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Hong DS, Van Tine BA, Biswas S, McAlpine C, Johnson ML, Olszanski AJ, Clarke JM, Araujo D, Blumenschein GR, Kebriaei P, Lin Q, Tipping AJ, Sanderson JP, Wang R, Trivedi T, Annareddy T, Bai J, Rafail S, Sun A, Fernandes L, Navenot JM, Bushman FD, Everett JK, Karadeniz D, Broad R, Isabelle M, Naidoo R, Bath N, Betts G, Wolchinsky Z, Batrakou DG, Van Winkle E, Elefant E, Ghobadi A, Cashen A, Grand'Maison A, McCarthy P, Fracasso PM, Norry E, Williams D, Druta M, Liebner DA, Odunsi K, Butler MO. Autologous T cell therapy for MAGE-A4 + solid cancers in HLA-A*02 + patients: a phase 1 trial. Nat Med 2023; 29:104-114. [PMID: 36624315 PMCID: PMC9873554 DOI: 10.1038/s41591-022-02128-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 11/09/2022] [Indexed: 01/11/2023]
Abstract
Affinity-optimized T cell receptors can enhance the potency of adoptive T cell therapy. Afamitresgene autoleucel (afami-cel) is a human leukocyte antigen-restricted autologous T cell therapy targeting melanoma-associated antigen A4 (MAGE-A4), a cancer/testis antigen expressed at varying levels in multiple solid tumors. We conducted a multicenter, dose-escalation, phase 1 trial in patients with relapsed/refractory metastatic solid tumors expressing MAGE-A4, including synovial sarcoma (SS), ovarian cancer and head and neck cancer ( NCT03132922 ). The primary endpoint was safety, and the secondary efficacy endpoints included overall response rate (ORR) and duration of response. All patients (N = 38, nine tumor types) experienced Grade ≥3 hematologic toxicities; 55% of patients (90% Grade ≤2) experienced cytokine release syndrome. ORR (all partial response) was 24% (9/38), 7/16 (44%) for SS and 2/22 (9%) for all other cancers. Median duration of response was 25.6 weeks (95% confidence interval (CI): 12.286, not reached) and 28.1 weeks (95% CI: 12.286, not reached) overall and for SS, respectively. Exploratory analyses showed that afami-cel infiltrates tumors, has an interferon-γ-driven mechanism of action and triggers adaptive immune responses. In addition, afami-cel has an acceptable benefit-risk profile, with early and durable responses, especially in patients with metastatic SS. Although the small trial size limits conclusions that can be drawn, the results warrant further testing in larger studies.
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Affiliation(s)
- David S Hong
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Brian A Van Tine
- Section of Medical Oncology, Division of Oncology, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Melissa L Johnson
- Sarah Cannon Cancer Institute, Tennessee Oncology/One Oncology, Nashville, TN, USA
| | - Anthony J Olszanski
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Dejka Araujo
- Department of Sarcoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George R Blumenschein
- Department of Thoracic-Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Partow Kebriaei
- Department of Stem Cell Transplantation and Cellular Therapy, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Quan Lin
- Adaptimmue, Philadelphia, PA, USA
| | | | | | | | | | | | - Jane Bai
- Adaptimmue, Philadelphia, PA, USA
| | | | - Amy Sun
- Adaptimmue, Philadelphia, PA, USA
| | | | | | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Derin Karadeniz
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | | | - Armin Ghobadi
- Section of Medical Oncology, Division of Oncology, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Amanda Cashen
- Section of Medical Oncology, Division of Oncology, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne Grand'Maison
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Philip McCarthy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | | | | | | | - Mihaela Druta
- Sarcoma Medical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - David A Liebner
- Department of Internal Medicine, Division of Medical Oncology, and Department of Biomedical Informatics, Division of Computational Biology and Bioinformatics, Ohio State University, Columbus, OH, USA
| | - Kunle Odunsi
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
| | - Marcus O Butler
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
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2
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Ramachandran I, Lowther DE, Dryer-Minnerly R, Wang R, Fayngerts S, Nunez D, Betts G, Bath N, Tipping AJ, Melchiori L, Navenot JM, Glod J, Mackall CL, D'Angelo SP, Araujo DM, Chow WA, Demetri GD, Druta M, Van Tine BA, Grupp SA, Abdul Razak AR, Wilky B, Iyengar M, Trivedi T, Winkle EV, Chagin K, Amado R, Binder GK, Basu S. Systemic and local immunity following adoptive transfer of NY-ESO-1 SPEAR T cells in synovial sarcoma. J Immunother Cancer 2019; 7:276. [PMID: 31651363 PMCID: PMC6813983 DOI: 10.1186/s40425-019-0762-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/26/2019] [Indexed: 12/31/2022] Open
Abstract
Background Gene-modified autologous T cells expressing NY-ESO-1c259, an affinity-enhanced T-cell receptor (TCR) reactive against the NY-ESO-1-specific HLA-A*02-restricted peptide SLLMWITQC (NY-ESO-1 SPEAR T-cells; GSK 794), have demonstrated clinical activity in patients with advanced synovial sarcoma (SS). The factors contributing to gene-modified T-cell expansion and the changes within the tumor microenvironment (TME) following T-cell infusion remain unclear. These studies address the immunological mechanisms of response and resistance in patients with SS treated with NY-ESO-1 SPEAR T-cells. Methods Four cohorts were included to evaluate antigen expression and preconditioning on efficacy. Clinical responses were assessed by RECIST v1.1. Engineered T-cell persistence was determined by qPCR. Serum cytokines were evaluated by immunoassay. Transcriptomic analyses and immunohistochemistry were performed on tumor biopsies from patients before and after T-cell infusion. Gene-modified T-cells were detected within the TME via an RNAish assay. Results Responses across cohorts were affected by preconditioning and intra-tumoral NY-ESO-1 expression. Of the 42 patients reported (data cut-off 4June2018), 1 patient had a complete response, 14 patients had partial responses, 24 patients had stable disease, and 3 patients had progressive disease. The magnitude of gene-modified T-cell expansion shortly after infusion was associated with response in patients with high intra-tumoral NY-ESO-1 expression. Patients receiving a fludarabine-containing conditioning regimen experienced increases in serum IL-7 and IL-15. Prior to infusion, the TME exhibited minimal leukocyte infiltration; CD163+ tumor-associated macrophages (TAMs) were the dominant population. Modest increases in intra-tumoral leukocytes (≤5%) were observed in a subset of subjects at approximately 8 weeks. Beyond 8 weeks post infusion, the TME was minimally infiltrated with a TAM-dominant leukocyte infiltrate. Tumor-associated antigens and antigen presentation did not significantly change within the tumor post-T-cell infusion. Finally, NY-ESO-1 SPEAR T cells trafficked to the TME and maintained cytotoxicity in a subset of patients. Conclusions Our studies elucidate some factors that underpin response and resistance to NY-ESO-1 SPEAR T-cell therapy. From these data, we conclude that a lymphodepletion regimen containing high doses of fludarabine and cyclophosphamide is necessary for SPEAR T-cell persistence and efficacy. Furthermore, these data demonstrate that non-T-cell inflamed tumors, which are resistant to PD-1/PD-L1 inhibitors, can be treated with adoptive T-cell based immunotherapy. Trial registration ClinicalTrials.gov, NCT01343043, Registered 27 April 2011.
