1
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Quaranta P, Basso-Ricci L, Jofra Hernandez R, Pacini G, Naldini MM, Barcella M, Seffin L, Pais G, Spinozzi G, Benedicenti F, Pietrasanta C, Cheong JG, Ronchi A, Pugni L, Dionisio F, Monti I, Giannelli S, Darin S, Fraschetta F, Barera G, Ferrua F, Calbi V, Ometti M, Di Micco R, Mosca F, Josefowicz SZ, Montini E, Calabria A, Bernardo ME, Cicalese MP, Gentner B, Merelli I, Aiuti A, Scala S. Circulating hematopoietic stem/progenitor cell subsets contribute to human hematopoietic homeostasis. Blood 2024; 143:1937-1952. [PMID: 38446574 PMCID: PMC11106755 DOI: 10.1182/blood.2023022666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/08/2024] Open
Abstract
ABSTRACT In physiological conditions, few circulating hematopoietic stem/progenitor cells (cHSPCs) are present in the peripheral blood, but their contribution to human hematopoiesis remain unsolved. By integrating advanced immunophenotyping, single-cell transcriptional and functional profiling, and integration site (IS) clonal tracking, we unveiled the biological properties and the transcriptional features of human cHSPC subpopulations in relationship to their bone marrow (BM) counterpart. We found that cHSPCs reduced in cell count over aging and are enriched for primitive, lymphoid, and erythroid subpopulations, showing preactivated transcriptional and functional state. Moreover, cHSPCs have low expression of multiple BM-retention molecules but maintain their homing potential after xenotransplantation. By generating a comprehensive human organ-resident HSPC data set based on single-cell RNA sequencing data, we detected organ-specific seeding properties of the distinct trafficking HSPC subpopulations. Notably, circulating multi-lymphoid progenitors are primed for seeding the thymus and actively contribute to T-cell production. Human clonal tracking data from patients receiving gene therapy (GT) also showed that cHSPCs connect distant BM niches and participate in steady-state hematopoietic production, with primitive cHSPCs having the highest recirculation capability to travel in and out of the BM. Finally, in case of hematopoietic impairment, cHSPCs composition reflects the BM-HSPC content and might represent a biomarker of the BM state for clinical and research purposes. Overall, our comprehensive work unveiled fundamental insights into the in vivo dynamics of human HSPC trafficking and its role in sustaining hematopoietic homeostasis. GT patients' clinical trials were registered at ClinicalTrials.gov (NCT01515462 and NCT03837483) and EudraCT (2009-017346-32 and 2018-003842-18).
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Affiliation(s)
- Pamela Quaranta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Luca Basso-Ricci
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Raisa Jofra Hernandez
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Guido Pacini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Maria Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Seffin
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Giulia Pais
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulio Spinozzi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Carlo Pietrasanta
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Jin Gyu Cheong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Andrea Ronchi
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lorenza Pugni
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesca Dionisio
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ilaria Monti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefania Giannelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Darin
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federico Fraschetta
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Graziano Barera
- Pediatric Department, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Ferrua
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valeria Calbi
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Ometti
- Department of Orthopedics and Traumatology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Raffaella Di Micco
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabio Mosca
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Steven Zvi Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Ester Bernardo
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Pia Cicalese
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Serena Scala
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
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2
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Mian SA, Ariza‐McNaughton L, Anjos‐Afonso F, Guring R, Jackson S, Kizilors A, Gribben J, Bonnet D. Influence of donor-recipient sex on engraftment of normal and leukemia stem cells in xenotransplantation. Hemasphere 2024; 8:e80. [PMID: 38774656 PMCID: PMC11107397 DOI: 10.1002/hem3.80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/12/2024] [Accepted: 04/09/2024] [Indexed: 05/24/2024] Open
Abstract
Immunodeficient mouse models are widely used for the assessment of human normal and leukemic stem cells. Despite the advancements over the years, reproducibility, as well as the differences in the engraftment of human cells in recipient mice remains to be fully resolved. Here, we used various immunodeficient mouse models to characterize the effect of donor-recipient sex on the engraftment of the human leukemic and healthy cells. Donor human cells and recipient immunodeficient mice demonstrate sex-specific engraftment levels with significant differences observed in the lineage output of normal CD34+ hematopoietic stem and progenitor cells upon xenotransplantation. Intriguingly, human female donor cells display heightened sensitivity to the recipient mice's gender, influencing their proliferation and resulting in significantly increased engraftment in female recipient mice. Our study underscores the intricate interplay taking place between donor and recipient characteristics, shedding light on important considerations for future studies, particularly in the context of pre-clinical research.
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Affiliation(s)
- Syed A. Mian
- Haematopoietic Stem Cell LabThe Francis Crick InstituteLondonUK
| | | | | | - Remisha Guring
- Haematopoietic Stem Cell LabThe Francis Crick InstituteLondonUK
| | - Sophie Jackson
- Laboratory for Molecular Haemato‐OncologyKing's College Hospital LondonLondonUK
| | - Aytug Kizilors
- Laboratory for Molecular Haemato‐OncologyKing's College Hospital LondonLondonUK
| | - John Gribben
- Department of Haemato‐Oncology, Barts Cancer InstituteQueen Mary University of LondonLondonUK
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3
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El Omar R, Abdellaoui N, Coulibaly ST, Fontenille L, Lanza F, Gachet C, Freund JN, Negroni M, Kissa K, Tavian M. Macrophage depletion overcomes human hematopoietic cell engraftment failure in zebrafish embryo. Cell Death Dis 2024; 15:305. [PMID: 38693109 PMCID: PMC11063059 DOI: 10.1038/s41419-024-06682-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/06/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
Zebrafish is widely adopted as a grafting model for studying human development and diseases. Current zebrafish xenotransplantations are performed using embryo recipients, as the adaptive immune system, responsible for host versus graft rejection, only reaches maturity at juvenile stage. However, transplanted primary human hematopoietic stem/progenitor cells (HSC) rapidly disappear even in zebrafish embryos, suggesting that another barrier to transplantation exists before the onset of adaptive immunity. Here, using a labelled macrophage zebrafish line, we demonstrated that engraftment of human HSC induces a massive recruitment of macrophages which rapidly phagocyte transplanted cells. Macrophages depletion, by chemical or pharmacological treatments, significantly improved the uptake and survival of transplanted cells, demonstrating the crucial implication of these innate immune cells for the successful engraftment of human cells in zebrafish. Beyond identifying the reasons for human hematopoietic cell engraftment failure, this work images the fate of human cells in real time over several days in macrophage-depleted zebrafish embryos.
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Affiliation(s)
- Reine El Omar
- University of Strasbourg, INSERM, EFS Grand-Est, BPPS UMR-S1255, Strasbourg, France
- Université de Lorraine, CITHEFOR, F-54505, Vandoeuvre Les Nancy, France
| | | | - Safiatou T Coulibaly
- University of Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
- ITI Innovec, Strasbourg, France
| | | | - François Lanza
- University of Strasbourg, INSERM, EFS Grand-Est, BPPS UMR-S1255, Strasbourg, France
| | - Christian Gachet
- University of Strasbourg, INSERM, EFS Grand-Est, BPPS UMR-S1255, Strasbourg, France
| | - Jean-Noel Freund
- ITI Innovec, Strasbourg, France
- University of Strasbourg, INSERM, IRFAC/UMR-S1113, Strasbourg, France
- INSERM, U1256 - NGERE, Université de Lorraine, 54500, Vandoeuvre-lès-Nancy, France
| | - Matteo Negroni
- University of Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
- ITI Innovec, Strasbourg, France
| | - Karima Kissa
- University of Montpellier, VBIC, INSERM U1047, Montpellier, France
- AZELEAD SAS, Montpellier, France
| | - Manuela Tavian
- University of Strasbourg, INSERM, EFS Grand-Est, BPPS UMR-S1255, Strasbourg, France.
- ITI Innovec, Strasbourg, France.
- University of Strasbourg, INSERM, IRFAC/UMR-S1113, Strasbourg, France.
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4
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Weng C, Yu F, Yang D, Poeschla M, Liggett LA, Jones MG, Qiu X, Wahlster L, Caulier A, Hussmann JA, Schnell A, Yost KE, Koblan LW, Martin-Rufino JD, Min J, Hammond A, Ssozi D, Bueno R, Mallidi H, Kreso A, Escabi J, Rideout WM, Jacks T, Hormoz S, van Galen P, Weissman JS, Sankaran VG. Deciphering cell states and genealogies of human haematopoiesis. Nature 2024; 627:389-398. [PMID: 38253266 PMCID: PMC10937407 DOI: 10.1038/s41586-024-07066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems2-5, simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.
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Affiliation(s)
- Chen Weng
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, P.R. China
| | - Dian Yang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular Pharmacology and Therapeutics, Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michael Poeschla
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - L Alexander Liggett
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew G Jones
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Genetics and Computer Science, BASE Research Initiative, Betty Irene Moore Children's Heart Center, Stanford University, Stanford, CA, USA
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey A Hussmann
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexandra Schnell
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kathryn E Yost
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke W Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jorge D Martin-Rufino
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph Min
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alessandro Hammond
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Ssozi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Raphael Bueno
- Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Hari Mallidi
- Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Antonia Kreso
- Division of Cardiac Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Javier Escabi
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William M Rideout
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA
| | - Tyler Jacks
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA
| | - Sahand Hormoz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter van Galen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA.
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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5
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Kitawi R, Ledger S, Kelleher AD, Ahlenstiel CL. Advances in HIV Gene Therapy. Int J Mol Sci 2024; 25:2771. [PMID: 38474018 DOI: 10.3390/ijms25052771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Early gene therapy studies held great promise for the cure of heritable diseases, but the occurrence of various genotoxic events led to a pause in clinical trials and a more guarded approach to progress. Recent advances in genetic engineering technologies have reignited interest, leading to the approval of the first gene therapy product targeting genetic mutations in 2017. Gene therapy (GT) can be delivered either in vivo or ex vivo. An ex vivo approach to gene therapy is advantageous, as it allows for the characterization of the gene-modified cells and the selection of desired properties before patient administration. Autologous cells can also be used during this process which eliminates the possibility of immune rejection. This review highlights the various stages of ex vivo gene therapy, current research developments that have increased the efficiency and safety of this process, and a comprehensive summary of Human Immunodeficiency Virus (HIV) gene therapy studies, the majority of which have employed the ex vivo approach.
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Affiliation(s)
- Rose Kitawi
- Kirby Institute, University of New South Wales, Kensington, NSW 2052, Australia
| | - Scott Ledger
- Kirby Institute, University of New South Wales, Kensington, NSW 2052, Australia
| | - Anthony D Kelleher
- Kirby Institute, University of New South Wales, Kensington, NSW 2052, Australia
- St. Vincent's Hospital, Darlinghurst, NSW 2010, Australia
- UNSW RNA Institute, University of New South Wales, Kensington, NSW 2052, Australia
| | - Chantelle L Ahlenstiel
- Kirby Institute, University of New South Wales, Kensington, NSW 2052, Australia
- UNSW RNA Institute, University of New South Wales, Kensington, NSW 2052, Australia
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6
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Jiang D, Chowdhury AY, Nogalska A, Contreras J, Lee Y, Vergel-Rodriguez M, Valenzuela M, Lu R. Quantitative association between gene expression and blood cell production of individual hematopoietic stem cells in mice. SCIENCE ADVANCES 2024; 10:eadk2132. [PMID: 38277455 PMCID: PMC10816716 DOI: 10.1126/sciadv.adk2132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024]
Abstract
Individual hematopoietic stem cells (HSCs) produce different amounts of blood cells upon transplantation. Taking advantage of the intercellular variation, we developed an experimental and bioinformatic approach to evaluating the quantitative association between gene expression and blood cell production across individual HSCs. We found that most genes associated with blood production exhibit the association only at some levels of blood production. By mapping gene expression with blood production, we identified four distinct patterns of their quantitative association. Some genes consistently correlate with blood production over a range of levels or across all levels, and these genes are found to regulate lymphoid but not myeloid production. Other genes exhibit one or more clear peaks of association. Genes with overlapping peaks are found to be coexpressed in other tissues and share similar molecular functions and regulatory motifs. By dissecting intercellular variations, our findings revealed four quantitative association patterns that reflect distinct dose-response molecular mechanisms modulating the blood cell production of HSCs.
