Non-invasive characterization of human bone marrow stimulation and reconstitution by cell-free messenger RNA sequencing

Abstract

Circulating cell-free mRNA (cf-mRNA) holds great promise as a non-invasive diagnostic biomarker. However, cf-mRNA composition and its potential clinical applications remain largely unexplored. Here we show, using Next Generation Sequencing-based profiling, that cf-mRNA is enriched in transcripts derived from the bone marrow compared to circulating cells. Further, longitudinal studies involving bone marrow ablation followed by hematopoietic stem cell transplantation in multiple myeloma and acute myeloid leukemia patients indicate that cf-mRNA levels reflect the transcriptional activity of bone marrow-resident hematopoietic lineages during bone marrow reconstitution. Mechanistically, stimulation of specific bone marrow cell populations in vivo using growth factor pharmacotherapy show that cf-mRNA reflects dynamic functional changes over time associated with cellular activity. Our results shed light on the biology of the circulating transcriptome and highlight the potential utility of cf-mRNA to non-invasively monitor bone marrow involved pathologies.

Territory-wide cohort study of Brugada syndrome in Hong Kong: predictors of long-term outcomes using random survival forests and non-negative matrix factorisation

“…This non-negativity makes the resulting matrices easier to inspect and makes the interpretation easier for real-world applications, such as identification of hidden stages in embryonic stem cell differentiation, 38 DNA methylation profiling of human cardiac tissue 39 and unsupervised cf-mRNA transcriptome decomposition. 40 NMF was recently used by our teams for mortality risk prediction in acquired long QT syndrome patients 41 and arrhythmic risk stratification in BrS patients. 42 In this study, these latent factors were then used as inputs an RSF model.…”

Data-Driven Modeling of Pregnancy-Related Complications

“…Sequencing technologies have enabled the quantification of both protein-coding mRNA and regulatory miRNAs, circular (circ)RNAs, and long noncoding (lnc)RNAs [176]. cfRNA from blood samples has also emerged as a promising application of transcriptomic profiling in the context of noninvasive biomarkers for use in clinical practice [177]. The limitations in cell-free transcriptomic data lie in the constraints of sequencing technology and our inability to determine the exact tissue of origin of the RNA sequenced.…”

Investigating Pregnancy and Its Complications Using Circulating Cell-Free RNA in Women's Blood During Gestation

“…Indeed, the connection between apoptosis and proliferation for both cfDNA as reviewed elsewhere ( 29 ), and by extension, cfRNA, points to apoptotic nucleic acid release as a means to understand both dying and living, proliferating cells. Recent convincing evidence outside the area of pregnancy also points to the possibility of active secretion ( 30 ). In longitudinal studies of cancer patients who underwent bone marrow ablation, Ibarra et al found that cf-mRNA captured active transcriptional activity.…”

“…cfRNA can be successfully extracted and amplified from a minimum of 0.5 ml of plasma with strong agreement between technical replicates ( 30 ). In a direct comparison, Munchel et al ( 4 ) recommended that 2–4 ml of plasma be used as starting material to minimize variability and maximize library complexity.…”

“…Following RNA extraction, samples may be prepared for sequencing or RT-qPCR. Library preparation for sequencing has converged on two key methods—total RNA sequencing with ribosomal RNA (rRNA) depletion ( 8 ) and exonic-focused (i.e., mRNA) sequencing via whole-exome enrichment ( 4 , 30 ). The appropriate method depends on desired downstream analyses.…”