Literature DB >> 31913361

Mechanisms of tissue and cell-type specificity in heritable traits and diseases.

Idan Hekselman1, Esti Yeger-Lotem2,3.   

Abstract

Hundreds of heritable traits and diseases that are caused by germline aberrations in ubiquitously expressed genes manifest in a remarkably limited number of cell types and tissues across the body. Unravelling mechanisms that govern their tissue-specific manifestations is critical for our understanding of disease aetiologies and may direct efforts to develop treatments. Owing to recent advances in high-throughput technologies and open resources, data and tools are now available to approach this enigmatic phenomenon at large scales, both computationally and experimentally. Here, we discuss the large prevalence of tissue-selective traits and diseases, describe common molecular mechanisms underlying their tissue-selective manifestation and present computational strategies and publicly available resources for elucidating the molecular basis of their genotype-phenotype relationships.

Entities:  

Mesh:

Year:  2020        PMID: 31913361     DOI: 10.1038/s41576-019-0200-9

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  151 in total

Review 1.  Exome sequencing as a tool for Mendelian disease gene discovery.

Authors:  Michael J Bamshad; Sarah B Ng; Abigail W Bigham; Holly K Tabor; Mary J Emond; Deborah A Nickerson; Jay Shendure
Journal:  Nat Rev Genet       Date:  2011-09-27       Impact factor: 53.242

Review 2.  Genetic determinants of myocardial dysfunction.

Authors:  Xianchi Li; Peiying Zhang
Journal:  J Med Genet       Date:  2016-11-21       Impact factor: 6.318

Review 3.  Genetics in Parkinson disease: Mendelian versus non-Mendelian inheritance.

Authors:  Dena G Hernandez; Xylena Reed; Andrew B Singleton
Journal:  J Neurochem       Date:  2016-04-18       Impact factor: 5.372

4.  A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes.

Authors:  Kasper Lage; Niclas Tue Hansen; E Olof Karlberg; Aron C Eklund; Francisco S Roque; Patricia K Donahoe; Zoltan Szallasi; Thomas Skøt Jensen; Søren Brunak
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-22       Impact factor: 11.205

Review 5.  Genetic modifiers of Mendelian disease: Huntington's disease and the trinucleotide repeat disorders.

Authors:  Peter A Holmans; Thomas H Massey; Lesley Jones
Journal:  Hum Mol Genet       Date:  2017-10-01       Impact factor: 6.150

6.  Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases.

Authors:  Ruth Barshir; Omer Shwartz; Ilan Y Smoly; Esti Yeger-Lotem
Journal:  PLoS Comput Biol       Date:  2014-06-12       Impact factor: 4.475

Review 7.  The Synucleinopathies: Twenty Years On.

Authors:  Michel Goedert; Ross Jakes; Maria Grazia Spillantini
Journal:  J Parkinsons Dis       Date:  2017       Impact factor: 5.568

8.  A revised airway epithelial hierarchy includes CFTR-expressing ionocytes.

Authors:  Daniel T Montoro; Adam L Haber; Moshe Biton; Vladimir Vinarsky; Brian Lin; Susan E Birket; Feng Yuan; Sijia Chen; Hui Min Leung; Jorge Villoria; Noga Rogel; Grace Burgin; Alexander M Tsankov; Avinash Waghray; Michal Slyper; Julia Waldman; Lan Nguyen; Danielle Dionne; Orit Rozenblatt-Rosen; Purushothama Rao Tata; Hongmei Mou; Manjunatha Shivaraju; Hermann Bihler; Martin Mense; Guillermo J Tearney; Steven M Rowe; John F Engelhardt; Aviv Regev; Jayaraj Rajagopal
Journal:  Nature       Date:  2018-08-01       Impact factor: 49.962

9.  Moving beyond neurons: the role of cell type-specific gene regulation in Parkinson's disease heritability.

Authors:  Sarah A Gagliano Taliun; Mina Ryten; Regina H Reynolds; Juan Botía; Mike A Nalls; John Hardy
Journal:  NPJ Parkinsons Dis       Date:  2019-04-17

10.  Role of duplicate genes in determining the tissue-selectivity of hereditary diseases.

Authors:  Ruth Barshir; Idan Hekselman; Netta Shemesh; Moran Sharon; Lena Novack; Esti Yeger-Lotem
Journal:  PLoS Genet       Date:  2018-05-03       Impact factor: 5.917

