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Nguyen H, Nguyen H, Tran D, Draghici S, Nguyen T. Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges. Nucleic Acids Res 2024; 52:4761-4783. [PMID: 38619038 PMCID: PMC11109966 DOI: 10.1093/nar/gkae267] [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: 10/26/2023] [Revised: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 04/16/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the measurement of the expression of all genes in each individual cell contained in a sample. Information at the single-cell level has been shown to be extremely useful in many areas. However, performing single-cell experiments is expensive. Although cellular deconvolution cannot provide the same comprehensive information as single-cell experiments, it can extract cell-type information from bulk RNA data, and therefore it allows researchers to conduct studies at cell-type resolution from existing bulk datasets. For these reasons, a great effort has been made to develop such methods for cellular deconvolution. The large number of methods available, the requirement of coding skills, inadequate documentation, and lack of performance assessment all make it extremely difficult for life scientists to choose a suitable method for their experiment. This paper aims to fill this gap by providing a comprehensive review of 53 deconvolution methods regarding their methodology, applications, performance, and outstanding challenges. More importantly, the article presents a benchmarking of all these 53 methods using 283 cell types from 30 tissues of 63 individuals. We also provide an R package named DeconBenchmark that allows readers to execute and benchmark the reviewed methods (https://github.com/tinnlab/DeconBenchmark).
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Affiliation(s)
- Hung Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
| | - Ha Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
| | - Duc Tran
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, USA
- Advaita Bioinformatics, Ann Arbor, MI, USA
| | - Tin Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
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Shidahara K, Katsuyama T, Hirose K, Matsumoto K, Nawachi S, Nakadoi T, Asano Y, Katayama Y, Miyawaki Y, Katsuyama E, Takano-Narazaki M, Matsumoto Y, Sada KE, Wada J. Infliximab biosimilar-induced lupus nephritis: A case report. Mod Rheumatol Case Rep 2023; 8:74-76. [PMID: 37902434 DOI: 10.1093/mrcr/rxad061] [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: 07/05/2023] [Revised: 09/25/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
We present a case of microhematuria, proteinuria and hypocomplementemia which developed in a 55-year-old female who was being treated with an infliximab biosimilar for rheumatoid arthritis. Renal biopsy showed lupus nephritis (ISN/RPS classification class IV + V). Treatment with the infliximab biosimilar was discontinued, and treatment with prednisolone, hydroxychloroquine and abatacept was started, resulting in clinical remission of lupus nephritis and RA. Although tumour necrosis factor-α α inhibitors are known to induce production of autoantibodies, symptoms are usually limited to skin involvement or arthritis, and renal complications are rare. Physicians should be aware of the risk of lupus nephritis and carefully monitor patients for the development of renal involvement during treatment with tumour necrosis factor-α inhibitors.
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Affiliation(s)
- Kenta Shidahara
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Takayuki Katsuyama
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kei Hirose
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kazuya Matsumoto
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Shoichi Nawachi
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Takato Nakadoi
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yosuke Asano
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yu Katayama
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yoshia Miyawaki
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Eri Katsuyama
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Mariko Takano-Narazaki
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yoshinori Matsumoto
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Ken-Ei Sada
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Department of Clinical Epidemiology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Jun Wada
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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Studham M, Vazquez‐Mateo C, Samy E, Haselmayer P, Aydemir A, Rolfe PA, Merrill JT, Morand EF, DeMartino J, Kao A, Townsend R. Identifying lupus Patient Subsets Through Immune Cell Deconvolution of Gene Expression Data in Two Atacicept Phase II Studies. ACR Open Rheumatol 2023; 5:536-546. [PMID: 37710418 PMCID: PMC10570667 DOI: 10.1002/acr2.11594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/06/2023] [Accepted: 07/03/2023] [Indexed: 09/16/2023] Open
Abstract
OBJECTIVE To use cell-based gene signatures to identify patients with systemic lupus erythematous (SLE) in the phase II/III APRIL-SLE and phase IIb ADDRESS II trials most likely to respond to atacicept. METHODS A published immune cell deconvolution algorithm based on Affymetrix gene array data was applied to whole blood gene expression from patients entering APRIL-SLE. Five distinct patient clusters were identified. Patient characteristics, biomarkers, and clinical response to atacicept were assessed per cluster. A modified immune cell deconvolution algorithm was developed based on RNA sequencing data and applied to ADDRESS II data to identify similar patient clusters and their responses. RESULTS Patients in APRIL-SLE (N = 105) were segregated into the following five clusters (P1-5) characterized by dominant cell subset signatures: high neutrophils, T helper cells and natural killer (NK) cells (P1), high plasma cells and activated NK cells (P2), high B cells and neutrophils (P3), high B cells and low neutrophils (P4), or high activated dendritic cells, activated NK cells, and neutrophils (P5). Placebo- and atacicept-treated patients in clusters P2,4,5 had markedly higher British Isles Lupus Assessment Group (BILAG) A/B flare rates than those in clusters P1,3, with a greater treatment effect of atacicept on lowering flares in clusters P2,4,5. In ADDRESS II, placebo-treated patients from P2,4,5 were less likely to be SLE Responder Index (SRI)-4, SRI-6, and BILAG-Based Combined Lupus Assessment responders than those in P1,3; the response proportions again suggested lower placebo effect and a greater treatment differential for atacicept in P2,4,5. CONCLUSION This exploratory analysis indicates larger differences between placebo- and atacicept-treated patients with SLE in a molecularly defined patient subset.
