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Lucero J, Alhumaid M, Novitzky-Basso I, Capo-Chichi JM, Stockley T, Gupta V, Bankar A, Chan S, Schuh AC, Minden M, Mattsson J, Kumar R, Sibai H, Tierens A, Kim DDH. Flow cytometry-based measurable residual disease (MRD) analysis identifies AML patients who may benefit from allogeneic hematopoietic stem cell transplantation. Ann Hematol 2024; 103:1187-1196. [PMID: 38291275 DOI: 10.1007/s00277-024-05639-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
Measurable residual disease (MRD) monitoring independently predicts long-term outcomes in patients with acute myeloid leukemia (AML). Of the various modalities available, multiparameter flow cytometry-based MRD analysis is widely used and relevant for patients without molecular targets. In the transplant (HCT) setting, the presence of MRD pre-HCT is associated with adverse outcomes. MRD-negative remission status pre-HCT was also associated with longer overall (OS) and progression-free survival and a lower risk of relapse. We hypothesize that the combination of disease risk and MRD at the time of first complete remission (CR1) could identify patients according to the benefit gained from HCT, especially for intermediate-risk patients. We performed a retrospective analysis comparing the outcomes of HCT versus non-HCT therapies based on MRD status in AML patients who achieved CR1. Time-dependent analysis was applied considering time-to-HCT as a time-dependent covariate and compared HCT versus non-HCT outcomes according to MRD status at CR1. Among 336 patients assessed at CR1, 35.1% were MRD positive (MRDpos) post-induction. MRDpos patients benefitted from HCT with improved OS and relapse-free survival (RFS), while no benefit was observed in MRDneg patients. In adverse-risk patients, HCT improved OS (HR for OS 0.55; p = 0.05). In intermediate-risk patients, HCT benefit was not significant for OS and RFS. Intermediate-risk MRDpos patients were found to have benefit from HCT with improved OS (HR 0.45, p = 0.04), RFS (HR 0.46, p = 0.02), and CIR (HR 0.41, p = 0.02). Our data underscore the benefit of HCT in adverse risk and MRDpos intermediate-risk AML patients.
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Affiliation(s)
- Josephine Lucero
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada.
| | | | - Igor Novitzky-Basso
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Jose-Mario Capo-Chichi
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Tracy Stockley
- Division of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Vikas Gupta
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Aniket Bankar
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Steven Chan
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Andre C Schuh
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Mark Minden
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Jonas Mattsson
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Rajat Kumar
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Hassan Sibai
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Anne Tierens
- Division of Hematology and Transfusion Medicine, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Dennis D H Kim
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada.
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2
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Davidson MB, Kennedy JA, Capo-Chichi JM, Shi Y, Xu W, Cheung V, Arruda A, Bankar A, Richard-Carpentier G, Chan S, Maze D, Minden MD, Schimmer AD, Schuh AC, Sibai H, Yee K, Tierens A, Viswabandya A, Gupta V. Outcomes of intensive and nonintensive blast-reduction strategies in accelerated and blast-phase MPN. Blood Adv 2024; 8:1281-1294. [PMID: 38170760 PMCID: PMC10918486 DOI: 10.1182/bloodadvances.2023011735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/28/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
ABSTRACT Transformation of BCR::ABL1-negative myeloproliferative neoplasms (MPN) to an accelerated or blast phase is associated with poor outcomes. The efficacy of acute myeloid leukemia (AML)-type intensive and nonintensive hypomethylating agent-based regimens is not well studied. We therefore performed a retrospective analysis of patients with MPN-AP/BP (N = 138) treated with intensive (N = 81) and nonintensive (N = 57) blast-reduction strategies. We used clinically relatable response criteria developed at the Princess Margaret Cancer Centre. The overall best response, comprising complete remission (CR), complete remission with incomplete hematologic recovery (CRi), and reversion to chronic phase MPN (cMPN), in the intensive and nonintensive groups was 77% (62 of 81) and 39% (21 of 54), respectively. Similar overall best response rates were observed in patients receiving induction with daunorubicin combined with cytarabine arabinoside (daunorubicin + ara-C) (74% [23 of 31]) or FLAG-IDA/NOVE-HiDAC (78% [39 of 50], P = .78). However, patients receiving daunorubicin + ara-C more often required second inductions (29% [9 of 31] vs 4% [2 of 50], P = .002). Most responses in the entire cohort were reversions to cMPN (55 of 83 [66%]). CR and CRi comprised 30% (25 of 83) and 4% (3 of 83) of responses, respectively. Mutations in TP53 (overall response [OR] 8.2 [95% confidence interval [CI] 2.01, 37.1], P = .004) and RAS pathway (OR 5.1 [95%CI 1.2, 23.7], P = .03) were associated with inferior treatment response for intensively treated patients, and poorer performance status (Eastern Cooperative Oncology Group) was associated with inferior treatment response in both intensively (OR 10.4 [95% CI 2.0, 78.5], P = .009) and nonintensively treated groups (OR 12 [95% CI 2.04, 230.3], P = .02). In patients with paired samples before and after therapy (N = 26), there was a significant residual mutation burden remaining irrespective of response to blast-reduction therapy.
