Integrative gene–tissue microarray-based approach for identification of human disease biomarkers: application to amyotrophic lateral sclerosis

• Published in: Human molecular genetics Vol. 19; no. 16; pp. 3233 - 3253
• Main Authors: Kudo, Lili C., Parfenova, Liubov, Vi, Nancy, Lau, Kimbley, Pomakian, Justine, Valdmanis, Paul, Rouleau, Guy A., Vinters, Harry V., Wiedau-Pazos, Martina, Karsten, Stanislav L.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15-08-2010
• Subjects: Adult; Aged; Aged, 80 and over; Amyotrophic Lateral Sclerosis - genetics; Amyotrophic Lateral Sclerosis - metabolism; Animals; Biological and medical sciences; Biomarkers - analysis; Degenerative and inherited degenerative diseases of the nervous system. Leukodystrophies. Prion diseases; Disease Models, Animal; Female; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; Genetic Predisposition to Disease - genetics; Genetics of eukaryotes. Biological and molecular evolution; Humans; Immunohistochemistry; Male; Medical sciences; Mice; Mice, Transgenic; Middle Aged; Molecular and cellular biology; Motor Neuron Disease - genetics; Motor Neuron Disease - metabolism; Mutation; Neurology; Oligonucleotide Array Sequence Analysis - methods; Postmortem Changes; Proteomics - methods; Reverse Transcriptase Polymerase Chain Reaction; Superoxide Dismutase - genetics; Superoxide Dismutase - metabolism; Superoxide Dismutase-1; tau Proteins - genetics; tau Proteins - metabolism; Tissue Array Analysis - methods; Human; Nervous system diseases; Gene; Central nervous system disease; Biological marker; Genetics; Amyotrophic lateral sclerosis; Degenerative disease; Identification; Tissue Microarray; Spinal cord disease
• ISSN: 0964-6906; 1460-2083
• DOI: 10.1093/hmg/ddq232

Advances in genomics and proteomics permit rapid identification of disease-relevant genes and proteins. Challenges include biological differences between animal models and human diseases, high discordance between DNA and protein expression data and a lack of experimental models to study human complex diseases. To overcome some of these limitations, we developed an integrative approach using animal models, postmortem human material and a combination of high-throughput microarray methods to identify novel molecular markers of amyotrophic lateral sclerosis (ALS). We used laser capture microdissection coupled with microarrays to identify early transcriptome changes occurring in spinal cord motor neurons or surrounding glial cells. Two models of familial motor neuron disease, SOD1G93A and TAUP301L, transgenic mice were used at the presymptomatic stage. Identified gene expression changes were predominantly model-specific. However, several genes were regulated in both models. The relevance of identified genes as clinical biomarkers was tested in the peripheral blood transcriptome of presymptomatic SOD1G93A animals using custom-designed ALS microarray. To confirm the relevance of identified genes in human sporadic ALS (SALS), selected corresponding protein products were examined by high-throughput immunoassays using tissue microarrays constructed from human postmortem spinal cord tissues. Genes that were identified by these experiments and located within a linkage region associated with familial ALS/frontotemporal dementia were sequenced in several families. This large-scale gene and protein expression study pointing to distinct molecular mechanisms of TAU- and SOD1-induced motor neuron degeneration identified several new SALS-relevant proteins (CNGA3, CRB1, OTUB2, MMP14, SLK, DDX58, RSPO2) and putative blood biomarkers, including Nefh, Prph and Mgll.