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Schnegg-Kaufmann AS, Thoms JAI, Bhuyan GS, Hampton HR, Vaughan L, Rutherford K, Kakadia PM, Lee HM, Johansson EMV, Failes TW, Arndt GM, Koval J, Lindeman R, Warburton P, Rodriguez-Meira A, Mead AJ, Unnikrishnan A, Davidson S, Polizzotto MN, Hertzberg M, Papaemmanuil E, Bohlander SK, Faridani OR, Jolly CJ, Zanini F, Pimanda JE. Contribution of mutant HSC clones to immature and mature cells in MDS and CMML, and variations with AZA therapy. Blood 2023; 141:1316-1321. [PMID: 36493342 PMCID: PMC10651766 DOI: 10.1182/blood.2022018602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/07/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
Myelodysplastic neoplasms (MDSs) and chronic myelomonocytic leukemia (CMML) are clonal disorders driven by progressively acquired somatic mutations in hematopoietic stem cells (HSCs). Hypomethylating agents (HMAs) can modify the clinical course of MDS and CMML. Clinical improvement does not require eradication of mutated cells and may be related to improved differentiation capacity of mutated HSCs. However, in patients with established disease it is unclear whether (1) HSCs with multiple mutations progress through differentiation with comparable frequency to their less mutated counterparts or (2) improvements in peripheral blood counts following HMA therapy are driven by residual wild-type HSCs or by clones with particular combinations of mutations. To address these questions, the somatic mutations of individual stem cells, progenitors (common myeloid progenitors, granulocyte monocyte progenitors, and megakaryocyte erythroid progenitors), and matched circulating hematopoietic cells (monocytes, neutrophils, and naïve B cells) in MDS and CMML were characterized via high-throughput single-cell genotyping, followed by bulk analysis in immature and mature cells before and after AZA treatment. The mutational burden was similar throughout differentiation, with even the most mutated stem and progenitor clones maintaining their capacity to differentiate to mature cell types in vivo. Increased contributions from productive mutant progenitors appear to underlie improved hematopoiesis in MDS following HMA therapy.
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Affiliation(s)
- Annatina S. Schnegg-Kaufmann
- School of Biomedical Sciences, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Julie A. I. Thoms
- School of Biomedical Sciences, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Golam Sarower Bhuyan
- School of Clinical Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Henry R. Hampton
- School of Biomedical Sciences, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Lachlin Vaughan
- School of Clinical Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, NSW, Australia
- Haematology Department, Westmead Hospital, Sydney, NSW, Australia
| | - Kayleigh Rutherford
- Department of Epidemiology and Biostatistics, Computational Oncology Service, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Purvi M. Kakadia
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Hui Mei Lee
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Emma M. V. Johansson
- Flow Cytometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Timothy W. Failes
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Australian Cancer Research Foundation (ACRF) Drug Discovery Centre for Childhood Cancer, Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Greg M. Arndt
- School of Clinical Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Australian Cancer Research Foundation (ACRF) Drug Discovery Centre for Childhood Cancer, Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Jason Koval
- Ramaciotti Centre for Genomics, UNSW Sydney, Sydney, NSW, Australia
| | - Robert Lindeman
- Department of Clinical Haematology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Pauline Warburton
- Department of Haematology, Wollongong Hospital, Wollongong, NSW, Australia
| | - Alba Rodriguez-Meira
- Haematopoietic Stem Cell Biology Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adam J. Mead
- Haematopoietic Stem Cell Biology Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ashwin Unnikrishnan
- School of Clinical Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Sarah Davidson
- ANU Clinical Hub for Interventional Research (CHOIR), John Curtin School of Medical Research, Canberra, Australia
| | - Mark N. Polizzotto
- ANU Clinical Hub for Interventional Research (CHOIR), John Curtin School of Medical Research, Canberra, Australia
| | - Mark Hertzberg
- Department of Clinical Haematology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Computational Oncology Service, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stefan K. Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Omid R. Faridani
- School of Biomedical Sciences, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Garvan-Weizmann Centre for Cellular Genomics, Sydney, NSW, Australia
- Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Christopher J. Jolly
- School of Biomedical Sciences, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Fabio Zanini
- School of Clinical Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Garvan-Weizmann Centre for Cellular Genomics, Sydney, NSW, Australia
- Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW, Australia
| | - John E. Pimanda
- School of Biomedical Sciences, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Department of Clinical Haematology, Prince of Wales Hospital, Sydney, NSW, Australia
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Anande G, Deshpande NP, Mareschal S, Batcha AMN, Hampton HR, Herold T, Lehmann S, Wilkins MR, Wong JWH, Unnikrishnan A, Pimanda JE. RNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia. Clin Cancer Res 2020; 26:3597-3607. [PMID: 32122925 DOI: 10.1158/1078-0432.ccr-20-0184] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/13/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE RNA splicing is a fundamental biological process that generates protein diversity from a finite set of genes. Recurrent somatic mutations of splicing factor genes are common in some hematologic cancers but are relatively uncommon in acute myeloid leukemia (AML, < 20% of patients). We examined whether RNA splicing differences exist in AML, even in the absence of splicing factor mutations. EXPERIMENTAL DESIGN We developed a bioinformatics pipeline to study alternative RNA splicing in RNA-sequencing data from large cohorts of patients with AML. RESULTS We have identified recurrent differential alternative splicing between patients with poor and good prognosis. These splicing events occurred even in patients without any discernible splicing factor mutations. Alternative splicing recurrently occurred in genes with specific molecular functions, primarily related to protein translation. Developing tools to predict the functional impact of alternative splicing on the translated protein, we discovered that approximately 45% of the splicing events directly affected highly conserved protein domains. Several splicing factors were themselves misspliced and the splicing of their target transcripts were altered. Studying differential gene expression in the same patients, we identified that alternative splicing of protein translation genes in ELNAdv patients resulted in the induction of an integrated stress response and upregulation of inflammation-related genes. Finally, using machine learning techniques, we identified a splicing signature of four genes which refine the accuracy of existing risk prognosis schemes and validated it in a completely independent cohort. CONCLUSIONS Our discoveries therefore identify aberrant alternative splicing as a molecular feature of adverse AML with clinical relevance.See related commentary by Bowman, p. 3503.
