1
|
Xie W, Ravi P, Buyse M, Halabi S, Kantoff P, Sartor O, Soule H, Clarke N, Dignam J, James N, Fizazi K, Gillessen S, Mottet N, Murphy L, Parulekar W, Sandler H, Tombal B, Williams S, Sweeney CJ. Validation of metastasis-free survival as a surrogate endpoint for overall survival in localized prostate cancer in the era of docetaxel for castration-resistant prostate cancer. Ann Oncol 2024; 35:285-292. [PMID: 38061427 PMCID: PMC10922430 DOI: 10.1016/j.annonc.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Prior work from the Intermediate Clinical Endpoints in Cancer of the Prostate (ICECaP) consortium (ICECaP-1) demonstrated that metastasis-free survival (MFS) is a valid surrogate for overall survival (OS) in localized prostate cancer (PCa). This was based on data from patients treated predominantly before 2004, prior to docetaxel being available for the treatment of metastatic castrate-resistant prostate cancer (mCRPC). We sought to validate surrogacy in a more contemporary era (ICECaP-2) with greater availability of docetaxel and other systemic therapies for mCRPC. PATIENTS AND METHODS Eligible trials for ICECaP-2 were those providing individual patient data (IPD) after publication of ICECaP-1 and evaluating adjuvant/salvage therapy for localized PCa, and which collected MFS and OS data. MFS was defined as distant metastases or death from any cause, and OS was defined as death from any cause. Surrogacy was evaluated using a meta-analytic two-stage validation model, with an R2 ≥ 0.7 defined a priori as clinically relevant. RESULTS A total of 15 164 IPD from 14 trials were included in ICECaP-2, with 70% of patients treated after 2004. The median follow-up was 8.3 years and the median postmetastasis survival was 3.1 years in ICECaP-2, compared with 1.9 years in ICECaP-1. For surrogacy condition 1, Kendall's tau was 0.92 for MFS with OS at the patient level, and R2 from weighted linear regression (WLR) of 8-year OS on 5-year MFS was 0.73 (95% confidence interval 0.53-0.82) at the trial level. For condition 2, R2 was 0.83 (95% confidence interval 0.64-0.89) from WLR of log[hazard ratio (HR)]-OS on log(HR)-MFS. The surrogate threshold effect on OS was an HR(MFS) of 0.81. CONCLUSIONS MFS remained a valid surrogate for OS in a more contemporary era, where patients had greater access to docetaxel and other systemic therapies for mCRPC. This supports the use of MFS as the primary outcome measure for ongoing adjuvant trials in localized PCa.
Collapse
Affiliation(s)
- W Xie
- Dana-Farber Cancer Institute, Boston, USA
| | - P Ravi
- Dana-Farber Cancer Institute, Boston, USA
| | - M Buyse
- International Drug Development Institute, Louvain-la-Neuve; I-BioStat, Hasselt University, Hasselt, Belgium
| | | | | | | | - H Soule
- Prostate Cancer Foundation, Santa Monica, USA
| | - N Clarke
- The Christie NHS Foundation Trust, Manchester, UK
| | - J Dignam
- University of Chicago, Chicago, USA
| | - N James
- The Institute of Cancer Research & The Royal Marsden NHS Foundation Trust, London, UK
| | - K Fizazi
- Institut Gustave Roussy, University of Paris Saclay, Villejuif, France
| | - S Gillessen
- Oncology Institute of Southern Switzerland, EOC, Bellinzona; Università della Svizzera Italiana, Lugano, Switzerland
| | - N Mottet
- Mutualite Francoise Loire, St Etienne, France
| | - L Murphy
- Medical Research Council at UCL, London, UK
| | - W Parulekar
- Queens University, Kingston, Ontario, Canada
| | - H Sandler
- Cedars-Sinai Medical Center, Los Angeles, USA
| | - B Tombal
- Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - S Williams
- Peter MacCallum Cancer Centre, Melbourne
| | - C J Sweeney
- South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, Australia.
| |
Collapse
|
2
|
McFeely O, Walsh PM, Desmond R, Enright H, Costa Blasco M, Wolinska A, Murphy L, Andrawis M, Beatty P, Doyle C, Tobin AM, O'Gorman S, Molloy K. Incidence of cutaneous T-cell lymphoma in the Republic of Ireland between 1994 and 2019. J Eur Acad Dermatol Venereol 2024; 38:e145-e147. [PMID: 37705380 DOI: 10.1111/jdv.19497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023]
Affiliation(s)
- O McFeely
- Department of Dermatology, Tallaght University Hospital, Dublin, Ireland
| | - P M Walsh
- National Cancer Registry of Ireland, Cork, Ireland
| | - R Desmond
- Department of Haematology, Tallaght University Hospital, Dublin, Ireland
| | - H Enright
- Department of Haematology, Tallaght University Hospital, Dublin, Ireland
| | - M Costa Blasco
- Department of Dermatology, Tallaght University Hospital, Dublin, Ireland
| | - A Wolinska
- Department of Dermatology, Tallaght University Hospital, Dublin, Ireland
| | - L Murphy
- Department of Dermatology, Tallaght University Hospital, Dublin, Ireland
| | - M Andrawis
- Department of Dermatology, Tallaght University Hospital, Dublin, Ireland
| | - P Beatty
- Department of Dermatology, Tallaght University Hospital, Dublin, Ireland
| | - C Doyle
- Department of Dermatology, Tallaght University Hospital, Dublin, Ireland
| | - A M Tobin
- Department of Dermatology, Tallaght University Hospital, Dublin, Ireland
| | - S O'Gorman
- Department of Dermatology, St. James's Hospital, Dublin, Ireland
| | - K Molloy
- Department of Dermatology, Tallaght University Hospital, Dublin, Ireland
| |
Collapse
|
3
|
Chybowska AD, Gadd DA, Cheng Y, Bernabeu E, Campbell A, Walker RM, McIntosh AM, Wrobel N, Murphy L, Welsh P, Sattar N, Price JF, McCartney DL, Evans KL, Marioni RE. Epigenetic Contributions to Clinical Risk Prediction of Cardiovascular Disease. Circ Genom Precis Med 2024; 17:e004265. [PMID: 38288591 PMCID: PMC10876178 DOI: 10.1161/circgen.123.004265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 11/30/2023] [Indexed: 02/21/2024]
Abstract
BACKGROUND Cardiovascular disease (CVD) is among the leading causes of death worldwide. The discovery of new omics biomarkers could help to improve risk stratification algorithms and expand our understanding of molecular pathways contributing to the disease. Here, ASSIGN-a cardiovascular risk prediction tool recommended for use in Scotland-was examined in tandem with epigenetic and proteomic features in risk prediction models in ≥12 657 participants from the Generation Scotland cohort. METHODS Previously generated DNA methylation-derived epigenetic scores (EpiScores) for 109 protein levels were considered, in addition to both measured levels and an EpiScore for cTnI (cardiac troponin I). The associations between individual protein EpiScores and the CVD risk were examined using Cox regression (ncases≥1274; ncontrols≥11 383) and visualized in a tailored R application. Splitting the cohort into independent training (n=6880) and test (n=3659) subsets, a composite CVD EpiScore was then developed. RESULTS Sixty-five protein EpiScores were associated with incident CVD independently of ASSIGN and the measured concentration of cTnI (P<0.05), over a follow-up of up to 16 years of electronic health record linkage. The most significant EpiScores were for proteins involved in metabolic, immune response, and tissue development/regeneration pathways. A composite CVD EpiScore (based on 45 protein EpiScores) was a significant predictor of CVD risk independent of ASSIGN and the concentration of cTnI (hazard ratio, 1.32; P=3.7×10-3; 0.3% increase in C-statistic). CONCLUSIONS EpiScores for circulating protein levels are associated with CVD risk independent of traditional risk factors and may increase our understanding of the etiology of the disease.
Collapse
Affiliation(s)
- Aleksandra D Chybowska
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer (A.D.C., D.A.G., Y.C., E.B., A.C., D.L.M., K.L.E., R.E.M.), The University of Edinburgh, United Kingdom
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer (A.D.C., D.A.G., Y.C., E.B., A.C., D.L.M., K.L.E., R.E.M.), The University of Edinburgh, United Kingdom
| | - Yipeng Cheng
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer (A.D.C., D.A.G., Y.C., E.B., A.C., D.L.M., K.L.E., R.E.M.), The University of Edinburgh, United Kingdom
| | - Elena Bernabeu
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer (A.D.C., D.A.G., Y.C., E.B., A.C., D.L.M., K.L.E., R.E.M.), The University of Edinburgh, United Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer (A.D.C., D.A.G., Y.C., E.B., A.C., D.L.M., K.L.E., R.E.M.), The University of Edinburgh, United Kingdom
| | - Rosie M Walker
- School of Psychology, University of Exeter, United Kingdom (R.M.W.)
| | - Andrew M McIntosh
- Division of Psychiatry, Royal Edinburgh Hospital (A.M.M.), The University of Edinburgh, United Kingdom
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, Western General Hospital (N.W., L.M.), The University of Edinburgh, United Kingdom
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital (N.W., L.M.), The University of Edinburgh, United Kingdom
| | - Paul Welsh
- Institute of Cardiovascular and Medical Sciences, British Heart Foundation Glasgow Cardiovascular Research Centre, University of Glasgow, United Kingdom (P.W., N.S.)
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, British Heart Foundation Glasgow Cardiovascular Research Centre, University of Glasgow, United Kingdom (P.W., N.S.)
| | - Jackie F Price
- Usher Institute, Old Medical School (J.F.P.), The University of Edinburgh, United Kingdom
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer (A.D.C., D.A.G., Y.C., E.B., A.C., D.L.M., K.L.E., R.E.M.), The University of Edinburgh, United Kingdom
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer (A.D.C., D.A.G., Y.C., E.B., A.C., D.L.M., K.L.E., R.E.M.), The University of Edinburgh, United Kingdom
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer (A.D.C., D.A.G., Y.C., E.B., A.C., D.L.M., K.L.E., R.E.M.), The University of Edinburgh, United Kingdom
| |
Collapse
|
4
|
Staplin N, Haynes R, Judge PK, Wanner C, Green JB, Emberson J, Preiss D, Mayne KJ, Ng SYA, Sammons E, Zhu D, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu WJ, Kadowaki T, Nangaku M, Levin A, Cherney D, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Petrini M, Seidi S, Landray MJ, Baigent C, Herrington WG, Abat S, Abd Rahman R, Abdul Cader R, Abdul Hafidz MI, Abdul Wahab MZ, Abdullah NK, Abdul-Samad T, Abe M, Abraham N, Acheampong S, Achiri P, Acosta JA, Adeleke A, Adell V, Adewuyi-Dalton R, Adnan N, Africano A, Agharazii M, Aguilar F, Aguilera A, Ahmad M, Ahmad MK, Ahmad NA, Ahmad NH, Ahmad NI, Ahmad Miswan N, Ahmad Rosdi H, Ahmed I, Ahmed S, Ahmed S, Aiello J, Aitken A, AitSadi R, Aker S, Akimoto S, Akinfolarin A, Akram S, Alberici F, Albert C, Aldrich L, Alegata M, Alexander L, Alfaress S, Alhadj Ali M, Ali A, Ali A, Alicic R, Aliu A, Almaraz R, Almasarwah R, Almeida J, Aloisi A, Al-Rabadi L, Alscher D, Alvarez P, Al-Zeer B, Amat M, Ambrose C, Ammar H, An Y, Andriaccio L, Ansu K, Apostolidi A, Arai N, Araki H, Araki S, Arbi A, Arechiga O, Armstrong S, Arnold T, Aronoff S, Arriaga W, Arroyo J, Arteaga D, Asahara S, Asai A, Asai N, Asano S, Asawa M, Asmee MF, Aucella F, Augustin M, Avery A, Awad A, Awang IY, Awazawa M, Axler A, Ayub W, Azhari Z, Baccaro R, Badin C, Bagwell B, Bahlmann-Kroll E, Bahtar AZ, Baigent C, Bains D, Bajaj H, Baker R, Baldini E, Banas B, Banerjee D, Banno S, Bansal S, Barberi S, Barnes S, Barnini C, Barot C, Barrett K, Barrios R, Bartolomei Mecatti B, Barton I, Barton J, Basily W, Bavanandan S, Baxter A, Becker L, Beddhu S, Beige J, Beigh S, Bell S, Benck U, Beneat A, Bennett A, Bennett D, Benyon S, Berdeprado J, Bergler T, Bergner A, Berry M, Bevilacqua M, Bhairoo J, Bhandari S, Bhandary N, Bhatt A, Bhattarai M, Bhavsar M, Bian W, Bianchini F, Bianco S, Bilous R, Bilton J, Bilucaglia D, Bird C, Birudaraju D, Biscoveanu M, Blake C, Bleakley N, Bocchicchia K, Bodine S, Bodington R, Boedecker S, Bolduc M, Bolton S, Bond C, Boreky F, Boren K, Bouchi R, Bough L, Bovan D, Bowler C, Bowman L, Brar N, Braun C, Breach A, Breitenfeldt M, Brenner S, Brettschneider B, Brewer A, Brewer G, Brindle V, Brioni E, Brown C, Brown H, Brown L, Brown R, Brown S, Browne D, Bruce K, Brueckmann M, Brunskill N, Bryant M, Brzoska M, Bu Y, Buckman C, Budoff M, Bullen M, Burke A, Burnette S, Burston C, Busch M, Bushnell J, Butler S, Büttner C, Byrne C, Caamano A, Cadorna J, Cafiero C, Cagle M, Cai J, Calabrese K, Calvi C, Camilleri B, Camp S, Campbell D, Campbell R, Cao H, Capelli I, Caple M, Caplin B, Cardone A, Carle J, Carnall V, Caroppo M, Carr S, Carraro G, Carson M, Casares P, Castillo C, Castro C, Caudill B, Cejka V, Ceseri M, Cham L, Chamberlain A, Chambers J, Chan CBT, Chan JYM, Chan YC, Chang E, Chang E, Chant T, Chavagnon T, Chellamuthu P, Chen F, Chen J, Chen P, Chen TM, Chen Y, Chen Y, Cheng C, Cheng H, Cheng MC, Cherney D, Cheung AK, Ching CH, Chitalia N, Choksi R, Chukwu C, Chung K, Cianciolo G, Cipressa L, Clark S, Clarke H, Clarke R, Clarke S, Cleveland B, Cole E, Coles H, Condurache L, Connor A, Convery K, Cooper A, Cooper N, Cooper Z, Cooperman L, Cosgrove L, Coutts P, Cowley A, Craik R, Cui G, Cummins T, Dahl N, Dai H, Dajani L, D'Amelio A, Damian E, Damianik K, Danel L, Daniels C, Daniels T, Darbeau S, Darius H, Dasgupta T, Davies J, Davies L, Davis A, Davis J, Davis L, Dayanandan R, Dayi S, Dayrell R, De Nicola L, Debnath S, Deeb W, Degenhardt S, DeGoursey K, Delaney M, Deo R, DeRaad R, Derebail V, Dev D, Devaux M, Dhall P, Dhillon G, Dienes J, Dobre M, Doctolero E, Dodds V, Domingo D, Donaldson D, Donaldson P, Donhauser C, Donley V, Dorestin S, Dorey S, Doulton T, Draganova D, Draxlbauer K, Driver F, Du H, Dube F, Duck T, Dugal T, Dugas J, Dukka H, Dumann H, Durham W, Dursch M, Dykas R, Easow R, Eckrich E, Eden G, Edmerson E, Edwards H, Ee LW, Eguchi J, Ehrl Y, Eichstadt K, Eid W, Eilerman B, Ejima Y, Eldon H, Ellam T, Elliott L, Ellison R, Emberson J, Epp R, Er A, Espino-Obrero M, Estcourt S, Estienne L, Evans G, Evans J, Evans S, Fabbri G, Fajardo-Moser M, Falcone C, Fani