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Aertgeerts M, Meyers S, Demeyer S, Segers H, Cools J. Unlocking the Complexity: Exploration of Acute Lymphoblastic Leukemia at the Single Cell Level. Mol Diagn Ther 2024:10.1007/s40291-024-00739-5. [PMID: 39190087 DOI: 10.1007/s40291-024-00739-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2024] [Indexed: 08/28/2024]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children. ALL originates from precursor lymphocytes that acquire multiple genomic changes over time, including chromosomal rearrangements and point mutations. While a large variety of genomic defects was identified and characterized in ALL over the past 30 years, it was only in recent years that the clonal heterogeneity was recognized. Thanks to the latest advancements in single-cell sequencing techniques, which have evolved from the analysis of a few hundred cells to the analysis of thousands of cells simultaneously, the study of tumor heterogeneity now becomes possible. Different modalities can be explored at the single-cell level: DNA, RNA, epigenetic modifications, and intracellular and cell surface proteins. In this review, we describe these techniques and highlight their advantages and limitations in the study of ALL biology. Moreover, multiomics technologies and the incorporation of the spatial dimension can provide insight into intercellular communication. We describe how the different single-cell sequencing technologies help to unravel the molecular complexity of ALL, shedding light on its development, its heterogeneity, its interaction with the leukemia microenvironment and possible relapse mechanisms.
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Affiliation(s)
- Margo Aertgeerts
- Department of Oncology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven-UZ Leuven, Leuven, Belgium
| | - Sarah Meyers
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven-UZ Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven-UZ Leuven, Leuven, Belgium
| | - Heidi Segers
- Department of Oncology, KU Leuven, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven-UZ Leuven, Leuven, Belgium.
- Department of Pediatric Hematology and Oncology, UZ Leuven, Leuven, Belgium.
| | - Jan Cools
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven-UZ Leuven, Leuven, Belgium.
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2
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Chen S, Looney MR. Understanding megakaryocyte phenotypes and the impact on platelet biogenesis. Transfusion 2024; 64:1372-1380. [PMID: 38923572 PMCID: PMC11251837 DOI: 10.1111/trf.17927] [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: 10/31/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 06/28/2024]
Affiliation(s)
- Shiyu Chen
- Departments of Medicine and Laboratory Medicine, University
of California, San Francisco, San Francisco, CA, U.SA
| | - Mark R. Looney
- Departments of Medicine and Laboratory Medicine, University
of California, San Francisco, San Francisco, CA, U.SA
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3
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Allaeys I, Lemaire G, Leclercq M, Lacasse E, Fleury M, Dubuc I, Gudimard L, Puhm F, Tilburg J, Stone A, Machlus KR, Droit A, Flamand L, Boilard E. SARS-CoV-2 infection modifies the transcriptome of the megakaryocytes in the bone marrow. Blood Adv 2024; 8:2777-2789. [PMID: 38522092 PMCID: PMC11176959 DOI: 10.1182/bloodadvances.2023012367] [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: 12/07/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/26/2024] Open
Abstract
ABSTRACT Megakaryocytes (MKs), integral to platelet production, predominantly reside in the bone marrow (BM) and undergo regulated fragmentation within sinusoid vessels to release platelets into the bloodstream. Inflammatory states and infections influence MK transcription, potentially affecting platelet functionality. Notably, COVID-19 has been associated with altered platelet transcriptomes. In this study, we investigated the hypothesis that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection could affect the transcriptome of BM MKs. Using spatial transcriptomics to discriminate subpopulations of MKs based on proximity to BM sinusoids, we identified ∼19 000 genes in MKs. Machine learning techniques revealed that the transcriptome of healthy murine BM MKs exhibited minimal differences based on proximity to sinusoid vessels. Furthermore, at peak SARS-CoV-2 viremia, when the disease primarily affected the lungs, MKs were not significantly different from those from healthy mice. Conversely, a significant divergence in the MK transcriptome was observed during systemic inflammation, although SARS-CoV-2 RNA was never detected in the BM, and it was no longer detectable in the lungs. Under these conditions, the MK transcriptional landscape was enriched in pathways associated with histone modifications, MK differentiation, NETosis, and autoimmunity, which could not be explained by cell proximity to sinusoid vessels. Notably, the type I interferon signature and calprotectin (S100A8/A9) were not induced in MKs under any condition. However, inflammatory cytokines induced in the blood and lungs of COVID-19 mice were different from those found in the BM, suggesting a discriminating impact of inflammation on this specific subset of cells. Collectively, our data indicate that a new population of BM MKs may emerge through COVID-19-related pathogenesis.
