1
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Lopes BA, Meyer C, Bouzada H, Külp M, Maciel ALT, Larghero P, Barbosa TC, Poubel CP, Barbieri C, Venn NC, Pozza LD, Barbaric D, Palmi C, Fazio G, Saitta C, Aguiar TF, Lins MM, Ikoma-Colturato MRV, Schramm M, Chapchap E, Cazzaniga G, Sutton R, Marschalek R, Emerenciano M. The recombinome of IKZF1 deletions in B-cell precursor ALL. Leukemia 2023; 37:1727-1731. [PMID: 37386080 DOI: 10.1038/s41375-023-01935-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Affiliation(s)
- Bruno A Lopes
- Program of Molecular Carcinogenesis and Division of Clinical Research, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil.
- DCAL, Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany.
| | - Claus Meyer
- DCAL, Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
| | - Heloysa Bouzada
- Program of Molecular Carcinogenesis and Division of Clinical Research, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Marius Külp
- DCAL, Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
| | - Ana Luiza Tardem Maciel
- Program of Molecular Carcinogenesis and Division of Clinical Research, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Patrizia Larghero
- DCAL, Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
| | - Thayana C Barbosa
- Program of Molecular Carcinogenesis and Division of Clinical Research, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Caroline P Poubel
- Program of Molecular Carcinogenesis and Division of Clinical Research, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Caroline Barbieri
- Program of Molecular Carcinogenesis and Division of Clinical Research, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Nicola C Venn
- Molecular Diagnostics, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Luciano Dalla Pozza
- Cancer Centre for Children, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | | | - Chiara Palmi
- Tettamanti Cente, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Grazia Fazio
- Tettamanti Cente, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Claudia Saitta
- Tettamanti Cente, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Thais F Aguiar
- Arthur Siqueira Cavalcanti Hematology Institute (HEMORIO), Rio de Janeiro, Brazil
| | - Mecneide M Lins
- Instituto de Medicina Integral Prof. Fernando Figueira (IMIP), Recife, Brazil
| | | | - Marcia Schramm
- Prontobaby Hospital da Criança, Rio de Janeiro, Brazil
- Serviço de Hematologia, Hospital do Câncer I, INCA, Rio de Janeiro, Brazil
| | | | - Gianni Cazzaniga
- Tettamanti Cente, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Medical Genetics, School of Medicine and Surgery, University of Milan Bicocca, Monza, Italy
| | - Rosemary Sutton
- Molecular Diagnostics, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Rolf Marschalek
- DCAL, Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
| | - Mariana Emerenciano
- Program of Molecular Carcinogenesis and Division of Clinical Research, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil.
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2
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Meyer C, Larghero P, Almeida Lopes B, Burmeister T, Gröger D, Sutton R, Venn NC, Cazzaniga G, Corral Abascal L, Tsaur G, Fechina L, Emerenciano M, Pombo-de-Oliveira MS, Lund-Aho T, Lundán T, Montonen M, Juvonen V, Zuna J, Trka J, Ballerini P, Lapillonne H, Van der Velden VHJ, Sonneveld E, Delabesse E, de Matos RRC, Silva MLM, Bomken S, Katsibardi K, Keernik M, Grardel N, Mason J, Price R, Kim J, Eckert C, Lo Nigro L, Bueno C, Menendez P, Zur Stadt U, Gameiro P, Sedék L, Szczepański T, Bidet A, Marcu V, Shichrur K, Izraeli S, Madsen HO, Schäfer BW, Kubetzko S, Kim R, Clappier E, Trautmann H, Brüggemann M, Archer P, Hancock J, Alten J, Möricke A, Stanulla M, Lentes J, Bergmann AK, Strehl S, Köhrer S, Nebral K, Dworzak MN, Haas OA, Arfeuille C, Caye-Eude A, Cavé H, Marschalek R. The KMT2A recombinome of acute leukemias in 2023. Leukemia 2023; 37:988-1005. [PMID: 37019990 PMCID: PMC10169636 DOI: 10.1038/s41375-023-01877-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/09/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023]
Abstract
Chromosomal rearrangements of the human KMT2A/MLL gene are associated with de novo as well as therapy-induced infant, pediatric, and adult acute leukemias. Here, we present the data obtained from 3401 acute leukemia patients that have been analyzed between 2003 and 2022. Genomic breakpoints within the KMT2A gene and the involved translocation partner genes (TPGs) and KMT2A-partial tandem duplications (PTDs) were determined. Including the published data from the literature, a total of 107 in-frame KMT2A gene fusions have been identified so far. Further 16 rearrangements were out-of-frame fusions, 18 patients had no partner gene fused to 5'-KMT2A, two patients had a 5'-KMT2A deletion, and one ETV6::RUNX1 patient had an KMT2A insertion at the breakpoint. The seven most frequent TPGs and PTDs account for more than 90% of all recombinations of the KMT2A, 37 occur recurrently and 63 were identified so far only once. This study provides a comprehensive analysis of the KMT2A recombinome in acute leukemia patients. Besides the scientific gain of information, genomic breakpoint sequences of these patients were used to monitor minimal residual disease (MRD). Thus, this work may be directly translated from the bench to the bedside of patients and meet the clinical needs to improve patient survival.
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Affiliation(s)
- C Meyer
- DCAL/Institute of Pharm. Biology, Goethe-University, Frankfurt/Main, Germany
| | - P Larghero
- DCAL/Institute of Pharm. Biology, Goethe-University, Frankfurt/Main, Germany
| | - B Almeida Lopes
- DCAL/Institute of Pharm. Biology, Goethe-University, Frankfurt/Main, Germany
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - T Burmeister
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Dept. of Hematology, Oncology and Tumor Immunology, Berlin, Germany
| | - D Gröger
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Dept. of Hematology, Oncology and Tumor Immunology, Berlin, Germany
| | - R Sutton
- Molecular Diagnostics, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - N C Venn
- Molecular Diagnostics, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - G Cazzaniga
- Tettamanti Research Center, Pediatrics, University of Milano-Bicocca/Fondazione Tettamanti, Monza, Italy
| | - L Corral Abascal
- Tettamanti Research Center, Pediatrics, University of Milano-Bicocca/Fondazione Tettamanti, Monza, Italy
| | - G Tsaur
- Regional Children's Hospital, Ekaterinburg, Russian Federation; Research Institute of Medical Cell Technologies, Ekaterinburg, Russian Federation
| | - L Fechina
- Regional Children's Hospital, Ekaterinburg, Russian Federation; Research Institute of Medical Cell Technologies, Ekaterinburg, Russian Federation
| | - M Emerenciano
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | | | - T Lund-Aho
- Laboratory of Clinical Genetics, Fimlab Laboratories, Tampere, Finland
| | - T Lundán
- Department of Clinical Chemistry and Laboratory Division, University of Turku and Turku University Hospital, Turku, Finland
| | - M Montonen
- Department of Clinical Chemistry and Laboratory Division, University of Turku and Turku University Hospital, Turku, Finland
| | - V Juvonen
- Department of Clinical Chemistry and Laboratory Division, University of Turku and Turku University Hospital, Turku, Finland
| | - J Zuna
- CLIP, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - J Trka
- CLIP, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - P Ballerini
- Biological Hematology, AP-HP A. Trousseau, Pierre et Marie Curie University, Paris, France
| | - H Lapillonne
- Biological Hematology, AP-HP A. Trousseau, Pierre et Marie Curie University, Paris, France
| | - V H J Van der Velden
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - E Sonneveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - E Delabesse
- Institut Universitaire du Cancer de Toulouse, Toulouse Cedex 9, France
| | - R R C de Matos
- Cytogenetics Department, Bone Marrow Transplantation Unit, National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - M L M Silva
- Cytogenetics Department, Bone Marrow Transplantation Unit, National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - S Bomken
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - K Katsibardi
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - M Keernik
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - N Grardel
- Department of Hematology, CHU Lille, France
| | - J Mason
- Northern Institute for Cancer Research, Newcastle University and the Great North Children's West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Birmingham, United Kingdom
| | - R Price
- Northern Institute for Cancer Research, Newcastle University and the Great North Children's West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Birmingham, United Kingdom
| | - J Kim
- DCAL/Institute of Pharm. Biology, Goethe-University, Frankfurt/Main, Germany
- Department of Laboratory Medicine, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - C Eckert
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Pediatric Oncology/Hematology, Berlin, Germany
| | - L Lo Nigro
- Centro di Riferimento Regionale di Ematologia ed Oncologia Pediatrica, Azienda Policlinico "G. Rodolico", Catania, Italy
| | - C Bueno
- Josep Carreras Leukemia Research Institute. Barcelona, Spanish Network for Advanced Therapies (RICORS-TERAV, ISCIII); Spanish Collaborative Cancer Network (CIBERONC. ISCIII); University of Barcelona, Barcelona, Spain
- Josep Carreras Leukemia Research Institute. Barcelona, Spanish Network for Advanced Therapies (RICORS-TERAV, ISCIII); Spanish Collaborative Cancer Network (CIBERONC. ISCIII); Department of Biomedicine. University of Barcelona; and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - P Menendez
- Centro di Riferimento Regionale di Ematologia ed Oncologia Pediatrica, Azienda Policlinico "G. Rodolico", Catania, Italy
| | - U Zur Stadt
- Pediatric Hematology and Oncology and CoALL Study Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - P Gameiro
- Instituto Português de Oncologia, Departament of Hematology, Lisbon, Portugal
| | - L Sedék
- Department of Pediatric Hematology and Oncology, Medical University of Silesia, Zabrze, Poland
| | - T Szczepański
- Department of Pediatric Hematology and Oncology, Medical University of Silesia, Zabrze, Poland
| | - A Bidet
- Laboratoire d'Hématologie Biologique, CHU Bordeaux, Bordeaux, France
| | - V Marcu
- Hematology Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - K Shichrur
- Molecular Oncology Laboratory, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - S Izraeli
- Pediatric Hematology-Oncology, Schneider Children's Medical Center, Petah Tikva, and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - H O Madsen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - B W Schäfer
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - S Kubetzko
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - R Kim
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, INSERM/CNRS U944/UMR7212, Institut de recherche Saint-Louis, Paris, France
| | - E Clappier
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, INSERM/CNRS U944/UMR7212, Institut de recherche Saint-Louis, Paris, France
| | - H Trautmann
- Laboratory for Specialized Hematological Diagnostics, Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - M Brüggemann
- Laboratory for Specialized Hematological Diagnostics, Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - P Archer
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, United Kingdom
| | - J Hancock
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, United Kingdom
| | - J Alten
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - A Möricke
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - M Stanulla
- Department of Pediatrics, MHH, Hanover, Germany
| | - J Lentes
- Institute of Human Genetics, Medical School Hannover, Hannover, Germany
| | - A K Bergmann
- Institute of Human Genetics, Medical School Hannover, Hannover, Germany
| | - S Strehl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - S Köhrer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - K Nebral
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - M N Dworzak
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
- St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - O A Haas
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
- St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - C Arfeuille
- Genetics Department, AP-HP, Hopital Robert Debré, Paris, France
| | - A Caye-Eude
- Genetics Department, AP-HP, Hopital Robert Debré, Paris, France
- Université Paris Cité, Inserm U1131, Institut de recherche Saint-Louis, Paris, France
| | - H Cavé
- Genetics Department, AP-HP, Hopital Robert Debré, Paris, France
- Université Paris Cité, Inserm U1131, Institut de recherche Saint-Louis, Paris, France
| | - R Marschalek
- DCAL/Institute of Pharm. Biology, Goethe-University, Frankfurt/Main, Germany.
