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Thorsson H, Henningsson R, Puente-Moncada N, Peña-Martínez P, Sjöström L, Ågerstam H, Sandén C, Rissler M, Castor A, Marquart H, Modvig S, Paulsson K, Pronk CJ, Schmiegelow K, Hyrenius-Wittsten A, Orsmark-Pietras C, Lilljebjörn H, Fioretos T. Single-cell genomics details the maturation block in BCP-ALL and identifies therapeutic vulnerabilities in DUX4-r cases. Blood 2024; 144:1399-1411. [PMID: 38968149 PMCID: PMC11451301 DOI: 10.1182/blood.2023021705] [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: 07/10/2023] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024] Open
Abstract
ABSTRACT B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) is the most common childhood malignancy and is driven by multiple genetic alterations that cause maturation arrest and accumulation of abnormal progenitor B cells. Current treatment protocols with chemotherapy have led to favorable outcomes but are associated with significant toxicity and risk of side effects, highlighting the necessity for highly effective, less toxic, targeted drugs, even in subtypes with a favorable outcome. Here, we used multimodal single-cell sequencing to delineate the transcriptional, epigenetic, and immunophenotypic characteristics of 23 childhood BCP-ALLs belonging to the BCR::ABL1+, ETV6::RUNX1+, high hyperdiploid, and recently discovered DUX4-rearranged (DUX4-r) subtypes. Projection of the ALL cells along the normal hematopoietic differentiation axis revealed a diversity in the maturation pattern between the different BCP-ALL subtypes. Although the BCR::ABL1+, ETV6::RUNX1+, and high hyperdiploidy cells mainly showed similarities to normal pro-B cells, DUX4-r ALL cells also displayed transcriptional signatures resembling mature B cells. Focusing on the DUX4-r subtype, we found that the blast population displayed not only multilineage priming toward nonhematopoietic cells, myeloid, and T-cell lineages, but also an activation of phosphatidylinositol 3-kinase (PI3K)/AKT signaling that sensitized the cells to PI3K inhibition in vivo. Given the multilineage priming of DUX4-r blasts with aberrant expression of myeloid marker CD371 (CLL-1), we generated chimeric antigen receptor T cells, which effectively eliminated DUX4-r ALL cells in vivo. These results provide a detailed characterization of BCP-ALL at the single-cell level and reveal therapeutic vulnerabilities in the DUX4-r subtype, with implications for the understanding of ALL biology and new therapeutic strategies.
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Affiliation(s)
- Hanna Thorsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Rasmus Henningsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Noelia Puente-Moncada
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Pablo Peña-Martínez
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ludvig Sjöström
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Helena Ågerstam
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Carl Sandén
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Marianne Rissler
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Castor
- Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
| | - Hanne Marquart
- Department of Clinical Medicine, Copenhagen University, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Signe Modvig
- Department of Clinical Medicine, Copenhagen University, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kajsa Paulsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Kjeld Schmiegelow
- Department of Clinical Medicine, Copenhagen University, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, The Juliane Marie Centre, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Axel Hyrenius-Wittsten
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Christina Orsmark-Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
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2
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Bełdzińska-Gądek K, Zarzycka E, Pastuszak K, Borman K, Lewandowski K, Zaucha JM, Prejzner W. Immune escape of B-cell lymphoblastic leukemic cells through a lineage switch to acute myeloid leukemia. Leuk Lymphoma 2024; 65:1292-1302. [PMID: 38775354 DOI: 10.1080/10428194.2024.2351194] [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: 10/24/2023] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 08/31/2024]
Abstract
Acute leukemia (AL) with a lineage switch (LS) is associated with poor prognosis. The predisposing factors of LS are unknown, apart from KMT2A rearrangements that have been reported to be associated with LS. Herein, we present two cases and review all 104 published cases to identify risk factors for LS. Most of the patients (75.5%) experienced a switch from the lymphoid phenotype to the myeloid phenotype. Eighteen patients (17.0%) experienced a transformation from acute myelogenous leukemia (AML) to acute lymphoblastic leukemia (ALL). Forty-nine (46.2%) patients carried a KMT2A rearrangement. Most of the cases involved LS from B-cell ALL (B-ALL) to AML (59.4%), and 49 patients (46.2%) carried KMT2A-rearrangements. Forty patients (37.7%) received lineage-specific immunotherapy. Our findings suggest that the prevalence of KMT2A rearrangements together with the lineage-specific immunotherapy may trigger LS, which supports the thesis of the existence of leukemia stem cells that are capable of lymphoid or myeloid differentiation.
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MESH Headings
- Humans
- Cell Lineage/genetics
- Cell Lineage/immunology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Gene Rearrangement/immunology
- Histone-Lysine N-Methyltransferase/genetics
- Immunophenotyping
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Myeloid-Lymphoid Leukemia Protein/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/diagnosis
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Tumor Escape/genetics
- Tumor Escape/immunology
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Affiliation(s)
- Karolina Bełdzińska-Gądek
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
- First Doctoral School, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Zarzycka
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Krzysztof Pastuszak
- Department of Algorithms and System Modelling, Gdansk University of Technology, Gdansk, Poland
- Department of Translational Oncology, Medical University of Gdańsk, Gdansk, Poland
- Centre of Biostatistics and Bioinformatics, Medical University of Gdańsk, Gdansk, Poland
| | - Katarzyna Borman
- Intercollegiate Biotechnology Doctoral School, University of Gdańsk and Medical University of Gdańsk, Gdansk, Poland
| | | | - Jan M Zaucha
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Witold Prejzner
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
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3
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Jamroze A, Liu X, Tang DG. Treatment-induced stemness and lineage plasticity in driving prostate cancer therapy resistance. CANCER HETEROGENEITY AND PLASTICITY 2024; 1:0005. [PMID: 39363904 PMCID: PMC11449474 DOI: 10.47248/chp2401010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
Most human cancers are heterogeneous consisting of cancer cells at different epigenetic and transcriptional states and with distinct phenotypes, functions, and drug sensitivities. This inherent cancer cell heterogeneity contributes to tumor resistance to clinical treatment, especially the molecularly targeted therapies such as tyrosine kinase inhibitors (TKIs) and androgen receptor signaling inhibitors (ARSIs). Therapeutic interventions, in turn, induce lineage plasticity (also called lineage infidelity) in cancer cells that also drives therapy resistance. In this Perspective, we focus our discussions on cancer cell lineage plasticity manifested as treatment-induced switching of epithelial cancer cells to basal/stem-like, mesenchymal, and neural lineages. We employ prostate cancer (PCa) as the prime example to highlight ARSI-induced lineage plasticity during and towards development of castration-resistant PCa (CRPC). We further discuss how the tumor microenvironment (TME) influences therapy-induced lineage plasticity. Finally, we offer an updated summary on the regulators and mechanisms driving cancer cell lineage infidelity, which should be therapeutically targeted to extend the therapeutic window and improve patients' survival.
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Affiliation(s)
- Anmbreen Jamroze
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Xiaozhuo Liu
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Dean G. Tang
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Experimental Therapeutics (ET) Graduate Program, University at Buffalo & Roswell Park Comprehensive Cancer Center, NY 14263, USA
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4
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Janssens DH, Duran M, Otto DJ, Wu W, Xu Y, Kirkey D, Mullighan CG, Yi JS, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S. KMT2A oncoproteins induce epigenetic resistance to targeted therapies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.29.573681. [PMID: 38234854 PMCID: PMC10793413 DOI: 10.1101/2023.12.29.573681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Chromosomal translocations involving the Lysine-Methyl-Transferase-2A ( KMT2A ) locus generate potent oncogenic fusion proteins (oncoproteins) that disrupt regulation of developmental gene expression. By profiling the oncoprotein-target sites of 36 broadly representative KMT2A -rearranged leukemia samples, including three samples that underwent a lymphoid-to-myeloid lineage-switching event in response to therapy, we find the genomic enrichment of the oncoprotein is highly variable between samples and subject to dynamic regulation. At high levels of expression, the oncoproteins preferentially activate either an acute lymphoblastic leukemia (ALL) program, enriched for pro-B-cell genes, or an acute myeloid leukemia (AML) program, enriched for hematopoietic-stem-cell genes. The fusion-partner-specific-binding patterns over these gene sets are highly correlated with the prevalence of each mutation in ALL versus AML. In lineage-switching samples the oncoprotein levels are reduced and the oncoproteins preferentially activate granulocyte-monocyte progenitor (GMP) genes. In a sample that lineage switched during treatment with the menin inhibitor revumenib, the oncoprotein and menin are reduced to undetectable levels, but ENL, a transcriptional cofactor of the oncoprotein, persists on numerous oncoprotein-target loci, including genes in the GMP-like lineage-switching program. We propose KMT2A oncoproteins promote lineage-switching events through dynamic chromatin binding and can induce epigenetic lesions, marked by ENL, that support resistance to targeted therapies.
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5
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Jeong Y, Ronen J, Kopp W, Lutsik P, Akalin A. scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data. BMC Bioinformatics 2024; 25:257. [PMID: 39107690 PMCID: PMC11304929 DOI: 10.1186/s12859-024-05880-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
The recent advances in high-throughput single-cell sequencing have created an urgent demand for computational models which can address the high complexity of single-cell multiomics data. Meticulous single-cell multiomics integration models are required to avoid biases towards a specific modality and overcome sparsity. Batch effects obfuscating biological signals must also be taken into account. Here, we introduce a new single-cell multiomics integration model, Single-cell Multiomics Autoencoder Integration (scMaui) based on variational product-of-experts autoencoders and adversarial learning. scMaui calculates a joint representation of multiple marginal distributions based on a product-of-experts approach which is especially effective for missing values in the modalities. Furthermore, it overcomes limitations seen in previous VAE-based integration methods with regard to batch effect correction and restricted applicable assays. It handles multiple batch effects independently accepting both discrete and continuous values, as well as provides varied reconstruction loss functions to cover all possible assays and preprocessing pipelines. We demonstrate that scMaui achieves superior performance in many tasks compared to other methods. Further downstream analyses also demonstrate its potential in identifying relations between assays and discovering hidden subpopulations.