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Affiliation(s)
| | | | | | - Ruoxi Wang
- Adaptimmune, Oxford, UK.,Adaptimmune, Philadelphia, PA, USA
| | | | - Daniel Nunez
- Adaptimmune, Oxford, UK.,Adaptimmune, Philadelphia, PA, USA
| | - Gareth Betts
- Adaptimmune, Oxford, UK.,Adaptimmune, Philadelphia, PA, USA
| | - Natalie Bath
- Adaptimmune, Oxford, UK.,Adaptimmune, Philadelphia, PA, USA
| | - Alex J Tipping
- Adaptimmune, Oxford, UK.,Adaptimmune, Philadelphia, PA, USA
| | - Luca Melchiori
- Adaptimmune, Oxford, UK.,Adaptimmune, Philadelphia, PA, USA
| | | | - John Glod
- National Cancer Institute, Bethesda, MD, USA
| | | | - Sandra P D'Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dejka M Araujo
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Brian A Van Tine
- Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Stephan A Grupp
- Pediatric Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Breelyn Wilky
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Malini Iyengar
- Adaptimmune, Oxford, UK.,Adaptimmune, Philadelphia, PA, USA
| | - Trupti Trivedi
- Adaptimmune, Oxford, UK.,Adaptimmune, Philadelphia, PA, USA
| | | | - Karen Chagin
- Adaptimmune, Oxford, UK.,Adaptimmune, Philadelphia, PA, USA
| | - Rafael Amado
- Adaptimmune, Oxford, UK.,Adaptimmune, Philadelphia, PA, USA
| | | | - Samik Basu
- Adaptimmune, Oxford, UK. .,Adaptimmune, Philadelphia, PA, USA.
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3
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Merryweather-Clarke AT, Tipping AJ, Lamikanra AA, Fa R, Abu-Jamous B, Tsang HP, Carpenter L, Robson KJH, Nandi AK, Roberts DJ. Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors. BMC Genomics 2016; 17:817. [PMID: 27769165 PMCID: PMC5073849 DOI: 10.1186/s12864-016-3134-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 09/27/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Human-induced pluripotent stem cells (hiPSCs) are a potentially invaluable resource for regenerative medicine, including the in vitro manufacture of blood products. HiPSC-derived red blood cells are an attractive therapeutic option in hematology, yet exhibit unexplained proliferation and enucleation defects that presently preclude such applications. We hypothesised that substantial differential regulation of gene expression during erythroid development accounts for these important differences between hiPSC-derived cells and those from adult or cord-blood progenitors. We thus cultured erythroblasts from each source for transcriptomic analysis to investigate differential gene expression underlying these functional defects. RESULTS Our high resolution transcriptional view of definitive erythropoiesis captures the regulation of genes relevant to cell-cycle control and confers statistical power to deploy novel bioinformatics methods. Whilst the dynamics of erythroid program elaboration from adult and cord blood progenitors were very similar, the emerging erythroid transcriptome in hiPSCs revealed radically different program elaboration compared to adult and cord blood cells. We explored the function of differentially expressed genes in hiPSC-specific clusters defined by our novel tunable clustering algorithms (SMART and Bi-CoPaM). HiPSCs show reduced expression of c-KIT and key erythroid transcription factors SOX6, MYB and BCL11A, strong HBZ-induction, and aberrant expression of genes involved in protein degradation, lysosomal clearance and cell-cycle regulation. CONCLUSIONS Together, these data suggest that hiPSC-derived cells may be specified to a primitive erythroid fate, and implies that definitive specification may more accurately reflect adult development. We have therefore identified, for the first time, distinct gene expression dynamics during erythroblast differentiation from hiPSCs which may cause reduced proliferation and enucleation of hiPSC-derived erythroid cells. The data suggest several mechanistic defects which may partially explain the observed aberrant erythroid differentiation from hiPSCs.
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Affiliation(s)
- Alison T Merryweather-Clarke
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK.,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK
| | - Alex J Tipping
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK.,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK
| | - Abigail A Lamikanra
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK. .,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK.
| | - Rui Fa
- Department of Electronic and Computer Engineering, Brunel University London, Middlesex, UB8 3PH, UK
| | - Basel Abu-Jamous
- Department of Electronic and Computer Engineering, Brunel University London, Middlesex, UB8 3PH, UK
| | - Hoi Pat Tsang
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK.,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK
| | - Lee Carpenter
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK.,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK
| | - Kathryn J H Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, OX3 9DU, Oxford, UK
| | - Asoke K Nandi
- Department of Electronic and Computer Engineering, Brunel University London, Middlesex, UB8 3PH, UK.,Distinguished Visiting Professor, The Key Laboratory of Embedded Systems and Service Computing, College of Electronic and Information Engineering, Tongji University, Shanghai, People's Republic of China
| | - David J Roberts
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK. .,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK.