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Affiliation(s)
| | | | | | | | | | | | - Joan T. Merrill
- University of Oklahoma Health Sciences CenterOklahoma CityOKUnited States
| | - Eric F. Morand
- Monash University School of Clinical SciencesClaytonAustralia
| | | | - Amy Kao
- EMD SeronoBillericaMAUnited States
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Gumkowska-Sroka O, Kotyla K, Mojs E, Palka K, Kotyla P. Novel Therapeutic Strategies in the Treatment of Systemic Sclerosis. Pharmaceuticals (Basel) 2023; 16:1066. [PMID: 37630981 PMCID: PMC10458905 DOI: 10.3390/ph16081066] [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: 05/29/2023] [Revised: 07/09/2023] [Accepted: 07/17/2023] [Indexed: 08/27/2023] Open
Abstract
Systemic sclerosis is a connective tissue disease of unknown origin and with an unpredictable course, with both cutaneous and internal organ manifestations. Despite the enormous progress in rheumatology and clinical immunology, the background of this disease is largely unknown, and no specific therapy exists. The therapeutic approach aims to treat and preserve the function of internal organs, and this approach is commonly referred to as organ-based treatment. However, in modern times, data from other branches of medicine may offer insight into how to treat disease-related complications, making it possible to find new drugs to treat this disease. In this review, we present therapeutic options aiming to stop the progression of fibrotic processes, restore the aberrant immune response, stop improper signalling from proinflammatory cytokines, and halt the production of disease-related autoantibodies.
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Affiliation(s)
- Olga Gumkowska-Sroka
- Department of Rheumatology and Clinical Immunology, Voivodeship Hospital No. 5 in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland;
- Department of Internal Medicine Rheumatology and Clinical Immunology, Medical University of Silesia, 40-055 Katowice, Poland; (K.K.); (K.P.)
| | - Kacper Kotyla
- Department of Internal Medicine Rheumatology and Clinical Immunology, Medical University of Silesia, 40-055 Katowice, Poland; (K.K.); (K.P.)
| | - Ewa Mojs
- Department of Clinical Psychology, Poznan University of Medical Sciences, 61-701 Poznan, Poland;
| | - Klaudia Palka
- Department of Internal Medicine Rheumatology and Clinical Immunology, Medical University of Silesia, 40-055 Katowice, Poland; (K.K.); (K.P.)
| | - Przemysław Kotyla
- Department of Rheumatology and Clinical Immunology, Voivodeship Hospital No. 5 in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland;
- Department of Internal Medicine Rheumatology and Clinical Immunology, Medical University of Silesia, 40-055 Katowice, Poland; (K.K.); (K.P.)
