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Laghouaouta H, Laplana M, Ros-Freixedes R, Fraile LJ, Pena RN. Sequence variants associated with resilient responses in growing pigs. J Anim Breed Genet 2024. [PMID: 38967062 DOI: 10.1111/jbg.12886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024]
Abstract
The current work aimed to identify genomic regions and candidate genes associated with resilience in pigs. In previous work, we proposed the body weight deviation from the expected growth curve (ΔBW) and the increase of the positive acute-phase protein haptoglobin (ΔHP) after a vaccine challenge as resilience indicators which may be improved through selective breeding in pigs. Individuals with steady growth rate and minor activation of haptoglobin (high ΔBW and low ΔHP values) were considered resilient. In contrast, pigs with perturbed growth rate and high activation of haptoglobin (low ΔBW and high ΔHP values) were considered susceptible. Both ∆BW and ∆HP were simultaneously considered to select the most resilient (N = 40) and susceptible (N = 40) pigs. A genome-wide association study was carried out for the pigs' response classification to the challenge test using whole-genome sequence data (7,760,720 variants). Eleven associated genomic regions were identified, harbouring relevant candidate genes related to the immune response (such as pro- and anti-inflammatory responses) and growth pathways. These associated genomic regions harboured 41 potential functional mutations (frameshift, splice donor, splice acceptor, start loss and stop loss/gain) in candidate genes. Overall, this study advances our knowledge about the genetic determinism of resilience, highlighting its polygenic nature and strong relationship with immunity and growth.
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Affiliation(s)
- Houda Laghouaouta
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Marina Laplana
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Roger Ros-Freixedes
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Lorenzo J Fraile
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
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2
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Yang JC, Hsu TH, Chen CS, Yu JH, Lin KI, Chen YJ. Enhanced Proteomic Coverage in Tissue Microenvironment by Immune Cell Subtype Library-Assisted DIA-MS. Mol Cell Proteomics 2024; 23:100792. [PMID: 38810695 PMCID: PMC11260568 DOI: 10.1016/j.mcpro.2024.100792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/30/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024] Open
Abstract
Immune cells that infiltrate the tumor microenvironment (TME) play crucial roles in shaping cancer development and influencing clinical outcomes and therapeutic responses. However, obtaining a comprehensive proteomic snapshot of tumor-infiltrating immunity in clinical specimens is often hindered by small sample amounts and a low proportion of immune infiltrating cells in the TME. To enable in-depth and highly sensitive profiling of microscale tissues, we established an immune cell-enriched library-assisted strategy for data-independent acquisition mass spectrometry (DIA-MS). Firstly, six immune cell subtype-specific spectral libraries were established from sorted cluster of differentiation markers, CD8+, CD4+ T lymphocytes, B lymphocytes, natural killer cells, dendritic cells, and macrophages in murine mesenteric lymph nodes (MLNs), covering 7815 protein groups with surface markers and immune cell-enriched proteins. The feasibility of microscale immune proteomic profiling was demonstrated on 1 μg tissue protein from the tumor of murine colorectal cancer (CRC) models using single-shot DIA; the immune cell-enriched library increased coverage to quantify 7419 proteins compared to directDIA analysis (6978 proteins). The enhancement enabled the mapping of 841 immune function-related proteins and exclusive identification of many low-abundance immune proteins, such as CD1D1, and CD244, demonstrating high sensitivity for immune landscape profiling. This approach was used to characterize the MLNs in CRC models, aiming to elucidate the mechanism underlying their involvement in cancer development within the TME. Even with a low percentage of immune cell infiltration (0.25-3%) in the tumor, our results illuminate downregulation in the adaptive immune signaling pathways (such as C-type lectin receptor signaling, and chemokine signaling), T cell receptor signaling, and Th1/Th2/Th17 cell differentiation, suggesting an immunosuppressive status in MLNs of CRC model. The DIA approach using the immune cell-enriched libraries showcased deep coverage and high sensitivity that can facilitate illumination of the immune proteomic landscape for microscale samples.
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Affiliation(s)
- Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Tzi-Hui Hsu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Jou-Hui Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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3
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Nauffal V, Klarqvist MDR, Hill MC, Pace DF, Di Achille P, Choi SH, Rämö JT, Pirruccello JP, Singh P, Kany S, Hou C, Ng K, Philippakis AA, Batra P, Lubitz SA, Ellinor PT. Noninvasive assessment of organ-specific and shared pathways in multi-organ fibrosis using T1 mapping. Nat Med 2024; 30:1749-1760. [PMID: 38806679 DOI: 10.1038/s41591-024-03010-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/22/2024] [Indexed: 05/30/2024]
Abstract
Fibrotic diseases affect multiple organs and are associated with morbidity and mortality. To examine organ-specific and shared biologic mechanisms that underlie fibrosis in different organs, we developed machine learning models to quantify T1 time, a marker of interstitial fibrosis, in the liver, pancreas, heart and kidney among 43,881 UK Biobank participants who underwent magnetic resonance imaging. In phenome-wide association analyses, we demonstrate the association of increased organ-specific T1 time, reflecting increased interstitial fibrosis, with prevalent diseases across multiple organ systems. In genome-wide association analyses, we identified 27, 18, 11 and 10 independent genetic loci associated with liver, pancreas, myocardial and renal cortex T1 time, respectively. There was a modest genetic correlation between the examined organs. Several loci overlapped across the examined organs implicating genes involved in a myriad of biologic pathways including metal ion transport (SLC39A8, HFE and TMPRSS6), glucose metabolism (PCK2), blood group antigens (ABO and FUT2), immune function (BANK1 and PPP3CA), inflammation (NFKB1) and mitosis (CENPE). Finally, we found that an increasing number of organs with T1 time falling in the top quintile was associated with increased mortality in the population. Individuals with a high burden of fibrosis in ≥3 organs had a 3-fold increase in mortality compared to those with a low burden of fibrosis across all examined organs in multivariable-adjusted analysis (hazard ratio = 3.31, 95% confidence interval 1.77-6.19; P = 1.78 × 10-4). By leveraging machine learning to quantify T1 time across multiple organs at scale, we uncovered new organ-specific and shared biologic pathways underlying fibrosis that may provide therapeutic targets.
