1
|
Sparks R, Rachmaninoff N, Lau WW, Hirsch DC, Bansal N, Martins AJ, Chen J, Liu CC, Cheung F, Failla LE, Biancotto A, Fantoni G, Sellers BA, Chawla DG, Howe KN, Mostaghimi D, Farmer R, Kotliarov Y, Calvo KR, Palmer C, Daub J, Foruraghi L, Kreuzburg S, Treat JD, Urban AK, Jones A, Romeo T, Deuitch NT, Moura NS, Weinstein B, Moir S, Ferrucci L, Barron KS, Aksentijevich I, Kleinstein SH, Townsley DM, Young NS, Frischmeyer-Guerrerio PA, Uzel G, Pinto-Patarroyo GP, Cudrici CD, Hoffmann P, Stone DL, Ombrello AK, Freeman AF, Zerbe CS, Kastner DL, Holland SM, Tsang JS. A unified metric of human immune health. Nat Med 2024:10.1038/s41591-024-03092-6. [PMID: 38961223 DOI: 10.1038/s41591-024-03092-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/28/2024] [Indexed: 07/05/2024]
Abstract
Immunological health has been challenging to characterize but could be defined as the absence of immune pathology. While shared features of some immune diseases and the concept of immunologic resilience based on age-independent adaptation to antigenic stimulation have been developed, general metrics of immune health and its utility for assessing clinically healthy individuals remain ill defined. Here we integrated transcriptomics, serum protein, peripheral immune cell frequency and clinical data from 228 patients with 22 monogenic conditions impacting key immunological pathways together with 42 age- and sex-matched healthy controls. Despite the high penetrance of monogenic lesions, differences between individuals in diverse immune parameters tended to dominate over those attributable to disease conditions or medication use. Unsupervised or supervised machine learning independently identified a score that distinguished healthy participants from patients with monogenic diseases, thus suggesting a quantitative immune health metric (IHM). In ten independent datasets, the IHM discriminated healthy from polygenic autoimmune and inflammatory disease states, marked aging in clinically healthy individuals, tracked disease activities and treatment responses in both immunological and nonimmunological diseases, and predicted age-dependent antibody responses to immunizations with different vaccines. This discriminatory power goes beyond that of the classical inflammatory biomarkers C-reactive protein and interleukin-6. Thus, deviations from health in diverse conditions, including aging, have shared systemic immune consequences, and we provide a web platform for calculating the IHM for other datasets, which could empower precision medicine.
Collapse
Grants
- 1ZIAAI001152 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 1ZIAAI001152 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 1ZIAAI001152 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 1ZIAAI001152 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 1ZIAAI001152 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 1ZIAAI001152 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 1ZIAAI001152 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 1ZIAAI001152 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 1ZIAAI001152 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 1ZIAAI001152 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- Z01 AI000825-24 LIR Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 1 ZIA AI001202-07 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- Z-01-A-00646 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- Z-01-A-00647 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- Z-01-A-00646 Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- 5R01AI170116 U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
- U19AI089992 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- U19AI089992 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- ZIA-HL006089-12 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- 1ZIAHG200371 U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)
- 1ZIAHG200373 U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)
- 1ZIAHG200374 U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)
Collapse
Affiliation(s)
- Rachel Sparks
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Nicholas Rachmaninoff
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- Graduate Program in Biological Sciences, University of Maryland, College Park, MD, USA
| | - William W Lau
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Dylan C Hirsch
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, Inflammation, and Autoimmunity, NIAID, NIH, Bethesda, MD, USA
| | - Candace C Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, Inflammation, and Autoimmunity, NIAID, NIH, Bethesda, MD, USA
| | - Laura E Failla
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Angelique Biancotto
- NIH Center for Human Immunology, Inflammation, and Autoimmunity, NIAID, NIH, Bethesda, MD, USA
| | - Giovanna Fantoni
- NIH Center for Human Immunology, Inflammation, and Autoimmunity, NIAID, NIH, Bethesda, MD, USA
| | - Brian A Sellers
- NIH Center for Human Immunology, Inflammation, and Autoimmunity, NIAID, NIH, Bethesda, MD, USA
| | - Daniel G Chawla
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Katherine N Howe
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Darius Mostaghimi
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Rohit Farmer
- NIH Center for Human Immunology, Inflammation, and Autoimmunity, NIAID, NIH, Bethesda, MD, USA
| | - Yuri Kotliarov
- NIH Center for Human Immunology, Inflammation, and Autoimmunity, NIAID, NIH, Bethesda, MD, USA
| | - Katherine R Calvo
- Hematology Section, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, MD, USA
| | - Cindy Palmer
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Janine Daub
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Ladan Foruraghi
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Samantha Kreuzburg
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Jennifer D Treat
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Amanda K Urban
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anne Jones
- Inflammatory Disease Section, NHGRI, NIH, Bethesda, MD, USA
| | - Tina Romeo
- Inflammatory Disease Section, NHGRI, NIH, Bethesda, MD, USA
| | | | | | | | - Susan Moir
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, NIA, Baltimore, MD, USA
| | - Karyl S Barron
- Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | | | - Steven H Kleinstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Neal S Young
- Hematology Branch, NHLBI, NIH, Bethesda, MD, USA
| | | | - Gulbu Uzel
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | | | | | | | | | | | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Christa S Zerbe
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | | | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
- NIH Center for Human Immunology, Inflammation, and Autoimmunity, NIAID, NIH, Bethesda, MD, USA.
- Center for Systems and Engineering Immunology, Departments of Immunobiology and Biomedical Engineering, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
2
|
Fogel A, Olcer M, Goel A, Feng X, Reder AT. Novel biomarkers and interferon signature in secondary progressive multiple sclerosis. J Neuroimmunol 2024; 389:578328. [PMID: 38471284 DOI: 10.1016/j.jneuroim.2024.578328] [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: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Multiple sclerosis (MS) exhibits poor immune regulation and subnormal interferon (IFN-β) signaling. Secondary Progressive MS displays waning exacerbations, relentless neurodegeneration, and diminished benefit of therapy. We find dysregulated serum protein balance (Th1/Th2) and excessive gene expression in Relapsing-Remitting MS vs. healthy controls (8700 differentially-expressed genes, DEG) and intermediate levels in SPMS (3900 DEG). Olfactory receptor genes (chemosensing), and WNT/ß-catenin (anti-inflammatory, repair) and metallothionein (anti-oxidant) gene pathways, have less expression in SPMS than RRMS. IFN-β treatment decreased pro-inflammatory and increased metallothionein gene expression in SPMS. These gene expression biomarkers suggest new targets for immune regulation and brain repair in this neurodegenerative disease.
Collapse
Affiliation(s)
- Avital Fogel
- Department of Neurology, University of Chicago, Chicago, IL 60637, USA
| | - Maya Olcer
- Department of Neurology, University of Chicago, Chicago, IL 60637, USA
| | - Aika Goel
- Department of Neurology, University of Chicago, Chicago, IL 60637, USA
| | - Xuan Feng
- Department of Neurology, University of Chicago, Chicago, IL 60637, USA.
| | - Anthony T Reder
- Department of Neurology, University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
3
|
Tripathi N, Saraf P, Bhardwaj N, Shrivastava SK, Jain SK. Identifying inflammation-related targets of natural lactones using network pharmacology, molecular modeling and in vitro approaches. J Biomol Struct Dyn 2024:1-16. [PMID: 38334283 DOI: 10.1080/07391102.2024.2310783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/20/2024] [Indexed: 02/10/2024]
Abstract
Natural lactones have been used in traditional and folklore medicine for centuries owing to their anti-inflammatory properties. The study uses a multifaceted approach to identify lead anti-inflammatory lactones from the SISTEMATX natural products database. The study analyzed the natural lactone database, revealing 18 lactones linked to inflammation targets. The primary targets were PTGES, PTGS1, COX-2, ALOX5 and IL1B. STX 12273 was the best hit, with the lowest binding energy and potential for inhibiting the COX-2 enzyme. The study suggested natural lactone, STX 12273, from the SISTEMATX database with anti-inflammatory potential and postulated its use for inflammation treatment or prevention.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Nancy Tripathi
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Poorvi Saraf
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Nivedita Bhardwaj
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Sushant Kumar Shrivastava
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Shreyans K Jain
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| |
Collapse
|
4
|
Gu Y, Tang J, Zhang H, Wu Q, Luo L, Sun J. MicroRNA-125b mediates Interferon-γ-induced downregulation of the vitamin D receptor in systemic lupus erythematosus. Z Rheumatol 2024; 83:132-139. [PMID: 36732450 PMCID: PMC9894746 DOI: 10.1007/s00393-023-01319-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2023] [Indexed: 02/04/2023]
Abstract
BACKGROUND The inflammatory factor interferon (IFN)-γ is related to the occurrence and development of systemic lupus erythematosus (SLE). The vitamin D receptor (VDR) has an anti-inflammatory effect and its downregulation is involved in the onset of SLE. Our previous studies have confirmed that the expression of VDR in SLE peripheral blood mononuclear cells (PBMCs) is downregulated, which is negatively correlated with disease activity and inflammation. However, the mechanism underlying VDR downregulation in SLE is unknown. METHODS Based on the results of computer simulation analysis, the expression of VDR and four microRNAs (miR-17-3p, miR-34a, miR-346, and miR-125b) in SLE PBMC cells was analyzed under proinflammatory cytokine IFN‑γ treatment, and miR-125b was identified as the target miRNA. The relationship between IFN‑γ, miR-125b, and VDR was further assessed in THP‑1 cells. RESULTS We showed that IFN‑γ inhibited the expression of VDR and miR-125b. Further study revealed that VDR mRNA was positively correlated with miR-125b in THP‑1 cells after IFN‑γ intervention. After transfection of miR-125b mimic or inhibitor, the expression of VDR in the miR-125b inhibitor group was lower than in the control group and miR-125b mimic group, while expression in the control group was lower than in miR-125b mimic group. Transfection of miR-125b inhibitor into THP‑1 cells could further promote the ability of IFN‑γ to inhibit VDR. CONCLUSION The decrease in VDR expression promotes development of inflammation and SLE. These data suggest that miR-125b may mediate inflammatory factor IFN-γ-induced downregulation of VDR in the pathogenesis of SLE.
Collapse
Affiliation(s)
- Yihong Gu
- Department of Nephrology and Rheumatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Juan Tang
- Department of Nephrology and Rheumatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Zhang
- Department of Nephrology and Rheumatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Qiongying Wu
- Department of Nephrology and Rheumatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Linjuan Luo
- Department of Nephrology and Rheumatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Jian Sun
- Department of Nephrology and Rheumatology, Third Xiangya Hospital, Central South University, Changsha, China.
| |
Collapse
|
5
|
Kim G, Chun H. Similarity-assisted variational autoencoder for nonlinear dimension reduction with application to single-cell RNA sequencing data. BMC Bioinformatics 2023; 24:432. [PMID: 37964243 PMCID: PMC10647110 DOI: 10.1186/s12859-023-05552-1] [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: 03/21/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Deep generative models naturally become nonlinear dimension reduction tools to visualize large-scale datasets such as single-cell RNA sequencing datasets for revealing latent grouping patterns or identifying outliers. The variational autoencoder (VAE) is a popular deep generative method equipped with encoder/decoder structures. The encoder and decoder are useful when a new sample is mapped to the latent space and a data point is generated from a point in a latent space. However, the VAE tends not to show grouping pattern clearly without additional annotation information. On the other hand, similarity-based dimension reduction methods such as t-SNE or UMAP present clear grouping patterns even though these methods do not have encoder/decoder structures. RESULTS To bridge this gap, we propose a new approach that adopts similarity information in the VAE framework. In addition, for biological applications, we extend our approach to a conditional VAE to account for covariate effects in the dimension reduction step. In the simulation study and real single-cell RNA sequencing data analyses, our method shows great performance compared to existing state-of-the-art methods by producing clear grouping structures using an inferred encoder and decoder. Our method also successfully adjusts for covariate effects, resulting in more useful dimension reduction. CONCLUSIONS Our method is able to produce clearer grouping patterns than those of other regularized VAE methods by utilizing similarity information encoded in the data via the highly celebrated UMAP loss function.
