1
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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 PMCID: PMC11393547 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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2
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Flynn A, Waszak SM, Weischenfeldt J. Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer. Mol Syst Biol 2024; 20:1006-1024. [PMID: 39026103 PMCID: PMC11369196 DOI: 10.1038/s44320-024-00054-5] [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: 12/07/2023] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/20/2024] Open
Abstract
Somatic hypermutation in cancer has gained momentum with the increased use of tumour mutation burden as a biomarker for immune checkpoint inhibitors. Spontaneous deamination of 5-methylcytosine to thymine at CpG dinucleotides is one of the most ubiquitous endogenous mutational processes in normal and cancer cells. Here, we performed a systematic investigation of somatic CpG hypermutation at a pan-cancer level. We studied 30,191 cancer patients and 103 cancer types and developed an algorithm to identify somatic CpG hypermutation. Across cancer types, we observed the highest prevalence in paediatric leukaemia (3.5%), paediatric high-grade glioma (1.7%), and colorectal cancer (1%). We discovered germline variants and somatic mutations in the mismatch repair complex MutSα (MSH2-MSH6) as genetic drivers of somatic CpG hypermutation in cancer, which frequently converged on CpG sites and TP53 driver mutations. We further observe an association between somatic CpG hypermutation and response to immune checkpoint inhibitors. Overall, our study identified novel cancer types that display somatic CpG hypermutation, strong association with MutSα-deficiency, and potential utility in cancer immunotherapy.
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Affiliation(s)
- Aidan Flynn
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Sebastian M Waszak
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Copenhagen, Denmark.
- Department of Urology, Charité University Hospital, Berlin, Germany.
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3
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Lill CB, Fitter S, Zannettino ACW, Vandyke K, Noll JE. Molecular and cellular mechanisms of chemoresistance in paediatric pre-B cell acute lymphoblastic leukaemia. Cancer Metastasis Rev 2024:10.1007/s10555-024-10203-9. [PMID: 39102101 DOI: 10.1007/s10555-024-10203-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
Paediatric patients with relapsed B cell acute lymphoblastic leukaemia (B-ALL) have poor prognosis, as relapse-causing clones are often refractory to common chemotherapeutics. While the molecular mechanisms leading to chemoresistance are varied, significant evidence suggests interactions between B-ALL blasts and cells within the bone marrow microenvironment modulate chemotherapy sensitivity. Importantly, bone marrow mesenchymal stem cells (BM-MSCs) and BM adipocytes are known to support B-ALL cells through multiple distinct molecular mechanisms. This review discusses the contribution of integrin-mediated B-ALL/BM-MSC signalling and asparagine supplementation in B-ALL chemoresistance. In addition, the role of adipocytes in sequestering anthracyclines and generating a BM niche favourable for B-ALL survival is explored. Furthermore, this review discusses the role of BM-MSCs and adipocytes in promoting a quiescent and chemoresistant B-ALL phenotype. Novel treatments which target these mechanisms are discussed herein, and are needed to improve dismal outcomes in patients with relapsed/refractory disease.
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Affiliation(s)
- Caleb B Lill
- Myeloma Research Laboratory, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
- Precision Cancer Medicine Theme, Solid Tumour Program, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Stephen Fitter
- Myeloma Research Laboratory, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
- Precision Cancer Medicine Theme, Solid Tumour Program, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Andrew C W Zannettino
- Myeloma Research Laboratory, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
- Precision Cancer Medicine Theme, Solid Tumour Program, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Kate Vandyke
- Myeloma Research Laboratory, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
- Precision Cancer Medicine Theme, Solid Tumour Program, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Jacqueline E Noll
- Myeloma Research Laboratory, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia.
- Precision Cancer Medicine Theme, Solid Tumour Program, South Australian Health and Medical Research Institute, Adelaide, Australia.
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4
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Torres-Diz M, Reglero C, Falkenstein CD, Castro A, Hayer KE, Radens CM, Quesnel-Vallières M, Ang Z, Sehgal P, Li MM, Barash Y, Tasian SK, Ferrando A, Thomas-Tikhonenko A. An Alternatively Spliced Gain-of-Function NT5C2 Isoform Contributes to Chemoresistance in Acute Lymphoblastic Leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557413. [PMID: 39091882 PMCID: PMC11291008 DOI: 10.1101/2023.09.14.557413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) is a major cause of pediatric cancer-related deaths. Relapse-specific mutations do not account for all chemotherapy failures in B- ALL patients, suggesting additional mechanisms of resistance. By mining RNA-seq datasets of paired diagnostic/relapse pediatric B-ALL samples, we discovered pervasive alternative splicing (AS) patterns linked to relapse and affecting drivers of resistance to glucocorticoids, anti-folates, and thiopurines. Most splicing variations represented cassette exon skipping, "poison" exon inclusion, and intron retention, phenocopying well-documented loss-of-function mutations. In contrast, relapse-associated AS of NT5C2 mRNA yielded an isoform with the functionally uncharacterized in-frame exon 6a. Incorporation of the 8-amino acid sequence SQVAVQKR into this enzyme created a putative phosphorylation site and resulted in elevated nucleosidase activity, which is a known consequence of gain-of-function mutations in NT5C2 and a common determinant of 6-mercaptopurine (6-MP) resistance. Consistent with this finding, NT5C2ex6a and the R238W hotspot variant conferred comparable levels of resistance to 6-MP in B-ALL cells both in vitro and in vivo. Furthermore, both the NT5C2ex6a and R238W variants induced collateral sensitivity to the inosine monophosphate dehydrogenase (IMPDH) inhibitor mizoribine. These results ascribe an important role for splicing perturbations in chemotherapy resistance in relapsed B-ALL and suggest that IMPDH inhibitors, including the commonly used immunosuppressive agent mycophenolate mofetil, could be a valuable therapeutic option for treating thiopurine-resistant leukemias.
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5
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Ahn WK, Yu K, Kim H, Lee ST, Choi JR, Han JW, Lyu CJ, Hahn S, Shin S. Monitoring measurable residual disease in paediatric acute lymphoblastic leukaemia using immunoglobulin gene clonality based on next-generation sequencing. Cancer Cell Int 2024; 24:218. [PMID: 38918782 PMCID: PMC11201849 DOI: 10.1186/s12935-024-03404-3] [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: 12/01/2023] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Assessment of measurable residual disease (MRD) is an essential prognostic tool for B-lymphoblastic leukaemia (B-ALL). In this study, we evaluated the utility of next-generation sequencing (NGS)-based MRD assessment in real-world clinical practice. METHOD The study included 93 paediatric patients with B-ALL treated at our institution between January 2017 and June 2022. Clonality for IGH or IGK rearrangements was identified in most bone marrow samples (91/93, 97.8%) obtained at diagnosis. RESULTS In 421 monitoring samples, concordance was 74.8% between NGS and multiparameter flow cytometry and 70.7% between NGS and reverse transcription-PCR. Elevated quantities of clones of IGH alone (P < 0.001; hazard ratio [HR], 22.2; 95% confidence interval [CI], 7.1-69.1), IGK alone (P = 0.011; HR, 5.8; 95% CI, 1.5-22.5), and IGH or IGK (P < 0.001; HR, 7.2; 95% CI, 2.6-20.0) were associated with an increased risk of relapse. Detection of new clone(s) in NGS was also associated with inferior relapse-free survival (P < 0.001; HR, 18.1; 95% CI, 3.0-108.6). Multivariable analysis confirmed age at diagnosis, BCR::ABL1-like mutation, TCF3::PBX1 mutation, and increased quantity of IGH or IGK clones during monitoring as unfavourable factors. CONCLUSION In conclusion, this study highlights the usefulness of NGS-based MRD as a routine assessment tool for prognostication of paediatric patients with B-ALL.
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Affiliation(s)
- Won Kee Ahn
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Kyunghee Yu
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hongkyung Kim
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Dxome Co. Ltd, Seongnam-si, , Gyeonggi-do, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Dxome Co. Ltd, Seongnam-si, , Gyeonggi-do, Korea
| | - Jung Woo Han
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Chuhl Joo Lyu
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Seungmin Hahn
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Saeam Shin
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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6
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Mohd Nippah NF, Abu N, Ab Mutalib NS, Alias H. Advances in next-generation sequencing for relapsed pediatric acute lymphoblastic leukemia: current insights and future directions. Front Genet 2024; 15:1394523. [PMID: 38894724 PMCID: PMC11183504 DOI: 10.3389/fgene.2024.1394523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Leukemia is one of the most common cancers in children; and its genetic diversity in the landscape of acute lymphoblastic leukemia (ALL) is important for diagnosis, risk assessment, and therapeutic approaches. Relapsed ALL remains the leading cause of cancer deaths among children. Almost 20% of children who are treated for ALL and achieve complete remission experience disease recurrence. Relapsed ALL has a poor prognosis, and relapses are more likely to have mutations that affect signaling pathways, chromatin patterning, tumor suppression, and nucleoside metabolism. The identification of ALL subtypes has been based on genomic alterations for several decades, using the molecular landscape at relapse and its clinical significance. Next-generation sequencing (NGS), also known as massive parallel sequencing, is a high-throughput, quick, accurate, and sensitive method to examine the molecular landscape of cancer. This has undoubtedly transformed the study of relapsed ALL. The implementation of NGS has improved ALL genomic analysis, resulting in the recent identification of various novel molecular entities and a deeper understanding of existing ones. Thus, this review aimed to consolidate and critically evaluate the most current information on relapsed pediatric ALL provided by NGS technology. In this phase of targeted therapy and personalized medicine, identifying the capabilities, benefits, and drawbacks of NGS will be essential for healthcare professionals and researchers offering genome-driven care. This would contribute to precision medicine to treat these patients and help improve their overall survival and quality of life.
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Affiliation(s)
- Nur Farhana Mohd Nippah
- Department of Pediatrics, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
| | - Nurul Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
| | - Hamidah Alias
- Department of Pediatrics, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
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7
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Li X, Lin S, Liao N, Mai H, Long X, Liu L, Wu B, Chen Q, Kong Q, Kong X, Liu L, Qin J, Fang J, Zhou D. The RAS-signaling-pathway-mutation-related prognosis in B-cell acute lymphoblastic leukemia: A report from South China children's leukemia group. Hematol Oncol 2024; 42:e3265. [PMID: 38564328 DOI: 10.1002/hon.3265] [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: 07/03/2023] [Revised: 01/24/2024] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
The next-generation sequencing technologies application discovers novel genetic alterations frequently in pediatric acute lymphoblastic leukemia (ALL). RAS signaling pathway mutations at the time of relapse ALL frequently appear as small subclones at the time of onset, which are considered as the drivers in ALL relapse. Whether subclones alterations in the RAS signaling pathway should be considered for risk group stratification of ALL treatment is not decided yet. In this work, we investigate the RAS signaling pathway mutation spectrum and the related prognosis in pediatric ALL. We employed an NGS panel comprising 220 genes. NGS results were collected from 202 pediatric ALL patients. 155 patients (76.7%) harbored at least one mutation. The incidences of RAS signaling pathway mutations are different significantly between T-ALL and B-ALL. In B-ALL, the RAS pathway is mostly involved, and NRAS (17.6%), KRAS (22.7%), and PTPN11 (7.7%) were the three most frequently mutated genes. Co-occurring mutations of CREBBP and NRAS, FLT3, or PTPN11 (p = 0.002, p = 0.009, and p = 0.003, respectively) were found in this cohort. The 3-year RFS rates for the RAS signaling pathway mutation-positive and negative cases was 76.5 % versus 89.7 % (p = 0.012). Four cases relapsed in the lately 3 years were RAS signaling pathway mutation-positive. RAS signaling pathway mutation is an important biomarker for poorer relapse-free survival in pediatric B-ALL patients despite good early MRD levels.
