scholarly journals Comprehensive single-cell gene and isoform expression analysis reveals signatures of ageing in haematopoietic stem and progenitor cells

2021 ◽  
Author(s):  
Laura Mincarelli ◽  
Vladimir Uzun ◽  
David Wright ◽  
Stuart Rushworth ◽  
Wilfried Haerty ◽  
...  
Keyword(s):  
Stem Cells ◽  
Single Cell ◽  
Progenitor Cells ◽  
Cell Type ◽  
Aberrant Expression ◽  
Hematopoietic Stem ◽  
Long Read ◽  
Stem And Progenitor Cells ◽  
Cell Type Specific ◽  
Isoform Expression

Abstract Single-cell approaches have revealed that the haematopoietic hierarchy is a continuum of differentiation, from stem cell to committed progenitor, marked by changes in gene expression. However, many of these approaches neglect isoform level information, and thus do not capture the extent and effect of alternative splicing within the system. Here, we present the first integrated short- and long-read single-cell RNA-seq of haematopoietic stem and progenitor cells. We demonstrate that over half of genes detected in standard short-read single-cell analyses are expressed as multiple, often functionally distinct, isoforms. This includes many transcription factors and key cytokine receptors, and in particular the Thrombopoietin receptor Mpl, which displays complex isoform expression patterns between individual hematopoietic stem cells. The dataset further reveals novel signatures of hematopoietic ageing, including a global increase in lncRNA expression. Strikingly, the long-read sequencing enables us to observe aberrant expression of full-length VJ-rearranged immunoglobulin kappa transcripts in aged haematopoietic stem cells, prior to lymphoid commitment. Integrating single cell and cell-type specific isoform landscape in normal and aged hematopoiesis provides a new reference for accurate molecular profiling of heterogeneous tissues, as well as novel insights into transcriptional complexity, cell-type specific splicing events and effects of ageing.

scholarly journals Combined single-cell gene and isoform expression analysis in haematopoietic stem and progenitor cells

2020 ◽  
Author(s):  
Laura Mincarelli ◽  
Vladimir Uzun ◽  
Stuart A. Rushworth ◽  
Wilfried Haerty ◽  
Iain C. Macaulay
Keyword(s):  
Single Cell ◽  
Progenitor Cells ◽  
Cell Types ◽  
Cell Phenotype ◽  
Hematopoietic Stem ◽  
Long Read ◽  
Stem And Progenitor Cells ◽  
Alternatively Spliced ◽  
Isoform Expression

AbstractSingle-cell RNA sequencing (scRNA-seq) enables gene expression profiling and characterization of novel cell types within heterogeneous cell populations. However, most approaches cannot detect alternatively spliced transcripts, which can profoundly shape cell phenotype by generating functionally distinct proteins from the same gene. Here, we integrate short- and long-read scRNA-seq of hematopoietic stem and progenitor cells to characterize changes in cell type abundance, gene and isoform expression during differentiation and ageing.

Single Cell Proteomics Reveals Novel Cytokine-Producing Function of Hematopoietic Stem and Progenitor Cells

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 26-26
Author(s):  
Jimmy L. Zhao ◽  
Chao Ma ◽  
Ryan O'Connell ◽  
Dinesh S. Rao ◽  
James Heath ◽  
...  
Keyword(s):  
Stem Cells ◽  
Immune Response ◽  
Single Cell ◽  
Progenitor Cells ◽  
Cytokine Production ◽  
Conflicts Of Interest ◽  
Severe Neutropenia ◽  
Hematopoietic Stem ◽  
Stem And Progenitor Cells

