ritap

• Pinto, Rita Isabel Morais; Sjurgard, Ingrid Vikan; Pharo, Heidi; Mala, Tom; Vedeld, Hege Marie & Lind, Guro Elisabeth (2025). Molecular stratification of esophageal adenocarcinoma: implications for prognosis and treatment strategy. Oncogene. ISSN 0950-9232. 45, s. 353–367. doi: 10.1038/s41388-025-03650-3. Fulltekst i vitenarkiv Vis sammendrag

  Genome-wide molecular profiling has emerged as a promising approach for advancing the clinical management of esophageal adenocarcinoma (EAC), with the potential to improve prognostic accuracy and enable more personalized treatment strategies. In this review, we summarize current evidence from genomic and epigenomic EAC stratification studies, highlighting the proposed molecular subtypes and evaluating their clinical relevance. We discuss how these subclassifications may inform disease outcomes, refine patient selection for specific therapies and uncover new treatment opportunities aligned with tumor molecular profiles. Additionally, we explore molecular subtypes associated with Barrett’s esophagus, a precursor lesion of EAC, and consider how these insights can help elucidate the mechanisms underlying EAC development. Such understanding may inform improved strategies for early tumor detection, risk stratification and prevention, ultimately aiming to reduce the burden of EAC. We also address the current challenges limiting the clinical application of these molecular classifiers, including restricted sample availability, insufficient validation and the difficulty of translating genome-wide findings into practical and clinical useful biomarkers. Integrating molecular subtyping into clinical workflows is a key step toward precision medicine in EAC, with the goal of enhancing treatment response rates and patient outcomes. Future advances will require collaborative efforts and robust clinical validation in large prospective studies to ensure that molecular stratification strategies can be effectively translated into improved management of EAC.

• Pharo, Heidi; Vedeld, Hege Marie; Sjurgard, Ingrid Vikan; Pinto, Rita Isabel Morais & Lind, Guro Elisabeth (2025). From concept to clinic: a roadmap for DNA methylation biomarkers in liquid biopsies. Oncogene. ISSN 0950-9232. 44, s. 4814–4831. doi: 10.1038/s41388-025-03624-5. Fulltekst i vitenarkiv Vis sammendrag

  Global cancer incidence continues to rise, emphasizing the urgent need for improved diagnostics and management strategies. DNA methylation biomarkers in liquid biopsies offer a promising, minimally invasive solution. Despite their potential, only a few tests have successfully transitioned from research to clinical practice. This review addresses key aspects influencing successful biomarker development and clinical implementation—including liquid biopsy source selection, biomarker discovery workflow and targeted validation in clinical sample series—and provide strategies to improve accuracy, reproducibility and clinical utility. Altogether, these considerations could aid in bridging the translational gap from research to clinical application, and to increase the number of clinically implemented liquid biopsy tests.

• Pinto, Rita Isabel Morais; Vedeld, Hege Marie; Lind, Guro Elisabeth & Jeanmougin, Marine Anne-Lise Francoise (2024). Unraveling epigenetic heterogeneity across gastrointestinal adenocarcinomas through a standardized analytical framework. Molecular Oncology. ISSN 1574-7891. doi: 10.1002/1878-0261.13772. Fulltekst i vitenarkiv Vis sammendrag

  In this study, we propose an alternative approach for stratifying genome-scale DNA methylation profiles of gastrointestinal (GI) adenocarcinomas based on a robust analytical framework. A set of 978 GI adenocarcinomas and 120 adjacent normal tissues from public repositories was quality controlled and analyzed. Hierarchical consensus clustering of the tumors, based on differential epigenetic variability between malignant and normal samples, identified six distinct subtypes defined either by a pan-GI or a lower GI-specific phenotype. In addition to methylation levels, aberrant methylation frequencies and the degree of DNA methylation instability contributed to the characterization of each subtype. We found significant differences in the outcome of patients, with the poorest overall survival seen for those belonging to a pan-GI subtype with infrequent aberrant methylation. In conclusion, our standardized approach contributes to a refined characterization of the epigenetic heterogeneity in GI adenocarcinomas, offering insights into subtype-specific methylation with the potential to support prognostication.

