Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

Summary Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats’ chronological age, the majority are specific to one organ. These may be a consequence of the organ’s physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats.

[1]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[2]  Ratan D. Bhardwaj,et al.  Retrospective Birth Dating of Cells in Humans , 2005, Cell.

[3]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[4]  I. Kohane,et al.  Gene regulation and DNA damage in the ageing human brain , 2004, Nature.

[5]  E. Wang,et al.  Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.

[6]  Robert W. Williams,et al.  Mitonuclear protein imbalance as a conserved longevity mechanism , 2013, Nature.

[7]  J. Sanes,et al.  Mammalian SAD Kinases Are Required for Neuronal Polarization , 2005, Science.

[8]  Gary D. Bader,et al.  An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.

[9]  M. Beck,et al.  Integrated Structural Analysis of the Human Nuclear Pore Complex Scaffold , 2013, Cell.

[10]  John R. Yates,et al.  Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures , 2013, Cell.

[11]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[12]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[13]  J. Yates,et al.  Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain , 2012, Science.

[14]  Korbinian Strimmer,et al.  fdrtool: a versatile R package for estimating local and tail area-based false discovery rates , 2008, Bioinform..

[15]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[16]  Nicholas T. Ingolia,et al.  Mammalian microRNAs predominantly act to decrease target mRNA levels , 2010, Nature.

[17]  Hilmar Bading,et al.  Nuclear calcium signalling in the regulation of brain function , 2013, Nature Reviews Neuroscience.

[18]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[19]  N. Perrimon,et al.  Protein Complex–Based Analysis Framework for High-Throughput Data Sets , 2013, Science Signaling.

[20]  R. Aebersold,et al.  An Essential Switch in Subunit Composition of a Chromatin Remodeling Complex during Neural Development , 2007, Neuron.

[21]  Andrew R. Jones,et al.  ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.

[22]  P G Schultz,et al.  The effects of aging on gene expression in the hypothalamus and cortex of mice. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[23]  J. Sanes,et al.  LKB1 and SAD Kinases Define a Pathway Required for the Polarization of Cortical Neurons , 2007, Cell.

[24]  H. Takagi,et al.  SAD: A Presynaptic Kinase Associated with Synaptic Vesicles and the Active Zone Cytomatrix that Regulates Neurotransmitter Release , 2006, Neuron.

[25]  Richard Weindruch,et al.  Gene-expression profile of the ageing brain in mice , 2000, Nature Genetics.

[26]  C. Barnes,et al.  Neural plasticity in the ageing brain , 2006, Nature Reviews Neuroscience.

[27]  P. Bork,et al.  Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines , 2013, Molecular systems biology.

[28]  Christian von Mering,et al.  STRING 8—a global view on proteins and their functional interactions in 630 organisms , 2008, Nucleic Acids Res..

[29]  Kevin G Becker,et al.  Transcriptional Profiling of Aging in Human Muscle Reveals a Common Aging Signature , 2006, PLoS genetics.

[30]  C Roskelley,et al.  A biomarker that identifies senescent human cells in culture and in aging skin in vivo. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[31]  D. Green,et al.  Mitochondria and the Autophagy–Inflammation–Cell Death Axis in Organismal Aging , 2011, Science.

[32]  B. Göttgens,et al.  Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. , 2014, Cell stem cell.

[33]  Hans Clevers,et al.  Signaling pathways in intestinal development and cancer. , 2004, Annual review of cell and developmental biology.

[34]  T. Prolla,et al.  Evolution of the Aging Brain Transcriptome and Synaptic Regulation , 2008, PloS one.

[35]  Johan Auwerx,et al.  The metabolic footprint of aging in mice , 2011, Scientific reports.

[36]  Peter J. Woolf,et al.  GAGE: generally applicable gene set enrichment for pathway analysis , 2009, BMC Bioinformatics.

[37]  M. Hetzer,et al.  A change in nuclear pore complex composition regulates cell differentiation. , 2012, Developmental cell.

[38]  Thomas Craig,et al.  Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome , 2012, AGE.

