A5025129892- Cancer Genomics and Diagnostics
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- PARP inhibition in cancer therapy
- Ferroptosis and cancer prognosis
- Cancer Immunotherapy and Biomarkers
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- DNA Repair Mechanisms
- RNA Research and Splicing
- Hippo pathway signaling and YAP/TAZ
- Genetic factors in colorectal cancer
- Protein Degradation and Inhibitors
- Molecular Biology Techniques and Applications
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Cancer Mechanisms and Therapy
- IL-33, ST2, and ILC Pathways
- Magnetic and Electromagnetic Effects
- Cancer Research and Treatments
- interferon and immune responses
- Virus-based gene therapy research
- Soil Moisture and Remote Sensing
- Breast Cancer Treatment Studies
- CRISPR and Genetic Engineering
- Cancer Cells and Metastasis
Chongqing Three Gorges University
2024
First Affiliated Hospital of Jinan University
2021-2024
Chongqing University
2024
Harbin Medical University
2016-2021
Deregulations of long non-coding RNAs (lncRNAs) have been implicated in cancer initiation and progression. Current methods can only capture differential expression lncRNAs at the population level ignore heterogeneous individual patients.We propose a method (LncRIndiv) to identify differentially expressed (DE) patients by exploiting disrupted ordering levels each disease sample comparison with stable normal ordering. LncRIndiv was applied lncRNA profiles lung adenocarcinoma (LUAD). Based on...
Long non-coding RNAs (lncRNAs) play key regulatory roles in breast cancer. However, population-level differential expression analysis methods disregard the heterogeneous of lncRNAs individual patients. Therefore, we individualized lncRNA profiles for invasive carcinoma (BRCA) using method LncRNA Individualization (LncRIndiv). After evaluating robustness LncRIndiv, constructed an differentially expressed (IDElncRNA) profile BRCA and investigated subtype-specific IDElncRNAs. The cancer...
Resistance to gemcitabine is the main challenge of chemotherapy for pancreatic ductal adenocarcinoma (PDAC). Hence, development a response signature essential precision therapy PDAC. However, existing quantitative signatures are susceptible batch effects and variations in sequencing platforms. Therefore, based on within-sample relative expression ordering pairwise genes, we developed transcriptome-based consisting 28 gene pairs (28-GPS) that could predict PDAC at individual level. The 28-GPS...
Pancreatic cancer (PC) with homologous recombination deficiency (HRD) has been reported to benefit from poly ADP-ribose polymerase (PARP) inhibitors. However, accurate identification of HRD status for PC patients the transcriptional level is still a great challenge. Here, based on relative expression ordering (REO)-based algorithm, we developed an signature including 24 gene pairs (24-GPS) using profiles The Cancer Genome Atlas (TCGA). samples classified by 24-GPS showed worse overall...
Results from numerous studies suggest an important role for somatic copy number alterations (SCNAs) in cancer progression. Our work aimed to identify the drivers (oncogenes or tumor suppressor genes) that reside recurrently aberrant genomic regions, including a large of genes non-coding genes, which remain challenge decoding SCNAs involved carcinogenesis. Here, we propose new approach comprehensively drivers, using 8740 samples involving 18 types The Cancer Genome Atlas (TCGA). On average,...
Cancer cells generally harbor hundreds of alterations in the cancer genomes and act as crucial factors development progression cancer. Gene genome form genetic interactions, which affect response patients to drugs. We developed an algorithm that mines copy number alteration whole-exome mutation profiles from The Genome Atlas (TCGA), well functional screen data generated identify potential interactions for specific types. As a result, 4,529 synthetic viability (SV) 10,637 lethality (SL) were...
Synthetic viability, which is defined as the combination of gene alterations that can rescue lethal effects a single alteration, may represent mechanism by cancer cells resist targeted drugs. Approaches to detect synthetic viable (SV) interactions in genome investigate drug resistance are still scarce. Here, we present computational method viability-induced (SVDR) integrating multidimensional data sets, including copy number whole-exome mutation, expression profile and clinical data. SVDR...
The non-cancerous components in tumor tissues, e.g., infiltrating stromal cells and immune cells, dilute purity might confound genomic mutation profile analyses the identification of pathological biomarkers. It is necessary to systematically evaluate influence purity. Here, using public gastric cancer samples from Cancer Genome Atlas (TCGA), we firstly showed that numbers mutation, separately called by four algorithms, were significant positively correlated with purities (all p <...
