title: Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics.
abstract: This study uses advanced proteogenomic approaches in a nonmodel organism to elucidate cardioprotective mechanisms used during mammalian hibernation. Mammalian hibernation is characterized by drastic reductions in body temperature, heart rate, metabolism, and oxygen consumption. These changes pose significant challenges to the physiology of hibernators, especially for the heart, which maintains function throughout the extreme conditions, resembling ischemia and reperfusion. To identify novel cardioadaptive strategies, we merged large-scale RNA-seq data with large-scale iTRAQ-based proteomic data in heart tissue from 13-lined ground squirrels (Ictidomys tridecemlineatus) throughout the circannual cycle. Protein identification and data analysis were run through Galaxy-P, a new multiomic data analysis platform enabling effective integration of RNA-seq and MS/MS proteomic data. Galaxy-P uses flexible, modular workflows that combine customized sequence database searching and iTRAQ quantification to identify novel ground squirrel-specific protein sequences and provide insight into molecular mechanisms of hibernation. This study allowed for the quantification of 2007 identified cardiac proteins, including over 350 peptide sequences derived from previously uncharacterized protein products. Identification of these peptides allows for improved genomic annotation of this nonmodel organism, as well as identification of potential splice variants, mutations, and genome reorganizations that provides insights into novel cardioprotective mechanisms used during hibernation.
authors.affiliation: Department of Biology, University of Minnesota Duluth , 1035 Kirby Drive, Duluth, Minnesota 55812, United States.
authors.forename: Katie L
authors.initials: KL
authors.lastname: Vermillion
authors.affiliation: Center for Mass Spectrometry and Proteomics, University of Minnesota , 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States.|Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota , 321 Church St SE, Minneapolis, Minnesota 55455, United States.
authors.forename: Pratik
authors.initials: P
authors.lastname: Jagtap
authors.affiliation: Minnesota Supercomputing Institute , 512 Walter Library 117 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.
authors.forename: James E
authors.initials: JE
authors.lastname: Johnson
authors.affiliation: Center for Mass Spectrometry and Proteomics, University of Minnesota , 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States.|Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota , 321 Church St SE, Minneapolis, Minnesota 55455, United States.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Griffin
authors.affiliation: Department of Biology, University of Minnesota Duluth , 1035 Kirby Drive, Duluth, Minnesota 55812, United States.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Andrews
mesh_terms: D000818:Animals; D001831:Body Temperature / Q000235:genetics; D005260:Female; D005786:Gene Expression Regulation; D006339:Heart Rate / Q000235:genetics; D006605:Hibernation / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D058977:Molecular Sequence Annotation; D009206:Myocardium / Q000737:chemistry* / Q000378:metabolism; D010101:Oxygen Consumption / Q000235:genetics; D010507:Periodicity; D020543:Proteome / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D040901:Proteomics / Q000295:instrumentation / Q000379:methods; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012589:Sciuridae / Q000235:genetics*; D012621:Seasons; D053719:Tandem Mass Spectrometry
chemical_list: D020543:Proteome; D012313:RNA
keywords: Galaxy-P; heart; hibernation; proteogenomics