1
|
Di Nardo M, Astigiano S, Baldari S, Pallotta MM, Porta G, Pigozzi S, Antonini A, Emionite L, Frattini A, Valli R, Toietta G, Soddu S, Musio A. The synergism of SMC1A cohesin gene silencing and bevacizumab against colorectal cancer. J Exp Clin Cancer Res 2024; 43:49. [PMID: 38365745 PMCID: PMC10870497 DOI: 10.1186/s13046-024-02976-2] [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: 01/02/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND SMC1A is a subunit of the cohesin complex that participates in many DNA- and chromosome-related biological processes. Previous studies have established that SMC1A is involved in cancer development and in particular, is overexpressed in chromosomally unstable human colorectal cancer (CRC). This study aimed to investigate whether SMC1A could serve as a therapeutic target for CRC. METHODS At first, we studied the effects of either SMC1A overexpression or knockdown in vitro. Next, the outcome of SMC1A knocking down (alone or in combination with bevacizumab, a monoclonal antibody against vascular endothelial growth factor) was analyzed in vivo. RESULTS We found that SMC1A knockdown affects cell proliferation and reduces the ability to grow in anchorage-independent manner. Next, we demonstrated that the silencing of SMC1A and the combo treatment were effective in increasing overall survival in a xenograft mouse model. Functional analyses indicated that both treatments lead to atypical mitotic figures and gene expression dysregulation. Differentially expressed genes were implicated in several pathways including gene transcription regulation, cellular proliferation, and other transformation-associated processes. CONCLUSIONS These results indicate that SMC1A silencing, in combination with bevacizumab, can represent a promising therapeutic strategy for human CRC.
Collapse
Affiliation(s)
- Maddalena Di Nardo
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Via Moruzzi, Pisa, 1 56124, Italy
| | | | - Silvia Baldari
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Maria Michela Pallotta
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Via Moruzzi, Pisa, 1 56124, Italy
| | - Giovanni Porta
- Dipartimento di Medicina e Chirurgia, Sezione di Biologia Generale e Genetica Medica, Università degli Studi dell'Insubria, Varese, Italy
| | - Simona Pigozzi
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate, Università degli Studi di Genova, Genoa, Italy
| | - Annalisa Antonini
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | | | - Annalisa Frattini
- Dipartimento di Medicina e Chirurgia, Sezione di Biologia Generale e Genetica Medica, Università degli Studi dell'Insubria, Varese, Italy
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Roberto Valli
- Dipartimento di Medicina e Chirurgia, Sezione di Biologia Generale e Genetica Medica, Università degli Studi dell'Insubria, Varese, Italy
| | - Gabriele Toietta
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Silvia Soddu
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Antonio Musio
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Via Moruzzi, Pisa, 1 56124, Italy.
| |
Collapse
|
2
|
Popescu-Hobeanu G, Riza AL, Streață I, Tudorache Ș, Comănescu A, Tănase F, Drăgușin RC, Pascu C, Dijmărescu AL, Cara ML, Dorobanțu Ș, Petre-Mandache B, Cucu M, Sosoi SS, Ioana M, Iliescu D, Burada F. Cytogenetic Analysis of Sporadic First-Trimester Miscarriage Specimens Using Karyotyping and QF-PCR: A Retrospective Romanian Cohort Study. Genes (Basel) 2022; 13:genes13122246. [PMID: 36553513 PMCID: PMC9778060 DOI: 10.3390/genes13122246] [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: 10/21/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
It is well known that first-trimester miscarriages are associated with chromosome abnormalities, with numerical chromosome abnormalities being the ones most commonly detected. Conventional karyotyping is still considered the gold standard in the analysis of products of conception, despite the extended use of molecular genetic techniques. However, conventional karyotyping is a laborious and time-consuming method, with a limited resolution of 5-10 Mb and hampered by maternal cell contamination and culture failure. The aim of our study was to assess the type and frequency of chromosomal abnormalities detected by conventional karyotyping in specimens of sporadic first-trimester miscarriages in a Romanian cohort, using QF-PCR to exclude maternal cell contamination. Long-term cultures were established and standard protocols were applied for cell harvesting, slide preparation, and GTG banding. All samples with 46,XX karyotype were tested for maternal cell contamination by QF-PCR, comparing multiple microsatellite markers in maternal blood with cell culture and tissue samples. Out of the initial 311 specimens collected from patients with sporadic first-trimester miscarriages, a total of 230 samples were successfully analyzed after the exclusion of 81 specimens based on unsuitable sampling, culture failure, or QF-PCR-proven maternal cell contamination. Chromosome abnormalities were detected in 135 cases (58.7%), with the most common type being single autosomal trisomy (71/135-52.6%), followed by monosomy (monosomy X being the only one detected, 24/135-17.8%), and polyploidy (23/135-17.0%). The subgroup analysis based on maternal age showed a statistically significant higher rate of single trisomy for women aged 35 years or older (40.3%) compared to the young maternal age group (26.1%) (p = 0.029). In conclusion, the combination of conventional karyotyping and QF-PCR can lead to an increased chromosome abnormality detection rate in first-trimester miscarriages. Our study provides reliable information for the genetic counseling of patients with first-trimester miscarriages, and further large-scale studies using different genetic techniques are required.
Collapse
Affiliation(s)
- Gabriela Popescu-Hobeanu
- Doctoral School, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Anca-Lelia Riza
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Ioana Streață
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
- Correspondence: (I.S.); (Ș.T.)
| | - Ștefania Tudorache
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Department of Obstetrics and Gynecology, Emergency Clinical County Hospital, 200642 Craiova, Romania
- Correspondence: (I.S.); (Ș.T.)
