Peter Gregersen - Academia.edu (original) (raw)

Papers by Peter Gregersen

Proceedings of the National Academy of Sciences

Significance There is growing evidence that preexisting autoantibodies neutralizing type I interf... more Significance There is growing evidence that preexisting autoantibodies neutralizing type I interferons (IFNs) are strong determinants of life-threatening COVID-19 pneumonia. It is important to estimate their quantitative impact on COVID-19 mortality upon SARS-CoV-2 infection, by age and sex, as both the prevalence of these autoantibodies and the risk of COVID-19 death increase with age and are higher in men. Using an unvaccinated sample of 1,261 deceased patients and 34,159 individuals from the general population, we found that autoantibodies against type I IFNs strongly increased the SARS-CoV-2 infection fatality rate at all ages, in both men and women. Autoantibodies against type I IFNs are strong and common predictors of life-threatening COVID-19. Testing for these autoantibodies should be considered in the general population.

Nature, 2022

Variants of UNC13A, a critical gene for synapse function, increase the risk of amyotrophic latera... more Variants of UNC13A, a critical gene for synapse function, increase the risk of amyotrophic lateral sclerosis and frontotemporal dementia1–3, two related neurodegenerative diseases defined by mislocalization of the RNA-binding protein TDP-434,5. Here we show that TDP-43 depletion induces robust inclusion of a cryptic exon in UNC13A, resulting in nonsense-mediated decay and loss of UNC13A protein. Two common intronic UNC13A polymorphisms strongly associated with amyotrophic lateral sclerosis and frontotemporal dementia risk overlap with TDP-43 binding sites. These polymorphisms potentiate cryptic exon inclusion, both in cultured cells and in brains and spinal cords from patients with these conditions. Our findings, which demonstrate a genetic link between loss of nuclear TDP-43 function and disease, reveal the mechanism by which UNC13A variants exacerbate the effects of decreased TDP-43 function. They further provide a promising therapeutic target for TDP-43 proteinopathies.

Additional file 1: Figure S1. Analysis of effect of methotrexate on TL1A levels from a second ind... more Additional file 1: Figure S1. Analysis of effect of methotrexate on TL1A levels from a second independent patient cohort. TL1A was measured in serum from an independent cohort of patients with RA treated with MTX for 4 months (66 good/moderate EULAR responders, 18 non-responders).

Background. Endometriosis is a common, complex disorder which is underrecognized and subject to p... more Background. Endometriosis is a common, complex disorder which is underrecognized and subject to prolonged delays in diagnosis. It is accompanied by significant changes in the eutopic endometrial lining. Methods. We have undertaken the first single cell RNA-sequencing (scRNA-Seq) comparison of endometrial tissues in freshly collected menstrual effluent (ME) from 33 subjects, including confirmed endometriosis patients (cases) and controls as well as symptomatic subjects (who have chronic symptoms suggestive of endometriosis but have not been diagnosed). Results. We identify a unique subcluster of proliferating uterine natural killer (uNK) cells in ME-tissues from controls that is almost absent from endometriosis cases, along with a striking reduction of total uNK cells in the ME of cases (p<10-16). In addition, an IGFBP1+ decidualized subset of endometrial stromal cells are abundant in the shed endometrium of controls when compared to cases (p<10-16) confirming findings of compr...

The primary goal for RA arthroplasty P1 studies are: To establish if molecular signatures and pat... more The primary goal for RA arthroplasty P1 studies are: To establish if molecular signatures and pathways identified using core AMP technologies differ between OA and RA in 20 RA surgical samples and 10 OA arthroplasty samples.

Residuals of the multivariate normal regression models of five included cohorts. (TIFF 114 kb)

BACKGROUND Rheumatoid arthritis is a chronic inflammatory disease with a substantial genetic comp... more BACKGROUND Rheumatoid arthritis is a chronic inflammatory disease with a substantial genetic component. Susceptibility to disease has been linked with a region on chromosome 2q. METHODS We tested single-nucleotide polymorphisms (SNPs) in and around 13 candidate genes within the previously linked chromosome 2q region for association with rheumatoid arthritis. We then performed fine mapping of the STAT1-STAT4 region in a total of 1620 case patients with established rheumatoid arthritis and 2635 controls, all from North America. Implicated SNPs were further tested in an independent casecontrol series of 1529 patients with early rheumatoid arthritis and 881 controls, all from Sweden, and in a total of 1039 case patients and 1248 controls from three series of patients with systemic lupus erythematosus. RESULTS A SNP haplotype in the third intron of STAT4 was associated with susceptibility to both rheumatoid arthritis and systemic lupus erythematosus. The minor alleles of the haplotype-defining SNPs were present in 27% of chromosomes of patients with established rheumatoid arthritis, as compared with 22% of those of controls (for the SNP rs7574865, P = 2.81×10 −7 ; odds ratio for having the risk allele in chromosomes of patients vs. those of controls, 1.32). The association was replicated in Swedish patients with recent-onset rheumatoid arthritis (P = 0.02) and matched controls. The haplotype marked by rs7574865 was strongly associated with lupus, being present on 31% of chromosomes of case patients and 22% of those of controls (P = 1.87×10 −9 ; odds ratio for having the risk allele in chromosomes of patients vs. those of controls, 1.55). Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis. CONCLUSIONS A haplotype of STAT4 is associated with increased risk for both rheumatoid arthritis and systemic lupus erythematosus, suggesting a shared pathway for these illnesses.