• Pinto, Rita; Hauge, Tobias; Jeanmougin, Marine; Pharo, Heidi Dietrichson; Kresse, Stine Henrichson & Honne, Hilde [Vis alle 13 forfattere av denne artikkelen] (2022). Targeted genetic and epigenetic profiling of esophageal adenocarcinomas and non-dysplastic Barrett’s esophagus. Clinical Epigenetics. 14(77), s. 1–11. doi: 10.1186/s13148-022-01287-7. Fulltekst i vitenarkiv Vis sammendrag

  Background Despite the efforts to describe the molecular landscape of esophageal adenocarcinoma (EAC) and its precursor lesion Barrett’s esophagus (BE), discrepant findings are reported. Here, we investigated the prevalence of selected genetic (TP53 mutations and microsatellite instability (MSI) status) and epigenetic (DNA promoter hypermethylation of APC, CDKN2A, MGMT, TIMP3 and MLH1) modifications in a series of 19 non-dysplastic BE and 145 EAC samples. Additional biopsies from adjacent normal tissue were also evaluated. State-of-the-art methodologies and well-defined scoring criteria were applied in all molecular analyses. Results Overall, we confirmed frequent TP53 mutations among EAC (28%) in contrast to BE, which harbored no mutations. We demonstrated that MSI and MLH1 promoter hypermethylation are rare events, both in EAC and in BE. Our findings further support that APC, CDKN2A, MGMT and TIMP3 promoter hypermethylation is frequently seen in both lesions (21–89%), as well as in a subset of adjacent normal samples (up to 12%). Conclusions Our study further enlightens the molecular background of BE and EAC. To the best of our knowledge, this is one of the largest studies addressing a targeted analysis of genetic and epigenetic modifications simultaneously across a combined series of non-dysplastic BE and EAC samples.

• Malecki, Jedrzej Mieczyslaw; O'Donohue, Marie-Francoise; Kim, Yeji; Jakobsson, Magnus; Gessa, Luca & Pinto, Rita [Vis alle 14 forfattere av denne artikkelen] (2021). Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function. Nucleic Acids Research (NAR). ISSN 0305-1048. 49(6), s. 3185–3203. doi: 10.1093/nar/gkab088. Fulltekst i vitenarkiv Vis sammendrag

  Abstract Protein methylation occurs primarily on lysine and arginine, but also on some other residues, such as histidine. METTL18 is the last uncharacterized member of a group of human methyltransferases (MTases) that mainly exert lysine methylation, and here we set out to elucidate its function. We found METTL18 to be a nuclear protein that contains a functional nuclear localization signal and accumulates in nucleoli. Recombinant METTL18 methylated a single protein in nuclear extracts and in isolated ribosomes from METTL18 knockout (KO) cells, identified as 60S ribosomal protein L3 (RPL3). We also performed an RPL3 interactomics screen and identified METTL18 as the most significantly enriched MTase. We found that His-245 in RPL3 carries a 3-methylhistidine (3MH; τ-methylhistidine) modification, which was absent in METTL18 KO cells. In addition, both recombinant and endogenous METTL18 were found to be automethylated at His-154, thus further corroborating METTL18 as a histidine-specific MTase. Finally, METTL18 KO cells displayed altered pre-rRNA processing, decreased polysome formation and codon-specific changes in mRNA translation, indicating that METTL18-mediated methylation of RPL3 is important for optimal ribosome biogenesis and function. In conclusion, we have here established METTL18 as the second human histidine-specific protein MTase, and demonstrated its functional relevance.

• Davydova, Erna; Shimazu, Tadahiro; Schuhmacher, Maren Kirstin; Jakobsson, Magnus E.; Willemen, Hanneke L.D.M. & Liu, Tongri [Vis alle 28 forfattere av denne artikkelen] (2021). The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes. Nature Communications. 12, s. 1–14. doi: 10.1038/s41467-020-20670-7. Fulltekst i vitenarkiv Vis sammendrag

  Abstract Post-translational methylation plays a crucial role in regulating and optimizing protein function. Protein histidine methylation, occurring as the two isomers 1- and 3-methylhistidine (1MH and 3MH), was first reported five decades ago, but remains largely unexplored. Here we report that METTL9 is a broad-specificity methyltransferase that mediates the formation of the majority of 1MH present in mouse and human proteomes. METTL9-catalyzed methylation requires a His-x-His (HxH) motif, where “x” is preferably a small amino acid, allowing METTL9 to methylate a number of HxH-containing proteins, including the immunomodulatory protein S100A9 and the NDUFB3 subunit of mitochondrial respiratory Complex I. Notably, METTL9-mediated methylation enhances respiration via Complex I, and the presence of 1MH in an HxH-containing peptide reduced its zinc binding affinity. Our results establish METTL9-mediated 1MH as a pervasive protein modification, thus setting the stage for further functional studies on protein histidine methylation.

