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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [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: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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2
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Zhang Z, Jing Y, Chen B, Zhang H, Liu T, Dong S, Zhang L, Yan X, Yang S, Chen L, Lin Y, Ru K. The application of targeted RNA sequencing for the analysis of fusion genes, gene mutations, IKZF1 intragenic deletion, and CRLF2 overexpression in acute lymphoblastic leukemia. Int J Lab Hematol 2024; 46:670-677. [PMID: 38553845 DOI: 10.1111/ijlh.14269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/07/2024] [Indexed: 07/04/2024]
Abstract
INTRODUCTION Acute lymphoblastic leukemia (ALL) is characterized by highly genetic heterogeneity, owing to recurrent fusion genes, gene mutations, intragenic deletion, and gene overexpression, which poses significant challenges in clinical detection. RNA sequencing (RNA-seq) is a powerful tool for detecting multiple genetic abnormalities, especially cryptic gene rearrangements, in a single test. METHODS Sixty samples (B-ALL, n = 49; T-ALL, n = 9; mixed phenotype acute leukemia (MPAL), n = 2) and 20 controls were analyzed by targeted RNA-seq panel of 507 genes developed by our lab. Of these, 16 patients were simultaneously analyzed for gene mutations at the DNA level using a next-generation sequencing panel of 51 genes. Fusion genes, CRLF2 expression, and IKZF1 intragenic deletion were also detected by reverse transcription-polymerase chain reaction (RT-PCR). Karyotype analysis was performed using the R-banding and G-banding technique on bone marrow cells after 24 hours of culture. Partial fusion genes were analyzed using fluorescence in situ hybridization (FISH). RESULTS Compared with the results of Karyotype analysis, FISH, and RT-PCR, the detection rate of fusion genes by targeted RNA-seq increased from 48.3% to 58.3%, and six unexpected fusion genes were discovered, along with one rare isoform of IKZF1 intragenic deletion (IK10). The DNA sequencing analysis of 16 ALL patients revealed that 96.2% (25/26) of gene mutations identified at the DNA level were also detectable at the RNA level, except for one mutation with a low variant allele fraction. The detection of CRLF2 overexpression exhibited complete concordance between RT-PCR and RNA-seq. CONCLUSION The utilization of RNA-seq enables the identification of clinically significant genetic abnormalities that may go undetected through conventional detection methods. Its robust analytical performance might bring great application value for clinical diagnosis, prognosis, and therapy in ALL.
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Affiliation(s)
- Zhenyu Zhang
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yu Jing
- Department of Haematology, The Fifth Medical centre of Chinese PLA General Hospital, Beijing, China
| | - Bin Chen
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Hong Zhang
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Tuo Liu
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Shuran Dong
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Lei Zhang
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Xiaoyan Yan
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Shaobin Yang
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Long Chen
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Yani Lin
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Kun Ru
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
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Tabassum N, Muhammad S, Mirza T, Butt Z, Mansoor N. Clinical Characteristics and Cytogenetics of Childhood Acute Lymphoblastic Leukemia in a Single Center in Pakistan. Glob Pediatr Health 2024; 11:2333794X241256863. [PMID: 39070153 PMCID: PMC11283658 DOI: 10.1177/2333794x241256863] [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: 09/26/2023] [Revised: 04/18/2024] [Accepted: 05/07/2024] [Indexed: 07/30/2024] Open
Abstract
Objectives. This study aimed to find the association between clinical characteristics, cytogenetics, and post-induction outcomes of childhood acute lymphoblastic leukemia. Methods. The study was conducted at the Indus Hospital in Karachi. Initial total leukocyte count (TLC), cytogenetics, CNS status, and post-induction remission status were recorded. Results. Out of 108 children diagnosed with ALL, 66 (61.1%) were male and 42 (38.9%) were female. The majority 90 (83.3%) had B-ALL. CNS1 status was observed in 76 (84.4%) B-ALL and 18 (88.9%) T-ALL. All T-ALL and 89 (98.8%) B-ALL achieved remission post-induction. In B-ALL, 50 (55.5%) had a normal diploid karyotype, and 22 (24.4%) had numerical abnormalities. No typical gene rearrangement was observed in 66 (73.3%), 11 (12.2%) had BCR::ABL1, 10 (11.1%) had ETV6::RUNX1 and 3 (3.3%) KMT2A on FISH. No significant difference was observed between cytogenetics and clinical characteristics (P > .05). Conclusion. The study provides valuable data on childhood acute lymphoblastic leukemia in the Pakistani population.
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Ojha A, Zhao SJ, Zhang JT, Simo KA, Liu JY. Gap-App: A sex-distinct AI-based predictor for pancreatic ductal adenocarcinoma survival as a web application open to patients and physicians. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597246. [PMID: 38895246 PMCID: PMC11185613 DOI: 10.1101/2024.06.04.597246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
In this study, using RNA-Seq gene expression data and advanced machine learning techniques, we identified distinct gene expression profiles between male and female pancreatic ductal adenocarcinoma (PDAC) patients. Building upon this insight, we developed sex-specific 3-year survival predictive models along with a single comprehensive model. These sex-specific models outperformed the single general model despite the smaller sample sizes. We further refined our models by using the most important features extracted from these initial models. The refined sex-specific predictive models achieved improved accuracies of 92.62% for males and 91.96% for females, respectively, versus an accuracy of 87.84% from the refined comprehensive model, further highlighting the value of sex-specific analysis. Based on these findings, we created Gap-App, a web application that enables the use of individual gene expression profiles combined with sex information for personalized survival predictions. Gap-App, the first online tool aiming to bridge the gap between complex genomic data and clinical application and facilitating more precise and individualized cancer care, marks a significant advancement in personalized prognosis. The study not only underscores the importance of acknowledging sex differences in personalized prognosis, but also sets the stage for the shift from traditional one-size-fits-all to more personalized and targeted medicine. The GAP-App service is freely available at www.gap-app.org.
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Affiliation(s)
- Anuj Ojha
- Department of Medicine, College of Medicine, University of Toledo, Toledo, OH, USA
- Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH, USA
| | - Shu-Jun Zhao
- Department of Medicine, College of Medicine, University of Toledo, Toledo, OH, USA
- Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH, USA
| | - Jian-Ting Zhang
- Department of Cell and Cancer Biology, College of Medicine, University of Toledo, Toledo, OH, USA
| | - Kerri A. Simo
- Department of Surgery, College of Medicine, University of Toledo, Toledo, OH, USA
- ProMedica Health System, ProMedica Cancer Institute, Toledo, OH, USA
| | - Jing-Yuan Liu
- Department of Medicine, College of Medicine, University of Toledo, Toledo, OH, USA
- Department of Cell and Cancer Biology, College of Medicine, University of Toledo, Toledo, OH, USA
- Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH, USA
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Li X, Huang Z, Zhu L, Lai W, Li Y, Chen H, Liu D, Huang J, Zhou D, Li Y, Weng W, Xu H, Xu L, Luo Z, Fang J. The potential role of RNA sequencing in diagnosing unexplained insensitivity to conventional chemotherapy in pediatric patients with B-cell acute lymphoblastic leukemia. BMC Med Genomics 2024; 17:149. [PMID: 38811988 PMCID: PMC11137891 DOI: 10.1186/s12920-024-01892-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Pediatric B-cell acute lymphoblastic leukemia (B-ALL) is a highly heterogeneous disease. According to large-scale RNA sequencing (RNA-seq) data, B-ALL patients can be divided into more than 10 subgroups. However, many genomic defects associated with resistance mechanisms have not yet been identified. As an individual clinical tool for molecular diagnostic risk classification, RNA-seq and gene expression pattern-based therapy could be potential upcoming strategies. In this study, we retrospectively analyzed the RNA-seq gene expression profiles of 45 children whose molecular diagnostic classifications were inconsistent with the response to chemotherapy. The relationship between the transcriptome and chemotherapy response was analyzed. Fusion gene identification was conducted for the included patients who did not have known high-risk associated fusion genes or gene mutations. The most frequently detected fusion gene pair in the high-risk group was the DHRSX duplication, which is a novel finding. Fusions involving ABL1, LMNB2, NFATC1, PAX5, and TTYH3 at onset were more frequently detected in the high-risk group, while fusions involving LFNG, TTYH3, and NFATC1 were frequently detected in the relapse group. According to the pathways involved, the underlying drug resistance mechanism is related to DNA methylation, autophagy, and protein metabolism. Overall, the implementation of an RNA-seq diagnostic system will identify activated markers associated with chemotherapy response, and guide future treatment adjustments.
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Affiliation(s)
- Xinyu Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Zaoli Huang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Liwen Zhu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Weixin Lai
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Yunyao Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Han Chen
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Diandian Liu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Dunhua Zhou
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Yang Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Wenjun Weng
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Honggui Xu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Luhong Xu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China.
| | - Zhenhua Luo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China.
| | - Jianpei Fang
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China.
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Podgorica M, Drivet E, Viken JK, Richman A, Vestbøstad J, Szodoray P, Kvam AK, Wik HS, Tjønnfjord GE, Munthe LA, Frietze S, Schjerven H. Transcriptome analysis of primary adult B-cell lineage acute lymphoblastic leukemia identifies pathogenic variants and gene fusions, and predicts subtypes for in depth molecular diagnosis. Eur J Haematol 2024; 112:731-742. [PMID: 38192186 PMCID: PMC10990798 DOI: 10.1111/ejh.14164] [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: 07/25/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND B-cell acute lymphoblastic leukemia (B-ALL) is classified into subgroups based on known driver oncogenes and molecular lesions, including translocations and recurrent mutations. However, the current diagnostic tests do not identify subtypes or oncogenic lesions for all B-ALL samples, creating a heterogeneous B-ALL group of unknown subtypes. METHODS We sorted primary adult B-ALL cells and performed transcriptome analysis by bulk RNA sequencing (RNA-seq). RESULTS Transcriptomic analysis of an adult B-ALL cohort allowed the classification of four patient samples with subtypes that were not previously revealed by standard gene panels. The leukemia of two patients were of the DUX4 subtype and two were CRLF2+ Ph-like B-ALL. Furthermore, single nucleotide variant analysis detected the oncogenic NRAS-G12D, KRAS-G12D, and KRAS-G13D mutations in three of the patient samples, presenting targetable mutations. Additional oncogenic variants and gene fusions were uncovered, as well as multiple variants in the PDE4DIP gene across five of the patient samples. CONCLUSION We demonstrate that RNA-seq is an effective tool for precision medicine in B-ALL by providing comprehensive molecular profiling of leukemia cells, identifying subtype and oncogenic lesions, and stratifying patients for appropriate therapy.
