1
|
Heng E, Thanedar S, Heng HH. The Importance of Monitoring Non-clonal Chromosome Aberrations (NCCAs) in Cancer Research. Methods Mol Biol 2024; 2825:79-111. [PMID: 38913304 DOI: 10.1007/978-1-0716-3946-7_4] [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
Cytogenetic analysis has traditionally focused on the clonal chromosome aberrations, or CCAs, and considered the large number of diverse non-clonal chromosome aberrations, or NCCAs, as insignificant noise. Our decade-long karyotype evolutionary studies have unexpectedly demonstrated otherwise. Not only the baseline of NCCAs is associated with fuzzy inheritance, but the frequencies of NCCAs can also be used to reliably measure genome or chromosome instability (CIN). According to the Genome Architecture Theory, CIN is the common driver of cancer evolution that can unify diverse molecular mechanisms, and genome chaos, including chromothripsis, chromoanagenesis, and polypoidal giant nuclear and micronuclear clusters, and various sizes of chromosome fragmentations, including extrachromosomal DNA, represent some extreme forms of NCCAs that play a key role in the macroevolutionary transition. In this chapter, the rationale, definition, brief history, and current status of NCCA research in cancer are discussed in the context of two-phased cancer evolution and karyotype-coded system information. Finally, after briefly describing various types of NCCAs, we call for more research on NCCAs in future cytogenetics.
Collapse
Affiliation(s)
- Eric Heng
- Stanford University, Stanford, CA, USA
| | - Sanjana Thanedar
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Henry H Heng
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA.
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA.
| |
Collapse
|
2
|
Frias S, Ramos S, Salas C, Molina B, Sánchez S, Rivera-Luna R. Nonclonal Chromosome Aberrations and Genome Chaos in Somatic and Germ Cells from Patients and Survivors of Hodgkin Lymphoma. Genes (Basel) 2019; 10:genes10010037. [PMID: 30634664 PMCID: PMC6357137 DOI: 10.3390/genes10010037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/10/2018] [Accepted: 01/04/2019] [Indexed: 12/27/2022] Open
Abstract
Anticancer regimens for Hodgkin lymphoma (HL) patients include highly genotoxic drugs that have been very successful in killing tumor cells and providing a 90% disease-free survival at five years. However, some of these treatments do not have a specific cell target, damaging both cancerous and normal cells. Thus, HL survivors have a high risk of developing new primary cancers, both hematologic and solid tumors, which have been related to treatment. Several studies have shown that after treatment, HL patients and survivors present persistent chromosomal instability, including nonclonal chromosomal aberrations. The frequency and type of chromosomal abnormalities appear to depend on the type of therapy and the cell type examined. For example, MOPP chemotherapy affects hematopoietic and germ stem cells leading to long-term genotoxic effects and azoospermia, while ABVD chemotherapy affects transiently sperm cells, with most of the patients showing recovery of spermatogenesis. Both regimens have long-term effects in somatic cells, presenting nonclonal chromosomal aberrations and genomic chaos in a fraction of noncancerous cells. This is a source of karyotypic heterogeneity that could eventually generate a more stable population acquiring clonal chromosomal aberrations and leading towards the development of a new cancer.
Collapse
Affiliation(s)
- Sara Frias
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Cd. De Mexico, P.O. Box 04530, Mexico.
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de Mexico, Cd. De Mexico, P.O. Box 04510, Mexico.
| | - Sandra Ramos
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Cd. De Mexico, P.O. Box 04530, Mexico.
| | - Consuelo Salas
- Laboratorio de Genética y Cáncer, Instituto Nacional de Pediatría, Cd. De Mexico, P.O. Box 04530, Mexico.
| | - Bertha Molina
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Cd. De Mexico, P.O. Box 04530, Mexico.
| | - Silvia Sánchez
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Cd. De Mexico, P.O. Box 04530, Mexico.
| | - Roberto Rivera-Luna
- Subdirección de Hemato-Oncología, Instituto Nacional de Pediatría, Cd. De Mexico, P.O. Box 04530, Mexico.
