1
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Su M, Fleischer T, Grosheva I, Horev MB, Olszewska M, Mattioli CC, Barr H, Plotnikov A, Carvalho S, Moskovich Y, Minden MD, Chapal-Ilani N, Wainstein A, Papapetrou EP, Dezorella N, Cheng T, Kaushansky N, Geiger B, Shlush LI. Targeting SRSF2 mutations in leukemia with RKI-1447: A strategy to impair cellular division and nuclear structure. iScience 2024; 27:109443. [PMID: 38558935 PMCID: PMC10981050 DOI: 10.1016/j.isci.2024.109443] [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: 06/23/2023] [Revised: 02/07/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Spliceosome machinery mutations are common early mutations in myeloid malignancies; however, effective targeted therapies against them are still lacking. In the current study, we used an in vitro high-throughput drug screen among four different isogenic cell lines and identified RKI-1447, a Rho-associated protein kinase inhibitor, as selective cytotoxic effector of SRSF2 mutant cells. RKI-1447 targeted SRSF2 mutated primary human samples in xenografts models. RKI-1447 induced mitotic catastrophe and induced major reorganization of the microtubule system and severe nuclear deformation. Transmission electron microscopy and 3D light microscopy revealed that SRSF2 mutations induce deep nuclear indentation and segmentation that are apparently driven by microtubule-rich cytoplasmic intrusions, which are exacerbated by RKI-1447. The severe nuclear deformation in RKI-1447-treated SRSF2 mutant cells prevents cells from completing mitosis. These findings shed new light on the interplay between microtubules and the nucleus and offers new ways for targeting pre-leukemic SRSF2 mutant cells.
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Affiliation(s)
- Minhua Su
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tom Fleischer
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Grosheva
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Melanie Bokstad Horev
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Malgorzata Olszewska
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Haim Barr
- Wohl Institute for Drug Discovery, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Plotnikov
- Wohl Institute for Drug Discovery, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia Carvalho
- Wohl Institute for Drug Discovery, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yoni Moskovich
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mark D. Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON Canada
| | - Noa Chapal-Ilani
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Wainstein
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eirini P. Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nili Dezorella
- Electron Microscopy Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Nathali Kaushansky
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Benjamin Geiger
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Liran I. Shlush
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
- Molecular Hematology Clinic, Maccabi Healthcare, Tel Aviv, Israel
- Division of Hematology, Rambam Healthcare Campus, Haifa, Israel
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2
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Zioni N, Bercovich AA, Chapal-Ilani N, Bacharach T, Rappoport N, Solomon A, Avraham R, Kopitman E, Porat Z, Sacma M, Hartmut G, Scheller M, Muller-Tidow C, Lipka D, Shlush E, Minden M, Kaushansky N, Shlush LI. Inflammatory signals from fatty bone marrow support DNMT3A driven clonal hematopoiesis. Nat Commun 2023; 14:2070. [PMID: 37045808 PMCID: PMC10097668 DOI: 10.1038/s41467-023-36906-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/20/2023] [Indexed: 04/14/2023] Open
Abstract
Both fatty bone marrow (FBM) and somatic mutations in hematopoietic stem cells (HSCs), also termed clonal hematopoiesis (CH) accumulate with human aging. However it remains unclear whether FBM can modify the evolution of CH. To address this question, we herein present the interaction between CH and FBM in two preclinical male mouse models: after sub-lethal irradiation or after castration. An adipogenesis inhibitor (PPARγ inhibitor) is used in both models as a control. A significant increase in self-renewal can be detected in both human and rodent DNMT3AMut-HSCs when exposed to FBM. DNMT3AMut-HSCs derived from older mice interacting with FBM have even higher self-renewal in comparison to DNMT3AMut-HSCs derived from younger mice. Single cell RNA-sequencing on rodent HSCs after exposing them to FBM reveal a 6-10 fold increase in DNMT3AMut-HSCs and an activated inflammatory signaling. Cytokine analysis of BM fluid and BM derived adipocytes grown in vitro demonstrates an increased IL-6 levels under FBM conditions. Anti-IL-6 neutralizing antibodies significantly reduce the selective advantage of DNMT3AMut-HSCs exposed to FBM. Overall, paracrine FBM inflammatory signals promote DNMT3A-driven clonal hematopoiesis, which can be inhibited by blocking the IL-6 pathway.