F, Faria-Shayler P, Farnia F, Farrugia D, Fechter M, Fellowes D, Feng F, Fernandez J, Ferraro P, Field A, Fikry S, Finch J, Finn H, Fioretto P, Fish R, Fleischer A, Fleming-Brown D, Fletcher L, Flora R, Foellinger C, Foligno N, Forest S, Forghani Z, Forsyth K, Fottrell-Gould D, Fox P, Frankel A, Fraser D, Frazier R, Frederick K, Freking N, French H, Froment A, Fuchs B, Fuessl L, Fujii H, Fujimoto A, Fujita A, Fujita K, Fujita Y, Fukagawa M, Fukao Y, Fukasawa A, Fuller T, Funayama T, Fung E, Furukawa M, Furukawa Y, Furusho M, Gabel S, Gaidu J, Gaiser S, Gallo K, Galloway C, Gambaro G, Gan CC, Gangemi C, Gao M, Garcia K, Garcia M, Garofalo C, Garrity M, Garza A, Gasko S, Gavrila M, Gebeyehu B, Geddes A, Gentile G, George A, George J, Gesualdo L, Ghalli F, Ghanem A, Ghate T, Ghavampour S, Ghazi A, Gherman A, Giebeln-Hudnell U, Gill B, Gillham S, Girakossyan I, Girndt M, Giuffrida A, Glenwright M, Glider T, Gloria R, Glowski D, Goh BL, Goh CB, Gohda T, Goldenberg R, Goldfaden R, Goldsmith C, Golson B, Gonce V, Gong Q, Goodenough B, Goodwin N, Goonasekera M, Gordon A, Gordon J, Gore A, Goto H, Goto S, Goto S, Gowen D, Grace A, Graham J, Grandaliano G, Gray M, Green JB, Greene T, Greenwood G, Grewal B, Grifa R, Griffin D, Griffin S, Grimmer P, Grobovaite E, Grotjahn S, Guerini A, Guest C, Gunda S, Guo B, Guo Q, Haack S, Haase M, Haaser K, Habuki K, Hadley A, Hagan S, Hagge S, Haller H, Ham S, Hamal S, Hamamoto Y, Hamano N, Hamm M, Hanburry A, Haneda M, Hanf C, Hanif W, Hansen J, Hanson L, Hantel S, Haraguchi T, Harding E, Harding T, Hardy C, Hartner C, Harun Z, Harvill L, Hasan A, Hase H, Hasegawa F, Hasegawa T, Hashimoto A, Hashimoto C, Hashimoto M, Hashimoto S, Haskett S, Hauske SJ, Hawfield A, Hayami T, Hayashi M, Hayashi S, Haynes R, Hazara A, Healy C, Hecktman J, Heine G, Henderson H, Henschel R, Hepditch A, Herfurth K, Hernandez G, Hernandez Pena A, Hernandez-Cassis C, Herrington WG, Herzog C, Hewins S, Hewitt D, Hichkad L, Higashi S, Higuchi C, Hill C, Hill L, Hill M, Himeno T, Hing A, Hirakawa Y, Hirata K, Hirota Y, Hisatake T, Hitchcock S, Hodakowski A, Hodge W, Hogan R, Hohenstatt U, Hohenstein B, Hooi L, Hope S, Hopley M, Horikawa S, Hosein D, Hosooka T, Hou L, Hou W, Howie L, Howson A, Hozak M, Htet Z, Hu X, Hu Y, Huang J, Huda N, Hudig L, Hudson A, Hugo C, Hull R, Hume L, Hundei W, Hunt N, Hunter A, Hurley S, Hurst A, Hutchinson C, Hyo T, Ibrahim FH, Ibrahim S, Ihana N, Ikeda T, Imai A, Imamine R, Inamori A, Inazawa H, Ingell J, Inomata K, Inukai Y, Ioka M, Irtiza-Ali A, Isakova T, Isari W, Iselt M, Ishiguro A, Ishihara K, Ishikawa T, Ishimoto T, Ishizuka K, Ismail R, Itano S, Ito H, Ito K, Ito M, Ito Y, Iwagaitsu S, Iwaita Y, Iwakura T, Iwamoto M, Iwasa M, Iwasaki H, Iwasaki S, Izumi K, Izumi K, Izumi T, Jaafar SM, Jackson C, Jackson Y, Jafari G, Jahangiriesmaili M, Jain N, Jansson K, Jasim H, Jeffers L, Jenkins A, Jesky M, Jesus-Silva J, Jeyarajah D, Jiang Y, Jiao X, Jimenez G, Jin B, Jin Q, Jochims J, Johns B, Johnson C, Johnson T, Jolly S, Jones L, Jones L, Jones S, Jones T, Jones V, Joseph M, Joshi S, Judge P, Junejo N, Junus S, Kachele M, Kadowaki T, Kadoya H, Kaga H, Kai H, Kajio H, Kaluza-Schilling W, Kamaruzaman L, Kamarzarian A, Kamimura Y, Kamiya H, Kamundi C, Kan T, Kanaguchi Y, Kanazawa A, Kanda E, Kanegae S, Kaneko K, Kaneko K, Kang HY, Kano T, Karim M, Karounos D, Karsan W, Kasagi R, Kashihara N, Katagiri H, Katanosaka A, Katayama A, Katayama M, Katiman E, Kato K, Kato M, Kato N, Kato S, Kato T, Kato Y, Katsuda Y, Katsuno T, Kaufeld J, Kavak Y, Kawai I, Kawai M, Kawai M, Kawase A, Kawashima S, Kazory A, Kearney J, Keith B, Kellett J, Kelley S, Kershaw M, Ketteler M, Khai Q, Khairullah Q, Khandwala H, Khoo KKL, Khwaja A, Kidokoro K, Kielstein J, Kihara M, Kimber C, Kimura S, Kinashi H, Kingston H, Kinomura M, Kinsella-Perks E, Kitagawa M, Kitajima M, Kitamura S, Kiyosue A, Kiyota M, Klauser F, Klausmann G, Kmietschak W, Knapp K, Knight C, Knoppe A, Knott C, Kobayashi M, Kobayashi R, Kobayashi T, Koch M, Kodama S, Kodani N, Kogure E, Koizumi M, Kojima H, Kojo T, Kolhe N, Komaba H, Komiya T, Komori H, Kon SP, Kondo M, Kondo M, Kong W, Konishi M, Kono K, Koshino M, Kosugi T, Kothapalli B, Kozlowski T, Kraemer B, Kraemer-Guth A, Krappe J, Kraus D, Kriatselis C, Krieger C, Krish P, Kruger B, Ku Md Razi KR, Kuan Y, Kubota S, Kuhn S, Kumar P, Kume S, Kummer I, Kumuji R, Küpper A, Kuramae T, Kurian L, Kuribayashi C, Kurien R, Kuroda E, Kurose T, Kutschat A, Kuwabara N, Kuwata H, La Manna G, Lacey M, Lafferty K, LaFleur P, Lai V, Laity E, Lambert A, Landray MJ, Langlois M, Latif F, Latore E, Laundy E, Laurienti D, Lawson A, Lay M, Leal I, Leal I, Lee AK, Lee J, Lee KQ, Lee R, Lee SA, Lee YY, Lee-Barkey Y, Leonard N, Leoncini G, Leong CM, Lerario S, Leslie A, Levin A, Lewington A, Li J, Li N, Li X, Li Y, Liberti L, Liberti ME, Liew A, Liew YF, Lilavivat U, Lim SK, Lim YS, Limon E, Lin H, Lioudaki E, Liu H, Liu J, Liu L, Liu Q, Liu WJ, Liu X, Liu Z, Loader D, Lochhead H, Loh CL, Lorimer A, Loudermilk L, Loutan J, Low CK, Low CL, Low YM, Lozon Z, Lu Y, Lucci D, Ludwig U, Luker N, Lund D, Lustig R, Lyle S, Macdonald C, MacDougall I, Machicado R, MacLean D, Macleod P, Madera A, Madore F, Maeda K, Maegawa H, Maeno S, Mafham M, Magee J, Maggioni AP, Mah DY, Mahabadi V, Maiguma M, Makita Y, Makos G, Manco L, Mangiacapra R, Manley J, Mann P, Mano S, Marcotte G, Maris J, Mark P, Markau S, Markovic M, Marshall C, Martin M, Martinez C, Martinez S, Martins G, Maruyama K, Maruyama S, Marx K, Maselli A, Masengu A, Maskill A, Masumoto S, Masutani K, Matsumoto M, Matsunaga T, Matsuoka N, Matsushita M, Matthews M, Matthias S, Matvienko E, Maurer M, Maxwell P, Mayne KJ, Mazlan N, Mazlan SA, Mbuyisa A, McCafferty K, McCarroll F, McCarthy T, McClary-Wright C, McCray K, McDermott P, McDonald C, McDougall R, McHaffie E, McIntosh K, McKinley T, McLaughlin S, McLean N, McNeil L, Measor A, Meek J, Mehta A, Mehta R, Melandri M, Mené P, Meng T, Menne J, Merritt K, Merscher S, Meshykhi C, Messa P, Messinger L, Miftari N, Miller R, Miller Y, Miller-Hodges E, Minatoguchi M, Miners M, Minutolo R, Mita T, Miura Y, Miyaji M, Miyamoto S, Miyatsuka T, Miyazaki M, Miyazawa I, Mizumachi R, Mizuno M, Moffat S, Mohamad Nor FS, Mohamad Zaini SN, Mohamed Affandi FA, Mohandas C, Mohd R, Mohd Fauzi NA, Mohd Sharif NH, Mohd Yusoff Y, Moist L, Moncada A, Montasser M, Moon A, Moran C, Morgan N, Moriarty J, Morig G, Morinaga H, Morino K, Morisaki T, Morishita Y, Morlok S, Morris A, Morris F, Mostafa S, Mostefai Y, Motegi M, Motherwell N, Motta D, Mottl A, Moys R, Mozaffari S, Muir J, Mulhern J, Mulligan S, Munakata Y, Murakami C, Murakoshi M, Murawska A, Murphy K, Murphy L, Murray S, Murtagh H, Musa MA, Mushahar L, Mustafa R, Mustafar R, Muto M, Nadar E, Nagano R, Nagasawa T, Nagashima E, Nagasu H, Nagelberg S, Nair H, Nakagawa Y, Nakahara M, Nakamura J, Nakamura R, Nakamura T, Nakaoka M, Nakashima E, Nakata J, Nakata M, Nakatani S, Nakatsuka A, Nakayama Y, Nakhoul G, Nangaku M, Naverrete G, Navivala A, Nazeer I, Negrea L, Nethaji C, Newman E, Ng SYA, Ng TJ, Ngu LLS, Nimbkar T, Nishi H, Nishi M, Nishi S, Nishida Y, Nishiyama A, Niu J, Niu P, Nobili G, Nohara N, Nojima I, Nolan J, Nosseir H, Nozawa M, Nunn M, Nunokawa S, Oda M, Oe M, Oe Y, Ogane K, Ogawa W, Ogihara T, Oguchi G, Ohsugi M, Oishi K, Okada Y, Okajyo J, Okamoto S, Okamura K, Olufuwa O, Oluyombo R, Omata A, Omori Y, Ong LM, Ong YC, Onyema J, Oomatia A, Oommen A, Oremus R, Orimo Y, Ortalda V, Osaki Y, Osawa Y, Osmond Foster J, O'Sullivan A, Otani T, Othman N, Otomo S, O'Toole J, Owen L, Ozawa T, Padiyar A, Page N, Pajak S, Paliege A, Pandey A, Pandey R, Pariani H, Park J, Parrigon M, Passauer J, Patecki M, Patel M, Patel R, Patel T, Patel Z, Paul R, Paul R, Paulsen L, Pavone L, Peixoto A, Peji J, Peng BC, Peng K, Pennino L, Pereira E, Perez E, Pergola P, Pesce F, Pessolano G, Petchey W, Petr EJ, Pfab T, Phelan P, Phillips R, Phillips T, Phipps M, Piccinni G, Pickett T, Pickworth S, Piemontese M, Pinto D, Piper J, Plummer-Morgan J, Poehler D, Polese L, Poma V, Pontremoli R, Postal A, Pötz C, Power A, Pradhan N, Pradhan R, Preiss D, Preiss E, Preston K, Prib N, Price L, Provenzano C, Pugay C, Pulido R, Putz F, Qiao Y, Quartagno R, Quashie-Akponeware M, Rabara R, Rabasa-Lhoret R, Radhakrishnan D, Radley M, Raff R, Raguwaran S, Rahbari-Oskoui F, Rahman M, Rahmat K, Ramadoss S, Ramanaidu S, Ramasamy S, Ramli R, Ramli S, Ramsey T, Rankin A, Rashidi A, Raymond L, Razali WAFA, Read K, Reiner H, Reisler A, Reith C, Renner J, Rettenmaier B, Richmond L, Rijos D, Rivera R, Rivers V, Robinson H, Rocco M, Rodriguez-Bachiller I, Rodriquez R, Roesch C, Roesch J, Rogers J, Rohnstock M, Rolfsmeier S, Roman M, Romo A, Rosati A, Rosenberg S, Ross T, Rossello X, Roura M, Roussel M, Rovner S, Roy S, Rucker S, Rump L, Ruocco M, Ruse S, Russo F, Russo M, Ryder M, Sabarai A, Saccà C, Sachson R, Sadler E, Safiee NS, Sahani M, Saillant A, Saini J, Saito C, Saito S, Sakaguchi K, Sakai M, Salim H, Salviani C, Sammons E, Sampson A, Samson F, Sandercock P, Sanguila S, Santorelli G, Santoro D, Sarabu N, Saram T, Sardell R, Sasajima H, Sasaki T, Satko S, Sato A, Sato D, Sato H, Sato H, Sato J, Sato T, Sato Y, Satoh M, Sawada K, Schanz M, Scheidemantel F, Schemmelmann M, Schettler E, Schettler V, Schlieper GR, Schmidt C, Schmidt G, Schmidt U, Schmidt-Gurtler H, Schmude M, Schneider A, Schneider I, Schneider-Danwitz C, Schomig M, Schramm T, Schreiber A, Schricker S, Schroppel B, Schulte-Kemna L, Schulz E, Schumacher B, Schuster A, Schwab A, Scolari F, Scott A, Seeger W, Seeger W, Segal M, Seifert L, Seifert M, Sekiya M, Sellars R, Seman MR, Shah S, Shah S, Shainberg L, Shanmuganathan M, Shao F, Sharma K, Sharpe C, Sheikh-Ali M, Sheldon J, Shenton C, Shepherd A, Shepperd M, Sheridan R, Sheriff Z, Shibata Y, Shigehara T, Shikata K, Shimamura K, Shimano H, Shimizu Y, Shimoda H, Shin K, Shivashankar G, Shojima N, Silva R, Sim CSB, Simmons K, Sinha S, Sitter T, Sivanandam S, Skipper M, Sloan K, Sloan L, Smith R, Smyth J, Sobande T, Sobata M, Somalanka S, Song X, Sonntag F, Sood B, Sor SY, Soufer J, Sparks H, Spatoliatore G, Spinola T, Squyres S, Srivastava A, Stanfield J, Staplin N, Staylor K, Steele A, Steen O, Steffl D, Stegbauer J, Stellbrink C, Stellbrink E, Stevens W, Stevenson A, Stewart-Ray V, Stickley J, Stoffler D, Stratmann B, Streitenberger S, Strutz F, Stubbs J, Stumpf J, Suazo N, Suchinda P, Suckling R, Sudin A, Sugamori K, Sugawara H, Sugawara K, Sugimoto D, Sugiyama H, Sugiyama H, Sugiyama T, Sullivan M, Sumi M, Suresh N, Sutton D, Suzuki H, Suzuki R, Suzuki Y, Suzuki Y, Suzuki Y, Swanson E, Swift P, Syed S, Szerlip H, Taal M, Taddeo M, Tailor C, Tajima K, Takagi M, Takahashi K, Takahashi K, Takahashi M, Takahashi T, Takahira E, Takai T, Takaoka M, Takeoka J, Takesada A, Takezawa M, Talbot M, Taliercio J, Talsania T, Tamori Y, Tamura R, Tamura Y, Tan CHH, Tan EZZ, Tanabe A, Tanabe K, Tanaka A, Tanaka A, Tanaka N, Tang S, Tang Z, Tanigaki K, Tarlac M, Tatsuzawa A, Tay JF, Tay LL, Taylor J, Taylor K, Taylor K, Te A, Tenbusch L, Teng KS, Terakawa A, Terry J, Tham ZD, Tholl S, Thomas G, Thong KM, Tietjen D, Timadjer A, Tindall H, Tipper S, Tobin K, Toda N, Tokuyama A, Tolibas M, Tomita A, Tomita T, Tomlinson J, Tonks L, Topf J, Topping S, Torp A, Torres A, Totaro F, Toth P, Toyonaga Y, Tripodi F, Trivedi K, Tropman E, Tschope D, Tse J, Tsuji K, Tsunekawa S, Tsunoda R, Tucky B, Tufail S, Tuffaha A, Turan E, Turner H, Turner J, Turner M, Tuttle KR, Tye YL, Tyler A, Tyler J, Uchi H, Uchida H, Uchida T, Uchida T, Udagawa T, Ueda S, Ueda Y, Ueki K, Ugni S, Ugwu E, Umeno R, Unekawa C, Uozumi K, Urquia K, Valleteau A, Valletta C, van Erp R, Vanhoy C, Varad V, Varma R, Varughese A, Vasquez P, Vasseur A, Veelken R, Velagapudi C, Verdel K, Vettoretti S, Vezzoli G, Vielhauer V, Viera R, Vilar E, Villaruel S, Vinall L, Vinathan J, Visnjic M, Voigt E, von-Eynatten M, Vourvou M, Wada J, Wada J, Wada T, Wada Y, Wakayama K, Wakita Y, Wallendszus K, Walters T, Wan Mohamad WH, Wang L, Wang W, Wang X, Wang X, Wang Y, Wanner C, Wanninayake S, Watada H, Watanabe K, Watanabe K, Watanabe M, Waterfall H, Watkins D, Watson S, Weaving L, Weber B, Webley Y, Webster A, Webster M, Weetman M, Wei W, Weihprecht H, Weiland L, Weinmann-Menke J, Weinreich T, Wendt R, Weng Y, Whalen M, Whalley G, Wheatley R, Wheeler A, Wheeler J, Whelton P, White K, Whitmore B, Whittaker S, Wiebel J, Wiley J, Wilkinson L, Willett M, Williams A, Williams E, Williams K, Williams T, Wilson A, Wilson P, Wincott L, Wines E, Winkelmann B, Winkler M, Winter-Goodwin B, Witczak J, Wittes J, Wittmann M, Wolf G, Wolf L, Wolfling R, Wong C, Wong E, Wong HS, Wong LW, Wong YH, Wonnacott A, Wood A, Wood L, Woodhouse H, Wooding N, Woodman A, Wren K, Wu J, Wu P, Xia S, Xiao H, Xiao X, Xie Y, Xu C, Xu Y, Xue H, Yahaya H, Yalamanchili H, Yamada A, Yamada N, Yamagata K, Yamaguchi M, Yamaji Y, Yamamoto A, Yamamoto S, Yamamoto S, Yamamoto T, Yamanaka A, Yamano T, Yamanouchi Y, Yamasaki N, Yamasaki Y, Yamasaki Y, Yamashita C, Yamauchi T, Yan Q, Yanagisawa E, Yang F, Yang L, Yano S, Yao S, Yao Y, Yarlagadda S, Yasuda Y, Yiu V, Yokoyama T, Yoshida S, Yoshidome E, Yoshikawa H, Young A, Young T, Yousif V, Yu H, Yu Y, Yuasa K, Yusof N, Zalunardo N, Zander B, Zani R, Zappulo F, Zayed M, Zemann B, Zettergren P, Zhang H, Zhang L, Zhang L, Zhang N, Zhang X, Zhao J, Zhao L, Zhao S, Zhao Z, Zhong H, Zhou N, Zhou S, Zhu D, Zhu L, Zhu S, Zietz M, Zippo M, Zirino F, Zulkipli FH. Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial. Lancet Diabetes Endocrinol 2024; 12:39-50. [PMID: 38061371 PMCID: PMC7615591 DOI: 10.1016/s2213-8587(23)00321-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial. METHODS EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110. FINDINGS Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001). INTERPRETATION Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor. FUNDING Boehringer Ingelheim and Eli Lilly.
