Systemic sclerosis (SSc) is a progressive fibrotic disorder with a high mortality rate, characterized by extensive autoantibody production. Despite recent advancements, effective treatments remain limited. Rituximab (RTX), a B-cell depleting agent, has shown promise in clinical trials. The DESIRES trial highlighted the reduction in modified Rodnan Skin Score (mRSS) and the association between serum immunoglobulin levels and RTX responsiveness. We employed proteome-wide autoantibody screening (PWAS) using wet protein arrays (WPAs) that display 13,455 human autoantigens to analyze serum samples from SSc patients in the DESIRES trial and age- and sex-matched healthy controls (HCs). As a result, the sum of autoantibody levels (SAL) was significantly higher in SSc patients compared to HCs. High responders (HRs) to RTX showed a greater initial SAL and significant reductions post-treatment, unlike low responders (LRs). Machine learning identified specific autoantibodies linked to disease status, and 58 autoantibodies were identified as clinically relevant. Some of those autoantibodies targeted membrane proteins including G protein-coupled receptors, associated with better differentiation between HRs and LRs. Our findings underscore the significance of autoantibodies in SSc pathogenesis and their potential role in predicting RTX responsiveness. This comprehensive autoantibody profiling could enhance diagnostic and therapeutic strategies, and moreover, better understanding of the pathophysiology of SSc.
{"title":"Deciphering autoantibody landscape of systemic sclerosis through systems-based approach: insights from a B-cell depletion clinical trial","authors":"Kazuki M Matsuda, Satoshi Ebata, Kazuhiro Iwadoh, Hirohito Kotani, Teruyoshi Hisamoto, Ai Kuzumi, Takemichi Fukasawa, Asako Yoshizaki-Ogawa, Shinichi Sato, Ayumi Yoshizaki","doi":"10.1101/2024.07.30.24311212","DOIUrl":"https://doi.org/10.1101/2024.07.30.24311212","url":null,"abstract":"Systemic sclerosis (SSc) is a progressive fibrotic disorder with a high mortality rate, characterized by extensive autoantibody production. Despite recent advancements, effective treatments remain limited. Rituximab (RTX), a B-cell depleting agent, has shown promise in clinical trials. The DESIRES trial highlighted the reduction in modified Rodnan Skin Score (mRSS) and the association between serum immunoglobulin levels and RTX responsiveness. We employed proteome-wide autoantibody screening (PWAS) using wet protein arrays (WPAs) that display 13,455 human autoantigens to analyze serum samples from SSc patients in the DESIRES trial and age- and sex-matched healthy controls (HCs). As a result, the sum of autoantibody levels (SAL) was significantly higher in SSc patients compared to HCs. High responders (HRs) to RTX showed a greater initial SAL and significant reductions post-treatment, unlike low responders (LRs). Machine learning identified specific autoantibodies linked to disease status, and 58 autoantibodies were identified as clinically relevant. Some of those autoantibodies targeted membrane proteins including G protein-coupled receptors, associated with better differentiation between HRs and LRs. Our findings underscore the significance of autoantibodies in SSc pathogenesis and their potential role in predicting RTX responsiveness. This comprehensive autoantibody profiling could enhance diagnostic and therapeutic strategies, and moreover, better understanding of the pathophysiology of SSc.","PeriodicalId":501527,"journal":{"name":"medRxiv - Allergy and Immunology","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141865269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-23DOI: 10.1101/2024.07.22.24310829
Austin J Van Asselt, Jeffrey J Beck, Brandon N Johnson, Casey T Finnicum, Noah Kallsen, Sarah Viet, Patricia Huizenga, Lannie Ligthart, Jouke-Jan Hottenga, René Pool, Anke H. Maitland-van der Zee, Susanne J Vijverberg, Eco de Geus, Dorret I Boomsma, Erik A Ehli, Jenny van Dongen
Background: Asthma, a complex respiratory disease, presents with inflammatory symptoms in the lungs, blood, and other tissues. We investigated the relationship between DNA methylation and 35 clinical markers of asthma. The Illumina Infinium EPIC v1 methylation array was used to evaluate 742,442 CpGs in whole blood samples from 319 participants. They were part of the Netherlands Twin Register from families with at least one member suffering from severe asthma. Repeat blood samples were taken after 10 years from 182 of these individuals. Principal component analysis (PCA) on the clinical markers yielded ten principal components (PCs) that explained 92.8% of the total variance. We performed epigenome-wide association studies (EWAS) for each of the ten PCs correcting for familial structure and other covariates. Results: 221 unique CpGs reached genome-wide significance at timepoint 1 (T1) after Bonferroni correction. PC7 accounted for the majority of associations (204), which correlated with loadings of eosinophil counts and immunoglobulin levels. Enrichment analysis via the EWAS Atlas identified 190 of these CpGs to be previously identified in EWASs of asthma and asthma-related traits. Proximity assessment to previously identified SNPs associated with asthma identified 17 unique SNPs within 1 MB of two of the 221 CpGs. EWAS in 182 individuals with epigenetic data at a second timepoint (T2) identified 49 significant CpGs. EWAS Atlas enrichment analysis indicated that 4 of the 49 were previously associated with asthma or asthma-related traits. Comparing the estimates of all the significant associations identified across the two time points (271 in total) yielded a correlation of 0.81. Conclusion: We identified 270 unique CpGs that were associated with PC scores generated from 35 clinical markers of asthma, either cross-sectionally or 10 years later. A strong correlation was present between effect sizes at the 2 timepoints. Most associations were identified for PC7, which captured blood eosinophil counts and immunoglobulin levels and many of these CpGs have previous associations in earlier studies of asthma and asthma-related traits. The results point to using this robust DNA methylation profile as a new, stable biomarker for asthma.
