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Yang J, Zhu X, Zhang H, Fu Y, Li Z, Xing Z, Yu Y, Cao P, Le J, Jiang J, Li J, Wang H, Qian M, Zhai X. Nomogram models predicting prognosis for patients with t(8;21) acute myeloid leukemia: a SEER-based study. Hematology 2024; 29:2381169. [PMID: 39046131 DOI: 10.1080/16078454.2024.2381169] [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: 01/17/2024] [Accepted: 07/10/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) with t(8;21) manifests as a diverse hematological malignancy. Although it was categorized into a favorable subtype, 30-40% of patients experience relapse. The objective of this research was to devise a nomogram for the accurate anticipation of both overall survival (OS) and cancer-specific survival (CSS) in t(8;21) AML. METHODS From the Surveillance, Epidemiology, and End Results (SEER) database, individuals diagnosed with t(8;21) AML from 2000 to 2018 were selected. Prognostic factors for t(8;21) AML were identified using Cox regression analysis and Akaike Information Criterion (AIC), forming the basis for constructing prognostic nomograms. RESULTS Key variables, including first primary tumor, age group, race, and chemotherapy, were identified and integrated into the nomogram. The C-index values for the nomograms predicting OS and CSS were 0.753 (validation: 0.765) and 0.764 (validation: 0.757), respectively. Ultimately, based on nomogram scores, patients were stratified into high-risk and low-risk groups, revealing significant disparities in both OS and CSS between these groups (P < 0.001). CONCLUSION This study innovatively crafted nomograms, incorporating clinical and therapeutic variables, to forecast the 1-, 3-, and 5-year survival rates for individuals with t(8;21) AML.
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MESH Headings
- Humans
- Nomograms
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/therapy
- Male
- Female
- SEER Program
- Middle Aged
- Adult
- Chromosomes, Human, Pair 8/genetics
- Chromosomes, Human, Pair 21/genetics
- Translocation, Genetic
- Prognosis
- Adolescent
- Aged
- Young Adult
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Affiliation(s)
- Jiapeng Yang
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Xiaohua Zhu
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Honghong Zhang
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Yang Fu
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Zifeng Li
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Ziping Xing
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Yi Yu
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Ping Cao
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Jun Le
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Junye Jiang
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Jun Li
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Hongsheng Wang
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Xiaowen Zhai
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, People's Republic of China
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Lints R, Walker CA, Delfi O, Prouse M, PohLui De Silva M, Bohlander SK, Wood AC. Mutational cooperativity of RUNX1::RUNX1T1 isoform 9a and oncogenic NRAS in zebrafish myeloid leukaemia. Biol Open 2024; 13:bio060523. [PMID: 39177514 PMCID: PMC11381922 DOI: 10.1242/bio.060523] [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: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024] Open
Abstract
RUNX1::RUNX1T1 (R::RT1) acute myeloid leukaemia (AML) remains a clinical challenge, and further research is required to model and understand leukaemogenesis. Previous zebrafish R::RT1 models were hampered by embryonic lethality and low penetrance of the malignant phenotype. Here, we overcome this by developing an adult zebrafish model in which the human R::RT1 isoform 9a is co-expressed with the frequently co-occurring oncogenic NRASG12D mutation in haematopoietic stem and progenitor cells (HSPCs), using the Runx1+23 enhancer. Approximately 50% of F0 9a+NRASG12D transgenic zebrafish developed signs of haematological disease between 5 and 14 months, with 27% exhibiting AML-like pathology: myeloid precursor expansion, erythrocyte reduction, kidney marrow hypercellularity and the presence of blasts. Moreover, only 9a+NRASG12D transplant recipients developed leukaemia with high rates of mortality within 40 days, inferring the presence of leukaemia stem cells. These leukaemic features were rare or not observed in animals expressing either the NRAS or 9a oncogenes alone, suggesting 9a and NRAS cooperation drives leukaemogenesis. This novel adult AML zebrafish model provides a powerful new tool for investigating the basis of R::RT1 - NRAS cooperativity with the potential to uncover new therapeutic targets.
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Affiliation(s)
- Robyn Lints
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
| | - Christina A Walker
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
| | - Omid Delfi
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
| | - Matthew Prouse
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
| | | | - Stefan K Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
| | - Andrew C Wood
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
- Starship Child Health, Starship Blood and Cancer Centre, Auckland 1023, New Zealand
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3
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Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey ALW, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A Pan-Cancer Gene Panel for Childhood Malignancies to Enhance Cancer Monitoring and Early Detection. Clin Cancer Res 2024; 30:4100-4114. [PMID: 39047169 DOI: 10.1158/1078-0432.ccr-24-1063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/14/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
PURPOSE The purpose of the study was to design a pan-cancer gene panel for childhood malignancies and validate it using clinically characterized patient samples. EXPERIMENTAL DESIGN In addition to 5,275 coding exons, SJPedPanel also covers 297 introns for fusions/structural variations and 7,590 polymorphic sites for copy-number alterations. Capture uniformity and limit of detection are determined by targeted sequencing of cell lines using dilution experiment. We validate its coverage by in silico analysis of an established real-time clinical genomics (RTCG) cohort of 253 patients. We further validate its performance by targeted resequencing of 113 patient samples from the RTCG cohort. We demonstrate its power in analyzing low tumor burden specimens using morphologic remission and monitoring samples. RESULTS Among the 485 pathogenic variants reported in RTCG cohort, SJPedPanel covered 86% of variants, including 82% of 90 rearrangements responsible for fusion oncoproteins. In our targeted resequencing cohort, 91% of 389 pathogenic variants are detected. The gene panel enabled us to detect ∼95% of variants at allele fraction (AF) 0.5%, whereas the detection rate is ∼80% at AF 0.2%. The panel detected low-frequency driver alterations from morphologic leukemia remission samples and relapse-enriched alterations from monitoring samples, demonstrating its power for cancer monitoring and early detection. CONCLUSIONS SJPedPanel enables the cost-effective detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions by targeted sequencing of ∼0.15% of human genome for childhood malignancies. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
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Affiliation(s)
- Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Vidya Balagopal
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Li Dong
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Quang Tran
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Heather Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anna L W Huskey
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Emily Plyler
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhikai Liang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jingqun Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Joy Nakitandwe
- Department of Pathology and Laboratory Medicine, Diagnostics Institute, Cleveland Clinic, Cleveland, Ohio
| | - Jiali Gu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Maria Namwanje
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jamie Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Saradhi Mallampati
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
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4
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Travaglini S, Silvestrini G, Attardi E, Fanciulli M, Scalera S, Antonelli S, Maurillo L, Palmieri R, Divona M, Ciuffreda L, Savi A, Paterno G, Ottone T, Barbieri C, Maciejewski JP, Gurnari C, Ciliberto G, Voso MT. Evolution of transcriptomic profiles in relapsed inv(16) acute myeloid leukemia. Leuk Res 2024; 145:107568. [PMID: 39180902 DOI: 10.1016/j.leukres.2024.107568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/01/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Acute myeloid leukemia (AML) with inv(16) is typically associated with a favourable prognosis. However, up to 40 % of patients will eventually experience disease relapse. Herein, we dissected the genomic and transcriptomic profile of inv(16) AML to identify potential prognostic markers and therapeutic vulnerabilities. Sequencing data from 222 diagnostic samples, including 44 relapse/refractory patients, revealed a median of 1 concomitant additional mutation, cooperating with inv(16) in leukemogenesis. Notably, the mutational landscape at diagnosis did not differ significantly between patients experiencing primary induction failure or relapse when compared to the rest of the cohort, except for an increase in the mutational burden in the relapse/refractory group. RNA-Seq of unpaired diagnostic(n=7) and relapse(n=6) samples allowed the identification of oxidative phosphorylation (OXPHOS) as one of the most significantly downregulated pathways at relapse. Considering that OXPHOS could be targeted by Venetoclax/Azacitidine combination, we explored its biological effects on an inv(16) cell-line ME-1, but there was no additional advantage in terms of cell death over Azacitidine alone. To enhance Venetoclax efficacy, we tested in vitro effects of Metformin as a potential drug able to enhance chemosensitivity of AML cells by inhibiting the mitochondrial transfer. By challenging ME-1 with this combination, we observed a significant synergistic interaction at least similar to that of Venetoclax/Azacitidine. In conclusions, we identified a downregulated expression of oxidative phosphorylation (OXPHOS) at relapse in AML with inv(16), and explored the in vitro effects of metformin as a potential drug to enhance chemosensitivity in this setting.
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Affiliation(s)
- Serena Travaglini
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giorgia Silvestrini
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Enrico Attardi
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Maurizio Fanciulli
- SAFU Laboratory, Department of Research, Advanced Diagnostic and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Stefano Scalera
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Silvia Antonelli
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Luca Maurillo
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Raffaele Palmieri
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Mariadomenica Divona
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy; Saint Camillus International University of Health Sciences, Rome, Italy
| | - Ludovica Ciuffreda
- SAFU Laboratory, Department of Research, Advanced Diagnostic and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Arianna Savi
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | | | - Tiziana Ottone
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy; Santa Lucia Foundation, I.R.C.C.S., Neuro-Oncohematology, Rome, Italy
| | | | - Jaroslaw P Maciejewski
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Carmelo Gurnari
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy; Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy; Santa Lucia Foundation, I.R.C.C.S., Neuro-Oncohematology, Rome, Italy.
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5
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Nagler A, Labopin M, Salmenniemi U, Wu D, Blaise D, Rambaldi A, Reményi P, Forcade E, Socié G, Chevallier P, von dem Borne P, Burns D, Schmid C, Maertens J, Kröger N, Bug G, Aljurf M, Vydra J, Halaburda K, Ciceri F, Mohty M. Trends in allogeneic transplantation for favorable risk acute myeloid leukemia in first remission: a longitudinal study of >15 years from the ALWP of the EBMT. Bone Marrow Transplant 2024:10.1038/s41409-024-02379-z. [PMID: 39164484 DOI: 10.1038/s41409-024-02379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 08/22/2024]
Abstract
We assessed outcomes of allogeneic transplantation (HSCT) in favorable risk AML in CR1 over 3 time periods. 1850 patients were included, 2005 to 2009- 222, 2010 to 2014 -392, and 2015 to 2021-1236; 526 with t (8:21), 625 with inv (16), and 699 with NPM1mutFLT3WT. Patients transplanted in 2015-2021 were older (p < 0.0001) with more patients ≥60 years of age (p < 0.0001). The most frequent diagnosis in 2015-2021 was NPM1mutFLT3WT vs. t (8:21) in the 2 earlier periods, (p < 0001). Haploidentical transplants (Haplo) increased from 5.9% to 14.5% (p < 0.0001). Graft-versus-host disease (GVHD) prophylaxis with post-transplant cyclophosphamide (PTCy) was more frequent in 2015-2021 vs. the other 2 periods (p < 0.0001). On multivariate analysis, incidence of total chronic GVHD was reduced in HSCTs performed ≥2015 vs. those performed in 2005-2009, hazard ratio (HR) = 0.74 (95% CI 0.56-0.99, p = 0.046) and GVHD-free, relapse-free survival (GRFS) improved for patients transplanted from 2010-2014 vs. those transplanted in 2005-2009, HR = 0.74 (95% CI 0.56-0.98, p = 0.037). Other HSCT outcomes did not differ with no improvement ≥2015. LFS, OS, and GRFS were inferior in patients with t (8:21) with HR = 1.32 (95% CI 1.03-1.68, p = 0.026), HR = 1.38 (95% CI 1.04-1.83, p = 0.027) and HR = 01.25 (95% CI 1.02-1.53, p = 0.035), respectively. In conclusion, this retrospective analysis of HSCT in patients with favorable risk AML, transplanted over 16 years showed an increased number of transplants in patients ≥60 years, from Haplo donors with PTCy. Most importantly, 3-year GRFS improved ≥2010 and total chronic GVHD reduced ≥2015, with no significant change in other HSCT outcomes.
