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Wang J, Zhang W, Xu X, Buglioni A, Li P, Chen X, Liu Y, Xu M, Herrick JL, Horna P, Zhang X, Song J, Jevremovic D, He R, Shi M, Yuan J. Clinicopathologic features and outcomes of acute leukemia harboring PICALM::MLLT10 fusion. Hum Pathol 2024; 151:105626. [PMID: 38971327 DOI: 10.1016/j.humpath.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
The PICALM::MLLT10 fusion is a rare but recurrent cytogenetic abnormality in acute leukemia, with limited clinicopathologic and outcome data available. Herein, we analyzed 156 acute leukemia patients with PICALM::MLLT10 fusion, including 12 patients from our institutions and 144 patients from the literature. The PICALM::MLLT10 fusion preferentially manifested in pediatric and young adult patients, with a median age of 24 years. T-lymphoblastic leukemia/lymphoma (T-ALL) constituted 65% of cases, acute myeloid leukemia (AML) 27%, and acute leukemia of ambiguous lineage (ALAL) 8%. About half of T-ALL were classified as an early T-precursor (ETP)-ALL. In our institutions' cohort, mediastinum was the most common extramedullary site of involvement. Eight of 12 patients were diagnosed with T-ALL exhibiting a pro-/pre-T stage phenotype (CD4/CD8-double negative, CD7-positive), and frequent CD79a expression. NGS revealed pathogenic mutations in 5 of 6 tested cases, including NOTCH1, and genes in RAS and JAK-STAT pathways and epigenetic modifiers. Of 138 cases with follow-up, pediatric patients (<18 years) had 5-year overall survival (OS) of 71%, significantly better than adults at 33%. The 5-year OS for AML patients was 25%, notably shorter than T-ALL patients at 54%; this distinction was observed in both pediatric and adult populations. Furthermore, adult but not pediatric ETP-ALL patients demonstrated inferior survival compared to non-ETP-ALL patients. Neither karyotype complexity nor transplant status had a discernible impact on OS. In conclusion, PICALM::MLLT10 fusion is most commonly seen in T-ALL patients, particularly those with an ETP phenotype. AML and adult ETP-ALL patients had adverse prognosis. PICALM::MLTT10 fusion testing should be considered in T-ALL, AML, and ALAL patients.
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Affiliation(s)
| | - Weiwei Zhang
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Xinjie Xu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Alessia Buglioni
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Peng Li
- Division of Hematopathology, Department of Pathology, University of Utah Health, Salt Lake City, UT, 84132, USA
| | - Xueyan Chen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, 98195, USA
| | - Yajuan Liu
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, 98195, USA
| | - Min Xu
- Department of Pathology, Seattle Children's Hospital, Seattle, WA, 98105, USA
| | - Jennifer L Herrick
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Pedro Horna
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xiaohui Zhang
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jinming Song
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Dragan Jevremovic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rong He
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Min Shi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ji Yuan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
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Botten GA, Zhang Y, Fuda F, Koduru P, Weinberg OK, Slone TL, Zheng R, Dickerson KE, Gagan JR, Chen W. T/myeloid mixed phenotype acute leukaemia harbouring TLX3::BCL11B with TLX3 activation. Br J Haematol 2024; 205:607-612. [PMID: 38385580 DOI: 10.1111/bjh.19363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
T/myeloid mixed phenotype acute leukaemia (MPAL) is a rare aggressive acute leukaemia with poorly understood pathogenesis. Herein, we report two cases of T/myeloid MPAL harbouring BCL11B-associated structural variants that activate TLX3 (TLX3::BCL11B-TLX3-activation) by genome sequencing and transcriptomic analyses. Both patients were young males with extramedullary involvement. Cooperative gene alterations characteristic of T/myeloid MPAL and T-lymphoblastic leukaemia (T-ALL) were detected. Both patients achieved initial remission following lineage-matched ALL-based therapy with one patient requiring a lineage-switched myeloid-based therapy. Our study is the first to demonstrate the clinicopathological and genomic features of TLX3::BCL11B-TLX3-activated T/myeloid MPAL and provide insights into leukaemogenesis.
