Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways

Cecilia Mancini, Paola Roncaglia, Alessandro Brussino, Giovanni Stevanin, Nicola Lo Buono, Helena Krmac, Francesca Maltecca, Elena Gazzano, Anna Bartoletti Stella, Maria A Calvaruso, Luisa Iommarini, Claudia Cagnoli, Sylvie Forlani, Isabelle Le Ber, Alexandra Durr, Alexis Brice, Dario Ghigo, Giorgio Casari, Anna M Porcelli, Ada Funaro, Giuseppe Gasparre, Stefano Gustincich and Alfredo Brusco

BMC Medical Genomics (Advanced online June 18, 2013)

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.


Gene expression was evaluated with the Affymetrix GeneChip Human Genome U133A 2.0 Arrays and data were validated by real-time PCR.


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.


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.


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