Supplementary material, approximately 1.21 MB.

Plasmacytoid dendritic cells [pDCs] represent a rare innate immune subset uniquely endowed with t... more Plasmacytoid dendritic cells [pDCs] represent a rare innate immune subset uniquely endowed with the capacity to produce substantial amounts of type-I interferons [IFN-I]. This function of pDCs is critical for effective antiviral defenses and has been implicated in autoimmunity. While IFN-I and select cytokines have been recognized as pDC secreted products, a comprehensive agnostic profiling of the pDC secretome in response to a physiologic stimulus has not been reported. We applied LC-MS/MS to catalogue the repertoire of proteins secreted by pDCs in response to challenge with live influenza H1N1. Additionally, using single-cell RNA-seq [scRNA-seq], we perform multidimensional analyses of pDC transcriptional diversification following stimulation. Our data reveal an abundance of protein species released by pDCs in addition to IFN-I, and evidence highly specialized roles within the pDC population ranging from dedicated cytokine super-producers to cells with APC-like functions. Moreover...

Frontiers in Reproductive Health, 2020

Endometriosis is a chronic inflammatory disorder characterized by the presence of endometrial-lik... more Endometriosis is a chronic inflammatory disorder characterized by the presence of endometrial-like tissue growing outside of the uterus. Although the cause is unknown, retrograde menstruation leads to deposition of endometrial cells into the peritoneal cavity. Lack of disease recognition and long diagnostic delays (6-10 years) lead to substantial personal, social and financial burdens, as well as delayed treatment. A non-invasive diagnostic for endometriosis is a major unmet clinical need. Here, we assessed whether differences in menstrual effluent-derived stromal fibroblast cells (ME-SFCs) from women with and without endometriosis provide the basis for a non-invasive diagnostic for endometriosis. In addition, we investigated whether treatment of control ME-SFCs with inflammatory cytokines (TNF and IL-1β) could induce an endometriosis-like phenotype. ME-SFCs from laparoscopically diagnosed endometriosis patients exhibit reduced decidualization capacity, measured by IGFBP1 production after exposure to cAMP. A receiver operating characteristic (ROC) curve developed using decidualization data from controls and endometriosis subjects yielded an area under the curve of 0.92. In addition, a significant reduction in ALDH1A1 gene expression and increased podoplanin surface expression were also observed in endometriosis ME-SFCs when compared to control ME-SFCs. These endometriosis-like phenotypes can be reproduced in control ME-SFCs by exposure to inflammatory cytokines (TNF and IL-1β) and are associated with increased cell migration. These results are consistent with the hypothesis that chronic intrauterine inflammation influences the development of endometriosis lesions following retrograde menstruation. In conclusion, the analysis of ME-SFCs can provide an accurate, rapid, and non-invasive diagnostic for endometriosis and insight into disease pathogenesis.

Genetics, Genomics and Epigenetics, 2018

Background The two Apolipoprotein L1 (APOL1) risk variants (RV), G1 and G2, are enriched in Afric... more Background The two Apolipoprotein L1 (APOL1) risk variants (RV), G1 and G2, are enriched in African populations due to resistance to Trypanosoma brucei, a parasite endemic in West Africa. This improved fitness comes with the cost of propensity toward renal disease by multiple causes including SLE. In Ghana, up to 60% of individuals are heterozygous and 30% are variant homozygous. However, APOL1 variant phenotypes have never been described in a Ghanaian SLE cohort. Further it remains unclear whether RV associated nephritis progression is driven by accelerated inflammation or intrinsic renal disease. Accordingly, we evaluated APOL1 genotype-phenotype traits in the context of SLE activity in 101 Ghanaian patients seeking care at Korle bu Teaching Hospital in Accra, Ghana. Methods 101 Ghanaian patients meeting at least 4 clinical criteria for SLE were stratified by APOL1 genotype PCR/ sequencing as follows: ancestral (G0/G0), RV heterozygotes (RV/G0), and RV homozygotes (RV/RV). DNA was extracted from saliva. Clinical endpoints including demographics, ACR criteria, SLEDAI score, and SLICC damage index were recorded at time of blood draw. Based on cytokines known to fluctuate with SLE activity in African Americans, a 12 cytokine array was performed on sera to determine active inflammatory pathways. Interferon signature as measured by the WISH cell assay was completed. Results The frequencies of the G0, G1, and G2 alleles were 63.3%, 24.2%, and 12.5% respectively. Subjects were 100% female, and 32.1 years of age with a disease duration of 2.9 years. There were no differences in demographics across the genotypes. The RV associated with higher BP: 107.4/72.3, 108.5/72.1, and 120.6/83.4 in the G0/G0, RV/G0, and RV/RV groups respectively (p: 0.013 systolic; 0.003 diastolic). Among those with nephritis, RV/RV associated with increased creatinine and proteinuria with creatinine values of 0.9, 1.1, and 2.5, and average (3 visit) urine dipstick values of 1.0, 1.2, and 3.33 in the G0/G0, RV/G0, and RV/RV groups respectively (creatinine: p=0.03; urine dipstick p=0.01). RV/RV carriers were on higher doses of prednisolone (17.2 mg) compared to G0/G0 or RV/G0 carriers (11.2 mg; 11.8 mg respectively). SLEDAI scores were comparable across the genotypes, however RV/RV associated with elevated SLICC damage index: G0/G0 or RV/G0: 0.95 vs RV/RV: 1.7; driven by renal, CVD, and neurologic manifestations G0/G0: 0.46, RV/G0: 0.39, RV/RV: 1.25; p=0.03 Despite more damage, RV/RV individuals had lower dsDNA titers (10.7 IU/mL) than G0/G0 (57.1 IU/mL) and RV/G0 (95.6 IU/mL) carriers (p: 0.03). Cytokine scores were also lower in RV/RV carriers compared to G0/G0 and RV/RV, for example serum IL8 levels were 34.6 pg, 33.2 pg, and 13.8 pg (IL-8: p=0.04). Both G0/G0 and RV/G0 individuals exhibited more elevated IFN signatures than RV/RV individuals (245.7, 81.3, and 24.3 respectively, p:0.04). Conclusions Taken together, the APOL1 RV associated with increased blood pressure, creatinine, proteinuria, and SLICC damage score in this Ghanaian SLE cohort. Paradoxically, RV homozygotes exhibited lower dsDNA titers and lower cytokine profiles than G0/G0 or RV/G0 patients. This suggests that RV homozygotes may have an intrinsic propensity toward organ damage independent of SLE activity.