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Affiliation(s)
- Giovanni A Botten
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Franklin Fuda
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Prasad Koduru
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Olga K Weinberg
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Tamra L Slone
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ruifang Zheng
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kathryn E Dickerson
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jeffrey R Gagan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Weina Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Mangum R, Lin FY, Parsons DW. Recent Advancements and Innovations in Pediatric Precision Oncology. J Pediatr Hematol Oncol 2024; 46:262-271. [PMID: 38857189 DOI: 10.1097/mph.0000000000002871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/29/2024] [Indexed: 06/12/2024]
Abstract
Precision oncology incorporates comprehensive genomic profiling into the individualized clinical care of pediatric cancer patients. In recent years, comprehensive pan-cancer analyses have led to the successful implementation of genomics-based pediatric trials and accelerated approval of novel targeted agents. In addition, disease-specific studies have resulted in molecular subclassification of myriad cancer types with subsequent tailoring of treatment intensity based on the patient's prognostic factors. This review discusses the progress of the field and highlights developments that are leading to more personalized cancer care and improved patient outcomes. Increased understanding of the evolution of precision oncology over recent decades emphasizes the tremendous impact of improved genomic applications. New technologies and improved diagnostic modalities offer further promise for future advancements within the field.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ
| | - Frank Y Lin
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
| | - D Williams Parsons
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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4
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Pagliaro L, Chen SJ, Herranz D, Mecucci C, Harrison CJ, Mullighan CG, Zhang M, Chen Z, Boissel N, Winter SS, Roti G. Acute lymphoblastic leukaemia. Nat Rev Dis Primers 2024; 10:41. [PMID: 38871740 DOI: 10.1038/s41572-024-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Acute lymphoblastic leukaemia (ALL) is a haematological malignancy characterized by the uncontrolled proliferation of immature lymphoid cells. Over past decades, significant progress has been made in understanding the biology of ALL, resulting in remarkable improvements in its diagnosis, treatment and monitoring. Since the advent of chemotherapy, ALL has been the platform to test for innovative approaches applicable to cancer in general. For example, the advent of omics medicine has led to a deeper understanding of the molecular and genetic features that underpin ALL. Innovations in genomic profiling techniques have identified specific genetic alterations and mutations that drive ALL, inspiring new therapies. Targeted agents, such as tyrosine kinase inhibitors and immunotherapies, have shown promising results in subgroups of patients while minimizing adverse effects. Furthermore, the development of chimeric antigen receptor T cell therapy represents a breakthrough in ALL treatment, resulting in remarkable responses and potential long-term remissions. Advances are not limited to treatment modalities alone. Measurable residual disease monitoring and ex vivo drug response profiling screening have provided earlier detection of disease relapse and identification of exceptional responders, enabling clinicians to adjust treatment strategies for individual patients. Decades of supportive and prophylactic care have improved the management of treatment-related complications, enhancing the quality of life for patients with ALL.
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Affiliation(s)
- Luca Pagliaro
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Cristina Mecucci
- Department of Medicine, Hematology and Clinical Immunology, University of Perugia, Perugia, Italy
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ming Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Nicolas Boissel
- Hôpital Saint-Louis, APHP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Stuart S Winter
- Children's Minnesota Cancer and Blood Disorders Program, Minneapolis, MN, USA
| | - Giovanni Roti
- Department of Medicine and Surgery, University of Parma, Parma, Italy.
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy.
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy.
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Neumann M, Beder T, Bastian L, Hänzelmann S, Bultmann M, Wolgast N, Hartmann A, Trautmann H, Ortiz-Tanchez J, Schlee C, Schroeder M, Fransecky L, Vosberg S, Fiedler W, Alakel N, Heberling L, Kondakci M, Starck M, Schwartz S, Raffel S, Müller-Tidow C, Schneller F, Reichle A, Burmeister T, Greif PA, Brüggemann M, Gökbuget N, Baldus CD. Molecular subgroups of T-cell acute lymphoblastic leukemia in adults treated according to pediatric-based GMALL protocols. Leukemia 2024; 38:1213-1222. [PMID: 38744920 PMCID: PMC11147771 DOI: 10.1038/s41375-024-02264-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/14/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
In contrast to B-cell precursor acute lymphoblastic leukemia (ALL), molecular subgroups are less well defined in T-lineage ALL. Comprehensive studies on molecular T-ALL subgroups have been predominantly performed in pediatric ALL patients. Currently, molecular characteristics are rarely considered for risk stratification. Herein, we present a homogenously treated cohort of 230 adult T-ALL patients characterized on transcriptome, and partly on DNA methylation and gene mutation level in correlation with clinical outcome. We identified nine molecular subgroups based on aberrant oncogene expression correlating to four distinct DNA methylation patterns. The subgroup distribution differed from reported pediatric T-ALL cohorts with higher frequencies of prognostic unfavorable subgroups like HOXA or LYL1/LMO2. A small subset (3%) of HOXA adult T-ALL patients revealed restricted expression of posterior HOX genes with aberrant activation of lncRNA HOTTIP. With respect to outcome, TLX1 (n = 44) and NKX2-1 (n = 4) had an exceptionally favorable 3-year overall survival (3y-OS) of 94%. Within thymic T-ALL, the non TLX1 patients had an inferior but still good prognosis. To our knowledge this is the largest cohort of adult T-ALL patients characterized by transcriptome sequencing with meaningful clinical follow-up. Risk classification based on molecular subgroups might emerge and contribute to improvements in outcome.