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Affiliation(s)
- N Zioni
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - A Akhiad Bercovich
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - N Chapal-Ilani
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Bacharach
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - N Rappoport
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - A Solomon
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - R Avraham
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - E Kopitman
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Z Porat
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - M Sacma
- Institute of Molecular Medicine Ulm University, Ulm, Germany
| | - G Hartmut
- Institute of Molecular Medicine Ulm University, Ulm, Germany
| | - M Scheller
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - C Muller-Tidow
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Heidelberg, Heidelberg, Germany
| | - D Lipka
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Heidelberg, Heidelberg, Germany
| | - E Shlush
- IVF Unit, Galilee Medical Center, Nahariya, Israel
| | - M Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
- Division of Hematology, University Health Network, Toronto, ON, Canada
| | - N Kaushansky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Liran I Shlush
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
- Hematology and Bone Marrow Transplantation Institute Rambam Healthcare campus Haifa, Haifa, Israel.
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3
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Kim KH, Kim T, Novitzky-Basso I, Lee H, Yoo Y, Ahn JS, Pasic I, Law A, Lam W, Michelis FV, Gerbitz A, Viswabandya A, Lipton J, Kumar R, Mattsson J, Zhang Z, Kaushansky N, Brilon Y, Chapal-Ilani N, Biezuner T, Shlush LI, Kim DDH. Clonal hematopoiesis in the donor does not adversely affect long-term outcomes following allogeneic hematopoietic stem cell transplantation: result from 13-year followup. Haematologica 2023. [PMID: 36727396 DOI: 10.3324/haematol.2022.281806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Indexed: 02/03/2023] Open
Abstract
Donor clonal hematopoiesis may be transferred to the recipient through allogeneic hematopoietic stem cell transplantation (HCT), but the potential for adverse long-term impact on transplant outcomes remains unknown. A total of 744 samples from 372 recipients who received HCT and the corresponding donors were included. Bar-coded error-corrected sequencing using a modified molecular inversion probe capture protocol was performed, which targeted 34 genes covering mutations involved in clonal hematopoiesis with indeterminate potential (CHIP) and other AML-related mutations. A total of 30 mutations were detected from 25 donors (6.7%): the most frequently mutated gene was TET2 (n=7, 28%), followed by DNMT3A (n=4, 16%), SMC3 (n=3, 12%) and SF3B1 (n=3, 12%). With a median follow-up duration of 13 years among survivors, the presence of CHIP in the donor was not associated with recipient overall survival (p=0.969), relapse incidence (p=0.600) or non-relapse mortality (p=0.570). Donor CHIP did not impair neutrophil (p=0.460) or platelet (p=0.250) engraftment, the rates of acute (p=0.490), or chronic graft-vs-host disease (p=0.220). No significant difference was noted for secondary malignancy following HCT between the two groups. The present study suggests that the presence of CHIP in allogeneic stem donors does not adversely affect transplant outcomes after HCT. Accordingly, further study is warranted to reach a clearer conclusion on whether molecular profiling to determine the presence of CHIP mutations is necessary for the pre-transplant evaluation of donors prior to stem cell donation.
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Affiliation(s)
- Kyoung Ha Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada; Department of Internal Medicine, Soonchunhyang University College of Medicine, Soonchunhyang University Hospital, Seoul
| | - TaeHyung Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON
| | - Igor Novitzky-Basso
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto
| | - Hyewon Lee
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada; Division of Rare and Refractory Cancer, Division of Hemato-Oncology, and Center for Hematologic Malignancy Research Institute and Hospital National Cancer Center
| | - Youngseok Yoo
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto
| | - Jae-Sook Ahn
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Gwangju
| | - Ivan Pasic
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto
| | - Arjun Law
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto
| | - Wilson Lam
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto
| | - Fotios V Michelis
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto
| | - Armin Gerbitz
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto
| | - Auro Viswabandya
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto
| | - Jeffrey Lipton
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto
| | - Rajat Kumar
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto
| | - Jonas Mattsson
- Gloria and Seymour Epstein Chair in Cell Therapy and Transplantation
| | - Zhaolei Zhang
- Department of Computer Science, University of Toronto, Toronto, ON, Canada; The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON
| | | | - Yardena Brilon
- Department of Immunology, Weizmann Institute of Science, Rehovot
| | - Noa Chapal-Ilani
- Department of Immunology, Weizmann Institute of Science, Rehovot
| | - Tamir Biezuner
- Department of Immunology, Weizmann Institute of Science, Rehovot
| | - Liran I Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot.
| | - Dennis Dong Hwan Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada; Institute for Medical Science, Faculty of Medicine, University of Toronto, Toronto.