Collapse
|
5
|
Judge PK, Staplin N, Mayne KJ, Wanner C, Green JB, Hauske SJ, Emberson JR, Preiss D, Ng SYA, Roddick AJ, Sammons E, Zhu D, Hill M, Stevens W, Wallendszus K, Brenner S, Cheung AK, Liu ZH, Li J, Hooi LS, Liu WJ, Kadowaki T, Nangaku M, Levin A, Cherney D, Maggioni AP, Pontremoli R, Deo R, Goto S, Rossello X, Tuttle KR, Steubl D, Massey D, Landray MJ, Baigent C, Haynes R, Herrington WG, Abat S, Abd Rahman R, Abdul Cader R, Abdul Hafidz MI, Abdul Wahab MZ, Abdullah NK, Abdul-Samad T, Abe M, Abraham N, Acheampong S, Achiri P, Acosta JA, Adeleke A, Adell V, Adewuyi-Dalton R, Adnan N, Africano A, Agharazii M, Aguilar F, Aguilera A, Ahmad M, Ahmad MK, Ahmad NA, Ahmad NH, Ahmad NI, Ahmad Miswan N, Ahmad Rosdi H, Ahmed I, Ahmed S, Ahmed S, Aiello J, Aitken A, AitSadi R, Aker S, Akimoto S, Akinfolarin A, Akram S, Alberici F, Albert C, Aldrich L, Alegata M, Alexander L, Alfaress S, Alhadj Ali M, Ali A, Ali A, Alicic R, Aliu A, Almaraz R, Almasarwah R, Almeida J, Aloisi A, Al-Rabadi L, Alscher D, Alvarez P, Al-Zeer B, Amat M, Ambrose C, Ammar H, An Y, Andriaccio L, Ansu K, Apostolidi A, Arai N, Araki H, Araki S, Arbi A, Arechiga O, Armstrong S, Arnold T, Aronoff S, Arriaga W, Arroyo J, Arteaga D, Asahara S, Asai A, Asai N, Asano S, Asawa M, Asmee MF, Aucella F, Augustin M, Avery A, Awad A, Awang IY, Awazawa M, Axler A, Ayub W, Azhari Z, Baccaro R, Badin C, Bagwell B, Bahlmann-Kroll E, Bahtar AZ, Baigent C, Bains D, Bajaj H, Baker R, Baldini E, Banas B, Banerjee D, Banno S, Bansal S, Barberi S, Barnes S, Barnini C, Barot C, Barrett K, Barrios R, Bartolomei Mecatti B, Barton I, Barton J, Basily W, Bavanandan S, Baxter A, Becker L, Beddhu S, Beige J, Beigh S, Bell S, Benck U, Beneat A, Bennett A, Bennett D, Benyon S, Berdeprado J, Bergler T, Bergner A, Berry M, Bevilacqua M, Bhairoo J, Bhandari S, Bhandary N, Bhatt A, Bhattarai M, Bhavsar M, Bian W, Bianchini F, Bianco S, Bilous R, Bilton J, Bilucaglia D, Bird C, Birudaraju D, Biscoveanu M, Blake C, Bleakley N, Bocchicchia K, Bodine S, Bodington R, Boedecker S, Bolduc M, Bolton S, Bond C, Boreky F, Boren K, Bouchi R, Bough L, Bovan D, Bowler C, Bowman L, Brar N, Braun C, Breach A, Breitenfeldt M, Brenner S, Brettschneider B, Brewer A, Brewer G, Brindle V, Brioni E, Brown C, Brown H, Brown L, Brown R, Brown S, Browne D, Bruce K, Brueckmann M, Brunskill N, Bryant M, Brzoska M, Bu Y, Buckman C, Budoff M, Bullen M, Burke A, Burnette S, Burston C, Busch M, Bushnell J, Butler S, Büttner C, Byrne C, Caamano A, Cadorna J, Cafiero C, Cagle M, Cai J, Calabrese K, Calvi C, Camilleri B, Camp S, Campbell D, Campbell R, Cao H, Capelli I, Caple M, Caplin B, Cardone A, Carle J, Carnall V, Caroppo M, Carr S, Carraro G, Carson M, Casares P, Castillo C, Castro C, Caudill B, Cejka V, Ceseri M, Cham L, Chamberlain A, Chambers J, Chan CBT, Chan JYM, Chan YC, Chang E, Chang E, Chant T, Chavagnon T, Chellamuthu P, Chen F, Chen J, Chen P, Chen TM, Chen Y, Chen Y, Cheng C, Cheng H, Cheng MC, Cherney D, Cheung AK, Ching CH, Chitalia N, Choksi R, Chukwu C, Chung K, Cianciolo G, Cipressa L, Clark S, Clarke H, Clarke R, Clarke S, Cleveland B, Cole E, Coles H, Condurache L, Connor A, Convery K, Cooper A, Cooper N, Cooper Z, Cooperman L, Cosgrove L, Coutts P, Cowley A, Craik R, Cui G, Cummins T, Dahl N, Dai H, Dajani L, D'Amelio A, Damian E, Damianik K, Danel L, Daniels C, Daniels T, Darbeau S, Darius H, Dasgupta T, Davies J, Davies L, Davis A, Davis J, Davis L, Dayanandan R, Dayi S, Dayrell R, De Nicola L, Debnath S, Deeb W, Degenhardt S, DeGoursey K, Delaney M, Deo R, DeRaad R, Derebail V, Dev D, Devaux M, Dhall P, Dhillon G, Dienes J, Dobre M, Doctolero E, Dodds V, Domingo D, Donaldson D, Donaldson P, Donhauser C, Donley V, Dorestin S, Dorey S, Doulton T, Draganova D, Draxlbauer K, Driver F, Du H, Dube F, Duck T, Dugal T, Dugas J, Dukka H, Dumann H, Durham W, Dursch M, Dykas R, Easow R, Eckrich E, Eden G, Edmerson E, Edwards H, Ee LW, Eguchi J, Ehrl Y, Eichstadt K, Eid W, Eilerman B, Ejima Y, Eldon H, Ellam T, Elliott L, Ellison R, Emberson J, Epp R, Er A, Espino-Obrero M, Estcourt S, Estienne L, Evans G, Evans J, Evans S, Fabbri G, Fajardo-Moser M, Falcone C, Fani F, Faria-Shayler P, Farnia F, Farrugia D, Fechter M, Fellowes D, Feng F, Fernandez J, Ferraro P, Field A, Fikry S, Finch J, Finn H, Fioretto P, Fish R, Fleischer A, Fleming-Brown D, Fletcher L, Flora R, Foellinger C, Foligno N, Forest S, Forghani Z, Forsyth K, Fottrell-Gould D, Fox P, Frankel A, Fraser D, Frazier R, Frederick K, Freking N, French H, Froment A, Fuchs B, Fuessl L, Fujii H, Fujimoto A, Fujita A, Fujita K, Fujita Y, Fukagawa M, Fukao Y, Fukasawa A, Fuller T, Funayama T, Fung E, Furukawa M, Furukawa Y, Furusho M, Gabel S, Gaidu J, Gaiser S, Gallo K, Galloway C, Gambaro G, Gan CC, Gangemi C, Gao M, Garcia K, Garcia M, Garofalo C, Garrity M, Garza A, Gasko S, Gavrila M, Gebeyehu B, Geddes A, Gentile G, George A, George J, Gesualdo L, Ghalli F, Ghanem A, Ghate T, Ghavampour S, Ghazi A, Gherman A, Giebeln-Hudnell U, Gill B, Gillham S, Girakossyan I, Girndt M, Giuffrida A, Glenwright M, Glider T, Gloria R, Glowski D, Goh BL, Goh CB, Gohda T, Goldenberg R, Goldfaden R, Goldsmith C, Golson B, Gonce V, Gong Q, Goodenough B, Goodwin N, Goonasekera M, Gordon A, Gordon J, Gore A, Goto H, Goto S, Goto S, Gowen D, Grace A, Graham J, Grandaliano G, Gray M, Green JB, Greene T, Greenwood G, Grewal B, Grifa R, Griffin D, Griffin S, Grimmer P, Grobovaite E, Grotjahn S, Guerini A, Guest C, Gunda S, Guo B, Guo Q, Haack S, Haase M, Haaser K, Habuki K, Hadley A, Hagan S, Hagge S, Haller H, Ham S, Hamal S, Hamamoto Y, Hamano N, Hamm M, Hanburry A, Haneda M, Hanf C, Hanif W, Hansen J, Hanson L, Hantel S, Haraguchi T, Harding E, Harding T, Hardy C, Hartner C, Harun Z, Harvill L, Hasan A, Hase H, Hasegawa F, Hasegawa T, Hashimoto A, Hashimoto C, Hashimoto M, Hashimoto S, Haskett S, Hauske SJ, Hawfield A, Hayami T, Hayashi M, Hayashi S, Haynes R, Hazara A, Healy C, Hecktman J, Heine G, Henderson H, Henschel R, Hepditch A, Herfurth K, Hernandez G, Hernandez Pena A, Hernandez-Cassis C, Herrington WG, Herzog C, Hewins S, Hewitt D, Hichkad L, Higashi S, Higuchi C, Hill C, Hill L, Hill M, Himeno T, Hing A, Hirakawa Y, Hirata K, Hirota Y, Hisatake T, Hitchcock S, Hodakowski A, Hodge W, Hogan R, Hohenstatt U, Hohenstein B, Hooi L, Hope S, Hopley M, Horikawa S, Hosein D, Hosooka T, Hou L, Hou W, Howie L, Howson A, Hozak M, Htet Z, Hu X, Hu Y, Huang J, Huda N, Hudig L, Hudson A, Hugo C, Hull R, Hume L, Hundei W, Hunt N, Hunter A, Hurley S, Hurst A, Hutchinson C, Hyo T, Ibrahim FH, Ibrahim S, Ihana N, Ikeda T, Imai A, Imamine R, Inamori A, Inazawa H, Ingell J, Inomata K, Inukai Y, Ioka M, Irtiza-Ali A, Isakova T, Isari W, Iselt M, Ishiguro A, Ishihara K, Ishikawa T, Ishimoto T, Ishizuka K, Ismail R, Itano S, Ito H, Ito K, Ito M, Ito Y, Iwagaitsu S, Iwaita Y, Iwakura T, Iwamoto M, Iwasa M, Iwasaki H, Iwasaki S, Izumi K, Izumi K, Izumi T, Jaafar SM, Jackson C, Jackson Y, Jafari G, Jahangiriesmaili M, Jain N, Jansson K, Jasim H, Jeffers L, Jenkins A, Jesky M, Jesus-Silva J, Jeyarajah D, Jiang Y, Jiao X, Jimenez G, Jin B, Jin Q, Jochims J, Johns B, Johnson C, Johnson T, Jolly S, Jones L, Jones L, Jones S, Jones T, Jones V, Joseph M, Joshi S, Judge P, Junejo N, Junus S, Kachele M, Kadowaki T, Kadoya H, Kaga H, Kai H, Kajio H, Kaluza-Schilling W, Kamaruzaman L, Kamarzarian A, Kamimura Y, Kamiya H, Kamundi C, Kan T, Kanaguchi Y, Kanazawa A, Kanda E, Kanegae S, Kaneko K, Kaneko K, Kang HY, Kano T, Karim M, Karounos D, Karsan W, Kasagi R, Kashihara N, Katagiri H, Katanosaka A, Katayama A, Katayama M, Katiman E, Kato K, Kato M, Kato N, Kato S, Kato T, Kato Y, Katsuda Y, Katsuno T, Kaufeld J, Kavak Y, Kawai I, Kawai M, Kawai M, Kawase A, Kawashima S, Kazory A, Kearney J, Keith B, Kellett J, Kelley S, Kershaw M, Ketteler M, Khai Q, Khairullah Q, Khandwala H, Khoo KKL, Khwaja A, Kidokoro K, Kielstein J, Kihara M, Kimber C, Kimura S, Kinashi H, Kingston H, Kinomura M, Kinsella-Perks E, Kitagawa M, Kitajima M, Kitamura S, Kiyosue A, Kiyota M, Klauser F, Klausmann G, Kmietschak W, Knapp K, Knight C, Knoppe A, Knott C, Kobayashi M, Kobayashi R, Kobayashi T, Koch M, Kodama S, Kodani N, Kogure E, Koizumi M, Kojima H, Kojo T, Kolhe N, Komaba H, Komiya T, Komori H, Kon SP, Kondo M, Kondo M, Kong W, Konishi M, Kono K, Koshino M, Kosugi T, Kothapalli B, Kozlowski T, Kraemer B, Kraemer-Guth A, Krappe J, Kraus D, Kriatselis C, Krieger C, Krish P, Kruger B, Ku Md Razi KR, Kuan Y, Kubota S, Kuhn S, Kumar P, Kume S, Kummer I, Kumuji R, Küpper A, Kuramae T, Kurian L, Kuribayashi C, Kurien R, Kuroda E, Kurose T, Kutschat A, Kuwabara N, Kuwata H, La Manna G, Lacey M, Lafferty K, LaFleur P, Lai V, Laity E, Lambert A, Landray MJ, Langlois M, Latif F, Latore E, Laundy E, Laurienti D, Lawson A, Lay M, Leal I, Leal I, Lee AK, Lee J, Lee KQ, Lee R, Lee SA, Lee YY, Lee-Barkey Y, Leonard N, Leoncini G, Leong CM, Lerario S, Leslie A, Levin A, Lewington A, Li J, Li N, Li X, Li Y, Liberti L, Liberti ME, Liew A, Liew YF, Lilavivat U, Lim SK, Lim YS, Limon E, Lin H, Lioudaki E, Liu H, Liu J, Liu L, Liu Q, Liu WJ, Liu X, Liu Z, Loader D, Lochhead H, Loh CL, Lorimer A, Loudermilk L, Loutan J, Low CK, Low CL, Low YM, Lozon Z, Lu Y, Lucci D, Ludwig U, Luker N, Lund D, Lustig R, Lyle S, Macdonald C, MacDougall I, Machicado R, MacLean D, Macleod P, Madera A, Madore F, Maeda K, Maegawa H, Maeno S, Mafham M, Magee J, Maggioni AP, Mah DY, Mahabadi V, Maiguma M, Makita Y, Makos G, Manco L, Mangiacapra R, Manley J, Mann P, Mano S, Marcotte G, Maris J, Mark P, Markau S, Markovic M, Marshall C, Martin M, Martinez C, Martinez S, Martins G, Maruyama K, Maruyama S, Marx K, Maselli A, Masengu A, Maskill A, Masumoto S, Masutani K, Matsumoto M, Matsunaga T, Matsuoka N, Matsushita M, Matthews M, Matthias S, Matvienko E, Maurer M, Maxwell P, Mayne KJ, Mazlan N, Mazlan SA, Mbuyisa A, McCafferty K, McCarroll F, McCarthy T, McClary-Wright C, McCray K, McDermott P, McDonald C, McDougall R, McHaffie E, McIntosh K, McKinley T, McLaughlin S, McLean N, McNeil L, Measor A, Meek J, Mehta A, Mehta R, Melandri M, Mené P, Meng T, Menne J, Merritt K, Merscher S, Meshykhi C, Messa P, Messinger L, Miftari N, Miller R, Miller Y, Miller-Hodges E, Minatoguchi M, Miners M, Minutolo R, Mita T, Miura Y, Miyaji M, Miyamoto S, Miyatsuka T, Miyazaki M, Miyazawa I, Mizumachi R, Mizuno M, Moffat S, Mohamad Nor FS, Mohamad Zaini SN, Mohamed Affandi FA, Mohandas C, Mohd R, Mohd Fauzi NA, Mohd Sharif NH, Mohd Yusoff Y, Moist L, Moncada A, Montasser M, Moon A, Moran C, Morgan N, Moriarty J, Morig G, Morinaga H, Morino K, Morisaki T, Morishita Y, Morlok S, Morris A, Morris F, Mostafa S, Mostefai Y, Motegi M, Motherwell N, Motta D, Mottl A, Moys R, Mozaffari S, Muir J, Mulhern J, Mulligan S, Munakata Y, Murakami C, Murakoshi M, Murawska A, Murphy K, Murphy L, Murray S, Murtagh H, Musa MA, Mushahar L, Mustafa R, Mustafar R, Muto M, Nadar E, Nagano R, Nagasawa T, Nagashima E, Nagasu H, Nagelberg S, Nair H, Nakagawa Y, Nakahara M, Nakamura J, Nakamura R, Nakamura T, Nakaoka M, Nakashima E, Nakata J, Nakata M, Nakatani S, Nakatsuka A, Nakayama Y, Nakhoul G, Nangaku M, Naverrete G, Navivala A, Nazeer I, Negrea L, Nethaji C, Newman E, Ng SYA, Ng TJ, Ngu LLS, Nimbkar T, Nishi H, Nishi M, Nishi S, Nishida Y, Nishiyama A, Niu J, Niu P, Nobili G, Nohara N, Nojima I, Nolan J, Nosseir H, Nozawa M, Nunn M, Nunokawa S, Oda M, Oe M, Oe Y, Ogane K, Ogawa W, Ogihara T, Oguchi G, Ohsugi M, Oishi K, Okada Y, Okajyo J, Okamoto S, Okamura K, Olufuwa O, Oluyombo R, Omata A, Omori Y, Ong LM, Ong YC, Onyema J, Oomatia A, Oommen A, Oremus R, Orimo Y, Ortalda V, Osaki Y, Osawa Y, Osmond Foster J, O'Sullivan A, Otani T, Othman N, Otomo S, O'Toole J, Owen L, Ozawa T, Padiyar A, Page N, Pajak S, Paliege A, Pandey A, Pandey R, Pariani H, Park J, Parrigon M, Passauer J, Patecki M, Patel M, Patel R, Patel T, Patel Z, Paul R, Paul R, Paulsen L, Pavone L, Peixoto A, Peji J, Peng BC, Peng K, Pennino L, Pereira E, Perez E, Pergola P, Pesce F, Pessolano G, Petchey W, Petr EJ, Pfab T, Phelan P, Phillips R, Phillips T, Phipps M, Piccinni G, Pickett T, Pickworth S, Piemontese M, Pinto D, Piper J, Plummer-Morgan J, Poehler D, Polese L, Poma V, Pontremoli R, Postal A, Pötz C, Power A, Pradhan N, Pradhan R, Preiss D, Preiss E, Preston K, Prib N, Price L, Provenzano C, Pugay C, Pulido R, Putz F, Qiao Y, Quartagno R, Quashie-Akponeware M, Rabara R, Rabasa-Lhoret R, Radhakrishnan D, Radley M, Raff R, Raguwaran S, Rahbari-Oskoui F, Rahman M, Rahmat K, Ramadoss S, Ramanaidu S, Ramasamy S, Ramli R, Ramli S, Ramsey T, Rankin A, Rashidi A, Raymond L, Razali WAFA, Read K, Reiner H, Reisler A, Reith C, Renner J, Rettenmaier B, Richmond L, Rijos D, Rivera R, Rivers V, Robinson H, Rocco M, Rodriguez-Bachiller I, Rodriquez R, Roesch C, Roesch J, Rogers J, Rohnstock M, Rolfsmeier S, Roman M, Romo A, Rosati A, Rosenberg S, Ross T, Rossello X, Roura M, Roussel M, Rovner S, Roy S, Rucker S, Rump L, Ruocco M, Ruse S, Russo F, Russo M, Ryder M, Sabarai A, Saccà C, Sachson R, Sadler E, Safiee NS, Sahani M, Saillant A, Saini J, Saito C, Saito S, Sakaguchi K, Sakai M, Salim H, Salviani C, Sammons E, Sampson A, Samson F, Sandercock P, Sanguila S, Santorelli G, Santoro D, Sarabu N, Saram T, Sardell R, Sasajima H, Sasaki T, Satko S, Sato A, Sato D, Sato H, Sato H, Sato J, Sato T, Sato Y, Satoh M, Sawada K, Schanz M, Scheidemantel F, Schemmelmann M, Schettler E, Schettler V, Schlieper GR, Schmidt C, Schmidt G, Schmidt U, Schmidt-Gurtler H, Schmude M, Schneider A, Schneider I, Schneider-Danwitz C, Schomig M, Schramm T, Schreiber A, Schricker S, Schroppel B, Schulte-Kemna L, Schulz E, Schumacher B, Schuster A, Schwab A, Scolari F, Scott A, Seeger W, Seeger W, Segal M, Seifert L, Seifert M, Sekiya M, Sellars R, Seman MR, Shah S, Shah S, Shainberg L, Shanmuganathan M, Shao F, Sharma K, Sharpe C, Sheikh-Ali M, Sheldon J, Shenton C, Shepherd A, Shepperd M, Sheridan R, Sheriff Z, Shibata Y, Shigehara T, Shikata K, Shimamura K, Shimano H, Shimizu Y, Shimoda H, Shin K, Shivashankar G, Shojima N, Silva R, Sim CSB, Simmons K, Sinha S, Sitter T, Sivanandam S, Skipper M, Sloan K, Sloan L, Smith R, Smyth J, Sobande T, Sobata M, Somalanka S, Song X, Sonntag F, Sood B, Sor SY, Soufer J, Sparks H, Spatoliatore G, Spinola T, Squyres S, Srivastava A, Stanfield J, Staplin N, Staylor K, Steele A, Steen O, Steffl D, Stegbauer J, Stellbrink C, Stellbrink E, Stevens W, Stevenson A, Stewart-Ray V, Stickley J, Stoffler D, Stratmann B, Streitenberger S, Strutz F, Stubbs J, Stumpf J, Suazo N, Suchinda P, Suckling R, Sudin A, Sugamori K, Sugawara H, Sugawara K, Sugimoto D, Sugiyama H, Sugiyama H, Sugiyama T, Sullivan M, Sumi M, Suresh N, Sutton D, Suzuki H, Suzuki R, Suzuki Y, Suzuki Y, Suzuki Y, Swanson E, Swift P, Syed S, Szerlip H, Taal M, Taddeo M, Tailor C, Tajima K, Takagi M, Takahashi K, Takahashi K, Takahashi M, Takahashi T, Takahira E, Takai T, Takaoka M, Takeoka J, Takesada A, Takezawa M, Talbot M, Taliercio J, Talsania T, Tamori Y, Tamura R, Tamura Y, Tan CHH, Tan EZZ, Tanabe A, Tanabe K, Tanaka A, Tanaka A, Tanaka N, Tang S, Tang Z, Tanigaki K, Tarlac M, Tatsuzawa A, Tay JF, Tay LL, Taylor J, Taylor K, Taylor K, Te A, Tenbusch L, Teng KS, Terakawa A, Terry J, Tham ZD, Tholl S, Thomas G, Thong KM, Tietjen D, Timadjer A, Tindall H, Tipper S, Tobin K, Toda N, Tokuyama A, Tolibas M, Tomita A, Tomita T, Tomlinson J, Tonks L, Topf J, Topping S, Torp A, Torres A, Totaro F, Toth P, Toyonaga Y, Tripodi F, Trivedi K, Tropman E, Tschope D, Tse J, Tsuji K, Tsunekawa S, Tsunoda R, Tucky B, Tufail S, Tuffaha A, Turan E, Turner H, Turner J, Turner M, Tuttle KR, Tye YL, Tyler A, Tyler J, Uchi H, Uchida H, Uchida T, Uchida T, Udagawa T, Ueda S, Ueda Y, Ueki K, Ugni S, Ugwu E, Umeno R, Unekawa C, Uozumi K, Urquia K, Valleteau A, Valletta C, van Erp R, Vanhoy C, Varad V, Varma R, Varughese A, Vasquez P, Vasseur A, Veelken R, Velagapudi C, Verdel K, Vettoretti S, Vezzoli G, Vielhauer V, Viera R, Vilar E, Villaruel S, Vinall L, Vinathan J, Visnjic M, Voigt E, von-Eynatten M, Vourvou M, Wada J, Wada J, Wada T, Wada Y, Wakayama K, Wakita Y, Wallendszus K, Walters T, Wan Mohamad WH, Wang L, Wang W, Wang X, Wang X, Wang Y, Wanner C, Wanninayake S, Watada H, Watanabe K, Watanabe K, Watanabe M, Waterfall H, Watkins D, Watson S, Weaving L, Weber B, Webley Y, Webster A, Webster M, Weetman M, Wei W, Weihprecht H, Weiland L, Weinmann-Menke J, Weinreich T, Wendt R, Weng Y, Whalen M, Whalley G, Wheatley R, Wheeler A, Wheeler J, Whelton P, White K, Whitmore B, Whittaker S, Wiebel J, Wiley J, Wilkinson L, Willett M, Williams A, Williams E, Williams K, Williams T, Wilson A, Wilson P, Wincott L, Wines E, Winkelmann B, Winkler M, Winter-Goodwin B, Witczak J, Wittes J, Wittmann M, Wolf G, Wolf L, Wolfling R, Wong C, Wong E, Wong HS, Wong LW, Wong YH, Wonnacott A, Wood A, Wood L, Woodhouse H, Wooding N, Woodman A, Wren K, Wu J, Wu P, Xia S, Xiao H, Xiao X, Xie Y, Xu C, Xu Y, Xue H, Yahaya H, Yalamanchili H, Yamada A, Yamada N, Yamagata K, Yamaguchi M, Yamaji Y, Yamamoto A, Yamamoto S, Yamamoto S, Yamamoto T, Yamanaka A, Yamano T, Yamanouchi Y, Yamasaki N, Yamasaki Y, Yamasaki Y, Yamashita C, Yamauchi T, Yan Q, Yanagisawa E, Yang F, Yang L, Yano S, Yao S, Yao Y, Yarlagadda S, Yasuda Y, Yiu V, Yokoyama T, Yoshida S, Yoshidome E, Yoshikawa H, Young A, Young T, Yousif V, Yu H, Yu Y, Yuasa K, Yusof N, Zalunardo N, Zander B, Zani R, Zappulo F, Zayed M, Zemann B, Zettergren P, Zhang H, Zhang L, Zhang L, Zhang N, Zhang X, Zhao J, Zhao L, Zhao S, Zhao Z, Zhong H, Zhou N, Zhou S, Zhu D, Zhu L, Zhu S, Zietz M, Zippo M, Zirino F, Zulkipli FH. Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial. Lancet Diabetes Endocrinol 2024; 12:51-60. [PMID: 38061372 DOI: 10.1016/s2213-8587(23)00322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population. METHODS EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110. FINDINGS Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1). INTERPRETATION In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease. FUNDING Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.
