Search

Your search keyword '"692/308/2056"' showing total 10 results
Start Over Descriptor "692/308/2056" Publication Year Range Last 3 years
10 results on '"692/308/2056"'

1. Genetic association analysis of 77,539 genomes reveals rare disease etiologies

Author

Greene, Daniel, Genomics England Research Consortium, Pirri, Daniela, Frudd, Karen, Sackey, Ege, Al-Owain, Mohammed, Giese, Arnaud PJ, Ramzan, Khushnooda, Riaz, Sehar, Yamanaka, Itaru, Boeckx, Nele, Thys, Chantal, Gelb, Bruce D, Brennan, Paul, Hartill, Verity, Harvengt, Julie, Kosho, Tomoki, Mansour, Sahar, Masuno, Mitsuo, Ohata, Takako, Stewart, Helen, Taibah, Khalid, Turner, Claire LS, Imtiaz, Faiqa, Riazuddin, Saima, Morisaki, Takayuki, Ostergaard, Pia, Loeys, Bart L, Morisaki, Hiroko, Ahmed, Zubair M, Birdsey, Graeme M, Freson, Kathleen, Mumford, Andrew, Turro, Ernest, Giese, Arnaud PJ [0000-0001-7228-9542], Yamanaka, Itaru [0000-0003-0293-8070], Gelb, Bruce D [0000-0001-8527-5027], Kosho, Tomoki [0000-0002-8344-7507], Riazuddin, Saima [0000-0002-8645-4761], Ostergaard, Pia [0000-0002-2190-1356], Loeys, Bart L [0000-0003-3703-9518], Ahmed, Zubair M [0000-0003-2914-4502], Birdsey, Graeme M [0000-0002-0981-8672], Turro, Ernest [0000-0002-1820-6563], Apollo - University of Cambridge Repository, Giese, Arnaud P J [0000-0001-7228-9542], Freson, Kathleen [0000-0002-4381-2442], Giese, Arnaud P. J. [0000-0001-7228-9542], Gelb, Bruce D. [0000-0001-8527-5027], Loeys, Bart L. [0000-0003-3703-9518], Ahmed, Zubair M. [0000-0003-2914-4502], Birdsey, Graeme M. [0000-0002-0981-8672], and Genomics England Research Consortium

Subjects
Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], 631/208/2489/144, Genotype, 631/208/514/2254, 692/308/2056, article, Membrane Proteins, Bayes Theorem, General Medicine, General Biochemistry, Genetics and Molecular Biology, Chemistry, 631/208, All institutes and research themes of the Radboud University Medical Center, Rare Diseases, Phenotype, 631/114/2398, Humans, Human medicine, Biology, Genome-Wide Association Study
Abstract

Acknowledgements: This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health and Social Care). The 100,000 Genomes Project is funded by the National Institute for Health Research and National Health Service (NHS) England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. GS was performed by Illumina at Illumina Laboratory Services and was overseen by Genomics England. We thank all NHS clinicians who have contributed clinical phenotype data to the 100,000 Genomes Rare Diseases Programme and all staff at Genomics England who have contributed to the sequencing, maintenance of the research environment and assembly of the standard bioinformatic files that were required for our analyses. We thank the participants of the rare diseases program who made this research possible. We are grateful to V. Keeley for providing access to paternal DNA (ERG), F. Elmslie for inviting a patient to the clinic (ERG) and T. Jaworek for technical assistance (GPR156). D.G. was supported by the Cambridge British Heart Foundation (BHF) Centre of Research Excellence (RE/18/1/34212) and the Wellcome Collaborative (219506/Z/19/Z). V.H. was supported by an Medical Research Council (MRC)/National Institute for Health and Care Research Clinical Academic Research Partnership (MR/V037617/1). G.M.B. and K. Frudd were funded by BHF (PG/17/33/32990). G.M.B. and D.P. were funded by BHF (PG/20/16/35047). E.S. was supported by the Swiss Federal National Fund for Scientific Research (CRSII5_177191/1). S.M. and P.O. were supported by the MRC (MR/P011543/1) and BHF (RG/17/7/33217). K. Freson was supported by Katholieke Universiteit (KU) Leuven Special Research Fund (BOF) (C14/19/096) and Research Foundation – Flanders (G072921N). Work at the University of Maryland, Baltimore was supported by the National Institute on Deafness and Other Communication Disorders/National Institutes of Health (R01DC016295 to Z.M.A.). M.A.-O., F.I. and K.R. were supported by the King Salman Center for Disability Research (85722). E.T. was supported by the Mindich Child Health and Development Institute, the Charles Bronfman Institute for Personalized Medicine and the Lowy Foundation USA., Funder: Cambridge BHF Centre of Research Excellence [RE/18/1/34212] and Wellcome Collaborative Award 219506/Z/19/Z, Funder: BHF Project grant PG/17/33/32990, Funder: Swiss National Science Foundation grant CRSII5_177191, Funder: King Salman Center for Disability Research # 85722, Funder: MRC/NIHR Clinical Academic Research Partnership MR/V037617/1, Funder: Medical Research Council grant MR/P011543/1 and British Heart Foundation grant RG/17/7/33217, Funder: NIDCD/NIH R01DC016295, Funder: BHF Project grants PG/20/16/35047 & PG/17/33/32990, Funder: KULeuven BOF grant C14/19/096, FWO grant G072921N, The genetic etiologies of more than half of rare diseases remain unknown. Standardized genome sequencing and phenotyping of large patient cohorts provide an opportunity for discovering the unknown etiologies, but this depends on efficient and powerful analytical methods. We built a compact database, the ‘Rareservoir’, containing the rare variant genotypes and phenotypes of 77,539 participants sequenced by the 100,000 Genomes Project. We then used the Bayesian genetic association method BeviMed to infer associations between genes and each of 269 rare disease classes assigned by clinicians to the participants. We identified 241 known and 19 previously unidentified associations. We validated associations with ERG, PMEPA1 and GPR156 by searching for pedigrees in other cohorts and using bioinformatic and experimental approaches. We provide evidence that (1) loss-of-function variants in the Erythroblast Transformation Specific (ETS)-family transcription factor encoding gene ERG lead to primary lymphoedema, (2) truncating variants in the last exon of transforming growth factor-β regulator PMEPA1 result in Loeys–Dietz syndrome and (3) loss-of-function variants in GPR156 give rise to recessive congenital hearing impairment. The Rareservoir provides a lightweight, flexible and portable system for synthesizing the genetic and phenotypic data required to study rare disease cohorts with tens of thousands of participants.

