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1.
Nature ; 615(7950): 127-133, 2023 03.
Article in English | MEDLINE | ID: mdl-36813966

ABSTRACT

Haematopoietic stem cells (HSCs) are a rare cell type that reconstitute the entire blood and immune systems after transplantation and can be used as a curative cell therapy for a variety of haematological diseases1,2. However, the low number of HSCs in the body makes both biological analyses and clinical application difficult, and the limited extent to which human HSCs can be expanded ex vivo remains a substantial barrier to the wider and safer therapeutic use of HSC transplantation3. Although various reagents have been tested in attempts to stimulate the expansion of human HSCs, cytokines have long been thought to be essential for supporting HSCs ex vivo4. Here we report the establishment of a culture system that allows the long-term ex vivo expansion of human HSCs, achieved through the complete replacement of exogenous cytokines and albumin with chemical agonists and a caprolactam-based polymer. A phosphoinositide 3-kinase activator, in combination with a thrombopoietin-receptor agonist and the pyrimidoindole derivative UM171, were sufficient to stimulate the expansion of umbilical cord blood HSCs that are capable of serial engraftment in xenotransplantation assays. Ex vivo HSC expansion was further supported by split-clone transplantation assays and single-cell RNA-sequencing analysis. Our chemically defined expansion culture system will help to advance clinical HSC therapies.


Subject(s)
Cell Culture Techniques , Cell Proliferation , Cytokines , Hematopoietic Stem Cells , Humans , Cell Proliferation/drug effects , Clone Cells/cytology , Clone Cells/drug effects , Clone Cells/metabolism , Fetal Blood/cytology , Hematopoietic Stem Cell Transplantation , Hematopoietic Stem Cells/cytology , Hematopoietic Stem Cells/drug effects , Hematopoietic Stem Cells/metabolism , Phosphatidylinositol 3-Kinases/metabolism , Cell Culture Techniques/methods , Albumins , Caprolactam , Polymers , Receptors, Thrombopoietin , Transplantation, Heterologous , Single-Cell Gene Expression Analysis
2.
Nature ; 608(7924): 724-732, 2022 08.
Article in English | MEDLINE | ID: mdl-35948631

ABSTRACT

The lymphocyte genome is prone to many threats, including programmed mutation during differentiation1, antigen-driven proliferation and residency in diverse microenvironments. Here, after developing protocols for expansion of single-cell lymphocyte cultures, we sequenced whole genomes from 717 normal naive and memory B and T cells and haematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells, with higher burdens in memory cells than in naive cells, and with T cells accumulating mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for approximately half of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every on-target IGHV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than in stem cells, with around 15% of deletions being attributable to off-target recombinase-activating gene activity. DNA damage from ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory cells. The mutation burden and signatures of normal B cells were broadly similar to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes that are active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.


Subject(s)
Lymphocytes , Mutation , B-Lymphocytes/cytology , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , B-Lymphocytes/pathology , Cell Differentiation , Cell Proliferation , Cellular Microenvironment , DNA Damage/genetics , DNA Damage/radiation effects , Germinal Center/cytology , Germinal Center/immunology , Humans , Immunologic Memory/genetics , Lymphocytes/cytology , Lymphocytes/immunology , Lymphocytes/metabolism , Lymphocytes/pathology , Neoplasms/genetics , Neoplasms/pathology
3.
Nature ; 606(7913): 343-350, 2022 06.
Article in English | MEDLINE | ID: mdl-35650442

ABSTRACT

Age-related change in human haematopoiesis causes reduced regenerative capacity1, cytopenias2, immune dysfunction3 and increased risk of blood cancer4-6, but the reason for such abrupt functional decline after 70 years of age remains unclear. Here we sequenced 3,579 genomes from single cell-derived colonies of haematopoietic cells across 10 human subjects from 0 to 81 years of age. Haematopoietic stem cells or multipotent progenitors (HSC/MPPs) accumulated a mean of 17 mutations per year after birth and lost 30 base pairs per year of telomere length. Haematopoiesis in adults less than 65 years of age was massively polyclonal, with high clonal diversity and a stable population of 20,000-200,000 HSC/MPPs contributing evenly to blood production. By contrast, haematopoiesis in individuals aged over 75 showed profoundly decreased clonal diversity. In each of the older subjects, 30-60% of haematopoiesis was accounted for by 12-18 independent clones, each contributing 1-34% of blood production. Most clones had begun their expansion before the subject was 40 years old, but only 22% had known driver mutations. Genome-wide selection analysis estimated that between 1 in 34 and 1 in 12 non-synonymous mutations were drivers, accruing at constant rates throughout life, affecting more genes than identified in blood cancers. Loss of the Y chromosome conferred selective benefits in males. Simulations of haematopoiesis, with constant stem cell population size and constant acquisition of driver mutations conferring moderate fitness benefits, entirely explained the abrupt change in clonal structure in the elderly. Rapidly decreasing clonal diversity is a universal feature of haematopoiesis in aged humans, underpinned by pervasive positive selection acting on many more genes than currently identified.