{"title":"Epigenetic Signatures of Asthma: A Comprehensive Study of DNA Methylation and Clinical Markers","authors":"Austin J Van Asselt, Jeffrey J Beck, Brandon N Johnson, Casey T Finnicum, Noah Kallsen, Sarah Viet, Patricia Huizenga, Lannie Ligthart, Jouke-Jan Hottenga, René Pool, Anke H. Maitland-van der Zee, Susanne J Vijverberg, Eco de Geus, Dorret I Boomsma, Erik A Ehli, Jenny van Dongen","doi":"10.1101/2024.07.22.24310829","DOIUrl":"https://doi.org/10.1101/2024.07.22.24310829","url":null,"abstract":"Background: Asthma, a complex respiratory disease, presents with inflammatory symptoms in the lungs, blood, and other tissues. We investigated the relationship between DNA methylation and 35 clinical markers of asthma. The Illumina Infinium EPIC v1 methylation array was used to evaluate 742,442 CpGs in whole blood samples from 319 participants. They were part of the Netherlands Twin Register from families with at least one member suffering from severe asthma. Repeat blood samples were taken after 10 years from 182 of these individuals. Principal component analysis (PCA) on the clinical markers yielded ten principal components (PCs) that explained 92.8% of the total variance. We performed epigenome-wide association studies (EWAS) for each of the ten PCs correcting for familial structure and other covariates.\u0000Results: 221 unique CpGs reached genome-wide significance at timepoint 1 (T1) after Bonferroni correction. PC7 accounted for the majority of associations (204), which correlated with loadings of eosinophil counts and immunoglobulin levels. Enrichment analysis via the EWAS Atlas identified 190 of these CpGs to be previously identified in EWASs of asthma and asthma-related traits. Proximity assessment to previously identified SNPs associated with asthma identified 17 unique SNPs within 1 MB of two of the 221 CpGs. EWAS in 182 individuals with epigenetic data at a second timepoint (T2) identified 49 significant CpGs. EWAS Atlas enrichment analysis indicated that 4 of the 49 were previously associated with asthma or asthma-related traits. Comparing the estimates of all the significant associations identified across the two time points (271 in total) yielded a correlation of 0.81.\u0000Conclusion: We identified 270 unique CpGs that were associated with PC scores generated from 35 clinical markers of asthma, either cross-sectionally or 10 years later. A strong correlation was present between effect sizes at the 2 timepoints. Most associations were identified for PC7, which captured blood eosinophil counts and immunoglobulin levels and many of these CpGs have previous associations in earlier studies of asthma and asthma-related traits. The results point to using this robust DNA methylation profile as a new, stable biomarker for asthma.","PeriodicalId":501527,"journal":{"name":"medRxiv - Allergy and Immunology","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141782432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-23DOI: 10.1101/2024.07.22.24310550
Evi Duthoo, Elien Beyls, Lynn Backers, Thorkell Gudjónsson, Peiquan Huang, Leander Jonckheere, Sebastian Riemann, Bram Parton, Likun Du, Veronique Debacker, Marieke De Bruyne, Levi Hoste, Ans Baeyens, Anne Vral, Eva Van Braeckel, Jens Staal, Geert Mortier, Tessa Kerre, Qiang Pan-Hammarström, Claus S Sørensen, Filomeen Haerynck, Kathleen BM Claes, Simon J Tavernier
ATR (Ataxia Telangiectasia and Rad3-related) kinase and its interacting protein ATRIP orchestrate the replication stress response. Two patients of independent ancestry with microcephaly, primordial dwarfism, and recurring infections were found to be homozygous for splice donor site variants of ATRIP exon 5, resulting in ATRIP deficiency. The c.829+5G>T patient exhibited autoimmune hemolytic anemia, lymphopenia, poor vaccine response, and intermittent neutropenia. Immunophenotyping revealed reduced CD16+ NK cells and absent naïve T cells, mucosal-associated invariant T cells (MAITs), and invariant natural killer T cells (iNKTs). Lymphocytic defects were characterized by T cell receptor (TCR) oligoclonality, abnormal class switch recombination (CSR), and impaired T cell proliferation. ATRIP deficiency resulted in low-grade ATR activation but impaired CHK1 phosphorylation upon genotoxic stress. Consequently, ATRIP deficient cells inadequately regulated DNA replication, leading to chromosomal instability, compromised cell cycle control, and impaired cell viability. CRISPR-SelectTIME confirmed reduced cell fitness induced by both variants. This study establishes ATRIP deficiency as a monogenic cause of microcephalic primordial dwarfism, highlights ATRIP′s critical role in protecting immune cells from replication stress, and brings a renewed perspective to the canonical functions of ATRIP.