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Affiliation(s)
- Arnon Nagler
- Division of Hematology, Sheba Medical Center, Tel Hashomer, Israel.
| | - Myriam Labopin
- EBMT Paris study office; Department of Haematology, Saint Antoine Hospital; INSERM UMR 938, Sorbonne University, Paris, France
- Sorbonne University, Department of Haematology, Saint Antoine Hospital; INSERM UMR 938, Paris, France
| | | | - Depei Wu
- First Affiliated Hospital of Soochow University, Suzhou, China
| | - Didier Blaise
- Programme de Transplantation & Therapie Cellulaire, Marseille, France
| | - Alessandro Rambaldi
- Department of Oncology and Hematology, University of Milan and Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | | | | | - Gérard Socié
- University Paris Cité, INSERM UMR 976, APHP- Saint-Louis Hospital, BMT Unit, Paris, France
| | | | | | - David Burns
- University Hospital Birmingham NHS Trust, Stoke, UK
| | | | | | | | - Gesine Bug
- Goethe-Universitaet, Frankfurt Main, Germany
| | - Mahmoud Aljurf
- King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Jan Vydra
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | | | - Fabio Ciceri
- IRCCS Osspedale San Raffaele, Vita-Salute San Raffaele University Haematology and BMT, Milano, Italy
| | - Mohamad Mohty
- EBMT Paris study office; Department of Haematology, Saint Antoine Hospital; INSERM UMR 938, Sorbonne University, Paris, France
- Sorbonne University, Department of Haematology, Saint Antoine Hospital; INSERM UMR 938, Paris, France
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6
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Halik A, Tilgner M, Silva P, Estrada N, Altwasser R, Jahn E, Heuser M, Hou HA, Pratcorona M, Hills RK, Metzeler KH, Fenwarth L, Dolnik A, Terre C, Kopp K, Blau O, Szyska M, Christen F, Krönke J, Vasseur L, Löwenberg B, Esteve J, Valk PJM, Duchmann M, Chou WC, Linch DC, Döhner H, Gale RE, Döhner K, Bullinger L, Yoshida K, Damm F. Genomic characterization of AML with aberrations of chromosome 7: a multinational cohort of 519 patients. J Hematol Oncol 2024; 17:70. [PMID: 39160538 PMCID: PMC11331663 DOI: 10.1186/s13045-024-01590-1] [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: 05/19/2024] [Accepted: 08/05/2024] [Indexed: 08/21/2024] Open
Abstract
BACKGROUND Deletions and partial losses of chromosome 7 (chr7) are frequent in acute myeloid leukemia (AML) and are linked to dismal outcome. However, the genomic landscape and prognostic impact of concomitant genetic aberrations remain incompletely understood. METHODS To discover genetic lesions in adult AML patients with aberrations of chromosome 7 [abn(7)], 60 paired diagnostic/remission samples were investigated by whole-exome sequencing in the exploration cohort. Subsequently, a gene panel including 66 genes and a SNP backbone for copy-number variation detection was designed and applied to the remaining samples of the validation cohort. In total, 519 patients were investigated, of which 415 received intensive induction treatment, typically containing a combination of cytarabine and anthracyclines. RESULTS In the exploration cohort, the most frequently mutated gene was TP53 (33%), followed by epigenetic regulators (DNMT3A, KMT2C, IDH2) and signaling genes (NRAS, PTPN11). Thirty percent of 519 patients harbored ≥ 1 mutation in genes located in commonly deleted regions of chr7-most frequently affecting KMT2C (16%) and EZH2 (10%). KMT2C mutations were often subclonal and enriched in patients with del(7q), de novo or core-binding factor AML (45%). Cancer cell fraction analysis and reconstruction of mutation acquisition identified TP53 mutations as mainly disease-initiating events, while del(7q) or -7 appeared as subclonal events in one-third of cases. Multivariable analysis identified five genetic lesions with significant prognostic impact in intensively treated AML patients with abn(7). Mutations in TP53 and PTPN11 (11%) showed the strongest association with worse overall survival (OS, TP53: hazard ratio [HR], 2.53 [95% CI 1.66-3.86]; P < 0.001; PTPN11: HR, 2.24 [95% CI 1.56-3.22]; P < 0.001) and relapse-free survival (RFS, TP53: HR, 2.3 [95% CI 1.25-4.26]; P = 0.008; PTPN11: HR, 2.32 [95% CI 1.33-4.04]; P = 0.003). By contrast, IDH2-mutated patients (9%) displayed prolonged OS (HR, 0.51 [95% CI 0.30-0.88]; P = 0.0015) and durable responses (RFS: HR, 0.5 [95% CI 0.26-0.96]; P = 0.036). CONCLUSION This work unraveled formerly underestimated genetic lesions and provides a comprehensive overview of the spectrum of recurrent gene mutations and their clinical relevance in AML with abn(7). KMT2C mutations are among the most frequent gene mutations in this heterogeneous AML subgroup and warrant further functional investigation.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/mortality
- Female
- Male
- Middle Aged
- Adult
- Chromosomes, Human, Pair 7/genetics
- Aged
- Mutation
- Cohort Studies
- Young Adult
- Chromosome Aberrations
- Prognosis
- Aged, 80 and over
- Adolescent
- Exome Sequencing
- DNA Copy Number Variations
- Tumor Suppressor Protein p53/genetics
- Genomics/methods
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics
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Affiliation(s)
- Adriane Halik
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marlon Tilgner
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Patricia Silva
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Natalia Estrada
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Robert Altwasser
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ekaterina Jahn
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- Department of Internal Medicine IV, University Hospital Halle (Saale), Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, and Division of General Medicine, Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung Shan South Road, Taipei City, Taiwan
| | - Marta Pratcorona
- Hospital de la Santa Creu i Sant Pau. Institut de Recerca Sant Pau. Department of Medicine, Universitat Autonoma of Barcelona, Barcelona, Spain
| | - Robert K Hills
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Klaus H Metzeler
- Department of Hematology, Cell Therapy, Hemostaseology and Infectious Diseases, University Hospital Leipzig, Leipzig, Germany
| | - Laurene Fenwarth
- Unité Mixte de Recherche (UMR) 9020-UMR1277, Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalo-Universitaire (CHU) Lille, Institut de Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Anna Dolnik
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christine Terre
- Laboratoire de Cytogénétique, Service de Biologie, CH de Versailles, Le Chesnay, France
| | - Klara Kopp
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Olga Blau
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Martin Szyska
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Friederike Christen
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jan Krönke
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany
| | - Loïc Vasseur
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | - Bob Löwenberg
- Department of Hematology, Erasmus MC Cancer Institute, and Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jordi Esteve
- Hematology Department, IDIBAPS, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, and Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Matthieu Duchmann
- Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Université Paris Cité, Paris, France
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, and Division of General Medicine, Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung Shan South Road, Taipei City, Taiwan
| | - David C Linch
- Department of Haematology, University College London Cancer Institute, London, UK
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Rosemary E Gale
- Department of Haematology, University College London Cancer Institute, London, UK
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany
| | - Kenichi Yoshida
- Division of Cancer Evolution, National Cancer Center Research Institute, Tokyo, Japan
| | - Frederik Damm
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
- German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany.
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7
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Duque-Afonso J, Veratti P, Rehman UU, Herzog H, Mitschke J, Greve G, Eble J, Berberich B, Thomas J, Pantic M, Waterhouse M, Gentile G, Heidenreich O, Miething C, Lübbert M. Identification of epigenetic modifiers essential for growth and survival of AML1/ETO-positive leukemia. Int J Cancer 2024. [PMID: 39146497 DOI: 10.1002/ijc.35134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 08/17/2024]
Abstract
Aberrant gene expression patterns in acute myeloid leukemia (AML) with balanced chromosomal translocations are often associated with dysregulation of epigenetic modifiers. The AML1/ETO (RUNX1/MTG8) fusion protein, caused by the translocation (8;21)(q22;q22), leads to the epigenetic repression of its target genes. We aimed in this work to identify critical epigenetic modifiers, on which AML1/ETO-positive AML cells depend on for proliferation and survival using shRNA library screens and global transcriptomics approaches. Using shRNA library screens, we identified 41 commonly depleted genes in two AML1/ETO-positive cell lines Kasumi-1 and SKNO-1. We validated, genetically and pharmacologically, DNMT1 and ATR using several AML1/ETO-positive and negative cell lines. We also demonstrated in vivo differentiation of myeloblasts after treatment with the DNMT1 inhibitor decitabine in a patient with an AML1/ETO-positive AML. Bioinformatic analysis of global transcriptomics after AML1/ETO induction in 9/14/18-U937 cells identified 973 differentially expressed genes (DEGs). Three genes (PARP2, PRKCD, and SMARCA4) were both downregulated after AML1/ETO induction, and identified in shRNA screens. In conclusion, using unbiased shRNA library screens and global transcriptomics, we have identified several driver epigenetic regulators for proliferation in AML1/ETO-positive AML. DNMT1 and ATR were validated and are susceptible to pharmacological inhibition by small molecules showing promising preclinical and clinical efficacy.
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Affiliation(s)
- Jesús Duque-Afonso
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - Pia Veratti
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
- German Cancer Consortium (DKTK), Partnering Site Freiburg, Freiburg, Germany
| | - Usama-Ur Rehman
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - Heike Herzog
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - Jan Mitschke
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
- German Cancer Consortium (DKTK), Partnering Site Freiburg, Freiburg, Germany
| | - Gabriele Greve
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Julian Eble
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - Bettina Berberich
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - Johanna Thomas
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - Milena Pantic
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - Miguel Waterhouse
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - Gaia Gentile
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - Olaf Heidenreich
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Cornelius Miething
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
- German Cancer Consortium (DKTK), Partnering Site Freiburg, Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology/Oncology/Stem Cell Transplantation, Faculty of Medicine, University of Freiburg Medical Center, Freiburg, Germany
- German Cancer Consortium (DKTK), Partnering Site Freiburg, Freiburg, Germany
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8
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Zhang Q, Ai Y, Abdel-Wahab O. Molecular impact of mutations in RNA splicing factors in cancer. Mol Cell 2024:S1097-2765(24)00617-8. [PMID: 39146933 DOI: 10.1016/j.molcel.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 08/17/2024]
Abstract
Somatic mutations in genes encoding components of the RNA splicing machinery occur frequently in multiple forms of cancer. The most frequently mutated RNA splicing factors in cancer impact intronic branch site and 3' splice site recognition. These include mutations in the core RNA splicing factor SF3B1 as well as mutations in the U2AF1/2 heterodimeric complex, which recruits the SF3b complex to the 3' splice site. Additionally, mutations in splicing regulatory proteins SRSF2 and RBM10 are frequent in cancer, and there has been a recent suggestion that variant forms of small nuclear RNAs (snRNAs) may contribute to splicing dysregulation in cancer. Here, we describe molecular mechanisms by which mutations in these factors alter splice site recognition and how studies of this process have yielded new insights into cancer pathogenesis and the molecular regulation of splicing. We also discuss data linking mutant RNA splicing factors to RNA metabolism beyond splicing.
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Affiliation(s)
- Qian Zhang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuxi Ai
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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9
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Cook JA, Lott L, Perry J, Eckel AM, Xu D, Hudson CA, Wells DA, Loken MR, Menssen AJ. Fusion-harboring mast cells can explain molecular positivity in flow cytometric MRD-negative core-binding factor AML. Blood 2024; 144:581-585. [PMID: 38749014 DOI: 10.1182/blood.2024024264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/09/2024] [Indexed: 08/02/2024] Open
Abstract
ABSTRACT Molecular measurable residual disease can persist in core-binding factor acute myeloid leukemia in otherwise disease-free patients. Utilizing cell sorting followed by fluorescent in situ hybridization, we show that detection is due to mast cells.
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MESH Headings
- Humans
- Mast Cells/metabolism
- Mast Cells/pathology
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/diagnosis
- Flow Cytometry/methods
- Neoplasm, Residual/diagnosis
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- In Situ Hybridization, Fluorescence
- RUNX1 Translocation Partner 1 Protein/genetics
- RUNX1 Translocation Partner 1 Protein/metabolism
- Male
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Female
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10
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Orsmark-Pietras C, Lyander A, Ladenvall C, Hallström B, Staffas A, Awier H, Krstic A, Baliakas P, Barbany G, Håkansson CB, Gellerbring A, Hagström A, Hellström-Lindberg E, Juliusson G, Lazarevic V, Munters A, Pandzic T, Wadelius M, Ås J, Fogelstrand L, Wirta V, Rosenquist R, Cavelier L, Fioretos T. Precision Diagnostics in Myeloid Malignancies: Development and Validation of a National Capture-Based Gene Panel. Genes Chromosomes Cancer 2024; 63:e23257. [PMID: 39031442 DOI: 10.1002/gcc.23257] [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: 05/07/2024] [Accepted: 06/23/2024] [Indexed: 07/22/2024] Open
Abstract
Gene panel sequencing has become a common diagnostic tool for detecting somatically acquired mutations in myeloid neoplasms. However, many panels have restricted content, provide insufficient sensitivity levels, or lack clinically validated workflows. We here describe the development and validation of the Genomic Medicine Sweden myeloid gene panel (GMS-MGP), a capture-based 191 gene panel including mandatory genes in contemporary guidelines as well as emerging candidates. The GMS-MGP displayed uniform coverage across all targets, including recognized difficult GC-rich areas. The validation of 117 previously described somatic variants showed a 100% concordance with a limit-of-detection of a 0.5% variant allele frequency (VAF), achieved by utilizing error correction and filtering against a panel-of-normals. A national interlaboratory comparison investigating 56 somatic variants demonstrated highly concordant results in both detection rate and reported VAFs. In addition, prospective analysis of 323 patients analyzed with the GMS-MGP as part of standard-of-care identified clinically significant genes as well as recurrent mutations in less well-studied genes. In conclusion, the GMS-MGP workflow supports sensitive detection of all clinically relevant genes, facilitates novel findings, and is, based on the capture-based design, easy to update once new guidelines become available. The GMS-MGP provides an important step toward nationally harmonized precision diagnostics of myeloid malignancies.