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Affiliation(s)
- Mirjam Podgorica
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Elsa Drivet
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jonas Krag Viken
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Laboratory Medicine, University of California San Francisco, CA, USA
| | - Alyssa Richman
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, USA
| | - Johanne Vestbøstad
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter Szodoray
- B Cell Receptor Signaling Group (BCRSG), Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Ann Kristin Kvam
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | | | - Geir E. Tjønnfjord
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Ludvig A. Munthe
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, USA
| | - Hilde Schjerven
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Laboratory Medicine, University of California San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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Jang MA. Genomic technologies for detecting structural variations in hematologic malignancies. Blood Res 2024; 59:1. [PMID: 38485792 PMCID: PMC10903520 DOI: 10.1007/s44313-024-00001-1] [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: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 03/18/2024] Open
Abstract
Genomic structural variations in myeloid, lymphoid, and plasma cell neoplasms can provide key diagnostic, prognostic, and therapeutic information while elucidating the underlying disease biology. Several molecular diagnostic approaches play a central role in evaluating hematological malignancies. Traditional cytogenetic diagnostic assays, such as chromosome banding and fluorescence in situ hybridization, are essential components of the current diagnostic workup that guide clinical care for most hematologic malignancies. However, each assay has inherent limitations, including limited resolution for detecting small structural variations and low coverage, and can only detect alterations in the target regions. Recently, the rapid expansion and increasing availability of novel and comprehensive genomic technologies have led to their use in clinical laboratories for clinical management and translational research. This review aims to describe the clinical relevance of structural variations in hematologic malignancies and introduce genomic technologies that may facilitate personalized tumor characterization and treatment.
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Affiliation(s)
- Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Korea.
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Lestringant V, Guermouche-Flament H, Jimenez-Pocquet M, Gaillard JB, Penther D. Cytogenetics in the management of hematological malignancies: An overview of alternative technologies for cytogenetic characterization. Curr Res Transl Med 2024; 72:103440. [PMID: 38447270 DOI: 10.1016/j.retram.2024.103440] [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: 07/10/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024]
Abstract
Genomic characterization is an essential part of the clinical management of hematological malignancies for diagnostic, prognostic and therapeutic purposes. Although CBA and FISH are still the gold standard in hematology for the detection of CNA and SV, some alternative technologies are intended to complement their deficiencies or even replace them in the more or less near future. In this article, we provide a technological overview of these alternatives. CMA is the historical and well established technique for the high-resolution detection of CNA. For SV detection, there are emerging techniques based on the study of chromatin conformation and more established ones such as RTMLPA for the detection of fusion transcripts and RNA-seq to reveal the molecular consequences of SV. Comprehensive techniques that detect both CNA and SV are the most interesting because they provide all the information in a single examination. Among these, OGM is a promising emerging higher-solution technique that offers a complete solution at a contained cost, at the expense of a relatively low throughput per machine. WGS remains the most adaptable solution, with long-read approaches enabling very high-resolution detection of CAs, but requiring a heavy bioinformatics installation and at a still high cost. However, the development of high-resolution genome-wide detection techniques for CAs allows for a much better description of chromoanagenesis. Therefore, we have included in this review an update on the various existing mechanisms and their consequences and implications, especially prognostic, in hematological malignancies.
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Affiliation(s)
| | | | | | - Jean-Baptiste Gaillard
- Unité de Génétique Chromosomique, Service de Génétique moléculaire et cytogénomique, CHU Montpellier, Montpellier, France
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Paolino J, Tsai HK, Harris MH, Pikman Y. IKZF1 Alterations and Therapeutic Targeting in B-Cell Acute Lymphoblastic Leukemia. Biomedicines 2024; 12:89. [PMID: 38255194 PMCID: PMC10813044 DOI: 10.3390/biomedicines12010089] [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: 11/21/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
IKZF1 encodes the transcription factor IKAROS, a zinc finger DNA-binding protein with a key role in lymphoid lineage development. IKAROS plays a critical role in the development of lineage-restricted mature lymphocytes. Deletions within IKZF1 in B-cell acute lymphoblastic leukemia (B-ALL) lead to a loss of normal IKAROS function, conferring leukemic stem cell properties, including self-renewal and subsequent uncontrolled growth. IKZF1 deletions are associated with treatment resistance and inferior outcomes. Early identification of IKZF1 deletions in B-ALL may inform the intensification of therapy and other potential treatment strategies to improve outcomes in this high-risk leukemia.
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Affiliation(s)
- Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Harrison K. Tsai
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA (M.H.H.)
| | - Marian H. Harris
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA (M.H.H.)
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
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10
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Lee SHR. Toward a Comprehensive One-Stop Shop for Somatic Genomic Profiling in Childhood Acute Lymphoblastic Leukemia. J Mol Diagn 2024; 26:2-4. [PMID: 37972852 DOI: 10.1016/j.jmoldx.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Affiliation(s)
- Shawn H R Lee
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore; Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Hu Z, Kovach AE, Yellapantula V, Ostrow D, Doan A, Ji J, Schmidt RJ, Gu Z, Bhojwani D, Raca G. Transcriptome Sequencing Allows Comprehensive Genomic Characterization of Pediatric B-Acute Lymphoblastic Leukemia in an Academic Clinical Laboratory. J Mol Diagn 2024; 26:49-60. [PMID: 37981088 PMCID: PMC10773144 DOI: 10.1016/j.jmoldx.2023.09.013] [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: 07/03/2023] [Revised: 09/16/2023] [Accepted: 09/28/2023] [Indexed: 11/21/2023] Open
Abstract
Studies have shown the power of transcriptome sequencing [RNA sequencing (RNA-Seq)] in identifying known and novel oncogenic drivers and molecular subtypes of B-acute lymphoblastic leukemia (B-ALL). The current study investigated whether the clinically validated RNA-Seq assay, coupled with a custom analysis pipeline, could be used for a comprehensive B-ALL classification. Following comprehensive clinical testing, RNA-Seq was performed on 76 retrospective B-ALL cases, 28 of which had known and 48 had undetermined subtype. Subtypes were accurately identified in all 28 known cases, and in 38 of 48 unknown cases (79%). The subtypes of the unknown cases included the following: PAX5alt (n = 12), DUX4-rearranged (n = 6), Philadelphia chromosome-like (n = 5), low hyperdiploid (n = 4), ETV6::RUNX1-like (n = 3), MEF2D-rearranged (n = 2), PAX5 P80R (n = 2), ZEB2/CEBP (n = 1), NUTM1-rearranged (n = 1), ZNF384-rearranged (n = 1), and TCF3::PBX1 (n = 1). In 15 of 38 cases (39%), classification based on expression profile was corroborated by detection of subtype-defining oncogenic drivers missed by clinical testing. RNA-Seq analysis also detected large copy number abnormalities, oncogenic hot-spot sequence variants, and intragenic IKZF1 deletions. This pilot study confirms the feasibility of implementing an RNA-Seq workflow for clinical diagnosis of molecular subtypes in pediatric B-ALL, reinforcing that RNA-Seq represents a promising global genomic assay for this heterogeneous leukemia.
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Affiliation(s)
- Zunsong Hu
- Department of Computational and Quantitative Medicine and Systems Biology, Beckman Research Institute of City of Hope, Duarte, California
| | - Alexandra E Kovach
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Venkata Yellapantula
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Dejerianne Ostrow
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Andrew Doan
- Children's Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Los Angeles, California
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine and Systems Biology, Beckman Research Institute of City of Hope, Duarte, California.
| | - Deepa Bhojwani
- Children's Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Los Angeles, California
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.
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12
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Gu A, Schmidt B, Lonsdale A, Jalaldeen R, Kosasih HJ, Brown LM, Sadras T, Ekert PG, Oshlack A. TALLSorts: a T-cell acute lymphoblastic leukemia subtype classifier using RNA-seq expression data. Blood Adv 2023; 7:7402-7406. [PMID: 37903323 PMCID: PMC10758738 DOI: 10.1182/bloodadvances.2023010385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/18/2023] [Accepted: 10/11/2023] [Indexed: 11/01/2023] Open
Affiliation(s)
- Allen Gu
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Breon Schmidt
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Andrew Lonsdale
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Roshan Jalaldeen
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Hansen J. Kosasih
- Children’s Cancer Institute, Kensington, NSW, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | | | - Teresa Sadras
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Paul G. Ekert
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Children’s Cancer Institute, Kensington, NSW, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- School of Clinical Medicine, University of New South Wales Medicine & Health, University of New South Wales, Kensington, NSW, Australia
| | - Alicia Oshlack
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia
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13
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Kovach AE, Wood BL. Updates on lymphoblastic leukemia/lymphoma classification and minimal/measurable residual disease analysis. Semin Diagn Pathol 2023; 40:457-471. [PMID: 37953192 DOI: 10.1053/j.semdp.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Lymphoblastic leukemia/lymphoma (ALL/LBL), especially certain subtypes, continues to confer morbidity and mortality despite significant therapeutic advances. The pathologic classification of ALL/LBL, especially that of B-ALL, has recently substantially expanded with the identification of several distinct and prognostically important genetic drivers. These discoveries are reflected in both current classification systems, the World Health Organization (WHO) 5th edition and the new International Consensus Classification (ICC). In this article, novel subtypes of B-ALL are reviewed, including DUX4, MEF2D and ZNF384-rearranged B-ALL; the rare pediatric entity B-ALL with TLF3::HLF, now added to the classifications, is discussed; updates to the category of B-ALL with BCR::ABL1-like features (Ph-like B-ALL) are summarized; and emerging genetic subtypes of T-ALL are presented. The second half of the article details current approaches to minimal/measurable residual disease (MRD) detection in B-ALL and T-ALL and presents anticipated challenges to current approaches in the burgeoning era of antigen-directed immunotherapy.
