scholarly journals Single-Cell Analysis of Murine Long-Term Hematopoietic Stem Cells Reveals Distinct Patterns of Gene Expression during Fetal Migration

PLoS ONE ◽  
2012 ◽  
Vol 7 (1) ◽  
pp. e30542 ◽  
Author(s):  
Jesús Ciriza ◽  
Dominique Hall ◽  
Alison Lu ◽  
Joseph Robert De Sena ◽  
Mufadhal Al-Kuhlani ◽  
...  
Author(s):  
Katherine H. M. Sturgess ◽  
Fernando J. Calero-Nieto ◽  
Berthold Göttgens ◽  
Nicola K. Wilson

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 105-105
Author(s):  
Jennifer Tsai ◽  
Kelsey R. Logas ◽  
Lauren D. Van Wassenhove ◽  
Beruh Dejene ◽  
Che-Hong Chen ◽  
...  

HSC loss in FA is due to failure to resolve DNA inter-strand crosslinks (ICL), which can be induced by reactive aldehydes, radiation, or other clastogenic agents. Aldehyde exposure may occur through environmental sources, e.g. ingestion, absorption, and inhalation, or endogenously as a byproduct of cellular metabolism. The ALDH2*2 genotype, a dominant-negative point mutation in the aldehyde dehydrogenase 2 (ALDH2) gene, causes the "Asian flushing syndrome" when ethanol (EtOH) is ingested, due to decreased metabolism of small aldehydes, particularly acetaldehyde. ALDH2*2 is a disease modifier in FA, causing more rapid bone marrow failure and earlier leukemia onset in doubly affected children. Similarly, mice experimentally doubly knocked out for FANCD2 and ALDH2 demonstrate increased HSC loss, which is accelerated by EtOH exposure. To reduce aldehyde exposure, we developed a small molecule ALDH activator, Alda-1, which increases the enzymatic activity of both wild type (WT) and mutant ALDH2. We hypothesized that DNA damage and HSC loss in FA would be prevented by reduction of the aldehyde load. To test the effects of Alda-1 mediated ALDH2 activation, we generated a novel murine FA model with FANCD2 KO and knock-in of the ALDH2*2 mutation into the murine locus. The FANCD2-/- ALDH2*1/*2 genetic model and parental controls were then tested after exogenous aldehydic challenge and/or therapeutic intervention with Alda-1. Increased aldehydic load was experimentally induced by EtOH administration 10 mg/kg/day IP, while Alda-1 10 ug/kg/day was continuously administered via osmotic pump. For each of these conditions, marrow was analyzed for HSC and progenitor cell (HSPC) number, HSC gene expression, and function. The importance of the altered aldehyde metabolism due to ALDH2*2 genotype was demonstrated by progressive loss of HSPC in ALDH2*2/*2 and FANCD2-/- ALDH2*1/*2 mice, e.g., 5-fold and 2-fold decline in long-term HSC (LT-HSC), respectively, by 36 weeks. Experimental EtOH challenge to increase the aldehyde load precipitously decreased HSC numbers of all genotypes. After 5 weeks of EtOH challenge, LT-HSC decreased 35-fold in FANCD2-/- ALDH2*1/*2, 12.5-fold in FANCD2-/-ALDH2*1/*1, and 10.5-fold in WT mice. Long-term Alda-1 treatment to decrease aldehydic load rescued FA mice from HSC loss. After 7 months of Alda-1 treatment, LT-HSC numbers in FANCD2-/-ALDH2*1/*2 and FANCD2-/-ALDH2*1/*1 were approximately 10-fold higher than untreated controls. There were no clinically observed adverse effects. Aldehyde exposure and Alda-1 treatment altered gene expression of HSC. Principal component analysis and clustering of HSC gene expression showed that the first principal component representing 40% of the variation in gene expression could be attributed to increased aldehydic load, either genetically (ALDH2*2 genotype) or environmentally (EtOH administration) induced, while Alda-1 treatment obviated these effects. HSC from Alda-1 treated mice clustered with those from control WT mice. To test whether Alda-1 improved HSC function as well as phenotypic number, engraftment potential was assessed with competitive repopulation assays of sorted HSC from congenic untreated donors vs short-term (3 weeks) Alda-1 treated donors. HSC from Alda-1 treated mice had 2-4 fold greater granulocyte repopulating capacity than those from the untreated donors. Our results demonstrate that Alda-1 treatment rescues HSC from aldehyde induced loss, whether from genetic variation (FANCD2- and/or ALDH2*2) or experimental challenge (EtOH administration). Furthermore, Alda-1 treatment prevents the abnormal HSC gene expression induced by increased aldehydic load. HSC function is improved by Alda-1 with greater repopulating capacity observed even after short-term treatment. These preclinical experiments provide compelling proof-of-concept that sustained activation of ALDH2 can prevent HSC loss in FA. Potential applications include long-term administration to prevent the development of marrow failure or leukemia, and HSC expansion to increase the number of cells available for gene therapy with autologous HSC. Our results suggest that a clinical trial of ALDH2 activation in FA patients to prevent marrow failure is warranted. Disclosures Van Wassenhove: U.S. Patent Office: Patents & Royalties: patent pending - submitted for ALDH2 activators to expand hematopoietic stem cells. Chen:Foresee Pharmaceuticals: Patents & Royalties: patents licensed to Foresee related to compounds that activate aldehyde dehydrogenase 2 (ALDH2) and correct the dysfunction in ALDH2*2; U.S. Patent Office: Patents & Royalties: patent pending - submitted for aldehyde dehydrogenase 2 (ALDH2) activators to expand hematopoietic stem cells. Mochly-Rosen:Foresee Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Patents & Royalties: patents licensed to Foresee related to compounds that activate aldehyde dehydrogenase 2 (ALDH2) and correct the dysfunction in ALDH2*2; U.S. Patent Office: Patents & Royalties: patent pending - submitted for aldehyde dehydrogenase 2 (ALDH2) activators to expand hematopoietic stem cells. Weinberg:U.S. Patent Office: Patents & Royalties: patent pending - submitted for aldehyde dehydrogenase 2 (ALDH2) activators to expand hematopoietic stem cells.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1267-1267
Author(s):  
Elisa Tomellini ◽  
Iman Fares ◽  
Bernhard Lehnertz ◽  
Jalila Chagraoui ◽  
Nadine Mayotte ◽  
...  