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4
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Billing M, Rörby E, May G, Tipping AJ, Soneji S, Brown J, Salminen M, Karlsson G, Enver T, Karlsson S. A network including TGFβ/Smad4, Gata2, and p57 regulates proliferation of mouse hematopoietic progenitor cells. Exp Hematol 2016; 44:399-409.e5. [DOI: 10.1016/j.exphem.2016.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/02/2016] [Accepted: 02/02/2016] [Indexed: 12/29/2022]
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5
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Lamikanra AA, Merryweather-Clarke AT, Tipping AJ, Roberts DJ. Correction: distinct mechanisms of inadequate erythropoiesis induced by tumor necrosis factor alpha or malarial pigment. PLoS One 2015; 10:e0127124. [PMID: 25901953 PMCID: PMC4406583 DOI: 10.1371/journal.pone.0127124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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6
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Lamikanra AA, Merryweather-Clarke AT, Tipping AJ, Roberts DJ. Distinct mechanisms of inadequate erythropoiesis induced by tumor necrosis factor alpha or malarial pigment. PLoS One 2015; 10:e0119836. [PMID: 25781011 PMCID: PMC4363658 DOI: 10.1371/journal.pone.0119836] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/19/2014] [Indexed: 12/18/2022] Open
Abstract
The role of infection in erythropoietic dysfunction is poorly understood. In children with P. falciparum malaria, the by-product of hemoglobin digestion in infected red cells (hemozoin) is associated with the severity of anemia which is independent of circulating levels of the inflammatory cytokine tumor necrosis alpha (TNF-α). To gain insight into the common and specific effects of TNF-α and hemozoin on erythropoiesis, we studied the gene expression profile of purified primary erythroid cultures exposed to either TNF-α (10ng/ml) or to hemozoin (12.5μg/ml heme units) for 24 hours. Perturbed gene function was assessed using co-annotation of associated gene ontologies and expression of selected genes representative of the profile observed was confirmed by real time PCR (rtPCR). The changes in gene expression induced by each agent were largely distinct; many of the genes significantly modulated by TNF-α were not affected by hemozoin. The genes modulated by TNF-α were significantly enriched for those encoding proteins involved in the control of type 1 interferon signalling and the immune response to viral infection. In contrast, genes induced by hemozoin were significantly enriched for functional roles in regulation of transcription and apoptosis. Further analyses by rtPCR revealed that hemozoin increases expression of transcription factors that form part of the integrated stress response which is accompanied by reduced expression of genes involved in DNA repair. This study confirms that hemozoin induces cellular stress on erythroblasts that is additional to and distinct from responses to inflammatory cytokines and identifies new genes that may be involved in the pathogenesis of severe malarial anemia. More generally the respective transcription profiles highlight the varied mechanisms through which erythropoiesis may be disrupted during infectious disease.
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Affiliation(s)
- Abigail A. Lamikanra
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9BQ, United Kingdom
- National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford OX3 9BQ, United Kingdom
- * E-mail:
| | - Alison T. Merryweather-Clarke
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9BQ, United Kingdom
- National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford OX3 9BQ, United Kingdom
| | - Alex J. Tipping
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9BQ, United Kingdom
- National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford OX3 9BQ, United Kingdom
| | - David J. Roberts
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9BQ, United Kingdom
- National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford OX3 9BQ, United Kingdom
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7
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Livak KJ, Wills QF, Tipping AJ, Datta K, Mittal R, Goldson AJ, Sexton DW, Holmes CC. Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells. Methods 2013; 59:71-9. [PMID: 23079396 PMCID: PMC3562442 DOI: 10.1016/j.ymeth.2012.10.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/18/2012] [Accepted: 10/05/2012] [Indexed: 01/10/2023] Open
Abstract
The stochastic nature of generating eukaryotic transcripts challenges conventional methods for obtaining and analyzing single-cell gene expression data. In order to address the inherent noise, detailed methods are described on how to collect data on multiple genes in a large number of single cells using microfluidic arrays. As part of a study exploring the effect of genotype on Wnt pathway activation, data were collected for 96 qPCR assays on 1440 lymphoblastoid cells. The description of methods includes preliminary data processing steps. The methods used in the collection and analysis of single-cell qPCR data are contrasted with those used in conventional qPCR.
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Affiliation(s)
- Kenneth J. Livak
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA
| | - Quin F. Wills
- Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
| | - Alex J. Tipping
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Krishnalekha Datta
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA
| | - Rowena Mittal
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA
| | - Andrew J. Goldson
- UEA Flow Cytometry Services, BioMedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Darren W. Sexton
- BioMedical Research Centre, Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Chris C. Holmes
- Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
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8
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Rodrigues NP, Tipping AJ, Wang Z, Enver T. GATA-2 mediated regulation of normal hematopoietic stem/progenitor cell function, myelodysplasia and myeloid leukemia. Int J Biochem Cell Biol 2011; 44:457-60. [PMID: 22192845 DOI: 10.1016/j.biocel.2011.12.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 12/05/2011] [Accepted: 12/07/2011] [Indexed: 01/22/2023]
Abstract
Unremitting blood cell production throughout the lifetime of an organism is reliant on hematopoietic stem cells (HSCs). A rare and relatively quiescent cell type, HSCs are, on entry into cell cycle fated to self-renew, undergo apoptosis or differentiate to progenitors (HPCs) that eventually yield specific classes of blood cells. Disruption of these HSC fate decisions is considered to be fundamental to the development of leukemia. Much effort has therefore been placed on understanding the molecular pathways that regulate HSC fate decisions and how these processes are undermined in leukemia. Transcription factors have emerged as critical regulators in this respect. Here we review the participation of zinc finger transcription factor GATA-2 in regulating normal hematopoietic stem and progenitor cell functionality, myelodysplasia and myeloid leukemia.