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Affiliation(s)
- Alexandra E Kovach
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
| | - Brent L Wood
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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14
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De Bie J, Quessada J, Tueur G, Lefebvre C, Luquet I, Toujani S, Cuccuini W, Lafage-Pochitaloff M, Michaux L. Cytogenetics in the management of T-cell acute lymphoblastic leukemia (T-ALL): Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103431. [PMID: 38016418 DOI: 10.1016/j.retram.2023.103431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Molecular analysis is the hallmark of T-cell acute lymphoblastic leukemia (T-ALL) categorization. Several T-ALL sub-groups are well recognized based on the aberrant expression of specific transcription factors. This recently resulted in the implementation of eight provisional T-ALL entities into the novel 2022 International Consensus Classification, albeit not into the updated World Health Organization classification system. Despite this extensive molecular characterization, cytogenetic analysis remains the backbone of T-ALL diagnosis in many countries as chromosome banding analysis and fluorescence in situ hybridization are relatively inexpensive techniques to obtain results of diagnostic, prognostic and therapeutic interest. Here, we provide an overview of recurrent chromosomal abnormalities detectable in T-ALL patients and propose guidelines regarding their detection. By referring in parallel to the more general molecular classification approach, we hope to offer a diagnostic framework useful in a broad clinical genetic setting.
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Affiliation(s)
- Jolien De Bie
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France; CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes, Marseille 13009, France
| | - Giulia Tueur
- Laboratoire d'hématologie, Hôpital Avicenne, AP-HP, Bobigny 93000, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble 38000, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, CHU Toulouse (IUCT-O), Toulouse 31000, France
| | - Saloua Toujani
- Service de Cytogénétique et Biologie Cellulaire, CHU de Rennes, Rennes 35033, France
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Unité de Cytogénétique, Hôpital Saint-Louis, AP-HP, Paris 75010, France
| | - Marina Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France
| | - Lucienne Michaux
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium; Katholieke Universiteit Leuven, Leuven 3000, Belgium.
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15
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Tueur G, Quessada J, De Bie J, Cuccuini W, Toujani S, Lefebvre C, Luquet I, Michaux L, Lafage-Pochitaloff M. Cytogenetics in the management of B-cell acute lymphoblastic leukemia: Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103434. [PMID: 38064905 DOI: 10.1016/j.retram.2023.103434] [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: 07/09/2023] [Revised: 10/20/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023]
Abstract
Cytogenetic analysis is mandatory at initial assessment of B-cell acute lymphoblastic leukemia (B-ALL) due to its diagnostic and prognostic value. Results from chromosome banding analysis and complementary FISH are taken into account in therapeutic protocols and further completed by other techniques (RT-PCR, SNP-array, MLPA, NGS, OGM). Indeed, new genomic entities have been identified by NGS, mostly RNA sequencing, such as Ph-like ALL that can benefit from targeted therapy. Here, we have attempted to establish cytogenetic guidelines by reviewing the most recent published data including the novel 5th World Health Organization and International Consensus Classifications. We also focused on newly described cytogenomic entities and indicate alternative diagnostic tools such as NGS technology, as its importance is vastly increasing in the diagnostic setting.
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Affiliation(s)
- Giulia Tueur
- Laboratoire d'hématologie, Hôpital Avicenne, AP-HP, Bobigny 93000, France
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France; CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes, Marseille 13009, France
| | - Jolien De Bie
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Unité de Cytogénétique, Hôpital Saint-Louis, AP-HP, Paris 75010, France
| | - Saloua Toujani
- Service de cytogénétique et biologie cellulaire, CHU de Rennes, Rennes 35033, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble 38000, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, CHU Toulouse (IUCT-O), Toulouse 31000, France
| | - Lucienne Michaux
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium; Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Marina Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France.
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16
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Tsai HK, Gogakos T, Lip V, Tsai JM, Li YD, Fisch AS, Weiss J, Yang W, Grimmett L, DiToro D, Schaefer EJ, Lindsley RC, Tran TH, Caron M, Langlois S, Sinnett D, Pikman Y, Nardi V, Kim AS, Silverman LB, Harris MH. Outlier Expression of Isoforms by Targeted or Total RNA Sequencing Identifies Clinically Significant Genomic Variants in Hematolymphoid Tumors. J Mol Diagn 2023; 25:665-681. [PMID: 37419244 PMCID: PMC10488324 DOI: 10.1016/j.jmoldx.2023.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 07/09/2023] Open
Abstract
Recognition of aberrant gene isoforms due to DNA events can impact risk stratification and molecular classification of hematolymphoid tumors. In myelodysplastic syndromes, KMT2A partial tandem duplication (PTD) was one of the top adverse predictors in the International Prognostic Scoring System-Molecular study. In B-cell acute lymphoblastic leukemia (B-ALL), ERG isoforms have been proposed as markers of favorable-risk DUX4 rearrangements, whereas deletion-mediated IKZF1 isoforms are associated with adverse prognosis and have been extended to the high-risk IKZF1plus signature defined by codeletions, including PAX5. In this limited study, outlier expression of isoforms as markers of IKZF1 intragenic or 3' deletions, DUX4 rearrangements, or PAX5 intragenic deletions were 92.3% (48/52), 90% (9/10), or 100% (9/9) sensitive, respectively, and 98.7% (368/373), 100% (35/35), or 97.1% (102/105) specific, respectively, by targeted RNA sequencing, and 84.0% (21/25), 85.7% (6/7), or 81.8% (9/11) sensitive, respectively, and 98.2% (109/111), 98.4% (127/129), or 98.7% (78/79) specific, respectively, by total RNA sequencing. Comprehensive split-read analysis identified expressed DNA breakpoints, cryptic splice sites associated with IKZF1 3' deletions, PTD of IKZF1 exon 5 spanning N159Y in B-ALL with mutated IKZF1 N159Y, and truncated KMT2A-PTD isoforms. Outlier isoforms were also effective targeted RNA markers for PAX5 intragenic amplifications (B-ALL), KMT2A-PTD (myeloid malignant cancers), and rare NOTCH1 intragenic deletions (T-cell acute lymphoblastic leukemia). These findings support the use of outlier isoform analysis as a robust strategy for detecting clinically significant DNA events.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Tasos Gogakos
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Va Lip
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan M Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yen-Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adam S Fisch
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Weiss
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weiping Yang
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie Grimmett
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel DiToro
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eva J Schaefer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Thai Hoa Tran
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada; Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Maxime Caron
- Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Sylvie Langlois
- Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Daniel Sinnett
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada; Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.
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17
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Kovach AE, Raca G. Modern Classification and Management of Pediatric B-cell Leukemia and Lymphoma. Surg Pathol Clin 2023; 16:249-266. [PMID: 37149359 DOI: 10.1016/j.path.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Although pediatric hematopathology overlaps with that of adults, certain forms of leukemia and lymphoma, and many types of reactive conditions affecting the bone marrow and lymph nodes, are unique to children. As part of this series focused on lymphomas, this article (1) details the novel subtypes of lymphoblastic leukemia seen primarily in children and described since the 2017 World Health Organization classification and (2) discusses unique concepts in pediatric hematopathology, including nomenclature changes and evaluation of surgical margins in selected lymphomas.
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Affiliation(s)
- Alexandra E Kovach
- Division of Laboratory Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.
| | - Gordana Raca
- Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA; Division of Genomic Medicine, Department of Pathology and Laboratory Medicine, Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
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18
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Lonsdale A, Halman A, Brown L, Kosasih H, Ekert P, Oshlack A. Toblerone: detecting exon deletion events in cancer using RNA-seq. F1000Res 2023; 12:130. [PMID: 37767021 PMCID: PMC10521068 DOI: 10.12688/f1000research.129490.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/27/2023] [Indexed: 09/29/2023] Open
Abstract
Cancer is driven by mutations of the genome that can result in the activation of oncogenes or repression of tumour suppressor genes. In acute lymphoblastic leukemia (ALL) focal deletions in IKAROS family zinc finger 1 (IKZF1) result in the loss of zinc-finger DNA-binding domains and a dominant negative isoform that is associated with higher rates of relapse and poorer patient outcomes. Clinically, the presence of IKZF1 deletions informs prognosis and treatment options. In this work we developed a method for detecting exon deletions in genes using RNA-seq with application to IKZF1. We developed a pipeline that first uses a custom transcriptome reference consisting of transcripts with exon deletions. Next, RNA-seq reads are mapped using a pseudoalignment algorithm to identify reads that uniquely support deletions. These are then evaluated for evidence of the deletion with respect to gene expression and other samples. We applied the algorithm, named Toblerone, to a cohort of 99 B-ALL paediatric samples including validated IKZF1 deletions. Furthermore, we developed a graphical desktop app for non-bioinformatics users that can quickly and easily identify and report deletions in IKZF1 from RNA-seq data with informative graphical outputs.
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Affiliation(s)
- Andrew Lonsdale
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre, Parkville, VIC, 3052, Australia
| | - Andreas Halman
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
- Peter MacCallum Cancer Centre, Parkville, VIC, 3052, Australia
| | - Lauren Brown
- Murdoch Children’s Research Institute, Parkville, VIC, 3052, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, 2052, Australia
- Children's Cancer Institute Australia, Sydney, NSW, 2052, Australia
| | - Hansen Kosasih
- Murdoch Children’s Research Institute, Parkville, VIC, 3052, Australia
| | - Paul Ekert
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre, Parkville, VIC, 3052, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, 2052, Australia
- Children's Cancer Institute Australia, Sydney, NSW, 2052, Australia
| | - Alicia Oshlack
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
- Peter MacCallum Cancer Centre, Parkville, VIC, 3052, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, 3010, Australia
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19
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Tran TH, Tasian SK. Clinical screening for Ph-like ALL and the developing role of TKIs. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2022; 2022:594-602. [PMID: 36485164 PMCID: PMC9821133 DOI: 10.1182/hematology.2022000357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a common subtype of B-lineage acute lymphoblastic leukemia (B-ALL) with increasing frequency across the age spectrum. Characterized by a kinase-activated gene expression profile and driven by a variety of genetic alterations involving cytokine receptors and kinases, Ph-like ALL is associated with high rates of residual disease and relapse in patients treated with conventional chemotherapy. In this case-based review, we describe the biology of the 2 major ABL-class and JAK pathway genetic subtypes of Ph-like ALL, discuss current diagnostic testing methodologies, and highlight targeted inhibitor and chemo/immunotherapy approaches under clinical investigation in children, adolescents, and adults with these high-risk leukemias.
