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Tuna M, Amos CI, Mills GB. Whole-chromosome arm acquired uniparental disomy in cancer development is a consequence of isochromosome formation. Neoplasia 2022; 25:9-17. [PMID: 35065533 PMCID: PMC8788198 DOI: 10.1016/j.neo.2021.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/09/2023]
Abstract
Using SNP-based microarray data from The Cancer Genome Atlas (TCGA), we investigated isochromosomes (deletion of one arm and duplication of the other arm) and related acquired uniparental disomy in 12 tumor types. We observed a high frequency of isochromosomes (25.98%) across all type of tumors except thyroid cancers. The highest frequency of isochromosomes was found in lung squamous cell carcinoma (54.18%). Moreover, whole-chromosome arm acquired uniparental disomy (aUPD) was common in the deleted arms of isochromosomes. These data are consistent with whole-chromosome arm aUPD likely being a consequence of isochromosomes formation. Our findings implicated aUPD as occurring through error-prone DNA repair of a deleted arm or segment of a chromosome that leads to homozygosity for existing alterations. Isochromosomes were significantly more frequent in TP53 mutated samples than wild types in 6 types of tumors with loss of TP53 function potentially contributing to development of isochromosomes. Isochromosomes are common alterations in cancer, and losing one arm of a chromosome could result in duplication of the lost arm. Duplication of the remaining arm leads promulgation of the effects on any defects in the remaining allele, due to subsequent homozygosity.
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Affiliation(s)
- Musaffe Tuna
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza room 100.23D, Houston, TX 77030, USA.
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza room 100.23D, Houston, TX 77030, USA; Institute of Clinical and Translational Medicine, Baylor College of Medicine, USA
| | - Gordon B Mills
- Department of Cell, Developmental & Cancer Biology, School of Medicine, Oregon Health Science University, Portland, OR, USA; Precision Oncology, Knight Cancer Institute, Portland, OR, USA
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Valli R, Minelli A, Galbiati M, D'Amico G, Frattini A, Montalbano G, Khan AW, Porta G, Millefanti G, Olivieri C, Cipolli M, Cesaro S, Pasquali F, Danesino C, Cazzaniga G, Maserati E. Shwachman-Diamond syndrome with clonal interstitial deletion of the long arm of chromosome 20 in bone marrow: haematological features, prognosis and genomic instability. Br J Haematol 2018; 184:974-981. [PMID: 30585299 DOI: 10.1111/bjh.15729] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/28/2018] [Indexed: 12/30/2022]
Abstract
In Shwachman-Diamond syndrome (SDS), deletion of the long arm of chromosome 20, del(20)(q), often acquired in bone marrow (BM), may imply a lower risk of developing myelodysplastic syndrome/acute myeloid leukaemia (MDS/AML), due to the loss of the EIF6 gene. The genes L3MBTL1 and SGK2, also on chromosome 20, are in a cluster of imprinted genes, and their loss implies dysregulation of BM function. We report here the results of array comparative genomic hybridization (a-CGH) performed on BM DNA of six patients which confirmed the consistent loss of EIF6 gene. Interestingly, array single nucleotide polymorphisms (SNPs) showed copy neutral loss of heterozygosity for EIF6 region in cases without del(20)(q). No preferential parental origin of the deleted chromosome 20 was detected by microsatellite analysis in six SDS patients. Our patients showed a very mild haematological condition, and none evolved into BM aplasia or MDS/AML. We extend the benign prognostic significance of del(20)(q) and loss of EIF6 to the haematological features of these patients, consistently characterized by mild hypoplastic BM, no or mild neutropenia, anaemia and thrombocytopenia. Some odd results obtained in microsatellite and SNP-array analysis demonstrate a peculiar genomic instability, in an attempt to improve BM function through the acquisition of the del(20)(q).
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Affiliation(s)
- Roberto Valli
- Genetica Umana e Medica, Dipartimento di Medicina e Chirurgia, Università dell'Insubria, Varese, Italy
| | - Antonella Minelli
- Genetica Medica, Fondazione IRCCS Policlinico S. Matteo and Università di Pavia, Pavia, Italy
| | - Marta Galbiati
- Immunology and Cell Therapy, Centro Ricerca Tettamanti, Paediatric Clinic, University of Milan Bicocca/MBBM, Monza, Italy
| | - Giovanna D'Amico
- Immunology and Cell Therapy, Centro Ricerca Tettamanti, Paediatric Clinic, University of Milan Bicocca/MBBM, Monza, Italy
| | - Annalisa Frattini
- Genetica Umana e Medica, Dipartimento di Medicina e Chirurgia, Università dell'Insubria, Varese, Italy.,Istituto di Ricerca Genetica e Biomedica, CNR, Milano, Italy
| | - Giuseppe Montalbano
- Genetica Umana e Medica, Dipartimento di Medicina e Chirurgia, Università dell'Insubria, Varese, Italy
| | - Abdul W Khan
- Genetica Umana e Medica, Dipartimento di Medicina e Chirurgia, Università dell'Insubria, Varese, Italy
| | - Giovanni Porta
- Genetica Umana e Medica, Dipartimento di Medicina e Chirurgia, Università dell'Insubria, Varese, Italy
| | - Giorgia Millefanti
- Genetica Umana e Medica, Dipartimento di Medicina e Chirurgia, Università dell'Insubria, Varese, Italy
| | - Carla Olivieri
- Genetica Medica, Fondazione IRCCS Policlinico S. Matteo and Università di Pavia, Pavia, Italy
| | - Marco Cipolli