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Affiliation(s)
- Neil P Rodrigues
- National Institutes of Health Center for Biomedical Research Excellence in Stem Cell Biology, Roger Williams Medical Center, Boston University School of Medicine, Providence, RI 02908, United States.
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9
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Schuh AH, Tipping AJ, Clark AJ, Hamlett I, Guyot B, Iborra FJ, Rodriguez P, Strouboulis J, Enver T, Vyas P, Porcher C. ETO-2 associates with SCL in erythroid cells and megakaryocytes and provides repressor functions in erythropoiesis. Mol Cell Biol 2005; 25:10235-50. [PMID: 16287841 PMCID: PMC1291220 DOI: 10.1128/mcb.25.23.10235-10250.2005] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [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: 04/15/2005] [Revised: 05/07/2005] [Accepted: 09/14/2005] [Indexed: 12/19/2022] Open
Abstract
Lineage specification and cellular maturation require coordinated regulation of gene expression programs. In large part, this is dependent on the activator and repressor functions of protein complexes associated with tissue-specific transcriptional regulators. In this study, we have used a proteomic approach to characterize multiprotein complexes containing the key hematopoietic regulator SCL in erythroid and megakaryocytic cell lines. One of the novel SCL-interacting proteins identified in both cell types is the transcriptional corepressor ETO-2. Interaction between endogenous proteins was confirmed in primary cells. We then showed that SCL complexes are shared but also significantly differ in the two cell types. Importantly, SCL/ETO-2 interacts with another corepressor, Gfi-1b, in red cells but not megakaryocytes. The SCL/ETO-2/Gfi-1b association is lost during erythroid differentiation of primary fetal liver cells. Genetic studies of erythroid cells show that ETO-2 exerts a repressor effect on SCL target genes. We suggest that, through its association with SCL, ETO-2 represses gene expression in the early stages of erythroid differentiation and that alleviation/modulation of the repressive state is then required for expression of genes necessary for terminal erythroid maturation to proceed.
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Affiliation(s)
- Anna H Schuh
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
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10
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Tipping AJ, Baluch S, Barnes DJ, Veach DR, Clarkson BM, Bornmann WG, Mahon FX, Goldman JM, Melo JV. Efficacy of dual-specific Bcr-Abl and Src-family kinase inhibitors in cells sensitive and resistant to imatinib mesylate. Leukemia 2004; 18:1352-6. [PMID: 15201856 DOI: 10.1038/sj.leu.2403416] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [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] [Indexed: 11/09/2022]
Abstract
Monotherapy of chronic myeloid leukemia (CML) with imatinib mesylate has been cast into shadow by the evolution of clinical resistance during therapy. Resistance to imatinib can arise by multiple mechanisms including amplification or mutation of Bcr-Abl, and continuity of imatinib therapy is probably a poor option for either of these patient groups. Recently, however, a structurally distinct new class of drugs, the pyrido[2,3-d]pyrimidines, has been described, and these compounds are predicted to make different molecular contacts in the Abl kinase domain. These drugs potently target both the Bcr-Abl and Src-family kinase activities, both of which are thought to be relevant to survival of the leukemic cell. We asked whether these drugs could selectively induce cell death in murine cell line models of CML cells sensitive and resistant to imatinib by different mechanisms. We show that whereas the pyrido[2,3-d] pyrimidines are indeed highly potent in suppressing proliferation of Bcr-Abl-overexpressing imatinib-resistant cells, they are almost completely ineffective against cells expressing the T315I mutant. This implies that despite structural differences from imatinib, these drugs are unlikely to be useful in patients expressing this mutant Bcr-Abl protein, but may be effective in cases where selection of cells overexpressing the oncoprotein leads to refractoriness to imatinib.
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MESH Headings
- Animals
- Benzamides
- Cell Division/drug effects
- Cell Line, Tumor
- Dose-Response Relationship, Drug
- Drug Delivery Systems
- Drug Resistance, Neoplasm
- Enzyme Inhibitors/pharmacology
- Enzyme Inhibitors/therapeutic use
- Fusion Proteins, bcr-abl/analysis
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Mice
- Piperazines/pharmacology
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Pyrimidines/pharmacology
- Pyrimidines/therapeutic use
- Treatment Outcome
- src-Family Kinases/antagonists & inhibitors
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Affiliation(s)
- A J Tipping
- Department of Haematology, Imperial College London, Hammersmith Hospital, London, UK
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11
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Tipping AJ, Melo JV. Comparative gene expression profile of p185(Bcr-Abl) versus p210(Bcr-Abl) expressing cells. Leuk Res 2003; 28:219-20. [PMID: 14687613 DOI: 10.1016/j.leukres.2003.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
MESH Headings
- Animals
- Bone Marrow Cells/metabolism
- Fusion Proteins, bcr-abl/biosynthesis
- Fusion Proteins, bcr-abl/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Mice
- Protein Isoforms/biosynthesis
- Protein Isoforms/genetics
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Fusion Proteins/genetics
- Transcription, Genetic
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12
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Tipping AJ, Vulliamy TJ, Morgan NV, Dokal I. Molecular Diagnosis of Fanconi Anemia and Dyskeratosis Congenita. Pediatric Hematology 2003; 91:3-17. [PMID: 14573926 DOI: 10.1385/1-59259-433-6:3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Tipping AJ, Deininger MW, Goldman JM, Melo JV. Comparative gene expression profile of chronic myeloid leukemia cells innately resistant to imatinib mesylate. Exp Hematol 2003; 31:1073-80. [PMID: 14585372] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
OBJECTIVE Resistance to imatinib mesylate monotherapy is clearly a barrier to successful treatment of chronic myeloid leukemia (CML) patients. In some patients, resistance arises due to powerful selective pressure on rare cells that carry amplified copies of the BCR-ABL fusion oncogene or point mutations in the Bcr-Abl tyrosine kinase domain that affect binding of the drug to the oncoprotein. However, in a proportion of patients neither mechanism operates, and resistance appears to be a priori, existing prior to exposure to the drug. These mechanisms of imatinib resistance are poorly understood and may be heterogeneous. MATERIALS AND METHODS We have previously described such innate resistance to imatinib in subclones of a myeloid leukemia cell line, KCL22, in which imatinib exposure inhibits the activity of Bcr-Abl and yet fails to induce apoptosis. We describe here whole-genome expression analysis of imatinib-sensitive and -resistant cells derived from the original KCL22 line, using Affymetrix microarray analysis. RESULTS We detected differential expression of 39 genes that correlate with the imatinib-resistant phenotype. The resistant cells overexpress several genes associated with the suppression of apoptosis or with conferral of a transformed phenotype. CONCLUSION Amongst the differentially-expressed genes correlating with imatinib resistance, several suggest the activation of alternative pathway(s) that maintain viability and growth independently of Bcr-Abl kinase activity. Given the high rate of primary imatinib resistance in blast crisis, the potential of activating such alternative pathways appears to correlate with disease progression.