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Affiliation(s)
- Marta B. Davidson
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - James A. Kennedy
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
- Medical Oncology and Hematology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Jose-Mario Capo-Chichi
- Department of Clinical Laboratory Genetics, Laboratory Medicine Program, Toronto, ON, Canada
| | - Yuliang Shi
- Biostatistics Department, University Health Network, Toronto, ON, Canada
| | - Wei Xu
- Biostatistics Department, University Health Network, Toronto, ON, Canada
| | - Verna Cheung
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Andrea Arruda
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Aniket Bankar
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Steven Chan
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Dawn Maze
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Mark D. Minden
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Aaron D. Schimmer
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Andre C. Schuh
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Hassan Sibai
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Karen Yee
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Anne Tierens
- Department of Hematopathology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Auro Viswabandya
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Vikas Gupta
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
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3
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Perusini MA, Zackova D, Kim T, Pagnano KBB, Pavlovsky C, Jeziskova I, Kvetková A, Jurcek T, Kim JJ, Yoo YS, Yi S, Lee H, Kim KH, Chang M, Capo-Chichi JM, Medeiros J, Arruda A, Minden MD, Zhang Z, Abelson S, Mayer J, Kim DDH. Mutations in myeloid transcription factors and activated signaling genes predict chronic myeloid leukemia outcomes. Blood Adv 2024:bloodadvances.2023012127. [PMID: 38447114 DOI: 10.1182/bloodadvances.2023012127] [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: 11/13/2023] [Revised: 01/17/2024] [Accepted: 02/15/2024] [Indexed: 03/08/2024] Open
Abstract
Advancements in genomics are transforming the clinical management of chronic myeloid leukemia (CML) towards precision medicine. The impact of somatic mutations on treatment outcomes is still under debate. We studied the association of somatic mutations in epigenetic modifiers genes and activated signaling/myeloid transcription factor (AS/MTF), with disease progression and treatment failure in CML patients following tyrosine kinase inhibitor (TKI) therapy. A total of 394 CML samples were sequenced, including 254 samples collected at initial diagnosis, and 140 samples taken during follow-up. Single-molecule molecular inversion probe (smMIP)-based next-generation sequencing (NGS) was conducted targeting recurrently mutated loci in 40 genes with a limit of detection of 0.2%. A total of 70 mutations were detected in 57 (22.4%) diagnostic samples, while 64 mutations were detected in 39 (27.9%) of the follow-up samples. Carrying any mutation at initial diagnosis was associated with worse outcomes following TKI therapy, particularly in AS/MTF genes. Patients having these mutations at initial diagnosis and treated with Imatinib showed higher risks of treatment failure (HR 2.53, 95% CI [1.13-5.66], p=0.0239). The adverse prognostic impact of the mutations was not clear for patients treated with second-generation TKIs (2G-TKI). The multivariate analysis affirmed that mutations in AS/MTF genes independently serve as adverse prognostic factors for molecular response, failure-free survival (FFS), and progression risk. Additionally, there was an observable non-significant trend indicating a heightened risk of progression to advanced disease and worse overall survival (OS). Conclusion: Mutations in the AS/MTF genes using smMIP-based NGS can help identify patients with a potential risk of both treatment failure and progression, even from initial diagnosis, and may help upfront TKI selection.
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Affiliation(s)
| | | | | | | | | | | | | | - Tomas Jurcek
- Masaryk University and University Hospital Brno, Brno, Czech Republic
| | | | | | - Seongyoon Yi
- Princess Margaret Cancer Centre, Korea, Republic of
| | - Hyewon Lee
- Princess Margaret Cancer Centre, Toronto, Canada
| | | | | | - Jose-Mario Capo-Chichi
- Department of Pathology, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | | | | | - Mark D Minden
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Zhaolei Zhang
- The Donnelly Centre for Cellular and Biomolecular Research, Donnelly Centre For Cellular & Biomolecular Research, Canada
| | - Sagi Abelson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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4
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England JT, Szuber N, Sirhan S, Dunne T, Cerquozzi S, Hill M, Villeneuve PJA, Ho JM, Sadikovic B, Bhai P, Krishnan N, Dowhanik S, Hillis C, Capo-Chichi JM, Tsui H, Cheung V, Gauthier K, Sibai H, Davidson MB, Bankar A, Kotchetkov R, Gupta V, Maze D. Clinical Features and Long-Term Outcomes of a Pan-Canadian Cohort of Adolescents and Young Adults with Myeloproliferative Neoplasms: A Canadian MPN Group Study. Leukemia 2024; 38:570-578. [PMID: 38321107 DOI: 10.1038/s41375-024-02155-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/27/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024]
Abstract
Myeloproliferative neoplasms (MPNs) are a group of chronic hematologic malignancies that lead to morbidity and early mortality due to thrombotic complications and progression to acute leukemia. Clinical and mutational risk factors have been demonstrated to predict outcomes in patients with MPNs and are used commonly to guide therapeutic decisions, including allogenic stem cell transplant, in myelofibrosis. Adolescents and young adults (AYA, age ≤45 years) comprise less than 10% of all MPN patients and have unique clinical and therapeutic considerations. The prevalence and clinical impact of somatic mutations implicated in myeloid disease has not been extensively examined in this population. We conducted a retrospective review of patients evaluated at eight Canadian centers for MPN patients diagnosed at ≤45 years of age. In total, 609 patients were included in the study, with median overall survival of 36.8 years. Diagnosis of prefibrotic or overt PMF is associated with the lowest OS and highest risk of AP/BP transformation. Thrombotic complications (24%), including splanchnic circulation thrombosis (9%), were frequent in the cohort. Mutations in addition to those in JAK2/MPL/CALR are uncommon in the initial disease phase in our AYA population (12%); but our data indicate they may be predictive of transformation to post-ET/PV myelofibrosis.
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Affiliation(s)
- James T England
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada.
