1
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Wang Z, Ciarlini PC, Oduro KA, Gadde R, O'Neill S, Zhao C, Meyerson HJ. Side scatter ratio of the CD105-positive and CD105-negative red blood cell fractions is useful for the detection of low-grade myelodysplastic neoplasms by flow cytometry. Am J Clin Pathol 2024:aqae021. [PMID: 38581145 DOI: 10.1093/ajcp/aqae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/29/2024] [Indexed: 04/08/2024] Open
Abstract
OBJECTIVES We assessed the utility of red blood cell (RBC) CD105 and side scatter (SSC) parameters by flow cytometry for the detection of low-grade myelodysplastic neoplasms (MDS) in bone marrow specimens. METHODS Ten RBC parameters incorporating CD105 or SSC combined with the Meyerson-Alayed scoring system (MASS) metrics were retrospectively evaluated by flow cytometry for utility in detecting low-grade MDS (n = 56) compared with cytopenic controls (n = 86). RESULTS Myelodysplastic neoplasms were associated with 7 of the RBC parameters in univariate analysis. Multivariate analysis using cutoff values based on optimal and 95% specificity levels of the RBC metrics and the MASS parameters revealed the SSC ratio of CD105-positive and CD105-negative RBC fractions (CD105+/- SSC); the percentage and coefficient of variation of the CD105-positive fraction of RBCs (CD105%, CD105+CV) emerged as significant RBC variables. Two simple scoring schemes using these RBC values along with MASS parameters were identified: 1 using CD105+/- SSC, CD105%, and CD105+CV combined with the percentage of CD177-positive granulocytes (CD177%), myeloblast percentage (CD34%), and granulocyte SSC (GranSSC), and the other incorporating CD105+/- SSC, CD105+CV, CD177%, CD34%, GranSSC, and B-cell progenitor percentage. Both demonstrated a sensitivity of approximately 80%, with a specificity of roughly 90% for the detection of MDS compared with cytopenic controls. CONCLUSIONS The red blood cell parameter, CD105+/- SSC, appears to be beneficial in the evaluation of low-grade MDS by flow cytometry.
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Affiliation(s)
- Zijan Wang
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University, Cleveland, OH, US
| | - Pedro C Ciarlini
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University, Cleveland, OH, US
| | - Kwadwo A Oduro
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University, Cleveland, OH, US
| | - Ramya Gadde
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University, Cleveland, OH, US
| | - Stacey O'Neill
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University, Cleveland, OH, US
| | - Chen Zhao
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University, Cleveland, OH, US
| | - Howard J Meyerson
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University, Cleveland, OH, US
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2
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Ijee S, Chambayil K, Chaudhury AD, Bagchi A, Modak K, Das S, Benjamin ESB, Rani S, Paul DZ, Nath A, Roy D, Palani D, Priyanka S, Ravichandran R, Kumary BK, Sivamani Y, S. V, Babu D, Nakamura Y, Thamodaran V, Balasubramanian P, Velayudhan SR. Efficient deletion of microRNAs using CRISPR/Cas9 with dual guide RNAs. Front Mol Biosci 2024; 10:1295507. [PMID: 38628442 PMCID: PMC11020096 DOI: 10.3389/fmolb.2023.1295507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/27/2023] [Indexed: 04/19/2024] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that play crucial roles in gene regulation, exerting post-transcriptional silencing, thereby influencing cellular function, development, and disease. Traditional loss-of-function methods for studying miRNA functions, such as miRNA inhibitors and sponges, present limitations in terms of specificity, transient effects, and off-target effects. Similarly, CRISPR/Cas9-based editing of miRNAs using single guide RNAs (sgRNAs) also has limitations in terms of design space for generating effective gRNAs. In this study, we introduce a novel approach that utilizes CRISPR/Cas9 with dual guide RNAs (dgRNAs) for the rapid and efficient generation of short deletions within miRNA genomic regions. Through the expression of dgRNAs through single-copy lentiviral integration, this approach achieves over a 90% downregulation of targeted miRNAs within a week. We conducted a comprehensive analysis of various parameters influencing efficient deletion formation. In addition, we employed doxycycline (Dox)-inducible expression of Cas9 from the AAVS1 locus, enabling homogeneous, temporal, and stage-specific editing during cellular differentiation. Compared to miRNA inhibitory methods, the dgRNA-based approach offers higher specificity, allowing for the deletion of individual miRNAs with similar seed sequences, without affecting other miRNAs. Due to the increased design space, the dgRNA-based approach provides greater flexibility in gRNA design compared to the sgRNA-based approach. We successfully applied this approach in two human cell lines, demonstrating its applicability for studying the mechanisms of human erythropoiesis and pluripotent stem cell (iPSC) biology and differentiation. Efficient deletion of miR-451 and miR-144 resulted in blockage of erythroid differentiation, and the deletion of miR-23a and miR-27a significantly affected iPSC survival. We have validated the highly efficient deletion of genomic regions by editing protein-coding genes, resulting in a significant impact on protein expression. This protocol has the potential to be extended to delete multiple miRNAs within miRNA clusters, allowing for future investigations into the cooperative effects of the cluster members on cellular functions. The protocol utilizing dgRNAs for miRNA deletion can be employed to generate efficient pooled libraries for high-throughput comprehensive analysis of miRNAs involved in different biological processes.
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Affiliation(s)
- Smitha Ijee
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Karthik Chambayil
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Sree Chitra Tirunal Institute of Science and Medical Technology, Thiruvananthapuram, India
| | - Anurag Dutta Chaudhury
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Regional Centre for Biotechnology, New Delhi, India
| | - Abhirup Bagchi
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Kirti Modak
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Regional Centre for Biotechnology, New Delhi, India
| | - Saswati Das
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Esther Sathya Bama Benjamin
- Sree Chitra Tirunal Institute of Science and Medical Technology, Thiruvananthapuram, India
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Sonam Rani
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Daniel Zechariah Paul
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Aneesha Nath
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Debanjan Roy
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Dhavapriya Palani
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Sweety Priyanka
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | | | - Betty K. Kumary
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Yazhini Sivamani
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Vijayanand S.
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Dinesh Babu
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Vasanth Thamodaran
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Tata Institute of Genetics and Society, Bengaluru, India
| | | | - Shaji R. Velayudhan
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Department of Haematology, Christian Medical College Campus, Vellore, India
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3
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Thompson EN, Carlino MJ, Scanlon VM, Grimes HL, Krause DS. Assay optimization for the objective quantification of human multilineage colony-forming units. Exp Hematol 2023; 124:36-44.e3. [PMID: 37271449 PMCID: PMC10527702 DOI: 10.1016/j.exphem.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/06/2023]
Abstract
Colony-forming unit (CFU) assays are a powerful tool in hematopoietic research because they allow researchers to functionally test the lineage potential of individual stem and progenitor cells. Assaying for lineage potential is important for determining and validating the identity of progenitor populations isolated by methods such as fluorescence-activated cell sorting (FACS). However, current methods for CFU assays are limited in their ability to robustly assay multipotent progenitors with the ability to differentiate down the myeloid, erythroid, and megakaryocytic lineages because of the lack of specific growth factors necessary for certain lineage outputs. In addition, manual counting of colony types is subjective resulting in user to user variability in assessments of cell types based on colony and cell morphologies. We demonstrate that the addition of granulocyte colony-stimulating factor (G-CSF), macrophage (M)-CSF, and granulocyte-macrophage (GM)-CSF into a collagen-based MegaCult medium containing IL-3, IL-6, SCF, EPO, and TPO allows for the differentiation of common myeloid progenitors into expected proportions of colonies containing granulocytic (G), monocytic (M), erythroid (E), and megakaryocytic (Mk) cells. Additionally, we demonstrate an objective method using in situ immunofluorescence (IF) with anti-CD66b, anti-CD14, anti-CD235a, and anti-CD41 to detect G, M, E, and Mk cells, respectively. IF stained colonies can be analyzed individually at a microscope or using high-throughput microscopy. Thus, our improvements to the culture conditions and method for assay readout increase the accuracy, reproducibility, and throughput of the myeloid CFU assay.
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Affiliation(s)
- Evrett N Thompson
- Department of Cell Biology, Yale School of Medicine, New Haven, CT; Yale Stem Cell Center, New Haven, CT
| | - Maximillian J Carlino
- Yale Stem Cell Center, New Haven, CT; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Vanessa M Scanlon
- Yale Stem Cell Center, New Haven, CT; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT; Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health, Farmington, CT
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Diane S Krause
- Department of Cell Biology, Yale School of Medicine, New Haven, CT; Yale Stem Cell Center, New Haven, CT; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT; Department of Pathology, Yale School of Medicine, New Haven, CT.
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4
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Sorigue M. Diagnosis of erythroid dysplasia by flow cytometry: a review. Expert Rev Hematol 2023; 16:1049-1062. [PMID: 38018383 DOI: 10.1080/17474086.2023.2289534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/27/2023] [Indexed: 11/30/2023]
Abstract
INTRODUCTION The diagnosis of myelodysplastic syndrome (MDS) is complex. Flow cytometric analysis of the myelomonocytic compartment can be helpful, but it is highly subjective and reproducibility by non-specialized groups is unclear. Analysis of the erythroid lineage by flow cytometry is emerging as potentially more reproducible and easier to conduct, while keeping a high diagnostic performance. AREAS COVERED We review the evidence in this area, including 1) the use of well-established markers - CD71 and CD36 - and other less well-established markers and parameters; 2) the use of flow cytometric scores for the erythroid lineage; and 3) additional aspects, including the emergence of computational tools and the roles of flow cytometry beyond diagnosis. Finally, we discuss the limitations with the current evidence, including 1) the impact of the sample processing protocol and reagents on the results, 2) the lack of a standard gating strategy, and 3) conceptualization and design issues in the available publications. EXPERT OPINION We end by offering our recommendations for the current use - and our personal take on the value - of the analysis of erythroid lineage by flow cytometry.
