51
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The evolution of viral integration site analysis. Blood 2020; 135:1192-1193. [PMID: 32271907 DOI: 10.1182/blood.2020005115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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52
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Bramlett C, Jiang D, Nogalska A, Eerdeng J, Contreras J, Lu R. Clonal tracking using embedded viral barcoding and high-throughput sequencing. Nat Protoc 2020; 15:1436-1458. [PMID: 32132718 PMCID: PMC7427513 DOI: 10.1038/s41596-019-0290-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 12/21/2019] [Indexed: 11/09/2022]
Abstract
Embedded viral barcoding in combination with high-throughput sequencing is a powerful technology with which to track single-cell clones. It can provide clonal-level insights into cellular proliferation, development, differentiation, migration, and treatment efficacy. Here, we present a detailed protocol for a viral barcoding procedure that includes the creation of barcode libraries, the viral delivery of barcodes, the recovery of barcodes, and the computational analysis of barcode sequencing data. The entire procedure can be completed within a few weeks. This barcoding method requires cells to be susceptible to viral transduction. It provides high sensitivity and throughput, and enables precise quantification of cellular progeny. It is cost efficient and does not require any advanced skills. It can also be easily adapted to many types of applications, including both in vitro and in vivo experiments.
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Affiliation(s)
- Charles Bramlett
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Du Jiang
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Anna Nogalska
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Jiya Eerdeng
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Jorge Contreras
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Rong Lu
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA, USA.
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53
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Wang Y, Sano S, Yura Y, Ke Z, Sano M, Oshima K, Ogawa H, Horitani K, Min KD, Miura-Yura E, Kour A, Evans MA, Zuriaga MA, Hirschi KK, Fuster JJ, Pietras EM, Walsh K. Tet2-mediated clonal hematopoiesis in nonconditioned mice accelerates age-associated cardiac dysfunction. JCI Insight 2020; 5:135204. [PMID: 32154790 PMCID: PMC7213793 DOI: 10.1172/jci.insight.135204] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/26/2020] [Indexed: 12/17/2022] Open
Abstract
Clonal hematopoiesis of indeterminate potential is prevalent in elderly individuals and associated with increased risks of all-cause mortality and cardiovascular disease. However, mouse models to study the dynamics of clonal hematopoiesis and its consequences on the cardiovascular system under homeostatic conditions are lacking. We developed a model of clonal hematopoiesis using adoptive transfer of unfractionated ten-eleven translocation 2-mutant (Tet2-mutant) bone marrow cells into nonirradiated mice. Consistent with age-related clonal hematopoiesis observed in humans, these mice displayed a progressive expansion of Tet2-deficient cells in multiple hematopoietic stem and progenitor cell fractions and blood cell lineages. The expansion of the Tet2-mutant fraction was also observed in bone marrow-derived CCR2+ myeloid cell populations within the heart, but there was a negligible impact on the yolk sac-derived CCR2- cardiac-resident macrophage population. Transcriptome profiling revealed an enhanced inflammatory signature in the donor-derived macrophages isolated from the heart. Mice receiving Tet2-deficient bone marrow cells spontaneously developed age-related cardiac dysfunction characterized by greater hypertrophy and fibrosis. Altogether, we show that Tet2-mediated hematopoiesis contributes to cardiac dysfunction in a nonconditioned setting that faithfully models human clonal hematopoiesis in unperturbed bone marrow. Our data support clinical findings that clonal hematopoiesis per se may contribute to diminished health span.
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Affiliation(s)
- Ying Wang
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Soichi Sano
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Yoshimitsu Yura
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Zhonghe Ke
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Miho Sano
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Kosei Oshima
- Molecular Cardiology/Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Hayato Ogawa
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Keita Horitani
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Kyung-Duk Min
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Emiri Miura-Yura
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Anupreet Kour
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Megan A. Evans
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Maria A. Zuriaga
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Karen K. Hirschi
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Jose J. Fuster
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Eric M. Pietras
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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54
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Black L, Zorina T. Cell-based immunomodulatory therapy approaches for type 1 diabetes mellitus. Drug Discov Today 2020; 25:380-391. [DOI: 10.1016/j.drudis.2019.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/11/2019] [Accepted: 11/30/2019] [Indexed: 12/14/2022]
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55
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Gulati GS, Zukowska M, Noh JJ, Zhang A, Wesche DJ, Sinha R, George BM, Weissman IL, Szade K. Neogenin-1 distinguishes between myeloid-biased and balanced Hoxb5+ mouse long-term hematopoietic stem cells. Proc Natl Acad Sci U S A 2019; 116:25115-25125. [PMID: 31754028 PMCID: PMC6911217 DOI: 10.1073/pnas.1911024116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Hematopoietic stem cells (HSCs) self-renew and generate all blood cells. Recent studies with single cell transplants and lineage tracing suggest that adult HSCs are diverse in their reconstitution and lineage potentials. However, prospective isolation of these subpopulations has remained challenging. Here, we identify Neogenin-1 (NEO1) as a unique surface marker on a fraction of mouse HSCs labeled with Hoxb5, a specific reporter of long-term HSCs (LT-HSCs). We show that NEO1+Hoxb5+ LT-HSCs expand with age and respond to myeloablative stress in young mice while NEO1-Hoxb5+ LT-HSCs exhibit no significant change in number. Furthermore, NEO1+Hoxb5+ LT-HSCs are more often in the G2/S cell cycle phase compared to NEO1-Hoxb5+ LT-HSCs in both young and old bone marrow. Upon serial transplantation, NEO1+Hoxb5+ LT-HSCs exhibit myeloid-biased differentiation and reduced reconstitution while NEO1-Hoxb5+ LT-HSCs are lineage-balanced and stably reconstitute recipients. Gene expression analysis reveals erythroid and myeloid priming in the NEO1+ fraction and association of quiescence and self-renewal-related transcription factors with NEO1- LT-HSCs. Finally, transplanted NEO1+Hoxb5+ LT-HSCs rarely generate NEO1-Hoxb5+ LT-HSCs while NEO1-Hoxb5+ LT-HSCs repopulate both LT-HSC fractions. This supports a model in which dormant, balanced NEO1-Hoxb5+ LT-HSCs can hierarchically precede active, myeloid-biased NEO1+Hoxb5+ LT-HSCs.