- Division of Medical Oncology & Malignant Hematology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.
| | - Natasha Szuber
- Maisonneuve-Rosemont Hospital, University of Montreal, Quebec, QC, Canada
| | - Shireen Sirhan
- Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Tom Dunne
- Division of Hematology, Newfoundland and Labrador Health Services, St. John's, NL, Canada
| | - Sonia Cerquozzi
- Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | - Madeleine Hill
- The Ottawa Hospital Research Institute, Ottawa, Ottawa, ON, Canada
| | - Pierre J A Villeneuve
- The Ottawa Hospital Research Institute, Ottawa, Ottawa, ON, Canada
- The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
| | - Jenny M Ho
- Division of Hematology, Department of Medicine, Western University, London Health Sciences Centre, London, ON, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON, Canada
| | - Pratibha Bhai
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON, Canada
| | - Nupur Krishnan
- Royal Victoria Regional Health Center, Barrie, ON, Canada
| | | | - Chris Hillis
- Department of Oncology, McMaster University, Hamilton, ON, Canada
| | - Jose-Mario Capo-Chichi
- Division of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Hubert Tsui
- Department of Hematopathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Verna Cheung
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Karine Gauthier
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Hassan Sibai
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Marta B Davidson
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Aniket Bankar
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | | | - Vikas Gupta
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Dawn Maze
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
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5
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Murphy T, Zou J, Arruda A, Wang TT, Zhao Z, Zheng Y, Gupta V, Maze D, McNamara C, Minden MD, Schimmer A, Sibai H, Yee K, Capo-Chichi JM, Stockley T, Schuh A, Bratman SV, Chan SM. Exclusion of persistent mutations in splicing factor genes and isocitrate dehydrogenase 2 improves the prognostic power of molecular measurable residual disease assessment in acute myeloid leukemia. Haematologica 2024; 109:671-675. [PMID: 37345484 PMCID: PMC10828788 DOI: 10.3324/haematol.2023.283510] [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: 05/10/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023] Open
Affiliation(s)
- Tracy Murphy
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Jinfeng Zou
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Andrea Arruda
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Ting Ting Wang
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Zhen Zhao
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Yangqiao Zheng
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Vikas Gupta
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Dawn Maze
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | | | - Mark D Minden
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Aaron Schimmer
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Hassan Sibai
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Karen Yee
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Jose-Mario Capo-Chichi
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto, ON
| | - Tracy Stockley
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto, ON
| | - Andre Schuh
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Scott V Bratman
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario
| | - Steven M Chan
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario.
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6
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Bergeron J, Capo-Chichi JM, Tsui H, Mahe E, Berardi P, Minden MD, Brandwein JM, Schuh AC. The Clinical Utility of FLT3 Mutation Testing in Acute Leukemia: A Canadian Consensus. Curr Oncol 2023; 30:10410-10436. [PMID: 38132393 PMCID: PMC10742150 DOI: 10.3390/curroncol30120759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
FMS-like tyrosine kinase 3 (FLT3) mutations are detected in approximately 20-30% of patients with acute myeloid leukemia (AML), with the presence of a FLT3 internal tandem duplication (FLT3-ITD) mutation being associated with an inferior outcome. Assessment of FLT3 mutational status is now essential to define optimal upfront treatment in both newly diagnosed and relapsed AML, to support post-induction allogeneic hematopoietic stem cell transplantation (alloSCT) decision-making, and to evaluate treatment response via measurable (minimal) residual disease (MRD) evaluation. In view of its importance in AML diagnosis and management, the Canadian Leukemia Study Group/Groupe canadien d'étude sur la leucémie (CLSG/GCEL) undertook the development of a consensus statement on the clinical utility of FLT3 mutation testing, as members reported considerable inter-center variability across Canada with respect to testing availability and timing of use, methodology, and interpretation. The CLSG/GCEL panel identified key clinical and hematopathological questions, including: (1) which patients should be tested for FLT3 mutations, and when?; (2) which is the preferred method for FLT3 mutation testing?; (3) what is the clinical relevance of FLT3-ITD size, insertion site, and number of distinct FLT3-ITDs?; (4) is there a role for FLT3 analysis in MRD assessment?; (5) what is the clinical relevance of the FLT3-ITD allelic burden?; and (6) how should results of FLT3 mutation testing be reported? The panel followed an evidence-based approach, taken together with Canadian clinical and laboratory experience and expertise, to create a consensus document to facilitate a more uniform approach to AML diagnosis and treatment across Canada.
