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Principal Investigator: Daniel Kastner
Organization: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
Fiscal Year: 2024
Award: $1,583,024
Funding agency: National Human Genome Research Institute
African American Scleroderma
During the current reporting period several collaborative projects have come close to fruition, and I anticipate that Dr. Gourh will have several manuscripts ready for submission within the next few months.
1) The role of NOTCH4 in the vasculopathy of SSc: Using a gene-based approach, we found that NOTCH4 is associated with SSc at an exome-wide significance and in patients with severe vascular disease. The risk haplotype defined by the missense (c.2824C>T) and promoter (c.-117G>A) variants was enriched in African Americans with SSc vs. controls and increased the risk of the combination of severe Raynauds, renal crisis, and pulmonary arterial hypertension. The c.-117A allele, residing in the glucocorticoid receptor binding site, was associated with increased NOTCH4 transcripts and protein expression. The c.2824 allele upregulated NOTCH4 in lymphoblastoid cell lines. SSc skin single-cell RNA sequencing identified NOTCH4 expression principally in endothelial cells, with dysregulated angiogenesis and endothelial-to-mesenchymal transition. NOTCH4 stimulation in an endothelial cell line and in c.-117A SSc primary endothelial cells attenuated tube formation. Inhibiting NOTCH4 rescued normal tube formation. Currently we are testing an FDA-approved NOTCH inhibitor drug, nirogacestat, in a Notch4 overexpression mouse model.
2) Admixture mapping: The goal of admixture mapping is to identify disease-associated variants that differ substantially in frequency between ancestral populations. We hypothesized that African American SSc patients would be enriched for African ancestry variants and carry a higher proportion of risk alleles at loci associated with SSc. We performed admixture mapping analysis to identify genes contained within the admixed regions followed by gene-based testing for enrichment of missense or loss-of-function variants in these genes. Admixture mapping of SSc identified one genome-wide significant and thirteen suggestive regions. Stratified analysis on SSc autoantibody subsets of SSc identified one genome-wide significant and several suggestive regions. Gene-based testing within these admixed regions identified enrichment of rare variants in twenty-seven genes in overall SSc and one, six, and three genes in the anti-fibrillarin, anti-topoisomerase, and anti-centromere subsets, respectively. Four genes (IL13, SLC29A2, OR10C1, and GDF9) were significant in both overall SSc and an autoantibody subset.
3) The possibility of molecular mimicry: This project is based on the hypothesis that SSc-associated autoantibodies may arise because of cross-reactivities between SSc-associated autoantigens and the antigens of naturally occurring pathogens, presented by SSc-associated HLA alleles. We have performed TCR sequencing in SSc patients and controls and plan to examine the specific sequences and amino acid composition of the TCRs. We have identified unique TCR clones in groups of SSc patients. Additional TCR sequence analysis identified five T cell clones that were present in 28% of samples and were also present in SSc skin. These clones had sequence homology to clones seen in SARS-CoV-2, suggesting a potential role for molecular mimicry between SSc-associated autoantigens and corona virus determinants.
4) The role of the IL1RAP gene in SSc susceptibility: The interleukin-1 receptor accessory protein (IL1RAP) is a co-receptor for the interleukin-1 family of cytokines. It plays an essential role in the signaling of IL-1, IL-33, and IL-36, which are known to mediate inflammation and fibrosis. In this study we examined the association of rare variants in the IL-1 family of ligands and receptors with SSc. In three of three gene-based tests, the IL1RAP gene was found to be enriched for rare variants in African Americans with SSc. Diffuse skin involvement was present in 15 of 17 patients (88.2%) with IL1RAP rare variants, whereas only 58.4% of the overall cohort had diffuse skin involvement. The IL1RAP association was even stronger in the diffuse skin subset, whereas no association was seen in the limited skin subset.
5) Genetic susceptibility to calcinosis in SSc: Calcinosis, deposition of insoluble calcium in the dermis and subcutaneous tissues, contributes to morbidity in SSc patients, leading to decreased quality of life. We have identified rare variants in pathways affecting calcinosis in SSc patients with severe calcinosis. Besides finding variants in genes known to cause Mendelian forms of calcinosis, we have also identified variants in genes leading to dysregulated phosphate metabolism. We have also identified, for the first time, HLA-DRB4 as a novel susceptibility allele in patients with SSc and severe calcinosis.
6) Effect of racial variability in autoantibody status on clinical outcomes: During the current reporting period we published a paper with colleagues in the Annals of the Rheumatic Diseases affirming already well-documented associations between race and autoantibody status but demonstrating that controlling for these associations does not completely explain racial differences in scleroderma outcome.