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Affiliation(s)
- Victor Nauffal
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew C Hill
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Danielle F Pace
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paolo Di Achille
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joel T Rämö
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James P Pirruccello
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
| | - Pulkit Singh
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shinwan Kany
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cardiology, University Heart and Vascular Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cody Hou
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenney Ng
- Center for Computational Health, IBM Research, Cambridge, MA, USA
| | - Anthony A Philippakis
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Puneet Batra
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven A Lubitz
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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4
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Chen Y, Liu P, Zhang Z, Ye Y, Yi S, Fan C, Zhao W, Liu J. Genetic overlap and causality between COVID-19 and multi-site chronic pain: the importance of immunity. Front Immunol 2024; 15:1277720. [PMID: 38633255 PMCID: PMC11022998 DOI: 10.3389/fimmu.2024.1277720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/13/2024] [Indexed: 04/19/2024] Open
Abstract
Background The existence of chronic pain increases susceptibility to virus and is now widely acknowledged as a prominent feature recognized as a major manifestation of long-term coronavirus disease 2019 (COVID-19) infection. Given the ongoing COVID-19 pandemic, it is imperative to explore the genetic associations between chronic pain and predisposition to COVID-19. Methods We conducted genetic analysis at the single nucleotide polymorphism (SNP), gene, and molecular levels using summary statistics of genome-wide association study (GWAS) and analyzed the drug targets by summary data-based Mendelian randomization analysis (SMR) to alleviate the multi-site chronic pain in COVID-19. Additionally, we performed a latent causal variable (LCV) method to investigate the causal relationship between chronic pain and susceptibility to COVID-19. Results The cross-trait meta-analysis identified 19 significant SNPs shared between COVID-19 and chronic pain. Coloc analysis indicated that the posterior probability of association (PPH4) for three loci was above 70% in both critical COVID-19 and COVID-19, with the corresponding top three SNPs being rs13135092, rs7588831, and rs13135092. A total of 482 significant overlapped genes were detected from MAGMA and CPASSOC results. Additionally, the gene ANAPC4 was identified as a potential drug target for treating chronic pain (P=7.66E-05) in COVID-19 (P=8.23E-03). Tissue enrichment analysis highlighted that the amygdala (P=7.81E-04) and prefrontal cortex (P=8.19E-05) as pivotal in regulating chronic pain of critical COVID-19. KEGG pathway enrichment further revealed the enrichment of pleiotropic genes in both COVID-19 (P=3.20E-03,Padjust=4.77E-02,hsa05171) and neurotrophic pathways (P=9.03E-04,Padjust =2.55E-02,hsa04621). Finally, the latent causal variable (LCV) model was applied to find the genetic component of critical COVID-19 was causal for multi-site chronic pain (P=0.015), with a genetic causality proportion (GCP) of was 0.60. Conclusions In this study, we identified several functional genes and underscored the pivotal role of the inflammatory system in the correlation between the paired traits. Notably, heat shock proteins emerged as potential objective biomarkers for chronic pain symptoms in individuals with COVID-19. Additionally, the ubiquitin system might play a role in mediating the impact of COVID-19 on chronic pain. These findings contribute to a more comprehensive understanding of the pleiotropy between COVID-19 and chronic pain, offering insights for therapeutic trials.
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Affiliation(s)
- Yanjing Chen
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Ping Liu
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhiyi Zhang
- Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yingling Ye
- Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Sijie Yi
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Chunhua Fan
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Zhao
- Clinical Research Center for Medical Imaging in Hunan Province, Changsha, Hunan, China
| | - Jun Liu
- Clinical Research Center for Medical Imaging in Hunan Province, Changsha, Hunan, China
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5
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van Eijck CWF, Sabroso-Lasa S, Strijk GJ, Mustafa DAM, Fellah A, Koerkamp BG, Malats N, van Eijck CHJ. A liquid biomarker signature of inflammatory proteins accurately predicts early pancreatic cancer progression during FOLFIRINOX chemotherapy. Neoplasia 2024; 49:100975. [PMID: 38335839 PMCID: PMC10873733 DOI: 10.1016/j.neo.2024.100975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is often treated with FOLFIRINOX, a chemotherapy associated with high toxicity rates and variable efficacy. Therefore, it is crucial to identify patients at risk of early progression during treatment. This study aims to explore the potential of a multi-omics biomarker for predicting early PDAC progression by employing an in-depth mathematical modeling approach. METHODS Blood samples were collected from 58 PDAC patients undergoing FOLFIRINOX before and after the first cycle. These samples underwent gene (GEP) and inflammatory protein expression profiling (IPEP). We explored the predictive potential of exclusively IPEP through Stepwise (Backward) Multivariate Logistic Regression modeling. Additionally, we integrated GEP and IPEP using Bayesian Kernel Regression modeling, aiming to enhance predictive performance. Ultimately, the FOLFIRINOX IPEP (FFX-IPEP) signature was developed. RESULTS Our findings revealed that proteins exhibited superior predictive accuracy than genes. Consequently, the FFX-IPEP signature consisted of six proteins: AMN, BANK1, IL1RL2, ITGB6, MYO9B, and PRSS8. The signature effectively identified patients transitioning from disease control to progression early during FOLFIRINOX, achieving remarkable predictive accuracy with an AUC of 0.89 in an independent test set. Importantly, the FFX-IPEP signature outperformed the conventional CA19-9 tumor marker. CONCLUSIONS Our six-protein FFX-IPEP signature holds solid potential as a liquid biomarker for the early prediction of PDAC progression during toxic FOLFIRINOX chemotherapy. Further validation in an external cohort is crucial to confirm the utility of the FFX-IPEP signature. Future studies should expand to predict progression under different chemotherapies to enhance the guidance of personalized treatment selection in PDAC.
