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Trine Ballestad Rounge

Professor - Section for Pharmacology and Pharmaceutical Biosciences

Email t.b.rounge@farmasi.uio.no

Phone +47 22 85 02 00

Mobile phone +47 22 85 02 00

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Visiting address Kristine Bonnevies Hus

Postal address Postboks 1068 Blindern 0316 Oslo

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Trine B. Rounge’s research focuses on genomics, epigenomics, transcriptomics and microbiome related research. Her primary goal is to identify biomarkers in tissues, biofluids, or associated microbes that reveal early-stage cancer progression.

With a broad background in bioinformatics and molecular biology, Trine specializes in designing and implementing sequencing protocols and performing advanced bioinformatics analyses. Bioinformatics tools develop in Rounge-lab include GENOMICON-Seq, VirMake, HoCoRT and TAME-seq.

Trine is the PI of the project CRCbiome funded by the Norwegian Cancer Society and HSØ, aiming to identify biomarkers in the gut microbiome for use in colorectal cancer screening. In collaboration with Paula Berstad they lead an effort to elucidate the interplay between the microbiome, lifestyle, diet and medication use on colorectal cancer development.

The Genome of Europe project, a part of the 1+MG initiative, is a project aiming to produce a European reference genome. Trine is the Norwegian PI for this project, in collaboration with Helsedirektoratet and Elixir.

Together with Hilde Langseth, Trine is the PI of a large project aiming to identify circulating RNAs cancer biomarkers using serum samples, funded by the Norwegian Research Council - JanusRNA. The research group have developed a small RNA sequencing protocol tailored for low RNA yield samples and done extensive characterization of RNA profiles of healthy individuals and confounding variables. In this project, they have profiled pre-diagnostic samples from seven different cancer sites. In total, more than 4000 samples have been analysed. Bioinformatic, regression and machine learning methods are applied. She also works with projects related to genome-wide differential DNA methylation in three different projects.

She is also one of the leaders in a cross-institutional group that works with development of methods and analyses of genomic events and variation in persistent infection of Human Papillomavirus, with aim to discover if the accumulation of these events can be used in cervical cancer screening.

Tags: bioinformatics, cancer, biomarkers, microbiome, epigenome, transcriptome, genomics, sequencing, virus