{"title":"ATRIP deficiency impairs the replication stress response and manifests as microcephalic primordial dwarfism and immunodeficiency.","authors":"Evi Duthoo, Elien Beyls, Lynn Backers, Thorkell Gudjónsson, Peiquan Huang, Leander Jonckheere, Sebastian Riemann, Bram Parton, Likun Du, Veronique Debacker, Marieke De Bruyne, Levi Hoste, Ans Baeyens, Anne Vral, Eva Van Braeckel, Jens Staal, Geert Mortier, Tessa Kerre, Qiang Pan-Hammarström, Claus S Sørensen, Filomeen Haerynck, Kathleen BM Claes, Simon J Tavernier","doi":"10.1101/2024.07.22.24310550","DOIUrl":"https://doi.org/10.1101/2024.07.22.24310550","url":null,"abstract":"ATR (Ataxia Telangiectasia and Rad3-related) kinase and its interacting protein ATRIP orchestrate the replication stress response. Two patients of independent ancestry with microcephaly, primordial dwarfism, and recurring infections were found to be homozygous for splice donor site variants of ATRIP exon 5, resulting in ATRIP deficiency. The c.829+5G>T patient exhibited autoimmune hemolytic anemia, lymphopenia, poor vaccine response, and intermittent neutropenia. Immunophenotyping revealed reduced CD16+ NK cells and absent naïve T cells, mucosal-associated invariant T cells (MAITs), and invariant natural killer T cells (iNKTs). Lymphocytic defects were characterized by T cell receptor (TCR) oligoclonality, abnormal class switch recombination (CSR), and impaired T cell proliferation. ATRIP deficiency resulted in low-grade ATR activation but impaired CHK1 phosphorylation upon genotoxic stress. Consequently, ATRIP deficient cells inadequately regulated DNA replication, leading to chromosomal instability, compromised cell cycle control, and impaired cell viability. CRISPR-SelectTIME confirmed reduced cell fitness induced by both variants. This study establishes ATRIP deficiency as a monogenic cause of microcephalic primordial dwarfism, highlights ATRIP′s critical role in protecting immune cells from replication stress, and brings a renewed perspective to the canonical functions of ATRIP.","PeriodicalId":501527,"journal":{"name":"medRxiv - Allergy and Immunology","volume":"50 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141782317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-10DOI: 10.1101/2024.07.10.24310202
Daan KJ Pieren, Aleix Benítez-Martínez, Vicente Descalzo, Maider Arando, Patricia Álvarez-López, Jorge N Garcia-Perez, Núria Massana, Júlia Castellón, Yannick Hoyos-Mallecot, Daniel Alvárez-Sierra, Clara Ramírez-Serra, Nuria Laia Rodriguez, Laura Mañalich-Barrachina, Cristina Centeno-Mediavilla, Josep Castellví, Vicenç Falcó, Maria J Buzón, Meritxell Genescà
Microbial imbalance in the female genital tract increases the risk for adverse health outcomes in women and may increase susceptibility to genital tract infections. The local mucosal immune system plays a fundamental role in maintaining microbial balance. Among different relevant immune subsets, inflammation-induced myeloid-derived suppressor cells (MDSCs) remain understudied in the context of female genital tract conditions. Here we show that frequency of an MDSC subset, Polymorphonuclear (PMN-) MDSCs, increased in the cervical mucosa, but not in blood, of women with Chlamydia trachomatis, bacterial vaginosis, or with a coinfection, but not in women with human papillomavirus. Mucosal PMN-MDSC frequencies correlated with mucosal IL-1β in C. trachomatis patients and ex vivo exposure of cervical tissue to C. trachomatis elevated both PMN-MDSC frequencies and IL-1β secretion. Likewise, exposure of cervical tissue to cervicovaginal lavage fluid from C. trachomatis and bacterial vaginosis patients also enhanced PMN-MDSC frequencies. Lastly, cervical MDSCs expressed suppressive mediators and functionally suppressed cytotoxic T-cell responses. Our study identifies IL-1β-stimulated PMN-MDSCs as an immune suppressive mediator in female genital tract infections, potentially contributing to susceptibility to acquiring secondary infections at this site.