Collapse
Affiliation(s)
- Gwangwoo Kim
- Graduate School of Data Science, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hyonho Chun
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
| |
Collapse
|
6
|
Zheng J, Wang Y, Fang X, Hu J. Exploration of common genomic signatures of systemic juvenile rheumatoid arthritis and type 1 diabetes. Sci Rep 2023; 13:15121. [PMID: 37704687 PMCID: PMC10500015 DOI: 10.1038/s41598-023-42209-8] [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: 05/04/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
To explore the genetic characteristics of systemic juvenile rheumatoid arthritis (sJRA) and type 1 diabetes mellitus (T1D). The microarray data of sJRA and T1D from Gene Expression Omnibus (GEO) were analyzed. The shared differentially expressed genes (SDEGs) were identified by the Meta-analysis, and genes of extracellular proteins were identified. Then, transcription factors (TFs) and their target genes in SDEGs were obtained by comparing databases from HumanTFDB, and hTFtarget. After that, functional enrichment analyses of the previously identified gene sets were performed by metascape tool. Finally, immune infiltration was analysed by CIBERSORT. We found 175 up-regulated and 245 down-regulated SDEGs, and by constructing a TFs-targeted SDEGs network, 3 key TFs (ARID3A, NEF2, RUNX3) were screened. Functional enrichment analyses and immune infiltration results suggested not only the adaptive immune system but also the innate immune system, and signaling pathways like JAK-STAT are important in the pathogenesis of sJRA and T1D, involving biological processes such as CD4 T cell functions and neutrophil degranulation. This work suggests that innate immune abnormalities also play important roles in sJRA and T1D, CD4 T cell functions, neutrophil degranulation and the JAK-STAT pathway may be involved. The regulatory roles of ARID3A, NEF2, and RUNX3 in this network need to be further investigated.
Collapse
Affiliation(s)
- Jie Zheng
- Department of Pediatric, FuJian Medical University Union Hospital, Fuzhou, 350001, China
| | - Yong Wang
- Department of Pediatric, FuJian Medical University Union Hospital, Fuzhou, 350001, China
| | - Xin Fang
- Department of Pediatric, FuJian Medical University Union Hospital, Fuzhou, 350001, China
| | - Jun Hu
- Department of Pediatric, FuJian Medical University Union Hospital, Fuzhou, 350001, China.
| |
Collapse
|
7
|
Fenton KA, Pedersen HL. Advanced methods and novel biomarkers in autoimmune diseases ‑ a review of the recent years progress in systemic lupus erythematosus. Front Med (Lausanne) 2023; 10:1183535. [PMID: 37425332 PMCID: PMC10326284 DOI: 10.3389/fmed.2023.1183535] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
There are several autoimmune and rheumatic diseases affecting different organs of the human body. Multiple sclerosis (MS) mainly affects brain, rheumatoid arthritis (RA) mainly affects joints, Type 1 diabetes (T1D) mainly affects pancreas, Sjogren's syndrome (SS) mainly affects salivary glands, while systemic lupus erythematosus (SLE) affects almost every organ of the body. Autoimmune diseases are characterized by production of autoantibodies, activation of immune cells, increased expression of pro-inflammatory cytokines, and activation of type I interferons. Despite improvements in treatments and diagnostic tools, the time it takes for the patients to be diagnosed is too long, and the main treatment for these diseases is still non-specific anti-inflammatory drugs. Thus, there is an urgent need for better biomarkers, as well as tailored, personalized treatment. This review focus on SLE and the organs affected in this disease. We have used the results from various rheumatic and autoimmune diseases and the organs involved with an aim to identify advanced methods and possible biomarkers to be utilized in the diagnosis of SLE, disease monitoring, and response to treatment.
Collapse
Affiliation(s)
- Kristin Andreassen Fenton
- UiT The Arctic University of Norway, Tromsø, Norway
- Centre of Clinical Research and Education, University Hospital of North Norway, Tromsø, Norway
| | - Hege Lynum Pedersen
- UiT The Arctic University of Norway, Tromsø, Norway
- Centre of Clinical Research and Education, University Hospital of North Norway, Tromsø, Norway
| |
Collapse
|
8
|
Jordan AA, Higgins PD. The role of upadacitinib in the treatment of ulcerative colitis. Immunotherapy 2023. [PMID: 37129377 DOI: 10.2217/imt-2022-0299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
The JAK signaling pathway plays a major role in the immunopathology of autoimmune diseases, including inflammatory bowel disease. JAK enzymes provide novel targets for rapidly effective inflammatory bowel disease therapy, particularly in ulcerative colitis. Upadacitinib is a targeted JAK1 inhibitor. In multiple phase III clinical trials, upadacitinib has demonstrated significant improvement in clinical and endoscopic outcomes and quality of life for patients with moderate-to-severe ulcerative colitis. In this drug evaluation we describe the role of the JAK signaling pathway in ulcerative colitis, the mechanism of action of upadacitinib and the current clinical evidence for its use in ulcerative colitis; we also review its safety and tolerability, including for special populations.
Collapse
Affiliation(s)
- Ariel A Jordan
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Dr Higgins
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Division of Gastroenterology & Hepatology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
9
|
Mulcahy V, Liaskou E, Martin JE, Kotagiri P, Badrock J, Jones RL, Rushbrook SM, Ryder SD, Thorburn D, Taylor-Robinson SD, Clark G, Cordell HJ, Sandford RN, Jones DE, Hirschfield GM, Mells GF. Regulation of immune responses in primary biliary cholangitis: a transcriptomic analysis of peripheral immune cells. Hepatol Commun 2023; 7:e0110. [PMID: 37026715 PMCID: PMC10079354 DOI: 10.1097/hc9.0000000000000110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/21/2022] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND AIMS In patients with primary biliary cholangitis (PBC), the serum liver biochemistry measured during treatment with ursodeoxycholic acid-the UDCA response-accurately predicts long-term outcome. Molecular characterization of patients stratified by UDCA response can improve biological understanding of the high-risk disease, thereby helping to identify alternative approaches to disease-modifying therapy. In this study, we sought to characterize the immunobiology of the UDCA response using transcriptional profiling of peripheral blood mononuclear cell subsets. METHODS We performed bulk RNA-sequencing of monocytes and TH1, TH17, TREG, and B cells isolated from the peripheral blood of 15 PBC patients with adequate UDCA response ("responders"), 16 PBC patients with inadequate UDCA response ("nonresponders"), and 15 matched controls. We used the Weighted Gene Co-expression Network Analysis to identify networks of co-expressed genes ("modules") associated with response status and the most highly connected genes ("hub genes") within them. Finally, we performed a Multi-Omics Factor Analysis of the Weighted Gene Co-expression Network Analysis modules to identify the principal axes of biological variation ("latent factors") across all peripheral blood mononuclear cell subsets. RESULTS Using the Weighted Gene Co-expression Network Analysis, we identified modules associated with response and/or disease status (q<0.05) in each peripheral blood mononuclear cell subset. Hub genes and functional annotations suggested that monocytes are proinflammatory in nonresponders, but antiinflammatory in responders; TH1 and TH17 cells are activated in all PBC cases but better regulated in responders; and TREG cells are activated-but also kept in check-in responders. Using the Multi-Omics Factor Analysis, we found that antiinflammatory activity in monocytes, regulation of TH1 cells, and activation of TREG cells are interrelated and more prominent in responders. CONCLUSIONS We provide evidence that adaptive immune responses are better regulated in patients with PBC with adequate UDCA response.
Collapse
Affiliation(s)
- Victoria Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Evaggelia Liaskou
- Centre for Liver and Gastrointestinal Research, National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre (BRC), University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, UK
- Institute of Immunology & Immunotherapy, University of Birmingham, Birmingham, UK
| | - Jose-Ezequiel Martin
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
- Cancer Molecular Diagnostic Laboratory, Oncology Department, University of Cambridge, Cambridge, UK
| | - Prasanti Kotagiri
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jonathan Badrock
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Rebecca L. Jones
- Leeds Liver Unit, The Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Simon M Rushbrook
- Department of Hepatology, Norwich Medical School, University of East Anglia, Norwich, UK
| | - Stephen D. Ryder
- NIHR Nottingham BRC, Nottingham University Hospitals NHS Trust, University of Nottingham, Nottingham, UK
| | - Douglas Thorburn
- The Sheila Sherlock Liver Centre, Royal Free London NHS Foundation Trust, London, UK
| | | | - Graeme Clark
- Stratified Medicine Core Laboratory (SMCL) Next Generation Sequencing Hub, NIHR Cambridge BRC, Cambridge, UK
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Richard N. Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - David E. Jones
- Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, UK
- NIHR Newcastle BRC, Newcastle University, Newcastle-upon-Tyne, UK
| | - Gideon M. Hirschfield
- Toronto Centre for Liver Disease, University Health Network and Department of Medicine, University of Toronto, Toronto, Canada
| | - George F. Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| |
Collapse
|
10
|
Tyagi N, Mehla K, Gupta D. Deciphering novel common gene signatures for rheumatoid arthritis and systemic lupus erythematosus by integrative analysis of transcriptomic profiles. PLoS One 2023; 18:e0281637. [PMID: 36928613 PMCID: PMC10019710 DOI: 10.1371/journal.pone.0281637] [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: 10/31/2022] [Accepted: 01/24/2023] [Indexed: 03/18/2023] Open
Abstract
Rheumatoid Arthritis (RA) and Systemic Lupus Erythematosus (SLE) are the two highly prevalent debilitating and sometimes life-threatening systemic inflammatory autoimmune diseases. The etiology and pathogenesis of RA and SLE are interconnected in several ways, with limited knowledge about the underlying molecular mechanisms. With the motivation to better understand shared biological mechanisms and determine novel therapeutic targets, we explored common molecular disease signatures by performing a meta-analysis of publicly available microarray gene expression datasets of RA and SLE. We performed an integrated, multi-cohort analysis of 1088 transcriptomic profiles from 14 independent studies to identify common gene signatures. We identified sixty-two genes common among RA and SLE, out of which fifty-nine genes (21 upregulated and 38 downregulated) had similar expression profiles in the diseases. However, antagonistic expression profiles were observed for ACVR2A, FAM135A, and MAPRE1 genes. Thirty genes common between RA and SLE were proposed as robust gene signatures, with persistent expression in all the studies and cell types. These gene signatures were found to be involved in innate as well as adaptive immune responses, bone development and growth. In conclusion, our analysis of multicohort and multiple microarray datasets would provide the basis for understanding the common mechanisms of pathogenesis and exploring these gene signatures for their diagnostic and therapeutic potential.
Collapse
Affiliation(s)
- Neetu Tyagi
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Kusum Mehla
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| |
Collapse
|
11
|
Lin P, Yan Y, Huang SY. DeepHomo2.0: improved protein-protein contact prediction of homodimers by transformer-enhanced deep learning. Brief Bioinform 2023; 24:6849483. [PMID: 36440949 DOI: 10.1093/bib/bbac499] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/08/2022] [Accepted: 10/21/2022] [Indexed: 11/30/2022] Open
Abstract
Protein-protein interactions play an important role in many biological processes. However, although structure prediction for monomer proteins has achieved great progress with the advent of advanced deep learning algorithms like AlphaFold, the structure prediction for protein-protein complexes remains an open question. Taking advantage of the Transformer model of ESM-MSA, we have developed a deep learning-based model, named DeepHomo2.0, to predict protein-protein interactions of homodimeric complexes by leveraging the direct-coupling analysis (DCA) and Transformer features of sequences and the structure features of monomers. DeepHomo2.0 was extensively evaluated on diverse test sets and compared with eight state-of-the-art methods including protein language model-based, DCA-based and machine learning-based methods. It was shown that DeepHomo2.0 achieved a high precision of >70% with experimental monomer structures and >60% with predicted monomer structures for the top 10 predicted contacts on the test sets and outperformed the other eight methods. Moreover, even the version without using structure information, named DeepHomoSeq, still achieved a good precision of >55% for the top 10 predicted contacts. Integrating the predicted contacts into protein docking significantly improved the structure prediction of realistic Critical Assessment of Protein Structure Prediction homodimeric complexes. DeepHomo2.0 and DeepHomoSeq are available at http://huanglab.phys.hust.edu.cn/DeepHomo2/.
Collapse
Affiliation(s)
- Peicong Lin
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Yumeng Yan
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| |
Collapse
|
12
|
Jahanbani F, Maynard RD, Sing JC, Jahanbani S, Perrino JJ, Spacek DV, Davis RW, Snyder MP. Phenotypic characteristics of peripheral immune cells of Myalgic encephalomyelitis/chronic fatigue syndrome via transmission electron microscopy: A pilot study. PLoS One 2022; 17:e0272703. [PMID: 35943990 PMCID: PMC9362953 DOI: 10.1371/journal.pone.0272703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/25/2022] [Indexed: 01/06/2023] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex chronic multi-systemic disease characterized by extreme fatigue that is not improved by rest, and worsens after exertion, whether physical or mental. Previous studies have shown ME/CFS-associated alterations in the immune system and mitochondria. We used transmission electron microscopy (TEM) to investigate the morphology and ultrastructure of unstimulated and stimulated ME/CFS immune cells and their intracellular organelles, including mitochondria. PBMCs from four participants were studied: a pair of identical twins discordant for moderate ME/CFS, as well as two age- and gender- matched unrelated subjects-one with an extremely severe form of ME/CFS and the other healthy. TEM analysis of CD3/CD28-stimulated T cells suggested a significant increase in the levels of apoptotic and necrotic cell death in T cells from ME/CFS patients (over 2-fold). Stimulated Tcells of ME/CFS patients also had higher numbers of swollen mitochondria. We also found a large increase in intracellular giant lipid droplet-like organelles in the stimulated PBMCs from the extremely severe ME/CFS patient potentially indicative of a lipid storage disorder. Lastly, we observed a slight increase in platelet aggregation in stimulated cells, suggestive of a possible role of platelet activity in ME/CFS pathophysiology and disease severity. These results indicate extensive morphological alterations in the cellular and mitochondrial phenotypes of ME/CFS patients' immune cells and suggest new insights into ME/CFS biology.
