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Tissue-specific and tissue-agnostic effects of genome sequence variation modulating blood pressure

Lee, Dongwon; Han, Seong Kyu; Yaacov, Or; Berk-Rauch, Hanna; Mathiyalagan, Prabhu; Ganesh, Santhi K; Chakravarti, Aravinda
Genome-wide association studies (GWASs) have identified numerous variants associated with polygenic traits and diseases. However, with few exceptions, a mechanistic understanding of which variants affect which genes in which tissues to modulate trait variation is lacking. Here, we present genomic analyses to explain trait heritability of blood pressure (BP) through the genetics of transcriptional regulation using GWASs, multiomics data from different tissues, and machine learning approaches. Approximately 500,000 predicted regulatory variants across four tissues explain 33.4% of variant heritability: 2.5%, 5.3%, 7.7%, and 11.8% for kidney-, adrenal-, heart-, and artery-specific variants, respectively. Variation in the enhancers involved shows greater tissue specificity than in the genes they regulate, suggesting that gene regulatory networks perturbed by enhancer variants in a tissue relevant to a phenotype are the major source of interindividual variation in BP. Thus, our study provides an approach to scan human tissue and cell types for their physiological contribution to any trait.
PMID: 37910504
ISSN: 2211-1247
CID: 5590312

Cardiac muscle-restricted partial loss of Nos1ap expression has limited but significant impact on electrocardiographic features

Smith, Alexa; Auer, Dallas; Johnson, Morgan; Sanchez, Ernesto; Ross, Holly; Ward, Christopher; Chakravarti, Aravinda; Kapoor, Ashish
Genome-wide association studies have identified sequence polymorphisms in a functional enhancer of the NOS1AP gene as the most common genetic regulator of QT interval and human cardiac NOS1AP gene expression in the general population. Functional studies based on in vitro overexpression in murine cardiomyocytes and ex vivo knockdown in zebrafish embryonic hearts, by us and others, have also demonstrated that NOS1AP expression levels can alter cellular electrophysiology. Here, to explore the role of NOS1AP in cardiac electrophysiology at an organismal level, we generated and characterized constitutive and heart muscle-restricted Nos1ap knockout mice to assess whether NOS1AP disruption alters the QT interval in vivo. Constitutive loss of Nos1ap led to genetic background-dependent variable lethality at or right before birth. Heart muscle-restricted Nos1ap knockout, generated using cardiac-specific alpha-myosin heavy chain promoter-driven tamoxifen-inducible Cre, resulted in tissue-level Nos1ap expression reduced by half. This partial loss of expression had no detectable effect on the QT interval or other electrocardiographic and echocardiographic parameters, except for a small but significant reduction in the QRS interval. Given that challenges associated with defining the end of the T wave on murine electrocardiogram can limit identification of subtle effects on the QT interval and that common noncoding NOS1AP variants are also associated with the QRS interval, our findings support the role of NOS1AP in regulation of the cardiac electrical cycle.
PMID: 37708408
ISSN: 2160-1836
CID: 5593352

RET enhancer haplotype-dependent remodeling of the human fetal gut development program

Chatterjee, Sumantra; Fries, Lauren E; Yaacov, Or; Hu, Nan; Berk-Rauch, Hanna E; Chakravarti, Aravinda
Hirschsprung disease (HSCR) is associated with deficiency of the receptor tyrosine kinase RET, resulting in loss of cells of the enteric nervous system (ENS) during fetal gut development. The major contribution to HSCR risk is from common sequence variants in RET enhancers with additional risk from rare coding variants in many genes. Here, we demonstrate that these RET enhancer variants specifically alter the human fetal gut development program through significant decreases in gene expression of RET, members of the RET-EDNRB gene regulatory network (GRN), other HSCR genes, with an altered transcriptome of 2,382 differentially expressed genes across diverse neuronal and mesenchymal functions. A parsimonious hypothesis for these results is that beyond RET's direct effect on its GRN, it also has a major role in enteric neural crest-derived cell (ENCDC) precursor proliferation, its deficiency reducing ENCDCs with relative expansion of non-ENCDC cells. Thus, genes reducing RET proliferative activity can potentially cause HSCR. One such class is the 23 RET-dependent transcription factors enriched in early gut development. We show that their knockdown in human neuroblastoma SK-N-SH cells reduces RET and/or EDNRB gene expression, expanding the RET-EDNRB GRN. The human embryos we studied had major remodeling of the gut transcriptome but were unlikely to have had HSCR: thus, genetic or epigenetic changes in addition to those in RET are required for aganglionosis.
PMID: 37948459
ISSN: 1553-7404
CID: 5607952