Clinical Cancer Research, 2018

Ovarian cancer is highly curable when diagnosed early as localized disease. Most women come to me... more Ovarian cancer is highly curable when diagnosed early as localized disease. Most women come to medical attention, however, with metastatic disease. For these women, cure rates are quite low; only 30% of patients with late-stage high-grade serous ovarian cancer (HGSOC) will live more than 5 years. Although initially sensitive to platinum-based chemotherapy, in most cases, drug resistance develops and a progressive disease course ensues. Therefore, in order to improve prognosis and overall survival, there is an urgent need to understand the basis of drug resistance and to identify new therapeutic targets. Previous studies have stressed the significant role that tumor heterogeneity and microenvironment have in clinical outcome. It is our goal to understand the genomics of metastatic lesions as compared to primary lesions, to identify the genetic drivers of metastasis and drug resistance, which we can then functionally investigate in order to develop novel therapies. Corresponding prima...

Blood, 2005

Interleukin-10 (IL-10), a cytokine that regulates inflammation, may play an important role in B-c... more Interleukin-10 (IL-10), a cytokine that regulates inflammation, may play an important role in B-cell chronic lymphocytic leukemia (B-CLL), because of the reported association of high serum IL-10 levels with a lower prognosis of survival. Using the Bio-Plex protein array system, we confirmed that B-CLL patients exhibit higher median IL-10 levels (3.54 pg/ml, n=50) as compared to controls (1.28 pg/ml, n=33) (p<0.0001). We are in the midst of determining B-CLL VH gene mutation status and IL-10 levels. To determine if elevated IL-10 levels are due to inherent genetic polymorphisms, we examined three single nucleotide polymorphisms (SNPs) in the proximal end of the promoter region of the IL-10 gene (-1082 A/G, −819 T/C, and −592 A/C) that may affect IL-10 transcription levels. DNA from an overlapping set of 54 B-CLL patients and 48 normals was genotyped using the Transgenomic WAVE system. The difference in allele frequencies at a single locus showed no trend towards significance betwe...

Arthritis Research & Therapy, 2012

Background: CD4 T cells help B cells produce antibodies following antigen challenge. This respons... more Background: CD4 T cells help B cells produce antibodies following antigen challenge. This response classically occurs in germinal centers (GC) located in B-cell follicles of secondary lymphoid organs (SLO), a site of immunoglobulin isotype switching and affinity maturation. GC formation requires specialized CD4 T cells, T-follicular helper (Tfh) cells, which localize to follicles and provide B cells with survival and differentiation signals that are essential for B-cell maturation into memory and long-lived plasma cells. Pathogenic autoantibodies in human and murine lupus arise in a like manner. Although Tfh cells are critical for GC development, their genesis in humans, role in promotion of autoimmunity, and potential as therapeutic targets in SLE are incompletely understood. To address these issues, we dissected Tfh cell development and function, defining their transcriptional regulation, migration, and function in vivo in normal and lupus-prone mice and ex vivo in normal humans and patients with SLE. Methods: We used a combination of approaches-flow cytometry, confocal microscopy, microarrays, quantitative chromatin immunoprecipitation and DNA sequencing (ChIP-seq), retroviral overexpression, and T-cell-B-cell helper assays-to characterize Tfh cells in normal mice and in lupus-prone strains, and from the tonsils of normal humans and the blood of patients with SLE. Results: We found that the transcription factor Bcl6 (B-cell CLL/lymphoma 6) is necessary and sufficient for Tfh development and function, via genetic control of Tfh proteins that are essential for their migration to B-cell follicles and GC and subsequent B-cell maturation. We dissected steps in Tfh development within SLO, beginning with their genesis in the T-cell zone followed by emigration to sites of B-cell interaction outside the B-cell follicle, where we have shown that B cells serve to provide signals for continued Tfh expansion and follicular migration. We have now begun to tease apart the factors that mediate T-cell-B-cell collaboration in the follicle; these represent therapeutic targets in SLE. Finally, we have shown that patients with SLE have expansion of Tfh cells in the blood, a finding that highlights their potential role in the pathogenesis of SLE and as likely therapeutic targets. Conclusion: These studies help define the developmental pathways for Tfh cells, and the steps that enable these cells to function in the B-cell follicle to promote immunoglobulin and autoantibody production. They have also helped define markers of Tfh cells in normals and autoimmune individuals, and suggest that they are a promising therapeutic target in patients.