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Affiliation(s)
- Du Jiang
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Adnan Y. Chowdhury
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Anna Nogalska
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jorge Contreras
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yeachan Lee
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mary Vergel-Rodriguez
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Melissa Valenzuela
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Rong Lu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
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7
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Hasan T, Pasala AR, Hassan D, Hanotaux J, Allan DS, Maganti HB. Homing and Engraftment of Hematopoietic Stem Cells Following Transplantation: A Pre-Clinical Perspective. Curr Oncol 2024; 31:603-616. [PMID: 38392038 PMCID: PMC10888387 DOI: 10.3390/curroncol31020044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024] Open
Abstract
Hematopoietic stem-cell (HSC) transplantation (HSCT) is used to treat various hematologic disorders. Use of genetically modified mouse models of hematopoietic cell transplantation has been critical in our fundamental understanding of HSC biology and in developing approaches for human patients. Pre-clinical studies in animal models provide insight into the journey of transplanted HSCs from infusion to engraftment in bone-marrow (BM) niches. Various signaling molecules and growth factors secreted by HSCs and the niche microenvironment play critical roles in homing and engraftment of the transplanted cells. The sustained equilibrium of these chemical and biologic factors ensures that engrafted HSCs generate healthy and durable hematopoiesis. Transplanted healthy HSCs compete with residual host cells to repopulate stem-cell niches in the marrow. Stem-cell niches, in particular, can be altered by the effects of previous treatments, aging, and the paracrine effects of leukemic cells, which create inhospitable bone-marrow niches that are unfavorable for healthy hematopoiesis. More work to understand how stem-cell niches can be restored to favor normal hematopoiesis may be key to reducing leukemic relapses following transplant.
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Affiliation(s)
- Tanvir Hasan
- Canadian Blood Services, Stem Cells and Centre for Innovation, Ottawa, ON K1G 4J5, Canada; (T.H.); (A.R.P.); (D.H.); (J.H.)
| | - Ajay Ratan Pasala
- Canadian Blood Services, Stem Cells and Centre for Innovation, Ottawa, ON K1G 4J5, Canada; (T.H.); (A.R.P.); (D.H.); (J.H.)
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Dhuha Hassan
- Canadian Blood Services, Stem Cells and Centre for Innovation, Ottawa, ON K1G 4J5, Canada; (T.H.); (A.R.P.); (D.H.); (J.H.)
| | - Justine Hanotaux
- Canadian Blood Services, Stem Cells and Centre for Innovation, Ottawa, ON K1G 4J5, Canada; (T.H.); (A.R.P.); (D.H.); (J.H.)
| | - David S. Allan
- Canadian Blood Services, Stem Cells and Centre for Innovation, Ottawa, ON K1G 4J5, Canada; (T.H.); (A.R.P.); (D.H.); (J.H.)
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8L6, Canada
- Clinical Epidemiology & Regenerative Medicine, Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - Harinad B. Maganti
- Canadian Blood Services, Stem Cells and Centre for Innovation, Ottawa, ON K1G 4J5, Canada; (T.H.); (A.R.P.); (D.H.); (J.H.)
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8L6, Canada
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8
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Zhang M, Liu D, Lan Y, Liu B, Li Z, Ni Y. Hematopoietic stem cell heterogeneity in non-human primates revealed by five-lineage output bias analysis. BLOOD SCIENCE 2024; 6:e00176. [PMID: 38213824 PMCID: PMC10781131 DOI: 10.1097/bs9.0000000000000176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024] Open
Abstract
Understanding hematopoietic stem cell (HSC) heterogeneity is crucial for treating malignant blood disorders. Compared with mice, we have limited knowledge of the heterogeneity of human HSCs. Fortunately, non-human primates (NHPs) have become the best animal models for studying human HSCs. Here, we employed a public dataset derived from NHP autologous bone marrow transplantation, and focused on a total of 820 HSC clones with reconstitution capacity of all available five lineages (granulocyte, monocyte, B cell, T cell, and natural killer cell) at two time points (11/12 and/or 42/43 months). Intriguingly, unsupervised clustering on these clones revealed six HSC subtypes, including a lymphoid/myeloid balanced (LM-balanced) subtype and five single-lineage-biased subtypes. We also observed that the subtypes of these HSC clones might change over time, and a given subtype could transition into any one of the other five subtypes, albeit with a certain degree of selectivity. Particularly, each of the six subtypes was more likely to turn into lymphoid-biased rather than myeloid-biased ones. Additionally, our five-lineage classification method exhibited strong correlation with traditional lymphoid/myeloid bias classification method. Specifically, our granulocyte- and monocyte-biased subtypes were predominantly attributed to α-HSCs, while LM-balanced, B cell-biased, and T cell-biased subtypes were primarily associated with β-HSCs. The γ-HSCs were composed of a small subset of B cell-biased and T cell-biased subtypes. In summary, our five-lineage classification identifies more finely tuned HSC subtypes based on lineage output bias. These findings enrich our understanding of HSC heterogeneity in NHPs and provide important insights for human research.
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Affiliation(s)
- Man Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing, China
| | - Di Liu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing, China
| | - Zongcheng Li
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing, China
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9
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Poletti V, Montepeloso A, Pellin D, Biffi A. Prostaglandin E2 as transduction enhancer affects competitive engraftment of human hematopoietic stem and progenitor cells. Mol Ther Methods Clin Dev 2023; 31:101131. [PMID: 37920236 PMCID: PMC10618226 DOI: 10.1016/j.omtm.2023.101131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Ex vivo gene therapy (GT) is a promising treatment for inherited genetic diseases. An ideal transduction protocol should determine high gene marking in long-term self-renewing hematopoietic stem cells (HSCs), preserving their repopulation potential during in vitro manipulation. In the context of the improvement of a clinically applicable transduction protocol, we tested prostaglandin E2 (PGE2) as a transduction enhancer (TE). The addition of PGE2 shortly before transduction of human CD34+ cells determined a significant transduction increase in the in vitro cell progeny paralleled by a significant reduction of their clonogenic potential. This effect increased with the duration of PGE2 exposure and correlated with an increase of CXCR4 expression. Blockage of CXCR4 with AMD3100 (plerixafor, Mozobil) did not affect transduction efficiency but partially rescued CD34+ clonogenic impairment in vitro. Once transplanted in vivo in a competitive repopulation assay, human CD34+ cells transduced with PGE2 contributed significantly less than cells transduced with a standard protocol to the repopulation of recipient mice, indicating a relative repopulation disadvantage of the PGE2-treated CD34+ cells and a counter-selection for the PGE2-treated cell progeny in vivo. In conclusion, our data indicate the need for risk/benefit evaluations in the use of PGE2 as a TE for clinical protocols of GT.
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Affiliation(s)
- Valentina Poletti
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Woman’s and Child Health Department, University of Padova, 35128 Padova, Italy
- Gene Therapy Program, Boston Children’s Dana-Farber Cancer and Blood Disorder Center, Boston, MA 02115, USA
- Pediatric Research Institute Città Della Speranza, 35127 Padova, Italy
| | - Annita Montepeloso
- Gene Therapy Program, Boston Children’s Dana-Farber Cancer and Blood Disorder Center, Boston, MA 02115, USA
| | - Danilo Pellin
- Gene Therapy Program, Boston Children’s Dana-Farber Cancer and Blood Disorder Center, Boston, MA 02115, USA
| | - Alessandra Biffi
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Woman’s and Child Health Department, University of Padova, 35128 Padova, Italy
- Gene Therapy Program, Boston Children’s Dana-Farber Cancer and Blood Disorder Center, Boston, MA 02115, USA
- Pediatric Research Institute Città Della Speranza, 35127 Padova, Italy
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10
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Uchiyama T, Kawai T, Nakabayashi K, Nakazawa Y, Goto F, Okamura K, Nishimura T, Kato K, Watanabe N, Miura A, Yasuda T, Ando Y, Minegishi T, Edasawa K, Shimura M, Akiba Y, Sato-Otsubo A, Mizukami T, Kato M, Akashi K, Nunoi H, Onodera M. Myelodysplasia after clonal hematopoiesis with APOBEC3-mediated CYBB inactivation in retroviral gene therapy for X-CGD. Mol Ther 2023; 31:3424-3440. [PMID: 37705244 PMCID: PMC10727956 DOI: 10.1016/j.ymthe.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
Stem cell gene therapy using the MFGS-gp91phox retroviral vector was performed on a 27-year-old patient with X-linked chronic granulomatous disease (X-CGD) in 2014. The patient's refractory infections were resolved, whereas the oxidase-positive neutrophils disappeared within 6 months. Thirty-two months after gene therapy, the patient developed myelodysplastic syndrome (MDS), and vector integration into the MECOM locus was identified in blast cells. The vector integration into MECOM was detectable in most myeloid cells at 12 months after gene therapy. However, the patient exhibited normal hematopoiesis until the onset of MDS, suggesting that MECOM transactivation contributed to clonal hematopoiesis, and the blast transformation likely arose after the acquisition of additional genetic lesions. In whole-genome sequencing, the biallelic loss of the WT1 tumor suppressor gene, which occurred immediately before tumorigenesis, was identified as a potential candidate genetic alteration. The provirus CYBB cDNA in the blasts contained 108 G-to-A mutations exclusively in the coding strand, suggesting the occurrence of APOBEC3-mediated hypermutations during the transduction of CD34-positive cells. A hypermutation-mediated loss of oxidase activity may have facilitated the survival and proliferation of the clone with MECOM transactivation. Our data provide valuable insights into the complex mechanisms underlying the development of leukemia in X-CGD gene therapy.
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Affiliation(s)
- Toru Uchiyama
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan.
| | - Toshinao Kawai
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Tokyo, Japan
| | - Yumiko Nakazawa
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Fumihiro Goto
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Center for Child Health and Development, Tokyo, Japan
| | - Toyoki Nishimura
- Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Koji Kato
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Nobuyuki Watanabe
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Akane Miura
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Toru Yasuda
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Yukiko Ando
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoko Minegishi
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Kaori Edasawa
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Marika Shimura
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Yumi Akiba
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Pediatric Hematology and Oncology, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoyuki Mizukami
- Department of Pediatrics, NHO Kumamoto Medical Center, Kumamoto, Japan
| | - Motohiro Kato
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Pediatric Hematology and Oncology, National Center for Child Health and Development, Tokyo, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Hiroyuki Nunoi
- Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Masafumi Onodera
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
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11
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Spencer Chapman M, Cull AH, Ciuculescu MF, Esrick EB, Mitchell E, Jung H, O'Neill L, Roberts K, Fabre MA, Williams N, Nangalia J, Quinton J, Fox JM, Pellin D, Makani J, Armant M, Williams DA, Campbell PJ, Kent DG. Clonal selection of hematopoietic stem cells after gene therapy for sickle cell disease. Nat Med 2023; 29:3175-3183. [PMID: 37973947 PMCID: PMC10719109 DOI: 10.1038/s41591-023-02636-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023]
Abstract
Gene therapy (GT) provides a potentially curative treatment option for patients with sickle cell disease (SCD); however, the occurrence of myeloid malignancies in GT clinical trials has prompted concern, with several postulated mechanisms. Here, we used whole-genome sequencing to track hematopoietic stem cells (HSCs) from six patients with SCD at pre- and post-GT time points to map the somatic mutation and clonal landscape of gene-modified and unmodified HSCs. Pre-GT, phylogenetic trees were highly polyclonal and mutation burdens per cell were elevated in some, but not all, patients. Post-GT, no clonal expansions were identified among gene-modified or unmodified cells; however, an increased frequency of potential driver mutations associated with myeloid neoplasms or clonal hematopoiesis (DNMT3A- and EZH2-mutated clones in particular) was observed in both genetically modified and unmodified cells, suggesting positive selection of mutant clones during GT. This work sheds light on HSC clonal dynamics and the mutational landscape after GT in SCD, highlighting the enhanced fitness of some HSCs harboring pre-existing driver mutations. Future studies should define the long-term fate of mutant clones, including any contribution to expansions associated with myeloid neoplasms.
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Affiliation(s)
- Michael Spencer Chapman
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alyssa H Cull
- York Biomedical Research Institute, University of York, York, UK
| | | | - Erica B Esrick
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | | | | | | | - Margarete A Fabre
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Joanne Quinton
- York Biomedical Research Institute, University of York, York, UK
| | - James M Fox
- York Biomedical Research Institute, University of York, York, UK
| | - Danilo Pellin
- Harvard Medical School, Boston, MA, USA
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Julie Makani
- Muhimbili University of Health and Allied Sciences (MUHAS), Dar-es-Salaam, Tanzania
- SickleInAfrica Clinical Coordinating Center, MUHAS, Dar-es-Salaam, Tanzania
- Imperial College London, London, UK
| | - Myriam Armant
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - David A Williams
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
| | - David G Kent
- York Biomedical Research Institute, University of York, York, UK.