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Affiliation(s)
- Casper W F van Eijck
- Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center, Madrid, Spain.
| | - Sergio Sabroso-Lasa
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center, Madrid, Spain; Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), Madrid, Spain
| | - Gaby J Strijk
- Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dana A M Mustafa
- Department of Clinical Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Amine Fellah
- Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bas Groot Koerkamp
- Department of Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center, Madrid, Spain; Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), Madrid, Spain
| | - Casper H J van Eijck
- Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center, Madrid, Spain.
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6
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Kortner TM, Afanasyev S, Koppang EO, Bjørgen H, Krogdahl Å, Krasnov A. A comprehensive transcriptional body map of Atlantic salmon unveils the vital role of the intestine in the immune system and highlights functional specialization within its compartments. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109422. [PMID: 38307300 DOI: 10.1016/j.fsi.2024.109422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/04/2024]
Abstract
The intestine is a barrier organ that plays an important role in the immune system of Atlantic salmon. The immune functions are distributed among the diffuse gut lymphoid tissue containing diverse immune cells, and other cell types. Comparison of intestinal transcriptomes with those of other organs and tissues offers an opportunity to elucidate the specific roles of the intestine and its relationship with other parts of the body. In this work, a meta-analysis was performed on a large volume of data obtained using a genome-wide DNA oligonucleotide microarray. The intestine ranks third by the expression level of immune genes after the spleen and head kidney. The activity of antigen presentation and innate antiviral immunity is higher in the intestine than in any other tissue. By comparing transcriptome profiles, intestine shows the greatest similarity with the gill, head kidney, spleen, epidermis, and olfactory rosette (descending order), which emphasizes the integrity of the peripheral mucosal system and its strong connections with the major lymphoid organs. T cells-specific genes dominate among the genes co-expressed in these tissues. The transcription signature of CD8+ (86 genes, r > 0.9) includes a master gene of immune tolerance foxp3 and other negative regulators. Different segments of the intestine were compared in a separate experiment, in which expression gradients along the intestine were found across several functional groups of genes. The expression of luminal and intracellular (lysosome) proteases is markedly higher in pyloric caeca and distal intestine respectively. Steroid metabolism and cytochromes P450 are highly expressed in pyloric caeca and mid intestine while the distal intestine harbors genes related to vitamin and iron metabolism. The expression of genes for antigen presenting proteins and immunoglobulins shows a gradual increase towards the distal intestine.
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Affiliation(s)
- Trond M Kortner
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Ås, Norway.
| | - Sergey Afanasyev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
| | - Erling Olaf Koppang
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Ås, Norway
| | - Håvard Bjørgen
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Ås, Norway
| | - Åshild Krogdahl
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Ås, Norway
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Carvalho NRG, He Y, Smadbeck P, Flannick J, Mercader JM, Udler M, Manrai AK, Moreno J, Patel CJ. Assessing the genetic contribution of cumulative behavioral factors associated with longitudinal type 2 diabetes risk highlights adiposity and the brain-metabolic axis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.30.24302019. [PMID: 38352440 PMCID: PMC10863013 DOI: 10.1101/2024.01.30.24302019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
While genetic factors, behavior, and environmental exposures form a complex web of interrelated associations in type 2 diabetes (T2D), their interaction is poorly understood. Here, using data from ~500K participants of the UK Biobank, we identify the genetic determinants of a "polyexposure risk score" (PXS) a new risk factor that consists of an accumulation of 25 associated individual-level behaviors and environmental risk factors that predict longitudinal T2D incidence. PXS-T2D had a non-zero heritability (h2 = 0.18) extensive shared genetic architecture with established clinical and biological determinants of T2D, most prominently with body mass index (genetic correlation [rg] = 0.57) and Homeostatic Model Assessment for Insulin Resistance (rg = 0.51). Genetic loci associated with PXS-T2D were enriched for expression in the brain. Biobank scale data with genetic information illuminates how complex and cumulative exposures and behaviors as a whole impact T2D risk but whose biology have been elusive in genome-wide studies of T2D.
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Affiliation(s)
- Nuno R. G. Carvalho
- School of Biological Sciences; Georgia Institute of Technology; Atlanta, GA, 30332, USA
| | - Yixuan He
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Boston, MA, 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Patrick Smadbeck
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Boston, MA, 02142, USA
| | - Jason Flannick
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Josep M. Mercader
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Boston, MA, 02142, USA
| | - Miriam Udler
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Boston, MA, 02142, USA
| | - Arjun K Manrai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jordi Moreno
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Boston, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
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Lochs SJA, van der Weide RH, de Luca KL, Korthout T, van Beek RE, Kimura H, Kind J. Combinatorial single-cell profiling of major chromatin types with MAbID. Nat Methods 2024; 21:72-82. [PMID: 38049699 PMCID: PMC10776404 DOI: 10.1038/s41592-023-02090-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/17/2023] [Indexed: 12/06/2023]
Abstract
Gene expression programs result from the collective activity of numerous regulatory factors. Studying their cooperative mode of action is imperative to understand gene regulation, but simultaneously measuring these factors within one sample has been challenging. Here we introduce Multiplexing Antibodies by barcode Identification (MAbID), a method for combinatorial genomic profiling of histone modifications and chromatin-binding proteins. MAbID employs antibody-DNA conjugates to integrate barcodes at the genomic location of the epitope, enabling combined incubation of multiple antibodies to reveal the distributions of many epigenetic markers simultaneously. We used MAbID to profile major chromatin types and multiplexed measurements without loss of individual data quality. Moreover, we obtained joint measurements of six epitopes in single cells of mouse bone marrow and during mouse in vitro differentiation, capturing associated changes in multifactorial chromatin states. Thus, MAbID holds the potential to gain unique insights into the interplay between gene regulatory mechanisms, especially for low-input samples and in single cells.
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Affiliation(s)
- Silke J A Lochs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Robin H van der Weide
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Kim L de Luca
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Tessy Korthout
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ramada E van Beek
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Jop Kind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands.