Avershina, Ekaterina; Birkeland, Einar Elvbakken; Johannessen, Cecilie Bucher - & Rounge, Trine Ballestad (2026). CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut. Gut microbes. ISSN 1949-0976. 18(1). doi: 10.1080/19490976.2026.2734649. Full text in Research Archive
Glenna, Susanne; Birkeland, Einar Elvbakken; Orr, Russell; Gilfillan, Gregor; Dalland, Marianne & Økstad, Ole Andreas Løchen [Show all 8 contributors for this article] (2026). Longitudinal analysis of the hand microbiome in response to chlorine-based antiseptic use during a military field exercise. Microbiology spectrum. 14(8). doi: 10.1128/spectrum.03771-25. Full text in Research Archive
Birkeland, Einar Elvbakken; Kværner, Ane Sørlie; Avershina, Ekaterina; Johannessen, Cecilie Bucher -; Bemanian, Vahid & Blix, Hege Salvesen [Show all 14 contributors for this article] (2026). Microbiome signatures for detection of colorectal lesions in population-based FIT screening. Nature Communications. 17. doi: 10.1038/s41467-026-75962-1. Full text in Research Archive Show summary
The gut microbiome has been linked to colorectal cancer (CRC) development, with microbe-based classifiers distinguishing between CRC patients and healthy controls. However, there is a lack of studies addressing the utility of the microbiome in screening-relevant settings, including both precancers and CRC. In this Norwegian population-based study, we used fecal immunochemical test (FIT) leftovers from 1034 FIT-positive (i.e. positive for occult blood) screening participants for gut metagenome profiling using shotgun sequencing. Using comprehensive clinical, demographic, and lifestyle data, we modeled gut microbiome associations with CRC screening outcomes. Combining microbial profiles with quantitative FIT values improved detection of premalignant lesions beyond optimizing the FIT value alone, even after incorporating established CRC risk factors. Still, the FIT value maintained superior discriminative ability for CRC. We confirmed enrichment of bacteria such as Fusobacterium nucleatum and Peptostreptococcus stomatis in CRC. In contrast, other bacteria previously associated with the presence of CRC, including Hungatella hathewayi and Clostridium symbiosum, as well as pks-negative Escherichia coli, were enriched in those with no neoplastic findings, suggesting that in a FIT-positive population their presence may reflect other conditions causing intestinal bleeding rather than underlying neoplasia. Microbial profiles were predominantly associated with distal rather than proximal lesions. Together, our findings highlight the potential for microbial markers to improve FIT-based CRC screening, especially by differentiating those with premalignant lesions from those who test FIT-positive for other reasons.
Kværner, Ane Sørlie; Birkeland, Einar Elvbakken; Avershina, Ekaterina; Botteri, Edoardo; Bucher-Johannessen, Cecilie & Knudsen, Markus Dines [Show all 14 contributors for this article] (2026). Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator. European Journal of Nutrition. ISSN 1436-6207. 65(4), p. 1–18. doi: 10.1007/s00394-026-03960-6. Full text in Research Archive Show summary
Background Alcohol consumption is one of the major risk factors of colorectal cancer (CRC), yet the mechanisms underlying this relationship, particularly the role of gut microbes, are not fully understood. Objective To study associations of alcohol intake with the gut microbiome and colorectal lesions among CRC screening participants. Of particular interest was the potential role of gut microbes in mediating the association between alcohol intake and colorectal lesions. Methods Screening participants with a positive faecal immunochemical test at ages 55–77 were eligible for the CRCbiome study. Alcohol intake was assessed using a validated, semi-quantitative food frequency questionnaire and linked with shotgun metagenome based gut microbial profiles to study associations with screen-detected colorectal lesions. The potential role of alcohol-associated gut microbes in mediating the association between alcohol intake and colorectal lesions was examined using causal mediation analysis. Results Of 1468 participants with dietary data, 414 were diagnosed with advanced lesions. Alcohol intake was positively associated with advanced lesions in a dose-dependent manner (ptrend = 0.008), with odds ratio of 1.09 (95% confidence interval, 1.00, 1.19) per 10 g/day increase. Compared to non-consumers, those consuming alcohol were characterized by a distinct microbial profile, manifested as modest, but consistent, shifts in α- and β-diversity, and differentially abundant bacteria. A causal mediation analysis showed that 12% of the association between alcohol intake and advanced lesions was mediated by alcohol-associated gut bacteria. Conclusion Alcohol consumption was associated with a distinct microbial profile, which partly explained the association between alcohol intake and advanced colorectal lesions.
Wojewodzic, Marcin Wlodzimierz; L.D., Volders, Ellen; Coby, Meijer,; Grotmol, Tom; J., Touw, Daan & Sjoukje, Lubberts, [Show all 9 contributors for this article] (2025). Changes in methylation associated with development of metabolic syndrome in testicular cancer patients treated with cisplatin chemotherapy. Scientific Reports. 15. doi: 10.1038/s41598-025-22918-y. Full text in Research Archive Show summary
Patients with metastatic testicular cancer (TC) treated with cisplatin-based chemotherapy (CBCT) are prone to develop metabolic syndrome (MetS). In an epigenome wide association study in patients with TC we have shown that DNA methylation was associated to CBCT. The aim of the study was to investigate whether there was a change in DNA methylation after treatment with CBCT, and if methylation status is related to the presence or development of MetS. In a prospective cohort of 67 TC patients who received CBCT, we assessed whole blood global methylation long interspersed nuclear element-1 (LINE-1) and DNA methylation at selected cytosine-phosphate-guanine dinucleotide (CpG) sites associated with MetS using targeted sequencing. Measured samples were taken before, one month after, and one year after CBCT. Development of MetS was assessed before and up to five years after CBCT. Serum platinum levels were measured to assess platinum exposure (PtAUC) within the first year after the start of CBCT. Data were used for paired comparisons, comparisons between groups, statistical modeling to account for covariates, and machine learning approaches to predict occurrence of MetS five years after diagnosis. Global methylation did not change during the first year after the start of CBCT (median 73.7% (25th -75th percentile 72.0–75.2) vs. 73.9% (72.5–75.1)). Seven out of the 16 other selected CpGs decreased. Patients with MetS before start of CBCT (N = 18) showed a larger decrease than patients without MetS (N = 49) for AC090023 (-11.6% vs. -8.2%, p = 0.008), NCAM2 (-6.5% vs. -1.6%, p = 0.030), and TOM1L2 (-5.8% vs. -2.6%, p = 0.003). The 15 patients who did not have MetS prior to CBCT, but developed MetS within five years after treatment showed an increase in global methylation (1.5% vs. − 0.6%, p = 0.008) after one year, and a decrease in TOM1L2 methylation (-4.0% vs. -1.6%, p = 0.015) when compared to patients who did not have prior to CBCT nor developed MetS (N = 34). There was no difference in PtAUC during the first year after the start of CBCT between the latter groups (70.0 vs. 67.9 days*mg/L, p = 0.206). Changes in global DNA methylation and TOM1L2 one year after the start of CBCT are associated with a higher risk for newly developing MetS within five years. This may indicate potential for tailored advice, based on epigenetic status, to patients treated with chemotherapy for TC to prevent development of MetS.
Mueller, Michael; Blandino, Alice; Scherer, Dominique; Zulantay, Inés; Apt, Werner & Varela, Nelson M. [Show all 18 contributors for this article] (2025). Small-RNA sequencing identifies serum microRNAs associated with abnormal electrocardiography findings in patients with Chagas disease. Journal of Infection. ISSN 0163-4453. 91(4). doi: 10.1016/j.jinf.2025.106613. Full text in Research Archive
Pestarino, Luca; Fortner, Shannon Renee Turzanski; Nøst, Therese Haugdahl; Fotopoulos, Ioannis; Urbarova, Ilona H. & Røe, Oluf Dimitri [Show all 8 contributors for this article] (2025). Recommendations for Validating Omics Prediction Models: Insights from a Lung Cancer RNA Biomarker Study. Cancer Epidemiology, Biomarkers and Prevention. ISSN 1055-9965. 34(10), p. 1852–1860. doi: 10.1158/1055-9965.epi-25-0787. Full text in Research Archive Show summary
Background: External validation of predictive models in medical research is crucial to ensure their generalizability and applicability across diverse populations. However, validation often reveals discrepancies in model performance due to cohort differences, sample collection and storage, overfitting, and inconsistencies in data handling. This study investigates the challenges encountered during external validation of predictive models for early lung cancer detection using small RNA biomarkers, tying these challenges to specific validation outcomes and deriving recommendations. Methods: Predictive models based on the XGBoost algorithm, developed from serum samples in the JanusRNA cohort, were externally validated in two independent Norwegian cohorts: HUNT and Norwegian Women and Cancer Study. These cohorts differed in sample types, RNA abundance, library preparation protocols, and lung cancer histologic classification. Strategies to harmonize data processing and address these discrepancies were used to ensure a robust validation process. Results: Validation revealed significant challenges due to cohort heterogeneity. Median AUC values ranged from 0.50 to 0.66 in validation cohorts, compared with 0.62 to 0.76 in the original models. Models performed worse in the female-only Norwegian Women and Cancer Study cohort, in which plasma was used, highlighting the impact of sample type and cohort characteristics on predictive accuracy. Conclusion: Based on the challenges encountered during validation, we propose seven recommendations to guide robust external validation of omics-based predictive models, including harmonizing data processing across cohorts, reevaluating overfitting, and critically assessing model performance for clinical applications. Impact: By highlighting practical issues in model validation and providing recommendations, this study supports more reliable and clinically applicable biomarker-based prediction models, ultimately aiding cancer screening and prevention efforts.
Glenna, Susanne; Birkeland, Einar Elvbakken; Orr, Russell; Gilfillan, Gregor; Dalland, Marianne & Økstad, Ole Andreas [Show all 8 contributors for this article] (2025). Skin bacterial community dynamics of hands and forearms before and after military field exercise. Microbiology spectrum. 13(5). doi: 10.1128/spectrum.02953-24. Full text in Research Archive Show summary
The human skin microbiome is crucial for health and immunity, especially under the extreme conditions military personnel face. Soldiers often encounter unique stressors and hygienic challenges that can alter their skin’s microbial composition, particularly in field environments. In this study, we aimed to investigate the impact of military field exercises on the diversity and composition of the skin bacterial microbiota using 16S rRNA sequencing. We conducted a longitudinal study of Norwegian soldiers (n = 19) participating in outdoor training operations during the NATO winter exercise Cold Response 2022. Skin swabs were taken from soldiers' hands and forearms before and after the 10-day military exercise, and following a 3-week post-exercise leave. Our results reveal hand- and forearm-specific shifts in bacterial populations associated with the exercise, likely influenced by environmental exposure, reduced hygiene, and heightened social contact. Alpha diversity increased on forearms while remaining stable on hands, which appeared more resilient to perturbations. Both sites exhibited temporal changes in composition, with soil- and water-associated bacteria enriched post-exercise; most being transient on hands but more sustained on forearms. The soldiers’ microbiomes converged during the exercise, then diverged in the post-exercise leave period, and neither skin site returned to baseline composition at follow-up. Our findings highlight the impact of collaborative outdoor activities on microbial communities and suggest that resilience and stability differ between skin sites. IMPORTANCE Optimizing soldier health and resilience is critical for maintaining military readiness and operational effectiveness. The skin, as the body’s first line of defense, is subjected to numerous challenges in military environments. Unique environmental and hygiene challenges can disrupt the skin microbiome and increase susceptibility to skin and soft tissue infections. This longitudinal research provides valuable insights into the effects of military service on the bacterial dynamics of the skin microbiome but can also inform hygiene management and disease prevention in comparable situations.
Blandino, Alice; Scherer, Dominique; Boekstegers, Felix; Rounge, Trine B.; Langseth, Hilde & Roessler, Stephanie [Show all 11 contributors for this article] (2025). Small-RNA sequencing reveals potential serum biomarkers for gallbladder cancer: Results from a three-stage collaborative study of large European prospective cohorts. European Journal of Cancer. ISSN 0959-8049. 214, p. 1–10. doi: 10.1016/j.ejca.2024.115138. Full text in Research Archive Show summary
Gallbladder cancer (GBC) is an aggressive disease with limited treatment options but high prevention potential. GBC tumours take 10–20 years to develop, a timeframe that holds potential for early detection. MicroRNAs (miRNAs) play a central role in abnormal cell processes, and circulating miRNAs may constitute valuable biomarkers of early disease. We used microarray data to pre-select differentially expressed miRNAs in formalin-fixed paraffin-embedded (FFPE) gallbladder tissue samples (GBC n = 40, normal n = 8). We then applied small-RNA sequencing to screen for miRNA expression differences in serum samples from three European prospective cohorts (n = 37 GBC case-control pairs), and validated the most promising candidates in three independent cohorts (n = 36 GBC case- control pairs). Statistical analyses included robust linear regression, pathway and meta-analysis, and examination of expression correlation between miRNAs and target genes. MiR-4533 and miR-671–5p were overexpressed in GBC tissue and serum samples, and meta-analysis confirmed the overexpression of miR-4533 in GBC serum samples from the prospective cohorts (p-value = 4.1×10-4), especially in individuals of female sex, under 63.5 years, or with a BMI below 26.2 kg/m2. Pathway and correlation analyses revealed that miR-4533 targets SIPA1L2 in the Rap1 signalling pathway, and SIPA1L2 was downregulated in GBC serum samples. Our study highlights the advantage of integrating small-RNA sequencing results from different types of samples and independent datasets, and the need for international research collaborations to identify and validate biomarkers for secondary prevention of rare tumours such as GBC. The function of miR-4533 and its interaction with SIPA1L2 in GBC development need to be further investigated.
Stosic, Milan; Costanzi, Jean-Marc; Ambur, Ole Herman & Rounge, Trine Ballestad (2025). GENOMICON-Seq enables realistic simulation of amplicon and exome sequencing for low-frequency mutation detection. Scientific Reports. 15. doi: 10.1038/s41598-025-05267-8. Full text in Research Archive
Burton, Joshua; Rounge, Trine Ballestad; Haugen, Trine B. & Wojewodzic, Marcin Wlodzimierz (2025). Networks of pre-diagnostic circulating RNA in testicular germ cell tumour. Scientific Reports. 15, p. 1–13. doi: 10.1038/s41598-024-84484-z. Full text in Research Archive Show summary
Testicular germ cell tumour (TGCT) is a malignancy with known inherited risk factors, affecting young men. We have previously identified several hundred differentially abundant circulating RNAs in pre-diagnostic serum from TGCT cases compared to healthy controls. In this study, we performed Weighted Gene Co-expression Network Analysis (WGCNA) on mRNA and miRNA data from these samples. Central genes (hub genes) enriched functional pathways, and regulatory feature prediction were identified for all TGCT subtypes together and according to histology. The TGCT susceptibility genes TEX14, NARS2, and G3BP2, were identified as hub genes in both seminoma and non-seminoma networks. We also identified UBCA1, RCC1, FMR1, OAS3, and UBE2W as hub genes associated with TGCT. The genes OAS3 and UBE2W have previously been associated with testicular dysgenesis. Furthermore, network module analysis indicated transcription factors for oestrogen-related receptors to have a potential role during development of TGCT. The overlap between mRNA network hub genes and TGCT susceptibility genes indicates a common role in TGCT development.
Zakhartseva, Ekaterina Avershina; Qureshi, Arfa Irej; Winther-Larsen, Hanne Cecilie & Rounge, Trine Ballestad (2025). Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases. Microbiome. 13(1). doi: 10.1186/s40168-025-02048-3. Full text in Research Archive Show summary
Background The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data. Results We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools’ performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used. Conclusion Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools’ performance. Video Abstract
