Hematopoietic stem cells (HSCs) are tightly controlled to maintain a balance between myeloid and lymphoid cell differentiation. Gata2 is a pivotal hematopoietic transcription factor required for HSC generation and maintenance. We generated a zebrafish mutant for the mouse Gata2 orthologue, gata2b. We found that in adult zebrafish, gata2b is required for both neutrophilic-and monocytic lineage differentiation. Single cell transcriptome analysis revealed that the myeloid defect present in Gata2b deficient zebrafish arise in the most immature hematopoietic stem and progenitor cell (HSPC) compartment and that this population is instead committed towards the lymphoid and erythroid lineage. Taken together, we find that Gata2b is vital for the fate choice between the myeloid and lymphoid lineages.
Introduction: Severe congenital neutropenia (SCN) is a genetically heterogeneous disease characterized by recurrent infections and a predisposition for malignant transformation. A wide variety of autosomal dominant or sporadic mutations in ELANE encoding neutrophil elastase (NE) are the most frequent cause of SCN, whereas recessive mutations in HAX1 are responsible for the autosomal recessive form of SCN known as Kostmann syndrome. How ELANE and HAX1 mutations cause SCN is still unclear. A prevailing hypothesis is that cellular stresses either caused by protein misfolding or malfunction in the case of ELANE-SCN, or by mitochondrial dysfunction in the case of HAX1-SCN, are drivers of the neutropenia. We focused on the role of the promyelocytic leukemia protein (PML) because PML is implicated in controlling cellular stress responses caused by reactive oxygen species (ROS) and protein misfolding and may exert both oncogenic and tumor-suppressive functions. Aims: (1) To elucidate which cellular stress mechanisms are involved in different genetic subtypes of SCN. (2) To assess the role of PML in SCN with a predicted ELANE misfolding mutation. Methods: We generated induced pluripotent stem cells (iPSCs) from healthy control and SCN patients with non-overlapping mutations: ELANE-I60F, ELANE-R103L and HAX1-W44X. CD34+CD45+ Hematopoietic Stem and Progenitor cells (HSPCs) were derived from iPSCs using the STEMdiff™ Hematopoietic Kit (STEMCELL Technologies). PML-/- iPSCs were created by introducing a stop codon in exon 3, shared by all PML isoforms, using CRISPR/Cas9 mediated genome editing. Results: HSPCs derived from the SCN-iPSCs showed increased ROS levels as measured with CellROX Deep Red. Consequently, nuclear translocation of the antioxidant regulatory factor NRF2 was significantly elevated in both ELANE- and HAX1-mutant SCN HSPCs relative to controls. Mutation prediction analysis (Venselaar, BMC Bioinformatics 2010) showed that ELANE-I60F likely causes NE protein misfolding, whereas the ELANE-R103L mutation predictably causes NE malfunction by disrupting interactions with other proteins. The mutation in HAX1 was predicted to result in nonsense-mediated mRNA decay. Transcriptome analysis using Gene Set Enrichment Analysis (GSEA) confirmed upregulation of the nonsense mediated decay pathway in HAX1 mutant HSPCs and in line with previous studies (Klein et al, 2008), FACS analysis using TMRM and Mitotracker Red showed that loss of HAX1 protein reduced mitochondrial membrane integrity. Surprisingly, and in apparent conflict with the mutation prediction analysis, GSEA on ELANE-I60F HSPCs did not show increased expression of the classical unfolded protein response (UPR) pathway. Because PML has been implicated as an alternative player involved in degrading misfolded proteins (Guo, Mol Cell 2014), we investigated a possible link between ELANE-I60F and PML. Immunofluorescent staining showed increased numbers of PML nuclear bodies (PML-NBs) in ELANE-I60F derived HPSCs, but not in ELANE-R103L or HAX1-W44X HSPCs. Furthermore, GSEA showed upregulation of transcripts associated with PML chromatin binding in ELANE-I60F, but not in ELANE-R103L or HAX1-W44X cells. Deletion of PML by CRISPR-Cas9 revealed that PML enhanced MYC and mTORC1-induced transcription and cell cycle signatures in HSPCs from ELANE-I60F, suggestive of an oncogenic role of PML by inducing proliferation and metabolism in ELANE-I60F. In contrast, PML inhibited these pathways in HSPCs derived from healthy control iPSCs, indicative of its tumor-suppressive function in normal HSPCs. Finally, and perhaps most intriguingly, transcriptome analysis revealed that ELANE-I60F HSPCs expressed 5-fold higher levels of (mutant) ELANE transcripts than control HSPCs, which were reduced to basal levels after deletion of PML. Conclusion: HAX1 and ELANE mutations cause oxidative stress in SCN-HSPCs by distinct mechanisms. We provide evidence for a dual role of PML in the pathogenesis of SCN caused by an ELANE mutation (I60F) associated with NE misfolding: (1) NE misfolding and increased oxidative stress cause elevated formation of PML-NBs, leading to increased expression of proliferation, cell cycle and metabolism associated transcripts, (2) PML strongly enhances the levels of ELANE transcripts, thus driving the expression of the disease causative ELANE mutant through a feed-forward mechanism. Disclosures No relevant conflicts of interest to declare.