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Affiliation(s)
- Xinyu Li
- Department of Pediatric Hematology/Oncology, Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shaofen Lin
- Department of Pediatric Hematology/Oncology, Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ning Liao
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Huirong Mai
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Shenzhen, China
| | - Xingjiang Long
- Department of Pediatrics, Liuzhou People's Hospital, Liuzhou, China
| | - Lili Liu
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Beiyan Wu
- Department of Pediatrics, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Qiwen Chen
- Department of Pediatrics, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qian Kong
- Department of Pediatrics, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xianling Kong
- Department of Pediatrics, Boai Hospital of Zhongshan, Zhongshan, China
| | - Lixia Liu
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd., Tianjin, China
| | - Jiayue Qin
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd., Tianjin, China
| | - Jianpei Fang
- Department of Pediatric Hematology/Oncology, Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dunhua Zhou
- Department of Pediatric Hematology/Oncology, Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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8
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Gong X, Hu T, Shen Q, Zhang L, Zhang W, Liu X, Zong S, Li X, Wang T, Yan W, Hu Y, Chen X, Zheng J, Zhang A, Wang J, Feng Y, Li C, Ma J, Gao X, Song Z, Zhang Y, Gale RP, Zhu X, Chen J. Gene expression prognostic of early relapse risk in low-risk B-cell acute lymphoblastic leukaemia in children. EJHAEM 2024; 5:333-345. [PMID: 38633121 PMCID: PMC11020147 DOI: 10.1002/jha2.872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/21/2024] [Indexed: 04/19/2024]
Abstract
ETV6::RUNX1 is the most common fusion gene in childhood acute lymphoblastic leukaemia (ALL) and is associated with favorable outcomes, especially in low-risk children. However, as many as 10% of children relapse within 3 years, and such early relapses have poor survival. Identifying children at risk for early relapse is an important challenge. We interrogated data from 87 children with low-risk ETV6::RUNX1-positive B-cell ALL and with available preserved bone marrow samples (discovery cohort). We profiled somatic point mutations in a panel of 559 genes and genome-wide transcriptome and single-nucleotide variants. We found high TIMD4 expression (> 85th-percentile value) at diagnosis was the most important independent prognostic factor of early relapse (hazard ratio [HR] = 5.07 [1.76, 14.62]; p = 0.03). In an independent validation cohort of low-risk ETV6::RUNX1-positive B-cell ALL (N = 68) high TIMD4 expression at diagnosis had an HR = 4.78 [1.07, 21.36] (p = 0.04) for early relapse. In another validation cohort including 78 children with low-risk ETV6::RUNX1-negative B-cell ALL, high TIMD4 expression at diagnosis had an HR = 3.93 [1.31, 11.79] (p = 0.01). Our results suggest high TIMD4 expression at diagnosis in low-risk B-cell ALL in children might be associated with high risk for early relapse.
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9
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Mosquera Orgueira A, Krali O, Pérez Míguez C, Peleteiro Raíndo A, Díaz Arias JÁ, González Pérez MS, Pérez Encinas MM, Fernández Sanmartín M, Sinnet D, Heyman M, Lönnerholm G, Norén-Nyström U, Schmiegelow K, Nordlund J. Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling. Clin Epigenetics 2024; 16:49. [PMID: 38549146 PMCID: PMC10976833 DOI: 10.1186/s13148-024-01662-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/16/2024] [Indexed: 04/02/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most prevalent cancer in children, and despite considerable progress in treatment outcomes, relapses still pose significant risks of mortality and long-term complications. To address this challenge, we employed a supervised machine learning technique, specifically random survival forests, to predict the risk of relapse and mortality using array-based DNA methylation data from a cohort of 763 pediatric ALL patients treated in Nordic countries. The relapse risk predictor (RRP) was constructed based on 16 CpG sites, demonstrating c-indexes of 0.667 and 0.677 in the training and test sets, respectively. The mortality risk predictor (MRP), comprising 53 CpG sites, exhibited c-indexes of 0.751 and 0.754 in the training and test sets, respectively. To validate the prognostic value of the predictors, we further analyzed two independent cohorts of Canadian (n = 42) and Nordic (n = 384) ALL patients. The external validation confirmed our findings, with the RRP achieving a c-index of 0.667 in the Canadian cohort, and the RRP and MRP achieving c-indexes of 0.529 and 0.621, respectively, in an independent Nordic cohort. The precision of the RRP and MRP models improved when incorporating traditional risk group data, underscoring the potential for synergistic integration of clinical prognostic factors. The MRP model also enabled the definition of a risk group with high rates of relapse and mortality. Our results demonstrate the potential of DNA methylation as a prognostic factor and a tool to refine risk stratification in pediatric ALL. This may lead to personalized treatment strategies based on epigenetic profiling.
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Affiliation(s)
- Adrián Mosquera Orgueira
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain.
- Health Research Institute of Santiago de Compostela, Compostela, Spain.
| | - Olga Krali
- Department of Medical Sciences, Molecular Precision Medicine, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Andrés Peleteiro Raíndo
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - José Ángel Díaz Arias
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - Marta Sonia González Pérez
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - Manuel Mateo Pérez Encinas
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - Manuel Fernández Sanmartín
- Health Research Institute of Santiago de Compostela, Compostela, Spain
- Department of Pediatric Medicine, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniel Sinnet
- Research Center, CHU Sainte-Justine, Montréal, Canada
- Department of Pediatrics, Université de Montréal, Montreal, Canada
| | - Mats Heyman
- Childhood Cancer Research Unit, Karolinska Institutet, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Ulrika Norén-Nyström
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Kjeld Schmiegelow
- Pediatrics and Adolescent Medicine, Rigshospitalet, and the Medical Faculty, Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Precision Medicine, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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10
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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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11
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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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12
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Contreras Yametti GP, Robbins G, Chowdhury A, Narang S, Ostrow TH, Kilberg H, Greenberg J, Kramer L, Raetz E, Tsirigos A, Evensen NA, Carroll WL. SETD2 mutations do not contribute to clonal fitness in response to chemotherapy in childhood B cell acute lymphoblastic leukemia. Leuk Lymphoma 2024; 65:78-90. [PMID: 37874744 DOI: 10.1080/10428194.2023.2273752] [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: 06/19/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023]
Abstract
Mutations in genes encoding epigenetic regulators are commonly observed at relapse in B cell acute lymphoblastic leukemia (B-ALL). Loss-of-function mutations in SETD2, an H3K36 methyltransferase, have been observed in B-ALL and other cancers. Previous studies on mutated SETD2 in solid tumors and acute myelogenous leukemia support a role in promoting resistance to DNA damaging agents. We did not observe chemoresistance, an impaired DNA damage response, nor increased mutation frequency in response to thiopurines using CRISPR-mediated knockout in wild-type B-ALL cell lines. Likewise, restoration of SETD2 in cell lines with hemizygous mutations did not increase sensitivity. SETD2 mutations affected the chromatin landscape and transcriptional output that was unique to each cell line. Collectively our data does not support a role for SETD2 mutations in driving clonal evolution and relapse in B-ALL, which is consistent with the lack of enrichment of SETD2 mutations at relapse in most studies.
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Affiliation(s)
- Gloria P Contreras Yametti
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gabriel Robbins
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ashfiyah Chowdhury
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Sonali Narang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Talia H Ostrow
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Harrison Kilberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Joshua Greenberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Lindsay Kramer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nikki A Evensen
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - William L Carroll
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
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13
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Song D, Hu F, Huang C, Lan J, She X, Zhao C, Wu H, Liu A, Wu Q, Chen Y, Luo X, Feng Y, Yang X, Xu C, Hu J, Wang G. Tiam1 methylation by NSD2 promotes Rac1 signaling activation and colon cancer metastasis. Proc Natl Acad Sci U S A 2023; 120:e2305684120. [PMID: 38113258 PMCID: PMC10756287 DOI: 10.1073/pnas.2305684120] [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: 04/15/2023] [Accepted: 10/03/2023] [Indexed: 12/21/2023] Open
Abstract
Metastasis is a major cause of cancer therapy failure and mortality. However, targeting metastatic seeding and colonization remains a significant challenge. In this study, we identified NSD2, a histone methyltransferase responsible for dimethylating histone 3 at lysine 36, as being overexpressed in metastatic tumors. Our findings suggest that NSD2 overexpression enhances tumor metastasis both in vitro and in vivo. Further analysis revealed that NSD2 promotes tumor metastasis by activating Rac1 signaling. Mechanistically, NSD2 combines with and activates Tiam1 (T lymphoma invasion and metastasis 1) and promotes Rac1 signaling by methylating Tiam1 at K724. In vivo and in vitro studies revealed that Tiam1 K724 methylation could be a predictive factor for cancer prognosis and a potential target for metastasis inhibition. Furthermore, we have developed inhibitory peptide which was proved to inhibit tumor metastasis through blocking the interaction between NSD2 and Tiam1. Our results demonstrate that NSD2-methylated Tiam1 promotes Rac1 signaling and cancer metastasis. These results provide insights into the inhibition of tumor metastasis.
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Affiliation(s)
- Da Song
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Fuqing Hu
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Changsheng Huang
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Jingqin Lan
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Xiaowei She
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Chongchong Zhao
- Department of Protein Chemistry and Proteinomics Facility at Technology Center for Protein Sciences, Tsinghua University, Beijing100084, China
| | - Hong Wu
- Department of Integrative Cancer Center and Cancer Clinical Research Center, Sichuan Cancer Hospital and Institute Sichuan Cancer Center, School of Medicine University of Electronic Science and Technology, Chengdu610000, China
| | - Anyi Liu
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Qi Wu
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Yaqi Chen
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Xuelai Luo
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Yongdong Feng
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Xiangping Yang
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Chuan Xu
- Department of Integrative Cancer Center and Cancer Clinical Research Center, Sichuan Cancer Hospital and Institute Sichuan Cancer Center, School of Medicine University of Electronic Science and Technology, Chengdu610000, China
| | - Junbo Hu
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Guihua Wang
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
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14
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Liao K, Yang Q, Xu Y, He Y, Wang J, Li Z, Wu C, Hu J, Wang X. Identification of signature of tumor-infiltrating CD8 T lymphocytes in prognosis and immunotherapy of colon cancer by machine learning. Clin Immunol 2023; 257:109811. [PMID: 37858752 DOI: 10.1016/j.clim.2023.109811] [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: 07/30/2022] [Revised: 09/25/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND To explore the specific marker of CD8+ T cell subsets which are closely related to the prognosis and immunotherapy of patients with colon cancer. METHODS 18 kinds of immune cell expression profile data sets were obtained from GEO database. Compared with other immune cell types, the specific markers of CD8 (+) T cells (TI-CD8) in colorectal cancer were screened. Regression analyses were used to further screen prognostic related genes and construct a prognostic evaluation model. The patients were stratified and analyzed according to the risk scores, KRAS mutation status, stage, lymphatic infiltration and other indicators. The landscape of infiltration level, mutation and copy number variation of immune subsets in high and low TI-CD8Sig score groups were compared and analyzed. The difference of drug response between high and low TI-CD8Sig score groups was analyzed. Differential expression of the model genes was verified by the HPA database. RESULTS Six prognostic-related CD8T cell-specific gene targets were further screened, and the prognostic evaluation model was constructed. The AUC value of the model is >0.75. FAT3 and UNC13C showed a high mutation state in the low-risk group, while USH2A, MUC5B et al. specifically showed a high mutation state in the high-risk group. Compared with the low-risk group, the high-risk group had lower effective rate of drug response. The expression of PD-1 gene was positively correlated with the level of TI-CD8Sig score. CONCLUSION The risk assessment model based on CD8T cell-specific marker genes can effectively predict the prognosis and the drug response of patients with CRC.
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Affiliation(s)
- Kaili Liao
- Department of Clinical Laboratory, the Second Affiliated Hospital of Nanchang University, Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, No. 1 Minde Road, Nanchang, Jiangxi 330006, China
| | - Qijun Yang
- Queen Mary College of Nanchang University, Xuefu Road, Nanchang, Jiangxi 330001, China
| | - Yuhan Xu
- Queen Mary College of Nanchang University, Xuefu Road, Nanchang, Jiangxi 330001, China
| | - Yingcheng He
- Queen Mary College of Nanchang University, Xuefu Road, Nanchang, Jiangxi 330001, China
| | - Jingyi Wang
- School of Public Health of Nanchang University, Nanchang, Jiangxi 330001, China
| | - Zimeng Li
- School of Public Health of Nanchang University, Nanchang, Jiangxi 330001, China
| | - Chengfeng Wu
- Department of Vascular Surgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, Jiangxi 330006, China
| | - Jialing Hu
- Department of Emergency, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, Jiangxi 330006, China
| | - Xiaozhong Wang
- Department of Clinical Laboratory, the Second Affiliated Hospital of Nanchang University, Jiangxi Province Key Laboratory of Laboratory Medicine, Jiangxi Provincial Clinical Research Center for Laboratory Medicine, No. 1 Minde Road, Nanchang, Jiangxi 330006, China.