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Affiliation(s)
- Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Monika Zukowska
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Joseph J Noh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Allison Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Daniel J Wesche
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Benson M George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305;
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Krzysztof Szade
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305;
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
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56
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Abstract
Genetic defects that accumulate in haematopoietic stem cells (HSCs) are thought to be responsible for age-related changes in haematopoiesis that include a decline in lymphopoiesis and skewing towards the myeloid lineage. This HSC-centric view is based largely on studies showing that HSCs from aged mice exhibit these lineage biases following transplantation into irradiated young recipient mice. In this Opinion article, we make the case that the reliance on this approach has led to inaccurate conclusions regarding the effects of ageing on blood-forming stem cells; we suggest instead that changes in the environment contribute to haematopoietic system ageing. We propose that a complete understanding of how ageing affects haematopoiesis depends on the analysis of blood cell production in unperturbed mice. We describe how this can be achieved using in situ fate mapping. This approach indicates that changes in downstream progenitors, in addition to any HSC defects, may explain the reduced lymphopoiesis and sustained myelopoiesis that occur during ageing.
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57
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Bigildeev AE, Petinati NA, Drize NJ. How Methods of Molecular Biology Shape Our Understanding of the Hematopoietic System. Mol Biol 2019. [DOI: 10.1134/s0026893319050029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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58
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Scala S, Aiuti A. In vivo dynamics of human hematopoietic stem cells: novel concepts and future directions. Blood Adv 2019; 3:1916-1924. [PMID: 31239246 PMCID: PMC6595260 DOI: 10.1182/bloodadvances.2019000039] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023] Open
Abstract
Unveiling the mechanisms and the cellular dynamics at the basis of human hematopoietic homeostasis has been a main focus for the scientific community since the discovery of a pool of multipotent hematopoietic stem cells (HSCs) capable of sustaining the hematopoietic output throughout life and after transplantation. Recently, new works shed light on the (1) differentiation paths, (2) size and replication rate of human HSC population at steady state, and (3) role of the distinct subpopulations comprising the hematopoietic stem and progenitor cell reservoir after transplantation. These papers exploited cutting-edge technologies, including vector integration site clonal tracking, spontaneous mutations, and deep transcriptome profiling. Here we discuss the latest updates in human hematopoietic system biology and in vivo dynamics, highlighting novel concepts and common findings deriving from different approaches and the future directions of these studies. Taken together, this information contributed to partially resolving the complexity of the in vivo HSC behavior and has major implications for HSC transplantation and gene therapy as well as for the development of future therapies.
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Affiliation(s)
- Serena Scala
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) and
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) and
- Pediatric Immunohematology and Stem Cell Programme, IRCCS San Raffaele Scientific Institute, Milan, Italy; and
- Medical School, Università Vita-Salute San Raffaele, Milan, Italy
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59
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Abstract
Ever since hematopoietic stem cells (HSCs) were first identified half a century ago, their differentiation roadmap has been extensively studied. The classical model of hematopoiesis has long held as a dogma that HSCs reside at the top of a hierarchy in which HSCs possess self-renewal capacity and can progressively give rise to all blood lineage cells. However, over the past several years, with advances in single cell technologies, this developmental scheme has been challenged. In this review, we discuss the evidence supporting heterogeneity within HSC and progenitor populations as well as the hierarchical models revised by novel approaches mainly in mouse system. These evolving views provide further understanding of hematopoiesis and highlight the complexity of hematopoietic differentiation.
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60
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Loss of hematopoietic diversity with age. Blood 2019; 133:1921-1922. [PMID: 31048301 DOI: 10.1182/blood-2019-03-900902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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61
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Chen J, Kao YR, Sun D, Todorova TI, Reynolds D, Narayanagari SR, Montagna C, Will B, Verma A, Steidl U. Myelodysplastic syndrome progression to acute myeloid leukemia at the stem cell level. Nat Med 2018; 25:103-110. [PMID: 30510255 PMCID: PMC6436966 DOI: 10.1038/s41591-018-0267-4] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/23/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Jiahao Chen
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yun-Ruei Kao
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Daqian Sun
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.,Stem Cell Isolation and Xenotransplantation Facility, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tihomira I Todorova
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - David Reynolds
- Genomics Core Facility, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Swathi-Rao Narayanagari
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.,Stem Cell Isolation and Xenotransplantation Facility, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA.,Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Medicine (Oncology), Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY, USA.,Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Amit Verma
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Medicine (Oncology), Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY, USA. .,Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Medicine (Oncology), Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY, USA. .,Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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