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Tassanakijpanich N, Wright R, Tassone F, Shankar SP, Hagerman R. Fragile X syndrome in a girl with variant Turner syndrome and an isodicentric X chromosome. BMJ Case Rep 2022; 15:e247901. [PMID: 35882436 PMCID: PMC9330300 DOI: 10.1136/bcr-2021-247901] [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: 11/03/2022] Open
Abstract
Fragile X (FXS) and Turner (TS) syndromes are X-chromosome-associated disorders. Herein, we report the case of a girl in middle childhood with bicuspid aortic valve in infancy, growth failure, global developmental delay (GDD), visual problems, and coexisting attention-deficit/hyperactivity and anxiety disorders. A high-resolution karyotype in 20 cells revealed 46,X,Idic(X)(p11.21)[19]/45,X[1], suggestive of variant TS. Given her atypical phenotype, subsequent DNA testing was performed. Four FMR1 cytosine-guanine-guanine repeats (30, 410, 580 and 800) were identified, confirming the additional FXS diagnosis. This case study highlights the importance of additional genetic testing in individuals with atypical variant TS, such as unexplained GDD and distinct facial characteristics. The additional FXS diagnosis prompted new therapeutic development for the patient to advance precision healthcare.
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Affiliation(s)
- Nattaporn Tassanakijpanich
- Pediatrics, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- UC Davis MIND Institute, UC Davis Health, Sacramento, California, USA
| | - Rachel Wright
- Biology, Texas A&M University, College Station, Texas, USA
| | - Flora Tassone
- UC Davis MIND Institute, UC Davis Health, Sacramento, California, USA
- Biochemistry and Molecular Medicine, UC Davis, School of Medicine, Davis, California, USA
| | - Suma P Shankar
- UC Davis MIND Institute, UC Davis Health, Sacramento, California, USA
- Pediatrics, UC Davis, School of Medicine, Sacramento, California, USA
| | - Randi Hagerman
- UC Davis MIND Institute, UC Davis Health, Sacramento, California, USA
- Pediatrics, UC Davis, School of Medicine, Sacramento, California, USA
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Stein A, Kubasch AS, Haferlach C, Platzbecker U. Case Report: Personalized Therapeutical Approaches with Lenalidomide in Del(5q): A Case Series. Front Oncol 2022; 12:866470. [PMID: 35433412 PMCID: PMC9008833 DOI: 10.3389/fonc.2022.866470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/09/2022] [Indexed: 12/30/2022] Open
Abstract
Myelodysplastic Syndrome (MDS) with del(5q) represents a unique WHO entity, which is often treated with lenalidomide according to standard clinical practice. Guidelines concerning treatment duration have thus far not been implemented, but rather comprise an indefinite therapy until loss of response. This review presents three red blood cell (RBC) transfusion-dependent MDS with del(5q) cases, starting with one rare case with an unbalanced translocation t(2;5), involving the breakpoint of del(5q) and loss of the 5q15-5q31 region. To the best of our knowledge, no comparable case has been described before with a response to lenalidomide. Strikingly, treatment-induced and maintained cytogenetic complete remission (cCR) in this patient. Furthermore, we report two cases of classical del(5q), in which lenalidomide was interrupted after a short period of lenalidomide therapy at the time cCR was achieved. Despite drug holiday cCR was maintained for seven and nine years, respectively. Then del(5q) re-emerged in the absence of novel molecular aberrations and re-treatment with lenalidomide could again achieve cCR in both cases. Together, this series presents three cases of personalized therapy of MDS with del(5q).
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Affiliation(s)
- Anna Stein
- Department of Hematology, Cellular Therapy and Hemostaseology, Leipzig University Hospital, Leipzig, Germany
| | - Anne Sophie Kubasch
- Department of Hematology, Cellular Therapy and Hemostaseology, Leipzig University Hospital, Leipzig, Germany
| | | | - Uwe Platzbecker
- Department of Hematology, Cellular Therapy and Hemostaseology, Leipzig University Hospital, Leipzig, Germany
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3
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Verdi G, Li D, Elsea SH, Nelson B, Bhoj EJ, Hakonarson H, Yearwood KR, Upadhya S, Gluschitz S, Smith JL, Sobering AK. A novel unbalanced translocation between chromosomes 5p and 18q leading to dysmorphology and global developmental delay. Mol Genet Genomic Med 2022; 10:e1900. [PMID: 35189041 PMCID: PMC9000934 DOI: 10.1002/mgg3.1900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/23/2021] [Accepted: 02/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background Individuals with various sized terminal duplications of chromosome 5p or terminal deletions of chromosome 18q have been described. These aberrations may cause congenital malformations and intellectual disability of varying severity. Methods Via an international collaborative effort, we obtained a cytogenetic diagnosis for a 5‐year‐old boy of Afro‐Caribbean ancestry who has global developmental delay, dysmorphology, hypotonia, feeding difficulties, bilateral club feet, and intellectual disability. Results Conventional G‐banded karyotyping showed additional chromatin of unknown origin on the long arm of chromosome 18. SNP microarray confirmed the loss of ~6.4 Mb from chromosome 18q: arr[hg19] 18q22.3‐q23(71,518,518‐77,943,115)x1. The source of the additional chromatin was determined from the microarray to be ~32 Mb from the short arm of chromosome 5 (arr[hg19] 5p13.3‐p15.33(51,045‐32,062,984)x3). The unbalanced translocation was verified by fluorescent in situ hybridization (FISH). Both parents are healthy and have normal karyotypes suggesting that this abnormality arose de novo in the proband, although gonadal mosaicism in a parent cannot be excluded. Conclusion The combination of clinical features in this individual is most likely due to the partial deletion of 18q and partial duplication of 5p, which to our knowledge has not been previously described.
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Affiliation(s)
- Giavanna Verdi
- Department of Biochemistry St. George's University School of Medicine True Blue Grenada
| | - Dong Li
- Center for Applied Genomics The Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas USA
| | - Beverly Nelson
- Clinical Teaching Unit St. George's University School of Medicine True Blue Grenada
| | - Elizabeth J. Bhoj
- Center for Applied Genomics The Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Hakon Hakonarson
- Center for Applied Genomics The Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | | | - Sharmila Upadhya
- Department of Biochemistry St. George's University School of Medicine True Blue Grenada
| | - Sarah Gluschitz
- Department of Anatomical Sciences St. George's University True Blue Grenada
| | - Janice L. Smith
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas USA
| | - Andrew K. Sobering
- Department of Biochemistry St. George's University School of Medicine True Blue Grenada
- AU/UGA Medical Partnership Athens Georgia USA
- Windward Islands Research and Education Foundation St. George's Grenada
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4
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Burada F, Streata I, Ungureanu A, Ruican D, Nagy R, Serban-Sosoi S, Stambouli D, Dimos L, Popescu-Hobeanu G, Mihai I, Iliescu D. Prenatal diagnosis of a pure 15q distal trisomy derived from a maternal pericentric inversion: A case report. Exp Ther Med 2021; 21:304. [PMID: 33717247 PMCID: PMC7885063 DOI: 10.3892/etm.2021.9735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/24/2020] [Indexed: 11/06/2022] Open
Abstract
Distal trisomy or duplication of 15q is a very rare chromosomal disorder; most of the previously reported cases were derived from unbalanced translocations involving chromosome 15 and another chromosome, whereas other mechanisms (e.g. duplication) have rarely been reported. We herein report a very rare prenatal case of a partial 15q trisomy, a 42.64-Mb duplication of 15q22.2-q26.3, arising from a maternal pericentric inversion of chromosome 15 (p11q22) that was not the result of an unbalanced translocation or duplication, and was not associated with concomitant partial monosomy. Fetal ultrasound revealed isolated thickened nuchal translucency at 12 weeks and multiple abnormalities in the second trimester, including early growth restriction, unilateral ventriculomegaly, narrow cavum septi pellucidi with hypoplasia of the corpus callosum, unilateral postaxial polydactyly, clenched hands and clubfoot with clawing of the toes, and a particular general dysplastic and hypotrophic aspect of the heart. The distinctive aspects of the present case may help to refine the phenotype associated with distal duplication 15q. To the best of our knowledge, this is the first report of a prenatal diagnosis with a 15q22.2-q26.3 duplication that did not result from an unbalanced translocation and did not have a concomitant monosomic component.
