1
|
Iriondo J, Gómez A, Zubicaray J, Garcia-Martinez J, Abad L, Matesanz C, Giménez R, Galán A, Sanz A, Sebastián E, González de Pablo J, de la Cruz A, Ramírez M, Sevilla J. Optical Genome Mapping as a New Tool to Overcome Conventional Cytogenetics Limitations in Patients with Bone Marrow Failure. Genes (Basel) 2024; 15:559. [PMID: 38790188 PMCID: PMC11121707 DOI: 10.3390/genes15050559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Cytogenetic studies are essential in the diagnosis and follow up of patients with bone marrow failure syndromes (BMFSs), but obtaining good quality results is often challenging due to hypocellularity. Optical Genome Mapping (OGM), a novel technology capable of detecting most types chromosomal structural variants (SVs) at high resolution, is being increasingly used in many settings, including hematologic malignancies. Herein, we compared conventional cytogenetic techniques to OGM in 20 patients with diverse BMFSs. Twenty metaphases for the karyotype were only obtained in three subjects (15%), and no SVs were found in any of the samples. One patient with culture failure showed a gain in chromosome 1q by fluorescence in situ hybridization, which was confirmed by OGM. In contrast, OGM provided good quality results in all subjects, and SVs were detected in 14 of them (70%), mostly corresponding to cryptic submicroscopic alterations not observed by standard techniques. Therefore, OGM emerges as a powerful tool that provides complete and evaluable results in hypocellular BMFSs, reducing multiple tests into a single assay and overcoming some of the main limitations of conventional techniques. Furthermore, in addition to confirming the abnormalities detected by conventional techniques, OGM found new alterations beyond their detection limits.
Collapse
Affiliation(s)
- June Iriondo
- Hematology and Hemotherapy Unit, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (J.Z.); (A.S.); (E.S.)
- Biomedical Research Foundation, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (J.G.d.P.); (A.d.l.C.)
| | - Ana Gómez
- Laboratory and Clinical Analysis Department, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (L.A.); (C.M.); (R.G.); (M.R.)
| | - Josune Zubicaray
- Hematology and Hemotherapy Unit, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (J.Z.); (A.S.); (E.S.)
- Biomedical Research Foundation, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (J.G.d.P.); (A.d.l.C.)
| | - Jorge Garcia-Martinez
- Pediatric Onco-Hematology Department, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain;
- Health Research Institute at Hospital de La Princesa (IIS-Princesa), 28006 Madrid, Spain
| | - Lorea Abad
- Laboratory and Clinical Analysis Department, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (L.A.); (C.M.); (R.G.); (M.R.)
| | - Carmen Matesanz
- Laboratory and Clinical Analysis Department, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (L.A.); (C.M.); (R.G.); (M.R.)
| | - Reyes Giménez
- Laboratory and Clinical Analysis Department, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (L.A.); (C.M.); (R.G.); (M.R.)
| | - Almudena Galán
- Biomedical Research Foundation, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (J.G.d.P.); (A.d.l.C.)
- Laboratory and Clinical Analysis Department, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (L.A.); (C.M.); (R.G.); (M.R.)
| | - Alejandro Sanz
- Hematology and Hemotherapy Unit, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (J.Z.); (A.S.); (E.S.)
- Biomedical Research Foundation, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (J.G.d.P.); (A.d.l.C.)
| | - Elena Sebastián
- Hematology and Hemotherapy Unit, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (J.Z.); (A.S.); (E.S.)
- Biomedical Research Foundation, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (J.G.d.P.); (A.d.l.C.)
| | - Jesús González de Pablo
- Biomedical Research Foundation, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (J.G.d.P.); (A.d.l.C.)
| | - Ana de la Cruz
- Biomedical Research Foundation, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (J.G.d.P.); (A.d.l.C.)
- Laboratory and Clinical Analysis Department, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (L.A.); (C.M.); (R.G.); (M.R.)
| | - Manuel Ramírez
- Laboratory and Clinical Analysis Department, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (L.A.); (C.M.); (R.G.); (M.R.)
- Pediatric Onco-Hematology Department, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain;
- Health Research Institute at Hospital de La Princesa (IIS-Princesa), 28006 Madrid, Spain
| | - Julián Sevilla
- Hematology and Hemotherapy Unit, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (J.Z.); (A.S.); (E.S.)
