Studies on Causes of Multiple Sclerosis : From Genes to Transcriptome

Multiple sclerosis (MS) is the most common cause of neurological disability in young adults, affecting more than two million people worldwide. It manifests as a chronic inflammation in the central nervous system (CNS) and causes demyelination and neurodegeneration. Depending on the location of the demyelinated plaques and axonal loss, a variety of symptoms can be observed including deficits in vision, coordination, balance and movement. With a typical age of onset at 20-40 years, the social and economic impacts of MS on lives of the patients and their families are considerable. Unfortunately the current treatments are relatively inefficient and the development of more effective treatments has been impeded by our limited understanding of the causes and pathogenesis of MS. Risk of MS is higher in biological relatives of MS patients than in the general population. Twin and adoption studies have shown that familial clustering of MS is explained by shared genetic factors rather than by shared familial environment. While the involvement of the human leukocyte antigen (HLA) genes was first discovered four decades ago, additional genetic risk factors have only recently been identified through genome-wide association studies (GWAS). Current evidence suggests that MS is a highly polygenic disease with perhaps hundreds of common variants with relatively modest effects contributing to susceptibility. Despite extensive research, the majority of these risk factors still remain to be identified. In this thesis the aim was to identify novel genes and pathways involved in MS. Using genome-wide microarray technology, gene expression levels in peripheral blood mononuclear cells (PBMC) from 12 MS patients and 15 controls were profiled and more than 600 genes with altered expression in MS were identified. Three of five selected findings, DEFA1A3, LILRA4 and TNFRSF25, were successfully replicated in an independent sample. Increased expression of DEFA1A3 in MS is a particularly interesting observation, because its elevated levels have previously been reported also in several other autoimmune diseases. A systematic review of seven microarray studies was then performed leading to identification of 229 genes, in which either decreased or increased expression in MS had been reported in at least two studies. In general there was relatively little overlap across the experiments: 11 of the 229 genes had been reported in three studies and only HSPA1A in four studies. Nevertheless, these 229 genes were associated with several immunological pathways including interleukin pathways related to type 2 and type 17 helper T cells and regulatory T cells. However, whether these pathways are involved in causing MS or related to secondary processes activated after disease onset remains to be investigated. The 229 genes were also compared with loci identified in published MS GWASs. Single nucleotide polymorphisms (SNP) in 17 of the 229 loci had been reported to be associated with MS with P-value less than 0.0001 including variants in CXCR4 and SAPS2, which were the only loci where evidence for correlation between the associated variant and gene expression was found. The CXCR4 variant was further tested for association with MS in a large case-control sample and the previously reported suggestive association was replicated (P-value is 0.0004). Finally, common genetic variants in candidate genes, which had been selected on the basis of showing association with other autoimmune diseases (MYO9B) or showing differential expression in MS in our study (DEFA1A3, LILRA4 and TNFRSF25), were tested for association with MS, but no evidence of association was found. In conclusion, through a systematic review of genome-wide expression studies in MS we have identified several promising candidate genes and pathways for future studies. In addition, we have replicated a previously suggested association of a SNP variant upstream of CXCR4 with MS. Keywords: autoimmune disease, common variant, CXCR4, DEFA1A3, HSPA1A,gene expression, genetic association, GWAS, MS, multiple sclerosis, systematic reviewPesäkekovettumatauti eli multippeli skleroosi (MS) on nuorten aikuisten yleisin neurologisiin häiriöihin johtava syy. Maailmanlaajuisesti sitä sairastaa yli kaksi miljoonaa ihmistä. Tauti ilmenee keskushermoston kroonisena tulehduksena ja johtaa myeliinikatoon ja keskushermoston rappeutumiseen. Oireet riippuvat leesioiden sijainnista keskushermostossa ja saattavat kohdistua esimerkiksi