Comprehensive microRNA expression profiling of the hematopoietic hierarchy

Abstract

The hematopoietic system produces a large number of highly specialized cell types that are derived through a hierarchical differentiation process from a common stem cell population. miRNAs are critical players in orchestrating this differentiation. Here, we report the development and application of a high-throughput microfluidic real-time quantitative PCR (RT-qPCR) approach for generating global miRNA profiles for 27 phenotypically distinct cell populations isolated from normal adult mouse hematopoietic tissues. A total of 80,000 RT-qPCR assays were used to map the landscape of miRNA expression across the hematopoietic hierarchy, including rare progenitor and stem cell populations. We show that miRNA profiles allow for the direct inference of cell lineage relations and functional similarity. Our analysis reveals a close relatedness of the miRNA expression patterns in multipotent progenitors and stem cells, followed by a major reprogramming upon restriction of differentiation potential to a single lineage. The analysis of miRNA expression in single hematopoietic cells further demonstrates that miRNA expression is very tightly regulated within highly purified populations, underscoring the potential of single-cell miRNA profiling for assessing compartment heterogeneity.RT-qPCR | stem cell | hematopoiesis | microfluidic | single cell

miR-99a/100∼125b tricistrons regulate hematopoietic stem and progenitor cell homeostasis by shifting the balance between TGFβ and Wnt signaling

“…S1C). A previously published data set confirmed this expression pattern in murine cells (Petriv et al 2010).…”

Deregulation of microRNAs in myelodysplastic syndrome

“…The most comprehensive analysis implicating miRNAs in hematopoiesis showed that certain miRNAs are distinctly expressed in mouse hematopoietic sub-populations. 15 This finding is supported by Dicerdeficient mice, which are unable to process any mature miRNA. The Dicer-deficient mice are depleted of HSC, 16 exhibit developmental defects in pro-B cells, 17 as well as impaired T-cell differentiation and cytokine production.…”

Encoded Hydrogel Microparticles for Sensitive and Multiplex microRNA Detection Directly from Raw Cell Lysates

“…8 Also, cell-to-cell expression is often heterogeneous, requiring large-scale analysis for the quantification of multiple miRNA expressions at the single-cell level. To translate to a single assay, one often relies on sequence-dependent target amplification via RT-PCR, 31,32 which potentially requires probe-set modification that may be difficult to scale-up. Instead, our versatile system is capable of incorporating a signal-based amplification scheme 23,33−35 such as rolling circle amplification (RCA) without a need for extensive optimization regardless of cell type or miRNA target.…”