- Biomedical Research Foundation, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain; (A.G.); (J.G.d.P.); (A.d.l.C.)
| |
Collapse
|
2
|
Zhang L, Deeb G, Deeb KK, Vale C, Peker Barclift D, Papadantonakis N. Measurable (Minimal) Residual Disease in Myelodysplastic Neoplasms (MDS): Current State and Perspectives. Cancers (Basel) 2024; 16:1503. [PMID: 38672585 PMCID: PMC11048433 DOI: 10.3390/cancers16081503] [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: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Myelodysplastic Neoplasms (MDS) have been traditionally studied through the assessment of blood counts, cytogenetics, and morphology. In recent years, the introduction of molecular assays has improved our ability to diagnose MDS. The role of Measurable (minimal) Residual Disease (MRD) in MDS is evolving, and molecular and flow cytometry techniques have been used in several studies. In this review, we will highlight the evolving concept of MRD in MDS, outline the various techniques utilized, and provide an overview of the studies reporting MRD and the correlation with outcomes.
Collapse
Affiliation(s)
- Linsheng Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - George Deeb
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kristin K. Deeb
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Colin Vale
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Deniz Peker Barclift
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nikolaos Papadantonakis
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
3
|
Finlay D, Murad R, Hong K, Lee J, Pang AWC, Lai CY, Clifford B, Burian C, Mason J, Hastie AR, Yin J, Vuori K. Detection of Genomic Structural Variations Associated with Drug Sensitivity and Resistance in Acute Leukemia. Cancers (Basel) 2024; 16:418. [PMID: 38254907 PMCID: PMC10814465 DOI: 10.3390/cancers16020418] [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: 11/20/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Acute leukemia is a particularly problematic collection of hematological cancers, and, while somewhat rare, the survival rate of patients is typically abysmal without bone marrow transplantation. Furthermore, traditional chemotherapies used as standard-of-care for patients cause significant side effects. Understanding the evolution of leukemia to identify novel targets and, therefore, drug treatment regimens is a significant medical need. Genomic rearrangements and other structural variations (SVs) have long been known to be causative and pathogenic in multiple types of cancer, including leukemia. These SVs may be involved in cancer initiation, progression, clonal evolution, and drug resistance, and a better understanding of SVs from individual patients may help guide therapeutic options. Here, we show the utilization of optical genome mapping (OGM) to detect known and novel SVs in the samples of patients with leukemia. Importantly, this technology provides an unprecedented level of granularity and quantitation unavailable to other current techniques and allows for the unbiased detection of novel SVs, which may be relevant to disease pathogenesis and/or drug resistance. Coupled with the chemosensitivities of these samples to FDA-approved oncology drugs, we show how an impartial integrative analysis of these diverse datasets can be used to associate the detected genomic rearrangements with multiple drug sensitivity profiles. Indeed, an insertion in the gene MUSK is shown to be associated with increased sensitivity to the clinically relevant agent Idarubicin, while partial tandem duplication events in the KMT2A gene are related to the efficacy of another frontline treatment, Cytarabine.
Collapse
Affiliation(s)
- Darren Finlay
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
| | - Rabi Murad
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
| | - Karl Hong
- Bionano Genomics Inc., San Diego, CA 92121, USA
| | - Joyce Lee
- Bionano Genomics Inc., San Diego, CA 92121, USA
| | | | - Chi-Yu Lai
- Bionano Genomics Inc., San Diego, CA 92121, USA
| | | | | | - James Mason
- Scripps MD Anderson, La Jolla, CA 92037, USA
| | | | - Jun Yin
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
| | - Kristiina Vuori
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Optical Genome Mapping for Cytogenetic Diagnostics in AML. Cancers (Basel) 2023; 15:cancers15061684. [PMID: 36980569 PMCID: PMC10046241 DOI: 10.3390/cancers15061684] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/24/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
The classification and risk stratification of acute myeloid leukemia (AML) is based on reliable genetic diagnostics. A broad and expanding variety of relevant aberrations are structural variants beyond single-nucleotide variants. Optical Genome Mapping is an unbiased, genome-wide, amplification-free method for the detection of structural variants. In this review, the current knowledge of Optical Genome Mapping (OGM) with regard to diagnostics in hematological malignancies in general, and AML in specific, is summarized. Furthermore, this review focuses on the ability of OGM to expand the use of cytogenetic diagnostics in AML and perhaps even replace older techniques such as chromosomal-banding analysis, fluorescence in situ hybridization, or copy number variation microarrays. Finally, OGM is compared to amplification-based techniques and a brief outlook for future directions is given.
Collapse
|