Model-based analysis uncovers mutations altering autophagy selectivity in human cancer

Zhu Han,Otto Baba,Zhidan Li,Yu Xue,Wanshan Ning,Xiaohui Liu,Wankun Deng,Da Jia,Lu Chen,Chenwei Wang,Zehua Shang,Weizhi Zhang,Xiaofei Shen,Tsuyoshi Morita

doi:10.1038/s41467-021-23539-5

Abstract

Autophagy can selectively target protein aggregates, pathogens, and dysfunctional organelles for the lysosomal degradation. Aberrant regulation of autophagy promotes tumorigenesis, while it is far less clear whether and how tumor-specific alterations result in autophagic aberrance. To form a link between aberrant autophagy selectivity and human cancer, we establish a computational pipeline and prioritize 222 potential LIR (LC3-interacting region) motif-associated mutations (LAMs) in 148 proteins. We validate LAMs in multiple proteins including ATG4B, STBD1, EHMT2 and BRAF that impair their interactions with LC3 and autophagy activities. Using a combination of transcriptomic, metabolomic and additional experimental assays, we show that STBD1, a poorly-characterized protein, inhibits tumor growth via modulating glycogen autophagy, while a patient-derived W203C mutation on LIR abolishes its cancer inhibitory function. This work suggests that altered autophagy selectivity is a frequently-used mechanism by cancer cells to survive during various stresses, and provides a framework to discover additional autophagy-related pathways that influence carcinogenesis.

Highlights

Autophagy can selectively target protein aggregates, pathogens, and dysfunctional organelles for the lysosomal degradation
To explore the link between aberrant autophagy selectivity and human cancer, we develop a pipeline named “inference of cancerassociated LC3-interacting region (LIR)-containing proteins”, which integrates a new algorithm named “prediction of the LIR motif”, a model-based algorithm named pLAM to predict LIR motifassociated mutations (LAMs), a pan-cancer analysis, and cell- and animal-based validations
We develop a new pipeline named inference of cancerassociated LIR-containing proteins” (iCAL) to form a link between aberrant autophagy selectivity and human cancer (Fig. 1)

Summary

Introduction

Autophagy can selectively target protein aggregates, pathogens, and dysfunctional organelles for the lysosomal degradation. The dual functions of autophagy in cancer pathogenesis is supported by the analysis of the genome, transcriptome, and proteome of human cancer samples, which revealed many recurrently altered ATG genes and autophagy regulators in human tumors[14,15] Despite these efforts, it remains unknown whether DNA alterations present in the cancer patient samples lead to changes in autophagy selectivity, and how cancer cells benefit from these changes. Using iCAL, we have identified 148 LIR-containing proteins (LIRCPs) that carry single point mutations within the LIR motif, including some well-established ATG genes and autophagy regulators as well as many novel candidate genes Among these candidate genes, we functionally confirm that starch-binding domain-containing protein 1 (STBD1), a gene involved in transporting glycogen to lysosomes, has a previously unappreciated role in suppressing cancer growth. Our study provides an integrative approach to discover and verify new autophagy pathways for the development of cancer

Methods

Results

Conclusion