COIMMR: a computational framework to reveal the contribution of herbal ingredients against human cancer via immune microenvironment and metabolic reprogramming

Author:

Tian Saisai12,Li Yanan12,Xu Jia23,Zhang Lijun4,Zhang Jinbo5,Lu Jinyuan6,Xu Xike2,Luan Xin4,Zhao Jing4,Zhang Weidong124

Affiliation:

1. College of Pharmacy, Ningxia Medical University , Yinchuan 750004 , China

2. School of Pharmacy, Second Military Medical University , Shanghai, 200433 , China

3. College of Pharmacy, Henan University , Kaifeng 475000 , China

4. The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine

5. Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China Department of Pharmacy, Tianjin Rehabilitation Center of Joint Logistics Support Force , Tianjin, 300110 , China

6. College of Pharmacy, Anhui University of Chinese Medicine , Anhui 230012 , China

Abstract

Abstract Immune evasion and metabolism reprogramming have been regarded as two vital hallmarks of the mechanism of carcinogenesis. Thus, targeting the immune microenvironment and the reprogrammed metabolic processes will aid in developing novel anti-cancer drugs. In recent decades, herbal medicine has been widely utilized to treat cancer through the modulation of the immune microenvironment and reprogrammed metabolic processes. However, labor-based herbal ingredient screening is time consuming, laborious and costly. Luckily, some computational approaches have been proposed to screen candidates for drug discovery rapidly. Yet, it has been challenging to develop methods to screen drug candidates exclusively targeting specific pathways, especially for herbal ingredients which exert anti-cancer effects by multiple targets, multiple pathways and synergistic ways. Meanwhile, currently employed approaches cannot quantify the contribution of the specific pathway to the overall curative effect of herbal ingredients. Hence, to address this problem, this study proposes a new computational framework to infer the contribution of the immune microenvironment and metabolic reprogramming (COIMMR) in herbal ingredients against human cancer and specifically screen herbal ingredients targeting the immune microenvironment and metabolic reprogramming. Finally, COIMMR was applied to identify isoliquiritigenin that specifically regulates the T cells in stomach adenocarcinoma and cephaelin hydrochloride that specifically targets metabolic reprogramming in low-grade glioma. The in silico results were further verified using in vitro experiments. Taken together, our approach opens new possibilities for repositioning drugs targeting immune and metabolic dysfunction in human cancer and provides new insights for drug development in other diseases. COIMMR is available at https://github.com/LYN2323/COIMMR.

Funder

National Key Research and Development Program of China

National Natural Science Foundation of China

Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine

Shanghai Sailing Program

Shanghai Frontiers Science Center of TCM Chemical Biology

Shanghai Municipal Health Commission Project

Three-year Action Plan for Shanghai TCM Development and Inheritance Program

Wild Goose Array Project, Zhengzhou Center of PLAJLSF

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Information Systems

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