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Affiliation(s)
- Martin Neumann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany.
- Clinical Research Unit 'CATCH ALL' (KFO 5010/1), Kiel, Germany.
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel and Lübeck, Germany.
| | - Thomas Beder
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel and Lübeck, Germany
| | - Lorenz Bastian
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit 'CATCH ALL' (KFO 5010/1), Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel and Lübeck, Germany
| | - Sonja Hänzelmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Miriam Bultmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel and Lübeck, Germany
| | - Nadine Wolgast
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit 'CATCH ALL' (KFO 5010/1), Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel and Lübeck, Germany
| | - Alina Hartmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit 'CATCH ALL' (KFO 5010/1), Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel and Lübeck, Germany
| | - Heiko Trautmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel and Lübeck, Germany
| | - Jutta Ortiz-Tanchez
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Cornelia Schlee
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Michael Schroeder
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Lars Fransecky
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel and Lübeck, Germany
| | - Sebastian Vosberg
- Department of Internal Medicine III, University Hospital LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Walter Fiedler
- Medical Department II, Hematology and Oncology, University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Nael Alakel
- Medical Department I, Carl Gustav Carus University Hospital Dresden, Dresden, Germany
| | - Lisa Heberling
- Medical Department I, Carl Gustav Carus University Hospital Dresden, Dresden, Germany
| | - Mustafa Kondakci
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Michael Starck
- Medical Department I, Hospital München-Schwabing, Schwabing, Germany
| | - Stefan Schwartz
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Simon Raffel
- Medical Department V, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Folker Schneller
- Medical Department III, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Albrecht Reichle
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - Thomas Burmeister
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Philipp A Greif
- Department of Internal Medicine III, University Hospital LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Monika Brüggemann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit 'CATCH ALL' (KFO 5010/1), Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel and Lübeck, Germany
| | - Nicola Gökbuget
- Department of Medicine II, Hematology/Oncology, University Hospital, Goethe University, Frankfurt/M, Germany
| | - Claudia D Baldus
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit 'CATCH ALL' (KFO 5010/1), Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel and Lübeck, Germany
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Li X, Huang Z, Zhu L, Lai W, Li Y, Chen H, Liu D, Huang J, Zhou D, Li Y, Weng W, Xu H, Xu L, Luo Z, Fang J. The potential role of RNA sequencing in diagnosing unexplained insensitivity to conventional chemotherapy in pediatric patients with B-cell acute lymphoblastic leukemia. BMC Med Genomics 2024; 17:149. [PMID: 38811988 PMCID: PMC11137891 DOI: 10.1186/s12920-024-01892-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Pediatric B-cell acute lymphoblastic leukemia (B-ALL) is a highly heterogeneous disease. According to large-scale RNA sequencing (RNA-seq) data, B-ALL patients can be divided into more than 10 subgroups. However, many genomic defects associated with resistance mechanisms have not yet been identified. As an individual clinical tool for molecular diagnostic risk classification, RNA-seq and gene expression pattern-based therapy could be potential upcoming strategies. In this study, we retrospectively analyzed the RNA-seq gene expression profiles of 45 children whose molecular diagnostic classifications were inconsistent with the response to chemotherapy. The relationship between the transcriptome and chemotherapy response was analyzed. Fusion gene identification was conducted for the included patients who did not have known high-risk associated fusion genes or gene mutations. The most frequently detected fusion gene pair in the high-risk group was the DHRSX duplication, which is a novel finding. Fusions involving ABL1, LMNB2, NFATC1, PAX5, and TTYH3 at onset were more frequently detected in the high-risk group, while fusions involving LFNG, TTYH3, and NFATC1 were frequently detected in the relapse group. According to the pathways involved, the underlying drug resistance mechanism is related to DNA methylation, autophagy, and protein metabolism. Overall, the implementation of an RNA-seq diagnostic system will identify activated markers associated with chemotherapy response, and guide future treatment adjustments.
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Affiliation(s)
- Xinyu Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Zaoli Huang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Liwen Zhu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Weixin Lai
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Yunyao Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Han Chen
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Diandian Liu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Dunhua Zhou
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Yang Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Wenjun Weng
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Honggui Xu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Luhong Xu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China.
| | - Zhenhua Luo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China.
| | - Jianpei Fang
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China.
