Open AccessPolyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids
Author(s) -
Liu Zhongzhen,
Wang Taifu,
Yang Xi,
Zhou Qing,
Zhu Sujun,
Zeng Juan,
Chen Haixiao,
Sun Jinghua,
Li Liqiang,
Xu Jinjin,
Geng Chunyu,
Xu Xun,
Wang Jian,
Yang Huanming,
Zhu Shida,
Chen Fang,
Wang WenJing
Publication year - 2022
Publication title -
clinical and translational medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.125
H-Index - 1
ISSN - 2001-1326
DOI - 10.1002/ctm2.987
Subject(s) - rna , messenger rna , polyadenylation , biology , ribonuclease , microrna , body fluid , non coding rna , microbiology and biotechnology , rna extraction , small nucleolar rna , saliva , gene , biochemistry , medicine , pathology
Background Cell‐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. Methods Here, 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. Results Using 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. Conclusion Together, PALM‐Seq enables a simultaneous characterization of cf‐mRNA and cf‐lncRNA, contributing to elucidating the biology and promoting the application of cfRNAs.