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15
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Antić Ž, Lentes J, Bergmann AK. Cytogenetics and genomics in pediatric acute lymphoblastic leukaemia. Best Pract Res Clin Haematol 2023; 36:101511. [PMID: 38092485 DOI: 10.1016/j.beha.2023.101511] [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: 03/22/2023] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 12/18/2023]
Abstract
The last five decades have witnessed significant improvement in diagnostics, treatment and management of children with acute lymphoblastic leukaemia (ALL). These advancements have become possible through progress in our understanding of the genetic and biological background of ALL, resulting in the introduction of risk-adapted treatment and novel therapeutic targets, e.g., tyrosine kinase inhibitors for BCR::ABL1-positive ALL. Further advances in the taxonomy of ALL and the discovery of new genetic biomarkers and therapeutic targets, as well as the introduction of targeted and immunotherapies into the frontline treatment protocols, may improve management and outcome of children with ALL. In this review we describe the current developments in the (cyto)genetic diagnostics and management of children with ALL, and provide an overview of the most important advances in the genetic classification of ALL. Furthermore, we discuss perspectives resulting from the development of new techniques, including artificial intelligence (AI).
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Affiliation(s)
- Željko Antić
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Jana Lentes
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Anke K Bergmann
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany.
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16
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Lorentzian AC, Rever J, Ergin EK, Guo M, Akella NM, Rolf N, James Lim C, Reid GSD, Maxwell CA, Lange PF. Targetable lesions and proteomes predict therapy sensitivity through disease evolution in pediatric acute lymphoblastic leukemia. Nat Commun 2023; 14:7161. [PMID: 37989729 PMCID: PMC10663560 DOI: 10.1038/s41467-023-42701-9] [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: 01/27/2023] [Accepted: 10/19/2023] [Indexed: 11/23/2023] Open
Abstract
Childhood acute lymphoblastic leukemia (ALL) genomes show that relapses often arise from subclonal outgrowths. However, the impact of clonal evolution on the actionable proteome and response to targeted therapy is not known. Here, we present a comprehensive retrospective analysis of paired ALL diagnosis and relapsed specimen. Targeted next generation sequencing and proteome analysis indicate persistence of actionable genome variants and stable proteomes through disease progression. Paired viably-frozen biopsies show high correlation of drug response to variant-targeted therapies but in vitro selectivity is low. Proteome analysis prioritizes PARP1 as a pan-ALL target candidate needed for survival following cellular stress; diagnostic and relapsed ALL samples demonstrate robust sensitivity to treatment with two PARP1/2 inhibitors. Together, these findings support initiating prospective precision oncology approaches at ALL diagnosis and emphasize the need to incorporate proteome analysis to prospectively determine tumor sensitivities, which are likely to be retained at disease relapse.
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Affiliation(s)
- Amanda C Lorentzian
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- Michael Cuccione Childhood Cancer Research Program at the BC Children's Hospital Research Institute, Vancouver, Canada
| | - Jenna Rever
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- Michael Cuccione Childhood Cancer Research Program at the BC Children's Hospital Research Institute, Vancouver, Canada
| | - Enes K Ergin
- Michael Cuccione Childhood Cancer Research Program at the BC Children's Hospital Research Institute, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Meiyun Guo
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- Michael Cuccione Childhood Cancer Research Program at the BC Children's Hospital Research Institute, Vancouver, Canada
| | - Neha M Akella
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- Michael Cuccione Childhood Cancer Research Program at the BC Children's Hospital Research Institute, Vancouver, Canada
| | - Nina Rolf
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- Michael Cuccione Childhood Cancer Research Program at the BC Children's Hospital Research Institute, Vancouver, Canada
| | - C James Lim
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- Michael Cuccione Childhood Cancer Research Program at the BC Children's Hospital Research Institute, Vancouver, Canada
| | - Gregor S D Reid
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- Michael Cuccione Childhood Cancer Research Program at the BC Children's Hospital Research Institute, Vancouver, Canada
| | - Christopher A Maxwell
- Department of Pediatrics, University of British Columbia, Vancouver, Canada.
- Michael Cuccione Childhood Cancer Research Program at the BC Children's Hospital Research Institute, Vancouver, Canada.
| | - Philipp F Lange
- Michael Cuccione Childhood Cancer Research Program at the BC Children's Hospital Research Institute, Vancouver, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
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17
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Jia MZ, Li WJ, Wang CJ, Zhang Q, Gao C, Huang XT, Zhu T, Zhang RD, Cui L, Li ZG. Tracing back of relapse clones by Ig/TCR gene rearrangements reveals complex patterns of recurrence in pediatric acute lymphoblastic leukemia. Int J Lab Hematol 2023; 45:717-725. [PMID: 37194559 DOI: 10.1111/ijlh.14100] [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: 12/15/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Relapse remained the major obstacle to improving the prognosis of children with acute lymphoblastic leukemia (ALL). This study aimed to investigate the changing patterns of Ig/TCR gene rearrangements between diagnosis and relapse and the clinical relevance and to explore the mechanism of leukemic relapse. METHODS Clonal Ig/TCR gene rearrangements were screened by multiplex PCR amplification in 85 paired diagnostic and relapse bone marrow (BM) samples from children with ALL. The new rearrangements presented at relapse were quantitatively assessed by the RQ-PCR approach targeting the patient-specific junctional region sequence in 19 diagnostic samples. The relapse clones were further back-traced to diagnostic and follow-up BM samples from 12 patients. RESULTS Comparison of Ig/TCR gene rearrangements between diagnosis and relapse showed that 40 (57.1%) B-ALL and 5 (33.3%) T-ALL patients exhibited a change from diagnosis to relapse, and 25 (35.7%) B-ALL patients acquired new rearrangements at relapse. The new relapse rearrangements were present in 15 of the 19 (78.9%) diagnostic samples as shown by RQ-PCR, with a median level of 5.26 × 10-2 . The levels of minor rearrangements correlated with B immunophenotype, WBC counts, age at diagnosis, and recurrence time. Furthermore, back-tracing rearrangements in 12 patients identified three patterns of relapse clone dynamics, which suggested the recurrence mechanisms not only through clonal selection of pre-existing subclones but also through an ongoing clonal evolution during remission and relapse. CONCLUSION Backtracking Ig/TCR gene rearrangements in relapse clones of pediatric ALL revealed complex patterns of clonal selection and evolution for leukemic relapse.
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Affiliation(s)
- Ming-Zhu Jia
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Wei-Jing Li
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Chan-Juan Wang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
| | - Qing Zhang
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Chao Gao
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Xiao-Tong Huang
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Ting Zhu
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Rui-Dong Zhang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
| | - Lei Cui
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Zhi-Gang Li
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
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18
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Caserta C, Nucera S, Barcella M, Fazio G, Naldini MM, Pagani R, Pavesi F, Desantis G, Zonari E, D'Angiò M, Capasso P, Lombardo A, Merelli I, Spinelli O, Rambaldi A, Ciceri F, Silvestri D, Valsecchi MG, Biondi A, Cazzaniga G, Gentner B. miR-126 identifies a quiescent and chemo-resistant human B-ALL cell subset that correlates with minimal residual disease. Leukemia 2023; 37:1994-2005. [PMID: 37640845 DOI: 10.1038/s41375-023-02009-5] [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: 03/14/2023] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023]
Abstract
Complete elimination of B-cell acute lymphoblastic leukemia (B-ALL) by a risk-adapted primary treatment approach remains a clinical key objective, which fails in up to a third of patients. Recent evidence has implicated subpopulations of B-ALL cells with stem-like features in disease persistence. We hypothesized that microRNA-126, a core regulator of hematopoietic and leukemic stem cells, may resolve intratumor heterogeneity in B-ALL and uncover therapy-resistant subpopulations. We exploited patient-derived xenograft (PDX) models with B-ALL cells transduced with a miR-126 reporter allowing the prospective isolation of miR-126(high) cells for their functional and transcriptional characterization. Discrete miR-126(high) populations, often characterized by MIR126 locus demethylation, were identified in 8/9 PDX models and showed increased repopulation potential, in vivo chemotherapy resistance and hallmarks of quiescence, inflammation and stress-response pathway activation. Cells with a miR-126(high) transcriptional profile were identified as distinct disease subpopulations by single-cell RNA sequencing in diagnosis samples from adult and pediatric B-ALL. Expression of miR-126 and locus methylation were tested in several pediatric and adult B-ALL cohorts, which received standardized treatment. High microRNA-126 levels and locus demethylation at diagnosis associate with suboptimal response to induction chemotherapy (MRD > 0.05% at day +33 or MRD+ at day +78).
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Affiliation(s)
- Carolina Caserta
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Silvia Nucera
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Grazia Fazio
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Matteo Maria Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Riccardo Pagani
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Francesca Pavesi
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - Giacomo Desantis
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Erika Zonari
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mariella D'Angiò
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Paola Capasso
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Lombardo
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Ivan Merelli
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Orietta Spinelli
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Alessandro Rambaldi
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Fabio Ciceri
- Vita-Salute San Raffaele University, Milan, Italy
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - Daniela Silvestri
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Maria Grazia Valsecchi
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Andrea Biondi
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
- Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italia
| | - Giovanni Cazzaniga
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Genetics, School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Hospital, Milan, Italy.
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland.
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19
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Sisoudiya SD, Mishra P, Li H, Schraw JM, Scheurer ME, Salvi S, Doddapaneni H, Muzny D, Mitchell D, Taylor O, Sabo A, Lupo PJ, Plon SE. Identification of USP9X as a leukemia susceptibility gene. Blood Adv 2023; 7:4563-4575. [PMID: 37289514 PMCID: PMC10425687 DOI: 10.1182/bloodadvances.2023009814] [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: 01/23/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 06/10/2023] Open
Abstract
We recently reported that children with multiple birth defects have a significantly higher risk of childhood cancer. We performed whole-genome sequencing on a cohort of probands from this study with birth defects and cancer and their parents. Structural variant analysis identified a novel 5 kb de novo heterozygous inframe deletion overlapping the catalytic domain of USP9X in a female proband with multiple birth defects, developmental delay, and B-cell acute lymphoblastic leukemia (B-ALL). Her phenotype was consistent with female-restricted X-linked syndromic intellectual developmental disorder-99 (MRXS99F). Genotype-phenotype analysis including previously reported female probands (n = 42) demonstrated that MRXS99F probands with B-ALL (n = 3) clustered with subjects with loss-of-function (LoF) USP9X variants and multiple anomalies. The cumulative incidence of B-ALL among these female probands (7.1%) was significantly higher than an age- and sex-matched cohort (0.003%) from the Surveillance, Epidemiology, and End Results database (P < .0001, log-rank test). There are no reports of LoF variants in males. Males with hypomorphic missense variants have neurodevelopmental disorders without birth defects or leukemia risk. In contrast, in sporadic B-ALL, somatic LoF USP9X mutations occur in both males and females, and expression levels are comparable in leukemia samples from both sexes (P = .54), with the highest expressors being female patients with extra copies of the X-chromosome. Overall, we describe USP9X as a novel female-specific leukemia predisposition gene associated with multiple congenital, neurodevelopmental anomalies, and B-ALL risk. In contrast, USP9X serves as a tumor suppressor in sporadic pediatric B-ALL in both sexes, with low expression associated with poorer survival in patients with high-risk B-ALL.