Collapse
|
6
|
Brierley CK, Yip BH, Orlando G, Goyal H, Wen S, Wen J, Levine MF, Jakobsdottir GM, Rodriguez-Meira A, Adamo A, Bashton M, Hamblin A, Clark SA, O'Sullivan J, Murphy L, Olijnik AA, Cotton A, Narina S, Pruett-Miller SM, Enshaei A, Harrison C, Drummond M, Knapper S, Tefferi A, Antony-Debré I, Thongjuea S, Wedge DC, Constantinescu S, Papaemmanuil E, Psaila B, Crispino JD, Mead AJ. Chromothripsis orchestrates leukemic transformation in blast phase MPN through targetable amplification of DYRK1A. bioRxiv 2023:2023.12.08.570880. [PMID: 38106192 PMCID: PMC10723394 DOI: 10.1101/2023.12.08.570880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Chromothripsis, the process of catastrophic shattering and haphazard repair of chromosomes, is a common event in cancer. Whether chromothripsis might constitute an actionable molecular event amenable to therapeutic targeting remains an open question. We describe recurrent chromothripsis of chromosome 21 in a subset of patients in blast phase of a myeloproliferative neoplasm (BP-MPN), which alongside other structural variants leads to amplification of a region of chromosome 21 in ∼25% of patients ('chr21amp'). We report that chr21amp BP-MPN has a particularly aggressive and treatment-resistant phenotype. The chr21amp event is highly clonal and present throughout the hematopoietic hierarchy. DYRK1A , a serine threonine kinase and transcription factor, is the only gene in the 2.7Mb minimally amplified region which showed both increased expression and chromatin accessibility compared to non-chr21amp BP-MPN controls. We demonstrate that DYRK1A is a central node at the nexus of multiple cellular functions critical for BP-MPN development, including DNA repair, STAT signalling and BCL2 overexpression. DYRK1A is essential for BP-MPN cell proliferation in vitro and in vivo , and DYRK1A inhibition synergises with BCL2 targeting to induce BP-MPN cell apoptosis. Collectively, these findings define the chr21amp event as a prognostic biomarker in BP-MPN and link chromothripsis to a druggable target.
Collapse
|
7
|
Merzbacher C, Ryan B, Goldsborough T, Hillary RF, Campbell A, Murphy L, McIntosh AM, Liewald D, Harris SE, McRae AF, Cox SR, Cannings TI, Vallejos CA, McCartney DL, Marioni RE. Integration of datasets for individual prediction of DNA methylation-based biomarkers. Genome Biol 2023; 24:278. [PMID: 38053194 PMCID: PMC10696831 DOI: 10.1186/s13059-023-03114-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Epigenetic scores (EpiScores) can provide biomarkers of lifestyle and disease risk. Projecting new datasets onto a reference panel is challenging due to separation of technical and biological variation with array data. Normalisation can standardise data distributions but may also remove population-level biological variation. RESULTS We compare two birth cohorts (Lothian Birth Cohorts of 1921 and 1936 - nLBC1921 = 387 and nLBC1936 = 498) with blood-based DNA methylation assessed at the same chronological age (79 years) and processed in the same lab but in different years and experimental batches. We examine the effect of 16 normalisation methods on a novel BMI EpiScore (trained in an external cohort, n = 18,413), and Horvath's pan-tissue DNA methylation age, when the cohorts are normalised separately and together. The BMI EpiScore explains a maximum variance of R2=24.5% in BMI in LBC1936 (SWAN normalisation). Although there are cross-cohort R2 differences, the normalisation method makes a minimal difference to within-cohort estimates. Conversely, a range of absolute differences are seen for individual-level EpiScore estimates for BMI and age when cohorts are normalised separately versus together. While within-array methods result in identical EpiScores whether a cohort is normalised on its own or together with the second dataset, a range of differences is observed for between-array methods. CONCLUSIONS Normalisation methods returning similar EpiScores, whether cohorts are analysed separately or together, will minimise technical variation when projecting new data onto a reference panel. These methods are important for cases where raw data is unavailable and joint normalisation of cohorts is computationally expensive.
Collapse
Affiliation(s)
| | - Barry Ryan
- School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | | | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - David Liewald
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Simon R Cox
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Timothy I Cannings
- Maxwell Institute for Mathematical Sciences, School of Mathematics, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Catalina A Vallejos
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Alan Turing Institute, London, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| |
Collapse
|
8
|
Gethin G, Murphy L, Sezgin D, Carr PJ, Mcintosh C, Probst S. Resigning oneself to a life of wound-related odour - A thematic analysis of patient experiences. J Tissue Viability 2023; 32:460-464. [PMID: 37495442 DOI: 10.1016/j.jtv.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/21/2023] [Accepted: 07/18/2023] [Indexed: 07/28/2023]
Abstract
AIMS To determine how patients with chronic wounds describe wound odour, identify what strategies they use to manage it and how effective these are. MATERIALS AND METHODS Using a qualitative descriptive approach, semi-structured interviews were conducted between July and August 2021 with seven patients living with an odorous chronic wound at home. Data were analysed using Braun and Clarke's thematic analysis framework. RESULTS The results were organised into two main themes: 1) becoming resigned to living with wound-related odour 2) strategies used to manage wound-related odour. Participants were sad, embarrassed and felt isolated but became resigned to living with this odour and accepting of it as a consequence of having a wound. Frequent dressing changes, household cleaning along with the use of sprays were the most frequently used tactics to manage odour none of which were deemed to be very effective. CONCLUSION This study highlights the problem of odour management in clinical practice and how individuals develop strategies to overcome odour. Sadly, patients were resigned to living with wound odour and were accepting of it as part of daily life. This highlights the importance for healthcare professionals to recognise, assess for and ensure a better understanding of how people experience wound odour, the impact it can have on them personally. Frequent dressing changes can help manage wound odour from the patient's perspective.
Collapse
Affiliation(s)
- G Gethin
- School of Nursing and Midwifery, University of Galway, Galway, Ireland; Alliance for Research and Innovation in Wounds, University of Galway, Galway, Ireland; Geneva School of Health Science, HES-SO University of Applied Sciences and Arts, Western Switzerland, Switzerland.
| | - L Murphy
- Alliance for Research and Innovation in Wounds, University of Galway, Galway, Ireland; Department of Nursing and Midwifery, Health Research Institute, University of Limerick, Limerick, Ireland.
| | - D Sezgin
- School of Nursing and Midwifery, University of Galway, Galway, Ireland; Alliance for Research and Innovation in Wounds, University of Galway, Galway, Ireland.
| | - P J Carr
- School of Nursing and Midwifery, University of Galway, Galway, Ireland; Alliance for Research and Innovation in Wounds, University of Galway, Galway, Ireland; AVATAR Group Menzies Health Institute Queensland Griffith University, Australia.
| | - C Mcintosh
- Alliance for Research and Innovation in Wounds, University of Galway, Galway, Ireland; Discipline of Podiatric Medicine, School of Health Science, University of Galway, Galway, Ireland.
| | - S Probst
- Alliance for Research and Innovation in Wounds, University of Galway, Galway, Ireland; Geneva School of Health Science, HES-SO University of Applied Sciences and Arts, Western Switzerland, Switzerland; School of Nursing, Monash University, Australia.
| |
Collapse
|
9
|
Patir A, Raper A, Fleming R, Henderson BEP, Murphy L, Henderson NC, Clark EL, Freeman TC, Barnett MW. Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis. G3 (Bethesda) 2023; 13:jkad178. [PMID: 37548242 PMCID: PMC10542211 DOI: 10.1093/g3journal/jkad178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 06/30/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023]
Abstract
It is estimated that animals pollinate 87.5% of flowering plants worldwide and that managed honey bees (Apis mellifera) account for 30-50% of this ecosystem service to agriculture. In addition to their important role as pollinators, honey bees are well-established insect models for studying learning and memory, behavior, caste differentiation, epigenetic mechanisms, olfactory biology, sex determination, and eusociality. Despite their importance to agriculture, knowledge of honey bee biology lags behind many other livestock species. In this study, we have used scRNA-Seq to map cell types to different developmental stages of the worker honey bee (prepupa at day 11 and pupa at day 15) and sought to determine their gene expression signatures. To identify cell-type populations, we examined the cell-to-cell network based on the similarity of the single-cells transcriptomic profiles. Grouping similar cells together we identified 63 different cell clusters of which 17 clusters were identifiable at both stages. To determine genes associated with specific cell populations or with a particular biological process involved in honey bee development, we used gene coexpression analysis. We combined this analysis with literature mining, the honey bee protein atlas, and gene ontology analysis to determine cell cluster identity. Of the cell clusters identified, 17 were related to the nervous system and sensory organs, 7 to the fat body, 19 to the cuticle, 5 to muscle, 4 to compound eye, 2 to midgut, 2 to hemocytes, and 1 to malpighian tubule/pericardial nephrocyte. To our knowledge, this is the first whole single-cell atlas of honey bees at any stage of development and demonstrates the potential for further work to investigate their biology at the cellular level.
Collapse
Affiliation(s)
- Anirudh Patir
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Anna Raper
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Robert Fleming
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Beth E P Henderson
- The Queen's Medical Research Institute, Centre for Inflammation Research, University of Edinburgh,Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Neil C Henderson
- The Queen's Medical Research Institute, Centre for Inflammation Research, University of Edinburgh,Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
- Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh,Edinburgh EH4 2XU, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Tom C Freeman
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Mark W Barnett
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
- Beebytes Analytics CIC, The Roslin Innovation Centre, University of Edinburgh, The Charnock Bradley Building, Easter Bush, Midlothian EH25 9RG, UK
| |
Collapse
|
10
|
Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature 2023; 619:E61. [PMID: 37433877 PMCID: PMC10371859 DOI: 10.1038/s41586-023-06383-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Affiliation(s)
- Erola Pairo-Castineira
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Pain Service, NHS Tayside, Ninewells Hospital and Medical School, Dundee, UK
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Marie Zechner
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Fiona Griffiths
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jonathan Millar
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ryan Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Charles Hinds
- William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Colin Begg
- Royal Hospital for Children, Glasgow, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Malak Abedalthagafi
- Genomic Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Andre D Luchessi
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Raquel Cruz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) Santiago de Compostela, Santiago de Compostela, Spain
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Clohisey Hendry
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
| |
Collapse
|
11
|
Hillary RF, McCartney DL, Smith HM, Bernabeu E, Gadd DA, Chybowska AD, Cheng Y, Murphy L, Wrobel N, Campbell A, Walker RM, Hayward C, Evans KL, McIntosh AM, Marioni RE. Blood-based epigenome-wide analyses of 19 common disease states: A longitudinal, population-based linked cohort study of 18,413 Scottish individuals. PLoS Med 2023; 20:e1004247. [PMID: 37410739 PMCID: PMC10325072 DOI: 10.1371/journal.pmed.1004247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/25/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND DNA methylation is a dynamic epigenetic mechanism that occurs at cytosine-phosphate-guanine dinucleotide (CpG) sites. Epigenome-wide association studies (EWAS) investigate the strength of association between methylation at individual CpG sites and health outcomes. Although blood methylation may act as a peripheral marker of common disease states, previous EWAS have typically focused only on individual conditions and have had limited power to discover disease-associated loci. This study examined the association of blood DNA methylation with the prevalence of 14 disease states and the incidence of 19 disease states in a single population of over 18,000 Scottish individuals. METHODS AND FINDINGS DNA methylation was assayed at 752,722 CpG sites in whole-blood samples from 18,413 volunteers in the family-structured, population-based cohort study Generation Scotland (age range 18 to 99 years). EWAS tested for cross-sectional associations between baseline CpG methylation and 14 prevalent disease states, and for longitudinal associations between baseline CpG methylation and 19 incident disease states. Prevalent cases were self-reported on health questionnaires at the baseline. Incident cases were identified using linkage to Scottish primary (Read 2) and secondary (ICD-10) care records, and the censoring date was set to October 2020. The mean time-to-diagnosis ranged from 5.0 years (for chronic pain) to 11.7 years (for Coronavirus Disease 2019 (COVID-19) hospitalisation). The 19 disease states considered in this study were selected if they were present on the World Health Organisation's 10 leading causes of death and disease burden or included in baseline self-report questionnaires. EWAS models were adjusted for age at methylation typing, sex, estimated white blood cell composition, population structure, and 5 common lifestyle risk factors. A structured literature review was also conducted to identify existing EWAS for all 19 disease states tested. The MEDLINE, Embase, Web of Science, and preprint servers were searched to retrieve relevant articles indexed as of March 27, 2023. Fifty-four of approximately 2,000 indexed articles met our inclusion criteria: assayed blood-based DNA methylation, had >20 individuals in each comparison group, and examined one of the 19 conditions considered. First, we assessed whether the associations identified in our study were reported in previous studies. We identified 69 associations between CpGs and the prevalence of 4 conditions, of which 58 were newly described. The conditions were breast cancer, chronic kidney disease, ischemic heart disease, and type 2 diabetes mellitus. We also uncovered 64 CpGs that associated with the incidence of 2 disease states (COPD and type 2 diabetes), of which 56 were not reported in the surveyed literature. Second, we assessed replication across existing studies, which was defined as the reporting of at least 1 common site in >2 studies that examined the same condition. Only 6/19 disease states had evidence of such replication. The limitations of this study include the nonconsideration of medication data and a potential lack of generalizability to individuals that are not of Scottish and European ancestry. CONCLUSIONS We discovered over 100 associations between blood methylation sites and common disease states, independently of major confounding risk factors, and a need for greater standardisation among EWAS on human disease.
