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Ye JC, Heng HH. The New Era of Cancer Cytogenetics and Cytogenomics. Methods Mol Biol 2024; 2825:3-37. [PMID: 38913301 DOI: 10.1007/978-1-0716-3946-7_1] [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] [Indexed: 06/25/2024]
Abstract
The promises of the cancer genome sequencing project, combined with various -omics technologies, have raised questions about the importance of cancer cytogenetic analyses. It is suggested that DNA sequencing provides high resolution, speed, and automation, potentially replacing cytogenetic testing. We disagree with this reductionist prediction. On the contrary, various sequencing projects have unexpectedly challenged gene theory and highlighted the importance of the genome or karyotype in organizing gene network interactions. Consequently, profiling the karyotype can be more meaningful than solely profiling gene mutations, especially in cancer where karyotype alterations mediate cellular macroevolution dominance. In this chapter, recent studies that illustrate the ultimate importance of karyotype in cancer genomics and evolution are briefly reviewed. In particular, the long-ignored non-clonal chromosome aberrations or NCCAs are linked to genome or chromosome instability, genome chaos is linked to genome reorganization under cellular crisis, and the two-phased cancer evolution reconciles the relationship between genome alteration-mediated punctuated macroevolution and gene mutation-mediated stepwise microevolution. By further synthesizing, the concept of karyotype coding is discussed in the context of information management. Altogether, we call for a new era of cancer cytogenetics and cytogenomics, where an array of technical frontiers can be explored further, which is crucial for both basic research and clinical implications in the cancer field.
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Affiliation(s)
- Jing Christine Ye
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Henry H Heng
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA.
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Yurov YB, Vorsanova SG, Iourov IY. FISHing for Chromosome Instability and Aneuploidy in the Alzheimer's Disease Brain. Methods Mol Biol 2022; 2561:191-204. [PMID: 36399271 DOI: 10.1007/978-1-0716-2655-9_10] [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: 11/19/2022]
Abstract
Fluorescence in situ hybridization (FISH) is the method of choice for visualizing chromosomal DNA in post-mitotic cells. The availability of chromosome-enumeration (centromeric), site-specific, and multicolor-banding DNA probes offers opportunities to uncover genomic changes, at the chromosomal level, in single interphase nuclei. Alzheimer's disease (AD) has been associated repeatedly with (sub)chromosome instability and aneuploidy, likely affecting the brain. Although the types and rates of chromosome instability in the AD brain remain a matter of debate, molecular cytogenetic analysis of brain cells appears to be important for uncovering mechanisms of neurodegeneration. Here, we describe a FISH protocol for studying chromosome instability and aneuploidy in the AD brain.
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Affiliation(s)
- Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan Y Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia. .,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia.
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Elnaggar MG, Mosad E, Makboul A, Shafik EA. Cytogenetic profile of adult acute myeloid leukemia in Egypt: a single-center experience. Mol Cytogenet 2022; 15:43. [PMID: 36195917 PMCID: PMC9533520 DOI: 10.1186/s13039-022-00621-1] [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] [Received: 06/09/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is a diverse disease characterized by the expansion of blasts of myeloid lineage. Cytogenetic testing is the cornerstone for risk stratification of AML patients. Geographical and environmental factors may play a very important role in the development of leukemia and several differences in genetic profile may be seen among different ethnicities. In our study, we evaluated cytogenetic findings of adult AML patients in South Egypt. Methods Cytogenetic testing (karyotyping and M-FISH) was performed for 120 adult patients with AML. Twenty metaphases were analyzed for each patient. Results In our study, the median age of AML patients was 36.5 years, with an age range between 18 and 86 years. 56.7% of patients had normal karyotypes and 43.3% of patients had clonal cytogenetic abnormalities. t (15;17) was the most detected structural abnormality, and + 8 was the most detected numerical abnormality. Regarding cytogenetic risk stratification, 65% of patients were in the intermediate-risk category. Conclusion The cytogenetic profile of AML patients in our locality showed some differences and some similarities with cytogenetic profiles in different Arab, Asian and Western countries. Further studies are needed using advanced techniques such as next-generation sequencing and optical genome mapping to elucidate more ethnic and geographic genetic heterogeneity among different countries.
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Affiliation(s)
- Mohamed G Elnaggar
- Clinical Pathology Department, South Egypt Cancer Institute, Assiut University, Assiut, 71515, Egypt.
| | - Eman Mosad
- Clinical Pathology Department, South Egypt Cancer Institute, Assiut University, Assiut, 71515, Egypt
| | - Ahmed Makboul
- Clinical Pathology Department, South Egypt Cancer Institute, Assiut University, Assiut, 71515, Egypt
| | - Engy Adel Shafik
- Clinical Pathology Department, South Egypt Cancer Institute, Assiut University, Assiut, 71515, Egypt
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Thielker J, Weise A, Othman MAK, Carreria IM, Melo JB, Von Eggeling F, Guntinas-Lichius O, Ziegler M, Liehr T. Molecular cytogenetic pilot study on pleomorphic adenomas of salivary glands. Oncol Lett 2019; 19:1125-1130. [PMID: 31966040 PMCID: PMC6955655 DOI: 10.3892/ol.2019.11198] [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: 06/25/2019] [Accepted: 09/24/2019] [Indexed: 01/17/2023] Open
Abstract
Pleomorphic adenomas (PAs) of salivary glands are the most frequent entity of solid parotid tumors. Nonetheless, their genetics is not yet well understood. Thus, the current study characterized 14 PAs using a unique combination of cytogenetic, molecular cytogenetic and/or molecular karyotyping based approaches. The current study applied G-banding based on trypsin treatment and Giemsa-staining in peripheral blood and tumor tissue. Additionally, fluorescence in situ hybridization was performed using whole chromosome painting or centromeric probes. Array-based comparative genomic hybridization was also conducted. In 5 of 14 cases, chromosomal and/or submicroscopic alterations were characterized. Balanced and unbalanced translocations, loss or gain of whole chromosomes and submicroscopic copy number alterations were detected. Furthermore, the first case of a so-called ‘jumping translocation’ in a PA was reported. The genes twist-related protein 1 and distal-less homeobox 5 were also involved in copy number variations in two PAs. In conclusion, approaches utilized in the current study are highly suited to characterize the genetic constitution of PAs.
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Affiliation(s)
- Jovanna Thielker
- Department of Otorhinolaryngology, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Moneeb A K Othman
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Isabel M Carreria
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal.,The Center of Investigation On Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal
| | - Joana B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal.,The Center of Investigation On Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal
| | - Ferdinand Von Eggeling
- Department of Otorhinolaryngology, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Orlando Guntinas-Lichius
- Department of Otorhinolaryngology, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Monika Ziegler
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
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