Recent advances in quantitative and chemical proteomics for autophagy studies

Abstract

Macroautophagy/autophagy is an evolutionarily well-conserved cellular degradative process with important biological functions that is closely implicated in health and disease. In recent years, quantitative mass spectrometry-based proteomics and chemical proteomics have emerged as important tools for the study of autophagy, through large-scale unbiased analysis of the proteome or through highly specific and accurate analysis of individual proteins of interest. At present, a variety of approaches have been successfully applied, including (i) expression and interaction proteomics for the study of protein post-translational modifications, (ii) investigating spatio-temporal dynamics of protein synthesis and degradation, and (iii) direct determination of protein activity and profiling molecular targets in the autophagic process. In this review, we attempted to provide an overview of principles and techniques relevant to the application of quantitative and chemical proteomics methods to autophagy, and outline the current landscape as well as future outlook of these methods in autophagy research.

Diurnal Rhythms Spatially and Temporally Organize Autophagy

“…Prior proteomic analyses adopted various standards for judging proteins as targets of autophagy as opposed to stable constituents of the autolysosome ( Cudjoe et al, 2017 ; Mancias et al, 2014 ; Schneider et al, 2014 ; Wong et al, 2017 ). We derived our standard for autophagy substrate detection based on the technical variability of our discovery platform, as estimated by two negative control datasets.…”

ANXA6 suppresses the tumorigenesis of cervical cancer through autophagy induction

“…To profile de novo protein synthesis during autophagy, the azide-tagged methionine analogue AHA (L-azidohomoalanine) is incorporated into protein synthesis. 12,28 Under 2 h starvation, there was still a lower signal intensity in Figure 1A. After the click reaction, we performed quantitative proteomics and identified 937 newly synthesized proteins.…”

Triptolide Induces Glioma Cell Autophagy and Apoptosis via Upregulating the ROS/JNK and Downregulating the Akt/mTOR Signaling Pathways

“…Apoptosis, or type I PCD, is critical for the development and homeostasis of multicellular organisms and is characterized by specific morphological and biochemical changes of dying cells, including cell shrinkage, nuclear condensation and fragmentation (17). Autophagy or type II PCD is an evolutionarily conserved catabolic process in which cellular material is delivered by double-membrane structures called autophagosomes to lysosomes for degradation (18). In general, apoptosis invariably contributes to cell death, whereas autophagy can play either pro-survival or pro-death roles during different stages of tumor development.…”