NeuCode Proteomics Reveals Bap1 Regulation of Metabolism

Joshua M. Baughman, Christopher M. Rose, Ganesh Kolumam, Joshua D. Webster, Emily M. Wilkerson, Anna E. Merrill, Timothy W. Rhoads, Rajkumar Noubade, Paula Katavolos, Justin Lesch, Donald S. Stapleton, Mary E. Rabaglia, Kathy L. Schueler, Raymond Asuncion, Melanie Domeyer, Jose Zavala-Solorio, Michael Reich, Jason DeVoss, Mark P. Keller, Alan D. AttieAlexander S. Hebert, Michael S. Westphall, Joshua J. Coon, Donald S. Kirkpatrick, Anwesha Dey

Research output: Contribution to journalArticlepeer-review

55 Scopus citations


We introduce neutron-encoded (NeuCode) amino acid labeling of mice as a strategy for multiplexed proteomic analysis in vivo. Using NeuCode, we characterize an inducible knockout mouse model of Bap1, a tumor suppressor and deubiquitinase whose in vivo roles outside of cancer are not well established. NeuCode proteomics revealed altered metabolic pathways following Bap1 deletion, including profound elevation of cholesterol biosynthetic machinery coincident with reduced expression of gluconeogenic and lipid homeostasis proteins in liver. Bap1 loss increased pancreatitis biomarkers and reduced expression of mitochondrial proteins. These alterations accompany a metabolic remodeling with hypoglycemia, hypercholesterolemia, hepatic lipid loss, and acinar cell degeneration. Liver-specific Bap1 null mice present with fully penetrant perinatal lethality, severe hypoglycemia, and hepatic lipid deficiency. This work reveals Bap1 as a metabolic regulator in liver and pancreas, and it establishes NeuCode as a reliable proteomic method for deciphering in vivo biology.

Original languageEnglish
Pages (from-to)583-595
Number of pages13
JournalCell Reports
Issue number2
StatePublished - Jul 12 2016


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