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9
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Wright M, Smed MK, Nelson JL, Olsen J, Hetland ML, Jewell NP, Zoffmann V, Jawaheer D. Pre-pregnancy gene expression signatures are associated with subsequent improvement/worsening of rheumatoid arthritis during pregnancy. Arthritis Res Ther 2023; 25:191. [PMID: 37794420 PMCID: PMC10548620 DOI: 10.1186/s13075-023-03169-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND While many women with rheumatoid arthritis (RA) improve during pregnancy and others worsen, there are no biomarkers to predict this improvement or worsening. In our unique RA pregnancy cohort that includes a pre-pregnancy baseline, we have examined pre-pregnancy gene co-expression networks to identify differences between women with RA who subsequently improve during pregnancy and those who worsen. METHODS Blood samples were collected before pregnancy (T0) from 19 women with RA and 13 healthy women enrolled in our prospective pregnancy cohort. RA improvement/worsening between T0 and 3rd trimester was assessed by changes in the Clinical Disease Activity Index (CDAI). Pre-pregnancy expression profiles were examined by RNA sequencing and differential gene expression analysis. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules correlated with the improvement/worsening of RA during pregnancy and to assess their functional relevance. RESULTS Of the 19 women with RA, 14 improved during pregnancy (RAimproved) while 5 worsened (RAworsened). At the T0 baseline, however, the mean CDAI was similar between the two groups. WGCNA identified one co-expression module related to B cell function that was significantly correlated with the worsening of RA during pregnancy and was significantly enriched in genes differentially expressed between the RAimproved and RAworsened groups. A neutrophil-related expression signature was also identified in the RAimproved group at the T0 baseline. CONCLUSION The pre-pregnancy gene expression signatures identified represent potential biomarkers to predict the subsequent improvement/worsening of RA during pregnancy, which has important implications for the personalized treatment of RA during pregnancy.
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Affiliation(s)
- Matthew Wright
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | | | - J Lee Nelson
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Jørn Olsen
- University of California Los Angeles, Los Angeles, CA, USA
- Aarhus University Hospital, Aarhus, Denmark
| | - Merete Lund Hetland
- DANBIO Registry and Copenhagen Centre for Arthritis Research, Centre for Rheumatology and Spine Diseases, Rigshospitalet, Glostrup, Denmark
- University of Copenhagen, Copenhagen, Denmark
| | | | - Vibeke Zoffmann
- Juliane Marie Centeret, Rigshospitalet, Copenhagen, Denmark
- University of Copenhagen, Copenhagen, Denmark
| | - Damini Jawaheer
- Children's Hospital Oakland Research Institute, Oakland, CA, USA.
- Division of Rheumatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
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10
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Carruthers NJ, Guo C, Gill R, Stemmer PM, Rosenspire AJ. Mercury intoxication disrupts tonic signaling in B cells, and may promote autoimmunity due to abnormal phosphorylation of STIM-1 and other autoimmunity risk associated phosphoproteins involved in BCR signaling. Toxicol Appl Pharmacol 2023; 474:116607. [PMID: 37348680 PMCID: PMC10534200 DOI: 10.1016/j.taap.2023.116607] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
Epidemiological studies link exposure to mercury with autoimmune disease. Unfortunately, in spite of considerable effort, no generally accepted mechanistic understanding of how mercury functions with respect to the etiology of autoimmune disease is currently available. Nevertheless, autoimmune disease often arises because of defective B cell signaling. Because B cell signaling is dependent on phosphorylation cascades, in this report, we have focused on how mercury intoxication alters phosphorylation of B cell proteins in antigen-non stimulated (tonic) mouse (BALB/c) splenic B cells. Specifically, we utilized mass spectrometric techniques to conduct a comprehensive unbiased global analysis of the effect of inorganic mercury (Hg2+) on the entire B cell phosphoproteome. We found that the effects were pleotropic in the sense that large numbers of pathways were impacted. However, confirming our earlier work, we found that the B cell signaling pathway stood out from the rest, in that phosphoproteins which had sites which were affected by Hg2+, exhibited a much higher degree of connectivity, than components of other pathways. Further analysis showed that many of these BCR pathway proteins had been previously linked to autoimmune disease. Finally, dose response analysis of these BCR pathway proteins showed STIM1_S575, and NFAT2_S259 are the two most Hg2+ sensitive of these sites. Because STIM1_S575 controls the ability of STIM1 to regulate internal Ca2+, we speculate that STIM1 may be the initial point of disruption, where Hg2+ interferes with B cell signaling leading to systemic autoimmunity, with the molecular effects pleiotropically propagated throughout the cell by virtue of Ca2+ dysregulation.
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Affiliation(s)
- N J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - C Guo
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States of America
| | - R Gill
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States of America
| | - P M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - A J Rosenspire
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States of America.
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11
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Huang SUS, Kulatunge O, O'Sullivan KM. Deciphering the Genetic Code of Autoimmune Kidney Diseases. Genes (Basel) 2023; 14:genes14051028. [PMID: 37239388 DOI: 10.3390/genes14051028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Autoimmune kidney diseases occur due to the loss of tolerance to self-antigens, resulting in inflammation and pathological damage to the kidneys. This review focuses on the known genetic associations of the major autoimmune kidney diseases that result in the development of glomerulonephritis: lupus nephritis (LN), anti-neutrophil cytoplasmic associated vasculitis (AAV), anti-glomerular basement disease (also known as Goodpasture's disease), IgA nephropathy (IgAN), and membranous nephritis (MN). Genetic associations with an increased risk of disease are not only associated with polymorphisms in the human leukocyte antigen (HLA) II region, which governs underlying processes in the development of autoimmunity, but are also associated with genes regulating inflammation, such as NFkB, IRF4, and FC γ receptors (FCGR). Critical genome-wide association studies are discussed both to reveal similarities in gene polymorphisms between autoimmune kidney diseases and to explicate differential risks in different ethnicities. Lastly, we review the role of neutrophil extracellular traps, critical inducers of inflammation in LN, AAV, and anti-GBM disease, where inefficient clearance due to polymorphisms in DNase I and genes that regulate neutrophil extracellular trap production are associated with autoimmune kidney diseases.