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Affiliation(s)
- Christina Orsmark-Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Anna Lyander
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Clinical Genomics Stockholm, Science Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Claes Ladenvall
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Björn Hallström
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Anna Staffas
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Hero Awier
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aleksandra Krstic
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Gisela Barbany
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Brunhoff Håkansson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Anna Gellerbring
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Anna Hagström
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Eva Hellström-Lindberg
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Gunnar Juliusson
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Vladimir Lazarevic
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Arielle Munters
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacogenomics, Uppsala University, Uppsala, Sweden
| | - Joel Ås
- Department of Medical Sciences, Clinical Pharmacogenomics, Uppsala University, Uppsala, Sweden
| | - Linda Fogelstrand
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Valtteri Wirta
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Clinical Genomics Stockholm, Science Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science Life Laboratory, Karolinska Institutet, Solna, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
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11
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Tarlock K, Gerbing RB, Ries RE, Smith JL, Leonti A, Huang BJ, Kirkey D, Robinson L, Peplinksi JH, Lange B, Cooper TM, Gamis AS, Kolb EA, Aplenc R, Pollard JA, Alonzo TA, Meshinchi S. Prognostic impact of cooccurring mutations in FLT3-ITD pediatric acute myeloid leukemia. Blood Adv 2024; 8:2094-2103. [PMID: 38295280 PMCID: PMC11063409 DOI: 10.1182/bloodadvances.2023011980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/28/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
ABSTRACT We sought to define the cooccurring mutational profile of FLT3-ITD-positive (ITDpos) acute myeloid leukemia (AML) in pediatric and young adult patients and to define the prognostic impact of cooperating mutations. We identified 464 patients with FLT3-ITD mutations treated on Children's Oncology Group trials with available sequencing and outcome data. Overall survival, event-free survival (EFS), and relapse risk were determined according to the presence of cooccurring risk stratifying mutations. Among the cohort, 79% of patients had cooccurring alterations across 239 different genes that were altered through mutations or fusions. Evaluation of the prognostic impact of the cooccurring mutations demonstrated that patients with ITDpos AML experienced significantly different outcomes according to the cooccurring mutational profile. Patients with ITDpos AML harboring a cooccurring favorable-risk mutation of NPM1, CEBPA, t(8;21), or inv(16) experienced a 5-year EFS of 64%, which was significantly superior to of 22.2% for patients with ITDpos AML and poor-risk mutations of WT1, UBTF, or NUP98::NSD1 as well to 40.9% for those who lacked either favorable-risk or poor-risk mutation (ITDpos intermediate; P < .001 for both). Multivariable analysis demonstrated that cooccurring mutations had significant prognostic impact, whereas allelic ratio had no impact. Therapy intensification, specifically consolidation transplant in remission, resulted in significant improvements in survival for ITDpos AML. However, patients with ITDpos/NUP98::NSD1 continued to have poor outcomes with intensified therapy, including sorafenib. Cooccurring mutational profile in ITDpos AML has significant prognostic impacts and is critical to determining risk stratification and therapeutic allocation. These clinical trials were registered at www.clinicaltrials.gov as NCT00002798, NCT00070174, NCT00372593, and NCT01371981.
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Affiliation(s)
- Katherine Tarlock
- Division of Hematology/Oncology, Seattle Children’s Hospital, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | | | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jenny L. Smith
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Amanda Leonti
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Benjamin J. Huang
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Danielle Kirkey
- Division of Hematology/Oncology, Seattle Children’s Hospital, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Leila Robinson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jack H. Peplinksi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Beverly Lange
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Todd M. Cooper
- Division of Hematology/Oncology, Seattle Children’s Hospital, Seattle, WA
| | - Alan S. Gamis
- Divisions of Hematology/Oncology, Children’s Mercy Hospital and Clinics, Kansas City, MO
| | - E. Anders Kolb
- Nemours Center for Cancer and Blood Disorders, Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Richard Aplenc
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Jessica A. Pollard
- Pediatric Oncology, Dana Farber Cancer Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Todd A. Alonzo
- Children’s Oncology Group, Monrovia, CA
- University of Southern California Keck School of Medicine, Los Angeles, CA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
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12
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Thomas ME, Qi W, Walsh MP, Ma J, Westover T, Abdelhamed S, Ezzell LJ, Rolle C, Xiong E, Rosikiewicz W, Xu B, Loughran AJ, Pruett-Miller SM, Janke LJ, Klco JM. Functional characterization of cooperating MGA mutations in RUNX1::RUNX1T1 acute myeloid leukemia. Leukemia 2024; 38:991-1002. [PMID: 38454121 PMCID: PMC11073986 DOI: 10.1038/s41375-024-02193-y] [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: 08/31/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024]
Abstract
MGA (Max-gene associated) is a dual-specificity transcription factor that negatively regulates MYC-target genes to inhibit proliferation and promote differentiation. Loss-of-function mutations in MGA have been commonly identified in several hematological neoplasms, including acute myeloid leukemia (AML) with RUNX1::RUNX1T1, however, very little is known about the impact of these MGA alterations on normal hematopoiesis or disease progression. We show that representative MGA mutations identified in patient samples abolish protein-protein interactions and transcriptional activity. Using a series of human and mouse model systems, including a newly developed conditional knock-out mouse strain, we demonstrate that loss of MGA results in upregulation of MYC and E2F targets, cell cycle genes, mTOR signaling, and oxidative phosphorylation in normal hematopoietic cells, leading to enhanced proliferation. The loss of MGA induces an open chromatin state at promoters of genes involved in cell cycle and proliferation. RUNX1::RUNX1T1 expression in Mga-deficient murine hematopoietic cells leads to a more aggressive AML with a significantly shortened latency. These data show that MGA regulates multiple pro-proliferative pathways in hematopoietic cells and cooperates with the RUNX1::RUNX1T1 fusion oncoprotein to enhance leukemogenesis.
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Affiliation(s)
- Melvin E Thomas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN, 38105, USA
| | - Wenqing Qi
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN, 38105, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN, 38105, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN, 38105, USA
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN, 38105, USA
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN, 38105, USA
| | - Lauren J Ezzell
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chandra Rolle
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN, 38105, USA
| | - Emily Xiong
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN, 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Allister J Loughran
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Laura J Janke
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN, 38105, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN, 38105, USA.
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13
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Gabellier L, Peterlin P, Thepot S, Hicheri Y, Paul F, Gallego-Hernanz MP, Bertoli S, Turlure P, Pigneux A, Guieze R, Ochmann M, Malfuson JV, Cluzeau T, Thomas X, Tavernier E, Jourdan E, Bonnet S, Tudesq JJ, Raffoux E. Hypomethylating agent monotherapy in core binding factor acute myeloid leukemia: a French multicentric retrospective study. Ann Hematol 2024; 103:759-769. [PMID: 38273140 PMCID: PMC10867066 DOI: 10.1007/s00277-024-05623-0] [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: 10/26/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024]
Abstract
Very few data are available about hypomethylating agent (HMA) efficiency in core binding factor acute myeloid leukemias (CBF-AML). Our main objective was to evaluate the efficacy and safety of HMA in the specific subset of CBF-AML. Here, we report the results of a multicenter retrospective French study about efficacy of HMA monotherapy, used frontline or for R/R CBF-AML. Forty-nine patients were included, and received a median of 5 courses of azacitidine (n = 46) or decitabine (n = 3). ORR was 49% for the whole cohort with a median time to response of 112 days. After a median follow-up of 72.3 months, median OS for the total cohort was 10.6 months. In multivariate analysis, hematological relapse of CBF-AML at HMA initiation was significantly associated with a poorer OS (HR: 2.13; 95%CI: 1.04-4.36; p = 0.038). Responders had a significantly improved OS (1-year OS: 75%) compared to non-responders (1-year OS: 15.3%; p < 0.0001). Hematological improvement occurred for respectively 28%, 33% and 48% for patients who were red blood cell or platelet transfusion-dependent, or who experienced grade 3/4 neutropenia at HMA initiation. Adverse events were consistent with the known safety profile of HMA. Our study highlights that HMA is a well-tolerated therapeutic option with moderate clinical activity for R/R CBF-AML and for patients who cannot handle intensive chemotherapy.
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Affiliation(s)
- Ludovic Gabellier
- Département d'Hématologie Clinique, CHU Montpellier, Université Montpellier-Nîmes, 80, Avenue Augustin Fliche, 34090, Montpellier, France.
| | - Pierre Peterlin
- Département d'Hématologie Clinique, CHU Nantes, Université de Nantes, Nantes, France
| | - Sylvain Thepot
- Département d'Hématologie Clinique, CHU Angers, Université d'Angers, Angers, France
| | - Yosr Hicheri
- Département d'Hématologie Clinique, Institut Paoli-Calmettes, Marseille, France
| | - Franciane Paul
- Département d'Hématologie Clinique, CHU Montpellier, Université Montpellier-Nîmes, 80, Avenue Augustin Fliche, 34090, Montpellier, France
| | | | - Sarah Bertoli
- Service d'Hématologie Clinique, CHU Toulouse, Institut Universitaire du Cancer de Toulouse - Oncopôle, Université Toulouse III - Paul Sabatier, Toulouse, France
| | - Pascal Turlure
- Département d'Hématologie Clinique, CHU Limoges, Université de Limoges, Limoges, France
| | - Arnaud Pigneux
- Département d'Hématologie Clinique, CHU Bordeaux, Université de Bordeaux, Bordeaux, France
| | - Romain Guieze
- Département d'Hématologie Clinique, CHU Clermont-Ferrand, Université de Clermont-Ferrand, Clermont-Ferrand, France
| | - Marlène Ochmann
- Département d'Hématologie Clinique, Orléans, Orléans, CH, France
| | - Jean-Valère Malfuson
- Département d'Hématologie Clinique, Hôpital d'instruction Des Armées, Percy, France
| | - Thomas Cluzeau
- Département d'Hématologie Clinique, CHU Nice, Université de Nice, Nice, France
| | - Xavier Thomas
- Département d'Hématologie Clinique, Hospices Civils de Lyon, CHU Lyon, Université de Lyon, Lyon, France
| | - Emmanuelle Tavernier
- Département d'Hématologie Clinique, Institut de Cancérologie Lucien Neuwirth, Université de Saint-Etienne, Saint-Etienne, France
| | - Eric Jourdan
- Département d'Hématologie Clinique, CHU Nîmes, Université de Montpellier-Nîmes, Nîmes, France
| | - Sarah Bonnet
- Département d'Hématologie Clinique, CHU Montpellier, Université Montpellier-Nîmes, 80, Avenue Augustin Fliche, 34090, Montpellier, France
| | - Jean-Jacques Tudesq
- Département d'Hématologie Clinique, CHU Montpellier, Université Montpellier-Nîmes, 80, Avenue Augustin Fliche, 34090, Montpellier, France
| | - Emmanuel Raffoux
- Département d'Hématologie Clinique Adultes, Hôpital Saint-Louis, APHP, Université Paris Diderot, Paris, France
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14
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Zhang Z, Yin J, Lian G, Bao X, Hu M, Liu Z, Yu Y, Mi R, Zuo Y, Shi P, Zheng W, Jiang Q, Chao H, Xiao P, Yu W, Han Y, Wu Y, Zeng Y, Wu D, Yang X, Chen S. A multicenter retrospective comparison between systemic mastocytosis with t(8;21) AML and KIT mutant t(8;21) AML. Blood Adv 2024; 8:889-894. [PMID: 38170739 PMCID: PMC10875270 DOI: 10.1182/bloodadvances.2023012006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Affiliation(s)
- Zhibo Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jia Yin
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Guoli Lian
- Department of Pediatrics, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiebing Bao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Meng Hu
- Department of Hematology, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhenfang Liu
- Department of Hematology, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuan Yu
- Department of Hematology, Qilu Hospital, Shandong University, Jinan, China
| | - Ruihua Mi
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Yabei Zuo
- Department of Hematology, Second Hospital of Hebei Medical University, Hebei Key Laboratory of Hematology, Shijiazhuang, China
| | - Pengcheng Shi
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weiyan Zheng
- Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Hongying Chao
- Department of Hematology, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, China
| | - Peifang Xiao
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, China
| | - Weijuan Yu
- Department of Hematology Laboratory, Yantai Yuhuangding Hospital, Yantai, China
| | - Yanqiu Han
- Department of Hematology, Affiliated Hospital of Inner Mongolia Medical University, Inner Mongolia, China
| | - Yu Wu
- Department of Hematology and Institute of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Zeng
- Department of Hematology, Chengdu Second People’s Hospital, Chengdu, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Xiaofei Yang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
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15
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Wachter F, Pikman Y. Pathophysiology of Acute Myeloid Leukemia. Acta Haematol 2024; 147:229-246. [PMID: 38228114 DOI: 10.1159/000536152] [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: 07/25/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a biologically heterogenous disease arising in clonally proliferating hematopoietic stem cells. Sequential acquisition of mutations leads to expanded proliferation of clonal myeloid progenitors and failure of differentiation, leading to fulminant AML. SUMMARY Here, we review the pathophysiology of AML with a focus on factors predisposing to AML development, including prior chemo- and radiation therapy, environmental factors, and germline predisposition. KEY MESSAGE Increasing genomic characterization of AML and insight into mechanisms of its development will be critical to improvement in AML prognostication and therapy.
