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Sánchez-Sanz A, Muñoz-Viana R, Sabín-Muñoz J, Moreno-Torres I, Brea-Álvarez B, Rodríguez-De la Fuente O, García-Merino A, Sánchez-López AJ. Response to Fingolimod in Multiple Sclerosis Patients Is Associated with a Differential Transcriptomic Regulation. Int J Mol Sci 2024; 25:1372. [PMID: 38338652 PMCID: PMC10855583 DOI: 10.3390/ijms25031372] [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: 12/22/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Fingolimod is an immunomodulatory sphingosine-1-phosphate (S1P) analogue approved for the treatment of relapsing-remitting multiple sclerosis (RRMS). The identification of biomarkers of clinical responses to fingolimod is a major necessity in MS to identify optimal responders and avoid the risk of disease progression in non-responders. With this aim, we used RNA sequencing to study the transcriptomic changes induced by fingolimod in peripheral blood mononuclear cells of MS-treated patients and their association with clinical response. Samples were obtained from 10 RRMS patients (five responders and five non-responders) at baseline and at 12 months of fingolimod therapy. Fingolimod exerted a vast impact at the transcriptional level, identifying 7155 differentially expressed genes (DEGs) compared to baseline that affected the regulation of numerous signaling pathways. These DEGs were predominantly immune related, including genes associated with S1P metabolism, cytokines, lymphocyte trafficking, master transcription factors of lymphocyte functions and the NF-kB pathway. Responder and non-responder patients exhibited a differential transcriptomic regulation during treatment, with responders presenting a higher number of DEGs (6405) compared to non-responders (2653). The S1P, NF-kB and TCR signaling pathways were differentially modulated in responder and non-responder patients. These transcriptomic differences offer the potential of being exploited as biomarkers of a clinical response to fingolimod.
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Affiliation(s)
- Alicia Sánchez-Sanz
- Neuroimmunology Unit, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, 28222 Madrid, Spain;
| | - Rafael Muñoz-Viana
- Bioinformatics Unit, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, 28222 Madrid, Spain;
| | - Julia Sabín-Muñoz
- Department of Neurology, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Madrid, Spain; (J.S.-M.); (O.R.-D.l.F.)
| | - Irene Moreno-Torres
- Demyelinating Diseases Unit, Hospital Universitario Fundación Jiménez Díaz, 28040 Madrid, Spain;
| | - Beatriz Brea-Álvarez
- Radiodiagnostic Division, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Madrid, Spain;
| | - Ofir Rodríguez-De la Fuente
- Department of Neurology, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Madrid, Spain; (J.S.-M.); (O.R.-D.l.F.)
| | - Antonio García-Merino
- Neuroimmunology Unit, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, 28222 Madrid, Spain;
- Department of Neurology, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Madrid, Spain; (J.S.-M.); (O.R.-D.l.F.)
- Department of Medicine, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Red Española de Esclerosis Múltiple (REEM), 08028 Barcelona, Spain
| | - Antonio J. Sánchez-López
- Neuroimmunology Unit, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, 28222 Madrid, Spain;
- Red Española de Esclerosis Múltiple (REEM), 08028 Barcelona, Spain
- Biobank, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, 28222 Madrid, Spain
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Sferruzza G, Clarelli F, Mascia E, Ferrè L, Ottoboni L, Sorosina M, Santoro S, Filippi M, Provero P, Esposito F. Transcriptional effects of fingolimod treatment on peripheral T cells in relapsing remitting multiple sclerosis patients. Pharmacogenomics 2022; 23:161-171. [PMID: 35068175 DOI: 10.2217/pgs-2021-0118] [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: 11/21/2022] Open
Abstract
Aim: To investigate the transcriptional changes induced by Fingolimod (FTY) in T cells of relapsing remitting multiple sclerosis patients. Patients & methods: Transcriptomic changes after 6 months of FTY therapy were evaluated on T cells from 24 relapsing remitting multiple sclerosis patients through RNA-sequencing, followed by technical validation and pathway analysis. Results: Among differentially expressed genes, CX3CR1 and CCR7 resulted strongly up- and down-regulated, respectively. Two relevant genes were validated with quantitative PCR and we largely confirmed findings from two previous microarray-based studies with similar design. Pathway analysis pointed to an involvement of processes related to immune function and cell migration. Conclusion: Our data support the evidence that FTY induces major transcriptional changes in genes involved in immune response and cell trafficking in T lymphocytes.
