Xiaotong Li
A5100371880- Cancer Genomics and Diagnostics
- Cancer Immunotherapy and Biomarkers
- Cancer-related molecular mechanisms research
- Nonmelanoma Skin Cancer Studies
- Genetic factors in colorectal cancer
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Atherosclerosis and Cardiovascular Diseases
- Head and Neck Cancer Studies
- Breast Cancer Treatment Studies
- MicroRNA in disease regulation
- Evolution and Genetic Dynamics
- Bioinformatics and Genomic Networks
- BRCA gene mutations in cancer
- Nutrition, Genetics, and Disease
- Dental Implant Techniques and Outcomes
- RNA Research and Splicing
- Immunotherapy and Immune Responses
- Genomics and Phylogenetic Studies
- Lung Cancer Treatments and Mutations
- dental development and anomalies
- Orthodontics and Dentofacial Orthopedics
- Epigenetics and DNA Methylation
- Cancer, Hypoxia, and Metabolism
- Gene expression and cancer classification
Zhejiang University
2025
China Pharmaceutical University
2020-2025
Capital Medical University
2023-2025
Shanxi Medical University
2024
Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences
2024
Beijing Institute of Education
2024
Beijing Tian Tan Hospital
2024
Yale University
2018-2023
Yale Cancer Center
2018-2023
Academy of Military Medical Sciences
2023
Abstract Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for resource lncRNAs with validated roles. Furthermore, it remains debated whether mutated can drive tumorigenesis, and such functions could be conserved during evolution. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, we introduce Cancer LncRNA Census (CLC), compilation 122 GENCODE causal roles in phenotypes. In contrast to existing databases, CLC requires...
Multi-omics datasets represent distinct aspects of the central dogma molecular biology. Such high-dimensional profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple using statistical fusion, rationalizes contributing evidence highlights associated genes. As part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing from...
Abstract ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds cell types, providing a universal annotation for genome interpretation. However, particular applications, it may be advantageous to use customized annotation. Here, we develop such custom by leveraging advanced assays, as eCLIP, Hi-C, whole-genome STARR-seq on number data-rich types. A key aspect this is comprehensive experimentally derived networks both transcription factors RNA-binding...
Abstract The catalog of cancer driver mutations in protein-coding genes has greatly expanded the past decade. However, non-coding are less well-characterized and only a handful recurrent mutations, most notably TERT promoter have been reported. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 across 38 tumor types, we perform multi-faceted pathway network analyses 2583 genomes 27 types compiled by PCAWG...
Multi-region sequencing is used to detect intratumor genetic heterogeneity (ITGH) in tumors. To assess whether genuine ITGH can be distinguished from artifacts, we performed whole-exome (WES) on three anatomically distinct regions of the same tumor with technical replicates estimate noise. Somatic variants were detected different WES pipelines and subsequently validated by high-depth amplicon sequencing. The cancer-only pipeline was unreliable, about 69% identified somatic being false...
How the immune microenvironment changes during neoadjuvant chemotherapy of primary breast cancer is not well understood.We analyzed pre- and post-treatment samples from 60 patients using NanoString PanCancer IO360™ assay to measure expression 750 immune-related genes corresponding 14 cell types various functions, assessed TIL counts PD-L1 protein by immunohistochemistry. Treatment associated in gene levels were compared t-test with Bonferroni correction. count, metagenes Wilcoxon test....
Neural stem cells (NSCs) are critical for brain development and maintenance of neurogenesis. However, the molecular mechanisms that regulate NSC proliferation differentiation remain unclear. Mysm1 is a deubiquitinase essential self-renewal several cells. It unknown whether plays an important role in NSCs. Here, we found was expressed NSCs its expression increased with age mice. Mice knockdown by crossing floxed mice Nestin-Cre exhibited abnormal microcephaly. deletion promoted apoptosis,...
Abstract The discovery of driver mutations is one the key motivations for cancer genome sequencing. Here , as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium which aggregated whole sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify in coding non-coding sites within genomes. Using total 1373 genomic features derived public sources, DriverPower’s...
Reprogramming of glucose metabolism is a key event in tumorigenesis and progression. Here, we show that active c-Src stimulates glycolysis by phosphorylating (Tyr194) activating PFKFB3, enzyme boosts producing fructose-2,6-bisphosphate PFK1. Increased intermediates replenish non-oxidative pentose phosphate pathway (PPP) serine for biosynthesis cancer cells. PFKFB3 knockout (KO) cells their counterpart reconstituted with PFKFB3-Y194F comparably impaired abilities proliferation, migration,...
A precise predictive biomarker for TNBC response to immunochemotherapy is urgently needed. We previously established a 27-gene IO signature derived from 101-gene model classifying TNBC. Here we report pilot study assess the performance of in predicting pCR preoperative immunochemotherapy. obtained RNA sequencing data primary tumors 55 patients with TNBC, who received neoadjuvant PD-L1 blocker durvalumab. determined power and accuracy immunomodulatory (IM) subtype identified by model,...