Subject(s)
Aging , Clonal Hematopoiesis , Clone Cells , Longevity , Adolescent , Adult , Aged , Aged, 80 and over , Aging/genetics , Child , Child, Preschool , Clonal Hematopoiesis/genetics , Clone Cells/cytology , Female , Hematologic Neoplasms/genetics , Hematologic Neoplasms/pathology , Hematopoietic Stem Cells/cytology , Humans , Infant , Infant, Newborn , Male , Middle Aged , Multipotent Stem Cells/cytology , Young Adult
4.
Nature ; 593(7859): 405-410, 2021 05.
Article in English | MEDLINE | ID: mdl-33911282

ABSTRACT

Somatic mutations drive the development of cancer and may contribute to ageing and other diseases1,2. Despite their importance, the difficulty of detecting mutations that are only present in single cells or small clones has limited our knowledge of somatic mutagenesis to a minority of tissues. Here, to overcome these limitations, we developed nanorate sequencing (NanoSeq), a duplex sequencing protocol with error rates of less than five errors per billion base pairs in single DNA molecules from cell populations. This rate is two orders of magnitude lower than typical somatic mutation loads, enabling the study of somatic mutations in any tissue independently of clonality. We used this single-molecule sensitivity to study somatic mutations in non-dividing cells across several tissues, comparing stem cells to differentiated cells and studying mutagenesis in the absence of cell division. Differentiated cells in blood and colon displayed remarkably similar mutation loads and signatures to their corresponding stem cells, despite mature blood cells having undergone considerably more divisions. We then characterized the mutational landscape of post-mitotic neurons and polyclonal smooth muscle, confirming that neurons accumulate somatic mutations at a constant rate throughout life without cell division, with similar rates to mitotically active tissues. Together, our results suggest that mutational processes that are independent of cell division are important contributors to somatic mutagenesis. We anticipate that the ability to reliably detect mutations in single DNA molecules could transform our understanding of somatic mutagenesis and enable non-invasive studies on large-scale cohorts.


Subject(s)
Blood Cells/metabolism , Cell Differentiation/genetics , DNA Mutational Analysis/methods , Muscle, Smooth/metabolism , Mutation , Neurons/metabolism , Single Molecule Imaging/methods , Stem Cells/metabolism , Alzheimer Disease/genetics , Blood Cells/cytology , Cell Division , Cohort Studies , Colon/cytology , Epithelium/metabolism , Granulocytes/cytology , Granulocytes/metabolism , Healthy Volunteers , Humans , Male , Middle Aged , Muscle, Smooth/cytology , Mutagenesis , Mutation Rate , Neurons/cytology , Stem Cells/cytology
5.
Blood ; 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38905596

ABSTRACT

The ribosomopathy Shwachman-Diamond syndrome (SDS) is a rare autosomal recessive inherited bone marrow failure syndrome (IBMFS) caused by mutations in the Shwachman-Bodian-Diamond syndrome (SBDS) gene, that is associated with an increased risk of myeloid malignancy. Tracking how hematopoietic stem cell (HSC) clonal dynamics change over time, assessing whether somatic genetic rescue mechanisms affect these dynamics, and mapping out when leukemic driver mutations are acquired is important to understand which individuals with SDS may go on to develop leukemia. In this review, we will discuss how new technologies that allow researchers to map mutations at the level of single HSC clones are generating important insights into genetic rescue mechanisms and their relative risk for driving evolution to leukemia, and how these data can inform the future development of personalized medicine approaches in SDS and other IBMFSs.