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Affiliation(s)
- Julie Bergeron
- CEMTL Installation Maisonneuve-Rosemont, Institut Universitaire d’Hématologie-Oncologie et de Thérapie Cellulaire, Université de Montréal, Montréal, QC H1T 2M4, Canada
| | - Jose-Mario Capo-Chichi
- Division of Clinical Laboratory Genetics, Department of Laboratory Medicine and Pathobiology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, ON M5G 2C4, Canada;
| | - Hubert Tsui
- Division of Hematological Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Precision Diagnostics and Therapeutics Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada;
- Department of Laboratory Medicine and Pathobiology, Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Etienne Mahe
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Division of Hematology and Hematological Malignancies, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Philip Berardi
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital/Eastern Ontario Regional Laboratory Association, Ottawa, ON K1H 8M2, Canada;
- Department of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mark D. Minden
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; (M.D.M.); (A.C.S.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Joseph M. Brandwein
- Division of Hematology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada;
| | - Andre C. Schuh
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; (M.D.M.); (A.C.S.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
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7
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Mullen D, Vajpeyi R, Capo-Chichi JM, Nowak K, Wong N, Chetty R. Gastrointestinal Stromal Tumours (GISTs) with KRAS Mutation: A Rare but Important Subset of GISTs. Case Rep Gastrointest Med 2023; 2023:4248128. [PMID: 37663588 PMCID: PMC10471449 DOI: 10.1155/2023/4248128] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/27/2022] [Accepted: 07/10/2023] [Indexed: 09/05/2023] Open
Abstract
Gastrointestinal stromal tumours (GISTs) are the most common mesenchymal tumours of the GI tract, usually found in the stomach, jejunum, and ileum. Typically, they are KIT or PDGFR-mutated, allowing for targetable treatments with tyrosine kinase inhibitors such as imatinib. Here, we present two KRAS-mutated wild-type gastrointestinal tumours (GISTs). Both cases occurred in the small bowel of females. Immunohistochemical studies on both tumours showed KIT and DOG-1 positivity, with SDHB retained. Molecular analysis revealed a KRAS G12D mutation and a KRAS G13D mutation, respectively. Wild-type GISTs are extremely uncommon. They typically occur in the stomach or the small bowel. KRAS is one of the genes implicated in this subset of GIST, with KRAS G12D being the most frequently encountered mutation. GIST KRAS mutations can arise alone or in conjunction with KIT, PDFRA, or BRAF mutations. Identification of these rare molecular subtypes is clinically important due to their resistance to imatinib therapy.
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Affiliation(s)
- Dorinda Mullen
- Division of Anatomical Pathology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, Canada
| | - Rajkumar Vajpeyi
- Division of Anatomical Pathology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, Canada
| | - Jose-Mario Capo-Chichi
- Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Klaudia Nowak
- Division of Anatomical Pathology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, Canada
| | - Newton Wong
- Department of Cellular Pathology, Southmead Hospital, Bristol, UK
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8
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Zhou Q, Zhao D, Eladl E, Capo-Chichi JM, Kim DDH, Chang H. Molecular genetic characterization of Philadelphia chromosome-positive acute myeloid leukemia. Leuk Res 2023; 124:107002. [PMID: 36563650 DOI: 10.1016/j.leukres.2022.107002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 11/06/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Philadelphia chromosome-positive acute myeloid leukemia (Ph+ AML) is a provisional disease entity in the 2016 WHO classification, while its genetic profile of Ph+ AML remains poorly defined. In addition, the differentiating features of Ph+ AML and chronic myeloid leukemia in myeloid blast crisis (CML-MBC) remain controversial. METHODS We conducted a retrospective study of 15 Ph+ AML patients to compare their clinical and laboratory profiles with 27 CML-MBC patients. RESULTS Compared to CML-MBC, Ph+ AML patients presented with significantly higher peripheral WBC count and bone marrow blast percentage. The immunophenotypic profiles were largely similar between Ph+ AML and CML-MBC, except for CD4 expression, which was significantly enriched in CML-MBC. Ph+ AML patients less frequently harboured co-occurring additional cytogenetic abnormalities (ACA) compared to CML-MBC, and trisomy 19 (23%) and IDH1/2 (46%) were the most common ACA and mutated genes in Ph+ AML, respectively. Overall survival (OS) did not significantly differ between Ph+ AML and CML-MBC. Ph+ AML without CML-like features appeared to have a better outcome compared to Ph+ AML with CML-like features; ACA in Ph+ AML may confer an even worse prognosis. CONCLUSIONS Our results indicate that patients with Ph+ AML share similar genetic profiles and clinical outcomes with those with CML-MBC, thus should be classified as a high-risk entity.
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Affiliation(s)
- Qianghua Zhou
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Haematology, University Health Network, Toronto, Ontario, Canada
| | - Davidson Zhao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Entsar Eladl
- Department of Laboratory Haematology, University Health Network, Toronto, Ontario, Canada; Pathology Department, Mansoura University, Egypt
| | - Jose-Mario Capo-Chichi
- Clinical Laboratory Genetics, Genome Diagnostics Laboratory Medicine Program, University of Toronto, Toronto, Ontario, Canada
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Hong Chang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Haematology, University Health Network, Toronto, Ontario, Canada.
