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Abstract
Genomic analyses have revolutionized our understanding of the biology of B-progenitor acute lymphoblastic leukemia (ALL). Studies of thousands of cases across the age spectrum have revised the taxonomy of B-ALL by identifying multiple new subgroups with diverse sequence and structural initiating events that vary substantially by age at diagnosis and prognostic significance. There is a growing appreciation of the role of inherited genetic variation in predisposition to ALL and drug responsiveness and of the nature of genetic variegation and clonal evolution that may be targeted for improved diagnostic, risk stratification, disease monitoring, and therapeutic intervention. This review provides an overview of the current state of knowledge of the genetic basis of B-ALL, with an emphasis on recent discoveries that have changed our approach to diagnosis and monitoring.
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Affiliation(s)
- Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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152
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Tsuzuki S, Yasuda T, Kojima S, Kawazu M, Akahane K, Inukai T, Imaizumi M, Morishita T, Miyamura K, Ueno T, Karnan S, Ota A, Hyodo T, Konishi H, Sanada M, Nagai H, Horibe K, Tomita A, Suzuki K, Muramatsu H, Takahashi Y, Miyazaki Y, Matsumura I, Kiyoi H, Hosokawa Y, Mano H, Hayakawa F. Targeting MEF2D-fusion Oncogenic Transcriptional Circuitries in B-cell Precursor Acute Lymphoblastic Leukemia. Blood Cancer Discov 2020; 1:82-95. [PMID: 34661142 PMCID: PMC8447276 DOI: 10.1158/2643-3230.bcd-19-0080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/14/2020] [Accepted: 05/11/2020] [Indexed: 11/16/2022] Open
Abstract
The cellular context that integrates gene expression, signaling, and metabolism dictates the oncogenic behavior and shapes the treatment responses in distinct cancer types. Although chimeric fusion proteins involving transcription factors (TF) are hallmarks of many types of acute lymphoblastic leukemia (ALL), therapeutically targeting the fusion proteins is a challenge. In this work, we characterize the core regulatory circuitry (CRC; interconnected autoregulatory loops of TFs) of B-ALL involving MEF2D-fusions and identify MEF2D-fusion and SREBF1 TFs as crucial CRC components. By gene silencing and pharmacologic perturbation, we reveal that the CRC integrates the pre-B-cell receptor (BCR) and lipid metabolism to maintain itself and govern malignant phenotypes. Small-molecule inhibitors of pre-BCR signaling and lipid biosynthesis disrupt the CRC and silence the MEF2D fusion in cell culture and show therapeutic efficacy in xenografted mice. Therefore, pharmacologic disruption of CRC presents a potential therapeutic strategy to target fusion protein-driven leukemia. SIGNIFICANCE Cancer type-specific gene expression is governed by transcription factors involved in a highly interconnected autoregulatory loop called CRC. Here, we characterized fusion protein-driven CRC and identified its pharmacologic vulnerabilities, opening therapeutic avenues to indirectly target fusion-driven leukemia by disrupting its CRC.See related commentary by Sadras and Müschen, p. 18. This article is highlighted in the In This Issue feature, p. 5.
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Affiliation(s)
- Shinobu Tsuzuki
- Department of Biochemistry, Aichi Medical University, School of Medicine, Nagakute, Aichi, Japan
| | - Takahiko Yasuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Shinya Kojima
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Koshi Akahane
- Department of Pediatrics, School of Medicine, University of Yamanashi, Chuo, Japan
| | - Takeshi Inukai
- Department of Pediatrics, School of Medicine, University of Yamanashi, Chuo, Japan
| | | | - Takanobu Morishita
- Department of Hematology, Japanese Red Cross Nagoya First Hospital, Nagoya, Aichi, Japan
| | - Koichi Miyamura
- Department of Hematology, Japanese Red Cross Nagoya First Hospital, Nagoya, Aichi, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Sivasundaram Karnan
- Department of Biochemistry, Aichi Medical University, School of Medicine, Nagakute, Aichi, Japan
| | - Akinobu Ota
- Department of Biochemistry, Aichi Medical University, School of Medicine, Nagakute, Aichi, Japan
| | - Toshinori Hyodo
- Department of Biochemistry, Aichi Medical University, School of Medicine, Nagakute, Aichi, Japan
| | - Hiroyuki Konishi
- Department of Biochemistry, Aichi Medical University, School of Medicine, Nagakute, Aichi, Japan
| | - Masashi Sanada
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Hirokazu Nagai
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Keizo Horibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Akihiro Tomita
- Department of Hematology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Itaru Matsumura
- Department of Hematology and Rheumatology, Kindai University Faculty of Medicine, Sayama, Osaka, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yoshitaka Hosokawa
- Department of Biochemistry, Aichi Medical University, School of Medicine, Nagakute, Aichi, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Fumihiko Hayakawa
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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153
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IKZF1 deletions in pediatric acute lymphoblastic leukemia: still a poor prognostic marker? Blood 2020; 135:252-260. [PMID: 31821407 DOI: 10.1182/blood.2019000813] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/21/2019] [Indexed: 12/31/2022] Open
Abstract
Improved personalized adjustment of primary therapy to the perceived risk of relapse by using new prognostic markers for treatment stratification may be beneficial to patients with acute lymphoblastic leukemia (ALL). Here, we review the advances that have shed light on the role of IKZF1 aberration as prognostic factor in pediatric ALL and summarize emerging concepts in this field. Continued research on the interplay of disease biology with exposure and response to treatment will be key to further improve treatment strategies.
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154
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Jung M, Schieck M, Hofmann W, Tauscher M, Lentes J, Bergmann A, Stelter M, Möricke A, Alten J, Schlegelberger B, Schrappe M, Zimmermann M, Stanulla M, Cario G, Steinemann D. Frequency and prognostic impact of PAX5 p.P80R in pediatric acute lymphoblastic leukemia patients treated on an AIEOP-BFM acute lymphoblastic leukemia protocol. Genes Chromosomes Cancer 2020; 59:667-671. [PMID: 32592278 PMCID: PMC7540392 DOI: 10.1002/gcc.22882] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 12/27/2022] Open
Abstract
PAX5 is a member of the paired box (PAX) family of transcription factors involved in B‐cell development. PAX5P80R has recently been described as a distinct genetic B‐cell precursor (BCP) acute lymphoblastic leukemia (ALL) subtype with a favorable prognosis in adults. In contrast, an unfavorable outcome has been observed in children. Our aim was to determine the frequency of PAX5P80R in childhood BCP‐ALL treated according to the Associazione Italiana Ematologia ed Oncologia Pediatrica‐Berlin‐Frankfurt‐Muenster (AIEOP‐BFM) ALL 2000 protocol and to evaluate its clinical significance within this study cohort. The analyses included 1237 patients with ALL treated in the AIEOP‐BFM ALL 2000 trial with complete information for copy number variations (CNVs) of IKZF1, PAX5, ETV6, RB1, BTG1, EBF1, CDKN2A, CDKN2B, and ERG. A customized TaqMan genotyping assay was used to screen for PAX5P80R. Sanger sequencing was used to confirm PAX5P80R‐positive results as well as to screen for second variants in PAX5. Agilent CGH + SNP arrays (e‐Array design 85 320; Agilent Technologies) were performed in PAX5P80R‐positive patients to verify additional CNVs. Almost 2% (20/1028) of our BCP‐ALL cohort were PAX5P80R‐positive. White blood cell counts higher than 50 000/μl as well as male sex were significantly (P < .05) associated with PAX5P80R. Most of the PAX5P80R‐positive cases were 10 years of age or older. PAX5P80R‐positive samples were enriched for deletions affecting PAX5, IKZF1, CDKN2A, and CDKN2B. Compared to PAX5P80R‐wildtype BCP‐ALL, PAX5P80R‐positive patients showed a significantly reduced 5‐year overall survival (P = .042). Further studies should evaluate the interaction of PAX5P80R with other genetic aberrations to further stratify intermediate risk pediatric BCP‐ALL.
