Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids
Abstract 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 bioflui...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-07-01
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| Series: | Clinical and Translational Medicine |
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| Online Access: | https://doi.org/10.1002/ctm2.987 |
| _version_ | 1828189308070133760 |
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| author | Zhongzhen Liu Taifu Wang Xi Yang Qing Zhou Sujun Zhu Juan Zeng Haixiao Chen Jinghua Sun Liqiang Li Jinjin Xu Chunyu Geng Xun Xu Jian Wang Huanming Yang Shida Zhu Fang Chen Wen‐Jing Wang |
| author_facet | Zhongzhen Liu Taifu Wang Xi Yang Qing Zhou Sujun Zhu Juan Zeng Haixiao Chen Jinghua Sun Liqiang Li Jinjin Xu Chunyu Geng Xun Xu Jian Wang Huanming Yang Shida Zhu Fang Chen Wen‐Jing Wang |
| author_sort | Zhongzhen Liu |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-12T08:03:42Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2001-1326 |
| language | English |
| last_indexed | 2024-04-12T08:03:42Z |
| publishDate | 2022-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Clinical and Translational Medicine |
| spelling | doaj.art-a4c0fb4281aa437cbdbe08f83297b6362022-12-22T03:41:14ZengWileyClinical and Translational Medicine2001-13262022-07-01127n/an/a10.1002/ctm2.987Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluidsZhongzhen Liu0Taifu Wang1Xi Yang2Qing Zhou3Sujun Zhu4Juan Zeng5Haixiao Chen6Jinghua Sun7Liqiang Li8Jinjin Xu9Chunyu Geng10Xun Xu11Jian Wang12Huanming Yang13Shida Zhu14Fang Chen15Wen‐Jing Wang16BGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaObstetrics Department Shenzhen Maternity and Child Healthcare Hospital Shenzhen Guangdong Province ChinaObstetrics Department Shenzhen Maternity and Child Healthcare Hospital Shenzhen Guangdong Province ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaBGI‐Shenzhen Shenzhen ChinaAbstract 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.https://doi.org/10.1002/ctm2.987cell‐free RNARNA sequencingbiofluidsin vitro diagnosis |
| spellingShingle | Zhongzhen Liu Taifu Wang Xi Yang Qing Zhou Sujun Zhu Juan Zeng Haixiao Chen Jinghua Sun Liqiang Li Jinjin Xu Chunyu Geng Xun Xu Jian Wang Huanming Yang Shida Zhu Fang Chen Wen‐Jing Wang Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids Clinical and Translational Medicine cell‐free RNA RNA sequencing biofluids in vitro diagnosis |
| title | Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids |
| title_full | Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids |
| title_fullStr | Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids |
| title_full_unstemmed | Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids |
| title_short | Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids |
| title_sort | polyadenylation ligation mediated sequencing palm seq characterizes cell free coding and non coding rnas in human biofluids |
| topic | cell‐free RNA RNA sequencing biofluids in vitro diagnosis |
| url | https://doi.org/10.1002/ctm2.987 |
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