A5051753526- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Cholangiocarcinoma and Gallbladder Cancer Studies
- RNA and protein synthesis mechanisms
- Animal Genetics and Reproduction
- Computational Drug Discovery Methods
- Viral Infectious Diseases and Gene Expression in Insects
- COVID-19 Clinical Research Studies
- Inhalation and Respiratory Drug Delivery
- Sex work and related issues
- COVID-19 diagnosis using AI
- Genomic variations and chromosomal abnormalities
- Bioinformatics and Genomic Networks
- Viral-associated cancers and disorders
- CRISPR and Genetic Engineering
- COVID-19 Impact on Reproduction
- Sexuality, Behavior, and Technology
- Single-cell and spatial transcriptomics
- COVID-19 and Mental Health
- Adolescent Sexual and Reproductive Health
- T-cell and B-cell Immunology
- Cancer-related molecular mechanisms research
- Viral Infections and Immunology Research
- Cytomegalovirus and herpesvirus research
Weill Cornell Medicine
2019-2024
Cornell University
2019-2024
Abstract Human endogenous retroviruses (HERVs) are repetitive elements previously implicated in major psychiatric conditions, but their role aetiology remains unclear. Here, we perform specialised transcriptome-wide association studies that consider HERV expression quantified to precise genomic locations, using RNA sequencing and genetic data from 792 post-mortem brain samples. In Europeans, identify 1238 HERVs with regulated cis , of which 26 represent signals associated disorders, ten...
SARS-CoV-2 promotes an imbalanced host response that underlies the development and severity of COVID-19. Infections with viruses are known to modulate transposable elements (TEs), which can exert downstream effects by modulating gene expression, innate immune sensing, or activities encoded their protein products. We investigated impact infection on TE expression using RNA-Seq data from cell lines primary patient samples. Using a bioinformatics tool, Telescope, we showed led upregulation...
Abstract Human endogenous retroviruses (HERVs) are the germline embedded proviral fragments of ancient retroviral infections that make up roughly 8% human genome. Our understanding HERVs in physiology primarily surrounds their non-coding functions, while protein coding capacity remains virtually uncharacterized. Therefore, we applied bioinformatic pipeline “hervQuant” to high-resolution ribosomal profiling healthy tissues provide a comprehensive overview translationally active HERVs. We find...
Alzheimer's disease (AD) is characterized by the pathological accumulation of amyloid β (Aβ) plaques and neurofibrillary tangles composed hyperphosphorylated tau. Microglia astrocytes respond to abnormal presence tau protein with induced transposable element (TE) transcription. In this Forum, we discuss new data that link dysregulated TE expression AD pathogenesis.
Abstract Human endogenous retroviruses (HERV) have been implicated in a variety of diseases including cancers. Recent research implicates HERVs epigenetic gene regulation. Here we utilize recently developed bioinformatics tool for identifying HERV expression at the locus-specific level to identify differential matched tumor-normal RNA-sequencing (RNA-seq) data from The Cancer Genome Atlas. Data 52 prostate cancer, 111 breast and 24 colon cancer cases were analyzed. Locus-specific analysis...
Abstract Background Vaccination programs have been launched worldwide to halt the spread of COVID-19. However, identification existing, safe compounds with combined treatment and prophylactic properties would be beneficial individuals who are waiting vaccinated, particularly in less economically developed countries, where vaccine availability may initially limited. Methods We used a data-driven approach, combining results from screening large transcriptomic database (L1000) molecular docking...
There have been more than 116,000 recorded deaths worldwide to-date caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), etiological agent of Coronavirus Disease 2019 (COVID-19), and over 1.8 million individuals are currently infected. Although there now hundreds clinical trials for COVID-19, no effective licensed treatments, while numbers infected continue to rise at an exponential rate in many parts world. Here, we used a data-driven approach utilizing...
Transposable elements (TEs) are mobile genomic sequences that encompass roughly 50% of the human genome. Class 1 TEs, or "retrotransposons," mobilize through production an RNA intermediate is then reverse transcribed to form complementary DNA (cDNA) molecules capable reinsertion. While TEs traditionally silenced maintain integrity, recognition immunostimulatory cues, such as those provided by microorganisms, drastically alters host transcription induce differential expression TEs. Emerging...
In people living with HIV (PLWH), chronic inflammation can lead to cancer initiation and progression, besides driving a dysregulated diminished immune responsiveness. infection also leads increased transcription of Human Endogenous Retroviruses (HERVs), which could increase an inflammatory environment create tumor growth suppressive high expression pro-inflammatory cytokines. order determine the impact HERV on breast microenvironment, we sequenced total RNA from formalin-fixed...
The heterogeneity of cancers are driven by diverse mechanisms underlying oncogenesis such as differential 'cell-of-origin' (COO) progenitors, mutagenesis, and viral infections. Classification B-cell lymphomas have been defined considering these characteristics. However, the expression contribution transposable elements (TEs) to B cell lymphoma or classification overlooked. We hypothesized that incorporating TE signatures would increase resolution identity during healthy malignant conditions....
Single cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex biological systems. However, most studies overlook contribution transposable element (TE) expression to transcriptome. In both scRNA-seq and bulk tissue (RNA-seq), quantification TE challenging due repetitive sequence content poorly characterized gene models. Here, we developed a tool analysis pipeline for Transposable Element Locus Level Analysis scRNA Sequencing (Stellarscope) that reassigns multi-mapped reads...
<p>There have been more than 116,000 recorded deaths worldwide to-date caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), etiological agent of Coronavirus Disease 2019 (COVID-19), and over 1.8 million individuals are currently infected. Although there now hundreds clinical trials for COVID-19, no effective licensed treatments, while numbers infected continue to rise at an exponential rate in many parts world. Here, we used a data-driven approach utilizing...
Objective Characterising the perceptions of groups most affected by HIV is fundamental in establishing guidelines for biomedical advancement. Although Brazil has successfully fought HIV/AIDS through several measures, transgender women still have a likelihood infection 55 times higher than general population. This study aimed to better understand perception and awareness cure research among trans-identifying population São Paulo, Brazil, determine factors that motivate or discourage...
<div>Abstract<p>Human endogenous retroviruses (HERV) have been implicated in a variety of diseases including cancers. Recent research implicates HERVs epigenetic gene regulation. Here we utilize recently developed bioinformatics tool for identifying HERV expression at the locus-specific level to identify differential matched tumor-normal RNA-sequencing (RNA-seq) data from The Cancer Genome Atlas. Data 52 prostate cancer, 111 breast and 24 colon cancer cases were analyzed....
Introduction: Clinical and pathological heterogeneity in aggressive B-cell non-Hodgkin lymphomas may be driven by several mechanisms of oncogenesis, such as translocations involving the immunoglobulin locus proto-oncogenes, 'cell-of-origin' from germinal center (GC), viral associations. Previous classifications have been defined one or more these characteristics transforming events. However, transposable elements (TEs), which make up roughly half human genome key regulatory functions,...
<p>Supplemental tables and figures as referenced in the manuscript.</p>
<p>Supplemental tables and figures as referenced in the manuscript.</p>
<div>Abstract<p>Human endogenous retroviruses (HERV) have been implicated in a variety of diseases including cancers. Recent research implicates HERVs epigenetic gene regulation. Here we utilize recently developed bioinformatics tool for identifying HERV expression at the locus-specific level to identify differential matched tumor-normal RNA-sequencing (RNA-seq) data from The Cancer Genome Atlas. Data 52 prostate cancer, 111 breast and 24 colon cancer cases were analyzed....