A5046363705- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Pluripotent Stem Cells Research
- Cancer-related gene regulation
- CRISPR and Genetic Engineering
- Immune cells in cancer
- Genomics and Rare Diseases
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Cancer Immunotherapy and Biomarkers
- Bioinformatics and Genomic Networks
- Osteoarthritis Treatment and Mechanisms
- RNA and protein synthesis mechanisms
- Congenital heart defects research
- Genetics and Neurodevelopmental Disorders
- Neurogenetic and Muscular Disorders Research
- Telomeres, Telomerase, and Senescence
- Ferroptosis and cancer prognosis
- RNA regulation and disease
- Immune Cell Function and Interaction
- Long-Term Effects of COVID-19
- Genetic Syndromes and Imprinting
University of Michigan
2017-2025
Peking University
2020-2025
Peking University Third Hospital
2020-2025
Chinese Academy of Sciences
2013-2021
Chinese Nutrition Society
2013-2021
University of Chinese Academy of Sciences
2013-2017
Abstract Improvement in the clinical outcome of human cancers requires characterization genetic alterations underlying their pathogenesis. Large‐scale genomic and transcriptomic papillary thyroid carcinomas (PTCs) Western populations has revealed multiple oncogenic drivers which are essential for understanding pathogenic mechanisms this disease, while, so far, landscape Chinese patients with PTC remains uncharacterized. Here, we conducted a large‐scale analysis PTCs from China to determine...
Osteoarthritis (OA) is a musculoskeletal disorder disease affecting about 500 million people worldwide and mesenchymal sem cells (MSCs) therapy has been demonstrated as potential strategy to treat OA. However, the shear forces during direct injection harsher condition of OA environments would lead significant cell damage inhibit therapeutic efficacy. Herein, DNA supramolecular hydrogel applied delivering material for MSCs severe model, which perform extraordinary protection in against force...
The prevalence of neutral mutations in cancer cell population impedes the distinguishing cancer-causing driver from passenger mutations. To systematically prioritize oncogenic ability somatic and genes, we constructed a useful platform, OncoVar (https://oncovar.org/), which employed published bioinformatics algorithms incorporated known events to identify genes. We identified 20 162 mutations, 814 genes 2360 pathogenic pathways with high-confidence by reanalyzing 10 769 exomes 33 types...
Osteochondral injury is a common and frequent orthopedic disease that can lead to more serious degenerative joint disease. Tissue engineering promising modality for osteochondral repair, but the implanted scaffolds are often immunogenic induce unwanted foreign body reaction (FBR). Here, we prepare polypept(o)ide-based PAA-RGD hydrogel using novel thiol/thioester dual-functionalized hyperbranched polypeptide P(EG3Glu-co-Cys) maleimide-functionalized polysarcosine under biologically benign...
The effects of pore size in additively manufactured biodegradable porous magnesium on the mechanical properties and biodegradation scaffolds as well new bone formation have rarely been reported. In this work, we found that high temperature oxidation improves corrosion resistance scaffold. And characteristics scaffolds, formation, were investigated using with three different sizes, namely, 500, 800, 1400 μm (P500, P800, P1400). We discovered P500 group much better than those other two groups....
Quiescence in stem cells is traditionally considered as a state of inactive dormancy or with poised potential. Naive mouse embryonic (ESCs) can enter quiescence spontaneously upon inhibition MYC fatty acid oxidation, mimicking diapause vivo. The molecular underpinning and developmental potential quiescent ESCs (qESCs) are relatively unexplored. Here we show that qESCs possess an expanded unrestricted cell fate, capable generating both extraembryonic types (e.g., trophoblast cells). These...
Papillary thyroid carcinoma (PTC) is the fastest-growing disease caused by numerous molecular alterations in addition to previously reported DNA mutations. There a compelling need identify novel transcriptomic that are associated with pathogenesis of PTC potential diagnostic and prognostic implications.
Murine rodents are excellent models for study of adaptive radiations and speciation. Brown Norway rats (Rattus norvegicus) successful global colonizers the contributions their domesticated laboratory strains to biomedical research well established. To identify nucleotide-based speciation timing rat genomic information contributing its colonization capabilities, we analyzed 51 whole-genome sequences wild-derived sibling species, R. nitidus, identified over 20 million genetic variants in wild...