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Affiliation(s)
- Govardhan Anande
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales Sydney, New South Wales, Australia
| | - Nandan P Deshpande
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, New South Wales, Australia
| | - Sylvain Mareschal
- Hematology Centre, Karolinska University Hospital and Department of Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Aarif M N Batcha
- Institute of Medical Data Processing, Biometrics and Epidemiology, Faculty of Medicine, LMU Munich, Munich, Germany.,Data Integration for Future Medicine, LMU Munich, Munich, Germany
| | - Henry R Hampton
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales Sydney, New South Wales, Australia
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Soren Lehmann
- Hematology Centre, Karolinska University Hospital and Department of Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, New South Wales, Australia
| | - Jason W H Wong
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales Sydney, New South Wales, Australia.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Ashwin Unnikrishnan
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales Sydney, New South Wales, Australia.
| | - John E Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales Sydney, New South Wales, Australia. .,Department of Pathology, School of Medical Sciences, University of New South Wales Sydney, New South Wales, Australia.,Department of Haematology, Prince of Wales Hospital, Sydney, New South Wales, Australia
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Abstract
Lymphatic vessels collect interstitial fluid that has extravasated from blood vessels and return it to the circulatory system. Another important function of the lymphatic network is to facilitate immune cell migration and antigen transport from the periphery to draining lymph nodes. This migration plays a crucial role in immune surveillance, initiation of immune responses and tolerance. Here we discuss the significance and mechanisms of lymphatic migration of innate and adaptive immune cells in homeostasis, inflammation and cancer.
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Affiliation(s)
| | - Tatyana Chtanova
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales Sydney, Kensington, NSW, Australia
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Suan D, Nguyen A, Moran I, Bourne K, Hermes JR, Arshi M, Hampton HR, Tomura M, Miwa Y, Kelleher AD, Kaplan W, Deenick EK, Tangye SG, Brink R, Chtanova T, Phan TG. T follicular helper cells have distinct modes of migration and molecular signatures in naive and memory immune responses. Immunity 2015; 42:704-18. [PMID: 25840682 DOI: 10.1016/j.immuni.2015.03.002] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/24/2014] [Accepted: 02/05/2015] [Indexed: 12/13/2022]
Abstract
B helper follicular T (Tfh) cells are critical for long-term humoral immunity. However, it remains unclear how these cells are recruited and contribute to secondary immune responses. Here we show that primary Tfh cells segregate into follicular mantle (FM) and germinal center (GC) subpopulations that display distinct gene expression signatures. Restriction of the primary Tfh cell subpopulation in the GC was mediated by downregulation of chemotactic receptor EBI2. Following collapse of the GC, memory T cells persisted in the outer follicle where they scanned CD169(+) subcapsular sinus macrophages. Reactivation and intrafollicular expansion of these follicular memory T cells in the subcapsular region was followed by their extrafollicular dissemination via the lymphatic flow. These data suggest that Tfh cells integrate their antigen-experience history to focus T cell help within the GC during primary responses but act rapidly to provide systemic T cell help after re-exposure to the antigen.
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Affiliation(s)
- Dan Suan
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, 390 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Akira Nguyen
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, 390 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Imogen Moran
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, 390 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Katherine Bourne
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Jana R Hermes
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Mehreen Arshi
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Centre for Applied Medical Research, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
| | - Henry R Hampton
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, 390 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Michio Tomura
- Kyoto University Graduate School of Medicine, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshihiro Miwa
- University of Tsukuba, Ibaraki Prefecture, Tsukuba 305-8572, Japan
| | - Anthony D Kelleher
- St Vincent's Centre for Applied Medical Research, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
| | - Warren Kaplan
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, 390 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Elissa K Deenick
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, 390 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Stuart G Tangye
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, 390 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Robert Brink
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, 390 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Tatyana Chtanova
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, 390 Victoria Street, Darlinghurst, NSW 2010, Australia.
| | - Tri Giang Phan
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, 390 Victoria Street, Darlinghurst, NSW 2010, Australia.
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