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3
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Lopes B, Meyer C, Maciel AL, Barbosa T, Venn NC, Sutton R, Fazio G, Cazzaniga G, Marschalek R, Emerenciano M. Unravelling the recombinome of IKZF1 deletions in
B-ALL. KLINISCHE PADIATRIE 2022. [DOI: 10.1055/s-0042-1748681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- B Lopes
- Molecular Cancer Study Group, Division of Clinical Research, Instituto
Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de
Janeiro, Brazil
| | - C Meyer
- Institute of Pharmaceutical Biology/DCAL, Goethe-University,
Frankfurt/Main, Germany
| | - AL Maciel
- Molecular Cancer Study Group, Division of Clinical Research, Instituto
Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de
Janeiro, Brazil
| | - T Barbosa
- Molecular Cancer Study Group, Division of Clinical Research, Instituto
Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de
Janeiro, Brazil
| | - NC Venn
- Children's Cancer Institute, Lowy Cancer Research Centre UNSW,
Sydney, New South Wales, Australia
| | - R Sutton
- Children's Cancer Institute, Lowy Cancer Research Centre UNSW,
Sydney, New South Wales, Australia
| | - G Fazio
- Centro Ricerca Tettamanti, Clinica Pediatrica, Dipartimento di Medicina
e Chirurgia, Università degli Studi di Milano-Bicocca, Fondazione MBBM,
Monza, Italy
| | - G Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica, Dipartimento di Medicina
e Chirurgia, Università degli Studi di Milano-Bicocca, Fondazione MBBM,
Monza, Italy
| | - R Marschalek
- Institute of Pharmaceutical Biology/DCAL, Goethe-University,
Frankfurt/Main, Germany
| | - M Emerenciano
- Molecular Cancer Study Group, Division of Clinical Research, Instituto
Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de
Janeiro, Brazil
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4
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McClure BJ, Pal M, Heatley SL, Rehn J, Schutz C, Breen J, Venn NC, Sutton R, Khaw SL, Yeung DT, White DL. Two novel cases of NUTM1-rearranged B-cell acute lymphoblastic leukaemia presenting with high-risk features. Br J Haematol 2021; 196:1407-1411. [PMID: 34897646 DOI: 10.1111/bjh.17995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 11/30/2021] [Indexed: 12/14/2022]
Affiliation(s)
- Barbara J McClure
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia
| | - Manika Pal
- Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Susan L Heatley
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Australian and New Zealand Children's Oncology Group (ANZCHOG), Clayton, VIC, Australia
| | - Jacqueline Rehn
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia
| | - Caitlin Schutz
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - James Breen
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,South Australian Genomics Centre (SAGC), SAHMRI, Adelaide, SA, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Nicola C Venn
- Molecular Diagnostics, Children's Cancer Institute, Sydney, NSW, Australia
| | - Rosemary Sutton
- Australian and New Zealand Children's Oncology Group (ANZCHOG), Clayton, VIC, Australia.,Molecular Diagnostics, Children's Cancer Institute, Sydney, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia.,Australian Genomics Health Alliance (AGHA), Parkville, VIC, Australia
| | - Seong Lin Khaw
- Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - David T Yeung
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia
| | - Deborah L White
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Australian and New Zealand Children's Oncology Group (ANZCHOG), Clayton, VIC, Australia.,Australian Genomics Health Alliance (AGHA), Parkville, VIC, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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5
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Chen D, Sutton R, Giles J, Venn NC, Huang L, Law T, Subhash VV, Trahair TN, Henderson MJ. Analytical Quality Controls for ddPCR Detection of Minimal Residual Disease in Acute Lymphoblastic Leukemia. Clin Chem 2021. [DOI: 10.1093/clinchem/hvab117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Background
Droplet digital PCR (ddPCR) is a promising technique for absolute quantification of minimal residual disease (MRD) in acute lymphoblastic leukemia (ALL), but there is no comprehensive quality assurance program to enable its application in clinical laboratories. Current guidelines for real-time quantitative PCR (qPCR) assays targeting immunoglobulin/T-cell receptor (Ig/TCR) gene rearrangements needed adaptation for ddPCR to cover droplet generation, intraassay variation, and interassay variation in the absence of standard curves.
Methods
Six qPCR MRD assays for Ig/TCR gene rearrangements and a standard albumin control gene assay were migrated to a ddPCR platform and used to test 82 remission samples from 6 patients with ALL. Three analytical quality controls (QC) were developed and evaluated for ddPCR MRD detection.
Results
Analytical QC for droplet number generation (DN-QC), for albumin ddPCR assay performance (Alb-QC) and for patient-specific marker assay performance (PS-QC) were established with pass/fail limits and corresponding QC rules. Compared to established qPCRs, the ddPCR assays had comparable sensitivity and quantitative range. Overall, there was close agreement (91%) of MRD results between qPCR and ddPCR (κ = 0.86, P < 0.0001) and stronger concordance in 32 quantifiable samples (R2 = 0.97, P < 0.0001).
Conclusions
The use of this newly developed quality control system for ddPCR MRD testing avoids the need to repeat standard curves and provides reliable results comparable to standardized qPCR methods for MRD detection in ALL.
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Affiliation(s)
- Dan Chen
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Rosemary Sutton
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Medicine, Randwick, Australia
| | - Jodie Giles
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Nicola C Venn
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Libby Huang
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Tamara Law
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Vinod Vijay Subhash
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Toby N Trahair
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Medicine, Randwick, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, Australia
| | - Michelle J Henderson
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Medicine, Randwick, Australia
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6
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Sutton R, Pozza LD, Khaw SL, Fraser C, Revesz T, Chamberlain J, Mitchell R, Trahair TN, Bateman CM, Venn NC, Law T, Ong E, Heatley SL, McClure BJ, Meyer C, Marschalek R, Henderson MJ, Cross S, White DL, Kotecha RS. Outcomes for Australian children with relapsed/refractory acute lymphoblastic leukaemia treated with blinatumomab. Pediatr Blood Cancer 2021; 68:e28922. [PMID: 33638292 DOI: 10.1002/pbc.28922] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/22/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023]
Abstract
We report on the Australian experience of blinatumomab for treatment of 24 children with relapsed/refractory precursor B-cell acute lymphoblastic leukaemia (B-ALL) and high-risk genetics, resulting in a minimal residual disease (MRD) response rate of 58%, 2-year progression-free survival (PFS) of 39% and 2-year overall survival of 63%. In total, 83% (n = 20/24) proceeded to haematopoietic stem cell transplant, directly after blinatumomab (n = 12) or following additional salvage therapy (n = 8). Four patients successfully received CD19-directed chimeric antigen receptor T-cell therapy despite prior blinatumomab exposure. Inferior 2-year PFS was associated with MRD positivity (20%, n = 15) and in KMT2A-rearranged infants (15%, n = 9). Our findings highlight that not all children with relapsed/refractory B-ALL respond to blinatumomab and factors such as blast genotype may affect prognosis.