6.
Development ; 149(20)2022 10 15.
Article in English | MEDLINE | ID: mdl-36217963

ABSTRACT

Haematopoietic stem cell (HSC) self-renewal is a process that is essential for the development and homeostasis of the blood system. Self-renewal expansion divisions, which create two daughter HSCs from a single parent HSC, can be harnessed to create large numbers of HSCs for a wide range of cell and gene therapies, but the same process is also a driver of the abnormal expansion of HSCs in diseases such as cancer. Although HSCs are first produced during early embryonic development, the key stage and location where they undergo maximal expansion is in the foetal liver, making this tissue a rich source of data for deciphering the molecules driving HSC self-renewal. Another equally interesting stage occurs post-birth, several weeks after HSCs have migrated to the bone marrow, when HSCs undergo a developmental switch and adopt a more dormant state. Characterising these transition points during development is key, both for understanding the evolution of haematological malignancies and for developing methods to promote HSC expansion. In this Spotlight article, we provide an overview of some of the key insights that studying HSC development have brought to the fields of HSC expansion and translational medicine, many of which set the stage for the next big breakthroughs in the field.


Subject(s)
Hematopoietic Stem Cells , Neoplasms , Cell Proliferation , Cell Self Renewal , Female , Hematopoiesis , Humans , Neoplasms/pathology , Neoplasms/therapy , Pregnancy
7.
Blood ; 142(6): 543-552, 2023 08 10.
Article in English | MEDLINE | ID: mdl-36735913

ABSTRACT

One of the most challenging aspects of stem cell research is the reliance on retrospective assays for ascribing function. This is especially problematic for hematopoietic stem cell (HSC) research in which the current functional assay that formally establishes its HSC identity involves long-term serial transplantation assays that necessitate the destruction of the initial cell state many months before knowing that it was, in fact, an HSC. In combination with the explosion of equally destructive single-cell molecular assays, the paradox facing researchers is how to determine the molecular state of a functional HSC when you cannot concomitantly assess its functional and molecular properties. In this review, we will give a historical overview of the functional and molecular assays in the field, identify new tools that combine molecular and functional readouts in populations of HSCs, and imagine the next generation of computational and molecular profiling tools that may help us better link cell function with molecular state.


Subject(s)
Hematopoietic Stem Cell Transplantation , Retrospective Studies , Hematopoietic Stem Cells , Cell Differentiation/physiology
8.
PLoS Biol ; 20(7): e3001680, 2022 07.
Article in English | MEDLINE | ID: mdl-35797414

ABSTRACT

Early career researchers (ECRs) are important stakeholders leading efforts to catalyze systemic change in research culture and practice. Here, we summarize the outputs from a virtual unconventional conference (unconference), which brought together 54 invited experts from 20 countries with extensive experience in ECR initiatives designed to improve the culture and practice of science. Together, we drafted 2 sets of recommendations for (1) ECRs directly involved in initiatives or activities to change research culture and practice; and (2) stakeholders who wish to support ECRs in these efforts. Importantly, these points apply to ECRs working to promote change on a systemic level, not only those improving aspects of their own work. In both sets of recommendations, we underline the importance of incentivizing and providing time and resources for systems-level science improvement activities, including ECRs in organizational decision-making processes, and working to dismantle structural barriers to participation for marginalized groups. We further highlight obstacles that ECRs face when working to promote reform, as well as proposed solutions and examples of current best practices. The abstract and recommendations for stakeholders are available in Dutch, German, Greek (abstract only), Italian, Japanese, Polish, Portuguese, Spanish, and Serbian.


Subject(s)
Research Personnel , Research Report , Humans , Power, Psychological
9.
Blood ; 140(14): 1592-1606, 2022 10 06.
Article in English | MEDLINE | ID: mdl-35767701

ABSTRACT

Adult hematopoietic stem cells (HSCs) are predominantly quiescent and can be activated in response to acute stress such as infection or cytotoxic insults. STAT1 is a pivotal downstream mediator of interferon (IFN) signaling and is required for IFN-induced HSC proliferation, but little is known about the role of STAT1 in regulating homeostatic hematopoietic stem/progenitor cells (HSPCs). Here, we show that loss of STAT1 altered the steady state HSPC landscape, impaired HSC function in transplantation assays, delayed blood cell regeneration following myeloablation, and disrupted molecular programs that protect HSCs, including control of quiescence. Our results also reveal STAT1-dependent functional HSC heterogeneity. A previously unrecognized subset of homeostatic HSCs with elevated major histocompatibility complex class II (MHCII) expression (MHCIIhi) displayed molecular features of reduced cycling and apoptosis and was refractory to 5-fluorouracil-induced myeloablation. Conversely, MHCIIlo HSCs displayed increased megakaryocytic potential and were preferentially expanded in CALR mutant mice with thrombocytosis. Similar to mice, high MHCII expression is a feature of human HSCs residing in a deeper quiescent state. Our results therefore position STAT1 at the interface of stem cell heterogeneity and the interplay between stem cells and the adaptive immune system, areas of broad interest in the wider stem cell field.


