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Ronaghy A, Yang RK, Khoury JD, Kanagal-Shamanna R. Clinical Applications of Chromosomal Microarray Testing in Myeloid Malignancies. Curr Hematol Malig Rep 2020; 15:194-202. [PMID: 32382988 DOI: 10.1007/s11899-020-00578-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE OF REVIEW Knowledge of both somatic mutations and copy number aberrations are important for the understanding of cancer pathogenesis and management of myeloid neoplasms. The currently available standard of care technologies for copy number assessment such as conventional karyotype and FISH are either limited by low resolution or restriction to targeted assessment. RECENT FINDINGS Chromosomal microarray (CMA) is effective in characterization of chromosomal and gene aberrations of diagnostic, prognostic, and therapeutic significance at a higher resolution than conventional karyotyping. These results are complementary to NGS mutation studies. Copy-neutral loss of heterozygosity (CN-LOH), which is prognostic in AML, is currently only identified by CMA. Yet, despite the widespread availability, CMA testing is not routinely performed in diagnostic laboratories due to lack of knowledge on best-testing practices for clinical work-up of myeloid neoplasms. In this review, we provide an overview of the clinical significance of CMA in acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and myelodysplastic/myeloproliferative neoplasms (MDS/MPN). We will also elaborate the specific clinical scenarios where CMA can provide additional information essential for management and could potentially alter treatment. Chromosomal microarray (CMA) is an effective technology for characterizing chromosomal copy number changes and copy-neutral loss of heterozygosity of diagnostic, prognostic, and therapeutic significance at a high resolution in myeloid malignancies.
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MESH Headings
- Chromosome Aberrations
- Chromosomes, Human
- Comparative Genomic Hybridization
- DNA Copy Number Variations
- Genetic Predisposition to Disease
- High-Throughput Nucleotide Sequencing
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myelomonocytic, Chronic/diagnosis
- Leukemia, Myelomonocytic, Chronic/genetics
- Loss of Heterozygosity
- Microarray Analysis
- Myelodysplastic Syndromes/diagnosis
- Myelodysplastic Syndromes/genetics
- Polymorphism, Single Nucleotide
- Predictive Value of Tests
- Prognosis
- Reproducibility of Results
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Affiliation(s)
- Arash Ronaghy
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Richard K Yang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA.
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Xiao X, He X, Li Q, Zhang W, Zhu H, Yang W, Li Y, Geng L, Liu H, Li L, Wang H, Fu R, Zhao M, Chen Z, Shao Z. Single-Nucleotide Polymorphism Array Technique Generating Valuable Risk-Stratification Information for Patients With Myelodysplastic Syndromes. Front Oncol 2020; 10:962. [PMID: 32733790 PMCID: PMC7358551 DOI: 10.3389/fonc.2020.00962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Chromosomal abnormalities play an important role in the diagnosis and prognosis of patients with myelodysplastic syndromes (MDSs). The single-nucleotide polymorphism array (SNP-A) technique has gained popularity due to its improved resolution compared to that of metaphase cytogenetic (MC) analysis. Methods: A total of 376 individuals were recruited from two medical centers in China, including 350 patients and 26 healthy individuals. Among these patients, 200 were diagnosed with de novo MDS, 25 with myeloproliferative neoplasm (MPN), 63 with primary acute myeloid leukemia (AML), and 62 with idiopathic cytopenia of undetermined significance (ICUS). We evaluated the significance of abnormal chromosomes detected by SNP-A in the diagnosis and prognosis of MDS-related disorders. Results: (1) When certain chromosomal abnormalities could not be detected by conventional MC methods, these abnormalities could be detected more efficiently by the SNP-A method. With SNP-A, the detection rates of submicroscopic or cryptic aberrations in the MDS, MPN, and AML patients with normal MC findings were 32.8, 30.8, and 30%, respectively. (2) The chromosomal abnormalities detected by SNP-A had a very important value for the prognosis of patients with MDSs, especially in the low-risk group. The survival of patients with abnormal chromosomes detected by SNP-A was significantly lower than that of patients with no detected chromosomal abnormalities; this difference was observed in overall survival (OS) (P = 0.001) and progression-free survival (PFS) [24 months vs. not reach (NR); P = 0.008]. The patients with multiple chromosomal abnormalities detected by SNP-A had an inferior prognosis, and SNP-A abnormalities (≥3 per patient) were found to be an independent predictor of poor prognosis in patients with MDSs [hazard ratio (HR) = 2.40, P = 0.002]. (3) Patients with ICUS may progress to myeloid malignancies, but most patients often maintain a stable ICUS status for many years without progression. An ICUS patient found to have an MDS-related karyotype would be rediagnosed with MDS. SNP-A can efficiently detect chromosomal abnormalities, which would be important for assessing the evolution of ICUS. In our study, 17 ICUS patients with SNP-A-detected abnormalities developed typical MDSs. Conclusions: SNP-A can help evaluate the prognosis of patients with MDSs and better assess the risk of disease progression for patients with ICUS.