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Affiliation(s)
- Rosemary Sutton
- Molecular Diagnostics, Children's Cancer Institute, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Luciano Dalla Pozza
- Cancer Centre for Children, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Seong Lin Khaw
- Children's Cancer Centre, The Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Chris Fraser
- Blood and Bone Marrow Transplant Program, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Tom Revesz
- Department of Clinical Haematology and Oncology, Women's and Children's Hospital, Adelaide, South Australia, Australia.,University of Adelaide, Adelaide, South Australia, Australia
| | - Janis Chamberlain
- John Hunter Children's Hospital, Newcastle, New South Wales, Australia
| | - Richard Mitchell
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Toby N Trahair
- Molecular Diagnostics, Children's Cancer Institute, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Caroline M Bateman
- Cancer Centre for Children, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Nicola C Venn
- Molecular Diagnostics, Children's Cancer Institute, Sydney, New South Wales, Australia
| | - Tamara Law
- Molecular Diagnostics, Children's Cancer Institute, Sydney, New South Wales, Australia
| | - Erika Ong
- Molecular Diagnostics, Children's Cancer Institute, Sydney, New South Wales, Australia
| | - Susan L Heatley
- University of Adelaide, Adelaide, South Australia, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Barbara J McClure
- University of Adelaide, Adelaide, South Australia, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Claus Meyer
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia, Goethe University, Frankfurt, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia, Goethe University, Frankfurt, Germany
| | - Michelle J Henderson
- Molecular Diagnostics, Children's Cancer Institute, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Siobhan Cross
- Children's Haematology/Oncology Centre, Christchurch Hospital, Christchurch, New Zealand
| | - Deborah L White
- University of Adelaide, Adelaide, South Australia, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,Australian Genomics Health Alliance, Parkville, Melbourne, Victoria, Australia
| | - Rishi S Kotecha
- Department of Clinical Haematology, Oncology and Bone Marrow Transplantation, Perth Children's Hospital, Perth, Western Australia, Australia.,Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
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7
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Fitter S, Bradey AL, Kok CH, Noll JE, Wilczek VJ, Venn NC, Law T, Paisitkriangkrai S, Story C, Saunders L, Dalla Pozza L, Marshall GM, White DL, Sutton R, Zannettino ACW, Revesz T. CKLF and IL1B transcript levels at diagnosis are predictive of relapse in children with pre-B-cell acute lymphoblastic leukaemia. Br J Haematol 2021; 193:171-175. [PMID: 33620089 DOI: 10.1111/bjh.17161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/30/2022]
Abstract
Disease relapse is the greatest cause of treatment failure in paediatric B-cell acute lymphoblastic leukaemia (B-ALL). Current risk stratifications fail to capture all patients at risk of relapse. Herein, we used a machine-learning approach to identify B-ALL blast-secreted factors that are associated with poor survival outcomes. Using this approach, we identified a two-gene expression signature (CKLF and IL1B) that allowed identification of high-risk patients at diagnosis. This two-gene expression signature enhances the predictive value of current at diagnosis or end-of-induction risk stratification suggesting the model can be applied continuously to help guide implementation of risk-adapted therapies.
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Affiliation(s)
- Stephen Fitter
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Alanah L Bradey
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Chung Hoow Kok
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Jacqueline E Noll
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Vicki J Wilczek
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Nicola C Venn
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Tamara Law
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | | | - Colin Story
- Department of Haematology-Oncology, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Lynda Saunders
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Department of Haematology-Oncology, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Luciano Dalla Pozza
- Cancer Centre for Children at The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, University of NSW, Sydney, NSW, Australia
| | - Deborah L White
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Rosemary Sutton
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia.,School of Women's and Children's Health, University of NSW, Sydney, NSW, Australia
| | - Andrew C W Zannettino
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Tamas Revesz
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia.,Department of Haematology-Oncology, Women's and Children's Hospital, Adelaide, SA, Australia
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8
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Yadav BD, Samuels AL, Wells JE, Sutton R, Venn NC, Bendak K, Anderson D, Marshall GM, Cole CH, Beesley AH, Kees UR, Lock RB. Heterogeneity in mechanisms of emergent resistance in pediatric T-cell acute lymphoblastic leukemia. Oncotarget 2018; 7:58728-42. [PMID: 27623214 PMCID: PMC5312271 DOI: 10.18632/oncotarget.11233] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 06/08/2016] [Accepted: 07/28/2016] [Indexed: 11/25/2022] Open
Abstract
Relapse in pediatric T-cell acute lymphoblastic leukemia (T-ALL) remains a significant clinical problem and is thought to be associated with clonal selection during treatment. In this study we used an established pre-clinical model of induction therapy to increase our understanding of the effect of engraftment and chemotherapy on clonal selection and acquisition of drug resistance in vivo. Immune-deficient mice were engrafted with patient diagnostic specimens and exposed to a repeated combination therapy consisting of vincristine, dexamethasone, L-asparaginase and daunorubicin. Any re-emergence of disease following therapy was shown to be associated with resistance to dexamethasone, no resistance was observed to the other three drugs. Immunoglobulin/T-cell receptor gene rearrangements closely matched those in respective diagnosis and relapse patient specimens, highlighting that these clonal markers do not fully reflect the biological changes associated with drug resistance. Gene expression profiling revealed the significant underlying heterogeneity of dexamethasone-resistant xenografts. Alterations were observed in a large number of biological pathways, yet no dominant signature was common to all lines. These findings indicate that the biological changes associated with T-ALL relapse and resistance are stochastic and highly individual, and underline the importance of using sophisticated molecular techniques or single cell analyses in developing personalized approaches to therapy.
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Affiliation(s)
- Babasaheb D Yadav
- Leukaemia Biology Program, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Amy L Samuels
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Julia E Wells
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Rosemary Sutton
- Molecular Diagnostics, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicola C Venn
- Molecular Diagnostics, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Katerina Bendak
- Leukaemia Biology Program, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Denise Anderson
- Division of Bioinformatics and Biostatistics, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Glenn M Marshall
- Kids Cancer Centre, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Catherine H Cole
- School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia
| | - Alex H Beesley
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Ursula R Kees
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Richard B Lock
- Leukaemia Biology Program, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
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9
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Lopes BA, Meyer C, Barbosa TC, Zur Stadt U, Horstmann M, Venn NC, Heatley S, White DL, Sutton R, Pombo-de-Oliveira MS, Marschalek R, Emerenciano M. COBL is a novel hotspot for IKZF1 deletions in childhood acute lymphoblastic leukemia. Oncotarget 2018; 7:53064-53073. [PMID: 27419633 PMCID: PMC5288169 DOI: 10.18632/oncotarget.10590] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 05/03/2016] [Accepted: 06/30/2016] [Indexed: 12/11/2022] Open
Abstract
IKZF1 deletion (ΔIKZF1) is an important predictor of relapse in childhood B-cell precursor acute lymphoblastic leukemia. Because of its clinical importance, we previously mapped breakpoints of intragenic deletions and developed a multiplex PCR assay to detect recurrent intragenic ΔIKZF1. Since the multiplex PCR was not able to detect complete deletions (IKZF1 Δ1-8), which account for ~30% of all ΔIKZF1, we aimed at investigating the genomic scenery of IKZF1 Δ1-8. Six samples of cases with IKZF1 Δ1-8 were analyzed by microarray assay, which identified monosomy 7, isochromosome 7q, and large interstitial deletions presenting breakpoints within COBL gene. Then, we established a multiplex ligation-probe amplification (MLPA) assay and screened copy number alterations within chromosome 7 in 43 diagnostic samples with IKZF1 Δ1-8. Our results revealed that monosomy and large interstitial deletions within chromosome 7 are the main causes of IKZF1 Δ1-8. Detailed analysis using long distance inverse PCR showed that six patients (16%) had large interstitial deletions starting within intronic regions of COBL at diagnosis, which is ~611 Kb downstream of IKZF1, suggesting that COBL is a hotspot for ΔIKZF1. We also investigated a series of 25 intragenic deletions (Δ2–8, Δ3–8 or Δ4–8) and 24 relapsed samples, and found one IKZF1-COBL tail-to-tail fusion, thus supporting that COBL is a novel hotspot for ΔIKZF1. Finally, using RIC score methodology, we show that breakpoint sequences of IKZF1 Δ1-8 are not analog to RAG-recognition sites, suggesting a different mechanism of error promotion than that suggested for intragenic ΔIKZF1.
