A5102925600- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Epigenetics and DNA Methylation
- Barrier Structure and Function Studies
- Genomics and Phylogenetic Studies
- Cancer, Hypoxia, and Metabolism
- Machine Learning in Bioinformatics
- Ferroptosis and cancer prognosis
- Biomedical Text Mining and Ontologies
- RNA modifications and cancer
- Biotin and Related Studies
- Cancer-related molecular mechanisms research
- Cancer Cells and Metastasis
- Analytical Chemistry and Chromatography
- Genetics, Bioinformatics, and Biomedical Research
- Lung Cancer Treatments and Mutations
- Cancer, Lipids, and Metabolism
- Hair Growth and Disorders
- Extracellular vesicles in disease
- Psoriasis: Treatment and Pathogenesis
- Cancer Immunotherapy and Biomarkers
- Cancer Mechanisms and Therapy
- Wnt/β-catenin signaling in development and cancer
- Tannin, Tannase and Anticancer Activities
Jilin University
2019-2025
Qinghai University
2023
Jilin Medical University
2020
First Bethune Hospital of Jilin University
2020
University of Liverpool
2012-2019
BGI Group (China)
2017-2019
China National GeneBank
2019
Tianjin Medical University Cancer Institute and Hospital
2009-2016
Digital Proteomics (United States)
2014-2015
Center for Systems Biology
2014
Estrogen receptor β (ERβ) has been reported to play an anti-cancer role in breast cancer, but the regulatory mechanism by which ERβ exerts this effect is not clear. Claudin-6 (CLDN6), a tight junction protein, acts as tumor suppressor gene cancer. Our previous studies have found that 17β-estradiol (E2) induces CLDN6 expression and inhibits MCF-7 cell migration invasion, underlying molecular mechanisms are still unclear. In study, we aimed investigate of process involved.Polymerase chain...
The range of heterogeneous approaches available for quantifying protein abundance via mass spectrometry (MS)(1) leads to considerable challenges in modeling, archiving, exchanging, or submitting experimental data sets as supplemental material journals. To date, there has been no widely accepted format capturing the evidence trail how quantitative analysis performed by software, transferring between software packages, public databases. In context Proteomics Standards Initiative, we have...
Abstract Background As a breast cancer suppressor gene, CLDN6 overexpression was found to inhibit metastasis in our previous studies, but the specific mechanism remains unclear. This study aimed clarify role and of inhibiting metastasis. Methods Western blot, immunofluorescence transmission electron microscopy were performed detect autophagy. Wound healing, transwell assays lung mouse models used examine Phalloidin staining immunofluorescent observe actin cytoskeleton. mRNA seq, RT-PCR,...
The ProteomeXchange (PX) consortium has been established to standardize and facilitate submission dissemination of MS-based proteomics data in the public domain. In consortium, PRIDE database at European Bioinformatics Institute, acts as initial point MS/MS sets. this manuscript, we explain step by process sets PX via PRIDE. We describe detail two available workflows: 'complete' 'partial' submissions, together with tools streamline process. Throughout will use one example set containing...
Mass spectrometry (MS) is one of the primary techniques used for large-scale analysis small molecules in metabolomics studies. To date, there has been little data format standardization this field, as different software packages export results formats represented XML or plain text, making sharing, database deposition, and reanalysis highly challenging. Working within consortia Metabolomics Standards Initiative, Proteomics Society, we have created mzTab-M to act a common output from...
Self-renewal is dependent on an intrinsic gene regulatory network centered OCT4 and atypical cell cycle G1/S transition, which also regulated by OCT4. p21, a negatively associated with self-renewal senescence marker, member of the universal cyclin-dependent kinase inhibitors (CDKIs) plays critical roles in regulation transition. The expression p21 can be OCT4-targeted DNA methyltransferases (DNMTs), play distinct maintaining pluripotency properties. aim this study was to determine role human...
We have previously described CLDN6 as a tumor suppressor gene in breast cancer. Here, new finding is that was upregulated under hypoxia, commonly recognized factor promotes metastasis. In this study, we aim to explain confusing and delineate the role of cancer metastasis induced by hypoxia.RNAi ChIP assays were used confirm transcriptional regulated HIF-1α. mRNA seq KEGG analysis performed define downstream pathways CLDN6. The roles CLDN6/SENP1/HIF-1α signaling on evaluated function...
Abstract We previously identified CLDN6 as a pivotal tumor suppressor in breast cancer and unexpectedly discovered that overexpression of resulted characteristic ultrastructural alterations ferroptosis. However, the exact mechanism by which triggers ferroptosis is still elusive cancer. Our study showed was associated with patients. The integration demonstrated remarkable predictive prognostic performance. observed NRF2-mediated vitro vivo. Mechanistically, enhanced nuclear export NRF2...