Background: Paroxysmal nocturnal haemoglobinuria (PNH) is a life-threatening clinical syndrome caused by acquired mutations in PIGA in the haemopoietic compartment. The clinicopathological features of PNH can overlap with aplastic anaemia (AA) and myelodysplastic syndrome (MDS) and these entities may represent different manifestations of a common underlying pathological process. To date, the landscape of acquired mutations in de novo PNH (i.e. not preceded by a formal diagnosis of AA/MDS) remains incompletely characterised. Aims: To characterise the spectrum of acquired mutations in the cellular and cell-free compartments in a cohort of patients with de novo PNH. Methods: DNA was extracted from peripheral blood leukocytes (n = 19) or bone marrow (n = 2) from 21 patients with a clinicopathological diagnosis of PNH (defined as a detectable PNH clone by flow cytometry, active haemolysis and not meeting formal diagnostic criteria for MDS or AA). Patients with a pre-existing diagnosis of AA or MDS were excluded. Cell-free DNA (cfDNA) was also collected from 19 patients. DNA sequencing libraries were prepared from cellular DNA using both the Peter MacCallum Cancer Centre PanHaem hybridisation and Myeloid amplicon panels (sensitivity 5%) which includes sequence variant detection for recurrently mutated genes associated with haematological malignancy and whole genome copy number assessment. A custom panel using Anchored Multiplex PCR target enrichment chemistry and unique molecular barcodes was used for cfDNA sequencing (sensitivity <1%). Results: At time of sampling 18 of 21 patients were two or more years post diagnosis (median time since diagnosis of 8 years) with a median age of 41 years (range 23 -82). 16 patients were being treated with complement inhibitor therapy. PIGA mutations were detected in 19 patients, with multiple mutations detected in half the cohort (11 patients, range 2 -9 PIGA mutations per patient). 21 mutations were detected in the cellular DNA, while cfDNA sequencing revealed 30 additional PIGA mutations at low allelic burden (median allele frequency 2.19%, range 0.57% -4.86%) (20 frameshift, 15 missense, 10 splice site, 6 nonsense). Two patients did not have a detectable PIGA mutation but instead harboured focal copy number losses at the PIGA locus, which also involved ZRSR2 in the minimal deleted region. Remarkably, 7 of 21 patients had truncating ASXL1 mutations detectable in both the cellular and cfDNA (9 frameshift, 3 nonsense); in 4 patients multiple ASXL1 mutations were detected. Clonal pathogenic mutations were also detected in U2AF1 (2 patients) and BCOR (1 patient). Patients with ASXL1 and/or U2AF1 mutations had significantly lower neutrophil counts (mean 1.7 vs 1.08, p = 0.021) compared to those without. Haemoglobin and platelet counts were not statistically different between the two groups. Summary/Conclusion: Multiple subclonal PIGA mutations are detectable in patients with PNH. In addition acquired pathogenic variants in ASXL1, U2AF1 and ZRSR2 were detected in a third of the cohort. L...
Background: C/EBPa is a lineage determining transcription factor, critical for terminal cell differentiation in different tissues including the bone marrow (BM), lung, liver, and adipocytes. Adequate CEBPA levels are needed to maintain the haematopoietic stem cell (HSC) pool and to promote neutrophilic differentiation. This knowledge points towards the importance of CEBPA dosage at different stages of differentiation. Aim: To investigate how CEBPA dosage is regulated at the transcriptional level by specific enhancer(s) and to study their role in haematopoiesis. Results: Chromatin immunoprecipitation for the active mark H3K27ac followed by deep sequencing (ChIP-seq), revealed eight putative regulatory elements within the CEBPA locus. One enhancer showed marked H3K27ac enrichment at +42Kb downstream of CEBPA particularly in CD34+ haematopoietic stem cells (HSCs), implying a role for CEBPA regulation at earlier stages of haematopoiesis. ChIP-Seq experiments revealed binding of RUNX1, ERG, PU.1, FLI1 and GATA2 to this +42Kb enhancer in CD34+ BM cells. Moreover, myeloid cell lines MOLM1 and U937 also showed H3K27ac enrichment at this enhancer, indicating that its activity is maintained upon myeloid differentiation. In contrast, active histone marks were completely devoid at this element in CEBPA expressing lung (A549) and liver (HepG2) cell lines, indicating hematopoietic specificity of this enhancer. Chromatin looping between the +42Kb enhancer and the CEBPA promoter was demonstrated by 4C-Seq, highlighting the specificity of this enhancer in CEBPA regulation. Furthermore, using CRISPR/Cas9 