Collapse
Affiliation(s)
- Fereshteh Jahanbani
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rajan D. Maynard
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Justin Cyril Sing
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shaghayegh Jahanbani
- Division of Immunology and Rheumatology, Stanford University School of Medicine, and VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - John J. Perrino
- Stanford Cell Sciences Imaging Facility (CSIF), Stanford University School of Medicine Stanford, Stanford, California, United States of America
| | - Damek V. Spacek
- Karius Incorporated, Redwood City, California, United States of America
| | - Ronald W. Davis
- ME/CFS Collaborative Research Center at Stanford, Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| |
Collapse
|
13
|
Hayat R, Manzoor M, Hussain A. Wnt Signaling Pathway: A Comprehensive Review. Cell Biol Int 2022; 46:863-877. [PMID: 35297539 DOI: 10.1002/cbin.11797] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/10/2022] [Accepted: 03/07/2022] [Indexed: 11/09/2022]
Abstract
Wnt signaling is an evolutionary cell-to-cell coordination mechanism and it is highly critical for a variety of physiological processes of an organism's body, including stem cell regeneration, proliferation, division, migration, polarity of a cell, determining fate of the cell and specification of neural crest, neural symmetry and morphogenesis. Wnts are extracellular secreted glycol proteins, consisted of a family of 19 human proteins that represent the complex nature of the regulatory structure and physiological efficiency of signaling. Moreover, a Wnt/β-catenin-dependent pathway and the β-catenin-independent pathway that is further classified into the Planar Cell Polarity and Wnt/Ca2+ pathways have been established as key signaling nodes downstream of the frizzled (Fz/Fzd) receptor, and these nodes are extensively analyzed at biochemical and molecular levels. Genetic and epigenetic activities that ultimately characterize the pathway and its subsequent responses contribute to Wnt-β-catenin signaling pathway hypo or hyper-activation and is associated with the variety of human disorders progression most significantly cancers. Recognizing how this mechanism operates is crucial to the advancement of cancer prevention therapies or regenerative medicine methods. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Rabia Hayat
- Institute of Evolution and Marine Biodiversity, Ocean university of China, Qingdao
| | - Maleeha Manzoor
- Department of Zoology, Government College University, Faisalabad
| | - Ali Hussain
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore
| |
Collapse
|
14
|
Santos AS, Cunha-Neto E, Gonfinetti NV, Bertonha FB, Brochet P, Bergon A, Moreira-Filho CA, Chevillard C, da Silva MER. Prevalence of Inflammatory Pathways Over Immuno-Tolerance in Peripheral Blood Mononuclear Cells of Recent-Onset Type 1 Diabetes. Front Immunol 2022; 12:765264. [PMID: 35058920 PMCID: PMC8764313 DOI: 10.3389/fimmu.2021.765264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
Background Changes in innate and adaptive immunity occurring in/around pancreatic islets had been observed in peripheral blood mononuclear cells (PBMC) of Caucasian T1D patients by some, but not all researchers. The aim of our study was to investigate whether gene expression patterns of PBMC of the highly admixed Brazilian population could add knowledge about T1D pathogenic mechanisms. Methods We assessed global gene expression in PBMC from two groups matched for age, sex and BMI: 20 patients with recent-onset T1D (≤ 6 months from diagnosis, in a time when the autoimmune process is still highly active), testing positive for one or more islet autoantibodies and 20 islet autoantibody-negative healthy controls. Results We identified 474 differentially expressed genes between groups. The most expressed genes in T1D group favored host defense, inflammatory and anti-bacterial/antiviral effects (LFT, DEFA4, DEFA1, CTSG, KCNMA1) and cell cycle progression. Several of the downregulated genes in T1D target cellular repair, control of inflammation and immune tolerance. They were related to T helper 2 pathway, induction of FOXP3 expression (AREG) and immune tolerance (SMAD6). SMAD6 expression correlated negatively with islet ZnT8 antibody. The expression of PDE12, that offers resistance to viral pathogens was decreased and negatively related to ZnT8A and GADA levels. The increased expression of long non coding RNAs MALAT1 and NEAT1, related to inflammatory mediators, autoimmune diseases and innate immune response against viral infections reinforced these data. Conclusions Our analysis suggested the activation of cell development, anti-infectious and inflammatory pathways, indicating immune activation, whereas immune-regulatory pathways were downregulated in PBMC from recent-onset T1D patients with a differential genetic profile.
Collapse
Affiliation(s)
- Aritania Sousa Santos
- Laboratorio de Carboidratos e Radioimunoensaios LIM 18, Faculdade de Medicina, University of Sao Paulo Hospital of Clinics, São Paulo, Brazil
| | - Edécio Cunha-Neto
- Laboratory of Immunology, Heart Institute, School of Medicine, University of São Paulo, São Paulo, Brazil
| | | | | | - Pauline Brochet
- Aix Marseille Université, Inserm, TAGC Theories and Approaches of Genomic Complexity, INSERM, UMR_1090, Marseille, France
| | - Aurelie Bergon
- Aix Marseille Université, Inserm, TAGC Theories and Approaches of Genomic Complexity, INSERM, UMR_1090, Marseille, France
| | | | - Christophe Chevillard
- Aix Marseille Université, Inserm, TAGC Theories and Approaches of Genomic Complexity, INSERM, UMR_1090, Marseille, France
| | - Maria Elizabeth Rossi da Silva
- Laboratorio de Carboidratos e Radioimunoensaios LIM 18, Faculdade de Medicina, University of Sao Paulo Hospital of Clinics, São Paulo, Brazil
| |
Collapse
|
15
|
Pathogenic TNF-α drives peripheral nerve inflammation in an Aire-deficient model of autoimmunity. Proc Natl Acad Sci U S A 2022; 119:2114406119. [PMID: 35058362 PMCID: PMC8795502 DOI: 10.1073/pnas.2114406119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 01/19/2023] Open
Abstract
Immune cells infiltrate the peripheral nervous system (PNS) after injury and with autoimmunity, but their net effect is divergent. After injury, immune cells are reparative, while in inflammatory neuropathies (e.g., Guillain Barré Syndrome and chronic inflammatory demyelinating polyneuropathy), immune cells are proinflammatory and promote autoimmune demyelination. An understanding of immune cell phenotypes that distinguish these conditions may, therefore, reveal new therapeutic targets for switching immune cells from an inflammatory role to a reparative state. In an autoimmune regulator (Aire)-deficient mouse model of inflammatory neuropathy, we used single-cell RNA sequencing of sciatic nerves to discover a transcriptionally heterogeneous cellular landscape, including multiple myeloid, innate lymphoid, and lymphoid cell types. Analysis of cell-cell ligand-receptor interactions uncovered a macrophage-mediated tumor necrosis factor-α (TNF-α) signaling axis that is induced by interferon-γ and required for initiation of autoimmune demyelination. Developmental trajectory visualization suggested that TNF-α signaling is associated with metabolic reprogramming of macrophages and polarization of macrophages from a reparative state in injury to a pathogenic, inflammatory state in autoimmunity. Autocrine TNF-α signaling induced macrophage expression of multiple genes (Clec4e, Marcksl1, Cxcl1, and Cxcl10) important in immune cell activation and recruitment. Genetic and antibody-based blockade of TNF-α/TNF-α signaling ameliorated clinical neuropathy, peripheral nerve infiltration, and demyelination, which provides preclinical evidence that the TNF-α axis may be effectively targeted to resolve inflammatory neuropathies.
Collapse
|
16
|
Lai HC, Ho UY, James A, De Souza P, Roberts TL. RNA metabolism and links to inflammatory regulation and disease. Cell Mol Life Sci 2021; 79:21. [PMID: 34971439 PMCID: PMC11072290 DOI: 10.1007/s00018-021-04073-5] [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: 01/13/2021] [Revised: 09/29/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022]
Abstract
Inflammation is vital to protect the host against foreign organism invasion and cellular damage. It requires tight and concise gene expression for regulation of pro- and anti-inflammatory gene expression in immune cells. Dysregulated immune responses caused by gene mutations and errors in post-transcriptional regulation can lead to chronic inflammatory diseases and cancer. The mechanisms underlying post-transcriptional gene expression regulation include mRNA splicing, mRNA export, mRNA localisation, mRNA stability, RNA/protein interaction, and post-translational events such as protein stability and modification. The majority of studies to date have focused on transcriptional control pathways. However, post-transcriptional regulation of mRNA in eukaryotes is equally important and related information is lacking. In this review, we will focus on the mechanisms involved in the pre-mRNA splicing events, mRNA surveillance, RNA degradation pathways, disorders or symptoms caused by mutations or errors in post-transcriptional regulation during innate immunity especially toll-like receptor mediated pathways.
Collapse
Affiliation(s)
- Hui-Chi Lai
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia.
- South West Sydney Clinical School, UNSW Australia, Liverpool, NSW, Australia.
| | - Uda Y Ho
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Alexander James
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Paul De Souza
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- School of Medicine, Western Sydney University, Macarthur, NSW, Australia
| | - Tara L Roberts
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- South West Sydney Clinical School, UNSW Australia, Liverpool, NSW, Australia
- School of Medicine, Western Sydney University, Macarthur, NSW, Australia
| |
Collapse
|
17
|
Louadi Z, Elkjaer ML, Klug M, Lio CT, Fenn A, Illes Z, Bongiovanni D, Baumbach J, Kacprowski T, List M, Tsoy O. Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. Genome Biol 2021; 22:327. [PMID: 34857024 PMCID: PMC8638120 DOI: 10.1186/s13059-021-02538-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023] Open
Abstract
Alternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis of AS-set events are lacking. To mitigate this, we developed NEASE, a tool integrating pathways with structural annotations of protein-protein interactions to functionally characterize AS events. We show in four application cases how NEASE can identify pathways contributing to tissue identity and cell type development, and how it highlights splicing-related biomarkers. With a unique view on AS, NEASE generates unique and meaningful biological insights complementary to classical pathways analysis.
Collapse
Affiliation(s)
- Zakaria Louadi
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607, Hamburg, Germany
| | - Maria L Elkjaer
- Department of Neurology, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Melissa Klug
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- Department of Internal Medicine I, School of Medicine, University hospital rechts der Isar, Technical University of Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Chit Tong Lio
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607, Hamburg, Germany
| | - Amit Fenn
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607, Hamburg, Germany
| | - Zsolt Illes
- Department of Neurology, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Dario Bongiovanni
- Department of Internal Medicine I, School of Medicine, University hospital rechts der Isar, Technical University of Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Cardiovascular Medicine, Humanitas Clinical and Research Center IRCCS and Humanitas University, Rozzano, Milan, Italy
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607, Hamburg, Germany
- Institute of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5000, Odense, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
| | - Olga Tsoy
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607, Hamburg, Germany.
| |
Collapse
|
18
|
Fox-Fisher I, Piyanzin S, Ochana BL, Klochendler A, Magenheim J, Peretz A, Loyfer N, Moss J, Cohen D, Drori Y, Friedman N, Mandelboim M, Rothenberg ME, Caldwell JM, Rochman M, Jamshidi A, Cann G, Lavi D, Kaplan T, Glaser B, Shemer R, Dor Y. Remote immune processes revealed by immune-derived circulating cell-free DNA. eLife 2021; 10:70520. [PMID: 34842142 PMCID: PMC8651286 DOI: 10.7554/elife.70520] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/24/2021] [Indexed: 01/08/2023] Open
Abstract
Blood cell counts often fail to report on immune processes occurring in remote tissues. Here, we use immune cell type-specific methylation patterns in circulating cell-free DNA (cfDNA) for studying human immune cell dynamics. We characterized cfDNA released from specific immune cell types in healthy individuals (N = 242), cross sectionally and longitudinally. Immune cfDNA levels had no individual steady state as opposed to blood cell counts, suggesting that cfDNA concentration reflects adjustment of cell survival to maintain homeostatic cell numbers. We also observed selective elevation of immune-derived cfDNA upon perturbations of immune homeostasis. Following influenza vaccination (N = 92), B-cell-derived cfDNA levels increased prior to elevated B-cell counts and predicted efficacy of antibody production. Patients with eosinophilic esophagitis (N = 21) and B-cell lymphoma (N = 27) showed selective elevation of eosinophil and B-cell cfDNA, respectively, which were undetectable by cell counts in blood. Immune-derived cfDNA provides a novel biomarker for monitoring immune responses to physiological and pathological processes that are not accessible using conventional methods.