Blood, 2011

2833 Introduction: In chronic lymphocytic leukemia (CLL), clonally expanded CD5+ B lymphocytes ev... more 2833 Introduction: In chronic lymphocytic leukemia (CLL), clonally expanded CD5+ B lymphocytes eventually overwhelm healthy immune cells, hindering normal immune function. To determine mechanisms fueling this expansion, gene expression data were gathered by microarray analysis of cells from CLL patients. Samples were grouped based on Ki-67 expression, an indicator of proliferation. To determine mechanisms correlating with B-cell proliferation and impacting on CLL B-cell biology, microarray profiles were compared using Gene Set Enrichment Analysis (GSEA) [Subramanian A, et al. PNAS 2005]. Methods: Samples were analyzed for intracellular expression of Ki-67 by flow cytometry and divided into 2 groups based on Ki-67 expression (cutoff at 5%). RNA was then purified from CD5+CD19+ CLL cells and gene expression microarray assays were performed using Illumina HumanHT12 beadchips. GSEA was carried out using a library of signatures by Dr. Louis Staudt [Shaffer AL, et al. Immunol Rev 2006] co...

Blood, 2011

3888 In B-CLL, mutations in the IGHV genes encoding the BCR are correlated with disease aggressiv... more 3888 In B-CLL, mutations in the IGHV genes encoding the BCR are correlated with disease aggressiveness: patients with unmutated BCR (U-CLL) typically have a worse prognosis than those with mutated BCR (M-CLL). Evidence that many U-CLL express BCR with specificity toward apoptotic cell antigens suggests that dying cells provide pro-survival signals for U-CLL clones. Thus progression of U-CLL may depend both on mechanisms that ensure the…

Blood, 2006

The transforming events that lead to B-cell chronic lymphocytic leukemia (B-CLL) are unknown, and... more The transforming events that lead to B-cell chronic lymphocytic leukemia (B-CLL) are unknown, and although genetic abnormalities appear to promote disease progression, none of these is seen in every patient. Therefore, we have applied a highly sensitive and specific method to probe, in greater depth, for genetic changes that can occur in B-CLL, and to explore if these correlate with disease development or progression. Utilizing ROMA to measure changes in gene copy number, we screened the entire genome of over two dozen B-CLL cases to identify characteristic and novel chromosomal changes. DNA from leukemic cells of patients was compared to the normal DNA from their unaffected neutrophils and to an unrelated, normal human control. By comparing normal DNA from each patient to an unrelated normal, we avoid inadvertently mistaking common copy number variation between people as possible candidates for lesions in B-CLL. ROMA was performed on both 85,000 and 390,000 probe microarrays enabli...

PLOS ONE, 2019

Background Previous studies of radiological damage in rheumatoid arthritis (RA) have used candida... more Background Previous studies of radiological damage in rheumatoid arthritis (RA) have used candidategene approaches, or evaluated single genome-wide association studies (GWAS). We undertook the first meta-analysis of GWAS of RA radiological damage to: (1) identify novel genetic loci for this trait; and (2) test previously validated variants. Methods Seven GWAS (2,775 RA cases, of a range of ancestries) were combined in a meta-analysis. Radiological damage was assessed using modified Larsen scores, Sharp van Der Heijde

Nature, 1998

CD8-positive T cells are thought to play an important role in the control of infection by human i... more CD8-positive T cells are thought to play an important role in the control of infection by human immunodeficiency virus (HIV) as a result of their cytotoxic activity and by releasing soluble factors. In AIDS patients, the absolute number of CD8+ T lymphocytes is decreased in peripheral blood and their turnover rate is increased, suggesting that there is more cell renewal and cell death occurring. Anti-retroviral therapy raises CD8+ T-cell counts in HIV-infected patients. Here we report that the death rate of CD8+ T cells by apoptosis increased markedly during HIV infection of peripheral blood mononuclear cells in vitro. Apoptosis is induced in a dose-dependent manner by recombinant envelope glycoprotein gp120 from HIV strain X4, or by stromal-derived factor-1 (SDF-1), the physiological ligand of the chemokine receptor CXCR4. Apoptosis is mediated by the interaction between tumour-necrosis factor-alpha bound to the membrane of macrophages (mbTNF) and a receptor on CD8+ T cells (TNF-receptor II, or TNFRII). The expression of both of these cell-surface proteins is upregulated by HIV infection or by treatment with recombinant gp120 or SDF-1. Apoptosis of CD8+ T cells isolated from HIV-infected patients is also mediated by macrophages through the interaction between mbTNF and TNFRII. These results indicate that the increased turnover of CD8+ T cells in HIV-infected subjects is mediated by the HIV envelope protein through the CXCR4 chemokine receptor.