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Affiliation(s)
- Mareike Jung
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Maximilian Schieck
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Marcel Tauscher
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Jana Lentes
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Anke Bergmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Marie Stelter
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Anja Möricke
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Julia Alten
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Martin Zimmermann
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Martin Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
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155
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Abdelrasoul H, Vadakumchery A, Werner M, Lenk L, Khadour A, Young M, El Ayoubi O, Vogiatzi F, Krämer M, Schmid V, Chen Z, Yousafzai Y, Cario G, Schrappe M, Müschen M, Halsey C, Mulaw MA, Schewe DM, Hobeika E, Alsadeq A, Jumaa H. Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia. Nat Commun 2020; 11:3194. [PMID: 32581241 PMCID: PMC7314847 DOI: 10.1038/s41467-020-16927-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 05/29/2020] [Indexed: 12/12/2022] Open
Abstract
Ph+ acute lymphoblastic leukemia (ALL) is characterized by the expression of an oncogenic fusion kinase termed BCR-ABL1. Here, we show that interleukin 7 receptor (IL7R) interacts with the chemokine receptor CXCR4 to recruit BCR-ABL1 and JAK kinases in close proximity. Treatment with BCR-ABL1 kinase inhibitors results in elevated expression of IL7R which enables the survival of transformed cells when IL7 was added together with the kinase inhibitors. Importantly, treatment with anti-IL7R antibodies prevents leukemia development in xenotransplantation models using patient-derived Ph+ ALL cells. Our results suggest that the association between IL7R and CXCR4 serves as molecular platform for BCR-ABL1-induced transformation and development of Ph+ ALL. Targeting this platform with anti-IL7R antibody eliminates Ph+ ALL cells including those with resistance to commonly used ABL1 kinase inhibitors. Thus, anti-IL7R antibodies may provide alternative treatment options for ALL in general and may suppress incurable drug-resistant leukemia forms.
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Affiliation(s)
- Hend Abdelrasoul
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Anila Vadakumchery
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Markus Werner
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Lennart Lenk
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Ahmad Khadour
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Marc Young
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Omar El Ayoubi
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Fotini Vogiatzi
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Markus Krämer
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Vera Schmid
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Zhengshan Chen
- Department of Systems Biology and City of Hope Comprehensive Cancer Center, Monrovia, CA, USA
| | - Yasar Yousafzai
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Gunnar Cario
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Martin Schrappe
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Markus Müschen
- Department of Systems Biology and City of Hope Comprehensive Cancer Center, Monrovia, CA, USA
| | - Christina Halsey
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Medhanie A Mulaw
- Institute of Experimental Cancer Research, Medical Faculty, University of Ulm, Ulm, Germany
| | - Denis M Schewe
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Elias Hobeika
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Ameera Alsadeq
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Hassan Jumaa
- Institute of Immunology, Ulm University Medical Center, 89081, Ulm, Germany.
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156
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Kimura S, Mullighan CG. Molecular markers in ALL: Clinical implications. Best Pract Res Clin Haematol 2020; 33:101193. [PMID: 33038982 DOI: 10.1016/j.beha.2020.101193] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/28/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and remains a main cause of death in children despite recent improvements in cure rates. In the past decade, development of massively parallel sequencing has enabled large scale genome profiling studies of ALL, which not only led to identification of new subtypes in both B-cell precursor ALL (BCP-ALL) and T-cell ALL (T-ALL), but has also identified potential new therapeutic approaches to target vulnerabilities of many subtypes. Several of these approaches have been validated in preclinical models and are now being formally evaluated in prospective clinical trials. In this review, we provide an overview of the recent advances in our knowledge of genomic bases of BCP-ALL, T-ALL, and relapsed ALL, and discuss their clinical implications.
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Affiliation(s)
- Shunsuke Kimura
- Department of Pathology, Hematological Malignancies Program, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, 38105, TN, USA
| | - Charles G Mullighan
- Department of Pathology, Hematological Malignancies Program, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, 38105, TN, USA.
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157
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Karol SE, Pui CH. Personalized therapy in pediatric high-risk B-cell acute lymphoblastic leukemia. Ther Adv Hematol 2020; 11:2040620720927575. [PMID: 32537116 PMCID: PMC7268159 DOI: 10.1177/2040620720927575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
Although cure rates for pediatric acute lymphoblastic leukemia (ALL) have now risen to more than 90%, subsets of patients with high-risk features continue to experience high rates of treatment failure and relapse. Recent work in minimal residual disease stratification and leukemia genomics have increased the ability to identify and classify these high-risk patients. In this review, we discuss this work to identify and classify patients with high-risk ALL. Novel therapeutics, which may have the potential to improve outcomes for these patients, are also discussed.
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Affiliation(s)
- Seth E Karol
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl., Mail Stop 260, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
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158
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Sun Y, Long S, Liu W. Observation of the molecular genetics among children with acute lymphoblastic leukemia: A retrospective study based on the SEER database. Medicine (Baltimore) 2020; 99:e20009. [PMID: 32481267 PMCID: PMC7249956 DOI: 10.1097/md.0000000000020009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is one of the most common malignancies of the hematologic system in children. Typically, ALL children with various genetic changes show different incidences, development, and prognoses. This study aimed to analyze the incidence of molecular genetic subtype among ALL children based on their clinical information, and to further investigate the relationship of genetic varieties with the prognostic factors.From 2010 to 2016, a total of 888 ALL children with TEL-AML1 fusion gene, hyperdiploidy, hypodiloidy, IL3-IGH rearranged, E2A PBX1 fusion gene, BCR-ABL1 fusion gene, or mixed lineage leukemia (MML) rearranged were selected and analyzed through the Surveillance, Epidemiology, and End Results database.Our results suggested that, ALL children who lived in the Northern Plains were more likely to experience genetic varieties. In addition, the TEL-AML1 fusion gene, hyperdiploidy, and hypodiloidy were more likely to be detected in ALL children aged 1 to 9 years, while MLL rearrangement was probably detected among ALL children aged <1 year. On the other hand, the 5-year overall survival varied depending on different regions (East: 42.21%; Alaska: 0.001%; Northern Plains: 1.8%; Pacific Coast: 16.3%; and Southwest: 8%), races (African American: 44.5%; white: 18.2%; and Other: 16.3%), and genetic features (TEL-AML1: 10.1%; hyperdiploidy: 19.4%; hypodiloidy: 64.7%; IL3-IGH: 0.01%; E2A PBX1: 14.2%; BCR-ABL1: 15.2%; MLL rearranged: 12.3%).In conclusion, our study found that genetic varieties among ALL children were closely related to their prognoses, and the detection rate of genetic molecules was associated with the age, race, and living area of children.