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Affiliation(s)
- Yunhee Jeong
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
- Faculty of Mathematics and Informatics, Heidelberg University, Im Neuenheimer Feld 205, Heidelberg, Germany
| | - Jonathan Ronen
- Bioinformatics and Omics Data Science Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Inceptive Nucleics, Inc., Palo Alto, CA, USA
| | - Wolfgang Kopp
- Bioinformatics and Omics Data Science Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Roche Diagnostics GmbH, Penzberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany.
- Department of Oncology, Catholic University (KU) Leuven, Leuven, Belgium.
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany.
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6
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de Bruijn I, Nikolov M, Lau C, Clayton A, Gibbs DL, Mitraka E, Pozhidayeva D, Lash A, Sumer SO, Altreuter J, Anton K, DeFelice M, Li X, Lisman A, R Longabaugh WJ, Muhlich J, Santagata S, Nandakumar S, Sorger PK, Suver C, Schultz N, Taylor AJ, Thorsson V, Cerami E, Eddy JA. Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure, and Community Engagement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.598921. [PMID: 38979389 PMCID: PMC11230241 DOI: 10.1101/2024.06.25.598921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The Data Coordinating Center (DCC) of the Human Tumor Atlas Network (HTAN) has played a crucial role in enabling the broad sharing and effective utilization of HTAN data within the scientific community. Data from the first phase of HTAN are now available publicly. We describe the diverse datasets and modalities shared, multiple access routes to HTAN assay data and metadata, data standards, technical infrastructure and governance approaches, as well as our approach to sustained community engagement. HTAN data can be accessed via the HTAN Portal, explored in visualization tools-including CellxGene, Minerva, and cBioPortal-and analyzed in the cloud through the NCI Cancer Research Data Commons nodes. We have developed a streamlined infrastructure to ingest and disseminate data by leveraging the Synapse platform. Taken together, the HTAN DCC's approach demonstrates a successful model for coordinating, standardizing, and disseminating complex cancer research data via multiple resources in the cancer data ecosystem, offering valuable insights for similar consortia, and researchers looking to leverage HTAN data.
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7
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Garcia C, Miller-Awe MD, Witkowski MT. Concepts in B cell acute lymphoblastic leukemia pathogenesis. J Leukoc Biol 2024; 116:18-32. [PMID: 38243586 DOI: 10.1093/jleuko/qiae015] [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: 10/26/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024] Open
Abstract
B cell acute lymphoblastic leukemia (B-ALL) arises from genetic alterations impacting B cell progenitors, ultimately leading to clinically overt disease. Extensive collaborative efforts in basic and clinical research have significantly improved patient prognoses. Nevertheless, a subset of patients demonstrate resistance to conventional chemotherapeutic approaches and emerging immunotherapeutic interventions. This review highlights the mechanistic underpinnings governing B-ALL transformation. Beginning with exploring normative B cell lymphopoiesis, we delineate the influence of recurrent germline and somatic genetic aberrations on the perturbation of B cell progenitor differentiation and protumorigenic signaling, thereby facilitating the neoplastic transformation underlying B-ALL progression. Additionally, we highlight recent advances in the multifaceted landscape of B-ALL, encompassing metabolic reprogramming, microbiome influences, inflammation, and the discernible impact of socioeconomic and racial disparities on B-ALL transformation and patient survival.
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Affiliation(s)
- Clarissa Garcia
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States
| | - Megan D Miller-Awe
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States
| | - Matthew T Witkowski
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States
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8
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Bandyopadhyay S, Duffy MP, Ahn KJ, Sussman JH, Pang M, Smith D, Duncan G, Zhang I, Huang J, Lin Y, Xiong B, Imtiaz T, Chen CH, Thadi A, Chen C, Xu J, Reichart M, Martinez Z, Diorio C, Chen C, Pillai V, Snaith O, Oldridge D, Bhattacharyya S, Maillard I, Carroll M, Nelson C, Qin L, Tan K. Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging. Cell 2024; 187:3120-3140.e29. [PMID: 38714197 PMCID: PMC11162340 DOI: 10.1016/j.cell.2024.04.013] [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: 07/03/2023] [Revised: 02/02/2024] [Accepted: 04/12/2024] [Indexed: 05/09/2024]
Abstract
Non-hematopoietic cells are essential contributors to hematopoiesis. However, heterogeneity and spatial organization of these cells in human bone marrow remain largely uncharacterized. We used single-cell RNA sequencing (scRNA-seq) to profile 29,325 non-hematopoietic cells and discovered nine transcriptionally distinct subtypes. We simultaneously profiled 53,417 hematopoietic cells and predicted their interactions with non-hematopoietic subsets. We employed co-detection by indexing (CODEX) to spatially profile over 1.2 million cells. We integrated scRNA-seq and CODEX data to link predicted cellular signaling with spatial proximity. Our analysis revealed a hyperoxygenated arterio-endosteal neighborhood for early myelopoiesis, and an adipocytic localization for early hematopoietic stem and progenitor cells (HSPCs). We used our CODEX atlas to annotate new images and uncovered mesenchymal stromal cell (MSC) expansion and spatial neighborhoods co-enriched for leukemic blasts and MSCs in acute myeloid leukemia (AML) patient samples. This spatially resolved, multiomic atlas of human bone marrow provides a reference for investigation of cellular interactions that drive hematopoiesis.
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Affiliation(s)
- Shovik Bandyopadhyay
- Cellular and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael P Duffy
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kyung Jin Ahn
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jonathan H Sussman
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Minxing Pang
- Applied Mathematics & Computational Science Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - David Smith
- Center for Single Cell Biology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gwendolyn Duncan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Iris Zhang
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeffrey Huang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Yulieh Lin
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Barbara Xiong
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tamjid Imtiaz
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Chia-Hui Chen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Anusha Thadi
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Changya Chen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jason Xu
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Melissa Reichart
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zachary Martinez
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Caroline Diorio
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chider Chen
- Department of Oral and Maxillofacial Surgery/Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vinodh Pillai
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oraine Snaith
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Derek Oldridge
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Siddharth Bhattacharyya
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ivan Maillard
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martin Carroll
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Charles Nelson
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ling Qin
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Kai Tan
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Single Cell Biology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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9
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Malyukova A, Lahnalampi M, Falqués-Costa T, Pölönen P, Sipola M, Mehtonen J, Teppo S, Akopyan K, Viiliainen J, Lohi O, Hagström-Andersson AK, Heinäniemi M, Sangfelt O. Sequential drug treatment targeting cell cycle and cell fate regulatory programs blocks non-genetic cancer evolution in acute lymphoblastic leukemia. Genome Biol 2024; 25:143. [PMID: 38822412 PMCID: PMC11143599 DOI: 10.1186/s13059-024-03260-4] [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: 05/15/2023] [Accepted: 04/26/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Targeted therapies exploiting vulnerabilities of cancer cells hold promise for improving patient outcome and reducing side-effects of chemotherapy. However, efficacy of precision therapies is limited in part because of tumor cell heterogeneity. A better mechanistic understanding of how drug effect is linked to cancer cell state diversity is crucial for identifying effective combination therapies that can prevent disease recurrence. RESULTS Here, we characterize the effect of G2/M checkpoint inhibition in acute lymphoblastic leukemia (ALL) and demonstrate that WEE1 targeted therapy impinges on cell fate decision regulatory circuits. We find the highest inhibition of recovery of proliferation in ALL cells with KMT2A-rearrangements. Single-cell RNA-seq and ATAC-seq of RS4;11 cells harboring KMT2A::AFF1, treated with the WEE1 inhibitor AZD1775, reveal diversification of cell states, with a fraction of cells exhibiting strong activation of p53-driven processes linked to apoptosis and senescence, and disruption of a core KMT2A-RUNX1-MYC regulatory network. In this cell state diversification induced by WEE1 inhibition, a subpopulation transitions to a drug tolerant cell state characterized by activation of transcription factors regulating pre-B cell fate, lipid metabolism, and pre-BCR signaling in a reversible manner. Sequential treatment with BCR-signaling inhibitors dasatinib, ibrutinib, or perturbing metabolism by fatostatin or AZD2014 effectively counteracts drug tolerance by inducing cell death and repressing stemness markers. CONCLUSIONS Collectively, our findings provide new insights into the tight connectivity of gene regulatory programs associated with cell cycle and cell fate regulation, and a rationale for sequential administration of WEE1 inhibitors with low toxicity inhibitors of pre-BCR signaling or metabolism.
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Affiliation(s)
- Alena Malyukova
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 171 77, Stockholm, Sweden.
| | - Mari Lahnalampi
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Ton Falqués-Costa
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Petri Pölönen
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mikko Sipola
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Juha Mehtonen
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Susanna Teppo
- Tampere Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Karen Akopyan
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Johanna Viiliainen
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Olli Lohi
- Tampere Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | | | - Merja Heinäniemi
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland.
| | - Olle Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 171 77, Stockholm, Sweden.
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10
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Xu Z, Qu HQ, Chan J, Kao C, Hakonarson H, Wang K. Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590597. [PMID: 38746128 PMCID: PMC11092450 DOI: 10.1101/2024.04.29.590597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The advent of long-read single-cell transcriptome sequencing (lr-scRNA-Seq) represents a significant leap forward in single-cell genomics. With the recent introduction of R10 flowcells by Oxford Nanopore, we propose that previous computational methods designed to handle high sequencing error rates are no longer relevant, and that the prevailing approach using short reads to compile "barcode space" (candidate barcode list) to de-multiplex long reads are no longer necessary. Instead, computational methods should now shift focus on harnessing the unique benefits of long reads to analyze transcriptome complexity. In this context, we introduce a comprehensive suite of computational methods named Single-Cell Omics for Transcriptome CHaracterization (SCOTCH). Our method is compatible with the single-cell library preparation platform from both 10X Genomics and Parse Biosciences, facilitating the analysis of special cell populations, such as neurons, hepatocytes and developing cardiomyocytes. We specifically re-formulated the transcript mapping problem with a compatibility matrix and addressed the multiple-mapping issue using probabilistic inference, which allows the discovery of novel isoforms as well as the detection of differential isoform usage between cell populations. We evaluated SCOTCH through analysis of real data across different combinations of single-cell libraries and sequencing technologies (10X + Illumina, Parse + Illumina, 10X + Nanopore_R9, 10X + Nanopore_R10, Parse + Nanopore_R10), and showed its ability to infer novel biological insights on cell type-specific isoform expression. These datasets enhance the availability of publicly available data for continued development of computational approaches. In summary, SCOTCH allows extraction of more biological insights from the new advancements in single-cell library construction and sequencing technologies, facilitating the examination of transcriptome complexity at the single-cell level.
