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Krzeminski P, Corchete LA, García JL, López-Corral L, Fermiñán E, García EM, Martín AA, Hernández-Rivas JM, García-Sanz R, San Miguel JF, Gutiérrez NC. Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse. Oncotarget 2018; 7:80664-80679. [PMID: 27811368 PMCID: PMC5348347 DOI: 10.18632/oncotarget.13025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 10/21/2016] [Indexed: 12/27/2022] Open
Abstract
Multiple myeloma (MM) remains incurable despite the introduction of novel agents, and a relapsing course is observed in most patients. Although the development of genomic technologies has greatly improved our understanding of MM pathogenesis, the mechanisms underlying relapse have been less thoroughly investigated. In this study, an integrative analysis of DNA copy number, DNA methylation and gene expression was conducted in matched diagnosis and relapse samples from MM patients. Overall, the acquisition of abnormalities at relapse was much more frequent than the loss of lesions present at diagnosis, and DNA losses were significantly more frequent in relapse than in diagnosis samples. Interestingly, copy number abnormalities involving more than 100 Mb of DNA at relapse significantly affect the gene expression of these samples, provoking a particular deregulation of the IL-8 pathway. On the other hand, no significant modifications of gene expression were observed in those samples with less than 100 Mb affected by chromosomal changes. Although several statistical approaches were used to identify genes whose abnormal expression at relapse was regulated by methylation, only two genes that were significantly deregulated in relapse samples (SORL1 and GLT1D1) showed a negative correlation between methylation and expression. Further analysis revealed that DNA methylation was involved in regulating SORL1 expression in MM. Finally, relevant changes in gene expression observed in relapse samples, such us downregulation of CD27 and P2RY8, were most likely not preceded by alterations in the corresponding DNA. Taken together, these results suggest that the genomic heterogeneity described at diagnosis remains at relapse.
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Affiliation(s)
- Patryk Krzeminski
- Departamento de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain.,Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Luis A Corchete
- Departamento de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain
| | - Juan L García
- Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Lucía López-Corral
- Departamento de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain.,Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Encarna Fermiñán
- Unidad de Genómica y Proteómica, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Eva M García
- Unidad de Genómica y Proteómica, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Ana A Martín
- Departamento de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain
| | - Jesús M Hernández-Rivas
- Departamento de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain.,Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Ramón García-Sanz
- Departamento de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain.,Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Jesús F San Miguel
- Clínica Universidad de Navarra, Centro de Investigaciones Médicas Aplicadas (CIMA), Pamplona, Spain
| | - Norma C Gutiérrez
- Departamento de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain.,Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
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Abáigar M, Robledo C, Benito R, Ramos F, Díez-Campelo M, Hermosín L, Sánchez-del-Real J, Alonso JM, Cuello R, Megido M, Rodríguez JN, Martín-Núñez G, Aguilar C, Vargas M, Martín AA, García JL, Kohlmann A, del Cañizo MC, Hernández-Rivas JM. Chromothripsis Is a Recurrent Genomic Abnormality in High-Risk Myelodysplastic Syndromes. PLoS One 2016; 11:e0164370. [PMID: 27741277 PMCID: PMC5065168 DOI: 10.1371/journal.pone.0164370] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 09/23/2016] [Indexed: 11/18/2022] Open
Abstract
To explore novel genetic abnormalities occurring in myelodysplastic syndromes (MDS) through an integrative study combining array-based comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) in a series of MDS and MDS/myeloproliferative neoplasms (MPN) patients. 301 patients diagnosed with MDS (n = 240) or MDS/MPN (n = 61) were studied at the time of diagnosis. A genome-wide analysis of DNA copy number abnormalities was performed. In addition, a mutational analysis of DNMT3A, TET2, RUNX1, TP53 and BCOR genes was performed by NGS in selected cases. 285 abnormalities were identified in 71 patients (23.6%). Three high-risk MDS cases (1.2%) displayed chromothripsis involving exclusively chromosome 13 and affecting some cancer genes: FLT3, BRCA2 and RB1. All three cases carried TP53 mutations as revealed by NGS. Moreover, in the whole series, the integrative analysis of aCGH and NGS enabled the identification of cryptic recurrent deletions in 2p23.3 (DNMT3A; n = 2.8%), 4q24 (TET2; n = 10%) 17p13 (TP53; n = 8.5%), 21q22 (RUNX1; n = 7%), and Xp11.4 (BCOR; n = 2.8%), while mutations in the non-deleted allele where found only in DNMT3A (n = 1), TET2 (n = 3), and TP53 (n = 4). These cryptic abnormalities were detected mainly in patients with normal (45%) or non-informative (15%) karyotype by conventional cytogenetics, except for those with TP53 deletion and mutation (15%), which had a complex karyotype. In addition to well-known copy number defects, the presence of chromothripsis involving chromosome 13 was a novel recurrent change in high-risk MDS patients. Array CGH analysis revealed the presence of cryptic abnormalities in genomic regions where MDS-related genes, such as TET2, DNMT3A, RUNX1 and BCOR, are located.