Abstract Purpose: We examined gene expression, germline variant, and somatic mutation features associated with pathologic response to neoadjuvant durvalumab plus chemotherapy in basal-like triple-negative breast cancer (bTNBC). Experimental Design: Germline whole-exome DNA RNA sequencing, programmed death ligand 1 (PD-L1) IHC, stromal tumor-infiltrating lymphocyte scoring were performed on 57 patients. validated our results using 162 patients from the GeparNuevo randomized trial. Results:...
Temporal predictive models have the potential to improve decisions in health care, public services, and other domains, yet they often fail effectively support decision-makers. Prior literature shows that many misalignments between model behavior decision-makers' expectations stem from issues of specification, namely how, when, for whom predictions are made. However, specifications tasks highly technical difficult non-data-scientist stakeholders interpret critique. To address this challenge...
Background Research data regarding the correlation between elevated oxidised low-density lipoprotein (oxLDL) cholesterol concentrations and unfavourable clinical outcomes in individuals experiencing minor acute ischaemic cerebrovascular events or transient attack (TIA) with presumed atherosclerotic aetiology are still limited. Methods This investigation incorporated a cohort of 5814 participants derived from Intensive Statin Antiplatelet Therapy for Acute High-Risk Intracranial Extracranial...
We previously reported that p38 MAPK signaling is required for osteoclast differentiation but not function. Here we further investigated the role of in function and mouse bone marrow macrophages (BMM phi), common precursors osteoclasts dendritic cells. Lipopolysaccharide (LPS) activated pathway BMM phi by sequential phosphorylation kinase 3/6, MAPK, activating transcription factor-2. Treatment with SB203580, a inhibitor, suppressed LPS-induced LPS stimulated production IL-1 beta, TNF alpha,...
// Qi Liu 1 , Zhen Cheng Lianzhong Luo 2 Yun Yang 3 Zhenzhu Zhang Huanhuan Ma Tao Chen Xi Huang Shu-Yong Lin Meijun Jin Qinxi Li Xiaotong State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Fujian 361102, China Central Laboratory, Medical College, Xiamen, 361008, Basic Xinxiang Henan 453003, Correspondence to: Li, e-mail: xtli@xmu.edu.cn liqinxi@xmu.edu.cn Keywords: MUC16, C-terminus, β-catenin, Wnt signaling, tumorigenesis Received: December 09,...
Salinity is a critical abiotic stress, which significantly impacts the agricultural yield worldwide. Identification of molecular mechanisms underlying salt tolerance in euhalophyte Suaeda salsa conducive to development salt-resistant crops. In present study, high-throughput RNA sequencing was performed after S. leaves were exposed 300 mM NaCl for 7 days, and 7,753 unigenes identified as differently expressed genes (DEGs) salsa, including 3,638 increased 4,115 decreased unigenes. Moreover,...
Sequence variations in coding and non-coding regions of the genome can affect gene expression signalling pathways, which turn may influence disease outcome. In this study, we integrated somatic mutations, clinical data from 930 breast cancer patients included TCGA database. Genes associated with single mutations molecular subtypes were identified by Mann-Whitney U-test their prognostic value was evaluated Kaplan-Meier Cox regression analyses. Results confirmed using profiles Metabric set (n...
Two hallmarks of cancer cells are their resistance to apoptosis and ability thrive despite reduced levels vital serum components. c-jun N-terminal kinase (JNK) activation is crucial for triggered by starvation (SS), isocitrate dehydrogenase 1 (IDH1) mutations tumorigenic, in part, because they produce the abnormal metabolite 2-hydroxyglutarate (2-HG). However, it unknown whether 2-HG-induced tumorigenesis partially due JNK inhibition thus defective SS-induced apoptosis. We show here, using...
Murine MARCO has been identified recently in subsets of macrophages located the peritoneum, marginal zone spleen, and medullary cord lymph nodes, where it proposed that serves as a bacteria‐binding receptor. A scavenger receptor family member with an extended collagenous domain, murine also demonstrated atherosclerotic lesions susceptible mice. We report here identification, tissue chromosomal localization, pharmacological characterization human (h)MARCO. hMARCO was from macrophage cDNA...
The human checkpoint kinase 2 (Chk2) plays a central role in regulation of the cellular response to DNA damage, resulting cell cycle arrest, repair, or apoptosis depending on severity damage and context. Chk2 inhibitors are being developed as sensitizers for chemotherapeutic agents. In contrast, here we report that direct activation alone (without agents) led potent inhibition cancer proliferation. absence de novo was achieved by increased expression, evidenced its phosphorylation at Thr68,...
EP300-interacting inhibitor of differentiation 1 (EID1) belongs to a protein family implicated in the control transcription, differentiation, DNA repair, and chromosomal maintenance. EID1 has very short half-life, especially G0 cells. We discovered that contains peptidic, modular degron is necessary sufficient for its polyubiquitylation proteasomal degradation. found this recognized by an Skp1, Cullin, F-box (SCF)-containing ubiquitin ligase complex uses Only Protein 21 (FBXO21) as substrate...