Phospho-small RNA-seq reveals circulating, extracellular mRNA/lncRNAs as potential biomarkers in human plasma: Hematopoietic Stem Cell Transplant [HSCT]

Extracellular RNAs (exRNAs) in blood and other biofluids have attracted great interest as potential biomarkers in liquid biopsy applications, as well as for their potential biological functions. Whereas it is well-established that extracellular microRNAs are present in human blood circulation, the degree to which messenger RNAs (mRNA) and long noncoding RNAs (lncRNA) are represented in plasma is less clear. Here we report that mRNA and lncRNA species are present as small fragments in plasma that are not detected by standard small RNA-seq methods, because they lack 5'-phosphorylation or carry 3'-phosphorylation. We developed a modified sequencing protocol (termed "phospho-sRNA-seq") that incorporates upfront RNA treatment with T4 polynucleotide kinase (which also has 3' phosphatase activity) and compared it to a standard small RNA-seq protocol, using as input both a pool of synthetic RNAs with diverse 5' and 3' end chemistries, as well exRNA isolated from human blood plasma. Using a custom, high-stringency pipeline for data analysis we identified mRNA and lncRNA transcriptome fingerprints in plasma, including multiple tissue-specific gene sets. In a longitudinal study of hematopoietic stem cell transplant (HSCT) patients, we found different sets corresponding to bone marrow- and liver- enriched genes, which tracked with bone marrow recovery or liver injury, providing proof-of-concept validation of this method as a biomarker approach. By accessing a previously unexplored realm of mRNA and lncRNA fragments in blood plasma, phospho-sRNA-seq opens up a new space for plasma transcriptome-based biomarker development in diverse clinical settings. Overall design: ExRNA-seq libraries were prepared from platelet-poor plasma obtained from serial blood draws collected from two individuals undergoing bone marrow transplantation. A total of 11 samples were collected from each individual, starting prior to chemotherapy/ratiation treatment (approximately 7 days pre-HSCT) the day of transplant, and then weekly up to approximately Day 63.

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Giraldez MD, Spengler RM, Etheridge A, Goicochea AJ, Tuck M, Choi SW, Galas DJ, Tewari M