Chromatin Immunoprecipitation (ChIP) Assay Development for FFPE human brain secti

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DESCRIPTION (provided by applicant): Depression is the leading cause of disability among individuals between the ages of 15-44, affecting approximately 21 million Americans and is the leading cause of suicide. Current diagnostic tools available for medical professionals are limited to questionnaires and other inherently subjective approaches. Improving accuracy of diagnosis has been cited as a pressing need in the field. Recent advances have shed light on the genetic basis for psychopathological conditions, which not only includes changes in gene expression, but also epigenomic changes as well. Epigenomic mechanisms, which regulate gene activity without altering the DNA code, consist fundamentally of DNA methylation of CpG-dinucleotides, which occurs at the fifth position of the cytosine pyrimidine ring, and regulation of chromatin structure through post-translational modification of histones. In this Phase I proposal , we intend to develop a Clinical Chromatin ImmunoPrecipitation assay (C- ChIP), for use with formaldehyde-fixed paraffin embedded (FFPE) human brain specimens, which will enable analysis of changes in histone post-translational modifications in normal and suicide brains samples. Chromatin immunoprecipitation is a powerful technique that captures DNA bound proteins, and enables quantification of the specific immunoprecipitated DNA sequences relative to input. Development of the C- ChIP assay will be achieved by first establishing a rat tissue model system, and in conjunction with the isolation of a panel of highly characterized and specific monoclonal antibodies to histone modifications associated with either transcriptionally active or repressed loci, will be used to systematically adapt existing ChIP protocols developed for in vitro cultured cells, into a highly sensitive assay compatible for use with FFPE sections. Assay validation with clinical samples will be performed collaboratively on a rat maternal care model and subsequently on FFPE control and suicide brain samples. The successful development of the C-ChIP assay will have two effects. First, would be the commercialization of the C-ChIP assay for the broad research market, providing for the first time, an assay which enables the functional genomic analysis of archived clinical samples. The second outcome of this Phase I application is that the C-ChIP assay will enable subsequent Phase II studies in which genomic-wide survey of a large cohort of suicide brains specimens will be examined for epigenetic alternations which could possibly serve as biomarkers for depression. With this information, it may be possible to subsequently identify peripheral markers that correlate with the brain markers, leading to the development of a diagnostic assay for assessing depression and suicide risk. PUBLIC HEALTH RELEVANCE: 1-3 Suicide and depression are major public health concerns . Recent studies have identified some of the molecular mechanisms involved in suicide and depression and these 7-15 mechanisms include changes in the regulation of gene expression in the brain . This Phase 1 application describes the development of an assay that will enable identification of gene expression changes through the whole genome, which could subsequently lead to the development of a much needed diagnostic for depression and suicide risk.