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Affiliation(s)
- Franziska Wachter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
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16
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Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A pan-cancer gene panel for childhood malignancies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.27.23299068. [PMID: 38076942 PMCID: PMC10705664 DOI: 10.1101/2023.11.27.23299068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. Results SJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate fusion oncoproteins, commonly amplified/deleted regions (e.g., MYCN for neuroblastoma, CDKN2A and PAX5 for B-/T-ALL, and SMARCB1 for AT/RT), and 7,590 polymorphism sites for interrogating tumors with aneuploidy, such as hyperdiploid and hypodiploid B-ALL or 17q gain neuroblastoma. We used driver alterations reported from an established real-time clinical genomics cohort (n=253) to validate this gene panel. Among the 485 pathogenic variants reported, our panel covered 417 variants (86%). For 90 rearrangements responsible for oncogenic fusions, our panel covered 74 events (82%). We re-sequenced 113 previously characterized clinical specimens at an average depth of 2,500X using SJPedPanel and recovered 354 (91%) of the 389 reported pathogenic variants. We then investigated the power of this panel in detecting mutations from specimens with low tumor purity (as low as 0.1%) using cell line-based dilution experiments and discovered that this gene panel enabled us to detect ∼80% variants with allele fraction of 0.2%, while the detection rate decreases to ∼50% when the allele fraction is 0.1%. We finally demonstrate its utility in disease monitoring on clinical specimens collected from AML patients in morphologic remission. Conclusions SJPedPanel enables the detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions for childhood cancers by targeted sequencing of ∼0.15% of human genome. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
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17
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Umeda M, Ma J, Westover T, Ni Y, Song G, Maciaszek JL, Rusch M, Rahbarinia D, Foy S, Huang BJ, Walsh MP, Kumar P, Liu Y, Yang W, Fan Y, Wu G, Baker SD, Ma X, Wang L, Alonzo TA, Rubnitz JE, Pounds S, Klco JM. A new genomic framework to categorize pediatric acute myeloid leukemia. Nat Genet 2024; 56:281-293. [PMID: 38212634 PMCID: PMC10864188 DOI: 10.1038/s41588-023-01640-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024]
Abstract
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas. To comprehensively define the genomic landscape of pAML, we systematically categorized 887 pAML into 23 mutually distinct molecular categories, including new major entities such as UBTF or BCL11B, covering 91.4% of the cohort. These molecular categories were associated with unique expression profiles and mutational patterns. For instance, molecular categories characterized by specific HOXA or HOXB expression signatures showed distinct mutation patterns of RAS pathway genes, FLT3 or WT1, suggesting shared biological mechanisms. We show that molecular categories were strongly associated with clinical outcomes using two independent cohorts, leading to the establishment of a new prognostic framework for pAML based on these updated molecular categories and minimal residual disease. Together, this comprehensive diagnostic and prognostic framework forms the basis for future classification of pAML and treatment strategies.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yonghui Ni
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jamie L Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Huang
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Priyadarshini Kumar
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sharyn D Baker
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Todd A Alonzo
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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18
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Rivera D, Naik U, Wang WJ, Cuglievan B, Yin CC, Chen L. Acute myeloid leukemia with inversion 16 and a novel PTPN11 mutation: A case report with literature review. Int J Lab Hematol 2024; 46:195-198. [PMID: 37872826 DOI: 10.1111/ijlh.14191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023]
Affiliation(s)
- Daniel Rivera
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Udit Naik
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Wei J Wang
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Branko Cuglievan
- Department of Leukemia and Lymphoma, Children's Cancer Hospital, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - C Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lei Chen
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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19
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Li Q, Guo H, Xu J, Li X, Wang D, Guo Y, Qing G, Van Vlierberghe P, Liu H. A helicase-independent role of DHX15 promotes MYC stability and acute leukemia cell survival. iScience 2024; 27:108571. [PMID: 38161423 PMCID: PMC10755364 DOI: 10.1016/j.isci.2023.108571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/13/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024] Open
Abstract
DHX15 has been implicated in RNA splicing and ribosome biogenesis, primarily functioning as an RNA helicase. To systematically assess the cellular role of DHX15, we conducted proteomic analysis to investigate the landscape of DHX15 interactome, and identified MYC as a binding partner. DHX15 co-localizes with MYC in cells and directly interacts with MYC in vitro. Importantly, DHX15 contributes to MYC protein stability at the post-translational level and independent of its RNA binding capacity. Mechanistic investigation reveals that DHX15 interferes the interaction between MYC and FBXW7, thereby preventing MYC polyubiquitylation and proteasomal degradation. Consequently, the abrogation of DHX15 drastically inhibits MYC-mediated transcriptional output. While DHX15 depletion blocks T cell development and leukemia cell survival as we recently reported, overexpression of MYC significantly rescues the phenotypic defects. These findings shed light on the essential role of DHX15 in mammalian cells and suggest that maintaining sufficient MYC expression is a significant contributor to DHX15-mediated cellular functions.
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Affiliation(s)
- Qilong Li
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, China
| | - Hao Guo
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, China
| | - Jin Xu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, China
| | - Xinlu Li
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, China
| | - Donghai Wang
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, China
| | - Ying Guo
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, China
| | - Guoliang Qing
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, China
| | | | - Hudan Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, China
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20
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Arnedo-Pac C, Muiños F, Gonzalez-Perez A, Lopez-Bigas N. Hotspot propensity across mutational processes. Mol Syst Biol 2024; 20:6-27. [PMID: 38177930 PMCID: PMC10883281 DOI: 10.1038/s44320-023-00001-w] [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: 10/05/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024] Open
Abstract
The sparsity of mutations observed across tumours hinders our ability to study mutation rate variability at nucleotide resolution. To circumvent this, here we investigated the propensity of mutational processes to form mutational hotspots as a readout of their mutation rate variability at single base resolution. Mutational signatures 1 and 17 have the highest hotspot propensity (5-78 times higher than other processes). After accounting for trinucleotide mutational probabilities, sequence composition and mutational heterogeneity at 10 Kbp, most (94-95%) signature 17 hotspots remain unexplained, suggesting a significant role of local genomic features. For signature 1, the inclusion of genome-wide distribution of methylated CpG sites into models can explain most (80-100%) of the hotspot propensity. There is an increased hotspot propensity of signature 1 in normal tissues and de novo germline mutations. We demonstrate that hotspot propensity is a useful readout to assess the accuracy of mutation rate models at nucleotide resolution. This new approach and the findings derived from it open up new avenues for a range of somatic and germline studies investigating and modelling mutagenesis.
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Affiliation(s)
- Claudia Arnedo-Pac
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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21
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Yan M, Liu M, Davis AG, Stoner SA, Zhang DE. Single-cell RNA sequencing of a new transgenic t(8;21) preleukemia mouse model reveals regulatory networks promoting leukemic transformation. Leukemia 2024; 38:31-44. [PMID: 37838757 PMCID: PMC10776403 DOI: 10.1038/s41375-023-02063-z] [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: 04/24/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
T(8;21)(q22;q22), which generates the AML1-ETO fusion oncoprotein, is a common chromosomal abnormality in acute myeloid leukemia (AML) patients. Despite having favorable prognosis, 40% of patients will relapse, highlighting the need for innovative models and application of the newest technologies to study t(8;21) leukemogenesis. Currently, available AML1-ETO mouse models have limited utility for studying the pre-leukemic stage because AML1-ETO produces mild hematopoietic phenotypes and no leukemic transformation. Conversely, overexpression of a truncated variant, AML1-ETO9a (AE9a), promotes fully penetrant leukemia and is too potent for studying pre-leukemic changes. To overcome these limitations, we devised a germline-transmitted Rosa26 locus AE9a knock-in mouse model that moderately overexpressed AE9a and developed leukemia with long latency and low penetrance. We observed pre-leukemic alterations in AE9a mice, including skewing of progenitors towards granulocyte/monocyte lineages and replating of stem and progenitor cells. Next, we performed single-cell RNA sequencing to identify specific cell populations that contribute to these pre-leukemic phenotypes. We discovered a subset of common myeloid progenitors that have heightened granulocyte/monocyte bias in AE9a mice. We also observed dysregulation of key hematopoietic transcription factor target gene networks, blocking cellular differentiation. Finally, we identified Sox4 activation as a potential contributor to stem cell self-renewal during the pre-leukemic stage.
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Affiliation(s)
- Ming Yan
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Mengdan Liu
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amanda G Davis
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Samuel A Stoner
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Dong-Er Zhang
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
- Department of Pathology, University of California San Diego, La Jolla, CA, USA.
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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22
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Day RB, Hickman JA, Xu Z, Katerndahl CD, Ferraro F, Ramakrishnan SM, Erdmann-Gilmore P, Sprung RW, Mi Y, Townsend RR, Miller CA, Ley TJ. Proteogenomic analysis reveals cytoplasmic sequestration of RUNX1 by the acute myeloid leukemia-initiating CBFB::MYH11 oncofusion protein. J Clin Invest 2023; 134:e176311. [PMID: 38061017 PMCID: PMC10866659 DOI: 10.1172/jci176311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/06/2023] [Indexed: 02/16/2024] Open
Abstract
Several canonical translocations produce oncofusion genes that can initiate acute myeloid leukemia (AML). Although each translocation is associated with unique features, the mechanisms responsible remain unclear. While proteins interacting with each oncofusion are known to be relevant for how they act, these interactions have not yet been systematically defined. To address this issue in an unbiased fashion, we fused a promiscuous biotin ligase (TurboID) in-frame with 3 favorable-risk AML oncofusion cDNAs (PML::RARA, RUNX1::RUNX1T1, and CBFB::MYH11) and identified their interacting proteins in primary murine hematopoietic cells. The PML::RARA- and RUNX1::RUNX1T1-TurboID fusion proteins labeled common and unique nuclear repressor complexes, implying their nuclear localization. However, CBFB::MYH11-TurboID-interacting proteins were largely cytoplasmic, probably because of an interaction of the MYH11 domain with several cytoplasmic myosin-related proteins. Using a variety of methods, we showed that the CBFB domain of CBFB::MYH11 sequesters RUNX1 in cytoplasmic aggregates; these findings were confirmed in primary human AML cells. Paradoxically, CBFB::MYH11 expression was associated with increased RUNX1/2 expression, suggesting the presence of a sensor for reduced functional RUNX1 protein, and a feedback loop that may attempt to compensate by increasing RUNX1/2 transcription. These findings may have broad implications for AML pathogenesis.
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Affiliation(s)
- Ryan B. Day
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, and
| | - Julia A. Hickman
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, and
| | - Ziheng Xu
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, and
| | - Casey D.S. Katerndahl
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, and
| | - Francesca Ferraro
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, and
| | | | - Petra Erdmann-Gilmore
- Division of Endocrinology, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Robert W. Sprung
- Division of Endocrinology, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Yiling Mi
- Division of Endocrinology, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - R. Reid Townsend
- Division of Endocrinology, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher A. Miller
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, and
| | - Timothy J. Ley
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, and
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Li XP, Dai Y, Zhang WN, Pan MM, Mao J, Zhao B, Jiang L, Gao Y. Single-cell RNA-seq reveals novel immune-associated biomarkers for predicting prognosis in AML patients with RUNX1::RUNX1T1. Int Immunopharmacol 2023; 125:111178. [PMID: 37951201 DOI: 10.1016/j.intimp.2023.111178] [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: 06/09/2023] [Revised: 10/15/2023] [Accepted: 11/01/2023] [Indexed: 11/13/2023]
Abstract
Acute myeloid leukemia (AML) with t(8;21)(q22;q22);(RUNX1::RUNX1T1) is highly heterogeneous and malignant. It has a relapse rate of nearly 40 %, resulting in clinical resistance or refractoriness to chemotherapy. Immune cells, particularly CD4(+) T and CD8(+) T lymphocytes, have been discovered to be dysfunctional in this condition, and functional recovery shows promising efficiency in preclinical trials. Here, with single-cell transcriptomic data from de novo AML patients with RUNX1::RUNX1T1 and at various stages following disease progression, we investigated the genes correlated with T-cell proliferation and activation. In leukemia cells, ADA, AHCY, GPN3 and LTBR were markedly highly expressed compared to those in T-cell at diagnosis, and they tended to increase with disease progression. Additionally, we discovered that AHCY was an effective biomarker to predict the overall survival as well as relapse-free survival of AML patients with RUNX1::RUNX1T1. The correlation of AHCY with infiltrated immune cells and immune checkpoints was also investigated. AML cohorts from two other independent studies, TCGA LAML (n = 145) and the GEO dataset (n = 104), also demonstrated an inferior outcome for AML patients with high AHCY expression. In conclusion, our research revealed that AHCY might function as a novel indicator to predict the prognosis and efficiency of T-cell proliferation and activation in AML patients with RUNX1::RUNX1T1.