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Affiliation(s)
- Alex J Tipping
- Department of Haematology, Imperial College London, Hammersmith Hospital, London, UK
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14
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Abstract
Imatinib mesylate (Gleevec) (formerly STI571) has secured a definitive role in the treatment of chronic myeloid leukemia (CML) due to its specificity and efficacy. Although some patients become resistant to the drug, it may still be possible to control the leukemia with imatinib-containing regimens. Front-line treatment with such combinations may indeed minimize the risk that resistance, and hence relapse, occurs. In this review, we discuss the published data on in vitro studies that address this question in a variety of models, and attempt to predict efficacious combinations for future clinical trials. These represent regimens where imatinib is combined with conventional chemotherapeutic drugs or with inhibitors of other key signal transduction molecules that may be preferentially activated in CML cells.
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Affiliation(s)
- Alex J Tipping
- Department of Haematology, Imperial College London, Hammersmith Hospital, London, UK
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15
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Tipping AJ, Mahon FX, Zafirides G, Lagarde V, Goldman JM, Melo JV. Drug responses of imatinib mesylate-resistant cells: synergism of imatinib with other chemotherapeutic drugs. Leukemia 2002; 16:2349-57. [PMID: 12454739 DOI: 10.1038/sj.leu.2402775] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2002] [Accepted: 08/27/2002] [Indexed: 11/09/2022]
Abstract
Imatinib mesylate (STI571, Glivec, Gleevec) is a powerful inhibitor of the tyrosine kinase activity of Bcr-Abl, the oncoprotein responsible for chronic myeloid leukemia (CML). The drug shows great efficacy in chronic phase, but is less effective in maintaining hematologic remissions in blast crisis patients. Our group has previously described several cell lines made resistant to imatinib. We now examine the question of cross-resistance to other chemotherapeutic drugs used in CML. Four paired imatinib-sensitive/resistant CML cell lines were assessed by caspase-3 and MTS assays for their proliferative response to cytosine arabinoside (Ara-C), daunorubicin (DNR), homoharringtonine (HHT) and hydroxyurea (HU), either alone or in combination with imatinib. Primary blasts from advanced-stage CML patients refractory to imatinib therapy were studied by semi-solid media clonogenic assays. We found that these drugs are generally capable of major inhibition of proliferation of the CML cell lines, although differential responses to DNR and HHT were noted between some sensitive and resistant cell line pairs, implying that resistance to imatinib may confer a growth advantage under such conditions. The four drugs were also effective in preventing the formation of progenitor cell colonies from CML patients both before treatment with imatinib, and after relapse on the drug. Isobolographic analysis implied that these drugs will generally combine well with imatinib, and in some cases will be synergistic. We conclude that Ara-C, DNR or HHT, either alone or in combination with imatinib, are likely to be the best therapeutic alternatives in the management of patients who become resistant to imatinib monotherapy.
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Affiliation(s)
- A J Tipping
- Dept of Haematology, Imperial College of Science, Technology and Medicine, Hammersmith Hospital, London, UK
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16
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Abstract
STI571 induces sustained hematologic remission in patients with chronic myeloid leukemia (CML) in chronic phase. However, in advanced phases, especially blast crisis, the leukemia usually becomes resistant within months. It has been investigated whether resistance to STI571 is stable and immutable or whether it can be reversed in selected CML cell lines. Withdrawal of STI571 for varying lengths of time from cultures of 3 resistant lines (K562-r, KCL22-r, and Baf/BCR-ABL-r1) did not restore sensitivity to the inhibitor. In contrast, LAMA84-resistant cells experienced a sharp reduction in survival and proliferation during the first week of STI571 withdrawal but recovered thereafter. Moreover, when left off the inhibitor for 2 months or longer, this cell line reacquired sensitivity to STI571. It is hypothesized, therefore, that patients who have become resistant to the drug may respond again if STI571 therapy is temporarily interrupted.