Collapse
Affiliation(s)
- Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Hannah M. Smith
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Elena Bernabeu
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Aleksandra D. Chybowska
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Yipeng Cheng
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- School of Psychology, University of Exeter, Exeter, United Kingdom
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew M. McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
12
|
Gillan JL, Chokshi M, Hardisty GR, Clohisey Hendry S, Prasca-Chamorro D, Robinson NJ, Lasota B, Clark R, Murphy L, Whyte MK, Baillie JK, Davidson DJ, Bao G, Gray RD. CAGE sequencing reveals CFTR-dependent dysregulation of type I IFN signaling in activated cystic fibrosis macrophages. Sci Adv 2023; 9:eadg5128. [PMID: 37235648 PMCID: PMC10219589 DOI: 10.1126/sciadv.adg5128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
An intense, nonresolving airway inflammatory response leads to destructive lung disease in cystic fibrosis (CF). Dysregulation of macrophage immune function may be a key facet governing the progression of CF lung disease, but the underlying mechanisms are not fully understood. We used 5' end centered transcriptome sequencing to profile P. aeruginosa LPS-activated human CF macrophages, showing that CF and non-CF macrophages deploy substantially distinct transcriptional programs at baseline and following activation. This includes a significantly blunted type I IFN signaling response in activated patient cells relative to healthy controls that was reversible upon in vitro treatment with CFTR modulators in patient cells and by CRISPR-Cas9 gene editing to correct the F508del mutation in patient-derived iPSC macrophages. These findings illustrate a previously unidentified immune defect in human CF macrophages that is CFTR dependent and reversible with CFTR modulators, thus providing new avenues in the search for effective anti-inflammatory interventions in CF.
Collapse
Affiliation(s)
- Jonathan L. Gillan
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mithil Chokshi
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Gareth R. Hardisty
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | | | | | - Nicola J. Robinson
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Benjamin Lasota
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Richard Clark
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Moira K. B. Whyte
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | | | - Donald J. Davidson
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Robert D. Gray
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| |
Collapse
|
13
|
Conole ELS, Vaher K, Cabez MB, Sullivan G, Stevenson AJ, Hall J, Murphy L, Thrippleton MJ, Quigley AJ, Bastin ME, Miron VE, Whalley HC, Marioni RE, Boardman JP, Cox SR. Immuno-epigenetic signature derived in saliva associates with the encephalopathy of prematurity and perinatal inflammatory disorders. Brain Behav Immun 2023; 110:322-338. [PMID: 36948324 DOI: 10.1016/j.bbi.2023.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/12/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Preterm birth is closely associated with a phenotype that includes brain dysmaturation and neurocognitive impairment, commonly termed Encephalopathy of Prematurity (EoP), of which systemic inflammation is considered a key driver. DNA methylation (DNAm) signatures of inflammation from peripheral blood associate with poor brain imaging outcomes in adult cohorts. However, the robustness of DNAm inflammatory scores in infancy, their relation to comorbidities of preterm birth characterised by inflammation, neonatal neuroimaging metrics of EoP, and saliva cross-tissue applicability are unknown. METHODS Using salivary DNAm from 258 neonates (n = 155 preterm, gestational age at birth 23.28 - 34.84 weeks, n = 103 term, gestational age at birth 37.00 - 42.14 weeks), we investigated the impact of a DNAm surrogate for C-reactive protein (DNAm CRP) on brain structure and other clinically defined inflammatory exposures. We assessed i) if DNAm CRP estimates varied between preterm infants at term equivalent age and term infants, ii) how DNAm CRP related to different types of inflammatory exposure (maternal, fetal and postnatal) and iii) whether elevated DNAm CRP associated with poorer measures of neonatal brain volume and white matter connectivity. RESULTS Higher DNAm CRP was linked to preterm status (-0.0107 ± 0.0008, compared with -0.0118 ± 0.0006 among term infants; p < 0.001), as well as perinatal inflammatory diseases, including histologic chorioamnionitis, sepsis, bronchopulmonary dysplasia, and necrotising enterocolitis (OR range |2.00 | to |4.71|, p < 0.01). Preterm infants with higher DNAm CRP scores had lower brain volume in deep grey matter, white matter, and hippocampi and amygdalae (β range |0.185| to |0.218|). No such associations were observed for term infants. Association magnitudes were largest for measures of white matter microstructure among preterms, where elevated epigenetic inflammation associated with poorer global measures of white matter integrity (β range |0.206| to |0.371|), independent of other confounding exposures. CONCLUSIONS Inflammatory-related DNAm captures the allostatic load of inflammatory burden in preterm infants. Such DNAm measures complement biological and clinical metrics when investigating the determinants of neurodevelopmental differences.
Collapse
Affiliation(s)
- Eleanor L S Conole
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
| | - Kadi Vaher
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Manuel Blesa Cabez
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Gemma Sullivan
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jill Hall
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Michael J Thrippleton
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alan J Quigley
- Imaging Department, Royal Hospital for Children and Young People, Edinburgh, EH16 4TJ, UK
| | - Mark E Bastin
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Veronique E Miron
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Heather C Whalley
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - James P Boardman
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Simon R Cox
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK.
| |
Collapse
|
14
|
Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature 2023; 617:764-768. [PMID: 37198478 PMCID: PMC10208981 DOI: 10.1038/s41586-023-06034-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/27/2023] [Indexed: 05/19/2023]
Abstract
Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown1 to be highly efficient for discovery of genetic associations2. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group3. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).
Collapse
Affiliation(s)
- Erola Pairo-Castineira
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Pain Service, NHS Tayside, Ninewells Hospital and Medical School, Dundee, UK
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Marie Zechner
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Fiona Griffiths
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jonathan Millar
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ryan Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Charles Hinds
- William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Colin Begg
- Royal Hospital for Children, Glasgow, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Malak Abedalthagafi
- Genomic Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Andre D Luchessi
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Raquel Cruz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) Santiago de Compostela, Santiago de Compostela, Spain
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Clohisey Hendry
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
| |
Collapse
|
15
|
Cheng Y, Gadd DA, Gieger C, Monterrubio-Gómez K, Zhang Y, Berta I, Stam MJ, Szlachetka N, Lobzaev E, Wrobel N, Murphy L, Campbell A, Nangle C, Walker RM, Fawns-Ritchie C, Peters A, Rathmann W, Porteous DJ, Evans KL, McIntosh AM, Cannings TI, Waldenberger M, Ganna A, McCartney DL, Vallejos CA, Marioni RE. Development and validation of DNA methylation scores in two European cohorts augment 10-year risk prediction of type 2 diabetes. Nat Aging 2023; 3:450-458. [PMID: 37117793 DOI: 10.1038/s43587-023-00391-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/27/2023] [Indexed: 04/30/2023]
Abstract
Type 2 diabetes mellitus (T2D) presents a major health and economic burden that could be alleviated with improved early prediction and intervention. While standard risk factors have shown good predictive performance, we show that the use of blood-based DNA methylation information leads to a significant improvement in the prediction of 10-year T2D incidence risk. Previous studies have been largely constrained by linear assumptions, the use of cytosine-guanine pairs one-at-a-time and binary outcomes. We present a flexible approach (via an R package, MethylPipeR) based on a range of linear and tree-ensemble models that incorporate time-to-event data for prediction. Using the Generation Scotland cohort (training set ncases = 374, ncontrols = 9,461; test set ncases = 252, ncontrols = 4,526) our best-performing model (area under the receiver operating characteristic curve (AUC) = 0.872, area under the precision-recall curve (PRAUC) = 0.302) showed notable improvement in 10-year onset prediction beyond standard risk factors (AUC = 0.839, precision-recall AUC = 0.227). Replication was observed in the German-based KORA study (n = 1,451, ncases = 142, P = 1.6 × 10-5).
Collapse
Affiliation(s)
- Yipeng Cheng
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Karla Monterrubio-Gómez
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Yufei Zhang
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Imrich Berta
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Michael J Stam
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | | | - Evgenii Lobzaev
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Cliff Nangle
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | - Chloe Fawns-Ritchie
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
- German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, München, Germany
| | - Wolfgang Rathmann
- German Center for Diabetes Research, München-Neuherberg, Germany
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Institute for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Catalina A Vallejos
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- The Alan Turing Institute, London, UK.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
16
|
Bernabeu E, McCartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, McIntosh AM, Robinson MR, Vallejos CA, Marioni RE. Refining epigenetic prediction of chronological and biological age. Genome Med 2023; 15:12. [PMID: 36855161 PMCID: PMC9976489 DOI: 10.1186/s13073-023-01161-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Epigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture. METHODS First, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women's Health Initiative study). RESULTS Through the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10-52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10-60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations. CONCLUSIONS The integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age.
Collapse
Affiliation(s)
- Elena Bernabeu
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Altos Labs, San Diego, USA
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, UK
| | - David Liewald
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Cathie Sudlow
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- BHF Data Science Centre, Health Data Research UK, London, UK
- Edinburgh Medical School, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Altos Labs, San Diego, USA
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | | | - Catalina A Vallejos
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- The Alan Turing Institute, London, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
17
|
Gethin G, Vellinga A, McIntosh C, Sezgin D, Probst S, Murphy L, Carr P, Ivory J, Cunningham S, Oommen AM, Joshi L, Ffrench C. Systematic review of topical interventions for the management of odour in patients with chronic or malignant fungating wounds. J Tissue Viability 2023; 32:151-157. [PMID: 36376189 DOI: 10.1016/j.jtv.2022.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/06/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022]
Abstract
Chronic wounds adversely affect the quality of life of individuals and odour is a well-recognised associated factor. Odour can affect sleep, well-being, social interactions, diet and potentially wound healing. This systematic review aims to examine the effectiveness of topical interventions in the management of odour associated with chronic and malignant fungating wounds. A systematic review guided by PRISMA recommendations of randomised controlled trials where odour intensity/odour is the primary outcome was undertaken. Inclusion criteria were adults (18 years and over) with chronic venous, arterial, diabetic or pressure ulcers or with malignant fungating wounds where odour has been managed through topical application of pharmacological/non-pharmacological agents. Searches were conducted in CENTRAL, CINAHL, EMBASE, MEDLINE, Scopus, and Web of Science. Eligibility screening, risk of bias assessment and data extraction was completed by authors working independently. Searches retrieved 171 titles and abstracts (157 post de-duplication). Thirteen studies were retained for full text review of which five (n = 137 individuals) examining the following treatments remained: metronidazole (n = 4), silver (n = 1). Meta-analysis was not possible but individual studies suggest improved outcomes (i.e., reduced odour) using metronidazole. Treatment options to manage wound odour are limited and hampered by lack of clinical trials, small sample sizes, and absence of standardised outcomes and consistent measurement. Whereas metronidazole and silver may have a role in controlling wound odour, robust and well-designed interventions with rigorous procedures and standardised odour outcomes are necessary to evaluate their contribution.
Collapse
Affiliation(s)
- G Gethin
- School of Nursing and Midwifery, University of Galway, Galway, Ireland; Alliance for Research and Innovation in Wounds, University of Galway, Galway, Ireland; Geneva School of Health Science, HES-SO University of Applied Sciences and Arts, Western, Switzerland; Faculty of Medicine Nursing and Health Sciences, Monash University, Australia; CÚRAM, SFI Research Centre for Medical Devices, Ireland.
| | - A Vellinga
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Ireland.
| | - C McIntosh
- Alliance for Research and Innovation in Wounds, University of Galway, Galway, Ireland; Discipline of Podiatric Medicine, School of Health Science, University of Galway, Galway, Ireland.
| | - D Sezgin
- School of Nursing and Midwifery, University of Galway, Galway, Ireland; Alliance for Research and Innovation in Wounds, University of Galway, Galway, Ireland.
| | - S Probst
- Geneva School of Health Science, HES-SO University of Applied Sciences and Arts, Western, Switzerland; Faculty of Medicine Nursing and Health Sciences, Monash University, Australia; Care Directorate, University Hospital Geneva, Switzerland.
| | - L Murphy
- School of Nursing and Midwifery, University of Galway, Galway, Ireland
| | - P Carr
- School of Nursing and Midwifery, University of Galway, Galway, Ireland
| | - J Ivory
- School of Nursing and Midwifery, University of Galway, Galway, Ireland; Alliance for Research and Innovation in Wounds, University of Galway, Galway, Ireland; Irish Research Council (IRC), Government of Ireland, Dublin, Ireland; Centre for Diabetes, Endocrinology and Metabolism, Galway University Hospital, Galway, Ireland
| | - S Cunningham
- Advance Glycoscience Research Cluster, School of Natural Sciences, University of Galway, Galway, Ireland; CÚRAM, SFI Research Centre for Medical Devices, Ireland
| | - A M Oommen
- Advance Glycoscience Research Cluster, School of Natural Sciences, University of Galway, Galway, Ireland; CÚRAM, SFI Research Centre for Medical Devices, Ireland
| | - Lokesh Joshi
- Advance Glycoscience Research Cluster, School of Natural Sciences, University of Galway, Galway, Ireland; CÚRAM, SFI Research Centre for Medical Devices, Ireland
| | - C Ffrench
- School of Nursing and Midwifery, University of Galway, Galway, Ireland; CÚRAM, SFI Research Centre for Medical Devices, Ireland; Centre for Pain Research, University of Galway, Ireland.
| |
Collapse
|
18
|
Jones C, Sachdeva A, Murphy L, Murray M, Brown L, Brown J, Mc Closkey E, Attard G, Parmar M, James N, Sydes M, Clarke N. Clinical fracture incidence in metastatic hormone-sensitive prostate cancer and risk-reduction following addition of zoledronic acid to androgen deprivation therapy with or without docetaxel: Long-term results from the STAMPEDE trial. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)01237-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
|
19
|
Stevenson AJ, McCartney DL, Gadd DA, Shireby G, Hillary RF, King D, Tzioras M, Wrobel N, McCafferty S, Murphy L, McColl BW, Redmond P, Taylor AM, Harris SE, Russ TC, McIntosh AM, Mill J, Smith C, Deary IJ, Cox SR, Marioni RE, Spires‐Jones TL. A comparison of blood and brain-derived ageing and inflammation-related DNA methylation signatures and their association with microglial burdens. Eur J Neurosci 2022; 56:5637-5649. [PMID: 35362642 PMCID: PMC9525452 DOI: 10.1111/ejn.15661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/18/2022] [Accepted: 03/29/2022] [Indexed: 12/31/2022]
Abstract
Inflammation and ageing-related DNA methylation patterns in the blood have been linked to a variety of morbidities, including cognitive decline and neurodegenerative disease. However, it is unclear how these blood-based patterns relate to patterns within the brain and how each associates with central cellular profiles. In this study, we profiled DNA methylation in both the blood and in five post mortem brain regions (BA17, BA20/21, BA24, BA46 and hippocampus) in 14 individuals from the Lothian Birth Cohort 1936. Microglial burdens were additionally quantified in the same brain regions. DNA methylation signatures of five epigenetic ageing biomarkers ('epigenetic clocks'), and two inflammatory biomarkers (methylation proxies for C-reactive protein and interleukin-6) were compared across tissues and regions. Divergent associations between the inflammation and ageing signatures in the blood and brain were identified, depending on region assessed. Four out of the five assessed epigenetic age acceleration measures were found to be highest in the hippocampus (β range = 0.83-1.14, p ≤ 0.02). The inflammation-related DNA methylation signatures showed no clear variation across brain regions. Reactive microglial burdens were found to be highest in the hippocampus (β = 1.32, p = 5 × 10-4 ); however, the only association identified between the blood- and brain-based methylation signatures and microglia was a significant positive association with acceleration of one epigenetic clock (termed DNAm PhenoAge) averaged over all five brain regions (β = 0.40, p = 0.002). This work highlights a potential vulnerability of the hippocampus to epigenetic ageing and provides preliminary evidence of a relationship between DNA methylation signatures in the brain and differences in microglial burdens.
Collapse
Affiliation(s)
- Anna J. Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Gemma Shireby
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Declan King
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
| | - Makis Tzioras
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
| | - Nicola Wrobel
- Edinburgh Clinical Research FacilityWestern General HospitalEdinburghUK
| | - Sarah McCafferty
- Edinburgh Clinical Research FacilityWestern General HospitalEdinburghUK
| | - Lee Murphy
- Edinburgh Clinical Research FacilityWestern General HospitalEdinburghUK
| | - Barry W. McColl
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
| | - Paul Redmond
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
| | | | - Sarah E. Harris
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Tom C. Russ
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Alzheimer Scotland Dementia Research Centre, 7 George SquareUniversity of EdinburghEdinburghUK
- Division of PsychiatryUniversity of Edinburgh, Royal Edinburgh HospitalEdinburghUK
| | - Andrew M. McIntosh
- Division of PsychiatryUniversity of Edinburgh, Royal Edinburgh HospitalEdinburghUK
| | - Jonathan Mill
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Colin Smith
- Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - Ian J. Deary
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Simon R. Cox
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
| | - Tara L. Spires‐Jones
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
| |
Collapse
|
20
|
Cunningham-Burley S, McCartney DL, Campbell A, Flaig R, Orange CEL, Porteous C, Aitken M, Mulholland C, Davidson S, McCafferty SM, Murphy L, Wrobel N, McCafferty S, Wallace K, StClair D, Kerr S, Hayward C, McIntosh AM, Sudlow C, Marioni RE, Pell J, Miedzybrodzka Z, Porteous DJ. Feasibility and ethics of using data from the Scottish newborn blood spot archive for research. Commun Med (Lond) 2022; 2:126. [PMID: 36210800 PMCID: PMC9537278 DOI: 10.1038/s43856-022-00189-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 09/21/2022] [Indexed: 11/05/2022] Open
Abstract
Background Newborn heel prick blood spots are routinely used to screen for inborn errors of metabolism and life-limiting inherited disorders. The potential value of secondary data from newborn blood spot archives merits ethical consideration and assessment of feasibility for public benefit. Early life exposures and behaviours set health trajectories in childhood and later life. The newborn blood spot is potentially well placed to create an unbiased and cost-effective population-level retrospective birth cohort study. Scotland has retained newborn blood spots for all children born since 1965, around 3 million in total. However, a moratorium on research access is currently in place, pending public consultation. Methods We conducted a Citizens' Jury as a first step to explore whether research use of newborn blood spots was in the public interest. We also assessed the feasibility and value of extracting research data from dried blood spots for predictive medicine. Results Jurors delivered an agreed verdict that conditional research access to the newborn blood spots was in the public interest. The Chief Medical Officer for Scotland authorised restricted lifting of the current research moratorium to allow a feasibility study. Newborn blood spots from consented Generation Scotland volunteers were retrieved and their potential for both epidemiological and biological research demonstrated. Conclusions Through the Citizens' Jury, we have begun to identify under what conditions, if any, should researchers in Scotland be granted access to the archive. Through the feasibility study, we have demonstrated the potential value of research access for health data science and predictive medicine.
