Genomic Analyses for Elucidating Novel Targets for Symptoms Management

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Most symptoms are multifactorial in origin with both genetic and environmental factors contributing to individual variations. Candidate gene studies on the basis of biological hypotheses have been performed to identify relevant genetic variation in complex traits such as pain. However, the complicated mesh of contributing factors and the thousands of molecules involved in different symptoms makes it difficult to detect responsible genetic variations for an individuals unique susceptibility to disorders. It is unlikely that common variations in a single gene act dominantly on complex traits; rather, the contribution of each gene seems to be subtle, acting on one of multiple biological pathways, making its signal difficult to detect. The combined impact of the rapid increase in knowledge of diseases and the ability to apply powerful and high capacity technology has raised expectations for more effective and safer medicines for various types of symptoms management. Developing new treatment strategies for symptoms management is also critically dependent on identifying new target molecules and defining phenotypes for specific types of disorders. Therefore the first step of this project has been to define the characteristics of experimental and clinical phenotypes. Recently, we launched multiple projects with next generation sequencing (NGS) technology, which allows us to perform entire and/or targeted genome sequencing. The role of genetic and epigenetic factors on symptoms in various disorders and/or conditions will continue to be studied. For example, in neurological disorders such as acute pain, mild traumatic brain injury and PTSD, we are using genotyping, gene and protein expression, and patient reported outcomes to better understand the reciprocal interplay between these factors and the numerous biologic/mechanistic pathways including the inflammatory cascade. Gene expression profiles from the soldiers back from war zone were presented at the multiple meetings (CNRM and ASN meeting) and have been published. We also started SNP assays and micro RNA analysis from similar samples from war zone soldiers. The results were also presented at multiple meetings and published. Two epigenetic studies using DNA methylation chromatin immunoprecipitation followed by whole genome scale sequencing were conducted from civilian and military groups. Epigenetic changes in the sports related concussion patients was presented at the ASHG meeting. This result was submitted for publication and currently under review. The second epigenetic study in military PTSD patients finished sequencing of first set of samples. After the primary data analysis, we increased sample size and will sequence more. Whole genome sequencing of special sensory disorder patient and control sibling were sequenced and will be analyzed. Using the targeted next generation sequencing technology, we also have 2 on-going microbiome projects to characterize population of microorganisms in human and/or animal body from different disease status. Using a next generation semiconductor sequencer, microbiome was analyzed with extensive sequencing of 16s rRNA region in an animal model of irritable bowel syndrome and human patients. The results were presented at the scientific meeting and submitted for publication. Another microbiome project for oral microbiome from the aplastic anemia patients was also on-going and finished the sample collection. So far, preliminary data analysis was finished and its result was presented at the IADR meeting and submitted for publication. Mainly both projects found that the microbiome composition is altered in specific disease conditions. Considering that the protein is the final product from DNA and RNA, protein analysis from those multiple projects has been recently launched. We especially focus on proteins showing trace amount only so that it makes difficult to detect with conventional protein assays such as ELISA. So far, we have successfully detect tau protein in plasma, which has not been measured with ELISA. Developing new analyzing methods for the high throughput big data generated by the next generation sequencers including whole genome sequencing, gene expression signatures, epigenetics and their interactions with other factors such as proteins and environment factors is another goal of these projects. From these results along with biological knowledge of multiple pathways in neurological disorders, we will be able to suggest molecular-genetic mechanisms of those diseases at the level of the individual. Finally, we can suggest integrative genomic analysis to develop new drugs and test them based on individual genetic information.