Genome-wide discovery of SLE genetic risk variant allelic enhancer activity

Lü, Xiaomei; X, Chen; Forney, Carmy; Donmez, Omer; Miller, Daniel; Parameswaran, Sreeja; Hong, Ted; Huang, Yongbo; Pujato, Mario; Cazares, Tareian; Er, Miraldi; Ray, John J.; Boer, Carl G. de; Jb, Harley; Mt, Weirauch; Kottyan, Leah C.

doi:10.1101/2020.01.20.906701

Cited by 5 publications

(4 citation statements)

References 128 publications

(196 reference statements)

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“…MPRA screening and publicly available data nominate the rs2431697-containing region as a potential cell-type-specific enhancer. Our massively parallel reporter assay (MPRA), which was used to screen allelic enhancer activity for all genome-wide significant SLE-associated genetic variants, discovered rs2431697 is a functional SNP with significant genotype-dependent enhancer activity (Supplementary Data 2) 46 . Likewise, using publicly available epigenetic data (NIH Roadmap Epigenomics Consortium, http://www.roadmapepigenomics.org) 47 , we observed strong H3K4me1 and H3K27ac signals, histone modifications that are hallmarks of active enhancers, overlapping rs2431697 in CD14+ monocytes.…”

Section: Resultsmentioning

confidence: 99%

SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression

Hou

Harley

et al. 2021

Nat Commun

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Since most variants that impact polygenic disease phenotypes localize to non-coding genomic regions, understanding the consequences of regulatory element variants will advance understanding of human disease mechanisms. Here, we report that the systemic lupus erythematosus (SLE) risk variant rs2431697 as likely causal for SLE through disruption of a regulatory element, modulating miR-146a expression. Using epigenomic analysis, genome-editing and 3D chromatin structure analysis, we show that rs2431697 tags a cell-type dependent distal enhancer specific for miR-146a that physically interacts with the miR-146a promoter. NF-kB binds the disease protective allele in a sequence-specific manner, increasing expression of this immunoregulatory microRNA. Finally, CRISPR activation-based modulation of this enhancer in the PBMCs of SLE patients attenuates type I interferon pathway activation by increasing miR-146a expression. Our work provides a strategy to define non-coding RNA functional regulatory elements using disease-associated variants and provides mechanistic links between autoimmune disease risk genetic variation and disease etiology.

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Section: Resultsmentioning

confidence: 99%

SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression

Hou

Harley

et al. 2021

Nat Commun

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“…Delivery of a library of DNA elements to cells, followed by RNA collection and sequencing, enables quantitative estimation of the expression driven by each element as a ratio of collected RNA barcode to delivered DNA barcode. These assays have recently been adapted to systematically identify SNPs with functional allelic TR differences from GWAS loci for several diseases [48][49][50][51][52][53][54][55][56] . Two key features make MPRAs advantageous for identifying both functional SNPs and their TR interactions.…”

Section: Introductionmentioning

confidence: 99%

Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays

Mulvey

Dougherty

2021

Preprint

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Family and population studies indicate clear heritability of major depressive disorder (MDD), though its underlying biology remains unclear. The majority of single-nucleotide polymorphism (SNP) linkage blocks associated with MDD by genome-wide association studies (GWASes) are believed to alter transcriptional regulators (e.g., enhancers, promoters), based on enrichment of marks correlated with these functions. A key to understanding MDD pathophysiology will be elucidation of which SNPs are functional and how such functional variants biologically converge to elicit the disease. Furthermore, retinoids can elicit MDD in patients, and promote depressive behaviors in rodent models, acting via a regulatory system of retinoid receptor transcription factors (TFs). We therefore sought to simultaneously identify functional genetic variants and assess retinoid pathway regulation of MDD risk loci. Using Massively Parallel Reporter Assays (MPRAs), we functionally screened over 1 000 SNPs prioritized from 39 neuropsychiatric trait/disease GWAS loci, with SNPs selected based on overlap with predicted regulatory features--including expression quantitative trait loci (eQTL) and histone marks--from human brains and cell cultures. We identified >100 SNPs with allelic effects on expression in a retinoid-responsive model system. Further, functional SNPs were enriched for binding sequences of retinoic acid-receptive transcription factors (TFs); with additional allelic differences unmasked by treatment with all-trans retinoic acid (ATRA). Finally, motifs overrepresented across functional SNPs corresponded to TFs highly specific to serotonergic neurons, suggesting an in vivo site of action. Our application of MPRAs to screen MDD-associated SNPs suggests a shared transcriptional regulatory program across loci, a subset of which are unmasked by retinoids.

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“…Evidence of this convergence is seen in de novo variants associated with ASD: several distinct variants disrupt binding sites for a single TF, NFIX (97). Such an approach was taken in a recent MPRA of lupusassociated SNPs, where identified functional variants were intersected with TF ChIP-seq datasets from pertinent cell types (leukocytes), identifying sets of recurrently disrupted TF binding sites (98).…”

Section: The Utility Of Mpras For Parsing Linked Variationmentioning

confidence: 99%

The Oft-Overlooked Massively Parallel Reporter Assay: Where, When, and Which Psychiatric Genetic Variants are Functional?

Mulvey¹,

Lagunas²,

Dougherty³

2020

Preprint

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Neuropsychiatric phenotypes have been long known to be influenced by heritable risk factors. The past decade of genetic studies have confirmed this directly, revealing specific common and rare genetic variants enriched in disease cohorts. However, the early hope for these studies-that only a small set of genes would be responsible for a given disorder-proved false. The picture that has emerged is far more complex: a given disorder may be influenced by myriad coding and noncoding variants of small effect size, and/or by rare but severe variants of large effect size, many de novo.Noncoding genomic sequences harbor a large portion of these variants, the molecular functions of which cannot usually be inferred from sequence alone. This creates a substantial barrier to understanding the higher-order molecular and biological systems underlying disease risk. Fortunately, a proliferation of genetic technologies-namely, scalable oligonucleotide synthesis, high-throughput RNA sequencing, CRISPR, and CRISPR derivatives-have opened novel avenues to experimentally identify biologically significant variants en masse. These advances have yielded an especially versatile technique adaptable to large-scale functional assays of variation in both untranscribed and untranslated regulatory features: Massively Parallel Reporter Assays (MPRAs). MPRAs are powerful molecular genetic tools that can be used to screen tens of thousands of predefined sequences for functional effects in a single experiment. This approach has several ideal features for psychiatric genetics, but remains underutilized in the field to date. To emphasize the opportunities MPRA holds for dissecting psychiatric polygenicity, we review here its applications in the literature, discuss its ability to test several biological variables implicated in psychiatric disorders, illustrate this flexibility with a proof-of-principle, in vivo cell-type specific implementation of the assay, and envision future outcomes of applying MPRA to both computational and experimental neurogenetics.

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Genome-wide discovery of SLE genetic risk variant allelic enhancer activity

Cited by 5 publications

References 128 publications

SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression

SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression

Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays

The Oft-Overlooked Massively Parallel Reporter Assay: Where, When, and Which Psychiatric Genetic Variants are Functional?

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