Proceedings of the National Academy of Sciences

Significance There is growing evidence that preexisting autoantibodies neutralizing type I interf... more Significance There is growing evidence that preexisting autoantibodies neutralizing type I interferons (IFNs) are strong determinants of life-threatening COVID-19 pneumonia. It is important to estimate their quantitative impact on COVID-19 mortality upon SARS-CoV-2 infection, by age and sex, as both the prevalence of these autoantibodies and the risk of COVID-19 death increase with age and are higher in men. Using an unvaccinated sample of 1,261 deceased patients and 34,159 individuals from the general population, we found that autoantibodies against type I IFNs strongly increased the SARS-CoV-2 infection fatality rate at all ages, in both men and women. Autoantibodies against type I IFNs are strong and common predictors of life-threatening COVID-19. Testing for these autoantibodies should be considered in the general population.

Nature, 2022

Variants of UNC13A, a critical gene for synapse function, increase the risk of amyotrophic latera... more Variants of UNC13A, a critical gene for synapse function, increase the risk of amyotrophic lateral sclerosis and frontotemporal dementia1–3, two related neurodegenerative diseases defined by mislocalization of the RNA-binding protein TDP-434,5. Here we show that TDP-43 depletion induces robust inclusion of a cryptic exon in UNC13A, resulting in nonsense-mediated decay and loss of UNC13A protein. Two common intronic UNC13A polymorphisms strongly associated with amyotrophic lateral sclerosis and frontotemporal dementia risk overlap with TDP-43 binding sites. These polymorphisms potentiate cryptic exon inclusion, both in cultured cells and in brains and spinal cords from patients with these conditions. Our findings, which demonstrate a genetic link between loss of nuclear TDP-43 function and disease, reveal the mechanism by which UNC13A variants exacerbate the effects of decreased TDP-43 function. They further provide a promising therapeutic target for TDP-43 proteinopathies.

Additional file 1: Figure S1. Analysis of effect of methotrexate on TL1A levels from a second ind... more Additional file 1: Figure S1. Analysis of effect of methotrexate on TL1A levels from a second independent patient cohort. TL1A was measured in serum from an independent cohort of patients with RA treated with MTX for 4 months (66 good/moderate EULAR responders, 18 non-responders).

Background. Endometriosis is a common, complex disorder which is underrecognized and subject to p... more Background. Endometriosis is a common, complex disorder which is underrecognized and subject to prolonged delays in diagnosis. It is accompanied by significant changes in the eutopic endometrial lining. Methods. We have undertaken the first single cell RNA-sequencing (scRNA-Seq) comparison of endometrial tissues in freshly collected menstrual effluent (ME) from 33 subjects, including confirmed endometriosis patients (cases) and controls as well as symptomatic subjects (who have chronic symptoms suggestive of endometriosis but have not been diagnosed). Results. We identify a unique subcluster of proliferating uterine natural killer (uNK) cells in ME-tissues from controls that is almost absent from endometriosis cases, along with a striking reduction of total uNK cells in the ME of cases (p<10-16). In addition, an IGFBP1+ decidualized subset of endometrial stromal cells are abundant in the shed endometrium of controls when compared to cases (p<10-16) confirming findings of compr...

The primary goal for RA arthroplasty P1 studies are: To establish if molecular signatures and pat... more The primary goal for RA arthroplasty P1 studies are: To establish if molecular signatures and pathways identified using core AMP technologies differ between OA and RA in 20 RA surgical samples and 10 OA arthroplasty samples.

Residuals of the multivariate normal regression models of five included cohorts. (TIFF 114 kb)

BACKGROUND Rheumatoid arthritis is a chronic inflammatory disease with a substantial genetic comp... more BACKGROUND Rheumatoid arthritis is a chronic inflammatory disease with a substantial genetic component. Susceptibility to disease has been linked with a region on chromosome 2q. METHODS We tested single-nucleotide polymorphisms (SNPs) in and around 13 candidate genes within the previously linked chromosome 2q region for association with rheumatoid arthritis. We then performed fine mapping of the STAT1-STAT4 region in a total of 1620 case patients with established rheumatoid arthritis and 2635 controls, all from North America. Implicated SNPs were further tested in an independent casecontrol series of 1529 patients with early rheumatoid arthritis and 881 controls, all from Sweden, and in a total of 1039 case patients and 1248 controls from three series of patients with systemic lupus erythematosus. RESULTS A SNP haplotype in the third intron of STAT4 was associated with susceptibility to both rheumatoid arthritis and systemic lupus erythematosus. The minor alleles of the haplotype-defining SNPs were present in 27% of chromosomes of patients with established rheumatoid arthritis, as compared with 22% of those of controls (for the SNP rs7574865, P = 2.81×10 −7 ; odds ratio for having the risk allele in chromosomes of patients vs. those of controls, 1.32). The association was replicated in Swedish patients with recent-onset rheumatoid arthritis (P = 0.02) and matched controls. The haplotype marked by rs7574865 was strongly associated with lupus, being present on 31% of chromosomes of case patients and 22% of those of controls (P = 1.87×10 −9 ; odds ratio for having the risk allele in chromosomes of patients vs. those of controls, 1.55). Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis. CONCLUSIONS A haplotype of STAT4 is associated with increased risk for both rheumatoid arthritis and systemic lupus erythematosus, suggesting a shared pathway for these illnesses.