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MESH Headings
- Animals
- Benzamides
- Caspase 3
- Caspases/metabolism
- Cell Division/drug effects
- Cell Survival/drug effects
- Drug Resistance, Neoplasm/genetics
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Gene Expression
- Imatinib Mesylate
- In Situ Hybridization, Fluorescence
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Mice
- Phosphorylation
- Piperazines
- Pyrimidines/administration & dosage
- Pyrimidines/pharmacology
- Pyrimidines/therapeutic use
- Tumor Cells, Cultured
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Affiliation(s)
- A J Tipping
- Department of Haematology, Imperial College School of Medicine, Hammersmith Hospital, London, United Kingdom
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17
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Laurenzi M, Tipping AJ, Marcus SE, Knox JP, Federico R, Angelini R, McPherson MJ. Analysis of the distribution of copper amine oxidase in cell walls of legume seedlings. Planta 2001; 214:37-45. [PMID: 11762169 DOI: 10.1007/s004250100600] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Copper-containing amine oxidase (CuAO) has been proposed to play a role in H2O2 production in plant cell walls during cell development and in response to pathogen attack. We have compared the localisation of CuAO in pea (Pisum sativum L.), lentil (Lens culinaris M.) and chick pea (Cicer arietinum L.) grown under different light conditions, using both immuno- and histochemical techniques. The enzyme was detected by indirect immunofluorescence in the cell walls of parenchyma tissues of etiolated pea and lentil plants and was particularly abundant at intercellular spaces. Upon de-etiolation, CuAO largely disappeared from cortical cell walls except in the region of intercellular spaces. In the apical internode of light-grown seedlings, CuAO occurred mainly in cortical cell walls and, to some extent, in cell walls of xylem vessels. In both the elongation zone and mature regions of roots, CuAO was restricted to cortical cell walls and some cell junctions close to the meristem. Extensin epitopes co-localised to intercellular spaces of the cortex in de-etiolated pea, indicating that CuAO may have a role in cell wall strengthening at intercellular spaces. In chick pea, the localisation of the enzyme varied between different cultivars that have differing susceptibility to the fungus Ascochyta rabiei. In a susceptible cultivar Calia, immunogold labelling localised CuAO to cell walls of the cortex, as in lentil and pea, while in a resistant cultivar Sultano, it was most abundant in xylem vessels and, in light-grown plants, in the epidermis. These expression patterns are discussed with regard to the possible functions of amine oxidase in cell growth, cell differentiation and pathogen resistance.
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Affiliation(s)
- M Laurenzi
- Dipartimento di Biologia, Università degli Studi Roma Tre, Viale Guglielmo Marconi 446, 00146 Rome, Italy
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18
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Tipping AJ, Pearson T, Morgan NV, Gibson RA, Kuyt LP, Havenga C, Gluckman E, Joenje H, de Ravel T, Jansen S, Mathew CG. Molecular and genealogical evidence for a founder effect in Fanconi anemia families of the Afrikaner population of South Africa. Proc Natl Acad Sci U S A 2001; 98:5734-9. [PMID: 11344308 PMCID: PMC33282 DOI: 10.1073/pnas.091402398] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2000] [Indexed: 02/03/2023] Open
Abstract
Fanconi anemia (FA) is a rare, genetically heterogeneous autosomal recessive disorder associated with progressive aplastic anemia, congenital abnormalities, and cancer. FA has a very high incidence in the Afrikaner population of South Africa, possibly due to a founder effect. Previously we observed allelic association between polymorphic markers flanking the FA group A gene (FANCA) and disease chromosomes in Afrikaners. We genotyped 26 FA families with microsatellite and single nucleotide polymorphic markers and detected five FANCA haplotypes. Mutation scanning of the FANCA gene revealed association of these haplotypes with four different mutations. The most common was an intragenic deletion of exons 12-31, accounting for 60% of FA chromosomes in 46 unrelated Afrikaner FA patients, while two other mutations accounted for an additional 20%. Screening for these mutations in the European populations ancestral to the Afrikaners detected one patient from the Western Ruhr region of Germany who was heterozygous for the major deletion. The mutation was associated with the same unique FANCA haplotype as in Afrikaner patients. Genealogical investigation of 12 Afrikaner families with FA revealed that all were descended from a French Huguenot couple who arrived at the Cape on June 5, 1688, whereas mutation analysis showed that the carriers of the major mutation were descendants of this same couple. The molecular and genealogical evidence is consistent with transmission of the major mutation to Western Germany and the Cape near the end of the 17th century, confirming the existence of a founder effect for FA in South Africa.
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Affiliation(s)
- A J Tipping
- Division of Medical and Molecular Genetics, Guy's, King's, and St. Thomas' School of Medicine, 8th Floor Guy's Tower, Guy's Hospital, London Bridge, London SE1 9RT, United Kingdom
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19
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Demuth I, Wlodarski M, Tipping AJ, Morgan NV, de Winter JP, Thiel M, Gräsl S, Schindler D, D'Andrea AD, Altay C, Kayserili H, Zatterale A, Kunze J, Ebell W, Mathew CG, Joenje H, Sperling K, Digweed M. Spectrum of mutations in the Fanconi anaemia group G gene, FANCG/XRCC9. Eur J Hum Genet 2000; 8:861-8. [PMID: 11093276 DOI: 10.1038/sj.ejhg.5200552] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
FANCG was the third Faconi anaemia gene identified and proved to be identical to the previously cloned XRCC9 gene. We present the pathogenic mutations and sequence variants we have so far identified in a panel of FA-G patients. Mutation screening was performed by PCR, single strand conformational polymorphism analysis and protein truncation tests. Altogether 18 mutations have been determined in 20 families - 97% of all expected mutant alleles. All mutation types have been found, with the exception of large deletions, the large majority is predicted to lead to shortened proteins. One stop codon mutation, E105X, has been found in several German patients and this founder mutation accounts for 44% of the mutant FANCG alleles in German FA-G patients. Comparison of clinical phenotypes shows that patients homozygous for this mutation have an earlier onset of the haematological disorder than most other FA-G patients. The mouse Fancg sequence was established in order to evaluate missense mutations. A putative missense mutation, L71P, in a possible leucine zipper motif may affect FANCG binding of FANCA and seems to be associated with a milder clinical phenotype.