Collapse
Affiliation(s)
- Sarah Cunningham-Burley
- grid.4305.20000 0004 1936 7988Centre for Biomedicine, Self and Society, Usher Institute, University of Edinburgh, 23 Buccleuch Place, Edinburgh, EH8 9LN UK
| | - Daniel L. McCartney
- grid.417068.c0000 0004 0624 9907Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU UK
| | - Archie Campbell
- grid.417068.c0000 0004 0624 9907Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU UK
| | - Robin Flaig
- grid.4305.20000 0004 1936 7988Centre for Medical Informatics, Usher Institute, University of Edinburgh, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4UX UK
| | - Clare E. L. Orange
- grid.511123.50000 0004 5988 7216NHS GGC Biorepository, Level 3, Laboratory Medicine Building, Queen Elizabeth University Hospital, 1345 Govan Road, Glasgow, G51 4TY UK
| | - Carol Porteous
- grid.4305.20000 0004 1936 7988Centre for Biomedicine, Self and Society, Usher Institute, University of Edinburgh, 23 Buccleuch Place, Edinburgh, EH8 9LN UK ,grid.417068.c0000 0004 0624 9907Present Address: Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU UK
| | - Mhairi Aitken
- grid.4305.20000 0004 1936 7988Centre for Biomedicine, Self and Society, Usher Institute, University of Edinburgh, 23 Buccleuch Place, Edinburgh, EH8 9LN UK ,grid.499548.d0000 0004 5903 3632Present Address: The Alan Turing Institute, British Library, 96 Euston Road, London, NW1 2DB UK
| | - Ciaran Mulholland
- grid.417068.c0000 0004 0624 9907Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU UK
| | - Sara Davidson
- grid.417068.c0000 0004 0624 9907Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU UK
| | - Selena M. McCafferty
- grid.511123.50000 0004 5988 7216NHS GGC Biorepository, Level 3, Laboratory Medicine Building, Queen Elizabeth University Hospital, 1345 Govan Road, Glasgow, G51 4TY UK
| | - Lee Murphy
- Ipsos MORI Scotland, Links House, 15 Links Pl, Edinburgh, EH6 7EZ UK
| | - Nicola Wrobel
- Ipsos MORI Scotland, Links House, 15 Links Pl, Edinburgh, EH6 7EZ UK
| | - Sarah McCafferty
- Ipsos MORI Scotland, Links House, 15 Links Pl, Edinburgh, EH6 7EZ UK
| | - Karen Wallace
- Medical Genetics, Room 2:041, School of Medicine, Medical Sciences and Nutrition, Polwarth Building, Foresterhill, Aberdeen, AB25 2ZD UK
| | - David StClair
- School of Medicine, Medical Sciences and Nutrition, Foresterhill Health Campus, Foresterhill Rd, Aberdeen, AB25 2ZN UK
| | - Shona Kerr
- grid.417068.c0000 0004 0624 9907MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU UK
| | - Caroline Hayward
- grid.417068.c0000 0004 0624 9907MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU UK
| | - Andrew M. McIntosh
- grid.4305.20000 0004 1936 7988Centre for Clinical Brain Sciences, Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF UK
| | - Cathie Sudlow
- grid.4305.20000 0004 1936 7988Centre for Medical Informatics, Usher Institute, University of Edinburgh, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4UX UK
| | - Riccardo E. Marioni
- grid.417068.c0000 0004 0624 9907Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU UK
| | - Jill Pell
- grid.8756.c0000 0001 2193 314XInstitute of Health and Wellbeing, University of Glasgow, Glasgow, G12 8RZ UK
| | - Zosia Miedzybrodzka
- Medical Genetics, Room 2:041, School of Medicine, Medical Sciences and Nutrition, Polwarth Building, Foresterhill, Aberdeen, AB25 2ZD UK
| | - David J. Porteous
- grid.417068.c0000 0004 0624 9907Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU UK
| |
Collapse
|
21
|
Murphy L, Alfano L, Brazzo K, Johnson N, Laurent J, Mathews K, Thiele S, Vissing J, Walter M, Woods L, Ørstavik K, Straub V. P.175 Global FKRP registry - the research database for limb girdle muscular dystrophy R9 (2I). Neuromuscul Disord 2022. [DOI: 10.1016/j.nmd.2022.07.313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
22
|
Simon SS, Fitzsimmons S, Murphy L, Muni-Lofra R, Blewit C, Group ASMARS, Bettolo CM. P.41 Adult SMA REACH: development and implementation data collection study in the UK Adult SMA population. Neuromuscul Disord 2022. [DOI: 10.1016/j.nmd.2022.07.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
23
|
Murphy L, Nightingale J, Calder P. Difficulties associated with Reporting Radiographer working practices - A narrative evidence synthesis. Radiography (Lond) 2022; 28:1101-1109. [PMID: 36075163 DOI: 10.1016/j.radi.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/28/2022] [Accepted: 08/17/2022] [Indexed: 12/01/2022]
Abstract
OBJECTIVES This narrative synthesis of evidence identifies and explores issues that impact upon the expansion or effectiveness of Reporting Radiographers working in all diagnostic modalities within the United Kingdom (UK). The publication focuses on working practices affecting trainees and qualified Reporting Radiographers. KEY FINDINGS Fourteen studies informed the themes of this article, they were published between 2014 and 2021. Delays to commencement of reporting roles and variance in performance monitoring was common. Lack of formalisation, overly restrictive and out of date scopes of practice were also found. Whilst, staffing shortages contributed to underutilisation. Failure to utilise skills was most prevalent in cross sectional imaging modalities. Considerable variance in practice was also found between centres. Meanwhile, Reporting Radiographer involvement in professional development, education and research is far from universal and often dependant on individuals sacrificing their own time. CONCLUSION Governance in many centres would benefit from renewal and standardisation, particularly relating to scopes of practice and performance monitoring audits. Measures are also required to encourage compliance with guidance, address staffing issues and reduce variation between centres. Failure to address these issues has the potential to impair collaboration, delay patient care and increase economic inefficiencies whilst negatively impacting satisfaction for service users and staff. Lack of involvement in professional development, education and research suggests Reporting Radiographers are not accomplishing their full potential, educating the next generation of the reporting workforce and driving evidence-based change for further development of the specialism. IMPLICATIONS FOR PRACTICE Better use of the existing workforce is essential to increase productivity, value, and security of Reporting Radiographer services, which are essential to improve patient outcomes and efficiency.
Collapse
Affiliation(s)
- L Murphy
- Radiology Department, Newcastle Upon Tyne NHS Foundation Trust, UK.
| | - J Nightingale
- Dept of Allied Health Professions, Sheffield Hallam University, UK
| | - P Calder
- Radiology Department, Newcastle Upon Tyne NHS Foundation Trust, UK
| |
Collapse
|
24
|
Attard G, Murphy L, Clarke N, Cross W, Gillessen S, Amos C, Brawley C, Jones R, Pezaro C, Malik Z, Montazeri A, Millman R, Cook A, Gilbert D, Langley R, Parker C, Sydes M, Brown L, Parmar M, James N. LBA62 Comparison of abiraterone acetate and prednisolone (AAP) or combination enzalutamide (ENZ) + AAP for metastatic hormone sensitive prostate cancer (mHSPC) starting androgen deprivation therapy (ADT): Overall survival (OS) results of 2 randomised phase III trials from the STAMPEDE protocol. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.08.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
25
|
Corvaro M, Johnson K, Himmelstein M, Bianchi E, Mingoia R, Bartels M, Reiss R, Terry C, LaRocca J, Murphy L, Gehen S. P06-13 Spinosad – mode of action and human relevance assessment of dystocia in rats. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
26
|
Murphy L, Nightingale J, Calder P. Difficulties associated with access to training and clinical support for Reporting Radiographers - A narrative evidence synthesis. Radiography (Lond) 2022; 28:1071-1079. [PMID: 35998381 DOI: 10.1016/j.radi.2022.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVES This narrative synthesis of evidence identifies and explores issues that impact upon the expansion or effectiveness of Reporting Radiographers working in all diagnostic modalities within the United Kingdom (UK). The publication focuses on accessibility to training for prospective Reporting Radiographers as well as clinical support within and beyond training. KEY FINDINGS Fifteen studies informed the themes of this article, they were published between 2014 and 2021. Reporting Radiographers often found it difficult find support during training and once qualified, this was usually due to the availability and workload of supervising staff. Although resistance and obstruction were experienced by many. Concerns relating to pay, promotion and interest were expressed by some respondents whilst access to courses and finance were highlighted as areas of variance across the UK. CONCLUSION Inadequate support of Reporting Radiographers is impairing expansion of the specialism, whilst impacting capability and morale. This increases risk of patient harm, delays to care and inefficiency, it also threatens the sustainability of services. Negative interactions between Reporting Radiographers and Radiologists or managers is disappointing considering development of the specialism; evidence of Reporting Radiographer effectiveness and current collaboration between Royal College of Radiologists and Society of Radiographers. Issues raised in relation to pay/promotion and litigation could be clarified with ease, this should be considered when guidance is updated. Access to finance and courses is a major barrier in some regions of the UK. Scope exists for further exploration of training. England has used grants to facilitate uptake, these may prove to be an important tool in other countries. IMPLICATIONS FOR PRACTICE Drivers to increase recruitment should be implemented alongside measures to facilitate accessibility to training and improvements to support infrastructure.
Collapse
Affiliation(s)
- L Murphy
- Radiology Department, Newcastle Upon Tyne NHS Foundation Trust, UK.
| | - J Nightingale
- Dept of Allied Health Professions, Sheffield Hallam University, UK
| | - P Calder
- Radiology Department, Newcastle Upon Tyne NHS Foundation Trust, UK
| |
Collapse
|
27
|
Robertson NA, Latorre-Crespo E, Terradas-Terradas M, Lemos-Portela J, Purcell AC, Livesey BJ, Hillary RF, Murphy L, Fawkes A, MacGillivray L, Copland M, Marioni RE, Marsh JA, Harris SE, Cox SR, Deary IJ, Schumacher LJ, Kirschner K, Chandra T. Longitudinal dynamics of clonal hematopoiesis identifies gene-specific fitness effects. Nat Med 2022; 28:1439-1446. [PMID: 35788175 PMCID: PMC9307482 DOI: 10.1038/s41591-022-01883-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/27/2022] [Indexed: 12/20/2022]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) increases rapidly in prevalence beyond age 60 and has been associated with increased risk for malignancy, heart disease and ischemic stroke. CHIP is driven by somatic mutations in hematopoietic stem and progenitor cells (HSPCs). Because mutations in HSPCs often drive leukemia, we hypothesized that HSPC fitness substantially contributes to transformation from CHIP to leukemia. HSPC fitness is defined as the proliferative advantage over cells carrying no or only neutral mutations. If mutations in different genes lead to distinct fitness advantages, this could enable patient stratification. We quantified the fitness effects of mutations over 12 years in older age using longitudinal sequencing and developed a filtering method that considers individual mutational context alongside mutation co-occurrence to quantify the growth potential of variants within individuals. We found that gene-specific fitness differences can outweigh inter-individual variation and, therefore, could form the basis for personalized clinical management.
Collapse
Affiliation(s)
| | | | - Maria Terradas-Terradas
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Jorge Lemos-Portela
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Alison C Purcell
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Louise MacGillivray
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Mhairi Copland
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Linus J Schumacher
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
| | - Kristina Kirschner
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
- Cancer Research UK Beatson Institute, Glasgow, UK.
| | - Tamir Chandra
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
28
|
Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK. Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature 2022; 607:97-103. [PMID: 35255492 PMCID: PMC9259496 DOI: 10.1038/s41586-022-04576-6] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2-4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.
Collapse
Affiliation(s)
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Xia Shen
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | | | | | | | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine and Institute in the Park, Alder Hey Children's Hospital and University of Liverpool, Liverpool, UK
| | | | | | | | | | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tom A Fowler
- Genomics England, London, UK
- Test and Trace, the Health Security Agency, Department of Health and Social Care, London, UK
| | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust: London, London, UK
| | | | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit and Research Centre, London, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Richard H Scott
- Genomics England, London, UK
- Great Ormond Street Hospital, London, UK
| | | | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Mark J Caulfield
- Genomics England, London, UK.
- William Harvey Research Institute, Queen Mary University of London, London, UK.
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
| |
Collapse
|
29
|
Kearns PKA, Martin SJ, Chang J, Meijboom R, York EN, Chen Y, Weaver C, Stenson A, Hafezi K, Thomson S, Freyer E, Murphy L, Harroud A, Foley P, Hunt D, McLeod M, O'Riordan J, Carod-Artal FJ, MacDougall NJJ, Baranzini SE, Waldman AD, Connick P, Chandran S. FutureMS cohort profile: a Scottish multicentre inception cohort study of relapsing-remitting multiple sclerosis. BMJ Open 2022; 12:e058506. [PMID: 35768080 PMCID: PMC9244691 DOI: 10.1136/bmjopen-2021-058506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
PURPOSE Multiple sclerosis (MS) is an immune-mediated, neuroinflammatory disease of the central nervous system and in industrialised countries is the most common cause of progressive neurological disability in working age persons. While treatable, there is substantial interindividual heterogeneity in disease activity and response to treatment. Currently, the ability to predict at diagnosis who will have a benign, intermediate or aggressive disease course is very limited. There is, therefore, a need for integrated predictive tools to inform individualised treatment decision making. PARTICIPANTS Established with the aim of addressing this need for individualised predictive tools, FutureMS is a nationally representative, prospective observational cohort study of 440 adults with a new diagnosis of relapsing-remitting MS living in Scotland at the time of diagnosis between May 2016 and March 2019. FINDINGS TO DATE The study aims to explore the pathobiology and determinants of disease heterogeneity in MS and combines detailed clinical phenotyping with imaging, genetic and biomarker metrics of disease activity and progression. Recruitment, baseline assessment and follow-up at year 1 is complete. Here, we describe the cohort design and present a profile of the participants at baseline and 1 year of follow-up. FUTURE PLANS A third follow-up wave for the cohort has recently begun at 5 years after first visit and a further wave of follow-up is funded for year 10. Longer-term follow-up is anticipated thereafter.
Collapse
Affiliation(s)
- Patrick K A Kearns
- Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh Centre for Clinical Brain Sciences, Edinburgh, UK
- Chromatin Lab, Genome Regulation Section, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
- Department of Clinical Neurosciences, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
- Department of Neurology, Institute of Clinical Neurosciences, NHS Greater Glasgow and Clyde, Glasgow, UK
- Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Sarah J Martin
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
- Department of Neurology, Institute of Clinical Neurosciences, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Jessie Chang
- Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh Centre for Clinical Brain Sciences, Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rozanna Meijboom
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Elizabeth N York
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Yingdi Chen
- Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh Centre for Clinical Brain Sciences, Edinburgh, UK
| | - Christine Weaver
- Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh Centre for Clinical Brain Sciences, Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Amy Stenson
- Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh Centre for Clinical Brain Sciences, Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | | | - Stacey Thomson
- Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Elizabeth Freyer
- Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Wellcome Trust Clinical Research Facility, Edinburgh, UK
| | - Adil Harroud
- Department of Neurology, Weill Institute of Clinical Neuroscience, San Francisco, California, USA
| | - Peter Foley
- Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh Centre for Clinical Brain Sciences, Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - David Hunt
- Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh Centre for Clinical Brain Sciences, Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Margaret McLeod
- Department of Neurology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Jonathon O'Riordan
- Tayside Centre for Clinical Neurosciences, University of Dundee Division of Neuroscience, Dundee, UK
| | | | - Niall J J MacDougall
- Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh Centre for Clinical Brain Sciences, Edinburgh, UK
- Department of Neurology, Wishaw General Hospital, Wishaw, UK
| | - Sergio E Baranzini
- Department of Neurology, Weill Institute of Clinical Neuroscience, San Francisco, California, USA
| | - Adam D Waldman
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Peter Connick
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh Centre for Clinical Brain Sciences, Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| |
Collapse
|
30
|
Wheater ENW, Galdi P, McCartney DL, Blesa M, Sullivan G, Stoye DQ, Lamb G, Sparrow S, Murphy L, Wrobel N, Quigley AJ, Semple S, Thrippleton MJ, Wardlaw JM, Bastin ME, Marioni RE, Cox SR, Boardman JP. DNA methylation in relation to gestational age and brain dysmaturation in preterm infants. Brain Commun 2022; 4:fcac056. [PMID: 35402911 PMCID: PMC8984700 DOI: 10.1093/braincomms/fcac056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/10/2021] [Accepted: 03/04/2022] [Indexed: 11/14/2022] Open
Abstract
Preterm birth is associated with dysconnectivity of structural brain networks and is a leading cause of neurocognitive impairment in childhood. Variation in DNA methylation is associated with early exposure to extrauterine life but there has been little research exploring its relationship with brain development. Using genome-wide DNA methylation data from the saliva of 258 neonates, we investigated the impact of gestational age on the methylome and performed functional analysis to identify enriched gene sets from probes that contributed to differentially methylated probes or regions. We tested the hypothesis that variation in DNA methylation could underpin the association between low gestational age at birth and atypical brain development by linking differentially methylated probes with measures of white matter connectivity derived from diffusion MRI metrics: peak width skeletonized mean diffusivity, peak width skeletonized fractional anisotropy and peak width skeletonized neurite density index. Gestational age at birth was associated with widespread differential methylation at term equivalent age, with genome-wide significant associations observed for 8870 CpG probes (P < 3.6 × 10-8) and 1767 differentially methylated regions. Functional analysis identified 14 enriched gene ontology terms pertaining to cell-cell contacts and cell-extracellular matrix contacts. Principal component analysis of probes with genome-wide significance revealed a first principal component that explained 23.5% of the variance in DNA methylation, and this was negatively associated with gestational age at birth. The first principal component was associated with peak width of skeletonized mean diffusivity (β = 0.349, P = 8.37 × 10-10) and peak width skeletonized neurite density index (β = 0.364, P = 4.15 × 10-5), but not with peak width skeletonized fraction anisotropy (β = -0.035, P = 0.510); these relationships mirrored the imaging metrics' associations with gestational age at birth. Low gestational age at birth has a profound and widely distributed effect on the neonatal saliva methylome that is apparent at term equivalent age. Enriched gene ontology terms related to cell-cell contacts reveal pathways that could mediate the effect of early life environmental exposures on development. Finally, associations between differential DNA methylation and image markers of white matter tract microstructure suggest that variation in DNA methylation may provide a link between preterm birth and the dysconnectivity of developing brain networks that characterizes atypical brain development in preterm infants.
