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Schmitt AD, Sikkink K, Ahmed AA, Melnyk S, Reid D, Van Meter L, Guest EM, Lansdon LA, Pastinen T, Pushel I, Yoo B, Farooqi MS. Evaluation of Hi-C Sequencing for Detection of Gene Fusions in Hematologic and Solid Tumor Pediatric Cancer Samples. Cancers (Basel) 2024; 16:2936. [PMID: 39272793 PMCID: PMC11394547 DOI: 10.3390/cancers16172936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/15/2024] [Accepted: 08/19/2024] [Indexed: 09/15/2024] Open
Abstract
Hi-C sequencing is a DNA-based next-generation sequencing method that preserves the 3D genome conformation and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate Hi-C as a potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia and sarcoma specimens. Archived viable and non-viable frozen leukemic cells and formalin-fixed paraffin-embedded (FFPE) tumor specimens were analyzed. Pediatric acute myeloid leukemia (AML) and alveolar rhabdomyosarcoma (A-RMS) specimens with known genomic rearrangements were subjected to Hi-C to assess analytical concordance. Subsequently, a discovery cohort consisting of AML and acute lymphoblastic leukemia (ALL) cases without known genomic rearrangements based on prior clinical diagnostic testing was evaluated to determine whether Hi-C could detect rearrangements. Using a standard sequencing depth of 50 million raw read-pairs per sample, or approximately 5X raw genomic coverage, we observed 100% concordance between Hi-C and previous clinical cytogenetic and molecular testing. In the discovery cohort, a clinically relevant gene fusion was detected in 45% of leukemia cases (5/11). This study provides an institutional proof of principle evaluation of Hi-C sequencing to medical diagnostic testing as it identified several clinically relevant rearrangements, including those that were missed by current clinical testing workflows.
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Affiliation(s)
| | - Kristin Sikkink
- Arima Genomics, 6354 Corte Del Abeto, Carlsbad, CA 92011, USA
| | - Atif A Ahmed
- Department of Pathology, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Shadi Melnyk
- Arima Genomics, 6354 Corte Del Abeto, Carlsbad, CA 92011, USA
| | - Derek Reid
- Arima Genomics, 6354 Corte Del Abeto, Carlsbad, CA 92011, USA
| | - Logan Van Meter
- Arima Genomics, 6354 Corte Del Abeto, Carlsbad, CA 92011, USA
| | - Erin M Guest
- Department of Pediatrics, Division of Hematology & Oncology, Children's Mercy Kansas City, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Lisa A Lansdon
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, 2411 Holmes St., Kansas City, MO 64108, USA
- Department of Pathology & Laboratory Medicine, Children's Mercy Kansas City, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Tomi Pastinen
- University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, 2411 Holmes St., Kansas City, MO 64108, USA
| | - Irina Pushel
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, 2411 Holmes St., Kansas City, MO 64108, USA
| | - Byunggil Yoo
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, 2411 Holmes St., Kansas City, MO 64108, USA
- Department of Pathology & Laboratory Medicine, Children's Mercy Kansas City, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Midhat S Farooqi
- University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, 2411 Holmes St., Kansas City, MO 64108, USA
- Department of Pathology & Laboratory Medicine, Children's Mercy Kansas City, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
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2
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Schmitt AD, Sikkink K, Ahmed AA, Melnyk S, Reid D, Van Meter L, Guest EM, Lansdon LA, Pastinen T, Pushel I, Yoo B, Farooqi MS. Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.10.24306838. [PMID: 38765974 PMCID: PMC11100933 DOI: 10.1101/2024.05.10.24306838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate HiC as a potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia and sarcoma specimens previously positive for clinically significant genomic rearrangements. Archived specimen types tested included viable and nonviable frozen leukemic cells, as well as formalin-fixed paraffin-embedded (FFPE) tumor tissues. Initially, pediatric acute myeloid leukemia (AML) and alveolar rhabdomyosarcoma (A-RMS) specimens with known genomic rearrangements were subjected to HiC analysis to assess analytical concordance. Subsequently, a discovery cohort consisting of AML and acute lymphoblastic leukemia (ALL) cases with no known genomic rearrangements based on prior clinical diagnostic testing were evaluated to determine whether HiC could detect rearrangements. Using a standard sequencing depth of 50 million raw read-pairs per sample, or approximately 5X raw genomic coverage, 100% concordance was observed between HiC and previous clinical cytogenetic and molecular testing. In the discovery cohort, a clinically relevant gene fusion was detected in 45% of leukemia cases (5/11). This study demonstrates the value of HiC sequencing to medical diagnostic testing as it identified several clinically significant rearrangements, including those that might have been missed by current clinical testing workflows. Key points HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome, facilitating detection of genomic rearrangements.HiC was 100% concordant with clinical diagnostic testing workflows for detecting clinically significant genomic rearrangements in pediatric leukemia and rhabdomyosarcoma specimens.HiC detected clinically significant genomic rearrangements not previously detected by prior clinical cytogenetic and molecular testing.HiC performed well with archived non-viable and viable frozen leukemic cell samples, as well as archived formalin-fixed paraffin-embedded tumor tissue specimens.