Bucher-Johannessen, Cecilie; Senthakumaran, Thulasika; Avershina, Ekaterina; Birkeland, Einar Elvbakken; Hoff, Geir Svein & Bemanian, Vahid [Show all 8 contributors for this article] (2024). Species-level verification of Phascolarctobacterium association with colorectal cancer. mSystems. 9(10). doi: 10.1128/msystems.00734-24. Full text in Research Archive Show summary
We have previously demonstrated an association between increased abundance of Phascolarctobacterium and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex specificity, the functional potential of the Phascolarctobacterium species, and their interaction with other microbial species. We analyze Phascolarctobacterium with 16S rRNA sequencing, shotgun metagenome sequencing, and species-specific qPCR, using 2350 samples from three Norwegian cohorts-CRCAhus, NORCCAP, and CRCbiome-and a large publicly available data set, curatedMetagenomicData. Using metagenome-assembled genomes from the CRCbiome study, we explore the genomic characteristics and functional potential of the Phascolarctobacterium pangenome. Three species of Phascolarctobacterium associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verifi
Senthakumaran, Thulasika; Tannæs, Tone Møller; Moen, Aina Elisabeth Fossum; Brackmann, Stephan Andreas; Jahanlu, David & Rounge, Trine Ballestad [Show all 8 contributors for this article] (2024). Detection of colorectal-cancer-associated bacterial taxa in fecal samples using next-generation sequencing and 19 newly established qPCR assays. Molecular Oncology. ISSN 1574-7891. 19(2), p. 412–429. doi: 10.1002/1878-0261.13700. Full text in Research Archive Show summary
We have previously identified increased levels of distinct bacterial taxa within mucosal biopsies from colorectal cancer (CRC) patients. Following prior research, the aim of this study was to investigate the detection of the same CRC-associated bacteria in fecal samples and to evaluate the suitability of fecal samples as a non-invasive material for the detection of CRC-associated bacteria. Next-generation sequencing (NGS) of the 16S ribosomal RNA (rRNA) V4 region was performed to evaluate the detection of the CRC-associated bacteria in the fecal microbiota of cancer patients, patients with adenomatous polyp and healthy controls. Furthermore, 19 novel species-specific quantitative PCR (qPCR) assays were established to detect the CRC-associated bacteria. Approximately, 75% of the bacterial taxa identified in biopsies were reflected in fecal samples. NGS failed to detect low-abundance CRC-associated taxa in fecal samples, whereas qPCR exhibited high sensitivity and specificity in identifying all targeted taxa. Comparison of fecal microbial composition between the different patient groups showed enrichment of Fusobacterium nucleatum, Parvimonas micra, and Gemella morbillorum in cancer patients. Our findings suggest that low-abundance mucosa-associated bacteria can be detected in fecal samples using sensitive qPCR assays.
Costanzi, Jean-Marc; Stosic, Milan; Løvestad, Alexander; Ambur, Ole Herman; Rounge, Trine Ballestad & Christiansen, Irene Kraus (2024). Changes in intrahost genetic diversity according to lesion severity in longitudinal HPV16 samples. Journal of Medical Virology. ISSN 0146-6615. 96(5). doi: 10.1002/jmv.29641. Full text in Research Archive Show summary
Human papillomavirus type 16 (HPV16) is the most common cause of cervical cancer, but most infections are transient with lesions not progressing to cancer. There is a lack of specific biomarkers for early cancer risk stratification. This study aimed to explore the intrahost HPV16 genomic variation in longitudinal samples from HPV16‐infected women with different cervical lesion severity (normal, low‐ grade, and high‐grade). The TaME‐seq deep sequencing protocol was used to generate whole genome HPV16 sequences of 102 samples collected over time from 40 individuals. Single nucleotide variants (SNVs) and intrahost SNVs (iSNVs) were identified in the viral genomes. A majority of individuals had a unique set of SNVs and these SNVs were stable over time. Overall, the number of iSNVs and APOBEC3‐ induced iSNVs were significantly lower in high‐grade relative to normal and low‐ grade samples. A significant increase in the number of APOBEC3‐induced iSNVs over time was observed for normal samples when compared to high‐grade. Our results indicates that the lower incidence of iSNVs and APOBEC3‐induced iSNVs in high‐grade lesions may have implications for novel biomarkers discoveries, potentially aiding early stratification of HPV‐induced cervical precancerous lesions.
Rostami, Sina; Rounge, Trine B.; Pestarino, Luca; Lyle, Robert; Fortner, Reneé Turzanski & Haaland, Øystein Ariansen [Show all 10 contributors for this article] (2024). Differential levels of circulating RNAs prior to endometrial cancer diagnosis. International Journal of Cancer. ISSN 0020-7136. 155(5), p. 946–956. doi: 10.1002/ijc.34951. Full text in Research Archive Show summary
Endometrial cancer (EC) is one of the most common female cancers and there is currently no routine screening strategy for early detection. An altered abundance of circulating microRNAs (miRNAs) and other RNA classes have the potential as early cancer biomarkers. We analyzed circulating RNA levels using small RNA sequencing, targeting RNAs in the size range of 17–47 nucleotides, in EC patients with samples collected prior to diagnosis compared to cancer-free controls. The analysis included 316 cases with samples collected 1–11 years prior to EC diagnosis, and 316 matched controls, both from the Janus Serum Bank cohort in Norway. We identified differentially abundant (DA) miRNAs, isomiRs, and small nuclear RNAs between EC cases and controls. The top EC DA miRNAs were miR-155-5p, miR-200b-3p, miR-589-5p, miR-151a-5p, miR-543, miR-485-5p, miR-625-p, and miR-671-3p. miR-200b-3p was previously reported to be among one of the top miRNAs with higher abundance in EC cases. We observed 47, 41, and 32 DA miRNAs for EC interacting with BMI, smoking status, and physical activity, respectively, including two miRNAs (miR-223-3p and miR-29b-3p) interacting with all three factors. The circulating RNAs are altered and show temporal dynamics prior to EC diagnosis. Notably, DA miRNAs for EC had the lowest q-value 4.39–6.66 years before diagnosis. Enrichment analysis of miRNAs showed that signaling pathways Fc epsilon RI, prolactin, toll-like receptor, and VEGF had the strongest associations.
Stawiski, Konrad; Fortner, Renee; Pestarino, Luca; Umu, Sinan Ugur; Kaaks, Rudolf & Rounge, Trine Ballestad [Show all 9 contributors for this article] (2024). Validation of miRNA signatures for ovarian cancer earlier detection in the pre-diagnosis setting using machine learning approaches. Frontiers in Oncology. 14, p. 1–8. doi: 10.3389/fonc.2024.1389066. Full text in Research Archive Show summary
Introduction: Effective strategies for early detection of epithelial ovarian cancer are lacking. We evaluated whether a panel of 14 previously established circulating microRNAs could discriminate between cases diagnosed <2 years after serum collection and those diagnosed 2–7 years after serum collection. miRNA sequencing data from subsequent ovarian cancer cases were obtained as part of the ongoing multi-cancer JanusRNA project, utilizing pre-diagnostic serum samples from the Janus Serum Bank and linked to the Cancer Registry of Norway for cancer outcomes. Methods: We included a total of 80 ovarian cancer cases contributing 80 serum samples and compared 40 serum samples from cases with samples collected <2 years prior to diagnosis with 40 serum samples from cases with sample collection ≥2 to 7 years. We employed the extreme gradient boosting (XGBoost) algorithm to train a binary classification model using 70% of the available data, while the model was tested on the remaining 30% of the dataset. Results: The performance of the model was evaluated using repeated holdout validation. The previously established set of miRNAs achieved a median area under the receiver operating characteristic curve (AUC) of 0.771 in the test sets. Four out of 14 miRNAs (hsa-miR-200a-3p, hsa-miR-1246, hsa-miR-203a-3p, hsa-miR-23b-3p) exhibited higher expression levels closer to diagnosis, consistent with the previously reported upregulation in cancer cases, with statistical significance observed only for hsa-miR-200a-3p (beta=0.14; p=0.04). Discussion: The discrimination potential of the selected models provides evidence of the robustness of the miRNA signature for ovarian cancer.
Istvan, Paula; Birkeland, Einar Elvbakken; Avershina, Ekaterina; Kværner, Ane Sørlie; Bemanian, Vahid & Pardini, Barbara [Show all 11 contributors for this article] (2024). Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study. Nature Communications. 15. doi: 10.1038/s41467-024-46033-0. Full text in Research Archive Show summary
Abstract Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.
Rao, Aakarsha; Stosic, Milan; Mohanty, Chitrasen; Suresh, Dhruthi; Wang, Albert R. & Lee, Denis L. [Show all 13 contributors for this article] (2024). Targeted inhibition of BET proteins in HPV16-positive head and neck squamous cell carcinoma reveals heterogeneous transcriptional responses. Frontiers in Oncology. 14. doi: 10.3389/fonc.2024.1440836. Full text in Research Archive Show summary
Human papilloma viruses (HPV), most commonly HPV16, are associated with a subset of head and neck squamous cell carcinoma (HNSCC) tumors, primarily oropharyngeal carcinomas, with integration of viral genomes into host chromosomes associated with worse survival outcomes. We analyzed TCGA data and found that HPV+ HNSCC expressed higher transcript levels of the bromodomain and extra terminal domain (BET) family of transcriptional co-regulators. The role of BET protein-mediated transcription of viral-cellular genes in the viral-HNSCC genomes needs to be better understood. Using a combination of TAME-Seq, qRT-PCR, and immunoblot analyses, we show that BET inhibition downregulates E6 and E7 significantly, with heterogeneity in the downregulation of viral transcription across different HPV+ HNSCC cell lines. Chemical BET inhibition was phenocopied with the knockdown of BRD4, mirroring the downregulation of viral E6 and E7 expression. We found that BET inhibition directly downregulated c-Myc and E2F expression and induced CDKN1A (p21) expression, leading to a G1-cell cycle arrest with apoptotic activity. Overall, our studies demonstrate that BET inhibition regulates both E6 and E7 viral and key cellular cell cycle regulator E2F gene expression and cellular gene expression in HPV-associated HNSCC and highlight the potential of BET inhibitors as a therapeutic strategy for this disease while also underscoring the importance of considering the heterogeneity in cellular responses to BET inhibition.
Løvestad, Alexander; Stosic, Milan; Costanzi, Jean-Marc; Christiansen, Irene Kraus; Aamot, Hege Vangstein & Ambur, Ole Herman [Show all 7 contributors for this article] (2023). TaME-seq2: tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling. Virology Journal. 20, p. 1–11. doi: 10.1186/s12985-023-02002-5. Full text in Research Archive Show summary
Background Previously developed TaME-seq method for deep sequencing of HPV, allowed simultaneous identification of the human papillomavirus (HPV) DNA consensus sequence, low-frequency variable sites, and chromosomal integration events. The method has been successfully validated and applied to the study of five carcinogenic high-risk (HR) HPV types (HPV16, 18, 31, 33, and 45). Here, we present TaME-seq2 with an updated laboratory workflow and bioinformatics pipeline. The HR-HPV type repertoire was expanded with HPV51, 52, and 59. As a proof-of-concept, TaME-seq2 was applied on SARS-CoV-2 positive samples showing the method’s flexibility to a broader range of viruses, both DNA and RNA. Results Compared to TaME-seq version 1, the bioinformatics pipeline of TaME-seq2 is approximately 40× faster. In total, 23 HPV-positive samples and seven SARS-CoV-2 clinical samples passed the threshold of 300× mean depth and were submitted to further analysis. The mean number of variable sites per 1 kb was ~ 1.5× higher in SARS-CoV-2 than in HPV-positive samples. Reproducibility and repeatability of the method were tested on a subset of samples. A viral integration breakpoint followed by a partial genomic deletion was found in within-run replicates of HPV59-positive sample. Identified viral consensus sequence in two separate runs was > 99.9% identical between replicates, differing by a couple of nucleotides identified in only one of the replicates. Conversely, the number of identical minor nucleotide variants (MNVs) differed greatly between replicates, probably caused by PCR-introduced bias. The total number of detected MNVs, calculated gene variability and mutational signature analysis, were unaffected by the sequencing run. Conclusion TaME-seq2 proved well suited for consensus sequence identification, and the detection of low-frequency viral genome variation and viral-chromosomal integrations. The repertoire of TaME-seq2 now encompasses seven HR-HPV types. Our goal is to further include all HR-HPV types in the TaME-seq2 repertoire. Moreover, with a minor modification of previously developed primers, the same method was successfully applied for the analysis of SARS-CoV-2 positive samples, implying the ease of adapting TaME-seq2 to other viruses.
Bucher-Johannessen, Cecilie; Birkeland, Einar Elvbakken; Vinberg, Elina; Bemanian, Vahid; Hoff, Geir Svein & Berstad, Paula [Show all 7 contributors for this article] (2023). Long-term follow-up of colorectal cancer screening attendees identifies differences in Phascolarctobacterium spp. using 16S rRNA and metagenome sequencing. Frontiers in Oncology. 13. doi: 10.3389/fonc.2023.1183039. Full text in Research Archive Show summary
Background: The microbiome has been implicated in the initiation and progression of colorectal cancer (CRC) in cross-sectional studies. However, there is a lack of studies using prospectively collected samples. Methods: From the Norwegian Colorectal Cancer Prevention (NORCCAP) trial, we analyzed 144 archived fecal samples from participants who were diagnosed with CRC or high-risk adenoma (HRA) at screening and from participants who remained cancer-free during 17 years of follow-up. We performed 16S rRNA sequencing of all the samples and metagenome sequencing on a subset of 47 samples. Differences in taxonomy and gene content between outcome groups were assessed for alpha and beta diversity and differential abundance. Results: Diversity and composition analyses showed no significant differences between CRC, HRA, and healthy controls. Phascolarctobacterium succinatutens was more abundant in CRC compared with healthy controls in both the 16S and metagenome data. The abundance of Bifidobacterium and Lachnospiraceae spp. was associated with time to CRC diagnosis. Conclusion: Using a longitudinal study design, we identified three taxa as being potentially associated with CRC. These should be the focus of further studies of microbial changes occurring prior to CRC diagnosis.
Abu-Halima, Masood; Keller, Andreas; Becker, Lea Simone; Fischer, Ulrike; Engel, Annika & Ludwig, Nicole [Show all 11 contributors for this article] (2023). Dynamic and static circulating cancer microRNA biomarkers – a validation study. RNA Biology. ISSN 1547-6286. 20(1), p. 1–9. doi: 10.1080/15476286.2022.2154470. Full text in Research Archive Show summary
For cancers and other pathologies, early diagnosis remains the most promising path to survival. Profiling of longitudinal cohorts facilitates insights into trajectories of biomarkers. We measured microRNA expression in 240 serum samples from patients with colon, lung, and breast cancer and from cancer-free controls. Each patient provided at least two serum samples, one prior to diagnosis and one following diagnosis. The median time interval between the samples was 11.6 years. Using computational models, we evaluated the circulating profiles of 21 microRNAs. The analysis yielded two sets of biomarkers, static ones that show an absolute difference between certain cancer types and controls and dynamic ones where the level over time provided higher diagnostic information content. In the first group, miR-99a-5p stands out for all three cancer types. In the second group, miR-155-5p allows to predict lung cancers and colon cancers. Classification in samples from cancer and non-cancer patients using gradient boosted trees reached an average accuracy of 79.9%. The results suggest that individual change over time or an absolute value at one time point may predict a disease with high specificity and sensitivity.
Senthakumaran, Thulasika; Moen, Aina Elisabeth Fossum; Tannæs, Tone Møller; Endres, Alexander; Brackmann, Stephan Andreas & Rounge, Trine Ballestad [Show all 8 contributors for this article] (2023). Microbial dynamics with CRC progression: a study of the mucosal microbiota at multiple sites in cancers, adenomatous polyps, and healthy controls. European Journal of Clinical Microbiology and Infectious Diseases. ISSN 0934-9723. 42, p. 305–322. doi: 10.1007/s10096-023-04551-7. Full text in Research Archive Show summary
