GenProMarkers™, Inc.

Microarray, Bioinformatics and Systems Biology for Discovery of Gene and Protein Biomarkers

Systems Biology

Systems biology is a biology-based inter-disciplinary study field that focuses on complex and holistic interactions in biological systems and aims at solving fundamental molecular mechanisms underlying biological phenomena and problems that cannot be answered by conventional individual approaches.  High-throughput technologies for generating enormous biological information, database for logistic organization of the information, computational methods for data mining, and comprehensive understanding of biological systems in study are all essential aspects of systems biology.  In biology, not only is the whole more than the sum of its parts, but it is also alive.


Canonical Pathways- and Diseases-Association of Dysregulated Genes

Molecular pathway analysis is based on the number of differentially expressed genes identified by microarray.  For example, our study of posttraumatic stress disorder demonstrated that the mitochondrial dysfunction and oxidative phosphorylation pathways contained the highest number of dysregulated genes.  To see functional relationships, we conducted the canonical pathway analysis on 119 dysregulated genes.  The results showed that out of 94 canonical pathways, 16 (17.0%) contained a significant number of dysregulated genes in some pathways.  Particularly, the mitochondrial dysfunction pathway contained 8 (4.8%) dysregulated genes (p=6.61x10-6) including upregulated APP, CAT, NDUFA10 and UCP2 and downregulated COX8A, NDUFB5, NDUFS2 and PDHA1.

Canonical pathways- and Diseases-Associated Dysregulated Genes.  The bar graphs indicate canonical pathways and neuropsychiatric and systemic disorders associated with dysregulated genes in the PTSD DLPFC BA46. (A)  10 canonical biochemical and molecular biology pathways with significantly (p<0.05, Fisher’s Exact Test) dysregulated genes, in the PTSD DLPFC BA46 group in comparison to the non-PTSD controls.  The ratio is calculated as the number of genes in a given pathway divided by a total number of genes that make up that pathway.  The mitochondrial dysfunction pathway contains 8 (4.8%) dysregulated genes (p=6.61x10-6) including upregulated APP, CAT, NDUFA10 and UCP2 and downregulated COX8A, NDUFB5, NDUFS2 and PDHA1.  (B) Six categories of abnormalities in which the significant (p<0.05, Fisher’s Exact Test) number of the dysregulated genes in the PTSD DLPFC BA46 are known to involve, by searching the literature in the NCBI PUBMED, DAVID, OMIM and Ingenuity databases.  Red: upregulation; green downregulation.

Mitochondrial Oxidative Phosphorylation Pathways Ninety percent (90%) cellular energy (ATP) is generated by mitochondrial oxidative phosphorylation pathways.  The pathways are extremely important in high energy demanding tissues including brain, eye, heart, etc. 

The mitochondrial oxidative phosphorylation pathways with significantly dysregulated genes the complex I, III and IV detected by hMitChip3 microarray and bioinformatics analysis of RNA samples from peripheral white blood cells.  Red stars indicate the dysregulated genes in the oxidative phosphorylation complex I, III and IV.

Cancer Cell Survival-Apoptosis Pathways

The aforementioned proapoptosis genes and antiapoptosis genes were mapped to known molecular signaling pathways that regulate survival and apoptosis of cells.  The results revealed mitochondria-centered signaling pathways with a total of 35 gene products.  Without UV irradiation, the expression of 10 proapoptotic genes (TNFSF10, FAS, BNIP1, BAK1 [encoded by 6p21.3], BCAP31, FDX1, FDXR, VDAC1, CASP6 and CASP3) and 3 antiapoptotic genes (BCL2L1, CLN3 and MCL1) were significantly (p<0.05) higher in the UACC903(+6) cell line (red) than in UACC903 (green).  Six genes (BBC3, BID, TP53, BAD, CYCS and APAF1) had no significant change in expression (black).  The known interactions of these genes are indicated in the pathways.  The survival-apoptosis signaling pathways predict and are in consistent with the UACC903(+6) cell line’s sensitivity, compared to the UACC903’s  resistance to apoptosis.

Heat map and survival-apoptosis pathways.  (A) Heat map of 15 proapoptotic, 3 antiapoptotic, and 5 DNA-damage-repair genes in UACC903(+6) and UACC903 cell lines before (0) and at 1.5-, 3-, 6-, and 12-hours after the UV treatment.  The color map illustrates a color change corresponding to a ratio change.  Each ratio was calculated by dividing an expression level of a given gene at the time point to the mathematic mean value of the gene expression levels in both UACC903(+6) and UACC903 cells without UV treatment.  The arrowheads and hyphens indicate overall expression changes of a gene in response to the UV treatment.  (B) The survival-apoptosis pathways with differentially expressed genes between UACC903(+6) and UACC903 cell lines without UV treatment.  Red, green and black correspond to those at the 0-hour time point in UACC903(+6) and UACC903 cell line listed in the panel (A).  The left and right half in each gene plate represents relative expression levels between UACC903(+6) and UACC903, respectively.  Solid line with solid arrowhead: direct activation of expression or activity; dashed line: indirect; open arrowhead: translocation; line with a short line at one end: inhibition; line with circle: leading to; square: cytokine; double circles or rhombus: group or complex; rhombus: enzymes; circle: named protein; membrane: cell membrane.

Neuron Function-Survival Molecular Networks with Drug Targets

Molecular networks for neuron function-survival with targets of neuropsychiatric drugs.  The networks have a total of 75 elements including 27 (36%) upregulated genes, 27 (36%) downregulated genes and 21 (28%) unchanged ones.  Twenty-one elements in white color include 7 genes present and 11 genes absent in the hMitChip3 microarray, and 3 small molecules.  The symbols in Legend illustrate the networks.  The genes in the blue boxes are the known targets for neuropsychiatric drugs.  For example: the ESR2 is a target of 17b-estradiol or related ligands.  The APP is a target for Bapineuzumab (AAB-001) that is currently used for the Phase 3 clinical trials for the treatment of patients with Alzheimer’s disease.    The ESR2 is a target for Tamoxifen that is used for the treatment of mania in patients with bipolar disorder.  The PRKCD is a target for both Tamoxifen, and rottlerin that has been used in preclinical treatment of Parkinson’s disease.  The PP2A is a target for Fostriecin that antagonize dopamine activities.  The VAMP1 is a target of the neurotoxin protein Dysport that is used in minute doses to treat painful muscle spasms.  The SLC1A6 is a target of Riluzole used to treat amyotrophic sclerosis.  The UCP2 is a target for protection of dopaminergic neurons from oxidative stress caused by 1,2,3,6-methyl-phenyl-tetrahydropyridine (MPTP) toxicity.