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Affiliation(s)
- Bruno Almeida Lopes
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Claus Meyer
- Diagnostic Center of Acute Leukemia/Institute of Pharmaceutical Biology/ZAFES, Goethe-University of Frankfurt, Biocenter, Germany
| | - Thayana Conceição Barbosa
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Udo Zur Stadt
- Center for Diagnostics, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Martin Horstmann
- Center for Diagnostics, University Medical Center Hamburg Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola C Venn
- Children's Cancer Institute, Lowy Cancer Research Centre UNSW, Sydney, New South Wales, Australia
| | - Susan Heatley
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Deborah L White
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Rosemary Sutton
- Children's Cancer Institute, Lowy Cancer Research Centre UNSW, Sydney, New South Wales, Australia
| | - Maria S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Rolf Marschalek
- Diagnostic Center of Acute Leukemia/Institute of Pharmaceutical Biology/ZAFES, Goethe-University of Frankfurt, Biocenter, Germany
| | - Mariana Emerenciano
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
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10
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Sutton R, Venn NC, Law T, Boer JM, Trahair TN, Ng A, Den Boer ML, Dissanayake A, Giles JE, Dalzell P, Mayoh C, Barbaric D, Revesz T, Alvaro F, Pieters R, Haber M, Norris MD, Schrappe M, Dalla Pozza L, Marshall GM. A risk score including microdeletions improves relapse prediction for standard and medium risk precursor B-cell acute lymphoblastic leukaemia in children. Br J Haematol 2017; 180:550-562. [DOI: 10.1111/bjh.15056] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Rosemary Sutton
- Children's Cancer Institute; Lowy Cancer Research Centre; UNSW; Sydney Australia
- School of Women's and Children's Health; UNSW; Sydney Australia
| | - Nicola C. Venn
- Children's Cancer Institute; Lowy Cancer Research Centre; UNSW; Sydney Australia
| | - Tamara Law
- Children's Cancer Institute; Lowy Cancer Research Centre; UNSW; Sydney Australia
| | - Judith M. Boer
- Department of Paediatric Oncology/Haematology; Erasmus Medical Centre; Sophia Children's Hospital; Rotterdam The Netherlands
- Princess Máxima Centre for Paediatric Oncology; Utrecht The Netherlands
| | - Toby N. Trahair
- Children's Cancer Institute; Lowy Cancer Research Centre; UNSW; Sydney Australia
- School of Women's and Children's Health; UNSW; Sydney Australia
- Kids Cancer Centre; Sydney Children's Hospital; Randwick Australia
| | - Anthea Ng
- Cancer Centre for Children; The Children's Hospital at Westmead; Westmead Australia
| | - Monique L. Den Boer
- Department of Paediatric Oncology/Haematology; Erasmus Medical Centre; Sophia Children's Hospital; Rotterdam The Netherlands
- Dutch Childhood Oncology Group; The Hague The Netherlands
| | | | - Jodie E. Giles
- Children's Cancer Institute; Lowy Cancer Research Centre; UNSW; Sydney Australia
| | | | - Chelsea Mayoh
- Children's Cancer Institute; Lowy Cancer Research Centre; UNSW; Sydney Australia
| | - Draga Barbaric
- Kids Cancer Centre; Sydney Children's Hospital; Randwick Australia
| | - Tamas Revesz
- Women's and Children's Hospital, SA Pathology; University of Adelaide; Adelaide Australia
| | - Frank Alvaro
- John Hunter Children's Hospital; Newcastle Australia
| | - Rob Pieters
- Princess Máxima Centre for Paediatric Oncology; Utrecht The Netherlands
- Dutch Childhood Oncology Group; The Hague The Netherlands
| | - Michelle Haber
- Children's Cancer Institute; Lowy Cancer Research Centre; UNSW; Sydney Australia
- School of Women's and Children's Health; UNSW; Sydney Australia
| | - Murray D. Norris
- Children's Cancer Institute; Lowy Cancer Research Centre; UNSW; Sydney Australia
- UNSW Centre for Childhood Cancer Research; Kensington Australia
| | - Martin Schrappe
- Christian-Albrechts-University Kiel and University Medical Centre Schleswig-Holstein; Kiel Germany
| | - Luciano Dalla Pozza
- Cancer Centre for Children; The Children's Hospital at Westmead; Westmead Australia
| | - Glenn M Marshall
- Children's Cancer Institute; Lowy Cancer Research Centre; UNSW; Sydney Australia
- School of Women's and Children's Health; UNSW; Sydney Australia
- Kids Cancer Centre; Sydney Children's Hospital; Randwick Australia
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11
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Afrin S, Zhang CRC, Meyer C, Stinson CL, Pham T, Bruxner TJC, Venn NC, Trahair TN, Sutton R, Marschalek R, Fink JL, Moore AS. Targeted Next-Generation Sequencing for Detecting MLL Gene Fusions in Leukemia. Mol Cancer Res 2017; 16:279-285. [PMID: 29133595 DOI: 10.1158/1541-7786.mcr-17-0569] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 10/17/2017] [Accepted: 10/30/2017] [Indexed: 11/16/2022]
Abstract
Mixed lineage leukemia (MLL) gene rearrangements characterize approximately 70% of infant and 10% of adult and therapy-related leukemia. Conventional clinical diagnostics, including cytogenetics and fluorescence in situ hybridization (FISH) fail to detect MLL translocation partner genes (TPG) in many patients. Long-distance inverse (LDI)-PCR, the "gold standard" technique that is used to characterize MLL breakpoints, is laborious and requires a large input of genomic DNA (gDNA). To overcome the limitations of current techniques, a targeted next-generation sequencing (NGS) approach that requires low RNA input was tested. Anchored multiplex PCR-based enrichment (AMP-E) was used to rapidly identify a broad range of MLL fusions in patient specimens. Libraries generated using Archer FusionPlex Heme and Myeloid panels were sequenced using the Illumina platform. Diagnostic specimens (n = 39) from pediatric leukemia patients were tested with AMP-E and validated by LDI-PCR. In concordance with LDI-PCR, the AMP-E method successfully identified TPGs without prior knowledge. AMP-E identified 10 different MLL fusions in the 39 samples. Only two specimens were discordant; AMP-E successfully identified a MLL-MLLT1 fusion where LDI-PCR had failed to determine the breakpoint, whereas a MLL-MLLT3 fusion was not detected by AMP-E due to low expression of the fusion transcript. Sensitivity assays demonstrated that AMP-E can detect MLL-AFF1 in MV4-11 cell dilutions of 10-7 and transcripts down to 0.005 copies/ng.Implications: This study demonstrates a NGS methodology with improved sensitivity compared with current diagnostic methods for MLL-rearranged leukemia. Furthermore, this assay rapidly and reliably identifies MLL partner genes and patient-specific fusion sequences that could be used for monitoring minimal residual disease. Mol Cancer Res; 16(2); 279-85. ©2017 AACR.
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Affiliation(s)
- Sadia Afrin
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Christine R C Zhang
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Claus Meyer
- Institute of Pharm. Biology/DCAL, Goethe-University, Frankfurt/Main, Germany
| | - Caedyn L Stinson
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Thy Pham
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Timothy J C Bruxner
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Nicola C Venn
- Children's Cancer Institute, University of New South Wales, Sydney, Australia
| | - Toby N Trahair
- Kids Cancer Centre, Sydney Children's Hospital, Sydney, Australia
| | - Rosemary Sutton
- Children's Cancer Institute, University of New South Wales, Sydney, Australia
| | - Rolf Marschalek
- Institute of Pharm. Biology/DCAL, Goethe-University, Frankfurt/Main, Germany
| | - J Lynn Fink
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Andrew S Moore
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia. .,Oncology Services Group, Children's Health Queensland Hospital and Health Service, Brisbane, Australia.,UQ Child Health Research Centre, The University of Queensland, Brisbane, Australia
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12
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Sadras T, Heatley SL, Kok CH, Dang P, Galbraith KM, McClure BJ, Muskovic W, Venn NC, Moore S, Osborn M, Revesz T, Moore AS, Hughes TP, Yeung D, Sutton R, White DL. Differential expression of MUC4, GPR110 and IL2RA defines two groups of CRLF2-rearranged acute lymphoblastic leukemia patients with distinct secondary lesions. Cancer Lett 2017; 408:92-101. [PMID: 28866095 DOI: 10.1016/j.canlet.2017.08.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 08/15/2017] [Accepted: 08/24/2017] [Indexed: 12/26/2022]
Abstract
CRLF2-rearrangements (CRLF2-r) occur frequently in Ph-like B-ALL, a high-risk ALL sub-type characterized by a signaling profile similar to Ph + ALL, however accumulating evidence indicates genetic heterogeneity within CRLF2-r ALL. We performed thorough genomic characterization of 35 CRLF2-r cases (P2RY8-CRLF2 n = 18; IGH-CRLF2 n = 17). Activating JAK2 mutations were present in 34% of patients, and a CRLF2-F232C mutation was identified in an additional 17%. IKZF1 deletions were detected in 63% of cases. The majority of patients (26/35) classified as Ph-like, and these were characterized by significantly higher levels of MUC4, GPR110 and IL2RA/CD25. In addition, Ph-like CRLF2-r samples were significantly enriched for IKZF1 deletions, JAK2/CRLF2 mutations and increased expression of JAK/STAT target genes (CISH, SOCS1), suggesting that mutation-driven CRLF2/JAK2 activation is more frequent in this sub-group. Less is known about the genomics of CRLF2-r cases lacking JAK2-pathway mutations, but KRAS/NRAS mutations were identified in 4/9 non-Ph-like samples. This work highlights the heterogeneity of secondary lesions which may arise and influence intracellular-pathway activation in CRLF2-r patients, and importantly presents distinct therapeutic targets within a group of patients harboring identical primary translocations, for whom efficient directed therapies are currently lacking.