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Affiliation(s)
- Zhuoran Xu
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hui-Qi Qu
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Joe Chan
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Charlly Kao
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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11
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Bernt KM. Mapping human hematopoiesis. Nat Immunol 2024; 25:590-591. [PMID: 38514889 DOI: 10.1038/s41590-024-01793-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Affiliation(s)
- Kathrin M Bernt
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania and Abramson Cancer Center, Philadelphia, PA, USA.
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12
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Ling RE, Cross JW, Roy A. Aberrant stem cell and developmental programs in pediatric leukemia. Front Cell Dev Biol 2024; 12:1372899. [PMID: 38601080 PMCID: PMC11004259 DOI: 10.3389/fcell.2024.1372899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Hematopoiesis is a finely orchestrated process, whereby hematopoietic stem cells give rise to all mature blood cells. Crucially, they maintain the ability to self-renew and/or differentiate to replenish downstream progeny. This process starts at an embryonic stage and continues throughout the human lifespan. Blood cancers such as leukemia occur when normal hematopoiesis is disrupted, leading to uncontrolled proliferation and a block in differentiation of progenitors of a particular lineage (myeloid or lymphoid). Although normal stem cell programs are crucial for tissue homeostasis, these can be co-opted in many cancers, including leukemia. Myeloid or lymphoid leukemias often display stem cell-like properties that not only allow proliferation and survival of leukemic blasts but also enable them to escape treatments currently employed to treat patients. In addition, some leukemias, especially in children, have a fetal stem cell profile, which may reflect the developmental origins of the disease. Aberrant fetal stem cell programs necessary for leukemia maintenance are particularly attractive therapeutic targets. Understanding how hijacked stem cell programs lead to aberrant gene expression in place and time, and drive the biology of leukemia, will help us develop the best treatment strategies for patients.
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Affiliation(s)
- Rebecca E. Ling
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Joe W. Cross
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Anindita Roy
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
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13
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Sussman JH, Oldridge DA, Yu W, Chen CH, Zellmer AM, Rong J, Parvaresh-Rizi A, Thadi A, Xu J, Bandyopadhyay S, Sun Y, Wu D, Emerson Hunter C, Brosius S, Ahn KJ, Baxter AE, Koptyra MP, Vanguri RS, McGrory S, Resnick AC, Storm PB, Amankulor NM, Santi M, Viaene AN, Zhang N, Raedt TD, Cole K, Tan K. A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583588. [PMID: 38496580 PMCID: PMC10942465 DOI: 10.1101/2024.03.06.583588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Pediatric high-grade glioma (pHGG) is an incurable central nervous system malignancy that is a leading cause of pediatric cancer death. While pHGG shares many similarities to adult glioma, it is increasingly recognized as a molecularly distinct, yet highly heterogeneous disease. In this study, we longitudinally profiled a molecularly diverse cohort of 16 pHGG patients before and after standard therapy through single-nucleus RNA and ATAC sequencing, whole-genome sequencing, and CODEX spatial proteomics to capture the evolution of the tumor microenvironment during progression following treatment. We found that the canonical neoplastic cell phenotypes of adult glioblastoma are insufficient to capture the range of tumor cell states in a pediatric cohort and observed differential tumor-myeloid interactions between malignant cell states. We identified key transcriptional regulators of pHGG cell states and did not observe the marked proneural to mesenchymal shift characteristic of adult glioblastoma. We showed that essential neuromodulators and the interferon response are upregulated post-therapy along with an increase in non-neoplastic oligodendrocytes. Through in vitro pharmacological perturbation, we demonstrated novel malignant cell-intrinsic targets. This multiomic atlas of longitudinal pHGG captures the key features of therapy response that support distinction from its adult counterpart and suggests therapeutic strategies which are targeted to pediatric gliomas.
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Affiliation(s)
- Jonathan H. Sussman
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Derek A. Oldridge
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Wenbao Yu
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman
School of Medicine, Philadelphia, PA
| | - Chia-Hui Chen
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Abigail M. Zellmer
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Jiazhen Rong
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Statistics and Data Science, University of
Pennsylvania, Philadelphia, PA
| | | | - Anusha Thadi
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Jason Xu
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Shovik Bandyopadhyay
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Cellular and Molecular Biology Graduate Group, Perelman School of
Medicine, University of Pennsylvania, PA
| | - Yusha Sun
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Neuroscience Graduate Group, Perelman School of Medicine,
University of Pennsylvania, PA
| | - David Wu
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - C. Emerson Hunter
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Stephanie Brosius
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kyung Jin Ahn
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Amy E. Baxter
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Mateusz P. Koptyra
- Department of Neurosurgery, Children’s Hospital of
Philadelphia, Philadelphia, PA
| | - Rami S. Vanguri
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Stephanie McGrory
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Adam C. Resnick
- Department of Neurosurgery, Children’s Hospital of
Philadelphia, Philadelphia, PA
| | - Phillip B. Storm
- Department of Neurosurgery, Children’s Hospital of
Philadelphia, Philadelphia, PA
| | - Nduka M. Amankulor
- Department of Neurosurgery, Perelman School of Medicine,
Philadelphia, PA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Angela N. Viaene
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Nancy Zhang
- Department of Statistics and Data Science, University of
Pennsylvania, Philadelphia, PA
| | - Thomas De Raedt
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Kristina Cole
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman
School of Medicine, Philadelphia, PA
| | - Kai Tan
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman
School of Medicine, Philadelphia, PA
- Center for Single Cell Biology, Children’s Hospital of
Philadelphia, Philadelphia, PA
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14
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Ang Z, Thomas-Tikhonenko A. Lymphoma immunotherapy: the garden of forking paths. Blood 2024; 143:655-657. [PMID: 38386427 DOI: 10.1182/blood.2023023202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Affiliation(s)
| | - Andrei Thomas-Tikhonenko
- Children's Hospital of Philadelphia
- Perelman School of Medicine at the University of Pennsylvania
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15
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Filipek-Gorzała J, Kwiecińska P, Szade A, Szade K. The dark side of stemness - the role of hematopoietic stem cells in development of blood malignancies. Front Oncol 2024; 14:1308709. [PMID: 38440231 PMCID: PMC10910019 DOI: 10.3389/fonc.2024.1308709] [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: 10/06/2023] [Accepted: 01/02/2024] [Indexed: 03/06/2024] Open
Abstract
Hematopoietic stem cells (HSCs) produce all blood cells throughout the life of the organism. However, the high self-renewal and longevity of HSCs predispose them to accumulate mutations. The acquired mutations drive preleukemic clonal hematopoiesis, which is frequent among elderly people. The preleukemic state, although often asymptomatic, increases the risk of blood cancers. Nevertheless, the direct role of preleukemic HSCs is well-evidenced in adult myeloid leukemia (AML), while their contribution to other hematopoietic malignancies remains less understood. Here, we review the evidence supporting the role of preleukemic HSCs in different types of blood cancers, as well as present the alternative models of malignant evolution. Finally, we discuss the clinical importance of preleukemic HSCs in choosing the therapeutic strategies and provide the perspective on further studies on biology of preleukemic HSCs.
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Affiliation(s)
- Jadwiga Filipek-Gorzała
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Patrycja Kwiecińska
- Laboratory of Stem Cell Biology, 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
| | - Krzysztof Szade
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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16
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Janssens DH, Greene JE, Wu SJ, Codomo CA, Minot SS, Furlan SN, Ahmad K, Henikoff S. Scalable single-cell profiling of chromatin modifications with sciCUT&Tag. Nat Protoc 2024; 19:83-112. [PMID: 37935964 PMCID: PMC11229882 DOI: 10.1038/s41596-023-00905-9] [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: 02/06/2023] [Accepted: 08/18/2023] [Indexed: 11/09/2023]
Abstract
Cleavage under targets and tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing immune precipitation-based methods, such as chromatin immunoprecipitation-sequencing. The efficiency of the method enables chromatin profiling in single cells but is limited by the numbers of cells that can be profiled. Here, we describe a combinatorial barcoding strategy for CUT&Tag that harnesses a nanowell dispenser for simple, high-resolution, high-throughput, single-cell chromatin profiling. In this single-cell combinatorial indexing CUT&Tag (sciCUT&Tag) protocol, lightly cross-linked nuclei are bound to magnetic beads and incubated with primary and secondary antibodies in bulk and then arrayed in a 96-well plate for a first round of cellular indexing by antibody-directed Tn5 tagmentation. The sample is then repooled, mixed and arrayed across 5,184 nanowells at a density of 12-24 nuclei per well for a second round of cellular indexing during PCR amplification of the sequencing-ready library. This protocol can be completed in 1.5 days by a research technician, and we illustrate the optimized protocol by profiling histone modifications associated with developmental gene repression (H3K27me3) as well as transcriptional activation (H3K4me1-2-3) in human peripheral blood mononuclear cells and use single-nucleotide polymorphisms to facilitate collision removal. We have also used sciCUT&Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&Tag make it an attractive platform to profile chromatin features in single cells.
