Research
Key Areas of Research
Brain function is governed by precise regulation of gene expression across anatomically distinct structures, circuits, and specific cell types. Gene expression is reasonably well stereotyped across individuals and the availability of comprehensive expression data at single cell type resolution has made it possible to identify how genes influence the development, function and disease mechanisms of the brain, and ultimately how we think, fell and behave.
Our group takes an integrative genomic approach to complex diseases, with a particular focus on neuropsychiatric diseases. We are currently studying the causes and consequences of molecular variation in the brain and the role this plays in development of PTSD, major depression, alcohol use, and suicidal behavior and are at the forefront of neuropsychiatric disease epigenomic research.
Molecular Technologies in the Girgenti Lab
Recent large genome-wide association studies (GWAS) have confirmed significant heritability in both sexes and identified reliable PTSD-associated loci that have not yet been linked with causal biological mechanisms. Brain molecular phenotypes, such as gene expression and chromatin assembly and modification, can be used to translate psychiatric GWAS loci into meaningful biological mechanisms and identify causal disease pathways.
RNA-sequencing and whole genome sequencing
RNA-seq is a giant leap ahead of microarray-based platforms to measure gene expression. In our lab, we perform whole genome and transcriptome (RNA) sequencing from brain tissue in-house. We are equipped to fully capture the functional diversity of the human brain transcriptome at various levels of gene feature resolution: whole transcript, exon and exon junction as published (Girgenti MJ et al, 2021).
Whole genome bisulfite (DNA methylation) sequencing
Since PTSD mechanisms derive from genes and the environment, it is critical to evaluate epigenetic marks such as DNA methylation in correlation with gene expression studies. We are performing whole genome bisulfite sequencing approaches to quantify DNA methylation with extensive genome-wide coverage.
Single Cell Multi-omics
PTSD arises from differences at various levels of gene regulation in diverse brain cell types that converge on specific pathways (e.g. glucocorticoid and GABAergic signaling) harboring clinical significance. However, the identity of the cell types and their individual contribution to the molecular pathology of PTSD is a significant research gap whose understanding will facilitate the development of diagnostics and personalized therapeutics. We are isolating nuclei from PTSD postmortem brains and perfroming single nuclei RNA, ATAC, and DNA methylation to generate single-cell type atlases of gene regulatory networks in primary brain regions.
Patient-derived cell lines
For nearly 10% of the postmortem brains collected at the NPBB (and all donors moving forward), we have viable dura mater derived fibroblast cell lines, thus permitting molecular characterization of targets for drug screening and development. The patient-derived PTSD cellular model best replicates the genetic risk architecture of PTSD patients.
Research Projects
- Understanding single cell gene expression regulation in the human brain
A major driving interest of our lab is to map the epigenomic variation that influences gene expression in the human brain, profiling chromatin assembly, three-dimensional nuclear structure, DNA and histone modifications across specific brain regions and cell types related to addiction and fear processing. This work is supported by the US Department of Veteran Affairs and has resulted in the systematic analysis of epigenomic processes in the human brain. We are particularly interested in how these changes affect the transcriptome through changes in gene expression levels, RNA editing and localization and alternative transcript usage and splicing.
2. Cell type-specific atlases of stress disorders
Our group is leading a major effort to map the single cell gene expression regulome of 10 discrete brain subregions within the prefrontal cortex, amygdala, hippocampus, hypothalamus, and nucleus accumbens. We are currently profiling three molecular modalities (transcriptome and epigenome) by snRNA-seq and snATAC-seq /snDNAm in these human brain regions across several neuropsychiatric disorders including PTSD, MDD, AUD, SUD, and suicidal behavior.
3. Profiling the transciptome and epigenome in health and disease
Our lab has coordinated the first systematic analyses of epigenetic and transcriptomic variation in the brain associated with PTSD, major depression, and alcohol use disorder, and are currently funded to perform large-scale studies in specific cell types. Our work in this area has had a considerable impact. We have assessed the epigenetic and transcriptional differences in PTSD brain, highlighting convergent and divergent molecular pathology with other neuropsychiatric disorders related to GABAergic signaling and neuroinflammatory processes. Finally, we are investigating transcriptional and regulatory alterations in rodent models of human brain disease. For example, we find genome-wide changes in rodent models of traumatic stress that overlap with genes and pathways identified in our analyses of human postmortem brain tissue.
4. Investigating genetic variation effects on gene expression and regulation in the human brain
We have undertaken systematic analyses of how genetic variation influences transcriptional and regulatory mechanisms in the human brain. We are expanding upon the rich transcriptomic and DNA methylation data generated from our postmortem brain tissue to show how cis-acting genetic influences on transcription (eQTLs) and DNAm (meQTLs) in the brain are enriched at genomic risk loci for stress and addiction. This the first step in translating genetic findings into potential therapeutics, by mapping SNP-to-gene-to-function and the availability of large genomic datasets from relevant case and control tissues is a critical component of this endeavor.
5. Exploring genetic, drug and stress effects in human iPSCs
We are investigating transcriptional and regulatory genomic alterations in cellular models of human brain disease. We are applying hiPSC-based approaches to manipulate the genotype and/or expression levels of putative causal risk genes identified in large GWAS and postmortem datasets for PTSD, major depression and drug/alcohol use to determine functional roles for these genes in disease.