| | - Alexandru Comănescu
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Department of Obstetrics and Gynecology, Emergency Clinical County Hospital, 200642 Craiova, Romania
| | - Florentina Tănase
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Department of Obstetrics and Gynecology, Emergency Clinical County Hospital, 200642 Craiova, Romania
| | - Roxana Cristina Drăgușin
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Department of Obstetrics and Gynecology, Emergency Clinical County Hospital, 200642 Craiova, Romania
| | | | - Anda Lorena Dijmărescu
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Department of Obstetrics and Gynecology, Clinical Municipal Hospital “Filantropia” of Craiova, 200143 Craiova, Romania
| | - Monica-Laura Cara
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
- Department of Public Health, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Ștefania Dorobanțu
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Bianca Petre-Mandache
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Mihai Cucu
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Simona Serban Sosoi
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Mihai Ioana
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Dominic Iliescu
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Department of Obstetrics and Gynecology, Emergency Clinical County Hospital, 200642 Craiova, Romania
| | - Florin Burada
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| |
Collapse
|
3
|
Molina-Ruiz FJ, Introna C, Bombau G, Galofre M, Canals JM. Standardization of Cell Culture Conditions and Routine Genomic Screening under a Quality Management System Leads to Reduced Genomic Instability in hPSCs. Cells 2022; 11:cells11131984. [PMID: 35805069 PMCID: PMC9265327 DOI: 10.3390/cells11131984] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 01/27/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) have generated unprecedented interest in the scientific community, given their potential applications in regenerative medicine, disease modeling, toxicology and drug screening. However, hPSCs are prone to acquire genomic alterations in vitro, mainly due to suboptimal culture conditions and inappropriate routines to monitor genome integrity. This poses a challenge to both the safety of clinical applications and the reliability of basic and translational hPSC research. In this study, we aim to investigate if the implementation of a Quality Management System (QMS) such as ISO9001:2015 to ensure reproducible and standardized cell culture conditions and genomic screening strategies can decrease the prevalence of genomic alterations affecting hPSCs used for research applications. To this aim, we performed a retrospective analysis of G-banding karyotype and Comparative Genomic Hybridization array (aCGH) data generated by our group over a 5-year span of different hESC and hiPSC cultures. This work demonstrates that application of a QMS to standardize cell culture conditions and genomic monitoring routines leads to a striking improvement of genomic stability in hPSCs cultured in vitro, as evidenced by a reduced probability of potentially pathogenic chromosomal aberrations and subchromosomal genomic alterations. These results support the need to implement QMS in academic laboratories performing hPSC research.
Collapse
Affiliation(s)
- Francisco J. Molina-Ruiz
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Clelia Introna
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Georgina Bombau
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Mireia Galofre
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Josep M. Canals
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Correspondence: ; Tel.: +34-934-035-288
| |
Collapse
|
4
|
McIntire E, Taapken S, Leonhard K, Larson AL. Genomic Stability Testing of Pluripotent Stem Cells. ACTA ACUST UNITED AC 2021; 52:e107. [PMID: 32105415 DOI: 10.1002/cpsc.107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pluripotent stem cell (PSC) cultures are subjected to selective pressures that can result in acquisition and expansion of recurrent genetic abnormalities at any time. These recurrent abnormalities enhance the variant cells harboring them with a competitive advantage over wild-type cells. Variant cells can eventually supplant wild-type cells entirely and become fixed in culture. Such variants can impact the efficacy of PSCs in research and clinical applications. Therefore, routine genomic characterization is required for reliable and effective use of PSCs. In this article we describe the capabilities and limitations of several assays commonly used for assessing PSC genomic stability. Based on this analysis, we provide a recommendation for integrating assays into a comprehensive testing regimen that maximizes coverage while minimizing cost. © 2020 by John Wiley & Sons, Inc.
Collapse
|
5
|
Halliwell J, Barbaric I, Andrews PW. Acquired genetic changes in human pluripotent stem cells: origins and consequences. Nat Rev Mol Cell Biol 2020; 21:715-728. [DOI: 10.1038/s41580-020-00292-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2020] [Indexed: 12/14/2022]
|
6
|
Martínez-Glez V, Tenorio J, Nevado J, Gordo G, Rodríguez-Laguna L, Feito M, de Lucas R, Pérez-Jurado LA, Ruiz Pérez VL, Torrelo A, Spinner NB, Happle R, Biesecker LG, Lapunzina P. A six-attribute classification of genetic mosaicism. Genet Med 2020; 22:1743-1757. [PMID: 32661356 PMCID: PMC8581815 DOI: 10.1038/s41436-020-0877-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Mosaicism denotes an individual who has at least two populations of cells with distinct genotypes that are derived from a single fertilized egg. Genetic variation among the cell lines can involve whole chromosomes, structural or copy number variants, small or single nucleotide variants, or epigenetic variants. The mutational events that underlie mosaic variants occur during mitotic cell divisions after fertilization and zygote formation. The initiating mutational event can occur in any types of cell at any time in development, leading to enormous variation in the distribution and phenotypic effect of mosaicism. A number of classification proposals have been put forward to classify genetic mosaicism into categories based on the location, pattern, and mechanisms of the disease. We here propose a new classification of genetic mosaicism that considers the affected tissue, the pattern and distribution of the mosaicism, the pathogenicity of the variant, the direction of the change (benign to pathogenic vs. pathogenic to benign), and the postzygotic mutational mechanism. The accurate and comprehensive categorization and subtyping of mosaicisms is important and has potential clinical utility to define the natural history of these disorders, tailor follow-up frequency and interventions, estimate recurrence risks, and guide therapeutic decisions.
Collapse
Affiliation(s)
- Víctor Martínez-Glez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
| | - Jair Tenorio
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Gema Gordo
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Lara Rodríguez-Laguna
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Marta Feito
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Raúl de Lucas
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra and Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Women's and Children's Hospital, South Australia Medical and Health Research Institute (SAHMRI) and University of Adelaide, Adelaide, SA, Australia
| | - Víctor L Ruiz Pérez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.,Instituto de Investigaciones Biomédicas de Madrid (CSIC-UAM), Madrid, Spain
| | - Antonio Torrelo
- Department of Pediatrics, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicines at The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rudolf Happle
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
| |
Collapse
|
7
|
Chromosome Missegregation in Single Human Oocytes Is Related to the Age and Gene Expression Profile. Int J Mol Sci 2020; 21:ijms21061934. [PMID: 32178390 PMCID: PMC7139522 DOI: 10.3390/ijms21061934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/16/2022] Open
Abstract
The growing trend for women to postpone childbearing has resulted in a dramatic increase in the incidence of aneuploid pregnancies. Despite the importance to human reproductive health, the events precipitating female age-related meiotic errors are poorly understood. To gain new insight into the molecular basis of age-related chromosome missegregation in human oocytes, we combined the transcriptome profiles of twenty single oocytes (derived from females divided into two groups according to age <35 and ≥35 years) with their chromosome status obtained by array comparative genomic hybridization (aCGH). Furthermore, we compared the transcription profile of the single oocyte with the surrounding cumulus cells (CCs). RNA-seq data showed differences in gene expression between young and old oocytes. Dysregulated genes play a role in important biological processes such as gene transcription regulation, cytoskeleton organization, pathways related to RNA maturation and translation. The comparison of the transcription profile of the oocyte and the corresponding CCs highlighted the differential expression of genes belonging to the G protein-coupled receptor superfamily. Finally, we detected the loss of a X chromosome in two oocytes derived from women belonging to the ≥35 years age group. These aneuploidies may be caused by the detriment of REEP4, an endoplasmic reticulum protein, in women aged ≥35 years. Here we gained new insight into the complex regulatory circuit between the oocyte and the surrounding CCs and uncovered a new putative molecular basis of age-related chromosome missegregation in human oocytes.