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Affiliation(s)
- Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jacob E Greene
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular Medicine and Mechanisms of Disease (M3D) PhD Program, University of Washington, Seattle, WA, USA
| | - Steven J Wu
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA
| | - Christine A Codomo
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Samuel S Minot
- Data Core, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Scott N Furlan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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17
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Winestone LE, Bhojwani D, Ghorashian S, Muffly L, Leahy AB, Chao K, Steineck A, Rössig C, Lamble A, Maude SL, Myers R, Rheingold SR. INSPIRED Symposium Part 4A: Access to CAR T Cell Therapy in Unique Populations with B Cell Acute Lymphoblastic Leukemia. Transplant Cell Ther 2024; 30:56-70. [PMID: 37821078 DOI: 10.1016/j.jtct.2023.10.005] [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: 08/28/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
The approval of tisagenlecleucel (tisa-cel) for use in children with B cell acute lymphoblastic leukemia (B-ALL) was based on the phase 2 ELIANA trial, a global registration study. However, the ELIANA trial excluded specific subsets of patients facing unique challenges and did not include a sufficient number of patients to adequately evaluate outcomes in rare subpopulations. Since the commercialization of tisa-cel, data have become available that support therapeutic indications beyond the specific cohorts previously eligible for chimeric antigen receptor (CAR) T cells targeted to CD19 (CD19 CAR-T) therapy on the registration clinical trial. Substantial real-world data and aggregate clinical trial data have addressed gaps in our understanding of response rates, longer-term efficacy, and toxicities associated with CD19 CAR-T in special populations and rare clinical scenarios. These include patients with central nervous system relapsed disease, who were excluded from ELIANA and other early CAR-T trials owing to concerns about risk of neurotoxicity that have not been born out. There is also interest in the use of CD19 CAR-T for very-high-risk patients earlier in the course of therapy, such as patients with persistent minimal residual disease after 2 cycles of upfront chemotherapy and patients with first relapse of B-ALL. However, these indications are not specified on the label for tisa-cel and historically were not included in eligibility criteria for most clinical trials; data addressing these populations are needed. Populations at high risk of relapse, including patients with high-risk cytogenetic lesions, infants with B-ALL, patients with trisomy 21, and young adults with B-ALL, also may benefit from earlier treatment with CD19 CAR-T. It is important to prospectively study patient-reported outcomes given the differential toxicity expected between CD19 CAR-T and the historic standard of care, hematopoietic cell transplantation. Now that CD19 CAR-T therapy is commercially available, studies evaluating potential access disparities created by this very expensive novel therapy are increasingly pressing.
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Affiliation(s)
- Lena E Winestone
- Division of Allergy, Immunology, and BMT, Department of Pediatrics, UCSF Benioff Children's Hospitals, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California.
| | - Deepa Bhojwani
- Division of Pediatric Hematology-Oncology, Children's Hospital Los Angeles, Norris Comprehensive Cancer Center and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Sara Ghorashian
- Haematology Department, Great Ormond Street Hospital, London UK, Developmental Biology and Cancer, UCL-Great Ormond Street Institute of Child Health, University College London, London United Kingdom
| | - Lori Muffly
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University, Stanford, California
| | - Allison Barz Leahy
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Karen Chao
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Angela Steineck
- MACC Fund Center for Cancer and Blood Disorders, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Claudia Rössig
- University Children's Hospital Muenster, Pediatric Hematology and Oncology, Muenster, Germany; Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Adam Lamble
- Division of Hematology and Oncology, Seattle Children's Hospital, Department of Pediatrics, University of Washington, Seattle, Washington
| | - Shannon L Maude
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Regina Myers
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Susan R Rheingold
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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18
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Lambo S, Trinh DL, Ries RE, Jin D, Setiadi A, Ng M, Leblanc VG, Loken MR, Brodersen LE, Dai F, Pardo LM, Ma X, Vercauteren SM, Meshinchi S, Marra MA. A longitudinal single-cell atlas of treatment response in pediatric AML. Cancer Cell 2023; 41:2117-2135.e12. [PMID: 37977148 DOI: 10.1016/j.ccell.2023.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/15/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Pediatric acute myeloid leukemia (pAML) is characterized by heterogeneous cellular composition, driver alterations and prognosis. Characterization of this heterogeneity and how it affects treatment response remains understudied in pediatric patients. We used single-cell RNA sequencing and single-cell ATAC sequencing to profile 28 patients representing different pAML subtypes at diagnosis, remission and relapse. At diagnosis, cellular composition differed between genetic subgroups. Upon relapse, cellular hierarchies transitioned toward a more primitive state regardless of subtype. Primitive cells in the relapsed tumor were distinct compared to cells at diagnosis, with under-representation of myeloid transcriptional programs and over-representation of other lineage programs. In some patients, this was accompanied by the appearance of a B-lymphoid-like hierarchy. Our data thus reveal the emergence of apparent subtype-specific plasticity upon treatment and inform on potentially targetable processes.
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Affiliation(s)
- Sander Lambo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Diane L Trinh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dan Jin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Audi Setiadi
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, Division of Hematopathology, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Michelle Ng
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Veronique G Leblanc
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | | | - Fangyan Dai
- Hematologics, Incorporated, Seattle, WA, USA
| | | | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Suzanne M Vercauteren
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, Division of Hematopathology, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
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19
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Kim R, Bergugnat H, Pastoret C, Pasquier F, Raffoux E, Larcher L, Passet M, Grardel N, Delabesse E, Kubetzko S, Caye-Eude A, Meyer C, Marschalek R, Lafage-Pochitaloff M, Thiebaut-Bertrand A, Balsat M, Escoffre-Barbe M, Blum S, Baumann M, Banos A, Straetmans N, Gallego-Hernanz MP, Chalandon Y, Graux C, Soulier J, Leguay T, Hunault M, Huguet F, Lhéritier V, Dombret H, Boissel N, Clappier E. Genetic alterations and MRD refine risk assessment for KMT2A-rearranged B-cell precursor ALL in adults: a GRAALL study. Blood 2023; 142:1806-1817. [PMID: 37595275 DOI: 10.1182/blood.2023021501] [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: 06/13/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023] Open
Abstract
KMT2A-rearranged (KMT2A-r) B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is widely recognized as a high-risk leukemia in both children and adults. However, there is a paucity of data on adults treated in recent protocols, and the optimal treatment strategy for these patients is still a matter of debate. In this study, we set out to refine the prognosis of adult KMT2A-r BCP-ALL treated with modern chemotherapy regimen and investigate the prognostic impact of comutations and minimal residual disease (MRD). Of 1091 adult patients with Philadelphia-negative BCP-ALL enrolled in 3 consecutive trials from the Group for Research on Adult Acute Lymphoblastic Leukemia (GRAALL), 141 (12.9%) had KMT2A-r, with 5-year cumulative incidence of relapse (CIR) and overall survival (OS) rates of 40.7% and 53.3%, respectively. Molecular profiling highlighted a low mutational burden in this subtype, reminiscent of infant BCP-ALL. However, the presence of TP53 and/or IKZF1 alterations defined a subset of patients with significantly poorer CIR (69.3% vs 36.2%; P = .001) and OS (28.1% vs 60.7%; P = .006) rates. Next, we analyzed the prognostic implication of MRD measured after induction and first consolidation, using both immunoglobulin (IG) or T-cell receptor (TR) gene rearrangements and KMT2A genomic fusion as markers. In approximately one-third of patients, IG/TR rearrangements were absent or displayed clonal evolution during the disease course, compromising MRD monitoring. In contrast, KMT2A-based MRD was highly reliable and strongly associated with outcome, with early good responders having an excellent outcome (3-year CIR, 7.1%; OS, 92.9%). Altogether, our study reveals striking heterogeneity in outcomes within adults with KMT2A-r BCP-ALL and provides new biomarkers to guide risk-based therapeutic stratification.
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Affiliation(s)
- Rathana Kim
- Hematology Laboratory, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- INSERM U944, CNRS UMR 7212 GenCellDis, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Hugo Bergugnat
- INSERM U944, CNRS UMR 7212 GenCellDis, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Cédric Pastoret
- Hematology Laboratory, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Florence Pasquier
- Department of Hematology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Emmanuel Raffoux
- Hematology Department, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Lise Larcher
- Hematology Laboratory, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- INSERM U944, CNRS UMR 7212 GenCellDis, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Marie Passet
- Hematology Laboratory, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nathalie Grardel
- Hematology Laboratory, Centre Hospitalier Régional Universitaire de Lille, Lille, France
| | - Eric Delabesse
- Hematology Laboratory, Institut Universitaire de Cancer Toulouse-Oncopole, INSERM 1037, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Susanne Kubetzko
- Department of Hematology, University Hospital of Zürich, Zürich, Switzerland
| | - Aurélie Caye-Eude
- Genetics Department, Molecular Genetics Unit, Hôpital Robert Debré, Assistance Publique-Hôpitaux de Paris, INSERM UMR_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France
| | - Claus Meyer
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia, Goethe University, Frankfurt/Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia, Goethe University, Frankfurt/Main, Germany
| | - Marine Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Hôpital Timone Enfant, Assistance Publique-Hôpitaux de Marseille, Aix-Marseille Université, Marseille, France
| | | | - Marie Balsat
- Department of Hematology, Hôpital Lyon Sud, Pierre Benite, France
| | | | - Sabine Blum
- Department of Hematology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Michael Baumann
- Klinik für Medizinische Onkologie und Hämatologie, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Anne Banos
- Department of Hematology, Centre Hospitalier de la Côte Basque, Bayonne, France
| | - Nicole Straetmans
- Department of Hematology, University Hospital Saint-Luc, Brussels, Belgium
| | | | - Yves Chalandon
- Division of Hematology, Department of Oncology, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland, for the Swiss Group for Clinical Cancer Research
- Swiss Group for Clinical Cancer Research
| | - Carlos Graux
- Department of Hematology, Université Catholique de Louvain, Centre Hospitalier Universitaire UCLouvain Namur-Godinne, Yvoir, Belgium
| | - Jean Soulier
- Hematology Laboratory, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- INSERM U944, CNRS UMR 7212 GenCellDis, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Thibaut Leguay
- Department of Hematology, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut-Levêque, Pessac, France
| | - Mathilde Hunault
- Département des Maladies du Sang, Centre Hospitalier Universitaire Angers, INSERM, CNRS, CRCI2NA, Fédération Hospitalo-Universitaire Grand Ouest Against Leukemia, Université d'Angers, Université de Nantes, Angers, France
| | - Françoise Huguet
- Department of Hematology, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire de Cancer Toulouse-Oncopole, Toulouse, France
| | - Véronique Lhéritier
- Coordination du Groupe Group for Research on Adult Acute Lymphoblastic Leukemia, Hospices Civils de Lyon, Hôpital Lyon Sud, Pierre Benite, France
| | - Hervé Dombret
- Hematology Department, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Nicolas Boissel
- Hematology Department, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Emmanuelle Clappier
- Hematology Laboratory, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- INSERM U944, CNRS UMR 7212 GenCellDis, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
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20
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Sperlazza J, Galeotti J, Hucks G, Alexander TB. Multiple lineage switches in KMT2A rearranged infant leukemia, responsive to combination therapy with CPX-351 and inotuzumab. Pediatr Blood Cancer 2023; 70:e30645. [PMID: 37638847 DOI: 10.1002/pbc.30645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/29/2023]
Affiliation(s)
- Justin Sperlazza
- Division of Pediatric Hematology-Oncology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Jonathan Galeotti
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - George Hucks
- Division of Pediatric Hematology-Oncology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Thomas B Alexander
- Division of Pediatric Hematology-Oncology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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21
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Schneider P, Crump NT, Arentsen-Peters STCJM, Smith AL, Hagelaar R, Adriaanse FRS, Bos RS, de Jong A, Nierkens S, Koopmans B, Milne TA, Pieters R, Stam RW. Modelling acquired resistance to DOT1L inhibition exhibits the adaptive potential of KMT2A-rearranged acute lymphoblastic leukemia. Exp Hematol Oncol 2023; 12:81. [PMID: 37740239 PMCID: PMC10517487 DOI: 10.1186/s40164-023-00445-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023] Open
Abstract
In KMT2A-rearranged acute lymphoblastic leukemia (ALL), an aggressive malignancy, oncogenic KMT2A-fusion proteins inappropriately recruit DOT1L to promote leukemogenesis, highlighting DOT1L as an attractive therapeutic target. Unfortunately, treatment with the first-in-class DOT1L inhibitor pinometostat eventually leads to non-responsiveness. To understand this we established acquired pinometostat resistance in pediatric KMT2A::AFF1+ B-ALL cells. Interestingly, these cells became mostly independent of DOT1L-mediated H3K79 methylation, but still relied on the physical presence of DOT1L, HOXA9 and the KMT2A::AFF1 fusion. Moreover, these cells selectively lost the epigenetic regulation and expression of various KMT2A-fusion target genes such as PROM1/CD133, while other KMT2A::AFF1 target genes, including HOXA9 and CDK6 remained unaffected. Concomitantly, these pinometostat-resistant cells showed upregulation of several myeloid-associated genes, including CD33 and LILRB4/CD85k. Taken together, this model comprehensively shows the adaptive potential of KMT2A-rearranged ALL cells upon losing dependency on one of its main oncogenic properties.