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Affiliation(s)
- Florin Burada
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania.,Regional Center of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Ioana Streata
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania.,Regional Center of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Anda Ungureanu
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania.,Department of Pediatric Cardiology, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Dan Ruican
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Rodica Nagy
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Simona Serban-Sosoi
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania.,Regional Center of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | | | - Luiza Dimos
- Cytogenomic Medical Laboratory, 014453 Bucharest, Romania
| | - Gabriela Popescu-Hobeanu
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Ioana Mihai
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania.,Regional Center 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
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Wishart DS, Bartok B, Oler E, Liang KYH, Budinski Z, Berjanskii M, Guo A, Cao X, Wilson M. MarkerDB: an online database of molecular biomarkers. Nucleic Acids Res 2021; 49:D1259-D1267. [PMID: 33245771 PMCID: PMC7778954 DOI: 10.1093/nar/gkaa1067] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/14/2020] [Accepted: 10/26/2020] [Indexed: 01/27/2023] Open
Abstract
MarkerDB is a freely available electronic database that attempts to consolidate information on all known clinical and a selected set of pre-clinical molecular biomarkers into a single resource. The database includes four major types of molecular biomarkers (chemical, protein, DNA [genetic] and karyotypic) and four biomarker categories (diagnostic, predictive, prognostic and exposure). MarkerDB provides information such as: biomarker names and synonyms, associated conditions or pathologies, detailed disease descriptions, detailed biomarker descriptions, biomarker specificity, sensitivity and ROC curves, standard reference values (for protein and chemical markers), variants (for SNP or genetic markers), sequence information (for genetic and protein markers), molecular structures (for protein and chemical markers), tissue or biofluid sources (for protein and chemical markers), chromosomal location and structure (for genetic and karyotype markers), clinical approval status and relevant literature references. Users can browse the data by conditions, condition categories, biomarker types, biomarker categories or search by sequence similarity through the advanced search function. Currently, the database contains 142 protein biomarkers, 1089 chemical biomarkers, 154 karyotype biomarkers and 26 374 genetic markers. These are categorized into 25 560 diagnostic biomarkers, 102 prognostic biomarkers, 265 exposure biomarkers and 6746 predictive biomarkers or biomarker panels. Collectively, these markers can be used to detect, monitor or predict 670 specific human conditions which are grouped into 27 broad condition categories. MarkerDB is available at https://markerdb.ca.
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Affiliation(s)
- David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.,Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada.,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Brendan Bartok
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Eponine Oler
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Kevin Y H Liang
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Zachary Budinski
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Mark Berjanskii
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - AnChi Guo
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Xuan Cao
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Michael Wilson
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.,OMx Personal Health Analytics, Inc., 406-10158 103 St NW, Edmonton, AB T5J 0X6, Canada
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6
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Chromosomal abnormality, laboratory techniques, tools and databases in molecular Cytogenetics. Mol Biol Rep 2020; 47:9055-9073. [DOI: 10.1007/s11033-020-05895-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/03/2020] [Indexed: 11/30/2022]
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7
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Abrams ZB, Li S, Zhang L, Coombes CE, Payne PRO, Heerema NA, Abruzzo LV, Coombes KR. CytoGPS: A large-scale karyotype analysis of CML data. Cancer Genet 2020; 248-249:34-38. [PMID: 33059160 DOI: 10.1016/j.cancergen.2020.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/11/2020] [Accepted: 09/25/2020] [Indexed: 01/19/2023]
Abstract
Karyotyping, the practice of visually examining and recording chromosomal abnormalities, is commonly used to diagnose diseases of genetic origin, including cancers. Karyotypes are recorded as text written in the International System for Human Cytogenetic Nomenclature (ISCN). Downstream analysis of karyotypes is conducted manually, due to the visual nature of analysis and the linguistic structure of the ISCN. The ISCN has not been computer-readable and, as such, prevents the full potential of these genomic data from being realized. In response, we developed CytoGPS, a platform to analyze large volumes of cytogenetic data using a Loss-Gain-Fusion model that converts the human-readable ISCN karyotypes into a machine-readable binary format. As proof of principle, we applied CytoGPS to cytogenetic data from the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer, a National Cancer Institute hosted database of over 69,000 karyotypes of human cancers. Using the Jaccard coefficient to determine similarity between karyotypes structured as binary vectors, we were able to identify novel patterns from 4,968 Mitelman CML karyotypes, such as the co-occurrence of trisomy 19 and 21. The CytoGPS platform unlocks the potential for large-scale, comparative analysis of cytogenetic data. This methodological platform is freely available at CytoGPS.org.
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Affiliation(s)
- Zachary B Abrams
- Department of Biomedical Informatics, Wexner Medical Center, The Ohio State University, 250 Lincoln Tower, 1800 Cannon Drive, Columbus, OH 43210, USA.
| | - Suli Li
- Department of Biomedical Informatics, Wexner Medical Center, The Ohio State University, 250 Lincoln Tower, 1800 Cannon Drive, Columbus, OH 43210, USA
| | - Lin Zhang
- Institute for Informatics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Caitlin E Coombes
- Department of Biomedical Informatics, Wexner Medical Center, The Ohio State University, 250 Lincoln Tower, 1800 Cannon Drive, Columbus, OH 43210, USA
| | - Philip R O Payne
- Institute for Informatics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Nyla A Heerema
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
| | - Lynne V Abruzzo
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
| | - Kevin R Coombes
- Department of Biomedical Informatics, Wexner Medical Center, The Ohio State University, 250 Lincoln Tower, 1800 Cannon Drive, Columbus, OH 43210, USA.
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8
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Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing. Sci Rep 2020; 10:2512. [PMID: 32054878 PMCID: PMC7018692 DOI: 10.1038/s41598-020-59214-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/23/2020] [Indexed: 12/15/2022] Open
Abstract
Structural chromosomal rearrangements that can lead to in-frame gene-fusions are a leading source of information for diagnosis, risk stratification, and prognosis in pediatric acute lymphoblastic leukemia (ALL). Traditional methods such as karyotyping and FISH struggle to accurately identify and phase such large-scale chromosomal aberrations in ALL genomes. We therefore evaluated linked-read WGS for detecting chromosomal rearrangements in primary samples of from 12 patients diagnosed with ALL. We assessed the effect of input DNA quality on phased haplotype block size and the detectability of copy number aberrations and structural variants in the ALL genomes. We found that biobanked DNA isolated by standard column-based extraction methods was sufficient to detect chromosomal rearrangements even at low 10x sequencing coverage. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements and aneuploidy assessment. With use of haplotype information from the linked-reads, we also identified previously unknown structural variants, such as a compound heterozygous deletion of ERG in a patient with the DUX4-IGH fusion gene. We conclude that linked-read WGS allows detection of important pathogenic variants in ALL genomes at a resolution beyond that of traditional karyotyping and FISH.
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9
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Vetro C, Haferlach T, Meggendorfer M, Stengel A, Jeromin S, Kern W, Haferlach C. Cytogenetic and molecular genetic characterization of KMT2A-PTD positive acute myeloid leukemia in comparison to KMT2A-Rearranged acute myeloid leukemia. Cancer Genet 2019; 240:15-22. [PMID: 31698332 DOI: 10.1016/j.cancergen.2019.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/23/2019] [Accepted: 10/28/2019] [Indexed: 12/19/2022]
Abstract
To define the biological differences in acute myeloid leukaemia (AML) with KMT2A gene involvements and their prognostic impact, we compared 190 de novo AML patients at diagnosis, 95 harbouring KMT2A-rearrangement (KMT2Ar) and 95 KMT2A-PTD by performing cytogenetic and molecular genetic analyses. Both AML subtypes had an unfavourable outcome, particularly in patients > 60 years. Patients with KMT2Ar were younger compared to patients with KMT2A-PTD (mean 52 vs 65 years, p < 0.001) and had a higher rate of additional cytogenetic abnormalities (ACA) (46% vs 25% of cases). In both groups, occurrence of ACA did not influence the overall survival (OS). Regarding molecular genetics, 66% of patients with KMT2Ar and 99% of patients with KMT2A-PTD had additional gene mutations. In multivariate analysis, KRAS mutations and 10p12 rearrangement resulted as adverse prognostic factors in KMT2Ar subgroup. In the KMT2A-PTD group, apart from age, only the occurrence of DNMT3A non-R882 mutations correlated with shorter OS.