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12
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Williams CMD, Noll JE, Bradey AL, Duggan J, Wilczek VJ, Masavuli MG, Grubor‐Bauk B, Panagopoulos RA, Hewett DR, Mrozik KM, Zannettino ACW, Vandyke K, Panagopoulos V. Myeloperoxidase creates a permissive microenvironmental niche for the progression of multiple myeloma. Br J Haematol 2023; 203:614-624. [PMID: 37699574 PMCID: PMC10952523 DOI: 10.1111/bjh.19102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/07/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Expression of myeloperoxidase (MPO), a key inflammatory enzyme restricted to myeloid cells, is negatively associated with the development of solid tumours. Activated myeloid cell populations are increased in multiple myeloma (MM); however, the functional consequences of myeloid-derived MPO within the myeloma microenvironment are unknown. Here, the role of MPO in MM pathogenesis was investigated, and the capacity for pharmacological inhibition of MPO to impede MM progression was evaluated. In the 5TGM1-KaLwRij mouse model of myeloma, the early stages of tumour development were associated with an increase in CD11b+ myeloid cell populations and an increase in Mpo expression within the bone marrow (BM). Interestingly, MM tumour cell homing was increased towards sites of elevated myeloid cell numbers and MPO activity within the BM. Mechanistically, MPO induced the expression of key MM growth factors, resulting in tumour cell proliferation and suppressed cytotoxic T-cell activity. Notably, tumour growth studies in mice treated with a small-molecule irreversible inhibitor of MPO (4-ABAH) demonstrated a significant reduction in overall MM tumour burden. Taken together, our data demonstrate that MPO contributes to MM tumour growth, and that MPO-specific inhibitors may provide a new therapeutic strategy to limit MM disease progression.
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Affiliation(s)
- Connor M. D. Williams
- Myeloma Research Laboratory, Faculty of Health and Medical Sciences, School of BiomedicineUniversity of AdelaideAdelaideAustralia
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
| | - Jacqueline E. Noll
- Myeloma Research Laboratory, Faculty of Health and Medical Sciences, School of BiomedicineUniversity of AdelaideAdelaideAustralia
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
| | - Alanah L. Bradey
- Myeloma Research Laboratory, Faculty of Health and Medical Sciences, School of BiomedicineUniversity of AdelaideAdelaideAustralia
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
| | - Jvaughn Duggan
- Myeloma Research Laboratory, Faculty of Health and Medical Sciences, School of BiomedicineUniversity of AdelaideAdelaideAustralia
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
| | - Vicki J. Wilczek
- Myeloma Research Laboratory, Faculty of Health and Medical Sciences, School of BiomedicineUniversity of AdelaideAdelaideAustralia
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
| | - Makutiro G. Masavuli
- Viral Immunology Group, Discipline of Surgery, Basil Hetzel Institute for Translational Health ResearchUniversity of AdelaideAdelaideAustralia
| | - Branka Grubor‐Bauk
- Viral Immunology Group, Discipline of Surgery, Basil Hetzel Institute for Translational Health ResearchUniversity of AdelaideAdelaideAustralia
| | - Romana A. Panagopoulos
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
- Breast Cancer Research Unit, Discipline of Surgery, Basil Hetzel Institute for Translational Health ResearchUniversity of AdelaideAdelaideAustralia
| | - Duncan R. Hewett
- Myeloma Research Laboratory, Faculty of Health and Medical Sciences, School of BiomedicineUniversity of AdelaideAdelaideAustralia
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
| | - Krzysztof M. Mrozik
- Myeloma Research Laboratory, Faculty of Health and Medical Sciences, School of BiomedicineUniversity of AdelaideAdelaideAustralia
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
| | - Andrew C. W. Zannettino
- Myeloma Research Laboratory, Faculty of Health and Medical Sciences, School of BiomedicineUniversity of AdelaideAdelaideAustralia
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
| | - Kate Vandyke
- Myeloma Research Laboratory, Faculty of Health and Medical Sciences, School of BiomedicineUniversity of AdelaideAdelaideAustralia
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
| | - Vasilios Panagopoulos
- Myeloma Research Laboratory, Faculty of Health and Medical Sciences, School of BiomedicineUniversity of AdelaideAdelaideAustralia
- Solid Tumour Program, Precision Cancer Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaideAustralia
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13
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Alhaj Hussen K, Chabaane E, Nelson E, Lekiashvili S, Diop S, Keita S, Evrard B, Lardenois A, Delord M, Verhoeyen E, Cornils K, Kasraian Z, Macintyre EA, Cumano A, Garrick D, Goodhardt M, Andrieu GP, Asnafi V, Chalmel F, Canque B. Multimodal cartography of human lymphopoiesis reveals B and T/NK/ILC lineages are subjected to differential regulation. iScience 2023; 26:107890. [PMID: 37766969 PMCID: PMC10520540 DOI: 10.1016/j.isci.2023.107890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The developmental cartography of human lymphopoiesis remains incompletely understood. Here, we establish a multimodal map demonstrating that lymphoid specification follows independent direct or stepwise hierarchic routes converging toward the emergence of newly characterized CD117lo multi-lymphoid progenitors (MLPs) that undergo a proliferation arrest before entering the CD127- (NK/ILC/T) or CD127+ (B) lymphoid pathways. While the differentiation of CD127- early lymphoid progenitors is mainly driven by Flt3 signaling, emergence of their CD127+ counterparts is regulated cell-intrinsically and depends exclusively on the divisional history of their upstream precursors, including hematopoietic stem cells. Further, transcriptional mapping of differentiation trajectories reveals that whereas myeloid granulomonocytic lineages follow continuous differentiation pathways, lymphoid trajectories are intrinsically discontinuous and characterized by sequential waves of cell proliferation allowing pre-commitment amplification of lymphoid progenitor pools. Besides identifying new lymphoid specification pathways and regulatory checkpoints, our results demonstrate that NK/ILC/T and B lineages are under fundamentally distinct modes of regulation. (149 words).
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Affiliation(s)
- Kutaiba Alhaj Hussen
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
- Service de Biochimie, Université de Paris Saclay, Hôpital Paul Brousse, AP-HP, Villejuif, Paris, France
| | - Emna Chabaane
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Elisabeth Nelson
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Shalva Lekiashvili
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Samuel Diop
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Seydou Keita
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Bertrand Evrard
- University Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Aurélie Lardenois
- University Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Marc Delord
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Els Verhoeyen
- CIRI, International Center for Infectiology Research, Université de Lyon, INSERM U1111, Lyon, France
- Centre Mediterranéen de Médecine Moléculaire (C3M), INSERM U1065, Nice, France
| | - Kerstin Cornils
- Division of Pediatric Stem Cell Transplantation and Immunology, Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf and Research Institute Children’s Cancer Center, Hamburg, Germany
| | - Zeinab Kasraian
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Elizabeth A. Macintyre
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Ana Cumano
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
| | - David Garrick
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Michele Goodhardt
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Guillaume P. Andrieu
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Vahid Asnafi
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Frederic Chalmel
- University Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Bruno Canque
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
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14
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Labrosse R, Chu JI, Armant MA, Everett JK, Pellin D, Kareddy N, Frelinger AL, Henderson LA, O’Connell AE, Biswas A, Coenen-van der Spek J, Miggelbrink A, Fiorini C, Adhikari H, Berry CC, Cantu VA, Fong J, Jaroslavsky J, Karadeniz DF, Li QZ, Reddy S, Roche AM, Zhu C, Whangbo JS, Dansereau C, Mackinnon B, Morris E, Koo SM, London WB, Baris S, Ozen A, Karakoc-Aydiner E, Despotovic JM, Forbes Satter LR, Saitoh A, Aizawa Y, King A, Nguyen MAT, Vu VDU, Snapper SB, Galy A, Notarangelo LD, Bushman FD, Williams DA, Pai SY. Outcomes of hematopoietic stem cell gene therapy for Wiskott-Aldrich syndrome. Blood 2023; 142:1281-1296. [PMID: 37478401 PMCID: PMC10731922 DOI: 10.1182/blood.2022019117] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/23/2023] Open
Abstract
Wiskott-Aldrich syndrome (WAS) is a rare X-linked disorder characterized by combined immunodeficiency, eczema, microthrombocytopenia, autoimmunity, and lymphoid malignancies. Gene therapy (GT) to modify autologous CD34+ cells is an emerging alternative treatment with advantages over standard allogeneic hematopoietic stem cell transplantation for patients who lack well-matched donors, avoiding graft-versus-host-disease. We report the outcomes of a phase 1/2 clinical trial in which 5 patients with severe WAS underwent GT using a self-inactivating lentiviral vector expressing the human WAS complementary DNA under the control of a 1.6-kB fragment of the autologous promoter after busulfan and fludarabine conditioning. All patients were alive and well with sustained multilineage vector gene marking (median follow-up: 7.6 years). Clinical improvement of eczema, infections, and bleeding diathesis was universal. Immune function was consistently improved despite subphysiologic levels of transgenic WAS protein expression. Improvements in platelet count and cytoskeletal function in myeloid cells were most prominent in patients with high vector copy number in the transduced product. Two patients with a history of autoimmunity had flares of autoimmunity after GT, despite similar percentages of WAS protein-expressing cells and gene marking to those without autoimmunity. Patients with flares of autoimmunity demonstrated poor numerical recovery of T cells and regulatory T cells (Tregs), interleukin-10-producing regulatory B cells (Bregs), and transitional B cells. Thus, recovery of the Breg compartment, along with Tregs appears to be protective against development of autoimmunity after GT. These results indicate that clinical and laboratory manifestations of WAS are improved with GT with an acceptable safety profile. This trial is registered at clinicaltrials.gov as #NCT01410825.
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Affiliation(s)
- Roxane Labrosse
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Immune Deficiency-Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Division of Allergy and Immunology, Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, QC, Canada
| | - Julia I. Chu
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, Benioff Children’s Hospital, University of California San Francisco, San Francisco, CA
| | - Myriam A. Armant
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - John K. Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Danilo Pellin
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
| | - Niharika Kareddy
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Andrew L. Frelinger
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | | | - Amy E. O’Connell
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA
| | - Amlan Biswas
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, MA
| | - Jet Coenen-van der Spek
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Alexandra Miggelbrink
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Claudia Fiorini
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Hriju Adhikari
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Charles C. Berry
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, UC San Diego, La Jolla, CA
| | - Vito Adrian Cantu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Johnson Fong
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Jason Jaroslavsky
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Derin F. Karadeniz
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Quan-Zhen Li
- Department of Immunology, Microarray and Immune Phenotyping Core Facility, University of Texas Southwestern Medical Center, Dallas, TX
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Aoife M. Roche
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Chengsong Zhu
- Department of Immunology, Microarray and Immune Phenotyping Core Facility, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jennifer S. Whangbo
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Colleen Dansereau
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
| | - Brenda Mackinnon
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
| | - Emily Morris
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
| | - Stephanie M. Koo
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
| | - Wendy B. London
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Safa Baris
- Department of Pediatrics, Division of Allergy and Immunology, Marmara University, Istanbul, Turkey
- The Işıl Berat Barlan Center for Translational Medicine, Marmara University, Istanbul, Turkey
| | - Ahmet Ozen
- Department of Pediatrics, Division of Allergy and Immunology, Marmara University, Istanbul, Turkey
- The Işıl Berat Barlan Center for Translational Medicine, Marmara University, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Department of Pediatrics, Division of Allergy and Immunology, Marmara University, Istanbul, Turkey
- The Işıl Berat Barlan Center for Translational Medicine, Marmara University, Istanbul, Turkey
| | - Jenny M. Despotovic
- Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
| | - Lisa R. Forbes Satter
- Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
| | - Akihiko Saitoh
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yuta Aizawa
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Alejandra King
- Hospital Luis Calvo Mackenna, Clínica Alemana De Santiago Universidad del Desarrollo, Santiago, Chile
| | - Mai Anh Thi Nguyen
- Department of Pediatrics, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Vy Do Uyen Vu
- Department of Pediatrics, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Scott B. Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, MA
| | - Anne Galy
- Genethon, Évry, France
- University of Paris-Saclay, University of Évry, INSERM, Genethon, Integrare Research Unit UMR_S951, Évry, France
| | - Luigi D. Notarangelo
- Division of Immunology, Boston Children’s Hospital, Boston, MA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David A. Williams
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Sung-Yun Pai
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Immune Deficiency-Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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15
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Yan KK, Condori J, Ma Z, Metais JY, Ju B, Ding L, Dhungana Y, Palmer LE, Langfitt DM, Ferrara F, Throm R, Shi H, Risch I, Bhatara S, Shaner B, Lockey TD, Talleur AC, Easton J, Meagher MM, Puck JM, Cowan MJ, Zhou S, Mamcarz E, Gottschalk S, Yu J. Integrome signatures of lentiviral gene therapy for SCID-X1 patients. SCIENCE ADVANCES 2023; 9:eadg9959. [PMID: 37801507 PMCID: PMC10558130 DOI: 10.1126/sciadv.adg9959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Lentiviral vector (LV)-based gene therapy holds promise for a broad range of diseases. Analyzing more than 280,000 vector integration sites (VISs) in 273 samples from 10 patients with X-linked severe combined immunodeficiency (SCID-X1), we discovered shared LV integrome signatures in 9 of 10 patients in relation to the genomics, epigenomics, and 3D structure of the human genome. VISs were enriched in the nuclear subcompartment A1 and integrated into super-enhancers close to nuclear pore complexes. These signatures were validated in T cells transduced with an LV encoding a CD19-specific chimeric antigen receptor. Intriguingly, the one patient whose VISs deviated from the identified integrome signatures had a distinct clinical course. Comparison of LV and gamma retrovirus integromes regarding their 3D genome signatures identified differences that might explain the lower risk of insertional mutagenesis in LV-based gene therapy. Our findings suggest that LV integrome signatures, shaped by common features such as genome organization, may affect the efficacy of LV-based cellular therapies.