Ret deficiency decreases neural crest progenitor proliferation and restricts fate potential during enteric nervous system development

Vincent, Elizabeth; Chatterjee, Sumantra; Cannon, Gabrielle H; Auer, Dallas; Ross, Holly; Chakravarti, Aravinda; Goff, Loyal A
The receptor tyrosine kinase RET plays a critical role in the fate specification of enteric neural crest-derived cells (ENCDCs) during enteric nervous system (ENS) development. RET loss of function (LoF) is associated with Hirschsprung disease (HSCR), which is marked by aganglionosis of the gastrointestinal (GI) tract. Although the major phenotypic consequences and the underlying transcriptional changes from Ret LoF in the developing ENS have been described, cell type- and state-specific effects are unknown. We performed single-cell RNA sequencing on an enriched population of ENCDCs from the developing GI tract of Ret null heterozygous and homozygous mice at embryonic day (E)12.5 and E14.5. We demonstrate four significant findings: 1) Ret-expressing ENCDCs are a heterogeneous population comprising ENS progenitors as well as glial- and neuronal-committed cells; 2) neurons committed to a predominantly inhibitory motor neuron developmental trajectory are not produced under Ret LoF, leaving behind a mostly excitatory motor neuron developmental program; 3) expression patterns of HSCR-associated and Ret gene regulatory network genes are impacted by Ret LoF; and 4) Ret deficiency leads to precocious differentiation and reduction in the number of proliferating ENS precursors. Our results support a model in which Ret contributes to multiple distinct cellular phenotypes during development of the ENS, including the specification of inhibitory neuron subtypes, cell cycle dynamics of ENS progenitors, and the developmental timing of neuronal and glial commitment.
PMID: 37585461
ISSN: 1091-6490
CID: 5595682

Interleukin-1 receptor antagonist gene ( IL1RN ) variants modulate the cytokine release syndrome and mortality of SARS-CoV-2

Attur, Mukundan; Petrilli, Christopher; Adhikari, Samrachana; Iturrate, Eduardo; Li, Xiyue; Tuminello, Stephanie; Hu, Nan; Chakravarti, Aravinda; Beck, David; Abramson, Steven B
OBJECTIVE/UNASSIGNED:, the gene encoding the anti-inflammatory IL-1 receptor antagonist (IL-1Ra), on the cytokine release syndrome and mortality. METHODS/UNASSIGNED:gene were assessed for association with laboratory markers of the cytokine release syndrome (CRS) and mortality. RESULTS/UNASSIGNED:rs419598 CC SNV exhibited lower inflammatory biomarker levels, and was associated with reduced mortality compared to the CT/TT genotype in men (OR 0.49 (0.23 - 1.00); 0.052), with the most pronounced effect observed between the ages of 55-74 [5.5% vs. 18.4%, p<0.001]. CONCLUSION/UNASSIGNED:modulates the COVID-19 cytokine release syndrome via endogenous " anti-inflammatory" mechanisms. SIGNIFICANCE STATEMENT/UNASSIGNED:merits further evaluation in severe SARS-CoV-2 infection.
PMID: 36711766
CID: 5602052

Quality assessment and refinement of chromatin accessibility data using a sequence-based predictive model