{"title":"Cervical mucosal inflammation expands functional polymorphonuclear myeloid-derived suppressor cells","authors":"Daan KJ Pieren, Aleix Benítez-Martínez, Vicente Descalzo, Maider Arando, Patricia Álvarez-López, Jorge N Garcia-Perez, Núria Massana, Júlia Castellón, Yannick Hoyos-Mallecot, Daniel Alvárez-Sierra, Clara Ramírez-Serra, Nuria Laia Rodriguez, Laura Mañalich-Barrachina, Cristina Centeno-Mediavilla, Josep Castellví, Vicenç Falcó, Maria J Buzón, Meritxell Genescà","doi":"10.1101/2024.07.10.24310202","DOIUrl":"https://doi.org/10.1101/2024.07.10.24310202","url":null,"abstract":"Microbial imbalance in the female genital tract increases the risk for adverse health outcomes in women and may increase susceptibility to genital tract infections. The local mucosal immune system plays a fundamental role in maintaining microbial balance. Among different relevant immune subsets, inflammation-induced myeloid-derived suppressor cells (MDSCs) remain understudied in the context of female genital tract conditions. Here we show that frequency of an MDSC subset, Polymorphonuclear (PMN-) MDSCs, increased in the cervical mucosa, but not in blood, of women with <em>Chlamydia trachomatis</em>, bacterial vaginosis, or with a coinfection, but not in women with human papillomavirus. Mucosal PMN-MDSC frequencies correlated with mucosal IL-1β in <em>C. trachomatis</em> patients and <em>ex vivo</em> exposure of cervical tissue to <em>C. trachomatis</em> elevated both PMN-MDSC frequencies and IL-1β secretion. Likewise, exposure of cervical tissue to cervicovaginal lavage fluid from <em>C. trachomatis</em> and bacterial vaginosis patients also enhanced PMN-MDSC frequencies. Lastly, cervical MDSCs expressed suppressive mediators and functionally suppressed cytotoxic T-cell responses. Our study identifies IL-1β-stimulated PMN-MDSCs as an immune suppressive mediator in female genital tract infections, potentially contributing to susceptibility to acquiring secondary infections at this site.","PeriodicalId":501527,"journal":{"name":"medRxiv - Allergy and Immunology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141584597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-07DOI: 10.1101/2024.07.05.24310017
Natalie S. Haddad, Andrea Morrison-Porter, Hannah Quehl, Violeta Capric, Pedro A. Lamothe, Fabliha Anam, Martin C. Runnstrom, Alex D. Truong, Adviteeya N. Dixit, Matthew C. Woodruff, Anting Chen, Jiwon Park, Doan C. Nguyen, Ian Hentenaar, Caroline Y. Kim, Shuya Kyu, Brandon Stewart, Elizabeth Wagman, Hannah Geoffroy, Daniel Sanz, Kevin S. Cashman, Richard P. Ramonell, Monica Cabrera-Mora, David N. Alter, John D. Roback, Michael C. Horwath, James B. O'Keefe, Alexandra W. Dretler, Ria Gripaldo, Samantha M. Yeligar, Ted Natoli, Viktoria Betin, Rahulkumar Patel, Kennedy Vela, Mindy Rodriguez Hernandez, Sabeena Usman, John Varghese, Anum Jalal, Saeyun Lee, Sang N. Le, R. Toby Amoss, John L. Daiss, Ignacio Sanz, F. Eun-Hyung Lee
Post-acute sequelae of SARS-CoV-2 (SARS2) infection (PASC) is a heterogeneous condition, but the main viral drivers are unknown. Here, we use MENSA, Media Enriched with Newly Synthesized Antibodies, secreted exclusively from circulating human plasmablasts, to provide an immune snapshot that defines the underlying viral triggers. We provide proof-of-concept testing that the MENSA technology can capture the new host immune response to accurately diagnose acute primary and breakthrough infections when known SARS2 virus or proteins are present. It is also positive after vaccination when spike proteins elicit an acute immune response. Applying the same principles for long-COVID patients, MENSA is positive for SARS2 in 40% of PASC vs none of the COVID recovered (CR) patients without any sequelae demonstrating ongoing SARS2 viral inflammation only in PASC. Additionally, in PASC patients, MENSAs are also positive for Epstein-Barr Virus (EBV) in 37%, Human Cytomegalovirus (CMV) in 23%, and herpes simplex virus 2 (HSV2) in 15% compared to 17%, 4%, and 4% in CR controls respectively. Combined, a total of 60% of PASC patients have a positive MENSA for SARS2, EBV, CMV, and/or HSV2. MENSA offers a unique antibody snapshot to reveal the underlying viral drivers in long-COVID thus demonstrating the persistence of SARS2 and reactivation of viral herpes in 60% of PASC patients.