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Affiliation(s)
- Teresa Sadras
- Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia; Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Susan L Heatley
- Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia; Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Chung H Kok
- Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia; Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Phuong Dang
- Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
| | - Kate M Galbraith
- Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
| | - Barbara J McClure
- Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
| | - Walter Muskovic
- Molecular Diagnostics Program, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, NSW, Australia
| | - Nicola C Venn
- Molecular Diagnostics Program, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, NSW, Australia
| | - Sarah Moore
- Department of Genetic Pathology, SA Pathology, Adelaide, SA, Australia
| | - Michael Osborn
- SA Pathology at Women's & Children's Hospital, Adelaide, SA, Australia; Australian Genomic Health Alliance, Adelaide, SA, Australia
| | - Tamas Revesz
- SA Pathology at Women's & Children's Hospital, Adelaide, SA, Australia
| | - Andrew S Moore
- The University of Queensland Diamantina Institute, UQ Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia; Oncology Services Group, Children's Health Queensland Hospital and Health Service, Brisbane, QLD, Australia
| | - Timothy P Hughes
- Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia; Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia; Department of Haematology, SA Pathology, Adelaide, SA, Australia
| | - David Yeung
- Department of Haematology, SA Pathology, Adelaide, SA, Australia
| | - Rosemary Sutton
- Molecular Diagnostics Program, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, NSW, Australia; Australian Genomic Health Alliance, Adelaide, SA, Australia; School of Women's and Children's Health, Medicine, University of NSW, Sydney, NSW, Australia
| | - Deborah L White
- Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia; Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia; Australian Genomic Health Alliance, Adelaide, SA, Australia.
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13
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Meyer C, Burmeister T, Gröger D, Tsaur G, Fechina L, Renneville A, Sutton R, Venn NC, Emerenciano M, Pombo-de-Oliveira MS, Barbieri Blunck C, Almeida Lopes B, Zuna J, Trka J, Ballerini P, Lapillonne H, De Braekeleer M, Cazzaniga G, Corral Abascal L, van der Velden VHJ, Delabesse E, Park TS, Oh SH, Silva MLM, Lund-Aho T, Juvonen V, Moore AS, Heidenreich O, Vormoor J, Zerkalenkova E, Olshanskaya Y, Bueno C, Menendez P, Teigler-Schlegel A, Zur Stadt U, Lentes J, Göhring G, Kustanovich A, Aleinikova O, Schäfer BW, Kubetzko S, Madsen HO, Gruhn B, Duarte X, Gameiro P, Lippert E, Bidet A, Cayuela JM, Clappier E, Alonso CN, Zwaan CM, van den Heuvel-Eibrink MM, Izraeli S, Trakhtenbrot L, Archer P, Hancock J, Möricke A, Alten J, Schrappe M, Stanulla M, Strehl S, Attarbaschi A, Dworzak M, Haas OA, Panzer-Grümayer R, Sedék L, Szczepański T, Caye A, Suarez L, Cavé H, Marschalek R. The MLL recombinome of acute leukemias in 2017. Leukemia 2017; 32:273-284. [PMID: 28701730 PMCID: PMC5808070 DOI: 10.1038/leu.2017.213] [Citation(s) in RCA: 460] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/25/2017] [Accepted: 06/21/2017] [Indexed: 12/16/2022]
Abstract
Chromosomal rearrangements of the human MLL/KMT2A gene are associated with infant, pediatric, adult and therapy-induced acute leukemias. Here we present the data obtained from 2345 acute leukemia patients. Genomic breakpoints within the MLL gene and the involved translocation partner genes (TPGs) were determined and 11 novel TPGs were identified. Thus, a total of 135 different MLL rearrangements have been identified so far, of which 94 TPGs are now characterized at the molecular level. In all, 35 out of these 94 TPGs occur recurrently, but only 9 specific gene fusions account for more than 90% of all illegitimate recombinations of the MLL gene. We observed an age-dependent breakpoint shift with breakpoints localizing within MLL intron 11 associated with acute lymphoblastic leukemia and younger patients, while breakpoints in MLL intron 9 predominate in AML or older patients. The molecular characterization of MLL breakpoints suggests different etiologies in the different age groups and allows the correlation of functional domains of the MLL gene with clinical outcome. This study provides a comprehensive analysis of the MLL recombinome in acute leukemia and demonstrates that the establishment of patient-specific chromosomal fusion sites allows the design of specific PCR primers for minimal residual disease analyses for all patients.
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Affiliation(s)
- C Meyer
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia (DCAL), Goethe-University, Frankfurt/Main, Germany
| | - T Burmeister
- Charité-Department of Hematology, Oncology and Tumorimmunology, Berlin, Germany
| | - D Gröger
- Charité-Department of Hematology, Oncology and Tumorimmunology, Berlin, Germany
| | - G Tsaur
- Regional Children Hospital 1, Research Institute of Medical Cell Technologies, Pediatric Oncology and Hematology Center, Ural Federal University, Ekaterinburg, Russia
| | - L Fechina
- Regional Children Hospital 1, Research Institute of Medical Cell Technologies, Pediatric Oncology and Hematology Center, Ural Federal University, Ekaterinburg, Russia
| | - A Renneville
- Laboratory of Hematology, Biology and Pathology Center, CHRU of Lille; INSERM, UMR-S 1172, Cancer Research Institute of Lille, Lille, France
| | - R Sutton
- Children's Cancer Institute Australia, Uinversity of NSW Sydney, Sydney, New South Wales, Australia
| | - N C Venn
- Children's Cancer Institute Australia, Uinversity of NSW Sydney, Sydney, New South Wales, Australia
| | - M Emerenciano
- Pediatric Hematology-Oncology Program-Research Center, Instituto Nacional de Cancer Rio de Janeiro, Rio de Janeiro, Brazil
| | - M S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program-Research Center, Instituto Nacional de Cancer Rio de Janeiro, Rio de Janeiro, Brazil
| | - C Barbieri Blunck
- Pediatric Hematology-Oncology Program-Research Center, Instituto Nacional de Cancer Rio de Janeiro, Rio de Janeiro, Brazil
| | - B Almeida Lopes
- Pediatric Hematology-Oncology Program-Research Center, Instituto Nacional de Cancer Rio de Janeiro, Rio de Janeiro, Brazil
| | - J Zuna
- CLIP, Department of Paediatric Haematology/Oncology, Charles University Prague, 2nd Faculty of Medicine, Prague, Czech Republic
| | - J Trka
- CLIP, Department of Paediatric Haematology/Oncology, Charles University Prague, 2nd Faculty of Medicine, Prague, Czech Republic
| | - P Ballerini
- Biological Hematology, AP-HP A. Trousseau, Pierre et Marie Curie University, Paris, France
| | - H Lapillonne
- Biological Hematology, AP-HP A. Trousseau, Pierre et Marie Curie University, Paris, France
| | - M De Braekeleer
- Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Laboratoire d'Histologie, Embryologie et Cytogénétique & INSERM-U1078, Brest, France
| | - G Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica Univ. Milano Bicocca, Monza, Italy
| | - L Corral Abascal
- Centro Ricerca Tettamanti, Clinica Pediatrica Univ. Milano Bicocca, Monza, Italy
| | | | - E Delabesse
- CHU Purpan, Laboratoire d'Hématologie, Toulouse, France
| | - T S Park
- Department of Laboratory Medicine, School of Medicine, Kyung Hee University, Seoul, Korea
| | - S H Oh
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Korea
| | - M L M Silva
- Cytogenetics Department, Bone Marrow Transplantation Unit, National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - T Lund-Aho
- Laboratory of Clinical Genetics, Fimlab Laboratories, Tampere, Finland
| | - V Juvonen
- Department of Clinical Chemistry and TYKSLAB, University of Turku and Turku University Central Hospital, Turku, Finland
| | - A S Moore
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - O Heidenreich
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - J Vormoor
- The Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - E Zerkalenkova
- Dmitry Rogachev National Scientific and Practical Center of Pediatric Hematology, Oncology and Immunology, Moscow
| | - Y Olshanskaya
- Dmitry Rogachev National Scientific and Practical Center of Pediatric Hematology, Oncology and Immunology, Moscow
| | - C Bueno
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,CIBER de Cancer (CIBERONC), ISCIII, Madrid, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - P Menendez
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,CIBER de Cancer (CIBERONC), ISCIII, Madrid, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - A Teigler-Schlegel
- Department of Experimental Pathology and Cytology, Institute of Pathology, Giessen, Germany
| | - U Zur Stadt
- Center for Diagnostic, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - J Lentes
- Department of Human Genetics, Hannover Medical School, Hanover, Germany
| | - G Göhring
- Department of Human Genetics, Hannover Medical School, Hanover, Germany
| | - A Kustanovich
- Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Republic of Belarus
| | - O Aleinikova
- Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Republic of Belarus
| | - B W Schäfer
- Department of Oncology, University Children's Hospital Zurich, Zurich, Switzerland
| | - S Kubetzko
- Department of Oncology, University Children's Hospital Zurich, Zurich, Switzerland
