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Raj A, Petreaca RC, Mirzaei G. Multi-Omics Integration for Liver Cancer Using Regression Analysis. Curr Issues Mol Biol 2024; 46:3551-3562. [PMID: 38666952 PMCID: PMC11049490 DOI: 10.3390/cimb46040222] [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: 02/18/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Genetic biomarkers have played a pivotal role in the classification, prognostication, and guidance of clinical cancer therapies. Large-scale and multi-dimensional analyses of entire cancer genomes, as exemplified by projects like The Cancer Genome Atlas (TCGA), have yielded an extensive repository of data that holds the potential to unveil the underlying biology of these malignancies. Mutations stand out as the principal catalysts of cellular transformation. Nonetheless, other global genomic processes, such as alterations in gene expression and chromosomal re-arrangements, also play crucial roles in conferring cellular immortality. The incorporation of multi-omics data specific to cancer has demonstrated the capacity to enhance our comprehension of the molecular mechanisms underpinning carcinogenesis. This report elucidates how the integration of comprehensive data on methylation, gene expression, and copy number variations can effectively facilitate the unsupervised clustering of cancer samples. We have identified regressors that can effectively classify tumor and normal samples with an optimal integration of RNA sequencing, DNA methylation, and copy number variation while also achieving significant p-values. Further, these regressors were trained using linear and logistic regression with k-means clustering. For comparison, we employed autoencoder- and stacking-based omics integration and computed silhouette scores to evaluate the clusters. The proof of concept is illustrated using liver cancer data. Our analysis serves to underscore the feasibility of unsupervised cancer classification by considering genetic markers beyond mutations, thereby emphasizing the clinical relevance of additional global cellular parameters that contribute to the transformative process in cells. This work is clinically relevant because changes in gene expression and genomic re-arrangements have been shown to be signatures of cellular transformation across cancers, as well as in liver cancers.
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Affiliation(s)
- Aditya Raj
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH 43210, USA;
| | - Ruben C. Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA;
- Cancer Biology Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Golrokh Mirzaei
- Department of Computer Science and Engineering, The Ohio State University, Marion, OH 43302, USA
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Lagunas-Rangel FA. Chromothripsis in hematologic malignancies. Exp Hematol 2024; 132:104172. [PMID: 38309572 DOI: 10.1016/j.exphem.2024.104172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
Chromotrypsis, a phenomenon resulting from catastrophic mitotic errors and genomic instability, is defined by the occurrence of multiple DNA double-strand breaks in one or more chromosomes, subsequently subject to error-prone repair mechanisms. This unique process results in extensive rearrangements in the affected chromosomes, leading to loss of tumor suppressor function, the creation of fusion genes, and/or activation of oncogenes. The importance of chromothripsis in cancer, especially in the field of hematologic disorders, underscores the intricate interplay between genomic instability and the genesis of alterations that contribute to cancer. This accentuates the critical need to unravel these complex processes for the targeted development of specific therapeutic interventions. This review delves into the analysis of chromothripsis cases in various hematologic diseases, such as leukemia, lymphoma, and myeloma, with the aim of unveiling its profound impact on patient prognosis. Furthermore, the study explores the intricate molecular mechanisms underlying chromothripsis and investigates its consequences.
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Affiliation(s)
- Francisco Alejandro Lagunas-Rangel
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico.
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3
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Sourty B, Basset L, Fontaine A, Garcion E, Rousseau A. Chromothripsis is rare in IDH-mutant gliomas compared to IDH-wild-type glioblastomas whereas whole-genome duplication is equally frequent in both tumor types. Neurooncol Adv 2024; 6:vdae059. [PMID: 38800696 PMCID: PMC11125406 DOI: 10.1093/noajnl/vdae059] [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: 05/29/2024] Open
Abstract
Background Adult-type diffuse gliomas comprise IDH (isocitrate dehydrogenase)-mutant astrocytomas, IDH-mutant 1p/19q-codeleted oligodendrogliomas (ODG), and IDH-wild-type glioblastomas (GBM). GBM displays genome instability, which may result from 2 genetic events leading to massive chromosome alterations: Chromothripsis (CT) and whole-genome duplication (WGD). These events are scarcely described in IDH-mutant gliomas. The better prognosis of the latter may be related to their genome stability compared to GBM. Methods Pangenomic profiles of 297 adult diffuse gliomas were analyzed at initial diagnosis using SNP arrays, including 192 GBM and 105 IDH-mutant gliomas (61 astrocytomas and 44 ODG). Tumor ploidy was assessed with Genome Alteration Print and CT events with CTLPScanner and through manual screening. Survival data were compared using the Kaplan-Meier method. Results At initial diagnosis, 37 GBM (18.7%) displayed CT versus 5 IDH-mutant gliomas (4.7%; P = .0008), the latter were all high-grade (grade 3 or 4) astrocytomas. WGD was detected at initial diagnosis in 18 GBM (9.3%) and 9 IDH-mutant gliomas (5 astrocytomas and 4 oligodendrogliomas, either low- or high-grade; 8.5%). Neither CT nor WGD was associated with overall survival in GBM or in IDH-mutant gliomas. Conclusions CT is less frequent in IDH-mutant gliomas compared to GBM. The absence of CT in ODG and grade 2 astrocytomas might, in part, explain their genome stability and better prognosis, while CT might underlie aggressive biological behavior in some high-grade astrocytomas. WGD is a rare and early event occurring equally in IDH-mutant gliomas and GBM.
