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Autophagy modulator scoring system: a user-friendly tool for quantitative analysis of methodological integrity of chemical autophagy modulator studies

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Version 2 2019-12-23, 08:44
Version 1 2019-12-15, 18:25
journal contribution
posted on 2019-12-23, 08:44 authored by Yu Dong, Yuanjia Hu, Sovan Sarkar, Wei-Xing Zong, Min Li, Du Feng, Ju-Xian Song, Diego L. Medina, Jieqiong Tan, Zhuohua Zhang, Zhenyu Yue, Jia-Hong Lu

Over the past 20 years (1999–2019), we have witnessed a rapid increase in publications involving chemical macroautophagy/autophagy modulators. However, an overview of the methodologies used in these studies is still lacking, and methodology flaws are frequently observed in some reports. To provide an objective and quantitative analysis of studies involving autophagy modulators, we present an Autophagy Modulator Scoring System (AMSS), which is designed to evaluate methodological integrity. AMSS-A includes the autophagy characterization by 4 aspects, namely, autophagosome quantification, autophagy-related biochemical changes, autophagy substrate degradation, and autophagic flux. AMSS-B contains the pharmacological and functional characteristics of chemical autophagy modulators, including lysosomal function, drug targets, autophagy-dependent pharmacological effects, and validation in multiple cell lines and in vivo models. Our analysis shows that of the 385 studies reporting chemical autophagy modulators, only 142 single studies had examined all 4 aspects of autophagy characterization in AMSS-A, and only 10 out of 142 studies had fulfilled all the AMSS criteria in a single study. A comprehensive analysis of the methodologies used in all the studies was made, along with a summary of studies that demonstrated the highest methodological integrity based on AMSS ranking. To test the reliability of the AMSS, a co-efficiency analysis of scores and co-citation values in the co-citation network was performed, and a significant co-efficiency was obtained. Collectively, AMSS provides insight into the methodological integrity of autophagy modulators studies and also offers a user-friendly toolkit to help choose appropriate assays to characterize autophagy modulators.

Abbreviations: 3-MA: 3-methyladenine; AMSS: Autophagy Modulator Scoring System; ATG: autophagy-related; BAF: bafilomycin A1; BECN1: beclin 1; CQ: chloroquine; GFP: green fluorescent protein; LC3: microtubule associated protein 1 light chain 3; mRFP: monomeric red fluorescent protein; MTOR: mechanistic target of rapamycin kinase; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate

Funding

This study was supported by the Science and Technology Development Fund, Macau SAR (File no. 092-2015-A3, 024-2017-AMJ) and the University of Macau grants (MYRG2017-00147-ICMS) awarded to Jia-Hong Lu, and the General Research Fund (HKBU 12101417,  HKBU 12100618) awarded to Min Li, and the Wellcome Trust Seed Award (109626/Z/15/Z), UKIERI (UK-India Education and Research Initiative) DST Thematic Partnership Award (2016-17-0087) awarded to Sovan Sarkar.

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