ArticleClinical and translational medicine2022
Polyadenylation ligation-mediated sequencing (PALM-Seq) characterizes cell-free coding and non-coding RNAs in human biofluids.
Article in Clinical and translational medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 27 citations in OpenAlex.
- Early characterization of pregnancy glycemic traits in gestational diabetes mellitus by plasma cell-free mRNA and non-coding RNA.Epigenetics · 2026Article
- Advancing the applications of liquid biopsies in oncology.Nature reviews. Genetics · 2026Review
- Deconformer: efficient cell-type composition profiling of cfRNA across diverse cell types.Briefings in bioinformatics · 2026Article
- Multifeature sequencing-based liquid biopsy for cancer diagnosis and monitoring.Genome medicine · 2026Review
- A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker).RNA (New York, N.Y.) · 2026Article
- Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples.Nature biotechnology · 2026Article
- MicroRNAs and Their Profiling via Single-Cell Sequencing Technologies.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring.RNA biology · 2025Article
- Cell-free RNAs in maternal peripheral blood as potential biomarkers of preeclampsia: a review.Reproductive biology and endocrinology : RB&E · 2025Review
- Urine Cell-Free RNA vs Plasma Cell-Free RNA for Monitoring of Kidney Injury and Immune Complications.Clinical chemistry · 2025Article
- Simultaneous Isolation and Characterization of Lipoprotein Classes in Plasma, Including HDL Subclasses and the Uncharacterized Dense HDL.bioRxiv : the preprint server for biology · 2025Article
- Liquid biopsy-based multi-cancer early detection: an exploration road from evidence to implementation.Science bulletin · 2025Review
- High-throughput assay confirmation of a T-cell receptor pre-mRNA fragment as a blood-based inflammatory breast cancer biomarker.medRxiv : the preprint server for health sciences · 2025Article
- A novel sequence-based transformer model architecture for integrating multi-omics data in preterm birth risk prediction.NPJ digital medicine · 2025Article
- Redefining cancer care: harnessing circulating tumor cells' potential for improved diagnosis and prognosis.Cancer cell international · 2025Review
- Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential.Genome biology · 2025Article
- Depletion-assisted multiplexed cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicles.Clinical and translational medicine · 2024Article
- Liquid Biopsy in Lung Cancer: Biomarkers for the Management of Recurrence and Metastasis.International journal of molecular sciences · 2023Review
- Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer.Cancers · 2023Review
- Integrated analysis of circulating cell free nucleic acids for cancer genotyping and immune phenotyping of tumor microenvironment.Frontiers in genetics · 2023Review
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Authors and funding
17 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCell-free messenger RNA (cf-mRNA) and long non-coding RNA (cf-lncRNA) are becoming increasingly important in liquid biopsy by providing biomarkers for disease prediction, diagnosis and prognosis, but the simultaneous characterization of coding and non-coding RNAs in human biofluids remains challenging.
methodsHere, we developed polyadenylation ligation-mediated sequencing (PALM-Seq), an RNA sequencing strategy employing treatment of RNA with T4 polynucleotide kinase to generate cell-free RNA (cfRNA) fragments with 5' phosphate and 3' hydroxyl and RNase H to deplete abundant RNAs, achieving simultaneous quantification and characterization of cfRNAs.
resultsUsing PALM-Seq, we successfully identified well-known differentially abundant mRNA, lncRNA and microRNA in the blood plasma of pregnant women. We further characterized cfRNAs in blood plasma, saliva, urine, seminal plasma and amniotic fluid and found that the detected numbers of different RNA biotypes varied with body fluids. The profiles of cf-mRNA reflected the function of originated tissues, and immune cells significantly contributed RNA to blood plasma and saliva. Short fragments (<50 nt) of mRNA and lncRNA were major in biofluids, whereas seminal plasma and amniotic fluid tended to retain long RNA. Body fluids showed distinct preferences of pyrimidine at the 3' end and adenine at the 5' end of cf-mRNA and cf-lncRNA, which were correlated with the proportions of short fragments.
conclusionTogether, PALM-Seq enables a simultaneous characterization of cf-mRNA and cf-lncRNA, contributing to elucidating the biology and promoting the application of cfRNAs.
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