Accumulating evidence has related the gut microbiota to colorectal cancer (CRC). Fusobacterium nucleatum has repeatedly been linked to colorectal tumorigenesis. The aim of this study was to investigate microbial composition in different sampling sites, in order to profile the microbial dynamics with CRC progression. Further, we characterized the tumor-associated F. nucleatum subspecies. Here, we conducted Illumina Miseq next-generation sequencing of the 16S rRNA V4 region in biopsy samples, to investigate microbiota alterations in cancer patients, patients with adenomatous polyp, and healthy controls in Norway. Further, Fusobacterium positive tumor biopsies were subjected to MinION nanopore sequencing of Fusobacterium- specific amplicons to characterize the Fusobacterium species and subspecies. We found enrichment of oral biofilm-associated bacteria, Fusobacterium, Gemella, Parvimonas, Granulicatella, Leptotrichia, Peptostreptococcus, Campylobacter, Seleno- monas, Porphyromonas, and Prevotella in cancer patients compared to adenomatous polyp patients and control patients. Higher abundance of amplicon sequence variants (ASVs) classified as Phascolarctobacterium, Bacteroides vulgatus, Bac- teroides plebeius, Bacteroides eggerthii, Tyzzerella, Desulfovibrio, Frisingicoccus, Eubacterium coprostanoligenes group, and Lachnospiraceae were identified in cancer and adenomatous polyp patients compared to healthy controls. F. nucleatum ssp. animalis was the dominating subspecies. F. nucleatum ssp. nucleatum, F. nucleatum ssp. vincentii, Fusobacterium pseudoperiodonticum, Fusobacterium necrophorum, and Fusobacterium gonidiaformans were identified in five samples. Several biofilm-associated bacteria were enriched at multiple sites in cancer patients. Another group of bacteria was enriched in both cancer and polyps, suggesting that they may have a role in polyp development and possibly early stages of CRC.
Umu, Sinan Ugur; Paynter, Vanessa Molin; Trondsen, Håvard; Buschmann, Tilo; Rounge, Trine Ballestad & Peterson, Kevin J. [Show all 7 contributors for this article] (2023). Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine. Cell Genomics. 3:100348(8), p. 1–15. doi: 10.1016/j.xgen.2023.100348. Full text in Research Archive Show summary
The annotation of microRNAs depends on the availability of transcriptomics data and expert knowledge. This has led to a gap between the availability of novel genomes and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families. These models are available in our tool MirMachine, which annotates conserved microRNAs within genomes. We successfully applied MirMachine to a range of animal species, including those with large genomes and genome duplications and extinct species, where small RNA sequencing is hard to achieve. We further describe a microRNA score of expected microRNAs that can be used to assess the completeness of genome assemblies. MirMachine closes a long-persisting gap in the microRNA field by facilitating automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms.
Rumbavicius, Ignas; Rounge, Trine Ballestad & Rognes, Torbjørn (2023). HoCoRT: host contamination removal tool. BMC Bioinformatics. 24(1). doi: 10.1186/s12859-023-05492-w. Full text in Research Archive Show summary
Background Shotgun metagenome sequencing data obtained from a host environment will usually be contaminated with sequences from the host organism. Host sequences should be removed before further analysis to avoid biases, reduce downstream computational load, or ensure privacy in the case of a human host. The tools that we identified, as designed specifically to perform host contamination sequence removal, were either outdated, not maintained, or complicated to use. Consequently, we have developed HoCoRT, a fast and user-friendly tool that implements several methods for optimised host sequence removal. We have evaluated the speed and accuracy of these methods. Results HoCoRT is an open-source command-line tool for host contamination removal. It is designed to be easy to install and use, offering a one-step option for genome indexing. HoCoRT employs a variety of well-known mapping, classification, and alignment methods to classify reads. The user can select the underlying classification method and its parameters, allowing adaptation to different scenarios. Based on our investigation of various methods and parameters using synthetic human gut and oral microbiomes, and on assessment of publicly available data, we provide recommendations for typical datasets with short and long reads. Conclusions To decontaminate a human gut microbiome with short reads using HoCoRT, we found the optimal combination of speed and accuracy with BioBloom, Bowtie2 in end-to-end mode, and HISAT2. Kraken2 consistently demonstrated the highest speed, albeit with a trade-off in accuracy. The same applies to an oral microbiome, but here Bowtie2 was notably slower than the other tools. For long reads, the detection of human host reads is more difficult. In this case, a combination of Kraken2 and Minimap2 achieved the highest accuracy and detected 59% of human reads. In comparison to the dedicated DeconSeq tool, HoCoRT using Bowtie2 in end-to-end mode proved considerably faster and slightly more accurate. HoCoRT is available as a Bioconda package, and the source code can be accessed at https://github.com/ignasrum/hocort along with the documentation. It is released under the MIT licence and is compatible with Linux and macOS (except for the BioBloom module).
Birkeland, Einar Elvbakken; Ferrero, Giulio; Pardini, Barbara; Umu, Sinan Ugur; Tarallo, Sonia & Bulfamante, Sara [Show all 10 contributors for this article] (2023). Profiling small RNAs in fecal immunochemical tests: is it possible? Molecular Cancer. 22:161(1), p. 1–7. doi: 10.1186/s12943-023-01869-w. Full text in Research Archive Show summary
Fecal microRNAs represent promising molecules with potential clinical interest as non-invasive diagnostic and prognostic biomarkers. Colorectal cancer (CRC) screening based on the fecal immunochemical test (FIT) is an effective tool for prevention of cancer development. However, due to the poor sensitivity of FIT especially for premalignant lesions, there is a need for implementation of complementary tests. Improving the identification of individuals who would benefit from further investigation with colonoscopy using molecular analysis, such as miRNA profiling of FIT samples, would be ideal due to their widespread use. In the present study, we assessed the feasibility of applying small RNA sequencing to measure human miRNAs in FIT leftover buffer in samples from two European screening populations. We showed robust detection of miRNAs with profiles similar to those obtained from specimens sampled using the established protocol of RNA stabilizing buffers, or in long-term archived samples. Detected miRNAs exhibited differential abundances for CRC, advanced adenoma, and control samples that were consistent for FIT and RNA-stabilizing buffers. Interestingly, the sequencing data also allowed for concomitant evaluation of small RNA-based microbial profiles. We demonstrated that it is possible to explore the human miRNome in FIT leftover samples across populations and envision that the analysis of small RNA biomarkers can complement the FIT in large scale screening settings.
Kværner, Ane Sørlie; Andersen, Astrid Riseth; Henriksen, Hege Berg; Knudsen, Markus Dines; Johansen, Anne Marte Wetting & Hjartåker, Anette [Show all 13 contributors for this article] (2023). Associations of the 2018 World Cancer Research Fund/American Institute of Cancer Research (WCRF/AICR) cancer prevention recommendations with stages of colorectal carcinogenesis. Cancer Medicine. 12(13), p. 14806–14819. doi: 10.1002/cam4.6119. Full text in Research Archive Show summary
Background: While adherence to cancer prevention recommendations is linked to lower risk of colorectal cancer (CRC), few have studied associations across the entire spectrum of colorectal carcinogenesis. Here, we studied the relationship of the standardized 2018 World Cancer Research Fund/American Institute for Cancer Research (WCRF/AICR) Score for cancer prevention recommendations with detection of colorectal lesions in a screening setting. As a secondary objective, we examined to what extent the recommendations were being followed in an external cohort of CRC patients. Methods: Adherence to the seven-point 2018 WCRF/AICR Score was measured in screening participants receiving a positive fecal immunochemical test and in CRC patients participating in an intervention study. Dietary intake, body fatness and physical activity were assessed using self-administered questionnaires. Multinomial logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for screen-detected lesions. Results: Of 1486 screening participants, 548 were free from adenomas, 524 had non-advanced adenomas, 349 had advanced lesions and 65 had CRC. Adherence to the 2018 WCRF/AICR Score was inversely associated with advanced lesions; OR 0.82 (95% CI 0.71, 0.94) per score point, but not with CRC. Of the seven individual components included in the score, alcohol, and BMI seemed to be the most influential. Of the 430 CRC patients included in the external cohort, the greatest potential for lifestyle improvement was seen for the recommendations concerning alcohol and red and processed meat, where 10% and 2% fully adhered, respectively. Conclusions: Adherence to the 2018 WCRF/AICR Score was associated with lower probability of screen-detected advanced precancerous lesions, but not CRC. Although some components of the score seemed to be more influential than others (i.e., alcohol and BMI), taking a holistic approach to cancer prevention is likely the best way to prevent the occurrence of precancerous colorectal lesions.
Burton, Joshua; Wojewodzic, Marcin Wlodzimierz; Rounge, Trine Ballestad & Haugen, Trine B. (2022). A Role of the TEX101 Interactome in the Common Aetiology Behind Male Subfertility and Testicular Germ Cell Tumor. Frontiers in Oncology. 12. doi: 10.3389/fonc.2022.892043. Full text in Research Archive Show summary
Patients who develop testicular germ cell tumours (TGCT) are at higher risk to be subfertile than the general population. The conditions are believed to originate during foetal life, however, the mechanisms behind a common aetiology of TGCT and male subfertility remains unknown. Testis-expressed 101 (TEX101) is a glycoprotein that is related to male fertility, and downregulation of the TEX101 gene was shown in pre-diagnostic TGCT patients. In this review, we summarize the current knowledge of TEX101 and its interactome related to fertility and TGCT development. We searched literature and compilation of data from curated databases. There are studies from both human and animals showing that disruption of TEX101 result in abnormal semen parameters and sperm function. Members of the TEX101 interactome, like SPATA19, Ly6k, PICK1, and ODF genes are important for normal sperm function. We found only two studies of TEX101 related to TGCT, however, several genes in its interactome may be associated with TGCT development, such as PLAUR, PRSS21, CD109, and ALP1. Some of the interactome members are related to both fertility and cancer. Of special interest is the presence of the glycosylphosphatidylinositol anchored proteins TEX101 and PRSS21 in basophils that may be coupled to the immune response preventing further development of TGCT precursor cells. The findings of this review indicate that members of the TEX101 interactome could be a part of the link between TGCT and male subfertility.
Umu, Sinan Ugur; Langseth, Hilde; Zuber, Verena; Helland, Åslaug; Lyle, Robert & Rounge, Trine Ballestad (2022). Serum RNAs can predict lung cancer up to 10 years prior to diagnosis. eLIFE. 11. doi: 10.7554/ELIFE.71035. Full text in Research Archive Show summary
Lung cancer (LC) prognosis is closely linked to the stage of disease when diagnosed. We investigated the biomarker potential of serum RNAs for the early detection of LC in smokers at different prediagnostic time intervals and histological subtypes. In total, 1061 samples from 925 individuals were analyzed. RNA sequencing with an average of 18 million reads per sample was performed. We generated machine learning models using normalized serum RNA levels and found that smokers later diagnosed with LC in 10 years can be robustly separated from healthy controls regardless of histology with an average area under the ROC curve (AUC) of 0.76 (95% CI, 0.68–0.83). Furthermore, the strongest models that took both time to diagnosis and histology into account successfully predicted non-small cell LC (NSCLC) between 6 and 8 years, with an AUC of 0.82 (95% CI, 0.76–0.88), and SCLC between 2 and 5 years, with an AUC of 0.89 (95% CI, 0.77–1.0), before diagnosis. The most important separators were microRNAs, miscellaneous RNAs, isomiRs, and tRNA-derived fragments. We have shown that LC can be detected years before diagnosis and manifestation of disease symptoms independently of histological subtype. However, the highest AUCs were achieved for specific subtypes and time intervals before diagnosis. The collection of models may therefore also predict the severity of cancer development and its histology. Our study demonstrates that serum RNAs can be promising prediagnostic biomarkers in an LC screening setting, from early detection to risk assessment.
Kværner, Ane Sørlie; Birkeland, Einar Elvbakken; Vinberg, Elina; Hoff, Geir; Hjartåker, Anette & Rounge, Trine Ballestad [Show all 7 contributors for this article] (2022). Associations of red and processed meat intake with screen-detected colorectal lesions. British Journal of Nutrition. ISSN 0007-1145. p. 1–36. doi: 10.1017/S0007114522002860. Full text in Research Archive Show summary
Limited data exist regarding the role of meat consumption in early-stage colorectal carcinogenesis. We examined associations of red and processed meat intake with screen-detected colorectal lesions in immunochemical fecal occult blood test (FIT)-positive participants, enrolled in the Norwegian CRCbiome study during 2017-2021, aged 55-77 years. Absolute and energy-adjusted intakes of red and processed meat (combined and individually) were assessed using a validated, semiquantitative food frequency questionnaire. Associations between meat intake and screen-detected colorectal lesions were examined using multinomial logistic regression analyses with adjustment for key covariates. Of 1,162 participants with available dietary data, 319 (27%) presented with advanced colorectal lesions at colonoscopy. High vs low energy-adjusted intakes of red and processed meat combined, as well as red meat alone, were borderline to significantly positively associated with advanced colorectal lesions (ORs (95% CIs) of 1.24 (0.98, 1.57) and 1.34 (1.07, 1.69), respectively). A significant dose-response-relationship was also observed for absolute intake levels (OR (95% CI) of 1.32 (1.09, 1.60) per 100 g/day increase in red and processed meat). For processed meat, no association was observed between energy-adjusted intakes and advanced colorectal lesions. A significant positive association was, however, observed for the small proportion of participants (10%) with absolute intake levels ≥100 vs <50 g/day (OR (95% CI) of 1.19 (1.09, 1.31)). In summary, high intakes of red and processed meat were associated with presence of advanced colorectal lesions at colonoscopy in FIT-positive participants. The study demonstrates a potential role of using dietary data to improve the performance of FIT-based screening.
Blandino, Alice; Scherer, Dominique; Rounge, Trine Ballestad; Umu, Sinan Ugur; Boekstegers, Felix & Ponce, Carol Barahona [Show all 41 contributors for this article] (2022). Identification of Circulating lncRNAs Associated with Gallbladder Cancer Risk by Tissue-Based Preselection, Cis-eQTL Validation, and Analysis of Association with Genotype-Based Expression. Cancers. 14(3). doi: 10.3390/cancers14030634. Full text in Research Archive Show summary
Long noncoding RNAs (lncRNAs) play key roles in cell processes and are good candidates for cancer risk prediction. Few studies have investigated the association between individual genotypes and lncRNA expression. Here we integrate three separate datasets with information on lncRNA expression only, both lncRNA expression and genotype, and genotype information only to identify circulating lncRNAs associated with the risk of gallbladder cancer (GBC) using robust linear and logistic regression techniques. In the first dataset, we preselect lncRNAs based on expression changes along the sequence “gallstones → dysplasia → GBC”. In the second dataset, we validate associations between genetic variants and serum expression levels of the preselected lncRNAs (cis-lncRNA-eQTLs) and build lncRNA expression prediction models. In the third dataset, we predict serum lncRNA expression based on individual genotypes and assess the association between genotype-based expression and GBC risk. AC084082.3 and LINC00662 showed increasing expression levels (p-value = 0.009), while C22orf34 expression decreased in the sequence from gallstones to GBC (p-value = 0.04). We identified and validated two cis-LINC00662-eQTLs (r2 = 0.26) and three cis-C22orf34-eQTLs (r2 = 0.24). Only LINC00662 showed a genotyped-based serum expression associated with GBC risk (OR = 1.25 per log2 expression unit, 95% CI 1.04–1.52, p-value = 0.02). Our results suggest that preselection of lncRNAs based on tissue samples and exploitation of cis-lncRNA-eQTLs may facilitate the identification of circulating noncoding RNAs linked to cancer risk.
Løvestad, Alexander; Repesa, Adina; Costanzi, Jean-Marc; Lagström, Sonja; Christiansen, Irene Kraus & Rounge, Trine Ballestad [Show all 7 contributors for this article] (2022). Differences in integration frequencies and APOBEC3 profiles of five high-risk HPV types adheres to phylogeny. Tumour Virus Research. 14. doi: 10.1016/j.tvr.2022.200247. Full text in Research Archive Show summary