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Affiliation(s)
- Pauline Schneider
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Nicholas T Crump
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
| | | | - Alastair L Smith
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | | | - Romy S Bos
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Anja de Jong
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Bianca Koopmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Thomas A Milne
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Ronald W Stam
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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22
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Beder T, Hansen BT, Hartmann AM, Zimmermann J, Amelunxen E, Wolgast N, Walter W, Zaliova M, Antić Ž, Chouvarine P, Bartsch L, Barz MJ, Bultmann M, Horns J, Bendig S, Kässens J, Kaleta C, Cario G, Schrappe M, Neumann M, Gökbuget N, Bergmann AK, Trka J, Haferlach C, Brüggemann M, Baldus CD, Bastian L. The Gene Expression Classifier ALLCatchR Identifies B-cell Precursor ALL Subtypes and Underlying Developmental Trajectories Across Age. Hemasphere 2023; 7:e939. [PMID: 37645423 PMCID: PMC10461941 DOI: 10.1097/hs9.0000000000000939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/26/2023] [Indexed: 08/31/2023] Open
Abstract
Current classifications (World Health Organization-HAEM5/ICC) define up to 26 molecular B-cell precursor acute lymphoblastic leukemia (BCP-ALL) disease subtypes by genomic driver aberrations and corresponding gene expression signatures. Identification of driver aberrations by transcriptome sequencing (RNA-Seq) is well established, while systematic approaches for gene expression analysis are less advanced. Therefore, we developed ALLCatchR, a machine learning-based classifier using RNA-Seq gene expression data to allocate BCP-ALL samples to all 21 gene expression-defined molecular subtypes. Trained on n = 1869 transcriptome profiles with established subtype definitions (4 cohorts; 55% pediatric / 45% adult), ALLCatchR allowed subtype allocation in 3 independent hold-out cohorts (n = 1018; 75% pediatric / 25% adult) with 95.7% accuracy (averaged sensitivity across subtypes: 91.1% / specificity: 99.8%). High-confidence predictions were achieved in 83.7% of samples with 98.9% accuracy. Only 1.2% of samples remained unclassified. ALLCatchR outperformed existing tools and identified novel driver candidates in previously unassigned samples. Additional modules provided predictions of samples blast counts, patient's sex, and immunophenotype, allowing the imputation in cases where these information are missing. We established a novel RNA-Seq reference of human B-lymphopoiesis using 7 FACS-sorted progenitor stages from healthy bone marrow donors. Implementation in ALLCatchR enabled projection of BCP-ALL samples to this trajectory. This identified shared proximity patterns of BCP-ALL subtypes to normal lymphopoiesis stages, extending immunophenotypic classifications with a novel framework for developmental comparisons of BCP-ALL. ALLCatchR enables RNA-Seq routine application for BCP-ALL diagnostics with systematic gene expression analysis for accurate subtype allocation and novel insights into underlying developmental trajectories.
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Affiliation(s)
- Thomas Beder
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Björn-Thore Hansen
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Alina M Hartmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Johannes Zimmermann
- Institute of Experimental Medicine, Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, Germany
| | - Eric Amelunxen
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nadine Wolgast
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | | | - Marketa Zaliova
- Childhood Leukaemia Investigation Prague, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Željko Antić
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Philippe Chouvarine
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Lorenz Bartsch
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Malwine J Barz
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Miriam Bultmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Johanna Horns
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sonja Bendig
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Jan Kässens
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christoph Kaleta
- Institute of Experimental Medicine, Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, Germany
| | - Gunnar Cario
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein Kiel, Germany
| | - Martin Schrappe
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein Kiel, Germany
| | - Martin Neumann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Nicola Gökbuget
- Department of Medicine II, Hematology/Oncology, Goethe University Hospital, Frankfurt/M., Germany
| | | | - Jan Trka
- Childhood Leukaemia Investigation Prague, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | | | - Monika Brüggemann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Claudia D Baldus
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Lorenz Bastian
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
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23
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Goyette MA, Lipsyc-Sharf M, Polyak K. Clinical and translational relevance of intratumor heterogeneity. Trends Cancer 2023; 9:726-737. [PMID: 37248149 PMCID: PMC10524913 DOI: 10.1016/j.trecan.2023.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023]
Abstract
Intratumor heterogeneity (ITH) is a driver of tumor evolution and a main cause of therapeutic resistance. Despite its importance, measures of ITH are still not incorporated into clinical practice. Consequently, standard treatment is frequently ineffective for patients with heterogeneous tumors as changes to treatment regimens are made only after recurrence and disease progression. More effective combination therapies require a mechanistic understanding of ITH and ways to assess it in clinical samples. The growth of technologies enabling the spatially intact analysis of tumors at the single-cell level and the development of sophisticated preclinical models give us hope that ITH will not simply be used as a predictor of a poor outcome but will guide treatment decisions from diagnosis through treatment.
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Affiliation(s)
- Marie-Anne Goyette
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marla Lipsyc-Sharf
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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24
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Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Commun Biol 2023; 6:765. [PMID: 37479893 PMCID: PMC10362028 DOI: 10.1038/s42003-023-05120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage composition of AML cells at time of therapy resistance. Here we leverage single-cell chromatin accessibility profiling of 22 AML bone marrow aspirates from eight patients at time of therapy resistance and following subsequent therapy to characterize their lineage landscape. Our findings reveal a complex lineage architecture of therapy-resistant AML cells that are primed for stem and progenitor lineages and spanning quiescent, activated and late stem cell/progenitor states. Remarkably, therapy-resistant AML cells are also composed of cells primed for differentiated myeloid, erythroid and even lymphoid lineages. The heterogeneous lineage composition persists following subsequent therapy, with early progenitor-driven features marking unfavorable prognosis in The Cancer Genome Atlas AML cohort. Pseudotime analysis further confirms the vast degree of heterogeneity driven by the dynamic changes in chromatin accessibility. Our findings suggest that therapy-resistant AML cells are characterized not only by stem and progenitor states, but also by a continuum of differentiated cellular lineages. The heterogeneity in lineages likely contributes to their therapy resistance by harboring different degrees of lineage-specific susceptibilities to therapy.
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Affiliation(s)
- Huihui Fan
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Zeng
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alex Murison
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Katarzyna Tomczak
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fatima Zahra Jelloul
- Department of Hematopathology, University of Texas M D Anderson Cancer Center, Houston, TX, USA
| | - Bofei Wang
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Praveen Barrodia
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Dick
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Naval Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein A Abbas
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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25
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Mendoza-Castrejon J, Magee JA. Layered immunity and layered leukemogenicity: Developmentally restricted mechanisms of pediatric leukemia initiation. Immunol Rev 2023; 315:197-215. [PMID: 36588481 PMCID: PMC10301262 DOI: 10.1111/imr.13180] [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] [Indexed: 01/03/2023]
Abstract
Hematopoietic stem cells (HSCs) and multipotent progenitor cells (MPPs) arise in successive waves during ontogeny, and their properties change significantly throughout life. Ontological changes in HSCs/MPPs underlie corresponding changes in mechanisms of pediatric leukemia initiation. As HSCs and MPPs progress from fetal to neonatal, juvenile and adult stages of life, they undergo transcriptional and epigenetic reprogramming that modifies immune output to meet age-specific pathogenic challenges. Some immune cells arise exclusively from fetal HSCs/MPPs. We propose that this layered immunity instructs cell fates that underlie a parallel layered leukemogenicity. Indeed, some pediatric leukemias, such as juvenile myelomonocytic leukemia, myeloid leukemia of Down syndrome, and infant pre-B-cell acute lymphoblastic leukemia, are age-restricted. They only present during infancy or early childhood. These leukemias likely arise from fetal progenitors that lose competence for transformation as they age. Other childhood leukemias, such as non-infant pre-B-cell acute lymphoblastic leukemia and acute myeloid leukemia, have mutation profiles that are common in childhood but rare in morphologically similar adult leukemias. These differences could reflect temporal changes in mechanisms of mutagenesis or changes in how progenitors respond to a given mutation at different ages. Interactions between leukemogenic mutations and normal developmental switches offer potential targets for therapy.