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7
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Singh M, Sharma P, Bhatia P, Trehan A, Thakur R, Sreedharanunni S. Integrated analysis of transcriptome and genome variations in pediatric T cell acute lymphoblastic leukemia: data from north Indian tertiary care center. BMC Cancer 2024; 24:325. [PMID: 38459434 PMCID: PMC10924344 DOI: 10.1186/s12885-024-12063-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/26/2024] [Indexed: 03/10/2024] Open
Abstract
INTRODUCTION T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease with poor prognosis and inferior outcome. Although multiple studies have been perform on genomics of T-ALL, data from Indian sub-continent is scarce. METHODS In the current study we aimed to identify the genetic variability of T-ALL in an Indian cohort of pediatric (age ≤ 12 years) T-ALL patients (n = 25) by whole transcriptome sequencing along with whole exome sequencing and correlated the findings with clinical characteristics and disease outcome. RESULTS The median age was 7 years (range 3 -12 years). RNA sequencing revealed a definitive fusion event in 14 cases (56%) (including a novel fusions) with STIL::TAL1 in 4 (16%), followed by NUP21::ABL1, TCF7::SPI1, ETV6::HDAC8, LMO1::RIC3, DIAPH1::JAK2, SETD2::CCDC12 and RCBTB2::LPAR6 in 1 (4%) case each. Significant aberrant expression was noted in RAG1 (64%), RAG2 (80%), MYCN (52%), NKX3-1 (52%), NKX3-2 (32%), TLX3 (28%), LMO1 (20%) and MYB (16%) genes. WES data showed frequent mutations in NOTCH1 (35%) followed by WT1 (23%), FBXW7 (12%), KRAS (12%), PHF6 (12%) and JAK3 (12%). Nearly 88.2% of cases showed a deletion of CDKN2A/CDKN2B/MTAP genes. Clinically significant association of a better EFS and OS (p=0.01) was noted with RAG2 over-expression at a median follow up of 22 months, while a poor EFS (p=0.041) and high relapse rate (p=0.045) was observed with MYB over-expression. CONCLUSION Overall, the present study demonstrates the frequencies of transcriptomic and genetic alterations from Indian cohort of pediatric T-ALL and is a salient addition to current genomics data sets available in T-ALL.
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Affiliation(s)
- Minu Singh
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Sector -12, 160012, Chandigarh, India.
| | - Pankaj Sharma
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Sector -12, 160012, Chandigarh, India
| | - Prateek Bhatia
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Sector -12, 160012, Chandigarh, India
| | - Amita Trehan
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Sector -12, 160012, Chandigarh, India
| | - Rozy Thakur
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Sector -12, 160012, Chandigarh, India
| | - Sreejesh Sreedharanunni
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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8
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Almeida A, T'Sas S, Pagliaro L, Fijalkowski I, Sleeckx W, Van Steenberge H, Zamponi R, Lintermans B, Van Loocke W, Palhais B, Reekmans A, Bardelli V, Demoen L, Reunes L, Deforce D, Van Nieuwerburgh F, Kentsis A, Ntziachristos P, Van Roy N, De Moerloose B, Mecucci C, La Starza R, Roti G, Goossens S, Van Vlierberghe P, Pieters T. Myb overexpression synergizes with the loss of Pten and is a dependency factor and therapeutic target in T-cell lymphoblastic leukemia. Hemasphere 2024; 8:e51. [PMID: 38463444 PMCID: PMC10924755 DOI: 10.1002/hem3.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/28/2024] [Indexed: 03/12/2024] Open
Abstract
T-lineage acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy that accounts for 10%-15% of pediatric and 25% of adult ALL cases. Although the prognosis of T-ALL has improved over time, the outcome of T-ALL patients with primary resistant or relapsed leukemia remains poor. Therefore, further progress in the treatment of T-ALL requires a better understanding of its biology and the development of more effective precision oncologic therapies. The proto-oncogene MYB is highly expressed in diverse hematologic malignancies, including T-ALLs with genomic aberrations that further potentiate its expression and activity. Previous studies have associated MYB with a malignant role in the pathogenesis of several cancers. However, its role in the induction and maintenance of T-ALL remains relatively poorly understood. In this study, we found that an increased copy number of MYB is associated with higher MYB expression levels, and might be associated with inferior event-free survival of pediatric T-ALL patients. Using our previously described conditional Myb overexpression mice, we generated two distinct MYB-driven T-ALL mouse models. We demonstrated that the overexpression of Myb synergizes with Pten deletion but not with the overexpression of Lmo2 to accelerate the development of T-cell lymphoblastic leukemias. We also showed that MYB is a dependency factor in T-ALL since RNA interference of Myb blocked cell cycle progression and induced apoptosis in both human and murine T-ALL cell lines. Finally, we provide preclinical evidence that targeting the transcriptional activity of MYB can be a useful therapeutic strategy for the treatment of T-ALL.