Persistent infection with Human Papillomavirus (HPV) is responsible for almost all cases of cervical cancers, and HPV16 and HPV18 associated with the majority of these. These types differ in the proportion of viral minor nucleotide variants (MNVs) caused by APOBEC3 mutagenesis as well as integration frequencies. Whether these traits extend to other types remains uncertain. This study aimed to investigate and compare genomic variability and chromosomal integration in the two phylogenetically distinct Alpha-7 and Alpha-9 clades of carcinogenic HPV types. The TaME-seq protocol was employed to sequence cervical cell samples positive for HPV31, HPV33 or HPV45 and combine these with data from a previous study on HPV16 and HPV18. APOBEC3 mutation signatures were found in Alpha-9 (HPV16/31/33) but not in Alpha-7 (HPV18/45). HPV45 had significantly more MNVs compared to the other types. Alpha-7 had higher integration frequency compared to Alpha-9. An increase in integration frequency with increased diagnostic severity was found for Alpha-7. The results highlight important differences and broaden our understanding of the molecular mechanisms behind cervical cancer induced by high-risk HPV types from the Alpha-7 and Alpha-9 clades.
Mandishora, Racheal S. Dube; Rounge, Trine Ballestad; Fitzpatrick, Megan; Christiansen, Hanne Irene Kraus; Ambur, Ole Herman & Lagström, Sonja [Show all 10 contributors for this article] (2021). Self-collected and clinician-collected anal swabs show modest agreement for HPV genotyping. PLOS ONE. 16(4). doi: 10.1371/journal.pone.0250426. Full text in Research Archive Show summary
Background & aim: Women with HIV/HPV coinfection and cervical lesions are at increased risk of developing HPV related anal cancer. Self-collection of anal swabs may facilitate HPV molecular testing in anal cancer screening, especially in high-risk groups, and yet it is not adequately studied. We evaluated level of agreement between self-collected anal swabs (SCAS) and clinician-collected anal swabs (CCAS) when used for HPV genotyping. We also described the anal HPV genotype distribution and HIV/HPV coinfection. Methods: We performed a cross sectional study with participants from a visual-inspection-with-acetic-acid and cervicography (VIAC) clinic, in Harare, Zimbabwe. In a clinic setting, the women aged ≥ 18 years provided anal swabs in duplicate; first CCAS and then SCAS immediately after. HPV detection and genotyping were performed using next generation amplicon sequencing of a 450bp region of the HPV L1 gene. Level of agreement of HPV genotypes between CCAS and SCAS was calculated using the kappa statistic. McNemar tests were used to evaluate agreement in the proportion of genotypes detected by either method. Results: Three-hundred women provided 600 samples for HPV genotyping. HPV genotypes were detected in 25% of SCAS and in 22% of CCAS. The most common genotypes with CCAS were HPV52, HPV62 and HPV70 and with SCAS were HPV62, HPV44, HPV52, HPV53 and HPV68. Total HPV genotypes detected in CCAS were more than those detected in SCAS, 32 versus 27. The agreement of HPV genotypes between the two methods was 0.55 in kappa value (k). The test of proportions using McNemar gave a Chi-square value of 0.75 (p = 0.39). Multiple HPV infections were detected in 28/75 and 29/67 women for CCAS and SCAS respectively. Conclusions: SCAS and CCAS anal swabs showed moderate agreement, with no statistically significant difference in the proportion of genotypes detected by either methods. Although the differences between the two methods were not statistically significant, CCAS detected more HPV genotypes than SCAS and more HPV infections were detected in SCAS than in CCAS. Our data suggest that self-collected anal swabs can be used as an alternative to clinician-collected anal swabs for HPV genotyping.
Wojewodzic, Marcin; Leithaug, Magnus; Lauritzen, Marianne; Lyle, Robert; Haglund, Sofia & Rubin, Carl-Johan [Show all 9 contributors for this article] (2021). Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes. Clinical Epigenetics. 13(107). doi: 10.1186/s13148-021-01097-3. Full text in Research Archive Show summary
Background Long-term stored serum is considered challenging for epigenomic analyses: as there are no cells, circulating DNA is scarce, and amplification removes epigenetic signals. Additionally, pre-analytical treatments and storage might introduce biases and fragmentation to the DNA. In particular, starting with low-input DNA can result in low-diversity libraries. However, successful whole-genome bisulphite sequencing (WGBS) of such serum samples has the potential to open biobanks for epigenetic analyses and deliver novel prediagnostic biomarkers. Here, we perform WGBS using the Accel-NGS library preparation kit on ultralow amounts of DNA from long-term archived samples with diverse pretreatments from the Janus Serum Bank. Results Ninety-four of the 96 samples produced satisfactory methylation calls; an average of 578 M reads per sample generated a mean coverage of 17× and mean duplication level of 35%. Failed samples were related to poor bisulphite conversion rather than to sequencing or library preparation. We demonstrate the feasibility of WGBS on ultralow DNA yields from serum samples stored up to 48 years. Conclusions Our results show the potential of large serum biobank collections for future epigenomic studies and biomarker discovery.
Lagström, Sonja; Løvestad, Alexander; Umu, Sinan Uğur; Ambur, Ole Herman; Nygård, Mari & Rounge, Trine Ballestad [Show all 7 contributors for this article] (2021). HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples. Tumour Virus Research. 12. doi: 10.1016/j.tvr.2021.200221. Full text in Research Archive Show summary
Human papillomavirus (HPV) 16 and 18 are the most predominant types in cervical cancer. Only a small fraction of HPV infections progress to cancer, indicating that additional factors and genomic events contribute to the carcinogenesis, such as minor nucleotide variation caused by APOBEC3 and chromosomal integration. We analysed intra-host minor nucleotide variants (MNVs) and integration in HPV16 and HPV18 positive cervical samples with different morphology. Samples were sequenced using an HPV whole genome sequencing protocol TaME-seq. A total of 80 HPV16 and 51 HPV18 positive samples passed the sequencing depth criteria of 300× reads, showing the following distribution: non-progressive disease (HPV16 n = 21, HPV18 n = 12); cervical intraepithelial neoplasia (CIN) grade 2 (HPV16 n = 27, HPV18 n = 9); CIN3/adenocarcinoma in situ (AIS) (HPV16 n = 27, HPV18 n = 30); cervical cancer (HPV16 n = 5). Similar numbers of MNVs in HPV16 and HPV18 samples were observed for most viral genes, with the exception of HPV18 E4 with higher numbers across clinical categories. APOBEC3 signatures were observed in HPV16 lesions, while similar mutation patterns were not detected for HPV18. The proportion of samples with integration was 13% for HPV16 and 59% for HPV18 positive samples, with a noticeable portion located within or close to cancer-related genes.
Kværner, Ane Sørlie; Birkeland, Einar Elvbakken; Bucher-Johannessen, Cecilie; Vinberg, Elina; Nordby, Jan Inge & Kangas, Harri [Show all 27 contributors for this article] (2021). The CRCbiome study: a large prospective cohort study examining the role of lifestyle and the gut microbiome in colorectal cancer screening participants. BMC Cancer. 21. doi: 10.1186/s12885-021-08640-8. Full text in Research Archive Show summary
Background: Colorectal cancer (CRC) screening reduces CRC incidence and mortality. However, current screening methods are either hampered by invasiveness or suboptimal performance, limiting their effectiveness as primary screening methods. To aid in the development of a non-invasive screening test with improved sensitivity and specificity, we have initiated a prospective biomarker study (CRCbiome), nested within a large randomized CRC screening trial in Norway. We aim to develop a microbiome-based classification algorithm to identify advanced colorectal lesions in screening participants testing positive for an immunochemical fecal occult blood test (FIT). We will also examine interactions with host factors, diet, lifestyle and prescription drugs. The prospective nature of the study also enables the analysis of changes in the gut microbiome following the removal of precancerous lesions. Methods: The CRCbiome study recruits participants enrolled in the Bowel Cancer Screening in Norway (BCSN) study, a randomized trial initiated in 2012 comparing once-only sigmoidoscopy to repeated biennial FIT, where women and men aged 50–74 years at study entry are invited to participate. Since 2017, participants randomized to FIT screening with a positive test result have been invited to join the CRCbiome study. Self-reported diet, lifestyle and demographic data are collected prior to colonoscopy after the positive FIT-test (baseline). Screening data, including colonoscopy findings are obtained from the BCSN database. Fecal samples for gut microbiome analyses are collected both before and 2 and 12 months after colonoscopy. Samples are analyzed using metagenome sequencing, with taxonomy profiles, and gene and pathway content as primary measures. CRCbiome data will also be linked to national registries to obtain information on prescription histories and cancer relevant outcomes occurring during the 10 year follow-up period. Discussion: The CRCbiome study will increase our understanding of how the gut microbiome, in combination with lifestyle and environmental factors, influences the early stages of colorectal carcinogenesis. This knowledge will be crucial to develop microbiome-based screening tools for CRC. By evaluating biomarker performance in a screening setting, using samples from the target population, the generalizability of the findings to future screening cohorts is likely to be high.
Engberg, Elina; Raju, Sajan; Figueiredo, Rejane A.O.; Weiderpass, Elisabete; Rounge, Trine Ballestad & Viljakainen, Heli (2021). Saliva microbiota differs between children with low and high sedentary screen times. Human Microbiome Journal. 20. doi: 10.1016/j.humic.2021.100080. Full text in Research Archive Show summary
This study examined whether the diversity, composition and functional capacity of the saliva microbiota differed between children with low and high sedentary screen times. We analyzed the saliva microbiota using 16S rRNA (V3–V4) sequencing from 193 children with low and 183 children with high TV/screen viewing times while sitting. Microbiota diversity was higher among children with low screen times compared to children with high screen times. Furthermore, microbiota composition differed between the screen time groups. In addition, we identified ten differentially abundant taxonomic groups, including Veillonella, Prevotella and Streptococcus, and five differentially present metabolic pathways between the screen time groups. Children with high screen times exhibited a higher capacity to synthesize the fatigue- and activity-related amino acids ornithine and arginine. To conclude, children with high sedentary screen (sitting) times exhibited a lower diversity and a different composition and functionality of the microbiota compared to children with low screen times.
Burton, Joshua; Umu, Sinan Uğur; Langseth, Hilde; Grotmol, Tom; Grimsrud, Tom Kristian & Haugen, Trine B. [Show all 7 contributors for this article] (2020). Serum RNA profiling in the 10-year period prior to diagnosis of testicular germ cell tumour. Frontiers in Oncology. 10, p. 1–13. doi: 10.3389/fonc.2020.574977. Full text in Research Archive Show summary
Although testicular germ cell tumor (TGCT) overall is highly curable, patients may experience late effects after treatment. An increased understanding of the mechanisms behind the development of TGCT may pave the way for better outcome for patients. To elucidate molecular changes prior to TGCT diagnosis we sequenced small RNAs in serum from 69 patients who were later diagnosed with TGCT and 111 matched controls. The deep RNA profiles, with on average 18 million sequences per sample, comprised of nine classes of RNA, including microRNA. We found that circulating RNA signals differed significantly between cases and controls regardless of time to diagnosis. Different levels of TSIX related to X-chromosome inactivation and TEX101 involved in spermatozoa production are among the interesting findings. The RNA signals differed between seminoma and non-seminoma TGCT subtypes, with seminoma cases showing lower levels of RNAs and non-seminoma cases showing higher levels of RNAs, compared with controls. The differentially expressed RNAs were typically associated with cancer related pathways. Our results indicate that circulating RNA profiles change during TGCT development according to histology and may be useful for early detection of this tumor type.
Viljakainen, Jannina; Raju, Sajan C.; Viljakainen, Heli; Figueiredo, Rejane Augusta de Oliveira; Roos, Eva & Weiderpass, Elisabete [Show all 7 contributors for this article] (2020). Meal Regularity Plays a Role in Shaping the Saliva Microbiota. Frontiers in Microbiology. 11. doi: 10.3389/fmicb.2020.00757. Full text in Research Archive Show summary
Background: Diet may influence health directly or indirectly via the human microbiota, emphasizing the need to unravel these complex relationships for future health benefits. Associations between eating habits and gut microbiota have been shown, but less is known about the association between eating habits and saliva microbiota. Objective: The aim of this study was to investigate if eating habits and meal patterns are associated with the saliva microbiota. Methods: In total, 842 adolescents, aged 11–14 years, from the Finnish Health in Teens (Fin-HIT) study cohort were included in this study. Eating habits and breakfast and dinner patterns were derived from a web-based questionnaire answered in school. Three major eating habit groups were identified: fruit and vegetable avoiders (FV avoiders), healthy and unhealthy. Microbiota profiles were produced from 16S rRNA gene (V3–V4) sequencing of DNA from the saliva samples. Statistical models were adjusted for gender, age, parental language, body mass index (BMI) categories, and sequencing depth. Results: Regular breakfast eaters had a higher alpha diversity (Shannon index with mean (standard error of means) 2.27 (0.03) vs. 2.22 (0.03), p = 0.06, inverse Simpson’s index with 6.27 (0.17) vs. 5.80 (0.02), p = 0.01), and slight differences in bacterial composition (PERMANOVA: p = 0.001) compared with irregular breakfast eaters. A similar trend in alpha diversity was observed between regular and irregular dinner eaters (Shannon index with 2.27 (0.03) vs. 2.22 (0.03), p = 0.054, inverse Simpson’s index with 6.23 (0.17) vs. 6.04 (0.22), p = 0.28), while no difference was found in composition (PERMANOVA: p = 0.08). No differences were identified between eating habit groups and saliva microbiota diversity (Shannon index p = 0.77, inverse Simpson’s index p = 0.94) or composition (PERMANOVA: p = 0.13). FV avoiders, irregular breakfast eaters and irregular dinner eaters had high abundances of Prevotella. Conclusion: Regularity of eating, especially breakfast eating, was associated with more diverse saliva microbiota and different composition compared with irregular eaters. However, the dissimilarities in composition were small between regular and irregular breakfast eaters. Our results suggest that Prevotella abundances in saliva were common in FV avoiders and meal skippers. However, the clinical implications of these findings need to be evaluated in future studies.
Keller, Andreas; Fehlmann, Tobias; Backes, Christina; Kern, Fabian; Gislefoss, Randi Elin & Langseth, Hilde [Show all 9 contributors for this article] (2020). Competitive learning suggests circulating miRNA profiles for cancers decades prior to diagnosis. RNA Biology. ISSN 1547-6286. 17(10), p. 1416–1426. doi: 10.1080/15476286.2020.1771945. Full text in Research Archive
Raju, Sajan C.; Viljakainen, Heli; Figueiredo, Rejane A.O.; Neuvonen, Pertti J.; Eriksson, Johan G. & Weiderpass, Elisabete [Show all 7 contributors for this article] (2020). Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition. Microbiome. 8, p. 1–13. doi: 10.1186/s40168-020-00893-y. Full text in Research Archive Show summary
