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Schump MD, Bernstein DI, Bravo FJ, Neff CP. Selection, activity, and nuclease stabilization of cross-neutralizing DNA aptamers targeting HSV-1 and HSV-2. Virology 2024; 589:109916. [PMID: 37925791 DOI: 10.1016/j.virol.2023.109916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/03/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Cross-neutralizing aptamers targeting both HSV-1 and HSV-2 were developed by selecting against the ectodomains of glycoprotein D (gD) from both viruses in parallel as well as sequentially using the SELEX method. Since gD facilitates viral invasion, sterically blocking the host-receptor interaction prevents infection. Candidate aptamers were screened, and lead aptamers were identified that exhibited exceptional neutralizing activity against both viruses in vitro. The specificity of the aptamers was confirmed by comparing their activity to scrambled versions of themselves. Modifications of the lead compounds were tested to define critical motifs to guide development. Stability of the aptamers was increased using phosphorothioate backbone linkages, and 2' methoxy substitutions of terminal and key internal bases. Aptamers were applied in a guinea pig vaginal HSV-2 infection model and found to reduce both the viral load of infected animals and the severity of the resulting disease. These results suggest that cross-neutralizing aptamers can be developed into on-demand antiviral interventions effective against both HSV-1 and HSV-2.
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Affiliation(s)
- Michael D Schump
- Apspeeda Biosciences, 12635 E. Montview Blvd., Ste 100, Aurora, CO, USA
| | - David I Bernstein
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Fernando J Bravo
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Charles P Neff
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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2
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Neff CP, Cikara M, Geiss BJ, Thomas Caltagirone G, Liao A, Atif SM, Macdonald B, Schaden R. Nucleocapsid protein binding DNA aptamers for detection of SARS-COV-2. Curr Res Biotechnol 2023; 5:100132. [PMID: 37275459 PMCID: PMC10223630 DOI: 10.1016/j.crbiot.2023.100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/07/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV-2) has infected millions of individuals and continues to be a major health concern worldwide. While reverse transcription-polymerase chain reaction remains a reliable method for detecting infections, limitations of this technology, particularly cost and the requirement of a dedicated laboratory, prevent rapid viral monitoring. Antigen tests filled this need to some extent but with limitations including sensitivity and specificity, particularly against emerging variants of concern. Here, we developed aptamers against the SARS-CoV-2 Nucleocapsid protein to complement or replace antibodies in antigen detection assays. As detection reagents in ELISA-like assays, our DNA aptamers were able to detect as low as 150 pg/mL of the protein and under 150 k copies of inactivated SARS-CoV-2 Wuhan Alpha strain in viral transport medium with little cross-reactivity to other human coronaviruses (HCoVs). Further, our aptamers were reselected against the SARS-CoV-2 Omicron variant of concern, and we found two sequences that had a more than two-fold increase in signal compared to our original aptamers when used as detection reagents against protein from the Omicron strain. These findings illustrate the use of aptamers as promising alternative detection reagents that may translate for use in current tests and our findings validate the method for the reselection of aptamers against emerging viral strains.