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159
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Biloglav A, Olsson-Arvidsson L, Theander J, Behrendtz M, Castor A, Johansson B. SFPQ-ABL1-positive B-cell precursor acute lymphoblastic leukemias. Genes Chromosomes Cancer 2020; 59:540-543. [PMID: 32306475 DOI: 10.1002/gcc.22852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/03/2020] [Accepted: 04/10/2020] [Indexed: 12/22/2022] Open
Abstract
In recent years, a subgroup of B-cell precursor acute lymphoblastic leukemia (BCP ALL) without an established abnormality ("B-other") has been shown to be characterized by rearrangements of ABL1, ABL2, CSF1R, or PDGFRB (a.k.a. ABL-class genes). Using FISH with probes for these genes, we screened 55 pediatric and 50 adult B-other cases. Three (6%) of the adult but none of the childhood B-other cases were positive for ABL-class aberrations. RT-PCR and sequencing confirmed a rare SFPQ-ABL1 fusion in one adult B-other case with t(1;9)(p34;q34). Only six SFPQ-ABL1-positive BCP ALLs have been reported, present case included. A review of these shows that all harbored fusions between exon 9 of SFPQ and exon 4 of ABL1, that the fusion is typically found in adolescents/younger adults without hyperleukocytosis, and that IKZF1 deletions are recurrent. The few patients not treated with tyrosine kinase inhibitors (TKIs) and/or allogeneic stem cell transplantation relapsed, strengthening the notion that TKI should be added to the therapy of SFPQ-ABL1-positive BCP ALL.
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Affiliation(s)
- Andrea Biloglav
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Linda Olsson-Arvidsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Division of Laboratory Medicine, Department of Clinical Genetics and Pathology, Lund, Sweden
| | - Johan Theander
- Department of Hematology, Skåne University Hospital, Lund, Sweden
| | - Mikael Behrendtz
- Department of Pediatrics, Linköping University Hospital, Linköping, Sweden
| | - Anders Castor
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Division of Laboratory Medicine, Department of Clinical Genetics and Pathology, Lund, Sweden
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160
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Saito Y, Koya J, Araki M, Kogure Y, Shingaki S, Tabata M, McClure MB, Yoshifuji K, Matsumoto S, Isaka Y, Tanaka H, Kanai T, Miyano S, Shiraishi Y, Okuno Y, Kataoka K. Landscape and function of multiple mutations within individual oncogenes. Nature 2020; 582:95-99. [PMID: 32494066 DOI: 10.1038/s41586-020-2175-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/13/2020] [Indexed: 01/09/2023]
Abstract
Sporadic reports have described cancer cases in which multiple driver mutations (MMs) occur in the same oncogene1,2. However, the overall landscape and relevance of MMs remain elusive. Here we carried out a pan-cancer analysis of 60,954 cancer samples, and identified 14 pan-cancer and 6 cancer-type-specific oncogenes in which MMs occur more frequently than expected: 9% of samples with at least one mutation in these genes harboured MMs. In various oncogenes, MMs are preferentially present in cis and show markedly different mutational patterns compared with single mutations in terms of type (missense mutations versus in-frame indels), position and amino-acid substitution, suggesting a cis-acting effect on mutational selection. MMs show an overrepresentation of functionally weak, infrequent mutations, which confer enhanced oncogenicity in combination. Cells with MMs in the PIK3CA and NOTCH1 genes exhibit stronger dependencies on the mutated genes themselves, enhanced downstream signalling activation and/or greater sensitivity to inhibitory drugs than those with single mutations. Together oncogenic MMs are a relatively common driver event, providing the underlying mechanism for clonal selection of suboptimal mutations that are individually rare but collectively account for a substantial proportion of oncogenic mutations.
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Affiliation(s)
- Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Mitsugu Araki
- Department of Clinical System Onco-Informatics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Sumito Shingaki
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Marni B McClure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kota Yoshifuji
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shigeyuki Matsumoto
- Medical Sciences Innovation Hub Program, RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
| | - Yuta Isaka
- Research and Development Group for In Silico Drug Discovery, Center for Cluster Development and Coordination, Foundation for Biomedical Research and Innovation, Kobe, Japan
| | - Hiroko Tanaka
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takanori Kanai
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuichi Shiraishi
- Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Yasushi Okuno
- Department of Clinical System Onco-Informatics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.
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161
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Evidence-based review of genomic aberrations in B-lymphoblastic leukemia/lymphoma: Report from the cancer genomics consortium working group for lymphoblastic leukemia. Cancer Genet 2020; 243:52-72. [PMID: 32302940 DOI: 10.1016/j.cancergen.2020.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 03/04/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
Abstract
Clinical management and risk stratification of B-lymphoblastic leukemia/ lymphoma (B-ALL/LBL) depend largely on identification of chromosomal abnormalities obtained using conventional cytogenetics and Fluorescence In Situ Hybridization (FISH) testing. In the last few decades, testing algorithms have been implemented to support an optimal risk-oriented therapy, leading to a large improvement in overall survival. In addition, large scale genomic studies have identified multiple aberrations of prognostic significance that are not routinely tested by existing modalities. However, as chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) technologies are increasingly used in clinical management of hematologic malignancies, these abnormalities may be more readily detected. In this article, we have compiled a comprehensive, evidence-based review of the current B-ALL literature, focusing on known and published subtypes described to date. More specifically, we describe the role of various testing modalities in the diagnosis, prognosis, and therapeutic relevance. In addition, we propose a testing algorithm aimed at assisting laboratories in the most effective detection of the underlying genomic abnormalities.
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162
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Xiong J, Cui BW, Wang N, Dai YT, Zhang H, Wang CF, Zhong HJ, Cheng S, Ou-Yang BS, Hu Y, Zhang X, Xu B, Qian WB, Tao R, Yan F, Hu JD, Hou M, Ma XJ, Wang X, Liu YH, Zhu ZM, Huang XB, Liu L, Wu CY, Huang L, Shen YF, Huang RB, Xu JY, Wang C, Wu DP, Yu L, Li JF, Xu PP, Wang L, Huang JY, Chen SJ, Zhao WL. Genomic and Transcriptomic Characterization of Natural Killer T Cell Lymphoma. Cancer Cell 2020; 37:403-419.e6. [PMID: 32183952 DOI: 10.1016/j.ccell.2020.02.005] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/06/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022]
Abstract
Natural killer/T cell lymphoma (NKTCL) is an aggressive and heterogeneous entity of non-Hodgkin lymphoma, strongly associated with Epstein-Barr virus (EBV) infection. To identify molecular subtypes of NKTCL based on genomic structural alterations and EBV sequences, we performed multi-omics study on 128 biopsy samples of newly diagnosed NKTCL and defined three prominent subtypes, which differ significantly in cell of origin, EBV gene expression, transcriptional signatures, and responses to asparaginase-based regimens and targeted therapy. Our findings thus identify molecular networks of EBV-associated pathogenesis and suggest potential clinical strategies on NKTCL.