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Affiliation(s)
- Koon-Kiu Yan
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jose Condori
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhijun Ma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jean-Yves Metais
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Bensheng Ju
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yogesh Dhungana
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Lance E. Palmer
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Deanna M. Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Francesca Ferrara
- Vector Development and Production Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert Throm
- Vector Development and Production Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hao Shi
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Isabel Risch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sheetal Bhatara
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Bridget Shaner
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Timothy D. Lockey
- Department of Therapeutics Production and Quality, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Aimee C. Talleur
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Michael M. Meagher
- Department of Therapeutics Production and Quality, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jennifer M. Puck
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA 94158, USA
| | - Morton J. Cowan
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA 94158, USA
| | - Sheng Zhou
- Experimental Cellular Therapeutics Laboratory, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ewelina Mamcarz
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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16
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Chen J, Gale RP, Feng Y, Hu Y, Qi S, Liu X, Zhu H, Gong X, Zhang W, Liu H, Sun Z. Are haematopoietic stem cell transplants stem cell transplants, is there a threshold dose of CD34-positive cells and how many are needed for rapid posttransplant granulocyte recovery? Leukemia 2023; 37:1963-1968. [PMID: 37474589 PMCID: PMC10539175 DOI: 10.1038/s41375-023-01973-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 06/29/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Affiliation(s)
- Junren Chen
- 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.
- Tianjin Institutes of Health Science, Tianjin, China.
| | - Robert Peter Gale
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College of Science, Technology and Medicine, London, UK
| | - Yahui Feng
- 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
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yu Hu
- 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
- Tianjin Institutes of Health Science, Tianjin, China
| | - Saibing Qi
- 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
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xueou Liu
- 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
- Tianjin Institutes of Health Science, Tianjin, China
| | - Huaiping Zhu
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
- Blood and Cell Therapy Institute, Division of Life Sciences and Medicine, Anhui Provincial Key Laboratory of Blood Research and Applications, University of Science and Technology of China, Hefei, China
| | - Xiaowen Gong
- 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
- Tianjin Institutes of Health Science, Tianjin, China
| | - Wei Zhang
- 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
- Tianjin Institutes of Health Science, Tianjin, China
| | - Huilan Liu
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
- Blood and Cell Therapy Institute, Division of Life Sciences and Medicine, Anhui Provincial Key Laboratory of Blood Research and Applications, University of Science and Technology of China, Hefei, China
| | - Zimin Sun
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China.
- Blood and Cell Therapy Institute, Division of Life Sciences and Medicine, Anhui Provincial Key Laboratory of Blood Research and Applications, University of Science and Technology of China, Hefei, China.
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17
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Casirati G, Cosentino A, Mucci A, Salah Mahmoud M, Ugarte Zabala I, Zeng J, Ficarro SB, Klatt D, Brendel C, Rambaldi A, Ritz J, Marto JA, Pellin D, Bauer DE, Armstrong SA, Genovese P. Epitope editing enables targeted immunotherapy of acute myeloid leukaemia. Nature 2023; 621:404-414. [PMID: 37648862 PMCID: PMC10499609 DOI: 10.1038/s41586-023-06496-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Despite the considerable efficacy observed when targeting a dispensable lineage antigen, such as CD19 in B cell acute lymphoblastic leukaemia1,2, the broader applicability of adoptive immunotherapies is hampered by the absence of tumour-restricted antigens3-5. Acute myeloid leukaemia immunotherapies target genes expressed by haematopoietic stem/progenitor cells (HSPCs) or differentiated myeloid cells, resulting in intolerable on-target/off-tumour toxicity. Here we show that epitope engineering of donor HSPCs used for bone marrow transplantation endows haematopoietic lineages with selective resistance to chimeric antigen receptor (CAR) T cells or monoclonal antibodies, without affecting protein function or regulation. This strategy enables the targeting of genes that are essential for leukaemia survival regardless of shared expression on HSPCs, reducing the risk of tumour immune escape. By performing epitope mapping and library screenings, we identified amino acid changes that abrogate the binding of therapeutic monoclonal antibodies targeting FLT3, CD123 and KIT, and optimized a base-editing approach to introduce them into CD34+ HSPCs, which retain long-term engraftment and multilineage differentiation ability. After CAR T cell treatment, we confirmed resistance of epitope-edited haematopoiesis and concomitant eradication of patient-derived acute myeloid leukaemia xenografts. Furthermore, we show that multiplex epitope engineering of HSPCs is feasible and enables more effective immunotherapies against multiple targets without incurring overlapping off-tumour toxicities. We envision that this approach will provide opportunities to treat relapsed/refractory acute myeloid leukaemia and enable safer non-genotoxic conditioning.
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Affiliation(s)
- Gabriele Casirati
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Milano-Bicocca University, Milan, Italy
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Andrea Cosentino
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Oncology and Hematology, University of Milan and Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Adele Mucci
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Mohammed Salah Mahmoud
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Zoology Department, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Iratxe Ugarte Zabala
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Denise Klatt
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Christian Brendel
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Harvard Medical School, Boston, MA, USA
| | - Alessandro Rambaldi
- Department of Oncology and Hematology, University of Milan and Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Jerome Ritz
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute, Boston, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Danilo Pellin
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Harvard Medical School, Boston, MA, USA
| | - Scott A Armstrong
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Harvard Medical School, Boston, MA, USA
| | - Pietro Genovese
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA.
- Harvard Medical School, Boston, MA, USA.
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18
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Rodriguez-Fraticelli AE. HSCs "shift and drift" during transplantation. Blood 2023; 142:3-4. [PMID: 37410506 DOI: 10.1182/blood.2023020189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Affiliation(s)
- Alejo E Rodriguez-Fraticelli
- Institute for Research in Biomedicine, Barcelona Institute for Science and Technology, and Catalan Institution for Research and Advanced Studies
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19
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Radtke S, Enstrom M, Pande D, Duke ER, Cardozo-Ojeda EF, Madhu R, Owen S, Kanestrom G, Cui M, Perez AM, Schiffer JT, Kiem HP. Stochastic fate decisions of HSCs after transplantation: early contribution, symmetric expansion, and pool formation. Blood 2023; 142:33-43. [PMID: 36821766 PMCID: PMC10935507 DOI: 10.1182/blood.2022018564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Hematopoietic stem cells (HSCs) are assumed to be rare, infrequently dividing, long-lived cells not involved in immediate recovery after transplantation. Here, we performed unprecedented high-density clonal tracking in nonhuman primates and found long-term persisting HSC clones to actively contribute during early neutrophil recovery, and to be the main source of blood production as early as 50 days after transplantation. Most surprisingly, we observed a rapid decline in the number of unique HSC clones, while persisting HSCs expanded, undergoing symmetric divisions to create identical siblings and formed clonal pools ex vivo as well as in vivo. In contrast to the currently assumed model of hematopoietic reconstitution, we provide evidence for contribution of HSCs in short-term recovery as well as symmetric expansion of individual clones into pools. These findings provide novel insights into HSC biology, informing the design of HSC transplantation and gene therapy studies.
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Affiliation(s)
- Stefan Radtke
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Mark Enstrom
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Dnyanada Pande
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Elizabeth R. Duke
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | | | - Ravishankar Madhu
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Staci Owen
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Greta Kanestrom
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Margaret Cui
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Anai M. Perez
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Pathology, University of Washington School of Medicine, Seattle, WA
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20
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Rai R, Naseem A, Vetharoy W, Steinberg Z, Thrasher AJ, Santilli G, Cavazza A. An improved medium formulation for efficient ex vivo gene editing, expansion and engraftment of hematopoietic stem and progenitor cells. Mol Ther Methods Clin Dev 2023; 29:58-69. [PMID: 36950452 PMCID: PMC10025975 DOI: 10.1016/j.omtm.2023.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/24/2023] [Indexed: 03/04/2023]
Abstract
Gene editing has emerged as a powerful tool for the therapeutic correction of monogenic diseases. CRISPR-Cas9 applied to hematopoietic stem and progenitor cells (HSPCs) has shown great promise in proof-of-principle preclinical studies to treat hematological disorders, and clinical trials using these tools are now under way. Nonetheless, there remain important challenges that need to be addressed, such as the efficiency of targeting primitive, long-term repopulating HSPCs and their in vitro expansion for clinical application. In this study, we assessed the effect of different culture medium compositions on the ability of HSPCs to proliferate and undergo homology-directed repair-mediated knock-in of a reporter gene, while preserving their stemness features during ex vivo culture. We demonstrated that by supplementing the culture medium with stem cell agonists and by fine-tuning its cytokine composition it is possible to achieve high levels of gene targeting in long-term repopulating HSPCs both in vitro and in vivo, with a beneficial balance between preservation of stemness and cell expansion. Overall, the implementation of this optimized ex vivo HSPC culture protocol can improve the efficacy, feasibility, and applicability of gene editing as a key step to unlocking the full therapeutic potential of this powerful technology.
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Affiliation(s)
- Rajeev Rai
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Asma Naseem
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Winston Vetharoy
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Zohar Steinberg
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Adrian J. Thrasher
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Giorgia Santilli
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Alessia Cavazza
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
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21
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Zhao HG, Deininger M. Always stressed but never exhausted: how stem cells in myeloid neoplasms avoid extinction in inflammatory conditions. Blood 2023; 141:2797-2812. [PMID: 36947811 PMCID: PMC10315634 DOI: 10.1182/blood.2022017152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/27/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
Chronic or recurrent episodes of acute inflammation cause attrition of normal hematopoietic stem cells (HSCs) that can lead to hematopoietic failure but they drive progression in myeloid malignancies and their precursor clonal hematopoiesis. Mechanistic parallels exist between hematopoiesis in chronic inflammation and the continuously increased proliferation of myeloid malignancies, particularly myeloproliferative neoplasms (MPNs). The ability to enter dormancy, a state of deep quiescence characterized by low oxidative phosphorylation, low glycolysis, reduced protein synthesis, and increased autophagy is central to the preservation of long-term HSCs and likely MPN SCs. The metabolic features of dormancy resemble those of diapause, a state of arrested embryonic development triggered by adverse environmental conditions. To outcompete their normal counterparts in the inflammatory MPN environment, MPN SCs co-opt mechanisms used by HSCs to avoid exhaustion, including signal attenuation by negative regulators, insulation from activating cytokine signals, anti-inflammatory signaling, and epigenetic reprogramming. We propose that new therapeutic strategies may be derived from conceptualizing myeloid malignancies as an ecosystem out of balance, in which residual normal and malignant hematopoietic cells interact in multiple ways, only few of which have been characterized in detail. Disrupting MPN SC insulation to overcome dormancy, interfering with aberrant cytokine circuits that favor MPN cells, and directly boosting residual normal HSCs are potential strategies to tip the balance in favor of normal hematopoiesis. Although eradicating the malignant cell clones remains the goal of therapy, rebalancing the ecosystem may be a more attainable objective in the short term.
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Affiliation(s)
- Helong Gary Zhao
- Versiti Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI
| | - Michael Deininger
- Versiti Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI
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22
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Corre G, Galy A. Evaluation of diversity indices to estimate clonal dominance in gene therapy studies. Mol Ther Methods Clin Dev 2023; 29:418-425. [PMID: 37251980 PMCID: PMC10220254 DOI: 10.1016/j.omtm.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/04/2023] [Indexed: 05/31/2023]
Abstract
In cell and gene therapy, achieving the stable engraftment of an abundant and highly polyclonal population of gene-corrected cells is one of the key factors to ensure the successful and safe treatment of patients. Because integrative vectors have been associated with possible risks of insertional mutagenesis leading to clonal dominance, monitoring the relative abundance of individual vector insertion sites in patients' blood cells has become an important safety assessment, particularly in hematopoietic stem cell-based therapies. Clinical studies often express clonal diversity using various metrics. One of the most commonly used is the Shannon index of entropy. However, this index aggregates two distinct aspects of diversity, the number of unique species and their relative abundance. This property hampers the comparison of samples with different richness. This prompted us to reanalyze published datasets and to model the properties of various indices as applied to the evaluation of clonal diversity in gene therapy. A normalized version of the Shannon index, such as Pielou's index, or Simpson's probability index is robust and useful to compare sample evenness between patients and trials. Clinically meaningful standard values for clonal diversity are herein proposed to facilitate the use of vector insertion site analyses in genomic medicine practice.
