RNA Fragmentomics
The future of next-generation diagnostics.
RNA is an unrealized analyte.
RNA isn’t the easiest to work with, especially when its chemical instability causes fragmentation. Current methods focus on unfragmented RNA and end up missing the more than 90% of cfRNA that is fragmented. And we believe sequencing that’s missing all that data is missing the point.
RNA fragments hold a wealth of information.
Hidden within these easily overlooked fragments of RNA is a rich and dynamic set of biological data. By leveraging RNA fragmentomics, our proprietary RiboMarker platform unlocks this hidden information and provides a greater level of insight into the transcriptome than ever before. Through a routine liquid biopsy, in-depth views into the progression of a disease and a patient’s clinical journey become possible.
Recent Publications Featuring Our Technology
2024
Ros-Moner, E., et al., Conservation of molecular responses upon viral infection in the non-vascular plant Marchantia polymorpha. Nature Communications, 2024. 15:8326.
Lenart, M., et al., Identification of miRNAs present in cell- and plasma-derived extracellular vesicles — possible biomarkers of colorectal cancer. Cancers, 2024. 16(13), 2464.
Zhan, J., et al., Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. Proceedings of the National Academy of Sciences, 2024. 121(21): p. e2402285121.
Weigl, M., et al., Profiling microRNA expression during senescence and aging: mining for a diagnostic tool of senescent-cell burden. bioRxiv, 2024: p. 2024.04. 10.588794.
Pultar, M., et al., Analysis of extracellular vesicle microRNA profiles reveals distinct blood and lymphatic endothelial cell origins. J Extracell Biol, 2024. 3(1): p. e134.
Paksoy, A., et al., MicroRNA expression analysis in peripheral blood and soft-tissue of patients with periprosthetic hip infection: a prospective controlled pilot study. Bone & Joint Open, 2024. 5(6): p. 479.
Mills, J., et al., Extracellular vesicle formation in Euryarchaeota is driven by a small GTPase. Proceedings of the National Academy of Sciences, 2024. 121(10): p. e2311321121.
Lehto, P., et al., Postmortem analyses of myocardial microRNA expression in sepsis. Research Square, 2024.
Lago-Docampo, M., et al., Overexpression of miR-3168 impairs angiogenesis in Pulmonary Arterial Hypertension: Insights from circulating miRNA analysis. medRxiv, 2024: p. 2024.04. 30.24306656.
Harkess, A., et al., The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza. G3 (Bethesda), 2024. 14(4): p. jkae004.
Hamdi, M., et al., Oviductal extracellular vesicles miRNA cargo varies in response to embryos and their quality. BMC genomics, 2024. 25(1): p. 520.
Erhart, F., et al., The plasma miRNome and venous thromboembolism in high-grade glioma: miRNA Sequencing of a nested case-control cohort. J Cell Mol Med, 2024. 28(8): p. e18149.
Chapagain, P., et al., Characterisation of sRNAs enriched in outer membrane vesicles of pathogenic Flavobacterium psychrophilum causing Bacterial Cold Water Disease in rainbow trout. J Extracell Biol, 2024. 3(6): p. e161.
Caldi Gomes, L., et al., Multiomic ALS signatures highlight subclusters and sex differences suggesting the MAPK pathway as therapeutic target. Nature Communications, 2024. 15(1): p. 4893.
Borniego, L., et al., Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs. bioRxiv, 2024: p. 2024.05. 15.594325.
Belanger, S., et al., Comparative transcriptome profiling identifies stage-specific phasiRNAs and co-expressed Argonaute genes in Bambusoideae and Pooideae species. bioRxiv, 2024: p. 2024.06. 12.598608.
2023
Stverakova, T., et al., Selection of endogenous control and identification of significant microRNA deregulations in cervical cancer. Front Oncol, 2023. 13: p. 1143691.
Reshi, Q.U.A., et al., Spermatozoa, acts as an external cue and alters the cargo and production of the extracellular vesicles derived from oviductal epithelial cells in vitro. J Cell Commun Signal, 2023. 17(3): p. 737-755.
Nguyen, L.D., et al., Small molecule regulators of microRNAs identified by high-throughput screen coupled with high-throughput sequencing. Nat Commun, 2023. 14(1): p. 7575.
Namous, H., et al., Longitudinal dynamics of circulating miRNAs in a swine model of familial hypercholesterolemia during early atherosclerosis. Sci Rep, 2023. 13(1): p. 19355.
Messner, Z., et al., Circulating miRNAs Respond to Denosumab Treatment After 2 Years in Postmenopausal Women With Osteoporosis-the MiDeTe study. J Clin Endocrinol Metab, 2023. 108(5): p. 1154-1165.