Abstract Hematopoietic stem cell (HSC) transplantation constitutes one of the most effective therapeutic strategies to treat numerous hematological diseases. Cord blood (CB) is one of the most attractive donor sources of stem cells for this procedure due to its rapid availability, HLA mismatches tolerance and low associated risk of chronic graft-versus-host disease. However, these advantages are offset by the limited cell dose in CB units, which can contribute to delayed hematopoietic engraftment following transplantation. Mastering ex vivo HSC expansion is therefore of great interest for clinical purposes and for genetic manipulation. HSCs can be functionally defined as either long-term (LT-HSC), providing life-long hematopoiesis and characterized by delayed engraftment pattern, or short-term repopulating stem cells (ST-HSC), providing early and transient hematopoietic recovery. Major hurdles hindering the study of these cell populations is the current inability to evaluate their content in cultured samples and the lack of understanding of the molecular mechanisms regulating stem cell self-renewal ex vivo. Those issues highly benefited from the discovery by our laboratory of the small molecule UM171, which promote HSC expansion ex vivo, as well as from the identification of EPCR as one of the most reliable surface markers for cultured HSCs. We now describe the identification of Integrin-α3 (ITGA3) as a novel marker for cultured HSCs. ITGA3 expression was found to be sufficient to split the primitive EPCR+CD90+CD133+CD34+CD45RA- HSC population in two functionally distinct fractions presenting only short-term (ITGA3-) and both short-term and long-term (ITGA3+) repopulating potential. ITGA3+ cells, as opposed to the ITGA3- fraction, exhibited robust multilineage differentiation potential and serial reconstitution ability in immunocompromised mice. This combination of markers identifies repopulating HSCs in culture by FACS beyond what is currently possible with other approaches, with a frequency of LT-HSC found in the ITGA3+ population estimated at 1:38 in day 7 UM171 expanded CB-cells. Moreover, lentiviral-mediated ITGA3 knockdown was shown to compromise the LT repopulating activity of cultured HSC in vivo. Gene expression profiling revealed striking molecular similarity between ITGA3+ and ITGA3- cells, showing overrepresentation of genes involved in fundamental hematopoietic programs known to govern HSC specification and function in both of these populations. However, ITGA3+ and ITGA3- subsets clearly clustered separately by principle component analysis, indicating broad differences in gene expression. Concordantly with their primitive phenotype, stem cell markers and cell quiescence are gene sets enriched in ITGA3+ cells, while progenitor markers, DNA replication, M/G1 and G2/M checkpoints, mRNA processing, reduction of hypoxia and Myc targets were significantly downregulated in these cells. Altogether, our results indicate that ITGA3 is a reliable marker for cultured HSCs, improving the accuracy of prospective HSC identification in culture. Deciphering the function of genes upregulated in primitive ITGA3+ HSCs will represent an invaluable resource for dissecting the genetic programs that govern hematopoietic stem cells biology. Disclosures Sauvageau: ExCellThera: Employment, Equity Ownership.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 725-725
Author(s):  
Pengxu Qian ◽  
Bony De Kumar ◽  
Youngwook Ahn ◽  
Christof Nolte ◽  
Ariel Paulson ◽  
...  