Subject(s)
Hematopoietic Stem Cells , Megakaryocytes , STAT1 Transcription Factor , Animals , Cell Proliferation , Fluorouracil/pharmacology , Hematopoietic Stem Cells/metabolism , Humans , Interferons , Megakaryocytes/metabolism , Mice , STAT1 Transcription Factor/genetics , STAT1 Transcription Factor/metabolism
10.
EMBO Rep ; 23(10): e55502, 2022 10 06.
Article in English | MEDLINE | ID: mdl-35971894

ABSTRACT

Hematopoietic stem cells (HSCs) cultured outside the body are the fundamental component of a wide range of cellular and gene therapies. Recent efforts have achieved > 200-fold expansion of functional HSCs, but their molecular characterization has not been possible since the majority of cells are non-HSCs and single cell-initiated cultures have substantial clone-to-clone variability. Using the Fgd5 reporter mouse in combination with the EPCR surface marker, we report exclusive identification of HSCs from non-HSCs in expansion cultures. By directly linking single-clone functional transplantation data with single-clone gene expression profiling, we show that the molecular profile of expanded HSCs is similar to proliferating fetal HSCs and reveals a gene expression signature, including Esam, Prdm16, Fstl1, and Palld, that can identify functional HSCs from multiple cellular states. This "repopulation signature" (RepopSig) also enriches for HSCs in human datasets. Together, these findings demonstrate the power of integrating functional and molecular datasets to better derive meaningful gene signatures and opens the opportunity for a wide range of functional screening and molecular experiments previously not possible due to limited HSC numbers.


Subject(s)
Follistatin-Related Proteins , Animals , Cells, Cultured , Endothelial Protein C Receptor/metabolism , Follistatin-Related Proteins/metabolism , Hematopoietic Stem Cells/metabolism , Humans , Mice , Transcription Factors/metabolism
11.
Nature ; 561(7724): 473-478, 2018 09.
Article in English | MEDLINE | ID: mdl-30185910

ABSTRACT

Haematopoietic stem cells drive blood production, but their population size and lifetime dynamics have not been quantified directly in humans. Here we identified 129,582 spontaneous, genome-wide somatic mutations in 140 single-cell-derived haematopoietic stem and progenitor colonies from a healthy 59-year-old man and applied population-genetics approaches to reconstruct clonal dynamics. Cell divisions from early embryogenesis were evident in the phylogenetic tree; all blood cells were derived from a common ancestor that preceded gastrulation. The size of the stem cell population grew steadily in early life, reaching a stable plateau by adolescence. We estimate the numbers of haematopoietic stem cells that are actively making white blood cells at any one time to be in the range of 50,000-200,000. We observed adult haematopoietic stem cell clones that generate multilineage outputs, including granulocytes and B lymphocytes. Harnessing naturally occurring mutations to report the clonal architecture of an organ enables the high-resolution reconstruction of somatic cell dynamics in humans.


Subject(s)
Blood Cells/cytology , Blood Cells/metabolism , Cell Lineage/genetics , DNA Mutational Analysis , Mutation , Adult Stem Cells/cytology , Bayes Theorem , Cell Count , Cell Division , Clone Cells/cytology , Clone Cells/metabolism , Embryonic Development/genetics , Genome, Human/genetics , Granulocytes/cytology , Granulocytes/metabolism , Hematopoiesis/genetics , Hematopoietic Stem Cells/cytology , Hematopoietic Stem Cells/metabolism , Humans , Lymphocytes/cytology , Lymphocytes/metabolism , Male , Middle Aged , Time Factors
12.
Blood ; 132(8): 791-803, 2018 08 23.
Article in English | MEDLINE | ID: mdl-29991556