Luxen, M., et al., Unique miRNome and transcriptome profiles underlie microvascular heterogeneity in mouse kidney. Am J Physiol Renal Physiol, 2023. 325(3): p. F299-F316.
Liu, Z.W., et al., Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis. Nucleic Acids Res, 2023. 51(12): p. 6039-6054.
Liang, L.W., et al., Comprehensive Transcriptomics Profiling of MicroRNA Reveals Plasma Circulating Biomarkers of Hypertrophic Cardiomyopathy and Dysregulated Signaling Pathways. Circ Heart Fail, 2023. 16(6): p. e010010.
Kusch, S., et al., Site-specific analysis reveals candidate cross-kingdom small RNAs, tRNA and rRNA fragments, and signs of fungal RNA phasing in the barley-powdery mildew interaction. Mol Plant Pathol, 2023. 24(6): p. 570-587.
Kopcho, S., et al., Alterations in Abundance and Compartmentalization of miRNAs in Blood Plasma Extracellular Vesicles and Extracellular Condensates during HIV/SIV Infection and Its Modulation by Antiretroviral Therapy (ART) and Delta-9-Tetrahydrocannabinol (Δ9-THC). Viruses, 2023. 15(3): p. 623.
Kopcho, S., et al., SIV Infection Regulates Compartmentalization of Circulating Blood Plasma miRNAs within Extracellular Vesicles (EVs) and Extracellular Condensates (ECs) and Decreases EV-Associated miRNA-128. Viruses, 2023. 15(3): p. 622.
Kim, J., et al., SARS-CoV-2 infection engenders heterogeneous ribonucleoprotein interactions to impede translation elongation in the lungs. Exp Mol Med, 2023. 55(12): p. 2541-2552.
Hadzimuratovic, B., et al., Longitudinal course of circulating miRNAs in a patient with hypophosphatasia: a case report. Osteologie, 2023. 32(03): p. P 42.
Freiria-Martinez, L., et al., Human Breast Milk microRNAs, Potential Players in the Regulation of Nervous System. Nutrients, 2023. 15(14): p. 3284.
de Las Heras, J.I., et al., Metabolic, fibrotic and splicing pathways are all altered in Emery-Dreifuss muscular dystrophy spectrum patients to differing degrees. Hum Mol Genet, 2023. 32(6): p. 1010-1031.
Beric, A., et al., Small RNAs, short but mighty: the unknown players in AD pathobiology. Alzheimer's & Dementia, 2023. 19: p. e076855.
Belanger, S., et al., Plastid dsRNA transgenes trigger phased small RNA-based gene silencing of nuclear-encoded genes. Plant Cell, 2023. 35(9): p. 3398-3412.
Alexander, L.M., et al., Novel and Engineered Type II CRISPR Systems from Uncultivated Microbes with Broad Genome Editing Capability. CRISPR J, 2023. 6(3): p. 261-277.
2022
Bélanger, S., Kramer, M.C., Payne, H.A., R. Keith Slotkin, Blake C. Meyers, Jeffrey M. Staub. Plastid double-strand RNA transgenes trigger small RNA-based gene silencing of nuclear-encoded genes. bioRxiv 2022.12.06.519219; doi: https://doi.org/10.1101/2022.12.06.519219
Zhou, X., et al., 24-nt phasiRNAs move from tapetal to meiotic cells in maize anthers. New Phytol, 2022. 235(2): p. 488-501.
Zand Karimi, H., et al., Arabidopsis apoplastic fluid contains sRNA- and circular RNA-protein complexes that are located outside extracellular vesicles. Plant Cell, 2022. 34(5): p. 1863-1881.
Vazquez-Villasenor, I., et al., RNA-Seq Profiling of Neutrophil-Derived Microvesicles in Alzheimer's Disease Patients Identifies a miRNA Signature That May Impact Blood-Brain Barrier Integrity. Int J Mol Sci, 2022. 23(11).
Ravishankar, P. and A. Daily, Tears as the next diagnostic biofluid: a comparative study between ocular fluid and blood. Applied Sciences, 2022. 12(6): p. 2884.
Liu, X., et al., A pro-metastatic tRNA fragment drives Nucleolin oligomerization and stabilization of its bound metabolic mRNAs. Mol Cell, 2022. 82(14): p. 2604-2617 e8.
Lattekivi, F., et al., Profiling Blood Serum Extracellular Vesicles in Plaque Psoriasis and Psoriatic Arthritis Patients Reveals Potential Disease Biomarkers. Int J Mol Sci, 2022. 23(7).
Khamina, K., et al., A MicroRNA Next-Generation-Sequencing Discovery Assay (miND) for Genome-Scale Analysis and Absolute Quantitation of Circulating MicroRNA Biomarkers. Int J Mol Sci, 2022. 23(3): p. 1226.