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Affiliation(s)
- André Almeida
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
| | - Sara T'Sas
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Luca Pagliaro
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Igor Fijalkowski
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Leukemia Therapy Resistance Laboratory and Center for Medical Genetics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Wouter Sleeckx
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Hannah Van Steenberge
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | | | - Béatrice Lintermans
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
| | - Wouter Van Loocke
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
| | - Bruno Palhais
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Leukemia Therapy Resistance Laboratory and Center for Medical Genetics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Alexandra Reekmans
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Valentina Bardelli
- Institute of Hematology and Center for Hemato‐Oncology ResearchUniversity of Perugia and S.M. Misericordia HospitalPerugiaItaly
| | - Lisa Demoen
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
| | - Lindy Reunes
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Leukemia Therapy Resistance Laboratory and Center for Medical Genetics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | | | - Alex Kentsis
- Tow Center for Developmental Oncology, Sloan Kettering Institute and Department of PediatricsMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Panagiotis Ntziachristos
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Leukemia Therapy Resistance Laboratory and Center for Medical Genetics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Nadine Van Roy
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Lab for Translational Oncogenomics and Bioinformatics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Pediatric Precision Oncology Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Barbara De Moerloose
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Department of Pediatric Hematology‐OncologyGhent University HospitalGhentBelgium
| | - Cristina Mecucci
- Institute of Hematology and Center for Hemato‐Oncology ResearchUniversity of Perugia and S.M. Misericordia HospitalPerugiaItaly
| | - Roberta La Starza
- Institute of Hematology and Center for Hemato‐Oncology ResearchUniversity of Perugia and S.M. Misericordia HospitalPerugiaItaly
| | - Giovanni Roti
- Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Steven Goossens
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Pieter Van Vlierberghe
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
| | - Tim Pieters
- Normal and Malignant Hematopoiesis Lab, Department of Biomolecular MedicineGhent UniversityGhentBelgium
- Cancer Research Institute Ghent (CRIG)GhentBelgium
- Unit for Translational Research in Oncology, Department of Diagnostic SciencesGhent UniversityGhentBelgium
- Leukemia Therapy Resistance Laboratory and Center for Medical Genetics, Department of Biomolecular MedicineGhent UniversityGhentBelgium
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9
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Liu Y, Wang Z, Zhuo Y, Wu H, Peng Y, Wang T, Peng T, Qiu L, Tan W. Aptamer-Based Multiparameter Analysis for Molecular Profiling of Hematological Malignancies. Anal Chem 2024; 96:3429-3435. [PMID: 38351845 DOI: 10.1021/acs.analchem.3c04717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The subtypes of hematological malignancies (HM) with minimal molecular profile differences display an extremely heterogeneous clinical course and a discrepant response to certain treatment regimens. Profiling the surface protein markers offers a potent solution for precision diagnosis of HM by differentiating among the subtypes of cancer cells. Herein, we report the use of Cell-SELEX technology to generate a panel of high-affinity aptamer probes that are able to discriminate subtle differences among surface protein profiles between different HM cells. Experimental results show that these aptamers with apparent dissociation constants (Kd) below 10 nM display a unique recognition pattern on different HM subtypes. By combining a machine learning model on the basis of partial least-squares discriminant analysis, 100% accuracy was achieved for the classification of different HM cells. Furthermore, we preliminarily validated the effectiveness of the aptamer-based multiparameter analysis strategy from a clinical perspective by accurately classifying complex clinical samples, thus providing a promising molecular tool for precise HM phenotyping.
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Affiliation(s)
- Yue Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Zhimin Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yuting Zhuo
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hui Wu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ying Peng
- NHC Key Laboratory of Birth Defect for Research and Prevention (Hunan Provincial Maternal and Child Health Care Hospital), Changsha, Hunan 410008, China
| | - Tong Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Tianhuan Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Vaidya P, Wang HY, Don MD, Hinds BR, Mangan JK. IDH2-mutated near ETP-ALL with aggressive leukemia cutis and brisk response to venetoclax and decitabine. Leuk Res Rep 2023; 21:100408. [PMID: 38269085 PMCID: PMC10805932 DOI: 10.1016/j.lrr.2023.100408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 01/26/2024] Open
Abstract
Near early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) is a rare hematologic malignancy, for which second line therapeutic options are limited. T-cell leukemias are also rarely associated with leukemia cutis, which is more often seen in leukemias of myeloid origin. We present the case of an adult male diagnosed with near ETP-ALL, with IDH2 and DNMT3A mutations, suggestive of a myeloid origin, and leukemia cutis. After the patient progressed on hyper-CVAD and nelarabine, we treated him with the BCL-2 inhibitor venetoclax and the hypomethylating agent decitabine. The regimen induced a rapid bone marrow response and resolution of the leukemia cutis.