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4
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Biezuner T, Brilon Y, Arye AB, Oron B, Kadam A, Danin A, Furer N, Minden MD, Hwan Kim DD, Shapira S, Arber N, Dick J, Thavendiranathan P, Moskovitz Y, Kaushansky N, Chapal-Ilani N, Shlush LI. An improved molecular inversion probe based targeted sequencing approach for low variant allele frequency. NAR Genom Bioinform 2022; 4:lqab125. [PMID: 35156021 PMCID: PMC8826764 DOI: 10.1093/nargab/lqab125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/25/2021] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
Deep targeted sequencing technologies are still not widely used in clinical practice due to the complexity of the methods and their cost. The Molecular Inversion Probes (MIP) technology is cost effective and scalable in the number of targets, however, suffers from low overall performance especially in GC rich regions. In order to improve the MIP performance, we sequenced a large cohort of healthy individuals (n = 4417), with a panel of 616 MIPs, at high depth in duplicates. To improve the previous state-of-the-art statistical model for low variant allele frequency, we selected 4635 potentially positive variants and validated them using amplicon sequencing. Using machine learning prediction tools, we significantly improved precision of 10–56.25% (P < 0.0004) to detect variants with VAF > 0.005. We further developed biochemically modified MIP protocol and improved its turn-around-time to ∼4 h. Our new biochemistry significantly improved uniformity, GC-Rich regions coverage, and enabled 95% on target reads in a large MIP panel of 8349 genomic targets. Overall, we demonstrate an enhancement of the MIP targeted sequencing approach in both detection of low frequency variants and in other key parameters, paving its way to become an ultrafast cost-effective research and clinical diagnostic tool.
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Affiliation(s)
- Tamir Biezuner
- Department of Immunology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Yardena Brilon
- Department of Immunology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Asaf Ben Arye
- Department of Statistics and Operations Research, Tel Aviv University, Ramat Aviv, Israel
| | - Barak Oron
- Department of Immunology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Aditee Kadam
- Department of Immunology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Adi Danin
- Department of Immunology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Nili Furer
- Department of Immunology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Department of Medical Oncology & Hematology, Toronto, ON, Canada
| | - Dennis Dong Hwan Kim
- Princess Margaret Cancer Centre, University Health Network (UHN), Department of Medical Oncology & Hematology, Toronto, ON, Canada
| | | | | | - John Dick
- Princess Margaret Cancer Centre, University Health Network (UHN), Department of Molecular Genetics, Toronto, ON, Canada
| | - Paaladinesh Thavendiranathan
- Department of Medicine, Division of Cardiology, Ted Rogers Program in Cardiotoxicity Prevention, Peter Munk Cardiac Center, Toronto General Hospital, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Yoni Moskovitz
- Department of Immunology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Nathali Kaushansky
- Department of Immunology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Noa Chapal-Ilani
- Department of Immunology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Liran I Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot 761001, Israel
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5
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Tao L, Raz O, Marx Z, Ghosh MS, Huber S, Greindl-Junghans J, Biezuner T, Amir S, Milo L, Adar R, Levy R, Onn A, Chapal-Ilani N, Berman V, Ben Arie A, Rom G, Oron B, Halaban R, Czyz ZT, Werner-Klein M, Klein CA, Shapiro E. Retrospective cell lineage reconstruction in humans by using short tandem repeats. Cell Rep Methods 2021; 1:None. [PMID: 34341783 PMCID: PMC8313865 DOI: 10.1016/j.crmeth.2021.100054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/29/2020] [Revised: 04/17/2021] [Accepted: 06/24/2021] [Indexed: 12/18/2022]
Abstract
Cell lineage analysis aims to uncover the developmental history of an organism back to its cell of origin. Recently, novel in vivo methods utilizing genome editing enabled important insights into the cell lineages of animals. In contrast, human cell lineage remains restricted to retrospective approaches, which still lack resolution and cost-efficient solutions. Here, we demonstrate a scalable platform based on short tandem repeats targeted by duplex molecular inversion probes. With this human cell lineage tracing method, we accurately reproduced a known lineage of DU145 cells and reconstructed lineages of healthy and metastatic single cells from a melanoma patient who matched the anatomical reference while adding further refinements. This platform allowed us to faithfully recapitulate lineages of developmental tissue formation in healthy cells. In summary, our lineage discovery platform can profile informative somatic mutations efficiently and provides solid lineage reconstructions even in challenging low-mutation-rate healthy single cells.