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Affiliation(s)
- Saumya Dushyant Sisoudiya
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Pamela Mishra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Jeremy M. Schraw
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Michael E. Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Sejal Salvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | | | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Danielle Mitchell
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Olga Taylor
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Philip J. Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
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20
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Montes-Rodríguez IM, Soto-Salgado M, Torres-Cintrón CR, Tomassini-Fernandini JC, Suárez E, Clavell LA, Cadilla CL. Incidence and Mortality Rates for Childhood Acute Lymphoblastic Leukemia in Puerto Rican Hispanics, 2012-2016. Cancer Epidemiol Biomarkers Prev 2023; 32:1030-1037. [PMID: 37222662 PMCID: PMC10524932 DOI: 10.1158/1055-9965.epi-22-1227] [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: 11/22/2022] [Revised: 02/24/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) accounts for 80% of all leukemias diagnosed in children. Although ALL age patterns are consistent across racial/ethnic groups, their incidence and mortality rates are highly variable. We assessed the age-standardized ALL incidence and mortality rates of Puerto Rican Hispanic (PRH) children and compared them with those of US mainland Hispanics (USH), non-Hispanic Whites (NHW), non-Hispanic Blacks (NHB), and Non-Hispanic Asian or Pacific Islanders (NHAPI). METHODS Differences between racial/ethnic groups were assessed by estimating the standardized rate ratio (SRR) for 2010 to 2014. Secondary data analyses of the Puerto Rico Central Cancer Registry and the National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) databases were performed for the 2001 to 2016 period. RESULTS PRH children had 31% lower incidence rates than USH, but 86% higher incidence rates than NHB. In addition, the incidence trends of ALL increased significantly from 2001 to 2016 among PRH and USH, with 5% and 0.9% per year, respectively. Moreover, PRH have a lower 5-year overall survival (81.7%) when compared with other racial/ethnic groups. CONCLUSIONS PRH children were found to have disparities in ALL incidence and mortality rates compared with other racial/ethnic groups in the US. Additional research is warranted to identify the genetic and environmental risk factors that may be associated with the disparities observed. IMPACT This is the first study reporting the incidence and mortality rates of childhood ALL for PRH and making comparisons with other racial/ethnic groups in the US. See related commentary by Mejía-Aranguré and Núñez-Enríquez, p. 999.
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Affiliation(s)
| | - Marievelisse Soto-Salgado
- Division of Cancer Control and Population Sciences, University of Puerto Rico Comprehensive Cancer Center, San Juan, PR
| | - Carlos R. Torres-Cintrón
- Puerto Rico Central Cancer Registry, University of Puerto Rico Comprehensive Cancer Center, San Juan, PR
| | | | - Erick Suárez
- Department of Biostatistics and Epidemiology, Graduate School of Public Health, Medical Sciences Campus, University of Puerto Rico, San Juan, PR
| | - Luis A. Clavell
- Division of Pediatric Oncology, San Jorge Children’s Hospital, San Juan, PR
| | - Carmen L. Cadilla
- Department of Biochemistry, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR
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21
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Sigvardsson M. Transcription factor networks link B-lymphocyte development and malignant transformation in leukemia. Genes Dev 2023; 37:703-723. [PMID: 37673459 PMCID: PMC10546977 DOI: 10.1101/gad.349879.122] [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] [Indexed: 09/08/2023]
Abstract
Rapid advances in genomics have opened unprecedented possibilities to explore the mutational landscapes in malignant diseases, such as B-cell acute lymphoblastic leukemia (B-ALL). This disease is manifested as a severe defect in the production of normal blood cells due to the uncontrolled expansion of transformed B-lymphocyte progenitors in the bone marrow. Even though classical genetics identified translocations of transcription factor-coding genes in B-ALL, the extent of the targeting of regulatory networks in malignant transformation was not evident until the emergence of large-scale genomic analyses. There is now evidence that many B-ALL cases present with mutations in genes that encode transcription factors with critical roles in normal B-lymphocyte development. These include PAX5, IKZF1, EBF1, and TCF3, all of which are targeted by translocations or, more commonly, partial inactivation in cases of B-ALL. Even though there is support for the notion that germline polymorphisms in the PAX5 and IKZF1 genes predispose for B-ALL, the majority of leukemias present with somatic mutations in transcription factor-encoding genes. These genetic aberrations are often found in combination with mutations in genes that encode components of the pre-B-cell receptor or the IL-7/TSLP signaling pathways, all of which are important for early B-cell development. This review provides an overview of our current understanding of the molecular interplay that occurs between transcription factors and signaling events during normal and malignant B-lymphocyte development.
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Affiliation(s)
- Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden; Division of Molecular Hematology, Lund University, 22184 Lund, Sweden
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22
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Hughes K, Evans K, Earley EJ, Smith CM, Erickson SW, Stearns T, Philip VM, Neuhauser SB, Chuang JH, Jocoy EL, Bult CJ, Teicher BA, Smith MA, Lock RB. In vivo activity of the dual SYK/FLT3 inhibitor TAK-659 against pediatric acute lymphoblastic leukemia xenografts. Pediatr Blood Cancer 2023; 70:e30503. [PMID: 37339930 PMCID: PMC10730772 DOI: 10.1002/pbc.30503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/27/2023] [Accepted: 06/04/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND While children with acute lymphoblastic leukemia (ALL) experience close to a 90% likelihood of cure, the outcome for certain high-risk pediatric ALL subtypes remains dismal. Spleen tyrosine kinase (SYK) is a prominent cytosolic nonreceptor tyrosine kinase in pediatric B-lineage ALL (B-ALL). Activating mutations or overexpression of Fms-related receptor tyrosine kinase 3 (FLT3) are associated with poor outcome in hematological malignancies. TAK-659 (mivavotinib) is a dual SYK/FLT3 reversible inhibitor, which has been clinically evaluated in several other hematological malignancies. Here, we investigate the in vivo efficacy of TAK-659 against pediatric ALL patient-derived xenografts (PDXs). METHODS SYK and FLT3 mRNA expression was quantified by RNA-seq. PDX engraftment and drug responses in NSG mice were evaluated by enumerating the proportion of human CD45+ cells (%huCD45+ ) in the peripheral blood. TAK-659 was administered per oral at 60 mg/kg daily for 21 days. Events were defined as %huCD45+ ≥ 25%. In addition, mice were humanely killed to assess leukemia infiltration in the spleen and bone marrow (BM). Drug efficacy was assessed by event-free survival and stringent objective response measures. RESULTS FLT3 and SYK mRNA expression was significantly higher in B-lineage compared with T-lineage PDXs. TAK-659 was well tolerated and significantly prolonged the time to event in six out of eight PDXs tested. However, only one PDX achieved an objective response. The minimum mean %huCD45+ was significantly reduced in five out of eight PDXs in TAK-659-treated mice compared with vehicle controls. CONCLUSIONS TAK-659 exhibited low to moderate single-agent in vivo activity against pediatric ALL PDXs representative of diverse subtypes.
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Affiliation(s)
- Keira Hughes
- Children's Cancer Institute, Lowy Cancer Research Centre, School of Clinical Medicine, UNSW Medicine & Health, Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Kathryn Evans
- Children's Cancer Institute, Lowy Cancer Research Centre, School of Clinical Medicine, UNSW Medicine & Health, Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Eric J Earley
- RTI International, Research Triangle Park, North Carolina, USA
| | - Christopher M Smith
- Children's Cancer Institute, Lowy Cancer Research Centre, School of Clinical Medicine, UNSW Medicine & Health, Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | | | - Tim Stearns
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | | | | | | | | | | | | | | | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre, School of Clinical Medicine, UNSW Medicine & Health, Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
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23
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[Chinese consensus on minimal residual disease detection and interpretation of patients with acute lymphoblastic leukemia (2023)]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2023; 44:267-275. [PMID: 37356994 PMCID: PMC10282871 DOI: 10.3760/cma.j.issn.0253-2727.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Indexed: 06/27/2023]
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24
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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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25
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Bo L, Wang Y, Li Y, Wurpel JND, Huang Z, Chen ZS. The Battlefield of Chemotherapy in Pediatric Cancers. Cancers (Basel) 2023; 15:cancers15071963. [PMID: 37046624 PMCID: PMC10093214 DOI: 10.3390/cancers15071963] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/12/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
The survival rate for pediatric cancers has remarkably improved in recent years. Conventional chemotherapy plays a crucial role in treating pediatric cancers, especially in low- and middle-income countries where access to advanced treatments may be limited. The Food and Drug Administration (FDA) approved chemotherapy drugs that can be used in children have expanded, but patients still face numerous side effects from the treatment. In addition, multidrug resistance (MDR) continues to pose a major challenge in improving the survival rates for a significant number of patients. This review focuses on the severe side effects of pediatric chemotherapy, including doxorubicin-induced cardiotoxicity (DIC) and vincristine-induced peripheral neuropathy (VIPN). We also delve into the mechanisms of MDR in chemotherapy to the improve survival and reduce the toxicity of treatment. Additionally, the review focuses on various drug transporters found in common types of pediatric tumors, which could offer different therapeutic options.
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Affiliation(s)
- Letao Bo
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA
| | - Youyou Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA
| | - Yidong Li
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA
| | - John N. D. Wurpel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA
| | - Zoufang Huang
- Ganzhou Key Laboratory of Hematology, Department of Hematology, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
- Correspondence: (Z.H.); (Z.-S.C.); Tel.: +86-138-797-27439 (Z.H.); +1-718-990-1432 (Z.-S.C.); Fax: +1-718-990-1877 (Z.-S.C.)
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA
- Institute for Biotechnology, St. John’s University, Queens, NY 11439, USA
- Correspondence: (Z.H.); (Z.-S.C.); Tel.: +86-138-797-27439 (Z.H.); +1-718-990-1432 (Z.-S.C.); Fax: +1-718-990-1877 (Z.-S.C.)
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26
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Sinclair PB, Cranston RE, Raninga P, Cheng J, Hanna R, Hawking Z, Hair S, Ryan SL, Enshaei A, Nakjang S, Rand V, Blair HJ, Moorman AV, Heidenreich O, Harrison CJ. Disruption to the FOXO-PRDM1 axis resulting from deletions of chromosome 6 in acute lymphoblastic leukaemia. Leukemia 2023; 37:636-649. [PMID: 36670235 PMCID: PMC9991907 DOI: 10.1038/s41375-023-01816-0] [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: 08/23/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
A common problem in the study of human malignancy is the elucidation of cancer driver mechanisms associated with recurrent deletion of regions containing multiple genes. Taking B-cell acute lymphoblastic leukaemia (B-ALL) and large deletions of 6q [del(6q)] as a model, we integrated analysis of functional cDNA clone tracking assays with patient genomic and transcriptomic data, to identify the transcription factors FOXO3 and PRDM1 as candidate tumour suppressor genes (TSG). Analysis of cell cycle and transcriptomic changes following overexpression of FOXO3 or PRDM1 indicated that they co-operate to promote cell cycle exit at the pre-B cell stage. FOXO1 abnormalities are absent in B-ALL, but like FOXO3, FOXO1 expression suppressed growth of TCF3::PBX1 and ETV6::RUNX1 B-ALL in-vitro. While both FOXOs induced PRDM1 and other genes contributing to late pre-B cell development, FOXO1 alone induced the key transcription factor, IRF4, and chemokine, CXCR4. CRISPR-Cas9 screening identified FOXO3 as a TSG, while FOXO1 emerged as essential for B-ALL growth. We relate this FOXO3-specific leukaemia-protective role to suppression of glycolysis based on integrated analysis of CRISPR-data and gene sets induced or suppressed by FOXO1 and FOXO3. Pan-FOXO agonist Selinexor induced the glycolysis inhibitor TXNIP and suppressed B-ALL growth at low dose (ID50 < 50 nM).
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Affiliation(s)
- Paul B Sinclair
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK.
| | - Ruth E Cranston
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Prahlad Raninga
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Joanna Cheng
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Rebecca Hanna
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Zoe Hawking
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Steven Hair
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Sarra L Ryan
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Amir Enshaei
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Sirintra Nakjang
- Bioinformatics Support Unit, Faculty of Medical Science, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Vikki Rand
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
- School of Health and Life Sciences, Teesside University, Middlesborough, UK
- National Horizons Centre, Teesside University, Darlington, UK
| | - Helen J Blair
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Anthony V Moorman
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Olaf Heidenreich
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
- Princess Maxima Centre for Paediatric Oncology, Utrecht, The Netherlands
| | - Christine J Harrison
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK.