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Affiliation(s)
- Marc Sorigue
- Medical Department, Trialing Health, Barcelona, Spain
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5
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Miljkovic M, Seguin A, Jia X, Cox JE, Catrow JL, Bergonia H, Phillips JD, Stephens WZ, Ward DM. Loss of the mitochondrial protein Abcb10 results in altered arginine metabolism in MEL and K562 cells and nutrient stress signaling through ATF4. J Biol Chem 2023:104877. [PMID: 37269954 PMCID: PMC10316008 DOI: 10.1016/j.jbc.2023.104877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/11/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023] Open
Abstract
Abcb10 is a mitochondrial membrane protein involved in hemoglobinization of red cells. Abcb10 topology and ATPase domain localization suggest it exports a substrate, likely biliverdin, out of mitochondria that is necessary for hemoglobinization. In this study we generated Abcb10 deletion cell lines in both mouse murine erythroleukemia (MEL) and human erythroid precursor human myelogenous leukemia (K562) cells to better understand the consequences of Abcb10 loss. Loss of Abcb10 resulted in an inability to hemoglobinize upon differentiation in both K562 and MEL cells with reduced heme and intermediate porphyrins and decreased levels of aminolevulinic acid synthase 2 activity. Metabolomic and transcriptional analyses revealed that Abcb10 loss gave rise to decreased cellular arginine levels, increased transcripts for cationic and neutral amino acid transporters with reduced levels of the citrulline to arginine converting enzymes argininosuccinate synthetase and argininosuccinate lyase. The reduced arginine levels in Abcb10 null cells gave rise to decreased proliferative capacity. Arginine supplementation improved both Abcb10 null proliferation and hemoglobinization upon differentiation. Abcb10 null cells showed increased phosphorylation of Eukaryotic Translation Initiation Factor 2 Subunit Alpha (eIF2A), increased expression of nutrient sensing transcription factor ATF4 and downstream targets DNA damage inducible transcript 3 (Chop), ChaC glutathione specific gamma-glutamylcyclotransferase 1 (Chac1) and arginyl-tRNA synthetase 1 (Rars). These results suggest that when the Abcb10 substrate is trapped in the mitochondria, the nutrient sensing machinery is turned on remodeling transcription to block protein synthesis necessary for proliferation and hemoglobin biosynthesis in erythroid models.
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Affiliation(s)
- Marisa Miljkovic
- Department of Pathology, Division of Microbiology and Immunology, Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Alexandra Seguin
- Department of Pathology, Division of Microbiology and Immunology, Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Xuan Jia
- Department of Pathology, Division of Microbiology and Immunology, Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - James E Cox
- Department of Biochemistry, Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; Metabolomics Core Research Facility, Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Jonathan Leon Catrow
- Metabolomics Core Research Facility, Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Hector Bergonia
- Iron and Heme Core Research Facility, Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - John D Phillips
- Department of Medicine, Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - W Zac Stephens
- Department of Pathology, Division of Microbiology and Immunology, Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Diane M Ward
- Department of Pathology, Division of Microbiology and Immunology, Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
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6
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Schippel N, Sharma S. Dynamics of Human Hematopoietic Stem and Progenitor Cell Differentiation to the Erythroid Lineage. Exp Hematol 2023:S0301-472X(23)00224-2. [PMID: 37172755 DOI: 10.1016/j.exphem.2023.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
Erythropoiesis, the development of erythrocytes from hematopoietic stem cells, occurs through four phases: erythroid progenitor development, early erythropoiesis, terminal erythroid differentiation (TED), and maturation. According to the classical model that is based on immunophenotypic profiles of cell populations, each of these phases comprises multiple differentiation states that arise in a hierarchical manner. After segregation of lymphoid potential, erythroid priming begins during progenitor development and progresses through progenitor cell types that have multilineage potential. Complete separation of the erythroid lineage is achieved during early erythropoiesis with the formation of unipotent erythroid progenitors: burst forming unit-erythroid and colony forming unit-erythroid. These erythroid committed progenitors undergo TED and maturation, which involves expulsion of the nucleus and remodeling to form functional biconcave, hemoglobin-filled erythrocytes. In the last decade or so, many studies employing advanced techniques such as single cell RNA-sequencing (scRNA-seq) as well as the conventional methods, including colony forming cell assays and immunophenotyping, have revealed heterogeneity within the stem, progenitor, and erythroblast stages, and uncovered alternate paths for segregation of erythroid lineage potential. In this review, we provide an in-depth account of immunophenotypic profiles of all cell types within erythropoiesis, highlight studies that demonstrate heterogeneous erythroid stages, and describe deviations to the classical model of erythropoiesis. Overall, although scRNA-seq approaches have provided new insights, flow cytometry remains relevant and is the primary method for validation of novel immunophenotypes.
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Affiliation(s)
- Natascha Schippel
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004.
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7
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Obi CD, Dailey HA, Jami-Alahmadi Y, Wohlschlegel JA, Medlock AE. Proteomic Analysis of Ferrochelatase Interactome in Erythroid and Non-Erythroid Cells. Life (Basel) 2023; 13. [PMID: 36836934 DOI: 10.3390/life13020577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/24/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Heme is an essential cofactor for multiple cellular processes in most organisms. In developing erythroid cells, the demand for heme synthesis is high, but is significantly lower in non-erythroid cells. While the biosynthesis of heme in metazoans is well understood, the tissue-specific regulation of the pathway is less explored. To better understand this, we analyzed the mitochondrial heme metabolon in erythroid and non-erythroid cell lines from the perspective of ferrochelatase (FECH), the terminal enzyme in the heme biosynthetic pathway. Affinity purification of FLAG-tagged-FECH, together with mass spectrometric analysis, was carried out to identify putative protein partners in human and murine cell lines. Proteins involved in the heme biosynthetic process and mitochondrial organization were identified as the core components of the FECH interactome. Interestingly, in non-erythroid cell lines, the FECH interactome is highly enriched with proteins associated with the tricarboxylic acid (TCA) cycle. Overall, our study shows that the mitochondrial heme metabolon in erythroid and non-erythroid cells has similarities and differences, and suggests new roles for the mitochondrial heme metabolon and heme in regulating metabolic flux and key cellular processes.
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Modepalli S, Martinez-Morilla S, Venkatesan S, Fasano J, Paulsen K, Görlich D, Hattangadi S, Kupfer GM. An In Vivo Model for Elucidating the Role of an Erythroid-Specific Isoform of Nuclear Export Protein Exportin 7 (Xpo7) in Murine Erythropoiesis. Exp Hematol 2022; 114:22-32. [PMID: 35973480 PMCID: PMC10165728 DOI: 10.1016/j.exphem.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 11/04/2022]
Abstract
Erythroid nuclear condensation is a complex process in which compaction to one-tenth its original size occurs in an active nucleus simultaneously undergoing transcription and cell division. We previously found that the nuclear exportin Exportin7 (Xpo7), which is erythroid- specific and highly induced during terminal erythropoiesis, facilitates nuclear condensation. We also identified a previously unannotated, erythroid-specific isoform of Xpo7 (Xpo7B) containing a novel first exon Xpo7-1b expressed only in late Ter119+ erythroblasts. To better understand the functional difference between the erythroid Xpo7B isoform and the ubiquitous isoform (Xpo7A) containing the original first exon Xpo7-1a, we created gene-targeted mouse models lacking either exon Xpo7-1a or Xpo7-1b, or both exons 4 and 5, which are completely null for Xpo7 expression. We found that deficiency in Xpo7A does not affect steady-state nor stress erythropoiesis. In contrast, mice lacking the erythroid isoform, Xpo7B, exhibit a mild anemia as well as altered stress erythropoiesis. Complete Xpo7 deficiency resulted in partially penetrant embryonic lethality at the stage when definitive erythropoiesis is prominent in the fetal liver. Inducible complete knockdown of Xpo7 confirms that both steady-state erythropoiesis and stress erythropoiesis are affected. We also observe that Xpo7 deficiency downregulates the expression of important stress response factors, such as Gdf15 and Smad3. We conclude that the erythroid-specific isoform of Xpo7 is important for both steady-state and stress erythropoiesis in mice.
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Affiliation(s)
- Susree Modepalli
- Department of Molecular Oncology, Georgetown University, Washington DC
| | | | - Srividhya Venkatesan
- Department of Pediatric Hematology-Oncology, Yale School of Medicine, New Haven, CT
| | - James Fasano
- Department of Pediatric Hematology-Oncology, Yale School of Medicine, New Haven, CT
| | - Katerina Paulsen
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Shilpa Hattangadi
- Division of Kidney, Urologic, and Hematologic Diseases, National Institutes of Health, Bethesda, MD.
| | - Gary M Kupfer
- Department of Molecular Oncology, Georgetown University, Washington DC.
