A5068012395- RNA modifications and cancer
- Colorectal Cancer Surgical Treatments
- Circadian rhythm and melatonin
- Colorectal Cancer Screening and Detection
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- Colorectal and Anal Carcinomas
- Cancer Genomics and Diagnostics
- Cancer-related molecular mechanisms research
- Bladder and Urothelial Cancer Treatments
- Tryptophan and brain disorders
- Genomics and Rare Diseases
- Animal Ecology and Behavior Studies
- Neuroendocrine regulation and behavior
- RNA Research and Splicing
- Ferroptosis and cancer prognosis
- Dietary Effects on Health
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Radiomics and Machine Learning in Medical Imaging
- Esophageal Cancer Research and Treatment
- Genetics, Aging, and Longevity in Model Organisms
- Genetic factors in colorectal cancer
- Genetic diversity and population structure
Peking University
2020-2025
Peking University Cancer Hospital
2020-2025
Institute of Zoology
2015-2023
Chinese Academy of Sciences
2013-2022
Chinese Nutrition Society
2013-2022
Ministry of Education of the People's Republic of China
2022
University of Chinese Academy of Sciences
2015-2018
Wenzhou Medical University
2010-2013
Institute of Psychology, Chinese Academy of Sciences
2009-2012
A growing number of genomic tools and databases were developed to facilitate the interpretation variants, particularly in coding regions. However, these are separately available different online websites or databases, making it challenging for general clinicians, geneticists biologists obtain first-hand information regarding some particular variants genes interest. Starting with regions splice sties, we artificially generated all possible single nucleotide (n = 110 154 363) cataloged...
Abstract Autism spectrum disorder (ASD) is a complex neurodevelopmental with male-to-female prevalence of 4:1. However, the genetic mechanisms underlying this gender difference remain unclear. Mutation burden analysis, TADA model, and co-expression functional network analyses were performed on de novo mutations (DNMs) corresponding candidate genes. We found that putative DNMs (loss-of-function predicted deleterious missense mutations) in females was significantly higher than males,...
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...
Highlights•Pak2+/− mice show lower spine density, defective LTP, and autism-related behaviors•LIMK1-cofilin-mediated actin polymerization was impaired in Pak2+/− mice•One de novo PAK2 nonsense mutation identified patients with ASD•PAK2 deficiency perturbed ASD-associated functional networksSummarySynaptic cytoskeleton dysfunction represents a common pathogenesis neurodevelopmental disorders, such as autism spectrum disorder (ASD). The serine/threonine kinase is critical regulator of...
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...
Preoperative neoadjuvant chemoradiotherapy (nCRT) is a standard treatment for locally advanced rectal cancer (LARC) patients, yet little known about the mediators underlying heterogeneous patient response. In this longitudinal study, we performed 16S rRNA sequencing on 353 fecal specimens and find reduced microbial diversity after nCRT. Multi-omics data integration reveals that Bacteroides vulgatus-mediated nucleotide biosynthesis associates with nCRT resistance in LARC nonresponsive tumors...
Abstract Indolent (lepidic) and aggressive (micropapillary, solid, poorly differentiated acinar) histologic subtypes often coexist within a tumor tissue of lung adenocarcinoma (LUAD), but the molecular features associated with different their transitions remain elusive. Here, we combine spatial transcriptomics multiplex immunohistochemistry to elucidate characteristics cellular plasticity distinct LUAD. We delineate transcriptional reprogramming dynamic cell signaling that determine subtype...
Abstract Hyperactive ribosome biogenesis (RiboSis) fuels unrestricted cell proliferation, whereas genomic hallmarks and therapeutic targets of RiboSis in cancers remain elusive, efficient approaches to quantify activity are still limited. Here, we have established an silico approach conveniently score based on individual transcriptome data. By employing this novel RNA-seq data 14 645 samples from TCGA/GTEx dataset 917 294 single-cell expression profiles across 13 cancer types, observed the...