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Thakur R, Bhatia P, Singh M, Sreedharanunni S, Sharma P, Singh A, Trehan A. Therapy-Acquired Clonal Mutations in Thiopurine Drug-Response Genes Drive Majority of Early Relapses in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia. Diagnostics (Basel) 2023; 13:diagnostics13050884. [PMID: 36900028 PMCID: PMC10001400 DOI: 10.3390/diagnostics13050884] [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: 01/19/2023] [Revised: 02/15/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
METHODS Forty pediatric (0-12 years) B-ALL DNA samples (20 paired Diagnosis-Relapse) and an additional six B-ALL DNA samples (without relapse at 3 years post treatment), as the non-relapse arm, were retrieved from the biobank for advanced genomic analysis. Deep sequencing (1050-5000X; mean 1600X) was performed using a custom NGS panel of 74 genes incorporating unique molecular barcodes. RESULTS A total 47 major clones (>25% VAF) and 188 minor clones were noted in 40 cases after bioinformatic data filtering. Of the forty-seven major clones, eight (17%) were diagnosis-specific, seventeen (36%) were relapse-specific and 11 (23%) were shared. In the control arm, no pathogenic major clone was noted in any of the six samples. The most common clonal evolution pattern observed was therapy-acquired (TA), with 9/20 (45%), followed by M-M, with 5/20 (25%), m-M, with 4/20 (20%) and unclassified (UNC) 2/20 (10%). The TA clonal pattern was predominant in early relapses 7/12 (58%), with 71% (5/7) having major clonal mutations in the NT5C2 or PMS2 gene related to thiopurine-dose response. In addition, 60% (3/5) of these cases were preceded by an initial hit in the epigenetic regulator, KMT2D. Mutations in common relapse-enriched genes comprised 33% of the very early relapses, 50% of the early and 40% of the late relapses. Overall, 14/46 (30%) of the samples showed the hypermutation phenotype, of which the majority (50%) had a TA pattern of relapse. CONCLUSIONS Our study highlights the high frequency of early relapses driven by TA clones, demonstrating the need to identify their early rise during chemotherapy by digital PCR.
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Affiliation(s)
- Rozy Thakur
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Prateek Bhatia
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
- Correspondence: ; Tel.: +91-0172-2755329
| | - Minu Singh
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Sreejesh Sreedharanunni
- Department of Haematology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Pankaj Sharma
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Aditya Singh
- Department of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
| | - Amita Trehan
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
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Zhu Y, Wang Z, Li Y, Peng H, Liu J, Zhang J, Xiao X. The Role of CREBBP/EP300 and Its Therapeutic Implications in Hematological Malignancies. Cancers (Basel) 2023; 15:cancers15041219. [PMID: 36831561 PMCID: PMC9953837 DOI: 10.3390/cancers15041219] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Disordered histone acetylation has emerged as a key mechanism in promoting hematological malignancies. CREB-binding protein (CREBBP) and E1A-binding protein P300 (EP300) are two key acetyltransferases and transcriptional cofactors that regulate gene expression by regulating the acetylation levels of histone proteins and non-histone proteins. CREBBP/EP300 dysregulation and CREBBP/EP300-containing complexes are critical for the initiation, progression, and chemoresistance of hematological malignancies. CREBBP/EP300 also participate in tumor immune responses by regulating the differentiation and function of multiple immune cells. Currently, CREBBP/EP300 are attractive targets for drug development and are increasingly used as favorable tools in preclinical studies of hematological malignancies. In this review, we summarize the role of CREBBP/EP300 in normal hematopoiesis and highlight the pathogenic mechanisms of CREBBP/EP300 in hematological malignancies. Moreover, the research basis and potential future therapeutic implications of related inhibitors were also discussed from several aspects. This review represents an in-depth insight into the physiological and pathological significance of CREBBP/EP300 in hematology.
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Affiliation(s)
- Yu Zhu
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Zi Wang
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Yanan Li
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Jing Liu
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Ji Zhang
- The Affiliated Nanhua Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang 421001, China
- Correspondence: (J.Z.); (X.X.); Tel.: +86-734-8279050 (J.Z.); +86-731-84805449 (X.X.)
| | - Xiaojuan Xiao
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
- Correspondence: (J.Z.); (X.X.); Tel.: +86-734-8279050 (J.Z.); +86-731-84805449 (X.X.)
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29
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Iacobucci I, Witkowski MT, Mullighan CG. Single-cell analysis of acute lymphoblastic and lineage-ambiguous leukemia: approaches and molecular insights. Blood 2023; 141:356-368. [PMID: 35926109 PMCID: PMC10023733 DOI: 10.1182/blood.2022016954] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/13/2022] [Accepted: 07/23/2022] [Indexed: 01/31/2023] Open
Abstract
Despite recent progress in identifying the genetic drivers of acute lymphoblastic leukemia (ALL), prognosis remains poor for those individuals who experience disease recurrence. Moreover, acute leukemias of ambiguous lineage lack a biologically informed framework to guide classification and therapy. These needs have driven the adoption of multiple complementary single-cell sequencing approaches to explore key issues in the biology of these leukemias, including cell of origin, developmental hierarchy and ontogeny, and the molecular heterogeneity driving pathogenesis, progression, and therapeutic responsiveness. There are multiple single-cell techniques for profiling a specific modality, including RNA, DNA, chromatin accessibility and methylation; and an expanding range of approaches for simultaneous analysis of multiple modalities. Single-cell sequencing approaches have also enabled characterization of cell-intrinsic and -extrinsic features of ALL biology. In this review we describe these approaches and highlight the extensive heterogeneity that underpins ALL gene expression, cellular differentiation, and clonal architecture throughout disease pathogenesis and treatment resistance. In addition, we discuss the importance of the dynamic interactions that occur between leukemia cells and the nonleukemia microenvironment. We discuss potential opportunities and limitations of single-cell sequencing for the study of ALL biology and treatment responsiveness.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN
| | - Matthew T. Witkowski
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Charles G. Mullighan
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN
- Hematological Malignancies Program, St Jude Children’s Research Hospital, Memphis, TN
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30
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Orgel E, Mittelman SD. From soup to nuts: Obesity impairs chemotherapy during early and late phases of acute lymphoblastic leukemia treatment. Cancer 2023; 129:15-17. [PMID: 36369919 DOI: 10.1002/cncr.34528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Etan Orgel
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Steve D Mittelman
- University of California, Los Angeles Children's Discovery and Innovation Institute, Los Angeles, California, USA
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31
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Islam SA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. CELL GENOMICS 2022; 2:None. [PMID: 36388765 PMCID: PMC9646490 DOI: 10.1016/j.xgen.2022.100179] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 04/10/2022] [Accepted: 08/31/2022] [Indexed: 12/09/2022]
Abstract
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.
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Affiliation(s)
- S.M. Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yang Wu
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mike Vella
- NVIDIA Corporation, 2788 San Tomas Expressway, Santa Clara, CA 95051, USA
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jon W. Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Clapham
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sergey Senkin
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Yun Rose Li
- Departments of Radiation Oncology and Cancer Genetics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Laura Riva
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Andreas J. Gruber
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, D-78464 Konstanz, Germany
| | - Christopher D. Steele
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David J. Adams
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Michael R. Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Steven G. Rozen
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
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32
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A Comprehensive Overview of Recent Advances in Epigenetics in Pediatric Acute Lymphoblastic Leukemia. Cancers (Basel) 2022; 14:cancers14215384. [DOI: 10.3390/cancers14215384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/21/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Recent years have brought a novel insight into our understanding of childhood acute lymphoblastic leukemia (ALL), along with several breakthrough treatment methods. However, multiple aspects of mechanisms behind this disease remain to be elucidated. Evidence suggests that leukemogenesis in ALL is widely influenced by epigenetic modifications. These changes include: DNA hypermethylation, histone modification and miRNA alteration. DNA hypermethylation in promoter regions, which leads to silencing of tumor suppressor genes, is a common epigenetic alteration in ALL. Histone modifications are mainly caused by an increased expression of histone deacetylases. A dysregulation of miRNA results in changes in the expression of their target genes. To date, several hundred genes were identified as suppressed by epigenetic mechanisms in ALL. What is promising is that epigenetic alterations in ALL may be used as potential biomarkers for classification of subtypes, predicting relapse and disease progression and assessing minimal residual disease. Furthermore, since epigenetic lesions are potentially reversible, an activation of epigenetically silenced genes with the use of hypomethylating agents or histone deacetylase inhibitors may be utilized as a therapeutic strategy for ALL. The following review summarizes our current knowledge about epigenetic modifications in ALL and describes potential uses of epigenetics in the clinical management of this disease.
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Ahn J, Kim T, Jung S, Ahn S, Song G, Kim M, Yang D, Lee J, Kim MY, Moon JH, Zhang Z, Kim H, Kim DDH. Next-generation sequencing-based analysis to assess the pattern of relapse in patients with Philadelphia-positive acute lymphoblastic leukemia. EJHAEM 2022; 3:1145-1153. [PMID: 36467841 PMCID: PMC9713221 DOI: 10.1002/jha2.514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 06/17/2023]
Abstract
In this study, we performed serial monitoring using targeted DNA sequencing to identify genetic alterations in adults with Philadelphia-positive acute lymphoblastic leukemia (Ph-ALL). Deep sequencing was performed by targeting the coding regions of 45 genes with recurrent driver mutations and 1129 single nucleotide polymorphism sites. Of the 43 patients that we examined, at least one case of genetic alterations was detected in 38 (88%) of the 43 patients at diagnosis (somatic mutations in 10 patients [23%] and copy number aberrations [CNA] in 36 patients [84%]). The most frequently detected CNA lesions were in IKZF1 (n = 25, 58%) and the most frequently mutated gene was SETD2 (n = 5). At least one genetic abnormality (loss, gain, or persistence) was observed in all the samples obtained at relapse that were available for analysis (n = 15), compared with the samples obtained at diagnosis (disappearance of any previously detected genetic alterations: 11 patients [73%]; new genetic abnormalities: nine patients [60%]; and persistent genetic abnormalities: eight patients [53%]]. The most frequently deleted lesions were in IKZF1 (n = 9, 60%), and the most frequently mutated gene was ABL1 (eight patients, 53%). Our data indicate that leukemic progression may be associated with complex genetic alterations in Ph-ALL during the course of treatment.
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Affiliation(s)
- Jae‐Sook Ahn
- Department of Internal Medicine, Chonnam National University Hwasun HospitalChonnam National UniversityGwangjuRepublic of Korea
- Genomic Research Center for Hematopoietic DiseasesChonnam National University Hwasun HospitalJeollanam‐doRepublic of Korea
| | - TaeHyung Kim
- The Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoOntarioCanada
- Department of Computer ScienceUniversity of TorontoTorontoOntarioCanada
| | - Sung‐Hoon Jung
- Department of Internal Medicine, Chonnam National University Hwasun HospitalChonnam National UniversityGwangjuRepublic of Korea
| | - Seo‐Yeon Ahn
- Department of Internal Medicine, Chonnam National University Hwasun HospitalChonnam National UniversityGwangjuRepublic of Korea
| | - Ga‐Young Song
- Department of Internal Medicine, Chonnam National University Hwasun HospitalChonnam National UniversityGwangjuRepublic of Korea
| | - Mihee Kim
- Department of Internal Medicine, Chonnam National University Hwasun HospitalChonnam National UniversityGwangjuRepublic of Korea
| | - Deok‐Hwan Yang
- Department of Internal Medicine, Chonnam National University Hwasun HospitalChonnam National UniversityGwangjuRepublic of Korea
| | - Je‐Jung Lee
- Department of Internal Medicine, Chonnam National University Hwasun HospitalChonnam National UniversityGwangjuRepublic of Korea
| | - Mi Yeon Kim
- Genomic Research Center for Hematopoietic DiseasesChonnam National University Hwasun HospitalJeollanam‐doRepublic of Korea
| | - Joon Ho Moon
- Department of Hematology‐OncologyKyungpook National University Hospital, School of Medicine, Kyungpook National UniversityDaeguRepublic of Korea
| | - Zhaolei Zhang
- The Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoOntarioCanada
- Department of Computer ScienceUniversity of TorontoTorontoOntarioCanada
- Department of Medical Oncology and Hematology, Princess Margaret Cancer CentreUniversity of TorontoTorontoOntarioCanada
| | - Hyeoung‐Joon Kim
- Department of Internal Medicine, Chonnam National University Hwasun HospitalChonnam National UniversityGwangjuRepublic of Korea
- Genomic Research Center for Hematopoietic DiseasesChonnam National University Hwasun HospitalJeollanam‐doRepublic of Korea
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34
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How Genetics and Genomics Advances Are Rewriting Pediatric Cancer Research and Clinical Care. Medicina (B Aires) 2022; 58:medicina58101386. [PMID: 36295546 PMCID: PMC9610804 DOI: 10.3390/medicina58101386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
In the last two decades, thanks to the data that have been obtained from the Human Genome Project and the development of next-generation sequencing (NGS) technologies, research in oncology has produced extremely important results in understanding the genomic landscape of pediatric cancers, which are the main cause of death during childhood. NGS has provided significant advances in medicine by detecting germline and somatic driver variants that determine the development and progression of many types of cancers, allowing a distinction between hereditary and non-hereditary cancers, characterizing resistance mechanisms that are also related to alterations of the epigenetic apparatus, and quantifying the mutational burden of tumor cells. A combined approach of next-generation technologies allows us to investigate the numerous molecular features of the cancer cell and the effects of the environment on it, discovering and following the path of personalized therapy to defeat an "ancient" disease that has had victories and defeats. In this paper, we provide an overview of the results that have been obtained in the last decade from genomic studies that were carried out on pediatric cancer and their contribution to the more accurate and faster diagnosis in the stratification of patients and the development of new precision therapies.
