Inferring gene expression from cell-free DNA fragmentation profiles Journal Article
| Authors: | Esfahani, M. S.; Hamilton, E. G.; Mehrmohamadi, M.; Nabet, B. Y.; Alig, S. K.; King, D. A.; Steen, C. B.; Macaulay, C. W.; Schultz, A.; Nesselbush, M. C.; Soo, J.; Schroers-Martin, J. G.; Chen, B.; Binkley, M. S.; Stehr, H.; Chabon, J. J.; Sworder, B. J.; Hui, A. B. Y.; Frank, M. J.; Moding, E. J.; Liu, C. L.; Newman, A. M.; Isbell, J. M.; Rudin, C. M.; Li, B. T.; Kurtz, D. M.; Diehn, M.; Alizadeh, A. A. |
| Article Title: | Inferring gene expression from cell-free DNA fragmentation profiles |
| Abstract: | Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed ‘epigenetic expression inference from cell-free DNA-sequencing’ (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential. © 2022, The Author(s), under exclusive licence to Springer Nature America, Inc. |
| Keywords: | adult; genetics; mutation; neoplasm; neoplasms; cytology; gene expression; patient monitoring; tumor marker; blood; dna; tumors; diagnosis; patient treatment; diseases; gene encoding; dna sequences; cancer detection; dna fragmentation; epigenomics; gene expression profiles; procedures; high throughput sequencing; high-throughput nucleotide sequencing; dna sequencing; humans; human; biomarkers, tumor; cell-free nucleic acids; cell-free; cell free nucleic acid; 'current; blood samples; genes expression; limited resolution |
| Journal Title: | Nature Biotechnology |
| Volume: | 40 |
| Issue: | 4 |
| ISSN: | 1087-0156 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2022-04-01 |
| Start Page: | 585 |
| End Page: | 597 |
| Language: | English |
| DOI: | 10.1038/s41587-022-01222-4 |
| PUBMED: | 35361996 |
| PROVIDER: | scopus |
| PMCID: | PMC9337986 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 2 May 2022 -- Source: Scopus |
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