Abstract Abstract 26 During infection, hematopoietic stem and progenitor cells (HSPCs) are called upon to proliferate and differentiate to produce more innate and adaptive immune cells to combat infection. Traditionally, HSPCs are thought to respond to depletion of downstream hematopoietic cells during infection. More recent evidence suggests that HSPCs may respond directly to infection and pro-inflammatory cytokines. However, little is known about the direct immune response of HSPCs and the molecular signaling regulating this response upon sensing an infection. In this study, we have combined transgenic and genetic knockout mouse models with a novel single cell barcode proteomics microchip technology to tackle these questions. We show that although long-term hematopoietic stem cells (HSCs) (defined by Lineage-cKit+Sca1+CD150+CD48-) do not secrete cytokines upon toll-like receptor (TLR) stimulation, short-term HSCs and multipotent progenitor cells (MPPs) (defined by Lineage-cKit+Sca1+, referred to as LKS thereafter) can produce copious amounts of cytokines upon direct TLR-4 and TLR-2 stimulation, indicating that LKS cells can directly participate in an immune response by producing a myriad of cytokines, upon a bacterial infection. Within the population of LKS cells we detect multiple functional subsets of cells, specialized in producing myeloid-like, lymphoid-like or both types of cytokines. Moreover, we show that the cytokine production by LKS cells is regulated by the NF-κB activity, as p50-deficient LKS cells show reduced cytokine production while microRNA-146a (miR-146a)-deficient LKS cells show significantly increased cytokine production. As long-term HSCs differentiate, they start to gain effector immune function much earlier than we had originally anticipated. In light of this finding, we should start to view the stepwise differentiation scheme of HSCs, and perhaps all other stem cells, as a strategy to sequentially gain functional capacity, instead of simply losing stemness and self-renewal ability. The remarkable ability of LKS cells to produce copious amounts of cytokines in response to bacteria may provide some protective immunity during severe neutropenia and lymphopenia or in the early stage of HSC transplantation. This study further extends the functions of NF-κB to include the regulation of primitive hematopoietic stem and progenitor cells and provides direct evidence of the bacteria-responding ability of HSPCs through the TLR/NF-κB axis. The single cell barcode proteomics technology can be widely applied to study proteomics of other rare cells or heterogeneous cell population at a single cell level. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Mechanism of Action of Diallyl Sulphide in Ameliorating the Hematopoietic Radiation Injury

2021 ◽  
Author(s):  
Omika Katoch ◽  
Mrinalini Tiwari ◽  
Namita Kalra ◽  
Paban K. Agrawala
Keyword(s):  
Stem Cells ◽  
Bone Marrow ◽  
Progenitor Cells ◽  
Hematopoietic Stem ◽  
Proliferation And Differentiation ◽  
Stem And Progenitor Cells ◽  
Radiation Induced ◽  
Medicinal Properties ◽  
Marrow Cellularity

AbstractDiallyl sulphide (DAS), the pungent component of garlic, is known to have several medicinal properties and has recently been shown to have radiomitigative properties. The present study was performed to better understand its mode of action in rendering radiomitigation. Evaluation of the colonogenic ability of hematopoietic progenitor cells (HPCs) on methocult media, proliferation and differentiation of hematopoietic stem cells (HSCs), and transplantation of stem cells were performed. The supporting tissue of HSCs was also evaluated by examining the histology of bone marrow and in vitro colony-forming unit–fibroblast (CFU-F) count. Alterations in the levels of IL-5, IL-6 and COX-2 were studied as a function of radiation or DAS treatment. It was observed that an increase in proliferation and differentiation of hematopoietic stem and progenitor cells occurred by postirradiation DAS administration. It also resulted in increased circulating and bone marrow homing of transplanted stem cells. Enhancement in bone marrow cellularity, CFU-F count, and cytokine IL-5 level were also evident. All those actions of DAS that could possibly add to its radiomitigative potential and can be attributed to its HDAC inhibitory properties, as was observed by the reversal radiation induced increase in histone acetylation.

scholarly journals Single-Cell RNA Sequencing of Hematopoietic Stem and Progenitor Cells Treated with Gemcitabine and Carboplatin

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 549
Author(s):  
Niclas Björn ◽  
Ingrid Jakobsen ◽  
Kourosh Lotfi ◽  
Henrik Gréen
Keyword(s):  
Cell Cycle ◽  
Cell Proliferation ◽  
Single Cell ◽  
Progenitor Cells ◽  
Myeloid Cell ◽  
Enrichment Analysis ◽  
Myelogenous Leukemia ◽  
Transcriptional Level ◽  
Hematopoietic Stem ◽  
Stem And Progenitor Cells

Treatments that include gemcitabine and carboplatin induce dose-limiting myelosuppression. The understanding of how human bone marrow is affected on a transcriptional level leading to the development of myelosuppression is required for the implementation of personalized treatments in the future. In this study, we treated human hematopoietic stem and progenitor cells (HSPCs) harvested from a patient with chronic myelogenous leukemia (CML) with gemcitabine/carboplatin. Thereafter, scRNA-seq was performed to distinguish transcriptional effects induced by gemcitabine/carboplatin. Gene expression was calculated and evaluated among cells within and between samples compared to untreated cells. Cell cycle analysis showed that the treatments effectively decrease cell proliferation, indicated by the proportion of cells in the G2M-phase dropping from 35% in untreated cells to 14.3% in treated cells. Clustering and t-SNE showed that cells within samples and between treated and untreated samples were affected differently. Enrichment analysis of differentially expressed genes showed that the treatments influence KEGG pathways and Gene Ontologies related to myeloid cell proliferation/differentiation, immune response, cancer, and the cell cycle. The present study shows the feasibility of using scRNA-seq and chemotherapy-treated HSPCs to find genes, pathways, and biological processes affected among and between treated and untreated cells. This indicates the possible gains of using single-cell toxicity studies for personalized medicine.