Collapse
|
8
|
Vogel I, Vestergaard EM, Lildballe DL, Christensen R, Hoseth GE, Petersen AC, Bogaard P, Sørensen AN. Placental mosaicism in the era of chromosomal microarrays. Eur J Med Genet 2019; 63:103778. [PMID: 31580923 DOI: 10.1016/j.ejmg.2019.103778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/15/2019] [Accepted: 09/29/2019] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Placental mosaicism for a subset of a chromosome, a structural chromosomal aberration, is thought to be a very rare finding in chorionic villus samples. Here, we present clinical and laboratory data on five cases with such mosaicism for structural chromosomal aberrations. METHODS During a period of 6 months, chromosomal microarray was carried out on DNA extracted from 100 uncultured chorion villous samples from high-risk pregnancies. RESULTS In five of 100 consecutively collected samples (5/100), mosaicism for a structural chromosomal aberration was detected. The mosaic aberration was subsequently detected in fetal tissue in three of the five cases. CONCLUSION Chromosomal microarray can detect placental mosaicism for structural chromosomal aberrations. This kind of mosaicism may be more frequent than previously anticipated, and the fetal involvement seems difficult to predict. These findings highlight the complexity of mosaicism for structural chromosomal aberrations in prenatal samples in the chromosomal microarray era.
Collapse
Affiliation(s)
- Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark; Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark.
| | - Else Marie Vestergaard
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark; Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Biochemistry, Horsens Regional Hospital, Horsens, Denmark
| | - Dorte Launtoft Lildballe
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark; Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Genetics, Vejle Hospital, Aarhus, Denmark
| | - Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark; Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark
| | - Gerd-Eva Hoseth
- Department of Gynecology and Obstetrics, Aalborg University Hospital, Denmark
| | | | - Pauline Bogaard
- Department of Pathology, Aalborg University Hospital, Denmark
| | - Anne Nødgaard Sørensen
- Department of Gynecology and Obstetrics, Aalborg University Hospital, Denmark; Department of Clinical Medicine, Aalborg University Hospital, Aalborg University, Denmark
| |
Collapse
|
9
|
The Genetic Landscape of Human Glioblastoma and Matched Primary Cancer Stem Cells Reveals Intratumour Similarity and Intertumour Heterogeneity. Stem Cells Int 2019; 2019:2617030. [PMID: 30984267 PMCID: PMC6431486 DOI: 10.1155/2019/2617030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/01/2019] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant human brain tumour, characterized by rapid progression, invasion, intense angiogenesis, high genomic instability, and resistance to therapies. Despite countless experimental researches for new therapeutic strategies and promising clinical trials, the prognosis remains extremely poor, with a mean survival of less than 14 months. GBM aggressive behaviour is due to a subpopulation of tumourigenic stem-like cells, GBM stem cells (GSCs), which hierarchically drive onset, proliferation, and tumour recurrence. The morbidity and mortality of this disease strongly encourage exploring genetic characteristics of GSCs. Here, using array-CGH platform, we investigated genetic and genomic aberration profiles of GBM parent tumour (n = 10) and their primarily derived GSCs. Statistical analysis was performed by using R software and complex heatmap and corrplot packages. Pearson correlation and K-means algorithm were exploited to compare genetic alterations and to group similar genetic profiles in matched pairs of GBM and derived GSCs. We identified, in both GBM and matched GSCs, recurrent copy number alterations, as chromosome 7 polysomy, chromosome 10 monosomy, and chromosome 9p21deletions, which are typical features of primary GBM, essential for gliomagenesis. These observations suggest a condition of strong genomic instability both in GBM as GSCs. Our findings showed the robust similarity between GBM mass and GSCs (Pearson corr.≥0.65) but also highlighted a marked variability among different patients. Indeed, the heatmap reporting Gain/Loss State for 21022 coding/noncoding genes demonstrated high interpatient divergence. Furthermore, K-means algorithm identified an impairment of pathways related to the development and progression of cancer, such as angiogenesis, as well as pathways related to the immune system regulation, such as T cell activation. Our data confirmed the preservation of the genomic landscape from tumour tissue to GSCs, supporting the relevance of this cellular model to test in vitro new target therapies for GBM.
Collapse
|
10
|
La Cognata V, Morello G, Gentile G, Cavalcanti F, Cittadella R, Conforti FL, De Marco EV, Magariello A, Muglia M, Patitucci A, Spadafora P, D’Agata V, Ruggieri M, Cavallaro S. NeuroArray: A Customized aCGH for the Analysis of Copy Number Variations in Neurological Disorders. Curr Genomics 2018; 19:431-443. [PMID: 30258275 PMCID: PMC6128384 DOI: 10.2174/1389202919666180404105451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/02/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neurological disorders are a highly heterogeneous group of pathological conditions that affect both the peripheral and the central nervous system. These pathologies are characterized by a complex and multifactorial etiology involving numerous environmental agents and genetic susceptibility factors. For this reason, the investigation of their pathogenetic basis by means of traditional methodological approaches is rather arduous. High-throughput genotyping technologies, including the microarray-based comparative genomic hybridization (aCGH), are currently replacing classical detection methods, providing powerful molecular tools to identify genomic unbalanced structural rearrangements and explore their role in the pathogenesis of many complex human diseases. METHODS In this report, we comprehensively describe the design method, the procedures, validation, and implementation of an exon-centric customized aCGH (NeuroArray 1.0), tailored to detect both single and multi-exon deletions or duplications in a large set of multi- and monogenic neurological diseases. This focused platform enables a targeted measurement of structural imbalances across the human genome, targeting the clinically relevant genes at exon-level resolution. CONCLUSION An increasing use of the NeuroArray platform may offer new insights in investigating potential overlapping gene signatures among neurological conditions and defining genotype-phenotype relationships.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sebastiano Cavallaro
- Address correspondence to this author at the Institute of Neurological Sciences, National Research Council, Via Paolo Gaifami 18, 95125, Catania, Italy; Tel: +39-095-7338111; E-mail:
| |
Collapse
|
11
|
Mokretar K, Pease D, Taanman JW, Soenmez A, Ejaz A, Lashley T, Ling H, Gentleman S, Houlden H, Holton JL, Schapira AHV, Nacheva E, Proukakis C. Somatic copy number gains of α-synuclein (SNCA) in Parkinson’s disease and multiple system atrophy brains. Brain 2018; 141:2419-2431. [DOI: 10.1093/brain/awy157] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 04/16/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Katya Mokretar
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