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10
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Denomy C, Germain S, Haave B, Vizeacoumar FS, Freywald A, Weaver BA, Vizeacoumar FJ. Banding Together: A Systematic Comparison of The Cancer Genome Atlas and the Mitelman Databases. Cancer Res 2019; 79:5181-5190. [PMID: 31416843 DOI: 10.1158/0008-5472.can-19-0585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/22/2019] [Accepted: 08/09/2019] [Indexed: 11/16/2022]
Abstract
Cytogenetic aberrations at the single-cell level represent an important characteristic of cancer cells relevant to tumor evolution and prognosis. However, with the advent of The Cancer Genome Atlas (TCGA), there has been a major shift in cancer research to the use of data from aggregate cell populations. Given that tumor cells harbor hundreds to thousands of biologically relevant genetic alterations that manifest as intratumor heterogeneity, these aggregate analyses may miss alterations readily observable at single-cell resolution. Using the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer, we developed an algorithm to parse International System for Cytogenetic Nomenclature notation for quantitative abnormalities. Comparison of the Mitelman database and TCGA demonstrated that the Mitelman database is a powerful resource, and that cytogenetic aberrations captured by traditional approaches used in Mitelman database are on par with population-based genomic analyses used in TCGA. This algorithm will help nonspecialists to overcome the challenges associated with the format and syntax of the Mitelman database. SIGNIFICANCE: A novel in silico approach compares cytogenetic data between the Mitelman database and TCGA, highlighting the advantages and limitations of both datasets.
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Affiliation(s)
- Connor Denomy
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Samuel Germain
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Bjorn Haave
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Beth A Weaver
- Department of Cell and Regenerative Biology, Department of Oncology/McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada. .,Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Canada
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11
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Wang J, LaFramboise T. CytoConverter: a web-based tool to convert karyotypes to genomic coordinates. BMC Bioinformatics 2019; 20:467. [PMID: 31510921 PMCID: PMC6739950 DOI: 10.1186/s12859-019-3062-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/29/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cytogenetic nomenclature is used to describe chromosomal aberrations (or lack thereof) in a collection of cells, referred to as the cells' karyotype. The nomenclature identifies locations on chromosomes using a system of cytogenetic bands, each with a unique name and region on a chromosome. Each band is microscopically visible after staining, and encompasses a large portion of the chromosome. More modern analyses employ genomic coordinates, which precisely specify a chromosomal location according to its distance from the end of the chromosome. Currently, there is no tool to convert cytogenetic nomenclature into genomic coordinates. Since locations of genes and other genomic features are usually specified by genomic coordinates, a conversion tool will facilitate the identification of the features that are harbored in the regions of chromosomal gain and loss that are implied by a karyotype. RESULTS Our tool, termed CytoConverter, takes as input either a single karyotype or a file consisting of multiple karyotypes from several individuals. All net chromosomal gains and losses implied by the karyotype are returned in standard genomic coordinates, along with the numbers of cells harboring each aberration if included in the input. CytoConverter also returns graphical output detailing areas of gains and losses of chromosomes and chromosomal segments. CONCLUSIONS CytoConverter is available as a web-based application at https://jxw773.shinyapps.io/Cytogenetic__software/ and as an R script at https://sourceforge.net/projects/cytoconverter/ . Supplemental Material detailing the underlying algorithms is available.
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Affiliation(s)
- Janet Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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12
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Tatsi C, Pankratz N, Lane J, Faucz FR, Hernández-Ramírez LC, Keil M, Trivellin G, Chittiboina P, Mills JL, Stratakis CA, Lodish MB. Large Genomic Aberrations in Corticotropinomas Are Associated With Greater Aggressiveness. J Clin Endocrinol Metab 2019; 104:1792-1801. [PMID: 30597087 PMCID: PMC6452317 DOI: 10.1210/jc.2018-02164] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/21/2018] [Indexed: 11/19/2022]
Abstract
CONTEXT Genomic losses/gains are associated with cancer progression and prognosis. In pituitary adenomas, analyses of copy number variations (CNVs) have shown that a subset of adenomas have higher genomic variability. However, whether CNVs are associated with tumor aggressiveness and prognosis has not been determined. OBJECTIVE We hypothesized that somatic CNVs of pituitary tumors may play a role in the progression and aggressiveness of pituitary corticotropinomas in children and adolescents. SAMPLES AND DESIGN Paired germline and tumor DNA samples from 27 pediatric patients with Cushing disease (CD), were subjected to whole exome sequencing. Somatic CNVs were identified using the ExomeDepth tool. Clinical, histological, and biochemical data from the patients were collected and correlated with the results of the CNV analysis. RESULTS Chromosomal instability, involving 23% to 59% of the tumor genome, was noted in 5 of the 27 samples (18.5%). The patients with tumors showing chromosomal instability had similar clinical and biochemical characteristics to the remaining patients, except for tumor size, which was larger (median size 18 mm vs 5.5 mm, P = 0.005). Tumors with chromosomal instability were also associated with a higher rate of invasion of the cavernous sinus (P = 0.029). There was insufficient information on persistence or recurrence of CD to determine whether the risk was higher in those with chromosomal instability. CONCLUSIONS A subgroup of corticotropinomas demonstrates chromosomal instability that is associated with markers of aggressiveness of these adenomas. It appears that more genomic gains/losses in a few, rare corticotropinomas may predict poorer prognosis for pediatric patients with CD.
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Affiliation(s)
- Christina Tatsi
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology University of Minnesota Medical School, Minneapolis, Minnesota
| | - John Lane
- Department of Laboratory Medicine and Pathology University of Minnesota Medical School, Minneapolis, Minnesota
| | - Fabio R Faucz
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Laura C Hernández-Ramírez
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Margaret Keil
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Giampaolo Trivellin
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Prashant Chittiboina
- Surgical Neurology Branch, National Institute of Neurologic Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - James L Mills
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institutes of Health, Bethesda, Maryland
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
- Correspondence and Reprint Requests: Constantine A. Stratakis, MD, National Institutes of Health, 10 Center Drive, Building 10, NIH-Clinical Research Center, Room 1-3330, MSC1103, Bethesda, Maryland 20892. E-mail:
| | - Maya B Lodish
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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Feurstein S, Thomay K, Hofmann W, Buesche G, Kreipe H, Thol F, Heuser M, Ganser A, Schlegelberger B, Göhring G. Routes of Clonal Evolution into Complex Karyotypes in Myelodysplastic Syndrome Patients with 5q Deletion. Int J Mol Sci 2018; 19:ijms19103269. [PMID: 30347879 PMCID: PMC6214088 DOI: 10.3390/ijms19103269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 02/01/2023] Open
Abstract
Myelodysplastic syndrome (MDS) can easily transform into acute myeloid leukemia (AML), a process which is often associated with clonal evolution and development of complex karyotypes. Deletion of 5q (del(5q)) is the most frequent aberration in complex karyotypes. This prompted us to analyze clonal evolution in MDS patients with del(5q). There were 1684 patients with low and intermediate-risk MDS and del(5q) with or without one additional cytogenetic abnormality, who were investigated cytogenetically in our department, involving standard karyotyping, fluorescence in situ hybridization (FISH) and multicolor FISH. We identified 134 patients (8%) with aspects of clonal evolution. There are two main routes of cytogenetic clonal evolution: a stepwise accumulation of cytogenetic events over time and a catastrophic event, which we defined as the occurrence of two or more aberrations present at the same time, leading to a sudden development of highly complex clones. Of the 134 patients, 61% underwent a stepwise accumulation of events whereas 39% displayed a catastrophic event. Patients with isolated del(5q) showed significantly more often a stepwise accumulation of events rather than a catastrophic event. The most frequent aberrations in the group of stepwise accumulation were trisomy 8 and trisomy 21 which were significantly more frequent in this group compared to the catastrophic event group. In the group with catastrophic events, del(7q)/-7 and del(17p)/-17 were the most common aberrations. A loss of 17p, containing the tumor suppressor gene TP53, was found significantly more frequent in this group compared to the group of stepwise accumulation. This leads to the assumption that the loss of TP53 is the driving force in patients with del(5q) who undergo a sudden catastrophic event and evolve into complex karyotypes.
