1
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Kirkham JK, Liu YC, Foy SG, Ma J, Gheorghe G, Furtado LV, Popescu MI, Klco JM, Karol SE, Blackburn PR. Clinical and genomic characterization of an ATRA-insensitive acute promyelocytic leukemia variant with a FNDC3B::RARB fusion. Genes Chromosomes Cancer 2023; 62:617-623. [PMID: 37283355 DOI: 10.1002/gcc.23180] [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: 04/06/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/08/2023] Open
Abstract
The promyelocytic leukemia-retinoic acid receptor-α (PML::RARA) fusion is the hallmark of acute promyelocytic leukemia (APL) and is observed in over 95% of APL cases. RARA and homologous receptors RARB and RARG are occasionally fused to other gene partners, which differentially affect sensitivity to targeted therapies. Most APLs without RARA fusions have rearrangements involving RARG or RARB, both of which frequently show resistance to all-trans-retinoic acid (ATRA) and/or multiagent chemotherapy for acute myeloid leukemia (AML). We present a 13-year-old male diagnosed with variant APL with a novel FNDC3B::RARB in-frame fusion that showed no response to ATRA but responded well to conventional AML therapy. While FNDC3B has been identified as a rare RARA translocation partner in ATRA-sensitive variant APL, it has never been reported as a fusion partner with RARB and it is only the second known fusion partner with RARB in variant APL. We also show that this novel fusion confers an RNA expression signature that is similar to APL, despite clinical resistance to ATRA monotherapy.
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MESH Headings
- Male
- Humans
- Adolescent
- Leukemia, Promyelocytic, Acute/drug therapy
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/metabolism
- Translocation, Genetic
- Tretinoin/therapeutic use
- Leukemia, Myeloid, Acute/genetics
- Retinoic Acid Receptor alpha/genetics
- Genomics
- Oncogene Proteins, Fusion/genetics
- Fibronectins/genetics
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Affiliation(s)
- Justin K Kirkham
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yen-Chun Liu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Scott G Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gabriela Gheorghe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Larissa V Furtado
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Marcela I Popescu
- Department of Pediatric Hematology and Oncology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Seth E Karol
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Patrick R Blackburn
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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2
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Mohebnasab M, Li P, Hong B, Dunlap J, Traer E, Fan G, Press RD, Moore SR, Xie W. Cytogenetically Cryptic Acute Promyelocytic Leukemia: A Diagnostic Challenge. Int J Mol Sci 2023; 24:13075. [PMID: 37685882 PMCID: PMC10488174 DOI: 10.3390/ijms241713075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
Cytogenetically cryptic acute promyelocytic leukemia (APL) is rare, characterized by typical clinical and morphological features, but lacks t(15;17)(q24;q21)/PML::RARA translocation seen in conventional karyotyping or FISH. The prompt diagnosis and treatment of APL are critical due to life-threatening complications associated with this disease. However, cryptic APL cases remain a diagnostic challenge that could mislead the appropriate treatment. We describe four cryptic APL cases and review reported cases in the literature. Reverse transcriptase polymerase chain reaction (RT-PCR) is the most efficient diagnostic modality to detect these cases, and alternative methods are also discussed. This study highlights the importance of using parallel testing methods to diagnose cryptic APL cases accurately and effectively.