- Department of Academic Haematology, University College London, UK
| | - Daniel Pease
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Jan-Willem Taanman
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Aynur Soenmez
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Ayesha Ejaz
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurodegenerative diseases, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Helen Ling
- Queen Square Brain Bank for Neurodegenerative diseases, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurodegenerative diseases, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Anthony H V Schapira
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | | | - Christos Proukakis
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| |
Collapse
|
12
|
Baker D, Hirst AJ, Gokhale PJ, Juarez MA, Williams S, Wheeler M, Bean K, Allison TF, Moore HD, Andrews PW, Barbaric I. Detecting Genetic Mosaicism in Cultures of Human Pluripotent Stem Cells. Stem Cell Reports 2017; 7:998-1012. [PMID: 27829140 PMCID: PMC5106530 DOI: 10.1016/j.stemcr.2016.10.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 10/10/2016] [Accepted: 10/10/2016] [Indexed: 02/07/2023] Open
Abstract
Genetic changes in human pluripotent stem cells (hPSCs) gained during culture can confound experimental results and potentially jeopardize the outcome of clinical therapies. Particularly common changes in hPSCs are trisomies of chromosomes 1, 12, 17, and 20. Thus, hPSCs should be regularly screened for such aberrations. Although a number of methods are used to assess hPSC genotypes, there has been no systematic evaluation of the sensitivity of the commonly used techniques in detecting low-level mosaicism in hPSC cultures. We have performed mixing experiments to mimic the naturally occurring mosaicism and have assessed the sensitivity of chromosome banding, qPCR, fluorescence in situ hybridization, and digital droplet PCR in detecting variants. Our analysis highlights the limits of mosaicism detection by the commonly employed methods, a pivotal requirement for interpreting the genetic status of hPSCs and for setting standards for safe applications of hPSCs in regenerative medicine. hPSCs conform to random sampling rules used for karyotyping Excluding mosaicism at <1% level requires sampling >500 metaphases qPCR is a rapid assay for detection of commonly amplified regions in hPSCs Cultures scored as normal by commonly used methods could harbor up to 10% variants
Collapse
Affiliation(s)
- Duncan Baker
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK; Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield S10 2TH, UK
| | - Adam J Hirst
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Paul J Gokhale
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Miguel A Juarez
- School of Mathematics and Statistics, The University of Sheffield, Sheffield S3 7RH, UK
| | - Steve Williams
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield S10 2TH, UK
| | - Mark Wheeler
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield S10 2TH, UK
| | - Kerry Bean
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield S10 2TH, UK
| | - Thomas F Allison
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Harry D Moore
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Peter W Andrews
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Ivana Barbaric
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK.
| |
Collapse
|
13
|
Ntai A, Baronchelli S, La Spada A, Moles A, Guffanti A, De Blasio P, Biunno I. A Review of Research-Grade Human Induced Pluripotent Stem Cells Qualification and Biobanking Processes. Biopreserv Biobank 2017; 15:384-392. [DOI: 10.1089/bio.2016.0097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Aikaterini Ntai
- Integrated Systems Engineering S.r.l. (ISENET), Milan, Italy
| | - Simona Baronchelli
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), Department of Biomedicine, Milan, Italy
| | - Alberto La Spada
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), Department of Biomedicine, Milan, Italy
| | | | | | | | - Ida Biunno
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), Department of Biomedicine, Milan, Italy
- IRCCS MultiMedica, Department of Stem Cell Research, Milan, Italy
| |
Collapse
|
14
|
Valli R, De Paoli E, Nacci L, Frattini A, Pasquali F, Maserati E. Novel recurrent chromosome anomalies in Shwachman-Diamond syndrome. Pediatr Blood Cancer 2017; 64. [PMID: 28130858 DOI: 10.1002/pbc.26454] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/24/2016] [Accepted: 12/19/2016] [Indexed: 01/20/2023]
Abstract
BACKGROUND Two chromosome anomalies are frequent in the bone marrow (BM) of patients with Shwachman-Diamond syndrome (SDS): an isochromosome of the long arm of chromosome 7, i(7)(q10), and an interstitial deletion of the long arm of chromosome 20, del(20)(q). These anomalies are associated with a lower risk of developing myelodysplasia (MDS) and/or acute myeloid leukemia. The chromosome anomalies may be due to an SDS-specific karyotype instability, reflected also by anomalies that are not clonal, but found in single cells in the BM or in peripheral blood (PB). PROCEDURE Starting in 1999, we have monitored the cytogenetic picture of a cohort of 91 Italian patients with SDS by all suitable cytogenetic and molecular methods. RESULTS Here, we report clonal chromosome anomalies that are different from the aforementioned, as well as changes found in single cells in BM/PB of the same patients. CONCLUSIONS Some of the newly recognized clonal anomalies in BM reported here are recurrent, especially unbalanced structural anomalies of chromosome 7, a further complex rearrangement of the del(20)(q) with duplicated and deleted portions, and an unbalanced translocation t(3;6), with partial trisomy of the long arm of chromosome 3 and partial monosomy of the long arm of chromosome 6. Firm conclusions on the possible prognostic relevance of these anomalies would require further study with larger patient cohorts, but our data are sufficient to suggest that these patients necessitate more frequent cytogenetic monitoring. The results on anomalies found in single cells confirm the presence of an SDS-specific karyotype instability.
Collapse
Affiliation(s)
- Roberto Valli
- Human and Medical Genetics, Department of Clinical and Experimental Medicine, University of Insubria, Varese, Italy
| | - Elena De Paoli
- Human and Medical Genetics, Department of Clinical and Experimental Medicine, University of Insubria, Varese, Italy
| | - Lucia Nacci
- Medical Genetics, Fondazione IRCCS Policlinico S. Matteo and University of Pavia, Pavia, Italy
| | - Annalisa Frattini
- Human and Medical Genetics, Department of Clinical and Experimental Medicine, University of Insubria, Varese, Italy.,IRGB, National Council of Research, Milano, Italy
| | - Francesco Pasquali
- Human and Medical Genetics, Department of Clinical and Experimental Medicine, University of Insubria, Varese, Italy
| | - Emanuela Maserati
- Human and Medical Genetics, Department of Clinical and Experimental Medicine, University of Insubria, Varese, Italy
| |
Collapse
|
15
|
DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation. PLoS One 2017; 12:e0180467. [PMID: 28683077 PMCID: PMC5500342 DOI: 10.1371/journal.pone.0180467] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 06/15/2017] [Indexed: 01/08/2023] Open
Abstract
Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array "waves", and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance.
