Involvement of epigenetic mechanisms in disease inheritance and pathogenesis of Multiple Sclerosis (MS) with a focus on genomic imprinting and DNA methylation in CD4+ T cells

Multiple Sclerosis (MS) is a chronic inflammatory and neurodegenerative disease driven by autoreactive CD4+ T cells. Disease etiology is mediated by a strong interplay between genetic and environmental factors implying a role for epigenetic mechanisms. Epigenetics is defined as the study of mechanisms, such as DNA methylation, histone modifications and non-coding RNAs, that result in changes of gene expression without altering the underlying genetic code. Genomic imprinting, one of the most-studied epigenetic marking processes, causes a gene to be expressed only from the maternally or paternally inherited chromosome. In this thesis we investigate the contribution of epigenetic mechanisms to the etiology and pathogenesis of MS and its animal model, experimental autoimmune encephalomyelitis (EAE). We investigated the impact of parent-of-origin, in particular genomic imprinting, using two large populations of reciprocal backcross rats and identified that epigenetic mechanisms play a role in EAE inheritance and pathogenesis. Using a transgenic mouse model, we discovered that the imprinted Dlk1 gene impacts the underlying immune responses in EAE. Further discovery of imprinted genes, using RNA sequencing in adult reciprocal hybrid rats, provided additional insights into the underlying mechanisms of how imprinted genes could interfere with the immune response in EAE by modulating CD4+ T cell function. Utilizing a genome-wide approach to identify DNA methylation changes between MS patients and controls in CD4+ T cells and monocytes revealed how DNA methylation as an epigenetic mark can impact the function of CD4+ T cells in MS. We identified that DNA methylation acts as a mediator of the major MS risk factor, the HLA-DRB1 gene, to impact expression of the HLA class II molecules that present antigens to CD4+ T cells. DNA methylation further affected CD4+ T cells directly through changed epigenetic marking of a microRNA, miR-21, impacting miR-21 expression and its target genes. Our findings collectively underline the importance of integrating multiple layers of gene regulation to identify novel mechanisms involved in the etiology and pathogenesis of complex diseases like MS. This will in turn open up for novel therapeutic approaches based on targeting dysregulated epigenomes in human disease

Microglial autophagy-associated phagocytosis is essential for recovery from neuroinflammation

Multiple sclerosis (MS) is a leading cause of incurable progressive disability in young adults caused by inflammation and neurodegeneration in the central nervous system (CNS). The capacity of microglia to clear tissue debris is essential for maintaining and restoring CNS homeostasis. This capacity diminishes with age, and age strongly associates with MS disease progression, although the underlying mechanisms are still largely elusive. Here, we demonstrate that the recovery from CNS inflammation in a murine model of MS is dependent on the ability of microglia to clear tissue debris. Microglia-specific deletion of the autophagy regulator Atg7, but not the canonical macroautophagy protein Ulk1, led to increased intracellular accumulation of phagocytosed myelin and progressive MS-like disease. This impairment correlated with a microglial phenotype previously associated with neurodegenerative pathologies. Moreover, Atg7-deficient microglia showed notable transcriptional and functional similarities to microglia from aged wild-type mice that were also unable to clear myelin and recover from disease. In contrast, induction of autophagy in aged mice using the disaccharide trehalose found in plants and fungi led to functional myelin clearance and disease remission. Our results demonstrate that a noncanonical form of autophagy in microglia is responsible for myelin degradation and clearance leading to recovery from MS-like disease and that boosting this process has a therapeutic potential for age-related neuroinflammatory conditions.Swedish Research CouncilSwedish Brain FoundationSwedish Association for Persons with Neurological DisabilitiesStockholm County Council (ALF project)AstraZeneca (AstraZeneca-Science for Life Laboratory collaboration)European Union Horizon 2020/European Research Council Consolidator Grant (Epi4MS)Knut and Alice Wallenbergs FoundationMargeretha af Ugglas FoundationAlltid Litt SterkereFoundation of Swedish MS researchNEURO SwedenKarolinska InstitutetAccepte

Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients

Multiple Sclerosis (MS) is an autoimmune disease of the central nervous system with prominent neurodegenerative components. The triggering and progression of MS is associated with transcriptional and epigenetic alterations in several tissues, including peripheral blood. The combined influence of transcriptional and epigenetic changes associated with MS has not been assessed in the same individuals. Here we generated paired transcriptomic (RNA-seq) and DNA methylation (Illumina 450 K array) profiles of CD4+ and CD8+ T cells (CD4, CD8), using clinically accessible blood from healthy donors and MS patients in the initial relapsing-remitting and subsequent secondary-progressive stage. By integrating the output of a differential expression test with a permutation-based non-parametric combination methodology, we identified 149 differentially expressed (DE) genes in both CD4 and CD8 cells collected from MS patients. Moreover, by leveraging the methylation-dependent regulation of gene expression, we identified the gene SH3YL1, which displayed significant correlated expression and methylation changes in MS patients. Importantly, silencing of SH3YL1 in primary human CD4 cells demonstrated its influence on T cell activation. Collectively, our strategy based on paired sampling of several cell-types provides a novel approach to increase sensitivity for identifying shared mechanisms altered in CD4 and CD8 cells of relevance in MS in small sized clinical materials

Auxilin is a novel susceptibility gene for congenital heart block which directly impacts fetal heart function

Objective: Neonatal lupus erythematosus (NLE) may develop after transplacental transfer of maternal autoantibodies with cardiac manifestations (congenital heart block, CHB) including atrioventricular block, atrial and ventricular arrhythmias, and cardiomyopathies. The association with anti-Ro/SSA antibodies is well established, but a recurrence rate of only 12%–16% despite persisting maternal autoantibodies suggests that additional factors are required for CHB development. Here, we identify fetal genetic variants conferring risk of CHB and elucidate their effects on cardiac function. Methods: A genome-wide association study was performed in families with at least one case of CHB. Gene expression was analysed by microarrays, RNA sequencing and PCR and protein expression by western blot, immunohistochemistry, immunofluorescence and flow cytometry. Calcium regulation and connectivity were analysed in primary cardiomyocytes and cells induced from pleuripotent stem cells. Fetal heart performance was analysed by Doppler/echocardiography. Results: We identified DNAJC6 as a novel fetal susceptibility gene, with decreased cardiac expression of DNAJC6 associated with the disease risk genotype. We further demonstrate that fetal cardiomyocytes deficient in auxilin, the protein encoded by DNAJC6, have abnormal connectivity and Ca2+ homoeostasis in culture, as well as decreased cell surface expression of the Cav1.3 calcium channel. Doppler echocardiography of auxilin-deficient fetal mice revealed cardiac NLE abnormalities in utero, including abnormal heart rhythm with atrial and ventricular ectopias, as well as a prolonged atrioventricular time intervals. Conclusions: Our study identifies auxilin as the first genetic susceptibility factor in NLE modulating cardiac function, opening new avenues for the development of screening and therapeutic strategies in CHB.publishedVersio

Functional Energetics of CD4+-Cellular Immunity in Monoclonal Antibody-Associated Progressive Multifocal Leukoencephalopathy in Autoimmune Disorders

BACKGROUND: Progressive multifocal leukoencephalopathy (PML) is an opportunistic central nervous system- (CNS-) infection that typically occurs in a subset of immunocompromised individuals. An increasing incidence of PML has recently been reported in patients receiving monoclonal antibody (mAb) therapy for the treatment of autoimmune diseases, particularly those treated with natalizumab, efalizumab and rituximab. Intracellular CD4(+)-ATP-concentration (iATP) functionally reflects cellular immunocompetence and inversely correlates with risk of infections during immunosuppressive therapy. We investigated whether iATP may assist in individualized risk stratification for opportunistic infections during mAb-treatment. METHODOLOGY/PRINCIPAL FINDINGS: iATP in PHA-stimulated, immunoselected CD4(+)-cells was analyzed using an FDA-approved assay. iATP of mAb-associated PML (natalizumab (n = 8), rituximab (n = 2), efalizumab (n = 1)), or other cases of opportunistic CNS-infections (HIV-associated PML (n = 2), spontaneous PML, PML in a psoriasis patient under fumaric acids, natalizumab-associated herpes simplex encephalitis (n = 1 each)) was reduced by 59% (194.5±29 ng/ml, mean±SEM) in comparison to healthy controls (HC, 479.9±19.8 ng/ml, p<0.0001). iATP in 14 of these 16 patients was at or below 3(rd) percentile of healthy controls, similar to HIV-patients (n = 18). In contrast, CD4(+)-cell numbers were reduced in only 7 of 15 patients, for whom cell counts were available. iATP correlated with mitochondrial transmembrane potential (ΔΨ(m)) (iATP/ΔΨ(m)-correlation:tau = 0.49, p = 0.03). Whereas mean iATP of cross-sectionally analysed natalizumab-treated patients was unaltered (448.7±12 ng/ml, n = 150), iATP was moderately decreased (316.2±26.1 ng/ml, p = 0.04) in patients (n = 7) who had been treated already during the pivotal phase III trials and had received natalizumab for more than 6 years. 2/92 (2%) patients with less than 24 months natalizumab treatment revealed very low iATP at or below the 3(rd) percentile of HC, whereas 10/58 (17%) of the patients treated for more than 24 months had such low iATP-concentrations. CONCLUSION: Our results suggest that bioenergetic parameters such as iATP may assist in risk stratification under mAb-immunotherapy of autoimmune disorders