näköaistiin, tasapainoon ja koordinaatio- ja liikuntakykyyn. MS-tauti puhkeaa yleensa 20-40 vuoden iässä, joten sen sosiaaliset ja ekonomiset vaikutukset potilaisiin ja näiden lähimmäisiin ovat merkittävät. Tehokkaiden hoitojen kehittämistä on vaikeuttanut se, että taudin syyt ja mekanismit tunnetaan toistaiseksi huonosti. Todennäköisyys sairastua MS-tautiin on suurempi MS-potilaiden biologisilla sukulaisilla kuin populaatiossa keskimäärin. Kaksos- ja adoptiotutkimuksissa on osoitettu, että taudin keskittyminen perheisiin selittyy jaetuilla perinnöllisillä alttiustekijöillä. Vaikka immunologisiin soluihin liittyvien HLA-varianttien yhteys MS-tautiin osoitettiin jo lähes neljä vuosikymmentä sitten, uusia geneettisiä alttiustekijöitä on onnistuttu paikantamaan vasta viime vuosina koko genomin laajuisten assosiaatiotutkimusten avulla. Nykyisten tutkimusten valossa MS-alttiuteen vaikuttavia geenivariantteja näyttäisi kuitenkin olevan jopa satoja ja suurin osa näistä on edelleen tunnistamatta. Tämän väitöskirjan tavoitteena oli tunnistaa uusia MS-tautiin liittyviä geenejä ja reaktioreittejä. Geenien ilmentymistasoja verrattiin ensin periferaalisissa mononukleaarisissa immuunisoluissa MS-potilaiden ja verrokkien välillä käyttäen mikrosirutekniikkaa, joka mahdollistaa kaikkien tunnettujen geenien samanaikaisen tarkastelun. Yli 600 geenin ilmentymisen havaittiin poikkeavan merkitsevästi MS-potilaiden ja verrokkien välillä. Tunnistetuista geeneistä viisi valittiin toistotutkimukseen, jossa kolmen geenin (DEFA1A3, LILRA4 ja TNFRSF25) tapauksessa ilmentymisero potilaiden ja verrokkien välillä toistui. Näistä geeneistä DEFA1A3 on erityisen kiinnostava, sillä sen ilmentymistason on havaittu olevan verrokkeja korkeampi myös muissa autoimmuunisairauksissa. Koska vastaavia mikosirututkimuksia on tehty MS-taudissa myös aiemmin, yhtenä väitöskirjan tavoitteena oli verrata tuloksia näistä tutkimuksista. Vertailuun otettiin kaikkiaan seitsemän tutkimusta, mukaan lukien tämän väitöskirjan osana tehty tutkimus. Tavoitteena oli tunnistaa geenit, joissa ilmentymisen oli raportoitu poikkeavan MS-potilaiden ja verrokkien välillä ainakin kahdessa tutkimuksessa. Vaikka tällaisia geenejä tunnistettiin 229, yleisesti ottaen tutkimustulosten välillä oli kuitenkin vähän päällekkäisyyttä: vain 11 geeniä oli raportoitu kolmessa tutkimuksessa ja ainoastaan yksi, HSPA1A, neljässä tutkimuksessa. Reaktioreittianalyysin avulla osoitettiin, että tunnistetut 229 geeniä assosioituvat merkittävästi useisiin mielenkiintoisiin immunologisiin reaktioreitteihin. Monet näistä liittyvät tiettyihin T-solutyppeihin, joiden merkitystä sekä MS-taudin alttiuden että taudin etenemisen ja patogeneesin kannalta on tulostemme perusteella syytä tutkia lisää. 229 geenistä ainoastaan 17 on aiemmin raportoitu assosioituvan MS-tautiin, mikä viittaisi siihen että nämä 229 geeniä eivät välttämättä ole merkittäviä taudin alttiuden lisäämisen kannalta, mutta voivat liittyä taudin mekanismeihin taudin puhkeamisen jälkeen. 17 geenistä ainoastaan SAPS2- ja CXCR4-geenien tapauksessa havaitsimme yhteyden geenin ilmentymisen ja geneettisen riskivariantin välillä siten, että molemmissa tapauksissa geenin ilmentyminen oli koholla riskialleelin kantajilla. Lopuksi väitöskirjassa testattiin tämän CXCR4-lokuksessa sijaitsevan variantin assosiaatiota MS-tautiin tuhansien henkilöiden potilas-kontrolli aineistossa ja aiemmissa tutkimuksissa havaittu assosiaatio toistettiin (P-arvo on 0.0004). Lisäksi tutkittiin valituissa ehdokasgeeneissä sijaitsevien yleisten geneettisten varianttien yhteyttä MS-tautiin. Edellä mikrosirututkimuksessa tunnistettujen DEFA1A3-, LILRA4- ja TNFRSF25-geenien lisäksi tarkasteltiin MYO9B-geeniä, jonka oli aiemmin havaittu assosioituvan muihin autoimmuunisairauksiin. Merkitsevää yhteyttä MS-taudin ja tarkasteltujen geneettisten varianttien välillä ei kuitenkaan havaittu. Yhteenvetona, tässä väitöskirjassa on geenien ilmentymistutkimusten ja niiden systemaattisen katsauksen avulla tunnistettu useita lupaavia ehdokasgeenejä (mm. DEFA1A3, LILRA4, TNFRSF25 ja HSPA1A) ja erityisesti T-soluihin liittyviä reaktioreittejä. Lisäksi väitöskirjassa on toistettu aiemmin raportoitu assosiaatio MS-taudin ja CXCR4-lokuksessa sijaitsevan geneettisen variantin välillä. Tunnistettujen geenien rooli MS-taudin patogeneesissä on kuitenkin toistaiseksi tuntematon, joten tarkempia jatkotutkimuksia tarvitaan. Avainsanat: CXCR4, DEFA1A3, HSPA1A, geenien ilmentyminen, geneettinen assosiaatio, GWAS, MS-tauti, multippeli skleroosi, pesäkekovettumatauti, yleinen variantt