scholarly journals Mouse acute leukemia develops independent of self-renewal and differentiation potentials in hematopoietic stem and progenitor cells

2019 ◽  
Vol 3 (3) ◽  
pp. 419-431 ◽  
Author(s):  
Fang Dong ◽  
Haitao Bai ◽  
Xiaofang Wang ◽  
Shanshan Zhang ◽  
Zhao Wang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Acute Leukemia ◽  
Progenitor Cells ◽  
Lymphoblastic Leukemia ◽  
The Self ◽  
Myelogenous Leukemia ◽  
Mouse Bone Marrow ◽  
Self Renewal ◽  
Hematopoietic Stem ◽  
Stem And Progenitor Cells

Abstract The cell of origin, defined as the normal cell in which the transformation event first occurs, is poorly identified in leukemia, despite its importance in understanding of leukemogenesis and improving leukemia therapy. Although hematopoietic stem cells (HSCs) and hematopoietic progenitor cells (HPCs) were used for leukemia models, whether their self-renewal and differentiation potentials influence the initiation and development of leukemia is largely unknown. In this study, the self-renewal and differentiation potentials in 2 distinct types of HSCs (HSC1 [CD150+CD41−CD34−Lineage−Sca-1+c-Kit+ cells] and HSC2 [CD150−CD41−CD34−Lineage−Sca-1+c-Kit+ cells]) and 3 distinct types of HPCs (HPC1 [CD150+CD41+CD34−Lineage−Sca-1+c-Kit+ cells], HPC2 [CD150+CD41+CD34+Lineage−Sca-1+c-Kit+ cells], and HPC3 [CD150−CD41−CD34+Lineage−Sca-1+c-Kit+ cells]) were isolated from adult mouse bone marrow, and examined by competitive repopulation assay. Then, cells from each population were retrovirally transduced to initiate MLL-AF9 acute myelogenous leukemia (AML) and the intracellular domain of NOTCH-1 T-cell acute lymphoblastic leukemia (T-ALL). AML and T-ALL similarly developed from all HSC and HPC populations, suggesting multiple cellular origins of leukemia. New leukemic stem cells (LSCs) were also identified in these AML and T-ALL models. Notably, switching between immunophenotypical immature and mature LSCs was observed, suggesting that heterogeneous LSCs play a role in the expansion and maintenance of leukemia. Based on this mouse model study, we propose that acute leukemia arises from multiple cells of origin independent of the self-renewal and differentiation potentials in hematopoietic stem and progenitor cells and is amplified by LSC switchover.

scholarly journals Single-cell RNA-seq reveals a distinct transcriptome signature of aneuploid hematopoietic cells

Blood ◽  
2017 ◽  
Vol 130 (25) ◽  
pp. 2762-2773 ◽  
Author(s):  
Xin Zhao ◽  
Shouguo Gao ◽  
Zhijie Wu ◽  
Sachiko Kajigaya ◽  
Xingmin Feng ◽  
...  
Keyword(s):  
Immune Response ◽  
Single Cell ◽  
Progenitor Cells ◽  
Rna Seq ◽  
Hematopoietic Stem ◽  
Monosomy 7 ◽  
Key Points ◽  
Stem And Progenitor Cells ◽  
Diploid Cells ◽  
Transcriptome Signature

Key Points We distinguished aneuploid cells from diploid cells within the hematopoietic stem and progenitor cells using scRNA-seq. Monosomy 7 cells showed downregulated pathways involved in immune response and maintenance of DNA stability.

scholarly journals The Making of Hematopoiesis: Developmental Ancestry and Environmental Nurture

2018 ◽  
Vol 19 (7) ◽  
pp. 2122 ◽  
Author(s):  
Geoffrey Brown ◽  
Rhodri Ceredig ◽  
Panagiotis Tsapogas
Keyword(s):  
Stem Cells ◽  
Hematopoietic Stem Cells ◽  
Progenitor Cells ◽  
Cell Fate ◽  
Hematopoietic Stem ◽  
Fate Determination ◽  
Intermediate Progenitors ◽  
Lineage Tree ◽  
Stem And Progenitor Cells ◽  
The Many