• Flatin, Bjørnar Tovson Bae; Vedeld, Hege Marie; Pinto, Rita; Langerud, Jonas; Lind, Guro Elisabeth & Lothe, Ragnhild A [Vis alle 8 forfattere av denne artikkelen] (2020). Multiregional assessment of CIMP in primary colorectal cancers: Phenotype concordance but marker variability. International Journal of Cancer. ISSN 0020-7136. s. 1–6. doi: 10.1002/ijc.33425. Fulltekst i vitenarkiv Vis sammendrag

  Intratumor heterogeneity of colorectal cancers (CRCs) is manifested both at the genomic and epigenomic levels. Early genetic aberrations in carcinogenesis are clonal and present throughout the tumors, but less is known about the heterogeneity of the epigenetic CpG island methylator phenotype (CIMP). CIMP characterizes a subgroup of CRCs thought to originate from specific precursor lesions, and it is defined by widespread DNA methylation within promoter regions. In this work, we investigated CIMP in two to four multiregional samples from 30 primary tumors (n = 86 samples) using the consensus Weisenberger gene panel (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1). Twenty‐nine of 30 tumors (97%) showed concordant CIMP status in all samples, and percent methylated reference (PMR) values of all five markers had higher intertumor than intratumor variation (P value = 1.5e−09). However, a third of the CIMP+ tumors exhibited discrepancies in methylation status in at least one of the five gene markers. To conclude, CIMP status was consistent within primary CRCs, and it is likely a clonal phenotype. However, spatial discordances of the individual genes suggest that large‐scale analysis of multiregional samples could be of interest for identifying CIMP markers that are robust to intratumor heterogeneity.

• Lopes, Nair Susana da Costa Florim Ribeiro; Bergsland, Christian Holst; Bruun, Jarle; Bjørnslett, Merete Pauline; Vieira, André Filipe & Mesquita, Patrícia [Vis alle 14 forfattere av denne artikkelen] (2020). A panel of intestinal differentiation markers (CDX2, GPA33, and LI-cadherin) identifies gastric cancer patients with favourable prognosis. Gastric Cancer. ISSN 1436-3291. 23(5), s. 811–823. doi: 10.1007/s10120-020-01064-6. Fulltekst i vitenarkiv
• Malecki, Jedrzej Mieczyslaw; Willemen, Hanneke L.D.M.; Pinto, Rita; Ho, Angela Yeuan Yen; Moen, Anders & Eijkelkamp, Niels [Vis alle 7 forfattere av denne artikkelen] (2019). Human FAM173A is a mitochondrial lysine-specific methyltransferase that targets adenine nucleotide translocase and affects mitochondrial respiration. Journal of Biological Chemistry. ISSN 0021-9258. 294(31), s. 11654–11664. doi: 10.1074/jbc.RA119.009045. Fulltekst i vitenarkiv
• Pinto, Rita; Vågbø, Cathrine Broberg; Jakobsson, Magnus; Yeji, Kim; Baltissen, Marijke P & O'Donohue, Marie-Francoise [Vis alle 16 forfattere av denne artikkelen] (2019). The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA. Nucleic Acids Research (NAR). ISSN 0305-1048. 48(2), s. 830–846. doi: 10.1093/nar/gkz1147. Fulltekst i vitenarkiv Vis sammendrag

  RNA methylations are essential both for RNA structure and function, and are introduced by a number of distinct methyltransferases (MTases). In recent years, N6-methyladenosine (m6A) modification of eukaryotic mRNA has been subject to intense studies, and it has been demonstrated that m6A is a reversible modification that regulates several aspects of mRNA function. However, m6A is also found in other RNAs, such as mammalian 18S and 28S ribosomal RNAs (rRNAs), but the responsible MTases have remained elusive. 28S rRNA carries a single m6A modification, found at position A4220 (alternatively referred to as A4190) within a stem–loop structure, and here we show that the MTase ZCCHC4 is the enzyme responsible for introducing this modification. Accordingly, we found that ZCCHC4 localises to nucleoli, the site of ribosome assembly, and that proteins involved in RNA metabolism are overrepresented in the ZCCHC4 interactome. Interestingly, the absence of m6A4220 perturbs codon-specific translation dynamics and shifts gene expression at the translational level. In summary, we establish ZCCHC4 as the enzyme responsible for m6A modification of human 28S rRNA, and demonstrate its functional significance in mRNA translation.