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Affiliation(s)
- Charles P Neff
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mile Cikara
- Precision Medicine Architects, LLC, PO Box 148, Wellington, CO 80549, United States
| | - Brian J Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Albert Liao
- Aptagen, LLC, 250 North Main Street, Jacobus, PA 17407, USA
| | - Shaikh M Atif
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bradley Macdonald
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Richard Schaden
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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3
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Littlefield KM, Schneider JM, Neff CP, Soesanto V, Siebert JC, Nusbacher NM, Moreno-Huizar N, Cartwright IM, Armstrong AJS, Colgen SP, Lozupone CA, Palmer BE. Elevated inflammatory fecal immune factors in men who have sex with men with HIV associate with microbiome composition and gut barrier function. Front Immunol 2022; 13:1072720. [PMID: 36605218 PMCID: PMC9808389 DOI: 10.3389/fimmu.2022.1072720] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction People living with HIV infection (PLWH) exhibit elevated levels of gastrointestinal inflammation. Potential causes of this inflammation include HIV infection and associated immune dysfunction, sexual behaviors among men who have sex with men (MSM) and gut microbiome composition. Methods To better understand the etiology of gastrointestinal inflammation we examined levels of 28 fecal soluble immune factors (sIFs) and the fecal microbiome in well-defined cohorts of HIV seronegative MSM (MSM-SN), MSM with untreated HIV infection (MSM-HIV) and MSM with HIV on anti-retroviral treatment (MSMART). Additionally, fecal solutes from these participants were used to stimulate T-84 colonic epithelial cells to assess barrier function. Results Both MSM cohorts with HIV had elevated levels of fecal calprotectin, a clinically relevant marker of GI inflammation, and nine inflammatory fecal sIFs (GM-CSF, ICAM-1, IL-1β, IL-12/23, IL-15, IL-16, TNF-β, VCAM-1, and VEGF). Interestingly, four sIFs (GM-CSF, ICAM-1, IL-7 and IL-12/23) were significantly elevated in MSM-SN compared to seronegative male non-MSM. Conversely, IL-22 and IL-13, cytokines beneficial to gut health, were decreased in all MSM with HIV and MSM-SN respectively. Importantly, all of these sIFs significantly correlated with calprotectin, suggesting they play a role in GI inflammation. Principal coordinate analysis revealed clustering of fecal sIFs by MSM status and significant associations with microbiome composition. Additionally, fecal solutes from participants in the MSM-HIV cohort significantly decreased colonic transcellular fluid transport in vitro, compared to non-MSM-SN, and this decrease associated with overall sIF composition and increased concentrations of eight inflammatory sIFs in participants with HIV. Lastly, elevated levels of plasma, sCD14 and sCD163, directly correlated with decreased transcellular transport and microbiome composition respectively, indicating that sIFs and the gut microbiome are associated with, and potentially contribute to, bacterial translocation. Conclusion Taken together, these data demonstrate that inflammatory sIFs are elevated in MSM, regardless of HIV infection status, and are associated with the gut microbiome and intestinal barrier function.
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Affiliation(s)
| | | | - Charles P. Neff
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Victoria Soesanto
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Janet C. Siebert
- Department of Medicine, University of Colorado, Aurora, CO, United States
- CytoAnalytics, Denver, CO, United States
| | - Nichole M. Nusbacher
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nancy Moreno-Huizar
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ian M. Cartwright
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Abigail J. S. Armstrong
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Sean P. Colgen
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Brent E. Palmer
- Department of Medicine, University of Colorado, Aurora, CO, United States
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4
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Tengesdal IW, Li S, Powers NE, May M, Neff CP, Joosten LAB, Marchetti C, Dinarello CA. Activation of Host-NLRP3 Inflammasome in Myeloid Cells Dictates Response to Anti-PD-1 Therapy in Metastatic Breast Cancers. Pharmaceuticals (Basel) 2022; 15:574. [PMID: 35631400 PMCID: PMC9144656 DOI: 10.3390/ph15050574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/22/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022] Open
Abstract
Tumor-associated inflammation leads to dysregulated cytokine production that promotes tumor immune evasion and anti-tumor immunity dysfunction. In advanced stage breast cancer, the proinflammatory cytokine IL-1β is overexpressed due to large proportions of activated myeloid cells in the tumor microenvironment (TME). Here, we demonstrate the role of the host nucleotide-binding domain, leucine-rich containing family, pyrin domain-containing 3 (NLRP3) inflammasome in metastatic breast cancer. In vitro, we show that stimulation of THP-1 cells with conditioned media collected from MDA-MB-468 cells induced NLRP3 activation and increased Pdcd1l1 expression. In vivo, mice deficient in NLRP3 orthotopically implanted with metastatic breast cancer cell line (E0771) showed significant reduction in tumor growth (p < 0.05) and increased survival (p < 0.01). Inhibition of NLRP3 with the small molecule OLT1177® reduced expression of Pdcd1l1 (p < 0.001), Casp1 (p < 0.01) and Il1b (p < 0.01) in primary tumors. Furthermore, tumor-bearing mice receiving OLT1177® showed reduced infiltration of myeloid-derived suppressor cells (MDSCs) (p < 0.001) and increased CD8+ T cells (p < 0.05) and NK cells (p < 0.05) in the TME. NLRP3 inhibition in addition to anti-PD-1 treatment significantly reduced tumor growth from the monotherapies (p < 0.05). These data define NLRP3 activation as a key driver of immune suppression in metastatic breast cancers. Furthermore, this study suggests NLRP3 as a valid target to increase efficacy of immunotherapy with checkpoint inhibitor in metastatic breast cancers.