| |
Collapse
|
3
|
Tang G, Medeiros LJ, Wang SA. How I investigate Clonal cytogenetic abnormalities of undetermined significance. Int J Lab Hematol 2018; 40:385-391. [PMID: 29624895 DOI: 10.1111/ijlh.12826] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 02/27/2018] [Indexed: 01/06/2023]
Abstract
Myelodysplastic syndromes are a group of hematopoietic stem cell diseases characterized by cytopenia(s), morphological dysplasia, and clonal hematopoiesis. In some patients, the cause of cytopenia(s) is uncertain, even after thorough clinical and laboratory evaluation. Evidence of clonal hematopoiesis has been used to support a diagnosis of myelodysplastic syndrome in this setting. In patients with cytopenia(s), the presence of clonal cytogenetic abnormalities, except for +8, del(20q) and -Y, can serve as presumptive evidence of myelodysplastic syndrome. Recent advances in next-generation sequencing have detected myeloid neoplasm-related mutations in patients who do not meet the diagnostic criteria for myelodysplastic syndrome. Various terms have been adopted to describe these cases, including clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS). Similarly, studies have shown that certain chromosomal abnormalities, including ones commonly detected in myelodysplastic syndrome, may not be associated necessarily with an underlying myelodysplastic syndrome. These clonal cytogenetic abnormalities of undetermined significance (CCAUS) are similar to CHIP and CCUS. Here, we review the features of CCAUS, distinguishing CCAUS from clonal cytogenetic abnormalities associated with myelodysplastic syndrome, and the potential impact of CCAUS on patient management.
Collapse
Affiliation(s)
- G Tang
- Department of Hematopathology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - L J Medeiros
- Department of Hematopathology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - S A Wang
- Department of Hematopathology, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| |
Collapse
|
4
|
New Insights in the Cytogenetic Practice: Karyotypic Chaos, Non-Clonal Chromosomal Alterations and Chromosomal Instability in Human Cancer and Therapy Response. Genes (Basel) 2017; 8:genes8060155. [PMID: 28587191 PMCID: PMC5485519 DOI: 10.3390/genes8060155] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 12/17/2022] Open
Abstract
Recently, non-clonal chromosomal alterations previously unappreciated are being proposed to be included in cytogenetic practice. The aim of this inclusion is to obtain a greater understanding of chromosomal instability (CIN) and tumor heterogeneity and their role in cancer evolution and therapy response. Although several genetic assays have allowed the evaluation of the variation in a population of cancer cells, these assays do not provide information at the level of individual cells, therefore limiting the information of the genomic diversity within tumors (heterogeneity). The karyotype is one of the few available cytogenetic techniques that allow us not only to identify the chromosomal alterations present within a single cell, but also allows us to profile both clonal (CCA) and non-clonal chromosomal alterations (NCCAs). A greater understanding of CIN and tumor heterogeneity in cancer could not only improve existing therapeutic regimens but could also be used as targets for the design of new therapeutic approaches. In this review we indicate the importance and significance of karyotypic chaos, NCCAs and CIN in the prognosis of human cancers.
Collapse
|
5
|
Heng HHQ, Regan SM, Liu G, Ye CJ. Why it is crucial to analyze non clonal chromosome aberrations or NCCAs? Mol Cytogenet 2016; 9:15. [PMID: 26877768 PMCID: PMC4752783 DOI: 10.1186/s13039-016-0223-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/03/2016] [Indexed: 12/28/2022] Open
Abstract
Current cytogenetics has largely focused its efforts on the identification of recurrent karyotypic alterations, also known as clonal chromosomal aberrations (CCAs). The rationale of doing so seems simple: recurrent genetic changes are relevant for diseases or specific physiological conditions, while non clonal chromosome aberrations (NCCAs) are insignificant genetic background or noise. However, in reality, the vast majority of chromosomal alterations are NCCAs, and it is challenging to identify commonly shared CCAs in most solid tumors. Furthermore, the karyotype, rather than genes, represents the system inheritance, or blueprint, and each NCCA represents an altered genome system. These realizations underscore the importance of the re-evaluation of NCCAs in cytogenetic analyses. In this concept article, we briefly review the definition of NCCAs, some historical misconceptions about them, and why NCCAs are not insignificant "noise," but rather a highly significant feature of the cellular population for providing genome heterogeneity and complexity, representing one important form of fuzzy inheritance. The frequencies of NCCAs also represent an index to measure both internally- and environmentally-induced genome instability. Additionally, the NCCA/CCA cycle is associated with macro- and micro-cellular evolution. Lastly, elevated NCCAs are observed in many disease/illness conditions. Considering all of these factors, we call for the immediate action of studying and reporting NCCAs. Specifically, effort is needed to characterize and compare different types of NCCAs, to define their baseline in various tissues, to develop methods to access mitotic cells, to re-examine/interpret the NCCAs data, and to develop an NCCA database.