Systemic Onset Juvenile Idiopathic Arthritis
During the current reporting period we published a paper in Arthritis and Rheumatology with colleagues demonstrating an enrichment of rare HLH variants in patients with sJIA compared with controls, driven by STXBP2 and UNC13D. Biallelic variation in HLH genes was associated with sJIA, driven by LYST. Only UNC13D displayed enrichment with MAS. The data suggest that HLH variants may contribute to the pathophysiology of sJIA, even without MAS.
VEXAS
During the current reporting period we published a paper in Blood examining the risk factors and frequency of thrombosis in VEXAS syndrome. We evaluated 119 patients with VEXAS syndrome for venous and arterial thrombosis and correlated their presence with clinical outcomes and survival. Thrombosis occurred in 49% of patients, mostly venous thromboembolism (VTE: 41%). Almost two-thirds of VTEs were unprovoked, 41% were recurrent, and 20% occurred despite anticoagulation. The cumulative incidence of VTE was 17% at 1 year from symptom onset and 40% by 5 years. Cardiac and pulmonary inflammatory manifestations were associated with time to VTE. M41L was positively associated specifically with pulmonary embolism by univariate and multivariate logistic regression. The cumulative incidence of arterial thrombosis was 6% at 1 year and 11% at 5 years. The overall survival of the entire patient cohort at median follow-up time of 4.8 years was 88%, and there was no difference in survival between patients with or without thrombosis. Patients with VEXAS syndrome are at high risk of VTE; thromboprophylaxis should be administered in high risk settings unless strongly contraindicated.
The concept of genetically transitional disease
Genetically transitional disease refers to disorders in which gene mutation is necessary but not sufficient to cause disease. With collaborators, Dr. Aksentijevich coauthored a paper in Nature Reviews Rheumatology exploring the possibility of applying this concept to rheumatic diseases.
Terms: <0-11 years old><2019 novel corona virus><2019 novel coronavirus><2019-nCoV><21+ years old><Active Follow-up><Adamantiades-Behcet's Syndrome><Adenitis><Adult><Adult Human><Affect><African American><African American group><African American individual><African American people><African American population><African Americans><African ancestry><African descent><Afro American><Afroamerican><Alleles><Allelomorphs><American><Amino Acids><Anticoagulation><Antigens><Aphthae><Aphthous Stomatitis><Aphthous Ulcer><Area><Arthritis><Atrophic Arthritis><Attenuated><Autoantibodies><Autoantigens><Autoimmune Diseases><Autoimmune Status><Autoimmunity><Autologous Antigens><Behcet Disease><Behcet Syndrome><Beige Protein><Binding Sites><Blood><Blood Reticuloendothelial System><CHS protein><CHS1><CHS1 Protein><CHS1 gene><COVID-19 virus><COVID19 virus><Calcinosis><Calcium><Canker Sore><Cardiac><Cell Body><Cell Communication and Signaling><Cell Line><Cell Signaling><CellLine><Cells><Centromere><Cervical><Chediak-Higashi Syndrome 1><Chediak-Higashi Syndrome 1 Gene><Child><Child Youth><Childhood><Children (0-21)><Chronic><Clinical><Clinical Investigator><Clone Cells><CoV-2><CoV2><Collaborations><Combining Site><Complex><Corium><Coronaviridae><Coronavirus><Cutis><DNA><Data><Deoxyribonucleic Acid><Deposit><Deposition><Dermis><Diffuse><Disease><Disorder><Drosophila Homolog of NOTCH 4><Dysfunction><EXTMR><Endothelial Cells><Endothelium><Enzyme Gene><Enzymes><Extramural><Extramural Activities><FDA approved><Faculty><Family><Fever><Fibrosis><Frequencies><Functional disorder><GDF-9><GDF9><GDF9 gene><Gene Alteration><Gene Expression><Gene Mutation><Gene Proteins><Genes><Genetic><Genetic Predisposition><Genetic Predisposition to Disease><Genetic Susceptibility><Genetic analyses><Genetic propensity><Genetic study><Genomics><Genotype><Glucocorticoid Receptor><Goals><Growth Differentiation Factor 9 Gene><Haplotypes><Human><Hypodermis><IL-1><IL-1 Receptors><IL-13><IL-1RAcP><IL1><IL1 Receptors><IL13><INT3><Incidence><Inflammation><Inflammatory><Inherited Predisposition><Inherited Susceptibility><Interleukin I><Interleukin-1><Interleukin-1 Receptors><Interleukin-13><Intermediary Metabolism><Intracellular Communication and Signaling><Investigation><Investigators><Journals><Juvenile-Onset Still's Disease><Kidney><Kidney Urinary System><LYST><Ligands><Link><Logistic Regressions><Lung><Lung Respiratory System><Lymphocyte-Stimulating Hormone><Lysosomal Trafficking Regulator><Macrophage Cell Factor><Magazine><Manuscripts><Mediating><Medicine><Mesenchymal><Metabolic Processes><Metabolism><Modern Man><Molecular Mimicry><Morbidity><Morbidity - disease