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 Antonietta Calvaruso, Luisa Iommarini, Claudia Cagnoli, Sylvie Forlani, Isabelle Le Ber, Alexandra Durr, Alexis Brice, Dario Ghigo, Giorgio Casari, Anna Maria Porcelli, Ada FunaroGiuseppe Gasparre, Stefano Gustincich, Alfredo Brusco

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Article number22
JournalBMC Medical Genomics
Volume6
Issue number1
DOIs
Publication statusPublished - 2013

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Genome
Cell Line
Growth
Mitochondrial DNA
Mitochondrial Dynamics
Gene Expression
Cell Cycle Resting Phase
G1 Phase
Human Genome
Ataxia
Electron Transport
Cell Adhesion
Lipid Peroxidation
Genes
Real-Time Polymerase Chain Reaction
Reactive Oxygen Species
Oxidative Stress
Homeostasis
Cell Death
Cell Count

Keywords

  • AFG3L2
  • Autosomal dominant cerebellar ataxia
  • Genome-wide expression
  • LCLs
  • SCA28
  • Spinocerebellar ataxia

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics

Cite this

Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways. / Mancini, Cecilia; Roncaglia, Paola; Brussino, Alessandro; Stevanin, Giovanni; Lo Buono, Nicola; Krmac, Helena; Maltecca, Francesca; Gazzano, Elena; Bartoletti Stella, Anna; Calvaruso, Maria Antonietta; Iommarini, Luisa; Cagnoli, Claudia; Forlani, Sylvie; Le Ber, Isabelle; Durr, Alexandra; Brice, Alexis; Ghigo, Dario; Casari, Giorgio; Porcelli, Anna Maria; Funaro, Ada; Gasparre, Giuseppe; Gustincich, Stefano; Brusco, Alfredo.

In: BMC Medical Genomics, Vol. 6, No. 1, 22, 2013.

Research output: Contribution to journalArticle

Mancini, C, Roncaglia, P, Brussino, A, Stevanin, G, Lo Buono, N, Krmac, H, Maltecca, F, Gazzano, E, Bartoletti Stella, A, Calvaruso, MA, Iommarini, L, Cagnoli, C, Forlani, S, Le Ber, I, Durr, A, Brice, A, Ghigo, D, Casari, G, Porcelli, AM, Funaro, A, Gasparre, G, Gustincich, S & Brusco, A 2013, 'Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways', BMC Medical Genomics, vol. 6, no. 1, 22. https://doi.org/10.1186/1755-8794-6-22
Mancini, Cecilia ; Roncaglia, Paola ; Brussino, Alessandro ; Stevanin, Giovanni ; Lo Buono, Nicola ; Krmac, Helena ; Maltecca, Francesca ; Gazzano, Elena ; Bartoletti Stella, Anna ; Calvaruso, Maria Antonietta ; Iommarini, Luisa ; Cagnoli, Claudia ; Forlani, Sylvie ; Le Ber, Isabelle ; Durr, Alexandra ; Brice, Alexis ; Ghigo, Dario ; Casari, Giorgio ; Porcelli, Anna Maria ; Funaro, Ada ; Gasparre, Giuseppe ; Gustincich, Stefano ; Brusco, Alfredo. / Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways. In: BMC Medical Genomics. 2013 ; Vol. 6, No. 1.
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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.",
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T1 - Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways

AU - Mancini, Cecilia

AU - Roncaglia, Paola

AU - Brussino, Alessandro

AU - Stevanin, Giovanni

AU - Lo Buono, Nicola

AU - Krmac, Helena

AU - Maltecca, Francesca

AU - Gazzano, Elena

AU - Bartoletti Stella, Anna

AU - Calvaruso, Maria Antonietta

AU - Iommarini, Luisa

AU - Cagnoli, Claudia

AU - Forlani, Sylvie

AU - Le Ber, Isabelle

AU - Durr, Alexandra

AU - Brice, Alexis

AU - Ghigo, Dario

AU - Casari, Giorgio

AU - Porcelli, Anna Maria

AU - Funaro, Ada

AU - Gasparre, Giuseppe

AU - Gustincich, Stefano

AU - Brusco, Alfredo

PY - 2013

Y1 - 2013

N2 - 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.

AB - 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.

KW - AFG3L2

KW - Autosomal dominant cerebellar ataxia

KW - Genome-wide expression

KW - LCLs

KW - SCA28

KW - Spinocerebellar ataxia

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