A5044533096- Genomic variations and chromosomal abnormalities
- Genomics and Rare Diseases
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Chromosomal and Genetic Variations
- RNA modifications and cancer
- Immunotherapy and Immune Responses
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Genetic Associations and Epidemiology
- Genetics and Neurodevelopmental Disorders
- Congenital heart defects research
- Epigenetics and DNA Methylation
- Immune Cell Function and Interaction
- Pluripotent Stem Cells Research
- Genetic Mapping and Diversity in Plants and Animals
- T-cell and B-cell Immunology
- RNA and protein synthesis mechanisms
- Invertebrate Immune Response Mechanisms
- Cancer-related gene regulation
- Genetic and phenotypic traits in livestock
- Soil Carbon and Nitrogen Dynamics
- SARS-CoV-2 detection and testing
Gaozhou People's Hospital
2025
Stanford University
2014-2024
Stanford Maternal and Child Health Research Institute
2024
Hainan Medical University
2024
Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital
2023
Daping Hospital
2023
Xinjiang Academy of Agricultural Sciences
2023
Temple University
2017-2023
Army Medical University
2023
Philadelphia University
2023
Somatic mosaicism in the human brain may alter function of individual neurons. We analyzed genomes single cells from forebrains three fetuses (15 to 21 weeks postconception) using clonal cell populations. detected 200 400 single-nucleotide variations (SNVs) per cell. SNV patterns resembled those found cancer genomes, indicating a role background mutagenesis cancer. SNVs with frequency >2% were also present spleen, revealing pregastrulation origin. reconstructed lineages for first five...
Caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time. We provide universal strategy for defining the coding potential of bacterial genomes applying ribosome profiling, RNA-seq, global 5′-RACE, liquid chromatography coupled with tandem mass spectrometry (LC-MS) data to 4-megabase C. genome. mapped transcript units at single base-pair resolution using RNA-seq together 5′-RACE. Additionally, profiling LC-MS, we translation...
Each Caulobacter cell cycle involves differentiation and an asymmetric division driven by a cyclical regulatory circuit comprised of four transcription factors (TFs) DNA methyltransferase. Using modified global 5′ RACE protocol, we globally mapped start sites (TSSs) at base-pair resolution, measured their levels multiple times in the cycle, identified factor binding sites. Out 2726 TSSs, 586 were shown to be cycle-regulated 529 for master regulators. Twenty-three percent promoters found...
Significance Caulobacter crescentus , a bacterium with an inherent asymmetric cell division, uses dynamic changes in chromosome methylation state to synchronize replication cell-cycle regulation. We identified the N 6 -methyladenine and 5-methylcytosine of every base pair at five times cycle show that 4,515 GANTC sites, recognized by CcrM methyltransferase, change from full- hemimethylation upon passage fork. Significantly, 27 sites are protected all times. also four previously unknown...
K562 is widely used in biomedical research. It one of three tier-one cell lines ENCODE and also most commonly for large-scale CRISPR/Cas9 screens. Although its functional genomic epigenomic characteristics have been extensively studied, genome sequence structural features never comprehensively analyzed. Such information essential the correct interpretation understanding vast troves existing genomics epigenomics data K562. We performed integrated deep-coverage whole-genome (short-insert),...
Abstract CTLA4 is a cell surface receptor on T cells that functions as an immune checkpoint molecule to enforce tolerance cognate antigens. Anti–CTLA4 immunotherapy highly effective at reactivating T-cell responses against melanoma, which postulated be due targeting cells. Here, we report also expressed by most human melanoma lines, well in normal melanocytes. Interferon-γ (IFNG) signaling activated the expression of gene melanocyte and cell–specific manner. Mechanistically, IFNG through...