[39]  S. Rafii,et al.  Critical Role of Histone Turnover in Neuronal Transcription and Plasticity , 2015, Neuron.

[40]  Sudhir Srivastava,et al.  Posttranslational Protein Modifications , 2006, Molecular & Cellular Proteomics.

[41]  V. Potter,et al.  Nuclei from Rat Liver: Isolation Method That Combines Purity with High Yield , 1966, Science.

[42]  G. Zajicek,et al.  [The streaming liver]. , 1991, Harefuah.

[43]  Daniel Kaganovich,et al.  Misfolded proteins partition between two distinct quality control compartments , 2008, Nature.

[44]  Manuel Serrano,et al.  The Hallmarks of Aging , 2013, Cell.

[45]  T. Hoppe,et al.  Ubiquitin sets the timer: impacts on aging and longevity , 2014, Nature Structural &Molecular Biology.

[46]  Rachael P. Huntley,et al.  QuickGO: a web-based tool for Gene Ontology searching , 2009, Bioinform..

[47]  M. Mann,et al.  Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.

[48]  J. Langston,et al.  Decreased α-synuclein expression in the aging mouse substantia nigra , 2009, Experimental Neurology.

[49]  M. Mann,et al.  Accurate Quantification of More Than 4000 Mouse Tissue Proteins Reveals Minimal Proteome Changes During Aging* , 2010, Molecular & Cellular Proteomics.

[50]  Alexis Battle,et al.  Impact of regulatory variation from RNA to protein , 2015, Science.

[51]  Israel Steinfeld,et al.  BMC Bioinformatics BioMed Central , 2008 .

[52]  U. Kutay,et al.  Exportin‐5‐mediated nuclear export of eukaryotic elongation factor 1A and tRNA , 2002, The EMBO journal.

[53]  Anna M. McGeachy,et al.  The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments , 2012, Nature Protocols.

[54]  M. Platzer,et al.  RNA-seq of the aging brain in the short-lived fish N. furzeri – conserved pathways and novel genes associated with neurogenesis , 2014, Aging cell.

[55]  U. Kutay,et al.  Nuclear Export of MicroRNA Precursors , 2004, Science.

[56]  M. D'Angelo,et al.  Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells , 2009, Cell.

[57]  E. Huang,et al.  Neurotrophins: roles in neuronal development and function. , 2001, Annual review of neuroscience.

[58]  João Pedro de Magalhães,et al.  Meta-analysis of age-related gene expression profiles identifies common signatures of aging , 2009, Bioinform..

[59]  M. Beck,et al.  The use of targeted proteomics to determine the stoichiometry of large macromolecular assemblies. , 2014, Methods in cell biology.

[60]  T. Breit,et al.  Delayed and Accelerated Aging Share Common Longevity Assurance Mechanisms , 2008, PLoS genetics.

[61]  Alma L. Burlingame,et al.  Widespread Protein Aggregation as an Inherent Part of Aging in C. elegans , 2010, PLoS biology.

[62]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[63]  Young-Ha Song,et al.  Cellular aging is associated with increased ubiquitylation of histone H2B in yeast telomeric heterochromatin. , 2013, Biochemical and biophysical research communications.

[64]  W. Bonner,et al.  Patterns of histone variant synthesis can distinguish go from G1 cells , 1982, Cell.

[65]  Gordon K. Smyth,et al.  limma: Linear Models for Microarray Data , 2005 .

[66]  Johannes Griss,et al.  The Proteomics Identifications (PRIDE) database and associated tools: status in 2013 , 2012, Nucleic Acids Res..

[67]  S. Henikoff,et al.  The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. , 2002, Molecular cell.

[68]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[69]  Hans-Werner Mewes,et al.  CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..

[70]  Brian E. Schwartz,et al.  Transcriptional activation triggers deposition and removal of the histone variant H3.3. , 2005, Genes & development.

[71]  Jürgen Sühnel,et al.  AgeFactDB—the JenAge Ageing Factor Database—towards data integration in ageing research , 2013, Nucleic Acids Res..

[72]  G Zajicek,et al.  The streaming liver. II. Hepatocyte life history. , 2008, Liver.