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Affiliation(s)
- Isak W. Tengesdal
- Department of Medicine, Radboud University Medical Center, 6525 Nijmegen, The Netherlands; (I.W.T.); (L.A.B.J.); (C.A.D.)
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; (S.L.); (N.E.P.); (M.M.); (C.P.N.)
| | - Suzhao Li
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; (S.L.); (N.E.P.); (M.M.); (C.P.N.)
| | - Nicholas E. Powers
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; (S.L.); (N.E.P.); (M.M.); (C.P.N.)
| | - Makenna May
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; (S.L.); (N.E.P.); (M.M.); (C.P.N.)
| | - Charles P. Neff
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; (S.L.); (N.E.P.); (M.M.); (C.P.N.)
| | - Leo A. B. Joosten
- Department of Medicine, Radboud University Medical Center, 6525 Nijmegen, The Netherlands; (I.W.T.); (L.A.B.J.); (C.A.D.)
| | - Carlo Marchetti
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; (S.L.); (N.E.P.); (M.M.); (C.P.N.)
| | - Charles A. Dinarello
- Department of Medicine, Radboud University Medical Center, 6525 Nijmegen, The Netherlands; (I.W.T.); (L.A.B.J.); (C.A.D.)
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; (S.L.); (N.E.P.); (M.M.); (C.P.N.)
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5
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Littlefield KM, Watson RO, Schneider JM, Neff CP, Yamada E, Zhang M, Campbell TB, Falta MT, Jolley SE, Fontenot AP, Palmer BE. SARS-CoV-2-specific T cells associate with inflammation and reduced lung function in pulmonary post-acute sequalae of SARS-CoV-2. PLoS Pathog 2022; 18:e1010359. [PMID: 35617421 PMCID: PMC9176759 DOI: 10.1371/journal.ppat.1010359] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/08/2022] [Accepted: 05/04/2022] [Indexed: 12/05/2022] Open
Abstract
As of January 2022, at least 60 million individuals are estimated to develop post-acute sequelae of SARS-CoV-2 (PASC) after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While elevated levels of SARS-CoV-2-specific T cells have been observed in non-specific PASC, little is known about their impact on pulmonary function which is compromised in the majority of these individuals. This study compares frequencies of SARS-CoV-2-specific T cells and inflammatory markers with lung function in participants with pulmonary PASC and resolved COVID-19 (RC). Compared to RC, participants with respiratory PASC had between 6- and 105-fold higher frequencies of IFN-γ- and TNF-α-producing SARS-CoV-2-specific CD4+ and CD8+ T cells in peripheral blood, and elevated levels of plasma CRP and IL-6. Importantly, in PASC participants the frequency of TNF-α-producing SARS-CoV-2-specific CD4+ and CD8+ T cells, which exhibited the highest levels of Ki67 indicating they were activity dividing, correlated positively with plasma IL-6 and negatively with measures of lung function, including forced expiratory volume in one second (FEV1), while increased frequencies of IFN-γ-producing SARS-CoV-2-specific T cells associated with prolonged dyspnea. Statistical analyses stratified by age, number of comorbidities and hospitalization status demonstrated that none of these factors affect differences in the frequency of SARS-CoV-2 T cells and plasma IL-6 levels measured between PASC and RC cohorts. Taken together, these findings demonstrate elevated frequencies of SARS-CoV-2-specific T cells in individuals with pulmonary PASC are associated with increased systemic inflammation and decreased lung function, suggesting that SARS-CoV-2-specific T cells contribute to lingering pulmonary symptoms. These findings also provide mechanistic insight on the pathophysiology of PASC that can inform development of potential treatments to reduce symptom burden.