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Affiliation(s)
- Giacomo Sferruzza
- Department of Neurology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Neuroimmunology Unit, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Ferdinando Clarelli
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit & INSPE, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Elisabetta Mascia
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit & INSPE, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Laura Ferrè
- Department of Neurology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit & INSPE, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Linda Ottoboni
- Neuroimmunology Unit, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Melissa Sorosina
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit & INSPE, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Silvia Santoro
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit & INSPE, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Massimo Filippi
- Department of Neurology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Paolo Provero
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Department of Neurosciences 'Rita Levi Montalcini,' University of Turin, Turin 10126, Italy
| | - Federica Esposito
- Department of Neurology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit & INSPE, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
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Transcriptomic Analysis of Peripheral Monocytes upon Fingolimod Treatment in Relapsing Remitting Multiple Sclerosis Patients. Mol Neurobiol 2021; 58:4816-4827. [PMID: 34181235 DOI: 10.1007/s12035-021-02465-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/20/2021] [Indexed: 12/14/2022]
Abstract
Fingolimod (FTY), a second-line oral drug approved for relapsing remitting Multiple Sclerosis (RRMS) acts in preventing lymphocyte migration outside lymph nodes; moreover, several lines of evidence suggest that it also inhibits myeloid cell activation. In this study, we investigated the transcriptional changes induced by FTY in monocytes in order to better elucidate its mechanism of action. CD14+ monocytes were collected from 24 RRMS patients sampled at baseline and after 6 months of treatment and RNA profiles were obtained through next-generation sequencing. We conducted pathway and sub-paths analysis, followed by centrality analysis of cell-specific interactomes on differentially expressed genes (DEGs). We investigated also the predictive role of baseline monocyte transcription profile in influencing the response to FTY therapy. We observed a marked down-regulation effect (60 down-regulated vs. 0 up-regulated genes). Most of the down-regulated DEGs resulted related with monocyte activation and migration like IL7R, CCR7 and the Wnt signaling mediators LEF1 and TCF7. The involvement of Wnt signaling was also confirmed by subpaths analyses. Furthermore, pathway and network analyses showed an involvement of processes related to immune function and cell migration. Baseline transcriptional profile of the HLA class II gene HLA-DQA1 and HLA-DPA1 were associated with evidence of disease activity after 2 years of treatment. Our data support the evidence that FTY induces major transcriptional changes in monocytes, mainly regarding genes involved in cell trafficking and immune cell activation. The baseline transcriptional levels of genes associated with antigen presenting function were associated with disease activity after 2 years of FTY treatment.
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Yang J, Zhang D, Motojima M, Kume T, Hou Q, Pan Y, Duan A, Zhang M, Jiang S, Hou J, Shi J, Qin Z, Liu Z. Super-Enhancer-Associated Transcription Factors Maintain Transcriptional Regulation in Mature Podocytes. J Am Soc Nephrol 2021; 32:1323-1337. [PMID: 33771836 PMCID: PMC8259645 DOI: 10.1681/asn.2020081177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/30/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Transcriptional programs control cell fate, and identifying their components is critical for understanding diseases caused by cell lesion, such as podocytopathy. Although many transcription factors (TFs) are necessary for cell-state maintenance in glomeruli, their roles in transcriptional regulation are not well understood. METHODS The distribution of H3K27ac histones in human glomerulus cells was analyzed to identify superenhancer-associated TFs, and ChIP-seq and transcriptomics were performed to elucidate the regulatory roles of the TFs. Transgenic animal models of disease were further investigated to confirm the roles of specific TFs in podocyte maintenance. RESULTS Superenhancer distribution revealed a group of potential TFs in core regulatory circuits in human glomerulus cells, including FOXC1/2, WT1, and LMX1B. Integration of transcriptome and cistrome data of FOXC1/2 in mice resolved transcriptional regulation in podocyte maintenance. FOXC1/2 regulated differentiation-associated transcription in mature podocytes. In both humans and animal models, mature podocyte injury was accompanied by deregulation of FOXC1/2 expression, and FOXC1/2 overexpression could protect podocytes in zebrafish. CONCLUSIONS FOXC1/2 maintain podocyte differentiation through transcriptional stabilization. The genome-wide chromatin resources support further investigation of TFs' regulatory roles in glomeruli transcription programs.