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Affiliation(s)
- Poorva Vaidya
- Department of Internal Medicine, Division of Hematology-Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
| | - Huan-You Wang
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
| | - Michelle D. Don
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
| | - Brian R. Hinds
- Department of Dermatology, University of California, San Diego, La Jolla, CA, United States
| | - James K. Mangan
- Department of Internal Medicine, Division of Blood and Marrow Transplantation, Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
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11
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Gu A, Schmidt B, Lonsdale A, Jalaldeen R, Kosasih HJ, Brown LM, Sadras T, Ekert PG, Oshlack A. TALLSorts: a T-cell acute lymphoblastic leukemia subtype classifier using RNA-seq expression data. Blood Adv 2023; 7:7402-7406. [PMID: 37903323 PMCID: PMC10758738 DOI: 10.1182/bloodadvances.2023010385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/18/2023] [Accepted: 10/11/2023] [Indexed: 11/01/2023] Open
Affiliation(s)
- Allen Gu
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Breon Schmidt
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Andrew Lonsdale
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Roshan Jalaldeen
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Hansen J. Kosasih
- Children’s Cancer Institute, Kensington, NSW, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | | | - Teresa Sadras
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Paul G. Ekert
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Children’s Cancer Institute, Kensington, NSW, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- School of Clinical Medicine, University of New South Wales Medicine & Health, University of New South Wales, Kensington, NSW, Australia
| | - Alicia Oshlack
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia
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12
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De Bie J, Quessada J, Tueur G, Lefebvre C, Luquet I, Toujani S, Cuccuini W, Lafage-Pochitaloff M, Michaux L. Cytogenetics in the management of T-cell acute lymphoblastic leukemia (T-ALL): Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103431. [PMID: 38016418 DOI: 10.1016/j.retram.2023.103431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Molecular analysis is the hallmark of T-cell acute lymphoblastic leukemia (T-ALL) categorization. Several T-ALL sub-groups are well recognized based on the aberrant expression of specific transcription factors. This recently resulted in the implementation of eight provisional T-ALL entities into the novel 2022 International Consensus Classification, albeit not into the updated World Health Organization classification system. Despite this extensive molecular characterization, cytogenetic analysis remains the backbone of T-ALL diagnosis in many countries as chromosome banding analysis and fluorescence in situ hybridization are relatively inexpensive techniques to obtain results of diagnostic, prognostic and therapeutic interest. Here, we provide an overview of recurrent chromosomal abnormalities detectable in T-ALL patients and propose guidelines regarding their detection. By referring in parallel to the more general molecular classification approach, we hope to offer a diagnostic framework useful in a broad clinical genetic setting.
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Affiliation(s)
- Jolien De Bie
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France; CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes, Marseille 13009, France
| | - Giulia Tueur
- Laboratoire d'hématologie, Hôpital Avicenne, AP-HP, Bobigny 93000, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble 38000, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, CHU Toulouse (IUCT-O), Toulouse 31000, France
| | - Saloua Toujani
- Service de Cytogénétique et Biologie Cellulaire, CHU de Rennes, Rennes 35033, France
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Unité de Cytogénétique, Hôpital Saint-Louis, AP-HP, Paris 75010, France
| | - Marina Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France
| | - Lucienne Michaux
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium; Katholieke Universiteit Leuven, Leuven 3000, Belgium.
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13
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Ehm P, Rietow R, Wegner W, Bußmann L, Kriegs M, Dierck K, Horn S, Streichert T, Horstmann M, Jücker M. SHIP1 Is Present but Strongly Downregulated in T-ALL, and after Restoration Suppresses Leukemia Growth in a T-ALL Xenotransplantation Mouse Model. Cells 2023; 12:1798. [PMID: 37443832 PMCID: PMC10341211 DOI: 10.3390/cells12131798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/23/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cause of cancer-related death in children. Despite significantly increased chances of cure, especially for high-risk ALL patients, it still represents a poor prognosis for a substantial fraction of patients. Misregulated proteins in central switching points of the cellular signaling pathways represent potentially important therapeutic targets. Recently, the inositol phosphatase SHIP1 (SH2-containing inositol 5-phosphatase) has been considered as a tumor suppressor in leukemia. SHIP1 serves as an important negative regulator of the PI3K/AKT signaling pathway, which is frequently constitutively activated in primary T-ALL. In contrast to other reports, we show for the first time that SHIP1 has not been lost in T-ALL cells, but is strongly downregulated. Reduced expression of SHIP1 leads to an increased activation of the PI3K/AKT signaling pathway. SHIP1-mRNA expression is frequently reduced in primary T-ALL samples, which is recapitulated by the decrease in SHIP1 expression at the protein level in seven out of eight available T-ALL patient samples. In addition, we investigated the change in the activity profile of tyrosine and serine/threonine kinases after the restoration of SHIP1 expression in Jurkat T-ALL cells. The tyrosine kinase receptor subfamilies of NTRK and PDGFR, which are upregulated in T-ALL subgroups with low SHIP1 expression, are significantly disabled after SHIP1 reconstitution. Lentiviral-mediated reconstitution of SHIP1 expression in Jurkat cells points to a decreased cellular proliferation upon transplantation into NSG mice in comparison to the control cohort. Together, our findings will help to elucidate the complex network of cell signaling proteins, further support a functional role for SHIP1 as tumor suppressor in T-ALL and, much more importantly, show that full-length SHIP1 is expressed in T-ALL samples.