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Affiliation(s)
- Katherine M. Littlefield
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Renée O. Watson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jennifer M. Schneider
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Charles P. Neff
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Eiko Yamada
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Min Zhang
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Thomas B. Campbell
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Michael T. Falta
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Sarah E. Jolley
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Andrew P. Fontenot
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Brent E. Palmer
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
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Li SX, Sen S, Schneider JM, Xiong KN, Nusbacher NM, Moreno-Huizar N, Shaffer M, Armstrong AJS, Severs E, Kuhn K, Neff CP, McCarter M, Campbell T, Lozupone CA, Palmer BE. Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection. PLoS Pathog 2019; 15:e1007611. [PMID: 30947289 PMCID: PMC6448819 DOI: 10.1371/journal.ppat.1007611] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/31/2019] [Indexed: 12/30/2022] Open
Abstract
Men who have sex with men (MSM) have differences in immune activation and gut microbiome composition compared with men who have sex with women (MSW), even in the absence of HIV infection. Gut microbiome differences associated with HIV itself when controlling for MSM, as assessed by 16S rRNA sequencing, are relatively subtle. Understanding whether gut microbiome composition impacts immune activation in HIV-negative and HIV-positive MSM has important implications since immune activation has been associated with HIV acquisition risk and disease progression. To investigate the effects of MSM and HIV-associated gut microbiota on immune activation, we transplanted feces from HIV-negative MSW, HIV-negative MSM, and HIV-positive untreated MSM to gnotobiotic mice. Following transplant, 16S rRNA gene sequencing determined that the microbiomes of MSM and MSW maintained distinct compositions in mice and that specific microbial differences between MSM and MSW were replicated. Immunologically, HIV-negative MSM donors had higher frequencies of blood CD38+ HLADR+ and CD103+ T cells and their fecal recipients had higher frequencies of gut CD69+ and CD103+ T cells, compared with HIV-negative MSW donors and recipients, respectively. Significant microbiome differences were not detected between HIV-negative and HIV-positive MSM in this small donor cohort, and immune differences between their recipients were trending but not statistically significant. A larger donor cohort may therefore be needed to detect immune-modulating microbes associated with HIV. To investigate whether our findings in mice could have implications for HIV replication, we infected primary human lamina propria cells stimulated with isolated fecal microbiota, and found that microbiota from MSM stimulated higher frequencies of HIV-infected cells than microbiota from MSW. Finally, we identified several microbes that correlated with immune readouts in both fecal recipients and donors, and with in vitro HIV infection, which suggests a role for gut microbiota in immune activation and potentially HIV acquisition in MSM.
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Affiliation(s)
- Sam X. Li
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Sharon Sen
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Jennifer M. Schneider
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Ka-Na Xiong
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Nichole M. Nusbacher
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Nancy Moreno-Huizar
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Michael Shaffer
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Abigail J. S. Armstrong
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Erin Severs
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Kristine Kuhn
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Charles P. Neff
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Martin McCarter
- Division of Colorectal Surgery, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Thomas Campbell
- Division of Infectious Diseases, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Catherine A. Lozupone
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Brent E. Palmer
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, United States of America
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7
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Jin Y, Roberts GHL, Ferrara TM, Ben S, van Geel N, Wolkerstorfer A, Ezzedine K, Siebert J, Neff CP, Palmer BE, Santorico SA, Spritz RA. Early-onset autoimmune vitiligo associated with an enhancer variant haplotype that upregulates class II HLA expression. Nat Commun 2019; 10:391. [PMID: 30674883 PMCID: PMC6344500 DOI: 10.1038/s41467-019-08337-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/03/2019] [Indexed: 01/28/2023] Open
Abstract
Vitiligo is an autoimmune disease in which melanocyte destruction causes skin depigmentation, with 49 loci known from previous GWAS. Aiming to define vitiligo subtypes, we discovered that age-of-onset is bimodal; one-third of cases have early onset (mean 10.3 years) and two-thirds later onset (mean 34.0 years). In the early-onset subgroup we found novel association with MHC class II region indel rs145954018, and independent association with the principal MHC class II locus from previous GWAS, represented by rs9271597; greatest association was with rs145954018del-rs9271597A haplotype (P = 2.40 × 10−86, OR = 8.10). Both rs145954018 and rs9271597 are located within lymphoid-specific enhancers, and the rs145954018del-rs9271597A haplotype is specifically associated with increased expression of HLA-DQB1 mRNA and HLA-DQ protein by monocytes and dendritic cells. Thus, for vitiligo, MHC regulatory variation confers extreme risk, more important than HLA coding variation. MHC regulatory variation may represent a significant component of genetic risk for other autoimmune diseases. GWAS have led to the identification of 49 genetic loci associated with vitiligo. Here, the authors observe a bimodal distribution of age-of-onset and find a novel genetic locus specifically associated with early-onset vitiligo, located in a regulatory element in the MHC class II region.