Published
2023
Full Text
View/download PDF

2. TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease

Author

Lindsey Van Haute, Emily O’Connor, Héctor Díaz-Maldonado, Benjamin Munro, Kiran Polavarapu, Daniella H. Hock, Gautham Arunachal, Alkyoni Athanasiou-Fragkouli, Mainak Bardhan, Magalie Barth, Dominique Bonneau, Nicola Brunetti-Pierri, Gerarda Cappuccio, Nikeisha J. Caruana, Natalia Dominik, Himanshu Goel, Guy Helman, Henry Houlden, Guy Lenaers, Karine Mention, David Murphy, Bevinahalli Nandeesh, Catarina Olimpio, Christopher A. Powell, Veeramani Preethish-Kumar, Vincent Procaccio, Rocio Rius, Pedro Rebelo-Guiomar, Cas Simons, Seena Vengalil, Maha S. Zaki, Alban Ziegler, David R. Thorburn, David A. Stroud, Reza Maroofian, John Christodoulou, Claes Gustafsson, Atchayaram Nalini, Hanns Lochmüller, Michal Minczuk, Rita Horvath, Van Haute, Lindsey [0000-0001-7809-1473], Polavarapu, Kiran [0000-0002-8879-6001], Hock, Daniella H [0000-0002-6940-4420], Bardhan, Mainak [0000-0002-4106-409X], Brunetti-Pierri, Nicola [0000-0002-6895-8819], Caruana, Nikeisha J [0000-0002-0817-1686], Helman, Guy [0000-0002-4784-7423], Houlden, Henry [0000-0002-2866-7777], Lenaers, Guy [0000-0003-2736-3349], Rius, Rocio [0000-0002-9871-3126], Rebelo-Guiomar, Pedro [0000-0002-5060-7519], Simons, Cas [0000-0003-3147-8042], Vengalil, Seena [0000-0002-0629-9221], Zaki, Maha S [0000-0001-7840-0002], Thorburn, David R [0000-0002-7725-9470], Stroud, David A [0000-0002-2048-3383], Christodoulou, John [0000-0002-8431-0641], Gustafsson, Claes [0000-0003-3531-8468], Minczuk, Michal [0000-0001-8242-1420], Horvath, Rita [0000-0002-9841-170X], Apollo - University of Cambridge Repository, Van Haute, Lindsey, O'Connor, Emily, Díaz-Maldonado, Héctor, Munro, Benjamin, Polavarapu, Kiran, Hock, Daniella H, Arunachal, Gautham, Athanasiou-Fragkouli, Alkyoni, Bardhan, Mainak, Barth, Magalie, Bonneau, Dominique, Brunetti-Pierri, Nicola, Cappuccio, Gerarda, Caruana, Nikeisha J, Dominik, Natalia, Goel, Himanshu, Helman, Guy, Houlden, Henry, Lenaers, Guy, Mention, Karine, Murphy, David, Nandeesh, Bevinahalli, Olimpio, Catarina, Powell, Christopher A, Preethish-Kumar, Veeramani, Procaccio, Vincent, Rius, Rocio, Rebelo-Guiomar, Pedro, Simons, Ca, Vengalil, Seena, Zaki, Maha S, Ziegler, Alban, Thorburn, David R, Stroud, David A, Maroofian, Reza, Christodoulou, John, Gustafsson, Clae, Nalini, Atchayaram, Lochmüller, Hann, Minczuk, Michal, and Horvath, Rita

Subjects
Transcription, Genetic, RNA, Mitochondrial, General Physics and Astronomy, 38/90, 13/106, 692/1807/1693, 14, DNA, Mitochondrial, General Biochemistry, Genetics and Molecular Biology, 38, 38/91, 82/80, Mitochondrial Proteins, 38/1, 692/420/2489/144, 692/617/375/374, 38/23, 38/22, Animals, Humans, Child, Zebrafish, 64, Multidisciplinary, 64/116, 692/308/2056, article, General Chemistry, 13/51, Mutation, 38/77, 692/700/139/422, Transcription Factors
Abstract

Funder: EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013)); doi: https://doi.org/10.13039/100011199; Grant(s): 309548, Funder: Lily Mae Foundation; doi: https://doi.org/10.13039/100012336, Mutations in the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA biology. The TEFM gene encodes the mitochondrial transcription elongation factor responsible for enhancing the processivity of mitochondrial RNA polymerase, POLRMT. We report for the first time that TEFM variants are associated with mitochondrial respiratory chain deficiency and a wide range of clinical presentations including mitochondrial myopathy with a treatable neuromuscular transmission defect. Mechanistically, we show muscle and primary fibroblasts from the affected individuals have reduced levels of promoter distal mitochondrial RNA transcripts. Finally, tefm knockdown in zebrafish embryos resulted in neuromuscular junction abnormalities and abnormal mitochondrial function, strengthening the genotype-phenotype correlation. Our study highlights that TEFM regulates mitochondrial transcription elongation and its defect results in variable, tissue-specific neurological and neuromuscular symptoms.