Hacquard, T., et al., The Arabidopsis F-box protein FBW2 targets AGO1 for degradation to prevent spurious loading of illegitimate small RNA. Cell Rep, 2022. 39(2): p. 110671.
Gutmann, C., et al., Association of cardiometabolic microRNAs with COVID-19 severity and mortality. Cardiovasc Res, 2022. 118(2): p. 461-474.
Fernandez, G.J., et al., Vitamin D boosts immune response of macrophages through a regulatory network of microRNAs and mRNAs. J Nutr Biochem, 2022. 109: p. 109105.
Fernandez, G.J., et al., Transcriptional and post-transcriptional mechanisms that regulate the genetic program in Zika virus-infected macrophages. Int J Biochem Cell Biol, 2022. 153: p. 106312.
Carro Vazquez, D., et al., Effect of Anti-Osteoporotic Treatments on Circulating and Bone MicroRNA Patterns in Osteopenic ZDF Rats. Int J Mol Sci, 2022. 23(12).
Baldrich, P., et al., An atlas of small RNAs from potato. Plant Direct, 2022. 6(12): p. e466.
Baker, M.E., et al., Investigation of MicroRNA Biomarkers in Equine Distal Interphalangeal Joint Osteoarthritis. Int J Mol Sci, 2022. 23(24).
Androvic, P., et al., Small RNA-Sequencing for Analysis of Circulating miRNAs: Benchmark Study. J Mol Diagn, 2022. 24(4): p. 386-394.
Amelkina, O., et al., Feline microRNAome in ovary and testis: Exploration of in-silico miRNA-mRNA networks involved in gonadal function and cellular stress response. Front Genet, 2022. 13: p. 1009220.
2021
Chapagain, P., et al., sRNAs enriched in outer membrane vesicles of pathogenic Flavobacterium psychrophilum interact with immune genes of rainbow trout. bioRxiv 2021.12.22.473952; doi: https://doi.org/10.1101/2021.12.22.473952.
Vollmers, A.C., et al., A conserved long noncoding RNA, GAPLINC, modulates the immune response during endotoxic shock. Proc Natl Acad Sci U S A, 2021. 118(7).
Pokhrel, S., et al., Pre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants. Nat Commun, 2021. 12(1): p. 4941.
Kaddour, H., et al., HIV-infection and cocaine use regulate semen extracellular vesicles proteome and miRNAome in a manner that mediates strategic monocyte haptotaxis governed by miR-128 network. Cell Mol Life Sci, 2021. 79(1): p. 5.
Castanheira, C., et al., Equine synovial fluid small non-coding RNA signatures in early osteoarthritis. BMC Vet Res, 2021. 17(1): p. 26.
Bissoondial, T.L., et al., Identification of disease-associated microRNA in a diet-induced model of nonalcoholic steatohepatitis. Mol Omics, 2021. 17(6): p. 911-916.
Benesova, S., et al., Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. Diagnostics (Basel), 2021. 11(6).
2020
Teng, C., et al., Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize. Nat Commun, 2020. 11(1): p. 2912.
Baldrich, P., et al., Ligation bias is a major contributor to nonstoichiometric abundances of secondary siRNAs and impacts analyses of microRNAs. bioRxiv, 2020: p. 2020.09.14.296616.
Sun, B., et al., Hepatitis C Virus Cure in Human Immunodeficiency Virus Coinfection Dampens Inflammation and Improves Cognition Through Multiple Mechanisms. J Infect Dis, 2020. 222(3): p. 396-406.
Ord, J., et al., Paternal effects in a wild-type zebrafish implicate a role of sperm-derived small RNAs. Mol Ecol, 2020. 29(14): p. 2722-2735.
Dargyte, M., et al., Splicing factor SRSF1 expands the regulatory logic of microRNA expression. bioRxiv 2020.05.12.092270; doi: https://doi.org/10.1101/2020.05.12.092270.
Hutter, K., et al., SAFB2 Enables the Processing of Suboptimal Stem-Loop Structures in Clustered Primary miRNA Transcripts. Mol Cell, 2020. 78(5): p. 876-889 e6.
Herbert, Z.T., et al., Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech, 2020. 31(2): p. 47-56.
Belanger, S., et al., Premeiotic, 24-Nucleotide Reproductive PhasiRNAs Are Abundant in Anthers of Wheat and Barley But Not Rice and Maize. Plant Physiol, 2020. 184(3): p. 1407-1423.
2018
Barberan-Soler, S., et al., Decreasing miRNA sequencing bias using a single adapter and circularization approach. Genome Biol, 2018. 19(1): p. 105.