Collapse
Affiliation(s)
- Ilana Fox-Fisher
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Sheina Piyanzin
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Bracha Lea Ochana
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ayelet Peretz
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joshua Moss
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Daniel Cohen
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yaron Drori
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel, and Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Nehemya Friedman
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel, and Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Michal Mandelboim
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel, and Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
| | - Julie M Caldwell
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
| | - Mark Rochman
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
| | | | | | - David Lavi
- Department of Hematology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Developmental Biology and Cancer Research, The Institute for Medical Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| |
Collapse
|
19
|
Metabolomics in Autoimmune Diseases: Focus on Rheumatoid Arthritis, Systemic Lupus Erythematous, and Multiple Sclerosis. Metabolites 2021; 11:metabo11120812. [PMID: 34940570 PMCID: PMC8708401 DOI: 10.3390/metabo11120812] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/18/2022] Open
Abstract
The metabolomics approach represents the last downstream phenotype and is widely used in clinical studies and drug discovery. In this paper, we outline recent advances in the metabolomics research of autoimmune diseases (ADs) such as rheumatoid arthritis (RA), multiple sclerosis (MuS), and systemic lupus erythematosus (SLE). The newly discovered biomarkers and the metabolic mechanism studies for these ADs are described here. In addition, studies elucidating the metabolic mechanisms underlying these ADs are presented. Metabolomics has the potential to contribute to pharmacotherapy personalization; thus, we summarize the biomarker studies performed to predict the personalization of medicine and drug response.
Collapse
|
20
|
Hong Z, Liu J, Chen Y. An interpretable machine learning method for homo-trimeric protein interface residue-residue interaction prediction. Biophys Chem 2021; 278:106666. [PMID: 34418678 DOI: 10.1016/j.bpc.2021.106666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 12/29/2022]
Abstract
Protein-protein interaction plays an important role in life activities. A more fine-grained analysis, such as residues and atoms level, will better benefit us to understand the mechanism for inter-protein interaction and drug design. The development of efficient computational methods to reduce trials and errors, as well as assisting experimental researchers to determine the complex structure are some of the ongoing studies in the field. The research of trimer protein interface, especially homotrimer, has been rarely studied. In this paper, we proposed an interpretable machine learning method for homo-trimeric protein interface residue pairs prediction. The structure, sequence, and physicochemical information are intergraded as feature input fed to model for training. Graph model is utilized to present spatial information for intra-protein. Matrix factorization captures the different features' interactions. Kernel function is designed to auto-acquire the adjacent information of our target residue pairs. The accuracy rate achieves 54.5% in an independent test set. Sequence and structure alignment exhibit the ability of model self-study. Our model indicates the biological significance between sequence and structure, and could be auxiliary for reducing trials and errors in the fields of protein complex determination and protein-protein docking, etc. SIGNIFICANCE: Protein complex structures are significant for understanding protein function and promising functional protein design. With data increasing, some computational tools have been developed for protein complex residue contact prediction, which is one of the most significant steps for complex structure prediction. But for homo-trimeric protein, the sequence-based deep learning predictors are infeasible for homologous sequences, and the algorithm black box prevents us from understanding of each step operation. In this way, we propose an interpreting machine learning method for homo-trimeric protein interface residue-residue interaction prediction, and the predictor shows a good performance. Our work provides a computational auxiliary way for determining the homo-trimeric proteins interface residue pairs which will be further verified by wet experiments, and and gives a hand for the downstream works, such as protein-protein docking, protein complex structure prediction and drug design.
Collapse
Affiliation(s)
- Zhonghua Hong
- Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing 314001, PR China.
| | - Jiale Liu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PR China
| | - Yinggao Chen
- Shantou Central Hospital, Shantou 515041, PR China.
| |
Collapse
|
21
|
Anchang CG, Xu C, Raimondo MG, Atreya R, Maier A, Schett G, Zaburdaev V, Rauber S, Ramming A. The Potential of OMICs Technologies for the Treatment of Immune-Mediated Inflammatory Diseases. Int J Mol Sci 2021; 22:ijms22147506. [PMID: 34299122 PMCID: PMC8306614 DOI: 10.3390/ijms22147506] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023] Open
Abstract
Immune-mediated inflammatory diseases (IMIDs), such as inflammatory bowel diseases and inflammatory arthritis (e.g., rheumatoid arthritis, psoriatic arthritis), are marked by increasing worldwide incidence rates. Apart from irreversible damage of the affected tissue, the systemic nature of these diseases heightens the incidence of cardiovascular insults and colitis-associated neoplasia. Only 40–60% of patients respond to currently used standard-of-care immunotherapies. In addition to this limited long-term effectiveness, all current therapies have to be given on a lifelong basis as they are unable to specifically reprogram the inflammatory process and thus achieve a true cure of the disease. On the other hand, the development of various OMICs technologies is considered as “the great hope” for improving the treatment of IMIDs. This review sheds light on the progressive development and the numerous approaches from basic science that gradually lead to the transfer from “bench to bedside” and the implementation into general patient care procedures.
Collapse
Affiliation(s)
- Charles Gwellem Anchang
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Cong Xu
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Maria Gabriella Raimondo
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Raja Atreya
- Department of Internal Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany;
| | - Andreas Maier
- Computer Science, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
| | - Georg Schett
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Vasily Zaburdaev
- Max-Planck-Zentrum für Physik und Medizin, 91054 Erlangen, Germany;
- Department of Biology, Mathematics in Life Sciences, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Simon Rauber
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
| | - Andreas Ramming
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum, 91054 Erlangen, Germany; (C.G.A.); (C.X.); (M.G.R.); (G.S.); (S.R.)
- Correspondence: ; Tel.: +49-9131-8543048; Fax: +49-9131-8536448
| |
Collapse
|
22
|
Do Autism Spectrum and Autoimmune Disorders Share Predisposition Gene Signature Due to mTOR Signaling Pathway Controlling Expression? Int J Mol Sci 2021; 22:ijms22105248. [PMID: 34065644 PMCID: PMC8156237 DOI: 10.3390/ijms22105248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/08/2021] [Accepted: 05/14/2021] [Indexed: 12/22/2022] Open
Abstract
Autism spectrum disorder (ASD) is characterized by uncommon genetic heterogeneity and a high heritability concurrently. Most autoimmune disorders (AID), similarly to ASD, are characterized by impressive genetic heterogeneity and heritability. We conducted gene-set analyses and revealed that 584 out of 992 genes (59%) included in a new release of the SFARI Gene database and 439 out of 871 AID-associated genes (50%) could be attributed to one of four groups: 1. FMRP (fragile X mental retardation protein) target genes, 2. mTOR signaling network genes, 3. mTOR-modulated genes, and 4. vitamin D3-sensitive genes. With the exception of FMRP targets, which are obviously associated with the direct involvement of local translation disturbance in the pathological mechanisms of ASD, the remaining categories are represented among AID genes in a very similar percentage as among ASD predisposition genes. Thus, mTOR signaling pathway genes make up 4% of ASD and 3% of AID genes, mTOR-modulated genes-31% of both ASD and AID genes, and vitamin D-sensitive genes-20% of ASD and 23% of AID genes. The network analysis revealed 3124 interactions between 528 out of 729 AID genes for the 0.7 cutoff, so the great majority (up to 67%) of AID genes are related to the mTOR signaling pathway directly or indirectly. Our present research and available published data allow us to hypothesize that both a certain part of ASD and AID comprise a connected set of disorders sharing a common aberrant pathway (mTOR signaling) rather than a vast set of different disorders. Furthermore, an immune subtype of the autism spectrum might be a specific type of autoimmune disorder with an early manifestation of a unique set of predominantly behavioral symptoms.
Collapse
|
23
|
Meta-analysis based gene expression profiling reveals functional genes in ovarian cancer. Biosci Rep 2021; 40:226877. [PMID: 33135729 PMCID: PMC7677829 DOI: 10.1042/bsr20202911] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/02/2023] Open
Abstract
Background: Ovarian cancer causes high mortality rate worldwide, and despite numerous attempts, the outcome for patients with ovarian cancer are still not well improved. Microarray-based gene expressional analysis provides with valuable information for discriminating functional genes in ovarian cancer development and progression. However, due to the differences in experimental design, the results varied significantly across individual datasets. Methods: In the present study, the data of gene expression in ovarian cancer were downloaded from Gene Expression Omnibus (GEO) and 16 studies were included. A meta-analysis based gene expression analysis was performed to identify differentially expressed genes (DEGs). The most differentially expressed genes in our meta-analysis were selected for gene expression and gene function validation. Results: A total of 972 DEGs with P-value < 0.001 were identified in ovarian cancer, including 541 up-regulated genes and 431 down-regulated genes, among which 92 additional DEGs were found as gained DEGs. Top five up- and down-regulated genes were selected for the validation of gene expression profiling. Among these genes, up-regulated CD24 molecule (CD24), SRY (sex determining region Y)-box transcription factor 17 (SOX17), WFDC2, epithelial cell adhesion molecule (EPCAM), innate immunity activator (INAVA), and down-regulated aldehyde oxidase 1 (AOX1) were revealed to be with consistent expressional patterns in clinical patient samples of ovarian cancer. Gene functional analysis demonstrated that up-regulated WFDC2 and INAVA promoted ovarian cancer cell migration, WFDC2 enhanced cell proliferation, while down-regulated AOX1 was functional in inducing cell apoptosis of ovarian cancer. Conclusion: Our study shed light on the molecular mechanisms underlying the development of ovarian cancer, and facilitated the understanding of novel diagnostic and therapeutic targets in ovarian cancer.
Collapse
|
24
|
Ghafouri-Fard S, Honarmand K, Taheri M. A comprehensive review on the role of chemokines in the pathogenesis of multiple sclerosis. Metab Brain Dis 2021; 36:375-406. [PMID: 33404937 DOI: 10.1007/s11011-020-00648-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023]
Abstract
Multiple sclerosis (MS) as a chronic inflammatory disorder of the central nervous system (CNS) is thought to be caused by the abnormal induction of immune responses. Chemokines as molecules that can engage leukocytes into the location of inflammation, actively participate in the pathogenesis of MS. Several members of this family of chemo attractants have been shown to be dysregulated in the peripheral blood, cerebrospinal fluid or CNS lesions of MS patients. Studies in animal models of MS particularly experimental autoimmune encephalomyelitis have indicated the critical roles of chemokines in the pathophysiology of MS. In the current review, we summarize the data regarding the role of CCL2, CCL3, CCL4, CCL11, CCL20, CXCL1, CXCL2, CXCL8, CXCL10, CXCL12 and CXCL13 in the pathogenesis of MS.
Collapse
Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kasra Honarmand
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
25
|
Bragde HG, Jansson U, Fredrikson M, Grodzinsky E, Söderman J. Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease. BMJ Open Gastroenterol 2020; 7:bmjgast-2020-000536. [PMID: 33323471 PMCID: PMC7745333 DOI: 10.1136/bmjgast-2020-000536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/05/2020] [Accepted: 11/21/2020] [Indexed: 12/20/2022] Open
Abstract
Introduction A coeliac disease (CD) diagnosis is likely in children with levels of tissue transglutaminase autoantibodies (anti-TG2) >10 times the upper reference value, whereas children with lower anti-TG2 levels need an intestinal biopsy to confirm or rule out CD. A blood sample is easier to obtain than an intestinal biopsy sample, and stabilised blood is suitable for routine diagnostics because transcript levels are preserved at sampling. Therefore, we investigated gene expression in stabilised whole blood to explore the possibility of gene expression-based diagnostics for the diagnosis and follow-up of CD. Design We performed RNA sequencing of stabilised whole blood from active CD cases (n=10), non-CD cases (n=10), and treated CD cases on a gluten-free diet (n=10) to identify diagnostic CD biomarkers and pathways involved in CD pathogenesis. Results No single gene was differentially expressed between the sample groups. However, by using gene set enrichment analysis (GSEA), significantly differentially expressed pathways were identified in active CD, and these pathways involved the inflammatory response, negative regulation of viral replication, translation, as well as cell proliferation, differentiation, migration, and survival. The results indicate that there are differences in pathway regulation in CD, which could be used for diagnostic purposes. Comparison between GSEA results based on stabilised blood with GSEA results based on small intestinal biopsies revealed that type I interferon response, defence response to virus, and negative regulation of viral replication were identified as pathways common to both tissues. Conclusions Stabilised whole blood is not a suitable sample for clinical diagnostics of CD based on single genes. However, diagnostics based on a pathway-focused gene expression panel may be feasible, but requires further investigation.