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Affiliation(s)
- Stephanie U-Shane Huang
- Department of Medicine, Centre for Inflammatory Diseases, Monash University, Clayton, VIC 3168, Australia
| | - Oneli Kulatunge
- Department of Medicine, Centre for Inflammatory Diseases, Monash University, Clayton, VIC 3168, Australia
| | - Kim Maree O'Sullivan
- Department of Medicine, Centre for Inflammatory Diseases, Monash University, Clayton, VIC 3168, Australia
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12
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Zeng X, Wang W, Zhang D, Li X, Zhang Y, Zhao Y, Zhao L, Wang J, Xu D, Cheng J, Li W, Zhou B, Lin C, Yang X, Zhai R, Ma Z, Liu J, Cui P, Weng X, Wu W, Zhang X, Zheng W. Expression of the Ovine Gene and the Relationship Between Its Polymorphism and Feed Efficiency Traits. DNA Cell Biol 2023; 42:194-202. [PMID: 36827437 DOI: 10.1089/dna.2022.0529] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
In the mutton industry, feed efficiency traits have the greatest influence on the economic benefits of sheep raised in housing conditions. In this study, quantitative real-time PCR (qRT-PCR), Sanger sequencing, and KASPar methods were used to detect the expression levels of the B cell scaffold protein with ankyrin repeats 1 (BANK1) gene and the relationship between its polymorphism and feed efficiency traits in Hu sheep. The qRT-PCR results showed that the BANK1 gene was extensively expressed in 10 tissues and it was expressed at remarkably higher levels in lymph than in other tissues (p < 0.05). Then, the polymorphism locus, g.93888 A > T, was detected in intron 4 of the BANK1 gene and proved to be remarkably associated with feed efficiency traits (p < 0.05). Hence, the BANK1 gene can be used as a candidate gene for improving the feed efficiency of Hu sheep and this locus could be used as a potential molecular marker for breeding high-feed efficiency sheep in future breeding efforts.
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Affiliation(s)
- Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,The State Key Laboratory of Grassland Agroecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agroecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- The State Key Laboratory of Grassland Agroecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agroecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiuxiu Weng
- The State Key Laboratory of Grassland Agroecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Science, Urumqi, China
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13
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Hendriks RW, Corneth OBJ. B Cell Signaling and Activation in Autoimmunity. Cells 2023; 12:cells12030499. [PMID: 36766841 PMCID: PMC9914404 DOI: 10.3390/cells12030499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Autoreactive B cells play a key role in the initiation or aggravation of many systemic and tissue-specific autoimmune disorders [...].
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14
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Zhang S, Li P, Wu P, Yang L, Liu X, Liu J, Zhang Y, Zeng J. Predictors of response of rituximab in rheumatoid arthritis by weighted gene co-expression network analysis. Clin Rheumatol 2023; 42:529-538. [PMID: 36374432 DOI: 10.1007/s10067-022-06438-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/14/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE The purpose of this study was to identify a biomarker that can predict the efficacy of rituximab (RTX) in the treatment of rheumatoid arthritis (RA) patients. METHODS Utilized weighted gene co-expression network analysis (WGCNA) and LASSO regression analysis of whole blood transcriptome data (GSE15316 and GSE37107) related to RTX treatment for RA from the GEO database, the critical modules, and key genes related to the efficacy of RTX treatment for RA were found. The biological functions were further explored through enrichment analysis. The area under the ROC curve (AUC) was validated using the GSE54629 dataset. RESULTS WGCNA screened 71 genes for a dark turquoise module that were correlated with the efficacy of RTX treatment for RA (r = 0.42, P < 0.05). Through the calculation of gene significance (GS) and module membership (MM), 12 important genes were identified; in addition, 21 important genes were screened by the LASSO regression model; two key genes were obtained from the intersection between the important genes. Then, BANK1 (AUC = 0.704, P < 0.05) was identified as a potential biomarker to predict the efficacy of RTX treatment for RA by ROC curve evaluation of the treatment and validation groups. BANK1 gene expression was significantly decreased after RTX treatment, and a statistically significant difference was found (log FC = - 2.08, P < 0.05). Immune cell infiltration analysis revealed that the infiltration of CD4 + T cell memory subset was increased in the group with high BANK1 expression, and a statistically significant difference was found (P < 0.05). CONCLUSIONS BANK1 can be used as a potential biomarker to predict the response of RTX treatment in RA patients. Key Points • Identifying the hub genes BANK1 as a potential biomarker to predict the response of RTX treatment in RA patients and confirming it in validation data. • Using the WGCNA approach and LASSO analyses to identify the BANK1 in a data set consisting of two GEO data merged and assessing the correlations between BANK1 and immune infiltration by CIBERSORT algorithm.
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Affiliation(s)
- Shan Zhang
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Peiting Li
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Pengjia Wu
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Lei Yang
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Xiaoxia Liu
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Jun Liu
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Yong Zhang
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Jiashun Zeng
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China.
