Genome-wide association studies (GWAS) have identified more than 50,000 unique associations with common human traits. While this represents a substantial step forward, establishing the biology underlying these associations has proven extremely difficult. Even determining which cell types and which particular gene(s) are relevant continues to be a challenge. Here, we conduct a cell-specific pathway analysis of the latest GWAS in multiple sclerosis (MS), which had analyzed a total of 47,351 cases and 68,284 healthy controls and found more than 200 non-MHC genome-wide associations. Our analysis identifies pan immune cell as well as cell-specific susceptibility genes in T cells, B cells and monocytes. Finally, genotype-level data from 2,370 patients and 412 controls is used to compute intraindividual and cell-specific susceptibility pathways that offer a biological interpretation of the individual genetic risk to MS. This approach could be adopted in any other complex trait for which genome-wide data is available. ; This investigation was supported in part by the following sources: NIH/NINDS awards R01NS088155 and 1R01NS099240, the Valhalla Charitable Foundation, and the Heidrich Family and Friends Foundation (Sergio E. Baranzini). US National Multiple Sclerosis Society (TA 3056-A-2), the Harvard NeuroDiscovery Center and an Intel Parallel Computing Center award (Nikolaos A. Patsopoulos). Swedish Medical Research Council; Swedish Research Council for Health, Working Life and Welfare, Knut and Alice Wallenberg Foundation, AFA insurance, Swedish Brain Foundation, the Swedish Association for Persons with Neurological Disabilities. Cambridge NIHR Biomedical Research Centre, UK Medical Research Council (G1100125) and the UK MS society (861/07). NIH/NINDS: R01 NS049477, NIH/NIAID: R01 AI059829, NIH/NIEHS: R01 ES0495103. Research Council of Norway grant 196776 and 240102. NINDS/NIH R01NS088155. Oslo MS association. Research Council KU Leuven, Research Foundation Flanders. AFM, AFM-Généthon, CIC, ARSEP, ANR-10-INBS-01 and ANR-10-IAIHU-06. Research Council KU Leuven, Research Foundation Flanders. Inserm ATIP-Avenir Fellowship and Connect-Talents Award. German Ministry for Education and Research, German Competence Network MS (BMBF KKNMS). Oslo MS association, Research Council of Norway grant 196776 and 240102. Dutch MS Research Foundation. TwinsUK is funded by the Wellcome Trust, Medical Research Council, European Union, the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust in partnership with King's College London. German Ministry for Education and Research, German Competence Network MS (BMBF KKNMS). Italian Foundation of Multiple Sclerosis (FISM). NMSS (RG 4680A1/1). German Ministry for Education and Research, German Competence Network MS (BMBF KKNMS). Lundbeck Foundation and Benzon Foundation. ; publishedVersion
In: Johnson , J O , Chia , R , Miller , D E , Li , R , Kumaran , R , Abramzon , Y , Alahmady , N , Renton , A E , Topp , S D , Gibbs , J R , Cookson , M R , Sabir , M S , Dalgard , C L , Troakes , C , Jones , A R , Shatunov , A , Iacoangeli , A , Al Khleifat , A , Ticozzi , N , Silani , V , Gellera , C , Blair , I P , Dobson-Stone , C , Kwok , J B , Bonkowski , E S , Palvadeau , R , Tienari , P J , Morrison , K E , Shaw , P J , Al-Chalabi , A , Brown , R H , Calvo , A , Mora , G , Al-Saif , H , Gotkine , M , Leigh , F , Chang , I J , Perlman , S J , Glass , I , Scott , A I , Shaw , C E , Basak , A N , Landers , J E , Chiò , A , Crawford , T O , Smith , B N , Traynor , B J , Smith , B N , Ticozzi , N , Fallini , C , Gkazi , A S , Topp , S D , Scotter , E L , Kenna , K P , Keagle , P , Tiloca , C , Vance , C , Troakes , C , Colombrita , C , King , A , Pensato , V , Castellotti , B , Baas , F , Ten Asbroek , A L M A , McKenna-Yasek , D , McLaughlin , R L , Polak , M , Asress , S , Esteban-Pérez , J , Stevic , Z , D'Alfonso , S , Mazzini , L , Comi , G P , Del Bo , R , Ceroni , M , Gagliardi , S , Querin , G , Bertolin , C , Van Rheenen , W , Rademakers , R , Van Blitterswijk , M , Lauria , G , Duga , S , Corti , S , Cereda , C , Corrado , L , Sorarù , G , Williams , K L , Nicholson , G A , Blair , I P , Leblond-Manry , C , Rouleau , G A , Hardiman , O , Morrison , K E , Veldink , J H , Van Den Berg , L H , Al-Chalabi , A , Pall , H , Shaw , P J , Turner , M R , Talbot , K , Taroni , F , García-Redondo , A , Wu , Z , Glass , J D , Gellera , C , Ratti , A , Brown , R H , Silani , V , Shaw , C E , Landers , J E , Dalgard , C L , Adeleye , A , Soltis , A R , Alba , C , Viollet , C , Bacikova , D , Hupalo , D N , Sukumar , G , Pollard , H B , Wilkerson , M D , Martinez , E M G , Abramzon , Y , Ahmed , S , Arepalli , S , Baloh , R H , Bowser , R , Brady , C B , Brice , A , Broach , J , Campbell , R H , Camu , W , Chia , R , Cooper-Knock , J , Ding , J , Drepper , C , Drory , V E , Dunckley , T L , Eicher , J D , England , B K , Faghri , F , Feldman , E , Floeter , M K , Fratta , P , Geiger , J T , Gerhard , G , Gibbs , J R , Gibson , S B , Glass , J D , Hardy , J , Harms , M B , Heiman-Patterson , T D , Hernandez , D G , Jansson , L , Kirby , J , Kowall , N W , Laaksovirta , H , Landeck , N , Landi , F , Le Ber , I , Lumbroso , S , Macgowan , D J L , Maragakis , N J , Mora , G , Mouzat , K , Murphy , N A , Myllykangas , L , Nalls , M A , Orrell , R W , Ostrow , L W , Pamphlett , R , Pickering-Brown , S , Pioro , E P , Pletnikova , O , Pliner , H A , Pulst , S M , Ravits , J M , Renton , A E , Rivera , A , Robberecht , W , Rogaeva , E , Rollinson , S , Rothstein , J D , Scholz , S W , Sendtner , M , Shaw , P J , Sidle , K C , Simmons , Z , Singleton , A B , Smith , N , Stone , D J , Tienari , P J , Troncoso , J C , Valori , M , Van Damme , P , Van Deerlin , V M , Van Den Bosch , L , Zinman , L , Landers , J E , Chiò , A , Traynor , B J , Angelocola , S M , Ausiello , F P , Barberis , M , Bartolomei , I , Battistini , S , Bersano , E , Bisogni , G , Borghero , G , Brunetti , M , Cabona , C , Calvo , A , Canale , F , Canosa , A , Cantisani , T A , Capasso , M , Caponnetto , C , Cardinali , P , Carrera , P , Casale , F , Chiò , A , Colletti , T , Conforti , F L , Conte , A , Conti , E , Corbo , M , Cuccu , S , Dalla Bella , E , D'Errico , E , Demarco , G , Dubbioso , R , Ferrarese , C , Ferraro , P M , Filippi , M , Fini , N , Floris , G , Fuda , G , Gallone , S , Gianferrari , G , Giannini , F , Grassano , M , Greco , L , Iazzolino , B , Introna , A , La Bella , V , Lattante , S , Lauria , G , Liguori , R , Logroscino , G , Logullo , F O , Lunetta , C , Mandich , P , Mandrioli , J , Manera , U , Manganelli , F , Marangi , G , Marinou , K , Marrosu , M G , Martinelli , I , Messina , S , Moglia , C , Mora , G , Mosca , L , Murru , M R , Origone , P , Passaniti , C , Petrelli , C , Petrucci , A , Pozzi , S , Pugliatti , M , Quattrini , A , Ricci , C , Riolo , G , Riva , N , Russo , M , Sabatelli , M , Salamone , P , Salivetto , M , Salvi , F , Santarelli , M , Sbaiz , L , Sideri , R , Simone , I , Simonini , C , Spataro , R , Tanel , R , Tedeschi , G , Ticca , A , Torriello , A , Tranquilli , S , Tremolizzo , L , Trojsi , F , Vasta , R , Vacchiano , V , Vita , G , Volanti , P , Zollino , M & Zucchi , E 2021 , ' Association of Variants in the SPTLC1 Gene with Juvenile Amyotrophic Lateral Sclerosis ' , JAMA neurology . https://doi.org/10.1001/jamaneurol.2021.2598
Importance: Juvenile amyotrophic lateral sclerosis (ALS) is a rare form of ALS characterized by age of symptom onset less than 25 years and a variable presentation. Objective: To identify the genetic variants associated with juvenile ALS. Design, Setting, and Participants: In this multicenter family-based genetic study, trio whole-exome sequencing was performed to identify the disease-associated gene in a case series of unrelated patients diagnosed with juvenile ALS and severe growth retardation. The patients and their family members were enrolled at academic hospitals and a government research facility between March 1, 2016, and March 13, 2020, and were observed until October 1, 2020. Whole-exome sequencing was also performed in a series of patients with juvenile ALS. A total of 66 patients with juvenile ALS and 6258 adult patients with ALS participated in the study. Patients were selected for the study based on their diagnosis, and all eligible participants were enrolled in the study. None of the participants had a family history of neurological disorders, suggesting de novo variants as the underlying genetic mechanism. Main Outcomes and Measures: De novo variants present only in the index case and not in unaffected family members. Results: Trio whole-exome sequencing was performed in 3 patients diagnosed with juvenile ALS and their parents. An additional 63 patients with juvenile ALS and 6258 adult patients with ALS were subsequently screened for variants in the SPTLC1 gene. De novo variants in SPTLC1 (p.Ala20Ser in 2 patients and p.Ser331Tyr in 1 patient) were identified in 3 unrelated patients diagnosed with juvenile ALS and failure to thrive. A fourth variant (p.Leu39del) was identified in a patient with juvenile ALS where parental DNA was unavailable. Variants in this gene have been previously shown to be associated with autosomal-dominant hereditary sensory autonomic neuropathy, type 1A, by disrupting an essential enzyme complex in the sphingolipid synthesis pathway. Conclusions and Relevance: These data broaden the phenotype associated with SPTLC1 and suggest that patients presenting with juvenile ALS should be screened for variants in this gene.