Collapse
|
16
|
Zakaria Z, Othman N, Ismail A, Kamaluddin NR, Esa E, Abdul Rahman EJ, Mat Yusoff Y, Mohd Fauzi F, Sew Keoh T. Whole-Exome Sequencing of ETV6/RUNX1 in Four Childhood Acute Lymphoblastic Leukaemia Cases. Asian Pac J Cancer Prev 2017; 18:1169-1175. [PMID: 28548470 PMCID: PMC5494233 DOI: 10.22034/apjcp.2017.18.4.1169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background: ETV6/RUNX1 gene fusion is the most frequently seen chromosomal abnormality in childhood acute lymphobastic leukamia (ALL). However, additional genetic changes are known to be required for the development of this type of leukaemia. Therefore, we here aimed to assess the somatic mutational profile of four ALL cases carrying the ETV6/RUNX1 fusion gene using whole-exome sequencing. Methods: DNA was isolated from bone marrow samples using a QIAmp DNA Blood Mini kit and subsequently sequenced using the Illumina MiSeq system. Results: We identified 12,960 to17,601 mutations in each sample, with a total of 16,466 somatic mutations in total. Some 15,533 variants were single nucleotide polymorphisms (SNPs), 129 were substitutions, 415 were insertions and 389 were deletions. When taking into account the coding region and protein impact, 1,875 variants were synonymous and 1,956 were non-synonymous SNPs. Among non-synonymous SNPs, 1,862 were missense, 13 nonsense, 35 frameshifts, 11 nonstop, 3 misstart, 15 splices disrupt and 17 in-frame indels. A total of 86 variants were located in leukaemia-related genes of which 32 variants were located in the coding regions of GLI2, SP140, GATA2, SMAD5, KMT2C, CDH17, CDX2, FLT3, PML and MOV10L1. Conclusions: Detection and identification of secondary genetic alterations are important in identifying new therapeutic targets and developing rationally designed treatment regimens with less toxicity in ALL patients.
Collapse
Affiliation(s)
- Zubaidah Zakaria
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, Kuala Lumpur 50588, Malaysia.
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Kyriakides O, Halliwell JA, Andrews PW. Acquired Genetic and Epigenetic Variation in Human Pluripotent Stem Cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 163:187-206. [PMID: 29071402 DOI: 10.1007/10_2017_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human pluripotent stem cells (hPSCs) can acquire non-random genomic variation during culture. Some of these changes are common in tumours and confer a selective growth advantage in culture. Additionally, there is evidence that reprogramming of human induced pluripotent stem cells (hiPSCs) introduces mutations. This poses a challenge to both the safety of clinical applications and the reliability of basic research using hPSCs carrying genomic variation. A number of methods are available for monitoring the genomic integrity of hPSCs, and a balance between practicality and sensitivity must be considered in choosing the appropriate methods for each use of hPSCs. Adjusting protocols by which hPSCs are derived and cultured is an evolving process that is important in minimising acquired genomic variation. Assessing genetic variation for its potential impact is becoming increasingly important as techniques to detect genome-wide variation improve.
Collapse
Affiliation(s)
- O Kyriakides
- Centre for Stem Cell Biology, Department Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - J A Halliwell
- Centre for Stem Cell Biology, Department Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - P W Andrews
- Centre for Stem Cell Biology, Department Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| |
Collapse
|
18
|
Edwards M, Brescianini S, Allgood C, Freelander M, Dunstan R, Patradoon-Ho P, Chin R, Morgan L, Pervez T, Legendre M, Burgess T, Amselem S, Whitehall J. Syndrome diagnosis with single-nucleotide polymorphism (SNP) microarray. J Paediatr Child Health 2016; 52:85-9. [PMID: 26228624 DOI: 10.1111/jpc.12981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/28/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Matthew Edwards
- Department of Clinical Genetics, Campbelltown Hospital, Campbelltown, New South Wales, Australia.,Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Sally Brescianini
- Department of Clinical Genetics, Campbelltown Hospital, Campbelltown, New South Wales, Australia
| | - Catherine Allgood
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Michael Freelander
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Richard Dunstan
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Patrick Patradoon-Ho
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia.,Department of Paediatrics, Mount Druitt Hospital, Mount Druitt, New South Wales, Australia
| | - Raymond Chin
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Lucy Morgan
- Department of Respiratory Medicine, Concord Hospital, Sydney, New South Wales, Australia
| | - Tasnuba Pervez
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Marie Legendre
- U.F. de Génétique Moléculaire, Hôpital Armand Trousseau, Paris, France
| | - Trent Burgess
- Molecular Cytogenetics, Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
| | - Serge Amselem
- Service de Génétique et d'Embryologie Médicales, UMR_S933 INSERM/UPMC, Paris, France
| | - John Whitehall
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| |
Collapse
|
19
|
Demily C, Rossi M, Chesnoy-Servanin G, Martin B, Poisson A, Sanlaville D, Edery P. Complex phenotype with social communication disorder caused by mosaic supernumerary ring chromosome 19p. BMC MEDICAL GENETICS 2014; 15:132. [PMID: 25496186 PMCID: PMC4411819 DOI: 10.1186/s12881-014-0132-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/02/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Deletions or duplications of chromosome 19 are rare and there is no previous report in the literature of a ring chromosome derived from proximal 19p. Copy Number Variants (CNVs) responsible for complex phenotypes with Social Communication Disorder (SCD), may contribute to improve knowledge about the distinction between intellectual deficiency and autism spectrum disorders. CASE PRESENTATION We report the clinical and cytogenetic characterization of a patient (male, 33 years-old, first child of healthy Portuguese non-consanguineous parents) presenting with a complex phenotype including SCD without intellectual deficiency and carrying a mosaic supernumerary ring chromosome 19p. Microarray-Based Comparative Genomic Hybridization and Fluorescence in situ Hybridization were performed. Genetic analysis showed a large mosaic interstitial duplication 19p13.12p12 of the short arm of chromosome 19, spanning 8.35 Mb. Our data suggested a putative association between psychosocial dysfunction and mosaic pure trisomy 19p13.2p12. CONCLUSION This clinical report demonstrated the need to analyze more discreet trait-based subsets of complex phenotypes to improve the ability to detect genetic effects. To address this question and the broader issue of deciphering the yet unknown genetic contributors to complex phenotype with SCD, we suggest performing systematic psychological and psychiatric assessments in patients with chromosomal abnormalities.
