Yongchao Dou
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View article: DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations
DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations Open
View article: Proteogenomic characterization unveils biomarkers associated with chemoresistance in muscle-invasive bladder cancer
Proteogenomic characterization unveils biomarkers associated with chemoresistance in muscle-invasive bladder cancer Open
To explore potential chemoresistance mechanisms and identify therapeutic opportunities in muscle-invasive bladder cancer (MIBC), we conduct comprehensive proteogenomic characterization of 46 pre- and 14 post-treatment MIBC tumors incorpora…
View article: Proteogenomic analysis of the CALGB 40601 (Alliance) HER2+ breast cancer neoadjuvant trial reveals resistance biomarkers
Proteogenomic analysis of the CALGB 40601 (Alliance) HER2+ breast cancer neoadjuvant trial reveals resistance biomarkers Open
View article: Author response: Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer
Author response: Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer Open
View article: Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer
Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer Open
ZNRF3 and RNF43 are closely related transmembrane E3 ubiquitin ligases with significant roles in development and cancer. Conventionally, their biological functions have been associated with regulating WNT signaling receptor ubiquitination …
View article: Tumor-associated antigen prediction using a single-sample gene expression state inference algorithm
Tumor-associated antigen prediction using a single-sample gene expression state inference algorithm Open
View article: A proteome-wide association study identifies putative causal proteins for breast cancer risk
A proteome-wide association study identifies putative causal proteins for breast cancer risk Open
Background Genome-wide association studies (GWAS) have identified more than 200 breast cancer risk-associated genetic loci, yet the causal genes and biological mechanisms for most loci remain elusive. Proteins, as final gene products, are …
View article: Pan-cancer proteogenomics expands the landscape of therapeutic targets
Pan-cancer proteogenomics expands the landscape of therapeutic targets Open
View article: Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer
Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer Open
ZNRF3 and RNF43 are closely related transmembrane E3 ubiquitin ligases with significant roles in development and cancer. Conventionally, their biological functions have been associated with regulating WNT signaling receptor ubiquitination …
View article: Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer
Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer Open
ZNRF3 and RNF43 are closely related transmembrane E3 ubiquitin ligases with significant roles in development and cancer. Conventionally, their biological functions have been associated with regulating WNT signaling receptor ubiquitination …
View article: Multiomics profiling of urothelial carcinoma in situ reveals CIS-specific gene signature and immune characteristics
Multiomics profiling of urothelial carcinoma in situ reveals CIS-specific gene signature and immune characteristics Open
Urothelial carcinoma in situ (CIS) is an aggressive phenotype of non-muscle-invasive bladder cancer. Molecular features unique to CIS compared to high-grade papillary tumors are underexplored. RNA sequencing of CIS, papillary tumors…
View article: Pan-cancer proteogenomics characterization of tumor immunity
Pan-cancer proteogenomics characterization of tumor immunity Open
View article: Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma
Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma Open
Background Omics characterization of pancreatic adenocarcinoma tissue is complicated by the highly heterogeneous and mixed populations of cells. We evaluate the feasibility and potential benefit of using a coring method to enrich specific …
View article: Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer
Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer Open
ZNRF3 and RNF43 are closely related transmembrane E3 ubiquitin ligases with significant roles in development and cancer. Conventionally, their biological functions have been associated with regulating WNT signaling receptor ubiquitination …
View article: Proteogenomics unveils mechanistic insights to precision oncology
Proteogenomics unveils mechanistic insights to precision oncology Open
Even though genomics plays a critical role in the development of precision treatments for cancer, the actual treatments overwhelmingly target proteins, which are responsible for most cellular function.1 Moreover, from genomic sequencing al…
View article: SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics
SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics Open
Shotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is challenging due to the extensive number of peptides shared across proteins, hindering our underst…
View article: A proteogenomics data-driven knowledge base of human cancer
A proteogenomics data-driven knowledge base of human cancer Open
View article: Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin
Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin Open
View article: Deep learning integrates histopathology and proteogenomics at a pan-cancer level
Deep learning integrates histopathology and proteogenomics at a pan-cancer level Open
View article: Proteogenomic insights suggest druggable pathways in endometrial carcinoma
Proteogenomic insights suggest druggable pathways in endometrial carcinoma Open
View article: Proteogenomic data and resources for pan-cancer analysis
Proteogenomic data and resources for pan-cancer analysis Open
View article: Pan-cancer proteogenomics connects oncogenic drivers to functional states
Pan-cancer proteogenomics connects oncogenic drivers to functional states Open
View article: Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation Open
View article: Figure S2 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Figure S2 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment Open
Figure S2. Binimetinib and fulvestrant inhibited the intended targets in the two PDXs that did not regress after treatment.
View article: FIGURE 1 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
FIGURE 1 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment Open
CNA complements mRNA for assessing NF1 status in ER+ PDX models. Sample map of 22 ER+ PDXs showing E2-dependent growth, patient disease state of sample used to generate the PDX, presence of recurring ESR1 mutat…
View article: Table S3 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Table S3 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment Open
Table S3. H-scores of NF1 protein levels in patient and PDX tumors as determined by IHC.
View article: Figure S1 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Figure S1 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment Open
Figure S1. NF1 gene structure and expression analyses.
View article: Figure S4 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Figure S4 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment Open
Figure S4. Tumor contents in the biopsy are comparable between the treatment sensitive and resistant groups.
View article: Figure S5 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Figure S5 from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment Open
Figure S5. IHC analysis on NF1 in baseline biopsies from the POL cohort.
View article: Data from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment
Data from Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor–positive Breast Cancers for Targeted Treatment Open
NF1 is a key tumor suppressor that represses both RAS and estrogen receptor-α (ER) signaling in breast cancer. Blocking both pathways by fulvestrant (F), a selective ER degrader, together with binimetinib (B), a MEK inhibitor, promotes tum…