Modern genome-wide genetic approaches to reveal intrinsic properties of stem cells

Functions and regulatory mechanisms of resting hematopoietic stem cells: a promising targeted therapeutic strategy

Hematopoietic stem cells (HSCs) are the common and essential precursors of all blood cells, including immune cells, and they are responsible for the lifelong maintenance and damage repair of blood tissue homeostasis. The vast majority (> 95%) of HSCs are in a resting state under physiological conditions and are only activated to play a functional role under stress conditions. This resting state affects their long-term survival and is also closely related to the lifelong maintenance of hematopoietic function; however, abnormal changes may also be an important factor leading to the decline of immune function in the body and the occurrence of diseases in various systems. While the importance of resting HSCs has attracted increasing research attention, our current understanding of this topic remains insufficient, and the direction of clinical targeted treatments is unclear. Here, we describe the functions of HSCs, analyze the regulatory mechanisms that affect their resting state, and discuss the relationship between resting HSCs and different diseases, with a view to providing guidance for the future clinical implementation of related targeted treatments.

Polycomb group proteins in hematopoietic stem cell aging and malignancies

Protection of the transcriptional "stemness" network is important to maintain a healthy hematopoietic stem cells (HSCs) compartment during the lifetime of the organism. Recent evidence shows that fundamental changes in the epigenetic status of HSCs might be one of the driving forces behind many age-related HSC changes and might pave the way for HSC malignant transformation and subsequent leukemia development, the incidence of which increases exponentially with age. Polycomb group (PcG) proteins are key epigenetic regulators of HSC cellular fate decisions and are often found to be misregulated in human hematopoietic malignancies. In this review, we speculate that PcG proteins balance HSC aging against the risk of developing cancer, since a disturbance in PcG genes and proteins affects several important cellular processes such as cell fate decisions, senescence, apoptosis, and DNA damage repair.

MicroRNAs play a role in the development of human hematopoietic stem cells

MicroRNAs (miRNAs) are a class of recently discovered noncoding RNA genes that post-transcriptionally regulate gene expression. It is becoming clear that miRNAs play an important role in the regulation of gene translation during development. However, in mammals, expression data are principally based on whole tissue analysis and are still very incomplete. We isolated CD34(+)CD38(-) hematopoietic stem cells (HSCs) from human umbilical cord blood, on the basis of cell-surface markers using fluorescence-activated cell sorting (FACS). Also, CD34(+) subpopulation was FACS isolated as the control. Next, using microarray containing oligonucleotides corresponding to 517 miRNAs from human, mouse, and rat genomes, we obtained miRNA gene expression profiles of both subpopulations. We focused on the HSCs correlative miRNAs with comparison to the control. The miRNAs of particular interest were confirmed by real-time RT-PCR. HSCs-overexpressed hsa-miR-520h and underexpressed hsa-miR-129 were selected for target prediction and analysis. The result showed that EIF2C3 and CAMTA1, genes related to miRNAs processing or transcription regulation, were proved to be real targets for hsa-miR-129. And ABCG2, involved in stemness maintaining, a real target for hsa-miR-520h. Finally, we chose hsa-miR-520h, enriched in HSCs but low in CD34(+) cells, for functional characterization, because of its possible role in differentiation of HSCs by regulating ABCG2. As a result, hsa-miR-520h transduction into CD34(+) cells greatly increased number of different progenitor colonies in Colony-Forming-Cell assays, suggesting that hsa-miR-520h may promote differentiation of HSCs into progenitor cells by inhibiting ABCG2 expression. This study paves the way for identifying HSC-specific miRNAs and their roles in HSC development.

Exploiting regulatory variation to identify genes underlying quantitative resistance to the wheat stem rust pathogen Puccinia graminis f. sp. tritici in barley