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9
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Baskar R, Chen AF, Favaro P, Reynolds W, Mueller F, Borges L, Jiang S, Park HS, Kool ET, Greenleaf WJ, Bendall SC. Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment. Cell Rep Methods 2022; 2:100188. [PMID: 35463156 PMCID: PMC9017139 DOI: 10.1016/j.crmeth.2022.100188] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/20/2022] [Accepted: 03/01/2022] [Indexed: 01/01/2023]
Abstract
Master transcription factors (TFs) directly regulate present and future cell states by binding DNA regulatory elements and driving gene-expression programs. Their abundance influences epigenetic priming to different cell fates at the chromatin level, especially in the context of differentiation. In order to link TF protein abundance to changes in TF motif accessibility and open chromatin, we developed InTAC-seq, a method for simultaneous quantification of genome-wide chromatin accessibility and intracellular protein abundance in fixed cells. Our method produces high-quality data and is a cost-effective alternative to single-cell techniques. We showcase our method by purifying bone marrow (BM) progenitor cells based on GATA-1 protein levels and establish high GATA-1-expressing BM cells as both epigenetically and functionally similar to erythroid-committed progenitors.
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Affiliation(s)
- Reema Baskar
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Cancer Biology Program, Stanford University, Stanford, CA 94305, USA
| | - Amy F. Chen
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Patricia Favaro
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Warren Reynolds
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Fabian Mueller
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Luciene Borges
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Hyun Shin Park
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
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10
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Abstract
Erythropoiesis is a process of enormous magnitude, with the average person generating two to three million red cells every second. Erythroid progenitors start as large cells with large nuclei, and over the course of three to four cell divisions they undergo a dramatic decrease in cell size accompanied by profound nuclear condensation, which culminates in enucleation. As maturing erythroblasts are undergoing these dramatic phenotypic changes, they accumulate hemoglobin and express high levels of other erythroid-specific genes, while silencing much of the non-erythroid transcriptome. These phenotypic and gene expression changes are associated with distinct changes in the chromatin landscape, and require close coordination between transcription factors and epigenetic regulators, as well as precise regulation of RNA polymerase II activity. Disruption of these processes are associated with inherited anemias and myelodysplastic syndromes. Here, we review the epigenetic mechanisms that govern terminal erythroid maturation, and their role in human disease.
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Affiliation(s)
- Maeve Wells
- Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Laurie Steiner
- Department of Pediatrics, University of Rochester, Rochester, NY, United States
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11
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Narayan RK, Asghar A, Ghosh SK, Bharti S. Adrenal Myelolipoma Mimics Ectopic Adrenal or Renal Tissue: An Incidental Finding During Cadaveric Dissection. Acta Endocrinol (Buchar) 2021; 17:111-116. [PMID: 34539918 DOI: 10.4183/aeb.2021.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Context On naked eye examination adrenal myelolipoma (AML) tissue appears to be an ectopic adrenal or renal tissue, based on the similarity to their external texture. This necessitates a histo-pathological study for confirming the origin of the tissue. Objective To establish the origin and histological features of the incidental AML tissue found during cadaveric dissection and review the literature for similar findings with clinical picture and treatment description. Subjects and Methods Unilateral adrenal gland obtained from cadaveric dissection was subjected to histological study by H & E staining of the slides prepared. The literature review was done from articles published in PubMed indexed journals. Case report A case of an incidental finding of AML during cadaveric dissection is presented which on naked eye examination was appearing to be an ectopic adrenal or renal tissue, based on the similarity to their external texture. On histological examination, a thin rim of adrenocortical tissue, surrounding the mature adipose tissue, and attenuated by islets of myeloid, erythroid and megakaryocytic cell lines in varying proportions, resembling the mature bone marrow morphology, was observed. The literature review on PubMed explains similar incidental post-mortem autopsy findings due to the asymptomatic nature of the tumor. The incidence of AML varied between 0.08% and 0.2% in the last decade of the 20th century, which increased up to 10 - 15% of incidental adrenal masses due to the widespread use of non-invasive imaging modalities leading to an increase in the diagnosis of the pathology. Conclusions Before considering the ectopic incidence of tissue during cadaveric dissection, a histo-pathological examination is mandatory for confirmation. Adreno-myelolipoma is an asymptomatic post-mortem finding in 10-15% of cases of adrenal tissue which mimics ectopic adrenal gland or renal tissue due to its external texture.
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Affiliation(s)
- R K Narayan
- All India Institute of Medical Sciences, Department of Anatomy, Patna, Bihar, India
| | - A Asghar
- All India Institute of Medical Sciences, Department of Anatomy, Patna, Bihar, India
| | - S K Ghosh
- All India Institute of Medical Sciences, Department of Anatomy, Patna, Bihar, India
| | - S Bharti
- All India Institute of Medical Sciences, Department of Pathology, Patna, Bihar, India
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12
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Daniels DE, Ferguson DCJ, Griffiths RE, Trakarnsanga K, Cogan N, MacInnes KA, Mordue KE, Andrienko T, Ferrer-Vicens I, Ramos Jiménez D, Lewis PA, Wilson MC, Canham MA, Kurita R, Nakamura Y, Anstee DJ, Frayne J. Reproducible immortalization of erythroblasts from multiple stem cell sources provides approach for sustainable RBC therapeutics. Mol Ther Methods Clin Dev 2021; 22:26-39. [PMID: 34485592 PMCID: PMC8390520 DOI: 10.1016/j.omtm.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 06/01/2021] [Indexed: 12/01/2022]
Abstract
Developing robust methodology for the sustainable production of red blood cells in vitro is essential for providing an alternative source of clinical-quality blood, particularly for individuals with rare blood group phenotypes. Immortalized erythroid progenitor cell lines are the most promising emergent technology for achieving this goal. We previously created the erythroid cell line BEL-A from bone marrow CD34+ cells that had improved differentiation and enucleation potential compared to other lines reported. In this study we show that our immortalization approach is reproducible for erythroid cells differentiated from bone marrow and also from far more accessible peripheral and cord blood CD34+ cells, consistently generating lines with similar improved erythroid performance. Extensive characterization of the lines shows them to accurately recapitulate their primary cell equivalents and provides a molecular signature for immortalization. In addition, we show that only cells at a specific stage of erythropoiesis, predominantly proerythroblasts, are amenable to immortalization. Our methodology provides a step forward in the drive for a sustainable supply of red cells for clinical use and for the generation of model cellular systems for the study of erythropoiesis in health and disease, with the added benefit of an indefinite expansion window for manipulation of molecular targets.
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Affiliation(s)
- Deborah E Daniels
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.,NIHR Blood and Transplant Research Unit, University of Bristol, Bristol BS8 1TD, UK
| | | | | | - Kongtana Trakarnsanga
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Nicola Cogan
- NIHR Blood and Transplant Research Unit, University of Bristol, Bristol BS8 1TD, UK.,Bristol Institute for Transfusion Sciences, National Health Service Blood and Transplant (NHSBT), Bristol BS34 7QH, UK
| | - Katherine A MacInnes
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.,NIHR Blood and Transplant Research Unit, University of Bristol, Bristol BS8 1TD, UK
| | - Kathryn E Mordue
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | | | | | - Phillip A Lewis
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | | | - Maurice A Canham
- Tissues, Cells & Advanced Therapeutics, Scottish National Blood Transfusion Service, The Jack Copland Centre, 52 Research Avenue North, Edinburgh, EH14 4BE, UK
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki, Japan
| | - David J Anstee
- NIHR Blood and Transplant Research Unit, University of Bristol, Bristol BS8 1TD, UK.,Bristol Institute for Transfusion Sciences, National Health Service Blood and Transplant (NHSBT), Bristol BS34 7QH, UK
| | - Jan Frayne
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.,NIHR Blood and Transplant Research Unit, University of Bristol, Bristol BS8 1TD, UK
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13
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Liao R, Zheng Y, Liu X, Zhang Y, Seim G, Tanimura N, Wilson GM, Hematti P, Coon JJ, Fan J, Xu J, Keles S, Bresnick EH. Discovering How Heme Controls Genome Function Through Heme-omics. Cell Rep 2021; 31:107832. [PMID: 32610133 DOI: 10.1016/j.celrep.2020.107832] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/03/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
Protein ensembles control genome function by establishing, maintaining, and deconstructing cell-type-specific chromosomal landscapes. A plethora of small molecules orchestrate cellular functions and therefore may link physiological processes with genome biology. The metabolic enzyme and hemoglobin cofactor heme induces proteolysis of a transcriptional repressor, Bach1, and regulates gene expression post-transcriptionally. However, whether heme controls genome function broadly or through prescriptive actions is unclear. Using assay for transposase-accessible chromatin sequencing (ATAC-seq), we establish a heme-dependent chromatin atlas in wild-type and mutant erythroblasts lacking enhancers that confer normal heme synthesis. Amalgamating chromatin landscapes and transcriptomes in cells with sub-physiological heme and post-heme rescue reveals parallel Bach1-dependent and Bach1-independent mechanisms that target heme-sensing chromosomal hotspots. The hotspots harbor a DNA motif demarcating heme-regulated chromatin and genes encoding proteins not known to be heme regulated, including metabolic enzymes. The heme-omics analysis establishes how an essential biochemical cofactor controls genome function and cellular physiology.