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Pillai PM, Mallory N, Pierro J, Saliba J, Newman D, Hu J, Bhatla T, Raetz E, Carroll WL, Evensen NA. Activation of the mitogen-activated protein kinase-extracellular signal-regulated kinase pathway in childhood B-cell acute lymphoblastic leukemia. Pediatr Blood Cancer 2022; 69:e29771. [PMID: 35593589 DOI: 10.1002/pbc.29771] [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: 02/22/2022] [Revised: 04/04/2022] [Accepted: 04/22/2022] [Indexed: 11/09/2022]
Abstract
RAS mutations are frequently observed in childhood B-cell acute lymphoblastic leukemia (B-ALL) and previous studies have yielded conflicting results as to whether they are associated with a poor outcome. We and others have demonstrated that the mitogen-activated protein kinase-extracellular signal-regulated kinase (MAPK) pathway can be activated through epigenetic mechanisms in the absence of RAS pathway mutations. Herein, we examined whether MAPK activation, as determined by measuring phosphorylated extracellular signal-regulated kinase (pERK) levels in 80 diagnostic patient samples using phosphoflow cytometry, could be used as a prognostic biomarker for pediatric B-ALL. The mean fluorescence intensity of pERK (MFI) was measured at baseline and after exogenous stimulation with or without pretreatment with the mitogen-activated protein kinase kinase (MEK) inhibitor trametinib. Activation levels (MFI stimulated/MFI baseline) ranged from 0.76 to 4.40 (median = 1.26), and inhibition indexes (MFI stimulated/MFI trametinib stimulated) ranged from 0.439 to 5.640 (median = 1.30), with no significant difference between patients with wildtype versus mutant RAS for either. Logistic regression demonstrated that neither MAPK activation levels nor RAS mutation status at diagnosis alone or in combination was prognostic of outcome. However, 35% of RAS wildtype samples showed MAPK inhibition indexes greater than the median, thus raising the possibility that therapeutic strategies to inhibit MAPK activation may not be restricted to patients whose blasts display Ras pathway defects.
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Affiliation(s)
- Pallavi M Pillai
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, Mount Sinai Kravis Children's Hospital, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nicole Mallory
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Joanna Pierro
- Northwell Health, Staten Island University Hospital, Staten Island, New York, USA
| | - Jason Saliba
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
| | - Daniel Newman
- Penn Medicine, University of Pennsylvania Health System, Philadelphia, Pennsylvania, USA
| | - Jiyuan Hu
- Department of Population Health, Division of Biostatistics, NYU Grossman School of Medicine, New York, New York, USA
| | - Teena Bhatla
- Department of Pediatrics, Children's Hospital of New Jersey at NBI, RWJBarnabas Health, Newark, New Jersey, USA
| | - Elizabeth Raetz
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA.,Department of Pediatrics, Division of Pediatric Hematology/Oncology, NYU Grossman School of Medicine, New York, New York, USA
| | - William L Carroll
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA.,Department of Pediatrics, Division of Pediatric Hematology/Oncology, NYU Grossman School of Medicine, New York, New York, USA
| | - Nikki A Evensen
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
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Closa A, Reixachs-Solé M, Fuentes-Fayos AC, Hayer K, Melero J, Adriaanse FRS, Bos R, Torres-Diz M, Hunger S, Roberts K, Mullighan C, Stam R, Thomas-Tikhonenko A, Castaño J, Luque R, Eyras E. A convergent malignant phenotype in B-cell acute lymphoblastic leukemia involving the splicing factor SRRM1. NAR Cancer 2022; 4:zcac041. [DOI: 10.1093/narcan/zcac041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/09/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Abstract
A significant proportion of infant B-cell acute lymphoblastic leukemia (B-ALL) patients remains with a dismal prognosis due to yet undetermined mechanisms. We performed a comprehensive multicohort analysis of gene expression, gene fusions, and RNA splicing alterations to uncover molecular signatures potentially linked to the observed poor outcome. We identified 87 fusions with significant allele frequency across patients and shared functional impacts, suggesting common mechanisms across fusions. We further identified a gene expression signature that predicts high risk independently of the gene fusion background and includes the upregulation of the splicing factor SRRM1. Experiments in B-ALL cell lines provided further evidence for the role of SRRM1 on cell survival, proliferation, and invasion. Supplementary analysis revealed that SRRM1 potentially modulates splicing events associated with poor outcomes through protein-protein interactions with other splicing factors. Our findings reveal a potential convergent mechanism of aberrant RNA processing that sustains a malignant phenotype independently of the underlying gene fusion and that could potentially complement current clinical strategies in infant B-ALL.
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Affiliation(s)
- Adria Closa
- The Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University , Canberra, Australia
- Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, Australian National University , Canberra, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University , Canberra, Australia
| | - Marina Reixachs-Solé
- The Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University , Canberra, Australia
- Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, Australian National University , Canberra, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University , Canberra, Australia
| | - Antonio C Fuentes-Fayos
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC) , Cordoba, Spain
- University of Cordoba (UCO) , Cordoba, Spain
- Reina Sofía University Hospital , Cordoba, Spain
| | - Katharina E Hayer
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia , Philadelphia, USA
| | - Juan L Melero
- The Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University , Canberra, Australia
- Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, Australian National University , Canberra, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University , Canberra, Australia
| | | | - Romy S Bos
- Princess Máxima Center for Pediatric Oncology , Utrecht, The Netherlands
| | - Manuel Torres-Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia , Philadelphia, USA
| | - Stephen P Hunger
- Division of Oncology, Children's Hospital of Philadelphia , Philadelphia, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital , Memphis, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital , Memphis, USA
| | - Ronald W Stam
- Princess Máxima Center for Pediatric Oncology , Utrecht, The Netherlands
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia , Philadelphia, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania , Philadelphia, USA
| | - Justo P Castaño
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC) , Cordoba, Spain
- University of Cordoba (UCO) , Cordoba, Spain
- Reina Sofía University Hospital , Cordoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición , (CIBERobn), Cordoba, Spain
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC) , Cordoba, Spain
- University of Cordoba (UCO) , Cordoba, Spain
- Reina Sofía University Hospital , Cordoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición , (CIBERobn), Cordoba, Spain
| | - Eduardo Eyras
- The Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University , Canberra, Australia
- Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, Australian National University , Canberra, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University , Canberra, Australia
- Catalan Institution for Research and Advanced Studies (ICREA) , Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM) , Barcelona, Spain
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Fan T, Xue L, Dong B, He H, Zhang W, Hao L, Ma W, Zang G, Han C, Dong Y. CDH1 overexpression predicts bladder cancer from early stage and inversely correlates with immune infiltration. BMC Urol 2022; 22:156. [PMID: 36131343 PMCID: PMC9494810 DOI: 10.1186/s12894-022-01103-7] [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: 04/18/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
Background Bladder cancer (BC) seriously endangers public health, but effective biomarkers for BC diagnosis, particularly in the early stage, are still lacking. Identification of reliable biomarkers associated with early-stage BC is of great importance to early treatment and an improved outcome. Methods Differentially expressed genes (DEGs) were identified using four publicly available early-stage BC gene-expression profiles. Protein–protein interaction (PPI) and survival analysis for hub genes was evaluated. The correlation between methylation of genes and prognosis was evaluated using the MethSurv database. Co-expressed genes were explored using Cancer Cell Line Encyclopedia database and the corresponding expression were assessed in vitro. The competing endogenous RNA network and the immune cell infiltration in BC were generated using data of The Cancer Genome Atlas. Results Ten hub genes of the 213 integrated DEGs were identified, including CDH1, IGFBP3, PPARG, SDC1, EPCAM, ACTA2, COL3A1, TPM1, ACTC1, and ACTN1. CDH1 appeared to increase from tumor initiation stage and negatively correlated with methylation. Six methylated sites in CDH1 indicated a good prognosis and one site indicated an aberrant prognosis. High CDH1 expression was negatively correlated with infiltrations by most immune cells, such as plasmacytoid dendritic cells (pDCs), regulatory T cells, macrophages, neutrophils, DCs, and natural killer cells. CDH1 was highly positively correlated with EPCAM and appeared to be directly regulated by miR-383. Conclusions The identified oncogenic alterations provide theoretical support for the development of novel biomarkers to advance early-stage BC diagnosis and personalized therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12894-022-01103-7.
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Affiliation(s)
- Tao Fan
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China.,Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China
| | - Liang Xue
- Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China
| | - Bingzheng Dong
- Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China.,Medical College of Soochow University, Soochow, China
| | - Houguang He
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China.,Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China
| | - Wenda Zhang
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China.,Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China
| | - Lin Hao
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China.,Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China.,Medical College of Soochow University, Soochow, China
| | - Weiming Ma
- Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China.,Medical College of Soochow University, Soochow, China
| | - Guanghui Zang
- Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China
| | - Conghui Han
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China. .,Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China. .,Medical College of Soochow University, Soochow, China.
| | - Yang Dong
- Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China. .,Medical College of Soochow University, Soochow, China.
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38
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Azagra A, Cobaleda C. NSD2 as a Promising Target in Hematological Disorders. Int J Mol Sci 2022; 23:11075. [PMID: 36232375 PMCID: PMC9569587 DOI: 10.3390/ijms231911075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Alterations of the epigenetic machinery are critically involved in cancer development and maintenance; therefore, the proteins in charge of the generation of epigenetic modifications are being actively studied as potential targets for anticancer therapies. A very important and widespread epigenetic mark is the dimethylation of Histone 3 in Lysine 36 (H3K36me2). Until recently, it was considered as merely an intermediate towards the generation of the trimethylated form, but recent data support a more specific role in many aspects of genome regulation. H3K36 dimethylation is mainly carried out by proteins of the Nuclear SET Domain (NSD) family, among which NSD2 is one of the most relevant members with a key role in normal hematopoietic development. Consequently, NSD2 is frequently altered in several types of tumors-especially in hematological malignancies. Herein, we discuss the role of NSD2 in these pathological processes, and we review the most recent findings in the development of new compounds aimed against the oncogenic forms of this novel anticancer candidate.
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Affiliation(s)
| | - César Cobaleda
- Immune System Development and Function Unit, Centro de Biología Molecular Severo Ochoa (CSIC–Universidad Autónoma de Madrid), 28049 Madrid, Spain
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39
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Brady SW, Roberts KG, Gu Z, Shi L, Pounds S, Pei D, Cheng C, Dai Y, Devidas M, Qu C, Hill AN, Payne-Turner D, Ma X, Iacobucci I, Baviskar P, Wei L, Arunachalam S, Hagiwara K, Liu Y, Flasch DA, Liu Y, Parker M, Chen X, Elsayed AH, Pathak O, Li Y, Fan Y, Michael JR, Rusch M, Wilkinson MR, Foy S, Hedges DJ, Newman S, Zhou X, Wang J, Reilly C, Sioson E, Rice SV, Pastor Loyola V, Wu G, Rampersaud E, Reshmi SC, Gastier-Foster J, Guidry Auvil JM, Gesuwan P, Smith MA, Winick N, Carroll AJ, Heerema NA, Harvey RC, Willman CL, Larsen E, Raetz EA, Borowitz MJ, Wood BL, Carroll WL, Zweidler-McKay PA, Rabin KR, Mattano LA, Maloney KW, Winter SS, Burke MJ, Salzer W, Dunsmore KP, Angiolillo AL, Crews KR, Downing JR, Jeha S, Pui CH, Evans WE, Yang JJ, Relling MV, Gerhard DS, Loh ML, Hunger SP, Zhang J, Mullighan CG. The genomic landscape of pediatric acute lymphoblastic leukemia. Nat Genet 2022; 54:1376-1389. [PMID: 36050548 PMCID: PMC9700506 DOI: 10.1038/s41588-022-01159-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Here, using whole-genome, exome and transcriptome sequencing of 2,754 childhood patients with ALL, we find that, despite a generally low mutation burden, ALL cases harbor a median of four putative somatic driver alterations per sample, with 376 putative driver genes identified varying in prevalence across ALL subtypes. Most samples harbor at least one rare gene alteration, including 70 putative cancer driver genes associated with ubiquitination, SUMOylation, noncoding transcripts and other functions. In hyperdiploid B-ALL, chromosomal gains are acquired early and synchronously before ultraviolet-induced mutation. By contrast, ultraviolet-induced mutations precede chromosomal gains in B-ALL cases with intrachromosomal amplification of chromosome 21. We also demonstrate the prognostic significance of genetic alterations within subtypes. Intriguingly, DUX4- and KMT2A-rearranged subtypes separate into CEBPA/FLT3- or NFATC4-expressing subgroups with potential clinical implications. Together, these results deepen understanding of the ALL genomic landscape and associated outcomes.