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Affiliation(s)
- Maedeh Mohebnasab
- Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, OR 97239, USA
- Division of Molecular Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
- Department of Molecular and Medical Genetics and Knight Diagnostics Laboratory, Oregon Health and Science University, Portland, OR 97239, USA
| | - Peng Li
- Division of Hematopathology, Department of Pathology, University of Utah Health, Salt Lake City, UT 84112, USA
| | - Bo Hong
- Division of Hematopathology, Department of Pathology, University of Utah Health, Salt Lake City, UT 84112, USA
| | - Jennifer Dunlap
- Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, OR 97239, USA
| | - Elie Traer
- Department of Molecular and Medical Genetics and Knight Diagnostics Laboratory, Oregon Health and Science University, Portland, OR 97239, USA
- Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Guang Fan
- Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, OR 97239, USA
| | - Richard D. Press
- Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics and Knight Diagnostics Laboratory, Oregon Health and Science University, Portland, OR 97239, USA
| | - Stephen R. Moore
- Department of Molecular and Medical Genetics and Knight Diagnostics Laboratory, Oregon Health and Science University, Portland, OR 97239, USA
| | - Wei Xie
- Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, OR 97239, USA
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3
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Pitel BA, Zuckerman EZ, Baughn LB. Mate Pair Sequencing: Next-Generation Sequencing for Structural Variant Detection. Methods Mol Biol 2023; 2621:127-149. [PMID: 37041444 DOI: 10.1007/978-1-0716-2950-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Structural variant detection by next-generation sequencing (NGS) methods have a higher molecular resolution than conventional cytogenetic techniques (Aypar et al., Eur J Haematol 102(1):87-96, 2019; Smadbeck et al., Blood Cancer J 9(12):103, 2019) and are particularly helpful in characterizing genomic rearrangements. Mate pair sequencing (MPseq) leverages a unique library preparation chemistry involving circularization of long DNA fragments, allowing for a unique application of paired-end sequencing of reads that are expected to map 2-5 kb apart in the genome. The unique orientation of the reads allows the user to estimate the location of breakpoints involved in a structural variant either within the sequenced reads or between the two reads. The precision of structural variant and copy number detection by this method allows for characterization of cryptic and complex rearrangements that may be otherwise undetectable by conventional cytogenetic methods (Singh et al., Leuk Lymphoma 60(5):1304-1307, 2019; Peterson et al., Blood Adv 3(8):1298-1302, 2019; Schultz et al., Leuk Lymphoma 61(4):975-978, 2020; Peterson et al., Mol Case Studies 5(2), 2019; Peterson et al., Mol Case Studies 5(3), 2019).
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Affiliation(s)
- Beth A Pitel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | | | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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4
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Gagnon MF, Berg HE, Meyer RG, Sukov WR, Van Dyke DL, Jenkins RB, Greipp PT, Thorland EC, Hoppman NL, Xu X, Baughn LB, Reichard KK, Ketterling RP, Peterson JF. Typical, atypical and cryptic t(15;17)(q24;q21) (PML::RARA) observed in acute promyelocytic leukemia: a retrospective review of 831 patients with concurrent chromosome and PML::RARA dual-color dual-fusion FISH studies. Genes Chromosomes Cancer 2022; 61:629-634. [PMID: 35639830 DOI: 10.1002/gcc.23070] [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: 03/25/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/07/2022] Open
Abstract
The diagnosis of acute promyelocytic leukemia (APL) relies on the identification of PML::RARA fusion. While the majority of APL cases harbor a typical t(15;17)(q24;q21), atypical genetic mechanisms leading to the oncogenic PML::RARA fusion have been reported yet their frequency and scope remain poorly characterized. We assessed the genetic findings of 831 cases with APL investigated with concurrent chromosome banding analysis and dual-color dual-fusion fluorescence in situ hybridization (D-FISH) analysis at our institution over an 18.5-year timeframe. Seven-hundred twenty-three (87%) cases had a typical balanced t(15;17) with both testing modalities. Atypical karyotypic results including complex translocations, unbalanced rearrangements and insertional events occurred in 50 (6%) cases, while 6 (0.7%) cases were cryptic by conventional chromosome studies despite PML::RARA fusion by D-FISH evaluation. Atypical FISH patterns were observed in 48 (6%) cases despite apparently balanced t(15;17) on chromosome banding analysis. Two-hundred fifty (30%) cases displayed additional chromosome abnormalities of which trisomy/tetrasomy 8 (37%), del(7q)/add(7q) (12%) and del(9q) (7%) were most frequent. Complex and very complex karyotypes were observed in 81 (10%) and 34 (4%) cases, respectively. In addition, 4 (0.5%) cases presented as an apparently doubled, near-tetraploid stemline clone. This report provides the largest appraisal of cytogenetic findings in APL with conventional chromosome and PML::RARA D-FISH analysis. By characterizing the frequency and breadth of typical and atypical results through the lens of these cytogenetic testing modalities, this study serves as a pragmatic source of information for those involved in the investigation of APL in both the clinical and research laboratory settings.