Collapse
Affiliation(s)
- Hanna Gustafsson Bragde
- Laboratory Medicine, Region Jönköping County, Jönköping, Sweden .,Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Ulf Jansson
- Department of Paediatrics, Region Jönköping County, Jönköping, Sweden
| | - Mats Fredrikson
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Ewa Grodzinsky
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Jan Söderman
- Laboratory Medicine, Region Jönköping County, Jönköping, Sweden.,Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| |
Collapse
|
26
|
Salas A, Hernandez-Rocha C, Duijvestein M, Faubion W, McGovern D, Vermeire S, Vetrano S, Vande Casteele N. JAK-STAT pathway targeting for the treatment of inflammatory bowel disease. Nat Rev Gastroenterol Hepatol 2020; 17:323-337. [PMID: 32203403 DOI: 10.1038/s41575-020-0273-0] [Citation(s) in RCA: 306] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/06/2020] [Indexed: 02/07/2023]
Abstract
Cytokines are involved in intestinal homeostasis and pathological processes associated with inflammatory bowel disease (IBD). The biological effects of cytokines, including several involved in the pathology of Crohn's disease and ulcerative colitis, occur as a result of receptor-mediated signalling through the Janus kinase (JAK) and signal transducer and activator of transcription (STAT) DNA-binding families of proteins. Although therapies targeting cytokines have revolutionized IBD therapy, they have historically targeted individual cytokines, and an unmet medical need exists for patients who do not respond to or lose response to these treatments. Several small-molecule inhibitors of JAKs that have the potential to affect multiple pro-inflammatory cytokine-dependent pathways are in clinical development for the treatment of IBD, with one agent, tofacitinib, already approved for ulcerative colitis and several other agents with demonstrated efficacy in early phase trials. This Review describes the current understanding of JAK-STAT signalling in intestinal homeostasis and disease and the rationale for targeting this pathway as a treatment for IBD. The available evidence for the efficacy, safety and pharmacokinetics of JAK inhibitors in IBD as well as the potential approaches to optimize treatment with these agents, such as localized delivery or combination therapy, are also discussed.
Collapse
Affiliation(s)
- Azucena Salas
- Department of Gastroenterology, IDIBAPS, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Cristian Hernandez-Rocha
- Zane Cohen Center for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| | - Marjolijn Duijvestein
- Gastroenterology and Hepatology, Amsterdam Gastroenterology and Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - William Faubion
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, MI, USA
| | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Severine Vermeire
- Department of Gastroenterology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Stefania Vetrano
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IBD Center, Laboratory of Immunology in Gastroenterology, Humanitas Clinical and Research Center IRCCS, Milan, Italy
| | - Niels Vande Casteele
- Robarts Clinical Trials, London, ON, Canada. .,Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
27
|
Andersson Svärd A, Maziarz M, Ramelius A, Lundgren M, Lernmark Å, Elding Larsson H. Decreased HLA-DQ expression on peripheral blood cells in children with varying number of beta cell autoantibodies. J Transl Autoimmun 2020; 3:100052. [PMID: 32743532 PMCID: PMC7388396 DOI: 10.1016/j.jtauto.2020.100052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022] Open
Abstract
The risk for type 1 diabetes is strongly associated with HLA-DQ and the appearance of beta cell autoantibodies against either insulin, glutamate decarboxylase (GAD65), insulinoma-associated protein-2 (IA-2), or zinc transporter 8 (ZnT8). Prolonged exposure to autoantibodies may be related to T cell exhaustion known to occur in chronic infections or autoimmune disorders. It was hypothesized that autoantibody exposure may affect HLA-DQ expression on peripheral blood cells and thereby contribute to T cell exhaustion thought to be associated with the pathogenesis of type 1 diabetes. The aim of this study was to determine whether autoantibody exposure as an expression of autoimmunity burden was related to peripheral blood cell HLA-DQ cell surface expression in either 1) a cross-sectional analysis or 2) cumulative as area under the trajectory of autoantibodies during long term follow-up in the Diabetes Prediction in Skåne (DiPiS) study. Children (n = 67), aged 10–15 years were analyzed for complete blood count, HLA-DQ cell surface median fluorescence intensity (MFI), autoantibody frequency, and HLA genotypes by Next Generation Sequencing. Decreased HLA-DQ cell surface MFI with an increasing number of autoantibodies was observed in CD16+, CD14+CD16−, CD4+ and CD8+ cells but not in CD19+ cells and neutrophils. HLA-DQ cell surface MFI was associated with HLA-DQ2/8 in CD4+ T cells, marginally in CD14+CD16− monocytes and CD8+ T cells. These associations appeared to be related to autoimmunity burden. The results suggest that HLA-DQ cell surface expression was related to HLA and autoimmunity burden. PBMC HLA-DQ surface expression in beta cell autoimmunity is poorly understood. Children, 10–15 years of age without or with beta cell autoantibodies were analyzed. HLA-DQ cell surface expression decreased with increasing number of autoantibodies. HLA-DQ cell surface expression was related to HLA and autoimmunity burden.
Collapse
Affiliation(s)
- Agnes Andersson Svärd
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, 205 02, Malmö, Sweden
| | - Marlena Maziarz
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, 205 02, Malmö, Sweden
| | - Anita Ramelius
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, 205 02, Malmö, Sweden
| | - Markus Lundgren
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, 205 02, Malmö, Sweden
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, 205 02, Malmö, Sweden
| | - Helena Elding Larsson
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, 205 02, Malmö, Sweden
| | | |
Collapse
|
28
|
Safari-Alighiarloo N, Taghizadeh M, Mohammad Tabatabaei S, Namaki S, Rezaei-Tavirani M. Identification of common key genes and pathways between type 1 diabetes and multiple sclerosis using transcriptome and interactome analysis. Endocrine 2020; 68:81-92. [PMID: 31912409 DOI: 10.1007/s12020-019-02181-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/27/2019] [Indexed: 01/24/2023]
Abstract
PURPOSE Type 1 diabetes (T1D) and multiple sclerosis (MS) are classified as T cell-mediated autoimmune diseases. Although convergent evidence proposed common genetic architecture for autoimmune diseases, it remains a challenge to identify them. This study aimed to determine common gene signature and pathways in T1D and MS via systems biology approach. METHODS Gene expression profiles of peripheral blood mononuclear cells (PBMCs) and pancreatic-β cells in T1D as well as PBMCs and cerebrospinal fluid (CSF) in MS were analyzed in our previous published data, and differential expressed genes were integrated with protein-protein interactions data to construct Query-Query PPI (QQPPI) networks. In this study, QQPPI networks were further analyzed to investigate more central genes, functional modules and complexes shared in T1D and MS progression. Lastly, the interaction of common genes with drugs was also explored. RESULTS Several cytokines such as IL-23A, IL-32, IL-34, and IL-37 tend to be differentially expressed in both diseases. In addition, PSMA1, MYC, SRPK1, YBX1, HNRNPM, NF-κB2, IKBKE, RAC1, FN1, ARRB2, ESR1, HSP90AB1, and PPP1CA were common high central genes in QQPPI networks corresponding to each disease. Proteasome, spliceosome, immune responses, apoptosis, cellular communication/signaling transduction mechanism, interaction with environment, and activity of intercellular mediators were shared biological processes in T1D and MS. Finally, azathioprine, melatonin, resveratrol, and geldanamycin identified as prioritized drugs for the treatment of patients with T1D and MS. CONCLUSIONS This study represented novel key genes and pathways shared between T1D and MS, which may facilitate the identification of potential therapeutic targets in these diseases.
Collapse
Affiliation(s)
- Nahid Safari-Alighiarloo
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Taghizadeh
- Bioinformatics Department, Institute of Biochemistry and Biophysics, Tehran University, Tehran, Iran
| | - Seyyed Mohammad Tabatabaei
- Medical Informatics Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Namaki
- Immunology Department, Faculty of Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
29
|
Ghavidel AA, Shiari R, Hassan-Zadeh V, Farivar S. The expression of DNMTs is dramatically decreased in peripheral blood mononuclear cells of male patients with juvenile idiopathic arthritis. Allergol Immunopathol (Madr) 2020; 48:182-186. [PMID: 31901404 DOI: 10.1016/j.aller.2019.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/07/2019] [Accepted: 08/28/2019] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Juvenile idiopathic arthritis (JIA) is an autoimmune rheumatic disease, which affects primarily the joints in children under 16 years old. The etiology of JIA is yet unknown but research has shown that JIA is a multifactorial disease implicating several genes and environmental factors. Environmental factors affect immune cells via epigenetic mechanisms. One of the most important epigenetic mechanisms is DNA methylation catalyzed by DNA methyltransferases (DNMTs) and usually associated with gene silencing. In this study, we analyzed the expression of three DNA methyltransferases namely DNMT1, DNMT3a and DNMT3b in peripheral blood mononuclear cells (PBMCs) of patients with JIA and compared it with the expression of these genes in healthy young individuals. MATERIALS AND METHODS Peripheral blood mononuclear cells of 28 JIA patients and 28 healthy controls were isolated. Total RNA was extracted, cDNA was synthesized and the transcript levels of DNMTs were analyzed by quantitative PCR. RESULTS Analysis of DNMT1, DNMT3a and DNMT3b relative gene expression in PBMCs of JIA patients and control individuals shows that the expression of DNMT1 and DNMT3a is reduced significantly by 7 folds and 5.5 folds, respectively, in JIA patients compared to healthy controls. Furthermore, the expression of all three DNMTs were significantly and drastically reduced in young affected males compared to healthy males. CONCLUSION This study shows that the expression of DNMTs is reduced in JIA patients and this reduction is severe in male JIA patients.
Collapse
Affiliation(s)
- Afshin Abdi Ghavidel
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, Iran; Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Shiari
- Department of Pediatrics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Mofid Children's Hospital, Pediatrics Infectious Research Center (PIRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahideh Hassan-Zadeh
- Department of Cell and Molecular Biology, School of Biology, Faculty of Science, University of Tehran, Tehran, Iran
| | - Shirin Farivar
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, Iran.
| |
Collapse
|
30
|
Toro-Domínguez D, Villatoro-García JA, Martorell-Marugán J, Román-Montoya Y, Alarcón-Riquelme ME, Carmona-Sáez P. A survey of gene expression meta-analysis: methods and applications. Brief Bioinform 2020; 22:1694-1705. [PMID: 32095826 DOI: 10.1093/bib/bbaa019] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 02/07/2023] Open
Abstract
The increasing use of high-throughput gene expression quantification technologies over the last two decades and the fact that most of the published studies are stored in public databases has triggered an explosion of studies available through public repositories. All this information offers an invaluable resource for reuse to generate new knowledge and scientific findings. In this context, great interest has been focused on meta-analysis methods to integrate and jointly analyze different gene expression datasets. In this work, we describe the main steps in the gene expression meta-analysis, from data preparation to the state-of-the art statistical methods. We also analyze the main types of applications and problems that can be approached in gene expression meta-analysis studies and provide a comparative overview of the available software and bioinformatics tools. Moreover, a practical guide for choosing the most appropriate method in each case is also provided.
Collapse
Affiliation(s)
- Daniel Toro-Domínguez
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
| | - Juan Antonio Villatoro-García
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
| | - Jordi Martorell-Marugán
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
| | - Yolanda Román-Montoya
- Department of Statistics and Operations Research, University of Granada, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain.,Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute, 171 67, Solna, Sweden
| | - Pedro Carmona-Sáez
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
| |
Collapse
|
31
|
Giudici F, Lombardelli L, Russo E, Cavalli T, Zambonin D, Logiodice F, Kullolli O, Giusti L, Bargellini T, Fazi M, Biancone L, Scaringi S, Clemente AM, Perissi E, Delfino G, Torcia MG, Ficari F, Tonelli F, Piccinni MP, Malentacchi C. Multiplex gene expression profile in inflamed mucosa of patients with Crohn’s disease ileal localization: A pilot study. World J Clin Cases 2019; 7:2463-2476. [PMID: 31559282 PMCID: PMC6745337 DOI: 10.12998/wjcc.v7.i17.2463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/12/2019] [Accepted: 07/27/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Crohn’s disease (CD) is a complex disorder resulting from the interaction of genetic, environmental, and microbial factors. The pathogenic process may potentially affect any segment of the gastrointestinal tract, but a selective location in the terminal ileum was reported in 50% of patients.
AIM To characterize clinical sub-phenotypes (colonic and/or ileal) within the same disease, in order to identify new therapeutic targets.