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15
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He J, Chen K, Sui Y, Yang Q. Effects of N-methyl-D-aspartate receptor knockdown and hypoxia/reoxygenation injury on the neuronal proteome and transcriptome. Front Mol Neurosci 2022; 15:1004375. [PMID: 36590918 PMCID: PMC9799235 DOI: 10.3389/fnmol.2022.1004375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Brain tissue is extremely sensitive to hypoxia/reoxygenation (H/R) injury, which can easily cause irreversible damage to neurons. H/R injury can induce neuronal apoptosis through glutamate-mediated excitotoxicity. N-methyl-d-aspartate receptor (NMDAR) is one of the main receptors of excitatory glutamate, and blocking NMDAR protects brain tissue from ischemic and hypoxic injury. However, NMDAR hypofunction can also cause psychotic symptoms or cognitive impairment. There is still a lack of systematic research on the changes in the proteome and transcriptome in neuronal cells under conditions of NMDAR hypofunction and H/R injury. Methods We compared the changes in the proteome, transcriptome and lncRNA expression levels in neurons after NMDAR knockdown and H/R by isobaric tags for relative and absolute quantitation (iTRAQ) and RNA sequencing (RNA-Seq). Results The results showed that the proteins Rps9, Rpl18 and Rpl15 and the lncRNAs XLOC_161072 and XLOC_065271 were significantly downregulated after NMDAR knockdown but upregulated after H/R; in contrast, the mRNAs Bank1 and Pcp4l1 and the lncRNAs XLOC_159404 and XLOC_031922 were significantly upregulated after NMDAR knockdown but downregulated after H/R. Discussion In this study, we demonstrated the characterization of protein, mRNA, and lncRNA expression profiles in neurons following NMDAR knockdown and H/R injury. These molecules are involved in multiple biological functions and signaling pathways, and their roles in neurons lacking NMDAR and subjected to H/R injury deserve further study. Additionally, we found that lncRNAs respond fastest to hypoxic stimulation and that Gapdh is not suitable as a reference protein for NMDAR-reduced neuron-related experiments.
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Affiliation(s)
- Jinting He
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Kaili Chen
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yujie Sui
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, Medical Research Center, Second Hospital of Jilin University, Changchun, Jilin, China
| | - Qiwei Yang
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, Medical Research Center, Second Hospital of Jilin University, Changchun, Jilin, China,*Correspondence: Qiwei Yang,
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16
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Corneth OBJ, Neys SFH, Hendriks RW. Aberrant B Cell Signaling in Autoimmune Diseases. Cells 2022; 11:cells11213391. [PMID: 36359789 PMCID: PMC9654300 DOI: 10.3390/cells11213391] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/15/2022] [Accepted: 10/24/2022] [Indexed: 11/30/2022] Open
Abstract
Aberrant B cell signaling plays a critical in role in various systemic and organ-specific autoimmune diseases. This is supported by genetic evidence by many functional studies in B cells from patients or specific animal models and by the observed efficacy of small-molecule inhibitors. In this review, we first discuss key signal transduction pathways downstream of the B cell receptor (BCR) that ensure that autoreactive B cells are removed from the repertoire or functionally silenced. We provide an overview of aberrant BCR signaling that is associated with inappropriate B cell repertoire selection and activation or survival of peripheral B cell populations and plasma cells, finally leading to autoantibody formation. Next to BCR signaling, abnormalities in other signal transduction pathways have been implicated in autoimmune disease. These include reduced activity of several phosphates that are downstream of co-inhibitory receptors on B cells and increased levels of BAFF and APRIL, which support survival of B cells and plasma cells. Importantly, pathogenic synergy of the BCR and Toll-like receptors (TLR), which can be activated by endogenous ligands, such as self-nucleic acids, has been shown to enhance autoimmunity. Finally, we will briefly discuss therapeutic strategies for autoimmune disease based on interfering with signal transduction in B cells.
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17
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Chen Y, Wu C, Wang X, Zhou X, Kang K, Cao Z, Yang Y, Zhong Y, Xiao G. Weighted gene co-expression network analysis identifies dysregulated B-cell receptor signaling pathway and novel genes in pulmonary arterial hypertension. Front Cardiovasc Med 2022; 9:909399. [PMID: 36277750 PMCID: PMC9583267 DOI: 10.3389/fcvm.2022.909399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022] Open
Abstract
Background Pulmonary arterial hypertension (PAH) is a devastating cardio-pulmonary vascular disease in which chronic elevated pulmonary arterial pressure and pulmonary vascular remodeling lead to right ventricular failure and premature death. However, the exact molecular mechanism causing PAH remains unclear. Methods RNA sequencing was used to analyze the transcriptional profiling of controls and rats treated with monocrotaline (MCT) for 1, 2, 3, and 4 weeks. Weighted gene co-expression network analysis (WGCNA) was employed to identify the key modules associated with the severity of PAH. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the potential biological processes and pathways of key modules. Real-time PCR and western blot analysis were used to validate the gene expression. The hub genes were validated by an independent dataset obtained from the Gene Expression Omnibus database. Results A total of 26 gene modules were identified by WGCNA. Of these modules, two modules showed the highest correlation with the severity of PAH and were recognized as the key modules. GO analysis of key modules showed the dysregulated inflammation and immunity, particularly B-cell-mediated humoral immunity in MCT-induced PAH. KEGG pathway analysis showed the significant enrichment of the B-cell receptor signaling pathway in the key modules. Pathview analysis revealed the dysregulation of the B-cell receptor signaling pathway in detail. Moreover, a series of humoral immune response-associated genes, such as BTK, BAFFR, and TNFSF4, were found to be differentially expressed in PAH. Additionally, five genes, including BANK1, FOXF1, TLE1, CLEC4A1, and CLEC4A3, were identified and validated as the hub genes. Conclusion This study identified the dysregulated B-cell receptor signaling pathway, as well as novel genes associated with humoral immune response in MCT-induced PAH, thereby providing a novel insight into the molecular mechanisms underlying inflammation and immunity and therapeutic targets for PAH.
