| RRC ID |
68962
|
| 著者 |
Khorsandi SE, Dokal AD, Rajeeve V, Britton DJ, Illingworth MS, Heaton N, Cutillas PR.
|
| タイトル |
Computational Analysis of Cholangiocarcinoma Phosphoproteomes Identifies Patient-Specific Drug Targets.
|
| ジャーナル |
Cancer Res
|
| Abstract |
Cholangiocarcinoma is a form of hepatobiliary cancer with an abysmal prognosis. Despite advances in our understanding of cholangiocarcinoma pathophysiology and its genomic landscape, targeted therapies have not yet made a significant impact on its clinical management. The low response rates of targeted therapies in cholangiocarcinoma suggest that patient heterogeneity contributes to poor clinical outcome. Here we used mass spectrometry-based phosphoproteomics and computational methods to identify patient-specific drug targets in patient tumors and cholangiocarcinoma-derived cell lines. We analyzed 13 primary tumors of patients with cholangiocarcinoma with matched nonmalignant tissue and 7 different cholangiocarcinoma cell lines, leading to the identification and quantification of more than 13,000 phosphorylation sites. The phosphoproteomes of cholangiocarcinoma cell lines and patient tumors were significantly correlated. MEK1, KIT, ERK1/2, and several cyclin-dependent kinases were among the protein kinases most frequently showing increased activity in cholangiocarcinoma relative to nonmalignant tissue. Application of the Drug Ranking Using Machine Learning (DRUML) algorithm selected inhibitors of histone deacetylase (HDAC; belinostat and CAY10603) and PI3K pathway members as high-ranking therapies to use in primary cholangiocarcinoma. The accuracy of the computational drug rankings based on predicted responses was confirmed in cell-line models of cholangiocarcinoma. Together, this study uncovers frequently activated biochemical pathways in cholangiocarcinoma and provides a proof of concept for the application of computational methodology to rank drugs based on efficacy in individual patients. SIGNIFICANCE: Phosphoproteomic and computational analyses identify patient-specific drug targets in cholangiocarcinoma, supporting the potential of a machine learning method to predict personalized therapies.
|
| 巻・号 |
81(22)
|
| ページ |
5765-5776
|
| 公開日 |
2021-11-15
|
| DOI |
10.1158/0008-5472.CAN-21-0955
|
| PII |
0008-5472.CAN-21-0955
|
| PMID |
34551960
|
| MeSH |
Antineoplastic Agents / pharmacology*
Bile Duct Neoplasms / drug therapy
Bile Duct Neoplasms / metabolism
Bile Duct Neoplasms / pathology
Biomarkers, Tumor / antagonists & inhibitors
Biomarkers, Tumor / metabolism
Cholangiocarcinoma / drug therapy
Cholangiocarcinoma / metabolism*
Cholangiocarcinoma / pathology
Computational Biology / methods*
Drug Discovery
Humans
Phosphoproteins / analysis
Phosphoproteins / antagonists & inhibitors
Phosphoproteins / metabolism*
Protein Kinase Inhibitors / pharmacology*
Protein Kinases / chemistry*
Proteome / analysis
Proteome / metabolism*
Tumor Cells, Cultured
|
| IF |
9.727
|
| リソース情報 |
| ヒト・動物細胞 |
HuH-28(RCB1943)
TGBC1TKB(RCB1129)
TGBC24TKB(RCB1196) |
