Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-treated Pancreatic Beta Cells

Gluth, Austin; Li, Xiaolu; Gritsenko, Marina A.; Gaffrey, Matthew J.; Kim, Doo Nam; Lalli, Priscila M.; Chu, Rosalie K.; Day, Nicholas J.; Sagendorf, Tyler J.; Monroe, Matthew E.; Feng, Song; Liu, Tao; Yang, Bin; Qian, Weijun; Zhang, Tong

doi:10.1016/j.mcpro.2024.100881

Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-treated Pancreatic Beta Cells

Journal Article · Tue Dec 31 00:00:00 EST 2024 · Molecular & Cellular Proteomics

DOI:https://doi.org/10.1016/j.mcpro.2024.100881· OSTI ID:2483890

Gluth, Austin ^[1]; Li, Xiaolu ^[2]; ^[2]; Gaffrey, Matthew J. ^[2]; Kim, Doo Nam ^[2]; Lalli, Priscila M. ^[2]; Chu, Rosalie K. ^[2]; Day, Nicholas J. ^[2]; ^[2]; ^[2]; ^[2]; ^[2]; Yang, Bin ^[1]; ^[2]; Zhang, Tong ^[2]

Washington State University Tri-Cities
BATTELLE (PACIFIC NW LAB)

Studying regulation of protein function at a systems level necessitates an understanding of the interplay among diverse post-translational modifications (PTMs). A variety of proteomics sample processing workflows are currently used to study specific PTMs but rarely characterize multiple types of PTMs from the same sample inputs. Method incompatibilities and laborious sample preparation steps complicate large-scale physiological investigations and can lead to variations in results. The single-pot, solid-phase-enhanced sample preparation (SP3) method for sample cleanup is compatible with different lysis buffers and amenable to automation, making it attractive for high-throughput multi-PTM profiling. Herein, we describe an integrative SP3 workflow for multiplexed quantification of protein abundance, cysteine thiol oxidation, phosphorylation, and acetylation. The broad applicability of this approach is demonstrated using cell and tissue samples, and its utility for studying interacting regulatory networks is highlighted in a time-course experiment of cytokine-treated ß-cells. We observed a swift response in global regulation of protein abundances consistent with rapid activation of JAK-STAT and NF-?B signaling pathways. Regulators of these pathways as well as proteins involved in their target processes displayed multi-PTM dynamics indicative of a complex cellular response stages: acute, adaptation, and chronic (prolonged stress). PARP14, a negative regulator of JAK-STAT, had multiple co-localized PTMs that may be involved in intraprotein regulatory crosstalk. Our workflow provides a high-throughput platform that can profile multi-PTMomes from the same sample set, which is valuable in unraveling the functional roles of PTMs and their co-regulation.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 2483890

Report Number(s):: PNNL-SA-202916

Journal Information:: Molecular & Cellular Proteomics, Vol. 23, Issue 12

Country of Publication:: United States

Language:: English

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