Collapse
Affiliation(s)
- Caroline Demily
- Centre de dépistage et de prises en charge des troubles psychiatriques d'origine génétique, Pôle Ouest, Centre Hospitalier le Vinatier, 95 bld Pinel, 69677, Bron cedex, France. .,Centre de Neuroscience Cognitive, UMR 5229 (CNRS et Université Lyon 1), Lyon, France.
| | - Massimiliano Rossi
- Hospices Civils de Lyon, service de génétique et centre de référence des anomalies du développement, GHE, Lyon, France. .,Centre de Recherche en Neurosciences de Lyon, Inserm U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France.
| | - Gabrielle Chesnoy-Servanin
- Centre de dépistage et de prises en charge des troubles psychiatriques d'origine génétique, Pôle Ouest, Centre Hospitalier le Vinatier, 95 bld Pinel, 69677, Bron cedex, France. .,Centre de Neuroscience Cognitive, UMR 5229 (CNRS et Université Lyon 1), Lyon, France.
| | - Brice Martin
- Centre de Neuroscience Cognitive, UMR 5229 (CNRS et Université Lyon 1), Lyon, France. .,Service Universitaire de Réhabilitation, Centre Hospitalier le Vinatier, Bron, France.
| | - Alice Poisson
- Centre de dépistage et de prises en charge des troubles psychiatriques d'origine génétique, Pôle Ouest, Centre Hospitalier le Vinatier, 95 bld Pinel, 69677, Bron cedex, France. .,Centre de Neuroscience Cognitive, UMR 5229 (CNRS et Université Lyon 1), Lyon, France.
| | - Damien Sanlaville
- Centre de Recherche en Neurosciences de Lyon, Inserm U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France. .,Hospices Civils de Lyon, service de génétique, centre de référence des anomalies du développement, laboratoire de cytogénétique, GHE, Lyon, France.
| | - Patrick Edery
- Hospices Civils de Lyon, service de génétique et centre de référence des anomalies du développement, GHE, Lyon, France. .,Centre de Recherche en Neurosciences de Lyon, Inserm U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France.
| |
Collapse
|
20
|
Mosaikbefunde in der Microarray-Diagnostik bei prä- und postnatalen Untersuchungen. MED GENET-BERLIN 2014. [DOI: 10.1007/s11825-014-0012-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Zusammenfassung
Die molekulare Karyotypisierung mithilfe der „Array“-basierten genomischen Hybridisierung (Microarrays) ermöglicht nicht nur den genomweiten, hochauflösenden Nachweis von Kopienzahlveränderungen, -zugewinnen und -verlusten, sondern auch die Detektion bestimmter Mosaike. Der Beitrag gibt eine Übersicht über Einflussgrößen beim Nachweis von Mosaiken mit Microarrays und über verschiedene Mosaikfälle, die sowohl mit Array-CGH (CGH: „comparative genomic hybridization“) als auch mit SNP-Arrays (SNP: „single nucleotide polymorphism“) erhoben wurden. Dabei wird anhand der Array-CGH eine Möglichkeit aufgezeigt, wie der Prozentsatz eines Mosaiks bestimmt werden kann.
Collapse
|
21
|
Jenderny J. Chromosome aberrations in a large series of spontaneous miscarriages in the German population and review of the literature. Mol Cytogenet 2014; 7:38. [PMID: 24976865 PMCID: PMC4073514 DOI: 10.1186/1755-8166-7-38] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/27/2014] [Indexed: 12/14/2022] Open
Abstract
Background In a review of the literature in 2000 the different cytogenetic aspects of spontaneous miscarriages were well documented. This review also included the spontaneous miscarriage results of one large German study published in 1990. However, to our knowledge there are no new data on spontaneous miscarriages in the German population. Therefore, the aim of the present retrospective large study was to find out the incidence and types of chromosome aberrations in an unselected series of spontaneous miscarriages in the German population, and whether our more recent results were different to data published previously. In case of culture failure we implemented a quantitative fluorescent polymerase chain reaction (QF-PCR) for chromosomes 13, 18, 21, X and Y. Results In the present German retrospective study cytogenetic analysis (CA) was attempted on 534 spontaneous miscarriages between weeks 7 and 34 of gestation, being successful in 73% (390/534) of them. Two hundred and thirty-seven of the cases (61%, 237/390) were chromosomally abnormal. Trisomy was the most common chromosome aberration and accounted for 53% (125/237) of the aberrant karyotypes. A multiple aneuploidy was observed in 7% (17/237) of the aberrant karyotypes. Chromosomes 16, 22, 15 and 21 were found most frequently involved in aneuploidies. Fifty-four cases (23%, 54/237) with a polyploidy were found in the present study. Single unbalanced structural chromosome aberrations accounted for 4% (10/237) of the aberrant karyotypes. Eleven samples (5%, 11/237) displayed a variety of numerical and/or structural chromosome aberrations. One hundred and forty-four spontaneous miscarriages (27%, 144/534) failed to grow in culture. A total of 27 cases were analysed by QF-PCR for chromosomes 13, 18, 21, X and Y, being informative in all cases. Conclusion In our German retrospective large study of spontaneous miscarriages, the incidence and types of chromosome aberrations by CA are within the reported range of other studies published previously before and after 2000. Therefore, we can conclude that cytogenetic aspects of spontaneous miscarriages have not changed over the years. Additionally 8 of 27 cases (30%) without cell growth showed a numerical chromosome aberration by QF-PCR. Therefore QF-PCR played an important role as a supplementary test when culture failure occurred.
Collapse
Affiliation(s)
- Jutta Jenderny
- Humangenetik, Labor Lademannbogen, Lademannbogen 61-63, DE-22339 Hamburg, Germany
| |
Collapse
|
22
|
Hall GK, Mackie FL, Hamilton S, Evans A, McMullan DJ, Williams D, Allen S, Kilby MD. Chromosomal microarray analysis allows prenatal detection of low level mosaic autosomal aneuploidy. Prenat Diagn 2014; 34:505-7. [PMID: 24464918 DOI: 10.1002/pd.4333] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/16/2014] [Accepted: 01/16/2014] [Indexed: 01/07/2023]
Affiliation(s)
- Georgina K Hall
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Edgbaston, Birmingham, UK
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Eltrombopag restores trilineage hematopoiesis in refractory severe aplastic anemia that can be sustained on discontinuation of drug. Blood 2013; 123:1818-25. [PMID: 24345753 DOI: 10.1182/blood-2013-10-534743] [Citation(s) in RCA: 280] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
About a quarter of patients with severe aplastic anemia remain pancytopenic despite immunosuppressive therapy. We have previously demonstrated that eltrombopag has efficacy in this setting with 44% (11/25) of patients having clinically significant hematologic responses. We now report safety and efficacy data on a further 18 patients and long-term follow-up on the entire cohort of 43 patients. The overall response rate was 17 of 43 patients (40%) at 3 to 4 months, including tri- and bilineage responses. The majority of patients who remained on eltrombopag in an extension study (14/17) continued to show improvement, and 7 eventually had significant increases in neutrophil, red cell, and platelet lineages. Five patients with robust near-normalization of blood counts had drug discontinued at a median of 28.5 months after entry (range, 9-37 months), and all maintained stable counts a median of 13 months (range, 1-15 months) off eltrombopag. Eight patients, including 6 nonresponders and 2 responders, developed new cytogenetic abnormalities on eltrombopag, including 5 with chromosome 7 loss or partial deletion. None evolved to acute myeloid leukemia to date. Eltrombopag is efficacious in a subset of patients with aplastic anemia refractory to immunosuppressive therapy, with frequent multilineage responses and maintenance of normalized hematopoiesis off treatment. This study is registered at www.clinicaltrials.gov as #NCT00922883.