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3
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Akkari Y, Baughn LB, Kim A, Karaca E, Raca G, Shao L, Mikhail FM. Section E6.1-6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes. Genet Med 2024; 26:101054. [PMID: 38349293 DOI: 10.1016/j.gim.2023.101054] [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: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 04/09/2024] Open
Abstract
Cytogenomic analyses of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes are instrumental in the clinical management of patients with hematologic neoplasms. Cytogenetic analyses assist in the diagnosis of such disorders and can provide important prognostic information. Furthermore, cytogenetic studies can provide crucial information regarding specific genetically defined subtypes of these neoplasms that may have targeted therapies. At time of relapse, cytogenetic analysis can confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the technical standards applicable to cytogenomic studies of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes. This updated Section E6.1-6.6 supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Technical Standards for Clinical Genetics Laboratories.
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Affiliation(s)
- Yassmine Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Annette Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Ender Karaca
- Department of Pathology, Baylor University Medical Center, Dallas, TX; Texas A&M School of Medicine, Texas A&M University, Dallas, TX
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lina Shao
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
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4
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Keskus A, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M. Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.22.24304756. [PMID: 38585974 PMCID: PMC10996739 DOI: 10.1101/2024.03.22.24304756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy. Here, we present Severus: a method for the accurate detection of different types of somatic SVs using a phased breakpoint graph approach. To benchmark various short- and long-read SV detection methods, we sequenced five tumor/normal cell line pairs with Illumina, Nanopore, and PacBio sequencing platforms; on this benchmark Severus showed the highest F1 scores (harmonic mean of the precision and recall) as compared to long-read and short-read methods. We then applied Severus to three clinical cases of pediatric cancer, demonstrating concordance with known genetic findings as well as revealing clinically relevant cryptic rearrangements missed by standard genomic panels.
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Affiliation(s)
- Ayse Keskus
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Byunggil Yoo
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | | | - Anton Goretsky
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Ataberk Donmez
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Lisa A. Lansdon
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Jimin Park
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Yuelin Liu
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Xiwen Cui
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | - Samuel Sacco
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Jyoti Shetty
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yongmei Zhao
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | | | | | | | | | - Erin K. Molloy
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Irina Pushel
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Erin Guest
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Tomi Pastinen
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Kishwar Shafin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Salem Malikic
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Chi-Ping Day
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Cenk Sahinalp
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Midhat S. Farooqi
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | | | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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Hoffmeister LM, Suttorp J, Walter C, Antoniou E, Behrens YL, Göhring G, Awada A, von Neuhoff N, Reinhardt D, Schneider M. Panel-based RNA fusion sequencing improves diagnostics of pediatric acute myeloid leukemia. Leukemia 2024; 38:538-544. [PMID: 38086945 PMCID: PMC10912021 DOI: 10.1038/s41375-023-02102-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/14/2023] [Accepted: 11/23/2023] [Indexed: 03/06/2024]
Abstract
New methods like panel-based RNA fusion sequencing (RNA-FS) promise improved diagnostics in various malignancies. We here analyzed the impact of RNA-FS on the initial diagnostics of 241 cases with pediatric acute myeloid leukemia (AML). We show that, compared to classical cytogenetics (CCG), RNA-FS reliably detected risk-relevant fusion genes in pediatric AML. In addition, RNA-FS strongly improved the detection of cryptic fusion genes like NUP98::NSD1, KMT2A::MLLT10 and CBFA2T3::GLIS2 and thereby resulted in an improved risk stratification in 25 patients (10.4%). Validation of additionally detected non-risk-relevant high confidence fusion calls identified PIM3::BRD1, C22orf34::BRD1, PSPC1::ZMYM2 and ARHGAP26::NR3C1 as common genetic variants and MYB::GATA1 as recurrent aberration, which we here describe in AML subtypes M0 and M7 for the first time. However, it failed to detect rare cytogenetically confirmed fusion events like MNX1::ETV6 and other chromosome 12p-abnormalities. As add-on benefit, the proportion of patients for whom measurable residual disease (MRD) monitoring became possible was increased by RNA-FS from 44.4 to 75.5% as the information on the fusion transcripts' sequence allowed the design of new MRD assays.
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Affiliation(s)
- Lina Marie Hoffmeister
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Julia Suttorp
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Christiane Walter
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Evangelia Antoniou
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Yvonne Lisa Behrens
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Amani Awada
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Nils von Neuhoff
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Markus Schneider
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany.
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6
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Kim Y, Kim B, Seong MW, Lee DS, Hong KT, Kang HJ, Yun J, Chang YH. Cryptic KMT2A/MLLT10 fusion detected by next-generation sequencing in a case of pediatric acute megakaryoblastic leukemia. Cancer Genet 2023; 276-277:36-39. [PMID: 37478796 DOI: 10.1016/j.cancergen.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 06/09/2023] [Accepted: 07/08/2023] [Indexed: 07/23/2023]
Abstract
KMT2A (11q23.3) gene rearrangements are found in acute leukemia and are associated with a poor or intermediate prognosis. MLLT10 is the fourth most common gene fusion partner for KMT2A. A reciprocal translocation t(10;11) is insufficient to produce an in-frame KMT2A/MLLT10 fusion, because the genes involved in the rearrangement have opposite transcriptional orientations. In order to bring KMT2A and MLLT10 into juxtaposition, complex rearrangements are required. Until now, conventional chromosome, fluorescence in situ hybridization (FISH), and reverse transcriptase-polymerase chain reaction (RT-PCR) studies have been used to detect KMT2A/MLLT10 fusions. However, conventional studies have limitations, such as poor and inconsistent resolution, when compared to next-generation sequencing (NGS). In this study, we report a pediatric patient with acute megakaryoblastic leukemia, in whom the cryptic KMT2A/MLLT10 fusion was not detected by KMT2A break-apart probe FISH and chromosome analysis, but detected by NGS. In this patient, NGS showed cryptic insertion of MLLT10 exons 9-24 into intron 9 of KMT2A, resulting in a KMT2A/MLLT10 fusion. Therefore, NGS is a valuable complementary option for the evaluation of structural aberrations, especially those with a cryptic size.