| | - H O Madsen
- Department of Clinical Immunology, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - B Gruhn
- Department of Pediatrics, Jena University Hospital, Jena, Germany
| | - X Duarte
- Department of Pediatrics, Portuguese Institute of Oncology of Lisbon, Lisbon, Portugal
| | - P Gameiro
- Hemato-Oncology Laboratory, UIPM, Portuguese Institute of Oncology of Lisbon, Lisbon, Portugal
| | - E Lippert
- Hématologie Biologique, CHU de Brest and INSERM U1078, Université de Bretagne Occidentale, Brest, France
| | - A Bidet
- Hématologie Biologique, CHU de Brest and INSERM U1078, Université de Bretagne Occidentale, Brest, France
| | - J M Cayuela
- Laboratoire d'hématologie, AP-HP Saint-Louis, Paris Diderot University, Paris, France
| | - E Clappier
- Laboratoire d'hématologie, AP-HP Saint-Louis, Paris Diderot University, Paris, France
| | - C N Alonso
- Hospital Nacional de Pediatría Prof Dr J. P. Garrahan, Servcio de Hemato-Oncología, Buenos Aires, Argentina
| | - C M Zwaan
- Department of Pediatric Oncology/Hematology, Erasmus MC, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - M M van den Heuvel-Eibrink
- Department of Pediatric Oncology/Hematology, Erasmus MC, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - S Izraeli
- The Chaim Sheba Medical Center, Department of Pediatric Hemato-Oncology and the Cancer Research Center, Tel Aviv, Israel.,Sackler Medical School Tel Aviv University, Tel Aviv, Israel
| | - L Trakhtenbrot
- The Chaim Sheba Medical Center, Department of Pediatric Hemato-Oncology and the Cancer Research Center, Tel Aviv, Israel.,Sackler Medical School Tel Aviv University, Tel Aviv, Israel
| | - P Archer
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - J Hancock
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - A Möricke
- Department of Pediatrics, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - J Alten
- Department of Pediatrics, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - M Schrappe
- Department of Pediatrics, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - M Stanulla
- Department of Pediatrics, MHH, Hanover, Germany
| | - S Strehl
- Children's Cancer Research Institute and St Anna Children's Hospital, Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - A Attarbaschi
- Children's Cancer Research Institute and St Anna Children's Hospital, Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - M Dworzak
- Children's Cancer Research Institute and St Anna Children's Hospital, Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - O A Haas
- Children's Cancer Research Institute and St Anna Children's Hospital, Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - R Panzer-Grümayer
- Children's Cancer Research Institute and St Anna Children's Hospital, Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - L Sedék
- Department of Microbiology and Immunology, Medical University of Silesia, Zabrze, Poland
| | - T Szczepański
- Department of Pediatric Hematology and Oncology, Medical University of Silesia, Zabrze, Poland
| | - A Caye
- Department of Genetics, AP-HP Robert Debré, Paris Diderot University, Paris, France
| | - L Suarez
- Department of Genetics, AP-HP Robert Debré, Paris Diderot University, Paris, France
| | - H Cavé
- Department of Genetics, AP-HP Robert Debré, Paris Diderot University, Paris, France
| | - R Marschalek
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia (DCAL), Goethe-University, Frankfurt/Main, Germany
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14
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Irving JAE, Enshaei A, Parker CA, Sutton R, Kuiper RP, Erhorn A, Minto L, Venn NC, Law T, Yu J, Schwab C, Davies R, Matheson E, Davies A, Sonneveld E, den Boer ML, Love SB, Harrison CJ, Hoogerbrugge PM, Revesz T, Saha V, Moorman AV. Integration of genetic and clinical risk factors improves prognostication in relapsed childhood B-cell precursor acute lymphoblastic leukemia. Blood 2016; 128:911-22. [PMID: 27229005 PMCID: PMC5026463 DOI: 10.1182/blood-2016-03-704973] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [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] [Received: 03/10/2016] [Accepted: 05/19/2016] [Indexed: 12/13/2022] Open
Abstract
Somatic genetic abnormalities are initiators and drivers of disease and have proven clinical utility at initial diagnosis. However, the genetic landscape and its clinical utility at relapse are less well understood and have not been studied comprehensively. We analyzed cytogenetic data from 427 children with relapsed B-cell precursor ALL treated on the international trial, ALLR3. Also we screened 238 patients with a marrow relapse for selected copy number alterations (CNAs) and mutations. Cytogenetic risk groups were predictive of outcome postrelapse and survival rates at 5 years for patients with good, intermediate-, and high-risk cytogenetics were 68%, 47%, and 26%, respectively (P < .001). TP53 alterations and NR3C1/BTG1 deletions were associated with a higher risk of progression: hazard ratio 2.36 (95% confidence interval, 1.51-3.70, P < .001) and 2.15 (1.32-3.48, P = .002). NRAS mutations were associated with an increased risk of progression among standard-risk patients with high hyperdiploidy: 3.17 (1.15-8.71, P = .026). Patients classified clinically as standard and high risk had distinct genetic profiles. The outcome of clinical standard-risk patients with high-risk cytogenetics was equivalent to clinical high-risk patients. Screening patients at relapse for key genetic abnormalities will enable the integration of genetic and clinical risk factors to improve patient stratification and outcome. This study is registered at www.clinicaltrials.org as #ISCRTN45724312.
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Affiliation(s)
- Julie A E Irving
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Amir Enshaei
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catriona A Parker
- Children's Cancer Group, Institute of Cancer, Faculty of Medical & Human Sciences, The University of Manchester, Manchester, United Kingdom; Royal Manchester Children's Hospital, Central Manchester University Hospitals Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Rosemary Sutton
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Roland P Kuiper
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Amy Erhorn
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lynne Minto
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nicola C Venn
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Tamara Law
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Jiangyan Yu
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claire Schwab
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rosanna Davies
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Elizabeth Matheson
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alysia Davies
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Monique L den Boer
- Dutch Childhood Oncology Group, The Hague, The Netherlands; Department of Paediatric Oncology and Haematology, Erasmus MC-Sophia Children's Hospital, University Medical Centre, Rotterdam, The Netherlands
| | - Sharon B Love
- Centre for Statistics in Medicine, University of Oxford, Oxford, United Kingdom
| | - Christine J Harrison
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Peter M Hoogerbrugge
- Dutch Childhood Oncology Group, The Hague, The Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Tamas Revesz
- Department of Haematology-Oncology, SA Pathology at Women's and Children's Hospital and University of Adelaide, Adelaide, Australia; and
| | - Vaskar Saha
- Children's Cancer Group, Institute of Cancer, Faculty of Medical & Human Sciences, The University of Manchester, Manchester, United Kingdom; Royal Manchester Children's Hospital, Central Manchester University Hospitals Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Tata Translational Cancer Research Centre, Tata Medical Center, New Town, Kolkata, India
| | - Anthony V Moorman
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
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15
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Andersson AK, Ma J, Wang J, Chen X, Gedman AL, Dang J, Nakitandwe J, Holmfeldt L, Parker M, Easton J, Huether R, Kriwacki R, Rusch M, Wu G, Li Y, Mulder H, Raimondi S, Pounds S, Kang G, Shi L, Becksfort J, Gupta P, Payne-Turner D, Vadodaria B, Boggs K, Yergeau D, Manne J, Song G, Edmonson M, Nagahawatte P, Wei L, Cheng C, Pei D, Sutton R, Venn NC, Chetcuti A, Rush A, Catchpoole D, Heldrup J, Fioretos T, Lu C, Ding L, Pui CH, Shurtleff S, Mullighan CG, Mardis ER, Wilson RK, Gruber TA, Zhang J, Downing JR. The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias. Nat Genet 2015; 47:330-7. [PMID: 25730765 PMCID: PMC4553269 DOI: 10.1038/ng.3230] [Citation(s) in RCA: 355] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 02/02/2015] [Indexed: 12/13/2022]
Abstract
Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non-MLL-R) and 20 older children (MLL-R cases) with leukemia. Our data demonstrated infant MLL-R ALL to have one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite the paucity of mutations, activating mutations in kinase/PI3K/RAS signaling pathways were detected in 47%. Surprisingly, however, these mutations were often sub-clonal and frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (a mean of 6.5/case versus 1.3/case, P=7.15×10−5) and contained frequent mutations (45%) in epigenetic regulators, a category of genes that with the exception of MLL was rarely mutated in infant MLL-R ALL.