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Affiliation(s)
- Simone Feurstein
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, 900 E 57th street, Chicago, IL 60637, USA.
| | - Kathrin Thomay
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Guntram Buesche
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Brigitte Schlegelberger
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
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Halgren C, Nielsen NM, Nazaryan-Petersen L, Silahtaroglu A, Collins RL, Lowther C, Kjaergaard S, Frisch M, Kirchhoff M, Brøndum-Nielsen K, Lind-Thomsen A, Mang Y, El-Schich Z, Boring CA, Mehrjouy MM, Jensen PK, Fagerberg C, Krogh LN, Hansen J, Bryndorf T, Hansen C, Talkowski ME, Bak M, Tommerup N, Bache I. Risks and Recommendations in Prenatally Detected De Novo Balanced Chromosomal Rearrangements from Assessment of Long-Term Outcomes. Am J Hum Genet 2018; 102:1090-1103. [PMID: 29805044 DOI: 10.1016/j.ajhg.2018.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/06/2018] [Indexed: 12/20/2022] Open
Abstract
The 6%-9% risk of an untoward outcome previously established by Warburton for prenatally detected de novo balanced chromosomal rearrangements (BCRs) does not account for long-term morbidity. We performed long-term follow-up (mean 17 years) of a registry-based nationwide cohort of 41 individuals carrying a prenatally detected de novo BCR with normal first trimester screening/ultrasound scan. We observed a significantly higher frequency of neurodevelopmental and/or neuropsychiatric disorders than in a matched control group (19.5% versus 8.3%, p = 0.04), which was increased to 26.8% upon clinical follow-up. Chromosomal microarray of 32 carriers revealed no pathogenic imbalances, illustrating a low prognostic value when fetal ultrasound scan is normal. In contrast, mate-pair sequencing revealed disrupted genes (ARID1B, NPAS3, CELF4), regulatory domains of known developmental genes (ZEB2, HOXC), and complex BCRs associated with adverse outcomes. Seven unmappable autosomal-autosomal BCRs with breakpoints involving pericentromeric/heterochromatic regions may represent a low-risk group. We performed independent phenotype-aware and blinded interpretation, which accurately predicted benign outcomes (specificity = 100%) but demonstrated relatively low sensitivity for prediction of the clinical outcome in affected carriers (sensitivity = 45%-55%). This sensitivity emphasizes the challenges associated with prenatal risk prediction for long-term morbidity in the absence of phenotypic data given the still immature annotation of the morbidity genome and poorly understood long-range regulatory mechanisms. In conclusion, we upwardly revise the previous estimates of Warburton to a morbidity risk of 27% and recommend sequencing of the chromosomal breakpoints as the first-tier diagnostic test in pregnancies with a de novo BCR.
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Thomay K, Fedder C, Hofmann W, Kreipe H, Stadler M, Titgemeyer J, Zander I, Schlegelberger B, Göhring G. Telomere shortening, TP53 mutations and deletions in chronic lymphocytic leukemia result in increased chromosomal instability and breakpoint clustering in heterochromatic regions. Ann Hematol 2017; 96:1493-1500. [PMID: 28691153 DOI: 10.1007/s00277-017-3055-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/19/2017] [Indexed: 01/09/2023]
Abstract
Complex karyotypes are associated with a poor prognosis in chronic lymphocytic leukemia (CLL). Using mFISH, iFISH, and T/C-FISH, we thoroughly characterized 59 CLL patients regarding parameters known to be involved in chromosomal instability: status of the genes ATM and TP53 and telomere length. Interestingly, a deletion of the ATM locus in 11q, independent of the cytogenetic context, was associated with significantly diminished risk (p<0.05) of carrying a mutation in TP53. In patients with loss or mutation of TP53, chromosomal breakage occurred more frequently (p<0.01) in (near-) heterochromatic regions. Median telomere length in patients with complex karyotypes was significantly shorter than that of healthy controls and shorter than in all other cytogenetic cohorts. Furthermore, the median telomere length of patients carrying a TP53 mutation was significantly shorter than without mutation. We conclude that telomere shortening in combination with loss of TP53 induces increased chromosomal instability with preferential involvement of (near-) heterochromatic regions.
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Affiliation(s)
- Kathrin Thomay
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany
| | - Caroline Fedder
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany
| | - Michael Stadler
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625, Hannover, Germany
| | - Jan Titgemeyer
- Onkologische Praxis Celle, Neumarkt 1, 29221, Celle, Germany
| | - Ingo Zander
- Onkologie am Raschplatz, Rundestr. 10, 30161, Hannover, Germany
| | - Brigitte Schlegelberger
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625, Hannover, Germany.
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Efficient Transformation of Primary Human Mesenchymal Stromal Cells by Adenovirus Early Region 1 Oncogenes. J Virol 2016; 91:JVI.01782-16. [PMID: 27795433 DOI: 10.1128/jvi.01782-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/15/2016] [Indexed: 11/20/2022] Open
Abstract
Previous observations that human amniotic fluid cells (AFC) can be transformed by human adenovirus type 5 (HAdV-5) E1A/E1B oncogenes prompted us to identify the target cells in the AFC population that are susceptible to transformation. Our results demonstrate that one cell type corresponding to mesenchymal stem/stroma cells (hMSCs) can be reproducibly transformed by HAdV-5 E1A/E1B oncogenes as efficiently as primary rodent cultures. HAdV-5 E1-transformed hMSCs exhibit all properties commonly associated with a high grade of oncogenic transformation, including enhanced cell proliferation, anchorage-independent growth, increased growth rate, and high telomerase activity as well as numerical and structural chromosomal aberrations. These data confirm previous work showing that HAdV preferentially transforms cells of mesenchymal origin in rodents. More importantly, they demonstrate for the first time that human cells with stem cell characteristics can be completely transformed by HAdV oncogenes in tissue culture with high efficiency. Our findings strongly support the hypothesis that undifferentiated progenitor cells or cells with stem cell-like properties are highly susceptible targets for HAdV-mediated cell transformation and suggest that virus-associated tumors in humans may originate, at least in part, from infections of these cell types. We expect that primary hMSCs will replace the primary rodent cultures in HAdV viral transformation studies and are confident that these investigations will continue to uncover general principles of viral oncogenesis that can be extended to human DNA tumor viruses as well. IMPORTANCE It is generally believed that transformation of primary human cells with HAdV-5 E1 oncogenes is very inefficient. However, a few cell lines have been successfully transformed with HAdV-5 E1A and E1B, indicating that there is a certain cell type which is susceptible to HAdV-mediated transformation. Interestingly, all those cell lines have been derived from human embryonic tissue, albeit the exact cell type is not known yet. We show for the first time the successful transformation of primary human mesenchymal stromal cells (hMSCs) by HAdV-5 E1A and E1B. Further, we show upon HAdV-5 E1A and E1B expression that these primary progenitor cells exhibit features of tumor cells and can no longer be differentiated into the adipogenic, chondrogenic, or osteogenic lineage. Hence, primary hMSCs represent a robust and novel model system to elucidate the underlying molecular mechanisms of adenovirus-mediated transformation of multipotent human progenitor cells.