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Affiliation(s)
- Xue-Ping Li
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China; State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei-Na Zhang
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Meng-Meng Pan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiaying Mao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China; Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Baitian Zhao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China; Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yan Gao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China; Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
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Zhai Y, Wang Q, Ji L, Ren H, Dong Y, Yang F, Yin Y, Liang Z, Wang Q, Liu W, Mei Y, Zhang L, Li Y. Clinical characteristics and prognostic factors analysis of core binding factor acute myeloid leukemia in real world. Cancer Med 2023; 12:21592-21604. [PMID: 38062912 PMCID: PMC10757144 DOI: 10.1002/cam4.6693] [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: 08/24/2023] [Revised: 10/13/2023] [Accepted: 10/26/2023] [Indexed: 12/31/2023] Open
Abstract
BACKGROUND Chromosomal translocations involving core binding factor (CBF) genes account for 15% of adult acute myeloid leukemia (AML) cases in China. Despite being classified as favorable-risk by European Leukemia Net (ELN), CBF-AML patients have a 40% relapse rate. This study aims to analyze clinical characteristics and prognosis of CBF-AML, compare its subtypes (inv(16) and t(8;21)), and validate prognostic factors. METHODS Retrospective analysis of 149 AML patients (75 CBF-AML, 74 non-CBF) at Peking University First Hospital (March 2012-March 2022). RESULTS CBF-AML patients have significantly lower disease-free survival (DFS) (p = 0.005) and higher non-relapse mortality (NRM) (p = 0.028) compared to non-CBF AML. inv (16) and t(8;21) show distinct co-occurring gene mutation patterns, with inv(16) being prone to central nervous system (CNS) leukemia. Multivariate analysis identifies age as a risk factor for overall survival (OS) and disease free survival (DFS), kinase mutation as a risk factor for DFS and Recurrence, while WT1 mutation as a risk factor for OS and non relapse mortality (NRM) risk in t(8;21) AML. Allogeneic hematopoietic stem cell transplantation (allo-HSCT) improves prognosis in low-risk t(8;21). CONCLUSION Prognosis of CBF-AML is poorer than ELN guidelines suggest. inv(16) and (8;21) are separate entities with relatively poor prognoses, requiring rational risk stratification strategies. Allo-HSCT may benefit low-risk t(8;21), but further research is needed for conclusive evidence.
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Affiliation(s)
- Yamei Zhai
- Department of HematologyPeking University First HospitalBeijingChina
| | - Qingya Wang
- Department of HematologyPeking University First HospitalBeijingChina
| | - Li Ji
- Department of HematologyPeking University First HospitalBeijingChina
| | - Hanyun Ren
- Department of HematologyPeking University First HospitalBeijingChina
| | - Yujun Dong
- Department of HematologyPeking University First HospitalBeijingChina
| | - Fan Yang
- Department of HematologyPeking University First HospitalBeijingChina
| | - Yue Yin
- Department of HematologyPeking University First HospitalBeijingChina
| | - Zeyin Liang
- Department of HematologyPeking University First HospitalBeijingChina
| | - Qian Wang
- Department of HematologyPeking University First HospitalBeijingChina
| | - Wei Liu
- Department of HematologyPeking University First HospitalBeijingChina
| | - Yan Mei
- Department of HematologyPeking University First HospitalBeijingChina
| | - Lu Zhang
- Department of HematologyPeking University First HospitalBeijingChina
| | - Yuan Li
- Department of HematologyPeking University First HospitalBeijingChina
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Chapilliquen Ramirez RM, Corbacho Pachas MTDJ, Zapata Dongo RJ. Prevalence and Prognosis of Secondary Genetic Aberrations Among Patients With Core Binding Factor Acute Myeloid Leukemia: A Mitelman Database Analysis. World J Oncol 2023; 14:488-498. [PMID: 38022406 PMCID: PMC10681777 DOI: 10.14740/wjon1661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Background Core binding factor acute myeloid leukemia (CBF-AML) comprises t(8;21) and inv(16) and usually has a favorable prognosis. However, a wide spectrum of secondary genetic aberrations has been shown to be associated with worse outcomes with respect to overall survival (OS) and relapse. We aimed to identify secondary molecular and chromosomal aberrations within each group of CBF-AML, i.e., t(8;21) and inv(16), and to evaluate their prognosis with OS. Methods Using the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer, we analyzed 193 cases of CBF-AML reported between 2011 and 2021. We conducted a survival analysis to determine the 5-year OS, and we conducted univariate and multivariate Cox regression to identify independent genetic factors related to OS. Results Among the 193 cases with CBF-AML, structural and numerical chromosome rearrangements were 25.9% and 40.9%, respectively, and secondary genetic mutations were 54.9%. The 5-year OS for the presence of del(7) and trisomy 22 was significantly worse. NRAS mutations had a worse 5-year OS in the t(8;21) group in the univariate analysis but showed no significant difference in the multivariate analysis. Conclusions CBF-AML has heterogeneous cytogenetic characteristics but no difference in the 5-year OS between the inv(16) and t(8;21) groups. Finally, the presence of del(7), trisomy 22 and NRAS mutations showed a potential prognostic impact in CBF-AML patients. Secondary genetic findings may need to be identified to determine its association to a worse prognosis, and in the future develop better targeted therapies in patients with CBF-AML.
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Darwish C, Farina K, Tremblay D. The core concepts of core binding factor acute myeloid leukemia: Current considerations for prognosis and treatment. Blood Rev 2023; 62:101117. [PMID: 37524647 DOI: 10.1016/j.blre.2023.101117] [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: 03/23/2023] [Revised: 07/04/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023]
Abstract
Core binding factor acute myeloid leukemia (CBF AML), defined by t(8;21) or inv(16), is a subset of favorable risk AML. Despite its association with a high complete remission rate after induction and relatively good prognosis overall compared with other subtypes of AML, relapse risk after induction chemotherapy remains high. Optimizing treatment planning to promote recurrence free survival and increase the likelihood of survival after relapse is imperative to improving outcomes. Recent areas of research have included evaluation of the role of gemtuzumab in induction and consolidation, the relative benefit of increased cycles of high dose cytarabine in consolidation, the utility of hypomethylating agents and kinase inhibitors, and the most appropriate timing of stem cell transplant. Surveillance with measurable residual disease testing is increasingly being utilized for monitoring disease in remission, and ongoing investigation seeks to determine how to use this tool for early identification of patients who would benefit from proceeding to transplant. In this review, we outline the current therapeutic approach from diagnosis to relapse while highlighting the active areas of investigation in each stage of treatment.
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Affiliation(s)
- Christina Darwish
- Tisch Cancer Institute, Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, Box 1079, New York, NY 10029, USA
| | - Kyle Farina
- Department of Pharmacy Practice, The Mount Sinai Hospital, New York, NY 10029, USA
| | - Douglas Tremblay
- Tisch Cancer Institute, Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, Box 1079, New York, NY 10029, USA.
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27
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Feng Q, Krick K, Chu J, Burge CB. Splicing quality control mediated by DHX15 and its G-patch activator SUGP1. Cell Rep 2023; 42:113223. [PMID: 37805921 PMCID: PMC10842378 DOI: 10.1016/j.celrep.2023.113223] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/27/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
Pre-mRNA splicing is surveilled at different stages by quality control (QC) mechanisms. The leukemia-associated DExH-box family helicase hDHX15/scPrp43 is known to disassemble spliceosomes after splicing. Here, using rapid protein depletion and analysis of nascent and mature RNA to enrich for direct effects, we identify a widespread splicing QC function for DHX15 in human cells, consistent with recent in vitro studies. We find that suboptimal introns with weak splice sites, multiple branch points, and cryptic introns are repressed by DHX15, suggesting a general role in promoting splicing fidelity. We identify SUGP1 as a G-patch factor that activates DHX15's splicing QC function. This interaction is dependent on both DHX15's ATPase activity and on SUGP1's U2AF ligand motif (ULM) domain. Together, our results support a model in which DHX15 plays a major role in splicing QC when recruited and activated by SUGP1.
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Affiliation(s)
- Qing Feng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA.
| | - Keegan Krick
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Jennifer Chu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA.
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28
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Zhang K, Zhang X, Xu Y, Xue S, Qiu H, Tang X, Han Y, Chen S, Sun A, Zhang Y, Wu D, Wang Y. Efficacy of venetoclax combined with hypomethylating agents in young, and unfit patients with newly diagnosed core binding factor acute myeloid leukemia. Blood Cancer J 2023; 13:155. [PMID: 37821435 PMCID: PMC10567686 DOI: 10.1038/s41408-023-00928-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/09/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Affiliation(s)
- Keyuan Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiang Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yang Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Shengli Xue
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Huiying Qiu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Xiaowen Tang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Yue Han
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Aining Sun
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Yanming Zhang
- Department of Hematology, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, No 62, Huaihai Road (S.), Huai'an, China.
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China.
| | - Ying Wang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China.
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29
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DeWolf S, Tallman MS, Rowe JM, Salman MY. What Influences the Decision to Proceed to Transplant for Patients With AML in First Remission? J Clin Oncol 2023; 41:4693-4703. [PMID: 37611216 PMCID: PMC10564290 DOI: 10.1200/jco.22.02868] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/12/2023] [Accepted: 06/14/2023] [Indexed: 08/25/2023] Open
Abstract
Although allogeneic hematopoietic cell transplantation (allo-HCT) remains the backbone of curative treatment for the majority of fit adults diagnosed with AML, there is indeed a subset of patients for whom long-term remission may be achieved without transplantation. Remarkable changes in our knowledge of AML biology in recent years has transformed the landscape of diagnosis, management, and treatment of AML. Specifically, markedly increased understanding of molecular characteristics of AML, the expanded application of minimal/measurable residual diseases testing, and an increased armamentarium of leukemia-directed therapeutic agents have created a new paradigm for the medical care of patients with AML. An attempt is herein made to decipher the decision to proceed to transplant for patients with AML in first complete remission on the basis of the current best available evidence. The focus is on factors affecting the biology and treatment of AML itself, rather than on variables related to allo-HCT, an area characterized by significant advancements that have reduced overall therapy-related complications. This review seeks to focus on areas of particular complexity, while simultaneously providing clarity on how our current knowledge and treatment strategies may, or may not, influence the decision to pursue allo-HCT in patients with AML.
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Affiliation(s)
- Susan DeWolf
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin S. Tallman
- Division of Hematology and Oncology Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Jacob M. Rowe
- Rambam Health Care Campus and Technion, Israel Institute of Technology, Haifa, Israel
- Department of Hematology, Shaare Zedek Medical Center, Jerusalem, Israel
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30
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Bidet A, Quessada J, Cuccuini W, Decamp M, Lafage-Pochitaloff M, Luquet I, Lefebvre C, Tueur G. Cytogenetics in the management of acute myeloid leukemia and histiocytic/dendritic cell neoplasms: Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103421. [PMID: 38016419 DOI: 10.1016/j.retram.2023.103421] [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: 07/04/2023] [Revised: 09/29/2023] [Accepted: 10/15/2023] [Indexed: 11/30/2023]
Abstract
Genetic data are becoming increasingly essential in the management of hematological neoplasms as shown by two classifications published in 2022: the 5th edition of the World Health Organization Classification of Hematolymphoid Tumours and the International Consensus Classification of Myeloid Neoplasms and Acute Leukemias. Genetic data are particularly important for acute myeloid leukemias (AMLs) because their boundaries with myelodysplastic neoplasms seem to be gradually blurring. The first objective of this review is to present the latest updates on the most common cytogenetic abnormalities in AMLs while highlighting the pitfalls and difficulties that can be encountered in the event of cryptic or difficult-to-detect karyotype abnormalities. The second objective is to enhance the role of cytogenetics among all the new technologies available in 2023 for the diagnosis and management of AML.
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Affiliation(s)
- Audrey Bidet
- Laboratoire d'Hématologie Biologique, CHU Bordeaux, Avenue Magellan, Bordeaux, Pessac F-33600, France.