{"title":"MENSA, a Media Enriched with Newly Synthesized Antibodies, to Identify SARS-CoV-2 Persistence and Latent Viral Reactivation in Long-COVID","authors":"Natalie S. Haddad, Andrea Morrison-Porter, Hannah Quehl, Violeta Capric, Pedro A. Lamothe, Fabliha Anam, Martin C. Runnstrom, Alex D. Truong, Adviteeya N. Dixit, Matthew C. Woodruff, Anting Chen, Jiwon Park, Doan C. Nguyen, Ian Hentenaar, Caroline Y. Kim, Shuya Kyu, Brandon Stewart, Elizabeth Wagman, Hannah Geoffroy, Daniel Sanz, Kevin S. Cashman, Richard P. Ramonell, Monica Cabrera-Mora, David N. Alter, John D. Roback, Michael C. Horwath, James B. O'Keefe, Alexandra W. Dretler, Ria Gripaldo, Samantha M. Yeligar, Ted Natoli, Viktoria Betin, Rahulkumar Patel, Kennedy Vela, Mindy Rodriguez Hernandez, Sabeena Usman, John Varghese, Anum Jalal, Saeyun Lee, Sang N. Le, R. Toby Amoss, John L. Daiss, Ignacio Sanz, F. Eun-Hyung Lee","doi":"10.1101/2024.07.05.24310017","DOIUrl":"https://doi.org/10.1101/2024.07.05.24310017","url":null,"abstract":"Post-acute sequelae of SARS-CoV-2 (SARS2) infection (PASC) is a heterogeneous condition, but the main viral drivers are unknown. Here, we use MENSA, Media Enriched with Newly Synthesized Antibodies, secreted exclusively from circulating human plasmablasts, to provide an immune snapshot that defines the underlying viral triggers. We provide proof-of-concept testing that the MENSA technology can capture the new host immune response to accurately diagnose acute primary and breakthrough infections when known SARS2 virus or proteins are present. It is also positive after vaccination when spike proteins elicit an acute immune response. Applying the same principles for long-COVID patients, MENSA is positive for SARS2 in 40% of PASC vs none of the COVID recovered (CR) patients without any sequelae demonstrating ongoing SARS2 viral inflammation only in PASC. Additionally, in PASC patients, MENSAs are also positive for Epstein-Barr Virus (EBV) in 37%, Human Cytomegalovirus (CMV) in 23%, and herpes simplex virus 2 (HSV2) in 15% compared to 17%, 4%, and 4% in CR controls respectively. Combined, a total of 60% of PASC patients have a positive MENSA for SARS2, EBV, CMV, and/or HSV2. MENSA offers a unique antibody snapshot to reveal the underlying viral drivers in long-COVID thus demonstrating the persistence of SARS2 and reactivation of viral herpes in 60% of PASC patients.","PeriodicalId":501527,"journal":{"name":"medRxiv - Allergy and Immunology","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141570459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-06DOI: 10.1101/2024.07.03.24309917
Eric Leslie, Marina Miller, Allison LaFuze, Sofya Svyatskaya, Gil-Soon Choi, David H Broide
PGAP3 is a glycosylphosphatidylinositol (GPI) phospholipase gene localized within chromosome 17q12-21, a region highly linked to asthma. Although much is known about the function of other chromosome 17q12-21 genes expressed at increased levels in bronchial epithelium such as ORMDL3 and GSDMB, little is known about the function of increased PGAP3 expression in bronchial epithelium in the context of asthma. The aim of this study was therefore to determine whether increased PGAP3 expression in human bronchial epithelial cells regulated expression of mRNA pathways important to the pathogenesis of asthma by utilizing RNA-sequencing and bioinformatic analysis. We performed RNA-sequencing on normal human bronchial epithelial cells transfected with PGAP3 for 24 and 48 hours. PGAP3 regulated genes were compared to asthma and respiratory virus (influenza A, rhinovirus, respiratory syncytial virus) reference data sets to identify PGAP3 target genes and pathways. Approximately 9% of the upregulated PGAP3- induced genes were found in an asthma reference data set, 41% in a rhinovirus reference data set, 33% in an influenza A reference data set, and 3% in a respiratory syncytial virus reference data set. PGAP3 significantly upregulated the expression of several genes associated with the innate immune response and viral signatures of respiratory viruses associated with asthma exacerbations. Two of the highest expressed genes induced by PGAP3 are RSAD2, OASL, and IFN-λ, which are anti-viral genes associated with asthma. PGAP3 also upregulated the antiviral gene BST2, which like PGAP3 is a GPI-anchored protein. We conclude that PGAP3 expression in human bronchial epithelial cells regulates expression of genes known to be linked to asthma, and also regulates the bronchial epithelial expression of genes pertinent to the pathogenesis of respiratory viral triggered asthma exacerbations.