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Affiliation(s)
- Jingping Yang
- Medical School of Nanjing University, Nanjing, China,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Difei Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Masaru Motojima
- Department of Clinical Pharmacology, Tokai University School of Medicine, Isehara, Japan
| | - Tsutomu Kume
- Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Qing Hou
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yu Pan
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Aiping Duan
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Mingchao Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Song Jiang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jinhua Hou
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jingsong Shi
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhaohui Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Zhihong Liu
- Medical School of Nanjing University, Nanjing, China,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
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Bonnan M, Berthelot E, Cabre P. Multiple sclerosis-like NMOSD patients suffer severe worsening of status after fingolimod initiation. Mult Scler Relat Disord 2021; 52:102975. [PMID: 33951589 DOI: 10.1016/j.msard.2021.102975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Initial clinical manifestations of NMOSD may rarely overlap with MS. Fingolimod may trigger severe attacks in patients with NMOSD previously misdiagnosed as MS. These cases are rare and their pathophysiology remains elusive. METHODS We recruited all NMOSD patients treated by fingolimod in a single-center cohort of Afro-Caribbean neuro-inflammatory patients in Fort-de-France (French West Indies). Six patients were collected from the literature. RESULTS Among 622 patients followed locally for MS, 101 received fingolimod and two suffered severe attacks revealing a typical NMOSD presentation. These two patients were found to have AQP4-IgG. The risk of misdiagnosed NMOSD in MS in our high-risk Afro-Caribbean patients was estimated to be 1.9% (0 to 4.7%). Among the whole cohort, relapses occurred within a month after fingolimod initiation in five patients. All attacks were severe and contrasted with previously benign attacks, suggesting a shift to a more severe disorder. An unusual finding in these patients was large brain lesions. CONCLUSION AQP4-IgG should be obtained before initiation of fingolimod in high-risk patients, especially in those from areas of high NMOSD prevalence.
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Affiliation(s)
- Mickael Bonnan
- Service de Neurologie, Centre Hospitalier de Pau, 4 Bd Hauterive, 64000 Pau, France.
| | - Emeline Berthelot
- Service de Neurologie, Hôpital Zobda Quitman, 97261 Fort-de-France, French West Indies
| | - Philippe Cabre
- Service de Neurologie, Hôpital Zobda Quitman, 97261 Fort-de-France, French West Indies
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Hao X, Gao M, He L, Ye X, Yang J, Zhang F, Liu R, Wei H. Deficiency of O-linked-glycosylation regulates activation of T cells and aggravates Concanavalin A-induced liver injury. Toxicology 2020; 433-434:152411. [PMID: 32081641 DOI: 10.1016/j.tox.2020.152411] [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: 10/20/2019] [Revised: 01/16/2020] [Accepted: 02/16/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Protein glycosylation is involved in immunological recognition and immune cell activation. The role of O-glycosylation in Concanavalin A (Con A)-induced autoimmune hepatitis (AIH) was elucidated in the present study. METHODS Mice were intravenously injected with Con A (10 mg/kg) to establish an AIH mouse model. Here, 24 h prior to administration of Con A, experimental mice were intragastrically administrated with O-glycosylation inhibitor (benzyl-α-GalNAc) at doses of 1 and 5 mg/kg, respectively, while control mice were administrated with the same volume of saline. Before and after administration of Con A for 6 and 12 h, mice were sacrificed and their plasma and livers were collected to score liver injury. Peripheral blood, spleen, and thymus were collected for flow cytometry analysis. The expression levels of neutrophilic alkaline phosphatase-3 (NALP3) and NALP6 in liver were evaluated as well. RESULTS Pre-treatment with benzyl-α-GalNAc increased the serum transaminase levels and induced more infiltration and necrosis in livers of Con A administrated mice. The levels of some pro-inflammation cytokines also increased in administrated mice. In addition, pretreatment with benzyl-α-GalNAc up-regulated the expression levels of NALP3 and NALP6. And benzyl-α-GalNAc inhibited the levels of apoptosis of thymus cells and influenced activation of T cells in peripheral blood and spleen of Con A administrated mice, especially that accelerated the physiological progression of CD4+CD25-CD69+ subset. CONCLUSION The present research demonstrated that benzyl-α-GalNAc aggravated Con A-induced AIH, and the role of the O-glycosylation inhibitor as the aggravation may be related to regulation of the levels of cytokines, as well as influencing proliferation of T cells.
