Yige Wu

Washington University in St. Louis

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Co-Authors

Li Ding

Washington University in St. Louis

Matthew A. Wyczalkowski

James S. McDonnell Foundation

Michael C. Wendl

Washington University in St. Louis

Ruiyang Liu

Guangzhou Vocational College of Science and Technology

Hui Zhang

Johns Hopkins University

Daniel Cui Zhou

Washington University in St. Louis

Chia-Kuei Mo

Washington University in St. Louis

Hua Sun

Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences

Ryan C. Fields

Washington University in St. Louis

Sherri R. Davies

Washington University in St. Louis

Cooperative Institutions

Washington University in St. Louis

263

The University of Texas MD Anderson Cancer Center

198

Harvard University

192

Baylor College of Medicine

142

National Institutes of Health

141

Memorial Sloan Kettering Cancer Center

128

Broad Institute

126

James S. McDonnell Foundation

125

National Cancer Institute

106

Dana-Farber Cancer Institute

102

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Proteogenomic Characterization of Endometrial Carcinoma

Cell (2020)

Yongchao Dou Emily Kawaler Daniel Cui Zhou Marina Gritsenko Chen Huang

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 of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. An extensive genome-wide acetylation survey yielded insights into regulatory mechanisms linking Wnt signaling and histone acetylation. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, identify new molecular associations of potential mechanistic significance in the development of endometrial cancers, and suggest novel approaches for identifying potential therapeutic targets.

Druggability

10.1016/j.cell.2020.01.026

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Citations (367)

Table S5 from Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Yige Wu Siqi Chen Xiaolu Yang Kazuhito Sato Preet Lal

Tumor volumes after 1-month and 2-month treatments

Cabozantinib

10.1158/0008-5472.24825772.v1

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Citations (0)

Table S1 from Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Yige Wu Siqi Chen Xiaolu Yang Kazuhito Sato Preet Lal

Clinical information for the patients and corresponding tumors

Cabozantinib

10.1158/0008-5472.24825784.v1

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Table S2 from Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Yige Wu Siqi Chen Xiaolu Yang Kazuhito Sato Preet Lal

Somatic mutations and copy number alterations for the tumors

Cabozantinib

10.1158/0008-5472.24825781.v1

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Proteogenomic data and resources for pan-cancer analysis

Cancer Cell (2023)

Yize Li Yongchao Dou Felipe da Veiga Leprevost Yifat Geffen Anna Calinawan

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data.

Proteogenomics

Harmonization

Proteome

10.1016/j.ccell.2023.06.009

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Citations (70)

Mechanism of hydroxy-safflower Yellow A inhibiting NLRP3 expression in microglia after ischemic stroke through TLR4/NF-κB signaling pathway to reduce neuroinflammatory injury

Journal of the Neurological Sciences (2023)

Yige Wu Lijuan Song Lijun Yin Kexin Liu Ruheng Wei

Stroke

10.1016/j.jns.2023.122373

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PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery

NAR Cancer (2022)

Soner Koc Michael W. Lloyd Jeffrey W. Grover Nan Xiao Sara Seepo

We created the PDX Network (PDXNet) portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources, to facilitate collaboration among researchers and to make these data easily available for research. The portal includes sections for resources, analysis results, metrics for PDXNet activities, data processing protocols and training materials for processing PDX data. Currently, the portal contains PDXNet model information and data resources from 334 new models across 33 cancer types. Tissue samples of these models were deposited in the NCI's Patient-Derived Model Repository (PDMR) for public access. These models have 2134 associated sequencing files from 873 samples across 308 patients, which are hosted on the Cancer Genomics Cloud powered by Seven Bridges and the NCI Cancer Data Service for long-term storage and access with dbGaP permissions. The portal includes results from freely available, robust, validated and standardized analysis workflows on PDXNet sequencing files and PDMR data (3857 samples from 629 patients across 85 disease types). The PDXNet portal is continuously updated with new data and is of significant utility to the cancer research community as it provides a centralized location for PDXNet resources, which support multi-agent treatment studies, determination of sensitivity and resistance mechanisms, and preclinical trials.

10.1093/narcan/zcac014

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Citations (16)

Supplementary Data 1 from Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Yige Wu Siqi Chen Xiaolu Yang Kazuhito Sato Preet Lal

Tumor size and body weight measurements by day

Cabozantinib

10.1158/0008-5472.24825790

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Supplementary Figures from Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Yige Wu Siqi Chen Xiaolu Yang Kazuhito Sato Preet Lal

Supplementary Figure S1-5

Cabozantinib

10.1158/0008-5472.24825787

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Prevalence of Escherichia coli and Antibiotic Resistance in Animal-Derived Food Samples — Six Districts, Beijing, China, 2020

China CDC Weekly (2021)

Hui Li Yanchao Liu Lu Yang Xuan Wu Yige Wu

Escherichia coli is an important hygiene indicator for animal-derived foods such as pork and chicken, and the contamination of retail meat is associated with the spread of antimicrobial resistance (AMR) and public health.The prevalence of E. coli in 6 different districts of Beijing was 64.1%. The contamination of chicken was more serious than pork in Beijing. E. coli isolates were highly resistant to sulfonamides (87.4%). TheampC1 and ampC2 genes were the main antibiotic resistance genotype (94.7% and 99.4%).This study highlights the need to strengthen the surveillance of antibiotic resistance of E. coli in animal-derived foods. A national or regional multicenter study is required to assess the dissemination and evolution of multidrug resistant (MDR) E. coli in clinical medicine and animal production for food.

Animal food

Food contaminant

Food hygiene

10.46234/ccdcw2021.243

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Citations (11)