Collapse
|
24
|
Valli R, Pressato B, Marletta C, Mare L, Montalbano G, Curto FL, Pasquali F, Maserati E. Different loss of material in recurrent chromosome 20 interstitial deletions in Shwachman-Diamond syndrome and in myeloid neoplasms. Mol Cytogenet 2013; 6:56. [PMID: 24330778 PMCID: PMC3914702 DOI: 10.1186/1755-8166-6-56] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/04/2013] [Indexed: 12/19/2022] Open
Abstract
Background An interstitial deletion of the long arms of chromosome 20, del(20)(q), is frequent in the bone marrow (BM) of patients with myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), and myeloproliferative neoplasms (MPN), and it is recurrent in the BM of patients with Shwachman-Diamond syndrome (SDS), who have a 30-40% risk of developing MDS and AML. Results We report the results obtained by microarray-based comparative genomic hybridization (a-CGH) in six patients with SDS, and we compare the loss of chromosome 20 material with one patient with MDS, and with data on 92 informative patients with MDS/AML/MPN and del(20)(q) collected from the literature. Conclusions The chromosome material lost in MDS/AML/MPN is highly variable with no identifiable common deleted regions, whereas in SDS the loss is more uniform: in 3/6 patients it was almost identical, and the breakpoints that we defined are probably common to most patients from the literature. In some SDS patients less material may be lost, due to different distal breakpoints, but the proximal breakpoint is in the same region, always leading to the loss of the EIF6 gene, an event which was related to a lower risk of MDS/AML in comparison with other patients.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Emanuela Maserati
- Dipartimento di Medicina Clinica e Sperimentale, Università dell'Insubria, Via J, H, Dunant, 5, I 21100 Varese, Italy.
| |
Collapse
|
25
|
Shaffer LG, Rosenfeld JA. Microarray-based prenatal diagnosis for the identification of fetal chromosome abnormalities. Expert Rev Mol Diagn 2013; 13:601-11. [PMID: 23895129 DOI: 10.1586/14737159.2013.811912] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The goal of prenatal cytogenetic testing is to provide reassurance to the couple seeking testing for their pregnancy, identify chromosome abnormalities in the fetus, if present, and provide treatments and medical management for affected babies. Cytogenetic analysis of banded chromosomes has been the standard for identifying chromosome abnormalities in the fetus for over 40 years. With chromosome analysis, whole chromosome aneuploidies and large structural rearrangements can be identified. The sequencing of the human genome has provided the resources to develop molecular tools that allow higher resolution observations of human chromosomes. The future holds the promise of sequencing that may identify chromosomal imbalances and deleterious single nucleotide variants. This review will focus on the use of genomic microarrays for the testing and identification of chromosome anomalies in prenatal diagnosis and will discuss the future directions of fetal testing.
Collapse
Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA.
| | | |
Collapse
|
26
|
Proukakis C, Houlden H, Schapira AH. Somatic alpha-synuclein mutations in Parkinson's disease: hypothesis and preliminary data. Mov Disord 2013; 28:705-12. [PMID: 23674490 PMCID: PMC3739940 DOI: 10.1002/mds.25502] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 03/13/2013] [Accepted: 04/01/2013] [Indexed: 02/02/2023] Open
Abstract
Alpha-synuclein (SNCA) is crucial in the pathogenesis of Parkinson's disease (PD), yet mutations in the SNCA gene are rare. Evidence for somatic genetic variation in normal humans, also involving the brain, is increasing, but its role in disease is unknown. Somatic SNCA mutations, arising in early development and leading to mosaicism, could contribute to PD pathogenesis and yet be absent or undetectable in DNA derived from peripheral lymphocytes. Such mutations could underlie the widespread pathology in PD, with the precise clinical outcome dependent on their type and the timing and location of their occurrence. We recently reported a novel SNCA mutation (c.150T>G, p.H50Q) in PD brain-derived DNA. To determine if there was mosaicism for this, a PCR and cloning strategy was used to take advantage of a nearby heterozygous intronic polymorphism. No evidence of mosaicism was found. High-resolution melting curve analysis of SNCA coding exons, which was shown to be sensitive enough to detect low proportions of 2 known mutations, did not reveal any further mutations in DNA from 28 PD brain-derived samples. We outline the grounds that make the somatic SNCA mutation hypothesis consistent with genetic, embryological, and pathological data. Further studies of brain-derived DNA are warranted and should include DNA from multiple regions and methods for detecting other types of genomic variation. © 2013 Movement Disorder Society
Collapse
Affiliation(s)
- Christos Proukakis
- Department of Clinical Neuroscience, Institute of Neurology, University College London, London, United Kingdom.
| | | | | |
Collapse
|
27
|
Density matters: comparison of array platforms for detection of copy-number variation and copy-neutral abnormalities. Genet Med 2013; 15:706-12. [DOI: 10.1038/gim.2013.36] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 02/20/2013] [Indexed: 01/20/2023] Open
|
28
|
Shaffer LG, Ballif BC, Schultz RA. The use of cytogenetic microarrays in myelodysplastic syndrome characterization. Methods Mol Biol 2013; 973:69-85. [PMID: 23412784 DOI: 10.1007/978-1-62703-281-0_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Various microarray platforms, including BAC, oligonucleotide, and SNP arrays, have been shown to -provide clinically useful diagnostic and prognostic information for patients with myelodysplastic syndromes (MDS). Clinically useful arrays are designed with specific purposes in mind and with attention to genomic content and probe density. All array types have been shown to detect genomic copy gains and losses, with SNP arrays having the added advantage of detecting copy neutral loss of heterozygosity (CNLOH). The finding of CNLOH has led to the identification of certain disease genes implicated in the initiation or progression of myeloid diseases. In addition, SNP karyotyping alone, or in conjunction with routine cytogenetics, can affect the outcome prediction and improve prognostic stratification of patients with MDS. Patients who were reclassified after array testing as having adverse-risk chromosomal findings correlated with poor survival. Results of over 25 published studies support the use of arrays in MDS testing. Because few balanced translocations are found in MDS, this disease is particularly amenable to microarray testing, and studies have shown better disease classification, identification of cryptic changes, and prognostication in this heterogeneous group of disorders. Novel genomic alterations identified by array testing may lead to better targeted therapies for treating patients with MDS.
