Human follicular helper T cell promoter connectomes reveal novel genes and regulatory elements at SLE GWAS loci

Abstract

22Systemic lupus erythematosus (SLE) is a complex inflammatory disease mediated by 23 autoreactive antibodies that damages multiple tissues in children and adults. wide association studies (GWAS) have statistically implicated hundreds of loci in the 25 susceptibility to human disease, including SLE, but the majority have failed to identify the 26 causal variants or the effector genes. As a physicochemical approach to detecting 27 functional variants and connecting them to target genes, we generated comprehensive, 28 high-resolution maps of SLE variant accessibility and gene connectivity in the context of 29 the three-dimensional chromosomal architecture of human tonsillar follicular helper T 30 cells (TFH), a cell type required for the production of anti-nuclear antibodies characteristic 31 of SLE. These spatial epigenomic maps identified a shortlist of over 400 potentially 32 functional variants across 48 GWAS-implicated SLE loci. Twenty percent of these 33 variants were located in open promoters of highly-expressed TFH genes, while 80% 34 reside in non-promoter genomic regions that are connected in 3D to genes that likewise 35 tend to be highly expressed in TFH. Importantly, we find that 90% of SLE-associated 36 variants exhibit spatial proximity to genes that are not nearby in the 1D sequence of the 37 genome, and over 60% of variants 'skip' the nearest gene to physically interact only with 38 the promoters of distant genes. Gene ontology confirmed that genes in spatial proximity 39 to SLE variants reside in highly SLE-relevant networks, including accessible variants that 40 loop 200-1000 kb to interact with the promoters of the canonical TFH genes BCL6 and 41 CXCR5. CRISPR-Cas9 genome editing confirmed that these variants reside in novel, 42 distal regulatory elements required for normal BCL6 and CXCR5 expression by T cells. 43Furthermore, SLE-associated SNP-promoter interactomes implicated a set of novel 44 51 52 GWAS has been an important tool in understanding the genetic basis of complex, 53 heritable diseases and traits. However, GWAS is typically powered to identify relatively 54 large blocks of the genome containing dozens to hundreds of single nucleotide 55 polymorphisms (SNP) in linkage disequilibrium (LD), any one of which could be 56 responsible for the association of the entire locus with disease susceptibility. Moreover, 57 ~90% of GWAS-implicated SNP are intergenic or intronic, and do not affect the coding 58 sequence of proteins. Therefore, the location of the GWAS signal per se does not identify 59 the culprit gene(s). Examples of this are the FTO GWAS signal in obesity 1,2 , and the 60 TCF7L2 GWAS signal in type 2 diabetes 3 , in which each suspected causal variant resides 61 in an intron of the local gene, but were shown instead to regulate expression of the distant 62 genes IRX3/5 and ACSL5, respectively. 63Systemic lupus erythematosus (SLE) is a complex inflammatory disease mediated by 64 autoreactive antibodies that damage skin, joints, kidneys, brain and other tissues in 65 children and ...

Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits

“…We also observed a trend for genes with higher expression interacting with more cREs (Kruskal Wallis test: p-value < 2.2 x10 -16 ) (Supplemental Figure 3F), which is in line with reports for other neuronal 38 and immune cells 22 .…”

“…Recently, we combined a suite of techniques to systematically evaluate GWAS signals located in distal elements [19][20][21][22] . Together, our integrated "variant-to-gene mapping" approach aims to physically fine-map significant GWAS loci by identifying open proxy SNPs in LD with each given sentinel signal that directly contact a gene promoter.…”

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal additional BMI loci

“…Over the past decade, sequencing technologies such aa RNA-seq ( Wang et al, 2009 ), ATAC-seq ( Buenrostro et al, 2013 ), and high-resolution promoter-focused Capture C Chesi et al, 2019 ; Hughes et al, 2014 ; Su et al, 2020 have been developed to facilitate the annotation of genes and their regulatory elements. Such data have been utilized to identify physical variant-to-gene interactions via three-dimensional genomics to implicate effector genes at GWAS loci where both sequence variant and gene reside within regions of open chromatin ( Arnold et al, 2015 ; Çalışkan et al, 2019 ; Chesi et al, 2019 ; Cousminer et al, 2020 ; Javierre et al, 2016 ; Smemo et al, 2014 ; Su et al, 2019 ; Su et al, 2020 ). By leveraging high-resolution promoter-focused Capture C with ATAC-seq, it is possible to physically connect putatively functional non-coding elements, such as enhancers, harboring disease-relevant SNPs to promoters of specific genes thereby potentially mechanistically implicated in the SNP-associated phenotype.…”