A5023474461- Cancer-related molecular mechanisms research
- Epigenetics and DNA Methylation
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Protein Degradation and Inhibitors
- Genomics and Chromatin Dynamics
- Ferroptosis and cancer prognosis
- Cancer-related gene regulation
- RNA Research and Splicing
- Bladder and Urothelial Cancer Treatments
- Acute Myeloid Leukemia Research
- Mechanisms of cancer metastasis
- MicroRNA in disease regulation
- Adipose Tissue and Metabolism
- Genomic variations and chromosomal abnormalities
- Glioma Diagnosis and Treatment
- Hippo pathway signaling and YAP/TAZ
- CRISPR and Genetic Engineering
- Genetic and phenotypic traits in livestock
- Histone Deacetylase Inhibitors Research
- Nanoplatforms for cancer theranostics
- Sarcoma Diagnosis and Treatment
- RNA and protein synthesis mechanisms
- Acute Lymphoblastic Leukemia research
The University of Texas Health Science Center at San Antonio
2024-2025
Northwestern University
2020-2025
The University of Texas Health Science Center at Houston
2024-2025
Shenyang Medical College
2022-2023
Shenyang First People's Hospital
2022-2023
Midwestern University
2022
Shanghai Jiao Tong University
2021-2022
Northwestern Medicine
2022
Huazhong Agricultural University
2016-2021
Ministry of Agriculture and Rural Affairs
2019
The Hi-C technique has been shown to be a promising method detect structural variations (SVs) in human genomes. However, algorithms that can use data for full-range SV detection have severely lacking. Current methods only identify interchromosomal translocations and long-range intrachromosomal SVs (>1 Mb) at less-than-optimal resolution. Therefore, we develop EagleC, framework combines deep-learning ensemble-learning strategies predict full range of high We show EagleC uniquely capture set...
Abstract Although major advances in genomics have initiated an exciting new era of research, a lack information regarding cis -regulatory elements has limited the genetic improvement or manipulation pigs as meat source and biomedical model. Here, we systematically characterize their functions 12 diverse tissues from four pig breeds by adopting similar strategies ENCODE Roadmap Epigenomics projects, which include RNA-seq, ATAC-seq, ChIP-seq. In total, generate 199 datasets identify more than...
Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression overall survival. Transcriptionally, FOXA1, GATA3, PPARG shown essential for subtype-specific gene regulation subtype switching, while TP63, STAT3, TFAP2 family members critical genes. Despite these advances, the underlying epigenetic mechanisms 3D chromatin architecture responsible in cancer remain...
Abstract Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanisms of FE essential for improvement. In this study, skeletal muscle proteome high-FE and low-FE pigs were investigated by iTRAQ approach. A total 1780 proteins identified, among which 124 differentially expressed between high- pigs, with 74 up-regulated 50 down-regulated pigs. Ten randomly selected (DEPs) validated Western blotting quantitative PCR (qPCR). Gene ontology...
Comprehensive profiling of the enhancer landscape and 3D genome structure in liposarcoma identifies extensive enhancer-oncogene coamplification hijacking events, deepening understanding how oncogenes are regulated cancer.
Feed efficiency (FE) is essential for pig production. In this study, 300 significantly differentially expressed (DE) transcripts, including 232 annotated genes, 28 cis-natural antisense transcripts (cis-NATs), and 40 long noncoding RNAs (lncRNAs), were identified between the liver of Yorkshire pigs with extremely high low FE. Among these 25 DE lncRNAs correlated 125 genes at a transcriptional level. These enriched primarily in vitamin A (VA), fatty acid, steroid hormone metabolism. VA...
The Hippo pathway plays a central role in tissue development and homeostasis. However, the function of pancreatic endocrine remains obscure. Here, we generated novel conditional genetically engineered mouse models to examine roles pathway-mediated YAP1/TAZ inhibition stages specification differentiation. While YAP1 protein was localized nuclei bipotent progenitor cells, Neurogenin 3 expressing progenitors completely lost expression. Using models, found that inactivation requires both an...
Hematopoietic stem cells (HSCs) rely on self-renewal to sustain cell potential and undergo differentiation generate mature blood cells. Mitochondrial fatty acid β-oxidation (FAO) is essential for HSC maintenance. However, the role of Carnitine palmitoyl transferase 1a (CPT1A), a key enzyme in FAO, remains unclear HSCs. Using Cpt1a hematopoietic specific conditional knock-out (Cpt1aΔ/Δ) mouse model, we found that loss leads defects, including quiescence self-renewal, increased...