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Affiliation(s)
- Jonny Mendoza-Castrejon
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110
| | - Jeffrey A. Magee
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110
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26
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Külp M, Larghero P, Alten J, Cario G, Eckert C, Caye-Eude A, Cavé H, Schmachtel T, Bardini M, Cazzaniga G, De Lorenzo P, Valsecchi MG, Bonig H, Meyer C, Rieger MA, Marschalek R. The EGR3 regulome of infant KMT2A-r acute lymphoblastic leukemia identifies differential expression of B-lineage genes predictive for outcome. Leukemia 2023:10.1038/s41375-023-01895-z. [PMID: 37100882 PMCID: PMC10132433 DOI: 10.1038/s41375-023-01895-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/28/2023]
Abstract
KMT2A-rearranged acute lymphoblastic infant leukemia (KMT2A-r iALL) is associated with outsize risk of relapse and relapse mortality. We previously reported strong upregulation of the immediate early gene EGR3 in KMT2A::AFF1 iALL at relapse; now we provide analyses of the EGR3 regulome, which we assessed through binding and expression target analysis of an EGR3-overexpressing t(4;11) cell culture model. Our data identify EGR3 as a regulator of early B-lineage commitment. Principal component analysis of 50 KMT2A-r iALL patients at diagnosis and 18 at relapse provided strictly dichotomous separation of patients based on the expression of four B-lineage genes. Absence of B-lineage gene expression translates to more than two-fold poorer long-term event-free survival. In conclusion, our study presents four B-lineage genes with prognostic significance, suitable for gene expression-based risk stratification of KMT2A-r iALL patients.
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Affiliation(s)
- Marius Külp
- Diagnostic Center of Acute Leukemia (DCAL), Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany.
- Department of Medicine, Hematology/Oncology, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany.
| | - Patrizia Larghero
- Diagnostic Center of Acute Leukemia (DCAL), Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany
| | - Julia Alten
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Cornelia Eckert
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Aurélie Caye-Eude
- Genetics Department, AP-HP, Hôpital Robert Debré, F-75019, Paris, France
- Université Paris Cité, Inserm U1131, Institut de recherche Saint-Louis, F-75010, Paris, France
| | - Hélène Cavé
- Genetics Department, AP-HP, Hôpital Robert Debré, F-75019, Paris, France
- Université Paris Cité, Inserm U1131, Institut de recherche Saint-Louis, F-75010, Paris, France
| | - Tessa Schmachtel
- Department of Medicine, Hematology/Oncology, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Michela Bardini
- Centro Ricerca Tettamanti, Pediatrics, University of Milan-Bicocca, Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM)/San Gerardo Hospital, Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Pediatrics, University of Milan-Bicocca, Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM)/San Gerardo Hospital, Monza, Italy
- Genetics, School of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Paola De Lorenzo
- Statistical Section, Pediatric Clinic, University of Milan-Bicocca, Monza, Italy
| | - Maria Grazia Valsecchi
- Center of Bioinformatics, Biostatistics and Bioimaging, University of Milan-Bicocca, Monza, Italy
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Goethe University, Frankfurt am Main, Germany
- German Red Cross Blood Service Baden-Württemberg-Hessen, Frankfurt am Main, Germany
- Department of Medicine, Division of Hematology, University of Washington School of Medicine, Seattle, WA, USA
| | - Claus Meyer
- Diagnostic Center of Acute Leukemia (DCAL), Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany
| | - Michael A Rieger
- Department of Medicine, Hematology/Oncology, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKZF), Heidelberg, Germany
- Cardio-Pulmonary Institute, Frankfurt am Main, Germany
| | - Rolf Marschalek
- Diagnostic Center of Acute Leukemia (DCAL), Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany.
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27
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Goodlad JR, Xiao W, Amador C, Cook JR, Happ L, Thakkar D, Dave S, Dogan A, Duffield A, Nejati R, Ott G, Wasik M, Czader M. Phenotypic and genotypic infidelity in B-lineage neoplasms, including transdifferentiation following targeted therapy: Report from the 2021 SH/EAHP Workshop. Am J Clin Pathol 2023:7135991. [PMID: 37085149 DOI: 10.1093/ajcp/aqad035] [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: 12/05/2022] [Accepted: 03/13/2023] [Indexed: 04/23/2023] Open
Abstract
OBJECTIVES Session 2 of the 2021 Society for Hematopathology and European Association for Haematopathology Workshop collected examples of lineage infidelity and transdifferentiation in B-lineage neoplasms, including after targeted therapy. METHODS Twenty cases were submitted. Whole-exome sequencing and genome-wide RNA expression analysis were available on a limited subsample. RESULTS A diagnosis of B-cell acute lymphoblastic leukemia (B-ALL) was rendered on at least 1 biopsy from 13 patients. There was 1 case of acute myeloid leukemia (AML); the remaining 6 cases were mature B-cell neoplasms. Targeted therapy was administered in 7 cases of B-ALL and 4 cases of mature B-cell neoplasms. Six cases of B-ALL underwent lineage switch to AML or mixed-phenotype acute leukemia at relapse, 5 of which had rearranged KMT2A. Changes in maturational state without lineage switch were observed in 2 cases. Examples of de novo aberrant T-cell antigen expression (n = 2) were seen among the mature B-cell lymphoma cohort, and their presence correlated with alterations in tumor cell gene expression patterns. CONCLUSIONS This cohort of cases enabled us to illustrate, discuss, and review current concepts of lineage switch and aberrant antigen expression in a variety of B-cell neoplasms and draw attention to the role targeted therapies may have in predisposing neoplasms to transdifferentiation as well as other, less expected changes in maturational status.
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Affiliation(s)
- John R Goodlad
- Department of Pathology, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Catalina Amador
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, US
| | - James R Cook
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, US
| | | | | | - Sandeep Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University School of Medicine, Durham, NC, US
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Amy Duffield
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, US
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Mariusz Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, US
| | - Magdalena Czader
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, US
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28
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Iacobucci I, Witkowski MT, Mullighan CG. Single-cell analysis of acute lymphoblastic and lineage-ambiguous leukemia: approaches and molecular insights. Blood 2023; 141:356-368. [PMID: 35926109 PMCID: PMC10023733 DOI: 10.1182/blood.2022016954] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/13/2022] [Accepted: 07/23/2022] [Indexed: 01/31/2023] Open
Abstract
Despite recent progress in identifying the genetic drivers of acute lymphoblastic leukemia (ALL), prognosis remains poor for those individuals who experience disease recurrence. Moreover, acute leukemias of ambiguous lineage lack a biologically informed framework to guide classification and therapy. These needs have driven the adoption of multiple complementary single-cell sequencing approaches to explore key issues in the biology of these leukemias, including cell of origin, developmental hierarchy and ontogeny, and the molecular heterogeneity driving pathogenesis, progression, and therapeutic responsiveness. There are multiple single-cell techniques for profiling a specific modality, including RNA, DNA, chromatin accessibility and methylation; and an expanding range of approaches for simultaneous analysis of multiple modalities. Single-cell sequencing approaches have also enabled characterization of cell-intrinsic and -extrinsic features of ALL biology. In this review we describe these approaches and highlight the extensive heterogeneity that underpins ALL gene expression, cellular differentiation, and clonal architecture throughout disease pathogenesis and treatment resistance. In addition, we discuss the importance of the dynamic interactions that occur between leukemia cells and the nonleukemia microenvironment. We discuss potential opportunities and limitations of single-cell sequencing for the study of ALL biology and treatment responsiveness.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN
| | - Matthew T. Witkowski
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Charles G. Mullighan
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN
- Hematological Malignancies Program, St Jude Children’s Research Hospital, Memphis, TN
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29
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Cheung LC, Aya-Bonilla C, Cruickshank MN, Chiu SK, Kuek V, Anderson D, Chua GA, Singh S, Oommen J, Ferrari E, Hughes AM, Ford J, Kunold E, Hesselman MC, Post F, Faulk KE, Breese EH, Guest EM, Brown PA, Loh ML, Lock RB, Kees UR, Jafari R, Malinge S, Kotecha RS. Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy. Leukemia 2023; 37:61-71. [PMID: 36380143 PMCID: PMC9883157 DOI: 10.1038/s41375-022-01746-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022]
Abstract
Infants with KMT2A-rearranged B-cell acute lymphoblastic leukemia (ALL) have a dismal prognosis. Survival outcomes have remained static in recent decades despite treatment intensification and novel therapies are urgently required. KMT2A-rearranged infant ALL cells are characterized by an abundance of promoter hypermethylation and exhibit high BCL-2 expression, highlighting potential for therapeutic targeting. Here, we show that hypomethylating agents exhibit in vitro additivity when combined with most conventional chemotherapeutic agents. However, in a subset of samples an antagonistic effect was seen between several agents. This was most evident when hypomethylating agents were combined with methotrexate, with upregulation of ATP-binding cassette transporters identified as a potential mechanism. Single agent treatment with azacitidine and decitabine significantly prolonged in vivo survival in KMT2A-rearranged infant ALL xenografts. Treatment of KMT2A-rearranged infant ALL cell lines with azacitidine and decitabine led to differential genome-wide DNA methylation, changes in gene expression and thermal proteome profiling revealed the target protein-binding landscape of these agents. The selective BCL-2 inhibitor, venetoclax, exhibited in vitro additivity in combination with hypomethylating or conventional chemotherapeutic agents. The addition of venetoclax to azacitidine resulted in a significant in vivo survival advantage indicating the therapeutic potential of this combination to improve outcome for infants with KMT2A-rearranged ALL.