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Affiliation(s)
- María Abáigar
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Cristina Robledo
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Rocío Benito
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Fernando Ramos
- IBIOMED, Instituto de Biomedicina, Universidad de León, León, Spain
- Servicio de Hematología, Hospital Universitario de León, León, Spain
| | - María Díez-Campelo
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Lourdes Hermosín
- Servicio de Hematología, Hospital Jerez de la Frontera, Cádiz, Spain
| | | | - Jose M. Alonso
- Servicio de Hematología, Hospital Río Carrión, Palencia, Spain
| | - Rebeca Cuello
- Servicio de Hematología, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Marta Megido
- Servicio de Hematología, Hospital del Bierzo, Ponferrada, Spain
| | | | | | - Carlos Aguilar
- Servicio de Hematología, Hospital General de Soria, Soria, Spain
| | - Manuel Vargas
- Servicio de Hematología, Hospital Comarcal de Jarrio, Jarrio-Coaña, Spain
| | - Ana A. Martín
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Juan L. García
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Alexander Kohlmann
- AstraZeneca, Personalized Healthcare and Biomarkers, Innovative Medicines and Early Development, Cambridge, United Kingdom
| | - M. Consuelo del Cañizo
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- IBSAL, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
| | - Jesús M. Hernández-Rivas
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- IBSAL, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- * E-mail:
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Misiewicz-Krzeminska I, Sarasquete ME, Vicente-Dueñas C, Krzeminski P, Wiktorska K, Corchete LA, Quwaider D, Rojas EA, Corral R, Martín AA, Escalante F, Bárez A, García JL, Sánchez-García I, García-Sanz R, San Miguel JF, Gutiérrez NC. Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma. Clin Cancer Res 2015; 22:207-17. [PMID: 26341922 DOI: 10.1158/1078-0432.ccr-14-2796] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 08/14/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Dysregulation of one of the three D-cyclin genes has been observed in virtually all multiple myeloma tumors. The mechanisms by which CCND2 is upregulated in a set of multiple myeloma are not completely deciphered. We investigated the role of post-transcriptional regulation through the interaction between miRNAs and their binding sites at 3'UTR in CCND2 overexpression in multiple myeloma. EXPERIMENTAL DESIGN Eleven myeloma cell lines and 45 primary myeloma samples were included in the study. Interactions between miRNAs deregulated in multiple myeloma and mRNA targets were analyzed by 3'UTR-luciferase plasmid assay. The presence of CCND2 mRNA isoforms different in length was explored using qRT-PCR, Northern blot, mRNA FISH, and 3' rapid amplification of cDNA ends (RACE)-PCR. RESULTS We detected the presence of short CCND2 mRNA, both in the multiple myeloma cell lines and primary cells. The results obtained by 3'RACE experiments revealed that changes in CCND2 3'UTR length are explained by alternative polyadenylation. The luciferase assays using plasmids harboring the truncated CCND2 mRNA strongly confirmed the loss of miRNA sites in the shorter CCND2 mRNA isoform. Those multiple myelomas with greater abundance of the shorter 3'UTR isoform were associated with significant higher level of total CCND2 mRNA expression. Furthermore, functional analysis showed significant CCND2 mRNA shortening after CCND1 silencing and an increased relative expression of longer isoform after CCND1 and CCND3 overexpression, suggesting that cyclin D1 and D3 could regulate CCND2 levels through modifications in polyadenylation-cleavage reaction. CONCLUSIONS Overall, these results highlight the impact of CCND2 3'UTR shortening on miRNA-dependent regulation of CCND2 in multiple myeloma.
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Affiliation(s)
- Irena Misiewicz-Krzeminska
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. National Medicines Institute, Warsaw, Poland
| | - María E Sarasquete
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Carolina Vicente-Dueñas
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. Experimental Therapeutics and Translational Oncology Program, Instituto de Biologia Molecular y Celular del Cancer, CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Patryk Krzeminski
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | | | - Luis Antonio Corchete
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Dalia Quwaider
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Elizabeta A Rojas
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Rocío Corral
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. Servicio de Hematología, Hospital Universitario, Salamanca, Spain
| | - Ana A Martín
- Servicio de Hematología, Hospital Universitario, Salamanca, Spain
| | | | | | - Juan Luis García
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Isidro Sánchez-García
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. Experimental Therapeutics and Translational Oncology Program, Instituto de Biologia Molecular y Celular del Cancer, CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Ramón García-Sanz
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. Servicio de Hematología, Hospital Universitario, Salamanca, Spain
| | - Jesús F San Miguel
- Clinica Universidad de Navarra, Centro de Investigaciones Medicas Aplicadas (CIMA), Pamplona, Spain
| | - Norma C Gutiérrez
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. Servicio de Hematología, Hospital Universitario, Salamanca, Spain.