Han, Seong Kyu; Muto, Yoshiharu; Wilson, Parker C; Humphreys, Benjamin D; Sampson, Matthew G; Chakravarti, Aravinda; Lee, Dongwon
Chromatin accessibility assays are central to the genome-wide identification of gene regulatory elements associated with transcriptional regulation. However, the data have highly variable quality arising from several biological and technical factors. To surmount this problem, we developed a sequence-based machine learning method to evaluate and refine chromatin accessibility data. Our framework, gapped k-mer SVM quality check (gkmQC), provides the quality metrics for a sample based on the prediction accuracy of the trained models. We tested 886 DNase-seq samples from the ENCODE/Roadmap projects to demonstrate that gkmQC can effectively identify "high-quality" (HQ) samples with low conventional quality scores owing to marginal read depths. Peaks identified in HQ samples are more accurately aligned at functional regulatory elements, show greater enrichment of regulatory elements harboring functional variants, and explain greater heritability of phenotypes from their relevant tissues. Moreover, gkmQC can optimize the peak-calling threshold to identify additional peaks, especially for rare cell types in single-cell chromatin accessibility data.
PMID: 36508674
ISSN: 1091-6490
CID: 5381942

RET enhancer haplotype-dependent remodeling of the human fetal gut development program [PrePrint]

Chatterjee, Sumantra; Fries, Lauren E; Yaacov, Or; Hu, Nan; Berk-Rauch, Hanna E; Chakravarti, Aravinda
ISSN: 2692-8205
CID: 5294112

Insights From a Large-Scale Whole-Genome Sequencing Study of Systolic Blood Pressure, Diastolic Blood Pressure, and Hypertension

Kelly, Tanika N; Sun, Xiao; He, Karen Y; Brown, Michael R; Taliun, Sarah A Gagliano; Hellwege, Jacklyn N; Irvin, Marguerite R; Mi, Xuenan; Brody, Jennifer A; Franceschini, Nora; Guo, Xiuqing; Hwang, Shih-Jen; de Vries, Paul S; Gao, Yan; Moscati, Arden; Nadkarni, Girish N; Yanek, Lisa R; Elfassy, Tali; Smith, Jennifer A; Chung, Ren-Hua; Beitelshees, Amber L; Patki, Amit; Aslibekyan, Stella; Blobner, Brandon M; Peralta, Juan M; Assimes, Themistocles L; Palmas, Walter R; Liu, Chunyu; Bress, Adam P; Huang, Zhijie; Becker, Lewis C; Hwa, Chii-Min; O'Connell, Jeffrey R; Carlson, Jenna C; Warren, Helen R; Das, Sayantan; Giri, Ayush; Martin, Lisa W; Craig Johnson, W; Fox, Ervin R; Bottinger, Erwin P; Razavi, Alexander C; Vaidya, Dhananjay; Chuang, Lee-Ming; Chang, Yen-Pei C; Naseri, Take; Jain, Deepti; Kang, Hyun Min; Hung, Adriana M; Srinivasasainagendra, Vinodh; Snively, Beverly M; Gu, Dongfeng; Montasser, May E; Reupena, Muagututi'a Sefuiva; Heavner, Benjamin D; LeFaive, Jonathon; Hixson, James E; Rice, Kenneth M; Wang, Fei Fei; Nielsen, Jonas B; Huang, Jianfeng; Khan, Alyna T; Zhou, Wei; Nierenberg, Jovia L; Laurie, Cathy C; Armstrong, Nicole D; Shi, Mengyao; Pan, Yang; Stilp, Adrienne M; Emery, Leslie; Wong, Quenna; Hawley, Nicola L; Minster, Ryan L; Curran, Joanne E; Munroe, Patricia B; Weeks, Daniel E; North, Kari E; Tracy, Russell P; Kenny, Eimear E; Shimbo, Daichi; Chakravarti, Aravinda; Rich, Stephen S; Reiner, Alex P; Blangero, John; Redline, Susan; Mitchell, Braxton D; Rao, Dabeeru C; Ida Chen, Yii-Der; Kardia, Sharon L R; Kaplan, Robert C; Mathias, Rasika A; He, Jiang; Psaty, Bruce M; Fornage, Myriam; Loos, Ruth J F; Correa, Adolfo; Boerwinkle, Eric; Rotter, Jerome I; Kooperberg, Charles; Edwards, Todd L; Abecasis, Gonçalo R; Zhu, Xiaofeng; Levy, Daniel; Arnett, Donna K; Morrison, Alanna C
BACKGROUND:The availability of whole-genome sequencing data in large studies has enabled the assessment of coding and noncoding variants across the allele frequency spectrum for their associations with blood pressure. METHODS:We conducted a multiancestry whole-genome sequencing analysis of blood pressure among 51 456 Trans-Omics for Precision Medicine and Centers for Common Disease Genomics program participants (stage-1). Stage-2 analyses leveraged array data from UK Biobank (N=383 145), Million Veteran Program (N=318 891), and Reasons for Geographic and Racial Differences in Stroke (N=10 643) participants, along with whole-exome sequencing data from UK Biobank (N=199 631) participants. RESULTS:, respectively). DISCUSSION/CONCLUSIONS:We report one promising but unconfirmed rare variant for blood pressure and, more importantly, contribute insights for future blood pressure sequencing studies. Our findings suggest promise of aggregate analyses to complement single variant analysis strategies and the need for larger, diverse samples, and family studies to enable robust rare variant identification.
PMID: 35652341
ISSN: 1524-4563
CID: 5236312

Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19

Nln, Ilona; Fernandez-Ruiz, Ruth; Muskardin, Theresa L Wampler; Paredes, Jacqueline L; Blazer, Ashira D; Tuminello, Stephanie; Attur, Mukundan; Iturrate, Eduardo; Petrilli, Christopher M; Abramson, Steven B; Chakravarti, Aravinda; Niewold, Timothy B
Type I interferon (IFN) is critical in our defense against viral infections. Increased type I IFN pathway activation is a genetic risk factor for systemic lupus erythematosus (SLE), and a number of common risk alleles contribute to the high IFN trait. We hypothesized that these common gain-of-function IFN pathway alleles may be associated with protection from mortality in acute COVID-19. We studied patients admitted with acute COVID-19 (756 European-American and 398 African-American ancestry). Ancestral backgrounds were analyzed separately, and mortality after acute COVID-19 was the primary outcome. In European-American ancestry, we found that a haplotype of interferon regulatory factor 5 (IRF5) and alleles of protein kinase cGMP-dependent 1 (PRKG1) were associated with mortality from COVID-19. Interestingly, these were much stronger risk factors in younger patients (OR=29.2 for PRKG1 in ages 45-54). Variants in the IRF7 and IRF8 genes were associated with mortality from COVID-19 in African-American subjects, and these genetic effects were more pronounced in older subjects. Combining genetic information with blood biomarker data such as C-reactive protein, troponin, and D-dimer resulted in significantly improved predictive capacity, and in both ancestral backgrounds the risk genotypes were most relevant in those with positive biomarkers (OR for death between 14 and 111 in high risk genetic/biomarker groups). This study confirms the critical role of the IFN pathway in defense against COVID-19 and viral infections, and supports the idea that some common SLE risk alleles exert protective effects in anti-viral immunity. BACKGROUND: We find that a number of IFN pathway lupus risk alleles significantly impact mortality following COVID-19 infection. These data support the idea that type I IFN pathway risk alleles for autoimmune disease may persist in high frequency in modern human populations due to a benefit in our defense against viral infections. TRANSLATIONAL SIGNIFICANCE: We develop multivariate prediction models which combine genetics and known biomarkers of severity to result in greatly improved prediction of mortality in acute COVID-19. The specific associated alleles provide some clues about key points in our defense against COVID-19.
PMID: 35114420
ISSN: 1878-1810
CID: 5153812

Ret loss-of-function decreases neural crest progenitor proliferation and restricts developmental fate potential during enteric nervous system development [PrePrint]

Vincent, Elizabeth; Chatterjee, Sumantra; Cannon, Gabrielle H; Auer, Dallas; Ross, Holly; Chakravarti, Aravinda; Goff, Loyal A
ISSN: 2692-8205
CID: 5294122