title: Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways.
abstract: BACKGROUND
  SCA28 is an autosomal dominant ataxia associated with AFG3L2 gene mutations. We performed a whole genome expression profiling using lymphoblastoid cell lines (LCLs) from four SCA28 patients and six unrelated healthy controls matched for sex and age.
  
  
  METHODS
  Gene expression was evaluated with the Affymetrix GeneChip Human Genome U133A 2.0 Arrays and data were validated by real-time PCR.
  
  
  RESULTS
  We found 66 genes whose expression was statistically different in SCA28 LCLs, 35 of which were up-regulated and 31 down-regulated. The differentially expressed genes were clustered in five functional categories: (1) regulation of cell proliferation; (2) regulation of programmed cell death; (3) response to oxidative stress; (4) cell adhesion, and (5) chemical homeostasis. To validate these data, we performed functional experiments that proved an impaired SCA28 LCLs growth compared to controls (p < 0.005), an increased number of cells in the G0/G1 phase (p < 0.001), and an increased mortality because of apoptosis (p < 0.05). We also showed that respiratory chain activity and reactive oxygen species levels was not altered, although lipid peroxidation in SCA28 LCLs was increased in basal conditions (p < 0.05). We did not detect mitochondrial DNA large deletions. An increase of TFAM, a crucial protein for mtDNA maintenance, and of DRP1, a key regulator of mitochondrial dynamic mechanism, suggested an alteration of fission/fusion pathways.
  
  
  CONCLUSIONS
  Whole genome expression profiling, performed on SCA28 LCLs, allowed us to identify five altered functional categories that characterize the SCA28 LCLs phenotype, the first reported in human cells to our knowledge.
authors.affiliation: Department of Medical Sciences, University of Torino, Via Santena 19, 10126 Torino, Italy.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Mancini
authors.forename: Paola
authors.initials: P
authors.lastname: Roncaglia
authors.forename: Alessandro
authors.initials: A
authors.lastname: Brussino
authors.forename: Giovanni
authors.initials: G
authors.lastname: Stevanin
authors.forename: Nicola
authors.initials: N
authors.lastname: Lo Buono
authors.forename: Helena
authors.initials: H
authors.lastname: Krmac
authors.forename: Francesca
authors.initials: F
authors.lastname: Maltecca
authors.forename: Elena
authors.initials: E
authors.lastname: Gazzano
authors.forename: Anna
authors.initials: A
authors.lastname: Bartoletti Stella
authors.forename: Maria Antonietta
authors.initials: MA
authors.lastname: Calvaruso
authors.forename: Luisa
authors.initials: L
authors.lastname: Iommarini
authors.forename: Claudia
authors.initials: C
authors.lastname: Cagnoli
authors.forename: Sylvie
authors.initials: S
authors.lastname: Forlani
authors.forename: Isabelle
authors.initials: I
authors.lastname: Le Ber
authors.forename: Alexandra
authors.initials: A
authors.lastname: Durr
authors.forename: Alexis
authors.initials: A
authors.lastname: Brice
authors.forename: Dario
authors.initials: D
authors.lastname: Ghigo
authors.forename: Giorgio
authors.initials: G
authors.lastname: Casari
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: Porcelli
authors.forename: Ada
authors.initials: A
authors.lastname: Funaro
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Gasparre
authors.forename: Stefano
authors.initials: S
authors.lastname: Gustincich
authors.forename: Alfredo
authors.initials: A
authors.lastname: Brusco
mesh_terms: D049069:ATP-Dependent Proteases / Q000235:genetics; D000074183:ATPases Associated with Diverse Cellular Activities; D017209:Apoptosis / Q000235:genetics*; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D004268:DNA-Binding Proteins / Q000378:metabolism; D034281:Dynamins; D059585:G1 Phase Cell Cycle Checkpoints; D020558:GTP Phosphohydrolases / Q000378:metabolism; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D015227:Lipid Peroxidation; D008869:Microtubule-Associated Proteins / Q000378:metabolism; D008928:Mitochondria / Q000378:metabolism; D024101:Mitochondrial Proteins / Q000378:metabolism; D010641:Phenotype; D020754:Spinocerebellar Ataxias / Q000151:congenital; D013132:Spinocerebellar Degenerations / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D008869:Microtubule-Associated Proteins; D024101:Mitochondrial Proteins; C499631:TFAM protein, human; D014157:Transcription Factors; D049069:ATP-Dependent Proteases; C120699:AFG3L2 protein, human; D020558:GTP Phosphohydrolases; D000074183:ATPases Associated with Diverse Cellular Activities; C110768:DNM1L protein, human; D034281:Dynamins