Supplementary material, approximately 1.21 MB.

Plasmacytoid dendritic cells [pDCs] represent a rare innate immune subset uniquely endowed with t... more Plasmacytoid dendritic cells [pDCs] represent a rare innate immune subset uniquely endowed with the capacity to produce substantial amounts of type-I interferons [IFN-I]. This function of pDCs is critical for effective antiviral defenses and has been implicated in autoimmunity. While IFN-I and select cytokines have been recognized as pDC secreted products, a comprehensive agnostic profiling of the pDC secretome in response to a physiologic stimulus has not been reported. We applied LC-MS/MS to catalogue the repertoire of proteins secreted by pDCs in response to challenge with live influenza H1N1. Additionally, using single-cell RNA-seq [scRNA-seq], we perform multidimensional analyses of pDC transcriptional diversification following stimulation. Our data reveal an abundance of protein species released by pDCs in addition to IFN-I, and evidence highly specialized roles within the pDC population ranging from dedicated cytokine super-producers to cells with APC-like functions. Moreover...

Frontiers in Reproductive Health, 2020

Endometriosis is a chronic inflammatory disorder characterized by the presence of endometrial-lik... more Endometriosis is a chronic inflammatory disorder characterized by the presence of endometrial-like tissue growing outside of the uterus. Although the cause is unknown, retrograde menstruation leads to deposition of endometrial cells into the peritoneal cavity. Lack of disease recognition and long diagnostic delays (6-10 years) lead to substantial personal, social and financial burdens, as well as delayed treatment. A non-invasive diagnostic for endometriosis is a major unmet clinical need. Here, we assessed whether differences in menstrual effluent-derived stromal fibroblast cells (ME-SFCs) from women with and without endometriosis provide the basis for a non-invasive diagnostic for endometriosis. In addition, we investigated whether treatment of control ME-SFCs with inflammatory cytokines (TNF and IL-1β) could induce an endometriosis-like phenotype. ME-SFCs from laparoscopically diagnosed endometriosis patients exhibit reduced decidualization capacity, measured by IGFBP1 production after exposure to cAMP. A receiver operating characteristic (ROC) curve developed using decidualization data from controls and endometriosis subjects yielded an area under the curve of 0.92. In addition, a significant reduction in ALDH1A1 gene expression and increased podoplanin surface expression were also observed in endometriosis ME-SFCs when compared to control ME-SFCs. These endometriosis-like phenotypes can be reproduced in control ME-SFCs by exposure to inflammatory cytokines (TNF and IL-1β) and are associated with increased cell migration. These results are consistent with the hypothesis that chronic intrauterine inflammation influences the development of endometriosis lesions following retrograde menstruation. In conclusion, the analysis of ME-SFCs can provide an accurate, rapid, and non-invasive diagnostic for endometriosis and insight into disease pathogenesis.

Genetics, Genomics and Epigenetics, 2018

Background The two Apolipoprotein L1 (APOL1) risk variants (RV), G1 and G2, are enriched in Afric... more Background The two Apolipoprotein L1 (APOL1) risk variants (RV), G1 and G2, are enriched in African populations due to resistance to Trypanosoma brucei, a parasite endemic in West Africa. This improved fitness comes with the cost of propensity toward renal disease by multiple causes including SLE. In Ghana, up to 60% of individuals are heterozygous and 30% are variant homozygous. However, APOL1 variant phenotypes have never been described in a Ghanaian SLE cohort. Further it remains unclear whether RV associated nephritis progression is driven by accelerated inflammation or intrinsic renal disease. Accordingly, we evaluated APOL1 genotype-phenotype traits in the context of SLE activity in 101 Ghanaian patients seeking care at Korle bu Teaching Hospital in Accra, Ghana. Methods 101 Ghanaian patients meeting at least 4 clinical criteria for SLE were stratified by APOL1 genotype PCR/ sequencing as follows: ancestral (G0/G0), RV heterozygotes (RV/G0), and RV homozygotes (RV/RV). DNA was extracted from saliva. Clinical endpoints including demographics, ACR criteria, SLEDAI score, and SLICC damage index were recorded at time of blood draw. Based on cytokines known to fluctuate with SLE activity in African Americans, a 12 cytokine array was performed on sera to determine active inflammatory pathways. Interferon signature as measured by the WISH cell assay was completed. Results The frequencies of the G0, G1, and G2 alleles were 63.3%, 24.2%, and 12.5% respectively. Subjects were 100% female, and 32.1 years of age with a disease duration of 2.9 years. There were no differences in demographics across the genotypes. The RV associated with higher BP: 107.4/72.3, 108.5/72.1, and 120.6/83.4 in the G0/G0, RV/G0, and RV/RV groups respectively (p: 0.013 systolic; 0.003 diastolic). Among those with nephritis, RV/RV associated with increased creatinine and proteinuria with creatinine values of 0.9, 1.1, and 2.5, and average (3 visit) urine dipstick values of 1.0, 1.2, and 3.33 in the G0/G0, RV/G0, and RV/RV groups respectively (creatinine: p=0.03; urine dipstick p=0.01). RV/RV carriers were on higher doses of prednisolone (17.2 mg) compared to G0/G0 or RV/G0 carriers (11.2 mg; 11.8 mg respectively). SLEDAI scores were comparable across the genotypes, however RV/RV associated with elevated SLICC damage index: G0/G0 or RV/G0: 0.95 vs RV/RV: 1.7; driven by renal, CVD, and neurologic manifestations G0/G0: 0.46, RV/G0: 0.39, RV/RV: 1.25; p=0.03 Despite more damage, RV/RV individuals had lower dsDNA titers (10.7 IU/mL) than G0/G0 (57.1 IU/mL) and RV/G0 (95.6 IU/mL) carriers (p: 0.03). Cytokine scores were also lower in RV/RV carriers compared to G0/G0 and RV/RV, for example serum IL8 levels were 34.6 pg, 33.2 pg, and 13.8 pg (IL-8: p=0.04). Both G0/G0 and RV/G0 individuals exhibited more elevated IFN signatures than RV/RV individuals (245.7, 81.3, and 24.3 respectively, p:0.04). Conclusions Taken together, the APOL1 RV associated with increased blood pressure, creatinine, proteinuria, and SLICC damage score in this Ghanaian SLE cohort. Paradoxically, RV homozygotes exhibited lower dsDNA titers and lower cytokine profiles than G0/G0 or RV/G0 patients. This suggests that RV homozygotes may have an intrinsic propensity toward organ damage independent of SLE activity.