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Affiliation(s)
- Ying Jin
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, 80045, CO, USA.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, 80045, CO, USA
| | - Genevieve H L Roberts
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, 80045, CO, USA
| | - Tracey M Ferrara
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, 80045, CO, USA
| | - Songtao Ben
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, 80045, CO, USA
| | - Nanja van Geel
- Department of Dermatology, Ghent University Hospital, Ghent, 9000, Belgium
| | - Albert Wolkerstorfer
- Netherlands Institute for Pigment Disorders, Department of Dermatology, Academic Medical Centre University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Khaled Ezzedine
- Department of Dermatology, Hôpital Henri Mondor, Université Paris-Est Créteil, Créteil, 94000, France
| | | | - Charles P Neff
- Department of Medicine, University of Colorado School of Medicine, Aurora, 80045, CO, USA
| | - Brent E Palmer
- Department of Medicine, University of Colorado School of Medicine, Aurora, 80045, CO, USA
| | - Stephanie A Santorico
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, 80045, CO, USA.,Department of Mathematical and Statistical Sciences, University of Colorado, Denver, 80204, CO, USA
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, 80045, CO, USA. .,Department of Pediatrics, University of Colorado School of Medicine, Aurora, 80045, CO, USA.
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8
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Li SX, Armstrong A, Neff CP, Shaffer M, Lozupone CA, Palmer BE. Complexities of Gut Microbiome Dysbiosis in the Context of HIV Infection and Antiretroviral Therapy. Clin Pharmacol Ther 2016; 99:600-11. [PMID: 26940481 DOI: 10.1002/cpt.363] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV) infection is associated with an altered gut microbiome that is not consistently restored with effective antiretroviral therapy (ART). Interpretation of the specific microbiome changes observed during HIV infection is complicated by factors like population, sample type, and ART-each of which may have dramatic effects on gut bacteria. Understanding how these factors shape the microbiome during HIV infection (which we refer to as the HIV-associated microbiome) is critical for defining its role in HIV disease, and for developing therapies that restore gut health during infection.
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Affiliation(s)
- S X Li
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ajs Armstrong
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - C P Neff
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - M Shaffer
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA.,Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - C A Lozupone
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - B E Palmer
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
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9
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Lozupone CA, Rhodes ME, Neff CP, Fontenot AP, Campbell TB, Palmer BE. HIV-induced alteration in gut microbiota: driving factors, consequences, and effects of antiretroviral therapy. Gut Microbes 2014; 5:562-70. [PMID: 25078714 DOI: 10.4161/gmic.32132] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Consistent with an important role for adaptive immunity in modulating interactions between intestinal bacteria and host, dramatic alteration in the composition of gut microbes during chronic HIV infection was recently reported by ourselves and independently by four other research groups. Here we evaluate our results in the context of these other studies and delve into the effects of antiretroviral therapy (ART). Although gut microbiota of HIV-positive individuals on ART usually does not resemble that of HIV-negative individuals, the degree to which ART restores health-associated prevalence varies across bacterial taxa. Finally, we discuss potential drivers and health consequences of gut microbiota alterations. We propose that understanding the mechanism of HIV-associated gut microbiota changes will elucidate the role of adaptive immunity in shaping gut microbiota composition, and lay the foundation for therapeutics targeting the microbiota to attenuate HIV disease progression and reduce the risk of gut-linked disease in people with HIV.
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Affiliation(s)
- Catherine A Lozupone
- Department of Medicine; University of Colorado Denver; Anschutz Medical Campus; Aurora, CO USA
| | - Matthew E Rhodes
- Department of Medicine; University of Colorado Denver; Anschutz Medical Campus; Aurora, CO USA
| | - Charles P Neff
- Department of Medicine; University of Colorado Denver; Anschutz Medical Campus; Aurora, CO USA
| | - Andrew P Fontenot
- Department of Medicine; University of Colorado Denver; Anschutz Medical Campus; Aurora, CO USA
| | - Thomas B Campbell
- Department of Medicine; University of Colorado Denver; Anschutz Medical Campus; Aurora, CO USA
| | - Brent E Palmer
- Department of Medicine; University of Colorado Denver; Anschutz Medical Campus; Aurora, CO USA
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