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Hoffmann MJ, Koutsogiannouli E, Skowron MA, Pinkerneil M, Niegisch G, Brandt A, Stepanow S, Rieder H, Schulz WA. The New Immortalized Uroepithelial Cell Line HBLAK Contains Defined Genetic Aberrations Typical of Early Stage Urothelial Tumors. Bladder Cancer 2016; 2:449-463. [PMID: 28035326 PMCID: PMC5181672 DOI: 10.3233/blc-160065] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Background: Cell culture models of normal urothelial cells are important for studying differentiation, disease mechanisms and anticancer drug development. Beyond primary cultures with their limitations in lifespan, interindividual heterogeneity and supply, few conditionally immortalized cell lines with limited applicability due to partial transformation or impaired differentiation capacity are available. We describe characteristics of the new spontaneously immortalized cell line HBLAK derived from a primary culture of uroepithelial cells. Objective: To characterize utility and limitations of HBLAK cells as an urothelial cell culture model. Methods: Differentiation markers were investigated by immunofluorescence and RT-PCR, genetic changes by standard karyotyping, array-CGH, PCR, RT-PCR and exome sequencing; expression of p53 and p21 by Western blotting. Results: HBLAK cells proliferated for >50 passages without senescing. They expressed cytokeratins of basal urothelial cells. Terminal differentiation markers appeared only after induction of differentiation by specific protocols. The karyotype was stable, with few chromosomal changes, especially gains of chromosomes 5 and 20 and a chromosome 9p21 deletion resulting in p16INK4A loss. A C228T TERT promoter mutation was present, but no other mutation typical of urothelial carcinoma. TP53 was wild-type and the cell cycle was arrested in response to genomic stress. Conclusions: HBLAK cells retain some differentiation potential and respond to cytotoxic agents similar to normal urothelial cells, but contain genetic changes contributing to immortalization in urothelial tumors. HBLAK may be valuable for evaluating the tumor specificity of novel cancer drugs, but may also be applied as an urothelial in vitro carcinogenesis model.
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Affiliation(s)
- Michèle J Hoffmann
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | | | - Margaretha A Skowron
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Maria Pinkerneil
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Günter Niegisch
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Artur Brandt
- Institute for Human Genetics, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Stefanie Stepanow
- Biological and Medical Research Center (BMFZ), Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Harald Rieder
- Institute for Human Genetics, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
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18
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Haberl S, Haferlach T, Stengel A, Jeromin S, Kern W, Haferlach C. MYC rearranged B-cell neoplasms: Impact of genetics on classification. Cancer Genet 2016; 209:431-439. [PMID: 27810071 DOI: 10.1016/j.cancergen.2016.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/11/2016] [Accepted: 08/21/2016] [Indexed: 12/12/2022]
Abstract
A cohort comprising 156 patients with B-cell neoplasms harboring an MYC rearrangement was analyzed with respect to phenotypic presentation, molecular markers (TP53, MYC and ID3) and additional cytogenetic abnormalities (concomitantly occurring BCL2, BCL6 and/or CCND1 rearrangements; double, triple or quadruple hit lymphomas = multiple hit lymphomas). MYC translocations occurred as single hit (only MYC rearranged, 63%) or multiple hit lymphoma (37%) and presented as acute leukemia (AL) (14%), Burkitt lymphoma (30%), chronic lymphocytic leukemia (CLL) (21%) or other mature B-cell neoplasms (35%). Multiple hit lymphomas more frequently showed a complex karyotype compared to single hit lymphomas (62% vs. 28%, p < 0.001). Single hit Burkitt lymphomas presented with specific characteristics, by translocation of MYC to an immunoglobulin locus, predominantly a non-complex karyotype (23% vs. 67%, p = 0.012) and a significantly higher ID3 and TP53 mutation frequency (ID3mut: 49% vs. 0%, p = 0.002; TP53mut: 69% vs. 33%, p = 0.045). Additionally, MYC rearranged CLL presented as outstanding group by often showing a non-complex karyotype (85%), absence of ID3 mutations, a high frequency of SF3B1 mutations, and a frequent involvement of non-immunoglobulin loci as MYC-partner genes (61%). Consequently, genetic characteristics distinguish different subgroups of MYC rearranged B-cell neoplasms and therefore may contribute to a new classification system.
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19
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Tang Z, Tang G, Wang SA, Lu X, Young KH, Bueso-Ramos CE, Alvarado Y, Medeiros LJ, Khoury JD. Simultaneous deletion of 3'ETV6 and 5'EWSR1 genes in blastic plasmacytoid dendritic cell neoplasm: case report and literature review. Mol Cytogenet 2016; 9:23. [PMID: 26925167 PMCID: PMC4769509 DOI: 10.1186/s13039-016-0232-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/22/2016] [Indexed: 12/11/2022] Open
Abstract
Background Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare hematologic malignancy. Based on literature reports of limited cases, over 50 % of BPDCN have chromosomal abnormalities, but no single chromosomal change has been identified as diagnostic of this entity. Case presentation In this report, we present a case of BPDCN with complicated chromosomal abnormalities involving chromosomes 12 and 22 and resulting in a simultaneous partial deletion of ETV6 and EWSR1. Notably, these aberrations were identified in bone marrow myeloid precursors in the absence of bone marrow involvement by BPDCN. Conclusion Analysis of 46 BPDCN cases with abnormal karyotypes (45 from literature reports plus this case) showed that 12p- is one of the most common structural aberrations in BPDCN. The ETV6 and CDKN1B on 12p deserve further investigations as potential markers of BPDCN.
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Affiliation(s)
- Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Sa A Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Xinyan Lu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Ken H Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Carlos E Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Yesid Alvarado
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 USA
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Aukema SM, Theil L, Rohde M, Bauer B, Bradtke J, Burkhardt B, Bonn BR, Claviez A, Gattenlöhner S, Makarova O, Nagel I, Oschlies I, Pott C, Szczepanowski M, Traulsen A, Kluin PM, Klapper W, Siebert R, Murga Penas EM. Sequential karyotyping in Burkitt lymphoma reveals a linear clonal evolution with increase in karyotype complexity and a high frequency of recurrent secondary aberrations. Br J Haematol 2015; 170:814-25. [DOI: 10.1111/bjh.13501] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/10/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Sietse M. Aukema
- Institute of Human Genetics; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
- Department of Pathology & Medical Biology; University Medical Centre Groningen; University of Groningen; Groningen the Netherlands
- Department of Haematology; University Medical Centre Groningen; University of Groningen; Groningen the Netherlands
| | - Laura Theil
- Institute of Human Genetics; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Marius Rohde
- Non-Hodgkin Lymphoma Berlin-Frankfurt-Münster Group Study Centre; Department of Paediatric Haematology and Oncology; Justus Liebig University; Gießen Germany
| | - Benedikt Bauer
- Department of Evolutionary Theory; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - Jutta Bradtke
- Institute of Pathology; University Hospital Giessen and Marburg; Justus-Liebig-University Giessen; Giessen Germany
| | - Birgit Burkhardt
- Non-Hodgkin Lymphoma Berlin-Frankfurt-Münster Group Study Center; Department of Pediatric Haematology and Oncology; University Children's Hospital; Münster Germany
| | - Bettina R. Bonn
- Non-Hodgkin Lymphoma Berlin-Frankfurt-Münster Group Study Center; Department of Pediatric Haematology and Oncology; University Children's Hospital; Münster Germany
| | - Alexander Claviez
- Department of Paediatrics; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University; Kiel Germany
| | - Stefan Gattenlöhner
- Institute of Pathology; University Hospital Giessen and Marburg; Justus-Liebig-University Giessen; Giessen Germany
| | - Olga Makarova
- Non-Hodgkin Lymphoma Berlin-Frankfurt-Münster Group Study Center; Department of Pediatric Haematology and Oncology; University Children's Hospital; Münster Germany
| | - Inga Nagel
- Institute of Human Genetics; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Ilske Oschlies
- Department of Pathology, Haematopathology Section and Lymph Node Registry; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Christiane Pott
- Second Medical Department; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Monika Szczepanowski
- Department of Pathology, Haematopathology Section and Lymph Node Registry; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Arne Traulsen
- Institute of Pathology; University Hospital Giessen and Marburg; Justus-Liebig-University Giessen; Giessen Germany
| | - Philip M. Kluin
- Department of Pathology & Medical Biology; University Medical Centre Groningen; University of Groningen; Groningen the Netherlands
| | - Wolfram Klapper
- Department of Pathology, Haematopathology Section and Lymph Node Registry; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Reiner Siebert
- Institute of Human Genetics; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
| | - Eva M. Murga Penas
- Institute of Human Genetics; University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel; Kiel Germany
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Bacher U, Haferlach T, Schnittger S, Zenger M, Meggendorfer M, Jeromin S, Roller A, Grossmann V, Krauth MT, Alpermann T, Kern W, Haferlach C. Investigation of 305 patients with myelodysplastic syndromes and 20q deletion for associated cytogenetic and molecular genetic lesions and their prognostic impact. Br J Haematol 2013; 164:822-33. [PMID: 24372512 DOI: 10.1111/bjh.12710] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/25/2013] [Indexed: 11/28/2022]
Abstract
In patients with myelodysplastic syndromes (MDS), sole 20q deletion [del(20q)] is a recurrent favourable abnormality. We studied additional molecular and cytogenetic lesions and their prognostic impact in 305 MDS patients with del(20q) (229 males/76 females; 29-90 years). All patients were investigated by cytomorphology and chromosome banding analysis (CBA), subsets by fluorescence in situ hybridization, molecular mutation screening, and array comparative genomic hybridization (aCGH). By aCGH (n = 30), the minimal common deleted region (CDR) was flanked by PTPRT (20q13·11) and EYA2 (20q13·12). 210 (68·9%) patients had 'early MDS' without blast increase, 95 (31·1%) 'advanced' MDS with blast increase (5-19%). Additional chromosomal abnormalities (ACAs) were detected in 88/305 (28·9%) patients. Patients with advanced MDS more frequently had ACAs (P = 0·003) and had a higher mean number of ACAs (P = 0·020) and of molecular mutations (P = 0·060). Spliceosome mutations were frequent (U2AF1: n = 31/155; 20·0%; SRSF2: n = 31/159; 19·5%; SF3B1mut: n = 8/159; 5·0%). ASXL1mut (25/153; 16·3%) were associated with advanced MDS (P = 0·001). Presence of ≥3 ACAs (P = 0·003) and ASXL1mut (P = 0·002) were associated with worse 2-year survival. In conclusion, the cytogenetic subgroup of MDS with del(20q) has a good prognosis but may be further subclassified by additional cytogenetic and molecular lesions. U2AF1mut is overrepresented in MDS with del(20q), and ASXL1mut is prognostically adverse.