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Affiliation(s)
- Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine & Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yunfeng Dai
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ashley N Hill
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pradyuamna Baviskar
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Wei
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sasi Arunachalam
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Diane A Flasch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Abdelrahman H Elsayed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Omkar Pathak
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - J Robert Michael
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mark R Wilkinson
- 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
| | - Dale J Hedges
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colleen Reilly
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen V Rice
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Victor Pastor Loyola
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shalini C Reshmi
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Jaime M Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Office of Data Sharing, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Malcolm A Smith
- Cancer Therapeutics Evaluation Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Naomi Winick
- Department of Pediatric Hematology Oncology and Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Richard C Harvey
- Department of Pathology, University of New Mexico Cancer Center, Albuquerque, NM, USA
| | | | - Eric Larsen
- Department of Pediatrics, Maine Children's Cancer Program, Scarborough, ME, USA
| | - Elizabeth A Raetz
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Michael J Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Brent L Wood
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - William L Carroll
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | | | - Karen R Rabin
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Kelly W Maloney
- Department of Pediatrics and Children's Hospital Colorado, University of Colorado, Aurora, CO, USA
| | - Stuart S Winter
- Children's Minnesota Research Institute and Cancer and Blood Disorders Program, Minneapolis, MN, USA
| | - Michael J Burke
- Division of Pediatric Hematology-Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Wanda Salzer
- Uniformed Services University, School of Medicine, Bethesda, MD, USA
| | | | | | - Kristine R Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sima Jeha
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, 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
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Stephen P Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Kaur G, Jena L, Gupta R, Farswan A, Gupta A, Sriram K. Correlation of changes in subclonal architecture with progression in the MMRF CoMMpass study. Transl Oncol 2022; 23:101472. [PMID: 35777247 PMCID: PMC9253848 DOI: 10.1016/j.tranon.2022.101472] [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: 09/11/2021] [Revised: 06/03/2022] [Accepted: 06/20/2022] [Indexed: 11/28/2022] Open
Abstract
Multiple myeloma (MM) is a heterogeneous plasma cell proliferative disorder that arises from its premalignant precursor stages through a complex cascade of interactions between clonal mutations and co-evolving microenvironment. The temporo-spatial evolutionary trajectories of MM are established early during myelomatogenesis in precursor stages and retained in MM. Such molecular events impact subsequent disease progression and clinical outcomes. Identification of clonal sweeps of actionable gene targets in MM could reveal potential vulnerabilities that may exist in early stages and thus potentiate prognostication and customization of early therapeutic interventions. We have evaluated clonal evolution at multiple time points in 76 MM patients enrolled in the MMRF CoMMpass study. The major findings of this study are (a) MM progresses predominantly through branching evolution, (b) there is a heterogeneous spectrum of mutational landscapes that include unique actionable gene targets at diagnosis compared to progression, (c) unique clonal gains/ losses of mutant driver genes can be identified in patients with different cytogenetic aberrations, (d) there is a significant correlation between co-occurring oncogenic mutations/ co-occurring subclones e.g., with mutated TP53+SYNE1, NRAS+MAGI3, and anticorrelative dependencies between FAT3+FCGBP gene pairs. Such co-trajectories may synchronize molecular events of drug response, myelomatogenesis and warrant future studies to explore their potential for early prognostication and development of risk stratified personalized therapies in MM.
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Affiliation(s)
- Gurvinder Kaur
- Laboratory Oncology Unit, Dr. B. R.A. IRCH, AIIMS, New Delhi
| | - Lingaraja Jena
- Laboratory Oncology Unit, Dr. B. R.A. IRCH, AIIMS, New Delhi
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B. R.A. IRCH, AIIMS, New Delhi.
| | - Akanksha Farswan
- SBILab, Department of Electronics and Communication Engineering, IIIT, Delhi
| | - Anubha Gupta
- SBILab, Department of Electronics and Communication Engineering, IIIT, Delhi.
| | - K Sriram
- Department of Computational Biology & Centre for Computational Biology, IIIT, Delhi
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41
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Multi-omics analysis defines highly refractory RAS burdened immature subgroup of infant acute lymphoblastic leukemia. Nat Commun 2022; 13:4501. [PMID: 36042201 PMCID: PMC9427775 DOI: 10.1038/s41467-022-32266-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/22/2022] [Indexed: 11/26/2022] Open
Abstract
KMT2A-rearranged infant acute lymphoblastic leukemia (ALL) represents the most refractory type of childhood leukemia. To uncover the molecular heterogeneity of this disease, we perform RNA sequencing, methylation array analysis, whole exome and targeted deep sequencing on 84 infants with KMT2A-rearranged leukemia. Our multi-omics clustering followed by single-sample and single-cell inference of hematopoietic differentiation establishes five robust integrative clusters (ICs) with different master transcription factors, fusion partners and corresponding stages of B-lymphopoietic and early hemato-endothelial development: IRX-type differentiated (IC1), IRX-type undifferentiated (IC2), HOXA-type MLLT1 (IC3), HOXA-type MLLT3 (IC4), and HOXA-type AFF1 (IC5). Importantly, our deep mutational analysis reveals that the number of RAS pathway mutations predicts prognosis and that the most refractory subgroup of IC2 possesses 100% frequency and the heaviest burden of RAS pathway mutations. Our findings highlight the previously under-appreciated intra- and inter-patient heterogeneity of KMT2A-rearranged infant ALL and provide a rationale for the future development of genomics-guided risk stratification and individualized therapy.
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Maintenance therapy for acute lymphoblastic leukemia: basic science and clinical translations. Leukemia 2022; 36:1749-1758. [PMID: 35654820 PMCID: PMC9252897 DOI: 10.1038/s41375-022-01591-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 01/21/2023]
Abstract
Maintenance therapy (MT) with oral methotrexate (MTX) and 6-mercaptopurine (6-MP) is essential for the cure of acute lymphoblastic leukemia (ALL). MTX and 6-MP interfere with nucleotide synthesis and salvage pathways. The primary cytotoxic mechanism involves the incorporation of thioguanine nucleotides (TGNs) into DNA (as DNA-TG), which may be enhanced by the inhibition of de novo purine synthesis by other MTX/6-MP metabolites. Co-medication during MT is common. Although Pneumocystis jirovecii prophylaxis appears safe, the benefit of glucocorticosteroid/vincristine pulses in improving survival and of allopurinol to moderate 6-MP pharmacokinetics remains uncertain. Numerous genetic polymorphisms influence the pharmacology, efficacy, and toxicity (mainly myelosuppression and hepatotoxicity) of MTX and thiopurines. Thiopurine S-methyltransferase (encoded by TPMT) decreases TGNs but increases methylated 6-MP metabolites (MeMPs); similarly, nudix hydrolase 15 (encoded by NUDT15) also decreases TGNs available for DNA incorporation. Loss-of-function variants in both genes are currently used to guide MT, but do not fully explain the inter-patient variability in thiopurine toxicity. Because of the large inter-individual variations in MTX/6-MP bioavailability and metabolism, dose adjustments are traditionally guided by the degree of myelosuppression, but this does not accurately reflect treatment intensity. DNA-TG is a common downstream metabolite of MTX/6-MP combination chemotherapy, and a higher level of DNA-TG has been associated with a lower relapse hazard, leading to the development of the Thiopurine Enhanced ALL Maintenance (TEAM) strategy-the addition of low-dose (2.5-12.5 mg/m2/day) 6-thioguanine to the 6-MP/MTX backbone-that is currently being tested in a randomized ALLTogether1 trial (EudraCT: 2018-001795-38). Mutations in the thiopurine and MTX metabolism pathways, and in the mismatch repair genes have been identified in early ALL relapses, providing valuable insights to assist the development of strategies to detect imminent relapse, to facilitate relapse salvage therapy, and even to bring about changes in frontline ALL therapy to mitigate this relapse risk.
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The Promise of Single-cell Technology in Providing New Insights Into the Molecular Heterogeneity and Management of Acute Lymphoblastic Leukemia. Hemasphere 2022; 6:e734. [PMID: 35651714 PMCID: PMC9148686 DOI: 10.1097/hs9.0000000000000734] [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: 02/22/2022] [Accepted: 04/28/2022] [Indexed: 11/26/2022] Open
Abstract
Drug resistance and treatment failure in pediatric acute lymphoblastic leukemia (ALL) are in part driven by tumor heterogeneity and clonal evolution. Although bulk tumor genomic analyses have provided some insight into these processes, single-cell sequencing has emerged as a powerful technique to profile individual cells in unprecedented detail. Since the introduction of single-cell RNA sequencing, we now have the capability to capture not only transcriptomic, but also genomic, epigenetic, and proteomic variation between single cells separately and in combination. This rapidly evolving field has the potential to transform our understanding of the fundamental biology of pediatric ALL and guide the management of ALL patients to improve their clinical outcome. Here, we discuss the impact single-cell sequencing has had on our understanding of tumor heterogeneity and clonal evolution in ALL and provide examples of how single-cell technology can be integrated into the clinic to inform treatment decisions for children with high-risk disease.
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Arunachalam S, Szlachta K, Brady SW, Ma X, Ju B, Shaner B, Mulder HL, Easton J, Raphael BJ, Myers M, Tinkle C, Allen SJ, Orr BA, Wetmore CJ, Baker SJ, Zhang J. Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor. Acta Neuropathol Commun 2022; 10:80. [PMID: 35642016 PMCID: PMC9153212 DOI: 10.1186/s40478-022-01381-0] [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: 03/10/2022] [Accepted: 05/12/2022] [Indexed: 11/11/2022] Open
Abstract
The majority of diffuse midline gliomas, H3 K27-altered (DMG-H3 K27-a), are infiltrating pediatric brain tumors that arise in the pons with no effective treatment. To understand how clonal evolution contributes to the tumor’s invasive spread, we performed exome sequencing and SNP array profiling on 49 multi-region autopsy samples from 11 patients with pontine DMG-H3 K27-a enrolled in a phase I clinical trial of PDGFR inhibitor crenolanib. For each patient, a phylogenetic tree was constructed by testing multiple possible clonal evolution models to select the one consistent with somatic mutations and copy number variations across all tumor regions. The tree was then used to deconvolute subclonal composition and prevalence at each tumor region to study convergent evolution and invasion patterns. Somatic variants in the PI3K pathway, a late event, are enriched in our cohort, affecting 70% of patients. Convergent evolution of PI3K at distinct phylogenetic branches was detected in 40% of the patients. 24 (~ 50%) of tumor regions were occupied by subclones of mixed lineages with varying molecular ages, indicating multiple waves of invasion across the pons and extrapontine. Subclones harboring a PDGFRA amplicon, including one that amplified a PDGRFAY849C mutant allele, were detected in four patients; their presence in extrapontine tumor and normal brain samples imply their involvement in extrapontine invasion. Our study expands the current knowledge on tumor invasion patterns in DMG-H3 K27-a, which may inform the design of future clinical trials.