Background The human microbiota contributes to health and well-being. Antimicrobials (AM) have an immediate effect on microbial diversity and composition in the gut, but next to nothing is known about their long-term contribution to saliva microbiota. Our objectives were to investigate the long-term impact of AM use on saliva microbiota diversity and composition in preadolescents. We compared the lifetime effects by gender and AMs. We used data from 808 randomly selected children in the Finnish Health In Teens (Fin-HIT) cohort with register-based data on AM purchases from the Social Insurance Institution of Finland. Saliva microbiota was assessed with 16S rRNA (V3-V4) sequencing. The sequences were aligned to the SILVA ribosomal RNA database and classified and counted using the mothur pipeline. Associations between AM use and alpha-diversity (Shannon index) were identified with linear regression, while associations between beta-diversity (Bray-Curtis dissimilarity) and low, medium or high AM use were identified with PERMANOVA. Results Of the children, 53.6% were girls and their mean age was 11.7 (0.4) years. On average, the children had 7.4 (ranging from 0 to 41) AM prescriptions during their lifespan. The four most commonly used AMs were amoxicillin (n = 2622, 43.7%), azithromycin (n = 1495, 24.9%), amoxicillin-clavulanate (n = 1123, 18.7%) and phenoxymethylpenicillin (n = 408, 6.8%). A linear inverse association was observed between the use of azithromycin and Shannon index (b − 0.015, p value = 0.002) in all children, the effect was driven by girls (b − 0.032, p value = 0.001), while not present in boys. Dissimilarities were marked between high, medium and low users of all AMs combined, in azithromycin users specifically, and in boys with amoxicillin use. Amoxicillin and amoxicillin-clavulanate use was associated with the largest decrease in abundance of Rikenellaceae. AM use in general and phenoxymethylpenicillin specifically were associated with a decrease of Paludibacter and pathways related to amino acid degradations differed in proportion between high and low AM users. Conclusions A systematic approach utilising reliable registry data on lifetime use of AMs demonstrated long-term effects on saliva microbiota diversity and composition. These effects are gender- and AM-dependent. We found that frequent lifelong use of AMs shifts bacterial profiles years later, which might have unforeseen health impacts in the future. Our findings emphasise a concern for high azithromycin use, which substantially decreases bacterial diversity and affects composition as well. Further studies are needed to determine the clinical implications of our findings. Video Abstract
Figueiredo, Rejane Augusta de Oliveira; Kajantie, Eero; Neuvonen, Pertti J.; Rounge, Trine Ballestad; Weiderpass, Elisabete & Viljakainen, Heli (2020). Lifetime antimicrobial use is associated with weight status in early adolescence—A register-based cohort study. Pediatric Obesity. ISSN 2047-6302. p. 1–10. doi: 10.1111/ijpo.12727. Full text in Research Archive
Brägelmann, Johannes; Ponce, Carol Barahona; Marcelain, Katherine; Roessler, Stephanie; Goeppert, Benjamin & Ivan, Gallegos [Show all 23 contributors for this article] (2020). Epigenome‐wide analysis of methylation changes in the sequence of gallstone disease, dysplasia, and gallbladder cancer. Hepatology. ISSN 0270-9139. doi: 10.1002/hep.31585. Full text in Research Archive
Scherer, Dominique; López, Marcela Dávila; Goeppert, Benjamin; Abrahamsson, Sanna; Silos, Rosa González & Nova, Igor [Show all 13 contributors for this article] (2020). RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling. Cancers. 12(9). doi: 10.3390/cancers12092510. Full text in Research Archive Show summary
Cancer cell lines allow the identification of clinically relevant alterations and the prediction of drug response. However, sequencing data for hepatobiliary cancer cell lines in general, and particularly gallbladder cancer (GBC), are sparse. Here, we apply RNA sequencing to characterize 10 GBC, eight hepatocellular carcinoma, and five cholangiocarcinoma (CCA) cell lines. RNA extraction, quality control, library preparation, sequencing, and pre-processing of sequencing data were implemented using state-of-the-art techniques. Public data from the MSK-IMPACT database and a large cohort of Japanese biliary tract cancer patients were used to illustrate the usage of the released data. The total number of exonic mutations varied from 7207 for the cell line NOZ to 9760 for HuCCT1. Researchers planning experiments that require TP53 mutations could use the cell lines NOZ, OCUG-1, SNU308, or YoMi. Mz-Cha-1 showed mutations in ATM, SNU308 presented SMAD4 mutations, and the only investigated cell line that showed ARID1A mutations was GB-d1. SNU478 was the cell line with the global gene expression pattern most similar to GBC, intrahepatic CCA, and extrahepatic CCA. EGFR, KMT2D, and KMT2C generally presented a higher expression in the investigated cell lines than in Japanese primary GBC tumors. We provide the scientific community with detailed mutation and gene expression data, together with three showcase applications, with the aim of facilitating the design of future in vitro cell culture assays for research on hepatobiliary cancer.
Engberg, Elina; Figueiredo, Rejane Augusta de Oliveira; Rounge, Trine Ballestad; Weiderpass, Elisabete & Viljakainen, Heli (2019). Heavy screen users are the heaviest among 10,000 children. Scientific Reports. 9(1), p. 11158–11158. doi: 10.1038/s41598-019-46971-6. Full text in Research Archive
Figueiredo, Rejane Augusta De Oliveira; Viljakainen, Jannina; Viljakainen, Heli; Roos, Eva; Rounge, Trine Ballestad & Weiderpass, Elisabete (2019). Identifying eating habits in Finnish children: A cross-sectional study. BMC Public Health. 19(312). doi: 10.1186/s12889-019-6603-x. Full text in Research Archive Show summary
Background - We aimed to identify different eating habits among Finnish children and to evaluate their association with meal patterns, breakfast consumption, and socio-demographic characteristics in a large, nationwide cohort of children. Methods - We evaluated 10,569 children aged 9–14 years into the Finnish Health in Teens cohort in a cross-sectional design. The hierarchical K-means method was used to identify groups of children with different eating habits, based on five factors obtained through factor analysis of 10 food items. Multiple correspondence analysis was used to show associations between groups with different eating habits and meal patterns, breakfast patterns, gender, age, and language spoken at home. Results - Analyses identified three groups: unhealthy eaters (12.3%), fruit and vegetable avoiders (43.3%), and healthy eaters (44.1%). Most children had regular meal and breakfast patterns. The proportion of boys was higher among unhealthy eaters. Unhealthy eaters also showed irregular meal and breakfast patterns, and had parents with low education level. There was a higher proportion of girls among healthy eaters. Healthy eaters also showed regular meal and breakfast patterns, and had parents with high education level. Conclusions - Although the number of unhealthy eaters was small, special attention should be still paid to these, mostly male children, as they have poor eating habits and they lack regular eating routine. Skipping breakfast was more common among older children and girls, although girls had healthier eating habits overall. Our results can contribute to public health efforts to improve eating behaviours, especially among children with poor eating habits and those skipping healthy food items.
Viljakainen, Heli; Dahlström, Emma; Figueiredo, Rejane; Sandholm, Niina; Rounge, Trine Ballestad & Weiderpass, Elisabete (2019). Genetic risk score predicts risk for overweight and obesity in Finnish preadolescents. Clinical Obesity. ISSN 1758-8103. 9(6). doi: 10.1111/cob.12342. Full text in Research Archive
Figueiredo, Rejane Augusta de Oliveira; Simola-Ström, Sabina; Rounge, Trine Ballestad; Viljakainen, Heli; Eriksson, Johan G. & Roos, Eva [Show all 7 contributors for this article] (2019). Cohort Profile: The Finnish Health in Teens (Fin-HIT) study: A population-based study. International Journal of Epidemiology. ISSN 0300-5771. 48(1), p. 22–24H. doi: 10.1093/ije/dyy189. Full text in Research Archive Show summary
The prevalence of overweight and obesity in children and adolescents is increasing globally. In high-income countries, the prevalence of obesity has plateaued, although the rate is still high. Children with overweight and obesity are likely to stay obese into adulthood and tend to develop certain diseases, such as pulmonary, cardiovascular and metabolic diseases, more frequently and at a younger age. Overweight and obesity develop as a consequence of the imbalance between energy intake and energy expenditure, and they are heavily influenced by poor eating habits, inadequate sleep and low physical activity level. Only about 20% of 13–15-year-old adolescents worldwide achieve the recommended 60 min per day of moderate-to-vigorous physical activity. At the same time, the number of hours per day that children and adolescents sit in front of a screen, especially in front of a computer screen, is increasing.
Umu, Sinan Uğur; Langseth, Hilde; Keller, Andreas; Meese, Eckart; Helland, Åslaug & Lyle, Robert [Show all 7 contributors for this article] (2019). A 10-year prediagnostic follow-up study shows that serum RNA signals are highly dynamic in lung carcinogenesis. Molecular Oncology. ISSN 1574-7891. 14(2), p. 235–247. doi: 10.1002/1878-0261.12620. Full text in Research Archive
Engberg, Elina; Figueiredo, Rejane Augusta de Oliveira; Rounge, Trine Ballestad; Weiderpass, Elisabete & Viljakainen, Heli (2019). Heavy Screen Use on Weekends in Childhood Predicts Increased Body Mass Index in Adolescence: A Three-Year Follow-Up Study. Journal of Adolescent Health. ISSN 1054-139X. p. 1–8. doi: 10.1016/j.jadohealth.2019.09.002. Full text in Research Archive
Viljakainen, Jannina; Figueiredo, Rejane Augusta de Oliveira; Viljakainen, Heli; Roos, Eva; Weiderpass, Elisabete & Rounge, Trine Ballestad (2019). Eating habits and weight status in Finnish adolescents. Public Health Nutrition (PHN). ISSN 1368-9800. doi: 10.1017/S1368980019001447. Full text in Research Archive Show summary
Objective: To investigate the association between eating habits and weight status in adolescents in Finland. Design: Cross-sectional study. Setting: The Finnish Health in Teens (Fin-HIT) study is a cohort study conducted in adolescents attending third to sixth grade in 496 schools in forty-four municipalities in Southern, Middle and Northern Finland in 2011–2014. Participants: Analyses included 10 569 adolescents from the Fin-HIT study aged 9–14 years (5005 boys and 5564 girls). Adolescents were categorized by their eating habits: healthy eaters (44·1 %; n 4661), unhealthy eaters (12·3 %; n 1298), and fruit and vegetable avoiders (43·6 %; n 4610); and they were grouped into weight status: underweight (11·1 %), normal weight (73·6 %) and excess weight (15·3 %). Results: We found an increased risk of underweight in fruit and vegetable avoiders (OR = 1·28; 95 % CI 1·12, 1·46). An irregular breakfast pattern showed an inverse association with underweight (OR = 0·70; 95 % CI 0·59, 0·84) and an increased risk of excess weight (OR = 1·56; 95 % CI 1·37, 1·77) compared with a regular breakfast pattern. An irregular dinner pattern was inversely associated with underweight (OR = 0·83; 95 % CI 0·69, 0·99) compared with a regular dinner pattern. Conclusions: Avoiding fruits and vegetables and following irregular breakfast and dinner patterns were associated with underweight and excess weight in adolescents.
Bucher-Johannessen, Cecilie; Page, Christian Magnus; Haugen, Trine B.; Wojewodzic, Marcin; Fosså, Sophie Dorothea & Grotmol, Tom [Show all 8 contributors for this article] (2019). Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome. Clinical Epigenetics. 11:179, p. 1–13. doi: 10.1186/s13148-019-0764-4. Full text in Research Archive Show summary
Background - Cisplatin-based chemotherapy (CBCT) is part of standard treatment of several cancers. In testicular cancer (TC) survivors, an increased risk of developing metabolic syndrome (MetS) is observed. In this epigenome-wide association study, we investigated if CBCT relates to epigenetic changes (DNA methylation) and if epigenetic changes render individuals susceptible for developing MetS later in life. We analyzed methylation profiles, using the MethylationEPIC BeadChip, in samples collected ~ 16 years after treatment from 279 Norwegian TC survivors with known MetS status. Among the CBCT treated (n = 176) and non-treated (n = 103), 61 and 34 developed MetS, respectively. We used two linear regression models to identify if (i) CBCT results in epigenetic changes and (ii) epigenetic changes play a role in development of MetS. Then we investigated if these changes in (i) and (ii) links to genes, functional networks, and pathways related to MetS symptoms. Results - We identified 35 sites that were differentially methylated when comparing CBCT treated and untreated TC survivors. The PTK6–RAS–MAPk pathway was significantly enriched with these sites and infers a gene network of 13 genes with CACNA1D (involved in insulin release) as a network hub. We found nominal MetS-associations and a functional gene network with ABCG1 and NCF2 as network hubs. Conclusion - Our results suggest that CBCT has long-term effects on the epigenome. We could not directly link the CBCT effects to the risk of developing MetS. Nevertheless, since we identified differential methylation occurring in genes associated with conditions pertaining to MetS, we hypothesize that epigenomic changes may also play a role in the development of MetS in TC survivors. Further studies are needed to validate this hypothesis.
Raju, Sajan C.; Lagström, Sonja; Ellonen, Pekka; Vos, Willem M. de; Eriksson, Johan G. & Weiderpass, Elisabete [Show all 7 contributors for this article] (2019). Gender-specific associations between saliva microbiota and body size. Frontiers in Microbiology. 10:767, p. 1–10. doi: 10.3389/fmicb.2019.00767. Full text in Research Archive Show summary
Objective: The human intestinal microbiota likely play an important role in the development of overweight and obesity. However, the associations between saliva microbiota and body mass index (BMI) have been sparsely studied. The aim of this study was to identify the associations between saliva microbiota and body size in Finnish children. Methods: The saliva microbiota of 900 Finnish children, aged 11–14 years with measured height and weight, was characterized using 16S rRNA (V3–V4) sequencing. Results: The core saliva microbiota consisted of 14 genera that were present in more than 95% of the Finnish children. The saliva microbiota profiles were gender-specific with higher alpha-diversity in boys than girls and significant differences between the genders in community composition and abundances. Alpha-diversity differed between normal weight and overweight girls and between normal weight and obese boys. The composition was dissimilar between normal weight and obese girls, but not in boys. The relative abundance profiles differed according to body size. Decrease in commensal saliva bacteria were observed in all the body sizes when compared to normal weight children. Notably, the relative abundance of bacteria related to, Veillonella, Prevotella, Selenomonas, and Streptococcus was reduced in obese children. Conclusion: Saliva microbiota diversity and composition were significantly associated with body size and gender in Finnish children. Body size–specific saliva microbiota profiles open new avenues for studying the potential roles of microbiota in weight development and management.
Rounge, Trine Ballestad; Lauritzen, Marianne; Erlandsen, Sten Even; Langseth, Hilde; Holmen, Oddgeir Lingaas & Gislefoss, Randi Elin (2019). Ultralow amounts of DNA from long-term archived serum samples produce quality genotypes. European Journal of Human Genetics. ISSN 1018-4813. doi: 10.1038/s41431-019-0543-x. Full text in Research Archive
Viljakainen, Heli T.; Figueiredo, Rejane Augusta de Oliveira; Rounge, Trine Ballestad & Weiderpass, Elisabete (2019). Picky eating - A risk factor for underweight in Finnish preadolescents. Appetite. ISSN 0195-6663. 133, p. 107–114. doi: 10.1016/j.appet.2018.10.025. Full text in Research Archive Show summary
Background - Picky eating (PE) is the most common cause of early-life feeding problems. However, the consequences of PE on food intake and weight development in general populations have not been established. Objectives - This study aims to investigate the associations of PE and food neophobia (FN) with weight status in 5700 Finnish preadolescents. In addition, we described food consumption by PE/FN status. Material and methods - We utilised the Finnish Health in Teens (Fin-HIT) cohort of 9–12-year-old preadolescents, who were categorised as having PE and FN based on answers from parental questionnaires. Weight was categorised as underweight, normal weight, and overweight/obesity based on body mass index (BMI) according to IOTF age- and sex-specific cut-offs. Eating patterns were obtained with a 16-item food frequency questionnaire. Multinomial logistic regression models were used to estimate odds ratios (OR) and 95% confidence intervals (CIs). Results - The overall prevalence of PE and FN were 34% and 14%, respectively. PE was inversely associated with overweight/obesity (OR = 0.7; 95% CI 0.6–0.8) and led to a higher risk of underweight (OR = 2.0; 95% CI 1.7–2.4), while this was not observed with FN. Compared with preadolescents without PE/FN, those with PE/FN reported consuming unhealthy foods such as pizza, hamburgers/hot dogs, and salty snacks more frequently (p < 0.0038). By the same token, these preadolescents reported consuming healthy foods such as cooked vegetables, fresh vegetables/salad, fruit/berries, milk/soured milk, and dark bread less frequently. Conclusions - Among Finnish preadolescents, only PE was associated with a higher risk for underweight and inversely with overweight/obesity. PE and FN were accompanied with unhealthy eating patterns. Management of PE in children may be explored as a potential strategy for improving healthy eating and avoiding underweight in preadolescents.
Lagström, Sonja; Weele, Pascal van der; Rounge, Trine Ballestad; Christiansen, Irene Kraus; King, Audrey & Ambur, Ole Herman (2019). HPV16 whole genome minority variants in persistent infections from young Dutch women. Journal of Clinical Virology. ISSN 1386-6532. 119, p. 24–30. doi: 10.1016/j.jcv.2019.08.003. Full text in Research Archive Show summary