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22
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Koch A, Hatina J, Rieder H, Seifert HH, Huckenbeck W, Jankowiak F, Florl AR, Stoehr R, Schulz WA. Discovery of TP53 splice variants in two novel papillary urothelial cancer cell lines. Cell Oncol (Dordr) 2012; 35:243-57. [PMID: 22669776 DOI: 10.1007/s13402-012-0082-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2012] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Using a novel cell culture technique, we established two new cell lines, BC44 and BC61, from papillary urothelial carcinoma and analyzed them for genetic changes typical of this tumor type. METHODS AND RESULTS Karyotyping revealed aneuploid karyotypes with loss of chromosome 9 and rearranged chromosome 5p. Molecular analysis showed CDKN2A deletions but wild-type PIK3CA. BC61 contained a G372C FGFR3 mutation. TP53 was not mutated in either cell line and BC61 expressed normal full-length protein. In contrast, BC44 exclusively expressed cytoplasmic and nuclear p53Δ40 and 133 isoforms from the alternative promoter P2 as revealed by Western blotting, immunocytochemistry and PCR. The only discernible difference in TP53 in BC44 was homozygosity for the deletion allele of the rs17878362 polymorphism in the P2 promoter. Expression of p53 isoforms was also detected in a few other urothelial carcinoma cell lines and tumor cultures and in 4 out of 28 carcinoma tissues. CONCLUSION In urothelial cancers, TP53 is typically inactivated by mutations in one allele and loss of the wildtype allele and more frequently in invasive compared to papillary carcinomas. We show that some urothelial carcinomas may predominantly or exclusively express isoforms which are not detected by commonly used antibodies to epitopes located in the p53 TA amino-terminal region. Expression of these isoforms may constitute a further mode of p53 inactivation in urothelial carcinoma. Our findings raise the question to which extent this mechanism may compromise wildtype p53 function in papillary tumors in particular, where point mutations in the gene are rare.
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Affiliation(s)
- Annemarie Koch
- Urologische Klinik, Heinrich-Heine-Universität, Düsseldorf, Germany
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Haferlach C, Bacher U, Schnittger S, Alpermann T, Zenger M, Kern W, Haferlach T. ETV6 rearrangements are recurrent in myeloid malignancies and are frequently associated with other genetic events. Genes Chromosomes Cancer 2012; 51:328-37. [PMID: 22162288 DOI: 10.1002/gcc.21918] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 11/03/2011] [Indexed: 02/01/2023] Open
Abstract
ETV6 (TEL) rearrangements are favorable in pediatric acute lymphoblastic leukemia but are less well characterized in myeloid malignancies. We investigated 9,550 patients with myeloid disorders for ETV6 rearrangements by chromosome banding analysis and interphase fluorescence in situ hybridization. ETV6 rearrangements were identified in 51 of 9,550 (0.5%) patients (range, 19.2-85.3 years). Frequencies were in detail: acute myeloid leukemia (AML): 40 of 3,798, 1.1%; myelodysplastic syndromes (MDS): 6 of 3,375, 0.2%; myeloproliferative neoplasms (MPNs): 5 of 1,720, 0.3%; MDS/MPN: 0 of 210; and chronic myelomonocytic leukemia: 0 of 447. Thirty-three different partner bands of ETV6 were identified, and most were recurrent: 3q26 (n = 10), 5q33 (n = 4), 17q11 (n = 3), 22q12 (n = 3), 5q31 (n = 2), and 2q31 (n = 2). Additional chromosomal abnormalities were identified in 29 of 51 (57%) ETV6 rearranged cases. In AML, ETV6 rearrangements were frequently associated with NPM1 (9/39, 23%) and RUNX1 mutations (6/31, 19%). The FAB M0 subtype was more frequent in ETV6 rearranged de novo AML than other AML (P < 0.001); expression of CD7 and CD34 by immunophenotyping was higher in ETV6 rearranged AML compared with other subgroups. Survival of 29 ETV6 rearranged de novo AML was compared with 818 AML from other cytogenetic subgroups. Median overall and event-free survival of ETV6 rearranged cases was similar to the intermediate-risk cohort (26.3 vs. 62.2 months and 14.0 vs. 15.4 months) defined according to Medical Research Council criteria. Our study confirms the variety of ETV6 rearrangements in AML, MDS, and MPNs often in association with other genetic events. Prognosis of ETV6 rearranged de novo AML seems to be intermediate, which should be independently confirmed.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antigens, CD34/biosynthesis
- Antigens, CD7/biosynthesis
- Chromosome Banding
- Core Binding Factor Alpha 2 Subunit/genetics
- Disease-Free Survival
- Female
- Gene Rearrangement
- Humans
- Immunophenotyping
- In Situ Hybridization, Fluorescence
- Karyotype
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Male
- Middle Aged
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/mortality
- Myelodysplastic Syndromes/pathology
- Myeloproliferative Disorders/genetics
- Myeloproliferative Disorders/mortality
- Myeloproliferative Disorders/pathology
- Nuclear Proteins/genetics
- Nucleophosmin
- Prognosis
- Proto-Oncogene Proteins c-ets/genetics
- Repressor Proteins/genetics
- Young Adult
- ETS Translocation Variant 6 Protein
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24
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Ozery-Flato M, Linhart C, Trakhtenbrot L, Izraeli S, Shamir R. Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy. Genome Biol 2011; 12:R61. [PMID: 21714908 PMCID: PMC3218849 DOI: 10.1186/gb-2011-12-6-r61] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 05/17/2011] [Accepted: 06/29/2011] [Indexed: 01/05/2023] Open
Abstract
Background Chromosomal aneuploidy, that is to say the gain or loss of chromosomes, is the most common abnormality in cancer. While certain aberrations, most commonly translocations, are known to be strongly associated with specific cancers and contribute to their formation, most aberrations appear to be non-specific and arbitrary, and do not have a clear effect. The understanding of chromosomal aneuploidy and its role in tumorigenesis is a fundamental open problem in cancer biology. Results We report on a systematic study of the characteristics of chromosomal aberrations in cancers, using over 15,000 karyotypes and 62 cancer classes in the Mitelman Database. Remarkably, we discovered a very high co-occurrence rate of chromosome gains with other chromosome gains, and of losses with losses. Gains and losses rarely show significant co-occurrence. This finding was consistent across cancer classes and was confirmed on an independent comparative genomic hybridization dataset of cancer samples. The results of our analysis are available for further investigation via an accompanying website. Conclusions The broad generality and the intricate characteristics of the dichotomy of aneuploidy, ranging across numerous tumor classes, are revealed here rigorously for the first time using statistical analyses of large-scale datasets. Our finding suggests that aneuploid cancer cells may use extra chromosome gain or loss events to restore a balance in their altered protein ratios, needed for maintaining their cellular fitness.