{"title":"PGAP3 regulates human bronchial epithelial cell mRNAs present in asthma and respiratory virus reference data sets","authors":"Eric Leslie, Marina Miller, Allison LaFuze, Sofya Svyatskaya, Gil-Soon Choi, David H Broide","doi":"10.1101/2024.07.03.24309917","DOIUrl":"https://doi.org/10.1101/2024.07.03.24309917","url":null,"abstract":"PGAP3 is a glycosylphosphatidylinositol (GPI) phospholipase gene localized within chromosome 17q12-21, a region highly linked to asthma. Although much is known about the function of other chromosome 17q12-21 genes expressed at increased levels in bronchial epithelium such as ORMDL3 and GSDMB, little is known about the function of increased PGAP3 expression in bronchial epithelium in the context of asthma. The aim of this study was therefore to determine whether increased PGAP3 expression in human bronchial epithelial cells regulated expression of mRNA pathways important to the pathogenesis of asthma by utilizing RNA-sequencing and bioinformatic analysis. We performed RNA-sequencing on normal human bronchial epithelial cells transfected with PGAP3 for 24 and 48 hours. PGAP3 regulated genes were compared to asthma and respiratory virus (influenza A, rhinovirus, respiratory syncytial virus) reference data sets to identify PGAP3 target genes and pathways. Approximately 9% of the upregulated PGAP3- induced genes were found in an asthma reference data set, 41% in a rhinovirus reference data set, 33% in an influenza A reference data set, and 3% in a respiratory syncytial virus reference data set. PGAP3 significantly upregulated the expression of several genes associated with the innate immune response and viral signatures of respiratory viruses associated with asthma exacerbations. Two of the highest expressed genes induced by PGAP3 are RSAD2, OASL, and IFN-λ, which are anti-viral genes associated with asthma. PGAP3 also upregulated the antiviral gene BST2, which like PGAP3 is a GPI-anchored protein. We conclude that PGAP3 expression in human bronchial epithelial cells regulates expression of genes known to be linked to asthma, and also regulates the bronchial epithelial expression of genes pertinent to the pathogenesis of respiratory viral triggered asthma exacerbations.","PeriodicalId":501527,"journal":{"name":"medRxiv - Allergy and Immunology","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141570458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-28DOI: 10.1101/2024.06.26.24309360
Maryam Vaseghi-Shanjani, Mehul Sharma, Pariya Yousefi, Simran Samra, Kaitlin U. Laverty, Arttu Jolma, Rozita Razavi, Ally H. W. Yang, Mihai Albu, Liam Golding, Anna F. Lee, Ryan Tan, Phillip A. Richmond, Marita Bosticardo, Jonathan H. Rayment, Connie L. Yang, Kyla J. Hildebrand, Rae Brager, Michelle K. Demos, Yu Lung Lau, Luigi D. Notarangelo, Timothy R. Hughes, Catherine M. Biggs, Stuart E. Turvey
ThPOK is best known as a regulator of CD4+ T cell lineage commitment, although it was initially cloned as a suppressor of collagen expression in the skin. The role of ThPOK has not been formally established in humans since individuals with damaging variants in ThPOK have not yet been identified. Here, we report the first case of a human with a damaging heterozygous de novo variant in ThPOK causing a syndrome encompassing CD4+ T cell deficiency, allergy, fibroinflammatory interstitial lung disease, developmental delay, and growth failure. The patient variant, ThPOK K360N, exhibited abnormal multimorphic activity, including interfering with ThPOK WT in regulating gene regulation (antimorph). Protein-DNA interaction assays showed inability of ThPOK K360N to bind to wild-type consensus sequences (amorph) and revealed a novel DNA-binding specificity (neomorph). Single-cell RNA sequencing of peripheral blood revealed potential developmental defects in maturation and activation of CD4+ and CD8+ T cells (hypomorph). To establish causality, we recapitulated the observed cellular defects in lentivirally transduced healthy control T cells and pulmonary fibroblasts. Transcriptomic analysis showed that T cells transduced with ThPOK K360N lacked the upregulation of activation, proliferation, and functional pathways observed in ThPOKWT-transduced cells. When overexpressed in healthy control fibroblasts, ThPOK K360N significantly increased the expression of pro-fibrotic genes implicated in pulmonary fibrosis, indicating a defect in regulating collagen expression. This novel human disease caused by a multimorphic variant in ThPOK confirms its role in CD4+ T cell development in an intact human context, while also revealing an unanticipated role for ThPOK in T cell function and the regulation of fibrotic pathways in fibroblasts.
ThPOK 最著名的作用是调节 CD4+ T 细胞系的形成，尽管它最初被克隆为皮肤胶原表达的抑制因子。ThPOK 在人类中的作用尚未正式确定，因为尚未发现 ThPOK 存在损伤性变异的个体。在这里，我们报告了第一例患有 ThPOK 从新变异的损伤性杂合变异体的人类病例，该变异体导致了一种包括 CD4+ T 细胞缺乏症、过敏症、纤维炎性间质性肺病、发育迟缓和生长发育障碍的综合征。患者的变异体 ThPOK K360N 表现出异常的多态性，包括干扰 ThPOK WT 的基因调控（抗多态性）。蛋白质-DNA相互作用测定显示，ThPOK K360N无法与野生型共识序列结合（amorph），并揭示了一种新的DNA结合特异性（neomorph）。外周血单细胞 RNA 测序显示，CD4+和 CD8+ T 细胞的成熟和活化存在潜在的发育缺陷（hypomorph）。为了确定因果关系，我们在慢病毒转导的健康对照 T 细胞和肺成纤维细胞中重现了观察到的细胞缺陷。转录组分析表明，转导 ThPOK K360N 的 T 细胞缺乏在转导 ThPOKWT 的细胞中观察到的活化、增殖和功能通路的上调。当 ThPOK K360N 在健康对照成纤维细胞中过表达时，会显著增加与肺纤维化有关的促纤维化基因的表达，这表明它在调节胶原表达方面存在缺陷。这种由 ThPOK 多态变异引起的新型人类疾病证实了 ThPOK 在完整人类环境中 CD4+ T 细胞发育中的作用，同时也揭示了 ThPOK 在 T 细胞功能和成纤维细胞纤维化途径调控中的意想不到的作用。