Abstract The balance between self-renewal and multilineage differentiation in hematopoietic stem cells (HSCs) is orchestrated by genetic regulatory networks, which are constituted by hundreds of thousands of cis-regulatory elements, such as promoters, enhancers, insulators, etc. Aberrant mutations in these cis-acting modules and their trans-acting factors have been frequently found in hematopoietic malignancies including leukemia. Although next-generation sequencing technologies have identified comprehensive maps of these modules, much remains unknown about their physiological functions and underlying mechanisms in HSC maintenance and leukemogenesis. Our transcriptome analysis in 17 murine hematopoietic cell types, including HSCs, committed progenitors and lineage cells, showed that most of HoxB cluster genes were predominantly enriched in the permanently reconstituting long-term (LT) HSCs. Interestingly, one of the two putative enhancers within HoxB cluster, identified by H3K27ac ChIP-Seq analysis, shared the same sequence as the retinoic acid responsive element DERARE, which was recently reported to regulate multiple HoxB gene expression in the central nervous system. To test whether DERARE is required for normal hematopoiesis, we utilized the DERARE knockout mouse and found that homozygous deletion of DERARE led to 2-fold reduction in both the frequency and absolute number of LT-HSCs. Functionally, limiting dilution, competitive repopulating unit assays showed a 2.5-fold decrease in functional HSCs of DERAREΔ mice compared to wildtype control. We further performed serial transplantation and observed a 4.3-fold reduction of repopulation rate after secondary transplantation of DERAREΔ HSCs, indicating long-term reconstitution capacity was impaired. Mechanistically, RNA-Seq in LT-HSCs from DERAREΔ mice exhibited significantly enriched apoptosis pathway in DERAREΔ compared with that from Wt control. Furthermore, DNA methylation analysis showed gradually gained methylation on DERARE during HSC differentiation, which is negatively correlated with HoxB cluster gene expression, suggesting DERARE might be a methylation-sensitive enhancer to control HoxB genes. Moreover, HoxB gene expression is markedly upregulated in Dnmt3a KO HSCs, indicating that Dnmt3a is responsible for the DERARE methylation in HSCs. Finally, the analysis of clinical data from acute myeloid leukemia 200 patients in the Cancer Genome Atlas project revealed that lowly methylated DERARE was significantly correlated with overexpression of HoxB genes, high cytogenetic risk, and poor prognosis, suggesting abnormal regulation of DERARE contributes to leukemogenesis. Collectively, our study demonstrates the essential roles of the cis-regulatory element DERARE in both maintenance of LT-HSCs and contribution to leukemogenesis through regulation of HoxB cluster genes. Disclosures No relevant conflicts of interest to declare.


