Genetic variation in NDFIP1 modifies the metabolic patterns in immune cells of multiple sclerosis patients

Autoinmunidad; Marcadores genéticos; Trastornos neurológicosAutoimmunitat; Marcadors genètics; Trastorns neurològicsAutoimmunity; Genetic markers; Neurological disordersOne of the 233 polymorphisms associated with multiple sclerosis (MS) susceptibility lies within the NDFIP1 gene, and it was previously identified as eQTL in healthy controls. NDFIP1 shows interesting immune functions and is involved in the development of the central nervous system. We aimed at studying the NDFIP1 variant on activation and metabolism of immune cells. NDFIP1 mRNA and protein expression were assessed in PBMCs by qPCR and western blot in 87 MS patients and 84 healthy controls genotyped for rs4912622. Immune activation after PHA stimulation was evaluated by CD69 upregulation, and metabolic function of both basal and PHA-activated lymphocytes was studied by Seahorse Xfp-Analyzer. In minor-allele homozygous controls but not in patients, we found higher NDFIP1 expression, significantly reduced protein levels, and CD69 upregulation in B- and T-cells. PBMCs from minor-allele homozygous controls showed significantly higher basal mitochondrial respiration and ATP production compared to major-allele carriers, while minor-allele homozygous patients showed significantly lower metabolic activity than carriers of the major allele. In conclusion, we describe associations in minor-allele homozygous controls with lower levels of NDFIP1 protein, CD69 upregulation, and raised mitochondrial activity, which are not replicated in MS patients, suggesting a NDFIP1 differential effect in health and disease.This work was supported by the projects PI16/01259 and PI20/01634, integrated in the Plan Nacional de I + D + I, AES 2013–2016 and 2017–2020; funded by the ISCIII and co-funded by the European Regional Development Fund (ERDF) "A way to make Europe”. LEP is recipient of a contract from “REEM: Red Española de Esclerosis Múltiple” (RETICS-REEM RD16/0015/0013; www.reem.es). AGJ and JAZ hold contracts from the program “Promoción de empleo joven y garantía juvenil-CAM” (PEJ2018-003125-A and PEJD-2019-PRE/SAL-16662)

Oral contraceptives do not modify the risk of a second attack and disability accrual in a prospective cohort of women with a clinically isolated syndrome and early multiple sclerosis

Cohort study; Oral contraceptives; Second relapseEstudio de cohorte; Anticonceptivos orales; Segunda recaídaEstudi de cohorts; Anticonceptius orals; Segona recaigudaObjective: To evaluate whether oral contraceptive (OC) use is associated with the risk of a second attack and disability accrual in women with a clinically isolated syndrome (CIS) and early multiple sclerosis (MS). Methods: Reproductive information from women included in the Barcelona CIS prospective cohort was collected through a self-reported cross-sectional survey. We examined the relationship of OC exposure with the risk of a second attack and confirmed Expanded Disability Status Scale of 3.0 using multivariate Cox regression models, adjusted by age, topography of CIS, oligoclonal bands, baseline brain T2 lesions, body size at menarche, smoking, and disease-modifying treatment (DMT). OC and DMT exposures were considered as time-varying variables. Findings were confirmed with sensitivity analyses using propensity score models. Results: A total of 495 women were included, 389 (78.6%) referred to ever use OC and 341 (68.9%) started OC before the CIS. Exposure to OC was not associated with a second attack (adjusted hazard ratio (aHR) = 0.73, 95% confidence interval (CI) = 0.33–1.61) or disability accrual (aHR = 0.81, 95% CI = 0.17–3.76). Sensitivity analyses confirmed these results. Conclusion: OC use does not modify the risk of second attack or disability accrual in patients with CIS and early MS, once considered as a time-dependent exposure and adjusted by other potential confounders.The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This project was supported by FIS PI15/0070 from Ministry of Economy and Competitiveness of Spain

Exome sequencing study in patients with multiple sclerosis reveals variants associated with disease course