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Affiliation(s)
- Isabelle Allaeys
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
- Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Faculté de Médecine de l'Université Laval, Québec, QC, Canada
| | - Guillaume Lemaire
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
- Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Faculté de Médecine de l'Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
| | - Emile Lacasse
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
- Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Faculté de Médecine de l'Université Laval, Québec, QC, Canada
| | - Maude Fleury
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
- Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Faculté de Médecine de l'Université Laval, Québec, QC, Canada
| | - Isabelle Dubuc
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
- Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Faculté de Médecine de l'Université Laval, Québec, QC, Canada
| | - Leslie Gudimard
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
- Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Faculté de Médecine de l'Université Laval, Québec, QC, Canada
| | - Florian Puhm
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
- Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Faculté de Médecine de l'Université Laval, Québec, QC, Canada
| | - Julia Tilburg
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA
| | - Andrew Stone
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA
| | - Kellie R. Machlus
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA
| | - Arnaud Droit
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
| | - Louis Flamand
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
- Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Faculté de Médecine de l'Université Laval, Québec, QC, Canada
| | - Eric Boilard
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
- Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Faculté de Médecine de l'Université Laval, Québec, QC, Canada
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Caetano CCS, Azamor T, Meyer NM, Onwubueke C, Calabrese CM, Calabrese LH, Visperas A, Piuzzi NS, Husni ME, Foo SS, Chen W. Mechanistic insights into bone remodelling dysregulation by human viral pathogens. Nat Microbiol 2024; 9:322-335. [PMID: 38316931 PMCID: PMC11045166 DOI: 10.1038/s41564-023-01586-6] [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: 05/13/2022] [Accepted: 12/12/2023] [Indexed: 02/07/2024]
Abstract
Bone-related diseases (osteopathologies) associated with human virus infections have increased around the globe. Recent findings have highlighted the intricate interplay between viral infection, the host immune system and the bone remodelling process. Viral infections can disrupt bone homeostasis, contributing to conditions such as arthritis and soft tissue calcifications. Osteopathologies can occur after arbovirus infections such as chikungunya virus, dengue virus and Zika virus, as well as respiratory viruses, such as severe acute respiratory syndrome coronavirus 2 and enteroviruses such as Coxsackievirus B. Here we explore how human viruses dysregulate bone homeostasis, detailing viral factors, molecular mechanisms, host immune response changes and bone remodelling that ultimately result in osteopathologies. We highlight model systems and technologies to advance mechanistic understanding of viral-mediated bone alterations. Finally, we propose potential prophylactic and therapeutic strategies, introduce 'osteovirology' as a research field highlighting the underestimated roles of viruses in bone-related diseases, and discuss research avenues for further investigation.
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Affiliation(s)
- Camila C S Caetano
- Infection Biology Program, Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Tamiris Azamor
- Infection Biology Program, Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nikki M Meyer
- Infection Biology Program, Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Chineme Onwubueke
- Infection Biology Program, Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Cassandra M Calabrese
- Department of Rheumatic and Immunologic Diseases, Cleveland Clinic, Cleveland, OH, USA
| | - Leonard H Calabrese
- Department of Rheumatic and Immunologic Diseases, Cleveland Clinic, Cleveland, OH, USA
| | - Anabelle Visperas
- Department of Orthopedic Surgery, Cleveland Clinic, Cleveland, OH, USA
| | - Nicolas S Piuzzi
- Department of Orthopedic Surgery, Cleveland Clinic, Cleveland, OH, USA
| | - M Elaine Husni
- Department of Rheumatic and Immunologic Diseases, Cleveland Clinic, Cleveland, OH, USA
| | - Suan-Sin Foo
- Infection Biology Program, Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| | - Weiqiang Chen
- Infection Biology Program, Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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5
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Puhm F, Laroche A, Boilard E. Diversity of Megakaryocytes. Arterioscler Thromb Vasc Biol 2023; 43:2088-2098. [PMID: 37675634 DOI: 10.1161/atvbaha.123.318782] [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: 05/17/2023] [Accepted: 08/14/2023] [Indexed: 09/08/2023]
Abstract
Megakaryocytes are commonly known as large, polyploid, bone marrow resident cells that contribute to hemostasis through the production of platelets. Soon after their discovery in the 19th century, megakaryocytes were described in tissue locations other than the bone marrow, specifically in the lungs and the blood circulation. However, the localization of megakaryocytes in the lungs and the contribution of lung megakaryocytes to the general platelet pool has only recently been appreciated. Moreover, the conception of megakaryocytes as uniform cells with the sole purpose of platelet production has been challenged. Here, we review the literature on megakaryocyte cell identity and location with a special focus on recent observations of megakaryocyte subpopulations identified by transcriptomic analyses.
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Affiliation(s)
- Florian Puhm
- Department of Infectious Diseases and Immunity, Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Canada (F.P., A.L., E.B.)
- Centre de Recherche ARThrite, Faculté de Médecine de l'Université Laval, Québec, Canada (F.P., A.L., E.B.)
| | - Audrée Laroche
- Department of Infectious Diseases and Immunity, Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Canada (F.P., A.L., E.B.)
- Centre de Recherche ARThrite, Faculté de Médecine de l'Université Laval, Québec, Canada (F.P., A.L., E.B.)
| | - Eric Boilard
- Department of Infectious Diseases and Immunity, Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Canada (F.P., A.L., E.B.)
- Centre de Recherche ARThrite, Faculté de Médecine de l'Université Laval, Québec, Canada (F.P., A.L., E.B.)
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