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Affiliation(s)
- Marie-France Gagnon
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Holly E Berg
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Reid G Meyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, 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
| | - Daniel L Van Dyke
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Robert B Jenkins
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Erik C Thorland
- 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
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kaaren K Reichard
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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5
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Karlin K, Bryke C, Dias A, Michaels P. Cytogenetically cryptic PML::RARA fusion in acute promyelocytic leukemia: Testing strategies in the modern era. Leuk Res Rep 2022; 17:100320. [PMID: 35572917 PMCID: PMC9092513 DOI: 10.1016/j.lrr.2022.100320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 11/30/2022] Open
Abstract
Cytogenetically cryptic PML::RARA fusions is an exceedingly rare phenomenon in acute promyelocytic leukemia Multiple methodologies may be employed for detecting the cryptic PML::RARA fusion Concurrent mutations can be identified in cases of acute promyelocytic leukemia with a cryptic PML::RARA fusion; however, a unifying genomic feature remains elusive For cases with a high clinical suspicion of acute promyelocytic leukemia and no cytogenetic evidence of a PML::RARA fusion, complementary techniques should be employed for further analysis
Acute promyelocytic leukemia (APL) is a unique leukemia that is characterized by the PML::RARA fusion. This fusion is often detected by conventional karyotype and fluorescence in situ hybridization (FISH); however, rare cases are cryptic and require molecular techniques to identify the PML::RARA fusion. Furthermore, as the incidence of these cases is rare, analysis by a targeted next-generation sequencing (NGS) panel of myeloid associated genes has never been reported. Herein, a clinical APL case is reported where the PML::RARA fusion was detected only by reverse transcriptase-polymerase chain reaction (RT-PCR), thus underscoring the necessity of utilizing complementary techniques when suspicion for APL is present.
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Affiliation(s)
- Kirill Karlin
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
| | - Christine Bryke
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
| | - Ajoy Dias
- Department of Hematology-Oncology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
| | - Phillip Michaels
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
- Corresponding author.
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Kanagal-Shamanna R, Bao H, Kearney H, Smoley S, Tang Z, Luthra R, Yang H, Zhang S, Lin P, Wu D, Medeiros LJ, Lu X. Molecular characterization of Novel ATM fusions in chronic lymphocytic leukemia and T-cell prolymphocytic leukemia. Leuk Lymphoma 2021; 63:865-875. [PMID: 34898335 DOI: 10.1080/10428194.2021.2010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
ATM deletions and/or mutations are recurrent in lymphoid neoplasms while rearrangements are rare. In this study, we used mate pair sequencing (MPseq) technology to characterize two novel ATM rearrangements in one patient with chronic lymphocytic leukemia (CLL) and one patient with T-prolymphocytic leukemia (T-PLL). Both patients showed chromosome 11q22 aberrations encompassing ATM by conventional karyotype and fluorescence in situ hybridization: isolated t(11;13)(q22;q14) in CLL and a complex karyotype with apparent 11q deletion and unbalanced der(14)t(11;14)(q22;p11.2) in T-PLL. MPseq identified ATM-LINC00371 fusion in CLL and ATM-USP28 in T-PLL, both of which led to ATM inactivation, confirmed by loss of immunohistochemical protein expression. Next-generation sequencing mutation analysis detected concurrent ATM mutation(s) CLL patient, while T-PLL lacked ATM mutation. ATM rearrangements, not apparently detectable using standard laboratory technologies, represent another mechanism of loss-of-function. Recent high-throughput technologies such as MPseq can uncover novel pathogenic gene fusions and resolve complex chromosomal rearrangements in hematologic malignancies.
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Haiyan Bao
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Hematology, SooChow University First Affiliated Hospital, Suzhou, Jiangsu, China
| | - Hutton Kearney
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Stephanie Smoley
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Hui Yang
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Shanshan Zhang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pei Lin
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Depei Wu
- Department of Hematology, SooChow University First Affiliated Hospital, Suzhou, Jiangsu, China
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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