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Affiliation(s)
- Baptiste Sourty
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
| | - Laëtitia Basset
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
| | - Alix Fontaine
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
| | - Emmanuel Garcion
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
| | - Audrey Rousseau
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000Angers, France
- Department of Pathology, University Hospital of Angers, Angers, France
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4
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Coccaro N, Zagaria A, Anelli L, Tarantini F, Tota G, Conserva MR, Cumbo C, Parciante E, Redavid I, Ingravallo G, Minervini CF, Minervini A, Specchia G, Musto P, Albano F. Optical Genome Mapping as a Tool to Unveil New Molecular Findings in Hematological Patients with Complex Chromosomal Rearrangements. Genes (Basel) 2023; 14:2180. [PMID: 38137002 PMCID: PMC10742895 DOI: 10.3390/genes14122180] [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: 10/27/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Standard cytogenetic techniques (chromosomal banding analysis-CBA, and fluorescence in situ hybridization-FISH) show limits in characterizing complex chromosomal rearrangements and structural variants arising from two or more chromosomal breaks. In this study, we applied optical genome mapping (OGM) to fully characterize two cases of complex chromosomal rearrangements at high resolution. In case 1, an acute myeloid leukemia (AML) patient showing chromothripsis, OGM analysis was fully concordant with classic cytogenetic techniques and helped to better refine chromosomal breakpoints. The OGM results of case 2, a patient with non-Hodgkin lymphoma, were only partially in agreement with previous cytogenetic analyses and helped to better define clonal heterogeneity, overcoming the bias related to clonal selection due to cell culture of cytogenetic techniques. In both cases, OGM analysis led to the identification of molecular markers, helping to define the pathogenesis, classification, and prognosis of the analyzed patients. Despite extensive efforts to study hematologic diseases, standard cytogenetic methods display unsurmountable limits, while OGM is a tool that has the power to overcome these limitations and provide a cytogenetic analysis at higher resolution. As OGM also shows limits in defining regions of a repetitive nature, combining OGM with CBA to obtain a complete cytogenetic characterization would be desirable.
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Affiliation(s)
- Nicoletta Coccaro
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Antonella Zagaria
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Luisa Anelli
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Francesco Tarantini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Giuseppina Tota
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Maria Rosa Conserva
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Cosimo Cumbo
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Elisa Parciante
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Immacolata Redavid
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Giuseppe Ingravallo
- Section of Molecular Pathology, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Crescenzio Francesco Minervini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Angela Minervini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Giorgina Specchia
- School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Pellegrino Musto
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Francesco Albano
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
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Samach A, Mafessoni F, Gross O, Melamed-Bessudo C, Filler-Hayut S, Dahan-Meir T, Amsellem Z, Pawlowski WP, Levy AA. CRISPR/Cas9-induced DNA breaks trigger crossover, chromosomal loss, and chromothripsis-like rearrangements. THE PLANT CELL 2023; 35:3957-3972. [PMID: 37497643 PMCID: PMC10615209 DOI: 10.1093/plcell/koad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
DNA double-stranded breaks (DSBs) generated by the Cas9 nuclease are commonly repaired via nonhomologous end-joining (NHEJ) or homologous recombination (HR). However, little is known about unrepaired DSBs and the type of damage they trigger in plants. We designed an assay that detects loss of heterozygosity (LOH) in somatic cells, enabling the study of a broad range of DSB-induced genomic events. The system relies on a mapped phenotypic marker which produces a light purple color (betalain pigment) in all plant tissues. Plants with sectors lacking the Betalain marker upon DSB induction between the marker and the centromere were tested for LOH events. Using this assay, we detected a tomato (Solanum lycopersicum) flower with a twin yellow and dark purple sector, corresponding to a germinally transmitted somatic crossover event. We also identified instances of small deletions of genomic regions spanning the T-DNA and whole chromosome loss. In addition, we show that major chromosomal rearrangements including loss of large fragments, inversions, and translocations were clearly associated with the CRISPR-induced DSB. Detailed characterization of complex rearrangements by whole-genome sequencing and molecular and cytological analyses supports a model in which a breakage-fusion-bridge cycle followed by chromothripsis-like rearrangements had been induced. Our LOH assay provides a tool for precise breeding via targeted crossover detection. It also uncovers CRISPR-mediated chromothripsis-like events in plants.