technology we deleted the +42Kb enhancer in the myeloid cell line THP-1 and showed 70% reduction of CEBPA mRNA levels. The +42Kb enhancer is conserved and located at +37Kb near Cebpa in mice. Using CRISPR/Cas9 system, we deleted the +37Kb enhancer in one-cell stage zygotes. Heterozygous mice were inter-crossed and F1 generation mice were born at normal mendelian ratios. Morphological and flow-cytometric analysis of peripheral blood and BM at 8-10 weeks of age, showed 10-20 fold decrease in (MAC1+/GR1+) neutrophil counts in homozygous +37Kb-/- mice, compared to +37Kbwt/wt and +37Kb-/wt controls. In line with the block of neutrophil development, flow-cytometric analysis revealed an increase (2 fold) in CD34+CD16/32low common myeloid progenitors and a decrease (2 fold) in the CD34+CD16/32high granulocyte/ monocyte progenitorsof +37Kb-/- mice. From these findings we hypothesized that the absence of the +37Kb enhancer disturbs the myeloid differentiation program via reduced Cebpa levels. In fact, Cebpa expression levels were reduced by 60-80% in bone marrow of +37Kb-/- mice, but unchanged in other Cebpa -expressing tissues such as lung and liver, indicating tissue specificity of this enhancer. Diminished Cebpa expression levels were accompanied by decreasedexpression of Cebpa target genes, including Csf3r. In line with this, bone marrow progenitor cells from +37Kb-/- mice were completely unresponsive to Csf3 in a colony forming assay. Given the importance of Cebpa in HSCs maintenance, we investigated the HSC population and found that long-term HSCs (CD48- CD150+) and short-term HSCs (CD48- CD150-) were depleted in the bone marrow of the +37Kb-/- mice. HSC depletion was accompanied by an increase in the CD48+/CD150- multipotent progenitors (MPPs). The +37Kb-/- MPPs, unlike controls, were able to serially replate in vitro under IL-3, GM-CSF, IL-6, SCF growth factor conditions with minimal evidence of differentiation, suggesting a leukemogenic potential. Reintroduction of Cebpa cDNA into +37Kb-/- MPPs fully recovered neutrophil development. Conclusion: We conclude that the +37Kb enhancer is tissue-specific and plays a central role in haematopoiesis regulating Cebpa dosage. Our study reveals that the bone marrow maintains its integrity through the activity of the +37Kb enhancer, which (1) prevents HSC exhaustion and (2) preserves neutrophilic development. The in vitro replating capacity of MPPs isolated from +37Kb-/- animals suggests that aberrant control of this enhancer may be a primary leukaemogenic event. In line with this, it is important to note that the conserved enhancer in humans (+42 KB) is a frequent target for oncogenic transcription factors such as AML1-ETO or EVI1, two oncogenes which are found in two distinct subtypes of AMLs with very low C/EBPa expression. Disclosures No relevant conflicts of interest to declare.
Cytotoxic CD8+ T lymphocytes (CTLs) play a major role in protection against chronic viral infections and tumors. Chronic antigen stimulation in both conditions leads to CTL exhaustion and failure of CTLs to efficiently eradicate tumors and virally infected cells. miRNAs are small, non-coding RNA molecules that participate in post-transcriptional gene regulation. This study aimed to determine the core miRNA signature of CTL exhaustion in mouse models of both tumors and chronic infection. Exhausted anti-tumor CTLs were isolated from tumors of mice that received 10^6 mouse mesothelioma cells (AE17sOVA) followed by an adoptive transfer of 10^4 CD45.1+ OT-I cells. Effector anti-viral CTLs were isolated from mice adoptively transferred with 10^4 CD45.1+ OT-I cells or P14 cells and infected with WSN-OVA or LCMV Armstrong respectively. For exhausted anti-viral CTLs, mice were adoptively transferred with 10^4 CD45.1+ P14 cells and infected with LCMV-Cl13. Single cell suspensions were prepared from the different tissues, live CTLs were FACS sorted, RNA isolated and small RNA-seq was performed. Principle component analysis (PCA) of miRNA expression revealed that exhausted anti-tumor CTLs and anti-LCMV Cl13 CTLs cluster apart from effector anti-viral CTLs (WSN-OVA and LCMV Armstrong). Differential expression analysis identified 73 miRNAs commonly shared between the exhausted day anti-tumor CTL and anti-viral CTL. Using RNA sequencing of two different models of exhaustion, distinct RNA profiles common in exhausted CTLs were found. This core miRNA signature can now be used to manipulate the expression of specific miRNA to potentially prevent or revert CTL exhaustion and improve the CTL response against tumors and/or chronic infections.
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