Collapse
Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer Inc., Spokane, WA, USA.
| | | | | |
Collapse
|
29
|
Krijgsman O, Israeli D, van Essen HF, Eijk PP, Berens MLM, Mellink CHM, Nieuwint AW, Weiss MM, Steenbergen RDM, Meijer GA, Ylstra B. Detection limits of DNA copy number alterations in heterogeneous cell populations. Cell Oncol (Dordr) 2012; 36:27-36. [PMID: 23117839 DOI: 10.1007/s13402-012-0108-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Array Comparative Genomic Hybridization (aCGH) is a widely used technique to assess chromosomal copy number alterations. Chromosomal content, however, is often not uniform throughout cell populations. Here we evaluated to what extent aCGH can detect DNA copy number alterations in heterogeneous cell populations. A systematic evaluation is currently lacking, despite its importance in diagnostics and research. The detection limits reported are a compound of analytical software and laboratory techniques and do not account for the number of probes in relation to sample homogeneity. METHODS Detection limits were explored with DNA isolated from a patient with intellectual disability (ID) and from tumor cell line BT474. Both were diluted with increasing amounts of normal DNA to simulate different levels of cellularity. Samples were hybridized on microarrays containing 180,880 oligonucleotides evenly distributed over the genome (spacing ~17 kb). RESULTS Single copy number alterations, represented by down to 249 probes (4 Mb) and present in 10 % of a cell population, could be detected. Alterations encompassing as few as 14 probes (~238 Kb) could also be detected, but for this a 35 % mosaic level was required. CONCLUSIONS DNA copy number alterations can be detected in cell populations containing 10 % abnormal cells. Detection of sub-megabase alterations requires a higher percentage of abnormal cells or microarrays with a higher probe density.
Collapse
Affiliation(s)
- Oscar Krijgsman
- Department of Pathology, VU University Medical Center, MB, Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Chromosome anomalies in bone marrow as primary cause of aplastic or hypoplastic conditions and peripheral cytopenia: disorders due to secondary impairment of RUNX1 and MPL genes. Mol Cytogenet 2012; 5:39. [PMID: 23025896 PMCID: PMC3542585 DOI: 10.1186/1755-8166-5-39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 09/06/2012] [Indexed: 11/18/2022] Open
Abstract
Background Chromosome changes in the bone marrow (BM) of patients with persistent cytopenia are often considered diagnostic for a myelodysplastic syndrome (MDS). Comprehensive cytogenetic evaluations may give evidence of the real pathogenetic role of these changes in cases with cytopenia without morphological signs of MDS. Results Chromosome anomalies were found in the BM of three patients, without any morphological evidence of MDS: 1) an acquired complex rearrangement of chromosome 21 in a boy with severe aplastic anaemia (SAA); the rearrangement caused the loss of exons 2–8 of the RUNX1 gene with subsequent hypoexpression. 2) a constitutional complex rearrangement of chromosome 21 in a girl with congenital thrombocytopenia; the rearrangement led to RUNX1 disruption and hypoexpression. 3) an acquired paracentric inversion of chromosome 1, in which two regions at the breakpoints were shown to be lost, in a boy with aplastic anaemia; the MPL gene, localized in chromosome 1 short arms was not mutated neither disrupted, but its expression was severely reduced: we postulate that the aplastic anaemia was due to position effects acting both in cis and in trans, and causing Congenital Amegakaryocytic Thrombocytopenia (CAMT). Conclusions A clonal anomaly in BM does not imply per se a diagnosis of MDS: a subgroup of BM hypoplastic disorders is directly due to chromosome structural anomalies with effects on specific genes, as was the case of RUNX1 and MPL in the patients here reported with diagnosis of SAA, thrombocytopenia, and CAMT. The anomaly may be either acquired or constitutional, and it may act by deletion/disruption of the gene, or by position effects. Full cytogenetic investigations, including a-CGH, should always be part of the diagnostic evaluation of patients with BM aplasia/hypoplasia and peripheral cytopenias.
Collapse
|
31
|
Uguen A, Talagas M, Quintin-Roué I, Abasq C, Coat C, Charles-Pétillon F, De Braekeleer M, Marcorelles P. [A silent-growing and fast-killing melanoma in a teenager]. Ann Pathol 2012; 32:254-8. [PMID: 23010398 DOI: 10.1016/j.annpat.2012.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/20/2012] [Accepted: 06/21/2012] [Indexed: 10/28/2022]
Abstract
Malignant melanoma is a relatively rare but potentially aggressive tumor in children and adolescents. We report the case of a metastatic malignant melanoma in a 17-year-old girl, first diagnosed on cytological features of a fine-needle lymph node aspiration and then histologically confirmed by both examination of the metastatic adenopathy and a clinically harmless skin lesion of the scalp, which harbored focal microscopic pattern of melanoma. A fluorescent in situ hybridization study revealed that both metastatic and primary cutaneous tumours contained the same and pejorative chromosomal aberration consisting in CCND1 amplification (11q13). This observation raises actual limits and challenges in the fields of diagnosis and treatment of fast-killing melanomas.
Collapse
Affiliation(s)
- Arnaud Uguen
- Service d'anatomie pathologique, pôle biologie-pathologie, CHRU de Brest, 2, avenue Foch, 29609 Brest cedex, France.
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Abstract
Genomic microarrays are now widely used diagnostically for the molecular karyotyping of patients with intellectual disability, congenital anomalies and autistic spectrum disorder and have more recently been applied for the detection of genomic imbalances in prenatal genetic diagnosis. We present an overview of the different arrays, protocols used and discuss methods of genomic array data analysis.
Collapse
Affiliation(s)
- Paul D Brady
- Laboratory for Cytogenetics and Genome Research, Centre for Human Genetics, University Hospital Leuven, K.U. Leuven, Leuven, Belgium
| | | |
Collapse
|
33
|
Vermeesch JR, Brady PD, Sanlaville D, Kok K, Hastings RJ. Genome-wide arrays: quality criteria and platforms to be used in routine diagnostics. Hum Mutat 2012; 33:906-15. [PMID: 22415865 DOI: 10.1002/humu.22076] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Whole-genome analysis using genome-wide arrays, also called "genomic arrays," "microarrays," or "arrays," has become the first-tier diagnostic test for patients with developmental abnormalities and/or intellectual disabilities. In addition to constitutional anomalies, genomic arrays are also used to diagnose acquired disorders. Despite the rapid implementation of these technologies in diagnostic laboratories, external quality control schemes (such as CEQA, EMQN, UK NEQAS, and the USA QA scheme CAP) and interlaboratory comparisons show that there are huge differences in quality, interpretation, and reporting among laboratories. We offer guidance to laboratories to help assure the quality of array experiments and to standardize minimum detection resolution, and we also provide guidelines to standardize interpretation and reporting.
Collapse
Affiliation(s)
- Joris R Vermeesch
- Laboratory for Cytogenetics and Genome Research, Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium.
| | | | | | | | | |
Collapse
|