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Affiliation(s)
- Yeseul Kim
- Department of Laboratory Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Boram Kim
- Department of Laboratory Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Dong Soon Lee
- Department of Laboratory Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Kyung Taek Hong
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyoung Jin Kang
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jiwon Yun
- Department of Laboratory Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Laboratory Medicine, Chung-Ang University Hospital, 102, Heukseok-ro, Dongjak-gu, Seoul 06973, Republic of Korea.
| | - Yoon Hwan Chang
- Department of Laboratory Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
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7
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Yamamoto K, Matsumoto H, Matsumoto S, Sakai R, Kitao A, Watanabe M, Goto H, Sugimoto T, Yano Y, Yakushijin K, Minami H. Unexpected appearance of KMT2A::MLLT10 fusion transcript in acute myeloid leukemia with t(5;11)(q31;q23.3). Cancer Genet 2023; 272-273:41-46. [PMID: 36774707 DOI: 10.1016/j.cancergen.2023.02.002] [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: 08/31/2022] [Revised: 01/11/2023] [Accepted: 02/02/2023] [Indexed: 02/06/2023]
Abstract
As an uncommon but nonrandom translocation in acute myeloid leukemia (AML) t(5;11)(q31;q23) results in fusion between KMT2A at 11q23 and ARHGAP26 at 5q31. The 5q31 region has another KMT2A partner, AFF4, which was identified in acute lymphoblastic leukemia harboring ins(5;11)(q31;q13q23). We report here a 65-year-old woman with AML M5b. G-banding and spectral karyotyping demonstrated 46,XX,t(5;11)(q31;q23.3). Fluorescence in situ hybridization revealed not only separated 5' and 3' KMT2A signals but a faint 5' KMT2A signal. Reverse transcription polymerase chain reaction (RT-PCR), using a KMT2A sense primer and ARHGAP26 antisense primer, detected no band whereas RT-PCR with a AFF4 antisense primer revealed an amplified band. However, sequence analysis unexpectedly disclosed that KMT2A exon 6 was connected with MLLT10 exons 15 to 18. This may be due to cross-hybridization between MLLT10 exon 18 and AFF4 antisense primer derived from AFF4 exon 10 since both exons had eight identical bases (AAGCAGCT). The MLLT10 gene is located at 10p12.31; a faint 5' KMT2A signal was probably present at this locus. These findings indicate that in AML the 5' KMT2A fragment containing exons 1 to 6 may be cryptically inserted into MLLT10 intron 14 when a reciprocal translocation t(5;11)(q31;q23.3) involving KMT2A occurred.
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Affiliation(s)
- Katsuya Yamamoto
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Hisayuki Matsumoto
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Sakuya Matsumoto
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Rina Sakai
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akihito Kitao
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Marika Watanabe
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hideaki Goto
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan; Department of Hematology and Oncology, Kita-Harima Medical Center, Ono, Japan
| | - Takeshi Sugimoto
- Department of Hematology and Oncology, Kita-Harima Medical Center, Ono, Japan
| | - Yoshihiko Yano
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Kimikazu Yakushijin
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hironobu Minami
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
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Xu ZJ, Zhang XL, Jin Y, Wang SS, Gu Y, Ma JC, Wen XM, Leng JY, Mao ZW, Lin J, Qian J. Pan-cancer analysis reveals distinct clinical, genomic, and immunological features of the LILRB immune checkpoint family in acute myeloid leukemia. Mol Ther Oncolytics 2022; 26:88-104. [PMID: 35795094 PMCID: PMC9233190 DOI: 10.1016/j.omto.2022.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/27/2022] [Indexed: 10/28/2022] Open
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9
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Duan Z, Chen Y, Ye M, Xiao L, Chen Y, Cao Y, Peng Y, Zhang J, Zhang Y, Yang T, Liu W, Feng S, Hu J. Differentiation and prognostic stratification of acute myeloid leukemia by serum-based spectroscopy coupling with metabolic fingerprints. FASEB J 2022; 36:e22416. [PMID: 35713583 DOI: 10.1096/fj.202200487r] [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: 04/02/2022] [Revised: 05/26/2022] [Accepted: 06/06/2022] [Indexed: 11/11/2022]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by complex molecular and cytogenetic abnormalities. New approaches to predict the prognosis of AML have increasingly attracted attention. There were 98 non-M3 AML cases and 48 healthy controls were enrolled in the current work. Clinically routine assays for cytogenetic and molecular genetic analyses were performed on the bone marrow samples of patients with AML. Meanwhile, metabolic profiling of these AML subjects was also performed on the serum samples by combining Ag nanoparticle-based surface-enhanced Raman spectroscopy (SERS) with proton nuclear magnetic resonance (NMR) spectroscopy. Although most of the routine biochemical test showed no significant differences between the M0-M2 and M5 groups, the metabolic profiles were significantly different either between AML subtypes or between prognostic risk subgroups. Specific SERS bands were screened to serve as potential markers for AML subtypes. The results demonstrated that the classification models for M0-M2 and M5 shared two bands (i.e., 1328 and 741 cm-1 ), all came from nucleic acid signals. Furthermore, Metabolic profiles provided various differential metabolites responsible for different AML subtypes, and we found altered pathways mainly included energy metabolism like glycolysis, pyruvate metabolism, and metabolisms of nucleic acid bases as well as specific amino acid metabolisms. It is concluded that integration of SERS and NMR provides the rational and could be reliable to reveal AML differentiation, and meanwhile lay the basis for experimental and clinical practice to monitor disease progression and prognostic evaluation.