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  26 in total

1.  A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids.

Authors:  Shweta Ramdas; Jonathan Judd; Sarah E Graham; Stavroula Kanoni; Yuxuan Wang; Ida Surakka; Brandon Wenz; Shoa L Clarke; Alessandra Chesi; Andrew Wells; Konain Fatima Bhatti; Sailaja Vedantam; Thomas W Winkler; Adam E Locke; Eirini Marouli; Greg J M Zajac; Kuan-Han H Wu; Ioanna Ntalla; Qin Hui; Derek Klarin; Austin T Hilliard; Zeyuan Wang; Chao Xue; Gudmar Thorleifsson; Anna Helgadottir; Daniel F Gudbjartsson; Hilma Holm; Isleifur Olafsson; Mi Yeong Hwang; Sohee Han; Masato Akiyama; Saori Sakaue; Chikashi Terao; Masahiro Kanai; Wei Zhou; Ben M Brumpton; Humaira Rasheed; Aki S Havulinna; Yogasudha Veturi; Jennifer Allen Pacheco; Elisabeth A Rosenthal; Todd Lingren; QiPing Feng; Iftikhar J Kullo; Akira Narita; Jun Takayama; Hilary C Martin; Karen A Hunt; Bhavi Trivedi; Jeffrey Haessler; Franco Giulianini; Yuki Bradford; Jason E Miller; Archie Campbell; Kuang Lin; Iona Y Millwood; Asif Rasheed; George Hindy; Jessica D Faul; Wei Zhao; David R Weir; Constance Turman; Hongyan Huang; Mariaelisa Graff; Ananyo Choudhury; Dhriti Sengupta; Anubha Mahajan; Michael R Brown; Weihua Zhang; Ketian Yu; Ellen M Schmidt; Anita Pandit; Stefan Gustafsson; Xianyong Yin; Jian'an Luan; Jing-Hua Zhao; Fumihiko Matsuda; Hye-Mi Jang; Kyungheon Yoon; Carolina Medina-Gomez; Achilleas Pitsillides; Jouke Jan Hottenga; Andrew R Wood; Yingji Ji; Zishan Gao; Simon Haworth; Ruth E Mitchell; Jin Fang Chai; Mette Aadahl; Anne A Bjerregaard; Jie Yao; Ani Manichaikul; Wen-Jane Lee; Chao Agnes Hsiung; Helen R Warren; Julia Ramirez; Jette Bork-Jensen; Line L Kårhus; Anuj Goel; Maria Sabater-Lleal; Raymond Noordam; Pala Mauro; Floris Matteo; Aaron F McDaid; Pedro Marques-Vidal; Matthias Wielscher; Stella Trompet; Naveed Sattar; Line T Møllehave; Matthias Munz; Lingyao Zeng; Jianfeng Huang; Bin Yang; Alaitz Poveda; Azra Kurbasic; Sebastian Schönherr; Lukas Forer; Markus Scholz; Tessel E Galesloot; Jonathan P Bradfield; Sanni E Ruotsalainen; E Warwick Daw; Joseph M Zmuda; Jonathan S Mitchell; Christian Fuchsberger; Henry Christensen; Jennifer A Brody; Phuong Le; Mary F Feitosa; Mary K Wojczynski; Daiane Hemerich; Michael Preuss; Massimo Mangino; Paraskevi Christofidou; Niek Verweij; Jan W Benjamins; Jorgen Engmann; Tsao L Noah; Anurag Verma; Roderick C Slieker; Ken Sin Lo; Nuno R Zilhao; Marcus E Kleber; Graciela E Delgado; Shaofeng Huo; Daisuke D Ikeda; Hiroyuki Iha; Jian Yang; Jun Liu; Ayşe Demirkan; Hampton L Leonard; Jonathan Marten; Carina Emmel; Börge Schmidt; Laura J Smyth; Marisa Cañadas-Garre; Chaolong Wang; Masahiro Nakatochi; Andrew Wong; Nina Hutri-Kähönen; Xueling Sim; Rui Xia; Alicia Huerta-Chagoya; Juan Carlos Fernandez-Lopez; Valeriya Lyssenko; Suraj S Nongmaithem; Alagu Sankareswaran; Marguerite R Irvin; Christopher Oldmeadow; Han-Na Kim; Seungho Ryu; Paul R H J Timmers; Liubov Arbeeva; Rajkumar Dorajoo; Leslie A Lange; Gauri Prasad; Laura Lorés-Motta; Marc Pauper; Jirong Long; Xiaohui