{"title":"A multimorphic variant in ThPOK causes a novel human disease characterized by T cell abnormalities, immunodysregulation, allergy, and fibrosis","authors":"Maryam Vaseghi-Shanjani, Mehul Sharma, Pariya Yousefi, Simran Samra, Kaitlin U. Laverty, Arttu Jolma, Rozita Razavi, Ally H. W. Yang, Mihai Albu, Liam Golding, Anna F. Lee, Ryan Tan, Phillip A. Richmond, Marita Bosticardo, Jonathan H. Rayment, Connie L. Yang, Kyla J. Hildebrand, Rae Brager, Michelle K. Demos, Yu Lung Lau, Luigi D. Notarangelo, Timothy R. Hughes, Catherine M. Biggs, Stuart E. Turvey","doi":"10.1101/2024.06.26.24309360","DOIUrl":"https://doi.org/10.1101/2024.06.26.24309360","url":null,"abstract":"ThPOK is best known as a regulator of CD4+ T cell lineage commitment, although it was initially cloned as a suppressor of collagen expression in the skin. The role of ThPOK has not been formally established in humans since individuals with damaging variants in ThPOK have not yet been identified. Here, we report the first case of a human with a damaging heterozygous de novo variant in ThPOK causing a syndrome encompassing CD4+ T cell deficiency, allergy, fibroinflammatory interstitial lung disease, developmental delay, and growth failure. The patient variant, ThPOK K360N, exhibited abnormal multimorphic activity, including interfering with ThPOK WT in regulating gene regulation (antimorph). Protein-DNA interaction assays showed inability of ThPOK K360N to bind to wild-type consensus sequences (amorph) and revealed a novel DNA-binding specificity (neomorph). Single-cell RNA sequencing of peripheral blood revealed potential developmental defects in maturation and activation of CD4+ and CD8+ T cells (hypomorph). To establish causality, we recapitulated the observed cellular defects in lentivirally transduced healthy control T cells and pulmonary fibroblasts. Transcriptomic analysis showed that T cells transduced with ThPOK K360N lacked the upregulation of activation, proliferation, and functional pathways observed in ThPOKWT-transduced cells. When overexpressed in healthy control fibroblasts, ThPOK K360N significantly increased the expression of pro-fibrotic genes implicated in pulmonary fibrosis, indicating a defect in regulating collagen expression. This novel human disease caused by a multimorphic variant in ThPOK confirms its role in CD4+ T cell development in an intact human context, while also revealing an unanticipated role for ThPOK in T cell function and the regulation of fibrotic pathways in fibroblasts.","PeriodicalId":501527,"journal":{"name":"medRxiv - Allergy and Immunology","volume":"166 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141505411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-24DOI: 10.1101/2024.06.20.24309228
Emily Stephenson, Erin Macdonald-Dunlop, Lisa M Dratva, Rik G.H. Lindeboom, Zewen Kelvin Tuong, Win Min Tun, Norzawani B Buang, Stephane Ballereau, Mia Cabantaus, Ana Penalver, Elena Prigmore, John R Ferdinand, Benjamin J Stewart, Jack Gisby, Talat Malik, Candice L Clarke, Nicholas Medjeral-Thomas, Maria Prendecki, Stephen McAdoo, Anais Portet, Michelle Willicombe, Eleanor Sandhu, Matthew C Pickering, Marina Botto, Sarah A Teichmann, Muzlifah Haniffa, Menna R Clatworthy, David C Thomas, James E Peters
Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. We performed longitudinal single cell multi-omic immune profiling of ESKD patients with COVID-19, sampled during two waves of the pandemic. Uniquely, for a subset of patients, we obtained samples before and during acute infection, allowing intra-individual comparison. Using single-cell transcriptome, surface proteome and immunoreceptor sequencing of 580,040 high-quality cells, derived from 187 longitudinal samples from 61 patients, we demonstrate widespread changes following infection. We identified gene expression signatures of severity, with the majority of pathways differentiating mild from severe disease in B cells and monocytes. For example, gene expression of PLAC8, a receptor known to modulate SARS-CoV-2 entry to cells, was a marker of severity in CD14+ monocytes. Longitudinal profiling demonstrated distinct temporal molecular trajectories in severe versus mild disease, including type 1 and type 2 interferon signalling, MHC gene expression and, in B cells, a proliferative signature (KRAS and MYC). Evaluation of clonal T cell dynamics showed that the fastest expanding clones were significantly enriched in known SARS-CoV-2 specific sequences and shared across multiple patients. Our analyses revealed novel TCR clones likely reactive to SARS-CoV-2. Finally, we identified a population of transcriptionally distinct monocytes that emerged in peripheral blood following glucocorticoid treatment. Overall, our data delineate the temporal dynamics of the immune response in COVID-19 in a high-risk population and provide a valuable open-access resource.