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Affiliation(s)
- Ruiqi Liao
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ye Zheng
- Department of Statistics, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Xin Liu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gretchen Seim
- Department of Nutritional Sciences, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Nobuyuki Tanimura
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Gary M Wilson
- Department of Chemistry, Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Peiman Hematti
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Joshua J Coon
- Department of Chemistry, Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jing Fan
- Department of Nutritional Sciences, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sunduz Keles
- Department of Statistics, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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14
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Iacobucci I, Mullighan C. Prognostic mutation constellations in acute myeloid leukaemia and myelodysplastic syndrome. Curr Opin Hematol 2021; 28:101-109. [PMID: 33427759 PMCID: PMC8174569 DOI: 10.1097/moh.0000000000000629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW In the past decade, numerous studies analysing the genome and transcriptome of large cohorts of acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS) patients have substantially improved our knowledge of the genetic landscape of these diseases with the identification of heterogeneous constellations of germline and somatic mutations with prognostic and therapeutic relevance. However, inclusion of integrated genetic data into classification schema is still far from a reality. The purpose of this review is to summarize recent insights into the prevalence, pathogenic role, clonal architecture, prognostic impact and therapeutic management of genetic alterations across the spectrum of myeloid malignancies. RECENT FINDINGS Recent multiomic-studies, including analysis of genetic alterations at the single-cell resolution, have revealed a high heterogeneity of lesions in over 200 recurrently mutated genes affecting disease initiation, clonal evolution and clinical outcome. Artificial intelligence and specifically machine learning approaches have been applied to large cohorts of AML and MDS patients to define in an unbiased manner clinically meaningful disease patterns including, disease classification, prognostication and therapeutic vulnerability, paving the way for future use in clinical practice. SUMMARY Integration of genomic, transcriptomic, epigenomic and clinical data coupled to conventional and machine learning approaches will allow refined leukaemia classification and risk prognostication and will identify novel therapeutic targets for these still high-risk leukaemia subtypes.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis (USA)
| | - Charles Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis (USA)
- Hematological Malignancies Program, St Jude Children’s Research Hospital, Memphis, TN, United States
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15
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Bagchi A, Nath A, Thamodaran V, Ijee S, Palani D, Rajendiran V, Venkatesan V, Datari P, Pai AA, Janet NB, Balasubramanian P, Nakamura Y, Srivastava A, Mohankumar KM, Thangavel S, Velayudhan SR. Direct Generation of Immortalized Erythroid Progenitor Cell Lines from Peripheral Blood Mononuclear Cells. Cells 2021; 10:523. [PMID: 33804564 PMCID: PMC7999632 DOI: 10.3390/cells10030523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/08/2021] [Accepted: 02/19/2021] [Indexed: 02/04/2023] Open
Abstract
Reliable human erythroid progenitor cell (EPC) lines that can differentiate to the later stages of erythropoiesis are important cellular models for studying molecular mechanisms of human erythropoiesis in normal and pathological conditions. Two immortalized erythroid progenitor cells (iEPCs), HUDEP-2 and BEL-A, generated from CD34+ hematopoietic progenitors by the doxycycline (dox) inducible expression of human papillomavirus E6 and E7 (HEE) genes, are currently being used extensively to study transcriptional regulation of human erythropoiesis and identify novel therapeutic targets for red cell diseases. However, the generation of iEPCs from patients with red cell diseases is challenging as obtaining a sufficient number of CD34+ cells require bone marrow aspiration or their mobilization to peripheral blood using drugs. This study established a protocol for culturing early-stage EPCs from peripheral blood (PB) and their immortalization by expressing HEE genes. We generated two iEPCs, PBiEPC-1 and PBiEPC-2, from the peripheral blood mononuclear cells (PBMNCs) of two healthy donors. These cell lines showed stable doubling times with the properties of erythroid progenitors. PBiEPC-1 showed robust terminal differentiation with high enucleation efficiency, and it could be successfully gene manipulated by gene knockdown and knockout strategies with high efficiencies without affecting its differentiation. This protocol is suitable for generating a bank of iEPCs from patients with rare red cell genetic disorders for studying disease mechanisms and drug discovery.
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Affiliation(s)
- Abhirup Bagchi
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Aneesha Nath
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Vasanth Thamodaran
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Dhavapriya Palani
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Vignesh Rajendiran
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Vigneshwaran Venkatesan
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Phaneendra Datari
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Aswin Anand Pai
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Nancy Beryl Janet
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Poonkuzhali Balasubramanian
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki 3050074, Japan;
| | - Alok Srivastava
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Kumarasamypet Murugesan Mohankumar
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Saravanabhavan Thangavel
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Shaji R. Velayudhan
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
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16
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Magee JA, Signer RAJ. Developmental Stage-Specific Changes in Protein Synthesis Differentially Sensitize Hematopoietic Stem Cells and Erythroid Progenitors to Impaired Ribosome Biogenesis. Stem Cell Reports 2021; 16:20-28. [PMID: 33440178 PMCID: PMC7815942 DOI: 10.1016/j.stemcr.2020.11.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/16/2022] Open
Abstract
Adult hematopoietic stem cell (HSC) self-renewal requires precise control of protein synthesis, but fetal and adult HSCs have distinct self-renewal mechanisms and lineage outputs. This raises the question of whether protein synthesis rates change with age. Here, we show that protein synthesis rates decline during HSC ontogeny, yet erythroid protein synthesis rates increase. A ribosomal mutation that impairs ribosome biogenesis (Rpl24Bst/+) disrupts both fetal and adult HSC self-renewal. However, the Rpl24Bst/+ mutation selectively impairs fetal erythropoiesis at differentiation stages that exhibit fetal-specific attenuation of protein synthesis. Developmental changes in protein synthesis thus differentially sensitize hematopoietic stem and progenitor cells to impaired ribosome biogenesis. Fetal HSCs synthesize much more protein per hour than young adult HSCs in vivo Fetal erythroid progenitors synthesize less protein than adult erythroid progenitors Differences in protein synthesis distinguish fetal and adult erythroid differentiation Rpl24Bst/+ impairs fetal and adult HSCs, but only impairs fetal erythroid progenitors
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Affiliation(s)
- Jeffrey A Magee
- Division of Hematology and Oncology, Department of Pediatrics, and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert A J Signer
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0652, USA.
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17
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Sarodaya N, Karapurkar J, Kim KS, Hong SH, Ramakrishna S. The Role of Deubiquitinating Enzymes in Hematopoiesis and Hematological Malignancies. Cancers (Basel) 2020; 12:E1103. [PMID: 32354135 PMCID: PMC7281754 DOI: 10.3390/cancers12051103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/11/2020] [Accepted: 04/26/2020] [Indexed: 12/24/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are responsible for the production of blood cells throughout the human lifespan. Single HSCs can give rise to at least eight distinct blood-cell lineages. Together, hematopoiesis, erythropoiesis, and angiogenesis coordinate several biological processes, i.e., cellular interactions during development and proliferation, guided migration, lineage programming, and reprogramming by transcription factors. Any dysregulation of these processes can result in hematological disorders and/or malignancies. Several studies of the molecular mechanisms governing HSC maintenance have demonstrated that protein regulation by the ubiquitin proteasomal pathway is crucial for normal HSC function. Recent studies have shown that reversal of ubiquitination by deubiquitinating enzymes (DUBs) plays an equally important role in hematopoiesis; however, information regarding the biological function of DUBs is limited. In this review, we focus on recent discoveries about the physiological roles of DUBs in hematopoiesis, erythropoiesis, and angiogenesis and discuss the DUBs associated with common hematological disorders and malignancies, which are potential therapeutic drug targets.
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Affiliation(s)
- Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (J.K.); (K.-S.K.)
| | - Janardhan Karapurkar
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (J.K.); (K.-S.K.)
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (J.K.); (K.-S.K.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (J.K.); (K.-S.K.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
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18
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Hawksworth J, Satchwell TJ, Meinders M, Daniels DE, Regan F, Thornton NM, Wilson MC, Dobbe JG, Streekstra GJ, Trakarnsanga K, Heesom KJ, Anstee DJ, Frayne J, Toye AM. Enhancement of red blood cell transfusion compatibility using CRISPR-mediated erythroblast gene editing. EMBO Mol Med 2019; 10:emmm.201708454. [PMID: 29700043 PMCID: PMC5991592 DOI: 10.15252/emmm.201708454] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Regular blood transfusion is the cornerstone of care for patients with red blood cell (RBC) disorders such as thalassaemia or sickle‐cell disease. With repeated transfusion, alloimmunisation often occurs due to incompatibility at the level of minor blood group antigens. We use CRISPR‐mediated genome editing of an immortalised human erythroblast cell line (BEL‐A) to generate multiple enucleation competent cell lines deficient in individual blood groups. Edits are combined to generate a single cell line deficient in multiple antigens responsible for the most common transfusion incompatibilities: ABO (Bombay phenotype), Rh (Rhnull), Kell (K0), Duffy (Fynull), GPB (S−s−U−). These cells can be differentiated to generate deformable reticulocytes, illustrating the capacity for coexistence of multiple rare blood group antigen null phenotypes. This study provides the first proof‐of‐principle demonstration of combinatorial CRISPR‐mediated blood group gene editing to generate customisable or multi‐compatible RBCs for diagnostic reagents or recipients with complicated matching requirements.