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Affiliation(s)
- Jie Xiong
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China
| | - Bo-Wen Cui
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China
| | - Nan Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China
| | - Yu-Ting Dai
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Zhang
- Department of Otolaryngology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao-Fu Wang
- Department of Pathology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui-Juan Zhong
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China
| | - Shu Cheng
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China
| | - Bin-Shen Ou-Yang
- Department of Pathology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Zhang
- Department of Hematology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Bin Xu
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Wen-Bin Qian
- Department of Hematology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Rong Tao
- Department of Hematology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Yan
- Department of Hematology, The Third Affiliated Hospital of Suzhou University, The First People's Hospital of Changzhou, Changzhou, People's Republic of China
| | - Jian-Da Hu
- Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Ming Hou
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, China
| | - Xue-Jun Ma
- Department of Medical Oncology, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xin Wang
- Department of Hematology, Shandong Province Hospital of Shandong University, Jinan, China
| | - Yuan-Hua Liu
- Department of Medical Oncology, Jiangsu Cancer Hospital, Nanjing, China
| | - Zun-Min Zhu
- Department of Hematology, Henan Province People's Hospital, Zhengzhou, China
| | - Xiao-Bin Huang
- Department of Hematology, Sichuan Provincial People's Hospital, Chengdu, China
| | - Li Liu
- Department of Hematology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Chong-Yang Wu
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou, Gansu, China
| | - Li Huang
- Department of Oncology and Hematology, Hospital (T.C.M) Affiliated to Southwest Medical University, Luzhou, China
| | - Yun-Feng Shen
- Department of Hematology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Rui-Bin Huang
- Department of Hematology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jing-Yan Xu
- Department of Hematology, Nanjing Drum Tower Hospital, Nanjing, China
| | - Chun Wang
- Department of Hematology, Shanghai General Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - De-Pei Wu
- Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Yu
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jian-Feng Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China
| | - Peng-Peng Xu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China
| | - Li Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China; Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China
| | - Jin-Yan Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China.
| | - Sai-Juan Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China; Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China.
| | - Wei-Li Zhao
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai 200025, China; Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China.
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163
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Brown LM, Lonsdale A, Zhu A, Davidson NM, Schmidt B, Hawkins A, Wallach E, Martin M, Mechinaud FM, Khaw SL, Bartolo RC, Ludlow LEA, Challis J, Brooks I, Petrovic V, Venn NC, Sutton R, Majewski IJ, Oshlack A, Ekert PG. The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia. Blood Adv 2020; 4:930-942. [PMID: 32150610 PMCID: PMC7065479 DOI: 10.1182/bloodadvances.2019001008] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/02/2020] [Indexed: 01/23/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy, and implementation of risk-adapted therapy has been instrumental in the dramatic improvements in clinical outcomes. A key to risk-adapted therapies includes the identification of genomic features of individual tumors, including chromosome number (for hyper- and hypodiploidy) and gene fusions, notably ETV6-RUNX1, TCF3-PBX1, and BCR-ABL1 in B-cell ALL (B-ALL). RNA-sequencing (RNA-seq) of large ALL cohorts has expanded the number of recurrent gene fusions recognized as drivers in ALL, and identification of these new entities will contribute to refining ALL risk stratification. We used RNA-seq on 126 ALL patients from our clinical service to test the utility of including RNA-seq in standard-of-care diagnostic pipelines to detect gene rearrangements and IKZF1 deletions. RNA-seq identified 86% of rearrangements detected by standard-of-care diagnostics. KMT2A (MLL) rearrangements, although usually identified, were the most commonly missed by RNA-seq as a result of low expression. RNA-seq identified rearrangements that were not detected by standard-of-care testing in 9 patients. These were found in patients who were not classifiable using standard molecular assessment. We developed an approach to detect the most common IKZF1 deletion from RNA-seq data and validated this using an RQ-PCR assay. We applied an expression classifier to identify Philadelphia chromosome-like B-ALL patients. T-ALL proved a rich source of novel gene fusions, which have clinical implications or provide insights into disease biology. Our experience shows that RNA-seq can be implemented within an individual clinical service to enhance the current molecular diagnostic risk classification of ALL.
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Affiliation(s)
- Lauren M Brown
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Andrew Lonsdale
- Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Andrea Zhu
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Royal Children's Hospital, Parkville, VIC, Australia
| | - Nadia M Davidson
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Breon Schmidt
- Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Anthony Hawkins
- Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Elise Wallach
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Royal Children's Hospital, Parkville, VIC, Australia
| | | | | | - Seong Lin Khaw
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Royal Children's Hospital, Parkville, VIC, Australia
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Ray C Bartolo
- Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Louise E A Ludlow
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Jackie Challis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Ian Brooks
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Vida Petrovic
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Nicola C Venn
- Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia
| | - Rosemary Sutton
- Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia
| | - Ian J Majewski
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne, Parkville, VIC, Australia; and
| | - Alicia Oshlack
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Paul G Ekert
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Royal Children's Hospital, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
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164
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McEvoy CR, Fox SB, Prall OWJ. Emerging entities in NUTM1-rearranged neoplasms. Genes Chromosomes Cancer 2020; 59:375-385. [PMID: 32060986 DOI: 10.1002/gcc.22838] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 12/11/2022] Open
Abstract
Structural alterations of NUTM1 were originally thought to be restricted to poorly differentiated carcinomas with variable squamous differentiation originating in the midline organs of children and adolescents. Termed NUT carcinomas (NCs), they were defined by a t(15;19) chromosomal rearrangement that was found to result in a BRD4-NUTM1 gene fusion. However, the use of DNA and RNA-based next-generation sequencing has recently revealed a multitude of new NUTM1 fusion partners in a diverse array of neoplasms including sarcoma-like tumors, poromas, and acute lymphoblastic leukemias (ALLs) that we propose to call NUTM1-rearranged neoplasms (NRNs). Intriguingly, the nosology of NRNs often correlates with the functional classification of the fusion partner, suggesting different oncogenic mechanisms within each NRN division. Indeed, whereas NCs are characterized by their aggressiveness and intransigence to standard therapeutic measures, the more positive clinical outcomes seen in some sarcoma and ALL NRNs may reflect these mechanistic differences. Here we provide a broad overview of the molecular, nosological, and clinical features in these newly discovered neoplastic entities. We describe how aberrant expression of NUTM1 due to fusion with an N-terminal DNA/chromatin-binding protein can generate a potentially powerful chromatin modifier that can give rise to oncogenic transformation in numerous cellular contexts. We also conclude that classification, clinical behavior, and therapeutic options may be best defined by the NUTM1 fusion partner rather than by tumor morphology or immunohistochemical profile.