Background: Chronic infections by one of the oncogenic human papillomaviruses (HPVs) are responsible for near 5% of the global cancer burden and HPV16 is the type most often found in cancers. HPV genomes displayunexpected levels of variation when deep-sequenced. Minor nucleotide variations (MNVs) may reveal HPVgenomic instability and HPV-related carcinogenic transformation of host cells. Objectives: The objective of this study was to investigate HPV16 genome variation at the minor variant level onpersisting HPV16 cervical infections from a population of young Dutch women. Study design:15 HPV16 infections were sequenced using a whole-HPV genome deep sequencing protocol (TaME-seq). One infection was followed over a three-year period, eight were followed over a two-year period, threewere followed over a one-year period and three infections had a single sampling point. Results and conclusions: Using a 1% variant frequency cutoff, we find on average 48 MNVs per HPV16 genomeand 1717 MNVs in total when sequencing coverage was > 100 × . Wefind the transition mutation T > C to be the most common, in contrast to other studies detecting APOBEC-related C > T mutation profiles in pre-cancerous and cancer samples. Our results suggest that the relative mutagenic footprint of HPV16 genomes may differ between the infections in this study and transforming lesions. In addition, we identify a number of MNVs that have previously been associated with higher incidence of high-grade lesions (CIN3+) in a population study. These findings may provide a starting point for future studies exploring causality between emerging HPV minorgenomic variants and cancer development.
Lagström, Sonja; Umu, Sinan Uğur; Lepistö, Maija; Ellonen, Pekka; Meisal, Roger & Christiansen, Irene Kraus [Show all 8 contributors for this article] (2019). TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration. Scientific Reports. 9:524, p. 1–12. doi: 10.1038/s41598-018-36669-6. Full text in Research Archive Show summary
HPV genomic variability and chromosomal integration are important in the HPV-induced carcinogenic process. To uncover these genomic events in an HPV infection, we have developed an innovative and cost-effective sequencing approach named TaME-seq (tagmentation-assisted multiplex PCR enrichment sequencing). TaME-seq combines tagmentation and multiplex PCR enrichment for simultaneous analysis of HPV variation and chromosomal integration, and it can also be adapted to other viruses. For method validation, cell lines (n = 4), plasmids (n = 3), and HPV16, 18, 31, 33 and 45 positive clinical samples (n = 21) were analysed. Our results showed deep HPV genome-wide sequencing coverage. Chromosomal integration breakpoints and large deletions were identified in HPV positive cell lines and in one clinical sample. HPV genomic variability was observed in all samples allowing identification of low frequency variants. In contrast to other approaches, TaME-seq proved to be highly efficient in HPV target enrichment, leading to reduced sequencing costs. Comprehensive studies on HPV intra-host variability generated during a persistent infection will improve our understanding of viral carcinogenesis. Efficient identification of both HPV variability and integration sites will be important for the study of HPV evolution and adaptability and may be an important tool for use in cervical cancer diagnostics.
Fehlmann, Tobias; Backes, Christina; Alles, Julia; Fischer, Ulrike; Hart, Martin & Kern, Fabian [Show all 20 contributors for this article] (2018). A high-resolution map of the human small non-coding transcriptome. Bioinformatics. ISSN 1367-4803. 34(10), p. 1621–1628. doi: 10.1093/bioinformatics/btx814. Full text in Research Archive
Rounge, Trine Ballestad; Umu, Sinan Uğur; Keller, Andreas; Meese, Eckart; Ursin, Giske & Tretli, Steinar [Show all 8 contributors for this article] (2018). Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity. Scientific Reports. 8( ). doi: 10.1038/s41598-018-35974-4. Full text in Research Archive Show summary
Small non-coding RNAs (sncRNA) are regulators of cell functions and circulating sncRNAs from the majority of RNA classes are potential non-invasive biomarkers. Understanding how common traits influence ncRNA expression is essential for assessing their biomarker potential. In this study, we identify associations between sncRNA expression and common traits (sex, age, self-reported smoking, body mass, self-reported physical activity). We used RNAseq data from 526 serum samples from the Janus Serum Bank and traits from health examination surveys. Ageing showed the strongest association with sncRNA expression, both in terms of statistical significance and number of RNAs, regardless of RNA class. piRNAs were abundant in the serum samples and they were associated to sex. Interestingly, smoking cessation generally restored RNA expression to non-smoking levels, although for some sncRNAs smoking-related expression levels persisted. Pathway analysis suggests that smoking-related sncRNAs target the cholinergic synapses and may therefore potentially play a role in smoking addiction. Our results show that common traits influence circulating sncRNA expression. It is clear that sncRNA biomarker analyses should be adjusted for age and sex. In addition, for specific sncRNAs, analyses should also be adjusted for body mass, smoking, physical activity and technical factors.
Rounge, Trine Ballestad; Meisal, Roger; Nordby, Jan Inge; Ambur, Ole Herman; Lange, Thomas de & Hoff, Geir (2018). Evaluating gut microbiota profiles from archived fecal samples. BMC Gastroenterology. 18(171). doi: 10.1186/s12876-018-0896-6. Full text in Research Archive Show summary
Background Associations between colorectal cancer and microbiota have been identified. Archived fecal samples might be valuable sample sources for investigating causality in carcinogenesis and biomarkers discovery due to the potential of performing longitudinal studies. However, the quality, quantity and stability of the gut microbiota in these fecal samples must be assessed prior to such studies. We evaluated i) cross-contamination during analysis for fecal blood and ii) evaporation in stored perforated fecal immunochemical tests (iFOBT) samples, iii) temperature stability as well as iv) comparison of the gut microbiota diversity and composition in archived, iFOBT and fresh fecal samples in order to assess feasibility of large scale microbiota studies. Methods The microbiota profiles were obtained by sequencing the V3-V4 region of 16S rDNA gene. Results The iFOBT does not introduce any cross-sample contamination detectable by qPCR. Neither could we detect evaporation during freeze-thaw cycle of perforated iFOBT samples. Our results confirm room temperature stability of the gut microbiome. Diverse microbial profiles were achieved in 100% of fresh, 81% of long-term archived and 96% of iFOBT samples. Microbial diversity and composition were comparable between fresh and iFOBT samples, however, diversity differed significantly between long-term archived, fresh and iFOBT samples. Conclusion Our data showed that it is feasible to exploit archived fecal sample sets originally collected for testing of fecal blood. The advantages of using these sample sets for microbial biomarker discovery and longitudinal observational studies are the availability of high-quality diagnostic and follow-up data. However, care must be taken when microbiota are profiled in long-term archived fecal samples.
Umu, Sinan Ugur; Langseth, Hilde; Bucher-Johannessen, Cecilie; Fromm, Bastian; Keller, Andreas & Meese, Eckart [Show all 10 contributors for this article] (2018). A comprehensive profile of circulating RNAs in human serum. RNA Biology. ISSN 1547-6286. 15(2), p. 242–250. doi: 10.1080/15476286.2017.1403003. Full text in Research Archive
Page, Christian; Vos, Linda; Rounge, Trine Ballestad; Harbo, Hanne Flinstad & Kulle, Bettina (2018). Assessing genome-wide significance for the detection of differentially methylated regions. Statistical Applications in Genetics and Molecular Biology. 17(6). doi: 10.1515/sagmb-2017-0050. Full text in Research Archive Show summary
DNA methylation plays an important role in human health and disease, and methods for the identification of differently methylated regions are of increasing interest. There is currently a lack of statistical methods which properly address multiple testing, i.e. control genome-wide significance for differentially methylated regions. We introduce a scan statistic (DMRScan), which overcomes these limitations. We benchmark DMRScan against two well established methods (bumphunter, DMRcate), using a simulation study based on real methylation data. An implementation of DMRScan is available from Bioconductor. Our method has higher power than alternative methods across different simulation scenarios, particularly for small effect sizes. DMRScan exhibits greater flexibility in statistical modeling and can be used with more complex designs than current methods. DMRScan is the first dynamic approach which properly addresses the multiple-testing challenges for the identification of differently methylated regions. DMRScan outperformed alternative methods in terms of power, while keeping the false discovery rate controlled.
Raju, Sajan C.; Lagström, Sonja; Ellonen, Pekka; Vos, Willem M. de; Eriksson, Johan Gunnar & Weiderpass, Elisabete [Show all 7 contributors for this article] (2018). Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling. Journal of Microbiological Methods. ISSN 0167-7012. 147, p. 76–86. doi: 10.1016/j.mimet.2018.03.003. Full text in Research Archive Show summary
Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 ± 0.097 and 13.56 ± 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.
Mandishora, Racheal Shamiso Dube; Gjøtterud, Kristina Stormo; Lagström, Sonja; Stray-Pedersen, Babill; Duri, Kerina & Chin'ombe, Nyasha [Show all 11 contributors for this article] (2018). Intra-host sequence variability in human papillomavirus. Papillomavirus Research. The Journal of HPV and other Small DNA Tumor Viruses. 5, p. 180–191. doi: 10.1016/j.pvr.2018.04.006. Full text in Research Archive Show summary
Human papillomaviruses (HPVs) co-evolve slowly with the human host and each HPV genotype displays epithelial tropisms. We assessed the evolution of intra HPV genotype variants within samples, and their association to anogenital site, cervical cytology and HIV status. Variability in the L1 gene of 35 HPV genotypes was characterized phylogenetically using maximum likelihood, and portrayed by phenotype. Up to a thousand unique variants were identiﬁed within individual samples. In-depth analyses of the most prevalent genotypes, HPV16, HPV18 and HPV52, revealed that the high diversity was dominated by a few abundant variants. This suggests high intra-host mutation rates. Clades of HPV16, HPV18 and HPV52 were associated to anatomical site and HIV co-infection. Particularly, we observed that one HPV16 clade was speciﬁc to vaginal cells and one HPV52 clade was speciﬁc to anal cells. One major HPV52 clade, present in several samples, was strongly associated with cervical neoplasia. Overall, our data suggest that tissue tropism and HIV immunosuppression are strong shapers of HPV evolution.
Jørgensen, Tor Erik; Karlsen, Bård Ove; Emblem, Åse; Breines, Ragna; Andreassen, morten & Rounge, Trine Ballestad [Show all 15 contributors for this article] (2018). Mitochondrial genome variation of Atlantic cod. BMC Research Notes. 11:397, p. 1–7. doi: 10.1186/s13104-018-3506-3. Full text in Research Archive Show summary
Objective: The objective of this study was to analyse intraspecifc sequence variation of Atlantic cod mitochondrial DNA, based on a comprehensive collection of completely sequenced mitochondrial genomes. Results: We determined the complete mitochondrial DNA sequence of 124 cod specimens from the eastern and western part of the species’ distribution range in the North Atlantic Ocean. All specimens harboured a unique mitochondrial DNA haplotype. Nine hundred and ffty-two polymorphic sites were identifed, including 109 non-synonymous sites within protein coding regions. Eighteen variable sites were identifed as indels, exclusively distributed in structural RNA genes and non-coding regions. Phylogeographic analyses based on 156 available cod mitochondrial genomes did not reveal a clear structure. There was a lack of mitochondrial genetic diferentiation between two ecotypes of cod in the eastern North Atlantic, but eastern and western cod were diferentiated and mitochondrial genome diversity was higher in the eastern than the western Atlantic, suggesting deviating population histories. The geographic distribution of mitochondrial genome variation seems to be governed by demographic processes and gene fow among ecotypes that are otherwise characterized by localized genomic divergence associated with chromosomal inversions.
Meisal, Roger; Rounge, Trine Ballestad; Christiansen, Irene Kraus; Eieland, Alexander Kirkeby; Worren, Merete Molton & Molden, Tor [Show all 10 contributors for this article] (2017). HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization. PLOS ONE. 12(1). doi: 10.1371/journal.pone.0169074. Full text in Research Archive Show summary
Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.
Keller, Andreas; Rounge, Trine Ballestad; Backes, Christina; Ludwig, Nicole; Gislefoss, Randi Elin & Leidinger, Petra [Show all 8 contributors for this article] (2017). Sources to variability in circulating human miRNA signatures. RNA Biology. ISSN 1547-6286. 14(12), p. 1791–1798. doi: 10.1080/15476286.2017.1367888. Full text in Research Archive
Mandishora, Racheal Shamiso Dube; Christiansen, Irene Kraus; Chin'ombe, Nyasha; Duri, Kerina; Ngara, Bernard & Rounge, Trine Ballestad [Show all 11 contributors for this article] (2017). Genotypic diversity of anogenital human papillomavirus in women attending cervical cancer screening in Harare, Zimbabwe. Journal of Medical Virology. ISSN 0146-6615. 89(9), p. 1671–1677. doi: 10.1002/jmv.24825. Full text in Research Archive
Sarkkola, Catharina; Rounge, Trine Ballestad; Simola-Ström, Sabina; Kraemer, Stephanie von; Roos, Eva & Weiderpass, Elisabete (2016). Validity of home-measured height, weight and waist circumference among adolescents. European Journal of Public Health. ISSN 1101-1262. 26(6), p. 975–977. doi: 10.1093/eurpub/ckw133. Full text in Research Archive
Rounge, Trine Ballestad; Page, Christian; Lepistö, Maija; Ellonen, Pekka; Andreassen, Bettina Kulle & Weiderpass, Elisabete (2016). Genome-wide DNA methylation in saliva and body size of adolescent girls. Epigenomics. ISSN 1750-1911. 8(11), p. 1495–1505. doi: 10.2217/epi-2016-0045. Full text in Research Archive Show summary
Aim: We performed an epigenome-wide association study within the Finnish Health in Teens cohort to identify differential DNA methylation and its association with BMI in adolescents. Materials & methods: Differential DNA methylation analyses of 3.1 million CpG sites were performed in saliva samples from 50 lean and 50 heavy adolescent girls by genome-wide targeted bisulfite-sequencing. Results: We identified 100 CpG sites with p-values < 0.000524, seven regions by ‘bumphunting’ and five CpG islands that differed significantly between the two groups. The ten CpG sites and regions most strongly associated with BMI substantially overlapped with obesity- and insulin-related genes, including MC2R, IGFBPL1, IP6K1 and IGF2BP1. Conclusion: Our findings suggest an association between the saliva methylome and BMI in adolescence.
Rounge, Trine Ballestad; Furu, Kari; Skotheim, Rolf Inge; Haugen, Trine B.; Grotmol, Tom & Enerly, Espen (2015). Profiling of the small RNA populations in human testicular germ cell tumors shows global loss of piRNAs. Molecular Cancer. 14(153). doi: 10.1186/s12943-015-0411-4. Full text in Research Archive Show summary
Background Small non-coding RNAs play essential roles in gene regulation, however, the interplay between RNA groups, their expression levels and deregulations in tumorigenesis requires additional exploration. In particular, a comprehensive analysis of microRNA (miRNA), PIWI-interacting RNAs (piRNAs), and tRNA-derived small RNAs in human testis and testicular germ cell tumor (TGCT) is lacking. Results We performed small RNA sequencing on 22 human TGCT samples from 5 histological subtypes, 3 carcinoma in situ, and 12 normal testis samples. miRNA was the most common group among the sequences 18–24 nt in length and showed histology-specific expression. In normal samples, most sequences 25–31 nucleotides in length displayed piRNA characteristics, whereas a large proportion of the sequences 32–36 nt length was derived from tRNAs. Expression analyses of the piRNA population demonstrated global loss in all TGCT subtypes compared to normal testis. In addition, three 5′ small tRNA fragments and 23 miRNAs showed significant (p < 10−6) differential expression in cancer vs normal samples. Conclusions We have documented significant changes in the small RNA populations in normal adult testicular tissue and TGCT samples. Although components of the same pathways might be involved in miRNA, piRNA and tRNA-derived small RNA biogenesis, our results showed that the response to the carcinogenic process differs between these pathways, suggesting independent regulation of their biogenesis. Overall, the small RNA deregulation in TGCT provides new insight into the small RNA interplay.
Rounge, Trine Ballestad; Lauritzen, Marianne; Langseth, Hilde; Enerly, Espen; Lyle, Robert & Gislefoss, Randi Elin (2015). MicroRNA biomarker discovery and high-throughput DNA sequencing are possible using long-term archived serum samples. Cancer Epidemiology, Biomarkers and Prevention. ISSN 1055-9965. 24(9), p. 1381–1387. doi: 10.1158/1055-9965.EPI-15-0289. Full text in Research Archive