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9
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Medeiros JJF, Capo-Chichi JM, Shlush LI, Dick JE, Arruda A, Minden MD, Abelson S. SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes-derived data. Bioinformatics 2022; 38:2088-2095. [PMID: 35150236 PMCID: PMC9004652 DOI: 10.1093/bioinformatics/btac081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 10/12/2021] [Revised: 01/13/2022] [Accepted: 02/07/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Single-molecule molecular inversion probes (smMIPs) provide an exceptionally cost-effective and modular approach for routine or large-cohort next-generation sequencing. However, processing the derived raw data to generate highly accurate variants calls remains challenging. RESULTS We introduce SmMIP-tools, a comprehensive computational method that promotes the detection of single nucleotide variants and short insertions and deletions from smMIP-based sequencing. Our approach delivered near-perfect performance when benchmarked against a set of known mutations in controlled experiments involving DNA dilutions and outperformed other commonly used computational methods for mutation detection. Comparison against clinically approved diagnostic testing of leukaemia patients demonstrated the ability to detect both previously reported variants and a set of pathogenic mutations that did not pass detection by clinical testing. Collectively, our results indicate that increased performance can be achieved when tailoring data processing and analysis to its related technology. The feasibility of using our method in research and clinical settings to benefit from low-cost smMIP technology is demonstrated. AVAILABILITY AND IMPLEMENTATION The source code for SmMIP-tools, its manual and additional scripts aimed to foster large-scale data processing and analysis are all available on github (https://github.com/abelson-lab/smMIP-tools). Raw sequencing data generated in this study have been submitted to the European Genome-Phenome Archive (EGA; https://ega-archive.org) and can be accessed under accession number EGAS00001005359. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jessie J F Medeiros
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada,Ontario Institute for Cancer Research, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jose-Mario Capo-Chichi
- Genome Diagnostics, Department of Clinical Laboratory Genetics, University Health Network, Toronto, ON, Canada
| | - Liran I Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada,Department of Hematology and Medical Oncology, University Health Network, Toronto, ON, Canada
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10
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England JT, McNamara CJ, Kennedy JA, Capo-Chichi JM, Huang J, Arruda A, Nye T, Cheung V, Claudio JO, Maze D, Sibai H, Tierens A, Tsui H, Bankar A, Xu W, Stockley T, Gupta V. Clinical and molecular correlates of JAK-inhibitor therapy failure in myelofibrosis: long-term data from a molecularly annotated cohort. Leukemia 2022; 36:1689-1692. [PMID: 35347238 PMCID: PMC9162913 DOI: 10.1038/s41375-022-01544-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/01/2022] [Accepted: 03/09/2022] [Indexed: 11/09/2022]
Affiliation(s)
- James T. England
- grid.415224.40000 0001 2150 066XMedical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - Caroline J. McNamara
- grid.415224.40000 0001 2150 066XMedical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - James A. Kennedy
- grid.413104.30000 0000 9743 1587Medical Oncology and Hematology, Sunnybrook Health Sciences Centre, Toronto, Ontario Canada
| | - Jose-Mario Capo-Chichi
- grid.231844.80000 0004 0474 0428Division of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario Canada
| | - Jingyue Huang
- grid.415224.40000 0001 2150 066XBiostatistics, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - Andrea Arruda
- grid.415224.40000 0001 2150 066XMedical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - Taylor Nye
- grid.415224.40000 0001 2150 066XMedical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - Verna Cheung
- grid.415224.40000 0001 2150 066XMedical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - Jaime O. Claudio
- grid.415224.40000 0001 2150 066XMedical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - Dawn Maze
- grid.415224.40000 0001 2150 066XMedical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - Hassan Sibai
- grid.415224.40000 0001 2150 066XMedical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - Anne Tierens
- grid.417184.f0000 0001 0661 1177Laboratory Hematology, Toronto General Hospital, Toronto, Ontario Canada
| | - Hubert Tsui
- grid.417184.f0000 0001 0661 1177Laboratory Hematology, Toronto General Hospital, Toronto, Ontario Canada
| | - Aniket Bankar
- grid.415224.40000 0001 2150 066XMedical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - Wei Xu
- grid.415224.40000 0001 2150 066XBiostatistics, Princess Margaret Cancer Centre, Toronto, Ontario Canada
| | - Tracy Stockley
- grid.231844.80000 0004 0474 0428Division of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario Canada
| | - Vikas Gupta
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
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11
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Bankar A, Alibhai S, Smith E, Yang D, Malik S, Cheung V, Siddiq N, Claudio J, Arruda A, Tsui H, Capo-Chichi JM, Kennedy JA, McNamara C, Sibai H, Maze D, Xu W, Gupta V. Association of frailty with clinical outcomes in myelofibrosis: a retrospective cohort study. Br J Haematol 2021; 194:557-567. [PMID: 34131896 PMCID: PMC8361997 DOI: 10.1111/bjh.17617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 03/28/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022]
Abstract
There is limited understanding of the impact of frailty on clinical outcomes in patients with myelofibrosis (MF). In this retrospective cohort study on 439 chronic phase MF patients [mean age: 68·7 ± 12 years; median follow-up: 3·4 years (IQR 0·4-8·6)] from 2004 till 2018, we used a 35-variable frailty index (FI) to categorise patient's frailty status as fit (FI < 0·2, reference), prefrail (FI 0·2-0·29) or frail (FI ≥ 0·3). The association of frailty with overall survival (OS) and cumulative JAK inhibitor (JAKi) therapy failure was measured using hazard ratio (HR, 95% CI). In multivariable analysis, prefrail (HR 1·7, 1·1-2·5) and frail patients (HR 2·9, 1·6-5·5), those with higher DIPSS score (HR 2·5, 1·6-3·9) and transfusion dependency (HR 1·9, 1·3-2·9) had shorter OS. In a subset analysis of patients on JAKi treatment (n = 222), frail patients (HR 2·5, 1·1-5·7), patients with higher DIPSS score (HR 1·7, 1·0-3·1) and transfusion dependence (HR 1·7, 1·1-2·7) had higher cumulative incidence of JAKi failure. Age, comorbidities, ECOG performance status, and MPN driver mutations did not impact outcomes. Thus, higher frailty scores are associated with worse OS and increased JAKi failure in MF, and is a superior indicator of fitness in comparison to age, comorbidities, and performance status.