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Affiliation(s)
- Thai Hoa Tran
- Division of Pediatric Hematology-Oncology, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics and Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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20
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Transcriptome-based molecular subtypes and differentiation hierarchies improve the classification framework of acute myeloid leukemia. Proc Natl Acad Sci U S A 2022; 119:e2211429119. [PMID: 36442087 PMCID: PMC9894241 DOI: 10.1073/pnas.2211429119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The current classification of acute myeloid leukemia (AML) relies largely on genomic alterations. Robust identification of clinically and biologically relevant molecular subtypes from nongenomic high-throughput sequencing data remains challenging. We established the largest multicenter AML cohort (n = 655) in China, with all patients subjected to RNA sequencing (RNA-Seq) and 619 (94.5%) to targeted or whole-exome sequencing (TES/WES). Based on an enhanced consensus clustering, eight stable gene expression subgroups (G1-G8) with unique clinical and biological significance were identified, including two unreported (G5 and G8) and three redefined ones (G4, G6, and G7). Apart from four well-known low-risk subgroups including PML::RARA (G1), CBFB::MYH11 (G2), RUNX1::RUNX1T1 (G3), biallelic CEBPA mutations or -like (G4), four meta-subgroups with poor outcomes were recognized. The G5 (myelodysplasia-related/-like) subgroup enriched clinical, cytogenetic and genetic features mimicking secondary AML, and hotspot mutations of IKZF1 (p.N159S) (n = 7). In contrast, most NPM1 mutations and KMT2A and NUP98 fusions clustered into G6-G8, showing high expression of HOXA/B genes and diverse differentiation stages, from hematopoietic stem/progenitor cell down to monocyte, namely HOX-primitive (G7), HOX-mixed (G8), and HOX-committed (G6). Through constructing prediction models, the eight gene expression subgroups could be reproduced in the Cancer Genome Atlas (TCGA) and Beat AML cohorts. Each subgroup was associated with distinct prognosis and drug sensitivities, supporting the clinical applicability of this transcriptome-based classification of AML. These molecular subgroups illuminate the complex molecular network of AML, which may promote systematic studies of disease pathogenesis and foster the screening of targeted agents based on omics.
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21
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Rehn J, Mayoh C, Heatley SL, McClure BJ, Eadie LN, Schutz C, Yeung DT, Cowley MJ, Breen J, White DL. RaScALL: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL). PLoS Genet 2022; 18:e1010300. [PMID: 36251721 PMCID: PMC9612819 DOI: 10.1371/journal.pgen.1010300] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/27/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022] Open
Abstract
RNA-sequencing (RNA-seq) efforts in acute lymphoblastic leukaemia (ALL) have identified numerous prognostically significant genomic alterations which can guide diagnostic risk stratification and treatment choices when detected early. However, integrating RNA-seq in a clinical setting requires rapid detection and accurate reporting of clinically relevant alterations. Here we present RaScALL, an implementation of the k-mer based variant detection tool km, capable of identifying more than 100 prognostically significant lesions observed in ALL, including gene fusions, single nucleotide variants and focal gene deletions. We compared genomic alterations detected by RaScALL and those reported by alignment-based de novo variant detection tools in a study cohort of 180 Australian patient samples. Results were validated using 100 patient samples from a published North American cohort. RaScALL demonstrated a high degree of accuracy for reporting subtype defining genomic alterations. Gene fusions, including difficult to detect fusions involving EPOR and DUX4, were accurately identified in 98% of reported cases in the study cohort (n = 164) and 95% of samples (n = 63) in the validation cohort. Pathogenic sequence variants were correctly identified in 75% of tested samples, including all cases involving subtype defining variants PAX5 p.P80R (n = 12) and IKZF1 p.N159Y (n = 4). Intragenic IKZF1 deletions resulting in aberrant transcript isoforms were also detectable with 98% accuracy. Importantly, the median analysis time for detection of all targeted alterations averaged 22 minutes per sample, significantly shorter than standard alignment-based approaches. The application of RaScALL enables rapid identification and reporting of previously identified genomic alterations of known clinical relevance.
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Affiliation(s)
- Jacqueline Rehn
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Chelsea Mayoh
- Children’s Cancer Institute, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Susan L Heatley
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, Victoria, Australia
| | - Barbara J McClure
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura N Eadie
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Caitlin Schutz
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - David T Yeung
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia
| | - Mark J Cowley
- Children’s Cancer Institute, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - James Breen
- Black Ochre Data Labs, Telethon Kids Institute, Adelaide, South Australia, Australia
- Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail:
| | - Deborah L White
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, Victoria, Australia
- Australian Genomics Health Alliance (AGHA), Parkville, Victoria, Australia
- Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
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22
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Hergott CB, Kim AS. Molecular Diagnostic Testing for Hematopoietic Neoplasms: Linking Pathogenic Drivers to Personalized Diagnosis. Clin Lab Med 2022; 42:325-347. [PMID: 36150815 DOI: 10.1016/j.cll.2022.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular diagnostics inhabit an increasingly central role in characterizing hematopoietic malignancies. This brief review summarizes the genomic targets important for many major categories of hematopoietic neoplasia by focusing on disease pathogenesis. In myeloid disease, recurrent mutations in key functional classes drive clonal hematopoiesis, on which additional variants can specify clinical presentation and accelerate progression. Lymphoblastic leukemias are frequently initiated by oncogenic fusions that block lymphoid maturation while, in concert with additional mutations, driving proliferation. The links between genetic aberrations and lymphoma patient outcomes have been clarified substantially through the clustering of genomic profiles. Finally, the addition of next-generation sequencing strategies to cytogenetics is refining risk stratification for plasma cell myeloma. In all categories, molecular diagnostics shed light on the unique mechanistic underpinnings of each individual malignancy, thereby empowering more rational, personalized care for these patients.
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Affiliation(s)
- Christopher B Hergott
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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23
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Lopes BA, Poubel CP, Teixeira CE, Caye-Eude A, Cavé H, Meyer C, Marschalek R, Boroni M, Emerenciano M. Novel Diagnostic and Therapeutic Options for KMT2A-Rearranged Acute Leukemias. Front Pharmacol 2022; 13:749472. [PMID: 35734412 PMCID: PMC9208280 DOI: 10.3389/fphar.2022.749472] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 05/04/2022] [Indexed: 11/24/2022] Open
Abstract
The KMT2A (MLL) gene rearrangements (KMT2A-r) are associated with a diverse spectrum of acute leukemias. Although most KMT2A-r are restricted to nine partner genes, we have recently revealed that KMT2A-USP2 fusions are often missed during FISH screening of these genetic alterations. Therefore, complementary methods are important for appropriate detection of any KMT2A-r. Here we use a machine learning model to unravel the most appropriate markers for prediction of KMT2A-r in various types of acute leukemia. A Random Forest and LightGBM classifier was trained to predict KMT2A-r in patients with acute leukemia. Our results revealed a set of 20 genes capable of accurately estimating KMT2A-r. The SKIDA1 (AUC: 0.839; CI: 0.799–0.879) and LAMP5 (AUC: 0.746; CI: 0.685–0.806) overexpression were the better markers associated with KMT2A-r compared to CSPG4 (also named NG2; AUC: 0.722; CI: 0.659–0.784), regardless of the type of acute leukemia. Of importance, high expression levels of LAMP5 estimated the occurrence of all KMT2A-USP2 fusions. Also, we performed drug sensitivity analysis using IC50 data from 345 drugs available in the GDSC database to identify which ones could be used to treat KMT2A-r leukemia. We observed that KMT2A-r cell lines were more sensitive to 5-Fluorouracil (5FU), Gemcitabine (both antimetabolite chemotherapy drugs), WHI-P97 (JAK-3 inhibitor), Foretinib (MET/VEGFR inhibitor), SNX-2112 (Hsp90 inhibitor), AZD6482 (PI3Kβ inhibitor), KU-60019 (ATM kinase inhibitor), and Pevonedistat (NEDD8-activating enzyme (NAE) inhibitor). Moreover, IC50 data from analyses of ex-vivo drug sensitivity to small-molecule inhibitors reveals that Foretinib is a promising drug option for AML patients carrying FLT3 activating mutations. Thus, we provide novel and accurate options for the diagnostic screening and therapy of KMT2A-r leukemia, regardless of leukemia subtype.
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Affiliation(s)
- Bruno A. Lopes
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Caroline Pires Poubel
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Cristiane Esteves Teixeira
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Aurélie Caye-Eude
- Département de Génétique, UF de Génétique moléculaire, Assistance Publique des Hópitaux de Paris (AP-HP), Hópital Robert Debré, Paris, France
- INSERM UMR_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France
| | - Hélène Cavé
- Département de Génétique, UF de Génétique moléculaire, Assistance Publique des Hópitaux de Paris (AP-HP), Hópital Robert Debré, Paris, France
- INSERM UMR_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France
| | - Claus Meyer
- DCAL/Institute of Pharmaceutical Biology, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Rolf Marschalek
- DCAL/Institute of Pharmaceutical Biology, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Mariana Boroni
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Mariana Emerenciano
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
- *Correspondence: Mariana Emerenciano,
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24
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Rack K, Bie J, Ameye G, Gielen O, Demeyer S, Cools J, Keersmaecker K, Vermeesch JR, Maertens J, Segers H, Michaux L, Dewaele B. Optimizing the diagnostic workflow for acute lymphoblastic leukemia by optical genome mapping. Am J Hematol 2022; 97:548-561. [PMID: 35119131 PMCID: PMC9314940 DOI: 10.1002/ajh.26487] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 12/11/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a malignancy that can be subdivided into distinct entities based on clinical, immunophenotypic and genomic features, including mutations, structural variants (SVs), and copy number alterations (CNA). Chromosome banding analysis (CBA) and Fluorescent In‐Situ Hybridization (FISH) together with Multiple Ligation‐dependent Probe Amplification (MLPA), array and PCR‐based methods form the backbone of routine diagnostics. This approach is labor‐intensive, time‐consuming and costly. New molecular technologies now exist that can detect SVs and CNAs in one test. Here we apply one such technology, optical genome mapping (OGM), to the diagnostic work‐up of 41 ALL cases. Compared to our standard testing pathway, OGM identified all recurrent CNAs and SVs as well as additional recurrent SVs and the resulting fusion genes. Based on the genomic profile obtained by OGM, 32 patients could be assigned to one of the major cytogenetic risk groups compared to 23 with the standard approach. The latter identified 24/34 recurrent chromosomal abnormalities, while OGM identified 33/34, misinterpreting only 1 case with low hypodiploidy. The results of MLPA were concordant in 100% of cases. Overall, there was excellent concordance between the results. OGM increased the detection rate and cytogenetic resolution, and abrogated the need for cascade testing, resulting in reduced turnaround times. OGM also provided opportunities for better patient stratification and accurate treatment options. However, for comprehensive cytogenomic testing, OGM still needs to be complemented with CBA or SNP‐array to detect ploidy changes and with BCR::ABL1 FISH to assign patients as soon as possible to targeted therapy.