Glioblastoma (GBM) is the most prevalent malignant brain tumor with poor prognosis. Although chromatin intratumoral heterogeneity a characteristic feature of GBM, current studies are conducted at single site. To investigate GBM-specific 3D genome organization and its heterogeneity, we Hi-C experiments in 21 GBM samples from nine patients, along three normal samples. We identified subcompartmentalization interactions specific to as well extensive intertumoral these levels. copy number...
Abstract Alterations in the 3D genome organization have been reported different types of cancer and linked with gene dysregulation progression. However, majority studies were performed using bulk chromatin interaction assays therefore, cannot address heterogeneity clone evolution primary human tumors. In this study, we generated single cell Hi-C ATAC-Seq data a cohort AML patients, comprising samples at disease stages, including diagnosis, remission, relapse. To our knowledge, is first large...
Pancreatic ductal adenocarcinoma (PDAC) occurs as a complex, multifaceted event driven by the interplay of tumor permissive genetic mutations, nature cellular origin and microenvironmental stress. In this study, using primary human pancreatic acinar 3D organoids, we performed CRISPR knockout screen targeting 199 previously underappreciated potential suppressors curated from clinical PDAC samples. Our data revealed significant enrichment list candidates, with NF2 emerging top target....
Feed efficiency (FE) is one of the main factors that determine production costs in pig industry. In this study, RNA Sequencing (RNA-seq) was applied to identify genes and long intergenic non-coding RNAs (lincRNAs) are differentially expressed (DE) adipose tissues Yorkshire pigs with extremely high low FE. total, 147 annotated 18 lincRNAs were identified as DE between high- low-FE pigs. Seventeen significantly correlated 112 at transcriptional level. Gene ontology (GO) analysis revealed...
Abstract >Emerging evidence indicates that microRNA (miRNA) plays an important role in adipogenesis and disease pathogenesis. To investigate the miRNA involved regulating different periods of adipogenesis, we performed a comprehensive study on microRNAome during stimulation by adipogenic differentiation cocktail C2C12 myoblasts at 0, 2, 4, 7 days using Solexa sequencing technology. In this study, identified 52 differentially expressed (DE) miRNA. Functional annotation indicated target...
miRNAs reportedly participate in various biological processes, such as skeletal muscle proliferation and differentiation. However, the regulation of differentially expressed (DE) their function myogenesis remain unclear. Herein, miRNA expression profiles during C2C12 differentiation were analyzed relation to chromatin states by RNA-seq, ATAC-seq, ChIP-seq. We identified 19 known nine novel at days 0, 1, 2, 4. The was related 113 surrounding open regions defined ATAC-seq peaks. Of these...
The domestic pig Sus scrofa domesticus originated from the wild boar S. about 10,000 years ago. During domestication, drastic morphological, physiological, and behavioral changes developed between pigs boars through artificial natural selection. long non-coding RNA (lncRNA) H19, which is located within imprinting gene cluster H19-IGF2, plays an important role in regulating muscle development humans mice. This study systematically analyzed molecular evolution of H19 its possible epigenetic...
Abstract Objective This study aims to clarify the mechanisms underlying transcriptional regulation and regulatory roles of lncRNAs in skeletal muscle cell differentiation. Methods We analysed expression patterns via time‐course RNA‐seq. Then, we further combined ATAC‐seq ChIP‐seq investigate governing differentially expressed (DE) lncRNAs. Weighted correlation network analysis GO were conducted identify transcription factor (TF)‐lncRNA pairs related Results identified 385 DE during C2C12...
Background: Cancer is considered one of the most lethal diseases worldwide. Venous thromboembolism (VTE) second leading cause death in cancer patients. As reproducible predictors thromboembolism, D-dimer level commonly by oncologists. Previous studies have demonstrated that correlated genes at are F3, F5 and FGA. Methods: Using data from TCGA multiple webtools, including GEPIA2, UALCAN, TIMER2.0, Kaplan-Meier Plotter CIBERSORTx, we analyzed tumor mutation burden (TMB), microsatellite...
Abstract Dynamic compartmentalization of eukaryotic DNA into active and repressed states enables diverse transcriptional programs to arise from a single genetic blueprint, whereas its dysregulation can be strongly linked broad spectrum diseases. While single-cell Hi-C experiments allow for chromosome conformation profiling across many cells, they are still expensive not widely available most labs. Here, we propose an alternate approach, scENCORE, computationally reconstruct chromatin...