Systematic review of genome-wide expression studies in multiple sclerosis

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Enterosgel for the treatment of adults with acute diarrhoea in a primary care setting : A randomised controlled trial

Background Acute intestinal infections are common conditions causing high morbidity and mortality especially in the young and elderly, resulting in a significant burden on health service resources and the economy. Current National Institute for Health and Care Excellence guidance are fluid and nutritional management; however, this does not reduce the duration of diarrhoea and the challenge of treating diarrhoea itself remains. We investigated the efficacy, tolerability and safety of intestinal adsorbent Enterosgel (polymethylsiloxane polyhydrate) compared with standard care in adults with acute diarrhoea. Methods This was a randomised controlled trial enrolling 105 subjects to receive the medical device Enterosgel up to six times daily for up to 8 days with standard care (oral rehydration solution), or standard care alone. The primary endpoint was the duration of diarrhoea (hours) from randomisation to first non-loose stool in the Enterosgel versus control group. Results A total of 51 subjects were randomised into the Enterosgel group and 54 into the control group, after excluding missing data, the data from 43 subjects in each group were analysed. Duration of diarrhoea was significantly shorter in the Enterosgel group at 27 hours versus 39 hours in the control group (HR was 1.74 [95% CI 1.06 to 2.87]) (p=0.03). This yielded a number needed to treat value of 5. Enterosgel was well tolerated and safe with no serious adverse events. One serious diarrhoea-related event resulting in hospitalisation was reported in the control group. Conclusions Enterosgel treatment was associated with a significant reduction in the duration of diarrhoea in adults with patient-reported acute diarrhoea, compared with standard care. These findings support the role of Enterosgel in acute diarrhoea especially in vulnerable groups where rapid resolution of symptoms is required. Reduction in symptom duration could translate to less healthcare costs and socioeconomic burden. Trial registration number ISRCTN20758708

Maximizing Adherence and Gaining New Information For Your Chronic Obstructive Pulmonary Disease (MAGNIFY COPD):Study Protocol for the Pragmatic, Cluster Randomized Trial Evaluating the Impact of Dual Bronchodilator with Add-On Sensor and Electronic Monitoring on Clinical Outcomes