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Affiliation(s)
- Liming Tao
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Ofir Raz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Zipora Marx
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Manjusha S. Ghosh
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Sandra Huber
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Julia Greindl-Junghans
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Tamir Biezuner
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Shiran Amir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Lilach Milo
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Rivka Adar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Ron Levy
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Amos Onn
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Noa Chapal-Ilani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Veronika Berman
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Asaf Ben Arie
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Guy Rom
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Barak Oron
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520-8059, USA
| | - Zbigniew T. Czyz
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Melanie Werner-Klein
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Christoph A. Klein
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
- Division of Personalized Tumor Therapy, Fraunhofer Institute for Experimental Medicine and Toxicology Regensburg, Am Biopark 9, 93053 Regensburg, Germany
| | - Ehud Shapiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
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6
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Feldman T, Bercovich A, Moskovitz Y, Chapal-Ilani N, Mitchell A, Medeiros JJF, Biezuner T, Kaushansky N, Minden MD, Gupta V, Milyavsky M, Livneh Z, Tanay A, Shlush LI. Recurrent deletions in clonal hematopoiesis are driven by microhomology-mediated end joining. Nat Commun 2021; 12:2455. [PMID: 33911081 PMCID: PMC8080710 DOI: 10.1038/s41467-021-22803-y] [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: 06/23/2020] [Accepted: 03/29/2021] [Indexed: 01/19/2023] Open
Abstract
The mutational mechanisms underlying recurrent deletions in clonal hematopoiesis are not entirely clear. In the current study we inspect the genomic regions around recurrent deletions in myeloid malignancies, and identify microhomology-based signatures in CALR, ASXL1 and SRSF2 loci. We demonstrate that these deletions are the result of double stand break repair by a PARP1 dependent microhomology-mediated end joining (MMEJ) pathway. Importantly, we provide evidence that these recurrent deletions originate in pre-leukemic stem cells. While DNA polymerase theta (POLQ) is considered a key component in MMEJ repair, we provide evidence that pre-leukemic MMEJ (preL-MMEJ) deletions can be generated in POLQ knockout cells. In contrast, aphidicolin (an inhibitor of replicative polymerases and replication) treatment resulted in a significant reduction in preL-MMEJ. Altogether, our data indicate an association between POLQ independent MMEJ and clonal hematopoiesis and elucidate mutational mechanisms involved in the very first steps of leukemia evolution.
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Affiliation(s)
- Tzah Feldman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Akhiad Bercovich
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Yoni Moskovitz
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Chapal-Ilani
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
| | - Jessie J F Medeiros
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Tamir Biezuner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nathali Kaushansky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | - Vikas Gupta
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | - Michael Milyavsky
- Department of Pathology, Tel-Aviv University, Tel-Aviv, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Zvi Livneh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Liran I Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada.
- Division of Hematology, Rambam Healthcare Campus, Haifa, Israel.