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Affiliation(s)
- Zhengwei Duan
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Yang Chen
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Minlu Ye
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Lijing Xiao
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Yanxin Chen
- Fujian Provincial Key Laboratory on Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yingping Cao
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yi Peng
- Department of Ophthalmology & Optometry, Fujian Medical University, Fuzhou, China
| | - Jingling Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yu Zhang
- Fujian Provincial Key Laboratory on Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Ting Yang
- Fujian Provincial Key Laboratory on Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Wuping Liu
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Department of Electronic Science, Xiamen University, Xiamen, China
| | - Shangyuan Feng
- Fujian Provincial Key Laboratory for Photonics Technology, Key Laboratory of Optoelectronic Science and Technology for Medicine, Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Jianda Hu
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory on Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
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10
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FISH improves risk stratification in acute leukemia by identifying KMT2A abnormal copy number and rearrangements. Sci Rep 2022; 12:9585. [PMID: 35688861 PMCID: PMC9187764 DOI: 10.1038/s41598-022-13545-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/25/2022] [Indexed: 11/26/2022] Open
Abstract
Most cases of acute leukemia (AL) with KMT2A rearrangement (KMT2A-r) have a dismal prognosis. Detection of this aberration in Chinese adult patients relies on reverse transcription polymerase chain reaction (RT-PCR) and chromosome banding analysis (CBA). The fluorescence in situ hybridization (FISH) probe for KMT2A detects KMT2A-r and copy number variation (CNV) but is not routinely used as a detection technique. This study investigated the potential value of FISH in the treatment of AL by performing FISH along with CBA and RT-PCR in 269 de novo cases of AL. The three detection techniques were compared in identification of KMT2A-r, and the applicability of FISH for detecting KMT2A CNV was evaluated. Twenty-three samples were identified as positive for KMT2A-r (20 using FISH, 15 using RT-PCR, 16 using CBA, and eight according to all three). FISH also identified 17 KMT2A CNV, 15 with gains and two with deletions. Ten patients with acute myeloid leukemia (AML) harboring KMT2A CNV had a complex karyotype, a negative prognostic factor in AML. Adding FISH of KMT2A to routine detection leads to more accurate detection of KMT2A-r and improved identification of KMT2A CNV, which would benefit patients by improving the risk stratification in AL.
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11
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Prognostic Lnc-S100B-2 Affects Cell Apoptosis and Microenvironment of Colorectal Cancer through MLLT10 Signaling. JOURNAL OF ONCOLOGY 2022; 2022:3565118. [PMID: 35126515 PMCID: PMC8808143 DOI: 10.1155/2022/3565118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 11/19/2022]
Abstract
Long noncoding RNA (LncRNA) is closely associated with the development of colorectal cancer (CRC). The chip data and clinical information of GSE104364 and GSE151021 were downloaded by GEOquery. Limma and Kaplan–Meier analysis were performed. Lnc-S100B-2 was obtained, and high expression of Lnc-S100B-2 was predicted to be associated with a lower survival rate. Online software was adopted to predict downstream regulatory genes, and miR-331-3p and Mixed Lineage Leukemia Translocated to 10 (MLLT10) were screened and verified. After silencing Lnc-S100B-2 and MLLT10, the proliferative activity of CRC cells decreased, and the apoptosis rate increased. At the gene and protein levels, the expressions of PCNA, Ki67, and Bcl-2 were decreased in the sh-Lnc-S100B-2 group, sh-MLLT10 group, and sh-Lnc-S100B-2 + sh-MLLT10 group, while the expressions of cleaved caspase 3, caspase 9, and Bax were increased. In vivo, the volume and mass of the tumor decreased in the sh-Lnc-S100B-2 + sh-MLLT10 group. Proliferation and apoptosis-related index (PCNA, Ki67, cleaved caspase 3, caspase 9, Bax, and Bcl-2) expression level was also altered. Meanwhile, the infiltration of immune cells (CD3 (-), CD16 (+), and CD11b (+) cells) decreased. The expressions of epithelial-mesenchymal transformation (EMT) related indicators (E-cadherin, N-cadherin, Vimentin, β-catenin, Snail, and Slug) were changed. E-cadherin and β-catenin were increased in the sh-Lnc-S100B-2 + sh-MLLT10 group, while N-cadherin, vimentin, snail, and slug were decreased. In conclusion, our study found that the expression of Lnc-S100B-2 was dysregulated in CRC. Lnc-S100B-2 could affect cell apoptosis and the microenvironment of CRC through regulating MLLT10.
