title: Proteomics of rimmed vacuoles define new risk allele in inclusion body myositis.
abstract: OBJECTIVE
  Sporadic inclusion body myositis (sIBM) pathogenesis is unknown; however, rimmed vacuoles (RVs) are a constant feature. We propose to identify proteins that accumulate within RVs.
  
  
  METHODS
  RVs and intact myofibers were laser microdissected from skeletal muscle of 18 sIBM patients and analyzed by a sensitive mass spectrometry approach using label-free spectral count-based relative protein quantification. Whole exome sequencing was performed on 62 sIBM patients. Immunofluorescence was performed on patient and mouse skeletal muscle.
  
  
  RESULTS
  A total of 213 proteins were enriched by >1.5 -fold in RVs compared to controls and included proteins previously reported to accumulate in sIBM tissue or when mutated cause myopathies with RVs. Proteins associated with protein folding and autophagy were the largest group represented. One autophagic adaptor protein not previously identified in sIBM was FYCO1. Rare missense coding FYCO1 variants were present in 11.3% of sIBM patients compared with 2.6% of controls (p = 0.003). FYCO1 colocalized at RVs with autophagic proteins such as MAP1LC3 and SQSTM1 in sIBM and other RV myopathies. One FYCO1 variant protein had reduced colocalization with MAP1LC3 when expressed in mouse muscle.
  
  
  CONCLUSIONS
  This study used an unbiased proteomic approach to identify RV proteins in sIBM that included a novel protein involved in sIBM pathogenesis. FYCO1 accumulates at RVs, and rare missense variants in FYCO1 are overrepresented in sIBM patients. These FYCO1 variants may impair autophagic function, leading to RV formation in sIBM patient muscle. FYCO1 functionally connects autophagic and endocytic pathways, supporting the hypothesis that impaired endolysosomal degradation underlies the pathogenesis of sIBM. Ann Neurol 2017;81:227-239.
authors.affiliation: Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Anne-Katrin
authors.initials: AK
authors.lastname: Güttsches
authors.affiliation: Department of Neurology, Southmead Hospital, Bristol, United Kingdom.
authors.forename: Stefen
authors.initials: S
authors.lastname: Brady
authors.affiliation: Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany.|Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Kathryn
authors.initials: K
authors.lastname: Krause
authors.affiliation: Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany.|Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Maerkens
authors.affiliation: Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Julian
authors.initials: J
authors.lastname: Uszkoreit
authors.affiliation: Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Eisenacher
authors.affiliation: Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Schreiner
authors.affiliation: Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Sara
authors.initials: S
authors.lastname: Galozzi
authors.affiliation: Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Janine
authors.initials: J
authors.lastname: Mertens-Rill
authors.affiliation: Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Tegenthoff
authors.affiliation: MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom.|Department of Molecular Neuroscience, Queen Square Brain Bank, UCL Institute of Neurology, London, United Kingdom.
authors.forename: Janice L
authors.initials: JL
authors.lastname: Holton
authors.affiliation: Department of Neurology, Columbia University, New York, NY.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Harms
authors.affiliation: Johns Hopkins University School of Medicine, Baltimore, MD.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Lloyd
authors.affiliation: Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Vorgerd
authors.affiliation: Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, Saint Louis, MO.
authors.forename: Conrad C
authors.initials: CC
authors.lastname: Weihl
authors.affiliation: Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Katrin
authors.initials: K
authors.lastname: Marcus
authors.affiliation: Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Rudolf A
authors.initials: RA
authors.lastname: Kley
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000483:Alleles; D000818:Animals; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D005260:Female; D006801:Humans; D008297:Male; D051379:Mice; D008869:Microtubule-Associated Proteins; D008875:Middle Aged; D018482:Muscle, Skeletal / Q000378:metabolism*; D018979:Myositis, Inclusion Body / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012306:Risk; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014617:Vacuoles / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; C460141:FYCO1 protein, human; D008869:Microtubule-Associated Proteins; D014157:Transcription Factors