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Cell types of origin of the cell-free transcriptome

Vorperian, Sevahn K., Moufarrej, Mira N., Tabula Sapiens Consortium, Overall Project Direction and Coordination, Jones, Robert C., Karkanias, Jim, Krasnow, Mark, Pisco, Angela Oliveira +173 more·2022·Nature Biotechnology
DOI 10.1038/s41587-021-01188-9PMC PMC9200634
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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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  • Most plasma miRNAs were RBC derived, followed by platelets, mesenchymal cells, and immune cells.

    “Similar to a recent manuscript on cell-free RNA in plasma [40] and consistent with other miRNA-based studies [41–43], we observed that most plasma miRNAs were RBC derived, followed by platelets, mesenchymal cells, and immune cells.”

    From A curated human cellular microRNAome based on 196 primary cell types (2022) · cites this paper as [40]

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Authors
Vorperian, S. K., Moufarrej, M. N., Tabula Sapiens Consortium, Overall Project Direction and Coordination, Jones, R. C., Karkanias, J., Krasnow, M., Pisco, A. O., Quake, S. R., Salzman, J., Yosef, N., Recruitment, D., Bulthaup, B., Brown, P., Harper, W., Hemenez, M., Ponnusamy, R., Salehi, A., Sanagavarapu, B. A., Spallino, E., Surgeons, Aaron, K. A., Concepcion, W., Gardner, J. M., Kelly, B., Neidlinger, N., Wang, Z., coordination, L., Crasta, S., Kolluru, S., Morri, M., Tan, S. Y., Travaglini, K. J., Xu, C., Processing, O., Alcántara-Hernández, M., Almanzar, N., Antony, J., Beyersdorf, B., Burhan, D., Calcuttawala, K., Carter, M. M., Chan, C. K. F., Chang, C. A., Chang, S., Colville, A., Culver, R. N., Cvijović, I., D’Amato, G., Ezran, C., Galdos, F. X., Gillich, A., Goodyer, W. R., Hang, Y., Hayashi, A., Houshdaran, S., Huang, X., Irwin, J. C., Jang, S., Juanico, J. V., Kershner, A. M., Kim, S., Kiss, B., Kong, W., Kumar, M. E., Kuo, A. H., Leylek, R., Li, B., Loeb, G. B., Lu, W.-J., Mantri, S., Markovic, M., McAlpine, P. L., de Morree, A., Mrouj, K., Mukherjee, S., Muser, T., Neuhöfer, P., Nguyen, T. D., Perez, K., Phansalkar, R., Puluca, N., Qi, Z., Rao, P., Raquer-McKay, H., Schaum, N., Scott, B., Seddighzadeh, B., Segal, J., Sen, S., Sikandar, S., Spencer, S. P., Steffes, L., Subramaniam, V. R., Swarup, A., Swift, M., Van Treuren, W., Trimm, E., Veizades, S., Vijayakumar, S., Vo, K. C., Vorperian, S. K., Wang, W., Weinstein, H. N. W., Winkler, J., Wu, T. T. H., Xie, J., Yung, A. R., Zhang, Y., Sequencing, Detweiler, A. M., Mekonen, H., Neff, N. F., Sit, R. V., Tan, M., Yan, J., Histology, Bean, G. R., Charu, V., Forgó, E., Martin, B. A., Ozawa, M. G., Silva, O., Toland, A., Vemuri, V. N. P., Analysis, D., Afik, S., Awayan, K., Bierman, R., Botvinnik, O. B., Byrne, A., Chen, M., Dehghannasiri, R., Gayoso, A., Granados, A. A., Li, Q., Mahmoudabadi, G., McGeever, A., Olivieri, J. E., Park, M., Ravikumar, N., Stanley, G., Tan, W., Tarashansky, A. J., Vanheusden, R., Wang, P., Wang, S., Xing, G., Xu, C., Yosef, N., Annotation, E. C. T., Culver, R., Dethlefsen, L., Ho, P.-Y., Liu, S., Maltzman, J. S., Metzger, R. J., Sasagawa, K., Sinha, R., Song, H., Wang, B., Tissue Expert Principal Investigators, Artandi, S. E., Beachy, P. A., Clarke, M. F., Giudice, L. C., Huang, F. W., Huang, K. C., Idoyaga, J., Kim, S. K., Kuo, C. S., Nguyen, P., Rando, T. A., Red-Horse, K., Reiter, J., Relman, D. A., Sonnenburg, J. L., Wu, A., Wu, S. M., Wyss-Coray, T., & Quake, S. R.
ORCID
Moufarrej, Mira N.
Venue
Nature Biotechnology
Publisher
Springer Science and Business Media LLC
Published
2022-02-07
Volume
40
Issue
6
Pages
855-861
ISSN
  • 1087-0156
  • 1546-1696
DOI
10.1038/s41587-021-01188-9
PMC
PMC9200634
Cited by
115
References
5
Language
en
Update notices
correction (2022-03-28)
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