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, Hôpital des enfants de la Timone, Assistance Publique-Hôpitaux de Marseille (APHM), Faculté de Médecine, Aix Marseille Université, Marseille 13005, France; CNRS, INSERM, CIML, Aix Marseille Université, Marseille 13009, France
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | | | - Marina Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Hôpital des enfants de la Timone, Assistance Publique-Hôpitaux de Marseille (APHM), Faculté de Médecine, Aix Marseille Université, Marseille 13005, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, CHU Toulouse, Site IUCT-O, Toulouse, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble, France
| | - Giulia Tueur
- Laboratoire d'Hématologie, CHU Avicenne, APHP, Bobigny, France
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31
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Duan W, Yang S, Zhao T, Hu L, Qin Y, Jia J, Wang J, Lu S, Jiang H, Zhang X, Xu L, Wang Y, Lai Y, Shi H, Huang X, Jiang Q. Comparison of efficacy between homoharringtonine, aclarubicin, cytarabine (HAA) and idarubicin, cytarabine (IA) regimens as induction therapy in patients with de novo core binding factor acute myeloid leukemia. Ann Hematol 2023; 102:2695-2705. [PMID: 37572135 DOI: 10.1007/s00277-023-05400-5] [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: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
To compare efficacy between homoharringtonine combined with cytarabine and aclarubicin (HAA) and idarubicin and cytarabine (IA) regimens as first induction chemotherapy in patients with core binding factor acute myeloid leukemia (CBF-AML). Cox regression model and propensity score matching (PSM) were used to identify the regimen associated with a better remission rate and outcomes. In total, 374 patients with CBF-AML (243 with RUNX1::RUXN1T1 and 131 with CBFB::MYH11) were included in this study. The patients received the HAA or IA regimen (187 each) as the first induction therapy. For patients with RUNX1::RUXN1T1, multivariate analyses showed that the HAA regimen was significantly associated with a higher CR/CRi rate after the first induction (hazard ratio [HR] = 5.3 [95% CI 2.3, 12.2]; p < 0.001) and more favorable relapse-free survival (RFS) (HR = 0.5 [0.3, 0.8], p = 0.01). In PSM analysis, the HAA regimen also had a higher CR/CRi rate (96% vs. 77%, p < 0.001), especially for those harboring wild-type KIT (KITWT) (96% vs. 83%, p = 0.02) or non-D816 KIT mutation (100% vs. 63%, p = 0.002), as well as more favorable RFS (p = 0.01), compared with the IA regimen. However, there was no difference in the remission rate or outcomes between the two regimens for patients with CBFB::MYH11. The HAA regimen as first induction chemotherapy resulted in a higher CR/CRi rate in AML patients with RUNX1::RUNX1T1, especially those harboring KITWT and non-D816 KIT mutation, and a more favorable RFS compared with the IA regimen. The efficacy between the two regimens did not differ in those with CBFB::MYH11.
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Affiliation(s)
- Wenbing Duan
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Sen Yang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Ting Zhao
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Lijuan Hu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Yazhen Qin
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Jinsong Jia
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Jing Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Shengye Lu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Hao Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Xiaohui Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Lanping Xu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Yu Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Yueyun Lai
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Hongxia Shi
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
| | - Xiaojun Huang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies, Chinese Academy of Medical Sciences, Beijing, China
| | - Qian Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, People's Republic of China.
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
- Peking University People's Hospital, Qingdao, China.
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Iaquinta G, Scalzulli E, Angeloni S, Carmosino I, Costa A, Ielo C, Passucci M, Masucci C, Martelli M, Grammatico P, Breccia M. CCND2 mutations in atypical chronic myeloid leukemia: a report of two cases. Leuk Lymphoma 2023; 64:1730-1732. [PMID: 37435984 DOI: 10.1080/10428194.2023.2232495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 06/25/2023] [Indexed: 07/13/2023]
Abstract
Atypical chronic myeloid leukemia (aCML) is a rare MDS/MPN disease characterized by the absence of BCR::ABL1 rearrangement and well known typical mutations associated with myeloproliferative disorders. Mutational landscape associated with this disease was recently described with frequent involvement of SETBP1 and ETNK1 mutations. CCND2 mutations have not been frequently detected in MPN or MDS/MPN patients. We describe two cases of aCML with two CCND2 mutations in 280 and 281 codons which rapidly develop progressive characteristics, and we reviewed the literature about this unfavorable association, suggesting a role as a new possible marker of aggressive disease.
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Affiliation(s)
- Giovanni Iaquinta
- U.O.C. Medical Genetics Laboratory, Department of Experimental Medicine, San Camillo-Forlanini Hospital - Sapienza University, Rome, Italy
| | - Emilia Scalzulli
- Department of Translational and Precision Medicine, Az. Policlinico Umberto I-Sapienza University, Rome, Italy
| | - Silvia Angeloni
- U.O.C. Medical Genetics Laboratory, Department of Experimental Medicine, San Camillo-Forlanini Hospital - Sapienza University, Rome, Italy
| | - Ida Carmosino
- Department of Translational and Precision Medicine, Az. Policlinico Umberto I-Sapienza University, Rome, Italy
| | - Alessandro Costa
- Department of Translational and Precision Medicine, Az. Policlinico Umberto I-Sapienza University, Rome, Italy
| | - Claudia Ielo
- Department of Translational and Precision Medicine, Az. Policlinico Umberto I-Sapienza University, Rome, Italy
| | - Mauro Passucci
- Department of Translational and Precision Medicine, Az. Policlinico Umberto I-Sapienza University, Rome, Italy
| | - Chiara Masucci
- Department of Translational and Precision Medicine, Az. Policlinico Umberto I-Sapienza University, Rome, Italy
| | - Maurizio Martelli
- Department of Translational and Precision Medicine, Az. Policlinico Umberto I-Sapienza University, Rome, Italy
| | - Paola Grammatico
- U.O.C. Medical Genetics Laboratory, Department of Experimental Medicine, San Camillo-Forlanini Hospital - Sapienza University, Rome, Italy
| | - Massimo Breccia
- Department of Translational and Precision Medicine, Az. Policlinico Umberto I-Sapienza University, Rome, Italy
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33
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Klco J, Thomas M, Qi W, Walsh M, Ma J, Westover T, Abdelhamed S, Ezzell L, Rolle C, Xiong E, Rosikiewicz W, Xu B, Pruett-Miller S, Loughran A, Janke L. Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia. RESEARCH SQUARE 2023:rs.3.rs-3315059. [PMID: 37790524 PMCID: PMC10543392 DOI: 10.21203/rs.3.rs-3315059/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
MGA (Max-gene associated) is a dual-specificity transcription factor that negatively regulates MYC-target genes to inhibit proliferation and promote differentiation. Loss-of-function mutations in MGA have been commonly identified in several hematological neoplasms, including acute myeloid leukemia (AML) with RUNX1::RUNX1T1, however, very little is known about the impact of these MGA alterations on normal hematopoiesis or disease progression. We show that representative MGA mutations identified in patient samples abolish protein-protein interactions and transcriptional activity. Using a series of human and mouse model systems, including a newly developed conditional knock-out mouse strain, we demonstrate that loss of MGA results in upregulation of MYC and E2F targets, cell cycle genes, mTOR signaling, and oxidative phosphorylation in normal hematopoietic cells, leading to enhanced proliferation. The loss of MGA induces an open chromatin state at promotors of genes involved in cell cycle and proliferation. RUNX1::RUNX1T1 expression in Mga-deficient murine hematopoietic cells leads to a more aggressive AML with a significantly shortened latency. These data show that MGA regulates multiple pro-proliferative pathways in hematopoietic cells and cooperates with the RUNX1::RUNX1 T1 fusion oncoprotein to enhance leukemogenesis.
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Affiliation(s)
| | | | | | | | - Jing Ma
- St. Jude Children's Research Hospital
| | | | | | | | | | | | | | - Beisi Xu
- St Jude Children's Research Hospital
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34
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Cooper TM, Alonzo TA, Tasian SK, Kutny MA, Hitzler J, Pollard JA, Aplenc R, Meshinchi S, Kolb EA. Children's Oncology Group's 2023 blueprint for research: Myeloid neoplasms. Pediatr Blood Cancer 2023; 70 Suppl 6:e30584. [PMID: 37480164 PMCID: PMC10614720 DOI: 10.1002/pbc.30584] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023]
Abstract
During the past decade, the outcomes of pediatric patients with acute myeloid leukemia (AML) have plateaued with 5-year event-free survival (EFS) and overall survival (OS) of approximately 46 and 64%, respectively. Outcomes are particularly poor for those children with high-risk disease, who have 5-year OS of 46%. Substantial survival improvements have been observed for a subset of patients treated with targeted therapies. Specifically, children with KMT2A-rearranged AML and/or FLT3 internal tandem duplication (FLT3-ITD) mutations benefitted from the addition of gemtuzumab ozogamicin, an anti-CD33 antibody-drug conjugate, in the AAML0531 clinical trial (NCT00372593). Sorafenib also improved response and survival in children with FLT3-ITD AML in the AAML1031 clinical trial (NCT01371981). Advances in characterization of prognostic cytomolecular events have helped to identify patients at highest risk of relapse and facilitated allocation to consolidative hematopoietic stem cell transplant (HSCT) in first remission. Some patients clearly have improved survival with HSCT, although the benefit is largely unknown for most patients. Finally, data-driven refinements in supportive care recommendations continue to evolve with meaningful and measurable reductions in toxicity and improvements in EFS and OS. As advances in application of targeted therapies, risk stratification, and improved supportive care measures are incorporated into current trials and become standard-of-care, there is every expectation that we will see improved survival with a reduction in toxic morbidity and mortality. The research agenda of the Children's Oncology Group's Myeloid Diseases Committee continues to build upon experience and outcomes with an overarching goal of curing more children with AML.
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Affiliation(s)
- Todd M Cooper
- Seattle Children’s Hospital Cancer and Blood Disorders Service, University of Washington School of Medicine; Seattle, Washington
| | | | - Sarah K Tasian
- Children’s Hospital of Philadelphia Division of Oncology and Center for Childhood Cancer Research and University of Pennsylvania School of Medicine; Philadelphia, Pennsylvania
| | - Matthew A Kutny
- University of Alabama at Birmingham, Department of Pediatrics, Division of Hematology/Oncology, Birmingham, Alabama
| | - Johann Hitzler
- Division of Hematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, ON, Canada; Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Jessica A Pollard
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children’s Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Richard Aplenc
- Children’s Hospital of Philadelphia Division of Oncology and Center for Childhood Cancer Research and University of Pennsylvania School of Medicine; Philadelphia, Pennsylvania
| | - Soheil Meshinchi
- Seattle Children’s Hospital Cancer and Blood Disorders Service, University of Washington School of Medicine; Seattle, Washington
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - E Anders Kolb
- Nemours Center for Cancer and Blood Disorders, Nemours Children’s Health, Wilmington, DE
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35
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Neldeborg S, Soerensen JF, Møller CT, Bill M, Gao Z, Bak RO, Holm K, Sorensen B, Nyegaard M, Luo Y, Hokland P, Stougaard M, Ludvigsen M, Holm CK. Dual intron-targeted CRISPR-Cas9-mediated disruption of the AML RUNX1-RUNX1T1 fusion gene effectively inhibits proliferation and decreases tumor volume in vitro and in vivo. Leukemia 2023; 37:1792-1801. [PMID: 37464068 PMCID: PMC10457201 DOI: 10.1038/s41375-023-01950-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/18/2023] [Accepted: 06/19/2023] [Indexed: 07/20/2023]
Abstract
Oncogenic fusion drivers are common in hematological cancers and are thus relevant targets of future CRISPR-Cas9-based treatment strategies. However, breakpoint-location variation in patients pose a challenge to traditional breakpoint-targeting CRISPR-Cas9-mediated disruption strategies. Here we present a new dual intron-targeting CRISPR-Cas9 treatment strategy, for targeting t(8;21) found in 5-10% of de novo acute myeloid leukemia (AML), which efficiently disrupts fusion genes without prior identification of breakpoint location. We show in vitro growth rate and proliferation reduction by 69 and 94% in AML t(8;21) Kasumi-1 cells, following dual intron-targeted disruption of RUNX1-RUNX1T1 compared to a non t(8;21) AML control. Furthermore, mice injected with RUNX1-RUNX1T1-disrupted Kasumi-1 cells had in vivo tumor growth reduction by 69 and 91% compared to controls. Demonstrating the feasibility of RUNX1-RUNX1T1 disruption, these findings were substantiated in isolated primary cells from a patient diagnosed with AML t(8;21). In conclusion, we demonstrate proof-of-principle of a dual intron-targeting CRISPR-Cas9 treatment strategy in AML t(8;21) without need for precise knowledge of the breakpoint location.
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Affiliation(s)
- Signe Neldeborg
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Johannes Frasez Soerensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Marie Bill
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Zongliang Gao
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Kasper Holm
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Boe Sorensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Hokland
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Danish Life Science Cluster, Copenhagen, Denmark
| | - Maja Ludvigsen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark.