Clinical Cancer Research, 2018

Ovarian cancer is highly curable when diagnosed early as localized disease. Most women come to me... more Ovarian cancer is highly curable when diagnosed early as localized disease. Most women come to medical attention, however, with metastatic disease. For these women, cure rates are quite low; only 30% of patients with late-stage high-grade serous ovarian cancer (HGSOC) will live more than 5 years. Although initially sensitive to platinum-based chemotherapy, in most cases, drug resistance develops and a progressive disease course ensues. Therefore, in order to improve prognosis and overall survival, there is an urgent need to understand the basis of drug resistance and to identify new therapeutic targets. Previous studies have stressed the significant role that tumor heterogeneity and microenvironment have in clinical outcome. It is our goal to understand the genomics of metastatic lesions as compared to primary lesions, to identify the genetic drivers of metastasis and drug resistance, which we can then functionally investigate in order to develop novel therapies. Corresponding prima...

Blood, 2005

Interleukin-10 (IL-10), a cytokine that regulates inflammation, may play an important role in B-c... more Interleukin-10 (IL-10), a cytokine that regulates inflammation, may play an important role in B-cell chronic lymphocytic leukemia (B-CLL), because of the reported association of high serum IL-10 levels with a lower prognosis of survival. Using the Bio-Plex protein array system, we confirmed that B-CLL patients exhibit higher median IL-10 levels (3.54 pg/ml, n=50) as compared to controls (1.28 pg/ml, n=33) (p<0.0001). We are in the midst of determining B-CLL VH gene mutation status and IL-10 levels. To determine if elevated IL-10 levels are due to inherent genetic polymorphisms, we examined three single nucleotide polymorphisms (SNPs) in the proximal end of the promoter region of the IL-10 gene (-1082 A/G, −819 T/C, and −592 A/C) that may affect IL-10 transcription levels. DNA from an overlapping set of 54 B-CLL patients and 48 normals was genotyped using the Transgenomic WAVE system. The difference in allele frequencies at a single locus showed no trend towards significance betwe...

Arthritis Research & Therapy, 2012

Background: CD4 T cells help B cells produce antibodies following antigen challenge. This respons... more Background: CD4 T cells help B cells produce antibodies following antigen challenge. This response classically occurs in germinal centers (GC) located in B-cell follicles of secondary lymphoid organs (SLO), a site of immunoglobulin isotype switching and affinity maturation. GC formation requires specialized CD4 T cells, T-follicular helper (Tfh) cells, which localize to follicles and provide B cells with survival and differentiation signals that are essential for B-cell maturation into memory and long-lived plasma cells. Pathogenic autoantibodies in human and murine lupus arise in a like manner. Although Tfh cells are critical for GC development, their genesis in humans, role in promotion of autoimmunity, and potential as therapeutic targets in SLE are incompletely understood. To address these issues, we dissected Tfh cell development and function, defining their transcriptional regulation, migration, and function in vivo in normal and lupus-prone mice and ex vivo in normal humans and patients with SLE. Methods: We used a combination of approaches-flow cytometry, confocal microscopy, microarrays, quantitative chromatin immunoprecipitation and DNA sequencing (ChIP-seq), retroviral overexpression, and T-cell-B-cell helper assays-to characterize Tfh cells in normal mice and in lupus-prone strains, and from the tonsils of normal humans and the blood of patients with SLE. Results: We found that the transcription factor Bcl6 (B-cell CLL/lymphoma 6) is necessary and sufficient for Tfh development and function, via genetic control of Tfh proteins that are essential for their migration to B-cell follicles and GC and subsequent B-cell maturation. We dissected steps in Tfh development within SLO, beginning with their genesis in the T-cell zone followed by emigration to sites of B-cell interaction outside the B-cell follicle, where we have shown that B cells serve to provide signals for continued Tfh expansion and follicular migration. We have now begun to tease apart the factors that mediate T-cell-B-cell collaboration in the follicle; these represent therapeutic targets in SLE. Finally, we have shown that patients with SLE have expansion of Tfh cells in the blood, a finding that highlights their potential role in the pathogenesis of SLE and as likely therapeutic targets. Conclusion: These studies help define the developmental pathways for Tfh cells, and the steps that enable these cells to function in the B-cell follicle to promote immunoglobulin and autoantibody production. They have also helped define markers of Tfh cells in normals and autoimmune individuals, and suggest that they are a promising therapeutic target in patients.