Collapse
Affiliation(s)
- Henry H. Q. Heng
- />Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201 USA
- />Department of Pathology, Wayne State University School of Medicine, 3226 Scott Hall, 540 E. Canfield, Detroit, MI 48201 USA
| | - Sarah M. Regan
- />Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201 USA
- />Division of Graduate Medical Sciences, Boston University School of Medicine, Boston, MA 02118 USA
| | - Guo Liu
- />Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - Christine J. Ye
- />The Division of Hematology/Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI USA
| |
Collapse
|
6
|
Yin CC, Peng J, Li Y, Kanagal-Shamanna R, Muzzafar T, DiNardo C, Khoury JD, Li S, Medeiros LJ, Wang SA, Tang G. Clinical significance of newly emerged isolated del(20q) in patients following cytotoxic therapies. Mod Pathol 2015; 28:1014-22. [PMID: 26044451 DOI: 10.1038/modpathol.2015.66] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/20/2015] [Accepted: 04/24/2015] [Indexed: 01/18/2023]
Abstract
Deletion 20q is a common chromosomal abnormality in myeloid neoplasms. Detection of del(20q) in patients following cytotoxic therapies raises concerns for an emerging therapy-related myeloid neoplasm. In this study, we identified 92 patients who acquired isolated del(20q) in their bone marrow following cytotoxic therapies for malignant neoplasms. Seventy-six patients showed interstitial and sixteen patients showed terminal 20q deletion. The median interval from prior cytotoxic therapies to detection of del(20q) was 58 months (range, 5-213 months). With a median follow-up of 23 months (range, 1-183 months), 21 (23%) patients developed therapy-related myeloid neoplasm and 71 (77%) patients did not. In patients who developed therapy-related myeloid neoplasm, del(20q) presented in a higher percentage of metaphases (60 vs 25%, P<0.0001); persisted for a longer period of time (24 vs 10 months, P=0.0487); and was more often a terminal deletion (33 vs 13%, P=0.0006) compared with patients who did not develop therapy-related myeloid neoplasm. Clonal evolution was only detected in patients with therapy-related myeloid neoplasm (4 patients, 19%). We conclude that del(20q) emerging after cytotoxic therapy represents an innocuous finding in more than two-thirds of patients. In patients who develop a therapy-related myeloid neoplasm, del(20q) often involves a higher percentage of metaphases, persists longer and more frequently is a terminal rather than an interstitial deletion.
Collapse
Affiliation(s)
- C Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jie Peng
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Li
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tariq Muzzafar
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Courtney DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoying Li
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sa A Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
7
|
Tang G, Wang SA, Lu V, Lee HC, Qazilbash MH, Wang XI, Yin CC, Orlowski R, Wang Y, Patel A, Medeiros LJ, Lu G. Clinically silent clonal cytogenetic abnormalities arising in patients treated for lymphoid neoplasms. Leuk Res 2014; 38:896-900. [PMID: 24939217 DOI: 10.1016/j.leukres.2014.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 02/03/2023]
Abstract
Newly emerged clonal cytogenetic abnormalities (CCA) in patients with prior cytotoxic therapy are highly concerning for therapy-related myeloid neoplasms (t-MN). In some patients, however, CCA appeared to be clinically "silent". In this study, we describe 25 patients who developed CCA after they received cytotoxic therapies for lymphoid neoplasms but never developed t-MN. These clinically "silent" CCA were always present as single abnormalities, often detected in a small subset of cells, and tended to disappear over time. We conclude that the occurrence of CCA is not always associated with t-MN. Clinical correlation is essential to guide a proper management of these patients.