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Affiliation(s)
- Christopher R McEvoy
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Owen W J Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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165
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Deak D, Pop C, Zimta AA, Jurj A, Ghiaur A, Pasca S, Teodorescu P, Dascalescu A, Antohe I, Ionescu B, Constantinescu C, Onaciu A, Munteanu R, Berindan-Neagoe I, Petrushev B, Turcas C, Iluta S, Selicean C, Zdrenghea M, Tanase A, Danaila C, Colita A, Colita A, Dima D, Coriu D, Einsele H, Tomuleasa C. Let's Talk About BiTEs and Other Drugs in the Real-Life Setting for B-Cell Acute Lymphoblastic Leukemia. Front Immunol 2020; 10:2856. [PMID: 31921126 PMCID: PMC6934055 DOI: 10.3389/fimmu.2019.02856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/20/2019] [Indexed: 01/07/2023] Open
Abstract
Background: Therapy for acute lymphoblastic leukemia (ALL) are currently initially efficient, but even if a high percentage of patients have an initial complete remission (CR), most of them relapse. Recent data shows that immunotherapy with either bispecific T-cell engagers (BiTEs) of chimeric antigen receptor (CAR) T cells can eliminate residual chemotherapy-resistant B-ALL cells. Objective: The objective of the manuscript is to present improvements in the clinical outcome for chemotherapy-resistant ALL in the real-life setting, by describing Romania's experience with bispecific antibodies for B-cell ALL. Methods: We present the role of novel therapies for relapsed B-cell ALL, including the drugs under investigation in phase I-III clinical trials, as a potential bridge to transplant. Blinatumomab is presented in a critical review, presenting both the advantages of this drug, as well as its limitations. Results: Bispecific antibodies are discussed, describing the clinical trials that resulted in its approval by the FDA and EMA. The real-life setting for relapsed B-cell ALL is described and we present the patients treated with blinatumomab in Romania. Conclusion: In the current manuscript, we present blinatumomab as a therapeutic alternative in the bridge-to-transplant setting for refractory or relapsed ALL, to gain a better understanding of the available therapies and evidence-based data for these patients in 2019.
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Affiliation(s)
- Dalma Deak
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania
| | - Cristina Pop
- Department of Pharmacology, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina-Andreea Zimta
- Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ancuta Jurj
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alexandra Ghiaur
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Sergiu Pasca
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Patric Teodorescu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Angela Dascalescu
- Department of Hematology, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania.,Department of Hematology, Regional Institute of Oncology, Iasi, Romania
| | - Ion Antohe
- Department of Hematology, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania.,Department of Hematology, Regional Institute of Oncology, Iasi, Romania
| | - Bogdan Ionescu
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Catalin Constantinescu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Anca Onaciu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Raluca Munteanu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Bobe Petrushev
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Turcas
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania
| | - Sabina Iluta
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Selicean
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania
| | - Alina Tanase
- Department of Stem Cell Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Catalin Danaila
- Department of Hematology, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania.,Department of Hematology, Regional Institute of Oncology, Iasi, Romania
| | - Anca Colita
- Department of Stem Cell Transplantation, Fundeni Clinical Institute, Bucharest, Romania.,Department of Pediatrics, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Andrei Colita
- Department of Hematology, Coltea Hospital, Bucharest, Romania.,Department of Hematology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Delia Dima
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Daniel Coriu
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania.,Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania.,Department of Hematology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Wurzburg, Würzburg, Germany
| | - Ciprian Tomuleasa
- Department of Hematology/Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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166
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Chen X, Wang F, Zhang Y, Ma X, Liu M, Cao P, Zhou L, Wang L, Zhang X, Wang T, Liu H. Identification of RNPC3 as a novel JAK2 fusion partner gene in B-acute lymphoblastic leukemia refractory to combination therapy including ruxolitinib. Mol Genet Genomic Med 2019; 8:e1110. [PMID: 31885183 PMCID: PMC7057088 DOI: 10.1002/mgg3.1110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/18/2019] [Accepted: 12/16/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Hematopoietic neoplasms with chromosomal translocations involving JAK2 are rare, and most of them show myeloproliferative neoplasm-associated features, followed by B-acute lymphoblastic leukemia (B-ALL). De novo B-ALL cases with JAK2 rearrangements are suggested to be appropriately considered as BCR-ABL1-like B-ALL, but its partners varied. METHODS Fluorescence in situ hybridization (FISH), RNA sequencing (RNA-Seq), whole-genome sequencing, and reverse transcription polymerase chain reaction (RT-PCR) were performed to identify the pathogenic fusion gene in a 29-year-old woman with relapsed B-ALL and rare t(1;9)(p13;p22) translocation. RESULTS We identified RNPC3 as a new JAK2 fusion partner in the patient. She was treated with a combination of chemotherapy and targeted drug ruxolitinib and chimeric antigen receptor T-cell therapy, but failed to achieve complete remission. She had no chance to undergo allogeneic hematopoietic stem cell transplantation and died of disease progression 7 months after the initial diagnosis. Her clinical course demonstrated that this novel RNPC3-JAK2 fusion might portend an unfavorable prognosis. CONCLUSION This finding adds to the expanding compendium of JAK2 fusions found in B-ALL and suggests the potential need for a diagnostic FISH analysis as well as RNA-Seq in the appropriate clinical setting.
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Affiliation(s)
- Xue Chen
- Divison of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Fang Wang
- Divison of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Yang Zhang
- Divison of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Xiaoli Ma
- Divison of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Mingyue Liu
- Divison of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Panxiang Cao
- Divison of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Lin Zhou
- Divison of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Lan Wang
- Divison of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Xian Zhang
- Department of Hematology, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Tong Wang
- Divison of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China.,Divison of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, Beijing, China
| | - Hongxing Liu
- Divison of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China.,Divison of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, Beijing, China.,Beijing Lu Daopei Institute of Hematology, Beijing, China
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167
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Eckert C, Groeneveld-Krentz S, Kirschner-Schwabe R, Hagedorn N, Chen-Santel C, Bader P, Borkhardt A, Cario G, Escherich G, Panzer-Grümayer R, Astrahantseff K, Eggert A, Sramkova L, Attarbaschi A, Bourquin JP, Peters C, Henze G, von Stackelberg A. Improving Stratification for Children With Late Bone Marrow B-Cell Acute Lymphoblastic Leukemia Relapses With Refined Response Classification and Integration of Genetics. J Clin Oncol 2019; 37:3493-3506. [DOI: 10.1200/jco.19.01694] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
PURPOSE Minimal residual disease (MRD) helps to accurately assess when children with late bone marrow relapses of B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) will benefit from allogeneic hematopoietic stem-cell transplantation (allo-HSCT). More detailed dissection of MRD response heterogeneity and the specific genetic aberrations could improve current practice. PATIENTS AND METHODS MRD was assessed after induction treatment and at different times during relapse treatment until allo-HSCT (indicated in poor responders to induction; MRD ≥ 10−3) for patients being treated for late BCP-ALL bone marrow relapses (n = 413; median follow-up, 9.4 years) in the ALL-REZ BFM 2002 trial/registry (ClinicalTrials.gov identifier: NCT00114348 ). RESULTS Patients with both good (MRD < 10−3) and poor responses to induction treatment reached excellent event-free survival (EFS; 72% v 65%) and overall survival (OS; 82% v 74%). Patients with MRD of 10−2 or greater after induction had reduced EFS (56%), and their MRD persisted until allo-HSCT more frequently than it did in patients with MRD of 10−3 or greater to less than 10−2 ( P = .037). Patients with 25% or more leukemic blasts after induction (early nonresponders) had the poorest prognosis (EFS, 22%). Interestingly, patients with MRD of 10−3 or greater before allo-HSCT (late nonresponders) still had an EFS of 50% and OS of 63%, which in principle justifies allo-HSCT in these patients. From a panel of selected candidate genes, TP53 alterations (frequency, 8%) were the only genetic alteration with independent prognostic value in any MRD-based response subgroup. CONCLUSION After induction treatment, MRD-based treatment stratification resulted in excellent survival in patients with late relapsed BCP-ALL. Prognosis could be further improved in very poor responders by intensifying treatment directly after induction. TP53 alterations can be defined as a novel genetic high-risk marker in all MRD response groups in late relapsed BCP-ALL. Here we identified early and late nonresponders to be considered as events in future trials.