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Affiliation(s)
- Patrick Ehm
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
- Research Institute Children’s Cancer Center Hamburg, Hamburg and Department of Pediatric Oncology and Hematology, University Medical Center, 20246 Hamburg, Germany
| | - Ruth Rietow
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
- Research Institute Children’s Cancer Center Hamburg, Hamburg and Department of Pediatric Oncology and Hematology, University Medical Center, 20246 Hamburg, Germany
| | - Wiebke Wegner
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Lara Bußmann
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- UCCH Kinomics Core Facility, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Malte Kriegs
- UCCH Kinomics Core Facility, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Center for Oncology, Clinic for Radiation Therapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kevin Dierck
- Research Institute Children’s Cancer Center Hamburg, Hamburg and Department of Pediatric Oncology and Hematology, University Medical Center, 20246 Hamburg, Germany
| | - Stefan Horn
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Thomas Streichert
- Institute for Clinical Chemistry, University Hospital Köln, 50937 Cologne, Germany
| | - Martin Horstmann
- Research Institute Children’s Cancer Center Hamburg, Hamburg and Department of Pediatric Oncology and Hematology, University Medical Center, 20246 Hamburg, Germany
| | - Manfred Jücker
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
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14
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Zerella JR, Homan CC, Arts P, Brown AL, Scott HS, Hahn CN. Transcription factor genetics and biology in predisposition to bone marrow failure and hematological malignancy. Front Oncol 2023; 13:1183318. [PMID: 37377909 PMCID: PMC10291195 DOI: 10.3389/fonc.2023.1183318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Transcription factors (TFs) play a critical role as key mediators of a multitude of developmental pathways, with highly regulated and tightly organized networks crucial for determining both the timing and pattern of tissue development. TFs can act as master regulators of both primitive and definitive hematopoiesis, tightly controlling the behavior of hematopoietic stem and progenitor cells (HSPCs). These networks control the functional regulation of HSPCs including self-renewal, proliferation, and differentiation dynamics, which are essential to normal hematopoiesis. Defining the key players and dynamics of these hematopoietic transcriptional networks is essential to understanding both normal hematopoiesis and how genetic aberrations in TFs and their networks can predispose to hematopoietic disease including bone marrow failure (BMF) and hematological malignancy (HM). Despite their multifaceted and complex involvement in hematological development, advances in genetic screening along with elegant multi-omics and model system studies are shedding light on how hematopoietic TFs interact and network to achieve normal cell fates and their role in disease etiology. This review focuses on TFs which predispose to BMF and HM, identifies potential novel candidate predisposing TF genes, and examines putative biological mechanisms leading to these phenotypes. A better understanding of the genetics and molecular biology of hematopoietic TFs, as well as identifying novel genes and genetic variants predisposing to BMF and HM, will accelerate the development of preventative strategies, improve clinical management and counseling, and help define targeted treatments for these diseases.
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Affiliation(s)
- Jiarna R. Zerella
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Claire C. Homan
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Peer Arts
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Anna L. Brown
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Hamish S. Scott
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Christopher N. Hahn
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
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15
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IL-15 Prevents the Development of T-ALL from Aberrant Thymocytes with Impaired DNA Repair Functions and Increased NOTCH1 Activation. Cancers (Basel) 2023; 15:cancers15030671. [PMID: 36765626 PMCID: PMC9913776 DOI: 10.3390/cancers15030671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
We previously reported that NOD.Scid mice lacking interleukin-15 (IL-15), or IL-15 receptor alpha-chain, develop T-acute lymphoblastic leukemia (T-ALL). To understand the mechanisms by which IL-15 signaling controls T-ALL development, we studied the thymocyte developmental events in IL-15-deficient Scid mice from NOD and C57BL/6 genetic backgrounds. Both kinds of mice develop T-ALL characterized by circulating TCR-negative cells expressing CD4, CD8 or both. Analyses of thymocytes in NOD.Scid.Il15-/- mice prior to T-ALL development revealed discernible changes within the CD4-CD8- double-negative (DN) thymocyte developmental stages and increased frequencies of CD4+CD8+ double-positive cells with a high proportion of TCR-negative CD4+ and CD8+ cells. The DN cells also showed elevated expressions of CXCR4 and CD117, molecules implicated in the expansion of DN thymocytes. T-ALL cell lines and primary leukemic cells from IL-15-deficient NOD.Scid and C57BL/6.Scid mice displayed increased NOTCH1 activation that was inhibited by NOTCH1 inhibitors and blockers of the PI3K/AKT pathway. Primary leukemic cells from NOD.Scid.Il15-/- mice survived and expanded when cultured with MS5 thymic stromal cells expressing Delta-like ligand 4 and supplemented with IL-7 and FLT3 ligand. These findings suggest that IL-15 signaling in the thymus controls T-ALL development from aberrant thymocytes with an impaired DNA repair capacity and increased NOTCH1 activation.