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Affiliation(s)
- Joseph Hawksworth
- School of Biochemistry, University of Bristol, Bristol, UK.,Bristol Institute for Transfusion Sciences, National Health Service Blood and Transplant (NHSBT), Bristol, UK
| | - Timothy J Satchwell
- School of Biochemistry, University of Bristol, Bristol, UK.,NIHR Blood and Transplant Research Unit, University of Bristol, Bristol, UK.,Bristol Institute for Transfusion Sciences, National Health Service Blood and Transplant (NHSBT), Bristol, UK
| | | | - Deborah E Daniels
- School of Biochemistry, University of Bristol, Bristol, UK.,NIHR Blood and Transplant Research Unit, University of Bristol, Bristol, UK
| | - Fiona Regan
- Imperial College Healthcare NHS Trust, London, UK.,NHS Blood & Transplant, London, UK
| | - Nicole M Thornton
- International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, Bristol, UK
| | | | - Johannes Gg Dobbe
- Department of Biomedical Engineering and Physics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Geert J Streekstra
- Department of Biomedical Engineering and Physics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Kongtana Trakarnsanga
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kate J Heesom
- School of Biochemistry, University of Bristol, Bristol, UK
| | - David J Anstee
- School of Biochemistry, University of Bristol, Bristol, UK.,NIHR Blood and Transplant Research Unit, University of Bristol, Bristol, UK.,Bristol Institute for Transfusion Sciences, National Health Service Blood and Transplant (NHSBT), Bristol, UK
| | - Jan Frayne
- School of Biochemistry, University of Bristol, Bristol, UK.,NIHR Blood and Transplant Research Unit, University of Bristol, Bristol, UK
| | - Ashley M Toye
- School of Biochemistry, University of Bristol, Bristol, UK .,NIHR Blood and Transplant Research Unit, University of Bristol, Bristol, UK.,Bristol Institute for Transfusion Sciences, National Health Service Blood and Transplant (NHSBT), Bristol, UK
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19
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Gould KA, Bresnick EH. Sequence determinants of DNA binding by the hematopoietic helix-loop-helix transcription factor TAL1: importance of sequences flanking the E-box core. Gene Expr 2018; 7:87-101. [PMID: 9699481 PMCID: PMC6190197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
TAL1 is a helix-loop-helix transcription factor that is essential for hematopoiesis. In vitro DNA binding site selection experiments have previously identified the preferred binding site for TAL1 heterodimers as AACAGATGGT. TAL1 homodimers do not bind DNA with significant affinity. A subset of other E-box sequences is also bound by TAL1 heterodimers. Here, we present an analysis of TAL1 heterodimer DNA binding specificity, using E-boxes derived from genomic clones, which were isolated by immunoadsorption of K562 erythroleukemia cell chromatin with a TAL1 antibody. We show that TAL1 heterodimer binding to a CAGATG E-box is strongly modulated by nucleotides flanking the E-box. A 10 base pair element consisting of the CAGATG E-box and two flanking nucleotides in both the 5' and 3' direction is sufficient for high-affinity binding. Certain mutations of nucleotides in either the 5' (-1 and -2) or 3' (+1 and +2) direction strongly inhibit binding. The importance of flanking nucleotides also exists in the context of nonpreferred E-boxes recognized by TAL1 heterodimers. Although there are no known target genes for TAL1, the regulatory regions of several genes involved in hematopoiesis contain the preferred E-box CAGATG. However, based on our results, the E-boxes in these potential target genes contain flanking sequences that would be expected to significantly reduce TAL1 heterodimer binding in vitro. Thus, additional stabilizing forces, such as protein-protein interactions between TAL1 heterodimers and accessory factors, may be required to confer high-affinity TAL1 heterodimer binding to such sequences.
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Affiliation(s)
- Karen A. Gould
- University of Wisconsin Medical School Department of Pharmacology, 1300 University Avenue, Madison, WI53706
| | - Emery H. Bresnick
- Address correspondence to Emery H. Bresnick. Tel: (608) 265-6446; Fax: (608) 262-1257; E-mail:
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20
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Mehta C, Johnson KD, Gao X, Ong IM, Katsumura KR, McIver SC, Ranheim EA, Bresnick EH. Integrating Enhancer Mechanisms to Establish a Hierarchical Blood Development Program. Cell Rep 2018; 20:2966-2979. [PMID: 28930689 DOI: 10.1016/j.celrep.2017.08.090] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/30/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic development requires the transcription factor GATA-2, and GATA-2 mutations cause diverse pathologies, including leukemia. GATA-2-regulated enhancers increase Gata2 expression in hematopoietic stem/progenitor cells and control hematopoiesis. The +9.5-kb enhancer activates transcription in endothelium and hematopoietic stem cells (HSCs), and its deletion abrogates HSC generation. The -77-kb enhancer activates transcription in myeloid progenitors, and its deletion impairs differentiation. Since +9.5-/- embryos are HSC deficient, it was unclear whether the +9.5 functions in progenitors or if GATA-2 expression in progenitors solely requires -77. We further dissected the mechanisms using -77;+9.5 compound heterozygous (CH) mice. The embryonic lethal CH mutation depleted megakaryocyte-erythrocyte progenitors (MEPs). While the +9.5 suffices for HSC generation, the -77 and +9.5 must reside on one allele to induce MEPs. The -77 generated burst-forming unit-erythroid through the induction of GATA-1 and other GATA-2 targets. The enhancer circuits controlled signaling pathways that orchestrate a GATA factor-dependent blood development program.
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Affiliation(s)
- Charu Mehta
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Kirby D Johnson
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Xin Gao
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Irene M Ong
- UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53705, USA
| | - Koichi R Katsumura
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Skye C McIver
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Erik A Ranheim
- Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Emery H Bresnick
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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21
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Salati S, Prudente Z, Genovese E, Pennucci V, Rontauroli S, Bartalucci N, Mannarelli C, Ruberti S, Zini R, Rossi C, Bianchi E, Guglielmelli P, Tagliafico E, Vannucchi AM, Manfredini R. Calreticulin Affects Hematopoietic Stem/Progenitor Cell Fate by Impacting Erythroid and Megakaryocytic Differentiation. Stem Cells Dev 2018; 27:225-236. [PMID: 29258411 DOI: 10.1089/scd.2017.0137] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Calreticulin (CALR) is a chaperone protein that localizes primarily to the endoplasmic reticulum (ER) lumen where it is responsible for the control of proper folding of neo-synthesized glycoproteins and the retention of calcium. Recently, mutations affecting exon 9 of the CALR gene have been described in approximately 40% of patients with myeloproliferative neoplasms (MPNs). Although the role of mutated CALR in the development of MPNs has begun to be clarified, there are still no data available on the function of wild-type (WT) CALR during physiological hematopoiesis. To shed light on the role of WT CALR during normal hematopoiesis, we performed gene silencing and overexpression experiments in hematopoietic stem progenitor cells (HSPCs). Our results showed that CALR overexpression is able to affect physiological hematopoiesis by enhancing both erythroid and megakaryocytic (MK) differentiation. In agreement with overexpression data, CALR silencing caused a significant decrease in both erythroid and MK differentiation of human HSPCs. Gene expression profiling (GEP) analysis showed that CALR is able to affect the expression of several genes involved in HSPC differentiation toward both the erythroid and MK lineages. Moreover, GEP data also highlighted the modulation of several genes involved in ER stress response, unfolded protein response (UPR), and DNA repair, and of several genes already described to play a role in MPN development, such as proinflammatory cytokines and hematological neoplasm-related markers. Altogether, our data unraveled a new and unexpected role for CALR in the regulation of normal hematopoietic differentiation. Moreover, by showing the impact of CALR on the expression of genes involved in several biological processes already described in cellular transformation, our data strongly suggest a more complex role for CALR in MPN development that goes beyond the activation of the THPO receptor and involves ER stress response, UPR, and DNA repair.
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Affiliation(s)
- Simona Salati
- Centre for Regenerative Medicine "Stefano Ferrari," University of Modena and Reggio Emilia, Modena, Italy
| | - Zelia Prudente
- Centre for Regenerative Medicine "Stefano Ferrari," University of Modena and Reggio Emilia, Modena, Italy
| | - Elena Genovese
- Centre for Regenerative Medicine "Stefano Ferrari," University of Modena and Reggio Emilia, Modena, Italy
| | - Valentina Pennucci
- Institute for Cell and Gene Therapy & Center for Chronic Immunodeficiency, University of Freiburg, Freiburg, Germany
| | - Sebastiano Rontauroli
- Centre for Regenerative Medicine "Stefano Ferrari," University of Modena and Reggio Emilia, Modena, Italy
| | - Niccolò Bartalucci
- CRIMM, Center for Research and Innovation for Myeloproliferative Neoplasms, Department of Experimental and Clinical Medicine, AOU Careggi, University of Florence, Florence, Italy
| | - Carmela Mannarelli
- CRIMM, Center for Research and Innovation for Myeloproliferative Neoplasms, Department of Experimental and Clinical Medicine, AOU Careggi, University of Florence, Florence, Italy
| | - Samantha Ruberti
- Centre for Regenerative Medicine "Stefano Ferrari," University of Modena and Reggio Emilia, Modena, Italy
| | - Roberta Zini
- Centre for Regenerative Medicine "Stefano Ferrari," University of Modena and Reggio Emilia, Modena, Italy
| | - Chiara Rossi
- Centre for Regenerative Medicine "Stefano Ferrari," University of Modena and Reggio Emilia, Modena, Italy
| | - Elisa Bianchi
- Centre for Regenerative Medicine "Stefano Ferrari," University of Modena and Reggio Emilia, Modena, Italy
| | - Paola Guglielmelli
- CRIMM, Center for Research and Innovation for Myeloproliferative Neoplasms, Department of Experimental and Clinical Medicine, AOU Careggi, University of Florence, Florence, Italy
| | - Enrico Tagliafico
- Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandro M Vannucchi
- CRIMM, Center for Research and Innovation for Myeloproliferative Neoplasms, Department of Experimental and Clinical Medicine, AOU Careggi, University of Florence, Florence, Italy
| | - Rossella Manfredini
- Centre for Regenerative Medicine "Stefano Ferrari," University of Modena and Reggio Emilia, Modena, Italy
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22
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Hewitt KJ, Katsumura KR, Matson DR, Devadas P, Tanimura N, Hebert AS, Coon JJ, Kim JS, Dewey CN, Keles S, Hao S, Paulson RF, Bresnick EH. GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia. Dev Cell 2017; 42:213-225.e4. [PMID: 28787589 DOI: 10.1016/j.devcel.2017.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/05/2017] [Accepted: 07/11/2017] [Indexed: 12/31/2022]
Abstract
An enhancer with amalgamated E-box and GATA motifs (+9.5) controls expression of the regulator of hematopoiesis GATA-2. While similar GATA-2-occupied elements are common in the genome, occupancy does not predict function, and GATA-2-dependent genetic networks are incompletely defined. A "+9.5-like" element resides in an intron of Samd14 (Samd14-Enh) encoding a sterile alpha motif (SAM) domain protein. Deletion of Samd14-Enh in mice strongly decreased Samd14 expression in bone marrow and spleen. Although steady-state hematopoiesis was normal, Samd14-Enh-/- mice died in response to severe anemia. Samd14-Enh stimulated stem cell factor/c-Kit signaling, which promotes erythrocyte regeneration. Anemia activated Samd14-Enh by inducing enhancer components and enhancer chromatin accessibility. Thus, a GATA-2/anemia-regulated enhancer controls expression of an SAM domain protein that confers survival in anemia. We propose that Samd14-Enh and an ensemble of anemia-responsive enhancers are essential for erythrocyte regeneration in stress erythropoiesis, a vital process in pathologies, including β-thalassemia, myelodysplastic syndrome, and viral infection.