Published
2023
Full Text
View/download PDF

3. FinnGen provides genetic insights from a well-phenotyped isolated population

Author

Kurki, Mitja I, Karjalainen, Juha, Palta, Priit, Sipilä, Timo P, Kristiansson, Kati, Donner, Kati M, Reeve, Mary P, Laivuori, Hannele, Aavikko, Mervi, Kaunisto, Mari A, Loukola, Anu, Lahtela, Elisa, Mattsson, Hannele, Laiho, Päivi, Della Briotta Parolo, Pietro, Lehisto, Arto A, Kanai, Masahiro, Mars, Nina, Rämö, Joel, Kiiskinen, Tuomo, Heyne, Henrike O, Veerapen, Kumar, Rüeger, Sina, Lemmelä, Susanna, Zhou, Wei, Ruotsalainen, Sanni, Pärn, Kalle, Hiekkalinna, Tero, Koskelainen, Sami, Paajanen, Teemu, Llorens, Vincent, Gracia-Tabuenca, Javier, Siirtola, Harri, Reis, Kadri, Elnahas, Abdelrahman G, Sun, Benjamin, Foley, Christopher N, Aalto-Setälä, Katriina, Alasoo, Kaur, Arvas, Mikko, Auro, Kirsi, Biswas, Shameek, Bizaki-Vallaskangas, Argyro, Carpen, Olli, Chen, Chia-Yen, Dada, Oluwaseun A, Ding, Zhihao, Ehm, Margaret G, Eklund, Kari, Färkkilä, Martti, Finucane, Hilary, Ganna, Andrea, Ghazal, Awaisa, Graham, Robert R, Green, Eric M, Hakanen, Antti, Hautalahti, Marco, Hedman, Åsa K, Hiltunen, Mikko, Hinttala, Reetta, Hovatta, Iiris, Hu, Xinli, Huertas-Vazquez, Adriana, Huilaja, Laura, Hunkapiller, Julie, Jacob, Howard, Jensen, Jan-Nygaard, Joensuu, Heikki, John, Sally, Julkunen, Valtteri, Jung, Marc, Junttila, Juhani, Kaarniranta, Kai, Kähönen, Mika, Kajanne, Risto, Kallio, Lila, Kälviäinen, Reetta, Kaprio, Jaakko, FinnGen, Kerimov, Nurlan, Kettunen, Johannes, Kilpeläinen, Elina, Kilpi, Terhi, Klinger, Katherine, Kosma, Veli-Matti, Kuopio, Teijo, Kurra, Venla, Laisk, Triin, Laukkanen, Jari, Lawless, Nathan, Liu, Aoxing, Longerich, Simonne, Mägi, Reedik, Mäkelä, Johanna, Mäkitie, Antti, Malarstig, Anders, Mannermaa, Arto, Maranville, Joseph, Matakidou, Athena, Meretoja, Tuomo, Mozaffari, Sahar V, Niemi, Mari EK, Niemi, Marianna, Niiranen, Teemu, O Donnell, Christopher J, Obeidat, Ma En, Okafo, George, Ollila, Hanna M, Palomäki, Antti, Palotie, Tuula, Partanen, Jukka, Paul, Dirk S, Pelkonen, Margit, Pendergrass, Rion K, Petrovski, Slavé, Pitkäranta, Anne, Platt, Adam, Pulford, David, Punkka, Eero, Pussinen, Pirkko, Raghavan, Neha, Rahimov, Fedik, Rajpal, Deepak, Renaud, Nicole A, Riley-Gillis, Bridget, Rodosthenous, Rodosthenis, Saarentaus, Elmo, Salminen, Aino, Salminen, Eveliina, Salomaa, Veikko, Schleutker, Johanna, Serpi, Raisa, Shen, Huei-Yi, Siegel, Richard, Silander, Kaisa, Siltanen, Sanna, Soini, Sirpa, Soininen, Hilkka, Sul, Jae Hoon, Tachmazidou, Ioanna, Tasanen, Kaisa, Tienari, Pentti, Toppila-Salmi, Sanna, Tukiainen, Taru, Tuomi, Tiinamaija, Turunen, Joni A, Ulirsch, Jacob C, Vaura, Felix, Virolainen, Petri, Waring, Jeffrey, Waterworth, Dawn, Yang, Robert, Nelis, Mari, Reigo, Anu, Metspalu, Andres, Milani, Lili, Esko, Tõnu, Fox, Caroline, Havulinna, Aki S, Perola, Markus, Ripatti, Samuli, Jalanko, Anu, Laitinen, Tarja, Mäkelä, Tomi P, Plenge, Robert, McCarthy, Mark, Runz, Heiko, Daly, Mark J, Palotie, Aarno, Palotie, Aarno [0000-0002-2527-5874], and Apollo - University of Cambridge Repository

Subjects
Estonia, 631/208/205/2138, 692/308/2056, 45/43, article, Middle Aged, United Kingdom, White People, 631/208/457/649/2219, Phenotype, Gene Frequency, Meta-Analysis as Topic, 631/208/727/2000, Humans, Disease, Genetic Predisposition to Disease, Finland, Genome-Wide Association Study
Abstract

Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored1,2. FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10-11) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of

