title: NeuCode Proteomics Reveals Bap1 Regulation of Metabolism.
abstract: 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.
authors.affiliation: Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Baughman
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Rose
authors.affiliation: Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Ganesh
authors.initials: G
authors.lastname: Kolumam
authors.affiliation: Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Webster
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Emily M
authors.initials: EM
authors.lastname: Wilkerson
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Anna E
authors.initials: AE
authors.lastname: Merrill
authors.affiliation: Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Timothy W
authors.initials: TW
authors.lastname: Rhoads
authors.affiliation: Department of Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Rajkumar
authors.initials: R
authors.lastname: Noubade
authors.affiliation: Department of Safety Assessment, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Paula
authors.initials: P
authors.lastname: Katavolos
authors.affiliation: Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Lesch
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Donald S
authors.initials: DS
authors.lastname: Stapleton
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Mary E
authors.initials: ME
authors.lastname: Rabaglia
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Kathy L
authors.initials: KL
authors.lastname: Schueler
authors.affiliation: Department of Transgenic Technology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Raymond
authors.initials: R
authors.lastname: Asuncion
authors.affiliation: Department of Transgenic Technology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Melanie
authors.initials: M
authors.lastname: Domeyer
authors.affiliation: Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Jose
authors.initials: J
authors.lastname: Zavala-Solorio
authors.affiliation: Department of Laboratory Animal Resources, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Reich
authors.affiliation: Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: DeVoss
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Mark P
authors.initials: MP
authors.lastname: Keller
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Alan D
authors.initials: AD
authors.lastname: Attie
authors.affiliation: Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Hebert
authors.affiliation: Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Westphall
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: jcoon@chem.wisc.edu.
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Coon
authors.affiliation: Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: kirkpatrick.donald@gene.com.
authors.forename: Donald S
authors.initials: DS
authors.lastname: Kirkpatrick
authors.affiliation: Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: dey.anwesha@gene.com.
authors.forename: Anwesha
authors.initials: A
authors.lastname: Dey
mesh_terms: D000818:Animals; D006410:Hematopoiesis; D006657:Histones / Q000378:metabolism; D007553:Isotope Labeling; D050356:Lipid Metabolism; D008239:Lysine / Q000378:metabolism; D008297:Male; D053858:Metabolic Networks and Pathways; D008810:Mice, Inbred C57BL; D008822:Mice, Transgenic; D008930:Mitochondria, Liver / Q000378:metabolism; D010179:Pancreas / Q000378:metabolism; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D025521:Tumor Suppressor Proteins / Q000502:physiology*; D043222:Ubiquitin Thiolesterase / Q000502:physiology*; D054875:Ubiquitination
chemical_list: C575444:BAP1 protein, mouse; D006657:Histones; D020543:Proteome; D025521:Tumor Suppressor Proteins; D043222:Ubiquitin Thiolesterase; D008239:Lysine