Die Darstellung epistemologischer Dimensionen von evidenzbasiertem Wissen in TV-Wissenschaftsmagazinen: Ein Lehrstück für die Bildungsforschung

Ergebnisse der empirischen Bildungsforschung werden seit den PISA-Studien verstärkt massenmedial und damit öffentlich dargestellt und diskutiert. Um die (Un)Gesichertheit der dabei präsentierten wissenschaftlichen Evidenz zu verstehen, müssen Rezipienten über ausgereifte epistemologische Überzeugungen verfügen. Ausgereifte epistemologische Überzeugungen sind Voraussetzung für das Verständnis von präsentiertem, evidenzbasiertem Wissen in TV-Wissenschaftsmagazinen und können gleichzeitig durch die implizit dargestellten epistemologischen Dimensionen von wissenschaftlichem Wissen beeinflusst werden. Empirisch gezeigt wird mittels Inhaltsanalyse, wie die epistemologischen Dimensionen wissenschaftlichen Wissens in TV-Wissenschaftsbeiträgen dargestellt werden. Mit Hilfe einer Framing-Analyse wird der Zusammenhang zwischen implizit dargestellten epistemologischen Dimensionen und typischen Darstellungsmustern der Wissenschaftsberichterstattung aufgezeigt. Aus den Ergebnissen werden Empfehlungen für die öffentliche Kommunikation von evidenzbasiertem Wissen der empirischen Bildungsforschung abgeleitet

Frames of scientific evidence: How journalists represent the (un)certainty of molecular medicine in science television programs

For laypeople, media coverage of science on television is a gateway to scientific issues. Defining scientific evidence is central to the field of science, but there are still questions if news coverage of science represents scientific research findings as certain or uncertain. The framing approach is a suitable framework to classify different media representations; it is applied here to investigate the frames of scientific evidence in film clips (n = 207) taken from science television programs. Molecular medicine is the domain of interest for this analysis, due to its high proportion of uncertain and conflicting research findings and risks. The results indicate that television clips vary in their coverage of scientific evidence of molecular medicine. Four frames were found: Scientific Uncertainty and Controversy, Scientifically Certain Data, Everyday Medical Risks, and Conflicting Scientific Evidence. They differ in their way of framing scientific evidence and risks of molecular medicine

Die Evidenzkraft von Bildern in der Wissenschaftskommunikation

Guenther L, Kessler SH, Reifegerste D. Die Evidenzkraft von Bildern in der Wissenschaftskommunikation. In: Ruhrmann G, Guenther L, Kessler SH, eds. Wissenschaftskommunikation zwischen Risiko und (Un)Sicherheit . Herbert von Halem Verlag; 2016: 171-192

Epigenetic epidemiology and alterations in type 2 diabetes and obesity

ype 2 diabetes (T2D) and obesity are multifactorial and polygenic metabolic diseases. Combinations of genetic and non-genetic risk factors such as risk SNPs, age, unhealthy diets, and physical inactivity increase the risk for these diseases. Emerging data also support a key role for epigenetic mechanisms in the pathogenesis of T2D and obesity. In this chapter, we summarize current knowledge of epigenetic alterations found in individuals with T2D and obesity. We present studies performed in blood, as well as human tissues important for metabolism, i.e., adipose tissue, skeletal muscle, liver, and pancreatic islets. These studies have found differential DNA methylation associated with both T2D and obesity. Although some studies exist, there is still limited information regarding histone modifications in human tissues linked to metabolic diseases. We finally explore how epigenetic mechanisms may be targeted by epigenetic editing and inhibitors of epigenetic enzymes for future therapies and precision medicine in T2D and obesity