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Affiliation(s)
- Katrina Rack
- Laboratory for the Cytogenetic and Molecular Diagnosis of Hematological Malignancies, Centre for Human Genetics University Hospitals Leuven Leuven Belgium
| | - Jolien Bie
- Laboratory for the Cytogenetic and Molecular Diagnosis of Hematological Malignancies, Centre for Human Genetics University Hospitals Leuven Leuven Belgium
- Laboratory for the Molecular Biology of Leukemia KU Leuven Leuven Belgium
| | - Geneviève Ameye
- Laboratory for the Cytogenetic and Molecular Diagnosis of Hematological Malignancies, Centre for Human Genetics University Hospitals Leuven Leuven Belgium
| | - Olga Gielen
- Laboratory for the Molecular Biology of Leukemia KU Leuven Leuven Belgium
- Centre for Cancer Biology Flemish Institute for Biotechnology (VIB) Leuven Belgium
| | - Sofie Demeyer
- Laboratory for the Molecular Biology of Leukemia KU Leuven Leuven Belgium
- Centre for Cancer Biology Flemish Institute for Biotechnology (VIB) Leuven Belgium
| | - Jan Cools
- Laboratory for the Molecular Biology of Leukemia KU Leuven Leuven Belgium
- Centre for Cancer Biology Flemish Institute for Biotechnology (VIB) Leuven Belgium
- Leuvens Kanker Instituut (LKI) KU Leuven – University Hospitals Leuven Leuven Belgium
| | - Kim Keersmaecker
- Leuvens Kanker Instituut (LKI) KU Leuven – University Hospitals Leuven Leuven Belgium
- Department of Oncology KU Leuven Leuven Belgium
| | - Joris R. Vermeesch
- Department of Human Genetics KU Leuven Leuven Belgium
- Centre for Human Genetics University Hospitals Leuven Leuven Belgium
| | - Johan Maertens
- Department of Hematology University Hospitals Leuven Leuven Belgium
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI) KU Leuven – University Hospitals Leuven Leuven Belgium
- Department of Pediatric Oncology‐Hematology University Hospitals Leuven Leuven Belgium
| | - Lucienne Michaux
- Laboratory for the Cytogenetic and Molecular Diagnosis of Hematological Malignancies, Centre for Human Genetics University Hospitals Leuven Leuven Belgium
| | - Barbara Dewaele
- Laboratory for the Cytogenetic and Molecular Diagnosis of Hematological Malignancies, Centre for Human Genetics University Hospitals Leuven Leuven Belgium
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25
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ALLSorts: a RNA-Seq subtype classifier for B-Cell Acute Lymphoblastic Leukemia. Blood Adv 2022; 6:4093-4097. [PMID: 35482550 PMCID: PMC9327546 DOI: 10.1182/bloodadvances.2021005894] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
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26
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Wang J, Bhakta N, Ayer Miller V, Revsine M, Litzow MR, Paietta E, Fedoriw Y, Roberts KG, Gu Z, Mullighan CG, Jones CD, Alexander TB. Acute Leukemia Classification Using Transcriptional Profiles From Low-Cost Nanopore mRNA Sequencing. JCO Precis Oncol 2022; 6:e2100326. [PMID: 35442720 PMCID: PMC9200386 DOI: 10.1200/po.21.00326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
PURPOSE Most cases of pediatric acute leukemia occur in low- and middle-income countries, where health centers lack the tools required for accurate diagnosis and disease classification. Recent research shows the robustness of using unbiased short-read RNA sequencing to classify genomic subtypes of acute leukemia. Compared with short-read sequencing, nanopore sequencing has low capital and consumable costs, making it suitable for use in locations with limited health infrastructure. MATERIALS AND METHODS We show the feasibility of nanopore mRNA sequencing on 134 cryopreserved acute leukemia specimens (26 acute myeloid leukemia [AML], 73 B-lineage acute lymphoblastic leukemia [B-ALL], 34 T-lineage acute lymphoblastic leukemia, and one acute undifferentiated leukemia). Using multiple library preparation approaches, we generated long-read transcripts for each sample. We developed a novel composite classification approach to predict acute leukemia lineage and major B-ALL and AML molecular subtypes directly from gene expression profiles. RESULTS We demonstrate accurate classification of acute leukemia samples into AML, B-ALL, or T-lineage acute lymphoblastic leukemia (96.2% of cases are classifiable with a probability of > 0.8, with 100% accuracy) and further classification into clinically actionable genomic subtypes using shallow RNA nanopore sequencing, with 96.2% accuracy for major AML subtypes and 94.1% accuracy for major B-lineage acute lymphoblastic leukemia subtypes. CONCLUSION Transcriptional profiling of acute leukemia samples using nanopore technology for diagnostic classification is feasible and accurate, which has the potential to improve the accuracy of cancer diagnosis in low-resource settings.
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Affiliation(s)
- Jeremy Wang
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Nickhill Bhakta
- Department of Global Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN
| | - Vanessa Ayer Miller
- Office of Clinical Translational Research, University of North Carolina, Chapel Hill, NC
| | - Mahler Revsine
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Mark R. Litzow
- Division of Hematology and Transplant Center, Mayo Clinic Rochester, Rochester, MN
| | | | - Yuri Fedoriw
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC
| | - Kathryn G. Roberts
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine & Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | | | - Corbin D. Jones
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Thomas B. Alexander
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC,Department of Pediatrics, University of North Carolina, Chapel Hill, NC,Thomas B. Alexander, MD, MPH, Department of Pediatrics and Department of Pathology and Laboratory Medicine, University of North Carolina Chapel Hill, 170 Manning Dr, 1185A Houpt Building, CB#7236, Chapel Hill, NC 27599;e-mail:
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27
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Mäkinen VP, Rehn J, Breen J, Yeung D, White DL. Multi-Cohort Transcriptomic Subtyping of B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2022; 23:ijms23094574. [PMID: 35562965 PMCID: PMC9099612 DOI: 10.3390/ijms23094574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022] Open
Abstract
RNA sequencing provides a snapshot of the functional consequences of genomic lesions that drive acute lymphoblastic leukemia (ALL). The aims of this study were to elucidate diagnostic associations (via machine learning) between mRNA-seq profiles, independently verify ALL lesions and develop easy-to-interpret transcriptome-wide biomarkers for ALL subtyping in the clinical setting. A training dataset of 1279 ALL patients from six North American cohorts was used for developing machine learning models. Results were validated in 767 patients from Australia with a quality control dataset across 31 tissues from 1160 non-ALL donors. A novel batch correction method was introduced and applied to adjust for cohort differences. Out of 18,503 genes with usable expression, 11,830 (64%) were confounded by cohort effects and excluded. Six ALL subtypes (ETV6::RUNX1, KMT2A, DUX4, PAX5 P80R, TCF3::PBX1, ZNF384) that covered 32% of patients were robustly detected by mRNA-seq (positive predictive value ≥ 87%). Five other frequent subtypes (CRLF2, hypodiploid, hyperdiploid, PAX5 alterations and Ph-positive) were distinguishable in 40% of patients at lower accuracy (52% ≤ positive predictive value ≤ 73%). Based on these findings, we introduce the Allspice R package to predict ALL subtypes and driver genes from unadjusted mRNA-seq read counts as encountered in real-world settings. Two examples of Allspice applied to previously unseen ALL patient samples with atypical lesions are included.
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Affiliation(s)
- Ville-Petteri Mäkinen
- Computational and Systems Biology Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- Australian Centre for Precision Health, UniSA Clinical & Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
- Computational Medicine, Faculty of Medicine, University of Oulu, FI-90014 Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, FI-90014 Oulu, Finland
- Correspondence: ; Tel.: +61-8-8128-4054
| | - Jacqueline Rehn
- Blood Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; (J.R.); (D.Y.); (D.L.W.)
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
| | - James Breen
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
- South Australian Genomics Centre, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - David Yeung
- Blood Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; (J.R.); (D.Y.); (D.L.W.)
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
- Australian and New Zealand Children’s Oncology Group, Clayton, VIC 3168, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA 5000, Australia
| | - Deborah L. White
- Blood Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; (J.R.); (D.Y.); (D.L.W.)
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
- Australian and New Zealand Children’s Oncology Group, Clayton, VIC 3168, Australia
- Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Australian Genomics Health Alliance, Parkville, VIC 3052, Australia
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28
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Akkari YM, Baughn LB, Dubuc AM, Smith AC, Mallo M, Dal Cin P, Diez Campelo M, Gallego MS, Granada Font I, Haase DT, Schlegelberger B, Slavutsky I, Mecucci C, Levine RL, Hasserjian RP, Solé F, Levy B, Xu X. Guiding the global evolution of cytogenetic testing for hematologic malignancies. Blood 2022; 139:2273-2284. [PMID: 35167654 PMCID: PMC9710485 DOI: 10.1182/blood.2021014309] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
Cytogenetics has long represented a critical component in the clinical evaluation of hematologic malignancies. Chromosome banding studies provide a simultaneous snapshot of genome-wide copy number and structural variation, which have been shown to drive tumorigenesis, define diseases, and guide treatment. Technological innovations in sequencing have ushered in our present-day clinical genomics era. With recent publications highlighting novel sequencing technologies as alternatives to conventional cytogenetic approaches, we, an international consortium of laboratory geneticists, pathologists, and oncologists, describe herein the advantages and limitations of both conventional chromosome banding and novel sequencing technologies and share our considerations on crucial next steps to implement these novel technologies in the global clinical setting for a more accurate cytogenetic evaluation, which may provide improved diagnosis and treatment management. Considering the clinical, logistic, technical, and financial implications, we provide points to consider for the global evolution of cytogenetic testing.