We previously mapped mRNA transcript abundance traits (expression-QTL or eQTL) using the Barley1 Affymetrix array and 'whole plant' tissue from 139 progeny of the Steptoe x Morex (St/Mx) reference barley mapping population. Of the 22,840 probesets (genes) on the array, 15,987 reported transcript abundance signals that were suitable for eQTL analysis, and this revealed a genome-wide distribution of 23,738 significant eQTLs. Here we have explored the potential of using these mRNA abundance eQTL traits as surrogates for the identification of candidate genes underlying the interaction between barley and the wheat stem rust fungus Puccinia graminis f. sp. tritici. We re-analysed quantitative 'resistance phenotype' data collected on this population in 1990/1991 and identified six loci associated with barley's reaction to stem rust. One of these coincided with the major stem rust resistance locus Rpg1, that we had previously positionally cloned using this population. Correlation analysis between phenotype values for rust infection and mRNA abundance values reported by the 22,840 GeneChip probe sets placed Rpg1, which is on the Barley1 GeneChip, in the top five candidate genes for the major QTL on chromosome 7H corresponding to the location of Rpg1. A second co-located with the rpg4/Rpg5 stem rust resistance locus that has been mapped in a different population and the remaining four were novel. Correlation analyses identified candidate genes for the rpg4/Rpg5 locus on chromosome 5H. By combining our data with additional published mRNA profiling data sets, we identify a putative sensory transduction histidine kinase as a strong candidate for a novel resistance locus on chromosome 2H and compile candidate gene lists for the other three loci.

Unique glycerophospholipid signature in retinal stem cells correlates with enzymatic functions of diverse long-chain acyl-CoA synthetases

Lipidomics is an emerging research field that comprehensively characterizes lipid molecular species and their metabolic regulation and biological roles. We performed the first lipidomics study on glycerophospholipids (GPLs) in adult mammalian retinal stem cells (RSCs) and non-RSC control cells. A unique GPL signature identified by electrospray ionization tandem mass spectrometry showed new prominent peaks of 16:0 (sn-1)-18:0 (sn-2) or 16:0-16:0 saturated fatty acids, instead of 18:0-20:4 or 18:0-22:6 polyunsaturated essential fatty acids, at 720 m/z of phosphatidylethanolamine, 764 m/z of phosphatidylserine, and 809 m/z of phosphatidylinositol in RSCs (sphere colony RSCs and enriched RSCs), but not in non-RSCs (retinal cells, ciliary cells, sphere colony-derived retinal cells, and nonretinal cells). To seek whether the GPL signature was associated with long-chain acyl-CoA synthetase (LACS), a potential modulator of fatty acid profiles in de novo GPL synthesis, we analyzed gene expression, catabolic activity, substrate selectivity, and inhibitor sensitivity of diverse LACSs. LACSs in RSCs mediated less utilization by GPLs of polyunsaturated essential fatty acids, including arachidonic acid (20:4 [n-6], a second messenger in cell signaling), which was accompanied by lower plasma membrane fluidity in proliferating RSCs compared with differentiated non-RSCs. These novel findings suggest that LACS-associated GPL signature and cell membrane fluidity may participate in regulating proliferation versus differentiation in RSCs and, perhaps, other types of stem cells.

Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis

Hematopoietic stem cells (HSC) produce all blood cell lineages by virtue of their capacity to self-renew and differentiate into progenitors with decreasing cellular potential. Recent studies suggest that epigenetic mechanisms play an important role in controlling stem cell potency and cell fate decisions. To investigate this hypothesis in HSC, we have modified the conventional chromatin immunoprecipitation assay allowing for the analysis of 50,000 prospectively purified stem and progenitor cells. Together with bisulfite sequencing analysis, we found that methylated H3K4 and AcH3 and unmethylated CpG dinucleotides colocalize across defined regulatory regions of lineage-affiliated genes in HSC. These active epigenetic histone modifications either accumulated or were replaced by increased DNA methylation and H3K27 trimethylation in committed progenitors consistent with gene expression. We also observed bivalent histone modifications at a lymphoid-affiliated gene in HSC and downstream transit-amplifying progenitors. Together, these data support a model in which epigenetic modifications serve as an important mechanism to control HSC multipotency.

Nitric oxide: emerging concepts about its use in cell-based therapies

Regenerative medicine is an emerging clinical discipline in which cell-based therapies are used to restore the functions of damaged or defective tissues and organs. Along with the well-established use of cells derived from bone marrow or pancreatic islets, novel approaches of cell therapy have recently emerged that appear particularly promising; that is, those using cell-based vaccines and stem cells. This review focuses on the recent developments of these experimental therapeutic approaches and their drawbacks, with specific focus on dendritic cell vaccines in tumours and mesoangioblasts in muscular dystrophies. The authors discuss how the unique properties of a gaseous messenger, NO, may be exploited to overcome some of the drawbacks of these cell-based approaches in combined therapies based on NO-releasing drugs and cell delivery.