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Affiliation(s)
- Kyle J Hewitt
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Koichi R Katsumura
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Daniel R Matson
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Prithvia Devadas
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Nobuyuki Tanimura
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Joshua J Coon
- Department of Chemistry, UW-Madison, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science and Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, South Korea
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Sunduz Keles
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Siyang Hao
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Robert F Paulson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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23
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Bebeshko VG, Bruslova KM, Pushkareva TI, Tsvyetkova NM, Lyashenko LO, Kuznyetsova OY, Kuzmenko VF, Gonchar LO, Yaatsemyrskyy SM. State of erythroid, granulocyte and platelet branches of hematopoiesis on stages of chemotherapy in children with acute lymphoblastic leukemia, who were exposed to ionizing radiation after the Chornobyl NPP accident. Probl Radiac Med Radiobiol 2016; 21:178-190. [PMID: 28027552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVE Evaluation of proliferation and differentiation processes of progenitor cells in bone marrow by the com position of elements of erythroid, granulocyte and platelet branches of hematopoiesis on the treatment stages in children with acute lymphoblastic leukemia (ALL), who were exposed to radiation from the Chornobyl NPP accident. MATERIALS AND METHODS The 46 children with ALL were studied, who lived in Kyiv, Zhytomyr and Chernihiv regions. Studies were conducted before the start of chemotherapy (ChT), on the 33 day of ChT (phase I), and after the com pletion of ChT (phase II). Exposure doses of patients, hemogram and myelogram parameters both with indices of mat uration of progenitor cells were evaluated. Signs of dysplasia of hematopoietic branch elements were revewed. RESULTS The 46 patients were studied. They have had the B ALL, namely pro B ALL (n=5), «common type» (n=36), pre B ALL (n=3), and T ALL in 2 other cases. In a debut of ALL the bone marrow was represented by lymphoblasts. Along with ChT conduction the bone marrow hematopoiesis recovered by such types, as erythroid, granulocyte, gran ulocyte whith monocytes, and uniform, when the cells number of all branches was within a normal quantity. At the phase ІІ of ChT the number of patients with hematopoiesis recovery by erythroid type decreased and number of chil dren with activation of granulocyte branch of hematopoiesis increased. In children with pro B ALL the number of erythroid elements was higher than normative at both ChT phases. A direct correlation was established between the number of myelokaryocytes (Mkc) and megakaryocytes (Mgkc) in both phase І and phase ІІ of treatment (Rs = +0.72; Rs = +0.56, respectively). There was no correlation between the radiation dose in patients (3.73 ± 0.12 mSv) and studied parameters. CONCLUSIONS Types of bone marrow recovery were established in ALL patients after the ChT indicating to the differ ent kinetic pathways of hematopoietic progenitor cells. Evaluation of reasons of prevalence of some hematopoietic branches will allow to reveal their role in leukemogenesis and to correct the treatment programs.
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Affiliation(s)
- V G Bebeshko
- State Institution National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Melnykov str., 53, Kyiv, 04050, Ukraine
| | - K M Bruslova
- State Institution National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Melnykov str., 53, Kyiv, 04050, Ukraine
| | - T I Pushkareva
- State Institution National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Melnykov str., 53, Kyiv, 04050, Ukraine
| | - N M Tsvyetkova
- State Institution National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Melnykov str., 53, Kyiv, 04050, Ukraine
| | - L O Lyashenko
- State Institution National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Melnykov str., 53, Kyiv, 04050, Ukraine
| | - O Ye Kuznyetsova
- State Institution National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Melnykov str., 53, Kyiv, 04050, Ukraine
| | - V F Kuzmenko
- State Institution National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Melnykov str., 53, Kyiv, 04050, Ukraine
| | - L O Gonchar
- State Institution National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Melnykov str., 53, Kyiv, 04050, Ukraine
| | - S M Yaatsemyrskyy
- State Institution National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Melnykov str., 53, Kyiv, 04050, Ukraine
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24
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Palis J. Hematopoietic stem cell-independent hematopoiesis: emergence of erythroid, megakaryocyte, and myeloid potential in the mammalian embryo. FEBS Lett 2016; 590:3965-3974. [PMID: 27790707 DOI: 10.1002/1873-3468.12459] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 10/10/2016] [Indexed: 01/20/2023]
Abstract
Steady-state production of all circulating blood cells in the adult ultimately depends on hematopoietic stem cells (HSCs), which first arise in small numbers beginning at embryonic day (E) 10.5 in large arterial vessels of the murine embryo. However, blood cell synthesis first begins in the yolk sac beginning at E7.25 and consists of two waves of hematopoietic progenitors. The first wave consists of primitive erythroid, megakaryocyte, and macrophage progenitors that rapidly give rise to maturing blood cells of all three lineages. This 'primitive' wave of progenitors is followed by a partially overlapping wave of 'erythro-myeloid progenitors', which contain definitive erythroid, megakaryocyte, macrophage, neutrophil, and mast cell progenitors that seed the fetal liver and jump-start hematopoiesis before the engraftment and expansion of HSCs. These two waves of progenitors that arise in the yolk sac are necessary and even sufficient to sustain the survival of the mouse embryo until birth in the absence of HSCs. They provide key signals to support HSC emergence. Finally, HSC-independent hematopoiesis also provides long-lived tissue-resident macrophage populations that function in multiple adult organs.
