title: Analysis of microRNA from archived formalin-fixed paraffin-embedded specimens of amyotrophic lateral sclerosis.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are noncoding small RNAs that regulate gene expression. This study investigated whether formalin-fixed paraffin-embedded (FFPE) specimens from postmortem cases of neurodegenerative disorders would be suitable for miRNA profiling.
  
  
  RESULTS
  Ten FFPE samples from 6 cases of amyotrophic lateral sclerosis (ALS) and 4 neurologically normal controls were selected for miRNA analysis on the basis of the following criteria for RNA quality: (i) a postmortem interval of less than 6 hours, (ii) a formalin fixation time of less than 4 weeks, (iii) an RNA yield per sample of more than 500 ng, and (iv) sufficient quality of the RNA agarose gel image. An overall RNA extraction success rate was 46.2%. For ALS, a total of 364 miRNAs were identified in the motor cortex, 91 being up-regulated and 233 down-regulated. Target genes were predicted using miRNA bioinformatics software, and the data applied to ontology analysis. This indicated that one of the miRNAs up-regulated in ALS (miR-338-3p) had already been identified in leukocytes, serum, cerebrospinal fluid and frozen spinal cord from ALS patients.
  
  
  CONCLUSIONS
  Although analysis was possible for just under half of the specimens examined, we were able to show that informative miRNA data can be derived from archived FFPE samples from postmortem cases of neurodegenerative disorders.
authors.affiliation: Department of Neuropathology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, 036-8562, Japan. koichi@cc.hirosaki-u.ac.jp.
authors.forename: Koichi
authors.initials: K
authors.lastname: Wakabayashi
authors.affiliation: Department of Neuropathology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, 036-8562, Japan. neuropal@cc.hirosaki-u.ac.jp.
authors.forename: Fumiaki
authors.initials: F
authors.lastname: Mori
authors.affiliation: Department of Pathological Neuroscience, Center for Bioresource-based Researches, Brain Research Institute, University of Niigata, Niigata, Japan. kakita@bri.niigata-u.ac.jp.
authors.forename: Akiyoshi
authors.initials: A
authors.lastname: Kakita
authors.affiliation: Department of Pathology, Brain Research Institute, University of Niigata, Niigata, Japan. hitoshi@bri.niigata-u.ac.jp.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Takahashi
authors.affiliation: Department of Neurology, Hokkaido University Graduate School of Medicine, Sapporo, Japan. jutsumi@pop.med.hokudai.ac.jp.
authors.forename: Jun
authors.initials: J
authors.lastname: Utsumi
authors.affiliation: Department of Neurology, Hokkaido University Graduate School of Medicine, Sapporo, Japan. h-isasak@med.hokudai.ac.jp.
authors.forename: Hidenao
authors.initials: H
authors.lastname: Sasaki
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000378:metabolism; D000368:Aged; D000369:Aged, 80 and over; D000690:Amyotrophic Lateral Sclerosis / Q000378:metabolism*; D000870:Anterior Horn Cells / Q000378:metabolism*; D064229:Biological Ontologies; D004587:Electrophoresis, Agar Gel; D005260:Female; D005557:Formaldehyde; D020869:Gene Expression Profiling; D006801:Humans; D007150:Immunohistochemistry; D008297:Male; D035683:MicroRNAs / Q000378:metabolism*; D008875:Middle Aged; D009044:Motor Cortex / Q000378:metabolism*; D016612:Paraffin Embedding / Q000379:methods; D012984:Software; D016707:Tissue Fixation / Q000379:methods
chemical_list: C553334:AMBRA1 protein, human; D048868:Adaptor Proteins, Signal Transducing; D035683:MicroRNAs; D005557:Formaldehyde