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12
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Walsh KM, Zhang C, Calvocoressi L, Hansen HM, Berchuck A, Schildkraut JM, Bondy ML, Wrensch M, Wiemels JL, Claus EB. Pleiotropic MLLT10 variation confers risk of meningioma and estrogen-mediated cancers. Neurooncol Adv 2022; 4:vdac044. [PMID: 35702670 PMCID: PMC9187056 DOI: 10.1093/noajnl/vdac044] [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] [Indexed: 11/18/2022] Open
Abstract
Background Risk of tumors of the breast, ovary, and meninges has been associated with hormonal factors and with one another. Genome-wide association studies (GWAS) identified a meningioma risk locus on 10p12 near previous GWAS hits for breast and ovarian cancers, raising the possibility of genetic pleiotropy. Methods We performed imputation-based fine-mapping in three case-control datasets of meningioma (927 cases, 790 controls), female breast cancer (28 108 cases, 22 209 controls), and ovarian cancer (25 509 cases, 40 941 controls). Analyses were stratified by sex (meningioma), estrogen receptor (ER) status (breast), and histotype (ovarian), then combined using subset-based meta-analysis in ASSET. Lead variants were assessed for association with additional traits in UK Biobank to identify potential effect-mediators. Results Two-sided subset-based meta-analysis identified rs7084454, an expression quantitative trait locus (eQTL) near the MLLT10 promoter, as lead variant (5.7 × 10-14). The minor allele was associated with increased risk of meningioma in females (odds ratio (OR) = 1.42, 95% Confidence Interval (95%CI):1.20-1.69), but not males (OR = 1.19, 95%CI: 0.91-1.57). It was positively associated with ovarian (OR = 1.09, 95%CI:1.06-1.12) and ER+ breast (OR = 1.05, 95%CI: 1.02-1.08) cancers, and negatively associated with ER- breast cancer (OR = 0.91, 95%CI: 0.86-0.96). It was also associated with several adiposity traits (P < 5.0 × 10-8), but adjusting for body mass index did not attenuate its association with meningioma. MLLT10 and ESR1 expression were positively correlated in normal meninges (P = .058) and meningioma tumors (P = .0065). Conclusions We identify a MLLT10 eQTL positively associated with risk of female meningioma, ER+ breast cancer, ovarian cancer, and obesity, and implicate a potential estrogenic mechanism underlying this pleiotropy.
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Affiliation(s)
- Kyle M Walsh
- Department of Neurosurgery and Duke Cancer Institute, Duke University School of Medicine. Durham, North Carolina, USA
| | - Chenan Zhang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Lisa Calvocoressi
- School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology and Duke Cancer Institute, Duke University School of Medicine. Durham, North Carolina, USA
| | | | - Melissa L Bondy
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, California, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, California, USA
| | - Elizabeth B Claus
- School of Public Health, Yale University, New Haven, Connecticut, USA
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13
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Cai X, Wang J, Lu J, Jia Z, Chen M, Liu J, Lu X, Chao H. Adult Acute Myeloid Leukemia with the KMT2A-Mixed Lineage Leukemia T10 Fusion: An Analysis of 10 Cases Showed Common Features and Frequent Mutations in the RAS Signaling Pathway. Acta Haematol 2021; 145:144-151. [PMID: 34551411 DOI: 10.1159/000518920] [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: 12/24/2020] [Accepted: 08/05/2021] [Indexed: 11/19/2022]
Abstract
Mixed lineage leukemia (MLL) T10 is a relatively rare partner for the KMT2A lysine (K)-specific methyltransferase 2A gene. The common features and coexisting mutations of acute myeloid leukemia (AML) patients with KMT2A-MLLT10 remain unknown. In this study, 10 adult AML patients with KMT2A-MLLT10 fusions were picked up from 496 AML patients by using RT-polymerase chain reaction (PCR) and/or fluorescence in situ hybridization, and then screened for mutations in the 49 genes panel with next-generation sequencing and PCR, followed by direct Sanger sequencing. Of the 10 unique individuals identified, 6 were male and 4 were female (M:F ratio, 1.5:1) with ages ranging from 19 to 52 years (median 39.5 years). Most (90%, 9/10) patients with KMT2A-MLLT10 were accompanied by additional mutations. Twelve mutated genes were detected, averaging 2.1 mutations per patient (range, 0-4). The most frequently mutated gene was NRAS (n = 5). Clinical and laboratory data pointed to common features: French American British-M5 subtype (n = 7), a high rate of relapse, and biomarkers CD33 (n = 10), CD117 (n = 9), CD13 (n = 8), and CD64 (n = 8). Overall, most patients harbored at least one mutation. A high incidence of mutations affecting the RAS signaling pathway or RAS regulating components was found in 50% (5/10) patients. The overall survival is about 12.0 months. Allogeneic-hematopoietic stem cell transplantation trends to improve survival in selected patients.
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Affiliation(s)
- Xiaohui Cai
- Department of Hematology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, China,
| | - Jinfei Wang
- Department of Hemopurification Center, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, China
| | - Jingtao Lu
- Department of Hematology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, China
| | - Zhuxia Jia
- Department of Hematology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, China
| | - Meiyu Chen
- Department of Hematology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, China
| | - Jianfang Liu
- Department of Hematology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, China
| | - Xuzhang Lu
- Department of Hematology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, China
| | - Hongying Chao
- Department of Hematology, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, China
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14
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Quessada J, Cuccuini W, Saultier P, Loosveld M, Harrison CJ, Lafage-Pochitaloff M. Cytogenetics of Pediatric Acute Myeloid Leukemia: A Review of the Current Knowledge. Genes (Basel) 2021; 12:924. [PMID: 34204358 PMCID: PMC8233729 DOI: 10.3390/genes12060924] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023] Open
Abstract
Pediatric acute myeloid leukemia is a rare and heterogeneous disease in relation to morphology, immunophenotyping, germline and somatic cytogenetic and genetic abnormalities. Over recent decades, outcomes have greatly improved, although survival rates remain around 70% and the relapse rate is high, at around 30%. Cytogenetics is an important factor for diagnosis and indication of prognosis. The main cytogenetic abnormalities are referenced in the current WHO classification of acute myeloid leukemia, where there is an indication for risk-adapted therapy. The aim of this article is to provide an updated review of cytogenetics in pediatric AML, describing well-known WHO entities, as well as new subgroups and germline mutations with therapeutic implications. We describe the main chromosomal abnormalities, their frequency according to age and AML subtypes, and their prognostic relevance within current therapeutic protocols. We focus on de novo AML and on cytogenetic diagnosis, including the practical difficulties encountered, based on the most recent hematological and cytogenetic recommendations.
