A5049113413- Chromosomal and Genetic Variations
- HIV Research and Treatment
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Genomic variations and chromosomal abnormalities
- Cytomegalovirus and herpesvirus research
- RNA modifications and cancer
- Immunodeficiency and Autoimmune Disorders
- Tracheal and airway disorders
- CRISPR and Genetic Engineering
- Neonatal Respiratory Health Research
- Viral-associated cancers and disorders
- Cystic Fibrosis Research Advances
- Single-cell and spatial transcriptomics
- Chromatin Remodeling and Cancer
Weill Cornell Medicine
2022-2024
Cornell University
2022-2024
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...
Endogenous retroelements (EREs), including human endogenous retroviruses (HERVs) and long interspersed nuclear elements (LINEs), comprise almost half of the genome. Our previous studies interferome in gut suggest potential mechanisms regarding how IFNb may drive HIV-1 pathogenesis. As ERE activity is suggested to partake type 1 immune responses incredibly sensitive viral infections, we sought elucidate underlying interactions between expression dynamics people living with (PLWH).
Germ cells are subject to exogenous retrovirus infections occasionally resulting in the genomic integration of retroviral gene sequences. These endogenized retroviruses (ERVs) found throughout mammalian genomes. Initially thought be inert, it is now appreciated that ERVs have often been co-opted for complex physiological processes. However, unregulated ERV transposition and expression a threat cellular fitness integrity, so must control through pre- post-transcriptional mechanisms. Here, we...
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...
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...
Summary Background Endogenous retroelements (EREs), including human endogenous retroviruses (HERVs) and long interspersed nuclear elements (LINEs), comprise almost half of the genome. HIV-1 infects a target cell already possessing ancient retroviral genetic material, exogenous infection modulates expression associated EREs. Following initial infection, there is rapid destruction CD4+ cells in gut lymphoid tissue (GALT). Our previous studies interferome suggest potential mechanisms regarding...