The chromatin landscape of healthy and injured cell types in the human kidney

• DOI: 10.1038/s41467-023-44467-6
• Publication Date: 2024-02-01T12:02:51Z
• Authors: Debora L. Gisch; Michelle Brennan; Blue B. Lake; Jeannine Basta; Mark S. Keller; Ricardo Melo Ferr...; Shreeram Akilesh; Reetika Ghag; Charles Lu; Ying-Hua Cheng; Kimberly S. Collins; Samir V. Parikh; Brad H. Rovin; Lynn Robbins; Lisa Stout; Kimberly Y. Conklin; Dinh Diep; Bo Zhang; Amanda Knoten; Daria Barwinska; Mahla Asghari; Angela R. Sabo; Michael J. Ferkowicz; Timothy A. Sutton; Katherine J. Kelly; Ian H. De Boer; Sylvia E. Rosas; Krzysztof Kiryluk; Jeffrey B. Hodgin; Fadhl Alakwaa; Seth Winfree; Nichole Jefferson; Aydın Türkmen; Joseph P. Gaut; Nils Gehlenborg; Carrie L. Phillips; Tarek M. El-Achkar; Pierre C. Dagher; Takashi Hato; Kun Zhang; Jonathan Himmelfarb; Matthias Kretzler; Shamim Mollah; ; Blue Lake; Alexander Morales; Isaac Stillman; Stewart Lecker; Steve Bogen; Ashish Verma; Guanghao Yu; Insa Schmidt; Joel Henderson; Laurence Beck; Pranav Yadati; Sushrut Waikar; Afolarin A. Amodu; Shana Maikhor; Titlayo Ilori; Mia R. Colona; Astrid Weins; Gearoid McMahon; Nir Hacohen; Anna Greka; Jamie L. Marshall; Paul J. Hoover; Vidya S. Viswanathan; Dana Crawford; Mark Aulisio; William Bush; Yijiang Chen; Anant Madabhushi; Charles O’Malley; Crystal Gadegbeku; Dianna Sendrey; Emilio Poggio; John O’Toole; John Sedor; Jonathan Taliercio; Lakeshia Bush; Leal Herlitz; Ellen Palmer; Jane Nguyen; Kassandra Spates-...; Leslie Cooperman; Stacey Jolly; Carissa Vinovskis; Andrew Bomback; Jonathan Barasch; Krzysztof Kiryluk; Paul Appelbaum; Vivette D’Agati; Cecilia Berrouet; Karla Mehl; Maya Sabatello; Ning Shang; Olivia Balderes; Pietro A. Canetta; Satoru Kudose; Joana de Pinho Go...; Lukasz Migas; Raf Van de Plas; Roy Lardenoije; Laura Barisoni; Helmut Rennke; Abraham Verdoes; Angela Sabo; Debora Lidia Gisch; James Williams; Katherine Kelly; Kenneth Dunn; Michael Eadon; Michael Ferkowicz; Pierre Dagher; Seth Winfree; Sharon Bledsoe; Stephanie Wofford; Timothy Sutton; William Bowen; Austen Slade; Elizabeth Record; Yinghua Cheng; Yashvardhan Jain; Bruce Herr; Ellen Quardokus; Ashley Wang; Celia Pamela Coro...; Chirag Parikh; Mohamed Atta; Steven Menez; Yumeng Wen; Alan Xu; Lauren Bernard; Camille Johansen; Sarah Chen; Sylvia Rosas; Isabel Donohoe; Jennifer Sun; Richard Knight; Anna Shpigel; Jack Bebiak; John Saul; Joseph Ardayfio; Robert Koewler; Roy Pinkeney; Taneisha Campbell; Evren Azeloglu; Girish Nadkarni; John He; Joji Tokita; Kirk Campbell; Marissa Patel; Sean Lefferts; Srinivas Ravi Iye...; Stephen Ward; Steven Coca; Cijang He; Yuguang Xiong; Pottumarthi Prasad; Brad Rovin; John P. Shapiro; Samir Parikh; Sethu M. Madhavan; Jessica Lukowski; Dusan Velickovic; Ljiljana Pasa-Tolic; George Oliver; Olga Troyanskaya; Rachel Sealfon; Weiguang Mao; Aaron Wong; Ari Pollack; Yury Goltsev; Brandon Ginley; Brendon Lutnick; Garry Nolan; Kavya Anjani; Tariq Mukatash; Zoltan G. Laszik; Baltazar Campos; Bijin Thajudeen; David Beyda; Erika Bracamonte; Frank Brosius; Gregory Woodhead; Katherine Mendoza; Nicole Marquez; Raymond Scott; Rebecca Tsosie; Milda Saunders; Adele Rike; E. Steve Woodle; Paul J. Lee; Rita R. Alloway; Tiffany Shi; Elena Hsieh; Jessica Kendrick; Joshua Thurman; Julia Wrobel; Laura Pyle; Petter Bjornstad; Nicholas Lucarelli; Pinaki Sarder; Amada Renteria; Ana