Massive Proteogenomic Reanalysis of Publicly Available Proteomic Datasets of Human Tissues in Search for Protein Recoding via Adenosine-to-Inosine RNA Editing

Abstract

The proteogenomic search pipeline developed in this work has been applied for reanalysis of 40 publicly available shotgun proteomic datasets from various human tissues comprising more than 8000 individual LC–MS/MS runs, of which 5442 .raw data files were processed in total. This reanalysis was focused on searching for ADAR-mediated RNA editing events, their clustering across samples of different origins, and classification. In total, 33 recoded protein sites were identified in 21 datasets. Of those, 18 sites were detected in at least two datasets, representing the core human protein editome. In agreement with prior artworks, neural and cancer tissues were found to be enriched with recoded proteins. Quantitative analysis indicated that recoding the rate of specific sites did not directly depend on the levels of ADAR enzymes or targeted proteins themselves, rather it was governed by differential and yet undescribed regulation of interaction of enzymes with mRNA. Nine recoding sites conservative between humans and rodents were validated by targeted proteomics using stable isotope standards in the murine brain cortex and cerebellum, and an additional one was validated in human cerebrospinal fluid. In addition to previous data of the same type from cancer proteomes, we provide a comprehensive catalog of recoding events caused by ADAR RNA editing in the human proteome.

Multi-tissue transition of A-to-I RNA editing pattern and its regulatory relevance in transcription, splicing, and translation during development

“…Notably, significant up-regulation of two missense editing c.284A>G (p.K95R) and c.232A>G (p.R78G) in the insulin-like growth factor binding protein 7 ( Igfbp7 ) gene were observed in the mouse brain, heart and kidney at the adult stage compared to the embryonic stage. These two conserved missense sites were also found in other mammals, such as humans and pigs 36 . Igfbp7 encodes a member of the soluble proteins that bind insulin growth factor (IGF) and suppress downstream signaling, thereby inhibiting protein synthesis, cell growth, and survival 36 .…”

“…These two conserved missense sites were also found in other mammals, such as humans and pigs 36 . Igfbp7 encodes a member of the soluble proteins that bind insulin growth factor (IGF) and suppress downstream signaling, thereby inhibiting protein synthesis, cell growth, and survival 36 . Recent studies have observed that K95R and R78G editing in IGFBP7 showed a high level in the adult brain and cardiovascular tissues, and are reported to be up-regulated in atherosclerosis and cardiomyopathies 37, 38 .…”

“…Notably, significant up-regulation of two missense editing c.284A>G (p.K95R) and c.232A>G (p.R78G) in the insulin-like growth factor binding protein 7 (Igfbp7) gene were observed in the mouse brain, heart and kidney at the adult stage compared to the embryonic stage. These two conserved missense sites were also found in other mammals, such as humans and pigs 36 .…”

Proteogenomics in Nephrology: A New Frontier in Nephrological Research

“…Genomic Data Integration: The pipeline initiates the collection and analysis of genomic data, which encompasses DNA sequencing to identify genetic variants, such as single nucleotide polymorphisms (SNPs), insertions, deletions, and structural variants. This genomic information provides the foundational layer for understanding genetic predispositions and alterations that may influence protein expression and function [13,14].…”

“…Standardization of Software: Establishing standards for proteogenomics software can ensure consistency across different research groups. This could involve creating common interfaces or formats for input and output data [13].…”