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Müller J, Walter W, Haferlach C, Müller H, Fuhrmann I, Müller ML, Ruge H, Meggendorfer M, Kern W, Haferlach T, Stengel A. How T-lymphoblastic leukemia can be classified based on genetics using standard diagnostic techniques enhanced by whole genome sequencing. Leukemia 2023; 37:217-221. [PMID: 36335263 PMCID: PMC9883150 DOI: 10.1038/s41375-022-01743-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Janine Müller
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wencke Walter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Heiko Müller
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Irene Fuhrmann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Martha-Lena Müller
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Henning Ruge
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Anna Stengel
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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Pre-T cell receptor self-MHC sampling restricts thymocyte dedifferentiation. Nature 2023; 613:565-574. [PMID: 36410718 PMCID: PMC9851994 DOI: 10.1038/s41586-022-05555-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/11/2022] [Indexed: 11/22/2022]
Abstract
Programming T cells to distinguish self from non-self is a vital, multi-step process that occurs in the thymus1-4. Signalling through the pre-T cell receptor (preTCR), a CD3-associated heterodimer comprising an invariant pTα chain and a clone-specific β chain, is a critical early checkpoint in thymocyte development within the αβ T cell lineage5,6. PreTCRs arrayed on CD4-CD8- double-negative thymocytes ligate peptides bound to major histocompatibility complex molecules (pMHC) on thymic stroma, similar to αβ T cell receptors that appear on CD4+CD8+ double-positive thymocytes, but via a different molecular docking strategy7-10. Here we show the consequences of these distinct interactions for thymocyte progression using synchronized fetal thymic progenitor cultures that differ in the presence or absence of pMHC on support stroma, and single-cell transcriptomes at key thymocyte developmental transitions. Although major histocompatibility complex (MHC)-negative stroma fosters αβ T cell differentiation, the absence of preTCR-pMHC interactions leads to deviant thymocyte transcriptional programming associated with dedifferentiation. Highly proliferative double-negative and double-positive thymocyte subsets emerge, with antecedent characteristics of T cell lymphoblastic and myeloid malignancies. Compensatory upregulation of diverse MHC class Ib proteins in B2m/H2-Ab1 MHC-knockout mice partially safeguards in vivo thymocyte progression, although disseminated double-positive thymic tumours may develop with ageing. Thus, as well as promoting β chain repertoire broadening for subsequent αβ T cell receptor utilization, preTCR-pMHC interactions limit cellular plasticity to facilitate normal thymocyte differentiation and proliferation that, if absent, introduce developmental vulnerabilities.
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Transcriptome-based molecular subtypes and differentiation hierarchies improve the classification framework of acute myeloid leukemia. Proc Natl Acad Sci U S A 2022; 119:e2211429119. [PMID: 36442087 PMCID: PMC9894241 DOI: 10.1073/pnas.2211429119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The current classification of acute myeloid leukemia (AML) relies largely on genomic alterations. Robust identification of clinically and biologically relevant molecular subtypes from nongenomic high-throughput sequencing data remains challenging. We established the largest multicenter AML cohort (n = 655) in China, with all patients subjected to RNA sequencing (RNA-Seq) and 619 (94.5%) to targeted or whole-exome sequencing (TES/WES). Based on an enhanced consensus clustering, eight stable gene expression subgroups (G1-G8) with unique clinical and biological significance were identified, including two unreported (G5 and G8) and three redefined ones (G4, G6, and G7). Apart from four well-known low-risk subgroups including PML::RARA (G1), CBFB::MYH11 (G2), RUNX1::RUNX1T1 (G3), biallelic CEBPA mutations or -like (G4), four meta-subgroups with poor outcomes were recognized. The G5 (myelodysplasia-related/-like) subgroup enriched clinical, cytogenetic and genetic features mimicking secondary AML, and hotspot mutations of IKZF1 (p.N159S) (n = 7). In contrast, most NPM1 mutations and KMT2A and NUP98 fusions clustered into G6-G8, showing high expression of HOXA/B genes and diverse differentiation stages, from hematopoietic stem/progenitor cell down to monocyte, namely HOX-primitive (G7), HOX-mixed (G8), and HOX-committed (G6). Through constructing prediction models, the eight gene expression subgroups could be reproduced in the Cancer Genome Atlas (TCGA) and Beat AML cohorts. Each subgroup was associated with distinct prognosis and drug sensitivities, supporting the clinical applicability of this transcriptome-based classification of AML. These molecular subgroups illuminate the complex molecular network of AML, which may promote systematic studies of disease pathogenesis and foster the screening of targeted agents based on omics.
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