BACKGROUND: It remains unclear whether disease course in multiple sclerosis (MS) is influenced by genetic polymorphisms. Here, we aimed to identify genetic variants associated with benign and aggressive disease courses in MS patients. METHODS: MS patients were classified into benign and aggressive phenotypes according to clinical criteria. We performed exome sequencing in a discovery cohort, which included 20 MS patients, 10 with benign and 10 with aggressive disease course, and genotyping in 2 independent validation cohorts. The first validation cohort encompassed 194 MS patients, 107 with benign and 87 with aggressive phenotypes. The second validation cohort comprised 257 patients, of whom 224 patients had benign phenotypes and 33 aggressive disease courses. Brain immunohistochemistries were performed using disease course associated genes antibodies. RESULTS: By means of single-nucleotide polymorphism (SNP) detection and comparison of allele frequencies between patients with benign and aggressive phenotypes, a total of 16 SNPs were selected for validation from the exome sequencing data in the discovery cohort. Meta-analysis of genotyping results in two validation cohorts revealed two polymorphisms, rs28469012 and rs10894768, significantly associated with disease course. SNP rs28469012 is located in CPXM2 (carboxypeptidase X, M14 family, member 2) and was associated with aggressive disease course (uncorrected p value < 0.05). SNP rs10894768, which is positioned in IGSF9B (immunoglobulin superfamily member 9B) was associated with benign phenotype (uncorrected p value < 0.05). In addition, a trend for association with benign phenotype was observed for a third SNP, rs10423927, in NLRP9 (NLR family pyrin domain containing 9). Brain immunohistochemistries in chronic active lesions from MS patients revealed expression of IGSF9B in astrocytes and macrophages/microglial cells, and expression of CPXM2 and NLRP9 restricted to brain macrophages/microglia. CONCLUSIONS: Genetic variants located in CPXM2, IGSF9B, and NLRP9 have the potential to modulate disease course in MS patients and may be used as disease activity biomarkers to identify patients with divergent disease courses. Altogether, the reported results from this study support the influence of genetic factors in MS disease course and may help to better understand the complex molecular mechanisms underlying disease pathogenesis

Búsqueda de Biomarcadores Asociados con la Respuesta al Tratamiento con Interferón-beta en Pacientes con Esclerosis Múltiple Remitente-Recurrente

El interferón-beta (IFNβ) es un tratamiento parcialmente efectivo en pacientes con esclerosis múltiple remitente-recurrente (EMRR). Disminuye el número de brotes y reduce la actividad y carga lesional de la enfermedad medidas por resonancia magnética. Sin embargo, el coste del IFNβ es elevado, el tratamiento tiene efectos secundarios y, sobretodo, existe una proporción relativamente importante de pacientes que no responden al mismo. En la actualidad, no disponemos de biomarcadores que se puedan asociar de forma fiable con la respuesta al IFNβ. En este contexto, el objetivo principal de esta tesis doctoral es la identificación de biomarcadores moleculares de respuesta al tratamiento con IFNβ en pacientes con EMRR. Mediante la aplicación de tecnologías denominadas “ómicas”, principalmente genómica y transcriptómica, se ha identificado un grupo de biomarcadores que presentan un denominador funcional común, su inducción predominante por los IFNs de tipo 1. De esta forma, las células de sangre periférica de pacientes con EMRR que no responden al tratamiento con IFNβ se caracterizan por una huella de expresión génica formada por genes de inducción predominante o selectiva por los IFNs de tipo 1, que ya se encuentra presente antes del tratamiento con IFNβ. Tambien se observó que algunos polimorfismos de genes que pertenecen a la vía de los IFNs de tipo 1 fueron los que mejor discriminaron entre pacientes con buena y mala respuestal al IFNβ. Los resultados de la presente tesis doctoral permiten concluir que la vía de los IFNs de tipo 1 se encuentra alterada en células de sangre periférica, posiblemente monocitos, de pacientes con mala respuesta al IFNβ, y propone un conjunto de biomarcadores con potencial uso en la práctica clínica para predecir la respuesta al tratamiento con IFNβ en el paciente con EM.Interferon-beta (IFNβ) is a partially effective treatment for patients with relapsing-remitting multiple sclerosis (RRMS). IFNβ has been shown to decrease clinical relapses and reduce brain magnetic resonance imaging activity. However, the cost of IFNβ is significant, the drug is associated with a number of adverse reactions, and there is a relatively large proportion of patients who do not respond to therapy. At present, there is a lack of biomarkers reliably associated with the response to IFNβ. In this context, the main objective of this doctoral thesis is the identification of IFNβ-treatment response molecular biomarkers in patients with RRMS. By applying omic technologies, particularly genomics and transcriptomics, we identified a group of biomarkers that had in common their predominant induction by type 1 IFNs. In this way, peripheral blood cells from RRMS patients who will not respond to IFNβ are characterized by a gene expression signature composed of genes predominantly or selectively induced by type 1 IFNs, which is already present before treatment with IFNβ. Furthermore, some polymorphisms of genes belonging to the type 1 IFN pathway discriminated well between responders and non-responders to IFNβ. The results from this doctoral thesis point to a dysregulation of the type 1 IFN pathway in peripheral blood cells, most likely monocytes, from patients who will show a lack of response to IFNβ, and propose molecular biomarkers that may potentially be used in clinical practice to predict the response to IFNβ in MS patients

