Multi-omics Technology Group

The Multi-omics Technology Group, under the direction of John Fullard, PhD, generates high-throughput omics data that provides the foundation for research by the other groups in the Center for Disease Neurogenomics (CDN). The group is the “wet lab” component of the CDN, generating much of the data analyzed by the other groups, and designing and performing validation experiments based on their observations.

We routinely perform bulk tissue and cell-type specific assays, including:

  • Genome (WGS, SNP arrays)
  • Transcriptome (RNA-seq)
  • Epigenome (ChIP-seq)
  • Chromatin structure (ATAC-seq, Hi-C)

We also routinely perform a range of single cell or single nucleus assays, including:

  • scRNA-seq and scATAC-seq
  • ECCITE-seq
  • CITE-seq
  • Spatial transcriptomics

Conducting Brain Omics at an Unprecedented Scale

The genetic basis of neuropsychiatric and neurodegenerative disease is highly complex, involving the interaction of numerous molecular perturbations, the majority of which are located in non-coding regions of the genome and are often cell-type specific in their effects. As the human brain is composed of a vast array of cell-types and sub-types, residing in functionally distinct regions of the brain, determining the mechanisms of action of these disease-associated risk variants is especially challenging. To further our understanding of brain disease, our group has been pioneering the application of state-of-the-art molecular techniques to maximize data generation from tiny amounts of precious clinical samples. We primarily work with fresh and frozen human brain specimens from controls and individuals affected by a diverse range of diseases, including schizophrenia, bipolar disorder, Alzheimer’s disease, and Parkinson’s disease. We have applied cell-type specific and single-cell technologies to examine disease-relevant cell types in thousands of clinical samples, providing the other groups of the Center with the statistical power they require to perform their analyses.

A Comprehensive Atlas of the Microglial Regulatory Landscape

A major focus of the Center is sifting through the thousands of variants associated with increased risk for brain disease and prioritizing their relevance. Most candidate mutations are non-coding and are thought to contribute to disease by disrupting cis-regulatory elements (CREs). CREs often function in a cell-type specific manner to determine when, where, and to what extent a gene is expressed. Microglia are resident macrophage of the brain, represent the active immune system of the central nervous system (CNS), and are implicated in a number of pathologies, in particular Alzheimer’s disease. We have optimized methods to isolate viable microglia from fresh human brain specimens, including both postmortem samples and biopsies, and subject them to a variety of molecular assays, allowing us to identify disease relevant CREs and their target genes. Integrative fine-mapping analysis of these data has, thus far, allowed us to identify putative regulatory mechanisms for 21 Alzheimer’s disease risk loci, of which 18 were refined to a single gene, including three new candidate risk genes (KCNN4, FIBP, and LRRC25).

Single Cell Analysis of the Human Brain

Recent technological developments have enabled researchers to perform molecular analysis at the level of individual cells. This is particularly applicable to the human brain, given its cellular complexity and the cell-type specific nature of many brain diseases. We routinely apply single cell, or single nuclei, assays to fresh as well as frozen archival brain material. To date, we have generated more than 2,500 single-cell RNA-seq libraries covering millions of cells, a range of brain regions, developmental time-points, and diseases (including Schizophrenia, Alzheimer’s, Parkinson’s and COVID-19). We have also processed more than 1,000 brain dissections using a multi-omics method that facilitates the simultaneous capture of gene expression (via RNA-seq) and chromatin structure (via ATAC-seq) in individual cells. Coupled with spatial transcriptomics and other in situ imaging approaches, we are using these data to better understand the genetic basis of disease and how specific cells of the brain interact with one another and their environment.

Validation and Functional Assays

Large scale omics datasets can lead to the identification of biologically, or clinically, relevant candidate genes. In order to validate these findings, we have established a facility enabling us to generate cell lines corresponding to the major cell types found in the human brain, including microglia and neurons. Coupled with functional assays (e.g. phagocytosis in the case of microglia) and gene expression analysis, we are using these cells to assess the impact of targeted perturbations (e.g. via CRISPR) or drug treatments on cellular function.