ABSTRACT

Recent advances in single-cell technologies have permitted the investigation of heterogeneous cell populations at previously unattainable resolution. Here we apply such approaches to resolve the molecular mechanisms driving disease in mouse hematopoietic stem cells (HSCs), using JAK2V617F mutant myeloproliferative neoplasms (MPNs) as a model. Single-cell gene expression and functional assays identified a subset of JAK2V617F mutant HSCs that display defective self-renewal. This defect is rescued at the single HSC level by crossing JAK2V617F mice with mice lacking TET2, the most commonly comutated gene in patients with MPN. Single-cell gene expression profiling of JAK2V617F-mutant HSCs revealed a loss of specific regulator genes, some of which were restored to normal levels in single TET2/JAK2 mutant HSCs. Of these, Bmi1 and, to a lesser extent, Pbx1 and Meis1 overexpression in JAK2-mutant HSCs could drive a disease phenotype and retain durable stem cell self-renewal in functional assays. Together, these single-cell approaches refine the molecules involved in clonal expansion of MPNs and have broad implications for deconstructing the molecular network of normal and malignant stem cells.


Subject(s)
Cell Self Renewal , Gene Expression Regulation, Neoplastic , Hematologic Neoplasms/metabolism , Hematopoietic Stem Cells/metabolism , Janus Kinase 2/metabolism , Mutation, Missense , Myeloproliferative Disorders/metabolism , Neoplasm Proteins/metabolism , Neoplastic Stem Cells/metabolism , Amino Acid Substitution , Animals , Hematologic Neoplasms/genetics , Hematologic Neoplasms/pathology , Hematopoietic Stem Cells/pathology , Janus Kinase 2/genetics , Mice , Mice, Transgenic , Myeloproliferative Disorders/genetics , Myeloproliferative Disorders/pathology , Neoplasm Proteins/genetics , Neoplastic Stem Cells/pathology
13.
Blood ; 131(21): e1-e11, 2018 05 24.
Article in English | MEDLINE | ID: mdl-29588278

ABSTRACT

Hematopoietic stem and progenitor cells (HSPCs) maintain the adult blood system, and their dysregulation causes a multitude of diseases. However, the differentiation journeys toward specific hematopoietic lineages remain ill defined, and system-wide disease interpretation remains challenging. Here, we have profiled 44 802 mouse bone marrow HSPCs using single-cell RNA sequencing to provide a comprehensive transcriptional landscape with entry points to 8 different blood lineages (lymphoid, megakaryocyte, erythroid, neutrophil, monocyte, eosinophil, mast cell, and basophil progenitors). We identified a common basophil/mast cell bone marrow progenitor and characterized its molecular profile at the single-cell level. Transcriptional profiling of 13 815 HSPCs from the c-Kit mutant (W41/W41) mouse model revealed the absence of a distinct mast cell lineage entry point, together with global shifts in cell type abundance. Proliferative defects were accompanied by reduced Myc expression. Potential compensatory processes included upregulation of the integrated stress response pathway and downregulation of proapoptotic gene expression in erythroid progenitors, thus providing a template of how large-scale single-cell transcriptomic studies can bridge between molecular phenotypes and quantitative population changes.


Subject(s)
Cell Differentiation/genetics , Cell Lineage/genetics , Hematopoietic Stem Cells/cytology , Hematopoietic Stem Cells/metabolism , Mutation , Proto-Oncogene Proteins c-kit/deficiency , Animals , Bone Marrow Cells/cytology , Bone Marrow Cells/metabolism , Cell Line, Tumor , Cells, Cultured , Gene Expression Profiling , Mice , Mice, Knockout , Proto-Oncogene Proteins c-kit/metabolism , Signal Transduction , Single-Cell Analysis , Transcriptome
14.
Blood ; 131(6): 649-661, 2018 02 08.
Article in English | MEDLINE | ID: mdl-29282219

ABSTRACT

Somatic mutations in the endoplasmic reticulum chaperone calreticulin (CALR) are detected in approximately 40% of patients with essential thrombocythemia (ET) and primary myelofibrosis (PMF). Multiple different mutations have been reported, but all result in a +1-bp frameshift and generate a novel protein C terminus. In this study, we generated a conditional mouse knockin model of the most common CALR mutation, a 52-bp deletion. The mutant novel human C-terminal sequence is integrated into the otherwise intact mouse CALR gene and results in mutant CALR expression under the control of the endogenous mouse locus. CALRdel/+ mice develop a transplantable ET-like disease with marked thrombocytosis, which is associated with increased and morphologically abnormal megakaryocytes and increased numbers of phenotypically defined hematopoietic stem cells (HSCs). Homozygous CALRdel/del mice developed extreme thrombocytosis accompanied by features of MF, including leukocytosis, reduced hematocrit, splenomegaly, and increased bone marrow reticulin. CALRdel/+ HSCs were more proliferative in vitro, but neither CALRdel/+ nor CALRdel/del displayed a competitive transplantation advantage in primary or secondary recipient mice. These results demonstrate the consequences of heterozygous and homozygous CALR mutations and provide a powerful model for dissecting the pathogenesis of CALR-mutant ET and PMF.