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Affiliation(s)
- Michal Ozery-Flato
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
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25
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de Souza MT, Mkrtchyan H, Hassan R, Ney-Garcia DR, de Azevedo AMB, da Costa ES, de Figueiredo AF, Liehr T, Abdelhay E, Silva MLM. Secondary abnormalities involving 1q or 13q and poor outcome in high stage Burkitt leukemia/lymphoma cases with 8q24 rearrangement at diagnosis. Int J Hematol 2011; 93:232-236. [DOI: 10.1007/s12185-010-0757-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 11/24/2010] [Accepted: 12/15/2010] [Indexed: 11/28/2022]
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26
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Reindl L, Bacher U, Dicker F, Alpermann T, Kern W, Schnittger S, Haferlach T, Haferlach C. Biological and clinical characterization of recurrent 14q deletions in CLL and other mature B-cell neoplasms. Br J Haematol 2010; 151:25-36. [PMID: 20649559 DOI: 10.1111/j.1365-2141.2010.08299.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
14q-deletions have been repeatedly described in mature B-cell neoplasms, but not yet characterized in a larger cohort. Based on chromosome banding analysis, the present study identified 47 del(14q) cases in 3054 mature B-cell neoplasms (1·5%) (chronic lymphocytic leukaemia [CLL]: 1·9%; CLL/prolymphocytic leukaemia [PL]: 9·0%; others: 0·2%). Interphase fluorescence in situ hybridization was performed with probes for 14q22.1, 14q24.1, 14q32.33, and IGH@ (14q32.3). The del(14q) had heterogeneous size but showed a breakpoint cluster at the centromeric site in 14q24.1 (62% of cases). At the telomeric side, the most frequent breakpoint was within the IGH@ locus (14q32.3) between IGH@ 3'-flanking and IGHV (IgVH) probes (45%). In 16 cases (34%), breakpoints occurred within 14q24.1 and 14q32.3. Eighty-one percent of del(14q) cases showed 1-3 additional cytogenetic alterations (in 45%, +12), and 56% were IGHV-unmutated. In all cases (16/16) with breakpoints in 14q24.1 and 14q32.3, a B-CLL immunophenotype was found. Clinical follow-up in 32 del(14q) patients was compared to 383 CLL and CLL/PL patients without del(14q). While 3-year-overall survival did not differ significantly, time to treatment was significantly shorter in the del(14q) cohort (21·0 months vs. 80·1 months, P = 0·015). In conclusion, the del(14q) is a rare recurrent alteration in diverse mature B-cell neoplasms, shows variable size but distinct clustering of breakpoints, and is associated with short time to treatment.
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Affiliation(s)
- Lena Reindl
- Munich Leukemia Laboratory, Munich Interdisciplinary Clinic for Stem Cell Transplantation, Max-Lebsche-Platz 31, Munich, Germany
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27
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Bacher U, Haferlach T, Alpermann T, Zenger M, Kröger N, Beelen DW, Kern W, Schnittger S, Haferlach C. Comparison of cytogenetic clonal evolution patterns following allogeneic hematopoietic transplantation versus conventional treatment in patients at relapse of AML. Biol Blood Marrow Transplant 2010; 16:1649-57. [PMID: 20558312 DOI: 10.1016/j.bbmt.2010.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Accepted: 06/07/2010] [Indexed: 11/27/2022]
Abstract
Relapse of acute myelogenous leukemia has been associated with clonal cytogenetic evolution, but no study focused specifically on relapse after allogeneic hematopoietic stem cell transplantation (HSCT). We compared karyotypes in 160 patients at both diagnosis and relapse either after allo-HSCT (n = 26) or standard chemotherapy (n = 134) using chromosome banding analysis combined with fluorescein in situ hybridization. There were 71 females and 89 males (19.7-80.6 years). At diagnosis, aberrant karyotypes were more frequent in the HSCT than in the chemotherapy cohort (16 of 26; 61.5% versus 63 of 134; 47.0%). This was most obvious in patients with unfavorable cytogenetics (8 of 26; 30.8% versus 19 of 134; 14.2%; P = .032). Differences in the karyotypes between diagnosis and relapse were more frequent in the allo-cohort (14 of 26; 53.8% versus 49 of 134; 36.6%) than in the conventional cohort (n.s.), mainly because of newly emerging cytogenetic alterations. Appearance of ≥ 3 new clonal alterations was more frequent in the allo-cohort (6 of 12; 50.0% with clonal evolution versus 5 of 41; 12.2%, P = .005). The mean number of cytogenetic alterations per patient was increasing from 2.0 at diagnosis to 4.0 at relapse in the allo-cohort, in the conventionally treated patients from 0.9 to 1.3 (both P < .001). Thus, higher frequencies of clonal evolution and increasing cytogenetic complexity were observed in the stem cell recipients probably related to the more unfavorable cytogenetic profiles already depicted at diagnosis.
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Affiliation(s)
- Ulrike Bacher
- Interdisciplinary Clinic for Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, Germany.
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28
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Abstract
Background Finding sequences of evolutionary operations that transform one genome into another is a classical problem in comparative genomics. While most of the genome rearrangement algorithms assume that there is exactly one copy of each gene in both genomes, this does not reflect the biological reality very well - most of the studied genomes contain duplicated gene content, which has to be removed before applying those algorithms. However, dealing with unequal gene content is a very challenging task, and only few algorithms allow operations like duplications and deletions, especially if the duplicated or deleted segments are of arbitrary size. Results We recently proposed a heuristic algorithm for sorting unichromosomal genomes by reversals, block interchanges, tandem duplications, and deletions. In this paper, we extend this approach to multichromosomal genomes. We are now able to sort a multichromosomal ancestral genome into a genome of a descendant by a large set of different operations, including tandem duplications and deletions of segments of arbitrary size. Conclusion Experimental results show that our algorithm finds sorting sequences that have a weight close to the true evolutionary distance.
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Affiliation(s)
- Martin Bader
- Institute of Theoretical Computer Science, Ulm University, 89069 Ulm, Germany.
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29
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Lange K, Gadzicki D, Schlegelberger B, Göhring G. Recurrent involvement of heterochromatic regions in multiple myeloma-a multicolor FISH study. Leuk Res 2009; 34:1002-6. [PMID: 20022374 DOI: 10.1016/j.leukres.2009.10.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 10/29/2009] [Accepted: 10/30/2009] [Indexed: 10/20/2022]
Abstract
Chromosome aberrations are important prognostic markers in multiple myeloma (MM), but their identification may be hampered by complexity of the karyotypes. Using multicolor fluorescence in situ hybridization (mFISH), we found cryptic aberrations in 7 of 10 patients with a complex karyotype. Moreover, in addition to typical aberrations involving 1q, 13q, 14q and 17p and structural aberrations in chromosomes 1, 6, 9 and 19, (iso)dicentric chromosomes and whole-arm translocations were detected. These chromosome aberrations were generated by breaks in heterochromatic regions indicating an increased breakage of these regions, which may predispose to the generation of chromosome aberrations in multiple myeloma.