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Affiliation(s)
- Yassmine M.N. Akkari
- Departments of Cytogenetics and Molecular Pathology, Legacy Health, Portland, OR
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Adrian M. Dubuc
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Adam C. Smith
- Laboratory Medicine Program, University Health Network and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Mar Mallo
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Maria Diez Campelo
- Hematology Department University Hospital of Salamanca, IBSAL, Salamanca, Spain
| | - Marta S. Gallego
- Laboratory of Cytogenetics and Molecular Cytogenetics, Department of Clinical Pathology, Italian Hospital, Buenos Aires, Argentina
| | - Isabel Granada Font
- Hematology Laboratory, Germans Trias i Pujol University Hospital–Catalan Institute of Oncology, Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Detlef T. Haase
- Clinics of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Irma Slavutsky
- Laboratory Genetics of Lymphoid Malignancies, Institute of Experimental Medicine, Buenos Aires, Argentina
| | - Cristina Mecucci
- Laboratory of Cytogenetics and Molecular Medicine, Hematology University of Perugia, Perugia, Italy
| | - Ross L. Levine
- Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Francesc Solé
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Brynn Levy
- College of Physicians and Surgeons, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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29
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Monitoring of Leukemia Clones in B-cell Acute Lymphoblastic Leukemia at Diagnosis and During Treatment by Single-cell DNA Amplicon Sequencing. Hemasphere 2022; 6:e700. [PMID: 35291210 PMCID: PMC8916209 DOI: 10.1097/hs9.0000000000000700] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is characterized by the presence of chromosomal changes, including numerical changes, translocations, and deletions, which are often associated with additional single-nucleotide mutations. In this study, we used single cell–targeted DNA sequencing to evaluate the clonal heterogeneity of B-ALL at diagnosis and during chemotherapy treatment. We designed a custom DNA amplicon library targeting mutational hotspot regions (in 110 genes) present in ALL, and we measured the presence of mutations and small insertions/deletions (indels) in bone marrow or blood samples from 12 B-ALL patients, with a median of 7973 cells per sample. Nine of the 12 cases showed at least 1 subclonal mutation, of which cases with PAX5 alterations or high hyperdiploidy (with intermediate to good prognosis) showed a high number of subclones (1 to 7) at diagnosis, defined by a variety of mutations in the JAK/STAT, RAS, or FLT3 signaling pathways. Cases with RAS pathway mutations had multiple mutations in FLT3, NRAS, KRAS, or BRAF in various clones. For those cases where we detected multiple mutational clones at diagnosis, we also studied blood samples during the first weeks of chemotherapy treatment. The leukemia clones disappeared during treatment with various kinetics, and few cells with mutations were easily detectable, even at low frequency (<0.1%). Our data illustrate that about half of the B-ALL cases show >2 subclones at diagnosis and that even very rare mutant cells can be detected at diagnosis or during treatment by single cell–targeted DNA sequencing.
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30
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SFPQ-ABL1 and BCR-ABL1 utilize different signalling networks to drive B-cell acute lymphoblastic leukaemia. Blood Adv 2022; 6:2373-2387. [PMID: 35061886 PMCID: PMC9006296 DOI: 10.1182/bloodadvances.2021006076] [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: 09/02/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
SFPQ-ABL1 is localized to the nuclear compartment and is a relatively weaker driver of cellular proliferation compared with BCR-ABL1. SFPQ-ABL1 and BCR-ABL1 activate distinct signaling networks, both of which converge on inhibiting apoptosis and driving proliferation.
Philadelphia-like (Ph-like) acute lymphoblastic leukemia (ALL) is a high-risk subtype of B-cell ALL characterized by a gene expression profile resembling Philadelphia chromosome–positive ALL (Ph+ ALL) in the absence of BCR-ABL1. Tyrosine kinase–activating fusions, some involving ABL1, are recurrent drivers of Ph-like ALL and are targetable with tyrosine kinase inhibitors (TKIs). We identified a rare instance of SFPQ-ABL1 in a child with Ph-like ALL. SFPQ-ABL1 expressed in cytokine-dependent cell lines was sufficient to transform cells and these cells were sensitive to ABL1-targeting TKIs. In contrast to BCR-ABL1, SFPQ-ABL1 localized to the nuclear compartment and was a weaker driver of cellular proliferation. Phosphoproteomics analysis showed upregulation of cell cycle, DNA replication, and spliceosome pathways, and downregulation of signal transduction pathways, including ErbB, NF-κB, vascular endothelial growth factor (VEGF), and MAPK signaling in SFPQ-ABL1–expressing cells compared with BCR-ABL1–expressing cells. SFPQ-ABL1 expression did not activate phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling and was associated with phosphorylation of G2/M cell cycle proteins. SFPQ-ABL1 was sensitive to navitoclax and S-63845 and promotes cell survival by maintaining expression of Mcl-1 and Bcl-xL. SFPQ-ABL1 has functionally distinct mechanisms by which it drives ALL, including subcellular localization, proliferative capacity, and activation of cellular pathways. These findings highlight the role that fusion partners have in mediating the function of ABL1 fusions.
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31
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Whole-transcriptome analysis in acute lymphoblastic leukemia: a report from the DFCI ALL Consortium Protocol 16-001. Blood Adv 2021; 6:1329-1341. [PMID: 34933343 PMCID: PMC8864659 DOI: 10.1182/bloodadvances.2021005634] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/27/2021] [Indexed: 11/25/2022] Open
Abstract
RNA-seq is feasible in the context of a prospective clinical trial for de novo ALL within a clinically sensitive turnaround time. RNA-seq identified several genetic alterations not detected by conventional methods that confer potential prognostic and therapeutic impact.
The molecular hallmark of childhood acute lymphoblastic leukemia (ALL) is characterized by recurrent, prognostic genetic alterations, many of which are cryptic by conventional cytogenetics. RNA sequencing (RNA-seq) is a powerful next-generation sequencing technology that can simultaneously identify cryptic gene rearrangements, sequence mutations and gene expression profiles in a single assay. We examined the feasibility and utility of incorporating RNA-seq into a prospective multicenter phase 3 clinical trial for children with newly diagnosed ALL. The Dana-Farber Cancer Institute ALL Consortium Protocol 16-001 enrolled 173 patients with ALL who consented to optional studies and had samples available for RNA-seq. RNA-seq identified at least 1 alteration in 157 patients (91%). Fusion detection was 100% concordant with results obtained from conventional cytogenetic analyses. An additional 56 gene fusions were identified by RNA-seq, many of which confer prognostic or therapeutic significance. Gene expression profiling enabled further molecular classification into the following B-cell ALL (B-ALL) subgroups: high hyperdiploid (n = 36), ETV6-RUNX1/-like (n = 31), TCF3-PBX1 (n = 7), KMT2A-rearranged (KMT2A-R; n = 5), intrachromosomal amplification of chromosome 21 (iAMP21) (n = 1), hypodiploid (n = 1), Philadelphia chromosome (Ph)-positive/Ph-like (n = 16), DUX4-R (n = 11), PAX5 alterations (PAX5 alt; n = 11), PAX5 P80R (n = 1), ZNF384-R (n = 4), NUTM1-R (n = 1), MEF2D-R (n = 1), and others (n = 10). RNA-seq identified 141 nonsynonymous mutations in 93 patients (54%); the most frequent were RAS-MAPK pathway mutations. Among 79 patients with both low-density array and RNA-seq data for the Philadelphia chromosome-like gene signature prediction, results were concordant in 74 patients (94%). In conclusion, RNA-seq identified several clinically relevant genetic alterations not detected by conventional methods, which supports the integration of this technology into front-line pediatric ALL trials. This trial was registered at www.clinicaltrials.gov as #NCT03020030.
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32
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Schmidt B, Cmero M, Ekert P, Davidson N, Oshlack A. Slinker: Visualising novel splicing events in RNA-Seq data. F1000Res 2021; 10:1255. [PMID: 35035899 PMCID: PMC8749905 DOI: 10.12688/f1000research.74836.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/29/2021] [Indexed: 11/30/2022] Open
Abstract
Visualisation of the transcriptome relative to a reference genome is fraught with sparsity. This is due to RNA sequencing (RNA-Seq) reads being predominantly mapped to exons that account for just under 3% of the human genome. Recently, we have used exon-only references, superTranscripts, to improve visualisation of aligned RNA-Seq data through the omission of supposedly unexpressed regions such as introns. However, variation within these regions can lead to novel splicing events that may drive a pathogenic phenotype. In these cases, the loss of information in only retaining annotated exons presents significant drawbacks. Here we present Slinker, a bioinformatics pipeline written in Python and Bpipe that uses a data-driven approach to assemble sample-specific superTranscripts. At its core, Slinker uses
Stringtie2 to assemble transcripts with any sequence across any gene. This assembly is merged with reference transcripts, converted to a superTranscript, of which rich visualisations are made through
Plotly with associated annotation and coverage information. Slinker was validated on five novel splicing events of rare disease samples from a cohort of primary muscular disorders. In addition, Slinker was shown to be effective in visualising deletion events within transcriptomes of tumour samples in the important leukemia gene, IKZF1. Slinker offers a succinct visualisation of RNA-Seq alignments across typically sparse regions and is freely available on Github.
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Affiliation(s)
- Breon Schmidt
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia
- School of BioScience, University of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Marek Cmero
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, 3000, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Paul Ekert
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, 3000, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, 3052, Australia
- Children’s Cancer Institute, Lowy Cancer Centre, Kensington, New South Wales, 2033, Australia
- School of Women’s and Children’s Health, University of New South Wales, Sydney, Victoria, 2052, Australia
| | - Nadia Davidson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia
- School of BioScience, University of Melbourne, Melbourne, Victoria, 3000, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Alicia Oshlack
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia
- School of BioScience, University of Melbourne, Melbourne, Victoria, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, 3000, Australia
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Transcriptional and Mutational Profiling of B-Other Acute Lymphoblastic Leukemia for Improved Diagnostics. Cancers (Basel) 2021; 13:cancers13225653. [PMID: 34830809 PMCID: PMC8616234 DOI: 10.3390/cancers13225653] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 12/11/2022] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common cancer in children, and significant progress has been made in diagnostics and the treatment of this disease based on the subtypes of BCP-ALL. However, in a large proportion of cases (B-other), recurrent BCP-ALL-associated genomic alterations remain unidentifiable by current diagnostic procedures. In this study, we performed RNA sequencing and analyzed gene fusions, expression profiles, and mutations in diagnostic samples of 185 children with BCP-ALL. Gene expression clustering showed that a subset of B-other samples partially clusters with some of the known subgroups, particularly DUX4-positive. Mutation analysis coupled with gene expression profiling revealed the presence of distinctive BCP-ALL subgroups, characterized by the presence of mutations in known ALL driver genes, e.g., PAX5 and IKZF1. Moreover, we identified novel fusion partners of lymphoid lineage transcriptional factors ETV6, IKZF1 and PAX5. In addition, we report on low blast count detection thresholds and show that the use of EDTA tubes for sample collection does not have adverse effects on sequencing and downstream analysis. Taken together, our findings demonstrate the applicability of whole-transcriptome sequencing for personalized diagnostics in pediatric ALL, including tentative classification of the B-other cases that are difficult to diagnose using conventional methods.