Li; Elizabeth Theusch; Fumihiko Takeuchi; Cassandra N Spracklen; Anu Loukola; Sailalitha Bollepalli; Sophie C Warner; Ya Xing Wang; Wen B Wei; Teresa Nutile; Daniela Ruggiero; Yun Ju Sung; Shufeng Chen; Fangchao Liu; Jingyun Yang; Katherine A Kentistou; Bernhard Banas; Anna Morgan; Karina Meidtner; Lawrence F Bielak; Jennifer A Smith; Prashantha Hebbar; Aliki-Eleni Farmaki; Edith Hofer; Maoxuan Lin; Maria Pina Concas; Simona Vaccargiu; Peter J van der Most; Niina Pitkänen; Brian E Cade; Sander W van der Laan; Kumaraswamy Naidu Chitrala; Stefan Weiss; Amy R Bentley; Ayo P Doumatey; Adebowale A Adeyemo; Jong Young Lee; Eva R B Petersen; Aneta A Nielsen; Hyeok Sun Choi; Maria Nethander; Sandra Freitag-Wolf; Lorraine Southam; Nigel W Rayner; Carol A Wang; Shih-Yi Lin; Jun-Sing Wang; Christian Couture; Leo-Pekka Lyytikäinen; Kjell Nikus; Gabriel Cuellar-Partida; Henrik Vestergaard; Bertha Hidalgo; Olga Giannakopoulou; Qiuyin Cai; Morgan O Obura; Jessica van Setten; Karen Y He; Hua Tang; Natalie Terzikhan; Jae Hun Shin; Rebecca D Jackson; Alexander P Reiner; Lisa Warsinger Martin; Zhengming Chen; Liming Li; Takahisa Kawaguchi; Joachim Thiery; Joshua C Bis; Lenore J Launer; Huaixing Li; Mike A Nalls; Olli T Raitakari; Sahoko Ichihara; Sarah H Wild; Christopher P Nelson; Harry Campbell; Susanne Jäger; Toru Nabika; Fahd Al-Mulla; Harri Niinikoski; Peter S Braund; Ivana Kolcic; Peter Kovacs; Tota Giardoglou; Tomohiro Katsuya; Dominique de Kleijn; Gert J de Borst; Eung Kweon Kim; Hieab H H Adams; M Arfan Ikram; Xiaofeng Zhu; Folkert W Asselbergs; Adriaan O Kraaijeveld; Joline W J Beulens; Xiao-Ou Shu; Loukianos S Rallidis; Oluf Pedersen; Torben Hansen; Paul Mitchell; Alex W Hewitt; Mika Kähönen; Louis Pérusse; Claude Bouchard; Anke Tönjes; Yii-Der Ida Chen; Craig E Pennell; Trevor A Mori; Wolfgang Lieb; Andre Franke; Claes Ohlsson; Dan Mellström; Yoon Shin Cho; Hyejin Lee; Jian-Min Yuan; Woon-Puay Koh; Sang Youl Rhee; Jeong-Taek Woo; Iris M Heid; Klaus J Stark; Martina E Zimmermann; Henry Völzke; Georg Homuth; Michele K Evans; Alan B Zonderman; Ozren Polasek; Gerard Pasterkamp; Imo E Hoefer; Susan Redline; Katja Pahkala; Albertine J Oldehinkel; Harold Snieder; Ginevra Biino; Reinhold Schmidt; Helena Schmidt; Stefania Bandinelli; George Dedoussis; Thangavel Alphonse Thanaraj; Patricia A Peyser; Norihiro Kato; Matthias B Schulze; Giorgia Girotto; Carsten A Böger; Bettina Jung; Peter K Joshi; David A Bennett; Philip L De Jager; Xiangfeng Lu; Vasiliki Mamakou; Morris Brown; Mark J Caulfield; Patricia B Munroe; Xiuqing Guo; Marina Ciullo; Jost B Jonas; Nilesh J Samani; Jaakko Kaprio; Päivi Pajukanta; Teresa Tusié-Luna; Carlos A Aguilar-Salinas; Linda S Adair; Sonny Augustin Bechayda; H Janaka de Silva; Ananda R Wickremasinghe; Ronald M Krauss; Jer-Yuarn Wu; Wei Zheng; Anneke I den Hollander; Dwaipayan Bharadwaj; Adolfo Correa; James G Wilson; Lars Lind; Chew-Kiat Heng; Amanda E Nelson; Yvonne M Golightly; James F Wilson; Brenda Penninx; Hyung-Lae Kim; John Attia; Rodney J Scott; D C Rao; Donna K Arnett; Mark Walker; Laura