Center for Spatial and Functional Genomics Research Overview

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Whole genome sequencing is revealing a myriad of variants for rare monogenic traits and genome-wide association studies (GWAS) are implicating hundreds of genomic loci in the susceptibility to human disease. But in the context of non-coding variants being implicated, such loci have been commonly blighted by the remaining need to pinpoint the precise causal variants or the culprit genes. A map of the three-dimensional, accessible structure of the genome in disease-relevant tissue offers mechanistic insights into the genetic basis of disease, but current chromosome conformation capture technologies lack the focus and resolution to precisely identify functional variants and map them to their target genes.

3D Genomics

To overcome these obstacles, we expanded on a high-resolution, massively parallel capture-C-based method to characterize the genome-wide interactomes of nearly all of the ~37,000 annotated human protein-coding and non-coding genes in any cell type. We are also increasingly leveraging Hi-C, which yields insights into every interaction in the genome. Only by uncovering the correct functional context of these genetic variants and understanding how they operate can we truly translate these high value GWAS reports into meaningful benefits for patient care.

We are working in a number of the key common disease areas.

We have already addressed the most significant genome-wide association studies (GWAS) finding in type 2 diabetes reported to date, namely genetic variation within the transcription factor 7-like 2 (TCF7L2) gene, which Struan Grant first described in 2006. Given that the type 2 diabetes genetics community widely consider the T allele of the intronic single nucleotide polymorphism (SNP), rs7903146, within TCF7L2 to be the causal variant at this locus, we utilized chromatin conformation capture and CRISPR/Cas9 genome editing techniques to target this specific genomic region. As a consequence, we have compelling evidence that the actual culprit gene at this locus is in fact acyl-CoA synthetase long chain family, member 5 (ACSL5). Given we already have a dedicated infrastructure in place to conduct such'variant to gene mapping efforts, our team is now working on an NIH-funded effort to determine how additional recently uncovered type 2 diabetes GWAS-implicated loci affect the expression and function of specific genes through the use of key cutting-edge molecular biology approaches. We are now scaling up this effort in type 2 diabetes to similarly tackle other established loci.

In addition, obesity is a major risk factor for type 2 diabetes, which in turn has serious complications including accelerated development of cardiovascular disease. Given the expected global increase in the prevalence of childhood obesity, prevention of this disease and its serious complications must be addressed in order to reduce individual morbidity and the economic burden on society. We are applying our battery of methods as part of an NIH-funded effort in order to elucidate the genomic underpinnings of pediatric adiposity.

Furthermore, we are employing similar approaches to address bone accretion during growth, which can result in suboptimal peak bone mass and bone fragility in older adulthood. Osteoporosis has a strong heritable component, and pediatric studies may be more effective in distilling the genetic component in this complex disease, because duration of environmental exposure has been less. We are using our advanced techniques to extract novel information about bone structural strength and quality, along with high resolution 3D Genomics and CRISPR-based techniques to pinpoint causal genetic variants and corresponding effector gene(s) contributing to pediatric bone phenotypes.

Genome-wide association studies (GWAS) have clearly revolutionized the field of complex disease genetics, where intense efforts by large-scale international collaborations have been successful in discovering key genetic variants robustly associated with Alzheimer's disease (AD). However, GWAS only reports genomic signals associated with a given trait and not necessarily the precise localization of culprit genes. Given the need for variant-to-gene mapping, plus the need to expand the collection of public domain genomic data relevant to brain tissue types, we are NIH funded to utilize 3D Genomic and CRISPR-based screens in induced puropotent stem cell-derived cell types to pinpoint the causal gene(s) at each key AD GWAS-implicated locus. We are going on to extend our approach to other neurological conditions that range from insomnia to schizophrenia.

Genome-wide association studies have been successful in uncovering multiple loci for various cancers, including those with a pediatric age of onset. We are applying our arsenal of approaches to many types of cancer, which currently include testicular, pancreatic, melanoma, and neuroblastoma.

The susceptibility to autoimmune diseases such as rheumatoid arthritis (RA), type 1 diabetes (T1D), multiple sclerosis (MS), celiac disease (CD), myasthenia gravis (MG), systemic lupus erythematosus (SLE) and the auto-inflammatory diseases psoriasis and inflammatory bowel disease (e.g., Crohns disease and ulcerative colitis) have strong but complex genetic components. We are applying our 3D genomics approaches to multiple, disease-relevant immune cell populations including monocytes, naïve B and T lymphocytes, regulatory T cells, follicular helper T cells, germinal center B cells, memory Th1, Th2, Th17, and CTL cells.

Recently, we completed a high-resolution open chromatin and 3D promoter interactomes in human follicular helper (TFH) T cells, a disease-relevant cell type required for the production of autoantibodies and use these maps to gain insight into the genetic basis of systemic lupus erythematosus (SLE). We identified ~350 putative functional SLE variants based on their accessibility in TFH open chromatin. Open promoter variants were enriched at genes highly expressed in TFH, and non-promoter open variants were enriched for enhancer signatures. Importantly, we find that 50 percent of non-promoter variants skip the nearest promoter to physically interact only with distant genes. Gene ontology confirmed that genes physically interacting with SLE variants in three dimensions reside in highly TFH- and SLE-relevant networks, while the set of genes residing nearest to these variants in one dimension do not. An example of this is an accessible intronic SLE variant at the LPP locus that loops over 1 Mb to interact with the promoter of the master TFH transcription factor gene BCL6. CRISPR/CAS9 genome editing confirmed that this variant resides in a novel distal enhancer required for normal expression of BCL6. This 3D variant-to-gene mapping approach gives crucial insight into the disease-associated regulatory architecture of the human genome.