Background: Poor treatment adherence in COPD patients is associated with poor clinical outcomes and increased healthcare burden. Personalized approaches for adherence management, supported with technology-based interventions, may offer benefits to patients and providers but are currently unproven in terms of clinical outcomes as opposed to adherence outcomes. Methods: Maximizing Adherence and Gaining New Information For Your COPD (MAGNIFY COPD study), a pragmatic cluster randomized trial, aims to evaluate the impact of an adherence technology package (interventional package), comprising an adherence review, ongoing provision of a dual bronchodilator but with an add-on inhaler sensor device and a connected mobile application. This will compare time to treatment failure and other clinical outcomes in patients identified at high risk of exacerbations with historic poor treatment adherence as measured by prescription collection to mono/dual therapy over one year (1312 patients) versus usual care. Treatment failure is defined as the first occurrence of one of the following: (1) moderate/severe COPD exacerbation, (2) prescription of triple therapy (inhaled corticosteroid/long-acting β2-agonist/long-acting muscarinic antagonist [ICS/LABA/LAMA]), (3) prescription of additional chronic therapy for COPD, or (4) respiratory-related death. Adherence, moderate/severe exacerbations, respiratory-related healthcare resource utilization and costs, and intervention package acceptance rate will also be assessed. Eligible primary care practices (N=176) participating in the Optimum Patient Care Quality Improvement Program will be randomized (1:1) to either adherence support cluster arm (suitable patients already receiving or initiated Ultibro® Breezhaler® [indacaterol/glycopyrronium] will be offered interventional package) or the control cluster arm (suitable patients continue to receive usual clinical care). Patients will be identified and outcomes collected from anonymized electronic medical records within the Optimum Patient Care Research Database. On study completion, electronic medical record data will be re-extracted to analyze outcomes in both study groups. Registration Number: ISRCTN10567920. Conclusion: MAGNIFY will explore patient benefits of technology-based interventions for electronic adherence monitoring

Changes in control status of COPD over time and their consequences : A prospective international, study

ACKNOWLEDGMENTS The study was designed and coordinated by the Respiratory Effectiveness Group (REG; www.effectivenessevaluation.org; Cambridge, UK) and delivered by Optimum Patient Care (OPC; www.optimumpatientcare.org). Funding: The study was funded by an unrestricted grant from Novartis AG.Peer reviewedPostprin

Comparison of clinical baseline characteristics between Asian and Western COPD patients in a prospective, international, multicenter study

The study was designed and coordinated by the Respiratory Effectiveness Group (REG; www.effectivenessevaluation.org; Cambridge, UK) and delivered by Optimum Patient Care (OPC; www.optimumpatientcare.org). The following investigators participated in the study: Spain: Marc Miravitlles, Cristina Esquinas, Miriam Barrecheguren, Alexa Nuñez, Hospital Universitari Vall d’Hebron, Barcelona. Bernardino Alcazar, Hospital de Alta Resolución de Loja. Juan Luis García-Rivero, Karina Hueso, Hospital Comarcal de Laredo, Cantabria. Miguel Roman-Rodríguez, Primary Health-care Center Son Pisà. IB-Salut. Palma de Mallorca. Poland: Pawel Sliwinsk Sliwinski, Katarzyna Iwan, Jacek Kolakowski, Institute of Tuberculosis and Lung Diseases, Warsaw. Korea: Chin Kook Rhee, Esther Ahn, St Mary’s Hospital. Seoul. Singapore: Jessica Tan, Therese Lapperre, Karen Tan Li Leng, Nicole Chia, Ong Thun How, Syifa Binte Shamsuddin, Sherine Lim Shu Gim, Yap Chwee Bee, Soh Rui Ya, Singapore General Hospital. Augustine Tee, Jun Jie Yan, Samuel Hong, William Tan, Jessica Tan, Changi General Hospital. UK: Victoria Carter, Latife Hardaker, Andrew McLaughlin, Optimum Patient Care, Cambridge. Malta: Caroline Gouder, Mater Dei Hospital. Ireland: Richard W Costello, Royal College of Surgeons. Dublin. The study was funded by an unrestricted grant from Novartis AG.Peer reviewedPublisher PD

Evaluation of criteria for clinical control in a prospective, international, multicenter study of patients with COPD