Published
2023
Full Text
View/download PDF

4. FinnGen provides genetic insights from a well-phenotyped isolated population

Author

Kurki, Mitja I, Karjalainen, Juha, Palta, Priit, Sipilä, Timo P, Kristiansson, Kati, Donner, Kati M, Reeve, Mary P, Laivuori, Hannele, Aavikko, Mervi, Kaunisto, Mari A, Loukola, Anu, Lahtela, Elisa, Mattsson, Hannele, Laiho, Päivi, Della Briotta Parolo, Pietro, Lehisto, Arto A, Kanai, Masahiro, Mars, Nina, Rämö, Joel, Kiiskinen, Tuomo, Heyne, Henrike O, Veerapen, Kumar, Rüeger, Sina, Lemmelä, Susanna, Zhou, Wei, Ruotsalainen, Sanni, Pärn, Kalle, Hiekkalinna, Tero, Koskelainen, Sami, Paajanen, Teemu, Llorens, Vincent, Gracia-Tabuenca, Javier, Siirtola, Harri, Reis, Kadri, Elnahas, Abdelrahman G, Sun, Benjamin, Foley, Christopher N, Aalto-Setälä, Katriina, Alasoo, Kaur, Arvas, Mikko, Auro, Kirsi, Biswas, Shameek, Bizaki-Vallaskangas, Argyro, Carpen, Olli, Chen, Chia-Yen, Dada, Oluwaseun A, Ding, Zhihao, Ehm, Margaret G, Eklund, Kari, Färkkilä, Martti, Finucane, Hilary, Ganna, Andrea, Ghazal, Awaisa, Graham, Robert R, Green, Eric M, Hakanen, Antti, Hautalahti, Marco, Hedman, Åsa K, Hiltunen, Mikko, Hinttala, Reetta, Hovatta, Iiris, Hu, Xinli, Huertas-Vazquez, Adriana, Huilaja, Laura, Hunkapiller, Julie, Jacob, Howard, Jensen, Jan-Nygaard, Joensuu, Heikki, John, Sally, Julkunen, Valtteri, Jung, Marc, Junttila, Juhani, Kaarniranta, Kai, Kähönen, Mika, Kajanne, Risto, Kallio, Lila, Kälviäinen, Reetta, Kaprio, Jaakko, Kerimov, Nurlan, Kettunen, Johannes, Kilpeläinen, Elina, Kilpi, Terhi, Klinger, Katherine, Kosma, Veli-Matti, Kuopio, Teijo, Kurra, Venla, Laisk, Triin, Laukkanen, Jari, Lawless, Nathan, Liu, Aoxing, Longerich, Simonne, Mägi, Reedik, Mäkelä, Johanna, Mäkitie, Antti, Malarstig, Anders, Mannermaa, Arto, Maranville, Joseph, Matakidou, Athena, Meretoja, Tuomo, Mozaffari, Sahar V, Niemi, Mari E K, Niemi, Marianna, Niiranen, Teemu, O Donnell, Christopher J, Obeidat, Ma En, Okafo, George, Ollila, Hanna M, Palomäki, Antti, Palotie, Tuula, Partanen, Jukka, Paul, Dirk S, Pelkonen, Margit, Pendergrass, Rion K, Petrovski, Slavé, Pitkäranta, Anne, Platt, Adam, Pulford, David, Punkka, Eero, Pussinen, Pirkko, Raghavan, Neha, Rahimov, Fedik, Rajpal, Deepak, Renaud, Nicole A, Riley-Gillis, Bridget, Rodosthenous, Rodosthenis, Saarentaus, Elmo, Salminen, Aino, Salminen, Eveliina, Salomaa, Veikko, Schleutker, Johanna, Serpi, Raisa, Shen, Huei-Yi, Siegel, Richard, Silander, Kaisa, Siltanen, Sanna, Soini, Sirpa, Soininen, Hilkka, Sul, Jae Hoon, Tachmazidou, Ioanna, Tasanen, Kaisa, Tienari, Pentti, Toppila-Salmi, Sanna, Tukiainen, Taru, Tuomi, Tiinamaija, Turunen, Joni A, Ulirsch, Jacob C, Vaura, Felix, Virolainen, Petri, Waring, Jeffrey, Waterworth, Dawn, Yang, Robert, Nelis, Mari, Reigo, Anu, Metspalu, Andres, Milani, Lili, Esko, Tõnu, Fox, Caroline, Havulinna, Aki S, Perola, Markus, Ripatti, Samuli, Jalanko, Anu, Laitinen, Tarja, Mäkelä, Tomi P, Plenge, Robert, McCarthy, Mark, Runz, Heiko, Daly, Mark J, Palotie, Aarno, Palotie, Aarno [0000-0002-2527-5874], Apollo - University of Cambridge Repository, Reis, Kadri [0000-0002-2144-5856], Kettunen, Johannes [0000-0002-3345-491X], and Paul, Dirk S [0000-0002-8230-0116]

Subjects
Estonia, 631/208/205/2138, 692/308/2056, 45/43, article, Middle Aged, United Kingdom, White People, 631/208/457/649/2219, Phenotype, Gene Frequency, Meta-Analysis as Topic, 631/208/727/2000, Humans, Disease, Genetic Predisposition to Disease, Finland, Genome-Wide Association Study
Abstract

Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored1,2. FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10-11) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of

Published
2023

5. A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria

Author

Hidayat Trimarsanto, Roberto Amato, Richard D. Pearson, Edwin Sutanto, Rintis Noviyanti, Leily Trianty, Jutta Marfurt, Zuleima Pava, Diego F. Echeverry, Tatiana M. Lopera-Mesa, Lidia M. Montenegro, Alberto Tobón-Castaño, Matthew J. Grigg, Bridget Barber, Timothy William, Nicholas M. Anstey, Sisay Getachew, Beyene Petros, Abraham Aseffa, Ashenafi Assefa, Awab G. Rahim, Nguyen H. Chau, Tran T. Hien, Mohammad S. Alam, Wasif A. Khan, Benedikt Ley, Kamala Thriemer, Sonam Wangchuck, Yaghoob Hamedi, Ishag Adam, Yaobao Liu, Qi Gao, Kanlaya Sriprawat, Marcelo U. Ferreira, Moses Laman, Alyssa Barry, Ivo Mueller, Marcus V. G. Lacerda, Alejandro Llanos-Cuentas, Srivicha Krudsood, Chanthap Lon, Rezika Mohammed, Daniel Yilma, Dhelio B. Pereira, Fe E. J. Espino, Cindy S. Chu, Iván D. Vélez, Chayadol Namaik-larp, Maria F. Villegas, Justin A. Green, Gavin Koh, Julian C. Rayner, Eleanor Drury, Sónia Gonçalves, Victoria Simpson, Olivo Miotto, Alistair Miles, Nicholas J. White, Francois Nosten, Dominic P. Kwiatkowski, Ric N. Price, Sarah Auburn, Pearson, Richard D [0000-0002-7386-3566], Sutanto, Edwin [0000-0002-2997-4648], Marfurt, Jutta [0000-0002-3846-0825], Echeverry, Diego F [0000-0003-0301-4478], Tobón-Castaño, Alberto [0000-0002-1671-2649], Grigg, Matthew J [0000-0001-9914-8352], Alam, Mohammad S [0000-0001-8330-5499], Khan, Wasif A [0000-0002-7650-8068], Ley, Benedikt [0000-0002-5734-0845], Mueller, Ivo [0000-0001-6554-6889], Lacerda, Marcus VG [0000-0003-3374-9985], Pereira, Dhelio B [0000-0002-7761-5498], Espino, Fe EJ [0000-0003-1690-1711], Koh, Gavin [0000-0002-7336-1566], Rayner, Julian C [0000-0002-9835-1014], Drury, Eleanor [0000-0002-9887-6961], Miotto, Olivo [0000-0001-8060-6771], Nosten, Francois [0000-0002-7951-0745], Kwiatkowski, Dominic P [0000-0002-5023-0176], Price, Ric N [0000-0003-2000-2874], Auburn, Sarah [0000-0002-4638-536X], and Apollo - University of Cambridge Repository

