Genome‐Wide Association Analyses of HPV16 and HPV18 Seropositivity Identify Susceptibility Loci for Cervical Cancer

Journal of Medical Virology, Journal Year: 2025, Volume and Issue: 97(2)

Published: Jan. 31, 2025

Infection by high-risk human papillomavirus is known to exacerbate cervical cancer development. The host immune response crucial in disease regression. Large-scale genetic association studies for have identified few susceptibility variants, mainly at the leukocyte antigen locus on chromosome 6. We hypothesized that modifies risk and performed three genome-wide analyses HPV16, HPV18 HPV16/18 seropositivity 7814, 7924, 7924 samples from UK Biobank, followed validation genotyping German Cervigen case-control series of dysplasia. In GWAS analyses, we two loci associated with HPV16 (6p21.32 15q26.2), (5q31.2 14q24.3), one and/or (at 6p21.32). MAGMA gene-based analysis HLA-DQA1 HLA-DQB1 as significant (GWS) genes. genotyping, lead variant 6p21.32, rs9272293 overall (OR = 0.86, p 0.004, 95% CI 0.78-0.95, n 3710) positive invasive 0.73, 0.005, 0.59-0.91, 1431). This was found be a robust eQTL HLA-DRB1, HLA-DQB1-AS1, C4B, HLA-DRB5, HLA-DRB6, HLA-DQB1, HLA-DPB1 epithelial tissue samples. additionally genotyped twenty-four HPV variants below GWS threshold out which eleven were our cohort, suggesting further may determine outcome. Our study identifies novel genomic associate type-specific dysplasia provides evidence candidate genes loci.

Language: Английский

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A survey on predicting microbe-disease associations: biological data and computational methods

Briefings in Bioinformatics, Journal Year: 2020, Volume and Issue: 22(3)

Published: June 22, 2020

Various microbes have proved to be closely related the pathogenesis of human diseases. While many computational methods for predicting microbe-disease associations (MDAs) been developed, few systematic reviews on these reported. In this study, we provide a comprehensive overview existing methods. Firstly, introduce data used in MDA prediction Secondly, classify those into different categories by their nature and describe algorithms strategies detail. Next, experimental evaluations are conducted representative using similarity calculation compare performances. Based principles results, discuss advantages disadvantages propose suggestions improvement Considering problems at present stage, future work from three perspectives including data, formulations end.

Language: Английский

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VirGrapher: a graph-based viral identifier for long sequences from metagenomes

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 25(2)

Published: Jan. 22, 2024

Abstract Viruses are the most abundant biological entities on earth and important components of microbial communities. A metagenome contains all microorganisms from an environmental sample. Correctly identifying viruses these mixed sequences is critical in viral analyses. It common to identify long sequences, which has already been passed thought pipelines assembly binning. Existing deep learning-based methods divide into short subsequences them separately. This makes relationships between be omitted, leading poor performance sequences. In this paper, VirGrapher proposed improve identification by constructing among ones. see a sequence as graph uses Graph Convolutional Network (GCN) model learn multilayer connections nodes after GCN-based node embedding model. achieves better AUC value accuracy validation set, than three benchmark methods.

Language: Английский

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Genome-wide chromatin accessibility and selective signals of meat rabbits reveal key Cis-regulatory elements and variants during postnatal development of skeletal muscles in rabbits

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 25, 2025

The development of skeletal muscles is intricately modulated by multiple genetic factors and significantly impacts the economic value meat rabbits. However, our knowledge epigenetics in rabbit remains largely unknown. In this study, we collected leg rabbits performed assays for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) to detect open across three developmental stages: birth (D1), weaning (D35), adulthood (D75). A total 126,959 accessible regions (ACRs) were identified samples, a broad increase decrease accessibility found from D1 D35 D75, respectively. Integrative analysis transcriptome data revealed ACRs that nearly closed at but highly D75 enriched muscle development. Cis-regulation further genes dominated enhancers mainly play roles neuron muscles. Moreover, detection selection signals footprinting transcription factor both base transversion (Chr13:12144967 A-> G) dynamics PRDM1 binding site might regulate ZSWIM5 during Our study provided category potential cis-regulatory elements understanding tissue level facilitate insights into growth regulation

Language: Английский

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Insights into the role of cis-regulatory elements of 5-HT2A gene in gene expression and regulation: an in silico approach

Research in Biotechnology, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 14

Published: Aug. 29, 2024

In multicellular organisms, coherent functioning of the central nervous system (CNS) and cellular diversity are driven by changes in high-fidelity gene expression. Crucial to these processes cis-gene regulatory elements (CRE elements), which control transcription response chemical physical stimuli. Variations components a major contributor several diseases humans that result particular phenotypic endpoints. The brain’s neuropsychological dependent on G-protein-coupled receptor (GPCR) activation, various neuropsychiatric disorders linked GPCR dysfunction. 5-HT2A plays key role many brain activities due its neurobiological signaling characteristics. distinct topography 5HT2A locus is outlined this work, including functions CRE elements. Further, imprinting methylation signatures’ was investigated. Our findings indicate non-coding antisense RNA transcript (HTR2A-AS1) present may expression levels HTR2A transcript. This region’s combinatorial DNA sequences include promoters, enhancers, silencers, CTCF all play crucial regulation Moreover, epigenetic inheritance be made possible tapestry chromatin architecture components, H3K27ac, DNase I hypersensitivity, binding regions found region. It also non-canonical structures repetitive promoter region contribute genomic stability. Together, flanking gene-specific gene. They might function as plausible indicators for human illnesses.

Language: Английский

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