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Kalatskaya I, Giovannoni G, Leist T, Cerra J, Boschert U, Rolfe PA. Revealing the immune cell subtype reconstitution profile in patients from the CLARITY study using deconvolution algorithms after cladribine tablets treatment. Sci Rep 2023; 13:8067. [PMID: 37202447 DOI: 10.1038/s41598-023-34384-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/28/2023] [Indexed: 05/20/2023] Open
Abstract
Immune Cell Deconvolution methods utilizing gene expression profiling to quantify immune cells in tissues and blood are an appealing alternative to flow cytometry. Our objective was to investigate the applicability of deconvolution approaches in clinical trial settings to better investigate the mode of action of drugs for autoimmune diseases. Popular deconvolution methods CIBERSORT and xCell were validated using gene expression from the publicly available GSE93777 dataset that has comprehensive matching flow cytometry. As shown in the online tool, ~ 50% of signatures show strong correlation (r > 0.5) with the remainder showing moderate correlation, or in a few cases, no correlation. Deconvolution methods were then applied to gene expression data from the phase III CLARITY study (NCT00213135) to evaluate the immune cell profile of relapsing multiple sclerosis patients treated with cladribine tablets. At 96 weeks after treatment, deconvolution scores showed the following changes vs placebo: naïve, mature, memory CD4+ and CD8+ T cells, non-class switched, and class switched memory B cells and plasmablasts were significantly reduced, naïve B cells and M2 macrophages were more abundant. Results confirm previously described changes in immune cell composition following cladribine tablets treatment and reveal immune homeostasis of pro- vs anti-inflammatory immune cell subtypes, potentially supporting long-term efficacy.
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Affiliation(s)
- Irina Kalatskaya
- EMD Serono Research & Development Institute, Inc. (an affiliate of Merck KGaA), 45 Middlesex Turnpike, Billerica, MA, 01821, USA.
| | - Gavin Giovannoni
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Thomas Leist
- Division of Clinical Neuroimmunology, Jefferson University, Comprehensive MS Center, Philadelphia, PA, USA
| | - Joseph Cerra
- EMD Serono Research & Development Institute, Inc. (an affiliate of Merck KGaA), 45 Middlesex Turnpike, Billerica, MA, 01821, USA
- BISC Global, Boston, MA, USA
| | - Ursula Boschert
- Ares Trading S.A. (an affiliate of Merck KGaA), Eysins, Switzerland
| | - P Alexander Rolfe
- EMD Serono Research & Development Institute, Inc. (an affiliate of Merck KGaA), 45 Middlesex Turnpike, Billerica, MA, 01821, USA
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Jabado O, Maldonado MA, Schiff M, Weinblatt ME, Fleischmann R, Robinson WH, He A, Patel V, Greenfield A, Saini J, Galbraith D, Connolly SE. Differential Changes in ACPA Fine Specificity and Gene Expression in a Randomized Trial of Abatacept and Adalimumab in Rheumatoid Arthritis. Rheumatol Ther 2021; 9:391-409. [PMID: 34878629 PMCID: PMC8964842 DOI: 10.1007/s40744-021-00404-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022] Open
Abstract
Introduction The biologics abatacept and adalimumab have different mechanisms of action (MoAs). We analyzed data from patients with rheumatoid arthritis treated in AMPLE (NCT00929864) to explore the pharmacodynamic effects of abatacept or adalimumab on anti-citrullinated protein antibodies (ACPAs) and gene expression. Methods AMPLE was a phase IIIb, 2-year, randomized, head-to-head trial of abatacept versus adalimumab. Post hoc analyses of baseline anti-cyclic citrullinated peptide-2 (anti-CCP2, an ACPA surrogate) positive (+) status and ACPA fine-specificity profiles over time, as well as transcriptional profiling (peripheral whole blood), were performed. Results Of 646 patients treated (abatacept, n = 318; adalimumab, n = 328), ACPA and gene expression data were available from 508 and 566 patients, respectively. In anti-CCP2+ patients (n = 388), baseline fine specificities for most ACPAs were highly correlated; over 2 years, levels decreased with abatacept but not adalimumab. By year 2, expression of genes associated with T cell co-stimulation and antibody production was lower for abatacept versus adalimumab; expression of genes associated with proinflammatory signaling was lower for adalimumab versus abatacept. Treatment modulated the expression of T- and B-cell gene signatures, with differences in CD8+ T cells, activated T cells, plasma cells, B cells, natural killer cells (all lower with abatacept versus adalimumab), and polymorphonuclear leukocytes (higher with abatacept versus adalimumab). Conclusions In AMPLE, despite similar clinical outcomes, data showed that pharmacodynamic/genetic changes after 2 years of abatacept or adalimumab were consistent with drug MoAs. Further assessment of the relationship between such changes and clinical outcomes, including prediction of response, is warranted. Trial Registration ClinicalTrials.gov identifier, NCT00929864. Supplementary Information The online version contains supplementary material available at 10.1007/s40744-021-00404-x.
