Jones, Robert C; Karkanias, Jim; Krasnow, Mark; Pisco, Angela Oliveira; Quake, Stephen R; Salzman, Julia; Yosef, Nir; Bulthaup, Bryan; Brown, Phillip; Harper, William; Hemenez, Marisa; Ponnusamy, Ravikumar; Salehi, Ahmad; Sanagavarapu, Bhavani A; Spallino, Eileen; Aaron, Ksenia A; Concepcion, Waldo; Gardner, James M; Kelly, Burnett; Neidlinger, Nikole; Wang, Zifa; Crasta, Sheela; Kolluru, Saroja; Morri, Maurizio; Tan, Serena Y; Travaglini, Kyle J; Xu, Chenling; Alcántara-Hernández, Marcela; Almanzar, Nicole; Antony, Jane; Beyersdorf, Benjamin; Burhan, Deviana; Calcuttawala, Kruti; Carter, Matthew M; Chan, Charles KF; Chang, Charles A; Chang, Stephen; Colville, Alex; Culver, Rebecca N; Cvijović, Ivana; D’Amato, Gaetano; Ezran, Camille; Galdos, Francisco X; Gillich, Astrid; Goodyer, William R; Hang, Yan; Hayashi, Alyssa; Houshdaran, Sahar; Huang, Xianxi; Irwin, Juan C; Jang, SoRi; Juanico, Julia Vallve; Kershner, Aaron M; Kim, Soochi; Kiss, Bernhard; Kong, William; Kumar, Maya E; Kuo, Angera H; Leylek, Rebecca; Li, Baoxiang; Loeb, Gabriel B; Lu, Wan-Jin; Mantri, Sruthi; Markovic, Maxim; McAlpine, Patrick L; de Morree, Antoine; Mrouj, Karim; Mukherjee, Shravani; Muser, Tyler; Neuhöfer, Patrick; Nguyen, Thi D; Perez, Kimberly; Phansalkar, Ragini; Puluca, Nazan; Qi, Zhen; Rao, Poorvi; Raquer-McKay, Hayley; Schaum, Nicholas; Scott, Bronwyn; Seddighzadeh, Bobak; Segal, Joe; Sen, Sushmita; Sikandar, Shaheen; Spencer, Sean P; Steffes, Lea

doi:10.1038/s41587-021-01188-9

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Cell types of origin of the cell-free transcriptome

2022

Jones, Robert C;
Karkanias, Jim;
Krasnow, Mark;
Pisco, Angela Oliveira;
Quake, Stephen R;
Salzman, Julia;
Yosef, Nir;
Bulthaup, Bryan;
Brown, Phillip;
Harper, William;
Hemenez, Marisa;
Ponnusamy, Ravikumar;
Salehi, Ahmad;
Sanagavarapu, Bhavani A;
Spallino, Eileen;
Aaron, Ksenia A;
Concepcion, Waldo;
Gardner, James M;
Kelly, Burnett;
Neidlinger, Nikole;
Wang, Zifa;
Crasta, Sheela;
Kolluru, Saroja;
Morri, Maurizio;
Tan, Serena Y;
Travaglini, Kyle J;
Xu, Chenling;
Alcántara-Hernández, Marcela;
Almanzar, Nicole;
Antony, Jane;
Beyersdorf, Benjamin;
Burhan, Deviana;
Calcuttawala, Kruti;
Carter, Matthew M;
Chan, Charles KF;
Chang, Charles A;
Chang, Stephen;
Colville, Alex;
Culver, Rebecca N;
Cvijović, Ivana;
D’Amato, Gaetano;
Ezran, Camille;
Galdos, Francisco X;
Gillich, Astrid;
Goodyer, William R;
Hang, Yan;
Hayashi, Alyssa;
Houshdaran, Sahar;
Huang, Xianxi;
Irwin, Juan C;
Jang, SoRi;
Juanico, Julia Vallve;
Kershner, Aaron M;
Kim, Soochi;
Kiss, Bernhard;
Kong, William;
Kumar, Maya E;
Kuo, Angera H;
Leylek, Rebecca;
Li, Baoxiang;
Loeb, Gabriel B;
Lu, Wan-Jin;
Mantri, Sruthi;
Markovic, Maxim;
McAlpine, Patrick L;
de Morree, Antoine;
Mrouj, Karim;
Mukherjee, Shravani;
Muser, Tyler;
Neuhöfer, Patrick;
Nguyen, Thi D;
Perez, Kimberly;
Phansalkar, Ragini;
Puluca, Nazan;
Qi, Zhen;
Rao, Poorvi;
Raquer-McKay, Hayley;
Schaum, Nicholas;
Scott, Bronwyn;
Seddighzadeh, Bobak;
Segal, Joe;
Sen, Sushmita;
Sikandar, Shaheen;
Spencer, Sean P;
Steffes, Lea;
Subramaniam, Varun R;
Swarup, Aditi;
Swift, Michael;
Van Treuren, Will;
Trimm, Emily;
Veizades, Stefan;
Vijayakumar, Sivakamasundari;
Vo, Kim Chi;
Vorperian, Sevahn K;
Wang, Wanxin;
Weinstein, Hannah NW;
Winkler, Juliane;
Wu, Timothy TH;
Xie, Jamie;
Yung, Andrea R;
Zhang, Yue;
Detweiler, Angela M;
Mekonen, Honey;
Neff, Norma F;
Sit, Rene V;
Tan, Michelle;
Yan, Jia;
Bean, Gregory R;
Charu, Vivek;
Forgó, Erna;
Martin, Brock A;
Ozawa, Michael G;
Silva, Oscar;
Toland, Angus;
Vemuri, Venkata NP;
Afik, Shaked;
Awayan, Kyle;
Bierman, Rob;
Botvinnik, Olga Borisovna;
Byrne, Ashley;
Chen, Michelle;
Dehghannasiri, Roozbeh;
Gayoso, Adam;
Granados, Alejandro A;
Li, Qiqing;
Mahmoudabadi, Gita;
McGeever, Aaron;
Olivieri, Julia Eve;
Park, Madeline;
Ravikumar, Neha;
Stanley, Geoff;
Tan, Weilun;
Tarashansky, Alexander J;
Vanheusden, Rohan;
Wang, Peter;
Wang, Sheng;
Xing, Galen;
Xu, Chenling;
Yosef, Nir;
Culver, Rebecca;
Dethlefsen, Les;
Ho, Po-Yi;
Liu, Shixuan;
Maltzman, Jonathan S;
Metzger, Ross J;
Sasagawa, Koki;
Sinha, Rahul;
Song, Hanbing;
Wang, Bruce;
Artandi, Steven E;
Beachy, Philip A;
Clarke, Michael F;
Giudice, Linda C;
Huang, Franklin W;
Huang, Kerwyn Casey;
Idoyaga, Juliana;
Kim, Seung K;
Kuo, Christin S;
Nguyen, Patricia;
Rando, Thomas A;
Red-Horse, Kristy;
Reiter, Jeremy;
Relman, David A;
Sonnenburg, Justin L;
Wu, Albert;
Wu, Sean M;
Wyss-Coray, Tony
et al.

Published Web Location

https://doi.org/10.1038/s41587-021-01188-9

Abstract

Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the Tabula Sapiens transcriptomic cell atlas as well as individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset. We define cell type signature scores, which allow the inference of cell types that contribute to cell-free RNA for a variety of diseases.

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Cell types of origin of the cell-free transcriptome

Published Web Location