Subjects
Likelihood Functions, Internet, Molecular medicine, 45, Epidemiology, 692/308/2056, article, Medicine (miscellaneous), 631/114/1305, General Biochemistry, Genetics and Molecular Biology, 692/4017, Malaria, Genetics research, Machine learning, Malaria, Vivax, 692/699/255/1629, Humans, PLASMODIUM, 692/308/174, Plasmodium vivax, General Agricultural and Biological Sciences
Abstract

Funder: HT was supported by a Charles Darwin University International PhD Scholarship (CDIPS), Funder: Malaysian Ministry of Health (BP00500420), Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.

Published
2022

6. Genetic variants associated with psychiatric disorders are enriched at epigenetically active sites in lymphoid cells

Author

Mary-Ellen Lynall, Blagoje Soskic, James Hayhurst, Jeremy Schwartzentruber, Daniel F. Levey, Gita A. Pathak, Renato Polimanti, Joel Gelernter, Murray B. Stein, Gosia Trynka, Menna R. Clatworthy, Ed Bullmore, Lynall, Mary-Ellen [0000-0002-1939-7525], Soskic, Blagoje [0000-0003-3173-4528], Levey, Daniel F [0000-0001-8431-9569], Polimanti, Renato [0000-0003-0745-6046], Gelernter, Joel [0000-0002-4067-1859], Stein, Murray B [0000-0001-9564-2871], Trynka, Gosia [0000-0002-6955-9529], and Apollo - University of Cambridge Repository

Subjects
141, Multidisciplinary, 45, Mental Disorders, 692/308/2056, 45/43, article, General Physics and Astronomy, General Chemistry, 45/15, Polymorphism, Single Nucleotide, 631/250/2152/1566/1618, General Biochemistry, Genetics and Molecular Biology, 38, 631/250/248, 631/378/371, Catalytic Domain, Schizophrenia, Humans, Genetic Predisposition to Disease, Lymphocytes, 692/699/476, Genome-Wide Association Study
Abstract

Multiple psychiatric disorders have been associated with abnormalities in both the innate and adaptive immune systems. The role of these abnormalities in pathogenesis, and whether they are driven by psychiatric risk variants, remains unclear. We test for enrichment of GWAS variants associated with multiple psychiatric disorders (cross-disorder or trans-diagnostic risk), or 5 specific disorders (cis-diagnostic risk), in regulatory elements in immune cells. We use three independent epigenetic datasets representing multiple organ systems and immune cell subsets. Trans-diagnostic and cis-diagnostic risk variants (for schizophrenia and depression) are enriched at epigenetically active sites in brain tissues and in lymphoid cells, especially stimulated CD4+ T cells. There is no evidence for enrichment of either trans-risk or cis-risk variants for schizophrenia or depression in myeloid cells. This suggests a possible model where environmental stimuli activate T cells to unmask the effects of psychiatric risk variants, contributing to the pathogenesis of mental health disorders.