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Affiliation(s)
- Xia Xiao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Xiaoyuan He
- Department of Clinical Medicine, Nankai University School of Medicine, Tianjin, China
| | - Qing Li
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Wei Zhang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Haibo Zhu
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Weihong Yang
- Wuhan Kindstar Diagnostics Co./Kindstar Global Gene (Beijing) Technology, Inc., Wuhan, China
| | - Yuming Li
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Li Geng
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Hui Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Lijuan Li
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Huaquan Wang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingfeng Zhao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China.,Department of Clinical Medicine, Nankai University School of Medicine, Tianjin, China
| | - Zhong Chen
- Wuhan Kindstar Diagnostics Co./Kindstar Global Gene (Beijing) Technology, Inc., Wuhan, China
| | - Zonghong Shao
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
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Response of high-risk MDS to azacitidine and lenalidomide is impacted by baseline and acquired mutations in a cluster of three inositide-specific genes. Leukemia 2019; 33:2276-2290. [PMID: 30787430 PMCID: PMC6733710 DOI: 10.1038/s41375-019-0416-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 12/26/2022]
Abstract
Specific myeloid-related and inositide-specific gene mutations can be linked to myelodysplastic syndromes (MDS) pathogenesis and therapy. Here, 44 higher-risk MDS patients were treated with azacitidine and lenalidomide and mutations analyses were performed at baseline and during the therapy. Results were then correlated to clinical outcome, overall survival (OS), leukemia-free-survival (LFS) and response to therapy. Collectively, 34/44 patients were considered evaluable for response, with an overall response rate of 76.25% (26/34 cases): 17 patients showed a durable response, 9 patients early lost response and 8 patients never responded. The most frequently mutated genes were ASXL1, TET2, RUNX1, and SRSF2. All patients early losing response, as well as cases never responding, acquired the same 3 point mutations during therapy, affecting respectively PIK3CD (D133E), AKT3 (D280G), and PLCG2 (Q548R) genes, that regulate cell proliferation and differentiation. Moreover, Kaplan–Meier analyses revealed that this mutated cluster was significantly associated with a shorter OS, LFS, and duration of response. All in all, a common mutated cluster affecting 3 inositide-specific genes is significantly associated with loss of response to azacitidine and lenalidomide therapy in higher risk MDS. Further studies are warranted to confirm these data and to further analyze the functional role of this 3-gene cluster.