J Scott; Heikki A Koistinen; Giriraj R Chandak; Josep M Mercader; Clicerio Gonzalez Villalpando; Lorena Orozco; Myriam Fornage; E Shyong Tai; Rob M van Dam; Terho Lehtimäki; Nish Chaturvedi; Mitsuhiro Yokota; Jianjun Liu; Dermot F Reilly; Amy Jayne McKnight; Frank Kee; Karl-Heinz Jöckel; Mark I McCarthy; Colin N A Palmer; Veronique Vitart; Caroline Hayward; Eleanor Simonsick; Cornelia M van Duijn; Zi-Bing Jin; Fan Lu; Haretsugu Hishigaki; Xu Lin; Winfried März; Vilmundur Gudnason; Jean-Claude Tardif; Guillaume Lettre; Leen M T Hart; Petra J M Elders; Daniel J Rader; Scott M Damrauer; Meena Kumari; Mika Kivimaki; Pim van der Harst; Tim D Spector; Ruth J F Loos; Michael A Province; Esteban J Parra; Miguel Cruz; Bruce M Psaty; Ivan Brandslund; Peter P Pramstaller; Charles N Rotimi; Kaare Christensen; Samuli Ripatti; Elisabeth Widén; Hakon Hakonarson; Struan F A Grant; Lambertus Kiemeney; Jacqueline de Graaf; Markus Loeffler; Florian Kronenberg; Dongfeng Gu; Jeanette Erdmann; Heribert Schunkert; Paul W Franks; Allan Linneberg; J Wouter Jukema; Amit V Khera; Minna Männikkö; Marjo-Riitta Jarvelin; Zoltan Kutalik; Cucca Francesco; Dennis O Mook-Kanamori; Ko Willems van Dijk; Hugh Watkins; David P Strachan; Niels Grarup; Peter Sever; Neil Poulter; Wayne Huey-Herng Sheu; Jerome I Rotter; Thomas M Dantoft; Fredrik Karpe; Matt J Neville; Nicholas J Timpson; Ching-Yu Cheng; Tien-Yin Wong; Chiea Chuen Khor; Hengtong Li; Charumathi Sabanayagam; Annette Peters; Christian Gieger; Andrew T Hattersley; Nancy L Pedersen; Patrik K E Magnusson; Dorret I Boomsma; Eco J C de Geus; L Adrienne Cupples; Joyce B J van Meurs; Arfan Ikram; Mohsen Ghanbari; Penny Gordon-Larsen; Wei Huang; Young Jin Kim; Yasuharu Tabara; Nicholas J Wareham; Claudia Langenberg; Eleftheria Zeggini; Jaakko Tuomilehto; Johanna Kuusisto; Markku Laakso; Erik Ingelsson; Goncalo Abecasis; John C Chambers; Jaspal S Kooner; Paul S de Vries; Alanna C Morrison; Scott Hazelhurst; Michèle Ramsay; Kari E North; Martha Daviglus; Peter Kraft; Nicholas G Martin; John B Whitfield; Shahid Abbas; Danish Saleheen; Robin G Walters; Michael V Holmes; Corri Black; Blair H Smith; Aris Baras; Anne E Justice; Julie E Buring; Paul M Ridker; Daniel I Chasman; Charles Kooperberg; Gen Tamiya; Masayuki Yamamoto; David A van Heel; Richard C Trembath; Wei-Qi Wei; Gail P Jarvik; Bahram Namjou; M Geoffrey Hayes; Marylyn D Ritchie; Pekka Jousilahti; Veikko Salomaa; Kristian Hveem; Bjørn Olav Åsvold; Michiaki Kubo; Yoichiro Kamatani; Yukinori Okada; Yoshinori Murakami; Bong-Jo Kim; Unnur Thorsteinsdottir; Kari Stefansson; Jifeng Zhang; Y Eugene Chen; Yuk-Lam Ho; Julie A Lynch; Philip S Tsao; Kyong-Mi Chang; Kelly Cho; Christopher J O'Donnell; John M Gaziano; Peter Wilson; Karen L Mohlke; Timothy M Frayling; Joel N Hirschhorn; Sekar Kathiresan; Michael Boehnke; Pradeep Natarajan; Yan V Sun; Andrew P Morris; Panos Deloukas; Gina Peloso; Themistocles L Assimes; Cristen J Willer; Xiang Zhu; Christopher D Brown
Journal:  Am J Hum Genet       Date:  2022-08-04       Impact factor: 11.043