Búsqueda de biomarcadores asociados con la respuesta al tratamiento con interferón-beta en pacientes con esclerosis múltiple remitente-recurrente

El interferón-beta (IFNβ) es un tratamiento parcialmente efectivo en pacientes con esclerosis múltiple remitente-recurrente (EMRR). Disminuye el número de brotes y reduce la actividad y carga lesional de la enfermedad medidas por resonancia magnética. Sin embargo, el coste del IFNβ es elevado, el tratamiento tiene efectos secundarios y, sobretodo, existe una proporción relativamente importante de pacientes que no responden al mismo. En la actualidad, no disponemos de biomarcadores que se puedan asociar de forma fiable con la respuesta al IFNβ. En este contexto, el objetivo principal de esta tesis doctoral es la identificación de biomarcadores moleculares de respuesta al tratamiento con IFNβ en pacientes con EMRR. Mediante la aplicación de tecnologías denominadas "ómicas", principalmente genómica y transcriptómica, se ha identificado un grupo de biomarcadores que presentan un denominador funcional común, su inducción predominante por los IFNs de tipo 1. De esta forma, las células de sangre periférica de pacientes con EMRR que no responden al tratamiento con IFNβ se caracterizan por una huella de expresión génica formada por genes de inducción predominante o selectiva por los IFNs de tipo 1, que ya se encuentra presente antes del tratamiento con IFNβ. Tambien se observó que algunos polimorfismos de genes que pertenecen a la vía de los IFNs de tipo 1 fueron los que mejor discriminaron entre pacientes con buena y mala respuestal al IFNβ. Los resultados de la presente tesis doctoral permiten concluir que la vía de los IFNs de tipo 1 se encuentra alterada en células de sangre periférica, posiblemente monocitos, de pacientes con mala respuesta al IFNβ, y propone un conjunto de biomarcadores con potencial uso en la práctica clínica para predecir la respuesta al tratamiento con IFNβ en el paciente con EM.Interferon-beta (IFNβ) is a partially effective treatment for patients with relapsing-remitting multiple sclerosis (RRMS). IFNβ has been shown to decrease clinical relapses and reduce brain magnetic resonance imaging activity. However, the cost of IFNβ is significant, the drug is associated with a number of adverse reactions, and there is a relatively large proportion of patients who do not respond to therapy. At present, there is a lack of biomarkers reliably associated with the response to IFNβ. In this context, the main objective of this doctoral thesis is the identification of IFNβ-treatment response molecular biomarkers in patients with RRMS. By applying omic technologies, particularly genomics and transcriptomics, we identified a group of biomarkers that had in common their predominant induction by type 1 IFNs. In this way, peripheral blood cells from RRMS patients who will not respond to IFNβ are characterized by a gene expression signature composed of genes predominantly or selectively induced by type 1 IFNs, which is already present before treatment with IFNβ. Furthermore, some polymorphisms of genes belonging to the type 1 IFN pathway discriminated well between responders and non-responders to IFNβ. The results from this doctoral thesis point to a dysregulation of the type 1 IFN pathway in peripheral blood cells, most likely monocytes, from patients who will show a lack of response to IFNβ, and propose molecular biomarkers that may potentially be used in clinical practice to predict the response to IFNβ in MS patients

Pharmacogenomic study in patients with multiple sclerosis Responders and nonresponders to IFN-β