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Fuchs O. Treatment of Lymphoid and Myeloid Malignancies by Immunomodulatory Drugs. Cardiovasc Hematol Disord Drug Targets 2019; 19:51-78. [PMID: 29788898 DOI: 10.2174/1871529x18666180522073855] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/05/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
Thalidomide and its derivatives (lenalidomide, pomalidomide, avadomide, iberdomide hydrochoride, CC-885 and CC-90009) form the family of immunomodulatory drugs (IMiDs). Lenalidomide (CC5013, Revlimid®) was approved by the US FDA and the EMA for the treatment of multiple myeloma (MM) patients, low or intermediate-1 risk transfusion-dependent myelodysplastic syndrome (MDS) with chromosome 5q deletion [del(5q)] and relapsed and/or refractory mantle cell lymphoma following bortezomib. Lenalidomide has also been studied in clinical trials and has shown promising activity in chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphoma (NHL). Lenalidomide has anti-inflammatory effects and inhibits angiogenesis. Pomalidomide (CC4047, Imnovid® [EU], Pomalyst® [USA]) was approved for advanced MM insensitive to bortezomib and lenalidomide. Other IMiDs are in phases 1 and 2 of clinical trials. Cereblon (CRBN) seems to have an important role in IMiDs action in both lymphoid and myeloid hematological malignancies. Cereblon acts as the substrate receptor of a cullin-4 really interesting new gene (RING) E3 ubiquitin ligase CRL4CRBN. This E3 ubiquitin ligase in the absence of lenalidomide ubiquitinates CRBN itself and the other components of CRL4CRBN complex. Presence of lenalidomide changes specificity of CRL4CRBN which ubiquitinates two transcription factors, IKZF1 (Ikaros) and IKZF3 (Aiolos), and casein kinase 1α (CK1α) and marks them for degradation in proteasomes. Both these transcription factors (IKZF1 and IKZF3) stimulate proliferation of MM cells and inhibit T cells. Low CRBN level was connected with insensitivity of MM cells to lenalidomide. Lenalidomide decreases expression of protein argonaute-2, which binds to cereblon. Argonaute-2 seems to be an important drug target against IMiDs resistance in MM cells. Lenalidomide decreases also basigin and monocarboxylate transporter 1 in MM cells. MM cells with low expression of Ikaros, Aiolos and basigin are more sensitive to lenalidomide treatment. The CK1α gene (CSNK1A1) is located on 5q32 in commonly deleted region (CDR) in del(5q) MDS. Inhibition of CK1α sensitizes del(5q) MDS cells to lenalidomide. CK1α mediates also survival of malignant plasma cells in MM. Though, inhibition of CK1α is a potential novel therapy not only in del(5q) MDS but also in MM. High level of full length CRBN mRNA in mononuclear cells of bone marrow and of peripheral blood seems to be necessary for successful therapy of del(5q) MDS with lenalidomide. While transfusion independence (TI) after lenalidomide treatment is more than 60% in MDS patients with del(5q), only 25% TI and substantially shorter duration of response with occurrence of neutropenia and thrombocytopenia were achieved in lower risk MDS patients with normal karyotype treated with lenalidomide. Shortage of the biomarkers for lenalidomide response in these MDS patients is the main problem up to now.
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Affiliation(s)
- Ota Fuchs
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic
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Kanagal-Shamanna R, Hodge JC, Tucker T, Shetty S, Yenamandra A, Dixon-McIver A, Bryke C, Huxley E, Lennon PA, Raca G, Xu X, Jeffries S, Quintero-Rivera F, Greipp PT, Slovak ML, Iqbal MA, Fang M. Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms. Cancer Genet 2018; 228-229:197-217. [PMID: 30377088 DOI: 10.1016/j.cancergen.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/16/2022]
Abstract
Multiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines for integrating CMA as a standard practice for diagnostic evaluation, assessment of prognosis and predicting treatment response are still lacking. CMA has not been recommended for clinical work-up of myeloid malignancies by the WHO 2016 or the NCCN 2017 guidelines but is a suggested test by the European LeukaemiaNet 2013 for the diagnosis of primary myelodysplastic syndrome (MDS). The Cancer Genomics Consortium (CGC) Working Group for Myeloid Neoplasms systematically reviewed peer-reviewed literature to determine the power of CMA in (1) improving diagnostic yield, (2) refining risk stratification, and (3) providing additional genomic information to guide therapy. In this manuscript, we summarize the evidence base for the clinical utility of array testing in the workup of MDS, myelodysplastic/myeloproliferative neoplasms (MDS/MPN) and myeloproliferative neoplasms (MPN). This review provides a list of recurrent CNAs and CN-LOH noted in this disease spectrum and describes the clinical significance of the aberrations and how they complement gene mutation findings by sequencing. Furthermore, for new or suspected diagnosis of MDS or MPN, we present suggestions for integrating genomic testing methods (CMA and mutation testing by next generation sequencing) into the current standard-of-care clinical laboratory testing (karyotype, FISH, morphology, and flow).
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston TX, USA.