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Affiliation(s)
- Guillaume Corre
- Genethon, 91000 Evry, France
- Université Paris-Saclay, University Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Anne Galy
- Genethon, 91000 Evry, France
- Université Paris-Saclay, University Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
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23
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Del Core L, Pellin D, Wit EC, Grzegorczyk MA. A mixed-effects stochastic model reveals clonal dominance in gene therapy safety studies. BMC Bioinformatics 2023; 24:228. [PMID: 37268887 DOI: 10.1186/s12859-023-05269-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/04/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Mathematical models of haematopoiesis can provide insights on abnormal cell expansions (clonal dominance), and in turn can guide safety monitoring in gene therapy clinical applications. Clonal tracking is a recent high-throughput technology that can be used to quantify cells arising from a single haematopoietic stem cell ancestor after a gene therapy treatment. Thus, clonal tracking data can be used to calibrate the stochastic differential equations describing clonal population dynamics and hierarchical relationships in vivo. RESULTS In this work we propose a random-effects stochastic framework that allows to investigate the presence of events of clonal dominance from high-dimensional clonal tracking data. Our framework is based on the combination between stochastic reaction networks and mixed-effects generalized linear models. Starting from the Kramers-Moyal approximated Master equation, the dynamics of cells duplication, death and differentiation at clonal level, can be described by a local linear approximation. The parameters of this formulation, which are inferred using a maximum likelihood approach, are assumed to be shared across the clones and are not sufficient to describe situation in which clones exhibit heterogeneity in their fitness that can lead to clonal dominance. In order to overcome this limitation, we extend the base model by introducing random-effects for the clonal parameters. This extended formulation is calibrated to the clonal data using a tailor-made expectation-maximization algorithm. We also provide the companion package RestoreNet, publicly available for download at https://cran.r-project.org/package=RestoreNet . CONCLUSIONS Simulation studies show that our proposed method outperforms the state-of-the-art. The application of our method in two in-vivo studies unveils the dynamics of clonal dominance. Our tool can provide statistical support to biologists in gene therapy safety analyses.
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Affiliation(s)
- Luca Del Core
- Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Groningen, The Netherlands.
- School of Mathematical Sciences, University of Nottingham, Nottingham, UK.
| | - Danilo Pellin
- Harvard Medical School, Harvard University, Boston, MA, USA.
| | - Ernst C Wit
- Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Groningen, The Netherlands.
- Institute of Computing, Università della Svizzera italiana, Lugano, Switzerland.
| | - Marco A Grzegorczyk
- Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Groningen, The Netherlands.
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24
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Scala S, Ferrua F, Basso-Ricci L, Dionisio F, Omrani M, Quaranta P, Jofra Hernandez R, Del Core L, Benedicenti F, Monti I, Giannelli S, Fraschetta F, Darin S, Albertazzi E, Galimberti S, Montini E, Calabria A, Cicalese MP, Aiuti A. Hematopoietic reconstitution dynamics of mobilized- and bone marrow-derived human hematopoietic stem cells after gene therapy. Nat Commun 2023; 14:3068. [PMID: 37244942 DOI: 10.1038/s41467-023-38448-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/28/2023] [Indexed: 05/29/2023] Open
Abstract
Mobilized peripheral blood is increasingly used instead of bone marrow as a source of autologous hematopoietic stem/progenitor cells for ex vivo gene therapy. Here, we present an unplanned exploratory analysis evaluating the hematopoietic reconstitution kinetics, engraftment and clonality in 13 pediatric Wiskott-Aldrich syndrome patients treated with autologous lentiviral-vector transduced hematopoietic stem/progenitor cells derived from mobilized peripheral blood (n = 7), bone marrow (n = 5) or the combination of the two sources (n = 1). 8 out of 13 gene therapy patients were enrolled in an open-label, non-randomized, phase 1/2 clinical study (NCT01515462) and the remaining 5 patients were treated under expanded access programs. Although mobilized peripheral blood- and bone marrow- hematopoietic stem/progenitor cells display similar capability of being gene-corrected, maintaining the engineered grafts up to 3 years after gene therapy, mobilized peripheral blood-gene therapy group shows faster neutrophil and platelet recovery, higher number of engrafted clones and increased gene correction in the myeloid lineage which correlate with higher amount of primitive and myeloid progenitors contained in hematopoietic stem/progenitor cells derived from mobilized peripheral blood. In vitro differentiation and transplantation studies in mice confirm that primitive hematopoietic stem/progenitor cells from both sources have comparable engraftment and multilineage differentiation potential. Altogether, our analyses reveal that the differential behavior after gene therapy of hematopoietic stem/progenitor cells derived from either bone marrow or mobilized peripheral blood is mainly due to the distinct cell composition rather than functional differences of the infused cell products, providing new frames of references for clinical interpretation of hematopoietic stem/progenitor cell transplantation outcome.
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Affiliation(s)
- Serena Scala
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Francesca Ferrua
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Luca Basso-Ricci
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Francesca Dionisio
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Maryam Omrani
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Department of Computer Science, Systems and Communication, University of Milano Bicocca, Milan, 20126, Italy
| | - Pamela Quaranta
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Università Vita-Salute San Raffaele, Milan, 20132, Italy
| | - Raisa Jofra Hernandez
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Luca Del Core
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- University of Groningen - Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, Groningen, 9747, Netherlands
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Ilaria Monti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Stefania Giannelli
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Federico Fraschetta
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Silvia Darin
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Elena Albertazzi
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Stefania Galimberti
- Center of Biostatistics for Clinical Epidemiology, University of Milano-Bicocca, Monza, 20900, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Maria Pia Cicalese
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Università Vita-Salute San Raffaele, Milan, 20132, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy.
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy.
- Università Vita-Salute San Raffaele, Milan, 20132, Italy.
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25
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Diamond B, Ziccheddu B, Maclachlan K, Taylor J, Boyle E, Ossa JA, Jahn J, Affer M, Totiger TM, Coffey D, Chandhok N, Watts J, Cimmino L, Lu SX, Bolli N, Bolton K, Landau H, Park JH, Ganesh K, McPherson A, Sekeres MA, Lesokhin A, Chung DJ, Zhang Y, Ho C, Roshal M, Tyner J, Nimer S, Papaemmanuil E, Usmani S, Morgan G, Landgren O, Maura F. Tracking the evolution of therapy-related myeloid neoplasms using chemotherapy signatures. Blood 2023; 141:2359-2371. [PMID: 36626250 PMCID: PMC10273163 DOI: 10.1182/blood.2022018244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Patients treated with cytotoxic therapies, including autologous stem cell transplantation, are at risk for developing therapy-related myeloid neoplasms (tMN). Preleukemic clones (ie, clonal hematopoiesis [CH]) are detectable years before the development of these aggressive malignancies, although the genomic events leading to transformation and expansion are not well defined. Here, by leveraging distinctive chemotherapy-associated mutational signatures from whole-genome sequencing data and targeted sequencing of prechemotherapy samples, we reconstructed the evolutionary life-history of 39 therapy-related myeloid malignancies. A dichotomy was revealed, in which neoplasms with evidence of chemotherapy-induced mutagenesis from platinum and melphalan were hypermutated and enriched for complex structural variants (ie, chromothripsis), whereas neoplasms with nonmutagenic chemotherapy exposures were genomically similar to de novo acute myeloid leukemia. Using chemotherapy-associated mutational signatures as temporal barcodes linked to discrete clinical exposure in each patient's life, we estimated that several complex events and genomic drivers were acquired after chemotherapy was administered. For patients with prior multiple myeloma who were treated with high-dose melphalan and autologous stem cell transplantation, we demonstrate that tMN can develop from either a reinfused CH clone that escapes melphalan exposure and is selected after reinfusion, or from TP53-mutant CH that survives direct myeloablative conditioning and acquires melphalan-induced DNA damage. Overall, we revealed a novel mode of tMN progression that is not reliant on direct mutagenesis or even exposure to chemotherapy. Conversely, for tMN that evolve under the influence of chemotherapy-induced mutagenesis, distinct chemotherapies not only select preexisting CH but also promote the acquisition of recurrent genomic drivers.
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Affiliation(s)
- Benjamin Diamond
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | | | - Kylee Maclachlan
- Division of Myeloma, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Eileen Boyle
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Juan Arango Ossa
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacob Jahn
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Maurizio Affer
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | | | - David Coffey
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Namrata Chandhok
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Justin Watts
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Luisa Cimmino
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Sydney X. Lu
- Division of Hematology, Stanford Hospital and Clinics, Stanford University, Stanford, CA
| | - Niccolò Bolli
- Department of Oncology and Onco-Hematology, Università degli Studi di Milano, Milan, Italy
- Hematology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Kelly Bolton
- Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Heather Landau
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jae H. Park
- Department of Medicine, Memorial Hospital, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karuna Ganesh
- Department of Medicine, Memorial Hospital, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrew McPherson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Alexander Lesokhin
- Division of Myeloma, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David J. Chung
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caleb Ho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mikhail Roshal
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jeffrey Tyner
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR
| | - Stephen Nimer
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Saad Usmani
- Division of Myeloma, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gareth Morgan
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Ola Landgren
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Francesco Maura
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
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26
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Lareau CA, Liu V, Muus C, Praktiknjo SD, Nitsch L, Kautz P, Sandor K, Yin Y, Gutierrez JC, Pelka K, Satpathy AT, Regev A, Sankaran VG, Ludwig LS. Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. Nat Protoc 2023; 18:1416-1440. [PMID: 36792778 PMCID: PMC10317201 DOI: 10.1038/s41596-022-00795-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 11/11/2022] [Indexed: 02/17/2023]
Abstract
Natural sequence variation within mitochondrial DNA (mtDNA) contributes to human phenotypes and may serve as natural genetic markers in human cells for clonal and lineage tracing. We recently developed a single-cell multi-omic approach, called 'mitochondrial single-cell assay for transposase-accessible chromatin with sequencing' (mtscATAC-seq), enabling concomitant high-throughput mtDNA genotyping and accessible chromatin profiling. Specifically, our technique allows the mitochondrial genome-wide inference of mtDNA variant heteroplasmy along with information on cell state and accessible chromatin variation in individual cells. Leveraging somatic mtDNA mutations, our method further enables inference of clonal relationships among native ex vivo-derived human cells not amenable to genetic engineering-based clonal tracing approaches. Here, we provide a step-by-step protocol for the use of mtscATAC-seq, including various cell-processing and flow cytometry workflows, by using primary hematopoietic cells, subsequent single-cell genomic library preparation and sequencing that collectively take ~3-4 days to complete. We discuss experimental and computational data quality control metrics and considerations for the extension to other mammalian tissues. Overall, mtscATAC-seq provides a broadly applicable platform to map clonal relationships between cells in human tissues, investigate fundamental aspects of mitochondrial genetics and enable additional modes of multi-omic discovery.