Collapse
Affiliation(s)
- Emily N. W. Wheater
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Paola Galdi
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Manuel Blesa
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Gemma Sullivan
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - David Q. Stoye
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Gillian Lamb
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Sarah Sparrow
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Nicola Wrobel
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alan J. Quigley
- Department of Paediatric Radiology, Royal Hospital for Sick Children, NHS Lothian, Edinburgh, UK
| | - Scott Semple
- Edinburgh Imaging, University of Edinburgh, EH16 4SB Edinburgh, UK
- Centre for Cardiovascular Science, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Michael J. Thrippleton
- Edinburgh Imaging, University of Edinburgh, EH16 4SB Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Joanna M. Wardlaw
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Mark E. Bastin
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Simon R. Cox
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - James P. Boardman
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| |
Collapse
|
31
|
Habota T, Sandu AL, Waiter GD, McNeil CJ, Steele JD, Macfarlane JA, Whalley HC, Valentine R, Younie D, Crouch N, Hawkins EL, Hirose Y, Romaniuk L, Milburn K, Buchan G, Coupar T, Stirling M, Jagpal B, MacLennan B, Priba L, Harris MA, Hafferty JD, Adams MJ, Campbell AI, MacIntyre DJ, Pattie A, Murphy L, Reynolds RM, Elliot R, Penton-Voak IS, Munafò MR, Evans KL, Seckl JR, Wardlaw JM, Lawrie SM, Haley CS, Porteous DJ, Deary IJ, Murray AD, McIntosh AM. Cohort profile for the STratifying Resilience and Depression Longitudinally (STRADL) study: A depression-focused investigation of Generation Scotland, using detailed clinical, cognitive, and neuroimaging assessments. Wellcome Open Res 2022; 4:185. [PMID: 35237729 PMCID: PMC8857525 DOI: 10.12688/wellcomeopenres.15538.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 11/20/2022] Open
Abstract
STratifying Resilience and Depression Longitudinally (STRADL) is a population-based study built on the Generation Scotland: Scottish Family Health Study (GS:SFHS) resource. The aim of STRADL is to subtype major depressive disorder (MDD) on the basis of its aetiology, using detailed clinical, cognitive, and brain imaging assessments. The GS:SFHS provides an important opportunity to study complex gene-environment interactions, incorporating linkage to existing datasets and inclusion of early-life variables for two longitudinal birth cohorts. Specifically, data collection in STRADL included: socio-economic and lifestyle variables; physical measures; questionnaire data that assesses resilience, early-life adversity, personality, psychological health, and lifetime history of mood disorder; laboratory samples; cognitive tests; and brain magnetic resonance imaging. Some of the questionnaire and cognitive data were first assessed at the GS:SFHS baseline assessment between 2006-2011, thus providing longitudinal measures relevant to the study of depression, psychological resilience, and cognition. In addition, routinely collected historic NHS data and early-life variables are linked to STRADL data, further providing opportunities for longitudinal analysis. Recruitment has been completed and we consented and tested 1,188 participants.
Collapse
|
32
|
Bengesser SA, Hohenberger H, Tropper B, Dalkner N, Birner A, Fellendorf FT, Platzer M, Rieger A, Maget A, Hamm C, Queissner R, Pilz R, Bauer K, Lenger M, Mörkl S, Wagner-Skacel J, Kapfhammer HP, Meier-Allard N, Stracke A, Holasek SJ, Murphy L, Reininghaus EZ. Gene expression analysis of MAOA and the clock gene ARNTL in individuals with bipolar disorder compared to healthy controls. World J Biol Psychiatry 2022; 23:287-294. [PMID: 34468263 DOI: 10.1080/15622975.2021.1973816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/30/2021] [Accepted: 08/24/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Circadian rhythms are associated with bipolar disorder (BD). This cross-sectional study aimed at investigating ARNTL and MAOA gene expression differences (1) between individuals with BD and controls, (2) between affective episodes, and (3) the relationship between ARNTL and MAOA expression. METHODS ARNTL and MAOA gene expression in peripheral mononuclear blood cells were analysed from fasting blood samples (BD n = 81, controls n = 54) with quantitative real-time PCR operating on TaqMan® assays (normalised to 18S RNA expression). ANCOVAs corrected for age, sex, body mass index, and medication was used to evaluate expression differences and correlation analyses for the relation between ARNTL and MAOA expression. RESULTS ARNTL gene expression differed between affective episodes (F(2,78) = 3.198, p = 0.047, Partial Eta2= 0.083), but not between BD and controls (n.s.). ARNTL and MAOA expression correlated positively in BD (r = 0.704, p < 0.001) and in controls (r = 0.932, p < 0.001). MAOA expression differed neither between BD and controls nor between affective episodes (n.s.). DISCUSSION Clock gene expression changes were observed in different affective states of BD. More precisely, ARNTL gene expression was significantly higher in euthymia than in depression. ARNTL and MAOA gene expression correlated significantly in BD and in controls, which emphasises the strong concatenation between circadian rhythms and neurotransmitter breakdown.
Collapse
Affiliation(s)
- S A Bengesser
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - H Hohenberger
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - B Tropper
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - N Dalkner
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - A Birner
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - F T Fellendorf
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - M Platzer
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - A Rieger
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - A Maget
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - C Hamm
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - R Queissner
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - R Pilz
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - K Bauer
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - M Lenger
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - S Mörkl
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - J Wagner-Skacel
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - H P Kapfhammer
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - N Meier-Allard
- Otto Loewi Research Center, Chair of Pathophysiology and Immunology, Medical University of Graz, Graz, Austria
| | - A Stracke
- Otto Loewi Research Center, Chair of Pathophysiology and Immunology, Medical University of Graz, Graz, Austria
| | - S J Holasek
- Otto Loewi Research Center, Chair of Pathophysiology and Immunology, Medical University of Graz, Graz, Austria
| | - L Murphy
- CAMH Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
| | - E Z Reininghaus
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| |
Collapse
|
33
|
Swan L, Horgan F, Cummins V, Doyle F, Galvin R, Burton E, Sorensen J, Jabakhanji SB, Skelton D, Townley B, Rooney D, Jackson G, Murphy L, Warters A, O'Sullivan M. 199 EMBEDDING PHYSICAL ACTIVITY WITHIN HOME CARE SERVICES FOR OLDER ADULTS IN IRELAND—A QUALITATIVE STUDY OF BARRIERS AND FACILITATORS. Age Ageing 2021. [DOI: 10.1093/ageing/afab216.199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Abstract
Background
In Ireland, over 53,000 older adults are supported in their community by formal home support, amounting to an estimated 19 million care hours annually. There is a growing need to move beyond care, to more proactive approaches to maintain physical function. In a feasibility study, we delivered the ‘Care to Move’ (CTM) programme through existing home support services. The aim of the present qualitative study was to explore the experience and perceptions of Health Care Assistants (HCAs), who were trained in, and delivered the CTM programme.
Methods
We conducted semi-structured telephone interviews with 22 HCAs involved in the delivery of the programme among older adults [n = 35, mean age 82.8 (7.8) years]. Interview transcripts were coded and analysed thematically to capture barriers and facilitators to programme delivery.
Results
Barriers and facilitators were identified under three main themes i) the programme ii) the care setting, iii) the clients. Overall, there was a positive perception of the programme’s focus on ‘movement prompts and motivators’, the ‘fit’ within home support services, and the training provided. Practical challenges of limited time and the task-orientation nature of home support were reported as recurring barriers for CTM. Many HCAs commented on the value and perceived positive benefits of the programme for their clients. Though negative perceptions of older adult’s motivation or ability to engage with physical activity also emerged. Risk, such as injury or pain, was identified but was not a dominant theme.
Conclusion
Our preliminary findings suggest that embedding physical activity initiatives within home support services could be feasible. Restructuring of services, engaging HCAs, and moving beyond traditional ‘task-oriented' care models to more personalised proactive approaches may facilitate this initiative and support ageing in place.
Collapse
Affiliation(s)
- L Swan
- Trinity College Dublin , Dublin, Ireland
| | - F Horgan
- Royal College of Surgeons in Ireland , Dublin, Ireland
| | - V Cummins
- Health Service Executive , Dublin, Ireland
| | - F Doyle
- Royal College of Surgeons in Ireland , Dublin, Ireland
| | - R Galvin
- University of Limerick , Limerick, Ireland
| | - E Burton
- Curtin University , Curtin, Australia
| | - J Sorensen
- Royal College of Surgeons in Ireland , Dublin, Ireland
| | | | - D Skelton
- Glasgow Caledonian University , Glasglow, United Kingdom
- Later Life Training, Northumberland , United Kingdom
| | - B Townley
- Later Life Training, Northumberland , United Kingdom
| | - D Rooney
- North Dublin Home Care , Dublin, Ireland
| | - G Jackson
- North Dublin Home Care , Dublin, Ireland
| | - L Murphy
- North Dublin Home Care , Dublin, Ireland
| | - A Warters
- Health Service Executive , Dublin, Ireland
| | | |
Collapse
|
34
|
Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, Wilson SJ. A prenylated dsRNA sensor protects against severe COVID-19. Science 2021; 374:eabj3624. [PMID: 34581622 PMCID: PMC7612834 DOI: 10.1126/science.abj3624] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022]
Abstract
Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that 2′-5′-oligoadenylate synthetase 1 (OAS1), through ribonuclease L, potently inhibits severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We show that a common splice-acceptor single-nucleotide polymorphism (Rs10774671) governs whether patients express prenylated OAS1 isoforms that are membrane-associated and sense-specific regions of SARS-CoV-2 RNAs or if they only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. In hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting that this antiviral defense is a major component of a protective antiviral response.
Collapse
Affiliation(s)
- Arthur Wickenhagen
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Elena Sugrue
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Spyros Lytras
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Srikeerthana Kuchi
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Marko Noerenberg
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Matthew L. Turnbull
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Colin Loney
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Vanessa Herder
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jay Allan
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Innes Jarmson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Natalia Cameron-Ruiz
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Margus Varjak
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Rute M. Pinto
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jeffrey Y. Lee
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Louisa Iselin
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natasha Palmalux
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Douglas G. Stewart
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Simon Swingler
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Edward J. D. Greenwood
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Thomas W. M. Crozier
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Quan Gu
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Emma L. Davies
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
| | - Monique Freire Santana
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
| | - Luiz Carlos de Lima Ferreira
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Alison Meynert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Graeme Grimes
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - ISARIC4C Investigators
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Joao Luiz Da Silva Filho
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Matthias Marti
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Eddie C. Y. Wang
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
| | - Antonia Ho
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ruth F. Jarrett
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Alfredo Castello
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - David L. Robertson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
| | - Massimo Palmarini
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Paul J. Lehner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Suzannah J. Rihn
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sam J. Wilson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| |
Collapse
|
35
|
Muni-Lofra R, Murphy L, Adcock K, Farrugia M, Irwin J, Lilleker J, McConville J, Merrison A, Parton M, Ryburn L, Scoto M, Marini-Bettolo C, Mayhew A. SMA – OUTCOME MEASURES AND REGISTRIES. Neuromuscul Disord 2021. [DOI: 10.1016/j.nmd.2021.07.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
36
|
Annoussamy M, Eggenspieler D, Camino E, Porter B, Bullivant J, Imber L, Murphy L, Hughes Z, Hughes W, Servais L. OUTCOME MEASURES. Neuromuscul Disord 2021. [DOI: 10.1016/j.nmd.2021.07.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
37
|
Bullivant J, Porter B, Murphy L, Render L, Bellgard M, Lennox A, Spring M, Hollander A, Bönnemann C, Jungbluth H, Buj-Bello A, Dowling J, Marini-Bettolo C. CONGENITAL MYOPATHIES – CENTRONUCLEAR MYOPATHIES. Neuromuscul Disord 2021. [DOI: 10.1016/j.nmd.2021.07.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
38
|
James E, Joffe J, Huddart R, Rustin G, Sohaib S, Murphy L, Noor D, Wade S, Schiavone F, Kaplan R, Cafferty F. 714P Prognostic factors in stage I seminoma: Data from the phase III, randomised TRial of Imaging and Surveillance in Seminoma Testis (TRISST). Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
39
|
Attard G, Brown L, Clarke N, Murphy L, Cross W, Jones R, Gillessen S, Russell J, Cook A, Bowen J, Lydon A, Pedley I, Parikh O, Chowdhury S, Malik Z, Matheson D, Parker C, Sydes M, Parmar M, James N. LBA4 Abiraterone acetate plus prednisolone (AAP) with or without enzalutamide (ENZ) added to androgen deprivation therapy (ADT) compared to ADT alone for men with high-risk non-metastatic (M0) prostate cancer (PCa): Combined analysis from two comparisons in the STAMPEDE platform protocol. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.2098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
40
|
Kirschner K, Robertson N, Latorre-Crespo E, Purcell A, Terradas-Terradas M, Fawkes A, MacGillivray L, Murphy L, Marsh J, Copland M, Marioni R, Harris S, Deary I, Simon C, Schumacher L, Chandra T. 3080 – CLONAL HAEMOPOIESIS IN LONGITUDINAL COHORTS OF AGEING. Exp Hematol 2021. [DOI: 10.1016/j.exphem.2021.12.298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
41
|
Habota T, Sandu AL, Waiter GD, McNeil CJ, Steele JD, Macfarlane JA, Whalley HC, Valentine R, Younie D, Crouch N, Hawkins EL, Hirose Y, Romaniuk L, Milburn K, Buchan G, Coupar T, Stirling M, Jagpal B, MacLennan B, Priba L, Harris MA, Hafferty JD, Adams MJ, Campbell AI, MacIntyre DJ, Pattie A, Murphy L, Reynolds RM, Elliot R, Penton-Voak IS, Munafò MR, Evans KL, Seckl JR, Wardlaw JM, Lawrie SM, Haley CS, Porteous DJ, Deary IJ, Murray AD, McIntosh AM. Cohort profile for the STratifying Resilience and Depression Longitudinally (STRADL) study: A depression-focused investigation of Generation Scotland, using detailed clinical, cognitive, and neuroimaging assessments. Wellcome Open Res 2021; 4:185. [PMID: 35237729 PMCID: PMC8857525 DOI: 10.12688/wellcomeopenres.15538.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 08/18/2023] Open
Abstract
STratifying Resilience and Depression Longitudinally (STRADL) is a population-based study built on the Generation Scotland: Scottish Family Health Study (GS:SFHS) resource. The aim of STRADL is to subtype major depressive disorder (MDD) on the basis of its aetiology, using detailed clinical, cognitive, and brain imaging assessments. The GS:SFHS provides an important opportunity to study complex gene-environment interactions, incorporating linkage to existing datasets and inclusion of early-life variables for two longitudinal birth cohorts. Specifically, data collection in STRADL included: socio-economic and lifestyle variables; physical measures; questionnaire data that assesses resilience, early-life adversity, personality, psychological health, and lifetime history of mood disorder; laboratory samples; cognitive tests; and brain magnetic resonance imaging. Some of the questionnaire and cognitive data were first assessed at the GS:SFHS baseline assessment between 2006-2011, thus providing longitudinal measures relevant to the study of depression, psychological resilience, and cognition. In addition, routinely collected historic NHS data and early-life variables are linked to STRADL data, further providing opportunities for longitudinal analysis. Recruitment has been completed and we consented and tested 1,188 participants.
Collapse
|
42
|
Bell RMB, Villalobos E, Nixon M, Miguelez-Crespo A, Murphy L, Fawkes A, Coutts A, Sharp MGF, Koerner MV, Allan E, Meijer OC, Houtman R, Odermatt A, Beck KR, Denham SG, Lee P, Homer NZM, Walker BR, Morgan RA. Carbonyl reductase 1 amplifies glucocorticoid action in adipose tissue and impairs glucose tolerance in lean mice. Mol Metab 2021; 48:101225. [PMID: 33785425 PMCID: PMC8095185 DOI: 10.1016/j.molmet.2021.101225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/09/2021] [Accepted: 03/24/2021] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE Carbonyl reductase 1 (Cbr1), a recently discovered contributor to tissue glucocorticoid metabolism converting corticosterone to 20β-dihydrocorticosterone (20β-DHB), is upregulated in adipose tissue of obese humans and mice and may contribute to cardiometabolic complications of obesity. This study tested the hypothesis that Cbr1-mediated glucocorticoid metabolism influences glucocorticoid and mineralocorticoid receptor activation in adipose tissue and impacts glucose homeostasis in lean and obese states. METHODS The actions of 20β-DHB on corticosteroid receptors in adipose tissue were investigated first using a combination of in silico, in vitro, and transcriptomic techniques and then in vivo administration in combination with receptor antagonists. Mice lacking one Cbr1 allele and mice overexpressing Cbr1 in their adipose tissue underwent metabolic phenotyping before and after induction of obesity with high-fat feeding. RESULTS 20β-DHB activated both the glucocorticoid and mineralocorticoid receptor in adipose tissue and systemic administration to wild-type mice induced glucose intolerance, an effect that was ameliorated by both glucocorticoid and mineralocorticoid receptor antagonism. Cbr1 haploinsufficient lean male mice had lower fasting glucose and improved glucose tolerance compared with littermate controls, a difference that was abolished by administration of 20β-DHB and absent in female mice with higher baseline adipose 20β-DHB concentrations than male mice. Conversely, overexpression of Cbr1 in adipose tissue resulted in worsened glucose tolerance and higher fasting glucose in lean male and female mice. However, neither Cbr1 haploinsfficiency nor adipose overexpression affected glucose dyshomeostasis induced by high-fat feeding. CONCLUSIONS Carbonyl reductase 1 is a novel regulator of glucocorticoid and mineralocorticoid receptor activation in adipose tissue that influences glucose homeostasis in lean mice.