rate><Mouse Mammary Tumor Virus Integration Site 3><Mucosa><Mucosal Tissue><Mucous Membrane><Musculoskeletal Pain Disorder><Myelogenous><Myeloid><NIAID><NIAMS><NIH><NOTCH4><NOTCH4 gene><National Institute of Allergy and Infectious Disease><National Institute of Arthritis, and Musculoskeletal, and Skin Diseases><National Institutes of Health><Nature><New England><New York><Northeastern United States><Oncogene INT3><Organ><Outcome><Paper><Pathologic Calcification><Pathway interactions><Patients><Periodicals><Pharyngitis><Phosphates><Physiopathology><Play><Population><Position><Positioning Attribute><Predisposition><Predisposition gene><Protein Gene Products><Publishing><Pulmonary Embolism><Pyrexia><QOL><Quality of life><Race><Races><Reactive Site><Receptor Protein><Recurrence><Recurrent><Reporting><Research Personnel><Researchers><Rheumatic Diseases><Rheumatism><Rheumatoid Arthritis><Rheumatologic Diseases><Rheumatologic Disorder><Rheumatology><Risk><Risk Factors><Risk-associated variant><Role><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV2><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><SEQ-AN><Sampling><Scleroderma><Self-Antigens><Sequence Analyses><Sequence Analysis><Sequence Homology><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome related corona virus 2><Signal Transduction><Signal Transduction Systems><Signaling><Skin><Somatic Mutation><Still's disease><Strains Cell Lines><Subcutaneous Tissue><Subcutis><Superficial Fascia><Susceptibility><Susceptibility Gene><Symptoms><Syndrome><System><T Helper Factor><T cell receptor repertoire sequencing><T cell receptor sequencing><T-Cells><T-Lymphocyte><TCR repertoire sequencing><TCR sequencing><TCR-seq><TCRseq><Tela Subcutanea><Testing><Thrombosis><Time><Tonsillar Tissue><Topoisomerase><Touraine's Aphthosis><Transcript><Triple Symptom complex of Behcet><Triple-Symptom Complex><Tube><Ubiquitin-Activating Enzyme E1><Ubiquitin-Activating Enzymes><Ubiquitination Activating Enzyme E1><Underserved Population><United States National Institutes of Health><Universities><Vacuole><Variant><Variation><Vascular Diseases><Vascular Disorder><Venous><Wuhan coronavirus><active followup><admixture mapping><adulthood><aminoacid><angiogenesis><arthritic><attenuate><attenuates><autoimmune antibody><autoimmune condition><autoimmune disorder><autoimmunity disease><autoinflammation><autoinflammatory><autoinflammatory diseases><autoinflammatory disorders><autoreactive antibody><biological signal transduction><blood vessel disorder><cohort><corona virus><coronavirus disease 2019 virus><coronavirus disease-19 virus><cross reactivity><cultured cell line><cutaneous fibrosis><cytokine><dermal fibrosis><dermatosclerosis><differences due to race><differences in race><differs by race><differs in race><exome><exomes><febrile><febris><fibrillarin><fibrotic skin><follow up><follow-up><followed up><followup><gene testing><gene-based testing><genetic analysis><genetic etiology><genetic mechanism of disease><genetic testing><genetic vulnerability><genetically predisposed><genome scale><genome-wide><genomewide><hCoV19><high risk><immunogen><inhibitor drug><inhibitor therapeutic><inhibitor therapy><inorganic phosphate><interest><interleukin-1 receptor accessory protein><kids><loss of function><lymphoblastoid cell line><lymphocyte activating factor><mortality><mouse model><multi-ethnic><multiethnic><murine model><nCoV2><novel><overexpress><overexpression><pathogen><pathophysiology><pathway><pediatric><periodic><periodical><predisposing gene><promoter><promotor><protein expression><pulmonary><pulmonary arterial hypertension><pulmonary artery hypertension><race based differences><race differences><race related differences><racial><racial background><racial difference><racial origin><racially different><rare allele><rare mutation><rare variant><receptor><renal><rheumatic arthritis><risk allele><risk gene><risk genotype><risk loci><risk locus><risk variant><scRNA-seq><self reactive antibody><single cell RNA-seq><single cell RNAseq><single cell expression profiling><single cell transcriptomic profiling><single-cell RNA sequencing><skin fibrosis><social role><somatic variant><subdermal tissue><susceptibility allele><susceptibility locus><susceptibility variant><systemic juvenile idiopathic arthritis><systemic onset juvenile idiopathic arthritis><tenure process><tenure track><thrombotic disease><thrombotic disorder><thymus derived lymphocyte><under served group><under served individual><under served people><under served population><underserved group><underserved individual><underserved people><vascular dysfunction><vasculopathy><venous thromboembolism><youngster>