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Affiliation(s)
| | | | | | | | - Roy Fleischmann
- Metroplex Clinical Research Center and University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Aiqing He
- Bristol Myers Squibb, Princeton, NJ, USA
| | | | | | | | | | - Sean E Connolly
- Bristol Myers Squibb, B4290 3401 Princeton Pike, Lawrenceville, NJ, 08648, USA.
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Vanarsa K, Soomro S, Zhang T, Strachan B, Pedroza C, Nidhi M, Cicalese P, Gidley C, Dasari S, Mohan S, Thai N, Truong VTT, Jordan N, Saxena R, Putterman C, Petri M, Mohan C. Quantitative planar array screen of 1000 proteins uncovers novel urinary protein biomarkers of lupus nephritis. Ann Rheum Dis 2020; 79:1349-1361. [PMID: 32651195 PMCID: PMC7839323 DOI: 10.1136/annrheumdis-2019-216312] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 12/30/2022]
Abstract
OBJECTIVE The goal of these studies is to discover novel urinary biomarkers of lupus nephritis (LN). METHODS Urine from systemic lupus erythematosus (SLE) patients was interrogated for 1000 proteins using a novel, quantitative planar protein microarray. Hits were validated in an independent SLE cohort with inactive, active non-renal (ANR) and active renal (AR) patients, in a cohort with concurrent renal biopsies, and in a longitudinal cohort. Single-cell renal RNA sequencing data from LN kidneys were examined to deduce the cellular origin of each biomarker. RESULTS Screening of 1000 proteins revealed 64 proteins to be significantly elevated in SLE urine, of which 17 were ELISA validated in independent cohorts. Urine Angptl4 (area under the curve (AUC)=0.96), L-selectin (AUC=0.86), TPP1 (AUC=0.84), transforming growth factor-β1 (TGFβ1) (AUC=0.78), thrombospondin-1 (AUC=0.73), FOLR2 (AUC=0.72), platelet-derived growth factor receptor-β (AUC=0.67) and PRX2 (AUC=0.65) distinguished AR from ANR SLE, outperforming anti-dsDNA, C3 and C4, in terms of specificity, sensitivity and positive predictive value. In multivariate regression analysis, urine Angptl4, L-selectin, TPP1 and TGFβ1 were highly associated with disease activity, even after correction for demographic variables. In SLE patients with serial follow-up, urine L-selectin (followed by urine Angptl4 and TGFβ1) were best at tracking concurrent or pending disease flares. Importantly, several proteins elevated in LN urine were also expressed within the kidneys in LN, either within resident renal cells or infiltrating immune cells, based on single-cell RNA sequencing analysis. CONCLUSION Unbiased planar array screening of 1000 proteins has led to the discovery of urine Angptl4, L-selectin and TGFβ1 as potential biomarker candidates for tracking disease activity in LN.
