Membrane protein-regulated networks across human cancers

Chun-Yu Lin; Chia-Hwa Lee; Yi-Hsuan Chuang; Jung-Yu Lee; Yi-Yuan Chiu; Yan-Hwa Wu Lee; Yuh-Jyh Jong; Jenn-Kang Hwang; Sing-Han Huangq; Li-Ching Chen; Chih-Hsiung Wu; Shih-Hsin Tu; Yuan-Soon Ho; Jinn-Moon Yang

doi:10.1038/s41467-019-10920-8

Membrane protein-regulated networks across human cancers

Chun-Yu Lin, Chia-Hwa Lee, Yi-Hsuan Chuang, Jung-Yu Lee, Yi-Yuan Chiu, Yan-Hwa Wu Lee, Yuh-Jyh Jong, Jenn-Kang Hwang, Sing-Han Huangq, Li-Ching Chen, Chih-Hsiung Wu, Shih-Hsin Tu, Yuan-Soon Ho^*, Jinn-Moon Yang^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

68 Scopus citations

Abstract

Alterations in membrane proteins (MPs) and their regulated pathways have been established as cancer hallmarks and extensively targeted in clinical applications. However, the analysis of MP-interacting proteins and downstream pathways across human malignancies remains challenging. Here, we present a systematically integrated method to generate a resource of cancer membrane protein-regulated networks (CaMPNets), containing 63,746 high-confidence protein-protein interactions (PPIs) for 1962 MPs, using expression profiles from 5922 tumors with overall survival outcomes across 15 human cancers. Comprehensive analysis of CaMPNets links MP partner communities and regulated pathways to provide MP-based gene sets for identifying prognostic biomarkers and druggable targets. For example, we identify CHRNA9 with 12 PPIs (e.g., ERBB2) can be a therapeutic target and find its anti-metastasis agent, bupropion, for treatment in nicotine-induced breast cancer. This resource is a study to systematically integrate MP interactions, genomics, and clinical outcomes for helping illuminate cancer-wide atlas and prognostic landscapes in tumor homo/heterogeneity.

Original language	English
Article number	3131
Pages (from-to)	1-17
Number of pages	17
Journal	Nature Communications
Volume	10
DOIs	https://doi.org/10.1038/s41467-019-10920-8
State	Published - 16 Jul 2019

Keywords

NICOTINIC ACETYLCHOLINE-RECEPTOR
WEB SERVER
ACTIVATION
DATABASE
BINDING
GENES
ANNOTATION
PREDICTION
PHENOTYPE
DISCOVERY

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41467-019-10920-8

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title = "Membrane protein-regulated networks across human cancers",

abstract = "Alterations in membrane proteins (MPs) and their regulated pathways have been established as cancer hallmarks and extensively targeted in clinical applications. However, the analysis of MP-interacting proteins and downstream pathways across human malignancies remains challenging. Here, we present a systematically integrated method to generate a resource of cancer membrane protein-regulated networks (CaMPNets), containing 63,746 high-confidence protein-protein interactions (PPIs) for 1962 MPs, using expression profiles from 5922 tumors with overall survival outcomes across 15 human cancers. Comprehensive analysis of CaMPNets links MP partner communities and regulated pathways to provide MP-based gene sets for identifying prognostic biomarkers and druggable targets. For example, we identify CHRNA9 with 12 PPIs (e.g., ERBB2) can be a therapeutic target and find its anti-metastasis agent, bupropion, for treatment in nicotine-induced breast cancer. This resource is a study to systematically integrate MP interactions, genomics, and clinical outcomes for helping illuminate cancer-wide atlas and prognostic landscapes in tumor homo/heterogeneity.",

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AU - Lin, Chun-Yu

AU - Lee, Chia-Hwa

AU - Chuang, Yi-Hsuan

AU - Lee, Jung-Yu

AU - Chiu, Yi-Yuan

AU - Wu Lee, Yan-Hwa

AU - Jong, Yuh-Jyh

AU - Hwang, Jenn-Kang

AU - Huangq, Sing-Han

AU - Chen, Li-Ching

AU - Wu, Chih-Hsiung

AU - Tu, Shih-Hsin

AU - Ho, Yuan-Soon

AU - Yang, Jinn-Moon

PY - 2019/7/16

Y1 - 2019/7/16

N2 - Alterations in membrane proteins (MPs) and their regulated pathways have been established as cancer hallmarks and extensively targeted in clinical applications. However, the analysis of MP-interacting proteins and downstream pathways across human malignancies remains challenging. Here, we present a systematically integrated method to generate a resource of cancer membrane protein-regulated networks (CaMPNets), containing 63,746 high-confidence protein-protein interactions (PPIs) for 1962 MPs, using expression profiles from 5922 tumors with overall survival outcomes across 15 human cancers. Comprehensive analysis of CaMPNets links MP partner communities and regulated pathways to provide MP-based gene sets for identifying prognostic biomarkers and druggable targets. For example, we identify CHRNA9 with 12 PPIs (e.g., ERBB2) can be a therapeutic target and find its anti-metastasis agent, bupropion, for treatment in nicotine-induced breast cancer. This resource is a study to systematically integrate MP interactions, genomics, and clinical outcomes for helping illuminate cancer-wide atlas and prognostic landscapes in tumor homo/heterogeneity.

AB - Alterations in membrane proteins (MPs) and their regulated pathways have been established as cancer hallmarks and extensively targeted in clinical applications. However, the analysis of MP-interacting proteins and downstream pathways across human malignancies remains challenging. Here, we present a systematically integrated method to generate a resource of cancer membrane protein-regulated networks (CaMPNets), containing 63,746 high-confidence protein-protein interactions (PPIs) for 1962 MPs, using expression profiles from 5922 tumors with overall survival outcomes across 15 human cancers. Comprehensive analysis of CaMPNets links MP partner communities and regulated pathways to provide MP-based gene sets for identifying prognostic biomarkers and druggable targets. For example, we identify CHRNA9 with 12 PPIs (e.g., ERBB2) can be a therapeutic target and find its anti-metastasis agent, bupropion, for treatment in nicotine-induced breast cancer. This resource is a study to systematically integrate MP interactions, genomics, and clinical outcomes for helping illuminate cancer-wide atlas and prognostic landscapes in tumor homo/heterogeneity.

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KW - WEB SERVER

KW - ACTIVATION

KW - DATABASE

KW - BINDING

KW - GENES

KW - ANNOTATION

KW - PREDICTION

KW - PHENOTYPE

KW - DISCOVERY

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JO - Nature Communications

JF - Nature Communications

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ER -

Membrane protein-regulated networks across human cancers

Abstract

Keywords

UN SDGs

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