Copy number variation (CNV) analysis is an integral component of the study human genomes in both research and clinical settings. Array-based CNV current first-tier approach cytogenetics. Decreasing costs high-throughput sequencing cloud computing have opened doors for development sequencing-based pipelines with fast turnaround times. We carry out a systematic quantitative comparative several low-coverage whole-genome (WGS) strategies to detect genome.We compared detection capabilities WGS...
We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 schizophrenia, and 59 autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, had 20 60 detectable single-nucleotide mutations, but ~6% harbored hundreds mutations. Hypermutability was associated age damaging in genes implicated cancers and, some brains, reflected vivo clonal expansions. Somatic duplications, likely arising during development, were found ~5% normal...
Few studies have been conducted to understand post-zygotic accumulation of mutations in cells the healthy human body. We reprogrammed 32 skin fibroblast from families donors into induced pluripotent stem cell (hiPSC) lines. The clonal nature hiPSC lines allows a high-resolution analysis genomes founder without being confounded by artifacts single-cell whole-genome amplification. estimate that on average children has 1035 mostly benign mosaic SNVs. On average, 235 SNVs could be directly...
HepG2 is one of the most widely used human cancer cell lines in biomedical research and main ENCODE. Although functional genomic epigenomic characteristics are extensively studied, its genome sequence has never been comprehensively analyzed higher order structural features largely unknown. The high degree aneuploidy renders traditional variant analysis methods challenging partially ineffective. Correct complete interpretation extensive genomics data from requires an understanding line’s...
Abstract Background Post-zygotic mutations incurred during DNA replication, repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in from non-cancerous tissues poses significant challenges, particularly if the only are present a small fraction cells. Results Here, Brain Mosaicism Network conducts coordinated, multi-institutional study examine ability existing methods...
CD9 and CD81 are closely related tetraspanins that regulate cell motility signaling by facilitating the organization of multimolecular membrane complexes, including integrins. We show down-regulated in smoking-related inflammatory response a macrophage line, RAW264.7. When functions were ablated with monoclonal antibody treatment, small interfering RNA transfection, or gene knock-out, macrophages less motile produced larger amounts matrix metalloproteinase (MMP)-2 MMP-9 than control cells...
Transcription factors regulate tissue patterning and cell fate determination during development; however, expression of early regulators frequently abates upon differentiation, suggesting that they may also play a role in maintaining an undifferentiated phenotype. The transcription factor paired box 3 (Pax3) is expressed by multipotent neural crest precursors implicated disorders humans such as Waardenburg syndrome. Pax3 required for development multiple lineages activation lineage-specific...
Abstract Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo RNA-binding proteins greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed a new computational approach, called BEAPR, to identify allele-specific (ASB) events eCLIP-Seq data. BEAPR takes into account crosslinking-induced sequence propensity...
Abstract When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant that evade surveillance can lead to cancer. Neurons with karyotypes arise during neurotypical brain development, but neurons almost never origin of cancers. Instead, mutations in bring about neurodevelopmental disorders, and contribute polygenic landscape neuropsychiatric neurodegenerative disease. A subset human harbors idiosyncratic copy number variants (CNVs, “CNV neurons”),...
Enkurin (ENKUR) is a tumor suppressor in some malignancies. However, its role endometrial cancer (EC) remains unknown. Here, we firstly observed that reduced ENKUR expression promotes progression and poor prognosis EC. Moreover,the overexpression of suppressed the proliferation, migration, invasion, intrahepatic dissemination EC vitro vivo. Repressing by small-interfering RNA significantly reversed inhibition cell proliferation invasion vitro. We used co-immunoprecipitation combined with...
Targeted protein degradation (TPD) is an emerging therapeutic modality in which small molecules are used to recruit targets the natural machinery of cell. Molecular glue degraders (MGD) monovalent that accomplish this by redirecting E3 ubiquitin ligases target proteins, offering potential degrade previously unliganded and ″undruggable″ proteins cancer, neurodegenerative, other diseases. While attractive due their drug-like properties, MGDs exceptionally hard discover have largely been...