Despite recent advances in imaging- and antibody-based methods, achieving in-depth, high-resolution protein mapping across entire tissues remains a significant challenge spatial proteomics. Here, we present parallel-flow projection transfer learning omics data (PLATO), an integrated framework combining microfluidics with deep to enable of thousands proteins whole tissue sections. We validated the PLATO by profiling proteome mouse cerebellum, identifying 2,564 groups single run. then applied...
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.
Abstract Background To analyse the performance of multicentre pre-treatment MRI-based radiomics (MBR) signatures combined with clinical baseline characteristics and neoadjuvant treatment modalities to predict complete response (chemo)radiotherapy in locally advanced rectal cancer (LARC). Methods Baseline MRI at four centres were collected. Decision tree, support vector machine five-fold cross-validation applied for two non-imaging three radiomics-based models’ development validation. Results...
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...
Extrachromosomal circular DNA is a hallmark of cancer, but its role in shaping the genome heterogeneity urothelial bladder carcinoma (UBC) remains poorly understood. Here, we comprehensively analyzed features extrachromosomal 80 UBC patients.
Abstract Extrachromosomal DNA (ecDNA) presents a promising target for cancer therapy; however, its spatial-temporal diversity and influence on tumor evolution the immune microenvironment remain largely unclear. We apply computational methods to analyze ecDNA from whole-genome sequencing data of 595 urothelial carcinoma (UC) patients. demonstrate that drives clonal through structural rearrangements during malignant transformation recurrence UC. This supports model wherein tumors evolve via...
The daily fluctuations of many physiologic and behavioral parameters are differentially influenced by either central or peripheral clocks in mammals. Since substance P (SP) oscillates some brain tissues plays an indispensable role modulating inflammatory pain at the spinal level, we speculated that SP mediates circadian nociception transmission level.In present study observation, real-time polymerase chain reaction, luciferase assay, chromatin immunoprecipitation, immunohistochemistry stain...
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...
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....
New sequencing technologies, such as Roche 454, ABI SOLiD and Illumina, have been increasingly developed at an astounding pace with the advantages of high throughput, reduced time cost. To satisfy impending need for deciphering large-scale data generated from next-generation sequencing, integrated software MagicViewer is to easily visualize short read mapping, identify annotate genetic variation based on reference genome. provides a user-friendly environment in which reads can be displayed...
Background: Esophageal squamous cell carcinoma (ESCC), one of the leading causes cancer mortality worldwide, is a heterogeneous with diverse clinical manifestations. However, little known about epigenetic heterogeneity and its relevance for this prevalent cancer. Methods: We generated 7.56 Tb single-base resolution whole-genome bisulfite sequencing data 84 ESCC paired paraneoplastic tissues. The analysis identified inter- intratumor DNA methylation (DNAm) heterogeneity, epigenome-wide DNAm...
Circadian rhythms govern various kinds of physiological and behavioral functions the living organisms, disruptions are highly detrimental to health. Although several databases have been built for circadian genes, a resource comprehensive post-transcriptional regulatory information RNAs expression patterns disease-related is still lacking. Here, we developed CirGRDB (http://cirgrdb.biols.ac.cn) by integrating more than 4936 genome-wide assays, with aim fulfilling growing need understand life....
Intratumor heterogeneity (ITH) has been shown to be inversely associated with immune infiltration in several cancers including clear cell renal carcinoma (ccRCC), but it remains unclear whether ITH is response immunotherapy (e.g. PD-1 blockade) ccRCC.We quantified using mutant-allele tumor heterogeneity, investigated the association of parameters patients ccRCC (n = 336) as well those papillary RCC (pRCC, n 280) from The Cancer Genome Atlas, and validations were conducted an independent...
The circadian rhythm plays a central role in immune function, and its disruption has been closely linked to the etiology of depression. However, mechanisms underlying association between depression remain unclear. We found that mice deficient Per2, clock component output, were resilient neuroinflammation-induced depressive behavior. After repeated lipopolysaccharide (LPS) injections, MCP-1, MIP-1β, RANTES increased wild type (WT) but not Per2-deficient mice. In addition,...