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Affiliation(s)
- Yuanrong Chen
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, China
| | - Chaoling Wu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, China
| | - Xiaoping Wang
- Department of Cardiology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xufeng Zhou
- Department of Cardiology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Kunpeng Kang
- Department of Cardiology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Zuofeng Cao
- Department of Cardiology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yihong Yang
- Department of Cardiology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yiming Zhong
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, China,Department of Cardiology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China,Gannan Branch Center of National Geriatric Disease Clinical Medical Research Center, Gannan Medical University, Ganzhou, China,*Correspondence: Yiming Zhong
| | - Genfa Xiao
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, China,Department of Cardiology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China,Gannan Branch Center of National Geriatric Disease Clinical Medical Research Center, Gannan Medical University, Ganzhou, China,Genfa Xiao
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18
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Wang Z, Yang S, Koga Y, Corbett SE, Shea C, Johnson W, Yajima M, Campbell JD. Celda: a Bayesian model to perform co-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data. NAR Genom Bioinform 2022; 4:lqac066. [PMID: 36110899 PMCID: PMC9469931 DOI: 10.1093/nargab/lqac066] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 08/09/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Single-cell RNA-seq (scRNA-seq) has emerged as a powerful technique to quantify gene expression in individual cells and to elucidate the molecular and cellular building blocks of complex tissues. We developed a novel Bayesian hierarchical model called Cellular Latent Dirichlet Allocation (Celda) to perform co-clustering of genes into transcriptional modules and cells into subpopulations. Celda can quantify the probabilistic contribution of each gene to each module, each module to each cell population and each cell population to each sample. In a peripheral blood mononuclear cell dataset, Celda identified a subpopulation of proliferating T cells and a plasma cell which were missed by two other common single-cell workflows. Celda also identified transcriptional modules that could be used to characterize unique and shared biological programs across cell types. Finally, Celda outperformed other approaches for clustering genes into modules on simulated data. Celda presents a novel method for characterizing transcriptional programs and cellular heterogeneity in scRNA-seq data.
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Affiliation(s)
- Zhe Wang
- Bioinformatics Program, Boston University, Boston, MA, USA
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Shiyi Yang
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Yusuke Koga
- Bioinformatics Program, Boston University, Boston, MA, USA
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Sean E Corbett
- Bioinformatics Program, Boston University, Boston, MA, USA
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Conor V Shea
- Bioinformatics Program, Boston University, Boston, MA, USA
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - W Evan Johnson
- Bioinformatics Program, Boston University, Boston, MA, USA
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Masanao Yajima
- Department of Mathematics and Statistics, Boston University, Boston, MA, USA
| | - Joshua D Campbell
- Bioinformatics Program, Boston University, Boston, MA, USA
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
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19
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Ortíz-Fernández L, Martín J, Alarcón-Riquelme ME. A Summary on the Genetics of Systemic Lupus Erythematosus, Rheumatoid Arthritis, Systemic Sclerosis, and Sjögren's Syndrome. Clin Rev Allergy Immunol 2022; 64:392-411. [PMID: 35749015 DOI: 10.1007/s12016-022-08951-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2022] [Indexed: 11/03/2022]
Abstract
Systemic lupus erythematosus, systemic sclerosis, rheumatoid arthritis, and Sjögren's syndrome are four major autoimmune rheumatic diseases characterized by the presence of autoantibodies, caused by a dysregulation of the immune system that leads to a wide variety of clinical manifestations. These conditions present complex etiologies strongly influenced by multiple environmental and genetic factors. The human leukocyte antigen (HLA) region was the first locus identified to be associated and still represents the strongest susceptibility factor for each of these conditions, particularly the HLA class II genes, including DQA1, DQB1, and DRB1, but class I genes have also been associated. Over the last two decades, the genetic component of these disorders has been extensively investigated and hundreds of non-HLA risk genetic variants have been uncovered. Furthermore, it is widely accepted that autoimmune rheumatic diseases share molecular disease pathways, such as the interferon (IFN) type I pathways, which are reflected in a common genetic background. Some examples of well-known pleiotropic loci for autoimmune rheumatic diseases are the HLA region, DNASEL13, TNIP1, and IRF5, among others. The identification of the causal molecular mechanisms behind the genetic associations is still a challenge. However, recent advances have been achieved through mouse models and functional studies of the loci. Here, we provide an updated overview of the genetic architecture underlying these four autoimmune rheumatic diseases, with a special focus on the HLA region.
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Affiliation(s)
- Lourdes Ortíz-Fernández
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Parque Tecnológico de La Salud, 18016, Granada, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Parque Tecnológico de La Salud, 18016, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO. Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av de la Ilustración 114, Parque Tecnológico de La Salud, 18016, Granada, Spain. .,Institute for Environmental Medicine, Karolinska Institutet, 171 77, Solna, Sweden.
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20
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Montaño JL, Wang BJ, Volk RF, Warrington SE, Garda VG, Hofmann KL, Chen LC, Zaro BW. Improved Electrophile Design for Exquisite Covalent Molecule Selectivity. ACS Chem Biol 2022; 17:1440-1449. [PMID: 35587148 DOI: 10.1021/acschembio.1c00980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Covalent inhibitors are viable therapeutics. However, off-target reactivity challenges the field. Chemists have attempted to solve this issue by varying the reactivity attributes of electrophilic warheads. Here, we report the development of an approach to increase the selectivity of covalent molecules that is independent of warhead reactivity features and can be used in concert with existing methods. Using the scaffold of the Bruton's tyrosine kinase (BTK) inhibitor Ibrutinib for our proof-of-concept, we reasoned that increasing the steric bulk of fumarate-based electrophiles on Ibrutinib should improve selectivity via the steric exclusion of off-targets but retain rates of cysteine reactivity comparable to that of an acrylamide. Using chemical proteomic techniques, we demonstrate that elaboration of the electrophile to a tert-butyl (t-Bu) fumarate ester decreases time-dependent off-target reactivity and abolishes time-independent off-target reactivity. While an alkyne-bearing probe analogue of Ibrutinib has 247 protein targets, our t-Bu fumarate probe analogue has only 7. Of these 7 targets, BTK is the only time-independent target. The t-Bu inhibitor itself is also more selective for BTK, reducing off-targets by 70%. We investigated the consequences of treatment with Ibrutinib and our t-Bu analogue and discovered that only 8 proteins are downregulated in response to treatment with the t-Bu analogue compared to 107 with Ibrutinib. Of these 8 proteins, 7 are also downregulated by Ibrutinib and a majority of these targets are associated with BTK biology. Taken together, these findings reveal an opportunity to increase cysteine-reactive covalent inhibitor selectivity through electrophilic structure optimization.