• Malecki, Jedrzej Mieczyslaw; Willemen, Hanneke L.D.M.; Pinto, Rita; Ho, Angela Yeuan Yen; Moen, Anders & Kjønstad, Ingrid Fadum [Vis alle 10 forfattere av denne artikkelen] (2018). Lysine methylation by the mitochondrial methyltransferase FAM173B optimizes the function of mitochondrial ATP synthase. Journal of Biological Chemistry. ISSN 0021-9258. 294(4), s. 1128–1141. doi: 10.1074/jbc.RA118.005473. Fulltekst i vitenarkiv Vis sammendrag

  Lysine methylation is an important post-translational modification that is also present on mitochondrial proteins, but the mitochondrial lysine-specific methyltransferases (KMTs) responsible for modification are in most cases unknown. Here, we set out to determine the function of human family with sequence similarity 173 member B (FAM173B), a mitochondrial methyltransferase (MTase) reported to promote chronic pain. Using bioinformatics analyses and biochemical assays, we found that FAM173B contains an atypical, noncleavable mitochondrial targeting sequence responsible for its localization to mitochondria. Interestingly, CRISPR/Cas9-mediated KO of FAM173B in mammalian cells abrogated trimethylation of Lys-43 in ATP synthase c-subunit (ATPSc), a modification previously reported as ubiquitous among metazoans. ATPSc methylation was restored by complementing the KO cells with enzymatically active human FAM173B or with a putative FAM173B orthologue from the nematode Caenorhabditis elegans. Interestingly, lack of Lys-43 methylation caused aberrant incorporation of ATPSc into the ATP synthase complex and resulted in decreased ATP-generating ability of the complex, as well as decreased mitochondrial respiration. In summary, we have identified FAM173B as the long-sought KMT responsible for methylation of ATPSc, a key protein in cellular ATP production, and have demonstrated functional significance of ATPSc methylation. We suggest renaming FAM173B to ATPSc-KMT (gene name ATPSCKMT).

• Jakobsson, Magnus; Malecki, Jedrzej Mieczyslaw; Halabelian, Levon; Nilges, Benedikt S.; Pinto, Rita & Kudithipudi, Srikanth [Vis alle 14 forfattere av denne artikkelen] (2018). The dual methyltransferase METTL13 targets N terminus and Lys55 of eEF1A and modulates codon-specific translation rates. Nature Communications. 9:3411, s. 1–15. doi: 10.1038/s41467-018-05646-y. Fulltekst i vitenarkiv Vis sammendrag

  Eukaryotic elongation factor 1 alpha (eEF1A) delivers aminoacyl-tRNA to the ribosome and thereby plays a key role in protein synthesis. Human eEF1A is subject to extensive post-translational methylation, but several of the responsible enzymes remain unknown. Using a wide range of experimental approaches, we here show that human methyltransferase (MTase)-like protein 13 (METTL13) contains two distinct MTase domains targeting the N terminus and Lys55 of eEF1A, respectively. Our biochemical and structural analyses provide detailed mechanistic insights into recognition of the eEF1A N terminus by METTL13. Moreover, through ribosome profiling, we demonstrate that loss of METTL13 function alters translation dynamics and results in changed translation rates of specific codons. In summary, we here unravel the function of a human MTase, showing that it methylates eEF1A and modulates mRNA translation in a codon-specific manner.

• Pinto, Rita; Hansen, Lars; Hintze, John; Almeida, Raquel; Larsen, Sylvester & Coskun, Mehmet [Vis alle 11 forfattere av denne artikkelen] (2017). Precise integration of inducible transcriptional elements (PrIITE) enables absolute control of gene expression. Nucleic Acids Research (NAR). ISSN 0305-1048. 45:e123(13), s. 1–15. doi: 10.1093/nar/gkx371. Fulltekst i vitenarkiv

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