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Affiliation(s)
- Aviva Samach
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Fabrizio Mafessoni
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Or Gross
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Cathy Melamed-Bessudo
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Shdema Filler-Hayut
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Tal Dahan-Meir
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Ziva Amsellem
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | | | - Avraham A Levy
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
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Coccaro N, Anelli L, Zagaria A, Tarantini F, Cumbo C, Tota G, Minervini CF, Minervini A, Conserva MR, Redavid I, Parciante E, Macchia MG, Specchia G, Musto P, Albano F. Feasibility of Optical Genome Mapping in Cytogenetic Diagnostics of Hematological Neoplasms: A New Way to Look at DNA. Diagnostics (Basel) 2023; 13:diagnostics13111841. [PMID: 37296693 DOI: 10.3390/diagnostics13111841] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Optical genome mapping (OGM) is a new genome-wide technology that can reveal both structural genomic variations (SVs) and copy number variations (CNVs) in a single assay. OGM was initially employed to perform genome assembly and genome research, but it is now more widely used to study chromosome aberrations in genetic disorders and in human cancer. One of the most useful OGM applications is in hematological malignancies, where chromosomal rearrangements are frequent and conventional cytogenetic analysis alone is insufficient, necessitating further confirmation using ancillary techniques such as fluorescence in situ hybridization, chromosomal microarrays, or multiple ligation-dependent probe amplification. The first studies tested OGM efficiency and sensitivity for SV and CNV detection, comparing heterogeneous groups of lymphoid and myeloid hematological sample data with those obtained using standard cytogenetic diagnostic tests. Most of the work based on this innovative technology was focused on myelodysplastic syndromes (MDSs), acute myeloid leukemia (AML), and acute lymphoblastic leukemia (ALL), whereas little attention was paid to chronic lymphocytic leukemia (CLL) or multiple myeloma (MM), and none was paid to lymphomas. The studies showed that OGM can now be considered as a highly reliable method, concordant with standard cytogenetic techniques but able to detect novel clinically significant SVs, thus allowing better patient classification, prognostic stratification, and therapeutic choices in hematological malignancies.
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Affiliation(s)
- Nicoletta Coccaro
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Luisa Anelli
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Antonella Zagaria
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Francesco Tarantini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Cosimo Cumbo
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Giuseppina Tota
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Crescenzio Francesco Minervini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Angela Minervini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Maria Rosa Conserva
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Immacolata Redavid
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Elisa Parciante
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Maria Giovanna Macchia
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Giorgina Specchia
- School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Pellegrino Musto
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Francesco Albano
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
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7
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Qin Y, Zhang H, Feng L, Wei H, Wu Y, Jiang C, Xu Z, Zhu H, Liu T. Combining metaphase cytogenetics with single nucleotide polymorphism arrays can improve the diagnostic yield and identify prognosis more precisely in myelodysplastic syndromes. Ann Med 2022; 54:2627-2636. [PMID: 36148999 PMCID: PMC9518301 DOI: 10.1080/07853890.2022.2125173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) encompass a group of heterogeneous haematopoietic stem cell malignancies characterised by ineffective haematopoiesis, cytological aberrations, and a propensity for progression to acute myeloid leukaemia. Diagnosis and disease prognostic stratification are much based on genomic abnormalities. The traditional metaphase cytogenetics analysis (MC) can detect about 40-60% aberrations. Single-nucleotide polymorphism arrays (SNP-A) karyotyping can detect copy number variations with a higher resolution and has a unique advantage in detection of copy number neutral loss of heterozygosity (CN-LOH). Combining these two methods may improve the diagnostic efficiency and accuracy for MDS. METHODS We retrospectively analysed the data of 110 MDS patients diagnosed from January 2012 to December 2019 to compare the detection yield of chromosomal abnormalities by MC with by SNP-A, and the relationship between chromosomal abnormalities and prognosis. RESULTS Our results showed that SNP-A improved the detection yield of chromosomal aberrations compared with MC (74.5 vs. 55.5%, p < .001). In addition, the positive yield could be further improved by combining MC with SNP-A to 77.3%, compared with MC alone. Univariate analysis showed that age >65 years, bone marrow blasts ≥5%, with acquired CN-LOH, new aberrations detected by SNP-A, TGA value > the median (81.435 Mb), higher risk by IPSS-R-MC, higher risk by IPSS-R-SNP-A all had poorer prognosis. More critically, multivariable analysis showed that age >65 years and higher risk by IPSS-R-SNP-A were independent predictors of inferior OS in MDS patients. CONCLUSION The combination of MC and SNP-A based karyotyping can further improve the diagnostic yield and provide more precise prognostic stratification in MDS patients. However, SNP-A may not completely replace MC because of its inability to detect balanced translocation and to detect different clones. From a practical point of view, we recommend the concurrent use of SNP-A and MC in the initial karyotypic evaluation for MDS patients on diagnosis and prognosis stratification.KEY MESSAGESSNP-A based karyotyping can further improve the MDS diagnostic yield and provide more precise prognostic stratification in MDS patients.Acquired CN-LOH is a characteristic chromosomal aberration of MDS, which should be integrated to the diagnostic project of MDS.The concurrent use of SNP-A and MC in the initial karyotypic evaluation for MDS patients can be recommended.