Blood, 2011

2833 Introduction: In chronic lymphocytic leukemia (CLL), clonally expanded CD5+ B lymphocytes ev... more 2833 Introduction: In chronic lymphocytic leukemia (CLL), clonally expanded CD5+ B lymphocytes eventually overwhelm healthy immune cells, hindering normal immune function. To determine mechanisms fueling this expansion, gene expression data were gathered by microarray analysis of cells from CLL patients. Samples were grouped based on Ki-67 expression, an indicator of proliferation. To determine mechanisms correlating with B-cell proliferation and impacting on CLL B-cell biology, microarray profiles were compared using Gene Set Enrichment Analysis (GSEA) [Subramanian A, et al. PNAS 2005]. Methods: Samples were analyzed for intracellular expression of Ki-67 by flow cytometry and divided into 2 groups based on Ki-67 expression (cutoff at 5%). RNA was then purified from CD5+CD19+ CLL cells and gene expression microarray assays were performed using Illumina HumanHT12 beadchips. GSEA was carried out using a library of signatures by Dr. Louis Staudt [Shaffer AL, et al. Immunol Rev 2006] co...

Blood, 2011

3888 In B-CLL, mutations in the IGHV genes encoding the BCR are correlated with disease aggressiv... more 3888 In B-CLL, mutations in the IGHV genes encoding the BCR are correlated with disease aggressiveness: patients with unmutated BCR (U-CLL) typically have a worse prognosis than those with mutated BCR (M-CLL). Evidence that many U-CLL express BCR with specificity toward apoptotic cell antigens suggests that dying cells provide pro-survival signals for U-CLL clones. Thus progression of U-CLL may depend both on mechanisms that ensure the…

Blood, 2006

The transforming events that lead to B-cell chronic lymphocytic leukemia (B-CLL) are unknown, and... more The transforming events that lead to B-cell chronic lymphocytic leukemia (B-CLL) are unknown, and although genetic abnormalities appear to promote disease progression, none of these is seen in every patient. Therefore, we have applied a highly sensitive and specific method to probe, in greater depth, for genetic changes that can occur in B-CLL, and to explore if these correlate with disease development or progression. Utilizing ROMA to measure changes in gene copy number, we screened the entire genome of over two dozen B-CLL cases to identify characteristic and novel chromosomal changes. DNA from leukemic cells of patients was compared to the normal DNA from their unaffected neutrophils and to an unrelated, normal human control. By comparing normal DNA from each patient to an unrelated normal, we avoid inadvertently mistaking common copy number variation between people as possible candidates for lesions in B-CLL. ROMA was performed on both 85,000 and 390,000 probe microarrays enabli...

PLOS ONE, 2019

Background Previous studies of radiological damage in rheumatoid arthritis (RA) have used candida... more Background Previous studies of radiological damage in rheumatoid arthritis (RA) have used candidategene approaches, or evaluated single genome-wide association studies (GWAS). We undertook the first meta-analysis of GWAS of RA radiological damage to: (1) identify novel genetic loci for this trait; and (2) test previously validated variants. Methods Seven GWAS (2,775 RA cases, of a range of ancestries) were combined in a meta-analysis. Radiological damage was assessed using modified Larsen scores, Sharp van Der Heijde

Nature, 1998

CD8-positive T cells are thought to play an important role in the control of infection by human i... more CD8-positive T cells are thought to play an important role in the control of infection by human immunodeficiency virus (HIV) as a result of their cytotoxic activity and by releasing soluble factors. In AIDS patients, the absolute number of CD8+ T lymphocytes is decreased in peripheral blood and their turnover rate is increased, suggesting that there is more cell renewal and cell death occurring. Anti-retroviral therapy raises CD8+ T-cell counts in HIV-infected patients. Here we report that the death rate of CD8+ T cells by apoptosis increased markedly during HIV infection of peripheral blood mononuclear cells in vitro. Apoptosis is induced in a dose-dependent manner by recombinant envelope glycoprotein gp120 from HIV strain X4, or by stromal-derived factor-1 (SDF-1), the physiological ligand of the chemokine receptor CXCR4. Apoptosis is mediated by the interaction between tumour-necrosis factor-alpha bound to the membrane of macrophages (mbTNF) and a receptor on CD8+ T cells (TNF-receptor II, or TNFRII). The expression of both of these cell-surface proteins is upregulated by HIV infection or by treatment with recombinant gp120 or SDF-1. Apoptosis of CD8+ T cells isolated from HIV-infected patients is also mediated by macrophages through the interaction between mbTNF and TNFRII. These results indicate that the increased turnover of CD8+ T cells in HIV-infected subjects is mediated by the HIV envelope protein through the CXCR4 chemokine receptor.