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Affiliation(s)
- Laurence C Cheung
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Carlos Aya-Bonilla
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | | | - Sung K Chiu
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Vincent Kuek
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Denise Anderson
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Grace-Alyssa Chua
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Sajla Singh
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Joyce Oommen
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Emanuela Ferrari
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Anastasia M Hughes
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Jette Ford
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Elena Kunold
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Maria C Hesselman
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Frederik Post
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Kelly E Faulk
- University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO, USA
| | - Erin H Breese
- Cancer and Blood Diseases Institute, Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Erin M Guest
- Division of Hematology, Oncology, Blood and Marrow Transplantation, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Patrick A Brown
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD, USA
| | - Mignon L Loh
- Division of Pediatric Hematology, Oncology, Bone Marrow Transplant and Cellular Therapy, Seattle Children's Hospital, Seattle, WA, USA
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre/School of Women's and Children's Health/UNSW Centre for Childhood Cancer Research, UNSW Sydney, Kensington, NSW, Australia
| | - Ursula R Kees
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Rozbeh Jafari
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Sébastien Malinge
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Rishi S Kotecha
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia.
- Curtin Medical School, Curtin University, Perth, WA, Australia.
- The University of Western Australia, Perth, WA, Australia.
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, WA, Australia.
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30
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Sussman JH, Xu J, Amankulor N, Tan K. Dissecting the tumor microenvironment of epigenetically driven gliomas: Opportunities for single-cell and spatial multiomics. Neurooncol Adv 2023; 5:vdad101. [PMID: 37706202 PMCID: PMC10496944 DOI: 10.1093/noajnl/vdad101] [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] [Indexed: 09/15/2023] Open
Abstract
Malignant gliomas are incurable brain neoplasms with dismal prognoses and near-universal fatality, with minimal therapeutic progress despite billions of dollars invested in research and clinical trials over the last 2 decades. Many glioma studies have utilized disparate histologic and genomic platforms to characterize the stunning genomic, transcriptomic, and immunologic heterogeneity found in gliomas. Single-cell and spatial omics technologies enable unprecedented characterization of heterogeneity in solid malignancies and provide a granular annotation of transcriptional, epigenetic, and microenvironmental states with limited resected tissue. Heterogeneity in gliomas may be defined, at the broadest levels, by tumors ostensibly driven by epigenetic alterations (IDH- and histone-mutant) versus non-epigenetic tumors (IDH-wild type). Epigenetically driven tumors are defined by remarkable transcriptional programs, immunologically distinct microenvironments, and incompletely understood topography (unique cellular neighborhoods and cell-cell interactions). Thus, these tumors are the ideal substrate for single-cell multiomic technologies to disentangle the complex intra-tumoral features, including differentiation trajectories, tumor-immune cell interactions, and chromatin dysregulation. The current review summarizes the applications of single-cell multiomics to existing datasets of epigenetically driven glioma. More importantly, we discuss future capabilities and applications of novel multiomic strategies to answer outstanding questions, enable the development of potent therapeutic strategies, and improve personalized diagnostics and treatment via digital pathology.
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Affiliation(s)
- Jonathan H Sussman
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Medical Scientist Training Program, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jason Xu
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Medical Scientist Training Program, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nduka Amankulor
- Department of Neurosurgery, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kai Tan
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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31
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IGH Rearrangement Evolution in Adult KMT2A-rearranged B-cell Precursor ALL: Implications for Cell-of-origin and MRD Monitoring. Hemasphere 2022; 7:e820. [PMID: 36570692 PMCID: PMC9771314 DOI: 10.1097/hs9.0000000000000820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022] Open
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32
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Updates in infant acute lymphoblastic leukemia and the potential for targeted therapy. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2022; 2022:611-617. [PMID: 36485124 PMCID: PMC9821252 DOI: 10.1182/hematology.2022000359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Outcomes for infants diagnosed under 1 year of age with KMT2A-rearranged acute lymphoblastic leukemia (ALL) have remained stagnant over the past 20 years. Successive treatment protocols have previously focused on intensification of conventional chemotherapy, but increased treatment-related toxicity and chemoresistance have led to a plateau in survival. We have now entered an era of immunotherapy with integration of agents, such as blinatumomab or chimeric antigen receptor T-cell therapy, into the standard chemotherapy backbone, showing significant promise for improving the dismal outcomes for this disease. There remains much optimism for the future as a wealth of preclinical studies have identified additional novel targeted agents, such as venetoclax or menin inhibitors, ready for incorporation into treatment, providing further ammunition to combat this aggressive disease. In contrast, infants with KMT2A-germline ALL have demonstrated excellent survival outcomes with current therapy, but there remains a high burden of treatment-related morbidity. Greater understanding of the underlying blast genetics for infants with KMT2A-germline ALL and incorporation of immunotherapeutic approaches may enable a reduction in the intensity of chemotherapy while maintaining the excellent outcomes.
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33
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34
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Wang J, Zhou C, Gao S, Song X, Yang X, Fan J, Ren S, Ma L, Zhao J, Cui M, Song K, Wang M, Li C, Zheng Y, Luo F, Miao K, Bai X, Hutchins AP, Li L, Chang G, Zhao XY. Single-cell multiomics sequencing reveals the reprogramming defects in embryos generated by round spermatid injection. SCIENCE ADVANCES 2022; 8:eabm3976. [PMID: 35947654 PMCID: PMC9365279 DOI: 10.1126/sciadv.abm3976] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Round spermatid injection (ROSI) technique holds great promise for clinical treatment of a proportion of infertile men. However, the compromised developmental potential of ROSI embryos largely limits the clinical application, and the mechanisms are not fully understood. Here, we describe the transcriptome, chromatin accessibility, and DNA methylation landscapes of mouse ROSI embryos derived from early-stage round spermatids using a single-cell multiomics sequencing approach. By interrogating these data, we identify the reprogramming defects in ROSI embryos at the pronuclear stages, which are mainly associated with the misexpression of a cohort of minor zygotic genome activation genes. We screen a small compound, A366, that can significantly increase the developmental potential of ROSI embryos, in which A366 can partially overcome the reprogramming defects by amending the epigenetic and transcriptomic states. Collectively, our study uncovers the reprogramming defects in ROSI embryos for understanding the mechanisms underlying compromised developmental potential and offers an avenue for ROSI technique optimization.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Cai Zhou
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Shuai Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China
| | - Xiuling Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Xinyan Yang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Jiaqi Fan
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Shaofang Ren
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Linzi Ma
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Jiexiang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Manman Cui
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Ke Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Mei Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Chaohui Li
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Yi Zheng
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Fang Luo
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Kai Miao
- Center for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau, SAR, China
| | - Xiaochun Bai
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Andrew P. Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518060, P. R. China
| | - Lin Li
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Gang Chang
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060, P. R. China
| | - Xiao-Yang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
- Guangdong Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, Guangdong 510700, P. R. China
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35
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Wen J, Zhou M, Shen Y, Long Y, Guo Y, Song L, Xiao J. Poor treatment responses were related to poor outcomes in pediatric B cell acute lymphoblastic leukemia with KMT2A rearrangements. BMC Cancer 2022; 22:859. [PMID: 35933338 PMCID: PMC9357304 DOI: 10.1186/s12885-022-09804-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/16/2022] [Indexed: 11/21/2022] Open
Abstract
Background The KMT2A gene, formerly named the MLL gene, is rearranged (KMT2Ar) in 70–75% of infants, 5–6% of children and 10–15% of adult patients with B cell acute lymphoblastic leukemia (B-ALL). The outcome after chemotherapy of pediatric cases remains poor, and only a few studies have investigated the clinical and laboratory features, treatment response and prognosis in Chinese populations. Methods A total of 48 B-ALL children with KMT2Ar were enrolled in the study, and clinical and laboratory data were collected and analyzed by age group. The relationship between prognosis and traditional risk factors and treatment response was investigated for these patients who received chemotherapy. Results The 48 enrolled patients included 28 males and 20 females; 18 (37.50%) or 30 (62.50%) patients were an age of < 12 m (infant B-ALL) or of > 12 m at onset. An initial WBC count of 300 × 109/L was detected in 7 (14.58%) patients; testicular leukemia (TL) or central nervous system involvement was found in 5 (10.41%) or 3 (6.25%) patients, respectively. Statistical differences were not found in the age groups of sex or initial WBC count, whereas TL was more common in the infant group (P < 0.05). 11q23 was detected in 18 patients; KMT2Ar was detected in 46 (95.83%) or 45 (93.75%) patients by FISH or multiplex RT–PCR technology, respectively; RNA-seq data were obtained for 18 patients, and 3 patients with uncommon KMT2Ar were identified. KMT2A-AFF1, KMT2A-MLLT3 and KMT2A-MLLT1 were the most common transcripts. Statistical differences were not found in treatment response by age groups, including dexamethasone induction, bone marrow (BM) smear status and minimal residual disease (MRD) level at different time points (TP), treatment-related mortality (TRM), or complete remission (CR) rate (P > 0.05); MRD levels monitored by FCM or PCR were unequal at the same TP. Four patients died of treatment, and TRM was 8.33%; 40 patients achieved CR, and the CR rate for the cohort was 83.33%. Seven patients quit, 15 patients relapsed, and the 5 yr cumulative relapse rate was 59.16 ± 9.16%; the 5 yr prospective EFS (pEFS) for patients who were included or excluded from the TRM group was 36.86 ± 8.48% or 40.84 ± 9.16%, respectively. Multivariate analysis for prognosis and hazard ratio was performed for 37 patients without TRM and revealed that an initial WBC count of > 300 × 109/L and a positive level of FCM-MRD were strongly related to a poor outcome for B-ALL patients with KMT2Ar (P < 0.05). Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09804-w.