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Affiliation(s)
- José L. Montaño
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Brian J. Wang
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Regan F. Volk
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Sara E. Warrington
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Virginia G. Garda
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Katherine L. Hofmann
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Leo C. Chen
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Balyn W. Zaro
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
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21
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Zhong J, Mao X, Li H, Shen G, Cao X, He N, Wang J, Xu L, Chen J, Song X, Liu S, Zhang X, Shen Y, Wang LL, Xiang C, Chen YY. Single-cell RNA sequencing analysis reveals the relationship of bone marrow and osteopenia in STZ-induced type 1 diabetic mice. J Adv Res 2022; 41:145-158. [PMID: 36328744 PMCID: PMC9637485 DOI: 10.1016/j.jare.2022.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/30/2021] [Accepted: 01/14/2022] [Indexed: 11/30/2022] Open
Abstract
scRNA-seq analysis reveals the profiles of bone marrow cells in STZ-induced T1D mice. scRNA-seq analysis reveals the heterogeneity of bone marrow immune cells in STZ-induced T1D mice. The ratio of BM-neutrophils to B lymphocytes is increased in the bone marrow of STZ-induced T1D mice. Osteopenia is occurred in STZ-induced T1D mice. This increased ratio is negatively correlated with osteopenia in STZ-induced T1D mice.
Introduction Type 1 diabetes (T1D) is a multifactorial autoimmune disease. Broad knowledge about the genetics, epidemiology and clinical management of T1D has been achieved, but understandings about the cell varieties in the bone marrow during T1D remain limited. Objectives We aimed to present a profile of the bone marrow cells and reveal the relationship of bone marrow and osteopenia in streptozotocin (STZ)-induced T1D mice. Methods The whole bone marrow cells from the femurs and tibias of healthy (group C) and STZ-induced T1D mice (group D) were collected for single-cell RNA sequencing analysis. Single-cell flow cytometry and immunohistochemistry were performed to confirm the proportional changes among bone marrow neutrophils (BM-neutrophils) (Cxcr2+, Ly6g+) and B lymphocytes (Cd19+). X-ray and micro-CT were performed to detect bone mineral density. The correlation between the ratio of BM-neutrophils/B lymphocytes and osteopenia in STZ-induced T1D mice was analyzed by nonparametric Spearman correlation analysis. Results The bone marrow cells in groups C and D were divided into 12 clusters, and 249 differentially expressed genes were found. The diversity of CD45+ immune cells between groups C and D were greatly affected: the proportion of BM-neutrophils showed a significant increase while the proportion of B lymphocytes in group D showed a significant decrease. X-ray and micro-CT analyses confirmed that osteopenia occurred in group D mice. In addition, the results of single-cell flow cytometry and correlation analysis showed that the ratio of BM-neutrophils/B lymphocytes negatively correlated with osteopenia in STZ-induced T1D mice. Conclusion A single-cell RNA sequencing analysis revealed the profile and heterogeneity of bone marrow immune cells in STZ-induced T1D mice for the first time. The ratio of BM-neutrophils/B lymphocytes negatively correlated with osteopenia in STZ-induced T1D mice, which may enhance understanding for treating T1D and preventing T1D-induced osteopenia.
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Affiliation(s)
- Jinjie Zhong
- Department of Basic Medicine Sciences, and Department of Obstetrics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xingjia Mao
- Department of Orthopedic, The Second Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Heyangzi Li
- Department of Basic Medicine Sciences, and Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Gerong Shen
- Department of Basic Medicine Sciences, and Department of Orthopaedics of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xi Cao
- Department of Basic Medicine Sciences, and Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ning He
- Department of Basic Medicine Sciences, and Department of Orthopaedics of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jingyu Wang
- Department of Neurosurgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Lintao Xu
- Department of Neurosurgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Jun Chen
- Department of Basic Medicine Sciences, and Department of Obstetrics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xinghui Song
- Core Facilities, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shuangshuang Liu
- Core Facilities, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaoming Zhang
- Department of Basic Medicine Sciences, and Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yueliang Shen
- Department of Basic Medicine Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lin-Lin Wang
- Department of Basic Medicine Sciences, and Department of Orthopaedics of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Chuan Xiang
- Department of Orthopedic, The Second Hospital of Shanxi Medical University, Taiyuan 030001, China.
| | - Ying-Ying Chen
- Department of Basic Medicine Sciences, and Department of Obstetrics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
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22
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The Immunogenetics of Systemic Sclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:259-298. [DOI: 10.1007/978-3-030-92616-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Satterthwaite AB. TLR7 Signaling in Lupus B Cells: New Insights into Synergizing Factors and Downstream Signals. Curr Rheumatol Rep 2021; 23:80. [PMID: 34817709 DOI: 10.1007/s11926-021-01047-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 12/19/2022]
Abstract
PURPOSE OF THE REVIEW Systemic lupus erythematosus (SLE) is driven by nucleic acid-containing antigens that stimulate endosomal TLRs. We review new advances in our understanding of how TLR7 signaling in B cells drives autoimmunity. RECENT FINDINGS Pathogenic B cell responses to TLR7 engagement are shaped by the disease-associated cytokine environment. TLR7, IFNγ, and IL-21 together promote the formation of autoreactive germinal centers and the ABC/DN2 B cell subset. BAFF and type 1 IFNs enhance autoantibody production from transitional B cells in concert with TLR7. TLR7 signaling components STAT1, BANK1, IRF5, SLC15A4, and CXorf21/TASL are associated genetically with SLE and important for lupus development in mice, while role of T-bet is controversial. Proper control of TLR7 trafficking by UNC93B1, syntenin-1, and αvβ3 integrin is critical for preventing autoimmunity. A better understanding of TLR7 signaling has revealed potential new therapeutic approaches for SLE, several of which are being tested in animal models or clinical trials.
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Affiliation(s)
- Anne B Satterthwaite
- Department of Internal Medicine, Rheumatic Diseases Division and Department of Immunology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8884, USA.
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