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Affiliation(s)
- Julie Quessada
- Hematological Cytogenetics Laboratory, Timone Children’s Hospital, Assistance Publique-Hôpitaux de Marseille (APHM), Faculté de Médecine, Aix Marseille University, 13005 Marseille, France;
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France;
| | - Wendy Cuccuini
- Hematological Cytogenetics Laboratory, Saint-Louis Hospital, Assistance Publique des Hôpitaux de Paris (APHP), 75010 Paris, France;
- Groupe Francophone de Cytogénétique Hématologique (GFCH), 1 Avenue Claude Vellefaux, 75475 Paris, France
| | - Paul Saultier
- APHM, La Timone Children’s Hospital Department of Pediatric Hematology and Oncology, 13005 Marseille, France;
- Faculté de Médecine, Aix Marseille University, INSERM, INRAe, C2VN, 13005 Marseille, France
| | - Marie Loosveld
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France;
- Hematology Laboratory, Timone Hospital, Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Christine J. Harrison
- Leukaemia Research Cytogenetics Group Translational and Clinical Research Institute, Newcastle University Centre for Cancer Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK;
| | - Marina Lafage-Pochitaloff
- Hematological Cytogenetics Laboratory, Timone Children’s Hospital, Assistance Publique-Hôpitaux de Marseille (APHM), Faculté de Médecine, Aix Marseille University, 13005 Marseille, France;
- Groupe Francophone de Cytogénétique Hématologique (GFCH), 1 Avenue Claude Vellefaux, 75475 Paris, France
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15
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Chen Y, Wang L, Lin X, Zhang Q, Xu Y, Lin D, Xu J, Feng S, Hu J. Cytological and spectroscopic characteristics of c-KIT N822K mutation in core binding factor acute myeloid leukemia cells. JOURNAL OF BIOPHOTONICS 2020; 13:e202000103. [PMID: 32390317 DOI: 10.1002/jbio.202000103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/24/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
The frequency of N822K mutation is high in the A-loop region of c-KIT which is highly associated with poor prognosis of core binding factor acute myeloid leukemia. The current work used common assays including cell cycle, apoptosis, clone formation and western blot to perform cytological detection for HL60 (wild type), NB4 (carrying t[15;17] chromosome translocation) and Kasumi-1 (with c-KIT N822K mutation); and meanwhile, the laser tweezers Raman spectroscopy (LTRS) was also used to perform label-free detection of single living cells. The results demonstrated that Kasumi-1 cell line bearing c-KIT N822K mutation has a stable cell cycle, while there was a significant difference between early and late apoptosis within 48 hours. The LTRS detection initially reflected the spectral differences induced by genetic abnormalities and highlighted progressive patterns of DNA and amino acids band contents which were appropriately consistent with that of cell clone ratio and the c-KIT phosphorylation level. It is concluded that methodology of LTRS-based single living cell characterization could be potential and effective to reveal gene mutation-induced cell differentiation.
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Affiliation(s)
- Yang Chen
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Lingyan Wang
- Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Xindi Lin
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Qian Zhang
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Yunchao Xu
- Key Laboratory of Optoelectronic Science and Technology for Medicine, Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Donghong Lin
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Jianping Xu
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Shangyuan Feng
- Key Laboratory of Optoelectronic Science and Technology for Medicine, Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Jianda Hu
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
- Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, China
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16
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Forgione MO, McClure BJ, Yeung DT, Eadie LN, White DL. MLLT10 rearranged acute leukemia: Incidence, prognosis, and possible therapeutic strategies. Genes Chromosomes Cancer 2020; 59:709-721. [PMID: 32720323 DOI: 10.1002/gcc.22887] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/07/2020] [Accepted: 07/13/2020] [Indexed: 12/22/2022] Open
Abstract
Rearrangements of the MLLT10 gene occur in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), most commonly T-lineage ALL (T-ALL), in patients of all ages. MLLT10 rearranged (MLLT10r) acute leukemia presents a complex diagnostic and therapeutic challenge due to frequent presentation of immature or mixed phenotype, and a lack of consensus regarding optimal therapy. Cases of MLLT10r AML or T-ALL bearing immature phenotype are at high risk of poor outcome, but the underlying molecular mechanisms and sensitivity to targeted therapies remain poorly characterized. This review addresses the incidence and prognostic significance of MLLT10r in acute leukemia, and how the aberrant gene expression profile of this disease can inform potential targeted therapeutic strategies. Understanding the underlying genomics of MLLT10r acute leukemia, both clinically and molecularly, will improve prognostic stratification and accelerate the development of targeted therapeutic strategies, to improve patient outcomes.