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Affiliation(s)
- I Demuth
- Institute of Human Genetics, Charité, Campus Virchow, Humboldt University, Berlin, Germany
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20
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Morgan NV, Tipping AJ, Joenje H, Mathew CG. High frequency of large intragenic deletions in the Fanconi anemia group A gene. Am J Hum Genet 1999; 65:1330-41. [PMID: 10521298 PMCID: PMC1288285 DOI: 10.1086/302627] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.7] [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: 06/29/1999] [Accepted: 09/20/1999] [Indexed: 11/03/2022] Open
Abstract
Fanconi anemia (FA) is an autosomal recessive disorder exhibiting chromosomal fragility, bone-marrow failure, congenital abnormalities, and cancer. At least eight complementation groups have been described, with group A accounting for 60%-65% of FA patients. Mutation screening of the group A gene (FANCA) is complicated by its highly interrupted genomic structure and heterogeneous mutation spectrum. Recent reports of several large deletions of FANCA, coupled with modest mutation-detection rates, led us to investigate whether many deletions might occur in the heterozygous state and thus fail to be detected by current screening protocols. We used a two-step screening strategy, in which small mutations were detected by fluorescent chemical cleavage of the FANCA transcript, and heterozygosity for gross deletions was detected by quantitative fluorescent multiplex PCR. We screened 26 cell lines from FA complementation group A for FANCA mutations and detected 33 different mutations, 23 of which were novel. Mutations were observed in all 26 cell lines and included 43 of a possible 52 mutant alleles (83%). Of the mutant alleles, 40% were large intragenic deletions that removed up to 31 exons from the gene, indicating that this may be the most prevalent form of mutation in FANCA. Several common deletion breakpoints were observed, and there was a highly significant correlation between the number of breakpoints detected in a given intron and the number of Alu repeats that it contained, which suggests that Alu-mediated recombination may explain the high prevalence of deletions in FANCA. The dual screening strategy that we describe may be useful for mutation screening in other genetic disorders in which mutation-detection rates are unexpectedly low.
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Affiliation(s)
- Neil V. Morgan
- Division of Medical and Molecular Genetics, GKT School of Medicine, Guy's Hospital, London; and Department of Human Genetics, Free University, Amsterdam
| | - Alex J. Tipping
- Division of Medical and Molecular Genetics, GKT School of Medicine, Guy's Hospital, London; and Department of Human Genetics, Free University, Amsterdam
| | - Hans Joenje
- Division of Medical and Molecular Genetics, GKT School of Medicine, Guy's Hospital, London; and Department of Human Genetics, Free University, Amsterdam
| | - Christopher G. Mathew
- Division of Medical and Molecular Genetics, GKT School of Medicine, Guy's Hospital, London; and Department of Human Genetics, Free University, Amsterdam
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21
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Crawford J, Ianzano L, Savino M, Whitmore S, Cleton-Jansen AM, Settasatian C, d'apolito M, Seshadri R, Pronk JC, Auerbach AD, Verlander PC, Mathew CG, Tipping AJ, Doggett NA, Zelante L, Callen DF, Savoia A. The PISSLRE gene: structure, exon skipping, and exclusion as tumor suppressor in breast cancer. Genomics 1999; 56:90-7. [PMID: 10036189 DOI: 10.1006/geno.1998.5676] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In sporadic breast cancer, loss of heterozygosity (LOH) frequently occurs in three discrete regions of the long arm of chromosome 16q, the most telomeric of which is located at 16q24.3. Among the genes mapped to this region, PISSLRE is a plausible candidate tumor suppressor gene. It codes for a putative cyclin-dependent kinase that, as with other members of this family, is likely to be involved in regulating the cell cycle and therefore may have a role in oncogenesis. We characterized the genomic structure of PISSLRE and found that the splicing of this gene is complex. A variety of different transcripts were identified, including those due to cryptic splice sites, exon skipping, insertion of intronic sequences, and exon scrambling. The last phenomenon was observed in a rare PISSLRE transcript in which exons are joined at a nonconsensus splice site in an order different from that predicted by the genomic sequence. To screen the PISSLRE gene in breast tumors with ascertained LOH at 16q24.3, we have analyzed each exon by single-strand conformational polymorphism. No variation was found in the coding sequence, leading us to conclude that another tumor suppressor must be targeted by LOH in sporadic breast cancer.
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Affiliation(s)
- J Crawford
- Department of Cytogenetics and Molecular Genetics, Adelaide Women's and Children's Hospital, North Adelaide, South Australia, 5006, Australia
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22
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Wijker M, Morgan NV, Herterich S, van Berkel CG, Tipping AJ, Gross HJ, Gille JJ, Pals G, Savino M, Altay C, Mohan S, Dokal I, Cavenagh J, Marsh J, van Weel M, Ortega JJ, Schuler D, Samochatova E, Karwacki M, Bekassy AN, Abecasis M, Ebell W, Kwee ML, de Ravel T. Heterogeneous spectrum of mutations in the Fanconi anaemia group A gene. Eur J Hum Genet 1999; 7:52-9. [PMID: 10094191 DOI: 10.1038/sj.ejhg.5200248] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [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] [Indexed: 11/09/2022] Open
Abstract
Fanconi anaemia (FA) is a genetically heterogeneous autosomal recessive disorder associated with chromosomal fragility, bone-marrow failure, congenital abnormalities and cancer. The gene for complementation group A (FAA), which accounts for 60-65% of all cases, has been cloned, and is composed of an open reading frame of 4.3 kb, which is distributed among 43 exons. We have investigated the molecular pathology of FA by screening the FAA gene for mutations in a panel of 90 patients identified by the European FA research group, EUFAR. A highly heterogeneous spectrum of mutations was identified, with 31 different mutations being detected in 34 patients. The mutations were scattered throughout the gene, and most are likely to result in the absence of the FAA protein. A surprisingly high frequency of intragenic deletions was detected, which removed between 1 and 30 exons from the gene. Most microdeletions and insertions occurred at homopolymeric tracts or direct repeats within the coding sequence. These features have not been observed in the other FA gene which has been cloned to date (FAC) and may be indicative of a higher mutation rate in FAA. This would explain why FA group A is much more common than the other complementation groups. The heterogeneity of the mutation spectrum and the frequency of intragenic deletions present a considerable challenge for the molecular diagnosis of FA. A scan of the entire coding sequence of the FAA gene may be required to detect the causative mutations, and scanning protocols will have to include methods which will detect the deletions in compound heterozygotes.