METHODS 14 consecutive patients undergoing surgery for ileal CD were recruited for this study. Peripheral blood samples from each patient were collected and the main polymorphisms of the gene Card15/Nod2 (R702W, G908R, and 1007fs) were analyzed in each sample. In addition, tissue samples were taken from both the tract affected by CD and from the apparently healthy and disease-free margins (internal controls). We used a multiplex gene assay in specimens obtained from patients with ileal localization of CD to evaluate the simultaneous expression of 24 genes involved in the pathogenesis of the disease. We also processed surgery gut samples with routine light microscopy (LM) and transmission electron microscopy (TEM) techniques to evaluate their structural and ultrastructural features.
RESULTS We found a significant increase of Th17 (IL17A and IL17F, IL 23R and CCR6) and Th1 (IFN-γ) gene expression in inflamed mucosa compared to non-inflamed sites of 14 CD patients. DEFB4 and HAMP, two genes coding for antimicrobial peptides, were also strongly activated in inflamed ileal mucosa, suggesting the overwhelming stimulation of epithelial cells by commensal microbiota. IFN-γ and CCR6 were more expressed in inflamed mucosa of CD patients with ileal localization compared with patients with colonic localization suggesting a more aggressive inflammation process in this site. Morphological analysis of the epithelial lining of Lieberkün crypts disclosed enhanced release activity from goblet mucocytes, whereas the lamina propria contained numerous cells pertaining to various lines.
CONCLUSION We observed that the expression of ileal genes related to Th1 and Th17 activity is strongly activated as well as the expression of genes involved in microbiota regulation.
Collapse
Affiliation(s)
- Francesco Giudici
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Letizia Lombardelli
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Edda Russo
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Tiziana Cavalli
- Dipartimento Chirurgico Ortopedico, Ospedale Carlo Poma di Mantova, Firenze 50134, Italy
| | - Daniela Zambonin
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Federica Logiodice
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Ornela Kullolli
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Lamberto Giusti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze 50134, Italy
| | - Tatiana Bargellini
- Surgical Unit, Department of Surgery and Translational Medicine, University of Firenze, Firenze 50134, Italy
| | - Marilena Fazi
- Surgical Unit, Department of Surgery and Translational Medicine, University of Firenze, Firenze 50134, Italy
| | - Livia Biancone
- Department of Internal Medicine, University of Roma Tor Vergata, Roma 00133, Italy
| | - Stefano Scaringi
- Surgical Unit, Department of Surgery and Translational Medicine, University of Firenze, Firenze 50134, Italy
| | - Ann Maria Clemente
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Eloisa Perissi
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Giovanni Delfino
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze 50134, Italy
| | - Maria G Torcia
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Ferdinando Ficari
- Surgical Unit, Department of Surgery and Translational Medicine, University of Firenze, Firenze 50134, Italy
| | - Francesco Tonelli
- Surgical Unit, Department of Surgery and Translational Medicine, University of Firenze, Firenze 50134, Italy
| | | | - Cecilia Malentacchi
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze 50134, Italy
| |
Collapse
|
32
|
Abstract
Autoimmune rheumatic diseases pose many problems that have, in general, already been solved in the field of cancer. The heterogeneity of each disease, the clinical similarities and differences between different autoimmune rheumatic diseases and the large number of patients that remain without a diagnosis underline the need to reclassify these diseases via new approaches. Knowledge about the molecular basis of systemic autoimmune diseases, along with the availability of bioinformatics tools capable of handling and integrating large volumes of various types of molecular data at once, offer the possibility of reclassifying these diseases. A new taxonomy could lead to the discovery of new biomarkers for patient stratification and prognosis. Most importantly, this taxonomy might enable important changes in clinical trial design to reach the expected outcomes or the design of molecularly targeted therapies. In this Review, we discuss the basis for a new molecular taxonomy for autoimmune rheumatic diseases. We highlight the evidence surrounding the idea that these diseases share molecular features related to their pathogenesis and development and discuss previous attempts to classify these diseases. We evaluate the tools available to analyse and combine different types of molecular data. Finally, we introduce PRECISESADS, a project aimed at reclassifying the systemic autoimmune diseases.
Collapse
|
33
|
Anderson AE, Maney NJ, Nair N, Lendrem DW, Skelton AJ, Diboll J, Brown PM, Smith GR, Carmody RJ, Barton A, Isaacs JD, Pratt AG. Expression of STAT3-regulated genes in circulating CD4+ T cells discriminates rheumatoid arthritis independently of clinical parameters in early arthritis. Rheumatology (Oxford) 2019; 58:1250-1258. [PMID: 30753680 PMCID: PMC6587924 DOI: 10.1093/rheumatology/kez003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/13/2018] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES Dysregulated signal transduction and activator of transcription-3 (STAT3) signalling in CD4+ T cells has been proposed as an early pathophysiological event in RA. We sought further evidence for this observation, and to determine its clinical relevance. METHODS Microarray technology was used to measure gene expression in purified peripheral blood CD4+ T cells from treatment-naïve RA patients and disease controls newly recruited from an early arthritis clinic. Analysis focused on 12 previously proposed transcripts, and concurrent STAT3 pathway activation was determined in the same cells by flow cytometry. A pooled analysis of previous and current gene expression findings incorporated detailed clinical parameters and employed multivariate analysis. RESULTS In an independent cohort of 161 patients, expression of 11 of 12 proposed signature genes differed significantly between RA patients and controls, robustly validating the earlier findings. Differential regulation was most pronounced for the STAT3 target genes PIM1, BCL3 and SOCS3 (>1.3-fold difference; P < 0.005), each of whose expression correlated strongly with paired intracellular phospho-STAT3. In a meta-analysis of 279 patients the same three genes accounted for the majority of the signature's ability to discriminate RA patients, which was found to be independent of age, joint involvement or acute phase response. CONCLUSION The STAT3-mediated dysregulation of BCL3, SOCS3 and PIM1 in circulating CD4+ T cells is a discriminatory feature of early RA that occurs independently of acute phase response. The mechanistic and functional implications of this observation at a cellular level warrant clarification.
Collapse
Affiliation(s)
- Amy E Anderson
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Nicola J Maney
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Nisha Nair
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, and NIHR Manchester Musculoskeletal Biomedical Research Centre, Manchester NHS Foundation Trust, Manchester, UK
| | - Dennis W Lendrem
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew J Skelton
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, UK
| | - Julie Diboll
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Philip M Brown
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Graham R Smith
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, UK
| | - Ruaidhrí J Carmody
- Centre for Immunobiology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, UK
| | - Anne Barton
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, and NIHR Manchester Musculoskeletal Biomedical Research Centre, Manchester NHS Foundation Trust, Manchester, UK
| | - John D Isaacs
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Arthur G Pratt
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| |
Collapse
|
34
|
Xu J, Huang G, Nagy T, Teng Q, Guo TL. Sex-dependent effects of bisphenol A on type 1 diabetes development in non-obese diabetic (NOD) mice. Arch Toxicol 2019; 93:997-1008. [PMID: 30600366 PMCID: PMC6511313 DOI: 10.1007/s00204-018-2379-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/13/2018] [Indexed: 12/17/2022]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease caused by immune-mediated pancreatic β-cell destruction. The endocrine disrupting chemical bisphenol A (BPA) has widespread human exposure and can modulate immune function and the gut microbiome (GMB), which may contribute to the increasing T1D incidence worldwide. It was hypothesized that BPA had sex-dependent effects on T1D by modulating immune homeostasis and GMB. Adult female and male non-obese diabetic (NOD) mice were orally administered BPA at environmentally relevant doses (30 or 300 µg/kg). Antibiotic-treated adult NOD females were exposed to 0 or 30 µg/kg BPA. BPA accelerated T1D development in females, but delayed males from T1D. Consistently, females had a shift towards pro-inflammation (e.g., increased macrophages and Bacteroidetes), while males had increases in anti-inflammatory immune factors and a decrease in both anti- and pro-inflammatory GMB. Although bacteria altered during sub-acute BPA exposure differed from bacteria altered from chronic BPA exposure in both sexes, the GMB profile was consistently pro-inflammatory in females, while males had a general decrease of both anti- and pro-inflammatory gut microbes. However, treatment of females with the antibiotic vancomycin failed to prevent BPA-induced glucose intolerance, suggesting changes in Gram-positive bacteria were not a primary mechanism. In conclusion, BPA exposure was found to have sex dimorphic effects on T1D with detrimental effects in females, and immunomodulation was identified as the primary mechanism.
Collapse
Affiliation(s)
- Joella Xu
- Department of Veterinary Biosciences and Diagnostic Imaging, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Guannan Huang
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Tamas Nagy
- Department of Pathology, University of Georgia, Athens, GA, 30602, USA
| | - Quincy Teng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, 30602, USA
| | - Tai L Guo
- Department of Veterinary Biosciences and Diagnostic Imaging, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
35
|
Bisphenol A alteration of type 1 diabetes in non-obese diabetic (NOD) female mice is dependent on window of exposure. Arch Toxicol 2019; 93:1083-1093. [PMID: 30826855 DOI: 10.1007/s00204-019-02419-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease in which pancreatic β-cell destruction can be mediated by dysbiosis, infiltration of pro-inflammatory immune cells, and cytokines/chemokines. Exposure to bisphenol A (BPA), an endocrine disruptor (ED), can lead to aberrant immunity and gut microbiota. We determined whether BPA had age-dependent effects on T1D by modulating immune homeostasis following various windows of exposure in non-obese diabetic (NOD) mice. Juvenile NOD females were orally exposed to 0 or 30 µg BPA/kg BW from postnatal day (PND) 28 to PND56. Adult NOD females were exposed to 0 or 300 µg BPA/kg BW. Female and male NOD offspring were exposed to 0 or 300 µg BPA/kg BW perinatally from gestation day 5 to PND28 by dosing the dams. It was found that BPA increased T1D risk in juvenile females with gut microbiota shifted towards pro-inflammation (e.g. increased Jeotgalicoccus). In agreement with our previous study, adult females had a trend of increased T1D and a general increase in immune responses. However, female offspring had a reduced T1D development. Consistently, female offspring had a shift towards anti-inflammation (e.g. decreased pro-inflammatory F4/80+Gr1+ cells). In contrast, BPA had minimal effects on immunity and T1D in male offspring. Thus, it was concluded that BPA had age- and sex-dependent effects on T1D with the alteration of gut microbiota and inflammation being the primary mechanisms for T1D exacerbation in juvenile exposure and decreases of inflammation being responsible for attenuated T1D in perinatally exposed females.
Collapse
|
36
|
Abstract
Purpose of Review The purpose is to discuss the advances that genetics and genomics have provided to better understand the molecular mechanisms behind SLE and how to solve its heterogeneity. I propose new ideas that can help us stratify lupus in order to find the best therapies for each patient, and the idea of substituting clinical diagnosis with molecular diagnosis according to their molecular patterns, an idea that may not only include lupus but also other diseases. Recent Findings The study of rare mutations may provide insight into groups of lupus patients where type I interferon signature is important and help understand those with an atypical clinical presentation. Recent papers used longitudinal blood transcriptome data correlating with disease activity scores to stratify lupus into molecular clusters. The implication of neutrophils in the risk to develop nephritis was established, but also that neutrophils and lymphocytes may correlate with activity differentiating the mechanisms of flares and separating patients into clinically separate groups. Summary The role of type I interferon signature is important; however, the stratification of SLE patients according to the genes and cellular compartments being modulated during disease activity may be even more important to define those patients who may benefit the most with new anti-type I IFN receptor therapies.