Collapse
Affiliation(s)
- Rachel M B Bell
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Elisa Villalobos
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Mark Nixon
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Allende Miguelez-Crespo
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Lee Murphy
- Genetics Core, Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom.
| | - Angie Fawkes
- Genetics Core, Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom.
| | - Audrey Coutts
- Genetics Core, Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom.
| | - Matthew G F Sharp
- Transgenics Core, Bioresearch & Veterinary Services, University of Edinburgh, Edinburgh, United Kingdom.
| | - Martha V Koerner
- Transgenics Core, Bioresearch & Veterinary Services, University of Edinburgh, Edinburgh, United Kingdom.
| | - Emma Allan
- Transgenics Core, Bioresearch & Veterinary Services, University of Edinburgh, Edinburgh, United Kingdom.
| | - Onno C Meijer
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Renè Houtman
- Pamgene International, Den Bosch, the Netherlands.
| | - Alex Odermatt
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| | - Katharina R Beck
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| | - Scott G Denham
- Mass Spectrometry Core Laboratory, Wellcome Trust Clinical Research Facility, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Patricia Lee
- Mass Spectrometry Core Laboratory, Wellcome Trust Clinical Research Facility, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Natalie Z M Homer
- Mass Spectrometry Core Laboratory, Wellcome Trust Clinical Research Facility, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Brian R Walker
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom; Clinical and Translational Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom.
| | - Ruth A Morgan
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom; Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom.
| |
Collapse
|
43
|
Wakeham K, Murray L, Muirhead R, Hawkins MA, Sebag-Montefiore D, Brown S, Murphy L, Thomas G, Bell S, Whibley M, Morgan C, Sleigh K, Gilbert DC. Multicentre Investigation of Prognostic Factors Incorporating p16 and Tumour Infiltrating Lymphocytes for Anal Cancer After Chemoradiotherapy. Clin Oncol (R Coll Radiol) 2021; 33:638-649. [PMID: 34024700 DOI: 10.1016/j.clon.2021.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/09/2021] [Accepted: 04/27/2021] [Indexed: 11/30/2022]
Abstract
AIMS Anal squamous cell carcinomas (ASCC) are strongly associated with human papillomaviruses. Standard of care is chemoradiotherapy at uniform doses with no treatment stratification. Immunohistochemical staining for p16INK4A (p16), a surrogate for human papillomaviruses, is prognostic for outcomes. We investigated this alongside clinical-pathological factors, including tumour infiltrating lymphocyte (TIL) scores. MATERIALS AND METHODS Using an independent, multicentre cohort of 257 ASCC treated with chemoradiotherapy, pretreatment biopsies were stained and scored for p16 and TIL. Kaplan-Meier curves were derived for outcomes (disease-free survival [DFS], overall survival and cancer-specific survival), by stage, p16 and TIL scores and Log-rank tests were carried out to investigate prognostic effect. A multivariate analysis was carried out using Cox regression. RESULTS Stage, sex, p16 and TILs were independently prognostic. Hazard ratios for death (overall survival) were 2.51 (95% confidence interval 1.36-4.63) for p16 negative versus p16 positive, 2.17 (1.34-3.5) for T3/4 versus T1/2, 2.42 (1.52-3.8) for males versus females and 3.30 (1.52-7.14) for TIL1 versus TIL3 (all P < 0.05). CONCLUSIONS We have refined prognostic factors in ASCC. p16 adds to stratification by stage with respect to DFS in early disease and overall survival/DFS in locally advanced cancers. Our data support the role of the host immune response in mediating outcomes. These factors will be prospectively evaluated in PLATO (ISRCTN88455282).
Collapse
Affiliation(s)
- K Wakeham
- Sussex Cancer Centre, Royal Sussex County Hospital, Brighton, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - L Murray
- Leeds Institute of Medical Research, University of Leeds, Leeds Cancer Centre, Leeds, UK
| | - R Muirhead
- Oxford University Hospitals NHS Trust, Department of Oncology, Churchill Hospital, Oxford, UK
| | - M A Hawkins
- University College London, Medical Physics and Biomedical Engineering, London, UK
| | - D Sebag-Montefiore
- Leeds Institute of Medical Research, University of Leeds, Leeds Cancer Centre, Leeds, UK
| | - S Brown
- Clinical Trials Research Unit, University of Leeds, Leeds, UK
| | - L Murphy
- MRC Clinical Trials Unit at UCL, London, UK
| | - G Thomas
- Department of Cellular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK; Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - S Bell
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - M Whibley
- Sussex Cancer Centre, Royal Sussex County Hospital, Brighton, UK
| | - C Morgan
- Sussex Cancer Centre, Royal Sussex County Hospital, Brighton, UK
| | - K Sleigh
- Sussex Cancer Centre, Royal Sussex County Hospital, Brighton, UK
| | - D C Gilbert
- MRC Clinical Trials Unit at UCL, London, UK.
| |
Collapse
|
44
|
Gadd DA, Stevenson AJ, Hillary RF, McCartney DL, Wrobel N, McCafferty S, Murphy L, Russ TC, Harris SE, Redmond P, Taylor AM, Smith C, Rose J, Millar T, Spires-Jones TL, Cox SR, Marioni RE. Epigenetic predictors of lifestyle traits applied to the blood and brain. Brain Commun 2021; 3:fcab082. [PMID: 34041477 PMCID: PMC8134833 DOI: 10.1093/braincomms/fcab082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/02/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022] Open
Abstract
Modifiable lifestyle factors influence the risk of developing many neurological diseases. These factors have been extensively linked with blood-based genome-wide DNA methylation, but it is unclear if the signatures from blood translate to the target tissue of interest-the brain. To investigate this, we apply blood-derived epigenetic predictors of four lifestyle traits to genome-wide DNA methylation from five post-mortem brain regions and the last blood sample prior to death in 14 individuals in the Lothian Birth Cohort 1936. Using these matched samples, we found that correlations between blood and brain DNA methylation scores for smoking, high-density lipoprotein cholesterol, alcohol and body mass index were highly variable across brain regions. Smoking scores in the dorsolateral prefrontal cortex had the strongest correlations with smoking scores in blood (r = 0.5, n = 14, P = 0.07) and smoking behaviour (r = 0.56, n = 9, P = 0.12). This was also the brain region which exhibited the largest correlations for DNA methylation at site cg05575921 - the single strongest correlate of smoking in blood-in relation to blood (r = 0.61, n = 14, P = 0.02) and smoking behaviour (r = -0.65, n = 9, P = 0.06). This suggested a particular vulnerability to smoking-related differential methylation in this region. Our work contributes to understanding how lifestyle factors affect the brain and suggest that lifestyle-related DNA methylation is likely to be both brain region dependent and in many cases poorly proxied for by blood. Though these pilot data provide a rarely-available opportunity for the comparison of methylation patterns across multiple brain regions and the blood, due to the limited sample size available our results must be considered as preliminary and should therefore be used as a basis for further investigation.
Collapse
Affiliation(s)
- Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh 2XU, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh 2XU, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh 2XU, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh 2XU, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sarah McCafferty
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Tom C Russ
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh EH8 9JZ, UK
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Sarah E Harris
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Paul Redmond
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Adele M Taylor
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Colin Smith
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Jamie Rose
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Tracey Millar
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Tara L Spires-Jones
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Simon R Cox
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh 2XU, UK
| |
Collapse
|
45
|
Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, Fourman MH, Russell CD, Furniss J, Richmond A, Gountouna E, Wrobel N, Harrison D, Wang B, Wu Y, Meynert A, Griffiths F, Oosthuyzen W, Kousathanas A, Moutsianas L, Yang Z, Zhai R, Zheng C, Grimes G, Beale R, Millar J, Shih B, Keating S, Zechner M, Haley C, Porteous DJ, Hayward C, Yang J, Knight J, Summers C, Shankar-Hari M, Klenerman P, Turtle L, Ho A, Moore SC, Hinds C, Horby P, Nichol A, Maslove D, Ling L, McAuley D, Montgomery H, Walsh T, Pereira AC, Renieri A, Shen X, Ponting CP, Fawkes A, Tenesa A, Caulfield M, Scott R, Rowan K, Murphy L, Openshaw PJM, Semple MG, Law A, Vitart V, Wilson JF, Baillie JK. Genetic mechanisms of critical illness in COVID-19. Nature 2021; 591:92-98. [PMID: 33307546 DOI: 10.1038/s41586-020-03065-y] [Citation(s) in RCA: 799] [Impact Index Per Article: 266.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 × 10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice.
Collapse
Affiliation(s)
- Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James Furniss
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Elvina Gountouna
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - David Harrison
- Intensive Care National Audit & Research Centre, London, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | | | | | | | - Zhijian Yang
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ranran Zhai
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chenqing Zheng
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | | | - Barbara Shih
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Chris Haley
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Paul Klenerman
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
- Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Victoria, Australia
- Intensive Care Unit, Alfred Hospital, Melbourne, Victoria, Australia
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | - Hugh Montgomery
- UCL Centre for Human Health and Performance, University College London, London, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Alexandre C Pereira
- Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- Heart Institute, University of São Paulo, São Paulo, Brazil
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Xia Shen
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Mark Caulfield
- Genomics England, London, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Richard Scott
- Genomics England, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust London, London, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Liverpool, UK
| | - Andrew Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
| |
Collapse
|
46
|
Masalmeh RHA, Taglini F, Rubio-Ramon C, Musialik KI, Higham J, Davidson-Smith H, Kafetzopoulos I, Pawlicka KP, Finan HM, Clark R, Wills J, Finch AJ, Murphy L, Sproul D. De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG islands. Nat Commun 2021; 12:694. [PMID: 33514701 PMCID: PMC7846778 DOI: 10.1038/s41467-020-20716-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
The aberrant gain of DNA methylation at CpG islands is frequently observed in colorectal tumours and may silence the expression of tumour suppressors such as MLH1. Current models propose that these CpG islands are targeted by de novo DNA methyltransferases in a sequence-specific manner, but this has not been tested. Using ectopically integrated CpG islands, here we find that aberrantly methylated CpG islands are subject to low levels of de novo DNA methylation activity in colorectal cancer cells. By delineating DNA methyltransferase targets, we find that instead de novo DNA methylation activity is targeted primarily to CpG islands marked by the histone modification H3K36me3, a mark associated with transcriptional elongation. These H3K36me3 marked CpG islands are heavily methylated in colorectal tumours and the normal colon suggesting that de novo DNA methyltransferase activity at CpG islands in colorectal cancer is focused on similar targets to normal tissues and not greatly remodelled by tumourigenesis.
Collapse
Affiliation(s)
| | - Francesca Taglini
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Cristina Rubio-Ramon
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Kamila I Musialik
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Jonathan Higham
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Ioannis Kafetzopoulos
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Kamila P Pawlicka
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Hannah M Finan
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Richard Clark
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Jimi Wills
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Andrew J Finch
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Duncan Sproul
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
47
|
Nguyen U, Tinsley B, Sen Y, Stein J, Palacios Y, Ceballos A, Welch C, Nzenkue K, Penn A, Murphy L, Leodones K, Casiquin J, Ivory I, Ghenta K, Danziger K, Widman E, Newman J, Triplehorn M, Hindi Z, Mulligan K. Exposure to bisphenol A differentially impacts neurodevelopment and behavior in Drosophila melanogaster from distinct genetic backgrounds. Neurotoxicology 2020; 82:146-157. [PMID: 33309840 DOI: 10.1016/j.neuro.2020.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/30/2020] [Accepted: 12/06/2020] [Indexed: 12/13/2022]
Abstract
Bisphenol A (BPA) is a ubiquitous environmental chemical that has been linked to behavioral differences in children and shown to impact critical neurodevelopmental processes in animal models. Though data is emerging, we still have an incomplete picture of how BPA disrupts neurodevelopment; in particular, how its impacts may vary across different genetic backgrounds. Given the genetic tractability of Drosophila melanogaster, they present a valuable model to address this question. Fruit flies are increasingly being used for assessment of neurotoxicants because of their relatively simple brain structure and variety of measurable behaviors. Here we investigated the neurodevelopmental impacts of BPA across two genetic strains of Drosophila-w1118 (control) and the Fragile X Syndrome (FXS) model-by examining both behavioral and neuronal phenotypes. We show that BPA induces hyperactivity in larvae, increases repetitive grooming behavior in adults, reduces courtship behavior, impairs axon guidance in the mushroom body, and disrupts neural stem cell development in the w1118 genetic strain. Remarkably, for every behavioral and neuronal phenotype examined, the impact of BPA in FXS flies was either insignificant or contrasted with the phenotypes observed in the w1118 strain. This data indicates that the neurodevelopmental impacts of BPA can vary widely depending on genetic background and suggests BPA may elicit a gene-environment interaction with Drosophila fragile X mental retardation 1 (dFmr1)-the ortholog of human FMR1, which causes Fragile X Syndrome and is associated with autism spectrum disorder.
Collapse
Affiliation(s)
- U Nguyen
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - B Tinsley
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - Y Sen
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - J Stein
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - Y Palacios
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - A Ceballos
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - C Welch
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - K Nzenkue
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - A Penn
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - L Murphy
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - K Leodones
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - J Casiquin
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - I Ivory
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - K Ghenta
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - K Danziger
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - E Widman
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - J Newman
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - M Triplehorn
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - Z Hindi
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States
| | - K Mulligan
- Department of Biological Sciences, California State University, Sacramento, 6000 J Street, Sacramento, CA, 95819, United States.
| |
Collapse
|
48
|
Gethin G, Vellinga A, Tawfick W, O'Loughlin A, McIntosh C, Mac Gilchrist C, Murphy L, Ejiugwo M, O'Regan M, Cameron A, Ivory JD. The profile of patients with venous leg ulcers: A systematic review and global perspective. J Tissue Viability 2020; 30:78-88. [PMID: 32839066 DOI: 10.1016/j.jtv.2020.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/05/2020] [Accepted: 08/05/2020] [Indexed: 01/24/2023]
Abstract
BACKGROUND A holistic profile that includes demographic, medical history and wound characteristics of individuals with venous leg ulceration is lacking. Lack of such a profile negatively impacts the ability to develop interventions to improve patient outcomes. OBJECTIVES To describe the profile of the patient population with venous leg ulceration from published observational (non-interventional) studies and to identify gaps in the knowledge base for future research in this area. METHODS A systematic review of observational studies that included more than 50 patients, from any world region, of any age and in any care setting. RESULTS twenty studies, involving 3395 patients, from all world regions met our criteria. Demographic characteristics were well reported and showed a female to male ratio of 1.2:1, average age of 47-65 years, high levels of co-morbidities including hypertension (53-71%) and diabetes (16-20%), and only one study reporting ethnicity. When reported, approximately 4-30% had high levels of depression. The average wound size was 18.6-43.39 cm2; mean wound duration was 13.8-65.5 months, mean number of recurrences was four. No study reported on demographic factors plus medical history plus wound characteristics together. CONCLUSION a comprehensive, holistic profile of the population with VLU is lacking. There is a critical need for more comprehensive profiling to enable the development of targeted interventions to improve outcomes.
Collapse
Affiliation(s)
- G Gethin
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland.
| | - A Vellinga
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland
| | - W Tawfick
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland
| | - A O'Loughlin
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland
| | - C McIntosh
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland
| | - C Mac Gilchrist
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland
| | - L Murphy
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland
| | - M Ejiugwo
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland
| | - M O'Regan
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland
| | - A Cameron
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland
| | - J D Ivory
- National University of Ireland, Galway, Ireland; Alliance for Research & Innovation in Wounds (ARIW), Ireland
| |
Collapse
|
49
|
Toombs J, Panther L, Ornelas L, Liu C, Gomez E, Martín-Ibáñez R, Cox SR, Ritchie SJ, Harris SE, Taylor A, Redmond P, Russ TC, Murphy L, Cooper JD, Burr K, Selvaraj BT, Browne C, Svendsen CN, Cowley SA, Deary IJ, Chandran S, Spires-Jones TL, Sareen D. Generation of twenty four induced pluripotent stem cell lines from twenty four members of the Lothian Birth Cohort 1936. Stem Cell Res 2020; 46:101851. [PMID: 32450543 PMCID: PMC7347008 DOI: 10.1016/j.scr.2020.101851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/01/2020] [Accepted: 05/13/2020] [Indexed: 11/19/2022] Open
Abstract
Cognitive decline is among the most feared aspects of ageing. We have generated induced pluripotent stem cells (iPSCs) from 24 people from the Lothian Birth Cohort 1936, whose cognitive ability was tested in childhood and in older age. Peripheral blood mononuclear cells (PBMCs) were reprogrammed using non-integrating oriP/EBNA1 backbone plasmids expressing six iPSC reprogramming factors (OCT3/4 (POU5F1), SOX2, KLF4, L-Myc, shp53, Lin28, SV40LT). All lines demonstrated STR matched karyotype and pluripotency was validated by multiple methods. These iPSC lines are a valuable resource to study molecular mechanisms underlying individual differences in cognitive ageing and resilience to age-related neurodegenerative diseases.
Collapse
Affiliation(s)
- Jamie Toombs
- Centre for Discovery Brain Sciences, UK Dementia Research Institute, The University of Edinburgh, UK
| | - Lindsay Panther
- iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA
| | - Loren Ornelas
- iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA
| | - Chunyan Liu
- iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA
| | - Emilda Gomez
- iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA
| | | | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Stuart J Ritchie
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Adele Taylor
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Tom C Russ
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK; Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - James D Cooper
- Dementia Research Institute at the University of Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Karen Burr
- Dementia Research Institute at the University of Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Bhuvaneish T Selvaraj
- Dementia Research Institute at the University of Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Cathy Browne
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Clive N Svendsen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Sally A Cowley
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; Oxford Parkinson's Disease Centre, Oxford, UK
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- Dementia Research Institute at the University of Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Tara L Spires-Jones
- Centre for Discovery Brain Sciences, UK Dementia Research Institute, The University of Edinburgh, UK.
| | - Dhruv Sareen
- iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA; Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
| |
Collapse
|
50
|
Keag OE, Murphy L, Bradley A, Deakin N, Whyte S, Norman JE, Stock SJ. Postal recruitment for genetic studies of preterm birth: A feasibility study. Wellcome Open Res 2020; 5:26. [PMID: 32322692 PMCID: PMC7160603 DOI: 10.12688/wellcomeopenres.15207.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2020] [Indexed: 11/28/2022] Open
Abstract
Background: Preterm birth (PTB) represents the leading cause of neonatal death. Large-scale genetic studies are necessary to determine genetic influences on PTB risk, but prospective cohort studies are expensive and time-consuming. We investigated the feasibility of retrospective recruitment of post-partum women for efficient collection of genetic samples, with self-collected saliva for DNA extraction from themselves and their babies, alongside self-recollection of pregnancy and birth details to phenotype PTB. Methods: 708 women who had participated in the OPPTIMUM trial (a randomised trial of progesterone pessaries to prevent PTB [ISRCTN14568373]) and consented to further contact were invited to provide self-collected saliva from themselves and their babies. DNA was extracted from Oragene OG-500 (adults) and OG-575 (babies) saliva kits and the yield measured by Qubit. Samples were analysed using a panel of Taqman single nucleotide polymorphism (SNP) assays. A questionnaire designed to meet the minimum data set required for phenotyping PTB was included. Questionnaire responses were transcribed and analysed for concordance with prospective trial data using Cohen’s kappa (
k). Results: Recruitment rate was 162/708 (23%) for self-collected saliva samples and 157/708 (22%) for questionnaire responses. 161 samples from the mother provided DNA with median yield 59.0µg (0.4-148.9µg). 156 samples were successfully genotyped (96.9%). 136 baby samples had a median yield 11.5µg (0.1-102.7µg); two samples failed DNA extraction. 131 baby samples (96.3%) were successfully genotyped. Concordance between self-recalled birth details and prospective birth details was excellent (
k>0.75) in 4 out of 10 key fields for phenotyping PTB (mode of delivery, labour onset, ethnicity and maternal age at birth). Conclusion: This feasibility study demonstrates that self-collected DNA samples from mothers and babies were sufficient for genetic analysis but yields were variable. Self-recollection of pregnancy and birth details was inadequate for accurately phenotyping PTB, highlighting the need for alternative strategies for investigating genetic links with PTB.
Collapse
Affiliation(s)
- Oonagh E Keag
- Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, EH4 2XU, UK
| | | | - Naomi Deakin
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Sonia Whyte
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Jane E Norman
- Faculty of Health Sciences, University of Bristol, Bristol, BS8 1UD, UK
| | - Sarah J Stock
- Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK.,Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH16 4UX, UK
| |
Collapse
|