- Cystic Fibrosis Center, AOU Ospedali Riuniti, Ancona, Italy
| | - Simone Cesaro
- Oncoematologia Pediatrica, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Francesco Pasquali
- Genetica Umana e Medica, Dipartimento di Medicina e Chirurgia, Università dell'Insubria, Varese, Italy
| | - Cesare Danesino
- Genetica Medica, Fondazione IRCCS Policlinico S. Matteo and Università di Pavia, Pavia, Italy
| | - Gianni Cazzaniga
- Immunology and Cell Therapy, Centro Ricerca Tettamanti, Paediatric Clinic, University of Milan Bicocca/MBBM, Monza, Italy
| | - Emanuela Maserati
- Genetica Umana e Medica, Dipartimento di Medicina e Chirurgia, Università dell'Insubria, Varese, Italy
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Affiliation(s)
- Roberto Valli
- Medical Genetic Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Annalisa Frattini
- UOS Milano, Institute of Genetics and Biomedical Research, National Research Council, Milano, Italy
- Department of Medicine and Surgery, University of Insubria, Milano, Italy
| | - Antonella Minelli
- Medical Genetic Unit, Department of Molecular Medicine, University of Pavia, Pavia, Italy
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Nacci L, Valli R, Maria Pinto R, Zecca M, Cipolli M, Morini J, Cesaro S, Boveri E, Rosti V, Corti P, Ambroni M, Pasquali F, Danesino C, Maserati E, Minelli A. Parental origin of the deletion del(20q) in Shwachman-Diamond patients and loss of the paternally derived allele of the imprintedL3MBTL1gene. Genes Chromosomes Cancer 2016; 56:51-58. [DOI: 10.1002/gcc.22401] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 11/11/2022] Open
Affiliation(s)
- Lucia Nacci
- Department of Molecular Medicine; University of Pavia; Pavia Italy
| | - Roberto Valli
- Department of Clinical and Experimental Medicine; University of Insubria; Varese Italy
| | - Rita Maria Pinto
- Ospedale Bambino Gesù IRCCS; Oncoematologia e Medicina Trasfusionale; Roma Italy
| | - Marco Zecca
- Oncoematologia Pediatrica, Fondazione IRCCS Policlinico San Matteo; Pavia Italy
| | - Marco Cipolli
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria; Verona Italy
| | | | - Simone Cesaro
- Oncoematologia Pediatrica, Azienda Ospedaliera Universitaria Integrata; Verona Italy
| | - Emanuela Boveri
- Fondazione IRCCS Policlinico; Anatomic Pathology Section; San Matteo, Pavia Italy
| | - Vittorio Rosti
- IRCCS Policlinico San Matteo; Center for the Study of Myelofibrosis, Biotechnology Research Area; Pavia Italy
| | - Paola Corti
- Pediatrics Unit, Fondazione Medico e Brianza per il Bambino e la sua Mamma; Monza Italy
| | - Maura Ambroni
- Cystic Fibrosis Regional Center, Ospedale M. Bufalini; Cesena Italy
| | - Francesco Pasquali
- Department of Clinical and Experimental Medicine; University of Insubria; Varese Italy
| | - Cesare Danesino
- Department of Molecular Medicine; University of Pavia; Pavia Italy
| | - Emanuela Maserati
- Department of Clinical and Experimental Medicine; University of Insubria; Varese Italy
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Donadieu J, Fenneteau O, Beaupain B, Beaufils S, Bellanger F, Mahlaoui N, Lambilliotte A, Aladjidi N, Bertrand Y, Mialou V, Perot C, Michel G, Fouyssac F, Paillard C, Gandemer V, Boutard P, Schmitz J, Morali A, Leblanc T, Bellanné-Chantelot C. Classification of and risk factors for hematologic complications in a French national cohort of 102 patients with Shwachman-Diamond syndrome. Haematologica 2012; 97:1312-9. [PMID: 22491737 DOI: 10.3324/haematol.2011.057489] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Patients with the Shwachman-Diamond syndrome often develop hematologic complications. No risk factors for these complications have so far been identified. The aim of this study was to classify the hematologic complications occurring in patients with Shwachman-Diamond syndrome and to investigate the risk factors for these complications. DESIGN AND METHODS One hundred and two patients with Shwachman-Diamond syndrome, with a median follow-up of 11.6 years, were studied. Major hematologic complications were considered in the case of definitive severe cytopenia (i.e. anemia <7 g/dL or thrombocytopenia <20 × 10(9)/L), classified as malignant (myelodysplasia/leukemia) according to the 2008 World Health Organization classification or as non-malignant. RESULTS Severe cytopenia was observed in 21 patients and classified as malignant severe cytopenia (n=9), non-malignant severe cytopenia (n=9) and malignant severe cytopenia preceded by non-malignant severe cytopenia (n=3). The 20-year cumulative risk of severe cytopenia was 24.3% (95% confidence interval: 15.3%-38.5%). Young age at first symptoms (<3 months) and low hematologic parameters both at diagnosis of the disease and during the follow-up were associated with severe hematologic complications (P<0.001). Fifteen novel SBDS mutations were identified. Genotype analysis showed no discernible prognostic value. CONCLUSIONS Patients with Shwachman-Diamond syndrome with very early symptoms or cytopenia at diagnosis (even mild anemia or thrombocytopenia) should be considered at a high risk of severe hematologic complications, malignant or non-malignant. Transient severe cytopenia or an indolent cytogenetic clone had no deleterious value.
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Affiliation(s)
- Jean Donadieu
- AP-HP Registre Français des Neutropénies Congénitales, Hôpital Trousseau, Service d’Hémato-oncologie Pédiatrique, APHP, Paris, France.
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