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36
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Rosli AA, Azlan A, Rajasegaran Y, Mot YY, Heidenreich O, Yusoff NM, Moses EJ. Cytogenetics analysis as the central point of genetic testing in acute myeloid leukemia (AML): a laboratory perspective for clinical applications. Clin Exp Med 2023; 23:1137-1159. [PMID: 36229751 DOI: 10.1007/s10238-022-00913-1] [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: 09/06/2022] [Accepted: 10/02/2022] [Indexed: 11/27/2022]
Abstract
Chromosomal abnormalities in acute myeloid leukemia (AML) have significantly contributed to scientific understanding of its molecular pathogenesis, which has aided in the development of therapeutic strategies and enhanced management of AML patients. The diagnosis, prognosis and treatment of AML have also rapidly transformed in recent years, improving initial response to treatment, remission rates, risk stratification and overall survival. Hundreds of rare chromosomal abnormalities in AML have been discovered thus far using chromosomal analysis and next-generation sequencing. As a result, the World Health Organization (WHO) has categorized AML into subgroups based on genetic, genomic and molecular characteristics, to complement the existing French-American classification which is solely based on morphology. In this review, we aim to highlight the most clinically relevant chromosomal aberrations in AML together with the technologies employed to detect these aberrations in laboratory settings.
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Affiliation(s)
- Aliaa Arina Rosli
- Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Adam Azlan
- Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Yaashini Rajasegaran
- Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Yee Yik Mot
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Olaf Heidenreich
- Prinses Máxima Centrum Voor Kinderoncologie, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Narazah Mohd Yusoff
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Emmanuel Jairaj Moses
- Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia.
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37
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Saleban M, Harris EL, Poulter JA. D-Type Cyclins in Development and Disease. Genes (Basel) 2023; 14:1445. [PMID: 37510349 PMCID: PMC10378862 DOI: 10.3390/genes14071445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
D-type cyclins encode G1/S cell cycle checkpoint proteins, which play a crucial role in defining cell cycle exit and progression. Precise control of cell cycle exit is vital during embryonic development, with defects in the pathways regulating intracellular D-type cyclins resulting in abnormal initiation of stem cell differentiation in a variety of different organ systems. Furthermore, stabilisation of D-type cyclins is observed in a wide range of disorders characterized by cellular over-proliferation, including cancers and overgrowth disorders. In this review, we will summarize and compare the roles played by each D-type cyclin during development and provide examples of how their intracellular dysregulation can be an underlying cause of disease.
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Affiliation(s)
- Mostafa Saleban
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
| | - Erica L Harris
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
| | - James A Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds LS2 9JT, UK
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38
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Liu Y, Klein J, Bajpai R, Dong L, Tran Q, Kolekar P, Smith JL, Ries RE, Huang BJ, Wang YC, Alonzo TA, Tian L, Mulder HL, Shaw TI, Ma J, Walsh MP, Song G, Westover T, Autry RJ, Gout AM, Wheeler DA, Wan S, Wu G, Yang JJ, Evans WE, Loh M, Easton J, Zhang J, Klco JM, Meshinchi S, Brown PA, Pruett-Miller SM, Ma X. Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication. Nat Commun 2023; 14:1739. [PMID: 37019972 PMCID: PMC10076316 DOI: 10.1038/s41467-023-37438-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 03/16/2023] [Indexed: 04/07/2023] Open
Abstract
Oncogenic fusions formed through chromosomal rearrangements are hallmarks of childhood cancer that define cancer subtype, predict outcome, persist through treatment, and can be ideal therapeutic targets. However, mechanistic understanding of the etiology of oncogenic fusions remains elusive. Here we report a comprehensive detection of 272 oncogenic fusion gene pairs by using tumor transcriptome sequencing data from 5190 childhood cancer patients. We identify diverse factors, including translation frame, protein domain, splicing, and gene length, that shape the formation of oncogenic fusions. Our mathematical modeling reveals a strong link between differential selection pressure and clinical outcome in CBFB-MYH11. We discover 4 oncogenic fusions, including RUNX1-RUNX1T1, TCF3-PBX1, CBFA2T3-GLIS2, and KMT2A-AFDN, with promoter-hijacking-like features that may offer alternative strategies for therapeutic targeting. We uncover extensive alternative splicing in oncogenic fusions including KMT2A-MLLT3, KMT2A-MLLT10, C11orf95-RELA, NUP98-NSD1, KMT2A-AFDN and ETV6-RUNX1. We discover neo splice sites in 18 oncogenic fusion gene pairs and demonstrate that such splice sites confer therapeutic vulnerability for etiology-based genome editing. Our study reveals general principles on the etiology of oncogenic fusions in childhood cancer and suggests profound clinical implications including etiology-based risk stratification and genome-editing-based therapeutics.
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Affiliation(s)
- Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathon Klein
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richa Bajpai
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Li Dong
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Quang Tran
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jenny L Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Benjamin J Huang
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Todd A Alonzo
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather L Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Timothy I Shaw
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Autry
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David A Wheeler
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon Loh
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute and the Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | | | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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39
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Familial 4p Interstitial Deletion Provides New Insights and Candidate Genes Underlying This Rare Condition. Genes (Basel) 2023; 14:genes14030635. [PMID: 36980907 PMCID: PMC10048360 DOI: 10.3390/genes14030635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Chromosome 4p deletions can lead to two distinct phenotypic outcomes: Wolf-–Hirschhorn syndrome (a terminal deletion at 4p16.3) and less frequently reported proximal interstitial deletions (4p11-p16). Proximal 4p interstitial deletions can result in mild to moderate intellectual disability, facial dysmorphisms, and a tall thin body habitus. To date, only 35 cases of proximal 4p interstitial deletions have been reported, and only two of these cases have been familial. The critical region for this syndrome has been narrowed down to 4p15.33-15.2, but the underlying causative genes remain unclear. In this study, we report the case of a 3-year-old female with failure to thrive, developmental and motor delays, and morphological features. The mother also had a 4p15.2-p14 deletion, and the proband was found to have a 13.4-Mb 4p15.2-p14 deletion by chromosome microarray analysis. The deleted region encompasses 16 genes, five of which have a high likelihood of contributing to the phenotype: PPARGC1A, DHX15, RBPJ, STIM2, and PCDH7. These findings suggest that multiple genes are involved in this rare proximal 4p interstitial deletion syndrome. This case highlights the need for healthcare providers to be aware of proximal 4p interstitial deletions and the potential phenotypic manifestations.
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40
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Ryland GL, Umeda M, Holmfeldt L, Lehmann S, Herlin MK, Ma J, Khanlari M, Rubnitz JE, Ries RE, Kosasih HJ, Ekert PG, Goh HN, Tiong IS, Grimmond SM, Haferlach C, Day RB, Ley TJ, Meshinchi S, Ma X, Blombery P, Klco JM. Description of a novel subtype of acute myeloid leukemia defined by recurrent CBFB insertions. Blood 2023; 141:800-805. [PMID: 36179268 PMCID: PMC10273080 DOI: 10.1182/blood.2022017874] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/29/2022] [Accepted: 09/16/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Georgina L. Ryland
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Linda Holmfeldt
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- The Beijer Laboratory, Uppsala, Sweden
| | - Sören Lehmann
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Morten Krogh Herlin
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Mahsa Khanlari
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Jeffrey E. Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Paul G. Ekert
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC, Australia
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Hwee Ngee Goh
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Ing S. Tiong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sean M. Grimmond
- Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | | | - Ryan B. Day
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Timothy J. Ley
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
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41
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Shiba N. Comprehensive molecular understanding of pediatric acute myeloid leukemia. Int J Hematol 2023; 117:173-181. [PMID: 36653696 DOI: 10.1007/s12185-023-03533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
Pediatric acute myeloid leukemia (AML) is a heterogeneous disease with various genetic abnormalities. Recent advances in genetic analysis have enabled the identification of causative genes in > 90% of pediatric AML cases. Fusion genes such as RUNX1::RUNX1T1, CBFB::MYH11, and KMT2A::MLLT3 are frequently detected in > 70% of pediatric AML cases, whereas FLT3-internal tandem duplication, CEBPA-bZip, and NPM1 mutations are detected in approximately 5-15% of cases, respectively. Conversely, mutations in DNMT3A, TET2, and IDH, which are common in adults, are extremely rare in pediatric AML. The genetic characteristics of pediatric AML are slightly different from those of adult AML. For accurate risk stratification and treatment intensity, genome analysis should be performed in a simple, fast, and inexpensive manner and the results should be returned to patients in real time. As with acute lymphoblastic leukemia, the presence or absence of minimal residual disease is an important factor in determining the success of treatment against AML, and it is important to predict prognosis and formulate treatment strategies considering the genetic abnormalities. For the development and clinical application of new molecularly targeted therapies based on identified genetic abnormalities, it is necessary to explore when and in which combinations drugs will be most effective.
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Affiliation(s)
- Norio Shiba
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, 3-9, Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan.
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George B, Yohannan B, Mohlere V, Gonzalez A. Therapy-related core binding factor acute myeloid leukemia. Int J Hematol Oncol 2023; 12:IJH43. [PMID: 36874378 PMCID: PMC9979104 DOI: 10.2217/ijh-2022-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Therapy-related acute myeloid leukemia (t-AML) usually stems from exposure of the bone marrow to cytotoxic chemotherapy and/or radiation therapy. t-AML is usually associated with poor overall survival, but occasionally t-AML can involve favorable-risk cytogenetics, including core binding factor AML (CBF-AML), which shows a recurrent chromosomal rearrangement with t(8;21) (q22;22) and 'inv(16) (p13.1;q22)/t(16;16)(p13.1;q22)', leading to 'RUNX1::RUNX1T1 and CBFB::MYH11' fusion genes, respectively. Therapy-related CBF-AML (t-CBF-AML) accounts for 5-15% of CBF-AML cases and tends to have better outcomes than t-AML with unfavorable cytogenetics. Although CBF-AML is sensitive to high-dose cytarabine, t-CBF-AML has worse overall survival than de novo CBF- AML. The objective of this review is to discuss the available data on the pathogenesis, mutations, and therapeutic options in patients with t-CBF-AML.
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Affiliation(s)
- Binsah George
- Department of Hematology/Oncology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, 6410 Fannin, Suite 830 Houston, TX 77030, USA
| | - Binoy Yohannan
- Department of Hematology/Oncology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, 6410 Fannin, Suite 830 Houston, TX 77030, USA
| | - Virginia Mohlere
- Department of Hematology/Oncology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, 6410 Fannin, Suite 830 Houston, TX 77030, USA
| | - Anneliese Gonzalez
- Department of Hematology/Oncology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, 6410 Fannin, Suite 830 Houston, TX 77030, USA
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Stelmach P, Trumpp A. Leukemic stem cells and therapy resistance in acute myeloid leukemia. Haematologica 2023; 108:353-366. [PMID: 36722405 PMCID: PMC9890038 DOI: 10.3324/haematol.2022.280800] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Indexed: 02/02/2023] Open
Abstract
A major obstacle in the treatment of acute myeloid leukemia (AML) is refractory disease or relapse after achieving remission. The latter arises from a few therapy-resistant cells within minimal residual disease (MRD). Resistant cells with long-term self-renewal capacity that drive clonal outgrowth are referred to as leukemic stem cells (LSC). The cancer stem cell concept considers LSC as relapse-initiating cells residing at the top of each genetically defined AML subclone forming epigenetically controlled downstream hierarchies. LSC display significant phenotypic and epigenetic plasticity, particularly in response to therapy stress, which results in various mechanisms mediating treatment resistance. Given the inherent chemotherapy resistance of LSC, targeted strategies must be incorporated into first-line regimens to prevent LSC-mediated AML relapse. The combination of venetoclax and azacitidine is a promising current strategy for the treatment of AML LSC. Nevertheless, the selection of patients who would benefit either from standard chemotherapy or venetoclax + azacitidine treatment in first-line therapy has yet to be established and the mechanisms of resistance still need to be discovered and overcome. Clinical trials are currently underway that investigate LSC susceptibility to first-line therapies. The era of single-cell multi-omics has begun to uncover the complex clonal and cellular architectures and associated biological networks. This should lead to a better understanding of the highly heterogeneous AML at the inter- and intra-patient level and identify resistance mechanisms by longitudinal analysis of patients' samples. This review discusses LSC biology and associated resistance mechanisms, potential therapeutic LSC vulnerabilities and current clinical trial activities.
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Affiliation(s)
- Patrick Stelmach
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM, gGmbH),Department of Medicine V, Heidelberg University Hospital
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM, gGmbH); Faculty of Biosciences, Heidelberg University; German Cancer Consortium (DKTK), Heidelberg.