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Affiliation(s)
- Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | - Vincent Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Samantha D Praktiknjo
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Lena Nitsch
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Pauline Kautz
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Karin Pelka
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Aviv Regev
- Genentech, South San Francisco, CA, USA.
| | - Vijay G Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Leif S Ludwig
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
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27
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Gallon R, Phelps R, Hayes C, Brugieres L, Guerrini-Rousseau L, Colas C, Muleris M, Ryan NAJ, Evans DG, Grice H, Jessop E, Kunzemann-Martinez A, Marshall L, Schamschula E, Oberhuber K, Azizi AA, Baris Feldman H, Beilken A, Brauer N, Brozou T, Dahan K, Demirsoy U, Florkin B, Foulkes W, Januszkiewicz-Lewandowska D, Jones KJ, Kratz CP, Lobitz S, Meade J, Nathrath M, Pander HJ, Perne C, Ragab I, Ripperger T, Rosenbaum T, Rueda D, Sarosiek T, Sehested A, Spier I, Suerink M, Zimmermann SY, Zschocke J, Borthwick GM, Wimmer K, Burn J, Jackson MS, Santibanez-Koref M. Constitutional Microsatellite Instability, Genotype, and Phenotype Correlations in Constitutional Mismatch Repair Deficiency. Gastroenterology 2023; 164:579-592.e8. [PMID: 36586540 DOI: 10.1053/j.gastro.2022.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 01/02/2023]
Abstract
BACKGROUND & AIMS Constitutional mismatch repair deficiency (CMMRD) is a rare recessive childhood cancer predisposition syndrome caused by germline mismatch repair variants. Constitutional microsatellite instability (cMSI) is a CMMRD diagnostic hallmark and may associate with cancer risk. We quantified cMSI in a large CMMRD patient cohort to explore genotype-phenotype correlations using novel MSI markers selected for instability in blood. METHODS Three CMMRD, 1 Lynch syndrome, and 2 control blood samples were genome sequenced to >120× depth. A pilot cohort of 8 CMMRD and 38 control blood samples and a blinded cohort of 56 CMMRD, 8 suspected CMMRD, 40 Lynch syndrome, and 43 control blood samples were amplicon sequenced to 5000× depth. Sample cMSI score was calculated using a published method comparing microsatellite reference allele frequencies with 80 controls. RESULTS Thirty-two mononucleotide repeats were selected from blood genome and pilot amplicon sequencing data. cMSI scoring using these MSI markers achieved 100% sensitivity (95% CI, 93.6%-100.0%) and specificity (95% CI 97.9%-100.0%), was reproducible, and was superior to an established tumor MSI marker panel. Lower cMSI scores were found in patients with CMMRD with MSH6 deficiency and patients with at least 1 mismatch repair missense variant, and patients with biallelic truncating/copy number variants had higher scores. cMSI score did not correlate with age at first tumor. CONCLUSIONS We present an inexpensive and scalable cMSI assay that enhances CMMRD detection relative to existing methods. cMSI score is associated with mismatch repair genotype but not phenotype, suggesting it is not a useful predictor of cancer risk.
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Affiliation(s)
- Richard Gallon
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - Rachel Phelps
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Christine Hayes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Laurence Brugieres
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Léa Guerrini-Rousseau
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France; Team "Genomics and Oncogenesis of pediatric Brain Tumors," INSERM U981, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Chrystelle Colas
- Département de Génétique, Institut Curie, Paris, France; INSERM U830, Université de Paris, Paris, France
| | - Martine Muleris
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre de Recherche Saint-Antoine, Paris, France
| | - Neil A J Ryan
- The Academic Women's Health Unit, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Department of Gynaecology Oncology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - D Gareth Evans
- Division of Evolution, Infection and Genomics, University of Manchester, Manchester, UK
| | - Hannah Grice
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Jessop
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Annabel Kunzemann-Martinez
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Centre for Inflammation and Tissue Repair, University College London, London, UK
| | - Lilla Marshall
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Esther Schamschula
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Klaus Oberhuber
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Amedeo A Azizi
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Andreas Beilken
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Nina Brauer
- Pediatric Oncology, Helios-Klinikum, Krefeld, Germany
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Karin Dahan
- Centre de Génétique Humaine, Institut de Pathologie et Génétique, Gosselies, Belgium
| | - Ugur Demirsoy
- Department of Pediatric Oncology, Kocaeli University, Kocaeli, Turkey
| | - Benoît Florkin
- Department of Pediatrics, Citadelle Hospital, University of Liège, Liège, Belgium
| | - William Foulkes
- Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada; Department of Medical Genetics, McGill University Health Centre, Montreal, Quebec, Canada; Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | | | - Kristi J Jones
- Department of Clinical Genetics, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, New South Wales, Australia; University of Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Stephan Lobitz
- Gemeinschaftsklinikum Mittelrhein, Department of Pediatric Hematology and Oncology, Koblenz, Germany
| | - Julia Meade
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Michaela Nathrath
- Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany; Department of Pediatrics, Pediatric Oncology Center, Technische Universität München, Munich, Germany
| | | | - Claudia Perne
- Institute of Human Genetics, Medical Faculty, University of Bonn and National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Iman Ragab
- Pediatrics Department, Hematology-Oncology Unit, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | - Daniel Rueda
- Hereditary Cancer Laboratory, University Hospital Doce de Octubre, i+12 Research Institute, Madrid, Spain
| | | | - Astrid Sehested
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn and National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stefanie-Yvonne Zimmermann
- Department of Pediatric Hematology and Oncology, Children's Hospital, University Hospital, Frankfurt, Germany
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Gillian M Borthwick
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katharina Wimmer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - John Burn
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Michael S Jackson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Mauro Santibanez-Koref
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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28
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Huo Y, Wu L, Pang A, Li Q, Hong F, Zhu C, Yang Z, Dai W, Zheng Y, Meng Q, Sun J, Ma S, Hu L, Zhu P, Dong F, Gao X, Jiang E, Hao S, Cheng T. Single-cell dissection of human hematopoietic reconstitution after allogeneic hematopoietic stem cell transplantation. Sci Immunol 2023; 8:eabn6429. [PMID: 36930730 DOI: 10.1126/sciimmunol.abn6429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Hematopoietic stem cell transplantation is an effective regenerative therapy for many malignant, inherited, or autoimmune diseases. However, our understanding of reconstituted hematopoiesis in transplant patients remains limited. Here, we uncover the reconstitution dynamics of human allogeneic hematopoietic stem and progenitor cells (HSPCs) at single-cell resolution after transplantation. Transplanted HSPCs underwent rapid and measurable changes during the first 30 days after transplantation, characterized by a strong proliferative response on the first day. Transcriptomic analysis of HSPCs enabled us to observe that immunoregulatory neutrophil progenitors expressing high levels of the S100A gene family were enriched in granulocyte colony-stimulating factor-mobilized peripheral blood stem cells. Transplant recipients who developed acute graft-versus-host disease (aGVHD) infused fewer S100Ahigh immunoregulatory neutrophil progenitors, immunophenotyped as Lin-CD34+CD66b+CD177+, than those who did not develop aGVHD. Therefore, our study provides insights into the regenerative process of transplanted HSPCs in human patients and identifies a potential criterion for identifying patients at high risk for developing aGVHD early after transplant.
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Affiliation(s)
- Yingying Huo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Linjie Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Aiming Pang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Qing Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Fang Hong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Caiying Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Zining Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Weiqian Dai
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Yawei Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Qianqian Meng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jiali Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shihui Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Linping Hu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Fang Dong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Xin Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Erlie Jiang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Sha Hao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
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29
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Radtke S. The unknown impact of conditioning on HSC engraftment and clonal dynamics. Mol Ther Methods Clin Dev 2023; 28:385-386. [PMID: 36874241 PMCID: PMC9982445 DOI: 10.1016/j.omtm.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Affiliation(s)
- Stefan Radtke
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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30
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Therapy-selected clonal hematopoiesis and its role in myeloid neoplasms. Leuk Res 2023; 126:107020. [PMID: 36696829 DOI: 10.1016/j.leukres.2023.107020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
Therapy-related myeloid neoplasms (t-MN) account for approximately 10-15% of all myeloid neoplasms and are associated with poor prognosis. Genomic characterization of t-MN to date has been limited in comparison to the considerable sequencing efforts performed for de novo myeloid neoplasms. Until recently, targeted deep sequencing (TDS) or whole exome sequencing (WES) have been the primary technologies utilized and thus limited the ability to explore the landscape of structural variants and mutational signatures. In the past decade, population-level studies have identified clonal hematopoiesis as a risk factor for the development of myeloid neoplasms. However, emerging research on clonal hematopoiesis as a risk factor for developing t-MN is evolving, and much is unknown about the progression of CH to t-MN. In this work, we will review the current knowledge of the genomic landscape of t-MN, discuss background knowledge of clonal hematopoiesis gained from studies of de novo myeloid neoplasms, and examine the recent literature studying the role of therapeutic selection of CH and its evolution under the effects of antineoplastic therapy. Finally, we will discuss the potential implications on current clinical practice and the areas of focus needed for future research into therapy-selected clonal hematopoiesis in myeloid neoplasms.
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31
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Wang X, Liu S, Yu J. Multi-lineage Differentiation from Hematopoietic Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:159-175. [PMID: 38228964 DOI: 10.1007/978-981-99-7471-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The hematopoietic stem cells (HSCs) have the ability to differentiate and give rise to all mature blood cells. Commitment to differentiation progressively limits the self-renewal potential of the original HSCs by regulating the level of lineage-specific gene expression. In this review, we will summarize the current understanding of the molecular mechanisms underlying HSC differentiation toward erythroid, myeloid, and lymphocyte lineages. Moreover, we will decipher how the single-cell technologies advance the lineage-biased HSC subpopulations and their differentiation potential.
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Affiliation(s)
- Xiaoshuang Wang
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China.
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu, China.
| | - Siqi Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China.
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu, China.
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32
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Pais G, Spinozzi G, Cesana D, Benedicenti F, Albertini A, Bernardo ME, Gentner B, Montini E, Calabria A. ISAnalytics enables longitudinal and high-throughput clonal tracking studies in hematopoietic stem cell gene therapy applications. Brief Bioinform 2022; 24:6955274. [PMID: 36545803 PMCID: PMC9910212 DOI: 10.1093/bib/bbac551] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Longitudinal clonal tracking studies based on high-throughput sequencing technologies supported safety and long-term efficacy and unraveled hematopoietic reconstitution in many gene therapy applications with unprecedented resolution. However, monitoring patients over a decade-long follow-up entails a constant increase of large data volume with the emergence of critical computational challenges, unfortunately not addressed by currently available tools. Here we present ISAnalytics, a new R package for comprehensive and high-throughput clonal tracking studies using vector integration sites as markers of cellular identity. Once identified the clones externally from ISAnalytics and imported in the package, a wide range of implemented functionalities are available to users for assessing the safety and long-term efficacy of the treatment, here described in a clinical trial use case for Hurler disease, and for supporting hematopoietic stem cell biology in vivo with longitudinal analysis of clones over time, proliferation and differentiation. ISAnalytics is conceived to be metadata-driven, enabling users to focus on biological questions and hypotheses rather than on computational aspects. ISAnalytics can be fully integrated within laboratory workflows and standard procedures. Moreover, ISAnalytics is designed with efficient and scalable data structures, benchmarked with previous methods, and grants reproducibility and full analytical control through interactive web-reports and a module with Shiny interface. The implemented functionalities are flexible for all viral vector-based clonal tracking applications as well as genetic barcoding or cancer immunotherapies.
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Affiliation(s)
- Giulia Pais
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | | | | | - Fabrizio Benedicenti
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Alessandra Albertini
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Maria Ester Bernardo
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy,IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Bernhard Gentner
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Eugenio Montini
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Andrea Calabria
- Corresponding author. Andrea Calabria, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS Ospedale San Raffaele, Milan, Italy. E-mail:
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33
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Abraham DM, Lozano RJ, Guitart X, Liang JA, Mortlock RD, Espinoza DA, Fan X, Krouse A, Bonifacino A, Hong SG, Singh K, Tisdale JF, Wu C, Dunbar CE. Comparison of busulfan and total body irradiation conditioning on hematopoietic clonal dynamics following lentiviral gene transfer in rhesus macaques. Mol Ther Methods Clin Dev 2022; 28:62-75. [PMID: 36620072 PMCID: PMC9798201 DOI: 10.1016/j.omtm.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The clonal dynamics following hematopoietic stem progenitor cell (HSPC) transplantation with busulfan conditioning are of great interest to the development of HSPC gene therapies. Compared with total body irradiation (TBI), busulfan is less toxic and more clinically relevant. We used a genetic barcoded HSPC autologous transplantation model to investigate the impact of busulfan conditioning on hematopoietic reconstitution in rhesus macaques. Two animals received lower busulfan dose and demonstrated lower vector marking levels compared with the third animal given a higher busulfan dose, despite similar busulfan pharmacokinetic analysis. We observed uni-lineage clonal engraftment at 1 month post-transplant, replaced by multilineage clones by 2 to 3 months in all animals. The initial multilineage clones in the first two animals were replaced by a second multilineage wave at 9 months; this clonal pattern disappeared at 13 months in the first animal, though was maintained in the second animal. The third animal maintained stable multilineage clones from 3 months to the most recent time point. In addition, busulfan animals exhibit more rapid HSPC clonal mixing across bone marrow sites and less CD16+ NK-biased clonal expansion compared with TBI animals. Therefore, busulfan conditioning regimens can variably impact the marrow niche, resulting in differences in clonal patterns with implications for HSPC gene therapies.
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Affiliation(s)
- Diana M. Abraham
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard J. Lozano
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xavi Guitart
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jialiu A. Liang
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryland D. Mortlock
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diego A. Espinoza
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xing Fan
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allen Krouse
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aylin Bonifacino
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - So Gun Hong
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Komudi Singh
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John F. Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding author Chuanfeng Wu, Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Building 10 CRC, Room 5E-3288, 10 Center Drive, Bethesda, MD 20892, USA.