2.  Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics.

Authors:  Karthik A Jagadeesh; Kushal K Dey; Daniel T Montoro; Rahul Mohan; Steven Gazal; Jesse M Engreitz; Ramnik J Xavier; Alkes L Price; Aviv Regev
Journal:  Nat Genet       Date:  2022-09-29       Impact factor: 41.307

3.  Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease.

Authors:  Hongbo Liu; Tomohito Doke; Dong Guo; Xin Sheng; Ziyuan Ma; Joseph Park; Ha My T Vy; Girish N Nadkarni; Amin Abedini; Zhen Miao; Matthew Palmer; Benjamin F Voight; Hongzhe Li; Christopher D Brown; Marylyn D Ritchie; Yan Shu; Katalin Susztak
Journal:  Nat Genet       Date:  2022-06-16       Impact factor: 41.307

4.  Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data.

Authors:  Martin Jinye Zhang; Kangcheng Hou; Kushal K Dey; Saori Sakaue; Karthik A Jagadeesh; Kathryn Weinand; Aris Taychameekiatchai; Poorvi Rao; Angela Oliveira Pisco; James Zou; Bruce Wang; Michael Gandal; Soumya Raychaudhuri; Bogdan Pasaniuc; Alkes L Price
Journal:  Nat Genet       Date:  2022-09-01       Impact factor: 41.307

5.  PCGA: a comprehensive web server for phenotype-cell-gene association analysis.

Authors:  Chao Xue; Lin Jiang; Miao Zhou; Qihan Long; Ying Chen; Xiangyi Li; Wenjie Peng; Qi Yang; Miaoxin Li
Journal:  Nucleic Acids Res       Date:  2022-05-26       Impact factor: 19.160

6.  Genetic mapping of etiologic brain cell types for obesity.

Authors:  Pascal N Timshel; Jonatan J Thompson; Tune H Pers
Journal:  Elife       Date:  2020-09-21       Impact factor: 8.140

7.  Integration of GWAS Summary Statistics and Gene Expression Reveals Target Cell Types Underlying Kidney Function Traits.

Authors:  Yong Li; Stefan Haug; Pascal Schlosser; Alexander Teumer; Adrienne Tin; Cristian Pattaro; Anna Köttgen; Matthias Wuttke
Journal:  J Am Soc Nephrol       Date:  2020-08-06       Impact factor: 10.121

Review 8.  Patient derived stem cells for discovery and validation of novel pathogenic variants in inherited retinal disease.

Authors:  Nathaniel K Mullin; Andrew P Voigt; Jessica A Cooke; Laura R Bohrer; Erin R Burnight; Edwin M Stone; Robert F Mullins; Budd A Tucker
Journal:  Prog Retin Eye Res       Date:  2020-10-29       Impact factor: 21.198

9.  Modeling regulatory network topology improves genome-wide analyses of complex human traits.

Authors:  Xiang Zhu; Zhana Duren; Wing Hung Wong
Journal:  Nat Commun       Date:  2021-05-14       Impact factor: 14.919

Review 10.  Disease-specific interactome alterations via epichaperomics: the case for Alzheimer's disease.

Authors:  Stephen D Ginsberg; Thomas A Neubert; Sahil Sharma; Chander S Digwal; Pengrong Yan; Calin Timbus; Tai Wang; Gabriela Chiosis
Journal:  FEBS J       Date:  2021-06-12       Impact factor: 5.622

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