Comprehensive microRNA expression profiling of the hematopoietic hierarchy.
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.
Petriv
O I
OI
Center for High-Throughput Biology, Department of Physics and Astronomy, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.
Kuchenbauer
F
F
Delaney
A D
AD
Lecault
V
V
White
A
A
Kent
D
D
Marmolejo
L
L
Heuser
M
M
Berg
T
T
Copley
M
M
Ruschmann
J
J
Sekulovic
S
S
Benz
C
C
Kuroda
E
E
Ho
V
V
Antignano
F
F
Halim
T
T
Giambra
V
V
Krystal
G
G
Takei
C J F
CJ
Weng
A P
AP
Piret
J
J
Eaves
C
C
Marra
M A
MA
Humphries
R K
RK
Hansen
C L
CL
D000818:Animals; D001854:Bone Marrow Cells / Q000166:cytology / Q000378:metabolism; D019070:Cell Lineage / Q000235:genetics*; D016000:Cluster Analysis; D005260:Female; D005434:Flow Cytometry; D020869:Gene Expression Profiling; D006412:Hematopoietic Stem Cells / Q000166:cytology / Q000378:metabolism*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
D035683:MicroRNAs