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding author Cynthia E. Dunbar, Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Building 10 CRC, Room 5E-3332, 10 Center Drive, Bethesda, MD 20892, USA.
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34
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Cornetta K, Lin TY, Pellin D, Kohn DB. Meeting FDA Guidance recommendations for replication-competent virus and insertional oncogenesis testing. Mol Ther Methods Clin Dev 2022; 28:28-39. [PMID: 36588821 PMCID: PMC9791246 DOI: 10.1016/j.omtm.2022.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Integrating vectors are associated with alterations in cellular function related to disruption of normal gene function. This has been associated with clonal expansion of cells and, in some instances, cancer. These events have been associated with replication-defective vectors and suggest that the inadvertent exposure to a replication-competent virus arising during vector manufacture would significantly increase the risk of treatment-related adverse events. These risks have led regulatory agencies to require specific monitoring for replication-competent viruses, both prior to and after treatment of patients with gene therapy products. Monitoring the risk of cell expansion and malignancy is also required. In this review, we discuss the rational potential approaches and challenges to meeting the US FDA expectations listed in current guidance documents.
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Affiliation(s)
- Kenneth Cornetta
- Gene Therapy Testing Laboratory, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA,National Gene Vector Biorepository, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA,Corresponding author Kenneth Cornetta, MD, Department of Medical and Molecular Genetics, Indiana University School of Medicine, R3 C602, 980 West Walnut Street, Indianapolis, IN 46202, USA.
| | - Tsai-Yu Lin
- Gene Therapy Testing Laboratory, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA,National Gene Vector Biorepository, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Danilo Pellin
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Donald B. Kohn
- Departments of Microbiology, Immunology and Molecular Genetics, and Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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35
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Skulimowska I, Sosniak J, Gonka M, Szade A, Jozkowicz A, Szade K. The biology of hematopoietic stem cells and its clinical implications. FEBS J 2022; 289:7740-7759. [PMID: 34496144 DOI: 10.1111/febs.16192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/19/2021] [Accepted: 09/07/2021] [Indexed: 01/14/2023]
Abstract
Hematopoietic stem cells (HSCs) give rise to all types of blood cells and self-renew their own population. The regeneration potential of HSCs has already been successfully translated into clinical applications. However, recent studies on the biology of HSCs may further extend their clinical use in future. The roles of HSCs in native hematopoiesis and in transplantation settings may differ. Furthermore, the heterogenic pool of HSCs dynamically changes during aging. These changes also involve the complex interactions of HSCs with the bone marrow niche. Here, we review the opportunities and challenges of these findings to improve the clinical use of HSCs. We describe new methods of HSCs mobilization and conditioning for the transplantation of HSCs. Finally, we highlight the research findings that may lead to overcoming the current limitations of HSC transplantation and broaden the patient group that can benefit from the clinical potential of HSCs.
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Affiliation(s)
- Izabella Skulimowska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Justyna Sosniak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Monika Gonka
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agata Szade
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alicja Jozkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Szade
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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36
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Sankaran VG, Weissman JS, Zon LI. Cellular barcoding to decipher clonal dynamics in disease. Science 2022; 378:eabm5874. [PMID: 36227997 PMCID: PMC10111813 DOI: 10.1126/science.abm5874] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cellular barcodes are distinct DNA sequences that enable one to track specific cells across time or space. Recent advances in our ability to detect natural or synthetic cellular barcodes, paired with single-cell readouts of cell state, have markedly increased our knowledge of clonal dynamics and genealogies of the cells that compose a variety of tissues and organs. These advances hold promise to redefine our view of human disease. Here, we provide an overview of cellular barcoding approaches, discuss applications to gain new insights into disease mechanisms, and provide an outlook on future applications. We discuss unanticipated insights gained through barcoding in studies of cancer and blood cell production and describe how barcoding can be applied to a growing array of medical fields, particularly with the increasing recognition of clonal contributions in human diseases.
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Affiliation(s)
- Vijay G Sankaran
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Leonard I Zon
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Stem Cell Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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37
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Hadj Abed L, Tak T, Cosgrove J, Perié L. CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data. Front Med (Lausanne) 2022; 9:919345. [PMID: 36275810 PMCID: PMC9581332 DOI: 10.3389/fmed.2022.919345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell’s progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapies. Analytical tools are needed to draw meaningful conclusions from lineage tracing measurements, which are characterized by high variability, sparsity and technical noise. However, the single cell lineage tracing field lacks versatile and easy-to-use tools for standardized and reproducible analyses, in particular tools accessible to biologists. Here we present CellDestiny, a RShiny app and associated web application developed for experimentalists without coding skills to perform visualization and analysis of single cell lineage-tracing datasets through a graphical user interface. We demonstrate the functionality of CellDestiny through the analysis of (i) lentiviral barcoding datasets of murine hematopoietic progenitors; (ii) published integration site data from Wiskott-Aldrich Symdrome patients undergoing gene-therapy treatment; and (iii) simultaneous barcoding and transcriptomic analysis of murine hematopoietic progenitor differentiation in vitro. In summary, CellDestiny is an easy-to-use and versatile toolkit that enables biologists to visualize and analyze single-cell lineage tracing data.
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Affiliation(s)
- Louisa Hadj Abed
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,Centre de Bio-Informatique, MINES ParisTech, Institut Curie, PSL University, Paris, France
| | - Tamar Tak
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,*Correspondence: Jason Cosgrove,
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,Leïla Perié,
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38
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Testa U, Castelli G, Pelosi E. Clonal Hematopoiesis: Role in Hematologic and Non-Hematologic Malignancies. Mediterr J Hematol Infect Dis 2022; 14:e2022069. [PMID: 36119457 PMCID: PMC9448266 DOI: 10.4084/mjhid.2022.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/18/2022] [Indexed: 02/08/2023] Open
Abstract
Hematopoietic stem cells (HSCs) ensure the coordinated and balanced production of all hematopoietic cell types throughout life. Aging is associated with a gradual decline of the self-renewal and regenerative potential of HSCs and with the development of clonal hematopoiesis. Clonal hematopoiesis of indeterminate potential (CHIP) defines the clonal expansion of genetically variant hematopoietic cells bearing one or more gene mutations and/or structural variants (such as copy number alterations). CHIP increases exponentially with age and is associated with cancers, including hematologic neoplasia, cardiovascular and other diseases. The presence of CHIP consistently increases the risk of hematologic malignancy, particularly in individuals who have CHIP in association with peripheral blood cytopenia.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
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39
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Naseem A, Steinberg Z, Cavazza A. Genome editing for primary immunodeficiencies: A therapeutic perspective on Wiskott-Aldrich syndrome. Front Immunol 2022; 13:966084. [PMID: 36059471 PMCID: PMC9433875 DOI: 10.3389/fimmu.2022.966084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Primary immunodeficiency diseases (PIDs) are a group of rare inherited disorders affecting the immune system that can be conventionally treated with allogeneic hematopoietic stem cell transplantation and with experimental autologous gene therapy. With both approaches still facing important challenges, gene editing has recently emerged as a potential valuable alternative for the treatment of genetic disorders and within a relatively short period from its initial development, has already entered some landmark clinical trials aimed at tackling several life-threatening diseases. In this review, we discuss the progress made towards the development of gene editing-based therapeutic strategies for PIDs with a special focus on Wiskott - Aldrich syndrome and outline their main challenges as well as future directions with respect to already established treatments.
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40
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Fu B, Liao J, Chen S, Li W, Wang Q, Hu J, Yang F, Hsiao S, Jiang Y, Wang L, Chen F, Zhang Y, Wang X, Li D, Liu M, Wu Y. CRISPR-Cas9-mediated gene editing of the BCL11A enhancer for pediatric β 0/β 0 transfusion-dependent β-thalassemia. Nat Med 2022; 28:1573-1580. [PMID: 35922667 DOI: 10.1038/s41591-022-01906-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 06/17/2022] [Indexed: 11/09/2022]
Abstract
Gene editing to disrupt the GATA1-binding site at the +58 BCL11A erythroid enhancer could induce γ-globin expression, which is a promising therapeutic strategy to alleviate β-hemoglobinopathy caused by HBB gene mutation. In the present study, we report the preliminary results of an ongoing phase 1/2 trial (NCT04211480) evaluating safety and efficacy of gene editing therapy in children with blood transfusion-dependent β-thalassemia (TDT). We transplanted BCL11A enhancer-edited, autologous, hematopoietic stem and progenitor cells into two children, one carrying the β0/β0 genotype, classified as the most severe type of TDT. Primary endpoints included engraftment, overall survival and incidence of adverse events (AEs). Both patients were clinically well with multilineage engraftment, and all AEs to date were considered unrelated to gene editing and resolved after treatment. Secondary endpoints included achieving transfusion independence, editing rate in bone marrow cells and change in hemoglobin (Hb) concentration. Both patients achieved transfusion independence for >18 months after treatment, and their Hb increased from 8.2 and 10.8 g dl-1 at screening to 15.0 and 14.0 g dl-1 at the last visit, respectively, with 85.46% and 89.48% editing persistence in bone marrow cells. Exploratory analysis of single-cell transcriptome and indel patterns in edited peripheral blood mononuclear cells showed no notable side effects of the therapy.
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Affiliation(s)
- Bin Fu
- Xiangya Hospital, Central South University, Hunan, China.
| | - Jiaoyang Liao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuanghong Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Wei Li
- Bioray Laboratories Inc., Shanghai, China
| | - Qiudao Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jian Hu
- Xiangya Hospital, Central South University, Hunan, China
| | - Fei Yang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shenlin Hsiao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yanhong Jiang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Liren Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Fangping Chen
- Xiangya Hospital, Central South University, Hunan, China
| | - Yuanjin Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xin Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China. .,Bioray Laboratories Inc., Shanghai, China.
| | - Mingyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China. .,Bioray Laboratories Inc., Shanghai, China.
| | - Yuxuan Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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41
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Palamenghi M, De Luca M, De Rosa L. The steep uphill path leading to ex vivo gene therapy for genodermatoses. Am J Physiol Cell Physiol 2022; 323:C896-C906. [PMID: 35912986 DOI: 10.1152/ajpcell.00117.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cell therapy, gene therapy and tissue engineering have the potential to revolutionize the field of regenerative medicine. In particular, gene therapy is understood as the therapeutical correction of mutated genes by addition of a correct copy of the gene or site-specific gene modifications. Gene correction of somatic stem cells sustaining renewing tissues is critical to ensure long-term clinical success of ex vivo gene therapy. To date, remarkable clinical outcomes arose from combined ex vivo cell and gene therapy of different genetic diseases, such as immunodeficiencies and genodermatoses. Despite the efforts of researchers around the world, only few of these advanced approaches has yet made it to routine therapy. In fact, gene therapy poses one of the greatest technical challenges in modern medicine, spanning safety and efficacy issues, regulatory constraints, registration and market access, all of which need to be addressed to make the therapy available to rare disease patients. In this review, we survey at some of the main challenges in the development of combined cell and gene therapy of genetic skin diseases.
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Affiliation(s)
- Michele Palamenghi
- Centre for Regenerative Medicine "Stefano Ferrari", University of Modena and Reggio Emilia, Modena, Italy
| | - Michele De Luca
- Centre for Regenerative Medicine "Stefano Ferrari", University of Modena and Reggio Emilia, Modena, Italy
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42
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Leonard A, Tisdale JF, Bonner M. Gene Therapy for Hemoglobinopathies. Hematol Oncol Clin North Am 2022; 36:769-795. [DOI: 10.1016/j.hoc.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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43
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Konturek-Ciesla A, Bryder D. Stem Cells, Hematopoiesis and Lineage Tracing: Transplantation-Centric Views and Beyond. Front Cell Dev Biol 2022; 10:903528. [PMID: 35573680 PMCID: PMC9091331 DOI: 10.3389/fcell.2022.903528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/12/2022] [Indexed: 12/26/2022] Open
Abstract
An appropriate production of mature blood cells, or hematopoiesis, is essential for organismal health and homeostasis. In this developmental cascade, hematopoietic stem cells (HSCs) differentiate into intermediate progenitor types, that subsequently give rise to the many distinct blood cell lineages. Here, we describe tools and methods that permit for temporal and native clonal-level HSC lineage tracing in the mouse, and that can now be combined with emerging single-cell molecular analyses. We integrate new insights derived from such experimental paradigms with past knowledge, which has predominantly been derived from transplantation-based approaches. Finally, we outline current knowledge and novel strategies derived from studies aimed to trace human HSC-derived hematopoiesis.