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Affiliation(s)
- M Wijker
- Department of Human Genetics, Free University of Amsterdam, The Netherlands
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23
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Whitmore SA, Settasatian C, Crawford J, Lower KM, McCallum B, Seshadri R, Cornelisse CJ, Moerland EW, Cleton-Jansen AM, Tipping AJ, Mathew CG, Savnio M, Savoia A, Verlander P, Auerbach AD, Van Berkel C, Pronk JC, Doggett NA, Callen DF. Characterization and screening for mutations of the growth arrest-specific 11 (GAS11) and C16orf3 genes at 16q24.3 in breast cancer. Genomics 1998; 52:325-31. [PMID: 9790751 DOI: 10.1006/geno.1998.5457] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [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] [Indexed: 11/22/2022]
Abstract
Loss of heterozygosity involving the long arm of chromosome 16 is a frequent event seen in a number of human carcinomas, including breast, prostate, hepatocellular, and ovarian cancers. A region found to be commonly deleted in breast and prostate carcinomas is located at 16q24.3, which suggests the presence of a tumor suppressor gene that may be altered in these two malignancies. A detailed physical and transcription map of this region that includes the loci defining the smallest region of deletion has been constructed. This report describes the characterization of a transcript located in this region, the growth arrest-specific 11 (GAS11) gene, which was viewed as a potential tumor suppressor gene due to the expression of its mouse homolog specifically during growth arrest. The gene consists of 11 exons spanning approximately 25 kb. Northern blot analysis identified two ubiquitously expressed mRNAs of 3.4 and 1.8 kb produced by the use of alternative polyadenylation sites. Another gene, C16orf3 (chromosome 16 open reading frame 3), was found to lie within intron 2 of GAS11. This gene appears intronless, is transcribed in the orientation opposite to that of GAS11, and is expressed at low levels. These genes were examined for mutations in breast tumor DNA, and both were excluded as tumor suppressor genes involved in breast cancer.
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Affiliation(s)
- S A Whitmore
- Centre for Medical Genetics, Department of Cytogenetics and Molecular Genetics, Women's and Children's Hospital, North Adelaide, South Australia, 5006, Australia.
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24
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Ianzano L, D'Apolito M, Centra M, Savino M, Levran O, Auerbach AD, Cleton-Jansen AM, Doggett NA, Pronk JC, Tipping AJ, Gibson RA, Mathew CG, Whitmore SA, Apostolou S, Callen DF, Zelante L, Savoia A. The genomic organization of the Fanconi anemia group A (FAA) gene. Genomics 1997; 41:309-14. [PMID: 9169126 DOI: 10.1006/geno.1997.4675] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [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] [Indexed: 02/04/2023]
Abstract
Fanconi anemia (FA) is a genetically heterogenous disease involving at least five genes on the basis of complementation analysis (FAA to FAE). The FAA gene has been recently isolated by two independent approaches, positional and functional cloning. In the present study we describe the genomic structure of the FAA gene. The gene contains 43 exons spanning approximately 80 kb as determined by the alignment of four cosmids and the fine localization of the first and the last exons in restriction fragments of these clones. Exons range from 34 to 188 bp. All but three of the splice sites were consistent with the ag-gt rule. We also describe three alternative splicing events in cDNA clones that result in the loss of exon 37, a 23-bp deletion at the 5' end of exon 41, and a GCAG insertion at the 3' portion also in exon 41. Sequence analysis of the 5' region upstream of the putative transcription start site showed no obvious TATA and CAAT boxes, but did show a GC-rich region, typical of housekeeping genes. Knowledge of the structure of the FAA gene will provide an invaluable resource for the discovery of mutations in the gene that accounts for about 60-66% of FA patients.
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Affiliation(s)
- L Ianzano
- Servizio di Genetica Medica, IRCCS-Ospedale CSS, San Giovanni Rotondo, Italy
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25
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Abstract
A pea seedling amine oxidase cDNA has been isolated and sequenced. A single long open reading frame has amino acid sequences corresponding to those determined from active site peptide (Janes, S.M., Palcic, M.M., Scaman, C.H., Smith, A.J., Brown, D.E., Dooley, D.M., Mure, M., and Klinman, J.P. (1992) Biochemistry 31, 12147-12154) and N-terminal sequencing experiments. The latter reveals the protein to have a 25-amino acid leader sequence with characteristics of a secretion signal peptide, as expected for this extracellular enzyme. Comparisons of the amino acid sequence of the mature pea enzyme (649 amino acids) with that of the mature lentil enzyme (569 amino acids; Rossi, A., Petruzzelli, R., and Finazzi-Agrò, A. (1992) FEBS Lett. 301, 253-257) reveal important and unexpected differences particularly with regard to protein length. Sequencing of part of the lentil gene identified several frameshift differences within the coding region resulting in a mature lentil protein of exactly the same length, 649 amino acids, as the pea enzyme. Multiple alignments of 10 copper amine oxidase sequences reveal 33 completely conserved residues of which 10 are found within 41 aligned residues at the C-terminal tails, the region missing from the original lentil sequence. One of only four conserved histidines is found in this region and may represent the third ligand to the copper. The pea enzyme contains around 3-4% carbohydrate as judged by deglycosylation experiments. We have also demonstrated by hybridization analysis that copper amine oxidase genes are present in a range of mono- and dicotyledonous plants.
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Affiliation(s)
- A J Tipping
- Department of Biochemistry and Molecular Biology, University of Leeds, United Kingdom
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26
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Affiliation(s)
- A J Tipping
- Department of Biochemistry and Molecular Biology, University of Leeds, U.K
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