Genomic Analyses for Elucidating Novel Targets for Symptoms Management

大多数症状是多因素的，遗传和环境因素都会导致个体差异。候选基因研究已经在生物学假设的基础上进行，以确定复杂性状（如疼痛）的相关遗传变异。然而，影响因素的复杂网络和涉及不同症状的数千个分子使得很难检测出对个体独特的疾病易感性负责的遗传变异。单一基因的常见变异不太可能对复杂性状起主导作用；相反，每个基因的作用似乎是微妙的，作用于多种生物途径中的一种，使其信号难以检测。

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 and chronic pain, mild traumatic brain injury and PTSD, we are using NGS for 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 using unbiased RNA-seq technology from soldiers who suffered from blast injury were presented at multiple meetings. We also presented micro RNA analysis from soldiers back from war zone. These results of gene expression profiles based on NGS data were also published. We recently launched a project of RNA-seq with multiple chronic pain conditions to decipher genetic roles in those symptoms and currently under sequencing. Based on the data generated from whole genome approaches, we also narrowed and used targeted analysis such as NanoString and validated NGS results of blast injury patients. We started targeted analysis of transcripts in adipose tissues in transplant patients to investigate the association between weight and sensory. Two epigenetic studies using DNA methylation chromatin immunoprecipitation followed by whole genome scale sequencing were conducted from civilian and military groups. The results were also presented at multiple meetings and published. Epigenetic changes in military PTSD patients was published while the epigenetic study in sports related concussion patients was submitted for publication and is currently under review. Whole genome sequencing of special sensory disorder patient and control sibling were sequenced and presented at the ASHG meeting. Using the targeted next generation sequencing technology, we also have finished a microbiome project to characterize population of microorganisms in human from different disease status. Using a next generation semiconductor sequencer, microbiome was analyzed with extensive sequencing of 16s rRNA region for oral microbiome from the aplastic anemia patients in 2 different ways, sequencing short but multiple sections in 16s rRNA region and full length of 16s rRNA sequencing. The data was presented at the IADR meeting and published. Following microbiome data of patient group was analyzed and currently the manuscript is in preparation for publication. Mainly the project 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 detected tau and p-tau protein in plasma, which has not been measured with ELISA. And its result of tau protein in military TBI patients was published. Multiplexing assays are now used for more effective and fast data collection. 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. Also, using gene editing technologies, we will try to develop a new treatment strategies based on genomics. Recent studies suggest central nervous system communicates with peripheral nervous system via exosomes. Therefore, we started exosome analysis using Nanosight 300 followed by either micro RNA analysis or protein analysis. Also, single cell assays using 2 different platforms, such as C1 from Fluidigm and ddSeq from BioRad were recently acquired and under the optimization process for future use. 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.