Subject(s)
Calreticulin/genetics , Cell Self Renewal/genetics , Hematopoietic Stem Cells/physiology , Primary Myelofibrosis/genetics , Thrombocytosis/genetics , Animals , Cells, Cultured , Homozygote , Leukocytosis/genetics , Leukocytosis/pathology , Mice , Mice, Inbred C57BL , Mice, Transgenic , Mutation, Missense , Splenomegaly/genetics , Splenomegaly/pathology , Thrombocythemia, Essential/genetics , Thrombocythemia, Essential/pathology
15.
Nature ; 510(7504): 268-72, 2014 Jun 12.
Article in English | MEDLINE | ID: mdl-24776803

ABSTRACT

The blood system is sustained by a pool of haematopoietic stem cells (HSCs) that are long-lived due to their capacity for self-renewal. A consequence of longevity is exposure to stress stimuli including reactive oxygen species (ROS), nutrient fluctuation and DNA damage. Damage that occurs within stressed HSCs must be tightly controlled to prevent either loss of function or the clonal persistence of oncogenic mutations that increase the risk of leukaemogenesis. Despite the importance of maintaining cell integrity throughout life, how the HSC pool achieves this and how individual HSCs respond to stress remain poorly understood. Many sources of stress cause misfolded protein accumulation in the endoplasmic reticulum (ER), and subsequent activation of the unfolded protein response (UPR) enables the cell to either resolve stress or initiate apoptosis. Here we show that human HSCs are predisposed to apoptosis through strong activation of the PERK branch of the UPR after ER stress, whereas closely related progenitors exhibit an adaptive response leading to their survival. Enhanced ER protein folding by overexpression of the co-chaperone ERDJ4 (also called DNAJB9) increases HSC repopulation capacity in xenograft assays, linking the UPR to HSC function. Because the UPR is a focal point where different sources of stress converge, our study provides a framework for understanding how stress signalling is coordinated within tissue hierarchies and integrated with stemness. Broadly, these findings reveal that the HSC pool maintains clonal integrity by clearance of individual HSCs after stress to prevent propagation of damaged stem cells.


Subject(s)
Endoplasmic Reticulum Stress , Hematopoietic Stem Cells/cytology , Unfolded Protein Response/physiology , Activating Transcription Factor 4/metabolism , Animals , Apoptosis/drug effects , Endoplasmic Reticulum Stress/drug effects , Eukaryotic Initiation Factor-2/metabolism , HSP40 Heat-Shock Proteins/metabolism , Hematopoietic Stem Cells/drug effects , Heterografts , Humans , Male , Membrane Proteins/metabolism , Mice , Molecular Chaperones/metabolism , Protein Folding , Protein Phosphatase 1/metabolism , Signal Transduction , Transcription Factor CHOP/metabolism , Tunicamycin/pharmacology , Unfolded Protein Response/drug effects , eIF-2 Kinase/metabolism
16.
Proc Natl Acad Sci U S A ; 114(23): 5822-5829, 2017 06 06.
Article in English | MEDLINE | ID: mdl-28584094

ABSTRACT

Adult blood contains a mixture of mature cell types, each with specialized functions. Single hematopoietic stem cells (HSCs) have been functionally shown to generate all mature cell types for the lifetime of the organism. Differentiation of HSCs toward alternative lineages must be balanced at the population level by the fate decisions made by individual cells. Transcription factors play a key role in regulating these decisions and operate within organized regulatory programs that can be modeled as transcriptional regulatory networks. As dysregulation of single HSC fate decisions is linked to fatal malignancies such as leukemia, it is important to understand how these decisions are controlled on a cell-by-cell basis. Here we developed and applied a network inference method, exploiting the ability to infer dynamic information from single-cell snapshot expression data based on expression profiles of 48 genes in 2,167 blood stem and progenitor cells. This approach allowed us to infer transcriptional regulatory network models that recapitulated differentiation of HSCs into progenitor cell types, focusing on trajectories toward megakaryocyte-erythrocyte progenitors and lymphoid-primed multipotent progenitors. By comparing these two models, we identified and subsequently experimentally validated a difference in the regulation of nuclear factor, erythroid 2 (Nfe2) and core-binding factor, runt domain, alpha subunit 2, translocated to, 3 homolog (Cbfa2t3h) by the transcription factor Gata2. Our approach confirms known aspects of hematopoiesis, provides hypotheses about regulation of HSC differentiation, and is widely applicable to other hierarchical biological systems to uncover regulatory relationships.