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7
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Shahar Gabay T, Chapal-Ilani N, Moskovitz Y, Biezuner T, Oron B, Brilon Y, Fridman-Dror A, Sabah R, Balicer R, Tanay A, Mendelson-Cohen N, Dann EJ, Fineman R, Kaushansky N, Yehudai-Reshef S, Zuckerman T, Shlush LI. Donor cell leukemia: reappearance of gene mutations in donor cells - more than an incidental phenomenon? Haematologica 2020; 105:2861-2863. [PMID: 33256388 PMCID: PMC7716367 DOI: 10.3324/haematol.2019.242347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Tal Shahar Gabay
- Hematology Research Center, Rambam Health Care Campus, Haifa, Israel
| | - Noa Chapal-Ilani
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yoni Moskovitz
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Tamir Biezuner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Barak Oron
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yardena Brilon
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Fridman-Dror
- Hematology Research Center, Rambam Health Care Campus, Haifa, Israel
| | - Rawan Sabah
- Hematology Research Center, Rambam Health Care Campus, Haifa, Israel
| | | | - Amos Tanay
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Netta Mendelson-Cohen
- Dept. of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Eldad J Dann
- Department of Hematology and BMT, Rambam Health Care Campus, Haifa, Israel
| | - Riva Fineman
- Department of Hematology and BMT, Rambam Health Care Campus, Haifa, Israel
| | - Nathali Kaushansky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Tsila Zuckerman
- Department of Hematology and BMT, Rambam Health Care Campus, Haifa, Israel
| | - Liran I Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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8
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Raz O, Biezuner T, Spiro A, Amir S, Milo L, Titelman A, Onn A, Chapal-Ilani N, Tao L, Marx T, Feige U, Shapiro E. Short tandem repeat stutter model inferred from direct measurement of in vitro stutter noise. Nucleic Acids Res 2019; 47:2436-2445. [PMID: 30698816 PMCID: PMC6412005 DOI: 10.1093/nar/gky1318] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 11/14/2022] Open
Abstract
Short tandem repeats (STRs) are polymorphic genomic loci valuable for various applications such as research, diagnostics and forensics. However, their polymorphic nature also introduces noise during in vitro amplification, making them difficult to analyze. Although it is possible to overcome stutter noise by using amplification-free library preparation, such protocols are presently incompatible with single cell analysis and with targeted-enrichment protocols. To address this challenge, we have designed a method for direct measurement of in vitro noise. Using a synthetic STR sequencing library, we have calibrated a Markov model for the prediction of stutter patterns at any amplification cycle. By employing this model, we have managed to genotype accurately cases of severe amplification bias, and biallelic STR signals, and validated our model for several high-fidelity PCR enzymes. Finally, we compared this model in the context of a naïve STR genotyping strategy against the state-of-the-art on a benchmark of single cells, demonstrating superior accuracy.
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Affiliation(s)
- Ofir Raz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Tamir Biezuner
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Adam Spiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Shiran Amir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Lilach Milo
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Alon Titelman
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Amos Onn
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Noa Chapal-Ilani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Liming Tao
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Tzipy Marx
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Uriel Feige
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Ehud Shapiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
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9
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Biezuner T, Spiro A, Raz O, Amir S, Milo L, Adar R, Chapal-Ilani N, Berman V, Fried Y, Ainbinder E, Cohen G, Barr HM, Halaban R, Shapiro E. A generic, cost-effective, and scalable cell lineage analysis platform. Genome Res 2016; 26:1588-1599. [PMID: 27558250 PMCID: PMC5088600 DOI: 10.1101/gr.202903.115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 08/11/2016] [Indexed: 02/05/2023]
Abstract
Advances in single-cell genomics enable commensurate improvements in methods for uncovering lineage relations among individual cells. Current sequencing-based methods for cell lineage analysis depend on low-resolution bulk analysis or rely on extensive single-cell sequencing, which is not scalable and could be biased by functional dependencies. Here we show an integrated biochemical-computational platform for generic single-cell lineage analysis that is retrospective, cost-effective, and scalable. It consists of a biochemical-computational pipeline that inputs individual cells, produces targeted single-cell sequencing data, and uses it to generate a lineage tree of the input cells. We validated the platform by applying it to cells sampled from an ex vivo grown tree and analyzed its feasibility landscape by computer simulations. We conclude that the platform may serve as a generic tool for lineage analysis and thus pave the way toward large-scale human cell lineage discovery.