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Affiliation(s)
- Aniket Bankar
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Elliot Smith
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Dongyang Yang
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Sarah Malik
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Verna Cheung
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Nancy Siddiq
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Jaime Claudio
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Hubert Tsui
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | | | | | | | - Hassan Sibai
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Dawn Maze
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Wei Xu
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Vikas Gupta
- Princess Margaret Cancer Centre, Toronto, ON, Canada
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12
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Jiang G, Capo-Chichi JM, Liu A, Atenafu EG, Guo R, Tierens A, Minden MD, Chang H. Acute myeloid leukemia with myelodysplasia-related changes diagnosed with multilineage dysplasia alone demonstrates a superior clinical outcome. Hum Pathol 2020; 104:117-126. [PMID: 32798550 DOI: 10.1016/j.humpath.2020.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/14/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022]
Abstract
Acute myeloid leukemia with myelodysplasia-related changes (AML-MRC) generally confers poor prognosis; however, the clinical outcome remains heterogeneous. We sought to further stratify this subentity of AML by performing a retrospective analysis of 179 adult patients with AML-MRC diagnosed at our institution. Based on 2016 World Health Organization diagnostic criteria, 44 (25%) patients had multilineage dysplasia alone (AML-MRC-M), 74 (41%) had history of myelodysplastic syndrome (MDS) or myelodysplastic/myeloproliferative disease (AML-MRC-H), and 61 (34%) had MDS-related cytogenetics (AML-MRC-C). AML-MRC-M and hematopoietic stem cell transplantation (HSCT) were associated with prolonged event-free survival (EFS) (P = 0.0051 and P < 0.0001, respectively) and overall survival (OS) (P = 0.0015 and P < 0.0001, respectively), whereas AML-MRC-C and age ≥60 years were associated with shorter EFS (P = 0.028 and P = 0.015, respectively) and OS (P = 0.021 and P = 0.013, respectively). Of note, NPM1mut did not affect the patient's outcome. Multivariable analysis confirmed HSCT and AML-MRC-C as independent predictors for EFS (P < 0.0001 and P = 0.0342, respectively) and OS (P < 0.0001 and P = 0.0295, respectively). AML-MRC-M was an independent predictor for OS (P = 0.0449). When compared with a control group of 105 patients with normal karyotype AML not otherwise specified (NK-AML-NOS), patients with AML-MRC-M had similar EFS and OS (P = 0.99 and P = 0.91, respectively). However, AML-MRC-H and AML-MRC-C were associated with shorter EFS and OS (P = 0.0002 and P < 0.0001, respectively) than the same control group. In a subset of patients, next-generation sequencing analysis showed AML-MRC-M was associated with ASXL1 mutation compared with NK-AML (56% vs 6%). In conclusion, AML-MRC-M demonstrates a superior clinical outcome compared with the rest of the AML-MRC group. They have comparable outcomes to NK-AML-NOS, and these data suggest AML-MRC-M may be considered not to be classified in the same group as patients with other AML-MRC.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Cell Lineage
- Female
- Genetic Predisposition to Disease
- Hematopoietic Stem Cell Transplantation/adverse effects
- Hematopoietic Stem Cell Transplantation/mortality
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/surgery
- Male
- Middle Aged
- Mutation
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/mortality
- Myelodysplastic Syndromes/pathology
- Myelodysplastic Syndromes/surgery
- Nuclear Proteins/genetics
- Nucleophosmin
- Progression-Free Survival
- Repressor Proteins/genetics
- Retrospective Studies
- Risk Assessment
- Risk Factors
- Time Factors
- Young Adult
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Affiliation(s)
- Gina Jiang
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada
| | - Jose-Mario Capo-Chichi
- Department of Clinical Laboratory Genetics, Genome Diagnostics, University Health Network, Canada
| | - Aijun Liu
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, China
| | | | - Robert Guo
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada
| | - Ann Tierens
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada
| | - Mark D Minden
- Department of Hematology and Medical Oncology, University Health Network, University of Toronto, Toronto, Canada
| | - Hong Chang
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada.
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13
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Jiang G, Capo-Chichi JM, Liu A, Atenafu EG, Kumar R, Minden MD, Chang H. Combination of FLT3-ITD Allelic Ratio, NPM1 Mutation, and Immunophenotypic Markers to Modulate Outcome Prediction in Patients with Normal Karyotype Acute Myelogenous Leukemia Undergoing Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2020; 26:1995-2000. [PMID: 32712325 DOI: 10.1016/j.bbmt.2020.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/06/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 12/01/2022]
Abstract
NPM1 mutation status and the allelic ratio (AR) of FLT3-internal tandem duplication (FLT3-ITD) are routinely tested for disease risk stratification in patients with normal karyotype (NK) acute myelogenous leukemia (AML); however, the predictive impact of immunophenotypic markers on different NPM1/FLT3 genotypes remains unclear. We performed a retrospective analysis of 423 patients with NK-AML subclassified into groups based on NPM1/FLT3 genotype. Allogeneic hematopoietic stem cell transplantation (HSCT) was performed in 124 of 423 patients (29%) and was significantly associated with longer event-free survival (EFS) and overall survival (OS), except for patients with the favorable genotype, defined as mutated NPM1 (NPM1mut) combined with normal FLT3 status (FLT3-ITDneg) or FLT3-ITD AR <.5 (FLT3-ITDlow). A subset of AML patients bearing the favorable NPM1mut/FLT3-ITDneg/low genotype share similar outcomes with AML patients who have the intermediate FLT3/NPM1 genotype defined by normal NPM1 (NPM1wt) and FLT3-ITDneg/low. In these individuals, the lack of CD13 expression (CD13neg) was associated with shorter EFS (P = .041) and OS (P = .017). CD13neg was an independent predictor for shorter OS (hazard ratio, 1.985; P = .028).
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Affiliation(s)
- Gina Jiang
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jose-Mario Capo-Chichi
- Department of Clinical Laboratory Genetics, Genome Diagnostics, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Aijun Liu
- Department of Hematology, Beijing Chaoyang Hospital, Capital University Beijing, Beijing, China
| | - Eshetu G Atenafu
- Department of Biostatistics, University Health Network, Toronto, Ontario, Canada
| | - Rajat Kumar
- Department of Hematology and Medical Oncology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Mark D Minden
- Department of Hematology and Medical Oncology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Hong Chang
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Ontario, Canada.