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Ren R, Horton JR, Chen Q, Yang J, Liu B, Huang Y, Blumenthal RM, Zhang X, Cheng X. Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia. J Biol Chem 2023; 299:102885. [PMID: 36626981 PMCID: PMC9932118 DOI: 10.1016/j.jbc.2023.102885] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Abstract
ZBTB7A belongs to a small family of transcription factors having three members in humans (7A, 7B, and 7C). They share a BTB/POZ protein interaction domain at the amino end and a zinc-finger DNA-binding domain at the carboxyl end. They control the transcription of a wide range of genes, having varied functions in hematopoiesis, oncogenesis, and metabolism (in particular glycolysis). ZBTB7A-binding profiles at gene promoters contain a consensus G(a/c)CCC motif, followed by a CCCC sequence in some instances. Structural and mutational investigations suggest that DNA-specific contacts with the four-finger tandem array of ZBTB7A are formed sequentially, initiated from ZF1-ZF2 binding to G(a/c)CCC before spreading to ZF3-ZF4, which bind the DNA backbone and the 3' CCCC sequence, respectively. Here, we studied some mutations found in t(8;21)-positive acute myeloid leukemia patients that occur within the ZBTB7A DNA-binding domain. We determined that these mutations generally impair ZBTB7A DNA binding, with the most severe disruptions resulting from mutations in ZF1 and ZF2, and the least from a frameshift mutation in ZF3 that results in partial mislocalization. Information provided here on ZBTB7A-DNA interactions is likely applicable to ZBTB7B/C, which have overlapping functions with ZBTB7A in controlling primary metabolism.
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Affiliation(s)
- Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Qin Chen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, Texas, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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Mao X, Yin R, Liu L, Zhou Y, Yang C, Fang C, Jiang H, Guo Q, Tian X. Clinical impact of c-KIT and CEBPA mutations in 33 patients with corebinding factor (Non-M3) acute myeloid leukemia. Pediatr Neonatol 2023:S1875-9572(23)00019-0. [PMID: 36809862 DOI: 10.1016/j.pedneo.2022.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/11/2022] [Accepted: 05/15/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Corebinding factor acute myeloid leukemia (CBF-AML) is the most common cytogenetic subtype of pediatric AML. CBF-AML is associated with a relatively favorable outcome, although the relapse rate of approximately 40% indicates a high degree of clinical heterogeneity. The clinical impact of additional cytogenetic aberrations, including c-KIT and CEBPA mutations, in pediatric CBF-AML has not been well characterized, especially in the multi-ethnic region of Yunnan Province in China. METHODS In this study, we retrospectively analyzed the clinical features, gene mutations, and prognoses of 72 pediatric patients newly diagnosed with non-M3 AML in Kunming Children's Hospital, China, from January 1, 2015 to May 31, 2020. RESULTS Of the 72 pediatric patients with AML, 46% (33/72) had CBF-AML. Thirteen patients with CBF-AML (39%) had c-KIT mutations, five (15%) had CEBPA mutations, and eleven (33.3%) had no other cytogenetic aberrations. The c-KIT mutations, resulting from single nucleotide substitutions and small insertions or deletions, occurred in exons 8 and 17. All of the CBF-AML-associated CEBPA mutations were single mutations and occurred in patients with RUNX1-RUNX1T1 fusion. We found no significant differences in the clinical data between CBF-AML patients with c-KIT or CEBPA mutations and CBF-AML patients without other aberrations, and no prognostic significance was established for these mutations. CONCLUSION Our study is the first to report the clinical impact of c-KIT and CEBPA mutations in pediatric patients with non-M3 CBF-AML from the multi-ethnic Yunnan Province, China. c-KIT and CEBPA mutations occurred at a higher frequency in CBF-AML cases and were associated with unique clinical characteristics; however, no potential molecular prognostic markers were identified.
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Affiliation(s)
- Xiaoyan Mao
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan 646000, China; Kunming Medical University, Kunming City, Yunnan province, China
| | - Runxiu Yin
- Department of Hematology, Kunming Children's Hospital (The Affiliated Children's Hospital of Kunming Medical University, Yunnan Key Laboratory of Children's Major Disease Research), Kunming Medical University, Kunming City, Yunnan province, China
| | - Li Liu
- Kunming Medical University, Kunming City, Yunnan province, China
| | - Yan Zhou
- Department of Hematology, Kunming Children's Hospital (The Affiliated Children's Hospital of Kunming Medical University, Yunnan Key Laboratory of Children's Major Disease Research), Kunming Medical University, Kunming City, Yunnan province, China
| | - Chunhui Yang
- Department of Hematology, Kunming Children's Hospital (The Affiliated Children's Hospital of Kunming Medical University, Yunnan Key Laboratory of Children's Major Disease Research), Kunming Medical University, Kunming City, Yunnan province, China
| | - Chunlian Fang
- Department of Hematology, Kunming Children's Hospital (The Affiliated Children's Hospital of Kunming Medical University, Yunnan Key Laboratory of Children's Major Disease Research), Kunming Medical University, Kunming City, Yunnan province, China
| | - Hongchao Jiang
- Department of Hematology, Kunming Children's Hospital (The Affiliated Children's Hospital of Kunming Medical University, Yunnan Key Laboratory of Children's Major Disease Research), Kunming Medical University, Kunming City, Yunnan province, China
| | - Qulian Guo
- Department of Pediatrics, Children Hematological Oncology and Birth Defects Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan 646000, China
| | - Xin Tian
- Department of Hematology, Kunming Children's Hospital (The Affiliated Children's Hospital of Kunming Medical University, Yunnan Key Laboratory of Children's Major Disease Research), Kunming Medical University, Kunming City, Yunnan province, China.
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DHX15 is involved in SUGP1-mediated RNA missplicing by mutant SF3B1 in cancer. Proc Natl Acad Sci U S A 2022; 119:e2216712119. [PMID: 36459648 PMCID: PMC9894173 DOI: 10.1073/pnas.2216712119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
SF3B1 is the most frequently mutated spliceosomal gene in cancer. Several hotspot mutations are known to disrupt the interaction of SF3B1 with another splicing factor, SUGP1, resulting in the RNA missplicing that characterizes mutant SF3B1 cancers. Properties of SUGP1, especially the presence of a G-patch motif, a structure known to function by activating DEAH-box RNA helicases, suggest the requirement of such an enzyme in SUGP1 function in splicing. However, the identity of this putative helicase has remained an important unanswered question. Here, using a variety of protein-protein interaction assays, we identify DHX15 as the critical helicase. We further show that depletion of DHX15 or expression of any of several DHX15 mutants, including one implicated in acute myeloid leukemia, partially recapitulates the splicing defects of mutant SF3B1. Moreover, a DHX15-SUGP1 G-patch fusion protein is able to incorporate into the spliceosome to rescue the splicing defects of mutant SF3B1. We also present the crystal structure of the human DHX15-SUGP1 G-patch complex, which reveals the molecular basis of their direct interaction. Our data thus demonstrate that DHX15 is the RNA helicase that functions with SUGP1 and additionally provide important insight into how mutant SF3B1 disrupts splicing in cancer.
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Gabra MM, Chow JTS, Kim T, Son MH, Arruda A, Woolley JF, Zhang Z, Minden MD, Salmena L. A 5-microRNA signature derived from core binding factor-AML is predictive in adult and childhood AML. Leuk Res 2022; 123:106968. [DOI: 10.1016/j.leukres.2022.106968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
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Zhang YF, Wang XL, Xu CH, Liu N, Zhang L, Zhang YM, Xie YY, Zhang YL, Huang QH, Wang L, Chen Z, Chen SJ, Roeder RG, Shen S, Xue K, Sun XJ. A direct comparison between AML1-ETO and ETO2-GLIS2 leukemia fusion proteins reveals context-dependent binding and regulation of target genes and opposite functions in cell differentiation. Front Cell Dev Biol 2022; 10:992714. [PMID: 36158200 PMCID: PMC9490184 DOI: 10.3389/fcell.2022.992714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
The ETO-family transcriptional corepressors, including ETO, ETO2, and MTGR1, are all involved in leukemia-causing chromosomal translocations. In every case, an ETO-family corepressor acquires a DNA-binding domain (DBD) to form a typical transcription factor—the DBD binds to DNA, while the ETO moiety manifests transcriptional activity. A directly comparative study of these “homologous” fusion transcription factors may clarify their similarities and differences in regulating transcription and leukemogenesis. Here, we performed a side-by-side comparison between AML1-ETO and ETO2-GLIS2, the most common fusion proteins in M2-and M7-subtypes of acute myeloid leukemia, respectively, by inducible expression of them in U937 leukemia cells. We found that, although AML1-ETO and ETO2-GLIS2 can use their own DBDs to bind DNA, they share a large proportion of genome-wide binding regions dependent on other cooperative transcription factors, including the ETS-, bZIP- and bHLH-family proteins. AML1-ETO acts as either transcriptional repressor or activator, whereas ETO2-GLIS2 mainly acts as activator. The repressor-versus-activator functions of AML1-ETO might be determined by the abundance of cooperative transcription factors/cofactors on the target genes. Importantly, AML1-ETO and ETO2-GLIS2 differentially regulate key transcription factors in myeloid differentiation including PU.1 and C/EBPβ. Consequently, AML1-ETO inhibits, but ETO2-GLIS2 facilitates, myeloid differentiation of U937 cells. This function of ETO2-GLIS2 is reminiscent of a similar effect of MLL-AF9 as previously reported. Taken together, this directly comparative study between AML1-ETO and ETO2-GLIS2 in the same cellular context provides insights into context-dependent transcription regulatory mechanisms that may underlie how these seemingly “homologous” fusion transcription factors exert distinct functions to drive different subtypes of leukemia.
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Shinriki S, Matsui H. Unique role of DDX41, a DEAD-box type RNA helicase, in hematopoiesis and leukemogenesis. Front Oncol 2022; 12:992340. [PMID: 36119490 PMCID: PMC9478608 DOI: 10.3389/fonc.2022.992340] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
In myeloid malignancies including acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), patient selection and therapeutic strategies are increasingly based on tumor-specific genetic mutations. Among these, mutations in DDX41, which encodes a DEAD-box type RNA helicase, are present in approximately 2–5% of AML and MDS patients; this disease subtype exhibits a distinctive disease phenotype characterized by late age of onset, tendency toward cytopenia in the peripheral blood and bone marrow, a relatively favorable prognosis, and a high frequency of normal karyotypes. Typically, individuals with a loss-of-function germline DDX41 variant in one allele later acquire the p.R525H mutation in the other allele before overt disease manifestation, suggesting that the progressive decrease in DDX41 expression and/or function is involved in myeloid leukemogenesis.RNA helicases play roles in many processes involving RNA metabolism by altering RNA structure and RNA-protein interactions through ATP-dependent helicase activity. A single RNA helicase can play multiple cellular roles, making it difficult to elucidate the mechanisms by which mutations in DDX41 are involved in leukemogenesis. Nevertheless, multiple DDX41 functions have been associated with disease development. The enzyme has been implicated in the regulation of RNA splicing, nucleic acid sensing in the cytoplasm, R-loop resolution, and snoRNA processing.Most of the mutated RNA splicing-related factors in MDS are involved in the recognition and determination of 3’ splice sites (SS), although their individual roles are distinct. On the other hand, DDX41 is likely incorporated into the C complex of the spliceosome, which may define a distinctive disease phenotype. This review summarizes the current understanding of how DDX41 is involved in this unique myeloid malignancy.
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Hug N, Aitken S, Longman D, Raab M, Armes H, Mann AR, Rio-Machin A, Fitzgibbon J, Rouault-Pierre K, Cáceres JF. A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its function in hematopoietic differentiation. RNA (NEW YORK, N.Y.) 2022; 28:1224-1238. [PMID: 35768279 PMCID: PMC9380745 DOI: 10.1261/rna.079277.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/22/2022] [Indexed: 05/27/2023]
Abstract
The DExD/H-box RNA helicase DHX34 is a nonsense-mediated decay (NMD) factor that together with core NMD factors coregulates NMD targets in nematodes and in vertebrates. Here, we show that DHX34 is also associated with the human spliceosomal catalytic C complex. Mapping of DHX34 endogenous binding sites using cross-linking immunoprecipitation (CLIP) revealed that DHX34 is preferentially associated with pre-mRNAs and locates at exon-intron boundaries. Accordingly, we observed that DHX34 regulates a large number of alternative splicing (AS) events in mammalian cells in culture, establishing a dual role for DHX34 in both NMD and pre-mRNA splicing. We previously showed that germline DHX34 mutations associated to familial myelodysplasia (MDS)/acute myeloid leukemia (AML) predisposition abrogate its activity in NMD. Interestingly, we observe now that DHX34 regulates the splicing of pre-mRNAs that have been linked to AML/MDS predisposition. This is consistent with silencing experiments in hematopoietic stem/progenitor cells (HSPCs) showing that loss of DHX34 results in differentiation blockade of both erythroid and myeloid lineages, which is a hallmark of AML development. Altogether, these data unveil new cellular functions of DHX34 and suggest that alterations in the levels and/or activity of DHX34 could contribute to human disease.
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Affiliation(s)
- Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Michaela Raab
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Hannah Armes
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Abigail R Mann
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Ana Rio-Machin
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Jude Fitzgibbon
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Kevin Rouault-Pierre
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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