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Affiliation(s)
- Cornelia Eckert
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, and German Cancer Research Center, Heidelberg, Germany
| | | | - Renate Kirschner-Schwabe
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, and German Cancer Research Center, Heidelberg, Germany
| | | | | | - Peter Bader
- University Hospital Frankfurt, Frankfurt, Germany
| | | | - Gunnar Cario
- University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Angelika Eggert
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, and German Cancer Research Center, Heidelberg, Germany
| | | | | | | | | | - Günter Henze
- Charité - Universitätsmedizin Berlin, Berlin, Germany
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168
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Characterization of novel, recurrent genomic rearrangements as sensitive MRD targets in childhood B-cell precursor ALL. Blood Cancer J 2019; 9:96. [PMID: 31784504 PMCID: PMC6884523 DOI: 10.1038/s41408-019-0257-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/01/2019] [Accepted: 11/06/2019] [Indexed: 12/20/2022] Open
Abstract
B-cell precursor (BCP) ALL carry a variety of classical V(D)J rearrangements as well as genomic fusions and translocations. Here, we assessed the value of genomic capture high-throughput sequencing (gc-HTS) in BCP ALL (n = 183) for the identification and implementation of targets for minimal residual disease (MRD) testing. For TRδ, a total of 300 clonal rearrangements were detected in 158 of 183 samples (86%). Beside clonal Vδ2-Dδ3, Dδ2-Dδ3, and Vδ2-Jα we identified a novel group of recurrent Dδ-Jα rearrangements, comprising Dδ2 or Dδ3 segments fused predominantly to Jα29. For IGH-JH, 329 clonal rearrangements were identified in 172 of 183 samples (94%) including novel types of V(D)J joining. Oligoclonality was found in ~1/3 (n = 57/183) of ALL samples. Genomic breakpoints were identified in 71 BCP-ALL. A distinct MRD high-risk subgroup of IGH-V(D)J-germline ALL revealed frequent deletions of IKZF1 (n = 7/11) and the presence of genomic fusions (n = 10/11). Quantitative measurement using genomic fusion breakpoints achieved equivalent results compared to conventional V(D)J-based MRD testing and could be advantageous upon persistence of a leukemic clone. Taken together, selective gc-HTS expands the spectrum of suitable MRD targets and allows for the identification of genomic fusions relevant to risk and treatment stratification in childhood ALL.
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169
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Sun J, Yu W, Zhang X. MEF2D-rearranged acute lymphoblastic leukemia resembles Burkitt lymphoma/leukemia. Ann Hematol 2019; 99:185-188. [DOI: 10.1007/s00277-019-03857-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 11/18/2019] [Indexed: 11/27/2022]
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170
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Yoon J, Yun JW, Jung CW, Ju HY, Koo HH, Kim SH, Kim HJ. Molecular characteristics of terminal deoxynucleotidyl transferase negative precursor B-cell phenotype Burkitt leukemia with IGH-MYC rearrangement. Genes Chromosomes Cancer 2019; 59:255-260. [PMID: 31705772 DOI: 10.1002/gcc.22825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/06/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
Precursor B cell phenotype Burkitt lymphoma/leukemia with IGH-MYC is a rare subtype of Burkitt lymphoma (BL). BL and B lymphoblastic leukemia/lymphoma (B-ALL/LBL) differ as regards treatment and the distinction between these two entities is crucial. Patients demonstrating a terminal deoxynucleotidyl transferase (TdT)-positive precursor B cell phenotype with IGH-MYC rearrangement have been reported to be molecularly distinct from BL and closer to B-ALL/LBL. We investigated the molecular characteristics of two cases of a rare but distinct TdT-negative precursor B cell phenotype BL. Both patients showed FAB L3 morphology with IGH-MYC translocation, but had precursor B cell immunophenotypes including dim to moderate expression of CD45 and absence of BCL6, CD20, monoclonal kappa, and lambda light chain expression. To characterize the molecular features, we performed exome sequencing and analyzed the breakpoint junction of the IGH-MYC rearrangement. We detected KMT2D mutations in both cases, a rarely acquired chromatin modifying gene mutation in BL. The breakpoint analysis revealed that the IGH-MYC rearrangement occurred due to an aberrant VDJ recombination in one case. The treatment protocols differed, including high-grade lymphoma treatment and standard B-ALL treatment. Complete remission was achieved in the patient who received B-ALL treatment. The degree of resemblance of BL and B-ALL differed between two cases, but the molecular pathogenesis and manifesting features of both TdT-negative precursor B cell phenotype BL case were distinct from classic BL, which indicates the need for a better understanding of this uncommon entity that does not fit in current diagnostic and classification categories.
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Affiliation(s)
- Jung Yoon
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jae Won Yun
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Chul Won Jung
- Department of Internal Medicine, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee Young Ju
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hong Hoe Koo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sun-Hee Kim
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee-Jin Kim
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, South Korea
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171
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Gyurina K, Kárai B, Ujfalusi A, Hevessy Z, Barna G, Jáksó P, Pálfi-Mészáros G, Póliska S, Scholtz B, Kappelmayer J, Zahuczky G, Kiss C. Coagulation FXIII-A Protein Expression Defines Three Novel Sub-populations in Pediatric B-Cell Progenitor Acute Lymphoblastic Leukemia Characterized by Distinct Gene Expression Signatures. Front Oncol 2019; 9:1063. [PMID: 31709175 PMCID: PMC6823876 DOI: 10.3389/fonc.2019.01063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Leukemic B-cell precursor (BCP) lymphoblasts were identified as a novel expression site for coagulation factor XIII subunit A (FXIII-A). Flow cytometry (FC) revealed three distinct expression patterns, i.e., FXIII-A negative, FXIII-A dim, and FXIII-A bright subgroups. The FXIII-A negative subgroup was significantly associated with the “B-other” genetic category and had an unfavorable disease outcome. Methods: RNA was extracted from bone marrow lymphoblasts of 42 pediatric patients with BCP-acute lymphoblastic leukemia (ALL). FXIII-A expression was determined by multiparameter FC. Genetic diagnosis was based on conventional cytogenetic method and fluorescence in situ hybridization. Affymetrix GeneChip Human Primeview array was used to analyze global expression pattern of 28,869 well-annotated genes. Microarray data were analyzed by Genespring GX14.9.1 software. Gene Ontology analysis was performed using Cytoscape 3.4.0 software with ClueGO application. Selected differentially expressed genes were validated by RT-Q-PCR. Results: We demonstrated, for the first time, the general expression of F13A1 gene in pediatric BCP-ALL samples. The intensity of F13A1 expression corresponded to the FXIII-A protein expression subgroups which defined three characteristic and distinct gene expression signatures detected by Affymetrix oligonucleotide microarrays. Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG, RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. Common enhancer elements of these genes revealed by in silico analysis suggest that common transcription factors may regulate the expression of these genes in a similar fashion. PLAC8 was downregulated in the FXIII-A bright subgroup. Gene expression signature of the FXIII-A negative subgroup showed an overlap with the signature of “B-other” samples. DFFA, GIGYF1, GIGYF2, and INTS3 were upregulated and CD3G was downregulated in the “B-other” subgroup. Validated genes proved biologically and clinically relevant. We described differential expression of genes not shown previously to be associated with pediatric BCP-ALL. Conclusions: Gene expression signature according to FXIII-A protein expression status defined three novel subgroups of pediatric BCP-ALL. Multiparameter FC appears to be an easy-to-use and affordable method to help in selecting FXIII-A negative patients who require a more elaborate and expensive molecular genetic investigation to design precision treatment.