Synthetic lethal (SL) interactions occur when alterations in two genes lead to cell death but alteration only one of them is not lethal. SL provide a new strategy for molecular-targeted cancer therapy. Currently, there are few drugs targeting that entered into clinical trials. Therefore, it necessary investigate the link between and drug sensitivity cells systematically development purpose. We identified by integrating high-throughput data from The Cancer Genome Atlas, small hairpin RNA...
Immune checkpoint inhibitors (ICI) have revolutionized the treatment for multiple cancers. However, most of patients encounter resistance. Synthetic viability (SV) between genes could induce In this study, we established SV signature to predict efficacy ICI melanoma.We collected features and predicted gene pairs by random forest classifier. This work prioritized based on CRISPR/Cas9 screens. were constructed response melanoma patients.This study robust 14 features. Filtered screens,...
Consensus molecular subtypes (CMSs) are emerging as critical factor for prognosis and treatment of colorectal cancer. Gene regulators, including chromatin regulator, RNA-binding protein transcriptional factor, modulators cancer hallmark, yet little is known regarding the underlying functional mechanism in CMSs. Herein, we identified a core set 235 gene regulators (FGRs) by integrating genome, epigenome, transcriptome interactome FGRs exhibited significant multi-omics alterations impacts on...
Interstitial lung disease (ILD) is a group of diffuse pulmonary diseases primarily affecting the interstitium and alveolar spaces, leading to restrictive ventilatory dysfunction diffusion impairment. Patients with ILD have higher risk developing cancer, which an indisputable factor for cancer. However, pathogenesis cancer (ILD-LC) remains unclear, there are few consensus documents specific diagnosis treatment ILD-LC date. This article reviews latest advancements in epidemiology, factors,...
Abstract The Hippo signaling pathway is a highly conserved controlling organ size, cell proliferation, apoptosis and other biological functions. Recent studies have shown that also plays important roles in cancer initiation progression. However, database offering multi-omics analyses visualization of genes cancer, as well comprehensive regulatory relationships still lacking. To fill this gap, we constructed the Regulation Pathway Cancer Genome (RHPCG) database. Currently, RHPCG focuses on...
RNA-sequencing enables accurate and low-cost transcriptome-wide detection. However, expression estimates vary as reference genomes gene annotations are updated, confounding existing expression-based prognostic signatures. Herein, 9-gene pair signature (GPS) was applied to 197 patients with stage I lung adenocarcinoma derived from previous latest data The Cancer Genome Atlas (TCGA) processed different annotations. For 9-GPS, 6.6% of exhibited discordant risk classifications between the two...
Identifying robust breast cancer subtypes will help to reveal the heterogeneity. However, previous were based on population-level quantitative gene expression, which is affected by batch effects and cannot be applied individuals. We detected differential genomic, epigenomic alterations identify driver expression at individual level. The reflected patients' heterogeneity revealed four subtypes. Mesenchymal subtype as most aggressive harbored deletion downregulated of genes in chromosome 11q23...
Cancer biomarkers are measurable indicators that play vital roles in clinical applications. Biomarkers body fluids have gained considerable attention since the development of liquid biopsy, and their data volume is rapidly increasing. Nevertheless, current research lacks compilation published cancer fluid into a centralized sustainable repository for researchers clinicians, despite handful small-scale specific resources. To fulfill this purpose, we developed biomarker (LiqBioer) containing...
The epithelial-mesenchymal transition (EMT) process is involved in cancer cell metastasis and immune system activation. Hence, identification of gene expression signatures capable predicting the EMT status cells essential for development therapeutic strategies. However, quantitative markers limited by batch effects, platform used, or normalization methods. We hypothesized that a set EMT-related relative orderings are highly stable epithelial samples yet reversed mesenchymal samples. To test...
Poly (ADPribose) polymerase inhibitors (PARPis) are clinically approved drugs designed according to the concept of synthetic lethality (SL) interaction. It is crucial expand scale patients who can benefit from PARPis, and overcome drug resistance associated with it. Genetic interactions (GIs) include SL viability (SV) that participate in response cancer cells. Based on hypothesis mutated genes or SV PARP1/2/3 potential sensitive resistant PARPis biomarkers, respectively, we developed a novel...
Abstract Background TMPRSS2-ERG (T2E) fusion is highly related to aggressive clinical features in prostate cancer (PC), which guides individual therapy. However, current prediction tools lacked enough accuracy and biomarkers were unable be applied individuals across different platforms due their quantitative nature. This study aims identify a transcriptome signature detect the T2E status of PC at level. Methods Based on 272 high-throughput mRNA expression profiles from Sboner dataset, we...