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Affiliation(s)
- Xiaohua Hao
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshun East Street, Chaoyang District, Beijing, 100015, China.
| | - Meixin Gao
- Department of Gastroenterology, Peking University Ditan Teaching Hospital, No. 8 Jingshun East Street, Chaoyang District, Beijing, 100015, China.
| | - Lingling He
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshun East Street, Chaoyang District, Beijing, 100015, China.
| | - Xiaohui Ye
- Department of Gastroenterology, Beijing Huaxin Hospital, the First Affiliated Hospital of Tsinghua Uinversity, A Neighborhood of No.6, Jiuxianqiao, Chaoyang District, Beijing, 100016, China.
| | - Junru Yang
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshun East Street, Chaoyang District, Beijing, 100015, China.
| | - Fuyang Zhang
- Department of Gastroenterology, Peking University Ditan Teaching Hospital, No. 8 Jingshun East Street, Chaoyang District, Beijing, 100015, China.
| | - Ran Liu
- Miyun Education Hospital, Capital Medicine University, No. 383 Yangguang Street, Miyun District, Beijing, 101500, China.
| | - Hongshan Wei
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshun East Street, Chaoyang District, Beijing, 100015, China; Department of Gastroenterology, Peking University Ditan Teaching Hospital, No. 8 Jingshun East Street, Chaoyang District, Beijing, 100015, China.
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de Jong JM, Wang P, Oomkens M, Baron W. Remodeling of the interstitial extracellular matrix in white matter multiple sclerosis lesions: Implications for remyelination (failure). J Neurosci Res 2020; 98:1370-1397. [PMID: 31965607 DOI: 10.1002/jnr.24582] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/29/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022]
Abstract
The extracellular matrix (ECM) provides protection, rigidity, and structure toward cells. It consists, among others, of a wide variety of glycoproteins and proteoglycans, which act together to produce a complex and dynamic environment, most relevant in transmembrane events. In the brain, the ECM occupies a notable proportion of its volume and maintains the homeostasis of central nervous system (CNS). In addition, remodeling of the ECM, that is transient changes in ECM proteins regulated by matrix metalloproteinases (MMPs), is an important process that modulates cell behavior upon injury, thereby facilitating recovery. Failure of ECM remodeling plays an important role in the pathogenesis of multiple sclerosis (MS), a neurodegenerative demyelinating disease of the CNS with an inflammatory response against protective myelin sheaths that surround axons. Remyelination of denuded axons improves the neuropathological conditions of MS, but this regeneration process fails over time, leading to chronic disease progression. In this review, we uncover abnormal ECM remodeling in MS lesions by discussing ECM remodeling in experimental demyelination models, that is when remyelination is successful, and compare alterations in ECM components to the ECM composition and MMP expression in the parenchyma of demyelinated MS lesions, that is when remyelination fails. Inter- and intralesional differences in ECM remodeling in the distinct white matter MS lesions are discussed in terms of consequences for oligodendrocyte behavior and remyelination (failure). Hence, the review will aid to understand how abnormal ECM remodeling contributes to remyelination failure in MS lesions and assists in developing therapeutic strategies to promote remyelination.