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Affiliation(s)
- Katalin Gyurina
- Department of Pediatrics, University of Debrecen, Debrecen, Hungary
| | - Bettina Kárai
- Department of Laboratory of Medicine, University of Debrecen, Debrecen, Hungary
| | - Anikó Ujfalusi
- Department of Laboratory of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsuzsanna Hevessy
- Department of Laboratory of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Barna
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Pál Jáksó
- Department of Pathology, University of Pécs, Pécs, Hungary
| | | | - Szilárd Póliska
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Beáta Scholtz
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Kappelmayer
- Department of Laboratory of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Zahuczky
- UD GenoMed Medical Genomic Technologies Ltd., Debrecen, Hungary
| | - Csongor Kiss
- Department of Pediatrics, University of Debrecen, Debrecen, Hungary
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172
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Abstract
Despite high cure rates in children, acute lymphoblastic leukemia (ALL) remains a leading cause of cancer death in the young, and the likelihood of treatment failure increases with age. With the exception of tyrosine kinase inhibitors, there have been few advances in repurposing or developing new therapeutic approaches tailored to vulnerabilities of ALL subtypes or individual cases. Large-scale genome profiling studies conducted over the last decade promise to improve ALL outcomes by refining risk stratification and modulation of therapeutic intensity, and by identifying new targets and pathways for immunotherapy. Many of these approaches have been validated in preclinical models and now merit testing in clinical trials. This review discusses the advances in our understanding of the genomic taxonomy and ontogeny of B-progenitor ALL, with an emphasis on those discoveries of clinical importance.
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173
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Pincez T, Landry J, Roussy M, Jouan L, Bilodeau M, Laramée L, Couture F, Sinnett D, Gendron P, Hébert J, Oligny L, Rouette A, Tran TH, Wilhelm BT, Bittencourt H, Cellot S. Cryptic recurrent
ACIN1
‐
NUTM1
fusions in non‐
KMT2A
‐rearranged infant acute lymphoblastic leukemia. Genes Chromosomes Cancer 2019; 59:125-130. [DOI: 10.1002/gcc.22808] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/21/2019] [Accepted: 09/11/2019] [Indexed: 01/05/2023] Open
Affiliation(s)
- Thomas Pincez
- Pediatric Hematology‐Oncology DivisionCharles‐Bruneau Cancer Center, CHU Sainte‐Justine Montréal Québec Canada
- Faculty of MedicineUniversité de Montréal Montréal Québec Canada
| | - Josette‐Renée Landry
- Pediatric Hematology‐Oncology DivisionCharles‐Bruneau Cancer Center, CHU Sainte‐Justine Montréal Québec Canada
- Faculty of MedicineUniversité de Montréal Montréal Québec Canada
- Streamline Genomics Montréal Québec Canada
| | - Mathieu Roussy
- Pediatric Hematology‐Oncology DivisionCharles‐Bruneau Cancer Center, CHU Sainte‐Justine Montréal Québec Canada
- Faculty of MedicineUniversité de Montréal Montréal Québec Canada
- Department of Biomedical SciencesUniversité de Montréal Montréal Québec Canada
| | - Loubna Jouan
- Integrated Centre for Pediatric Clinical Genomics, CHU Sainte‐Justine Montréal Québec Canada
| | - Mélanie Bilodeau
- Pediatric Hematology‐Oncology DivisionCharles‐Bruneau Cancer Center, CHU Sainte‐Justine Montréal Québec Canada
| | - Louise Laramée
- Pediatric Hematology‐Oncology DivisionCharles‐Bruneau Cancer Center, CHU Sainte‐Justine Montréal Québec Canada
| | - Françoise Couture
- Molecular Diagnostic Laboratory, CHU Sainte‐Justine Montréal Québec Canada
| | - Daniel Sinnett
- Pediatric Hematology‐Oncology DivisionCharles‐Bruneau Cancer Center, CHU Sainte‐Justine Montréal Québec Canada
- Faculty of MedicineUniversité de Montréal Montréal Québec Canada
| | - Patrick Gendron
- Bioinformatics Core Facility, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal Montréal Québec Canada
| | - Josée Hébert
- Faculty of MedicineUniversité de Montréal Montréal Québec Canada
- Division of HematologyMaisonneuve‐Rosemont Hospital Montréal Québec Canada
- Quebec Leukemia Cell Bank, Maisonneuve‐Rosemont Hospital Montréal Québec Canada
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal Montréal Québec Canada
| | - Luc Oligny
- Faculty of MedicineUniversité de Montréal Montréal Québec Canada
- Department of PathologyCHU Sainte‐Justine Montréal Québec Canada
| | - Alexandre Rouette
- Integrated Centre for Pediatric Clinical Genomics, CHU Sainte‐Justine Montréal Québec Canada
| | - Thai H. Tran
- Pediatric Hematology‐Oncology DivisionCharles‐Bruneau Cancer Center, CHU Sainte‐Justine Montréal Québec Canada
- Faculty of MedicineUniversité de Montréal Montréal Québec Canada
| | - Brian T. Wilhelm
- Faculty of MedicineUniversité de Montréal Montréal Québec Canada
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal Montréal Québec Canada
- Laboratory for High Throughput Biology, IRIC, Université de Montréal Montréal Québec Canada
| | - Henrique Bittencourt
- Pediatric Hematology‐Oncology DivisionCharles‐Bruneau Cancer Center, CHU Sainte‐Justine Montréal Québec Canada
- Faculty of MedicineUniversité de Montréal Montréal Québec Canada
| | - Sonia Cellot
- Pediatric Hematology‐Oncology DivisionCharles‐Bruneau Cancer Center, CHU Sainte‐Justine Montréal Québec Canada
- Faculty of MedicineUniversité de Montréal Montréal Québec Canada
- Quebec Leukemia Cell Bank, Maisonneuve‐Rosemont Hospital Montréal Québec Canada
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174
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Frisch A, Ofran Y. How I diagnose and manage Philadelphia chromosome-like acute lymphoblastic leukemia. Haematologica 2019; 104:2135-2143. [PMID: 31582548 PMCID: PMC6821607 DOI: 10.3324/haematol.2018.207506] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/03/2019] [Indexed: 01/31/2023] Open
Abstract
Advances in our understanding of mechanisms of leukemogenesis and driver mutations in acute lymphoblastic leukemia (ALL) lead to a more precise and informative sub-classification, mainly of B-cell ALL. In parallel, in recent years, novel agents have been approved for the therapy of B-cell ALL, and many others are in active clinical research. Among the newly recognized disease subtypes, Philadelphia-chromosome-like ALL is the most heterogeneous and thus, diagnostically challenging. Given that this subtype of B-cell ALL is associated with a poorer prognosis, improvement of available therapeutic approaches and protocols is a burning issue. Herein, we summarize, in a clinically relevant manner, up-to-date information regarding diagnostic strategies developed for the identification of patients with Philadelphia-chromosome-like ALL. Common therapeutic dilemmas, presented as several case scenarios, are also discussed. It is currently acceptable that patients with B-cell ALL, treated with an aim of cure, irrespective of their age, be evaluated for a Philadelphia-chromosome-like signature as early as possible. Following Philadelphia-chromosome-like recognition, a higher risk of resistance or relapse must be realized and treatment should be modified based on the patient’s specific genetic driver and clinical features. However, while active targeted therapeutic options are limited, there is much more to do than just prescribe a matched inhibitor to the identified mutated driver genes. In this review, we present a comprehensive evidence-based approach to the diagnosis and management of Philadelphia-chromosome-like ALL at different time-points during the disease course.