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Affiliation(s)
- Kathrin Lange
- Institute of Cell and Molecular Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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30
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Ozery-Flato M, Shamir R. Sorting cancer karyotypes by elementary operations. J Comput Biol 2009; 16:1445-60. [PMID: 19754273 DOI: 10.1089/cmb.2009.0083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Since the discovery of the "Philadelphia chromosome" in chronic myelogenous leukemia in 1960, there has been ongoing intensive research of chromosomal aberrations in cancer. These aberrations, which result in abnormally structured genomes, became a hallmark of cancer. Many studies provide evidence for the connection between chromosomal alterations and aberrant genes involved in the carcinogenesis process. An important problem in the analysis of cancer genomes is inferring the history of events leading to the observed aberrations. Cancer genomes are usually described in the form of karyotypes, which present the global changes in the genomes' structure. In this study, we propose a mathematical framework for analyzing chromosomal aberrations in cancer karyotypes. We introduce the problem of sorting karyotypes by elementary operations, which seeks a shortest sequence of elementary chromosomal events transforming a normal karyotype into a given (abnormal) cancerous karyotype. Under certain assumptions, we prove a lower bound for the elementary distance, and present a polynomial-time 3-approximation algorithm for the problem. We applied our algorithm to karyotypes from the Mitelman database, which records cancer karyotypes reported in the scientific literature. Approximately 94% of the karyotypes in the database, totaling 58,464 karyotypes, supported our assumptions, and each of them was subjected to our algorithm. Remarkably, even though the algorithm is only guaranteed to generate a 3-approximation, it produced a sequence whose length matched the lower bound (and hence optimal) in 99.9% of the tested karyotypes.
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Affiliation(s)
- Michal Ozery-Flato
- The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.
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31
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Similar patterns of chromosome abnormalities in CML occur in addition to the Philadelphia chromosome with or without tyrosine kinase inhibitor treatment. Leukemia 2009; 24:638-40. [DOI: 10.1038/leu.2009.222] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Krayenbühl N, Pravdenkova S, Al-Mefty O. De novo versus transformed atypical and anaplastic meningiomas: comparisons of clinical course, cytogenetics, cytokinetics, and outcome. Neurosurgery 2007; 61:495-503; discussion 503-4. [PMID: 17881961 DOI: 10.1227/01.neu.0000290895.92695.22] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE The clinical course of atypical and anaplastic meningiomas is heterogeneous. As malignant gliomas, aggressive meningiomas may arise de novo or transform from a benign tumor. This study aims to compare differences in clinical behavior, cytogenetics, cytokinetics, receptor status, and outcome between de novo malignant meningiomas and meningiomas that progressed to malignancy. METHODS Data from 36 patients with atypical or anaplastic meningiomas were selected for retrospective analysis and divided into two subgroups: 1) de novo atypical or anaplastic tumors and 2) tumors that progressed from a lower grade. We analyzed data concerning patients' sex, age, tumor location, number of operations, status of hormone receptors, proliferative indices, cytogenetic findings, additional therapy, and survival. For meningiomas with progression, we calculated the interval between initial diagnosis and tumor progression. RESULTS For atypical meningiomas, the subgroups had significant differences in status of progesterone receptors, proliferative indices, cytogenetics, and patients' outcome. The anaplastic group had similar differences, but they did not reach statistical significance because of the small numbers. There was a loss of part or monosomy of chromosome 10 and an increased monosomy or derivative chromosome 1 combined with monosomy of chromosome 14. These phenomena occurred mainly in patients with malignant transformation who had a worse outcome. CONCLUSION De novo malignant meningiomas and meningiomas with malignant transformation may represent distinct subgroups of atypical and anaplastic meningiomas.
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Affiliation(s)
- Niklaus Krayenbühl
- Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
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33
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Haferlach C, Dicker F, Schnittger S, Kern W, Haferlach T. Comprehensive genetic characterization of CLL: a study on 506 cases analysed with chromosome banding analysis, interphase FISH, IgVH status and immunophenotyping. Leukemia 2007; 21:2442-51. [PMID: 17805327 DOI: 10.1038/sj.leu.2404935] [Citation(s) in RCA: 246] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In CLL data from chromosome banding analysis (CBA) have been scarce due to the low proliferative activity of CLL cells in vitro. We improved the cultivation technique using an immunostimulatory CpG-oligonucleotide DSP30 and IL-2. A total of 506 CLL samples were analysed with CBA and interphase FISH using probes for the detection of trisomy 12, IgH rearrangements and deletions of 6q21, 11q22.3 (ATM), 13q14 (D13S25 and D13S319) and 17p13 (TP53). A total of 500 of 506 (98.8%) cases were successfully stimulated for metaphase generation and are subject to this study. Aberrations were detected in 415 of 500 (83.0%) cases by CBA and in 392 of 500 (78.4%) cases by FISH. CBA detected 832 abnormalities and FISH only 502. Therefore, CBA offers important information in addition to FISH. (1) CLL is characterized mainly by genomic imbalances and reciprocal translocations are rare. (2) A subgroup with complex aberrant karyotype (16.4%) is identified which is associated with an unmutated IgV(H) status and CD38 expression (P=0.034 and 0.02, respectively). (3) Additional abnormalities are detectable providing new biological insights into different CLL subclasses revealing a much more heterogeneous pattern of cytogenetic abnormalities as assumed so far based on FISH data only. Therefore, prospective clinical trials should evaluate the prognostic impact of newly available CBA data.
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MESH Headings
- ADP-ribosyl Cyclase 1/biosynthesis
- ADP-ribosyl Cyclase 1/genetics
- Adult
- Aged
- Aged, 80 and over
- Cell Culture Techniques/methods
- Chromosome Aberrations
- Chromosome Banding
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Gene Rearrangement, B-Lymphocyte, Heavy Chain
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Variable Region/genetics
- Immunophenotyping
- In Situ Hybridization, Fluorescence
- Interleukin-2/pharmacology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Membrane Glycoproteins/biosynthesis
- Membrane Glycoproteins/genetics
- Middle Aged
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Tumor Cells, Cultured/drug effects
- Tumor Cells, Cultured/metabolism
- Tumor Cells, Cultured/ultrastructure
- ZAP-70 Protein-Tyrosine Kinase/biosynthesis
- ZAP-70 Protein-Tyrosine Kinase/genetics
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Affiliation(s)
- C Haferlach
- MLL Munich Leukemia Laboratory, Munich, Germany.
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34
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Detection and molecular cytogenetic characterization of a novel ring chromosome in a histological variant of Ewing sarcoma. ACTA ACUST UNITED AC 2007; 172:12-22. [PMID: 17175374 DOI: 10.1016/j.cancergencyto.2006.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 06/23/2006] [Accepted: 07/05/2006] [Indexed: 10/23/2022]
Abstract
Ewing sarcoma/peripheral primitive neuro-ectodermal tumor (PNET) is a round-cell sarcoma that may show varying degrees of neuro-ectodermal differentiation. These tumors are identified by a characteristic round-cell morphology and immunohistochemical profile, as well as by specific translocations involving the EWS gene on chromosome 22 and the 3' portion of the E26 transformation-specific family of transcription factors. These translocations result in fusion proteins that act as aberrant transcription factors. The majority of Ewing sarcoma cases are characterized by a balanced t(11;22). Specific chromosomal abnormalities often correlate with distinct morphologic or phenotypic subtypes of tumors and play an important role in prognosis. Here we describe the molecular cytogenetic investigation of a case of Ewing sarcoma in the proximal humerus of a 39-year-old male using COBRA (combined binary ratio labelling) fluorescent in situ hybridization karyotyping, array comparative genomic hybridization, and EWS-gene specific fluorescence in situ hybridization. Multiple chromosomal aberrations were identified, including a der(22)r(20;22), resulting in an amplification of the proximal region of the EWS gene. This is the first time that both translocation and amplification involving the EWS gene and an unidentified gene are described. This case adds to the spectrum of both morphology and genetic rearrangements in Ewing sarcoma, and shows the importance of combined molecular cytogenetic approaches in identifying uncommon rearrangements in sarcomas.
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