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Rounge, Trine Ballestad & Paulsen, Jonas (2025). Highly sensitive method captures rare RNAs in blood to search for disease. Nature. ISSN 0028-0836. 641(8063), p. 599–600. doi: 10.1038/d41586-025-01127-7. Full text in Research Archive
Scherer, Dominique; Ponce, Carol Barahona; Mengoa, Claudio; Montenegro, Paola; Losada, Hector & Garcia, Ana Lineth [Show all 31 contributors for this article] (2025). Data Resource Profile: EULAT Eradicate GBC: the European-Latin American Research Consortium towards Eradication of Preventable Gallbladder Cancer. International Journal of Epidemiology. ISSN 0300-5771. 54(4). doi: 10.1093/ije/dyaf127. Full text in Research Archive
Rounge, Trine Ballestad (2023). Building epigenetic clocks for estimating accelerating aging in patients with testicular cancer treated with cisplatin-based chemotherapy. Full text in Research Archive
Wojewodzic, Marcin Wlodzimierz; Burton, Joshua; Rounge, Trine Ballestad & Haugen, Trine B. (2023). Pre-diagnostic circulating RNAs networks identify testicular germ cell tumour susceptibility genes. Full text in Research Archive
Wojewodzic, Marcin Wlodzimierz; Sydhagen, Kristin Aurora & Rounge, Trine Ballestad (2023). Building epigenetic clocks for estimating accelerating aging in patients with testicular cancer treated with cisplatin-based chemotherapy. Journal of Clinical Oncology. ISSN 0732-183X. 41. doi: 10.1200/JCO.2023.41.16_suppl.e24099. Full text in Research Archive Show summary
e24099 Background: DNA methylation is highly correlated with chronological age. This is essential for constructing epigenetic clocks. Epigenetic clocks can shade light not only about the biological age, but also describe the functional state of the body after chemotherapy (CT). Patients with testicular cancer (TC) treated with CT are prone to develop metabolic syndrome (MetS) later in life, that may be also mediated through epigenetic changes (Bucher, Clin Epigenetics. 2019; 11:179). If age acceleration is also a mediator in the CT~MetS relationship remains unknown. We developed an epigenetic clock, and then analyzed differences in biological age acceleration between groups of TC patients 16 years after CT. TC patients had undergone one of two treatments: either surgery or a combination of CT or surgery only. Half of the patients in both treatment-groups had developed MetS. Methods: First, we used an elastic net to develop epigenetic clocks based on DNA methylation from publicly available data sets (EPIC array). We tested the differences in age accelerations (residual and intrinsic age acceleration) between groups of TC patients that received CT and orchiectomy with those TC patients with orchiectomy only. Also, the linear regression used treatment type and MetS diagnosis as independent variables. Results: Five epigenetic clocks were developed, of which one, performing best, was chosen to be used in further analyses. This clock, the Aurora’s clock, had a root mean square error of 3.1/3.8 and R2 of 0.95/0.9 shown in two different test sets. In addition to Aurora’s clock, eABEC and Levine DNAm PhenoAge were used (Lee, BMC Genomics. 2020, 21, 747; Levine, Aging. 2018, 2018,10:573-591). The linear regressions indicated a lower age acceleration for the group treated with both CT and surgery, compared to the group treated with surgery only. The significance level varied between the clocks, with a p-value ranging from 0.03 to 0.17. All three clocks estimated a higher age acceleration for patients diagnosed with MetS, but this was only significant when applying Levine DNAm PhenoAge (p = 0.03 for residual age acceleration, and p = 0.045 for intrinsic age acceleration). Conclusions: These findings indicate that CT does not lead to increased age acceleration 16 years after treatment. However, individuals diagnosed with MetS can have an elevated age acceleration. These findings can have clinical implications for managing patients' after TC diagnosis (i.e. MetS can be predicted from age acceleration). Testing the clocks in an independent cohort of TC is needed for validation of our results.
Rostami, Sina; Langseth, Hilde; lyle, robert; Bjørge, Tone; Pestarino, Luca & Rounge, Trine Ballestad (2022). Pre-diagnostic circulating RNAs in endometrial cancer – impact of body mass index. Full text in Research Archive
Rounge, Trine Ballestad (2022). Predicting colorectal cancer using gut microbiome. Full text in Research Archive
Langseth, Hilde; Kymre, Kristina; Slyngstad, Tove; Rounge, Trine Ballestad; Gislefoss, Randi Elin & Lauritzen, Marianne (2022). Janus serumbank – jakten på biomarkører for kreft. Norsk Epidemiologi. ISSN 0803-2491. 30(1-2), p. 87–92. doi: 10.5324/nje.v30i1-2.4983. Full text in Research Archive
Avershina, Ekaterina; Birkeland, Einar Elvbakken; Berstad, Paula; Hoff, Geir Svein & Rounge, Trine Ballestad (2022). Total neoplastic polyp volume is correlated to several bacterial taxa in faecal immunochemical test-positive CRC-screening participants. Full text in Research Archive
Avershina, Ekaterina; Birkeland, Einar Elvbakken; Berstad, Paula; Hoff, Geir Svein & Rounge, Trine Ballestad (2022). Total neoplastic polyp volume is correlated to several bacterial taxa in faecal immunochemical test-positive CRC-screening participants. Full text in Research Archive
Istvan, Paula; Birkeland, Einar Elvbakken; Rognes, Torbjørn & Rounge, Trine Ballestad (2021). Profiling gut viruses from metagenomes of Bowel Cancer Screening participants. Full text in Research Archive
Løvestad, Alexander; Lagström, Sonja; Christiansen, Irene Kraus; Rounge, Trine Ballestad & Ambur, Ole Herman (2020). Investigating intra-host genomic events of HPV 31, HPV33 and HPV45 positive cervical samples using deep sequencing. Full text in Research Archive
Lagström, Sonja; Løvestad, Alexander; Umu, Sinan Uğur; Ambur, Ole Herman; Rounge, Trine Ballestad & Christiansen, Irene Kraus (2020). Chromosomal integration and APOBEC profiles differ between HPV16 and HPV18 positive cervical samples. Full text in Research Archive
Lagström, Sonja; Weele, Pascal van der; Rounge, Trine Ballestad; Christiansen, Irene Kraus; King, Audrey J. & Ambur, Ole Herman (2020). Erratum to “HPV16 whole genome minority variants in persistent infections from young Dutch women” (Journal of Clinical Virology (2019) 119 (24–30), (S1386653219301726), (10.1016/j.jcv.2019.08.003)). Journal of Clinical Virology. ISSN 1386-6532. 124. doi: 10.1016/j.jcv.2020.104286. Full text in Research Archive
Lagström, Sonja; Umu, Sinan Uğur; Lepistö, Maija; Ellonen, Pekka; Meisal, Roger & Christiansen, Irene Kraus [Show all 8 contributors for this article] (2018). TaME-seq: An efficient sequencing approach to characterize human papillomavirus genomic variability and chromosomal integration. Full text in Research Archive
Lagström, Sonja; Umu, Sinan Uğur; Lepistö, Maija; Ellonen, Pekka; Meisal, Roger & Christiansen, Irene Kraus [Show all 8 contributors for this article] (2018). TaME-seq: An efficient sequencing approach to characterise HPV genomic variability and chromosomal integration. Full text in Research Archive
Bucher-Johannessen, Cecilie; Page, Christian M.; Haugen, Trine B.; Fosså, Sophie Dorothea; Haugnes, Hege Sagstuen & Grotmol, Tom [Show all 7 contributors for this article] (2018). Epigenetic changes in testicular cancer survivors treated with cisplatin. Full text in Research Archive
Burton, Joshua; Hammer, Hugo Lewi; Umu, Sinan Uğur; Langseth, Hilde; Grotmol, Tom & Grimsrud, Tom Kristian [Show all 8 contributors for this article] (2018). Small non-coding RNA in serum from testicular germ cell tumour patients identified by machine learning. Full text in Research Archive
Burton, Joshua; Hammer, Hugo Lewi; Umu, Sinan Uğur; Langseth, Hilde; Grotmol, Tom & Grimsrud, Tom Kristian [Show all 8 contributors for this article] (2018). Differentially expressed small non-coding RNA in serum from testicular germ cell tumour patients and controls. Full text in Research Archive
Burton, Joshua; Hammer, Hugo Lewi; Umu, Sinan Uğur; Langseth, Hilde; Grotmol, Tom & Grimsrud, Tom Kristian [Show all 8 contributors for this article] (2018). Differentially expressed small non-coding RNA in serum from testicular germ cell tumour patients and controls. Full text in Research Archive
Mandishora, RS; Gjøtterud, Kristina Stormo; Stray-Pedersen, Babill; Chin'ombe, Nyasha; Duri, Kerina & Nygård, Mari [Show all 10 contributors for this article] (2017). Anal and vaginal HPV52: Understanding site-specific variance in women reporting for routine cervical cancer screening. Full text in Research Archive
Lagström, Sonja; Gjøtterud, Kristina Stormo; Nygård, Mari; Christiansen, Irene Kraus; Ambur, Ole Herman & Rounge, Trine Ballestad (2017). Intra-HPV type genetic variation in liquid based cytology screening samples. Full text in Research Archive
Mandishora, RS; Christiansen, Irene Kraus; Chin`ombe, N; Duri, Kerina; Rounge, Trine Ballestad & Meisal, Roger [Show all 9 contributors for this article] (2017). Do HIV-infected and Uninfected Women Have Different Human Papilloma Virus Genotypes Distribution: A Cross Sectional Study Carried out in Zimbabwe. AIDS Research and Human Retroviruses. ISSN 0889-2229. 32, p. 280–280. Full text in Research Archive Show summary
Abstract Background: Although anogenital cancers have been on a gradual rise in developing countries in the past few decades, they have been understudied. Objective: To investigate genotypic diversity of anogenital HPV amongst women reporting for routine cervical cancer screening in Harare in Zimbabwe. Methods: A cross sectional study that enrolled 144 women ≥18 years from a cervical cancer-screening clinic was performed. Each woman provided a self-collected cervico-vaginal swab (VS) and a clinician collected anal swab (CCAS). HIV testing was offered and cervical cytology was performed. Both VS and CCAS samples were HPV genotyped, using amplicon sequencing of the L1 gene region with Illumina technology. Results: Mean age of the women was 39.9 (range 18-83 years, SD ±11.0). HPV prevalence was 72%(104/144) in VS and 48% (69/144) in CCAS. The most common genotypes detected in both VS and CCAS were HPV18, HPV52 and HPV16. Sixty two percent of the subjects had multiple genotypic HPV infections. The odds of being HPV-positive among HIV-infected women were higher than in HIV-negative women in both the vagina and the anus (CCAS OR = 4.8; CI 2.4-9.8, p<0.001) and (VS OR=2.9; CI 1.3-6.4, p=0.005). Conclusion: High HPV prevalence and diverse genotypes were detected in both the vagina and anus. Anal oncogenic HPV infection was common. HPV 52 was one of the most common oncogenic genotypes in both the vagina and anus. HIV co-infection played a significant role in the prevalence of HPV. These data have implications for design of primary and secondary programs for prevention of anogenital cancer in Zimbabwe.
Lagström, Sonja; Umu, Sinan Uğur; Lepistö, Maija; Ellonen, Pekka; Meisal, Roger & Christiansen, Irene Kraus [Show all 8 contributors for this article] (2017). Human Papillomavirus whole genome sequencing reveals genetic diversity and human genome integration sites. Full text in Research Archive
Hansen, Mona; Kristiansen-Haugland, Hanne; Saltyte-Benth, Jurate; Myrvang, Ellen; Meisal, Roger & Rounge, Trine Ballestad [Show all 7 contributors for this article] (2016). Analytical performance of HPV genotyping methods on cervical liquid based cytology samples. Full text in Research Archive
Christiansen, Irene Kraus; Lagström, Sonja; Meisal, Roger; Myrvang, Ellen; Kristiansen-Haugland, Hanne & Hansen, Mona [Show all 10 contributors for this article] (2015). Human papillomavirus genotyping by next generation sequencing; evaluation of amplification targets and sequencing parameters. Full text in Research Archive
Rounge, Trine Ballestad; Furu, Kari; Skotheim, Rolf Inge; Haugen, Trine B.; Enerly, Espen & Grotmol, Tom (2015). Small RNA profiling of human testicular cancer tissue samples shows abundant tRNA fragments and global loss of piRNA. Full text in Research Archive
Rounge, Trine Ballestad; Berstad, Paula Marianna; Bøhn, Siv Kjølsrud & Fjørtoft, Jenny Helene Mary Storvik (2023). Place of Residence and the Gut Microbiome. Norges miljø- og biovitenskapelige universitet (NMBU). Full text in Research Archive Show summary
Background: Early detection of colorectal cancer (CRC) in screening programs is important to reduce development of CRC from precursor lesions. The CRCbiome study, nested within the screening pilot Bowel Cancer Screening in Norway (BCSN), aims to identify microbial biomarkers for early CRC detection. Preliminary results from the CRCbiome study have shown diet, lifestyle and sociodemographic differences and differences in CRC incidence between the populations of the two screening centers (Bærum and Moss). The main purpose of the master’s project was to investigate regional gut microbiome differences and investigate whether there was an association between diet, lifestyle and sociodemographic factors and the microbiome profiles. Methods: A total of 1036 participants from the CRCbiome study were included. Regional microbial differences were examined using three regional determinants: 1) screening center (Bærum and Moss), 2) the centrality class of their address (centrality class 1, 2 and >3), and 3) driving time from their home to the screening center (short and long driving time). Comparative metagenomic analysis of gut microbiome was performed by investigating the diversity within-groups (α-diversity) and between-groups (β-diversity), followed by differential abundance analysis of bacterial species. Connections between differentially abundant bacteria and diet, lifestyle and sociodemographic factors were investigated using Spearman correlation coefficients as inputs in principal component analysis (PCA) and hierarchical clustering. Results: Overall, there were no regional differences in α-diversity for any of the three regional determinants investigated, but small differences in β-diversity were observed, with deviating findings when analyzing the age segment of 55-65 years, males, those with no neoplasia and those with advanced neoplasia. β-diversity did not significantly differ when comparing centrality class 2 versus class >3. Analysis of differential abundance revealed enrichment in beneficial species associated with healthier diet and lifestyle, and higher socioeconomic status, for participants affiliated to the Bærum screening center, for participants residing centrally and for those having short driving time to the screening center. The differences were mainly driven by the Firmicutes phylum, most prominently in the Bacilli and Clostridia classes. Conclusion: De-central residency and long driving time were associated with CRC risk factors and correlated with disadvantageous microbiome profiles. The study also found that beneficial microbiome profiles were correlated with factors known to reduce the risk of developing CRC. However, while the results provide valuable insights into the regional differences in the gut microbiome, further research is required to fully comprehend the impact of the differences.

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Published June 25, 2020 1:23 PM - Last modified Oct. 2, 2026 2:21 PM

Trine Ballestad Rounge

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Trine Ballestad Rounge

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