Collapse
|
37
|
Jelcic I, Al Nimer F, Wang J, Lentsch V, Planas R, Jelcic I, Madjovski A, Ruhrmann S, Faigle W, Frauenknecht K, Pinilla C, Santos R, Hammer C, Ortiz Y, Opitz L, Grönlund H, Rogler G, Boyman O, Reynolds R, Lutterotti A, Khademi M, Olsson T, Piehl F, Sospedra M, Martin R. Memory B Cells Activate Brain-Homing, Autoreactive CD4 + T Cells in Multiple Sclerosis. Cell 2018; 175:85-100.e23. [PMID: 30173916 PMCID: PMC6191934 DOI: 10.1016/j.cell.2018.08.011] [Citation(s) in RCA: 289] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/04/2018] [Accepted: 08/03/2018] [Indexed: 12/16/2022]
Abstract
Multiple sclerosis is an autoimmune disease that is caused by the interplay of genetic, particularly the HLA-DR15 haplotype, and environmental risk factors. How these etiologic factors contribute to generating an autoreactive CD4+ T cell repertoire is not clear. Here, we demonstrate that self-reactivity, defined as “autoproliferation” of peripheral Th1 cells, is elevated in patients carrying the HLA-DR15 haplotype. Autoproliferation is mediated by memory B cells in a HLA-DR-dependent manner. Depletion of B cells in vitro and therapeutically in vivo by anti-CD20 effectively reduces T cell autoproliferation. T cell receptor deep sequencing showed that in vitro autoproliferating T cells are enriched for brain-homing T cells. Using an unbiased epitope discovery approach, we identified RASGRP2 as target autoantigen that is expressed in the brain and B cells. These findings will be instrumental to address important questions regarding pathogenic B-T cell interactions in multiple sclerosis and possibly also to develop novel therapies. Autoproliferation of CD4+ T cells and B cells is involved in multiple sclerosis The main genetic factor of MS, HLA-DR15, plays a central role in autoproliferation Memory B cells drive autoproliferation of Th1 brain-homing CD4+ T cells Autoproliferating T cells recognize antigens expressed in B cells and brain lesions
Collapse
Affiliation(s)
- Ivan Jelcic
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Faiez Al Nimer
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland; Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Jian Wang
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Verena Lentsch
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Raquel Planas
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Ilijas Jelcic
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Aleksandar Madjovski
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Sabrina Ruhrmann
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Wolfgang Faigle
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Katrin Frauenknecht
- Institute of Neuropathology, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Clemencia Pinilla
- Torrey Pines Institute for Molecular Studies (TPIMS), San Diego, CA, USA
| | - Radleigh Santos
- Torrey Pines Institute for Molecular Studies (TPIMS), Port St. Lucie, FL, USA
| | - Christian Hammer
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Yaneth Ortiz
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology and University of Zurich, 8057 Zurich, Switzerland
| | - Hans Grönlund
- Therapeutic Immune Design Unit, Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Richard Reynolds
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - Andreas Lutterotti
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Mohsen Khademi
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Fredrik Piehl
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Mireia Sospedra
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, 8091 Zurich, Switzerland.
| |
Collapse
|
38
|
Eguchi R, Karim MB, Hu P, Sato T, Ono N, Kanaya S, Altaf-Ul-Amin M. An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease. BMC Bioinformatics 2018; 19:264. [PMID: 30005591 PMCID: PMC6043997 DOI: 10.1186/s12859-018-2251-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 06/18/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND There are different and complicated associations between genes and diseases. Finding the causal associations between genes and specific diseases is still challenging. In this work we present a method to predict novel associations of genes and pathways with inflammatory bowel disease (IBD) by integrating information of differential gene expression, protein-protein interaction and known disease genes related to IBD. RESULTS We downloaded IBD gene expression data from NCBI's Gene Expression Omnibus, performed statistical analysis to determine differentially expressed genes, collected known IBD genes from DisGeNet database, which were used to construct a IBD related PPI network with HIPPIE database. We adapted our graph-based clustering algorithm DPClusO to cluster the disease PPI network. We evaluated the statistical significance of the identified clusters in the context of determining the richness of IBD genes using Fisher's exact test and predicted novel genes related to IBD. We showed 93.8% of our predictions are correct in the context of other databases and published literatures related to IBD. CONCLUSIONS Finding disease-causing genes is necessary for developing drugs with synergistic effect targeting many genes simultaneously. Here we present an approach to identify novel disease genes and pathways and discuss our approach in the context of IBD. The approach can be generalized to find disease-associated genes for other diseases.
Collapse
Affiliation(s)
- Ryohei Eguchi
- Graduate School of Science and Technology & NAIST Data Science Center, Nara Institute of Science and Technology, Nara, Japan
| | - Mohammand Bozlul Karim
- Graduate School of Science and Technology & NAIST Data Science Center, Nara Institute of Science and Technology, Nara, Japan
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada.,George and Fay Yee Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Canada.,Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
| | - Tetsuo Sato
- Graduate School of Science and Technology & NAIST Data Science Center, Nara Institute of Science and Technology, Nara, Japan.,Department of Radiological Technology, Gunma Prefectural College of Health Sciences, Gunma, Japan
| | - Naoaki Ono
- Graduate School of Science and Technology & NAIST Data Science Center, Nara Institute of Science and Technology, Nara, Japan
| | - Shigehiko Kanaya
- Graduate School of Science and Technology & NAIST Data Science Center, Nara Institute of Science and Technology, Nara, Japan
| | - Md Altaf-Ul-Amin
- Graduate School of Science and Technology & NAIST Data Science Center, Nara Institute of Science and Technology, Nara, Japan.
| |
Collapse
|
39
|
Kalantar K, LaHue SC, DeRisi JL, Sample HA, Contag CA, Josephson SA, Wilson MR, Douglas VC. Whole-Genome mRNA Gene Expression Differs Between Patients With and Without Delirium. J Geriatr Psychiatry Neurol 2018; 31:203-210. [PMID: 29991314 PMCID: PMC6817976 DOI: 10.1177/0891988718785774] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To identify differences in gene expression between patients with in-hospital delirium from a known etiology (urinary tract infection [UTI]) and patients with delirium from an unknown etiology, as well as from nondelirious patients. METHODS Thirty patients with delirium (8 with UTI) and 21 nondelirious patients (11 with UTI) were included in this prospective case-control study. Transcriptomic profiles from messenger RNA sequencing of peripheral blood were analyzed for gene expression and disease-specific pathway enrichment patterns, correcting for systemic inflammatory response syndrome. Genes and pathways with significant differential activity based on Fisher exact test ( P < .05, |Z score| >2) are reported. RESULTS Patients with delirium with UTI, compared to patients with delirium without UTI, exhibited significant activation of interferon signaling, upstream cytokines, and transcription regulators, as well as significant inhibition of actin cytoskeleton, integrin, paxillin, glioma invasiveness signaling, and upstream growth factors. All patients with delirium, compared to nondelirious patients, had significant complement system activation. Among patients with delirium without UTI, compared to nondelirious patients without UTI, there was significant activation of elF4 and p7056 K signaling. CONCLUSIONS Differences exist in gene expression between delirious patients due to UTI presence, as well as due to the presence of delirium alone. Transcriptional profiling may help develop etiology-specific biomarkers for patients with delirium.
Collapse
Affiliation(s)
- Katrina Kalantar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Sara C. LaHue
- Department of Neurology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA,Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Hannah A. Sample
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Caitlin A. Contag
- School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Scott A. Josephson
- Department of Neurology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA,Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Michael R. Wilson
- Department of Neurology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA,Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Vanja C. Douglas
- Department of Neurology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA,Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| |
Collapse
|
40
|
Reynés B, Priego T, Cifre M, Oliver P, Palou A. Peripheral Blood Cells, a Transcriptomic Tool in Nutrigenomic and Obesity Studies: Current State of the Art. Compr Rev Food Sci Food Saf 2018; 17:1006-1020. [DOI: 10.1111/1541-4337.12363] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Bàrbara Reynés
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
- Inst. d'Investigació Sanitària Illes Balears (IdISBa); Palma Spain
| | - Teresa Priego
- Dept. of Physiology, Faculty of Medicine; Univ. Complutense de Madrid; Madrid Spain
| | - Margalida Cifre
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
| | - Paula Oliver
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
- Inst. d'Investigació Sanitària Illes Balears (IdISBa); Palma Spain
| | - Andreu Palou
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
- Inst. d'Investigació Sanitària Illes Balears (IdISBa); Palma Spain
| |
Collapse
|
41
|
Mehdi AM, Hamilton-Williams EE, Cristino A, Ziegler A, Bonifacio E, Le Cao KA, Harris M, Thomas R. A peripheral blood transcriptomic signature predicts autoantibody development in infants at risk of type 1 diabetes. JCI Insight 2018. [PMID: 29515040 DOI: 10.1172/jci.insight.98212] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Autoimmune-mediated destruction of pancreatic islet β cells results in type 1 diabetes (T1D). Serum islet autoantibodies usually develop in genetically susceptible individuals in early childhood before T1D onset, with multiple islet autoantibodies predicting diabetes development. However, most at-risk children remain islet-antibody negative, and no test currently identifies those likely to seroconvert. We sought a genomic signature predicting seroconversion risk by integrating longitudinal peripheral blood gene expression profiles collected in high-risk children included in the BABYDIET and DIPP cohorts, of whom 50 seroconverted. Subjects were followed for 10 years to determine time of seroconversion. Any cohort effect and the time of seroconversion were corrected to uncover genes differentially expressed (DE) in seroconverting children. Gene expression signatures associated with seroconversion were evident during the first year of life, with 67 DE genes identified in seroconverting children relative to those remaining antibody negative. These genes contribute to T cell-, DC-, and B cell-related immune responses. Near-birth expression of ADCY9, PTCH1, MEX3B, IL15RA, ZNF714, TENM1, and PLEKHA5, along with HLA risk score predicted seroconversion (AUC 0.85). The ubiquitin-proteasome pathway linked DE genes and T1D susceptibility genes. Therefore, a gene expression signature in infancy predicts risk of seroconversion. Ubiquitination may play a mechanistic role in diabetes progression.
Collapse
Affiliation(s)
- Ahmed M Mehdi
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Emma E Hamilton-Williams
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Alexandre Cristino
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Anette Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum Munchen, Neuherberg, and Forschergruppe Diabetes, Klinikum rechts der Isar, Institut für Diabetesforschung, Neuherberg, Germany
| | - Ezio Bonifacio
- CRTD-DFG Research Center for Regenerative Therapies Dresden, Medical Faculty Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Kim-Anh Le Cao
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Mark Harris
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia.,Lady Cilento Children's Hospital, South Brisbane, Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| |
Collapse
|
42
|
Katiyar A, Sharma S, Singh TP, Kaur P. Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis. Front Genet 2018; 9:42. [PMID: 29503661 PMCID: PMC5820528 DOI: 10.3389/fgene.2018.00042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/30/2018] [Indexed: 01/21/2023] Open
Abstract
Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune diseases predominantly multiple sclerosis (MS). Though EMS and MS are evidently diverse in their phenotype, they are linked by a common autoimmune condition or immunodeficiency which could play a role in the expansion of endometriosis and possibly increase the risk of developing MS in women with EMS. However, the common molecular links connecting EMS with MS are still unclear. We conducted a meta-analysis of microarray experiments focused on EMS and MS with their respective controls. The GEO2R web application discovered a total of 711 and 1516 genes that are differentially expressed across the experimental conditions in EMS and MS, respectively with 129 shared DEGs between them. The functional enrichment analysis of DEGs predicts the shared gene expression signatures as well as the overlapping biological processes likely to infer the co-occurrence of EMS with MS. Network based meta-analysis unveiled six interaction networks/crosstalks through overlapping edges between commonly dysregulated pathways of EMS and MS. The PTPN1, ERBB3, and CDH1 were observed to be the highly ranked hub genes connected with disease-related genes of both EMS and MS. Androgen receptor (AR) and nuclear factor-kB p65 (RelA) were observed to be the most enriched transcription factor in the upstream of shared down-regulated and up-regulated genes, respectively. The two disease sample sets compared through crosstalk interactions between shared pathways revealed commonly up- and down-regulated expressions of 10 immunomodulatory proteins as probable linkers between EMS and MS. This study pinpoints the number of shared genes, pathways, protein kinases, and upstream regulators that may help in the development of biomarkers for diagnosis of MS and endometriosis at the same time through improved understanding of shared molecular signatures and crosstalk.
Collapse
Affiliation(s)
- Amit Katiyar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
43
|
Biomarker-guided stratification of autoimmune patients for biologic therapy. Curr Opin Immunol 2017; 49:56-63. [DOI: 10.1016/j.coi.2017.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/22/2017] [Accepted: 09/22/2017] [Indexed: 02/07/2023]
|
44
|
Barturen G, Alarcón-Riquelme ME. SLE redefined on the basis of molecular pathways. Best Pract Res Clin Rheumatol 2017; 31:291-305. [PMID: 29224672 DOI: 10.1016/j.berh.2017.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 09/01/2017] [Indexed: 12/11/2022]
Abstract
The implementation of precision medicine requires the recruiting of patients in statistically enough numbers, the possibility of obtaining enough materials, and the integration of data from various platforms, which are all real limitations. These types of studies have been performed extensively in cancer but barely on systemic lupus erythematosus (SLE) or other rheumatic diseases. To consider the practical use of the information obtained from such studies, we have to take into account the best biological fluid to use, the ease to perform the analysis in clinical practice, and its relevance to clinical practice. Here we review the most relevant studies that have performed analyses that attempt to classify or stratify SLE. We focus on two types of studies: those that stratify individuals diagnosed with SLE and those that compare SLE with other autoimmune diseases, defining differences and similarities that may be clinically relevant in the future.