OBJECTIVES: We aimed to investigate the association between polymorphisms located in type I interferon (IFN)-induced genes, genes belonging to the toll-like receptor (TLR) pathway, and genes encoding neurotransmitter receptors and the response to IFN-β treatment in patients with multiple sclerosis (MS). METHODS: In a first or screening phase of the study, 384 polymorphisms were genotyped in 830 patients with MS classified into IFN-β responders (n = 416) and nonresponders (n = 414) according to clinical criteria. In a second or validation phase, the most significant polymorphisms associated with IFN-β response were genotyped in an independent validation cohort of 555 patients with MS (281 IFN-β responders and 274 nonresponders). RESULTS: Seven single nucleotide polymorphisms (SNPs) were selected from the screening phase for further validation: rs832032 (GABRR3; p = 0.0006), rs6597 (STUB1; p = 0.019), rs3747517 (IFIH1; p = 0.010), rs2277302 (PELI3; p = 0.017), rs10958713 (IKBKB; p = 0.003), rs2834202 (IFNAR1; p = 0.030), and rs4422395 (CXCL1; p = 0.017). None of these SNPs were significantly associated with IFN-β response when genotyped in an independent cohort of patients. Combined analysis of these SNPs in all patients with MS (N = 1,385) revealed 2 polymorphisms associated with IFN-β response: rs2277302 (PELI3; p = 0.008) and rs832032 (GABRR3; p = 0.006). CONCLUSIONS: These findings do not support an association between polymorphisms located in genes related to the type I IFN or TLR pathways or genes encoding neurotransmitter receptors and the clinical response to IFN-β. Nevertheless, additional genetic and functional studies of PELI3 and GABRR3 are warranted.SM is early stage researcher of the FP7 (2007-2013) Marie Curie Initial Training Network "UEPHA*MS" (2008-2012; Grant Agreement Number 212877). Spanish Ministry of Economy and Competitiveness, SAF/ 2012-34670, MS research, 2013-2015. Ministerio de Economía y Competitividad (MINECO) Convocatoria Proyectos de Investigación 2012 (Madrid, Spain); Funciones intracelulares de tipo-no-citoquina de las subunidades de la familia IL-12; SAF2012-32118. Dirección General de Investigación Científica y Técnica - DGICYT. Spanish Government (BFU2012-38236)

CSF Chitinase 3–Like 2 Is Associated With Long-term Disability Progression in Patients With Progressive Multiple Sclerosis

Objective: This study aimed to identify long-term prognostic protein biomarkers associated with disease progression in patients with progressive multiple sclerosis (MS). Methods: CSF samples were collected from a discovery cohort of 28 patients with progressive MS who participated in a clinical trial with interferon beta. Patients were classified into high and low disability progression phenotypes according to numeric progression rates (NPR) and step-based progression rates (SPR) after a mean follow-up time of 12 years. Protein abundance was measured by shotgun proteomics. Selected proteins from the discovery cohort were quantified by parallel reaction monitoring in CSF samples from an independent validation cohort of 41 patients with progressive MS classified also into high and low disability progression phenotypes after a mean follow-up time of 7 years. Results: Of 2,548 CSF proteins identified in the discovery cohort, 10 were selected for validation based on their association with long-term disability progression: SPATS2-like protein, chitinase 3-like 2 (CHI3L2), plasma serine protease inhibitor, metallothionein-3, phospholipase D4, beta-hexosaminidase, neurexophilin-1, adipocyte enhancer-binding protein 1, cathepsin L1, and lipopolysaccharide-binding protein. Only CHI3L2 was validated, and patients with high disability progression exhibited significantly higher CSF protein levels compared with patients with low disability progression (p = 0.03 for NPR and p = 0.02 for SPR). CHI3L2 levels showed good performance to discriminate between high and low disability progression in patients with progressive MS (area under the curve 0.73; sensitivity 90% and specificity 63%). Conclusions: Although further confirmatory studies are needed, we propose CSF CHI3L2 as a prognostic protein biomarker associated with long-term disability progression in patients with progressive MS

Search for Specific Biomarkers of IFNb Bioactivity in Patients with Multiple Sclerosis

Myxovirus A (MxA), a protein encoded by the MX1 gene with antiviral activity, has proven to be a sensitive measure of IFNβ bioactivity in multiple sclerosis (MS). However, the use of MxA as a biomarker of IFNβ bioactivity has been criticized for the lack of evidence of its role on disease pathogenesis and the clinical response to IFNβ. Here, we aimed to identify specific biomarkers of IFNβ bioactivity in order to compare their gene expression induction by type I IFNs with the MxA, and to investigate their potential role in MS pathogenesis. Gene expression microarrays were performed in PBMC from MS patients who developed neutralizing antibodies (NAB) to IFNβ at 12 and/or 24 months of treatment and patients who remained NAB negative. Nine genes followed patterns in gene expression over time similar to the MX1, which was considered the gold standard gene, and were selected for further experiments: IFI6, IFI27, IFI44L, IFIT1, HERC5, LY6E, RSAD2, SIGLEC1, and USP18. In vitro experiments in PBMC from healthy controls revealed specific induction of selected biomarkers by IFNβ but not IFNγ, and several markers, in particular USP18 and HERC5, were shown to be significantly induced at lower IFNβ concentrations and more selective than the MX1 as biomarkers of IFNβ bioactivity. In addition, USP18 expression was deficient in MS patients compared with healthy controls (p = 0.0004). We propose specific biomarkers that may be considered in addition to the MxA to evaluate IFNβ bioactivity, and to further explore their implication in MS pathogenesis