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Affiliation(s)
- Michelle O Forgione
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Barbara J McClure
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - David T Yeung
- Cancer Program, Precision Medicine Theme, South Australian Health and 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, Adelaide, South Australia, Australia
| | - Laura N Eadie
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Deborah L White
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian Genomics Health Alliance (AGHA), The Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Australian and New Zealand Children's Oncology Group (ANZCHOG), Hudson Institute, Clayton, Victoria, Australia
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17
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Tian QQ, Xia J, Zhang X, Gao BQ, Wang W. miR-331-3p Inhibits Tumor Cell Proliferation, Metastasis, Invasion by Targeting MLLT10 in Non-Small Cell Lung Cancer. Cancer Manag Res 2020; 12:5749-5758. [PMID: 32765078 PMCID: PMC7368563 DOI: 10.2147/cmar.s249686] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/24/2020] [Indexed: 12/18/2022] Open
Abstract
Objective Mounting research has established the role of microRNAs (miRNAs) as oncogenes or anti-oncogenes (tumor suppressors) in the development and progression of several cancers. The purpose of our current study is to delineate the roles and functional mechanisms of miR-331-3p and MLLT10 in non-small cell lung cancer (NSCLC) tumorigenesis. Patients and Methods Quantitative reverse transcription-polymerase chain reaction (RT-qPCR) was employed to measure miR-331-3p expression levels in twenty-six matched tumor tissues and non-cancerous tissues collected from patients suffering from NSCLC, and from six NSCLC cell lines separately: A549, H1650, H292, H1299, H1944 and BEAS-2b. We employed the dual-luciferase activity assay to check whether the putative gene, MLLT10, was a downstream target of miR-331-3p in NSCLC pathogenesis and development. Western blot was conducted to analyze the protein expression levels of MLLT10 (AF10), E-cadherin, Vimentin, and GAPDH. CCK-8 assay, transwell migration assay, and transwell invasion assay were carried out to observe the functions of miR-331-3p and MLLT10 on NSCLC tumor cell proliferation, metastasis, and invasion, respectively. To identify whether the metastasis of NSCLC tumor cells was EMT-mediated, supplementary experiments involving E-cadherin and Vimentin were implemented. Results miR-331-3p was downregulated in NSCLC, which promoted tumor cell proliferation, whereas the overexpression of miR-331-3p inhibited tumor cell proliferation. Being a direct target of miR-331-3p, MLLT10 was negatively modulated by miR-331-3p, which suppressed tumor cell proliferation, migration, and invasion in NSCLC. However, MLLT10 overexpression alleviated the above inhibitory effects. Furthermore, EMT-mediated metastasis was proved to be present in NSCLC. Conclusion miR-331-3p played a suppressor role in NSCLC tumor cell proliferation, EMT-mediated metastasis, and invasion by targeting MLLT10. Our findings highlighted that miR-331-3p/MLLT10 axis could be useful as a clinical diagnostic marker and therapeutic target in NSCLC patients.
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Affiliation(s)
- Qing-Qing Tian
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jing Xia
- General Department of Houhu, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xin Zhang
- Department of Radiology, The Fourth People's Hospital of Huai'an, Huai'an, Huai'an, People's Republic of China
| | - Bao-Qin Gao
- Operating Room, Huai'an Second People's Hospital and the Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, People's Republic of China
| | - Wei Wang
- Department of Oncology, Huai'an Second People's Hospital and the Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, People's Republic of China
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18
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Dalland JC, Meyer R, Ketterling RP, Reichard KK. Myeloid Sarcoma With CBFB-MYH11 Fusion (inv(16) or t(16;16)) Prevails in the Abdomen. Am J Clin Pathol 2020; 153:333-341. [PMID: 31671434 DOI: 10.1093/ajcp/aqz168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Myeloid sarcoma with CBFB-MYH11 fusion may be enriched in abdominal sites. The clinicopathologic features of 11 cases are reported. METHODS We collected clinical features, morphology, immunophenotype, and bone marrow (BM) involvement of myeloid sarcoma cases with CBFB-MYH11 fusion. RESULTS Eleven of 29 total myeloid sarcoma cases were CBFB-MYH11 positive and all 11 involved abdominal sites. The blastic infiltrate was associated with eosinophils in four of 11 cases and plasmacytoid dendritic cell (pDC) nodules in four of six cases. CD34, CD117, and myeloperoxidase were expressed in eight of nine, 10 of 10, and 10 of 10 cases, respectively. Ten of 10 cases showed no BM involvement. CONCLUSIONS Our current series, combined with a literature review, identifies a compelling series of 31 (94%) of 33 cases of myeloid sarcoma with CBFB-MYH11 fusion showing a marked predilection for abdominal sites. In addition, the lack of obvious associated eosinophils, presence of pDC nodules, and lack of concurrent BM involvement suggest that "myeloid sarcoma with CBFB-MYH11 fusion" may represent a unique phenomenon.
