Academic Journal
A high-throughput, end-to-end pipeline for extracellular miRNA biomarker discovery from human biofluids.
| Τίτλος: | A high-throughput, end-to-end pipeline for extracellular miRNA biomarker discovery from human biofluids. |
|---|---|
| Συγγραφείς: | Hakim A; Department of Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA., Chousal JN; Department of Pathology, University of California, San Diego, La Jolla, CA 92037, USA., Srinivasan S; Department of Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA., Castro-Martinez A; Department of Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA., ElGhayati B; Department of Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA., Mochizuki M; Department of Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA., Ostrander T; Department of Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA., Wauer C; Department of Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA., De Hoff P; Department of Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA., Pantham P; Department of Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA. Electronic address: ppantham@health.ucsd.edu., Laurent LC; Department of Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA. Electronic address: llaurent@health.ucsd.edu. |
| Πηγή: | Cell reports methods [Cell Rep Methods] 2026 Aug 17; Vol. 6 (8), pp. 101502. Date of Electronic Publication: 2026 Jun 19. |
| Τύπος έκδοσης: | Journal Article |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Elsevier Inc Country of Publication: United States NLM ID: 9918227360606676 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2667-2375 (Electronic) Linking ISSN: 26672375 NLM ISO Abbreviation: Cell Rep Methods Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: [New York] : Elsevier Inc., [2021]- |
| Ιατρικοί όροι (MeSH): | MicroRNAs*/genetics , MicroRNAs*/blood , MicroRNAs*/urine , Biomarkers*/blood , Biomarkers*/urine , Biomarkers*/metabolism , Body Fluids*/metabolism , High-Throughput Nucleotide Sequencing*/methods, Gene Expression Profiling/methods ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Humans ; Female ; Pregnancy ; Reproducibility of Results |
| Περίληψη: | We developed a scalable pipeline for extracellular miRNA (ex-miRNA) profiling that integrates automated exRNA extraction, small RNA sequencing, and bioinformatic analysis including data processing and normalization. Automated extraction protocols, including doubling input volume or lyophilization to increase RNA yield, were benchmarked against leading manual methods, with donor pregnancy status serving as the primary biological variable. Small RNA sequencing was performed across conditions, enabling systematic evaluation of data quality and comparison of normalization strategies. Across methods and biofluids, DESeq2 most effectively reduced technical variability while preserving biological signal. Comparing specimen types, plasma exhibited the highest reproducibility and retention of biological signal, followed by serum, while urine exhibited greater variability and less differentially expressed miRNAs. Pregnancy-associated ex-miRNA signatures, including C19MC miRNAs, were consistently detected in both plasma and serum. Together, this study establishes a robust framework for scalable exRNA extraction and profiling, supporting standardized assay development for biomarker discovery and clinical applications. (Copyright © 2026 The Author(s). Published by Elsevier Inc. All rights reserved.) |
| Competing Interests: | Declaration of interests The authors declare no competing interests. |
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| Grant Information: | R00 HD096125 United States HD NICHD NIH HHS; S10 OD026929 United States OD NIH HHS; U54 DA049115 United States DA NIDA NIH HHS; UH3 CA241687 United States CA NCI NIH HHS |
| Contributed Indexing: | Keywords: CP: biotechnology; CP: molecular biology; automation; biofluid; biomarker; exRNA; high-throughput; miRNA |
| Substance Nomenclature: | 0 (MicroRNAs) 0 (Biomarkers) |
| Entry Date(s): | Date Created: 20260619 Date Completed: 20260817 Latest Revision: 20260824 |
| Update Code: | 20260824 |
| PubMed Central ID: | PMC13494534 |
| DOI: | 10.1016/j.crmeth.2026.101502 |
| PMID: | 42320480 |
| Βάση Δεδομένων: | MEDLINE |
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