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Wu S, Liu L, Chu X, Zheng J, Chen Z, Gao L, Xiao P, Lu J, Ji Q, Ling J, Cao S, Pan J, Qin J, Hu S. Dynamic change of variant allele frequency reveals disease status, clonal evolution and survival in pediatric relapsed B-cell acute lymphoblastic leukaemia. Clin Transl Med 2022; 12:e892. [PMID: 35605061 PMCID: PMC9126496 DOI: 10.1002/ctm2.892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/02/2022] Open
Affiliation(s)
- Shuiyan Wu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.,Pediatric Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, China
| | - Lixia Liu
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd., Tianjin, China
| | - Xinran Chu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Jiajia Zheng
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Zixing Chen
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Gao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Peifang Xiao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Jun Lu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Qi Ji
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Jing Ling
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Shanbo Cao
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd., Tianjin, China
| | - Jian Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Jiayue Qin
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd., Tianjin, China
| | - Shaoyan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
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Umeda M, Ma J, Huang BJ, Hagiwara K, Westover T, Abdelhamed S, Barajas JM, Thomas ME, Walsh MP, Song G, Tian L, Liu Y, Chen X, Kolekar P, Tran Q, Foy SG, Maciaszek JL, Kleist AB, Leonti AR, Ju B, Easton J, Wu H, Valentine V, Valentine MB, Liu YC, Ries RE, Smith JL, Parganas E, Iacobucci I, Hiltenbrand R, Miller J, Myers JR, Rampersaud E, Rahbarinia D, Rusch M, Wu G, Inaba H, Wang YC, Alonzo TA, Downing JR, Mullighan CG, Pounds S, Babu MM, Zhang J, Rubnitz JE, Meshinchi S, Ma X, Klco JM. Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia. Blood Cancer Discov 2022; 3:194-207. [PMID: 35176137 PMCID: PMC9780084 DOI: 10.1158/2643-3230.bcd-21-0160] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 08/27/2021] [Accepted: 01/24/2022] [Indexed: 01/21/2023] Open
Abstract
The genetics of relapsed pediatric acute myeloid leukemia (AML) has yet to be comprehensively defined. Here, we present the spectrum of genomic alterations in 136 relapsed pediatric AMLs. We identified recurrent exon 13 tandem duplications (TD) in upstream binding transcription factor (UBTF) in 9% of relapsed AML cases. UBTF-TD AMLs commonly have normal karyotype or trisomy 8 with cooccurring WT1 mutations or FLT3-ITD but not other known oncogenic fusions. These UBTF-TD events are stable during disease progression and are present in the founding clone. In addition, we observed that UBTF-TD AMLs account for approximately 4% of all de novo pediatric AMLs, are less common in adults, and are associated with poor outcomes and MRD positivity. Expression of UBTF-TD in primary hematopoietic cells is sufficient to enhance serial clonogenic activity and to drive a similar transcriptional program to UBTF-TD AMLs. Collectively, these clinical, genomic, and functional data establish UBTF-TD as a new recurrent mutation in AML. SIGNIFICANCE We defined the spectrum of mutations in relapsed pediatric AML and identified UBTF-TDs as a new recurrent genetic alteration. These duplications are more common in children and define a group of AMLs with intermediate-risk cytogenetic abnormalities, FLT3-ITD and WT1 alterations, and are associated with poor outcomes. See related commentary by Hasserjian and Nardi, p. 173. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Benjamin J. Huang
- Department of Pediatrics, University of California, Benioff Children's Hospital, San Francisco, California
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Juan M. Barajas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Melvin E. Thomas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael P. Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liqing Tian
- 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
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Pandurang Kolekar
- 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
| | - Scott G. Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jamie L. Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew B. Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Amanda R. Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Bengsheng Ju
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Yen-Chun Liu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jenny L. Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Evan Parganas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jonathan Miller
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jason R. Myers
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Todd A. Alonzo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - James R. Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - M. Madan Babu
- Department of Structural Biology and the Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffrey E. Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Xiaotu Ma
- 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
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Nakajima K, Kubota H, Kato I, Isobe K, Ueno H, Kozuki K, Tanaka K, Kawabata N, Mikami T, Tamefusa K, Nishiuchi R, Saida S, Umeda K, Hiramatsu H, Adachi S, Takita J. PAX5 alterations in an infant case of KMT2A-rearranged leukemia with lineage switch. Cancer Sci 2022; 113:2472-2476. [PMID: 35467057 PMCID: PMC9277256 DOI: 10.1111/cas.15380] [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: 03/04/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/27/2022] Open
Abstract
Lineage switch is a rare event at leukemic relapse. While mostly known to occur in KMT2A-rearranged infant leukemia, the underlying mechanism is yet to be depicted. This case report describes a female infant who achieved remission of KMT2A-MLLT3-rearranged acute monocytic leukemia, but six months thereafter, relapsed as KMT2A-MLLT3-rearranged acute lymphocytic leukemia. Whole exome sequencing of the bone marrow obtained pre-post lineage switch revealed two somatic mutations of PAX5 in the relapse sample. These two PAX5 alterations were suggested to be loss of function, thus to have played the driver role in the lineage switch from AML to ALL.
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Affiliation(s)
- Koji Nakajima
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hirohito Kubota
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kiyotaka Isobe
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroo Ueno
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kagehiro Kozuki
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kuniaki Tanaka
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoko Kawabata
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Mikami
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosuke Tamefusa
- Department of Pediatrics, Kochi Health Sciences Center, Kochi, Japan
| | - Ritsuo Nishiuchi
- Department of Pediatrics, Kochi Health Sciences Center, Kochi, Japan
| | - Satoshi Saida
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsutsugu Umeda
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidefumi Hiramatsu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Souichi Adachi
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Barsan V, Xia Y, Klein D, Gonzalez-Pena V, Youssef S, Inaba Y, Mahmud O, Natarajan S, Agarwal V, Pang Y, Autry R, Pui CH, Inaba H, Evans W, Gawad C. Simultaneous monitoring of disease and microbe dynamics through plasma DNA sequencing in pediatric patients with acute lymphoblastic leukemia. SCIENCE ADVANCES 2022; 8:eabj1360. [PMID: 35442732 PMCID: PMC9020671 DOI: 10.1126/sciadv.abj1360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/19/2022] [Indexed: 05/09/2023]
Abstract
Treatment of acute lymphoblastic leukemia (ALL) necessitates continuous risk assessment of leukemic disease burden and infections that arise in the setting of immunosuppression. This study was performed to assess the feasibility of a hybrid capture next-generation sequencing panel to longitudinally measure molecular leukemic disease clearance and microbial species abundance in 20 pediatric patients with ALL throughout induction chemotherapy. This proof of concept helps establish a technical and conceptual framework that we anticipate will be expanded and applied to additional patients with leukemia, as well as extended to additional cancer types. Molecular monitoring can help accelerate the attainment of insights into the temporal biology of host-microbe-leukemia interactions, including how those changes correlate with and alter anticancer therapy efficacy. We also anticipate that fewer invasive bone marrow examinations will be required, as these methods improve with standardization and are validated for clinical use.
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Affiliation(s)
- Valentin Barsan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Yuntao Xia
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - David Klein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Veronica Gonzalez-Pena
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sarah Youssef
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yuki Inaba
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ousman Mahmud
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sivaraman Natarajan
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Vibhu Agarwal
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Yakun Pang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert Autry
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - William Evans
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charles Gawad
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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49
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Semchenkova A, Mikhailova E, Komkov A, Gaskova M, Abasov R, Matveev E, Kazanov M, Mamedov I, Shmitko A, Belova V, Miroshnichenkova A, Illarionova O, Olshanskaya Y, Tsaur G, Verzhbitskaya T, Ponomareva N, Bronin G, Kondratchik K, Fechina L, Diakonova Y, Vavilova L, Myakova N, Novichkova G, Maschan A, Maschan M, Zerkalenkova E, Popov A. Lineage Conversion in Pediatric B-Cell Precursor Acute Leukemia under Blinatumomab Therapy. Int J Mol Sci 2022; 23:4019. [PMID: 35409391 PMCID: PMC8999738 DOI: 10.3390/ijms23074019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/24/2022] [Accepted: 04/02/2022] [Indexed: 12/28/2022] Open
Abstract
We report incidence and deep molecular characteristics of lineage switch in 182 pediatric patients affected by B-cell precursor acute lymphoblastic leukemia (BCP-ALL), who were treated with blinatumomab. We documented six cases of lineage switch that occurred after or during blinatumomab exposure. Therefore, lineage conversion was found in 17.4% of all resistance cases (4/27) and 3.2% of relapses (2/63). Half of patients switched completely from BCP-ALL to CD19-negative acute myeloid leukemia, others retained CD19-positive B-blasts and acquired an additional CD19-negative blast population: myeloid or unclassifiable. Five patients had KMT2A gene rearrangements; one had TCF3::ZNF384 translocation. The presented cases showed consistency of gene rearrangements and fusion transcripts across initially diagnosed leukemia and lineage switch. In two of six patients, the clonal architecture assessed by IG/TR gene rearrangements was stable, while in others, loss of clones or gain of new clones was noted. KMT2A-r patients demonstrated very few additional mutations, while in the TCF3::ZNF384 case, lineage switch was accompanied by a large set of additional mutations. The immunophenotype of an existing leukemia sometimes changes via different mechanisms and with different additional molecular changes. Careful investigation of all BM compartments together with all molecular -minimal residual disease studies can lead to reliable identification of lineage switch.
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Affiliation(s)
- Alexandra Semchenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Ekaterina Mikhailova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Alexander Komkov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117998 Moscow, Russia
| | - Marina Gaskova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Ruslan Abasov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Evgenii Matveev
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Institute for Information Transmission Problems (the Kharkevich Institute, RAS), 127051 Moscow, Russia
| | - Marat Kazanov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Institute for Information Transmission Problems (the Kharkevich Institute, RAS), 127051 Moscow, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Ilgar Mamedov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117998 Moscow, Russia
| | - Anna Shmitko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 119334 Moscow, Russia; (A.S.); (V.B.)
| | - Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 119334 Moscow, Russia; (A.S.); (V.B.)
| | - Anna Miroshnichenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Olga Illarionova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Grigory Tsaur
- Regional Clinical Children Hospital, 620149 Ekaterinburg, Russia; (G.T.); (T.V.); (L.F.)
- Research Institute of Medical Cell Technologies, 620026 Ekaterinburg, Russia
| | - Tatiana Verzhbitskaya
- Regional Clinical Children Hospital, 620149 Ekaterinburg, Russia; (G.T.); (T.V.); (L.F.)
- Research Institute of Medical Cell Technologies, 620026 Ekaterinburg, Russia
| | | | - Gleb Bronin
- Morozov City Children Clinical Hospital, 119049 Moscow, Russia; (G.B.); (K.K.)
| | | | - Larisa Fechina
- Regional Clinical Children Hospital, 620149 Ekaterinburg, Russia; (G.T.); (T.V.); (L.F.)
- Research Institute of Medical Cell Technologies, 620026 Ekaterinburg, Russia
| | - Yulia Diakonova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Liudmila Vavilova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Natalia Myakova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Alexey Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Michael Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Elena Zerkalenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Alexander Popov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
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Distinct genomic landscape of Chinese pediatric acute myeloid leukemia impacts clinical risk classification. Nat Commun 2022; 13:1640. [PMID: 35347147 PMCID: PMC8960760 DOI: 10.1038/s41467-022-29336-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/09/2022] [Indexed: 12/17/2022] Open
Abstract
Studies have revealed key genomic aberrations in pediatric acute myeloid leukemia (AML) based on Western populations. It is unknown to what extent the current genomic findings represent populations with different ethnic backgrounds. Here we present the genomic landscape of driver alterations of Chinese pediatric AML and discover previously undescribed genomic aberrations, including the XPO1-TNRC18 fusion. Comprehensively comparing between the Chinese and Western AML cohorts reveal a substantially distinct genomic alteration profile. For example, Chinese AML patients more commonly exhibit mutations in KIT and CSF3R, and less frequently mutated of genes in the RAS signaling pathway. These differences in mutation frequencies lead to the detection of previously uncharacterized co-occurring mutation pairs. Importantly, the distinct driver profile is clinical relevant. We propose a refined prognosis risk classification model which better reflected the adverse event risk for Chinese AML patients. These results emphasize the importance of genetic background in precision medicine. The genomic landscape of pediatric acute myeloid leukemia (AML) has mostly been characterised for Western populations. Here, the authors identify potential driver alterations in Chinese pediatric AML, which differ from Western populations, and propose a prognostic risk classification model.
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