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Affiliation(s)
- Jody M de Jong
- Section Molecular Neurobiology, Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Peng Wang
- Section Molecular Neurobiology, Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Michelle Oomkens
- Section Molecular Neurobiology, Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Wia Baron
- Section Molecular Neurobiology, Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Hecker M, Rüge A, Putscher E, Boxberger N, Rommer PS, Fitzner B, Zettl UK. Aberrant expression of alternative splicing variants in multiple sclerosis - A systematic review. Autoimmun Rev 2019; 18:721-732. [PMID: 31059848 DOI: 10.1016/j.autrev.2019.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Alternative splicing is an important form of RNA processing that affects nearly all human genes. The differential expression of specific transcript and protein isoforms holds the potential of novel biomarkers for complex diseases. In this systematic review, we compiled the existing literature on aberrant alternative splicing events in multiple sclerosis (MS). METHODS A systematic literature search in the PubMed database was carried out and supplemented by screening the reference lists of the identified articles. We selected only MS-related original research studies which compared the levels of different isoforms of human protein-coding genes. A narrative synthesis of the research findings was conducted. Additionally, we performed a case-control analysis using high-density transcriptome microarray data to reevaluate the genes that were examined in the reviewed studies. RESULTS A total of 160 records were screened. Of those, 36 studies from the last two decades were included. Most commonly, peripheral blood samples were analyzed (32 studies), and PCR-based techniques were usually employed (27 studies) for measuring the expression of selected genes. Two studies used an exploratory genome-wide approach. Overall, 27 alternatively spliced genes were investigated. Nine of these genes appeared in at least two studies (CD40, CFLAR, FOXP3, IFNAR2, IL7R, MOG, PTPRC, SP140 and TNFRSF1A). The microarray data analysis confirmed differential alternative pre-mRNA splicing for 19 genes. CONCLUSIONS An altered RNA processing of genes mediating immune signaling pathways has been repeatedly implicated in MS. The analysis of individual exon-level expression patterns is stimulated by the advancement of transcriptome profiling technologies. In particular, the examination of genes encoded in MS-associated genetic regions may provide important insights into the pathogenesis of the disease and help to identify new biomarkers.
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Affiliation(s)
- Michael Hecker
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany.
| | - Annelen Rüge
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Elena Putscher
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Nina Boxberger
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Paulus Stefan Rommer
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany; Medical University of Vienna, Department of Neurology, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Brit Fitzner
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Uwe Klaus Zettl
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
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Moreno-Torres I, González-García C, Marconi M, García-Grande A, Rodríguez-Esparragoza L, Elvira V, Ramil E, Campos-Ruíz L, García-Hernández R, Al-Shahrour F, Fustero-Torre C, Sánchez-Sanz A, García-Merino A, Sánchez López AJ. Immunophenotype and Transcriptome Profile of Patients With Multiple Sclerosis Treated With Fingolimod: Setting Up a Model for Prediction of Response in a 2-Year Translational Study. Front Immunol 2018; 9:1693. [PMID: 30090102 PMCID: PMC6068231 DOI: 10.3389/fimmu.2018.01693] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 07/10/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Fingolimod is a functional sphingosine-1-phosphate antagonist approved for the treatment of multiple sclerosis (MS). Fingolimod affects lymphocyte subpopulations and regulates gene expression in the lymphocyte transcriptome. Translational studies are necessary to identify cellular and molecular biomarkers that might be used to predict the clinical response to the drug. In MS patients, we aimed to clarify the differential effects of fingolimod on T, B, and natural killer (NK) cell subsets and to identify differentially expressed genes in responders and non-responders (NRs) to treatment. MATERIALS AND METHODS Samples were obtained from relapsing-remitting multiple sclerosis patients before and 6 months after starting fingolimod. Forty-eight lymphocyte subpopulations were measured by flow cytometry based on surface and intracellular marker analysis. Transcriptome sequencing by next-generation technologies was used to define the gene expression profiling in lymphocytes at the same time points. NEDA-3 (no evidence of disease activity) and NEDA-4 scores were measured for all patients at 1 and 2 years after beginning fingolimod treatment to investigate an association with cellular and molecular characteristics. RESULTS Fingolimod affects practically all lymphocyte subpopulations and exerts a strong effect on genetic transcription switching toward an anti-inflammatory and antioxidant response. Fingolimod induces a differential effect in lymphocyte subpopulations after 6 months of treatment in responder and NR patients. Patients who achieved a good response to the drug compared to NR patients exhibited higher percentages of NK bright cells and plasmablasts, higher levels of FOXP3, glucose phosphate isomerase, lower levels of FCRL1, and lower Expanded Disability Status Scale at baseline. The combination of these possible markers enabled us to build a probabilistic linear model to predict the clinical response to fingolimod. CONCLUSION MS patients responsive to fingolimod exhibit a recognizable distribution of lymphocyte subpopulations and a different pretreatment gene expression signature that might be useful as a biomarker.
