Ádám Györkei

• Györkei, Ádám; Johansen, Finn-Eirik & Qiao, Shuo-Wang (2026). Characterization of T-cell receptor loci and expressed repertoire reveals a capacity for robust T-cell response in Atlantic cod (Gadus morhua). Scientific Reports. 16. doi: 10.1038/s41598-026-45018-x. Full text in Research Archive
• Györkei, Ádám; Johansen, Finn-Eirik & Qiao, Shuo-Wang (2024). Systematic characterization of immunoglobulin loci and deep sequencing of the expressed repertoire in the Atlantic cod (Gadus morhua). BMC Genomics. 25(1). doi: 10.1186/s12864-024-10571-0. Full text in Research Archive Show summary

  Background The Atlantic cod is a prolific species in the Atlantic, despite its inconsistent specific antibody response. It presents a peculiar case within vertebrate immunology due to its distinct immune system, characterized by the absence of MHCII antigen presentation pathway, required for T cell-dependent antibody responses. Thorough characterisation of immunoglobulin loci and analysis of the antibody repertoire is necessary to further our understanding of the Atlantic cod’s immune response on a molecular level. Results A comprehensive search of the cod genome (gadmor3.0) identified the complete set of IgH genes organized into three sequential translocons on chromosome 2, while IgL genes were located on chromosomes 2 and 5. The Atlantic cod displayed a moderate germline V gene diversity, comprising four V gene families for both IgH and IgL, each with distinct chromosomal locations and organizational structures. 5’RACE sequencing revealed a diverse range of heavy chain CDR3 sequences and relatively limited CDR3 diversity in light chains. The analysis highlighted a differential impact of V-gene germline CDR3 length on receptor CDR3 length between heavy and light chains, underlining different recombination processes. Conclusions This study reveals that the Atlantic cod, despite its inconsistent antibody response, maintains a level of immunoglobulin diversity comparable to other fish species. The findings suggest that the extensive recent duplications of kappa light chain genes do not result in increased repertoire diversity. This research provides a comprehensive view of the Atlantic cod's immunoglobulin gene organization and repertoire, necessary for future studies of antibody responses at the molecular level.

• Porras, Adrian Lopez; Berg, Ragnhild Stenberg; Burgerhout, Erik; Hansen, Øyvind J; Györkei, Ádám & Qiao, Shuo-Wang [Show all 7 contributors for this article] (2024). CRISPR-Cas9/Cas12a-based genome editing in Atlantic cod (Gadus morhua). Aquaculture. ISSN 0044-8486. 581, p. 1–9. doi: 10.1016/j.aquaculture.2023.740440. Full text in Research Archive Show summary

  Aquaculture is the fastest-growing food sector worldwide but faces sustainability challenges that need to be addressed in many ways, including genetic enhancement. Atlantic cod has re-emerged as an aquaculture species and tools for genetic manipulation are needed. Thus, we compared five formats of CRISPR to determine which was most efficient to generate knock outs in Atlantic cod. Cas9 protein was presented in preformed ribonucleoprotein (RNP) complexes with single guide or with duplex guide RNAs or an mRNA encoding Cas9 was used with the same two formats of guide RNAs. Cas12a was tested as RNP complexes with single guide RNAs. We found Cas9 mRNA with single guide RNA to be the most efficient format to knock out both alleles of the slc45a2 gene, which resulted in an albino-like phenotype in up to 75% of surviving larvae. DNA analysis of individual larvae revealed mosaic genotypes with variable indel mutations. The mortality of injected eggs was high, resulting in low overall efficiency. Nevertheless, this study lays the foundation for further genetic and functional research using the CRISPR/Cas9 genome editing system in Atlantic cod.

• Németh-Szatmári, Orsolya; Nagy-Mikó, Bence; Györkei, Ádám; Varga, Dániel; Kovács, Bálint Barna H & Igaz, Nóra [Show all 18 contributors for this article] (2023). Phase-separated ribosome-nascent chain complexes in genotoxic stress response. RNA: A publication of the RNA Society. ISSN 1355-8382. 29(10), p. 1557–1574. doi: 10.1261/rna.079755.123. Full text in Research Archive Show summary

  Assemblysomes are EDTA- and RNase-resistant ribonucleoprotein (RNP) complexes of paused ribosomes with protruding nascent polypeptide chains. They have been described in yeast and human cells for the proteasome subunit Rpt1, and the disordered amino-terminal part of the nascent chain was found to be indispensable for the accumulation of the Rpt1-RNP into assemblysomes. Motivated by this, to find other assemblysome-associated RNPs we used bioinformatics to rank subunits of Saccharomyces cerevisiae protein complexes according to their amino-terminal disorder propensity. The results revealed that gene products involved in DNA repair are enriched among the top candidates. The Sgs1 DNA helicase was chosen for experimental validation. We found that indeed nascent chains of Sgs1 form EDTA-resistant RNP condensates, assemblysomes by definition. Moreover, upon exposure to UV, SGS1 mRNA shifted from assemblysomes to polysomes, suggesting that external stimuli are regulators of assemblysome dynamics. We extended our studies to human cell lines. The BLM helicase, ortholog of yeast Sgs1, was identified upon sequencing assemblysome-associated RNAs from the MCF7 human breast cancer cell line, and mRNAs encoding DNA repair proteins were overall enriched. Using the radiation-resistant A549 cell line, we observed by transmission electron microscopy that 1,6-hexanediol, an agent known to disrupt phase-separated condensates, depletes ring ribosome structures compatible with assemblysomes from the cytoplasm of cells and makes the cells more sensitive to X-ray treatment. Taken together, these findings suggest that assemblysomes may be a component of the DNA damage response from yeast to human.

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