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Cmero M, Schmidt B, Majewski IJ, Ekert PG, Oshlack A, Davidson NM. MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data. Genome Biol 2021; 22:296. [PMID: 34686194 PMCID: PMC8532352 DOI: 10.1186/s13059-021-02507-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/27/2021] [Indexed: 12/13/2022] Open
Abstract
Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify all types of variants in transcriptomes we developed MINTIE, an integrated pipeline for RNA-seq data. We take a reference-free approach, combining de novo assembly of transcripts with differential expression analysis to identify up-regulated novel variants in a case sample. We compare MINTIE with eight other approaches, detecting > 85% of variants while no other method is able to achieve this. We posit that MINTIE will be able to identify new disease variants across a range of disease types.
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Affiliation(s)
- Marek Cmero
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Parkville, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Breon Schmidt
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Parkville, Australia.,School of BioSciences, University of Melbourne, Parkville, Australia
| | - Ian J Majewski
- Walter and Eliza Hall Institute, Parkville, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Paul G Ekert
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Parkville, Australia.,Children's Cancer Institute, UNSW, Sydney, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Alicia Oshlack
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Parkville, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia. .,School of BioSciences, University of Melbourne, Parkville, Australia.
| | - Nadia M Davidson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Parkville, Australia. .,School of BioSciences, University of Melbourne, Parkville, Australia.
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Schwab CJ, Murdy D, Butler E, Enshaei A, Winterman E, Cranston RE, Ryan S, Barretta E, Hawking Z, Murray J, Antony G, Vora A, Moorman AV, Harrison CJ. Genetic characterisation of childhood B-other-acute lymphoblastic leukaemia in UK patients by fluorescence in situ hybridisation and Multiplex Ligation-dependent Probe Amplification. Br J Haematol 2021; 196:753-763. [PMID: 34676543 DOI: 10.1111/bjh.17869] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/26/2022]
Abstract
While next-generation sequencing technologies provide excellent strategies to screen for newly defined genetic abnormalities of prognostic or therapeutic significance in patients with B-other-acute lymphoblastic leukaemia (ALL), they are not widely available. We used a dual screening approach, incorporating fluorescence in situ hybridisation (FISH) and Multiplex Ligation-dependent Probe Amplification (MLPA), to establish the frequency and long-term outcome of a representative cohort of specific subgroups of B-other-ALL recruited to the childhood ALL trial, UKALL2003. We focussed on abnormalities of known prognostic significance, including ABL-class fusions and ERG deletions, as a surrogate marker for DUX4-rearranged ALL. ABL-class fusions accounted for ~4% of B-other-ALL and were associated with high levels of minimal residual disease (MRD; 14/23 with MRD >5%) and a high relapse rate (55·7%) following treatment without tyrosine kinase inhibitor (TKI), confirming the importance of prospective screening with a view to incorporating TKI into therapy. Patients with deletions of ERG (~10% of B-other-ALL) had a 10-year event-free-survival of 97·2%, validating previous reports of their excellent outcome. Rearrangements of ZNF384, MEF2D and NUTM1 were observed at low frequencies. Here, we estimate that approximately one third of B-other-ALL patients can be reliably classified into one of the known genetic subgroups using our dual screening method. This approach is rapid, accurate and readily incorporated into routine testing.
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Affiliation(s)
- Claire J Schwab
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Daniel Murdy
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Ellie Butler
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Amir Enshaei
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Emily Winterman
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Ruth E Cranston
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Sarra Ryan
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Emilio Barretta
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Zoe Hawking
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - James Murray
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Grace Antony
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Ajay Vora
- Department of Haematology, Great Ormond Street Hospital, London, UK
| | - Anthony V Moorman
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
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Lilljebjörn H, Orsmark-Pietras C, Mitelman F, Hagström-Andersson A, Fioretos T. Transcriptomics paving the way for improved diagnostics and precision medicine of acute leukemia. Semin Cancer Biol 2021; 84:40-49. [PMID: 34606984 DOI: 10.1016/j.semcancer.2021.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/26/2022]
Abstract
Transcriptional profiling of acute leukemia, specifically by RNA-sequencing or whole transcriptome sequencing (WTS), has provided fundamental insights into its underlying disease biology and allows unbiased detection of oncogenic gene fusions, as well as of gene expression signatures that can be used for improved disease classification. While used as a research tool for many years, RNA-sequencing is becoming increasingly used in clinical diagnostics. Here, we highlight key transcriptomic studies of acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) that have improved our biological understanding of these heterogeneous malignant disorders and have paved the way for translation into clinical diagnostics. Recent single-cell transcriptomic studies of ALL and AML, which provide new insights into the cellular ecosystem of acute leukemia and point to future clinical utility, are also reviewed. Finally, we discuss current challenges that need to be overcome for a more wide-spread adoption of RNA-sequencing in clinical diagnostics and how this technology significantly can aid the identification of genetic alterations in current guidelines and of newly emerging disease entities, some of which are critical to identify because of the availability of targeted therapies, thereby paving the way for improved precision medicine of acute leukemia.
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Affiliation(s)
- Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Christina Orsmark-Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anna Hagström-Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Center for Translational Genomics, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Center for Translational Genomics, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.
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Ni Chin WH, Li Z, Jiang N, Lim EH, Suang Lim JY, Lu Y, Chiew KH, Yin Kham SK, Zhi Oh BL, Tan AM, Ariffin H, Yang JJ, Eng-Juh Yeoh A. Practical Considerations for Using RNA Sequencing in Management of B-Cell Acute Lymphoblastic Leukemia: Malaysia-Singapore Acute Lymphoblastic Leukemia-Sequencing 2020 Implementation Strategy. J Mol Diagn 2021; 23:1359-1372. [PMID: 34365011 DOI: 10.1016/j.jmoldx.2021.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 12/31/2022] Open
Abstract
Despite the immense genetic heterogeneity of B-cell acute lymphoblastic leukemia (ALL), RNA sequencing (RNA-Seq) could comprehensively interrogate its genetic drivers, assigning a specific molecular subtype in >90% of patients. However, study groups have only started to use RNA-Seq. For broader clinical use, technical, quality control, and appropriate performance validation are needed. We describe the development and validation of an RNA-Seq workflow for subtype classification, TPMT/NUDT15/TP53 variant discovery, and IGH disease clone identification for Malaysia-Singapore ALL sequencing (ALL-Seq) 2020. We validated this workflow in 377 patients in our preceding Malaysia-Singapore ALL-Seq 2003/Malaysia-Singapore ALL-Seq 2010 studies and proposed the quality control measures for RNA quality, library size, sequencing, and data analysis using the International Organization for Standardization 15189 quality and competence standard for medical laboratories. Compared with conventional methods, we achieved >95% accuracy in oncogene fusion identification, digital karyotyping, and TPMT and NUDT15 variant discovery. We found seven pathogenic TP53 mutations, confirmed with Sanger sequencing, which conferred a poorer outcome. Applying this workflow prospectively to the first 21 patients in Malaysia-Singapore ALL-Seq 2020, we identified the genetic drivers and IGH disease clones in >90% of patients with concordant TPMT, NUDT15, and TP53 variants using PCR-based methods. The median turnaround time was 12 days, which was clinically actionable. In conclusion, RNA-Seq workflow could be used clinically in management of B-cell ALL patients.
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Affiliation(s)
- Winnie H Ni Chin
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zhenhua Li
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Nan Jiang
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Evelyn H Lim
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Joshua Y Suang Lim
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yi Lu
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kean H Chiew
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shirley K Yin Kham
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bernice L Zhi Oh
- Viva-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore
| | - Ah M Tan
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Hany Ariffin
- University of Malaya Cancer Research Institute, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Allen Eng-Juh Yeoh
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Viva-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore.
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Haferlach C, Walter W, Stengel A, Meggendorfer M, Hutter S, Kern W, Haferlach T. The diverse landscape of fusion transcripts in 25 different hematological entities. Leuk Lymphoma 2021; 62:3292-3295. [PMID: 34282718 DOI: 10.1080/10428194.2021.1953009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ribera JM. Philadelphia chromosome-like acute lymphoblastic leukemia. Still a pending matter. Haematologica 2021; 106:1514-1516. [PMID: 34060295 PMCID: PMC8168492 DOI: 10.3324/haematol.2020.270645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 12/21/2022] Open
Affiliation(s)
- Josep-Maria Ribera
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona and Universitat Autònoma de Barcelona.
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Mäkinen A, Nikkilä A, Mehtonen J, Teppo S, Oksa L, Nordlund J, Rounioja S, Pohjolainen V, Laukkanen S, Heinäniemi M, Paavonen T, Lohi O. Expression of BCL6 in paediatric B-cell acute lymphoblastic leukaemia and association with prognosis. Pathology 2021; 53:875-882. [PMID: 34049715 DOI: 10.1016/j.pathol.2021.02.013] [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: 11/03/2020] [Revised: 01/30/2021] [Accepted: 02/15/2021] [Indexed: 11/28/2022]
Abstract
B-cell lineage acute lymphoblastic leukaemia (B-ALL) is the most common paediatric malignancy. Transcription factor B-cell lymphoma 6 (BCL6) is essential to germinal centre formation and antibody affinity maturation and plays a major role in mature B-cell malignancies. More recently, it was shown to act as a critical downstream regulator in pre-BCR+ B-ALL. We investigated the expression of the BCL6 protein in a population-based cohort of paediatric B-ALL cases and detected moderate to strong positivity through immunohistochemistry in 7% of cases (8/117); however, only two of eight BCL6 cases (25%) co-expressed the ZAP70 protein. In light of these data, the subtype with active pre-BCR signalling constitutes a rare entity in paediatric B-ALL. In three independent larger cohorts with gene expression data, high BCL6 mRNA levels were associated with the TCF3-PBX1, Ph-like, NUTM1, MEF2D and PAX5-alt subgroups and the 'metagene' signature for pre-BCR-associated genes. However, higher-than-median BCL6 mRNA level alone was associated with favourable event free survival in the Nordic paediatric cohort, indicating that using BCL6 as a diagnostic marker requires careful design, and evaluation of protein level is needed alongside the genetic or transcriptomic data.