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Affiliation(s)
- Joanna C Dalland
- Department of Laboratory Medicine and Pathology, Divisions of Hematopathology, Rochester, MN
| | - Reid Meyer
- Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Divisions of Hematopathology, Rochester, MN
- Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Kaaren K Reichard
- Department of Laboratory Medicine and Pathology, Divisions of Hematopathology, Rochester, MN
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19
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Schultz MJ, Blackburn PR, Cogbill CH, Pitel BA, Smadbeck JB, Johnson SH, Vasmatzis G, Rech KL, Sukov WR, Greipp PT, Hoppman NL, Baughn LB, Ketterling RP, Peterson JF. Characterization of a cryptic PML-RARA fusion by mate-pair sequencing in a case of acute promyelocytic leukemia with a normal karyotype and negative RARA FISH studies. Leuk Lymphoma 2019; 61:975-978. [PMID: 31809670 DOI: 10.1080/10428194.2019.1699081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Matthew J Schultz
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patrick R Blackburn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Beth A Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Karen L Rech
- Division of Hematopathology, Department of Laboratory Medicine and Genomics, Mayo Clinic, Rochester, MN, USA
| | - William R Sukov
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Division of Hematopathology, Department of Laboratory Medicine and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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20
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Xu H, Muise ES, Javaid S, Chen L, Cristescu R, Mansueto MS, Follmer N, Cho J, Kerr K, Altura R, Machacek M, Nicholson B, Addona G, Kariv I, Chen H. Identification of predictive genetic signatures of Cytarabine responsiveness using a 3D acute myeloid leukaemia model. J Cell Mol Med 2019; 23:7063-7077. [PMID: 31449347 PMCID: PMC6787505 DOI: 10.1111/jcmm.14608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/25/2019] [Accepted: 07/30/2019] [Indexed: 12/31/2022] Open
Abstract
This study reports the establishment of a bone marrow mononuclear cell (BMMC) 3D culture model and the application of this model to define sensitivity and resistance biomarkers of acute myeloid leukaemia (AML) patient bone marrow samples in response to Cytarabine (Ara-C) treatment. By mimicking physiological bone marrow microenvironment, the growth conditions were optimized by using frozen BMMCs derived from healthy donors. Healthy BMMCs are capable of differentiating into major hematopoietic lineages and various types of stromal cells in this platform. Cryopreserved BMMC samples from 49 AML patients were characterized for ex vivo growth and sensitivity to Ara-C. RNA sequencing was performed for 3D and 2D cultures to determine differential gene expression patterns. Specific genetic mutations and/or gene expression signatures associated with the ability of the ex vivo expansion and response to Ara-C were elucidated by whole-exome and RNA sequencing. Data analysis identified unique gene expression signatures and novel genetic mutations associated with sensitivity to Ara-C treatment of proliferating AML specimens and can be used as predictive therapeutic biomarkers to determine the optimal treatment regimens. Furthermore, these data demonstrate the translational value of this ex vivo platform which should be widely applicable to evaluate other therapies in AML.
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Affiliation(s)
- Haiyan Xu
- Department of Pharmacology, Merck & Co., Inc., Boston, MA, USA
| | - Eric S Muise
- Department of Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | - Sarah Javaid
- Department of Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | - Lan Chen
- Department of Strategic Planning & Research Informatics, Merck & Co., Inc., Beijing, China
| | - Razvan Cristescu
- Department of Precision Oncology Biomarkers, Merck & Co., Inc., Boston, MA, USA
| | - My Sam Mansueto
- Department of Pharmacology, Merck & Co., Inc., Boston, MA, USA
| | - Nicole Follmer
- Department of Oncology Early Discovery, Merck & Co., Inc., Boston, MA, USA
| | - Jennifer Cho
- Department of Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | - Kimberley Kerr
- Department of Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | - Rachel Altura
- Department of Oncology Early Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Michelle Machacek
- Department of Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA
| | - Benjamin Nicholson
- Department of Oncology Early Discovery, Merck & Co., Inc., Boston, MA, USA
| | - George Addona
- Department of Pharmacology, Merck & Co., Inc., Boston, MA, USA
| | - Ilona Kariv
- Department of Pharmacology, Merck & Co., Inc., Boston, MA, USA
| | - Hongmin Chen
- Department of Pharmacology, Merck & Co., Inc., Boston, MA, USA
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21
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Chen S, Dickson BC, Mohammed S, Aldape K, Swanson D, Coulombe J, Zakhari N, Karimi S, Nassiri F, Zadeh G, Mamatjan Y, Wang T, Lo B, Woulfe J. A dural-based spindle cell neoplasm characterized by a novel MN1-KMT2A fusion gene. Neuro Oncol 2019; 21:1082-1083. [PMID: 31095693 DOI: 10.1093/neuonc/noz091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Suzan Chen
- Neurosciences Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Brendan C Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Safraz Mohammed
- Division of Neurosurgery, Department of Surgery, University of Ottawa, The Ottawa Hospital Civic Campus, Ottawa, Ontario, Canada
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute/Center for Cancer Research, Bethesda, Maryland, USA
| | - David Swanson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Josee Coulombe
- Neurosciences Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Nader Zakhari
- Division of Neuroradiology Department of Radiology University of Ottawa, The Ottawa Hospital Civic and General Campus, Ottawa, Ontario, Canada
| | - Shirin Karimi
- Princess Margaret Cancer Center, MacFeeters-Hamilton Center for Neuro-Oncology Research, Toronto, Ontario, Canada
| | - Farshad Nassiri
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Yasin Mamatjan
- Princess Margaret Cancer Center, MacFeeters-Hamilton Center for Neuro-Oncology Research, Toronto, Ontario, Canada
| | - Tao Wang
- Department of Pathology and Molecular Medicine, Queen's University, Richardson Laboratory, Kingston, Ontario, Canada
| | - Bryan Lo
- Division of Anatomical Pathology, Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - John Woulfe
- Neurosciences Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Eastern Ontario Regional Laboratory Association/Association des Laboratoires Régionaux de l'Est de l'Ontario (EORLA/ALREO), The Ottawa Hospital, Civic Campus, Laboratory Medicine Building, Ottawa, Ontario, Canada
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22
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Characterization of a cryptic KMT2A/AFF1 gene fusion by mate-pair sequencing (MPseq) in a young adult with newly diagnosed B-lymphoblastic leukemia. J Hematop 2019. [DOI: 10.1007/s12308-019-00355-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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