Collapse
Affiliation(s)
- Guillermo Barturen
- Pfizer - University of Granada - Andalusian Government Center for Genomics and Oncological Research (GENYO), Av de la Ilustración 114, PTS, 18016, Granada, Spain.
| | - Marta E Alarcón-Riquelme
- Pfizer - University of Granada - Andalusian Government Center for Genomics and Oncological Research (GENYO), Av de la Ilustración 114, PTS, 18016, Granada, Spain; Unit of Inflammatory Chronic Diseases, Institute of Environmental Medicine, Karolinska Institutet, Solna, 17777, Sweden.
| |
Collapse
|
45
|
López-Urrutia E, Campos-Parra A, Herrera LA, Pérez-Plasencia C. Alternative splicing regulation in tumor necrosis factor-mediated inflammation. Oncol Lett 2017; 14:5114-5120. [PMID: 29113151 PMCID: PMC5656035 DOI: 10.3892/ol.2017.6905] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 07/07/2017] [Indexed: 02/06/2023] Open
Abstract
It is generally accepted that alternative splicing has an effect on disease when it leads to conspicuous changes in relevant proteins, but that the combinatorial effect of several small modifications can have marked outcomes as well. Inflammation is a complex process involving numerous signaling pathways, among which the tumor necrosis factor (TNF) pathway is one of the most studied. Signaling pathways are commonly represented as intricate cascades of molecular interactions that eventually lead to the activation of one or several genes. Alternative splicing is a common means of controlling protein expression in time and space; therefore, it can modulate the outcome of signaling pathways through small changes in their elements. Notably, the overall process is tightly regulated, which is easily overlooked when analyzing the pathway as a whole. The present review summarizes recent studies of the alternative splicing of key players of the TNF pathway leading to inflammation, and hypothesizes on the cumulative results of those modifications and the impact on cancer development.
Collapse
Affiliation(s)
- Eduardo López-Urrutia
- Genomics Laboratory, UBIMED, Faculty of Higher Studies-Iztacala, National Autonomous University, Tlalnepantla, 54090 State of Mexico, Mexico
| | - Alma Campos-Parra
- Genomics Laboratory, National Cancer Institute of Mexico, Tlalpan, 14680 Mexico City, Mexico
| | - Luis Alonso Herrera
- Epigenetics Laboratory, National Cancer Institute of Mexico, Tlalpan, 14680 Mexico City, Mexico
| | - Carlos Pérez-Plasencia
- Genomics Laboratory, UBIMED, Faculty of Higher Studies-Iztacala, National Autonomous University, Tlalnepantla, 54090 State of Mexico, Mexico.,Genomics Laboratory, National Cancer Institute of Mexico, Tlalpan, 14680 Mexico City, Mexico
| |
Collapse
|
46
|
Banchereau R, Cepika AM, Banchereau J, Pascual V. Understanding Human Autoimmunity and Autoinflammation Through Transcriptomics. Annu Rev Immunol 2017; 35:337-370. [PMID: 28142321 PMCID: PMC5937945 DOI: 10.1146/annurev-immunol-051116-052225] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated diseases. Applied to immunomonitoring, transcriptomics is starting to unravel diagnostic and prognostic signatures that stratify patients, track molecular changes associated with disease activity, define personalized treatment strategies, and generally inform clinical practice. Herein, we review the use of transcriptomics to define mechanistic, diagnostic, and predictive signatures in human autoimmunity and autoinflammation. We discuss some of the analytical approaches applied to extract biological knowledge from high-dimensional data sets. Finally, we touch upon emerging applications of transcriptomics to study eQTLs, B and T cell repertoire diversity, and isoform usage.
Collapse
Affiliation(s)
| | | | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06030;
| | - Virginia Pascual
- Baylor Institute for Immunology Research, Dallas, Texas 75204; , ,
| |
Collapse
|
47
|
Hudson M, Bernatsky S, Colmegna I, Lora M, Pastinen T, Klein Oros K, Greenwood CMT. Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis. Epigenetics 2017; 12:433-440. [PMID: 28387599 DOI: 10.1080/15592294.2017.1303581] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We undertook this study to identify DNA methylation signatures of three systemic autoimmune rheumatic diseases (SARDs), namely rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis, compared to healthy controls. Using a careful design to minimize confounding, we restricted our study to subjects with incident disease and performed our analyses on purified CD4+ T cells, key effector cells in SARD. We identified differentially methylated (using the Illumina Infinium HumanMethylation450 BeadChip array) and expressed (using the Illumina TruSeq stranded RNA-seq protocol) sites between cases and controls, and investigated the biological significance of this SARD signature using gene annotation databases. We recruited 13 seropositive rheumatoid arthritis, 19 systemic sclerosis, 12 systemic lupus erythematosus subjects, and 8 healthy controls. We identified 33 genes that were both differentially methylated and expressed (26 over- and 7 under-expressed) in SARD cases versus controls. The most highly overexpressed gene was CD1C (log fold change in expression = 1.85, adjusted P value = 0.009). In functional analysis (Ingenuity Pathway Analysis), the top network identified was lipid metabolism, molecular transport, small molecule biochemistry. The top canonical pathways included the mitochondrial L-carnitine shuttle pathway (P = 5E-03) and PTEN signaling (P = 8E-03). The top upstream regulator was HNF4A (P = 3E-05). This novel SARD signature contributes to ongoing work to further our understanding of the molecular mechanisms underlying SARD and provides novel targets of interest.
Collapse
Affiliation(s)
- Marie Hudson
- a Lady Davis Research Institute , Montréal , QC , Canada.,b Division of Rheumatology , Jewish General Hospital , Montréal , QC , Canada.,c Department of Medicine , McGill University , Montréal , QC , Canada
| | - Sasha Bernatsky
- c Department of Medicine , McGill University , Montréal , QC , Canada.,d The Research Institute of the McGill University Health Centre , Montréal , QC , Canada
| | - Ines Colmegna
- c Department of Medicine , McGill University , Montréal , QC , Canada.,d The Research Institute of the McGill University Health Centre , Montréal , QC , Canada
| | - Maximilien Lora
- d The Research Institute of the McGill University Health Centre , Montréal , QC , Canada
| | - Tomi Pastinen
- e McGill University and Genome Quebec Innovation Centre , McGill University , Montréal , QC , Canada
| | | | - Celia M T Greenwood
- a Lady Davis Research Institute , Montréal , QC , Canada.,f Department of Human Genetics , McGill University , Montréal , QC , Canada.,g Department of Oncology , McGill University , Montréal , QC , Canada.,h Department of Epidemiology , Biostatistics & Occupational Health, McGill University , Montréal , QC , Canada
| |
Collapse
|
48
|
Jha PK, Vijay A, Sahu A, Ashraf MZ. Comprehensive Gene expression meta-analysis and integrated bioinformatic approaches reveal shared signatures between thrombosis and myeloproliferative disorders. Sci Rep 2016; 6:37099. [PMID: 27892526 PMCID: PMC5125005 DOI: 10.1038/srep37099] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/25/2016] [Indexed: 02/06/2023] Open
Abstract
Thrombosis is a leading cause of morbidity and mortality in patients with myeloproliferative disorders (MPDs), particularly polycythemia vera (PV) and essential thrombocythemia (ET). Despite the attempts to establish a link between them, the shared biological mechanisms are yet to be characterized. An integrated gene expression meta-analysis of five independent publicly available microarray data of the three diseases was conducted to identify shared gene expression signatures and overlapping biological processes. Using INMEX bioinformatic tool, based on combined Effect Size (ES) approaches, we identified a total of 1,157 differentially expressed genes (DEGs) (697 overexpressed and 460 underexpressed genes) shared between the three diseases. EnrichR tool's rich library was used for comprehensive functional enrichment and pathway analysis which revealed "mRNA Splicing" and "SUMO E3 ligases SUMOylate target proteins" among the most enriched terms. Network based meta-analysis identified MYC and FN1 to be the most highly ranked hub genes. Our results reveal that the alterations in biomarkers of the coagulation cascade like F2R, PROS1, SELPLG and ITGB2 were common between the three diseases. Interestingly, the study has generated a novel database of candidate genetic markers, pathways and transcription factors shared between thrombosis and MPDs, which might aid in the development of prognostic therapeutic biomarkers.
Collapse
Affiliation(s)
| | - Aatira Vijay
- Defence Institute of Physiology and Allied Sciences, Delhi, INDIA
| | - Anita Sahu
- Defence Institute of Physiology and Allied Sciences, Delhi, INDIA
| | | |
Collapse
|
49
|
Pellino G, Pallante P, Selvaggi F. Novel biomarkers of fibrosis in Crohn’s disease. World J Gastrointest Pathophysiol 2016; 7:266-275. [PMID: 27574564 PMCID: PMC4981766 DOI: 10.4291/wjgp.v7.i3.266] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/27/2016] [Accepted: 07/22/2016] [Indexed: 02/06/2023] Open
Abstract
Fibrosis represents a major challenge in Crohn’s disease (CD), and many CD patients will develop fibrotic strictures requiring treatment throughout their lifetime. There is no drug that can reverse intestinal fibrosis, and so endoscopic balloon dilatation and surgery are the only effective treatments. Since patients may need repeated treatments, it is important to obtain the diagnosis at an early stage before strictures become symptomatic with extensive fibrosis. Several markers of fibrosis have been proposed, but most need further validation. Biomarkers can be measured either in biological samples obtained from the serum or bowel of CD patients, or using imaging tools and tests. The ideal tool should be easily obtained, cost-effective, and reliable. Even more challenging is fibrosis occurring in ulcerative colitis. Despite the important burden of intestinal fibrosis, including its detrimental effect on outcomes and quality of life in CD patients, it has received less attention than fibrosis occurring in other organs. A common mechanism that acts via a specific signaling pathway could underlie both intestinal fibrosis and cancer. A comprehensive overview of recently introduced biomarkers of fibrosis in CD is presented, along with a discussion of the controversial areas remaining in this field.
Collapse
|
50
|
Thorsen SU, Jakobsen C, Cohen A, Lundqvist M, Thygesen LC, Pipper C, Ascherio A, Svensson J. Perinatal vitamin D levels are not associated with later risk of developing pediatric-onset inflammatory bowel disease: a Danish case-cohort study. Scand J Gastroenterol 2016; 51:927-33. [PMID: 26872831 DOI: 10.3109/00365521.2016.1144218] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Objective Basic and epidemiologic studies on inflammatory bowel disease (IBD) have suggested an association between vitamin D and IBD risk. Though, the literature on IBD - especially pediatric-onset IBD - and vitamin D is still in its cradle. We therefore wanted to examine if levels of 25(OH)D at birth were associated with increased risk of developing pediatric-onset IBD. Material and methods A case-cohort study composed of cases diagnosed with Crohn's disease, ulcerative colitis or indeterminate/unclassified colitis and healthy controls. Cases and controls were matched on date of birth and were born in the period 1981-2004. Cases were diagnosed before the age of 18 years. The concentration of 25(OH)D was assessed from neonatal dried blood spots using a highly sensitive liquid chromatography tandem mass spectrometry. Odds ratios (OR) were calculated using conditional logistic regression and two-way ANOVA were used to test for season and birth year 25(OH)D variations. A total of 384 matched pairs were included in the statistical analyses. Results No significant association were found between levels of 25(OH)D and IBD risk in the adjusted model (OR [95% CI] (per 25 nmol/L increase), 1.12 [0.88; 1.42], p = 0.35). 25(OH)D levels were found to fluctuate significantly with season (p < 0.001) and year (p < 0.001). Median/Q1-Q3 values for 25(OH)D were 27.1/16.5-39.5 nmol/L for cases and 25.7/16.1-39.4 nmol/L for controls. Conclusion Our study do not suggest that a window of vulnerability exist around time of birth in regards to 25(OH)D levels and later pediatric-onset IBD risk.
Collapse
Affiliation(s)
- Steffen U Thorsen
- a Department of Paediatrics, Copenhagen Diabetes Research Center (CPH-DIRECT) , Herlev University Hospital , Herlev , Denmark ;,b Faculty of Health and Medical Sciences , University of Copenhagen , Copenhagen , Denmark
| | - Christian Jakobsen
- c Department of Paediatrics , Hvidovre University Hospital , Hvidovre , Denmark
| | - Arieh Cohen
- d Department of Congenital Disorders , Statens Serum Institute , Copenhagen S , Denmark
| | - Marika Lundqvist
- d Department of Congenital Disorders , Statens Serum Institute , Copenhagen S , Denmark
| | - Lau C Thygesen
- e National Institute of Public Health , University of Southern Denmark , Copenhagen K , Denmark
| | - Christian Pipper
- f Department of Public Health, Section of Biostatistics , University of Copenhagen , Copenhagen K , Denmark
| | - Alberto Ascherio
- g Department of Nutrition , Harvard T.H. Chan School of Public Health , Boston , MA , USA
| | - Jannet Svensson
- a Department of Paediatrics, Copenhagen Diabetes Research Center (CPH-DIRECT) , Herlev University Hospital , Herlev , Denmark
| |
Collapse
|