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Affiliation(s)
- Artturi Mäkinen
- Faculty of Medicine and Health Technology, Tampere Center for Child Health Research, Tampere University, Tampere, Finland; Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland.
| | - Atte Nikkilä
- Faculty of Medicine and Health Technology, Tampere Center for Child Health Research, Tampere University, Tampere, Finland
| | - Juha Mehtonen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Susanna Teppo
- Faculty of Medicine and Health Technology, Tampere Center for Child Health Research, Tampere University, Tampere, Finland
| | - Laura Oksa
- Faculty of Medicine and Health Technology, Tampere Center for Child Health Research, Tampere University, Tampere, Finland
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Samuli Rounioja
- Fimlab Laboratories, Department of Hematology, Tampere University Hospital, Tampere, Finland
| | - Virva Pohjolainen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Saara Laukkanen
- Faculty of Medicine and Health Technology, Tampere Center for Child Health Research, Tampere University, Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Timo Paavonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland; Department of Pathology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli Lohi
- Faculty of Medicine and Health Technology, Tampere Center for Child Health Research, Tampere University, Tampere, Finland; Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
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Féral K, Jaud M, Philippe C, Di Bella D, Pyronnet S, Rouault-Pierre K, Mazzolini L, Touriol C. ER Stress and Unfolded Protein Response in Leukemia: Friend, Foe, or Both? Biomolecules 2021; 11:biom11020199. [PMID: 33573353 PMCID: PMC7911881 DOI: 10.3390/biom11020199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
The unfolded protein response (UPR) is an evolutionarily conserved adaptive signaling pathway triggered by a stress of the endoplasmic reticulum (ER) lumen compartment, which is initiated by the accumulation of unfolded proteins. This response, mediated by three sensors-Inositol Requiring Enzyme 1 (IRE1), Activating Transcription Factor 6 (ATF6), and Protein Kinase RNA-Like Endoplasmic Reticulum Kinase (PERK)—allows restoring protein homeostasis and maintaining cell survival. UPR represents a major cytoprotective signaling network for cancer cells, which frequently experience disturbed proteostasis owing to their rapid proliferation in an usually unfavorable microenvironment. Increased basal UPR also participates in the resistance of tumor cells against chemotherapy. UPR activation also occurs during hematopoiesis, and growing evidence supports the critical cytoprotective role played by ER stress in the emergence and proliferation of leukemic cells. In case of severe or prolonged stress, pro-survival UPR may however evolve into a cell death program called terminal UPR. Interestingly, a large number of studies have revealed that the induction of proapoptotic UPR can also strongly contribute to the sensitization of leukemic cells to chemotherapy. Here, we review the current knowledge on the consequences of the deregulation of UPR signaling in leukemias and their implications for the treatment of these diseases.
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Affiliation(s)
- Kelly Féral
- Inserm UMR1037-Cancer Research Center of Toulouse, 2 avenue Hubert Curien, Oncopole entrée C, CS 53717, 31037 Toulouse, France; (K.F.); (M.J.); (S.P.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France
| | - Manon Jaud
- Inserm UMR1037-Cancer Research Center of Toulouse, 2 avenue Hubert Curien, Oncopole entrée C, CS 53717, 31037 Toulouse, France; (K.F.); (M.J.); (S.P.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France
| | - Céline Philippe
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (K.R.-P.)
| | - Doriana Di Bella
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (K.R.-P.)
| | - Stéphane Pyronnet
- Inserm UMR1037-Cancer Research Center of Toulouse, 2 avenue Hubert Curien, Oncopole entrée C, CS 53717, 31037 Toulouse, France; (K.F.); (M.J.); (S.P.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France
| | - Kevin Rouault-Pierre
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (K.R.-P.)
| | - Laurent Mazzolini
- Inserm UMR1037-Cancer Research Center of Toulouse, 2 avenue Hubert Curien, Oncopole entrée C, CS 53717, 31037 Toulouse, France; (K.F.); (M.J.); (S.P.)
- CNRS ERL5294, CRCT, F-31037 Toulouse, France
- Correspondence: (L.M.); (C.T.)
| | - Christian Touriol
- Inserm UMR1037-Cancer Research Center of Toulouse, 2 avenue Hubert Curien, Oncopole entrée C, CS 53717, 31037 Toulouse, France; (K.F.); (M.J.); (S.P.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France
- Correspondence: (L.M.); (C.T.)
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Emerging molecular subtypes and therapeutic targets in B-cell precursor acute lymphoblastic leukemia. Front Med 2021; 15:347-371. [PMID: 33400146 DOI: 10.1007/s11684-020-0821-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by genetic alterations with high heterogeneity. Precise subtypes with distinct genomic and/or gene expression patterns have been recently revealed using high-throughput sequencing technology. Most of these profiles are associated with recurrent non-overlapping rearrangements or hotspot point mutations that are analogous to the established subtypes, such as DUX4 rearrangements, MEF2D rearrangements, ZNF384/ZNF362 rearrangements, NUTM1 rearrangements, BCL2/MYC and/or BCL6 rearrangements, ETV6-RUNX1-like gene expression, PAX5alt (diverse PAX5 alterations, including rearrangements, intragenic amplifications, or mutations), and hotspot mutations PAX5 (p.Pro80Arg) with biallelic PAX5 alterations, IKZF1 (p.Asn159Tyr), and ZEB2 (p.His1038Arg). These molecular subtypes could be classified by gene expression patterns with RNA-seq technology. Refined molecular classification greatly improved the treatment strategy. Multiagent therapy regimens, including target inhibitors (e.g., imatinib), immunomodulators, monoclonal antibodies, and chimeric antigen receptor T-cell (CAR-T) therapy, are transforming the clinical practice from chemotherapy drugs to personalized medicine in the field of risk-directed disease management. We provide an update on our knowledge of emerging molecular subtypes and therapeutic targets in BCP-ALL.
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MLL-TFE3: a novel and aggressive KMT2A fusion identified in infant leukemia. Blood Adv 2020; 4:4918-4923. [PMID: 33035331 DOI: 10.1182/bloodadvances.2020002708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/30/2020] [Indexed: 12/24/2022] Open
Abstract
Key Points
A novel KMT2A-rearrangement, MLL-TFE3, was identified in an infant leukemia patient. MLL-TFE3 expression produces aggressive leukemia in a mouse model.
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Rehn JA, O’Connor MJ, White DL, Yeung DT. DUX Hunting-Clinical Features and Diagnostic Challenges Associated with DUX4-Rearranged Leukaemia. Cancers (Basel) 2020; 12:cancers12102815. [PMID: 33007870 PMCID: PMC7599557 DOI: 10.3390/cancers12102815] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary DUX4-rearrangement (DUX4r) is a recently discovered recurrent genomic lesion reported in 4–7% of childhood B cell acute lymphoblastic leukaemia (B-ALL) cases. This subtype has favourable outcomes, especially in children and adolescents treated with intensive chemotherapy. The fusion most commonly links the hypervariable IGH gene to DUX4 a gene located within the D4Z4 macrosatellite repeat on chromosome 4. DUX4r is cryptic to most standard diagnostic techniques, and difficult to identify even with next generation sequencing assays. This review summarises the clinical features and molecular genetics of DUX4r B-ALL and proposes prospective new diagnostic methods. Abstract DUX4-rearrangement (DUX4r) is a recently discovered recurrent genomic lesion reported in 4–7% of childhood B cell acute lymphoblastic leukaemia (B-ALL) cases. This subtype has favourable outcomes, especially in children and adolescents treated with intensive chemotherapy. The fusion most commonly links the hypervariable IGH gene to DUX4 a gene located within the D4Z4 macrosatellite repeat on chromosome 4, with a homologous polymorphic repeat on chromosome 10. DUX4r is cryptic to most standard diagnostic techniques, and difficult to identify even with next generation sequencing assays. This review summarises the clinical features and molecular genetics of DUX4r B-ALL and proposes prospective new diagnostic methods.
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Affiliation(s)
- Jacqueline A. Rehn
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia; (J.A.R.); (D.T.Y.)
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA 5000, Australia
| | - Matthew J. O’Connor
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia; (J.A.R.); (D.T.Y.)
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA 5000, Australia
- Michael Rice Centre for Haematology and Oncology, Womens’s & Children’s Hospital, North Adelaide, SA 5006, Australia
| | - Deborah L. White
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia; (J.A.R.); (D.T.Y.)
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA 5000, Australia
- Australian Genomics, The Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, VIC 3168, Australia
- Correspondence:
| | - David T. Yeung
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia; (J.A.R.); (D.T.Y.)
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA 5000, Australia
- Department of Haematology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
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Comprehensive Custom NGS Panel Validation for the Improvement of the Stratification of B-Acute Lymphoblastic Leukemia Patients. J Pers Med 2020; 10:jpm10030137. [PMID: 32967112 PMCID: PMC7565730 DOI: 10.3390/jpm10030137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/13/2020] [Accepted: 09/19/2020] [Indexed: 01/06/2023] Open
Abstract
Background: B-acute lymphoblastic leukemia (B-ALL) is a hematological neoplasm of the stem lymphoid cell of the B lineage, characterized by the presence of genetic alterations closely related to the course of the disease. The number of alterations identified in these patients grows as studies of the disease progress, but in clinical practice, the conventional techniques frequently used are only capable of detecting the most common alterations. However, techniques, such as next-generation sequencing (NGS), are being implemented to detect a wide spectrum of new alterations that also include point mutations. Methods: In this study, we designed and validated a comprehensive custom NGS panel to detect the main genetic alterations present in the disease in a single step. For this purpose, 75 B-ALL diagnosis samples from patients previously characterized by standard-of-care diagnostic techniques were sequenced. Results: The use of the custom NGS panel allowed the correct detection of the main genetic alterations present in B-ALL patients, including the presence of an aneuploid clone in 14 of the samples and some of the recurrent fusion genes in 35 of the samples. The panel was also able to successfully detect a number of secondary alterations, such as single nucleotide variants (SNVs) and copy number variations (CNVs) in 66 and 46 of the samples analyzed, respectively, allowing for further refinement of the stratification of patients. The custom NGS panel could also detect alterations with a high level of sensitivity and reproducibility when the findings obtained by NGS were compared with those obtained from other conventional techniques. Conclusions: The use of this custom NGS panel allows us to quickly and efficiently detect the main genetic alterations present in B-ALL patients in a single assay (SNVs and insertions/deletions (INDELs), recurrent fusion genes, CNVs, aneuploidies, and single nucleotide polymorphisms (SNPs) associated with pharmacogenetics). The application of this panel would thus allow us to speed up and simplify the molecular diagnosis of patients, helping patient stratification and management.
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