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Affiliation(s)
- Irene Moreno-Torres
- Neuroimmunology Unit, Puerta de Hierro-Segovia de Arana Health Research Institute, Madrid, Spain
- Autonomous University of Madrid, Madrid, Spain
| | - Coral González-García
- Neuroimmunology Unit, Puerta de Hierro-Segovia de Arana Health Research Institute, Madrid, Spain
| | - Marco Marconi
- Centre for Plant Biotechnology and Genomics, Madrid, Spain
| | - Aranzazu García-Grande
- Flow Cytometry Core Facility, Puerta de Hierro-Segovia de Arana Health Research Institute, Madrid, Spain
| | | | - Víctor Elvira
- IMT Lille Douai & CRIStAL, Univ. de Lille, Douai, France
| | - Elvira Ramil
- Sequencing Core Facility, Puerta de Hierro-Segovia de Arana Health Research Institute, Madrid, Spain
| | - Lucía Campos-Ruíz
- Neuroimmunology Unit, Puerta de Hierro-Segovia de Arana Health Research Institute, Madrid, Spain
| | - Ruth García-Hernández
- Neuroimmunology Unit, Puerta de Hierro-Segovia de Arana Health Research Institute, Madrid, Spain
- Autonomous University of Madrid, Madrid, Spain
| | - Fátima Al-Shahrour
- Bioinformatics Unit of Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Coral Fustero-Torre
- Bioinformatics Unit of Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Alicia Sánchez-Sanz
- Neuroimmunology Unit, Puerta de Hierro-Segovia de Arana Health Research Institute, Madrid, Spain
| | - Antonio García-Merino
- Neuroimmunology Unit, Puerta de Hierro-Segovia de Arana Health Research Institute, Madrid, Spain
- Autonomous University of Madrid, Madrid, Spain
- Neurology Department, Puerta de Hierro University Hospital, Madrid, Spain
- Red Española de Esclerosis Múltiple (REEM), Barcelona, Spain
| | - Antonio José Sánchez López
- Neuroimmunology Unit, Puerta de Hierro-Segovia de Arana Health Research Institute, Madrid, Spain
- Red Española de Esclerosis Múltiple (REEM), Barcelona, Spain
- Biobank, Puerta de Hierro University Hospital-IDIPHISA, Madrid, Spain
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Koczan D, Fitzner B, Klaus Zettl U, Hecker M. Microarray data of transcriptome shifts in blood cell subsets during S1P receptor modulator therapy. Sci Data 2018; 5:180145. [PMID: 30040082 PMCID: PMC6057441 DOI: 10.1038/sdata.2018.145] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/21/2018] [Indexed: 12/29/2022] Open
Abstract
Treatment with fingolimod, a sphingosine-1-phosphate (S1P) receptor modulator, prevents the egress of immune cell subpopulations from lymphoid tissues into the blood. We obtained peripheral blood samples from patients with relapsing multiple sclerosis before the initiation of fingolimod therapy, after one day and after 3 months. To investigate the differential expression induced by the drug, five different cell populations were isolated. We then employed 150 Human Transcriptome Arrays (HTA 2.0) interrogating >245,000 protein-coding and >40,000 non-coding transcript isoforms. After 3 months of treatment, CD4+ and CD8+ T-cells showed huge transcriptome shifts, whereas the profiles of B-cells (CD19+) were slightly altered and those of monocytes (CD14+) and natural killer cells (CD56+) remained unaffected. With >6 million probes for exons and splice junctions, our large HTA 2.0 dataset provides a deep view into alternative splicing patterns in immune cell subsets. Our data may also be useful for comparing the effects on gene expression signatures of novel S1P receptor modulators, which are currently tested in clinical trials for other autoimmune and neurodegenerative diseases.
