Evidence map›Paper›PMID 42320480›Full record

ArticleCell reports methods2026

A high-throughput, end-to-end pipeline for extracellular miRNA biomarker discovery from human biofluids.

Abbas Hakim, Jennifer N Chousal, Srimeenakshi Srinivasan, Anelizze Castro-Martinez, Basant ElGhayati, Marina Mochizuki, Tyler Ostrander, Cassandra Wauer, Peter De Hoff, Priyadarshini Pantham and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Abbas HakimDepartment 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.
Jennifer N ChousalDepartment of Pathology, University of California, San Diego, La Jolla, CA 92037, USA.
Srimeenakshi SrinivasanDepartment 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.
Anelizze Castro-MartinezDepartment 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.
Basant ElGhayatiDepartment 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.
Marina MochizukiDepartment 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.
Tyler OstranderDepartment 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.
Cassandra WauerDepartment 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.
Peter De HoffDepartment 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.
Priyadarshini PanthamDepartment 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.
Louise C LaurentDepartment 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.

Funding

Omics Data Generation Center (ODGC) for the Acute to Chronic Pain Signatures (A2CPS) Program - A2CPS Extension Administrative SupplementU54DA049115 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FISCH, KATHLEEN MARIE, JEPSEN, KRISTEN LYNN · 2019 to 2025
$4.9M
Development and application of a scalable workflow for immunomagnetic separation of exRNA carrier subclasses and molecular analysis of their cargoUH3CA241687 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LAURENT, LOUISE CHANG · 2021 to 2022
$2.0M
Extracellular Vesicles as a Link Between Placental and Renal Dysfunction in PreeclampsiaR00HD096125 · NICHD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PANTHAM, PRIYADARSHINI · 2021 to 2023
$747k
Illumina NovaSeq 6000 Sequencing SystemS10OD026929 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEPSEN, KRISTEN LYNN · 2019 to 2019
$600k
NCI NIH HHS UH3 CA241687NICHD NIH HHS R00 HD096125NIDA NIH HHS U54 DA049115NIH HHS S10 OD026929
6 · The paper itself

Abstract

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.

Indexed as

BiomarkersBody FluidsHigh-Throughput Nucleotide SequencingMicroRNAsComputational BiologyFemaleGene Expression ProfilingHumansPregnancyReproducibility of ResultsSequence Analysis, RNABiomarkersMicroRNAsautomationbiofluidbiomarkerCP: biotechnologyCP: molecular biologyexRNAhigh-throughputmiRNA

Identifiers

PMID42320480
PMCPMC13494534

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.