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Affiliation(s)
- Tamir Biezuner
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Adam Spiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Ofir Raz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Shiran Amir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Lilach Milo
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Rivka Adar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Noa Chapal-Ilani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Veronika Berman
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Yael Fried
- Department of Biological Services, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Elena Ainbinder
- Department of Biological Services, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Galit Cohen
- Maurice and Vivienne Wohl Institute for Drug Discovery, G-INCPM, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Haim M Barr
- Maurice and Vivienne Wohl Institute for Drug Discovery, G-INCPM, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut 06520-8059, USA
| | - Ehud Shapiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 761001, Israel
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10
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Chapal-Ilani N, Maruvka YE, Spiro A, Reizel Y, Adar R, Shlush LI, Shapiro E. Comparing algorithms that reconstruct cell lineage trees utilizing information on microsatellite mutations. PLoS Comput Biol 2013; 9:e1003297. [PMID: 24244121 PMCID: PMC3828138 DOI: 10.1371/journal.pcbi.1003297] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 09/09/2013] [Indexed: 11/18/2022] Open
Abstract
Organism cells proliferate and die to build, maintain, renew and repair it. The cellular history of an organism up to any point in time can be captured by a cell lineage tree in which vertices represent all organism cells, past and present, and directed edges represent progeny relations among them. The root represents the fertilized egg, and the leaves represent extant and dead cells. Somatic mutations accumulated during cell division endow each organism cell with a genomic signature that is unique with a very high probability. Distances between such genomic signatures can be used to reconstruct an organism's cell lineage tree. Cell populations possess unique features that are absent or rare in organism populations (e.g., the presence of stem cells and a small number of generations since the zygote) and do not undergo sexual reproduction, hence the reconstruction of cell lineage trees calls for careful examination and adaptation of the standard tools of population genetics. Our lab developed a method for reconstructing cell lineage trees by examining only mutations in highly variable microsatellite loci (MS, also called short tandem repeats, STR). In this study we use experimental data on somatic mutations in MS of individual cells in human and mice in order to validate and quantify the utility of known lineage tree reconstruction algorithms in this context. We employed extensive measurements of somatic mutations in individual cells which were isolated from healthy and diseased tissues of mice and humans. The validation was done by analyzing the ability to infer known and clear biological scenarios. In general, we found that if the biological scenario is simple, almost all algorithms tested can infer it. Another somewhat surprising conclusion is that the best algorithm among those tested is Neighbor Joining where the distance measure used is normalized absolute distance. We include our full dataset in Tables S1, S2, S3, S4, S5 to enable further analysis of this data by others.
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Affiliation(s)
- Noa Chapal-Ilani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
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11
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Reizel Y, Itzkovitz S, Adar R, Elbaz J, Jinich A, Chapal-Ilani N, Maruvka YE, Nevo N, Marx Z, Horovitz I, Wasserstrom A, Mayo A, Shur I, Benayahu D, Skorecki K, Segal E, Dekel N, Shapiro E. Cell lineage analysis of the mammalian female germline. PLoS Genet 2012; 8:e1002477. [PMID: 22383887 PMCID: PMC3285577 DOI: 10.1371/journal.pgen.1002477] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 11/23/2011] [Indexed: 01/11/2023] Open
Abstract
Fundamental aspects of embryonic and post-natal development, including maintenance of the mammalian female germline, are largely unknown. Here we employ a retrospective, phylogenetic-based method for reconstructing cell lineage trees utilizing somatic mutations accumulated in microsatellites, to study female germline dynamics in mice. Reconstructed cell lineage trees can be used to estimate lineage relationships between different cell types, as well as cell depth (number of cell divisions since the zygote). We show that, in the reconstructed mouse cell lineage trees, oocytes form clusters that are separate from hematopoietic and mesenchymal stem cells, both in young and old mice, indicating that these populations belong to distinct lineages. Furthermore, while cumulus cells sampled from different ovarian follicles are distinctly clustered on the reconstructed trees, oocytes from the left and right ovaries are not, suggesting a mixing of their progenitor pools. We also observed an increase in oocyte depth with mouse age, which can be explained either by depth-guided selection of oocytes for ovulation or by post-natal renewal. Overall, our study sheds light on substantial novel aspects of female germline preservation and development. Many aspects of mammalian female germline development during embryogenesis and throughout adulthood are either unknown or under debate. In this study we applied a novel method for the reconstruction of cell lineage trees utilizing microsatellite mutations, accumulated during mouse life, in oocytes and other cells, sampled from young and old mice. Analysis of the reconstructed cell lineage trees shows that oocytes are clustered separately from bone-marrow derived cells, that oocytes from different ovaries share common progenitors, and that oocyte depth (number of cell divisions since the zygote) increases significantly with mouse age.
