Table 1.

Summary of gene profiling studies in grey matter tissue

TISSUE	BRAIN AREA/SAMPLE TYPE	COMPARATIVE TOOL	Q-PCR	FINDING
6 MS (SP, PP) 6 Ctl	Motor cortex Frozen	Affymetrix HG-U133A,B ~39,000 probes	Yes	Non-lesioned motor cortex from MS brains was compared to control motor cortex. Major findings include decreases in genes related to mitochondrial function and inhibitory neurotransmission. These results provide a mechanism of axonal degeneration through energy imbalance. In the same dataset, genes from the CNTF-mediated neuroprotective signaling pathway were increased, possibly reflecting an endogenous neuroprotective response.	13 20
6 MS (SP, PR, NA) 8 Ctl	Cerebral Cortex Frozen	Applied Biosystems Human Genome Survey Microarray v1.0 ~31,700 probes	Yes	Non-lesioned and lesioned cortex from MS brains was compared to control cortex. No genes were found to be significantly different between MS lesioned and non-lesioned cortex. Compared to controls, 532 genes were altered in MS cortex. Major findings of the study include increased mRNA levels of IgG-related genes, possibly due to meningeal plasma cells that are not infected by Epstein-Barr virus.	26
8 MS (SP, PP) 4 Ctl	Hippocampus Frozen	Affymetrix HG-U133A ~13,000 probes	Yes	Non-lesioned MS hippocampus was compared to lesioned MS and control hippocampus. There were 799 genes significantly altered between non-lesioned and lesioned hippocampus. A significant loss of neurons was not reported. Major findings of the study include decreases in mRNA and proteins belonging to axonal transport, glutamate neurotransmission, synaptic maintenance and memory/learning.	43
3 MS (SP) 3 Ctl	Frontal Cortex Frozen	Custom PCR array containing 92 Protein Tyrosine Phosphatases (PTPs)	NA	PTP levels in white matter and grey matter non-lesioned and lesioned tissues were compared. 52 PTPs were altered in MS white matter compared to 9 in grey matter. The study identified VHY/Dusp15 as a regulator of oligodendrocyte differentiation.	40
3 MS (SP) 3 TM 3 AD 3 Ctl	Frontal/Parietal/Temporal cortex Paraffin embedded	Agilent-Whole-Human Genome Microarrays ~ 41000 probes	Yes	Cortical lesions were divided into 1 active lesion and 2 chronic active lesions. MS cases were compared to all remaining samples (Tuberous meningitis, Alzheimer’s disease and control). One of the major aspects of this study was identifying 109 genes specific to MS and belonging to inflammation, cell death, DNA repair, transcription and translation. Although statistical analysis could not be performed, comparison of one single MS case (active lesion) with remaining samples (MS cortex, Tuberculous meningitis, Alzheimer’s disease and control cortex) led to changes in similar biological categories.	31

SP: secondary progressive MS; PP: Primary progressive MS; Ctl: control; PR: Progressive relapsing; NA: not available TM: Tuberculous meningitis AD: Alzheimer’s disease; Q-PCR: Quantitative polymerase chain reaction