Ricardo; Anand Srivastava; Devona Redmond; Eunice Carmona-Po...; James Bui; James Lash; Monica Fox; Natalie Meza; Ron Gaba; Suman Setty; Tanika Kelly; Chrysta Lienczewski; Dawit Demeke; Edgar Otto; Heather Ascani; Jeff Hodgin; Jennifer Schaub; John Hartman; Laura Mariani; Markus Bitzer; Michael Rose; Nikki Bonevich; Ninive Conser; Phillip McCown; Rachel Dull; Rajasree Menon; Rebecca Reamy; Sean Eddy; Ul Balis; Victoria Blanc; Viji Nair; Yongqun Oliver He; Zachary Wright; Becky Steck; Jinghui Luo; Renee Frey; Alyson Coleman; Dorisann Henderso...; Jerica Berge; Maria Luiza Caramori; Oyedele Adeyi; Patrick Nachman; Sami Safadi; Siobhan Flanagan; Sisi Ma; Susan Klett; Susan Wolf; Tasma Harindhanav...; Via Rao; Amy Mottl; Anne Froment; Evan Zeitler; Peter Bream; Sara Kelley; Matthew Rosengart; Michele Elder; Paul Palevsky; Raghavan Murugan; Daniel E. Hall; Filitsa Bender; James Winters; John A. Kellum; Matthew Gilliam; Mitchell Tublin; Roderick Tan; Guanshi Zhang; Kumar Sharma; Manjeri Venkatach...; Allen Hendricks; Asra Kermani; Jose Torrealba; Miguel Vazquez; Nancy Wang; Qi Cai; Richard Tyler Miller; Shihong Ma; Susan Hedayati; Andrew Hoofnagle; Artit Wangperawong; Ashley Berglund; Ashveena L. Dighe; Bessie Young; Brandon Larson; Brooke Berry; Charles Alpers; Christine Limonte; Christy Stutzke; Glenda Roberts; Ian de Boer; Jaime Snyder; Jimmy Phuong; Jonas Carson; Kasra Rezaei; Katherine Tuttle; Keith Brown; Kristina Blank; Natalya Sarkisova; Nichole Jefferson; Robyn McClelland; Sean Mooney; Yunbi Nam; Adam Wilcox; Christopher Park; Frederick Dowd; Kayleen Williams; Stephanie M. Grew...; Stephen Daniel; Stuart Shankland; Annapurna Pamreddy; Hongping Ye; Richard Montellano; Shweta Bansal; Anil Pillai; Dianbo Zhang; Harold Park; Jiten Patel; Kamalanathan Samb...; Mujeeb Basit; Natasha Wen; Orson W. Moe; Robert D. Toto; Simon C. Lee; Kavya Sharman; Richard M. Caprioli; Agnes Fogo; Jamie Allen; Jeffrey Spraggins; Katerina Djambazova; Mark de Caestecker; Martin Dufresne; Melissa Farrow; Anitha Vijayan; Brittany Minor; Gerald Nwanne; Joseph Gaut; Kristine Conlon; Madhurima Kaushal; Sabine M. Diettman; Angela M. Victori...; Dennis Moledina; Francis P. Wilson; Gilbert Moeckel; Lloyd Cantley; Melissa Shaw; Vijayakumar Kakade; Tanima Arora; Sanjay Jain; Michael Rauchman; Michael T. Eadon
• Keywords: Human kidney

There is a need to define regions of gene activation or repression that control human kidney cells in states health, injury, and repair understand the molecular pathogenesis disease design therapeutic strategies. Comprehensive integration expression with epigenetic features regulatory elements remains significant challenge. We measure dual single nucleus RNA chromatin accessibility, DNA methylation, H3K27ac, H3K4me1, H3K4me3, H3K27me3 histone modifications decipher landscape regulation reference adaptive injury states. establish spatially-anchored epigenomic atlas kidney's active, silent, accessible across genome. Using this atlas, we note distinct different epithelial cell types. A proximal tubule transcription factor network ELF3, KLF6, KLF10 regulates transition between health while thick ascending limb regulated by NR2F1. Further, combined perturbation distinguishes two tubular subtypes, one which manifested trajectory after knockout. This will serve as foundation facilitate targeted cell-specific therapeutics reprogramming networks.