Published
2022
Full Text
View/download PDF

7. Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention

Author

Wang, Zhe, Emmerich, Andrew, Pillon, Nicolas J., Moore, Tim, Hemerich, Daiane, Cornelis, Marilyn C., Mazzaferro, Eugenia, Broos, Siacia, Ahluwalia, Tarunveer S., Bartz, Traci M., Bentley, Amy R., Bielak, Lawrence F., Chong, Mike, Chu, Audrey Y., Berry, Diane, Dorajoo, Rajkumar, Dueker, Nicole D., Kasbohm, Elisa, Feenstra, Bjarke, Feitosa, Mary F., Gieger, Christian, Graff, Mariaelisa, Hall, Leanne M., Haller, Toomas, Hartwig, Fernando P., Hillis, David A., Huikari, Ville, Heard-Costa, Nancy, Holzapfel, Christina, Jackson, Anne U., Johansson, Åsa, Jørgensen, Anja Moltke, Kaakinen, Marika A., Karlsson, Robert, Kerr, Kathleen F., Kim, Boram, Koolhaas, Chantal M., Kutalik, Zoltan, Lagou, Vasiliki, Lind, Penelope A., Lorentzon, Mattias, Lyytikäinen, Leo-Pekka, Mangino, Massimo, Metzendorf, Christoph, Monroe, Kristine R., Pacolet, Alexander, Pérusse, Louis, Pool, Rene, Richmond, Rebecca C., Rivera, Natalia V., Robiou-du-Pont, Sebastien, Schraut, Katharina E., Schulz, Christina-Alexandra, Stringham, Heather M., Tanaka, Toshiko, Teumer, Alexander, Turman, Constance, van der Most, Peter J., Vanmunster, Mathias, van Rooij, Frank J. A., van Vliet-Ostaptchouk, Jana V., Zhang, Xiaoshuai, Zhao, Jing-Hua, Zhao, Wei, Balkhiyarova, Zhanna, Balslev-Harder, Marie N., Baumeister, Sebastian E., Beilby, John, Blangero, John, Boomsma, Dorret I., Brage, Søren Karl, Braund, Peter S., Brody, Jennifer A., Bruinenberg, Marcel, Ekelund, Ulf, Liu, Ching-Ti, Cole, John W., Collins, Francis S., Cupples, L. Adrienne, Esko, Tõnu, Enroth, Stefan, Faul, Jessica D., Fernandez-Rhodes, Lindsay, Fohner, Alison E., Franco, Oscar H., Galesloot, Tessel E., Gordon, Scott D., Grarup, Niels, Hartman, Catharina A., Heiss, Gerardo, Hui, Jennie, Illig, Thomas, Jago, Russell, James, Alan, Joshi, Peter K., Jung, Taeyeong, Kähönen, Mika, Kilpeläinen, Tuomas O., Koh, Woon-Puay, Kolcic, Ivana, Kraft, Peter P., Kuusisto, Johanna, Launer, Lenore J., Li, Aihua, Linneberg, Allan, Luan, Jian’an, Vidal, Pedro Marques, Medland, Sarah E., Milaneschi, Yuri, Moscati, Arden, Musk, Bill, Nelson, Christopher P., Nolte, Ilja M., Pedersen, Nancy L., Peters, Annette, Peyser, Patricia A., Power, Christine, Raitakari, Olli T., Reedik, Mägi, Reiner, Alex P., Ridker, Paul M., Rudan, Igor, Ryan, Kathy, Sarzynski, Mark A., Scott, Laura J., Scott, Robert A., Sidney, Stephen, Siggeirsdottir, Kristin, Smith, Albert V., Smith, Jennifer A., Sonestedt, Emily, Strøm, Marin, Tai, E. Shyong, Teo, Koon K., Thorand, Barbara, Tönjes, Anke, Tremblay, Angelo, Uitterlinden, Andre G., Vangipurapu, Jagadish, van Schoor, Natasja, Völker, Uwe, Willemsen, Gonneke, Williams, Kayleen, Wong, Quenna, Xu, Huichun, Young, Kristin L., Yuan, Jian Min, Zillikens, M. Carola, Zonderman, Alan B., Ameur, Adam, Bandinelli, Stefania, Bis, Joshua C., Boehnke, Michael, Bouchard, Claude, Chasman, Daniel I., Smith, George Davey, de Geus, Eco J. C., Deldicque, Louise, Dörr, Marcus, Evans, Michele K., Ferrucci, Luigi, Fornage, Myriam, Fox, Caroline, Garland, Theodore, Gudnason, Vilmundur, Gyllensten, Ulf, Hansen, Torben, Hayward, Caroline, Horta, Bernardo L., Hyppönen, Elina, Jarvelin, Marjo-Riitta, Johnson, W. Craig, Kardia, Sharon L. R., Kiemeney, Lambertus A., Laakso, Markku, Langenberg, Claudia, Lehtimäki, Terho, Marchand, Loic Le, Alizadeh, Behrooz Z., Boezen, H. Marike, Franke, Lude, Swertz, Morris, Wijmenga, Tjitske Nienke, van der Harst, Pim, Navis, Gerjan, Rots, Marianne, Wolffenbuttel, Bruce H. R., Magnusson, Patrik K. E., Martin, Nicholas G., Melbye, Mads, Metspalu, Andres, Meyre, David, North, Kari E., Ohlsson, Claes, Oldehinkel, Albertine J., Orho-Melander, Marju, Pare, Guillaume, Park, Taesung, Pedersen, Oluf, Penninx, Brenda W. J. H., Pers, Tune H., Polasek, Ozren, Prokopenko, Inga, Rotimi, Charles N., Samani, Nilesh J., Sim, Xueling, Snieder, Harold, Sørensen, Thorkild I. A., Spector, Tim D., Timpson, Nicholas J., van Dam, Rob M., van der Velde, Nathalie, van Duijn, Cornelia M., Vollenweider, Peter, Völzke, Henry, Voortman, Trudy, Waeber, Gérard, Wareham, Nicholas J., Weir, David R., Wichmann, Heinz-Erich, Wilson, James F., Hevener, Andrea L., Krook, Anna, Zierath, Juleen R., Thomis, Martine A. I., Loos, Ruth J. F., Hoed, Marcel den, Epidemiology, Internal Medicine, Tampere University, Department of Clinical Chemistry, Clinical Medicine, Department of Clinical Physiology and Nuclear Medicine, Wang, Zhe, Emmerich, Andrew, Pillon, Nicolas J, Moore, Tim, Hyppönen, Elina, den Hoed, Marcel, Lifelines Cohort Study, Alizadeh, B.Z., Boezen, H.M., Franke, L., Swertz, M., Wijmenga, C., van der Harst, P., Navis, G., Rots, M., Wolffenbuttel, BHR, Wang, Zhe [0000-0002-8046-4969], Emmerich, Andrew [0000-0002-0908-9924], Pillon, Nicolas J [0000-0003-1107-9490], Moore, Tim [0000-0003-4250-3370], Ameur, Adam [0000-0001-6085-6749], Bis, Joshua C [0000-0002-3409-1110], Boehnke, Michael [0000-0002-6442-7754], Bouchard, Claude [0000-0002-0048-491X], Chasman, Daniel I [0000-0003-3357-0862], Smith, George Davey [0000-0002-1407-8314], de Geus, Eco JC [0000-0001-6022-2666], Dörr, Marcus [0000-0001-7471-475X], Ferrucci, Luigi [0000-0002-6273-1613], Fornage, Myriam [0000-0003-0677-8158], Garland, Theodore [0000-0002-7916-3552], Gyllensten, Ulf [0000-0002-6316-3355], Hansen, Torben [0000-0001-8748-3831], Horta, Bernardo L [0000-0001-9843-412X], Hyppönen, Elina [0000-0003-3670-9399], Johnson, W Craig [0000-0002-3161-3753], Kiemeney, Lambertus A [0000-0002-2368-1326], Laakso, Markku [0000-0002-3394-7749], Langenberg, Claudia [0000-0002-5017-7344], Lehtimäki, Terho [0000-0002-2555-4427], Magnusson, Patrik KE [0000-0002-7315-7899], Martin, Nicholas G [0000-0003-4069-8020], Melbye, Mads [0000-0001-8264-6785], Metspalu, Andres [0000-0002-3718-796X], Meyre, David [0000-0003-4850-7444], North, Kari E [0000-0002-8903-0366], Ohlsson, Claes [0000-0002-9633-2805], Oldehinkel, Albertine J [0000-0003-3925-3913], Orho-Melander, Marju [0000-0002-3578-2503], Pare, Guillaume [0000-0002-6795-4760], Park, Taesung [0000-0002-8294-590X], Pedersen, Oluf [0000-0002-3321-3972], Pers, Tune H [0000-0003-0207-4831], Polasek, Ozren [0000-0002-5765-1862], Prokopenko, Inga [0000-0003-1624-7457], Rotimi, Charles N [0000-0001-5759-053X], Sim, Xueling [0000-0002-1233-7642], Snieder, Harold [0000-0003-1949-2298], Sørensen, Thorkild IA [0000-0003-4821-430X], Spector, Tim D [0000-0002-9795-0365], Timpson, Nicholas J [0000-0002-7141-9189], Voortman, Trudy [0000-0003-2830-6813], Waeber, Gérard [0000-0003-4193-788X], Wareham, Nicholas J [0000-0003-1422-2993], Weir, David R [0000-0002-1661-2402], Wilson, James F [0000-0001-5751-9178], Krook, Anna [0000-0002-0891-0258], Zierath, Juleen R [0000-0001-6891-7497], Thomis, Martine AI [0000-0001-9093-2191], Loos, Ruth JF [0000-0002-8532-5087], Hoed, Marcel den [0000-0001-8081-428X], Apollo - University of Cambridge Repository, Center for Liver, Digestive and Metabolic Diseases (CLDM), Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Life Course Epidemiology (LCE), Geriatrics, AMS - Ageing & Vitality, APH - Aging & Later Life, Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, APH - Mental Health, APH - Methodology, and AMS - Sports