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Affiliation(s)
- Kamala Vanarsa
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Sanam Soomro
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Ting Zhang
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Briony Strachan
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Claudia Pedroza
- Center for Clinical Research and Evidence-based Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Malavika Nidhi
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Pietro Cicalese
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Christopher Gidley
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Shobha Dasari
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Shree Mohan
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Nathan Thai
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Van Thi Thanh Truong
- Center for Clinical Research and Evidence-based Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Nicole Jordan
- Division of Rheumatology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ramesh Saxena
- Division of Nephrology, Department of Medicine, UT Southwestern Medical, Dallas, Texas, USA
| | - Chaim Putterman
- Division of Rheumatology, Albert Einstein College of Medicine, Bronx, New York, USA
- Azrieli Faculty of Medicine, Bar-Ilan University, Zefat, Israel
- Research Institute, Galilee Medical Center, Nahariya, Israel
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
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Moore E, Putterman C. Are lupus animal models useful for understanding and developing new therapies for human SLE? J Autoimmun 2020; 112:102490. [PMID: 32535128 DOI: 10.1016/j.jaut.2020.102490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 01/13/2023]
Abstract
Systemic lupus erythematosus is a systemic autoimmune disease driven by a complex combination of genetic, environmental, and other immunoregulatory factors. The development of targeted therapies is complicated by heterogeneous clinical manifestations, varying organ involvement, and toxicity. Despite advances in understanding the mechanisms contributing to SLE, only one biologic drug, belimumab, is FDA-approved. The identification and development of potential therapies have largely been driven by studies in lupus animal models. Therefore, direct comparison of both the therapeutic and immunological findings in human and murine SLE studies is critical and can reveal important insights into indeed how useful and relevant are murine studies in SLE drug development. Studies involving belimumab, mycophenolate mofetil, abatacept, rituximab, and anti-interferon strategies generally demonstrated analogous findings in the attenuation of SLE manifestations and modulation of select immune cell populations in human and murine SLE. While further basic and translational studies are needed to identify SLE patient subsets likely to respond to particular therapeutic modalities and in dissecting complex mechanisms, we believe that despite some inherent weaknesses SLE mouse models will continue to be integral in developing targeted SLE therapies.
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Affiliation(s)
- Erica Moore
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Chaim Putterman
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA; Division of Rheumatology, Albert Einstein College of Medicine, Bronx, NY, USA; Bar-Ilan University Azrieli Faculty of Medicine, Safed, Israel; Research Institute, Galilee Medical Center, Nahariya, Israel.
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Molecular profiling of rheumatoid arthritis patients reveals an association between innate and adaptive cell populations and response to anti-tumor necrosis factor. Arthritis Res Ther 2019; 21:216. [PMID: 31647025 PMCID: PMC6813112 DOI: 10.1186/s13075-019-1999-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/06/2019] [Indexed: 12/13/2022] Open
Abstract
Background The goal of this study is to use comprehensive molecular profiling to characterize clinical response to anti-TNF therapy in a real-world setting and identify reproducible markers differentiating good responders and non-responders in rheumatoid arthritis (RA). Methods Whole-blood mRNA, plasma proteins, and glycopeptides were measured in two cohorts of biologic-naïve RA patients (n = 40 and n = 36) from the Corrona CERTAIN (Comparative Effectiveness Registry to study Therapies for Arthritis and Inflammatory coNditions) registry at baseline and after 3 months of anti-TNF treatment. Response to treatment was categorized by EULAR criteria. A cell type-specific data analysis was conducted to evaluate the involvement of the most common immune cell sub-populations. Findings concordant between the two cohorts were further assessed for reproducibility using selected NCBI-GEO datasets and clinical laboratory measurements available in the CERTAIN database. Results A treatment-related signature suggesting a reduction in neutrophils, independent of the status of response, was indicated by a high level of correlation (ρ = 0.62; p < 0.01) between the two cohorts. A baseline, response signature of increased innate cell types in responders compared to increased adaptive cell types in non-responders was identified in both cohorts. This result was further assessed by applying the cell type-specific analysis to five other publicly available RA datasets. Evaluation of the neutrophil-to-lymphocyte ratio at baseline in the remaining patients (n = 1962) from the CERTAIN database confirmed the observation (odds ratio of good/moderate response = 1.20 [95% CI = 1.03–1.41, p = 0.02]). Conclusion Differences in innate/adaptive immune cell type composition at baseline may be a major contributor to response to anti-TNF treatment within the first 3 months of therapy.
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Litman T. Personalized medicine-concepts, technologies, and applications in inflammatory skin diseases. APMIS 2019; 127:386-424. [PMID: 31124204 PMCID: PMC6851586 DOI: 10.1111/apm.12934] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 01/31/2019] [Indexed: 12/19/2022]
Abstract
The current state, tools, and applications of personalized medicine with special emphasis on inflammatory skin diseases like psoriasis and atopic dermatitis are discussed. Inflammatory pathways are outlined as well as potential targets for monoclonal antibodies and small-molecule inhibitors.
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Affiliation(s)
- Thomas Litman
- Department of Immunology and MicrobiologyUniversity of CopenhagenCopenhagenDenmark
- Explorative Biology, Skin ResearchLEO Pharma A/SBallerupDenmark
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