Open Access Highly Accessed Research article

A parallel genome-wide mRNA and microRNA profiling of the frontal cortex of HIV patients with and without HIV-associated dementia shows the role of axon guidance and downstream pathways in HIV-mediated neurodegeneration

Li Zhou1, Gulietta M Pupo2, Priyanka Gupta1, Bing Liu3, Sieu L Tran2, Raany Rahme1, Bin Wang1, Rejane Rua1, Helen Rizos2, Adam Carroll3, Murray J Cairns34 and Nitin K Saksena1*

Author Affiliations

1 Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Westmead, NSW 2145, Sydney, Australia

2 Westmead Institute for Cancer Research, University of Sydney at Westmead Millennium Institute, Westmead, NSW, 2145, Australia

3 School of Biomedical Sciences and Pharmacy, Faculty of Health and the Hunter Medical Research Institute, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia

4 Schizophrenia Research Institute, Darlinghurst, Sydney NSW, Australia

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BMC Genomics 2012, 13:677  doi:10.1186/1471-2164-13-677

Published: 28 November 2012

Additional files

Additional file 1:

Table S1. DE gene list.

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Additional file 2:

Figure S1. Hierarchical clustering analysis of global mRNA and miRNA profiles obtained from the frontal cortex tissue at autopsy of HIV patients with and without dementia. Pearson correlation algorithm was chosen to evaluate and visualize the mRNA and miRNA expression patterns using GenomeStudio v3 and GeneSpring respectively. A. mRNA clustering. HAD samples are highlighted with (red square), and HIV negative control samples are highlighted with (sky-blue square) while HIV positive non-dementia patient samples are highlighted with (green square). B miRNA clustering.

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Additional file 3:

Table S2. DE miRNA list.

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Additional file 4:

Figure S2. Target of hsa-miR-137.

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Additional file 5:

Table S3. Low and high stringency G-seed search for miR-137, miR-153 and miR-218 targets.

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Additional file 6:

Table S4: Gene sets significantly enriched by GSEA analysis.

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Additional file 7:

Table S5. Validation of non-changed miRNA.

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Additional file 8:

Figure S3. Significantly dysregulated genes on long term potentiation pathway in HAD brains compared to HIV non-dementia brains.

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Additional file 9:

Figure S4. Western blot validation of MAP2K2 and MAP2K4. MAP2K2 and MAP2K4 encoding proteins MEK2 (A) and JNK (B) with relative molecular weight 45 and 46kD respectively were separated on 12% SDSpolyacrylamide gel and blotting with specific antibodies against them. Semiquantitative analysis has been carried out by comparing the relative protein level (standardized by Actin (C)) in HAD and HIV non-dementia patients. The quantification result demonstrated the trend similar to the one observed in microarray and qPCR for HAD patients when compared to HIV non-dementia patients.

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Additional file 10:

Figure S5. Significantly dysregulated genes on calcium signalling pathway in HAD brains compared to HIV non-dementia brains.

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Additional file 11:

Figure S6. Significantly dysregulated genes on Jak-STAT signalling pathway in HAD brains compared to HIV non-dementia brains.

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Additional file 12:

Figure S7. Significantly dysregulated genes on VEGF signalling pathway in HAD brains compared to HIV non-dementia brains.

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Additional file 13:

Table S6. DE miRNAs and their target pathways.

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Additional file 14:

Table S7. Patient details.

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Additional file 15:

Table S8. qPCR primers.

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