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Affiliation(s)
- Avraham Frisch
- Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa
| | - Yishai Ofran
- Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa .,Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
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175
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Yamamoto H, Hayakawa F, Yasuda T, Odaira K, Minamikawa Y, Tange N, Hirano D, Kojima Y, Morishita T, Tsuzuki S, Naoe T, Kiyoi H. ZNF384-fusion proteins have high affinity for the transcriptional coactivator EP300 and aberrant transcriptional activities. FEBS Lett 2019; 593:2151-2161. [PMID: 31234226 DOI: 10.1002/1873-3468.13506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 11/07/2022]
Abstract
Zinc-finger protein 384 (ZNF384) fusion (Z-fusion) genes have recently been identified as recurrent fusion genes in B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) and have been detected in 7-17% of Philadelphia chromosome-negative BCP-ALL cases. We selected SALL4 and ID2 as potential Z-fusion-specific transcriptional targets that might lead to the differentiation disorder of Z-fusion-positive ALL. The introduction of EP300-ZNF384 and SYNRG-ZNF384 induced the expression of these genes. Z-fusion proteins exhibited stronger transcriptional activities on the promoter or enhancer region of these genes than Wild-Z. Furthermore, GST pull-down assay revealed that Z-fusion proteins associated more strongly with EP300 than Wild-Z. Coexpression of EP300 specifically enhanced the transcriptional activities of Z-fusion proteins. We propose the increased EP300 binding of Z-fusion proteins as a mechanism for their increased transcriptional activities.
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Affiliation(s)
- Hideyuki Yamamoto
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
| | - Fumihiko Hayakawa
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan.,Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Japan
| | - Takahiko Yasuda
- Clinical Research Center, Nagoya Medical Center, National Hospital Organization, Nagoya, Japan
| | - Koya Odaira
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Japan
| | - Yuka Minamikawa
- Department of Analytical Neurobiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Naoyuki Tange
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
| | - Daiki Hirano
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
| | - Yuki Kojima
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
| | - Takanobu Morishita
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
| | - Shinobu Tsuzuki
- Department of Biochemistry, School of Medicine, Aichi Medical University, Japan
| | - Tomoki Naoe
- Nagoya Medical Center, National Hospital Organization, Nagoya, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
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176
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Relevant subtypes in childhood ALL. Hemasphere 2019; 3:HemaSphere-2019-0049. [PMID: 35309767 PMCID: PMC8925679 DOI: 10.1097/hs9.0000000000000245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/01/2019] [Indexed: 11/26/2022] Open
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177
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Coccaro N, Anelli L, Zagaria A, Specchia G, Albano F. Next-Generation Sequencing in Acute Lymphoblastic Leukemia. Int J Mol Sci 2019; 20:ijms20122929. [PMID: 31208040 PMCID: PMC6627957 DOI: 10.3390/ijms20122929] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.
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Affiliation(s)
- Nicoletta Coccaro
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
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178
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Pui CH, Tang JY, Yang JJ, Chen SJ, Chen Z. International Collaboration to Save Children With Acute Lymphoblastic Leukemia. J Glob Oncol 2019; 5:1-2. [PMID: 31045474 PMCID: PMC6550034 DOI: 10.1200/jgo.19.00010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2019] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Jing-Yan Tang
- Shanghai Children’s Medical Center, Shanghai Jiao Tong University, Shanghai, China
| | - Jun J. Yang
- St Jude Children’s Research Hospital, Memphis, TN
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, Shanghai Jiao Tong University, Shanghai, China
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179
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Zia S, Shahid R. Mutagenic players in ALL progression and their associated signaling pathways. Cancer Genet 2019; 233-234:7-20. [DOI: 10.1016/j.cancergen.2019.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/10/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022]
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180
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Hormann FM, Hoogkamer AQ, Beverloo HB, Boeree A, Dingjan I, Wattel MM, Stam RW, Escherich G, Pieters R, den Boer ML, Boer JM. NUTM1 is a recurrent fusion gene partner in B-cell precursor acute lymphoblastic leukemia associated with increased expression of genes on chromosome band 10p12.31-12.2. Haematologica 2019; 104:e455-e459. [PMID: 30872366 DOI: 10.3324/haematol.2018.206961] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Femke M Hormann
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Alex Q Hoogkamer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - H Berna Beverloo
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Aurélie Boeree
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Ilse Dingjan
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Moniek M Wattel
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ronald W Stam
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Gabriele Escherich
- COALL - German Cooperative Study Group for Childhood Acute Lymphoblastic Leukemia, Hamburg, Germany
| | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,DCOG - Dutch Childhood Oncology Group, Utrecht, the Netherlands
| | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands.,DCOG - Dutch Childhood Oncology Group, Utrecht, the Netherlands.,Department of Pediatric Oncology and Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands .,Oncode Institute, Utrecht, the Netherlands
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181
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PAX5 biallelic genomic alterations define a novel subgroup of B-cell precursor acute lymphoblastic leukemia. Leukemia 2019; 33:1895-1909. [PMID: 30842609 DOI: 10.1038/s41375-019-0430-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 11/08/2022]
Abstract
Chromosomal rearrangements and specific aneuploidy patterns are initiating events and define subgroups in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Here we analyzed 250 BCP-ALL cases and identified a novel subgroup ('PAX5-plus', n = 19) by distinct DNA methylation and gene expression profiles. All patients in this subgroup harbored mutations in the B-lineage transcription factor PAX5, with p.P80R as hotspot. Mutations either affected two independent codons, consistent with compound heterozygosity, or suffered LOH predominantly through chromosome 9p aberrations. These biallelic events resulted in disruption of PAX5 transcriptional programs regulating B-cell differentiation and tumor suppressor functions. Homozygous CDKN2A/B deletions and RAS-activating hotspot mutations were highly enriched as cooperating events in the genomic profile of PAX5-plus ALL. Together, this defined a specific pattern of triple alterations, exclusive to the novel subgroup. PAX5-plus ALL was observed in pediatric and adult patients. Although restricted by the limited sample size, a tendency for more favorable clinical outcome was observed, with 10 of 12 adult PAX5-plus patients achieving long-term survival. PAX5-plus represents the first BCP-ALL subgroup defined by sequence alterations in contrast to gross chromosomal events and exemplifies how deregulated differentiation (PAX5), impaired cell cycle control (CDKN2A/B) and sustained proliferative signaling (RAS) cooperatively drive leukemogenesis.
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