Collapse
Affiliation(s)
- Guilin Tang
- Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX, USA.
| | - Sa A Wang
- Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Victoria Lu
- Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Hans Chulhee Lee
- Department of Stem Cell Transplantation, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Muzaffar H Qazilbash
- Department of Stem Cell Transplantation, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaohong I Wang
- Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - C Cameron Yin
- Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Orlowski
- Department of Lymphoma/Myeloma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yaping Wang
- Department of Biostatistics, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Gary Lu
- Department of Hematopathology, UT MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
8
|
Justewicz DM, Shokes JE, Reavis B, Boyd SA, Burnette TB, Halberstadt CR, Spencer T, Ludlow JW, Bertram TA, Jain D. Characterization of the human smooth muscle cell secretome for regenerative medicine. Tissue Eng Part C Methods 2012; 18:797-816. [PMID: 22530582 DOI: 10.1089/ten.tec.2012.0054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Smooth muscle cells (SMC) play a central role in maintaining the structural and functional integrity of muscle tissue. Little is known about the early in vitro events that guide the assembly of 'bioartificial tissue' (constructs) and recapitulate the key aspects of smooth muscle differentiation and development before surgical implantation. Biomimetic approaches have been proposed that enable the identification of in vitro processes which allow standardized manufacturing, thus improving both product quality and the consistency of patient outcomes. One essential element of this approach is the description of the SMC secretome, that is, the soluble and deposited factors produced within the three-dimensional (3D) extracellular matrix (ECM) microenvironment. In this study, we utilized autologous SMC from multiple tissue types that were expanded ex vivo and generated with a rigorous focus on operational phenotype and genetic stability. The objective of this study was to characterize the spatiotemporal dynamics of the first week of organoid maturation using a well-defined in vitro-like, 3D-engineered scale model of our validated manufacturing process. Functional proteomics was used to identify the topological properties of the networks of interacting proteins that were derived from the SMC secretome, revealing overlapping central nodes related to SMC differentiation and proliferation, actin cytoskeleton regulation, and balanced ECM accumulation. The critical functions defined by the Ingenuity Pathway Analysis included cell signaling, cellular movement and proliferation, and cellular and organismal development. The results confirm the phenotypic and functional similarity of the SMC generated by our platform technology at the molecular level. Furthermore, these data validate the biomimetic approaches that have been established to maintain manufacturing consistency.
Collapse
Affiliation(s)
- Dominic M Justewicz
- Department of Bioprocess Research & Development, Tengion, Inc., 3929 Westpoint Blvd., Suite G, Winston-Salem, NC 27103, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Gümüş G, Sunguroğlu A, Tükün A, Sayin DB, Bökesoy I. Common fragile sites associated with the breakpoints of chromosomal aberrations in hematologic neoplasms. CANCER GENETICS AND CYTOGENETICS 2002; 133:168-71. [PMID: 11943347 DOI: 10.1016/s0165-4608(01)00569-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Fragile sites are specific regions of chromosomes prone to breakage when cells are cultured under specific conditions. These sites are divided into two classes: common and rare. Common fragile sites are expressed in all individuals at different frequencies, whereas rare ones are found only in certain individuals. Common and rare fragile sites have been shown to display a number of characteristics of instability being preferential sites for chromosomal deletions, duplications, and rearrangements. Moreover, a majority of mapped oncogenes are located at or near these fragile sites. These observations have led to the suggestion that both classes of fragile sites may play a significant role in chromosomal rearrangements involved in oncogene activation or tumor supressor gene inactivation. For these reasons, involvement of common and rare fragile sites and their relevance to specific chromosome breakpoints in cancer have received much attention. In this study, which reports on the cytogenetic findings obtained from 256 patients with chronic myelocytic leukemia, 103 with acute myelocytic leukemia, 40 with acute lymphocytic leukemia, 33 with myelodysplastic syndrome, we documented the fragile sites involved in chromosomal aberrations involving oncogenes, tumor supressor genes, and other known genes important in cell cycle regulation localized at these sites.
Collapse
MESH Headings
- Bone Marrow/pathology
- Chromosome Aberrations
- Chromosome Fragile Sites
- Chromosome Fragility/genetics
- Genes, Tumor Suppressor/physiology
- Genes, cdc/physiology
- Humans
- Karyotyping
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/pathology
- Oncogenes/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
Collapse
Affiliation(s)
- Güvem Gümüş
- Ankara University, Faculty of Medicine, Medical Biology Department, Ankara, Turkey.
| | | | | | | | | |
Collapse
|