Subject(s)
Gene Regulatory Networks , Hematopoiesis/genetics , Hematopoietic Stem Cells/cytology , Algorithms , Animals , Cell Differentiation , Mice, Inbred C57BL , Transcription Factors/genetics , Transcription Factors/metabolism , Transcription Factors/physiology
17.
Curr Opin Hematol ; 26(4): 214-221, 2019 07.
Article in English | MEDLINE | ID: mdl-31170109

ABSTRACT

PURPOSE OF REVIEW: The recent emergence of single-cell technologies has permitted unprecedented insight into the molecular drivers of fate choice in blood stem and progenitor cells. This review gives a broad overview of current efforts to understand the molecular regulators of malignant hematopoietic stem cells (HSCs) at the single-cell level. RECENT FINDINGS: The large-scale adoption of single-cell approaches has allowed extensive description of the transcriptional profiles and functional properties of single HSCs. These techniques are now beginning to be applied to malignant HSCs isolated directly from patients or from mouse models of malignancy. However, these studies have generally struggled to pinpoint the functional regulators of malignant characteristics, since malignant HSCs often differ in more than one property when compared with normal HSCs. Moreover, both normal and malignant populations are complicated by HSC heterogeneity. SUMMARY: Despite the existence of single-cell gene expression profiling tools, relatively few publications have emerged. Here, we review these studies from recent years with a specific focus on those undertaking single-cell measurements in malignant stem and progenitor cells. We anticipate this to be the tip of the iceberg, expecting the next 2-3 years to produce datasets that will facilitate a much broader understanding of malignant HSCs.


Subject(s)
Gene Expression Regulation , Hematologic Diseases/classification , Hematologic Diseases/pathology , Hematopoietic Stem Cells/cytology , Single-Cell Analysis/methods , Animals , Cell Differentiation , Cell Lineage , Hematologic Diseases/etiology , Hematopoietic Stem Cells/physiology , Humans , Signal Transduction
18.
N Engl J Med ; 372(7): 601-612, 2015 Feb 12.
Article in English | MEDLINE | ID: mdl-25671252

ABSTRACT

BACKGROUND: Cancers result from the accumulation of somatic mutations, and their properties are thought to reflect the sum of these mutations. However, little is known about the effect of the order in which mutations are acquired. METHODS: We determined mutation order in patients with myeloproliferative neoplasms by genotyping hematopoietic colonies or by means of next-generation sequencing. Stem cells and progenitor cells were isolated to study the effect of mutation order on mature and immature hematopoietic cells. RESULTS: The age at which a patient presented with a myeloproliferative neoplasm, acquisition of JAK2 V617F homozygosity, and the balance of immature progenitors were all influenced by mutation order. As compared with patients in whom the TET2 mutation was acquired first (hereafter referred to as "TET2-first patients"), patients in whom the Janus kinase 2 (JAK2) mutation was acquired first ("JAK2-first patients") had a greater likelihood of presenting with polycythemia vera than with essential thrombocythemia, an increased risk of thrombosis, and an increased sensitivity of JAK2-mutant progenitors to ruxolitinib in vitro. Mutation order influenced the proliferative response to JAK2 V617F and the capacity of double-mutant hematopoietic cells and progenitor cells to generate colony-forming cells. Moreover, the hematopoietic stem-and-progenitor-cell compartment was dominated by TET2 single-mutant cells in TET2-first patients but by JAK2-TET2 double-mutant cells in JAK2-first patients. Prior mutation of TET2 altered the transcriptional consequences of JAK2 V617F in a cell-intrinsic manner and prevented JAK2 V617F from up-regulating genes associated with proliferation. CONCLUSIONS: The order in which JAK2 and TET2 mutations were acquired influenced clinical features, the response to targeted therapy, the biology of stem and progenitor cells, and clonal evolution in patients with myeloproliferative neoplasms. (Funded by Leukemia and Lymphoma Research and others.).