{"title":"Temporal multi-omic analysis of COVID-19 in end-stage kidney disease","authors":"Emily Stephenson, Erin Macdonald-Dunlop, Lisa M Dratva, Rik G.H. Lindeboom, Zewen Kelvin Tuong, Win Min Tun, Norzawani B Buang, Stephane Ballereau, Mia Cabantaus, Ana Penalver, Elena Prigmore, John R Ferdinand, Benjamin J Stewart, Jack Gisby, Talat Malik, Candice L Clarke, Nicholas Medjeral-Thomas, Maria Prendecki, Stephen McAdoo, Anais Portet, Michelle Willicombe, Eleanor Sandhu, Matthew C Pickering, Marina Botto, Sarah A Teichmann, Muzlifah Haniffa, Menna R Clatworthy, David C Thomas, James E Peters","doi":"10.1101/2024.06.20.24309228","DOIUrl":"https://doi.org/10.1101/2024.06.20.24309228","url":null,"abstract":"Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. We performed longitudinal single cell multi-omic immune profiling of ESKD patients with COVID-19, sampled during two waves of the pandemic. Uniquely, for a subset of patients, we obtained samples before and during acute infection, allowing intra-individual comparison. Using single-cell transcriptome, surface proteome and immunoreceptor sequencing of 580,040 high-quality cells, derived from 187 longitudinal samples from 61 patients, we demonstrate widespread changes following infection. We identified gene expression signatures of severity, with the majority of pathways differentiating mild from severe disease in B cells and monocytes. For example, gene expression of PLAC8, a receptor known to modulate SARS-CoV-2 entry to cells, was a marker of severity in CD14+ monocytes. Longitudinal profiling demonstrated distinct temporal molecular trajectories in severe versus mild disease, including type 1 and type 2 interferon signalling, MHC gene expression and, in B cells, a proliferative signature (KRAS and MYC). Evaluation of clonal T cell dynamics showed that the fastest expanding clones were significantly enriched in known SARS-CoV-2 specific sequences and shared across multiple patients. Our analyses revealed novel TCR clones likely reactive to SARS-CoV-2. Finally, we identified a population of transcriptionally distinct monocytes that emerged in peripheral blood following glucocorticoid treatment. Overall, our data delineate the temporal dynamics of the immune response in COVID-19 in a high-risk population and provide a valuable open-access resource.","PeriodicalId":501527,"journal":{"name":"medRxiv - Allergy and Immunology","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141505380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-31DOI: 10.1101/2024.05.30.24308189
Jennifer G. Cox, James H. Cole, Matthew J. Kempton, Steven C. R. Williams, Marius de Groot
Brain white matter disruptions have been implicated in contributing to fatigue, brain fog and other central symptoms commonly reported in inflammatory diseases. In this study, we included 252 RA patients with 756 age and sex matched controls and 240 UC patients with 720 age and sex matched controls using the UK Biobank imaging dataset. We looked for differences in total volume of white matter hyperintensities (WMH) between patients compared to controls. Then, using voxelwise analysis, we explored the spatial distribution of these white matter hyperintensities and differences in these between patients and controls and between disease groups.
{"title":"Volume and Distribution of White Matter Hyperintensities in Rheumatoid Arthritis and Ulcerative Colitis Patients","authors":"Jennifer G. Cox, James H. Cole, Matthew J. Kempton, Steven C. R. Williams, Marius de Groot","doi":"10.1101/2024.05.30.24308189","DOIUrl":"https://doi.org/10.1101/2024.05.30.24308189","url":null,"abstract":"Brain white matter disruptions have been implicated in contributing to fatigue, brain fog and other central symptoms commonly reported in inflammatory diseases. In this study, we included 252 RA patients with 756 age and sex matched controls and 240 UC patients with 720 age and sex matched controls using the UK Biobank imaging dataset. We looked for differences in total volume of white matter hyperintensities (WMH) between patients compared to controls. Then, using voxelwise analysis, we explored the spatial distribution of these white matter hyperintensities and differences in these between patients and controls and between disease groups.","PeriodicalId":501527,"journal":{"name":"medRxiv - Allergy and Immunology","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141256833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-27DOI: 10.1101/2024.05.24.24307786
Shashika Dayarathna, Bhagya Senadheera, Chandima Jeewandara, Madushika Dissanayaka, Farha Bary, Graham S. Ogg, Gathsaurie Neelika Malavige
Background While dengue NS1 antigen has been shown to be associated with disease pathogenesis in some studies, it has not been linked in other studies, with the reasons remaining unclear. NS1 antigen levels in acute dengue are often associated with increased disease severity, but there have been a wide variation in results based on past dengue infection and infecting dengue virus (DENV) serotype. As NS1 engages with many host lipids, we hypothesize that the type of NS1-lipid interactions alters its pathogenicity.
{"title":"Dengue NS1 interaction with lipids alters its pathogenic effects on monocyte derived macrophages","authors":"Shashika Dayarathna, Bhagya Senadheera, Chandima Jeewandara, Madushika Dissanayaka, Farha Bary, Graham S. Ogg, Gathsaurie Neelika Malavige","doi":"10.1101/2024.05.24.24307786","DOIUrl":"https://doi.org/10.1101/2024.05.24.24307786","url":null,"abstract":"<strong>Background</strong> While dengue NS1 antigen has been shown to be associated with disease pathogenesis in some studies, it has not been linked in other studies, with the reasons remaining unclear. NS1 antigen levels in acute dengue are often associated with increased disease severity, but there have been a wide variation in results based on past dengue infection and infecting dengue virus (DENV) serotype. As NS1 engages with many host lipids, we hypothesize that the type of NS1-lipid interactions alters its pathogenicity.","PeriodicalId":501527,"journal":{"name":"medRxiv - Allergy and Immunology","volume":"73 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141171741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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