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Affiliation(s)
- James Palis
- Department of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, NY, USA
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25
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Affiliation(s)
- Nicole Mende
- a Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden , Dresden , Germany
| | - Susann Rahmig
- a Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden , Dresden , Germany
| | - Claudia Waskow
- a Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden , Dresden , Germany
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26
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McIver SC, Katsumura KR, Davids E, Liu P, Kang YA, Yang D, Bresnick EH. Exosome complex orchestrates developmental signaling to balance proliferation and differentiation during erythropoiesis. eLife 2016; 5. [PMID: 27543448 PMCID: PMC5040589 DOI: 10.7554/elife.17877] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/18/2016] [Indexed: 12/11/2022] Open
Abstract
Since the highly conserved exosome complex mediates the degradation and processing of multiple classes of RNAs, it almost certainly controls diverse biological processes. How this post-transcriptional RNA-regulatory machine impacts cell fate decisions and differentiation is poorly understood. Previously, we demonstrated that exosome complex subunits confer an erythroid maturation barricade, and the erythroid transcription factor GATA-1 dismantles the barricade by transcriptionally repressing the cognate genes. While dissecting requirements for the maturation barricade in Mus musculus, we discovered that the exosome complex is a vital determinant of a developmental signaling transition that dictates proliferation/amplification versus differentiation. Exosome complex integrity in erythroid precursor cells ensures Kit receptor tyrosine kinase expression and stem cell factor/Kit signaling, while preventing responsiveness to erythropoietin-instigated signals that promote differentiation. Functioning as a gatekeeper of this developmental signaling transition, the exosome complex controls the massive production of erythroid cells that ensures organismal survival in homeostatic and stress contexts. DOI:http://dx.doi.org/10.7554/eLife.17877.001 Red blood cells supply an animal’s tissues with the oxygen they need to survive. These cells circulate for a certain amount of time before they die. To replenish the red blood cells that are lost, first a protein called stem cell factor (SCF) instructs stem cells and precursor cells to proliferate, and a second protein, known as erythropoietin, then signals to these cells to differentiate into mature red blood cells. It is important to maintain this balance between these two processes because too much proliferation can lead to cancer while too much differentiation will exhaust the supply of stem cells. Previous work has shown that a collection of proteins called the exosome complex can block steps leading towards mature red blood cells. The exosome complex controls several processes within cells by modifying or degrading a variety of messenger RNAs, the molecules that serve as intermediates between DNA and protein. However, it was not clear how the exosome complex sets up the differentiation block and whether it is somehow connected to the signaling from SCF and erythropoietin. McIver et al. set out to address this issue by isolating precursor cells with the potential to become red blood cells from mouse fetal livers and experimentally reducing the levels of the exosome complex. The experiments showed that these cells were no longer able to respond when treated with SCF in culture, whereas the control cells responded as normal. Further experiments showed that cells with less of the exosome complex also made less of a protein named Kit. Normally, SCF interacts with Kit to instruct cells to multiply. Lastly, although the experimental cells could no longer respond to these proliferation signals, they could react to erythropoietin, which promotes differentiation. Thus, normal levels of the exosome complex keep the delicate balance between proliferation and differentiation, which is crucial to the development of red blood cells. In future, it will be important to study the exosome complex in living mice and in human cells, and to see whether it also controls other signaling pathways. Furthermore, it is worth exploring whether this new knowledge can help efforts to produce red blood cells on an industrial scale, which could then be used to treat patients with conditions such as anemia. DOI:http://dx.doi.org/10.7554/eLife.17877.002
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Affiliation(s)
- Skye C McIver
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, United States.,UW-Madison Blood Research Program, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Koichi R Katsumura
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, United States.,UW-Madison Blood Research Program, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Elsa Davids
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, United States.,UW-Madison Blood Research Program, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Peng Liu
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Yoon-A Kang
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, United States.,UW-Madison Blood Research Program, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - David Yang
- Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, United States.,UW-Madison Blood Research Program, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States
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27
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Sundaravel S, Duggan R, Bhagat T, Ebenezer DL, Liu H, Yu Y, Bartenstein M, Unnikrishnan M, Karmakar S, Liu TC, Torregroza I, Quenon T, Anastasi J, McGraw KL, Pellagatti A, Boultwood J, Yajnik V, Artz A, Le Beau MM, Steidl U, List AF, Evans T, Verma A, Wickrema A. Reduced DOCK4 expression leads to erythroid dysplasia in myelodysplastic syndromes. Proc Natl Acad Sci U S A 2015; 112:E6359-68. [PMID: 26578796 DOI: 10.1073/pnas.1516394112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Anemia is the predominant clinical manifestation of myelodysplastic syndromes (MDS). Loss or deletion of chromosome 7 is commonly seen in MDS and leads to a poor prognosis. However, the identity of functionally relevant, dysplasia-causing, genes on 7q remains unclear. Dedicator of cytokinesis 4 (DOCK4) is a GTPase exchange factor, and its gene maps to the commonly deleted 7q region. We demonstrate that DOCK4 is underexpressed in MDS bone marrow samples and that the reduced expression is associated with decreased overall survival in patients. We show that depletion of DOCK4 levels leads to erythroid cells with dysplastic morphology both in vivo and in vitro. We established a novel single-cell assay to quantify disrupted F-actin filament network in erythroblasts and demonstrate that reduced expression of DOCK4 leads to disruption of the actin filaments, resulting in erythroid dysplasia that phenocopies the red blood cell (RBC) defects seen in samples from MDS patients. Reexpression of DOCK4 in -7q MDS patient erythroblasts resulted in significant erythropoietic improvements. Mechanisms underlying F-actin disruption revealed that DOCK4 knockdown reduces ras-related C3 botulinum toxin substrate 1 (RAC1) GTPase activation, leading to increased phosphorylation of the actin-stabilizing protein ADDUCIN in MDS samples. These data identify DOCK4 as a putative 7q gene whose reduced expression can lead to erythroid dysplasia.
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28
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Tan E, Abrams-Ogg ACG, Defarges A, Bienzle D. Automated hematologic analysis of bone marrow aspirate samples from healthy Beagle dogs. Vet Clin Pathol 2014; 43:342-51. [PMID: 25135758 DOI: 10.1111/vcp.12175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Interpretation of bone marrow (BM) smears typically is comprised of qualitative assessment and differential counting of cells. Analysis of BM fluid with automated hematology analyzers may provide rapid characterization of cells to supplement microscopic interpretation. OBJECTIVES The purpose of the study was to examine the practicality and utility of analyzing BM samples in the Advia 2120 hematology analyzer; to determine if results correlate with smear assessment; and to establish descriptive statistics from hematologically normal and clinically healthy Beagle dogs. METHODS Anticoagulated BM aspirates from 3 different sites of 26 adult Beagle dogs were collected. BM samples were analyzed in the Advia 2120, and numerical results were correlated with microscopic assessment of corresponding BM smears. Results from automated analyses and manual 500-cell differential counts were statistically analyzed. RESULTS Forty-six samples were suitable for complete analysis. Results were available in approximately 2 (Advia) and 30 (stained and cover-slipped smear) minutes. Advia nucleated cell concentration was significantly correlated with microscopic assessment of smear particle number and smear cellularity. Significant correlations were also identified for Advia percent neutrophils with segmented, band and metamylocyte neutrophils, Advia percent lymphocytes with rubricytes, and Advia percent large unstained cells (LUC) with myeloblasts and promyelocytes. CONCLUSIONS Automated analysis of BM aspirates was practicable, although techniques to obtain cellular samples and avoid clot formation could be improved. Automated analysis may provide rapid and useful preliminary information regarding sample cellularity, and granulocytic and erythrocytic components. Automated analysis should not supplant microscopic assessment, but may be a useful adjunct.
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Affiliation(s)
- E Tan
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
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Duncan MT, Shin S, Wu JJ, Mays Z, Weng S, Bagheri N, Miller WM, Shea LD. Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation. Biotechnol Bioeng 2014; 111:2082-94. [PMID: 24853077 DOI: 10.1002/bit.25262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 02/23/2014] [Accepted: 03/31/2014] [Indexed: 01/19/2023]
Abstract
The directed differentiation toward erythroid (E) or megakaryocytic (MK) lineages by the MK-E progenitor (MEP) could enhance the ex vivo generation of red blood cells and platelets for therapeutic transfusions. The lineage choice at the MEP bifurcation is controlled in large part by activity within the intracellular signal transduction network, the output of which determines the activity of transcription factors (TFs) and ultimately gene expression. Although many TFs have been implicated, E or MK differentiation is a complex process requiring multiple days, and the dynamics of TF activities during commitment and terminal maturation are relatively unexplored. Herein, we applied a living cell array for the large-scale, dynamic quantification of TF activities during MEP bifurcation. A panel of hematopoietic TFs (GATA-1, GATA-2, SCL/TAL1, FLI-1, NF-E2, PU.1, c-Myb) was characterized during E and MK differentiation of bipotent K562 cells. Dynamic TF activity profiles associated with differentiation towards each lineage were identified, and validated with previous reports. From these activity profiles, we show that GATA-1 is an important hub during early hemin- and PMA-induced differentiation, and reveal several characteristic TF interactions for E and MK differentiation that confirm regulatory mechanisms documented in the literature. Additionally, we highlight several novel TF interactions at various stages of E and MK differentiation. Furthermore, we investigated the mechanism by which nicotinamide (NIC) promoted terminal MK maturation using an MK-committed cell line, CHRF-288-11 (CHRF). Concomitant with its enhancement of ploidy, NIC strongly enhanced the activity of three TFs with known involvement in terminal MK maturation: FLI-1, NF-E2, and p53. Dynamic profiling of TF activity represents a novel tool to complement traditional assays focused on mRNA and protein expression levels to understand progenitor cell differentiation.
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Affiliation(s)
- Mark T Duncan
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
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Wangen JR, Eidenschink Brodersen L, Stolk TT, Wells DA, Loken MR. Assessment of normal erythropoiesis by flow cytometry: important considerations for specimen preparation. Int J Lab Hematol 2013; 36:184-96. [PMID: 24118926 DOI: 10.1111/ijlh.12151] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/15/2013] [Indexed: 11/30/2022]
Abstract
INTRODUCTION The extension of quantitative flow cytometric studies to the erythroid lineage in patients with suspected myelodysplastic syndrome has prompted a reassessment of cell surface antigen expression during normal erythropoiesis. Erythropoiesis in normal and pathologic bone marrows was studied to determine the expected antigenic relationships of maturing erythroid cells. METHODS A total of 200 bone marrow specimens were evaluated by multidimensional flow cytometry (MDF). Samples were prepared using either NH4 Cl lysis or Ficoll density gradient separation. RESULTS Normal erythroid development is described as a two-step process observable with the intensity relationships between CD235a, CD71, CD45, CD105, CD34, CD117, and CD36. The variability of these intensities (CV) was determined. A comparison of processing techniques determined lysis is the optimal analytic technique for the analysis of early-stage erythroid cells. Nucleic acid staining with DRAQ5 revealed that Ficoll allows for the analysis of reticulocytes and mature erythrocytes otherwise eliminated by lysis. CONCLUSION These data demonstrate while lysis alters the light scatter characteristics of erythroid precursors, it did not alter quantitative antigen expression or nucleic acid content. The expected variability in antigen intensities is defined. These studies provide a basis for a comparison of erythroid development between normal individuals and those with erythroid dysplasia associated with myelodysplastic syndromes.