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44
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Gotzhein F, Aranyossy T, Thielecke L, Sonntag T, Thaden V, Fehse B, Müller I, Glauche I, Cornils K. The Reconstitution Dynamics of Cultivated Hematopoietic Stem Cells and Progenitors Is Independent of Age. Int J Mol Sci 2022; 23:ijms23063160. [PMID: 35328579 PMCID: PMC8948791 DOI: 10.3390/ijms23063160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/10/2022] Open
Abstract
Hematopoietic stem cell transplantation (HSCT) represents the only curative treatment option for numerous hematologic malignancies. While the influence of donor age and the composition of the graft have already been examined in clinical and preclinical studies, little information is available on the extent to which different hematological subpopulations contribute to the dynamics of the reconstitution process and on whether and how these contributions are altered with age. In a murine model of HSCT, we therefore simultaneously tracked different cultivated and transduced hematopoietic stem and progenitor cell (HSPC) populations using a multicolor-coded barcode system (BC32). We studied a series of age-matched and age-mismatched transplantations and compared the influence of age on the reconstitution dynamics. We show that reconstitution from these cultured and assembled grafts was substantially driven by hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) independent of age. The reconstitution patterns were polyclonal and stable in all age groups independently of the variability between individual animals, with higher output rates from MPPs than from HSCs. Our experiments suggest that the dynamics of reconstitution and the contribution of cultured and individually transduced HSPC subpopulations are largely independent of age. Our findings support ongoing efforts to expand the application of HSCT in older individuals as a promising strategy to combat hematological diseases, including gene therapy applications.
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Affiliation(s)
- Frauke Gotzhein
- Clinic of Pediatric Hematology and Oncology, Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.G.); (V.T.); (I.M.)
- Research Institute Children’s Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Tim Aranyossy
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (T.A.); (T.S.); (B.F.)
| | - Lars Thielecke
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (L.T.); (I.G.)
| | - Tanja Sonntag
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (T.A.); (T.S.); (B.F.)
| | - Vanessa Thaden
- Clinic of Pediatric Hematology and Oncology, Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.G.); (V.T.); (I.M.)
- Research Institute Children’s Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (T.A.); (T.S.); (B.F.)
| | - Ingo Müller
- Clinic of Pediatric Hematology and Oncology, Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.G.); (V.T.); (I.M.)
- Research Institute Children’s Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (L.T.); (I.G.)
| | - Kerstin Cornils
- Clinic of Pediatric Hematology and Oncology, Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.G.); (V.T.); (I.M.)
- Research Institute Children’s Cancer Center Hamburg, 20251 Hamburg, Germany
- Correspondence: ; Tel.: +49-40-7410-52721
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45
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Karuppusamy KV, Demosthenes JP, Venkatesan V, Christopher AC, Babu P, Azhagiri MK, Jacob A, Ramalingam VV, Rangaraj S, Murugesan MK, Marepally SK, Varghese GM, Srivastava A, Kannangai R, Thangavel S. The CCR5 Gene Edited CD34+CD90+ Hematopoietic Stem Cell Population Serves as an Optimal Graft Source for HIV Gene Therapy. Front Immunol 2022; 13:792684. [PMID: 35359982 PMCID: PMC8963924 DOI: 10.3389/fimmu.2022.792684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Transplantation of allogenic hematopoietic stem and progenitor cells (HSPCs) with C-C chemokine receptor type 5 (CCR5) Δ32 genotype generates HIV-1 resistant immune cells. CCR5 gene edited autologous HSPCs can be a potential alternative to hematopoietic stem cell transplantation (HSCT) from HLA-matched CCR5 null donor. However, the clinical application of gene edited autologous HSPCs is critically limited by the quality of the graft, as HIV also infects the HSPCs. In this study, by using mobilized HSPCs from healthy donors, we show that the CD34+CD90+ hematopoietic stem cells (HSCs) express 7-fold lower CD4/CCR5 HIV receptors, higher levels of SAMHD1 anti-viral restriction factor, and possess lower susceptibility to HIV infection than the CD34+CD90- hematopoietic progenitor cells. Further, the treatment with small molecule cocktail of Resveratrol, UM729 and SR1(RUS) improved the in vivo engraftment potential of CD34+CD90+ HSCs. To demonstrate that CD34+CD90+ HSC population as an ideal graft for HIV gene therapy, we sort purified CD34+CD90+ HSCs, treated with RUS and then gene edited the CCR5 with single sgRNA. On transplantation, 100,000 CD34+CD90+ HSCs were sufficient for long-term repopulation of the entire bone marrow of NBSGW mice. Importantly, the gene editing efficiency of ~90% in the infused product was maintained in vivo, facilitating the generation of CCR5 null immune cells, resistant to HIV infection. Altogether, CCR5 gene editing of CD34+CD90+ HSCs provide an ideal gene manipulation strategy for autologous HSCT based gene therapy for HIV infection.
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Affiliation(s)
- Karthik V. Karuppusamy
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | | | - Vigneshwaran Venkatesan
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Abisha Crystal Christopher
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Vellore, India
- Thiruvalluvar University, Vellore, India
| | - Prathibha Babu
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Manojkumar K. Azhagiri
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Annlin Jacob
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | | | - Sumathi Rangaraj
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Vellore, India
| | | | | | - George M. Varghese
- Department of Infectious Diseases, Christian Medical College, Vellore, India
| | - Alok Srivastava
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Vellore, India
- Department of Hematology, Christian Medical College, Vellore, India
| | - Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Vellore, India
- *Correspondence: Saravanabhavan Thangavel,
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46
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Del Core L, Cesana D, Gallina P, Secanechia YNS, Rudilosso L, Montini E, Wit EC, Calabria A, Grzegorczyk MA. Normalization of clonal diversity in gene therapy studies using shape constrained splines. Sci Rep 2022; 12:3836. [PMID: 35264585 PMCID: PMC8907296 DOI: 10.1038/s41598-022-05837-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 12/09/2021] [Indexed: 12/27/2022] Open
Abstract
Viral vectors are used to insert genetic material into semirandom genomic positions of hematopoietic stem cells which, after reinfusion into patients, regenerate the entire hematopoietic system. Hematopoietic cells originating from genetically modified stem cells will harbor insertions in specific genomic positions called integration sites, which represent unique genetic marks of clonal identity. Therefore, the analysis of vector integration sites present in the genomic DNA of circulating cells allows to determine the number of clones in the blood ecosystem. Shannon diversity index is adopted to evaluate the heterogeneity of the transduced population of gene corrected cells. However, this measure can be affected by several technical variables such as the DNA amount used and the sequencing depth of the library analyzed and therefore the comparison across samples may be affected by these confounding factors. We developed an advanced spline-regression approach that leverages on confounding effects to provide a normalized entropy index. Our proposed method was first validated and compared with two state of the art approaches in a specifically designed in vitro assay. Subsequently our approach allowed to observe the expected impact of vector genotoxicity on entropy level decay in an in vivo model of hematopoietic stem cell gene therapy based on tumor prone mice.
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Affiliation(s)
- L Del Core
- University of Groningen - Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, Groningen, Netherlands. .,IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy.
| | - D Cesana
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - P Gallina
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Y N Serina Secanechia
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - L Rudilosso
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - E Montini
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - E C Wit
- Università della Svizzera italiana - Institute of Computing, Lugano, Switzerland.
| | - A Calabria
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy.
| | - M A Grzegorczyk
- University of Groningen - Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, Groningen, Netherlands.
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47
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Post-natal conservation of human blood and marrow-specific CD34+ hematopoietic phenotypes. Exp Hematol 2022; 109:18-26. [DOI: 10.1016/j.exphem.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 11/18/2022]
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48
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Rodriguez Y Baena A, Rajendiran S, Manso BA, Krietsch J, Boyer SW, Kirschmann J, Forsberg EC. New transgenic mouse models enabling pan-hematopoietic or selective hematopoietic stem cell depletion in vivo. Sci Rep 2022; 12:3156. [PMID: 35210475 PMCID: PMC8873235 DOI: 10.1038/s41598-022-07041-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/07/2022] [Indexed: 12/22/2022] Open
Abstract
Hematopoietic stem cell (HSC) multipotency and self-renewal are typically defined through serial transplantation experiments. Host conditioning is necessary for robust HSC engraftment, likely by reducing immune-mediated rejection and by clearing limited HSC niche space. Because irradiation of the recipient mouse is non-specific and broadly damaging, there is a need to develop alternative models to study HSC performance at steady-state and in the absence of radiation-induced stress. We have generated and characterized two new mouse models where either all hematopoietic cells or only HSCs can be specifically induced to die in vivo or in vitro. Hematopoietic-specific Vav1-mediated expression of a loxP-flanked diphtheria-toxin receptor (DTR) renders all hematopoietic cells sensitive to diphtheria toxin (DT) in “Vav-DTR” mice. Crossing these mice to Flk2-Cre mice results in “HSC-DTR” mice which exhibit HSC-selective DT sensitivity. We demonstrate robust, rapid, and highly selective cell ablation in these models. These new mouse models provide a platform to test whether HSCs are required for long-term hematopoiesis in vivo, for understanding the mechanisms regulating HSC engraftment, and interrogating in vivo hematopoietic differentiation pathways and mechanisms regulating hematopoietic homeostasis.
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Affiliation(s)
- Alessandra Rodriguez Y Baena
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA.,Program in Biomedical Sciences and Engineering, Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Smrithi Rajendiran
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA.,Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Bryce A Manso
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA.,Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jana Krietsch
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA.,Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Scott W Boyer
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA.,Program in Biomedical Sciences and Engineering, Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jessica Kirschmann
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA
| | - E Camilla Forsberg
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA. .,Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA.
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49
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Aging and Clonal Behavior of Hematopoietic Stem Cells. Int J Mol Sci 2022; 23:ijms23041948. [PMID: 35216063 PMCID: PMC8878540 DOI: 10.3390/ijms23041948] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 12/19/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are the only cell population that possesses both a self-renewing capacity and multipotency, and can give rise to all lineages of blood cells throughout an organism’s life. However, the self-renewal capacity of HSCs is not infinite, and cumulative evidence suggests that HSCs alter their function and become less active during organismal aging, leading ultimately to the disruption of hematopoietic homeostasis, such as anemia, perturbed immunity and increased propensity to hematological malignancies. Thus, understanding how HSCs alter their function during aging is a matter of critical importance to prevent or overcome these age-related changes in the blood system. Recent advances in clonal analysis have revealed the functional heterogeneity of murine HSC pools that is established upon development and skewed toward the clonal expansion of functionally poised HSCs during aging. In humans, next-generation sequencing has revealed age-related clonal hematopoiesis that originates from HSC subsets with acquired somatic mutations, and has highlighted it as a significant risk factor for hematological malignancies and cardiovascular diseases. In this review, we summarize the current fate-mapping strategies that are used to track and visualize HSC clonal behavior during development or after stress. We then review the age-related changes in HSCs that can be inherited by daughter cells and act as a cellular memory to form functionally distinct clones. Altogether, we link aging of the hematopoietic system to HSC clonal evolution and discuss how HSC clones with myeloid skewing and low regenerative potential can be expanded during aging.
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50
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Nishi K, Sakamaki T, Sadaoka K, Fujii M, Takaori-Kondo A, Chen JY, Miyanishi M. Identification of the minimum requirements for successful haematopoietic stem cell transplantation. Br J Haematol 2021; 196:711-723. [PMID: 34927242 PMCID: PMC9300074 DOI: 10.1111/bjh.17867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 11/26/2022]
Abstract
Historically, defining haematopoietic subsets, including self‐renewal, differentiation and lineage restriction, has been elucidated by transplanting a small number of candidate cells with many supporting bone marrow (BM) cells. While this approach has been invaluable in characterising numerous distinct subsets in haematopoiesis, this approach is arguably flawed. The haematopoietic stem cell (HSC) has been proposed as the critical haematopoietic subset necessary for transplantation. However, due to the presence of supporting cells, the HSC has never demonstrated sufficiency. Utilising the homeobox B5 (Hoxb5)‐reporter system, we found that neither long‐term (LT) HSCs nor short‐term (ST) HSCs alone were sufficient for long‐term haematopoietic reconstitution. Critically, reconstitution can be rescued by transplanting combined LT‐ and ST‐HSCs, without supporting cells; a fraction we term the ‘Minimum Subset for Transplantation’ (MST). The MST accounts for only 0·005% of nucleated cells within mouse BM, and this MST can be cultured, expanded and genetically modified while preserving its rapid haematopoietic engraftment potential. These results support the consideration of an MST approach for clinical translation, especially for gene therapy approaches that require HSC compartment modification.
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Affiliation(s)
- Katsuyuki Nishi
- RIKEN Centre for Biosystems Dynamics Research, Kobe, Hyogo, Japan.,Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Taro Sakamaki
- RIKEN Centre for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Kay Sadaoka
- RIKEN Centre for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Momo Fujii
- RIKEN Centre for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - James Y Chen
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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