BACKGROUND: The concept of clinical control in COPD has been developed to help in treatment decisions, but it requires validation in prospective studies. METHOD: This international, multicenter, prospective study aimed to validate the concept of control in COPD [control = stability (no exacerbations or impairment in CAT scores) + low impact (low level of symptoms)]. Data from the screening visit was used to: investigate the level of control, compare characteristics of patients according to the control status, and perform a sensitivity analysis of the levels of control using either clinical criteria or questionnaires (COPD Assessment Test -CAT- or Clinical COPD Questionnaire -CCQ-). RESULTS: A total of 314 patients were analysed, mean age was 68.5 years and mean FEV1 was 52.6% of predicted. According to the prespecified criteria 21% of patients were classified as controlled, all of them with mild/moderate COPD (Body mass index, Obstruction, Dyspnea and Exacerbations, -BODEx-index <5). A high level of dyspnea, a high CAT score or an exacerbation in the previous 3 months were found, using univariate analysis, to be the main reasons for patients not being classified as controlled. Multivariate analysis showed that female sex, chronic bronchitis and having exacerbations in the previous year were associated with uncontrolled COPD. Changing the severity cut off of BODEx from 5 to 3 did not change significantly the percentage of patients fulfilling the criteria of control. CONCLUSIONS: The proposed criteria of control were only fulfilled by 21% of patients. The suggested cut offs and their predictive value for poor outcomes need to be refined in prospective studies

Predictive value of control of COPD for risk of exacerbations : An international, prospective study

Acknowledgements Collaborators/REG Investigators: Spain: Marc Miravitlles, Cristina Esquinas, Miriam Barrecheguren, Alexa Nuñez, Hospital Universitari Vall d'Hebron, Barcelona. Bernardino Alcazar, Hospital de Alta Resolución de Loja. Juan Luis García‐Rivero, Karina Hueso, Hospital Comarcal de Laredo, Cantabria. Miguel Roman‐Rodríguez, Primary Health‐Care Center Son Pisà, IB‐Salut, Palma de Mallorca. Poland: Pawel Sliwinsk, Katarzyna Iwan, Jacek Kolakowski, Institute of Tuberculosis and Lung Diseases, Warsaw. Korea: Chin Kook Rhee, Esther Ahn, St Mary's Hospital, Seoul. Singapore: Jessica Tan, Therese Laperre, Karen Tan Li Leng, Nicole Chia, Ong Thun How, Syifa Binte Shamsuddin, Sherine Lim Shu Gim, Yap Chwee Bee, Soh Rui Ya, Singapore General Hospital. Augustine Tee, Jun Jie Yan, Samuel Hong, William Tan, Changi General Hospital. UK: Victoria Carter, Latife Hardaker, Andrew McLaughlin, Optimum Patient Care, Cambridge. Malta: Caroline Gouder, Mater Dei Hospital. Ireland: Richard W Costello, Royal College of Surgeons, Dublin. The study was funded by an unrestricted grant from Novartis AG. The study was designed and coordinated by the Respiratory Effectiveness Group (REG; www.effectivenessevaluation.org; Cambridge, UK) and delivered by Optimum Patient Care (OPC; www.optimumpatientcare.org).Peer reviewedPostprin

Characteristics of patients in platform C19, a COVID-19 research database combining primary care electronic health record and patient reported information

Background Data to better understand and manage the COVID-19 pandemic is urgently needed. However, there are gaps in information stored within even the best routinely-collected electronic health records (EHR) including test results, remote consultations for suspected COVID-19, shielding, physical activity, mental health, and undiagnosed or untested COVID-19 patients. Observational and Pragmatic Research Institute (OPRI) Singapore and Optimum Patient Care (OPC) UK established Platform C19, a research database combining EHR data and bespoke patient questionnaire. We describe the demographics, clinical characteristics, patient behavior, and impact of the COVID-19 pandemic using data within Platform C19. Methods EHR data from Platform C19 were extracted from 14 practices across UK participating in the OPC COVID-19 Quality Improvement program on a continuous, monthly basis. Starting 7th August 2020, consenting patients aged 18–85 years were invited in waves to fill an online questionnaire. Descriptive statistics were summarized using all data available up to 22nd January 2021. Findings From 129,978 invitees, 31,033 responded. Respondents were predominantly female (59.6%), white (93.5%), and current or ex-smokers (52.6%). Testing for COVID-19 was received by 23.8% of respondents, of which 7.9% received positive results. COVID-19 symptoms lasted ≥4 weeks in 19.5% of COVID-19 positive respondents. Up to 39% respondents reported a negative impact on questions regarding their mental health. Most (67%-76%) respondents with asthma, Chronic Obstructive Pulmonary Disease (COPD), diabetes, heart, or kidney disease reported no change in the condition of their diseases. Interpretation Platform C19 will enable research on key questions relating to COVID-19 pandemic not possible using EHR data alone