Subjects
Vascular damage Radboud Institute for Health Sciences [Radboudumc 16], 631/208/205/2138, 610 Medicine & health, heritability, Actinin/genetics, Cross-Sectional Studies, Exercise/physiology, Genome-Wide Association Study, Humans, Leisure Activities, Sedentary Behavior, apolipoprotein-e genotype, Lifelines Cohort Study, 360 Social problems & social services, 692/308/575, Genetics, Actinin, Exercise, Medicinsk genetik, exercise, APOLIPOPROTEIN-E GENOTYPE, LD SCORE REGRESSION, GENE-EXPRESSION, EXERCISE, COMPLEX, PERFORMANCE, GWAS, HERITABILITY, MORTALITY, FITNESS, 360 Soziale Probleme, Sozialdienste, 692/308/2056, article, gwas, gene-expression, mortality, 3142 Public health care science, environmental and occupational health, fitness, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], LD score regression, 3111 Biomedicine, 610 Medizin und Gesundheit, Medical Genetics, complex, performance
Abstract

Funder: Kjell och Märta Beijers Stiftelse (Kjell and Marta Beijer Foundation); doi: https://doi.org/10.13039/501100006353, Although physical activity and sedentary behavior are moderately heritable, little is known about the mechanisms that influence these traits. Combining data for up to 703,901 individuals from 51 studies in a multi-ancestry meta-analysis of genome-wide association studies yields 99 loci that associate with self-reported moderate-to-vigorous intensity physical activity during leisure time (MVPA), leisure screen time (LST) and/or sedentary behavior at work. Loci associated with LST are enriched for genes whose expression in skeletal muscle is altered by resistance training. A missense variant in ACTN3 makes the alpha-actinin-3 filaments more flexible, resulting in lower maximal force in isolated type IIA muscle fibers, and possibly protection from exercise-induced muscle damage. Finally, Mendelian randomization analyses show that beneficial effects of lower LST and higher MVPA on several risk factors and diseases are mediated or confounded by body mass index (BMI). Our results provide insights into physical activity mechanisms and its role in disease prevention.

Published
2022
Full Text
View/download PDF

8. Diverse mutational landscapes in human lymphocytes

Author

Machado, Heather E, Mitchell, Emily, Øbro, Nina F, Kübler, Kirsten, Davies, Megan, Leongamornlert, Daniel, Cull, Alyssa, Maura, Francesco, Sanders, Mathijs A, Cagan, Alex TJ, McDonald, Craig, Belmonte, Miriam, Shepherd, Mairi S, Vieira Braga, Felipe A, Osborne, Robert J, Mahbubani, Krishnaa, Martincorena, Iñigo, Laurenti, Elisa, Green, Tony, Getz, Gad, Polak, Paz, Saeb-Parsy, Kourosh, Hodson, Daniel, Kent, David G, Campbell, Peter J, Hematology, Leongamornlert, Daniel [0000-0002-3486-3168], Cagan, Alex TJ [0000-0002-7857-4771], Mahbubani, Krishnaa [0000-0002-1327-2334], Martincorena, Iñigo [0000-0003-1122-4416], Laurenti, Elisa [0000-0002-9917-9092], Green, Tony [0000-0002-9795-0218], Getz, Gad [0000-0002-0936-0753], Saeb-Parsy, Kourosh [0000-0002-0633-3696], Hodson, Daniel [0000-0001-6225-2033], Kent, David G [0000-0001-7871-8811], Campbell, Peter J [0000-0002-3921-0510], Apollo - University of Cambridge Repository, Hodson, Daniel J [0000-0001-6225-2033], Center of Experimental and Molecular Medicine, and AGEM - Amsterdam Gastroenterology Endocrinology Metabolism