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Affiliation(s)
- Yao Qin
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Hang Zhang
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Lin Feng
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Haichen Wei
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Yuling Wu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Chaoran Jiang
- Sichuan Hua Xi Kindstar Medical Diagnostic Centre, Chengdu, Sichuan, P. R. China
| | - Zhihong Xu
- Sichuan Hua Xi Kindstar Medical Diagnostic Centre, Chengdu, Sichuan, P. R. China
| | - Huanling Zhu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Ting Liu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
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8
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Amendola M, Brusson M, Miccio A. CRISPRthripsis: The Risk of CRISPR/Cas9-induced Chromothripsis in Gene Therapy. Stem Cells Transl Med 2022; 11:1003-1009. [PMID: 36048170 PMCID: PMC9585945 DOI: 10.1093/stcltm/szac064] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/23/2022] [Indexed: 12/22/2022] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 nuclease system has allowed the generation of disease models and the development of therapeutic approaches for many genetic and non-genetic disorders. However, the generation of large genomic rearrangements has raised safety concerns for the clinical application of CRISPR/Cas9 nuclease approaches. Among these events, the formation of micronuclei and chromosome bridges due to chromosomal truncations can lead to massive genomic rearrangements localized to one or few chromosomes. This phenomenon, known as chromothripsis, was originally described in cancer cells, where it is believed to be caused by defective chromosome segregation during mitosis or DNA double-strand breaks. Here, we will discuss the factors influencing CRISPR/Cas9-induced chromothripsis, hereafter termed CRISPRthripsis, and its outcomes, the tools to characterize these events and strategies to minimize them.
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Affiliation(s)
- Mario Amendola
- Genethon, Evry, France.,Integrare Research Unit UMR_S951, Université Paris-Saclay, Univ Evry, Inserm, Genethon, Evry, France
| | - Mégane Brusson
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Université Paris Cité, Imagine Institute, Paris, France
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Université Paris Cité, Imagine Institute, Paris, France
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Burssed B, Zamariolli M, Bellucco FT, Melaragno MI. Mechanisms of structural chromosomal rearrangement formation. Mol Cytogenet 2022; 15:23. [PMID: 35701783 PMCID: PMC9199198 DOI: 10.1186/s13039-022-00600-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/31/2022] [Indexed: 12/31/2022] Open
Abstract
Structural chromosomal rearrangements result from different mechanisms of formation, usually related to certain genomic architectural features that may lead to genetic instability. Most of these rearrangements arise from recombination, repair, or replication mechanisms that occur after a double-strand break or the stalling/breakage of a replication fork. Here, we review the mechanisms of formation of structural rearrangements, highlighting their main features and differences. The most important mechanisms of constitutional chromosomal alterations are discussed, including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), Fork Stalling and Template Switching (FoSTeS), and Microhomology-Mediated Break-Induced Replication (MMBIR). Their involvement in chromoanagenesis and in the formation of complex chromosomal rearrangements, inverted duplications associated with terminal deletions, and ring chromosomes is also outlined. We reinforce the importance of high-resolution analysis to determine the DNA sequence at, and near, their breakpoints in order to infer the mechanisms of formation of structural rearrangements and to reveal how cells respond to DNA damage and repair broken ends.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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