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Affiliation(s)
- Jinquan Wen
- Department of Pediatric Hematology, Caihong Hospital of Xianyang, Xi'an, People's Republic of China
| | - Min Zhou
- Department of Hematology, Chengdu Women and Children's Central Hospital, Chengdu, People's Republic of China
| | - Yali Shen
- Department of Hematology, Children's Hospital of Chongqing Medical University, Yuzhong District, Zhongshan 2nd Road, Chongqing, 400014, People's Republic of China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, People's Republic of China
| | - Yueting Long
- Department of Pediatrics, The Second Affiliated Hospital of Guizhou Medical University, Kaili, People's Republic of China
| | - Yuxia Guo
- Department of Hematology, Children's Hospital of Chongqing Medical University, Yuzhong District, Zhongshan 2nd Road, Chongqing, 400014, People's Republic of China.,National Clinical Research Center for Child Health and Disorders, Chongqing, People's Republic of China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, People's Republic of China
| | - Lin Song
- Department of Pharmacy, Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China.,Chongqing Key Laboratory of Pediatrics, Chongqing, People's Republic of China
| | - Jianwen Xiao
- Department of Hematology, Children's Hospital of Chongqing Medical University, Yuzhong District, Zhongshan 2nd Road, Chongqing, 400014, People's Republic of China.
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36
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Bertrums EJ, Rosendahl Huber AK, de Kanter JK, Brandsma AM, van Leeuwen AJ, Verheul M, van den Heuvel-Eibrink MM, Oka R, van Roosmalen MJ, de Groot-Kruseman HA, Zwaan CM, Goemans BF, van Boxtel R. Elevated Mutational Age in Blood of Children Treated for Cancer Contributes to Therapy-Related Myeloid Neoplasms. Cancer Discov 2022; 12:1860-1872. [PMID: 35678530 PMCID: PMC7613255 DOI: 10.1158/2159-8290.cd-22-0120] [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: 01/28/2022] [Revised: 05/06/2022] [Accepted: 06/07/2022] [Indexed: 01/07/2023]
Abstract
Childhood cancer survivors are confronted with various chronic health conditions like therapy-related malignancies. However, it is unclear how exposure to chemotherapy contributes to the mutation burden and clonal composition of healthy tissues early in life. Here, we studied mutation accumulation in hematopoietic stem and progenitor cells (HSPC) before and after cancer treatment of 24 children. Of these children, 19 developed therapy-related myeloid neoplasms (t-MN). Posttreatment HSPCs had an average mutation burden increase comparable to what treatment-naïve cells accumulate during 16 years of life, with excesses up to 80 years. In most children, these additional mutations were induced by clock-like processes, which are also active during healthy aging. Other patients harbored mutations that could be directly attributed to treatments like platinum-based drugs and thiopurines. Using phylogenetic inference, we demonstrate that most t-MN in children originate after the start of treatment and that leukemic clones become dominant during or directly after chemotherapy exposure. SIGNIFICANCE Our study shows that chemotherapy increases the mutation burden of normal blood cells in cancer survivors. Only few drugs damage the DNA directly, whereas in most patients, chemotherapy-induced mutations are caused by processes similar to those present during normal aging. This article is highlighted in the In This Issue feature, p. 1825.
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Affiliation(s)
- Eline J.M. Bertrums
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands.,Department of Pediatric Oncology, Erasmus Medical Center – Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Axel K.M. Rosendahl Huber
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Jurrian K. de Kanter
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Arianne M. Brandsma
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Anaïs J.C.N. van Leeuwen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | | | - Rurika Oka
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Markus J. van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | | | - C. Michel Zwaan
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pediatric Oncology, Erasmus Medical Center – Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Bianca F. Goemans
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands.,Corresponding Author: Ruben van Boxtel, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands. Phone: 0031 (0)889727272; E-mail:
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37
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Small noncoding RNAs play superior roles in maintaining hematopoietic stem cell homeostasis. BLOOD SCIENCE 2022; 4:125-132. [DOI: 10.1097/bs9.0000000000000123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 11/25/2022] Open
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38
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Kurzer JH, Weinberg OK. To B- or not to B-: A review of lineage switched acute leukemia. Int J Lab Hematol 2022; 44 Suppl 1:64-70. [PMID: 35770493 DOI: 10.1111/ijlh.13923] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
Abstract
Acute leukemia is a heterogeneous disorder of hematologic malignancies composed primarily of hematopoietic precursors that have acquired unregulated self-renewal and proliferation. Hematology classification systems typically divide these neoplasms into lymphoid (B- or T-) and myeloid-lineage subtypes, with therapy dependent upon this distinction. Infrequently, certain acute leukemias may undergo a complete lineage switch at relapse, subsequently complicating the diagnosis and treatment of these recurrent diseases. Transformation from B-lineage to myeloid lineage is the most common switch observed, and is frequently associated with a balanced 11q23 translocation, involving KMT2A. The mechanisms involved in the lineage-switch are unclear, but modern therapies targeting the B-cell-specific marker, CD19, have proven to promote this conversion as one means of treatment escape. Broadly speaking, therapy-mediated selection of alternate lineage-committed subclones derived from the same initial pluripotent progenitors, clonal evolution and reprogramming of lineage-committed blasts, and de novo clonally unrelated leukemias may account for the clinical impression of lineage switched acute leukemia during treatment. This review will explore the phenomenon and potential mechanisms of lineage transformation during the treatment of acute leukemia.
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Affiliation(s)
- Jason H Kurzer
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Olga K Weinberg
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas, USA
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39
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Qin B, Dong X, Ding J. Neonatal congenital leukemia caused by several missense mutations and AFF1‑KMT2A fusion: A case report. Oncol Lett 2022; 24:283. [PMID: 35814831 PMCID: PMC9260735 DOI: 10.3892/ol.2022.13403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/13/2022] [Indexed: 11/30/2022] Open
Abstract
Neonatal leukemia, a congenital form of leukemia, is a rare and fatal disease occurring in the neonatal period. Its etiology and pathogenesis have remained to be fully elucidated and the clinical manifestations differ due to age variability. Acute myeloid leukemia (AML) occurring after birth indicates genetic abnormalities and possibly intrauterine exposure to radiation, drugs or other toxins. The present report described the case of a premature neonate without phenotypic signs of Down syndrome, but with an elevated white blood cell count, mainly pertaining to the monocytes of peripheral blood. At 31 weeks of gestation, delivery by Caesarean section was performed due to fetal distress; however, the infant died three days after birth. Further laboratory examination indicated pediatric myeloid leukemia. The present case report described a case of fetal AML. According to the results of peripheral blood smear and targeted-panel sequencing, 5 missense mutations with clinical significance and a novel AFF1-KMT2A fusion gene were detected, which may be the main causes of AML and death.
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Affiliation(s)
- Bo Qin
- Clinical Laboratory, Shaoxing Women and Children's Hospital, Shaoxing, Zhejiang 312000, P.R. China
| | - Xiaoqian Dong
- Clinical Laboratory, Shaoxing Women and Children's Hospital, Shaoxing, Zhejiang 312000, P.R. China
| | - Jinlong Ding
- Clinical Laboratory, Shaoxing Women and Children's Hospital, Shaoxing, Zhejiang 312000, P.R. China
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40
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The use of single-cell multi-omics in immuno-oncology. Nat Commun 2022; 13:2728. [PMID: 35585090 PMCID: PMC9117235 DOI: 10.1038/s41467-022-30549-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/06/2022] [Indexed: 11/22/2022] Open
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41
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Morris V, Wang D, Li Z, Marion W, Hughes T, Sousa P, Harada T, Sui SH, Naumenko S, Kalfon J, Sensharma P, Falchetti M, Vinicius da Silva R, Candelli T, Schneider P, Margaritis T, Holstege FCP, Pikman Y, Harris M, Stam RW, Orkin SH, Koehler AN, Shalek AK, North TE, Pimkin M, Daley GQ, Lummertz da Rocha E, Rowe RG. Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells. Cell Rep 2022; 39:110752. [PMID: 35476984 PMCID: PMC9099058 DOI: 10.1016/j.celrep.2022.110752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/24/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023] Open
Abstract
High-risk forms of B-acute lymphoblastic leukemia (B-ALL) remain a therapeutic challenge. Leukemia-initiating cells (LICs) self-renew and spark relapse and therefore have been the subject of intensive investigation; however, the properties of LICs in high-risk B-ALL are not well understood. Here, we use single-cell transcriptomics and quantitative xenotransplantation to understand LICs in MLL-rearranged (MLL-r) B-ALL. Compared with reported LIC frequencies in acute myeloid leukemia (AML), engraftable LICs in MLL-r B-ALL are abundant. Although we find that multipotent, self-renewing LICs are enriched among phenotypically undifferentiated B-ALL cells, LICs with the capacity to replenish the leukemic cellular diversity can emerge from more mature fractions. While inhibiting oxidative phosphorylation blunts blast proliferation, this intervention promotes LIC emergence. Conversely, inhibiting hypoxia and glycolysis impairs MLL-r B-ALL LICs, providing a therapeutic benefit in xenotransplantation systems. These findings provide insight into the aggressive nature of MLL-r B-ALL and provide a rationale for therapeutic targeting of hypoxia and glycolysis.
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Affiliation(s)
- Vivian Morris
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dahai Wang
- Stem Cell Transplantation Program, Department of Hematology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Zhiheng Li
- Stem Cell Transplantation Program, Department of Hematology, Boston Children's Hospital, Boston, MA 02115, USA
| | - William Marion
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Travis Hughes
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Patricia Sousa
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - Shannan Ho Sui
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sergey Naumenko
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jérémie Kalfon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Prerana Sensharma
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Stem Cell Transplantation Program, Department of Hematology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Marcelo Falchetti
- Graduate Program of Pharmacology, Center for Biological Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Renan Vinicius da Silva
- Graduate Program of Pharmacology, Center for Biological Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Tito Candelli
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Pauline Schneider
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | | | - Yana Pikman
- Harvard Medical School, Boston, MA 02115, USA; Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - Marian Harris
- Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ronald W Stam
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Stuart H Orkin
- Harvard Medical School, Boston, MA 02115, USA; Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Angela N Koehler
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alex K Shalek
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Trista E North
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Maxim Pimkin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis Santa Catarina 88040-900, Brazil
| | - R Grant Rowe
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Stem Cell Transplantation Program, Department of Hematology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA.
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42
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Plasticity and immune evasion in childhood ALL. Blood 2022; 139:2096-2097. [PMID: 35389444 DOI: 10.1182/blood.2021015117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/20/2022] Open
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