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Affiliation(s)
- Dirk Koczan
- University of Rostock, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany
| | - Brit Fitzner
- Steinbeis Transfer Centre for Proteome Analysis, Schillingallee 70, 18057 Rostock, Germany
| | - Uwe Klaus Zettl
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Michael Hecker
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
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11
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Angerer IC, Hecker M, Koczan D, Roch L, Friess J, Rüge A, Fitzner B, Boxberger N, Schröder I, Flechtner K, Thiesen HJ, Winkelmann A, Meister S, Zettl UK. Transcriptome profiling of peripheral blood immune cell populations in multiple sclerosis patients before and during treatment with a sphingosine-1-phosphate receptor modulator. CNS Neurosci Ther 2018; 24:193-201. [PMID: 29314605 DOI: 10.1111/cns.12793] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/07/2017] [Accepted: 12/07/2017] [Indexed: 12/11/2022] Open
Abstract
AIMS Fingolimod is a sphingosine-1-phosphate (S1P) receptor modulator approved for the treatment of the relapsing form of multiple sclerosis (MS). It prevents the egress of lymphocyte subpopulations from lymphoid tissues into the circulation. Here, we explored the broad effects of fingolimod on gene expression in different immune cell subsets. METHODS Utilizing 150 high-resolution microarrays from Affymetrix, we obtained the transcriptome profiles of 5 cell populations, which were separated from the peripheral blood of MS patients prior to and following oral administration of fingolimod. RESULTS After 3 months of treatment, significant transcriptome shifts were seen in CD4+ and CD8+ cells, which is mainly attributable to the selective homing of naive T cells and central memory T cells. Although the number of B cells was greatly reduced in the blood of fingolimod-treated MS patients, the analysis of differential expression in CD19+ cells identified only a small set of 42 genes, which indicated a slightly higher frequency of transitional B cells. The transcriptome signatures of CD14+ monocytes and CD56+ natural killer cells were not affected. CONCLUSION Our study corroborates changes in the composition of circulating immune cells in response to fingolimod and delineates the respective implications at the RNA level. Our data may be valuable for comparing the effects of novel S1P receptor modulating agents, which may be a therapeutic option for patients with secondary progressive MS as well.
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Affiliation(s)
- Ines C Angerer
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
| | - Michael Hecker
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany.,Steinbeis Transfer Center for Proteome Analysis, Rostock, Germany
| | - Dirk Koczan
- Steinbeis Transfer Center for Proteome Analysis, Rostock, Germany.,Institute of Immunology, University of Rostock, Rostock, Germany
| | - Luisa Roch
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
| | - Jörg Friess
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
| | - Annelen Rüge
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
| | - Brit Fitzner
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany.,Steinbeis Transfer Center for Proteome Analysis, Rostock, Germany
| | - Nina Boxberger
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
| | - Ina Schröder
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
| | | | - Hans-Jürgen Thiesen
- Steinbeis Transfer Center for Proteome Analysis, Rostock, Germany.,Institute of Immunology, University of Rostock, Rostock, Germany
| | - Alexander Winkelmann
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
| | - Stefanie Meister
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
| | - Uwe K Zettl
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
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12
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Role of Immunological Memory Cells as a Therapeutic Target in Multiple Sclerosis. Brain Sci 2017; 7:brainsci7110148. [PMID: 29112130 PMCID: PMC5704155 DOI: 10.3390/brainsci7110148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/31/2017] [Accepted: 11/02/2017] [Indexed: 12/14/2022] Open
Abstract
Pharmacological targeting of memory cells is an attractive treatment strategy in various autoimmune diseases, such as psoriasis and rheumatoid arthritis. Multiple sclerosis is the most common inflammatory disorder of the central nervous system, characterized by focal immune cell infiltration, activation of microglia and astrocytes, along with progressive damage to myelin sheaths, axons, and neurons. The current review begins with the identification of memory cell types in the previous literature and a recent description of the modulation of these cell types in T, B, and resident memory cells in the presence of different clinically approved multiple sclerosis drugs. Overall, this review paper tries to determine the potential of memory cells to act as a target for the current or newly-developed drugs.
