Characterization of Human Endogenous Retroviruses in Gastric Cancer with Helicobacter pylori: A Study from Northern Brazil

da Conceicao, M.; Pinto, J. B. A.; Pereira, D.; da Silva, V. C. S.; Avelar, D. d. S.; Mourao, R. M. d. S.; Ramos, S. A. A.; Demachki, S.; Casseb, S. M.; Neotti, T.; Anaissi, A. K. M.; Barra, W. F.; Ishak, G.; Assumpcao, P. P.; Burbano, R. M. R.; da Silva, J. M. C.; Moreira, F. C.

doi:10.1101/2025.09.06.674554

bioRxiv · 10.1101/2025.09.06.674554

Characterization of Human Endogenous Retroviruses in Gastric Cancer with Helicobacter pylori: A Study from Northern Brazil

da Conceicao, M.·Pinto, J. B. A.·Pereira, D.·da Silva, V. C. S.·Avelar, D. d. S.·Mourao, R. M. d. S.·Ramos, S. A. A.·Demachki, S.·Casseb, S. M.·Neotti, T.·Anaissi, A. K. M.·Barra, W. F.·Ishak, G.·Assumpcao, P. P.·Burbano, R. M. R.·da Silva, J. M. C.·Moreira, F. C.

View original source ↗Export metadata ↓

Abstract

Human endogenous retroviruses (HERVs) are retroelements that have integrated their genetic material into the human genome, accumulating mutations over time and accounting for approximately 8% of the genome. Under abnormal deregulation conditions, these elements can be expressed and contribute to the development of diseases, such as gastric cancer. This malignancy may be associated with infections, including those caused by Helicobacter pylori. However, the scientific literature does not yet provide clear evidence regarding the relationship between HERVs and H. pylori in the context of gastric cancer. Thus, HERVs may represent potential biomarkers for this neoplasm, as well as possible therapeutic targets. This study aimed to characterize HERV expression in gastric cancer using next-generation sequencing (NGS). We analyzed 46 tumor tissue samples and 42 peritumoral tissue samples from patients diagnosed with gastric adenocarcinoma, collected at HUJBB and Ophir Loyola hospitals. Among the tumor samples, 38 tested positive for H. pylori infection. For library preparation, 1 g of total RNA per sample was used, with integrity assessed via TapeStation ([~]260 bp band). cDNA libraries were sequenced using the Illumina NextSeq 500 platform (paired-end), following the ID Output V2 kit protocol. Alignment was performed with STAR software, and HERVs were identified and quantified using Telescope. Differential expression analysis of HERVs was performed on transcript data using DESeq2. A total of 183 HERVs were found to be differentially expressed in tumor tissues compared to adjacent tissues. In tumor samples associated with H. pylori infection, 44 HERVs showed differential expression. Overall, tumor tissues exhibited higher HERV transcription compared to adjacent tissues.

Explore related subjects

genetics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

da Conceicao, M., Pinto, J. B. A., Pereira, D., da Silva, V. C. S., Avelar, D. d. S., Mourao, R. M. d. S., Ramos, S. A. A., Demachki, S., Casseb, S. M., Neotti, T., Anaissi, A. K. M., Barra, W. F., Ishak, G., Assumpcao, P. P., Burbano, R. M. R., da Silva, J. M. C., Moreira, F. C.. 2025-09-08. Characterization of Human Endogenous Retroviruses in Gastric Cancer with Helicobacter pylori: A Study from Northern Brazil. https://doi.org/10.1101/2025.09.06.674554

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Generation of a transgenic cephalopod

Coleoid cephalopods (cuttlefish, octopus, and squid) are marine mollusks with elaborate nervous systems that support a diverse repertoire of complex behaviors. These include the neural control of the color, pattern, and texture of the skin, facilitating both adaptive camouflage and innate patterning that may reflect internal state. The development of transgenic cephalopods expressing fluorescent proteins, optogenetic actuators, and reporters of neural activity would contribute a new and important technology to cephalopod biology. The generation of transgenic cephalopods, however, has remained a major challenge. Here, we report the development of stable transgenic dwarf cuttlefish (Ascarosepion bandense) expressing ubiquitous nuclear-localized mScarlet, a red fluorescent protein. We evaluated multiple strategies for transgenesis, and established cuttlefish lines using both CRISPR and the transposons Sleeping Beauty and Minos. The stable expression of transgenes enabled live imaging of cell dynamics during embryonic development. The Minos transposon emerged as the most efficient transgenesis strategy and is adaptable to promoters and transgenes of choice. These strategies now enable the generation of diverse genetic tools for mechanistic studies of cephalopod biology.

genetics↗

bioRxiv2026

Large language model-based bibliometric evaluation of population descriptors in human genetics

As the use of population descriptors such as race, ethnicity, and ancestry have become increasingly common in modern genetics research, there have been growing calls to critically examine their use. Most notably, in 2023, the National Academies of Science, Engineering, and Medicine (NASEM) published a report titled Using Population Descriptors in Genetics and Genomics Research: A New Framework for an Evolving Field, which included eight specific and actionable recommendations for researchers to implement the ethical and accurate use of population descriptors in genetic research. Here, we use the 2023 NASEM report as a benchmark to analyze the use of population descriptors in genome-wide association studies (GWAS). We develop a general toolkit for large language model-based bibliometrics, operationalize the report's recommendations into an evaluation framework, and apply this framework to evaluate all 4,007 papers from the GWAS Catalog published between 2007 and 2025 with full text available on PubMedCentral. We find significant improvements in adherence to NASEM report recommendations over time. However, most improvements predate the publication of the NASEM report itself, suggesting the report functioned primarily as a synthesis of existing best practices rather than a catalyst for change. We conclude by highlighting opportunities for growth in the field of human genetics.

genetics↗

bioRxiv2026

Mitigating biases of rescaling in forward-in-time population genetic simulations

Forward-in-time population genetic simulations are widely used in evolutionary analyses, but simulating large populations and long genomic regions remains computationally demanding. To reduce this cost, parameter rescaling is widely employed, in which the original evolutionary process is approximated by one with a smaller population size and fewer generations. Recently, several studies using the SLiM simulator have raised concerns about the accuracy of this rescaling approach. In this study, we show that many of the biases reported in these studies can be mitigated by using a different simulation algorithm. These results reveal that the accuracy of parameter rescaling depends on how well the simulation algorithm preserves diffusion-limit properties under rescaling.

genetics↗