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14
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Gupta V, Kennedy J, Capo-Chichi JM, Kim S, Ahn KW, Hu ZH, Alyea EP, Popat UR, Sobecks RM, Scott BL, Nakamura R, Saber W. Impact of Genetic Mutations on the Outcomes of Allogeneic Hematopoietic Cell Transplantation in Patients with Acute Myeloid Leukemia with Antecedent Myeloproliferative Neoplasm. Biol Blood Marrow Transplant 2020. [DOI: 10.1016/j.bbmt.2019.12.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Capitano M, Capo-Chichi JM, Minden MD, Chang H. Mixed phenotype acute leukaemia with predominant myeloid blasts and a small subset of B/myeloid blasts shares the same mutation profile. Br J Haematol 2019; 188:e60-e63. [PMID: 31828776 DOI: 10.1111/bjh.16325] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mario Capitano
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jose-Mario Capo-Chichi
- Laboratory Medicine Program and Department of Medical Oncology and Hematology, University Health Network, University of Toronto, Ottawa, ON, Canada
| | - Mark D Minden
- Laboratory Medicine Program and Department of Medical Oncology and Hematology, University Health Network, University of Toronto, Ottawa, ON, Canada
| | - Hong Chang
- Laboratory Medicine Program and Department of Medical Oncology and Hematology, University Health Network, University of Toronto, Ottawa, ON, Canada
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16
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Serra S, Capo-Chichi JM, McCarthy AJ, Sabatini P, Chetty R. Unique MLH1 mutations in colonic adenomas in an obligate germline Lynch syndrome carrier. J Clin Pathol 2019; 73:291-295. [PMID: 31649038 DOI: 10.1136/jclinpath-2019-206234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/24/2019] [Accepted: 10/05/2019] [Indexed: 11/03/2022]
Abstract
BACKGROUND An obligate germline Lynch syndrome carrier had four colonic adenomas removed. MATERIALS AND METHODS The adenomas were evaluated for grade of dysplasia, MLH1, PMS2, MSH2 and MSH6 protein expression, microsatellite instability (MSI), BRAF, methylation status and a next-generation sequencing (NGS) panel of 52 cancer genes. RESULTS There were four tubular or tubulovillous adenomas from the hepatic flexure, rectosigmoid and rectum; one with low-grade and high-grade dysplasia, one with high-grade dysplasia only and two with low-grade dysplasia. All four adenomas showed retention of MLH1, MHS2 and MSH6 but complete loss of PMS2 in both low-grade and high-grade dysplasia areas.Two of the four adenomas were MSI-high, BRAF V600E wild type and were not MLH1 methylated. NGS identified an MLH1 germline variant: NM_000249.3: c.1558+1 G>A, p.(?) in all tissue (adenomas and normal), which likely explains the pathophysiology of Lynch syndrome in this patient. Other variants were also detected in MLH1 and MSH6 in all four adenomas tested; these being reported previously in somatic colorectal cancers. CONCLUSION We highlight an MLH1 variant in the colonic adenomas in an obligate Lynch syndrome carrier that resulted in PMS2 protein loss in the absence of mutations of the PMS2 gene.
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Affiliation(s)
- Stefano Serra
- Laboratory Medicine Program, Divisions of Anatomical Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | | | - Aoife J McCarthy
- Laboratory Medicine Program, Divisions of Anatomical Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Peter Sabatini
- Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada
| | - Runjan Chetty
- Laboratory Medicine Program, Divisions of Anatomical Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
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17
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Capo-Chichi JM, Michaels P, Tremblay-Le May R, Abelson S, Hasserjian RP, Xia D. Emerging patterns in clonal haematopoiesis. J Clin Pathol 2019; 72:453-459. [PMID: 31164443 DOI: 10.1136/jclinpath-2019-205851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 12/31/2022]
Abstract
Clonal haematopoiesis (CH) is defined by the presence of acquired mutations and/or cytogenetic abnormalities in haematopoietic cells. By definition, these premalignant clones do not meet criteria for haematopoietic neoplasms listed in the Revised Fourth Edition of the WHO classification. CH is fairly common in elderly individuals and is associated with higher risks for haematological cancers, in particular myelodysplastic syndrome and acute myeloid leukaemia (AML), as well as cardiovascular events. Similar small clones have also been detected during follow-up in patients with AML in morphological remission, in individuals with aplastic anaemia, and in pre-chemotherapy blood samples from patients with other types of cancers. In each of these contexts, the presence of mutations carries different clinical implications, and sometimes demonstrates unique genetic profiles. Emerging research suggests that the number and identity of mutations, the size of the mutant clones and various other factors, including age, immune status and history of exogenous drugs/toxins, are important for disease biology and progression. This review focuses specifically on the subset of CH with gene mutations detected by sequencing, and includes discussions of nomenclature and molecular technologies that detect and quantify gene mutations.