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13
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Boral D, Vishnoi M, Liu HN, Yin W, Sprouse ML, Scamardo A, Hong DS, Tan TZ, Thiery JP, Chang JC, Marchetti D. Molecular characterization of breast cancer CTCs associated with brain metastasis. Nat Commun 2017; 8:196. [PMID: 28775303 PMCID: PMC5543046 DOI: 10.1038/s41467-017-00196-1] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 06/09/2017] [Indexed: 12/30/2022] Open
Abstract
The enumeration of EpCAM-positive circulating tumor cells (CTCs) has allowed estimation of overall metastatic burden in breast cancer patients. However, a thorough understanding of CTCs associated with breast cancer brain metastasis (BCBM) is necessary for early identification and evaluation of treatment response to BCBM. Here we report that BCBM CTCs is enriched in a distinct sub-population of cells identifiable by their biomarker expression and mutational content. Deriving from a comprehensive analysis of CTC transcriptomes, we discovered a unique "circulating tumor cell gene signature" that is distinct from primary breast cancer tissues. Further dissection of the circulating tumor cell gene signature identified signaling pathways associated with BCBM CTCs that may have roles in potentiating BCBM. This study proposes CTC biomarkers and signaling pathways implicated in BCBM that may be used either as a screening tool for brain micro-metastasis detection or for making rational treatment decisions and monitoring therapeutic response in patients with BCBM.Characterization of CTCs derived from breast cancer patients with brain metastasis (BCBM) may allow for early diagnosis of brain metastasis and/or help for treatment choice and its efficacy. In this study, the authors identify a unique signature, based on patient-derived CTCs transcriptomes, for BCBM- CTCs that is different from primary tumors.
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Affiliation(s)
- Debasish Boral
- Biomarker Research Program Center, Houston Methodist Research Institute, Houston,, 77030, TX, USA
| | - Monika Vishnoi
- Biomarker Research Program Center, Houston Methodist Research Institute, Houston,, 77030, TX, USA
| | - Haowen N Liu
- Biomarker Research Program Center, Houston Methodist Research Institute, Houston,, 77030, TX, USA
| | - Wei Yin
- Biomarker Research Program Center, Houston Methodist Research Institute, Houston,, 77030, TX, USA
| | - Marc L Sprouse
- Biomarker Research Program Center, Houston Methodist Research Institute, Houston,, 77030, TX, USA
| | - Antonio Scamardo
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston,, 77030, TX, USA
| | - David S Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston,, 77030, TX, USA
| | - Tuan Z Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Jean P Thiery
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Jenny C Chang
- Institute for Academic Medicine, Houston Methodist Hospital, Houston,, 77030, TX, USA
| | - Dario Marchetti
- Biomarker Research Program Center, Houston Methodist Research Institute, Houston,, 77030, TX, USA.
- Institute for Academic Medicine, Houston Methodist Hospital, Houston,, 77030, TX, USA.
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14
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Fingolimod alters the transcriptome profile of circulating CD4+ cells in multiple sclerosis. Sci Rep 2017; 7:42087. [PMID: 28155899 PMCID: PMC5290459 DOI: 10.1038/srep42087] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/04/2017] [Indexed: 01/09/2023] Open
Abstract
Multiple sclerosis is a demyelinating disease affecting the central nervous system. T cells are known to contribute to this immune-mediated condition. Fingolimod modulates sphingosine-1-phosphate receptors, thereby preventing the egress of lymphocytes, especially CCR7-expressing CD8+ and CD4+ T cells, from lymphoid tissues. Using Affymetrix Human Transcriptome Arrays (HTA 2.0), we performed a transcriptome profiling analysis of CD4+ cells obtained from the peripheral blood of patients with highly active relapsing-remitting multiple sclerosis. The samples were drawn before the first administration of fingolimod as well as 24 hours and 3 months after the start of therapy. Three months after treatment initiation, 890 genes were found to be differentially expressed with fold-change >2.0 and t-test p-value < 0.001, among them several microRNA precursors. A subset of 272 genes were expressed at lower levels, including CCR7 as expected, while 618 genes showed an increase in expression, e.g., CCR2, CX3CR1, CD39, CD58 as well as LYN, PAK1 and TLR2. To conclude, we studied the gene expression of CD4+ cells to evaluate the effects of fingolimod treatment, and we identified 890 genes to be altered in expression after continuous drug administration. T helper cells circulating in the blood during fingolimod therapy present a distinct gene expression signature.
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