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Affiliation(s)
- Anna K Andersson
- 1] Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Department of Clinical Genetics, Lund University, Lund, Sweden
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jianmin Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Amanda Larson Gedman
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jinjun Dang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Joy Nakitandwe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Linda Holmfeldt
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John Easton
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Robert Huether
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Heather Mulder
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Susana Raimondi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Guolian Kang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jared Becksfort
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Pankaj Gupta
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Bhavin Vadodaria
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kristy Boggs
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Donald Yergeau
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jayanthi Manne
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Panduka Nagahawatte
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lei Wei
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rosemary Sutton
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicola C Venn
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Albert Chetcuti
- Tumor Bank, Children's Cancer Research Unit, Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Amanda Rush
- Tumor Bank, Children's Cancer Research Unit, Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Daniel Catchpoole
- Tumor Bank, Children's Cancer Research Unit, Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Jesper Heldrup
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Lund University, Lund, Sweden
| | - Charles Lu
- 1] Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA. [2] Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Li Ding
- 1] Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA. [2] Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Ching-Hon Pui
- 1] Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sheila Shurtleff
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Elaine R Mardis
- 1] Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA. [2] Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Richard K Wilson
- 1] Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA. [2] Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Tanja A Gruber
- 1] Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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16
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Richmond J, Carol H, Evans K, High L, Mendomo A, Robbins A, Meyer C, Venn NC, Marschalek R, Henderson M, Sutton R, Kurmasheva RT, Kees UR, Houghton PJ, Smith MA, Lock RB. Effective targeting of the P53-MDM2 axis in preclinical models of infant MLL-rearranged acute lymphoblastic leukemia. Clin Cancer Res 2015; 21:1395-405. [PMID: 25573381 DOI: 10.1158/1078-0432.ccr-14-2300] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Although the overall cure rate for pediatric acute lymphoblastic leukemia (ALL) approaches 90%, infants with ALL harboring translocations in the mixed-lineage leukemia (MLL) oncogene (infant MLL-ALL) experience shorter remission duration and lower survival rates (∼50%). Mutations in the p53 tumor-suppressor gene are uncommon in infant MLL-ALL, and drugs that release p53 from inhibitory mechanisms may be beneficial. The purpose of this study was to assess the efficacy of the orally available nutlin, RG7112, against patient-derived MLL-ALL xenografts. EXPERIMENTAL DESIGN Eight MLL-ALL patient-derived xenografts were established in immune-deficient mice, and their molecular features compared with B-lineage ALL and T-ALL xenografts. The sensitivity of MLL-ALL xenografts to RG7112 was assessed in vitro and in vivo, and the ability of RG7112 to induce p53, cell-cycle arrest, and apoptosis in vivo was evaluated. RESULTS Gene-expression analysis revealed that MLL-ALL, B-lineage ALL, and T-ALL xenografts clustered according to subtype. Moreover, genes previously reported to be overexpressed in MLL-ALL, including MEIS1, CCNA1, and members of the HOXA family, were significantly upregulated in MLL-ALL xenografts, confirming their ability to recapitulate the clinical disease. Exposure of MLL-ALL xenografts to RG7112 in vivo caused p53 upregulation, cell-cycle arrest, and apoptosis. RG7112 as a single agent induced significant regressions in infant MLL-ALL xenografts. Therapeutic enhancement was observed when RG7112 was assessed using combination treatment with an induction-type regimen (vincristine/dexamethasone/L-asparaginase) against an MLL-ALL xenograft. CONCLUSIONS The utility of targeting the p53-MDM2 axis in combination with established drugs for the management of infant MLL-ALL warrants further investigation.
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Affiliation(s)
- Jennifer Richmond
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - Hernan Carol
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - Kathryn Evans
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - Laura High
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - Agnes Mendomo
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - Alissa Robbins
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - Claus Meyer
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia (DCAL), Goethe-University of Frankfurt, Frankfurt/Main, Germany
| | - Nicola C Venn
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia (DCAL), Goethe-University of Frankfurt, Frankfurt/Main, Germany
| | - Michelle Henderson
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - Rosemary Sutton
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | | | - Ursula R Kees
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Peter J Houghton
- Center for Childhood Cancer, Nationwide Children's Hospital, Columbus, Ohio
| | | | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, Australia.
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17
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Henderson MJ, Choi S, Beesley AH, Sutton R, Venn NC, Marshall GM, Kee UR, Haber M, Norris MD. Mechanism of relapse in pediatric acute lymphoblastic leukemia. Cell Cycle 2014; 7:1315-20. [DOI: 10.4161/cc.7.10.5885] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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18
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Sutton R, Shaw PJ, Venn NC, Law T, Dissanayake A, Kilo T, Haber M, Norris MD, Fraser C, Alvaro F, Revesz T, Trahair TN, Dalla-Pozza L, Marshall GM, O'Brien TA. Persistent MRD before and after allogeneic BMT predicts relapse in children with acute lymphoblastic leukaemia. Br J Haematol 2014; 168:395-404. [DOI: 10.1111/bjh.13142] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/26/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Rosemary Sutton
- Children's Cancer Institute Australia; Lowy Cancer Research Centre, UNSW; Randwick NSW Australia
| | - Peter J. Shaw
- Oncology Unit; The Children's Hospital at Westmead; Westmead NSW Australia
| | - Nicola C. Venn
- Children's Cancer Institute Australia; Lowy Cancer Research Centre, UNSW; Randwick NSW Australia
| | - Tamara Law
- Children's Cancer Institute Australia; Lowy Cancer Research Centre, UNSW; Randwick NSW Australia
| | - Anuruddhika Dissanayake
- Children's Cancer Institute Australia; Lowy Cancer Research Centre, UNSW; Randwick NSW Australia
| | - Tatjana Kilo
- Oncology Unit; The Children's Hospital at Westmead; Westmead NSW Australia
| | - Michelle Haber
- Children's Cancer Institute Australia; Lowy Cancer Research Centre, UNSW; Randwick NSW Australia
| | - Murray D. Norris
- Children's Cancer Institute Australia; Lowy Cancer Research Centre, UNSW; Randwick NSW Australia
| | - Chris Fraser
- Royal Children's Hospital; Brisbane Qld Australia
| | - Frank Alvaro
- John Hunter Children's Hospital; Newcastle NSW Australia
| | - Tamas Revesz
- Women and Children's Hospital; Adelaide SA Australia
| | - Toby N. Trahair
- Children's Cancer Institute Australia; Lowy Cancer Research Centre, UNSW; Randwick NSW Australia
- Kids Cancer Centre; Sydney Children's Hospital; Randwick NSW Australia
| | | | - Glenn M. Marshall
- Children's Cancer Institute Australia; Lowy Cancer Research Centre, UNSW; Randwick NSW Australia
- Kids Cancer Centre; Sydney Children's Hospital; Randwick NSW Australia
| | - Tracey A. O'Brien
- Children's Cancer Institute Australia; Lowy Cancer Research Centre, UNSW; Randwick NSW Australia
- Kids Cancer Centre; Sydney Children's Hospital; Randwick NSW Australia
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Karsa M, Dalla Pozza L, Venn NC, Law T, Shi R, Giles JE, Bahar AY, Cross S, Catchpoole D, Haber M, Marshall GM, Norris MD, Sutton R. Improving the identification of high risk precursor B acute lymphoblastic leukemia patients with earlier quantification of minimal residual disease. PLoS One 2013; 8:e76455. [PMID: 24146872 PMCID: PMC3795712 DOI: 10.1371/journal.pone.0076455] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/28/2013] [Indexed: 01/05/2023] Open
Abstract
The stratification of patients with acute lymphoblastic leukemia (ALL) into treatment risk groups based on quantification of minimal residual disease (MRD) after induction therapy is now well accepted but the relapse rate of about 20% in intermediate risk patients remains a challenge. The purpose of this study was to further improve stratification by MRD measurement at an earlier stage. MRD was measured in stored day 15 bone marrow samples for pediatric patients enrolled on ANZCHOG ALL8 using Real-time Quantitative PCR to detect immunoglobulin and T-cell receptor gene rearrangements with the same assays used at day 33 and day 79 in the original MRD stratification. MRD levels in bone marrow at day 15 and 33 were highly predictive of outcome in 223 precursor B-ALL patients (log rank Mantel-Cox tests both P<0.001) and identified patients with poor, intermediate and very good outcomes. The combined use of MRD at day 15 (≥1×10−2) and day 33 (≥5×1−5) identified a subgroup of medium risk precursor B-ALL patients as poor MRD responders with 5 year relapse-free survival of 55% compared to 84% for other medium risk patients (log rank Mantel-Cox test, P = 0.0005). Risk stratification of precursor B-ALL but not T-ALL could be improved by using MRD measurement at day 15 and day 33 instead of day 33 and day 79 in similar BFM-based protocols for children with this disease.