Transcription factors bind to the genome by forming specific contacts with primary DNA sequence; however, RNA-binding proteins (RBPs) have greater scope achieve binding specificity through RNA secondary structure. It has been revealed that single nucleotide variants (SNVs) alter structure, also known as RiboSNitches, exhibit 3-fold local structure changes than replicates of same sequence, demonstrated fact depletion RiboSNitches could result in alteration shapes at thousands sites, including...
The Ten Eleven Translocation 1 (TET1) protein is a DNA demethylase that regulates gene expression through altering statue of methylation. However, recent studies have demonstrated TET1 could modulate transcriptional independent its demethylation activity; yet, the detailed mechanisms underlying TET1's role in such regulation remain not well understood. Here, we uncovered Tet1 formed chromatin complex with histone acetyltransferase Mof and scaffold Sin3a mouse embryonic stem cells by...
RNAi and
Rapid advances in high-throughput sequencing technologies have led to the discovery of thousands extrachromosomal circular DNAs (eccDNAs) human genome. Loss-of-function experiments are difficult conduct on and linear chromosomes, as they usually overlap. Hence, it is challenging interpret molecular functions eccDNAs. Here, we present CircleBase (http://circlebase.maolab.org), an integrated resource analysis platform used curate eccDNAs multiple cell types. identifies putative functional by...
Polycomb group (PcG) proteins are widely utilized for transcriptional repression in eukaryotes. Here, we characterize, the protist Tetrahymena thermophila, EZL1 (E(z)-like 1) complex, with components conserved metazoan Repressive Complexes 1 and 2 (PRC1 PRC2). The complex is required histone H3 K27 K9 methylation, heterochromatin formation, transposable element control, programmed genome rearrangement. interacts EMA1, a helicase RNA interference (RNAi). This interaction implicated...
Abstract ASH1L histone methyltransferase plays a crucial role in the pathogenesis of different diseases, including acute leukemia. While represents an attractive drug target, developing inhibitors is challenging, as catalytic SET domain adapts inactive conformation with autoinhibitory loop blocking access to active site. Here, by applying fragment-based screening followed medicinal chemistry and structure-based design, we developed first-in-class small molecule domain. The crystal structures...
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers, the vast majority them are located outside coding sequences, making it challenging to directly interpret their functional effects. With rapid advances in high-throughput technologies, genome-scale long-range chromatin interactions were detected, distal target genes regulatory elements determined using three-dimensional (3D) looping. Herein, we present OncoBase...
Abstract Somatic synonymous mutations are one of the most frequent genetic variants occurring in coding region cancer genomes, while their contributions to development remain largely unknown. To assess whether involved post-transcriptional regulation contribute etiology cancers, we collected whole exome data from 8,320 patients across 22 types. By employing our developed algorithm, PIVar, identified a total 22,948 posttranscriptionally impaired SNVs (pisSNVs) spanning 2,042 genes. In...
Abstract Recent cryo-EM structures show the highly dynamic nature of MLL1-NCP (nucleosome core particle) interaction. Functional implication and regulation such dynamics remain unclear. Here we that DPY30 intrinsically disordered regions (IDRs) ASH2L work together in restricting rotational MLL1 complex on NCP. We binding to leads stabilization integration IDRs into establishes new ASH2L-NCP contacts. The significance ASH2L-DPY30 interactions is demonstrated by requirement both for dramatic...
Optimal methods could effectively improve the accuracy of predicting and identifying candidate driver genes. Various computational based on mutational frequency, network function approaches have been developed to identify mutation genes in cancer genomes. However, a comprehensive evaluation performance levels network-, function- frequency-based is lacking. In present study, we assessed compared eight criteria for network-based, one function-based three algorithms using benchmark datasets....
RRAD (Ras-related associated with diabetes) is a small Ras-related GTPase that frequently inactivated by DNA methylation of the CpG island in its promoter region cancer tissues. However, role methylation-induced inactivation tumorigenesis remains unclear. In this study, Ras-regulated transcriptome and epigenome were profiled comparing T29H (a RasV12-transformed human ovarian epithelial cell line) T29 (an immortalized but non-transformed through reduced representation bisulfite sequencing...
Abstract The current challenge in cancer research is to increase the resolution of driver prediction from gene-level mutation-level, which more closely aligned with goal precision medicine. Improved methods distinguish drivers passengers are urgently needed dig out mutations increasing exome sequencing studies. Here, we developed an ensemble method, AI-Driver (AI-based classifier, https://github.com/hatchetProject/AI-Driver), predict status somatic missense based on 23 pathogenicity...