Numerous software packages exist to provide support for quantifying peptides and proteins from mass spectrometry (MS) data. However, many only a subset of experimental methods or instrument types, meaning that laboratories often have use multiple packages. The Progenesis LC-MS package Nonlinear Dynamics is solution label-free quantitation. using also wish employ stable isotope-based are not natively supported in Progenesis. We developed Java programming interface can the output files...
Breast cancer (BC) ranks as the third most fatal malignant tumor worldwide, with a strong reliance on fatty acid metabolism. CLDN6, candidate BC suppressor gene, was previously identified regulator of biosynthesis; however, underlying mechanism remains elusive. In this research, we aim to clarify specific through which CLDN6 modulates anabolism and its impact growth metastasis.
Abstract Objective POU5F1 (OCT4) is implicated in cancer stem cell self‐renewal. Currently, some studies have shown that OCT4 has a dual function suppressing or promoting progression. However, the precise molecular mechanism of breast progression remains unclear. Materials and Methods RT‐PCR Western blot were utilized to investigate expression tissues cells. Cell proliferation assays mouse models applied determine effects on proliferation. DNMT1 inhibitors, ChIP, CoIP, IHC ERα inhibitors...
Rice (Oryza sativa) is one of the most important worldwide crops. The genome has been available for over 10 years and undergone several rounds annotation. We created a comprehensive database transcripts from 29 public RNA sequencing data sets, officially predicted genes Ensembl plants, common contaminants in which to search protein-level evidence. re-analyzed nine publicly accessible rice proteomics sets. In total, we identified 420K peptide spectrum matches 47K peptides 8,187 protein...
The paper presents an ontology for the description of Drug Discovery Investigation (DDI).This has been developed through use a Robot Scientist "Eve", and in consultation with industry. DDI aims to define principle entities relations research development phase drug discovery pipeline. is highly transferable extendable due its adherence accepted standards, compliance existing resources. This enables be integrated such related ontologies as Vaccine Ontology, Advancing Clinico-Genomic Trials on...
Phosphorylation is one of the most prevalent post-translational modifications and plays a key role in regulating cellular processes. We carried out bioinformatics analysis pre-existing phosphoproteomics data, to profile two model species representing largest subclasses flowering plants dicot Arabidopsis thaliana monocot Oryza sativa, understand extent which phosphorylation signaling function conserved across evolutionary divergent plants. identified 6537 phosphopeptides from 3189...
Abstract Paclitaxel (PTX) has been used in a variety of malignancies for inhibiting tumor development and improving survival. However, its clinical application is limited due to poor solubility, drug resistance, gastrointestinal reactions. Natural borneol (NB), as promoter, could help improve absorption. Therefore, the aims present study were investigate ability NB synergize with PTX induce human esophageal squamous cell carcinoma (ESCC) cells apoptosis underlying mechanism synergistic...
Summary The paper presents an ontology for the description of Drug Discovery Investigation (DDI). This has been developed through use a Robot Scientist “Eve”, and in consultation with industry. DDI aims to define principle entities relations research development phase drug discovery pipeline. is highly transferable extendable due its adherence accepted standards, compliance existing resources. enables be integrated such related ontologies as Vaccine Ontology, Advancing Clinico-Genomic Trials...
Claudin 6 (CLDN6) was found to be a breast cancer suppressor gene, which is lowly expressed in and inhibits cell proliferation upon overexpression. However, the mechanism by CLDN6 unclear. Here, we investigated this issue elucidated molecular mechanisms proliferation. First, verified that tissues patients with lower expression had worse prognosis. Next, confirmed inhibited through vitro vivo experiments. As for mechanism, c–MYC–mediated aerobic glycolysis based on metabolomic analysis of...
M2 macrophages are associated with the prognosis of bladder cancer. CLDN6 has been linked to immune infiltration and is crucial for predicting in multi-tumor. The effect on cancer remains elusive. Here, we compared a total 40 machine learning algorithms, then selected optimal algorithm develop macrophages-related signature (MMRS) based identified related module. MMRS predicted better than other models immunotherapy response. CLDN6, as an important variable MMRS, was independent factor poor...
The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for called jmzQuantML. API provides robust bridges between classes elements in files allows random access to any part file. read write capabilities, is designed be embedded other software packages, enabling support added proteomics tools...
The mzQuantML data standard was designed to capture the output of quantitative software in proteomics, support submissions public repositories, development visualization and pipeline/modular approaches. is around a common core that can be extended particular types technique through release semantic rules are checked by validation software. first supported four proteomics techniques via sets rules: (i) intensity‐based (MS 1 ) label free, (ii) MS label‐based (such as SILAC or N 15 ), (iii) 2...
The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features LC-MS peptides, proteins or groups that have quantified multiple samples. In this article we report development an open source Java-based library routines mzQuantML, called mzqLibrary, associated software visualising...