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Affiliation(s)
- Mawar Karsa
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of NSW, Sydney, Australia
| | | | - Nicola C. Venn
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of NSW, Sydney, Australia
| | - Tamara Law
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of NSW, Sydney, Australia
| | - Rachael Shi
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of NSW, Sydney, Australia
| | - Jodie E. Giles
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of NSW, Sydney, Australia
| | - Anita Y. Bahar
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of NSW, Sydney, Australia
| | - Shamira Cross
- The Oncology Unit, The Children’s Hospital at Westmead, Westmead, Australia
| | - Daniel Catchpoole
- The Oncology Unit, The Children’s Hospital at Westmead, Westmead, Australia
| | - Michelle Haber
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of NSW, Sydney, Australia
| | - Glenn M. Marshall
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of NSW, Sydney, Australia
- Centre for Children’s Cancer and Blood Disorders, Sydney’s Children’s Hospital, Randwick, Australia
| | - Murray D. Norris
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of NSW, Sydney, Australia
| | - Rosemary Sutton
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of NSW, Sydney, Australia
- * E-mail:
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Marshall GM, Dalla Pozza L, Sutton R, Ng A, de Groot-Kruseman HA, van der Velden VH, Venn NC, van den Berg H, de Bont ESJM, Maarten Egeler R, Hoogerbrugge PM, Kaspers GJL, Bierings MB, van der Schoot E, van Dongen J, Law T, Cross S, Mueller H, de Haas V, Haber M, Révész T, Alvaro F, Suppiah R, Norris MD, Pieters R. High-risk childhood acute lymphoblastic leukemia in first remission treated with novel intensive chemotherapy and allogeneic transplantation. Leukemia 2013; 27:1497-503. [PMID: 23407458 DOI: 10.1038/leu.2013.44] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Revised: 02/03/2013] [Accepted: 02/07/2013] [Indexed: 12/20/2022]
Abstract
Children with acute lymphoblastic leukemia (ALL) and high minimal residual disease (MRD) levels after initial chemotherapy have a poor clinical outcome. In this prospective, single arm, Phase 2 trial, 111 Dutch and Australian children aged 1-18 years with newly diagnosed, t(9;22)-negative ALL, were identified among 1041 consecutively enrolled patients as high risk (HR) based on clinical features or high MRD. The HR cohort received the AIEOP-BFM (Associazione Italiana di Ematologia ed Oncologia Pediatrica (Italy)-Berlin-Frankfurt-Münster ALL Study Group) 2000 ALL Protocol I, then three novel HR chemotherapy blocks, followed by allogeneic transplant or chemotherapy. Of the 111 HR patients, 91 began HR treatment blocks, while 79 completed the protocol. There were 3 remission failures, 12 relapses, 7 toxic deaths in remission and 10 patients who changed protocol due to toxicity or clinician/parent preference. For the 111 HR patients, 5-year event-free survival (EFS) was 66.8% (±5.5) and overall survival (OS) was 75.6% (±4.3). The 30 patients treated as HR solely on the basis of high MRD levels had a 5-year EFS of 63% (±9.4%). All patients experienced grade 3 or 4 toxicities during HR block therapy. Although cure rates were improved compared with previous studies, high treatment toxicity suggested that novel agents are needed to achieve further improvement.
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Affiliation(s)
- G M Marshall
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, New South Wales, Australia.
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Sutton R, Venn NC, Tolisano J, Bahar AY, Giles JE, Ashton LJ, Teague L, Rigutto G, Waters K, Marshall GM, Haber M, Norris MD. Clinical significance of minimal residual disease at day 15 and at the end of therapy in childhood acute lymphoblastic leukaemia. Br J Haematol 2009; 146:292-9. [PMID: 19500099 DOI: 10.1111/j.1365-2141.2009.07744.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detection of minimal residual disease (MRD) after induction and consolidation therapy is highly predictive of outcome for childhood acute lymphoblastic leukaemia (ALL) and is used to identify patients at high risk of relapse in several current clinical trials. To evaluate the prognostic significance of MRD at other treatment phases, MRD was measured by real-time quantitative polymerase chain reaction on a selected group of 108 patients enrolled on the Australian and New Zealand Children's Cancer Study Group Study VII including 36 patients with a bone marrow or central nervous system relapse and 72 matched patients in first remission. MRD was prognostic of outcome at all five treatment phases tested: at day 15 (MRD > or = 5 x 10(-2), log rank P < 0.0001), day 35 (> or =1 x 10(-2), P = 0.0001), 4 months (> or =5 x 10(-4), P < 0.0001), 12 months (MRD > or = 1 x 10(-4), P = 0.006) and 24 months (MRD > or = 1 x 10(-4), P < 0.0001). Day 15 was the best early MRD time-point to differentiate between patients with high, intermediate and low risk of relapse. MRD testing at 12 and particularly at 24 months, detected molecular relapses in some patients up to 6 months before clinical relapse. This raised the question of whether a strategy of late monitoring and salvage therapy will improve outcome.
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Affiliation(s)
- Rosemary Sutton
- Children's Cancer Institute Australia for Medical Research, University of NSW, Sydney, NSW, Australia.
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Morley AA, Latham S, Brisco MJ, Sykes PJ, Sutton R, Hughes E, Wilczek V, Budgen B, van Zanten K, Kuss BJ, Venn NC, Norris MD, Crock C, Storey C, Revesz T, Waters K. Sensitive and specific measurement of minimal residual disease in acute lymphoblastic leukemia. J Mol Diagn 2009; 11:201-10. [PMID: 19324989 DOI: 10.2353/jmoldx.2009.080048] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A sensitive and specific quantitative real-time polymerase chain reaction method, involving three rounds of amplification with two allele-specific oligonucleotide primers directed against an rearrangement, was developed to quantify minimal residual disease (MRD) in B-lineage acute lymphoblastic leukemia (ALL). For a single sample containing 10 microg of good quality DNA, MRD was quantifiable down to approximately 10(-6), which is at least 1 log more sensitive than current methods. Nonspecific amplification was rarely observed. The standard deviation of laboratory estimations was 0.32 log units at moderate or high levels of MRD, but increased markedly as the level of MRD and the number of intact marker gene rearrangements in the sample fell. In 23 children with ALL studied after induction therapy, the mean MRD level was 1.6 x 10(-5) and levels ranged from 1.5 x 10(-2) to less than 10(-7). Comparisons with the conventional one-round quantitative polymerase chain reaction method on 29 samples from another 24 children who received treatment resulted in concordant results for 22 samples and discordant results for seven samples. The sensitivity and specificity of the method are due to the use of nested polymerase chain reaction, one segment-specific and two allele-specific oligonucleotide primers, and the use of a large amount of good quality DNA. This method may improve MRD-based decisions on treatment for ALL patients, and the principles should be applicable to DNA-based MRD measurements in other disorders.
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Affiliation(s)
- Alexander A Morley
- Department of Haematology and Genetic Pathology, Flinders University and Medical Centre, Adelaide, Australia.
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Brisco MJ, Latham S, Sutton R, Hughes E, Wilczek V, van Zanten K, Budgen B, Bahar AY, Malec M, Sykes PJ, Kuss BJ, Waters K, Venn NC, Giles JE, Haber M, Norris MD, Marshall GM, Morley AA. Determining the repertoire of IGH gene rearrangements to develop molecular markers for minimal residual disease in B-lineage acute lymphoblastic leukemia. J Mol Diagn 2009; 11:194-200. [PMID: 19324994 DOI: 10.2353/jmoldx.2009.080047] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular markers for minimal residual disease in B-lineage acute lymphoblastic leukemia were identified by determining, at the time of diagnosis, the repertoire of rearrangements of the immunoglobulin heavy chain (IGH) gene using segment-specific variable (V), diversity (D), and junctional (J) primers in two different studies that involved a total study population of 75 children and 18 adults. This strategy, termed repertoire analysis, was compared with the conventional strategy of identifying markers using family-specific V, D, and J primers for a variety of antigen receptor genes. Repertoire analysis detected significantly more markers for the major leukemic clone than did the conventional strategy, and one or more IgH rearrangements that were suitable for monitoring the major clone were detected in 96% of children and 94% of adults. Repertoire analysis also detected significantly more IGH markers for minor clones. Some minor clones were quite large and a proportion of them would not be able to be detected by a minimal residual disease test directed to the marker for the major clone. IGH repertoire analysis at diagnosis has potential advantages for the identification of molecular markers for the quantification of minimal residual disease in acute lymphoblastic leukemia cases. An IGH marker enables very sensitive quantification of the major leukemic clone, and the detection of minor clones may enable early identification of additional patients who are prone to relapse.
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Affiliation(s)
- Michael J Brisco
- Department of Hematology and Genetic Pathology, Flinders University and Medical Centre, Adelaide, Australia
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Choi S, Henderson MJ, Kwan E, Beesley AH, Sutton R, Bahar AY, Giles J, Venn NC, Pozza LD, Baker DL, Marshall GM, Kees UR, Haber M, Norris MD. Relapse in children with acute lymphoblastic leukemia involving selection of a preexisting drug-resistant subclone. Blood 2007; 110:632-9. [PMID: 17371950 DOI: 10.1182/blood-2007-01-067785] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Relapse following remission induction chemotherapy remains a barrier to survival in approximately 20% of children suffering from acute lymphoblastic leukemia (ALL). To investigate the mechanism of relapse, 27 matched diagnosis and relapse ALL samples were analyzed for clonal populations using polymerase chain reaction (PCR)-based detection of multiple antigen receptor gene rearrangements. These clonal markers revealed the emergence of apparently new populations at relapse in 13 patients. More sensitive clone-specific PCR revealed that, in 8 cases, these "relapse clones" were present at diagnosis and a significant relationship existed between presence of the relapse clone at diagnosis and time to first relapse (P < .007). Furthermore, in cases where the relapse clone could be quantified, time to first relapse was dependent on the amount of the relapse clone at diagnosis (r = -0.84; P = .018). This observation, together with demonstrated differential chemosensitivity between subclones at diagnosis, argues against therapy-induced acquired resistance as the mechanism of relapse in the informative patients. Instead these data indicate that relapse in ALL patients may commonly involve selection of a minor intrinsically resistant subclone that is undetectable by routine PCR-based methods. Relapse prediction may be improved with strategies to detect minor potentially resistant subclones early during treatment, hence allowing intensification of therapy.
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Affiliation(s)
- Seoyeon Choi
- Children's Cancer Institute Australia for Medical Research, Sydney, Australia
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