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DeVilbiss AW, Boyer ME, Bresnick EH. Establishing a hematopoietic genetic network through locus-specific integration of chromatin regulators. Proc Natl Acad Sci U S A 2013; 110:E3398-407. [PMID: 23959865 DOI: 10.1073/pnas.1302771110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The establishment and maintenance of cell type-specific transcriptional programs require an ensemble of broadly expressed chromatin remodeling and modifying enzymes. Many questions remain unanswered regarding the contributions of these enzymes to specialized genetic networks that control critical processes, such as lineage commitment and cellular differentiation. We have been addressing this problem in the context of erythrocyte development driven by the transcription factor GATA-1 and its coregulator Friend of GATA-1 (FOG-1). As certain GATA-1 target genes have little to no FOG-1 requirement for expression, presumably additional coregulators can mediate GATA-1 function. Using a genetic complementation assay and RNA interference in GATA-1-null cells, we demonstrate a vital link between GATA-1 and the histone H4 lysine 20 methyltransferase PR-Set7/SetD8 (SetD8). GATA-1 selectively induced H4 monomethylated lysine 20 at repressed, but not activated, loci, and endogenous SetD8 mediated GATA-1-dependent repression of a cohort of its target genes. GATA-1 used different combinations of SetD8, FOG-1, and the FOG-1-interacting nucleosome remodeling and deacetylase complex component Mi2β to repress distinct target genes. Implicating SetD8 as a context-dependent GATA-1 corepressor expands the repertoire of coregulators mediating establishment/maintenance of the erythroid cell genetic network, and provides a biological framework for dissecting the cell type-specific functions of this important coregulator. We propose a coregulator matrix model in which distinct combinations of chromatin regulators are required at different GATA-1 target genes, and the unique attributes of the target loci mandate these combinations.
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Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB. Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell 2009; 36:682-95. [PMID: 19941827 PMCID: PMC2800995 DOI: 10.1016/j.molcel.2009.11.002] [Citation(s) in RCA: 245] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 09/05/2009] [Accepted: 10/30/2009] [Indexed: 01/29/2023]
Abstract
The transcription factor GATA-1 is required for terminal erythroid maturation and functions as an activator or repressor depending on gene context. Yet its in vivo site selectivity and ability to distinguish between activated versus repressed genes remain incompletely understood. In this study, we performed GATA-1 ChIP-seq in erythroid cells and compared it to GATA-1-induced gene expression changes. Bound and differentially expressed genes contain a greater number of GATA-binding motifs, a higher frequency of palindromic GATA sites, and closer occupancy to the transcriptional start site versus nondifferentially expressed genes. Moreover, we show that the transcription factor Zbtb7a occupies GATA-1-bound regions of some direct GATA-1 target genes, that the presence of SCL/TAL1 helps distinguish transcriptional activation versus repression, and that polycomb repressive complex 2 (PRC2) is involved in epigenetic silencing of a subset of GATA-1-repressed genes. These data provide insights into GATA-1-mediated gene regulation in vivo.
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Affiliation(s)
- Ming Yu
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Laura Riva
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Huafeng Xie
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yocheved Schindler
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tyler B. Moran
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yong Cheng
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Duonan Yu
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ross Hardison
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Mitchell J Weiss
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stuart H. Orkin
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Bradley E. Bernstein
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School and the Broad Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, USA
| | - Alan B. Cantor
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Johnson KD, Kim SI, Bresnick EH. Differential sensitivities of transcription factor target genes underlie cell type-specific gene expression profiles. Proc Natl Acad Sci U S A 2006; 103:15939-44. [PMID: 17043224 PMCID: PMC1635106 DOI: 10.1073/pnas.0604041103] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Indexed: 02/05/2023] Open
Abstract
Changes in transcription factor levels and activities dictate developmental fate. Such a change might affect the full ensemble of target genes for a factor or only uniquely sensitive targets. We investigated the relationship among activity of the hematopoietic transcription factor GATA-1, chromatin occupancy, and target gene sensitivity. Graded activation of GATA-1 in GATA-1-null cells revealed high-, intermediate-, and low-sensitivity targets. GATA-1 activity requirements for occupancy and transcription often correlated. A GATA-1 amino-terminal deletion mutant severely deregulated the low-sensitivity gene Tac-2. Thus, cells expressing different levels of a cell type-specific activator can have qualitatively distinct target gene expression patterns, and factor mutations preferentially deregulate low-sensitivity genes. Unlike other target genes, GATA-1-mediated Tac-2 regulation was bimodal, with activation followed by repression, and the coregulator Friend of GATA-1 (FOG-1) selectively mediated repression. A GATA-1 mutant defective in FOG-1 binding occupied a Tac-2 regulatory region at levels higher than wild-type GATA-1, whereas FOG-1 facilitated chromatin occupancy at a distinct target site. These results indicate that FOG-1 is a determinant of GATA factor target gene sensitivity by either facilitating or opposing chromatin occupancy.
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Affiliation(s)
- Kirby D. Johnson
- Molecular and Cellular Pharmacology Program, Department of Pharmacology, University of Wisconsin School of Medicine, 383 Medical Sciences Center, 1300 University Avenue, Madison, WI 53706
| | - Shin-Il Kim
- Molecular and Cellular Pharmacology Program, Department of Pharmacology, University of Wisconsin School of Medicine, 383 Medical Sciences Center, 1300 University Avenue, Madison, WI 53706
| | - Emery H. Bresnick
- Molecular and Cellular Pharmacology Program, Department of Pharmacology, University of Wisconsin School of Medicine, 383 Medical Sciences Center, 1300 University Avenue, Madison, WI 53706
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Kiekhaefer CM, Grass JA, Johnson KD, Boyer ME, Bresnick EH. Hematopoietic-specific activators establish an overlapping pattern of histone acetylation and methylation within a mammalian chromatin domain. Proc Natl Acad Sci U S A 2002; 99:14309-14. [PMID: 12379744 PMCID: PMC137880 DOI: 10.1073/pnas.212389499] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2002] [Indexed: 11/18/2022] Open
Abstract
Posttranslational modification of histones through acetylation, methylation, and phosphorylation is a common mode of regulating chromatin structure and, therefore, diverse nuclear processes. One such modification, methylated histone H3 at lysine-4 (H3-meK4), colocalizes with hyperacetylated histones H3 and H4 in mammalian chromatin. Whereas activators directly recruit acetyltransferases, the process whereby H3-meK4 is established is unknown. We tested whether the hematopoietic-specific activators NF-E2 and GATA-1, which mediate transactivation of the beta-globin genes, induce both histone acetylation and H3-meK4. Through the use of NF-E2- and GATA-1-null cell lines, we show that both activators induce H3 acetylation at the promoter upon transcriptional activation. However, analysis of H3-mek4 revealed that NF-E2 and GATA-1 differentially regulate chromatin modifications at the betamajor promoter. NF-E2, but not GATA-1, induces H3-meK4 at the promoter. Thus, under conditions in which NF-E2 and GATA-1 activate the transcription of an endogenous gene at least 570-fold, these activators differ in their capacity to induce H3-meK4. Despite strong H3-meK4 at hypersensitive site 2 of the upstream locus control region, neither factor was required to establish H3-meK4 at this site. These results support a model in which multiple tissue-specific activators collectively function to assemble a composite histone modification pattern, consisting of overlapping histone acetylation and methylation. As GATA-1 induced H3 acetylation, but not H3-meK4, at the promoter, H3 acetylation and H3-meK4 components of a composite histone modification pattern can be established independently.
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Affiliation(s)
- Carol M Kiekhaefer
- Molecular and Cellular Pharmacology Program, Department of Pharmacology, University of Wisconsin Medical School, 1300 University Avenue, 383 Medical Sciences Center, Madison, WI 53706, USA
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Abstract
The human beta-globin locus control region (LCR) consists of four erythroid-specific DNaseI hypersensitive sites (HSs) at the 5' end of the beta-globin cluster. The LCR functions over a long distance on chromosome 11 to regulate transcription and replication of the beta-globin genes. To determine whether the HSs function independently or as an integrated unit, we analyzed the requirements for long-range transcriptional activation. If the HSs function independently, individual HSs would be expected to have long-range activity. In contrast, if long-range activity requires multiple HSs, individual HSs would have a limited functional distance. HS2, HS3, and a miniLCR containing multiple HSs, were separated from a gamma-globin promoter by fragments of phage lambda DNA. After stable transfection into K562 cells, HS2 had strong enhancer activity, but only when positioned close to the promoter. HS3 also had strong enhancer activity, although it was weaker than HS2 and more sensitive to the spacer DNA. The miniLCR had the strongest enhancer activity and functioned even at a distance of 7.3 kb. A model is proposed in which synergistic interactions between HSs confer long-range activation by creating a stable LCR nucleoprotein structure, which is competent for recruiting chromatin-modifying enzymes. These enzymes would mediate the well-characterized activity of the LCR to modulate chromatin structure.
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Affiliation(s)
- E H Bresnick
- University of Wisconsin Medical School, Department of Pharmacology, 387 Medical Science, 1300 University Avenue, Madison, WI 53706, USA
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Nienhuis AW, Anderson WF. Hemoglobin switching in sheep and goats: change in functional globin messenger RNA in reticulocytes and bone marrow cells. Proc Natl Acad Sci U S A 1972; 69:2184-8. [PMID: 4506088 PMCID: PMC426896 DOI: 10.1073/pnas.69.8.2184] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
ANEMIA CAUSES A CHANGE IN THE TYPE OF CIRCULATING HEMOGLOBIN IN GOATS AND CERTAIN SHEEP: HbA (alpha(2)beta(2) (A)) is replaced by HbC (alpha(2)beta(2) (C)). We have isolated globin mRNA from erythroid cells of anemic and nonanemic animals to investigate the mechanism whereby anemia causes this switch. To study several stages in transition from beta(A) to beta(C) synthesis, active globin mRNA was isolated from bone marrow cells, as well as from reticulocytes. By assaying these globin mRNAs in a rabbit reticulocyte cell-free system, we have demonstrated that the switch from beta(A) to beta(C) globin synthesis is mediated via a change in functional globin mRNA.
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