Evidence from studies of the behaviour of stem and progenitor cells and of the influence of cytokines on their fate determination, has recently led to a revised view of the process by which hematopoietic stem cells and their progeny give rise to the many different types of blood and immune cells. The new scenario abandons the classical view of a rigidly demarcated lineage tree and replaces it with a much more continuum-like view of the spectrum of fate options open to hematopoietic stem cells and their progeny. This is in contrast to previous lineage diagrams, which envisaged stem cells progressing stepwise through a series of fairly-precisely described intermediate progenitors in order to close down alternative developmental options. Instead, stem and progenitor cells retain some capacity to step sideways and adopt alternative, closely related, fates, even after they have “made a lineage choice.” The stem and progenitor cells are more inherently versatile than previously thought and perhaps sensitive to lineage guidance by environmental cues. Here we examine the evidence that supports these views and reconsider the meaning of cell lineages in the context of a continuum model of stem cell fate determination and environmental modulation.

scholarly journals Kinetics of normal hematopoietic stem and progenitor cells in a Notch1-induced leukemia model

Blood ◽  
2009 ◽  
Vol 114 (18) ◽  
pp. 3783-3792 ◽  
Author(s):  
Xiaoxia Hu ◽  
Hongmei Shen ◽  
Chen Tian ◽  
Hui Yu ◽  
Guoguang Zheng ◽  
...  
Keyword(s):  
Stem Cells ◽  
Hematopoietic Stem Cells ◽  
Progenitor Cells ◽  
Quiescent State ◽  
Hematopoietic Stem ◽  
Definitive Evidence ◽  
Accelerated Proliferation ◽  
Stem And Progenitor Cells ◽  
Underlying Mechanisms ◽  
The Impact

Abstract The predominant outgrowth of malignant cells over their normal counterparts in a given tissue is a shared feature for all types of cancer. However, the impact of a cancer environment on normal tissue stem and progenitor cells has not been thoroughly investigated. We began to address this important issue by studying the kinetics and functions of hematopoietic stem and progenitor cells in mice with Notch1-induced leukemia. Although hematopoiesis was progressively suppressed during leukemia development, the leukemic environment imposed distinct effects on hematopoietic stem and progenitor cells, thereby resulting in different outcomes. The normal hematopoietic stem cells in leukemic mice were kept in a more quiescent state but remained highly functional on transplantation to nonleukemic recipients. In contrast, the normal hematopoietic progenitor cells in leukemic mice demonstrated accelerated proliferation and exhaustion. Subsequent analyses on multiple cell-cycle parameters and known regulators (such as p21, p27, and p18) further support this paradigm. Therefore, our current study provides definitive evidence and plausible underlying mechanisms for hematopoietic disruption but reversible inhibition of normal hematopoietic stem cells in a leukemic environment. It may also have important implications for cancer prevention and treatment in general.

The AML1-ETO fusion protein promotes the expansion of human hematopoietic stem cells

Blood ◽  
2002 ◽  
Vol 99 (1) ◽  
pp. 15-23 ◽  
Author(s):  
James C. Mulloy ◽  
Jörg Cammenga ◽  
Karen L. MacKenzie ◽  
Francisco J. Berguido ◽  
Malcolm A. S. Moore ◽  
...  
Keyword(s):  
Stem Cells ◽  
Fusion Protein ◽  
Progenitor Cells ◽  
Protein Interactions ◽  
Dominant Negative ◽  
Myelogenous Leukemia ◽  
Hematopoietic Stem ◽  
Stem And Progenitor Cells

The acute myelogenous leukemia–1 (AML1)–ETO fusion protein is generated by the t(8;21), which is found in 40% of AMLs of the French-American-British M2 subtype. AML1-ETO interferes with the function of the AML1 (RUNX1, CBFA2) transcription factor in a dominant-negative fashion and represses transcription by binding its consensus DNA–binding site and via protein-protein interactions with other transcription factors. AML1 activity is critical for the development of definitive hematopoiesis, and haploinsufficiency of AML1 has been linked to a propensity to develop AML. Murine experiments suggest that AML1-ETO expression may not be sufficient for leukemogenesis; however, like the BCR-ABL isoforms, the cellular background in which these fusion proteins are expressed may be critical to the phenotype observed. Retroviral gene transfer was used to examine the effect of AML1-ETO on the in vitro behavior of human hematopoietic stem and progenitor cells. Following transduction of CD34+ cells, stem and progenitor cells were quantified in clonogenic assays, cytokine-driven expansion cultures, and long-term stromal cocultures. Expression of AML1-ETO inhibited colony formation by committed progenitors, but enhanced the growth of stem cells (cobblestone area-forming cells), resulting in a profound survival advantage of transduced over nontransduced cells. AML1-ETO–expressing cells retained progenitor activity and continued to express CD34 throughout the 5-week long-term culture. Thus, AML1-ETO enhances the self-renewal of pluripotent stem cells, the physiological target of many acute myeloid leukemias.

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