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Affiliation(s)
- Yitzhak Reizel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rivka Adar
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Judith Elbaz
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Adrian Jinich
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Chapal-Ilani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef E. Maruvka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Nava Nevo
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Zipora Marx
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Horovitz
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Adam Wasserstrom
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Irena Shur
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Dafna Benayahu
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Karl Skorecki
- Rappaport Faculty of Medicine and Research Institute, Technion and Rambam Medical Center, Haifa, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Nava Dekel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (ND); (ES)
| | - Ehud Shapiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (ND); (ES)
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12
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Segev E, Shefer G, Adar R, Chapal-Ilani N, Itzkovitz S, Horovitz I, Reizel Y, Benayahu D, Shapiro E. Muscle-bound primordial stem cells give rise to myofiber-associated myogenic and non-myogenic progenitors. PLoS One 2011; 6:e25605. [PMID: 22022423 PMCID: PMC3194814 DOI: 10.1371/journal.pone.0025605] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 09/07/2011] [Indexed: 12/14/2022] Open
Abstract
Myofiber cultures give rise to myogenic as well as to non-myogenic cells. Whether these myofiber-associated non-myogenic cells develop from resident stem cells that possess mesenchymal plasticity or from other stem cells such as mesenchymal stem cells (MSCs) remain unsolved. To address this question, we applied a method for reconstructing cell lineage trees from somatic mutations to MSCs and myogenic and non-myogenic cells from individual myofibers that were cultured at clonal density. Our analyses show that (i) in addition to myogenic progenitors, myofibers also harbor non-myogenic progenitors of a distinct, yet close, lineage; (ii) myofiber-associated non-myogenic and myogenic cells share the same muscle-bound primordial stem cells of a lineage distinct from bone marrow MSCs; (iii) these muscle-bound primordial stem-cells first part to individual muscles and then differentiate into myogenic and non-myogenic stem cells.
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Affiliation(s)
- Elad Segev
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Gabi Shefer
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Rivka Adar
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Chapal-Ilani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Horovitz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Reizel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Dafna Benayahu
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ehud Shapiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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13
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Reizel Y, Chapal-Ilani N, Adar R, Itzkovitz S, Elbaz J, Maruvka YE, Segev E, Shlush LI, Dekel N, Shapiro E. Colon stem cell and crypt dynamics exposed by cell lineage reconstruction. PLoS Genet 2011; 7:e1002192. [PMID: 21829376 PMCID: PMC3145618 DOI: 10.1371/journal.pgen.1002192] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/05/2011] [Indexed: 12/22/2022] Open
Abstract
Stem cell dynamics in vivo are often being studied by lineage tracing methods. Our laboratory has previously developed a retrospective method for reconstructing cell lineage trees from somatic mutations accumulated in microsatellites. This method was applied here to explore different aspects of stem cell dynamics in the mouse colon without the use of stem cell markers. We first demonstrated the reliability of our method for the study of stem cells by confirming previously established facts, and then we addressed open questions. Our findings confirmed that colon crypts are monoclonal and that, throughout adulthood, the process of monoclonal conversion plays a major role in the maintenance of crypts. The absence of immortal strand mechanism in crypts stem cells was validated by the age-dependent accumulation of microsatellite mutations. In addition, we confirmed the positive correlation between physical and lineage proximity of crypts, by showing that the colon is separated into small domains that share a common ancestor. We gained new data demonstrating that colon epithelium is clustered separately from hematopoietic and other cell types, indicating that the colon is constituted of few progenitors and ruling out significant renewal of colonic epithelium from hematopoietic cells during adulthood. Overall, our study demonstrates the reliability of cell lineage reconstruction for the study of stem cell dynamics, and it further addresses open questions in colon stem cells. In addition, this method can be applied to study stem cell dynamics in other systems. The study of stem cell and tissue dynamics in vivo is often carried out by lineage tracing methods that depend on the presence of specific markers and on the availability of stem cells. In the current study, we applied a novel method for the reconstruction of cell lineage trees from microsatellite mutations accumulated during mouse life. We focused on the intestinal epithelium, since its stem cells were intensively studied by various tracing methods that clarified many aspects of their dynamics. We first showed the reliability of our method by confirming three previously established facts: the existence of “monoclonal conversion,” the absence of an immortal strand mechanism in colon stem cells, and the separation of the colon into small domains each with a common ancestor. We also answered a few open questions, showing that the colon's lineage is separated from other lineages such as the hematopoietic and pancreatic lineages. Overall, our work presents a new approach for the study of stem cell dynamics and can similarly be used for studying stem cell dynamics in other systems.
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Affiliation(s)
- Yitzhak Reizel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Chapal-Ilani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Rivka Adar
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Judith Elbaz
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef E. Maruvka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Elad Segev
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Liran I. Shlush
- Rappaport Faculty of Medicine and Research Institute, Technion and Rambam Medical Center, Haifa, Israel
| | - Nava Dekel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Ehud Shapiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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