2004 ◽  
Vol 199 (3) ◽  
pp. 295-302 ◽  
Author(s):  
Hina Takano ◽  
Hideo Ema ◽  
Kazuhiro Sudo ◽  
Hiromitsu Nakauchi

How hematopoietic stem cells (HSCs) commit to a particular lineage is unclear. A high degree of HSC purification enabled us to address this issue at the clonal level. Single-cell transplantation studies revealed that 40% of the CD34−/low, c-Kit+, Sca-1+, and lineage marker− (CD34−KSL) cells in adult mouse bone marrow were able, as individual cells, to reconstitute myeloid and B- and T-lymphoid lineages over the long-term. Single-cell culture showed that >40% of CD34−KSL cells could form neutrophil (n)/macrophage (m)/erythroblast (E)/megakaryocyte (M) (nmEM) colonies. Assuming that a substantial portion of long-term repopulating cells can be detected as nmEM cells within this population, we compared differentiation potentials between individual pairs of daughter and granddaughter cells derived in vitro from single nmEM cells. One of the two daughter or granddaughter cells remained an nmEM cell. The other showed a variety of combinations of differentiation potential. In particular, an nmEM cell directly gave rise, after one cell division, to progenitor cells committed to nm, EM, or M lineages. The probability of asymmetric division of nmEM cells depended on the cytokines used. These data strongly suggest that lineage commitment takes place asymmetrically at the level of HSCs under the influence of external factors.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3773-3773
Author(s):  
Meaghan Boileau ◽  
Selin Jessa ◽  
Samantha Worme ◽  
Damien Faury ◽  
Nada Jabado ◽  
...  

Acute myeloid leukemia (AML) develops in a step-wise manner from pre-leukemic clonal expansion to full-blown disease driven by aberrant epigenetic changes. Indeed, regulators of the epigenome such as DNMT3A, TET2, IDH1/2, EZH2 and ASXL1 are often mutated in pre-leukemia and myeloid malignancies. We and others identified K27M/I mutations in histone H3 in AML (Boileau et al. Nat Commun, 2019; Lehnertz et al. Blood, 2017). We demonstrated that K27 mutations are found in pre-leukemic hematopoietic stem cells (HSCs), are enriched in secondary AML, expand the functional human HSC pool and increase leukemic aggressiveness. Transcriptomic and epigenomic analysis determined that K27 mutations alter gene expression through a global decrease in promoter H3K27 tri-methylation and a gene-specific increase in H3K27 acetylation in leukemic cells (Boileau et al. Nat Commun, 2019). Here, we have analyzed the effects of the K27M mutation on HSCs at the single-cell level to understand its role in pre-leukemic clonal expansion. Healthy CD34+CD38- human cord blood cells were transduced with HIST1H3H WT or K27M and injected intrafemorally into sub-lethally irradiated NSG mice. After 14 weeks, bone marrow cells from the femur were collected and sorted for CD34+ transduced (GFP+) cells. Single-cell transcriptomics were performed by generating gene expression libraries from ~8,000 CD34+ cells using the 10X Genomics technology and sequenced using HiSeq4000. We have performed initial clustering and dimensionality reduction (t-SNE and UMAP) and identified 10 and 11 distinct clusters in the WT and K27M samples, respectively. Gene sets distinguishing the individual clusters have been determined. Using published gene lists for primitive hematopoietic cell types, the clusters have been assigned to specific cell types such as HSC, granulocyte-monocyte progenitors (GMP), common myeloid progenitors (CMP), multi-lymphoid progenitors (MLP) and megakaryocyte-erythroid progenitors (MEP) (Laurenti et al. Nat Immunol, 2013). Preliminary joint clustering analysis indicates the presence of two distinct clusters for the WT and K27M samples that were both assigned as "HSCs" in individual clustering. Further analysis to identify the differences in the clusters and cell populations between WT and K27M samples is being performed and will be presented at this meeting. Overall, this single-cell transcriptomic analysis will aid in determining the mechanism of action of the K27M mutant histone in pre-leukemic HSC clonal expansion. In addition, we will be performing similar single-cell analysis on HSCs expressing mutant ASXL1 as a comparison. Further understanding of the role of mutations in epigenetic regulators, such as histone H3 and ASXL1, in pre-leukemic clonal hematopoiesis will provide valuable insight on how to better prevent and treat AML and other myeloid malignancies. Disclosures No relevant conflicts of interest to declare.


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