Xi Steven Chen
A5047514480- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Cancer Cells and Metastasis
- Ferroptosis and cancer prognosis
- Epigenetics and DNA Methylation
- CRISPR and Genetic Engineering
- Prostate Cancer Treatment and Research
- Genetic factors in colorectal cancer
- Sperm and Testicular Function
- Colorectal Cancer Treatments and Studies
- Cancer-related molecular mechanisms research
- Breast Cancer Treatment Studies
- Lung Cancer Treatments and Mutations
- Urologic and reproductive health conditions
- Gene expression and cancer classification
- RNA modifications and cancer
- Colorectal Cancer Surgical Treatments
- Genomics and Chromatin Dynamics
- Bacteriophages and microbial interactions
- Renal cell carcinoma treatment
- Sexual Differentiation and Disorders
- CAR-T cell therapy research
- Fibroblast Growth Factor Research
- Gut microbiota and health
- Single-cell and spatial transcriptomics
University of Miami
2018-2025
Sylvester Comprehensive Cancer Center
2018-2024
The University of Texas MD Anderson Cancer Center
2024
Baylor College of Medicine
2024
First Affiliated Hospital of Fujian Medical University
2024
Chinese Academy of Medical Sciences & Peking Union Medical College
2024
Fujian Medical University
2024
University of Hong Kong
2024
To elucidate the deregulated functional modules that drive clear cell renal carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration proteogenomic measurements uniquely protein dysregulation cellular mechanisms impacted by alterations, including...
The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this "proteogenomics" approach was applied to 122 treatment-naive primary breast cancers accrued preserve post-translational modifications, including protein phosphorylation acetylation. Proteogenomics challenged standard cancer diagnoses, provided detailed analysis the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint...
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences perturbations to the p53 Wnt/β-catenin pathways, identified potential role for circRNAs in epithelial-mesenchymal transition, provided information about proteomic markers clinical genomic tumor subgroups, including relationships known druggable pathways. An extensive genome-wide...
Abstract Cancer driver gene alterations influence cancer development, occurring in oncogenes, tumor suppressors, and dual role genes. Discovering genes is difficult because of their elusive context-dependent behavior. We define oncogenic mediators as controlling biological processes. With them, we classify genes, unveiling roles mechanisms. To this end, present Moonlight, a tool that incorporates multiple -omics data to identify critical analyze 8000+ samples from 18 types, discovering 3310...
<div>Abstract<p>Castration-resistant prostate cancer (CRPC) is incurable and fatal, making the second leading cancer-related cause of death for American men. CRPC results from therapeutic resistance to standard-of-care androgen deprivation (AD) treatments, through incompletely understood molecular mechanisms, lacks durable options. In this study, we identified enhanced soluble guanylyl cyclase (sGC) signaling as a mechanism that restrains initiation growth. Patients with...
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Abstract Background: Radiation therapy in rectal cancer treatment is limited by variable tumor responses among patients and harmful effects on normal tissues. We developed a translational human tumoroid-organoid platform to assess novel tumor-specific strategies for radiation sensitization using matched patient-derived models. Methods: Fifteen cancer-derived tumoroids three tissue-derived organoids were established from patients, representing primary tumors, metastases, recurrences. Four...
Abstract Rectal cancer patients display heterogeneous responses to neoadjuvant treatment—including the intensive total therapy (TNT)—and reliable biomarkers are lacking guide which tumors will benefit most from these regimens. Here, we profiled DNA methylation in tumor tissue and matched patient-derived organoids (PDOs) 18 rectal cases (50 samples), leveraging Illumina MethylationEPIC array quality control filters that retained 771,964 CpG sites. Analyses used linear models (for tissue-only...
Chondrosarcomas are a heterogeneous group of malignant bone tumors that produce hyaline cartilaginous matrix. Mutations in isocitrate dehydrogenase enzymes (IDH1/2) were recently described several cancers, including conventional and dedifferentiated chondrosarcomas. These mutations lead to the inability IDH convert into α-ketoglutarate (α-KG). Instead, α-KG is reduced D-2-hydroxyglutarate (D-2HG), an oncometabolite. D-2HG thought contribute tumorigenesis due role as competitive inhibitor...
Identifying molecular characteristics that are associated with aggressive cancer phenotypes through gene expression profiling can help predict treatment responses and clinical outcomes. Claudins deregulated in colorectal (CRC). In CRC, increased claudin-1 results epithelial-to-mesenchymal transition metastasis, while claudin-7 functions as a tumor suppressor. this study, we have developed signature based on poor patient survival chemoresistance. This was validated using an integrated...
Triple-negative breast cancer (TNBC) is a highly heterogeneous disease with different molecular subtypes. Although progress has been made, the identification of TNBC subtype-associated biomarkers still hindered by traditional RNA-seq or array technologies, since bulk data detected them usually have some non-disease tissue samples, they are confined to measure averaged properties whole tissues. To overcome these constraints and discover subtype-specific prognosis signatures (TSPSigs), we...
Helicobacter pylori (H. pylori) is the leading risk factor for gastric carcinogenesis. Fibroblast growth receptor 4 (FGFR4) a member of transmembrane tyrosine kinase receptors that are activated in cancer. We investigated role FGFR4 regulating cellular response to H. infection High levels oxidative stress signature and expression were detected cancer samples. Gene set enrichment analysis (GSEA) demonstrated NRF2 samples with high levels. induced reactive oxygen species (ROS) manifested by an...
Abstract Prediction of driver genes (tumor suppressors and oncogenes) is an essential step in understanding cancer development discovering potential novel treatments. We recently proposed Moonlight as a bioinformatics framework to predict analyze them system-biology-oriented manner based on -omics integration. uses gene expression primary data source combines it with patterns related hallmarks regulatory networks identify oncogenic mediators. Once the mediators are identified, important...
Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection public health. In WWTPs, activated sludge (AS) plays major removing contaminants pathogens from wastewater. While metagenomics has advanced our understanding microbial communities, it still faces challenges revealing the genomic heterogeneity cells, uncovering dark matter, establishing precise links between genetic elements their host...
Combination chemotherapy remains essential for clinical management of triple-negative breast cancer (TNBC). Consequently, responses to individual agents cannot be easily delineated at the single patient level, even though some patients might not require all drugs in combination. Herein, we conduct multi-omic analyses orthotopic TNBC patient-derived xenografts (PDXs) treated with agent carboplatin, docetaxel, or were usually no better than best agent, enhanced response only ~13% PDX, and...
Cancer driver gene alterations influence cancer development, occurring in oncogenes, tumor suppressors, and dual role genes. Discovering genes is difficult because of their elusive context-dependent behavior. We define oncogenic mediators as controlling biological processes. With them, we classify genes, unveiling roles mechanisms. To this end, present Moonlight, a tool that incorporates multiple -omics data to identify critical analyze 8000+ tumor samples from 18 types, discovering 3310...
Abstract Rectal cancer (RC) presents significant treatment challenges, particularly in the context of chemotherapy resistance. Addressing this, our study pioneers use matched RC tumor tissue and patient-derived organoid (PDO) models coupled with innovative computational tool, Moonlight, to explore gene expression landscape tumors their response chemotherapy. We analyzed 18 samples 32 PDOs, ensuring a high-fidelity representation bioloy. Our comprehensive integration strategy involved...