title: Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples.
abstract: The ongoing ascent of sequencing technologies has enabled researchers to gain unprecedented insights into the RNA content of biological samples. MiRNAs, a class of small non-coding RNAs, play a pivotal role in regulating gene expression. The discovery that miRNAs are stably present in circulation has spiked interest in their potential use as minimally-invasive biomarkers. However, sequencing of blood-derived samples (serum, plasma) is challenging due to the often low RNA concentration, poor RNA quality and the presence of highly abundant RNAs that dominate sequencing libraries. In murine serum for example, the high abundance of tRNA-derived small RNAs called 5' tRNA halves hampers the detection of other small RNAs, like miRNAs. We therefore evaluated two complementary approaches for targeted depletion of 5' tRNA halves in murine serum samples. Using a protocol based on biotinylated DNA probes and streptavidin coated magnetic beads we were able to selectively deplete 95% of the targeted 5' tRNA half molecules. This allowed an unbiased enrichment of the miRNA fraction resulting in a 6-fold increase of mapped miRNA reads and 60% more unique miRNAs detected. Moreover, when comparing miRNA levels in tumor-carrying versus tumor-free mice, we observed a three-fold increase in differentially expressed miRNAs.
authors.affiliation: Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), Ghent University Ghent, Belgium.
authors.forename: Alan
authors.initials: A
authors.lastname: Van Goethem
authors.affiliation: Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), Ghent University Ghent, Belgium.
authors.forename: Nurten
authors.initials: N
authors.lastname: Yigit
authors.affiliation: Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), Ghent University Ghent, Belgium.|Bioinformatics Institute Ghent (BIG), Ghent University, Ghent, Belgium.
authors.forename: Celine
authors.initials: C
authors.lastname: Everaert
authors.affiliation: Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas, United States.
authors.forename: Myrthala
authors.initials: M
authors.lastname: Moreno-Smith
authors.affiliation: Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), Ghent University Ghent, Belgium.
authors.forename: Liselot M
authors.initials: LM
authors.lastname: Mus
authors.affiliation: Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas, United States.
authors.forename: Eveline
authors.initials: E
authors.lastname: Barbieri
authors.affiliation: Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), Ghent University Ghent, Belgium.
authors.forename: Frank
authors.initials: F
authors.lastname: Speleman
authors.affiliation: Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), Ghent University Ghent, Belgium.|Bioinformatics Institute Ghent (BIG), Ghent University, Ghent, Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Mestdagh
authors.affiliation: Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas, United States.
authors.forename: Jason
authors.initials: J
authors.lastname: Shohet
authors.affiliation: Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), Ghent University Ghent, Belgium.
authors.forename: Tom
authors.initials: T
authors.lastname: Van Maerken
authors.affiliation: Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), Ghent University Ghent, Belgium.|Bioinformatics Institute Ghent (BIG), Ghent University, Ghent, Belgium.
authors.forename: Jo
authors.initials: J
authors.lastname: Vandesompele
mesh_terms: D000818:Animals; D014408:Biomarkers, Tumor / Q000235:genetics; D005260:Female; D015870:Gene Expression / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008297:Male; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D044967:Serum / Q000378:metabolism*
chemical_list: D014408:Biomarkers, Tumor; D035683:MicroRNAs; D012343:RNA, Transfer