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Affiliation(s)
| | - Phillip Michaels
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | | | - Sagi Abelson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Daniel Xia
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
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18
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McCarthy AJ, Capo-Chichi JM, Spence T, Grenier S, Stockley T, Kamel-Reid S, Serra S, Sabatini P, Chetty R. Heterogenous loss of mismatch repair (MMR) protein expression: a challenge for immunohistochemical interpretation and microsatellite instability (MSI) evaluation. J Pathol Clin Res 2018; 5:115-129. [PMID: 30387329 PMCID: PMC6463865 DOI: 10.1002/cjp2.120] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/01/2018] [Accepted: 10/24/2018] [Indexed: 01/18/2023]
Abstract
Immunohistochemistry (IHC) for mismatch repair (MMR) proteins is used to identify MMR status: being diffusely positive (intact/retained nuclear staining) or showing loss of nuclear tumour staining (MMR protein deficient). Four colonic adenocarcinomas and a gastric adenocarcinoma with associated dysplasia that displayed heterogenous IHC staining patterns in at least one of the four MMR proteins were characterised by next‐generation sequencing (NGS). In order to examine a potential molecular mechanism for these staining patterns, the respective areas were macrodissected, analysed for microsatellite instability (MSI) and investigated by NGS and multiplex ligation‐dependent probe amplification (MLPA) analysis of MLH1, MSH2, MSH6 and PMS2 genes, including MLH1 methylation analysis. One colonic adenocarcinoma showed heterogenous MSH6 IHC staining and molecular analysis demonstrated increasing allelic burden of two MSH6 frameshift variants (c.3261delC and c.3261dupC) in areas with MSH6 protein loss compared to areas where MSH6 was retained. Two colonic adenocarcinomas with heterogenous MLH1 staining showed no differences in sequence variants. In one of these cases, however, MLH1 was hypermethylated in the area of MLH1 loss. Another colon carcinoma with heterogenous PMS2 staining (but with retained MSH6) showed both MSH6 c.3261dupC and 3260_3261dupCC where PMS2 protein was lost and only c.3261dupC where PMS2 was retained. The gastric carcinoma showed complete loss of MSH6 in dysplastic foci, while the underlying invasive carcinoma showed retention of MSH6. Both these areas, however, were MSI‐high and showed the same MSH6 variant: c.3261delC. The gastric dysplasia additionally showed MSH6 c.3261dupC. In four of the five cases where MMR protein was lost, these areas were MSI‐high. Heterogenous MMR IHC (focal and/or zonal within the same tumour or between invasive and dysplastic preinvasive areas) is not always due to artefact and is invariably related to MSI‐high status in the areas of loss. An interesting aspect to this study is the presence of MSH6 somatic mutations irrespective of whether MSH6 IHC staining was intact or lost.
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Affiliation(s)
- Aoife J McCarthy
- Department of Anatomical Pathology, Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, Canada
| | - Jose-Mario Capo-Chichi
- Department of Anatomical Pathology, Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, Canada
| | - Tara Spence
- Clinical Laboratory Genetics, University Health Network and University of Toronto, Toronto, Canada
| | - Sylvie Grenier
- Clinical Laboratory Genetics, University Health Network and University of Toronto, Toronto, Canada
| | - Tracy Stockley
- Clinical Laboratory Genetics, University Health Network and University of Toronto, Toronto, Canada
| | - Suzanne Kamel-Reid
- Clinical Laboratory Genetics, University Health Network and University of Toronto, Toronto, Canada
| | - Stefano Serra
- Department of Anatomical Pathology, Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, Canada
| | - Peter Sabatini
- Clinical Laboratory Genetics, University Health Network and University of Toronto, Toronto, Canada
| | - Runjan Chetty
- Department of Anatomical Pathology, Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, Canada
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19
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Hamdan FF, Srour M, Capo-Chichi JM, Daoud H, Nassif C, Patry L, Massicotte C, Ambalavanan A, Spiegelman D, Diallo O, Henrion E, Dionne-Laporte A, Fougerat A, Pshezhetsky AV, Venkateswaran S, Rouleau GA, Michaud JL. De novo mutations in moderate or severe intellectual disability. PLoS Genet 2014; 10:e1004772. [PMID: 25356899 PMCID: PMC4214635 DOI: 10.1371/journal.pgen.1004772] [Citation(s) in RCA: 295] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 09/22/2014] [Indexed: 01/09/2023] Open
Abstract
Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband). We observed a significant excess of de novo single nucleotide substitutions and loss-of-function mutations in these cases compared to control subjects, suggesting that at least a subset of these variations are pathogenic. A total of 12 likely pathogenic DNMs were identified in genes previously associated with ID (ARID1B, CHD2, FOXG1, GABRB3, GATAD2B, GRIN2B, MBD5, MED13L, SETBP1, TBR1, TCF4, WDR45), resulting in a diagnostic yield of ∼29%. We also identified 12 possibly pathogenic DNMs in genes (HNRNPU, WAC, RYR2, SET, EGR1, MYH10, EIF2C1, COL4A3BP, CHMP2A, PPP1CB, VPS4A, PPP2R2B) that have not previously been causally linked to ID. Interestingly, no case was explained by inherited mutations. Protein network analysis indicated that the products of many of these known and candidate genes interact with each other or with products of other ID-associated genes further supporting their involvement in ID. We conclude that DNMs represent a major cause of moderate or severe ID.
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Affiliation(s)
| | - Myriam Srour
- CHU Sainte-Justine Research Center, Montreal, Canada
- Division of Pediatric Neurology, Montreal Children's Hospital, Montreal, Canada
| | | | - Hussein Daoud
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | | | - Lysanne Patry
- CHU Sainte-Justine Research Center, Montreal, Canada
| | | | | | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Ousmane Diallo
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Edouard Henrion
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | | | - Anne Fougerat
- CHU Sainte-Justine Research Center, Montreal, Canada
| | | | | | - Guy A. Rouleau
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Jacques L. Michaud
- CHU Sainte-Justine Research Center, Montreal, Canada
- Department of Pediatrics and Department of Neurosciences, University of Montreal, Montreal, Canada
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