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, Cancer Genetics Laboratory, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Shashi Shetty
- Department of Pathology, UHCMC, University Hospitals and Case Western Reserve University, Cleveland, OH, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Christine Bryke
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emma Huxley
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Xinjie Xu
- ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Sally Jeffries
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Marilyn L Slovak
- TriCore Reference Laboratories, University of New Mexico, Albuquerque, NM, USA
| | - M Anwar Iqbal
- University of Rochester Medical Center, Rochester, NY, USA
| | - Min Fang
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle, WA, USA.
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Yeung C, McElhone S, Chen XY, Ng D, Storer B, Deeg HJ, Fang M. Impact of copy neutral loss of heterozygosity and total genome aberrations on survival in myelodysplastic syndrome. Mod Pathol 2018; 31:569-580. [PMID: 29243741 PMCID: PMC5906151 DOI: 10.1038/modpathol.2017.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 12/17/2022]
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of diseases with varying genetic aberrations. Half of MDS patients have normal karyotype, obscuring the underlying condition indicating a need for new markers for improved diagnostics and prognosis. We performed a retrospective review of sequential MDS patients who underwent chromosomal genetic array testing (CGAT) between November 2008 and March 2014. Total Genomic Aberration (TGA) scores, with and without copy-neutral loss of heterozygosity (cnLOH), were compared to pathology and clinical data. Of 68 MDS participants, 50 patients (73%) had abnormal CGAT results. 32% showedcnLOH, 41% had no cnLOH but displayed copy number aberration (CNAs). Of 26 patients with normal cytogenetics, 46% had clonal abnormalities by CGAT. Abnormal CGAT results were associated with lower overall survival (P=0.04). Overall survival in patients with TGA above the median (68.6 Mb) was significantly inferior to those below the median (HR=2.9, 95% CI=1.3-6.8, P=0.01). Furthermore, there was an observed association between increased TGA and increased dysplastic lineages (Ptrend=0.003). CGAT studies provide important findings that extend beyond current standard testing. Clinical utility of CGAT includes improved diagnostic yield, correlation of extent of TGA and increased dysplastic features, and survival.
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Affiliation(s)
- Cecilia Yeung
- Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
- Seattle Cancer Care Alliance, Seattle, WA
| | | | | | | | - Barry Storer
- Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - H. Joachim Deeg
- Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - Min Fang
- Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
- Seattle Cancer Care Alliance, Seattle, WA
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Stevens-Kroef MJ, Olde Weghuis D, ElIdrissi-Zaynoun N, van der Reijden B, Cremers EMP, Alhan C, Westers TM, Visser-Wisselaar HA, Chitu DA, Cunha SM, Vellenga E, Klein SK, Wijermans P, de Greef GE, Schaafsma MR, Muus P, Ossenkoppele GJ, van de Loosdrecht AA, Jansen JH. Genomic array as compared to karyotyping in myelodysplastic syndromes in a prospective clinical trial. Genes Chromosomes Cancer 2017; 56:524-534. [DOI: 10.1002/gcc.22455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/16/2017] [Accepted: 02/16/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Daniel Olde Weghuis
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - Bert van der Reijden
- Department of Laboratory Medicine; Radboud University Medical Center; Nijmegen The Netherlands
| | - Eline M. P. Cremers
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Canan Alhan
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Theresia M. Westers
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Heleen A. Visser-Wisselaar
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Dana A. Chitu
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Sonia M. Cunha
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Edo Vellenga
- Department of Experimental Hematology; University Medical Center Groningen; Groningen The Netherlands
| | - Saskia K. Klein
- Department of Internal Medicine; Meander Medisch Centrum; Amersfoort The Netherlands
| | - Pierre Wijermans
- Department of Internal Medicine; Haga Ziekenhuis; The Hague The Netherlands
| | - Georgine E. de Greef
- Department of Hematology; Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - M. Ron Schaafsma
- Department of Internal Medicine; Medisch Centrum Twente; Enschede The Netherlands
| | - Petra Muus
- Department of Hematology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Gert J. Ossenkoppele
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Arjan A. van de Loosdrecht
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Joop H. Jansen
- Department of Laboratory Medicine; Radboud University Medical Center; Nijmegen The Netherlands
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