Subjects
B-Lymphocytes, Multidisciplinary, 45, Cambridge Stem Cell Institute, 631/208/212/2306, 692/308/2056, article, 45/23, Cell Differentiation, 631/208/212/2304, 13, Germinal Center, SDG 3 - Good Health and Well-being, Cellular Microenvironment, Neoplasms, Mutation, 631/250/232/2058, Humans, Lymphocytes, Immunologic Memory, Cell Proliferation, DNA Damage
Abstract

Funder: Wellcome Trust, The lymphocyte genome is prone to many threats, including programmed mutation during differentiation1, antigen-driven proliferation and residency in diverse microenvironments. Here, after developing protocols for expansion of single-cell lymphocyte cultures, we sequenced whole genomes from 717 normal naive and memory B and T cells and haematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells, with higher burdens in memory cells than in naive cells, and with T cells accumulating mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for approximately half of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every on-target IGHV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than in stem cells, with around 15% of deletions being attributable to off-target recombinase-activating gene activity. DNA damage from ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory cells. The mutation burden and signatures of normal B cells were broadly similar to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes that are active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.

Published
2022
Full Text
View/download PDF

9. Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis

Author

Siddhartha P. Kar, Pedro M. Quiros, Muxin Gu, Tao Jiang, Jonathan Mitchell, Ryan Langdon, Vivek Iyer, Clea Barcena, M. S. Vijayabaskar, Margarete A. Fabre, Paul Carter, Slavé Petrovski, Stephen Burgess, George S. Vassiliou, Kar, Siddhartha P [0000-0002-2314-1426], Quiros, Pedro M [0000-0002-7793-6291], Burgess, Stephen [0000-0001-5365-8760], Vassiliou, George S [0000-0003-4337-8022], Apollo - University of Cambridge Repository, Gu, Muxin [0000-0003-4376-795X], and Vassiliou, George [0000-0003-4337-8022]

Subjects
692/308/2056, 631/208/205/2138, article, 692/699/1541, Hematopoiesis, Cell Transformation, Neoplastic, Risk Factors, Mutation, Genetics, Humans, Genetic Predisposition to Disease, ICEP, Clonal Hematopoiesis, Genome-Wide Association Study
Abstract

Funder: British Heart Foundation, Clonal hematopoiesis (CH), the clonal expansion of a blood stem cell and its progeny driven by somatic driver mutations, affects over a third of people, yet remains poorly understood. Here we analyze genetic data from 200,453 UK Biobank participants to map the landscape of inherited predisposition to CH, increasing the number of germline associations with CH in European-ancestry populations from 4 to 14. Genes at new loci implicate DNA damage repair (PARP1, ATM, CHEK2), hematopoietic stem cell migration/homing (CD164) and myeloid oncogenesis (SETBP1). Several associations were CH-subtype-specific including variants at TCL1A and CD164 that had opposite associations with DNMT3A- versus TET2-mutant CH, the two most common CH subtypes, proposing key roles for these two loci in CH development. Mendelian randomization analyses showed that smoking and longer leukocyte telomere length are causal risk factors for CH and that genetic predisposition to CH increases risks of myeloproliferative neoplasia, nonhematological malignancies, atrial fibrillation and blood epigenetic ageing.

Published
2022
Full Text
View/download PDF

10. Gut mucosa dissociation protocols influence cell type proportions and single-cell gene expression levels

Author

Werna T. C. Uniken Venema, Aarón D. Ramírez-Sánchez, Emilia Bigaeva, Sebo Withoff, Iris Jonkers, Rebecca E. McIntyre, Mennatallah Ghouraba, Tim Raine, Rinse K. Weersma, Lude Franke, Eleonora A. M. Festen, Monique G. P. van der Wijst, Uniken Venema, Werna TC [0000-0002-1515-0920], Jonkers, Iris [0000-0003-2304-7939], Ghouraba, Mennatallah [0000-0003-4671-3500], van der Wijst, Monique GP [0000-0003-1520-3970], Apollo - University of Cambridge Repository, Molecular Neuroscience and Ageing Research (MOLAR), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), and Stem Cell Aging Leukemia and Lymphoma (SALL)

Subjects
Multidisciplinary, Sequence Analysis, RNA, Gene Expression Profiling, Single-Cell Analysis/methods, 692/308/2056, article, Gene Expression, 631/337/2019, Sequence Analysis, RNA/methods, Flow Cytometry, Flow Cytometry/methods, Collagenases, Single-Cell Analysis, Gene Expression Profiling/methods, Intestinal Mucosa, RNA/methods, Sequence Analysis, Peptide Hydrolases
Abstract

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of the cellular landscape of organs. Most single-cell protocols require fresh material, which limits sample size per experiment, and consequently, introduces batch effects. This is especially true for samples acquired through complex medical procedures, such as intestinal mucosal biopsies. Moreover, the tissue dissociation procedure required for obtaining single cells is a major source of noise; different dissociation procedures applied to different compartments of the tissue induce artificial gene expression differences between cell subsets. To overcome these challenges, we have developed a one-step dissociation protocol and demonstrated its use on cryopreserved gut mucosal biopsies. Using flow cytometry and scRNA-seq analysis, we compared this one-step dissociation protocol with the current gold standard, two-step collagenase digestion, and an adaptation of a recently published alternative, three-step cold-active Bacillus licheniformus protease digestion. Both cell viability and cell type composition were comparable between the one-step and two-step collagenase dissociation, with the former being more time-efficient. The cold protease digestion resulted in equal cell viability, but better preserves the epithelial cell types. Consequently, to analyze the rarer cell types, such as glial cells, larger total biopsy cell numbers are required as input material. The multi-step protocols affected cell types spanning multiple compartments differently. In summary, we show that cryopreserved gut mucosal biopsies can be used to overcome the logistical challenges and batch effects in large scRNA-seq studies. Furthermore, we demonstrate that using cryopreserved biopsies digested using a one-step collagenase protocol enables large-scale scRNA-seq, FACS, organoid generation and intraepithelial lymphocyte expansion.

Published
2022

Catalog

Books, media, physical & digital resources
See catalog results