Subject(s)
DNA-Binding Proteins/genetics , Hematopoietic Stem Cells/physiology , Janus Kinase 2/genetics , Mutation , Myeloproliferative Disorders/genetics , Proto-Oncogene Proteins/genetics , Age of Onset , Cell Proliferation/genetics , DNA Mutational Analysis , Dioxygenases , Gene Expression , Homozygote , Humans , Polycythemia Vera/genetics , Thrombocythemia, Essential/genetics , Thrombosis/genetics , Transcription, Genetic , Up-Regulation
19.
Blood ; 128(8): e20-31, 2016 08 25.
Article in English | MEDLINE | ID: mdl-27365425

ABSTRACT

Maintenance of the blood system requires balanced cell fate decisions by hematopoietic stem and progenitor cells (HSPCs). Because cell fate choices are executed at the individual cell level, new single-cell profiling technologies offer exciting possibilities for mapping the dynamic molecular changes underlying HSPC differentiation. Here, we have used single-cell RNA sequencing to profile more than 1600 single HSPCs, and deep sequencing has enabled detection of an average of 6558 protein-coding genes per cell. Index sorting, in combination with broad sorting gates, allowed us to retrospectively assign cells to 12 commonly sorted HSPC phenotypes while also capturing intermediate cells typically excluded by conventional gating. We further show that independently generated single-cell data sets can be projected onto the single-cell resolution expression map to directly compare data from multiple groups and to build and refine new hypotheses. Reconstruction of differentiation trajectories reveals dynamic expression changes associated with early lymphoid, erythroid, and granulocyte-macrophage differentiation. The latter two trajectories were characterized by common upregulation of cell cycle and oxidative phosphorylation transcriptional programs. By using external spike-in controls, we estimate absolute messenger RNA (mRNA) levels per cell, showing for the first time that despite a general reduction in total mRNA, a subset of genes shows higher expression levels in immature stem cells consistent with active maintenance of the stem-cell state. Finally, we report the development of an intuitive Web interface as a new community resource to permit visualization of gene expression in HSPCs at single-cell resolution for any gene of choice.


Subject(s)
Cell Differentiation , Hematopoietic Stem Cells/cytology , Single-Cell Analysis/methods , Animals , Biomarkers/metabolism , Cell Cycle/genetics , Cell Differentiation/genetics , Female , Gene Expression Profiling , Gene Expression Regulation , Hematopoietic Stem Cells/metabolism , Mice, Inbred C57BL , Phenotype , RNA, Messenger/genetics , RNA, Messenger/metabolism , Transcription, Genetic
20.
Blood ; 123(20): 3139-51, 2014 May 15.
Article in English | MEDLINE | ID: mdl-24692758

ABSTRACT

Genomic regions of acquired uniparental disomy (UPD) are common in malignancy and frequently harbor mutated oncogenes. Homozygosity for such gain-of-function mutations is thought to modulate tumor phenotype, but direct evidence has been elusive. Polycythemia vera (PV) and essential thrombocythemia (ET), 2 subtypes of myeloproliferative neoplasms, are associated with an identical acquired JAK2V617F mutation but the mechanisms responsible for distinct clinical phenotypes remain unclear. We provide direct genetic evidence and demonstrate that homozygosity for human JAK2V617F in knock-in mice results in a striking phenotypic switch from an ET-like to PV-like phenotype. The resultant erythrocytosis is driven by increased numbers of early erythroid progenitors and enhanced erythroblast proliferation, whereas reduced platelet numbers are associated with impaired platelet survival. JAK2V617F-homozygous mice developed a severe hematopoietic stem cell defect, suggesting that additional lesions are needed to sustain clonal expansion. Together, our results indicate that UPD for 9p plays a causal role in the PV phenotype in patients as a consequence of JAK2V617F homozygosity. The generation of a JAK2V617F allelic series of mice with a dose-dependent effect on hematopoiesis provides a powerful model for studying the consequences of mutant JAK2 homozygosity.


Subject(s)
Janus Kinase 2/genetics , Mutation , Polycythemia Vera/genetics , Thrombocythemia, Essential/genetics , Animals , Blood Platelets/metabolism , Blood Platelets/pathology , Erythroblasts/metabolism , Erythroblasts/pathology , Female , Gene Knock-In Techniques , Homozygote , Humans , Male , Megakaryocytes/metabolism , Megakaryocytes/pathology , Mice , Mice, Inbred C57BL , Phenotype , Polycythemia Vera/pathology , Thrombocythemia, Essential/pathology , Uniparental Disomy/genetics , Uniparental Disomy/pathology
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