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4
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Krzeminski P, Sarasquete ME, Misiewicz-Krzeminska I, Corral R, Corchete LA, Martín AA, García-Sanz R, San Miguel JF, Gutiérrez NC. Insights into epigenetic regulation of microRNA-155 expression in multiple myeloma. Biochim Biophys Acta 2014; 1849:353-66. [PMID: 25497370 DOI: 10.1016/j.bbagrm.2014.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/07/2014] [Accepted: 12/02/2014] [Indexed: 11/28/2022]
Abstract
CONTEXT MiR-155 plays a critical role in the development of B-cell malignancies. Previous studies have shown a deregulation of miR-155 in specific cytogenetic subtypes of multiple myeloma (MM). However, the mechanisms that regulate miR-155 expression in MM are not fully understood. OBJECTIVE In the present study, we explored the regulation of miRNA-155 in MM by DNA methylation mechanisms and the impact of miR-155 expression in survival of MM patients. METHOD Primary samples were obtained from 95 patients with newly diagnosed myeloma. Methylation was analyzed by Methylation Specific PCR, sequencing of bisulfite treated DNA and luciferase assay. RESULTS qRT-PCR analysis revealed that miR-155 was differentially expressed in MM and its upregulation was associated with longer survival. DNA methylation of CpG island present in the first exon of miR-155 host gene was associated with its low expression in MM cell lines and patient samples. Our results showed for the first time that in vitro methylation of part of the promoter and first exon abrogated the miR-155 expression. We further showed that miR-155 expression in MM cell lines was increased by demethylating 5-aza-dC treatment and decreased by RNA-directed DNA methylation. Additionally, we found that LPS "immunological challenge" was insufficient to induce miR-155 expression in MM cell lines with methylated DNA around transcription start site (TSS). CONCLUSION This study provides evidence that DNA methylation contributes to miR-155 expression in myeloma cells. Interestingly, the survival data showed an association between miR-155 expression and outcome of MM.
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Affiliation(s)
- Patryk Krzeminski
- Servicio de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain.
| | - María E Sarasquete
- Servicio de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain
| | - Irena Misiewicz-Krzeminska
- Servicio de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain; National Medicines Institute, Warsaw, Poland
| | - Rocío Corral
- Servicio de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain
| | - Luis A Corchete
- Servicio de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain
| | - Ana A Martín
- Servicio de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain
| | - Ramón García-Sanz
- Servicio de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain
| | - Jesús F San Miguel
- Clínica Universidad de Navarra, Centro de Investigación Médica Aplicada, Pamplona, Navarra, Spain
| | - Norma C Gutiérrez
- Servicio de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain.
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Martín AA, Galán YH, Rodríguez AJ, Graupera M, Lorenzo-Luaces P, Fernández LM, Camacho R, Lezcano M. The Cuban National Cancer Registry: 1986-1990. Eur J Epidemiol 1998; 14:287-97. [PMID: 9663522 DOI: 10.1023/a:1007463826932] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In Cuba, the illness that produces most deaths among 1-64-year-olds is cancer. Over 65, it is the second cause of death after heart diseases. A National Cancer Registry was created 1964. Its main goals are to register all malignant neoplasms diagnosed in the country, to study this disease from the statistical and epidemiological point of view and to aid in the health control and planning of cancer fighting resources. This paper presents the results based on cases registered from 1986 to 1990. More than 50% of incidence and mortality caused by cancer is confined to the five major primary sites: lung, prostate, colon, breast and cervix. World population standardised rates by 100,000 inhabitants for the period 1986-1990 were 218.2 in males and 183.7 in females for incidence and 138.4 in males and 95.1 in females for mortality. Cancer incidence distribution by provinces shows two major regions: western-central, where higher risks of lung, breast, prostate and colon cancers are found, and eastern where very high risk of cervix cancer is observed. Although an improvement of the information quality indexes has been reported by the National Cancer registry in the studied period of time, quality of the data remained very poor according to the international standards. However, the results obtained by the National Cancer Registry seem to be a valuable tool to evaluate the cancer burden and, in particular, to control and eventually modify the tasks of the National Cancer Control Program in Cuba.
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Affiliation(s)
- A A Martín
- National Cancer Registry, National Institute of Oncology, Havana, Cuba.
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Abstract
Cancer is an infrequent disease in childhood. However, it is responsible for 13.06% of child deaths between 1 and 14 years in Cuba. The aim of our work was to describe the incidence of childhood cancer in the period 1986 to 1990 using data reported to the National Cancer Registry (NCR) of Cuba. All cancer cases between 0 and 14 years of age reported to the NCR in the period 1986 to 1990, were included. The cases were classified histologically, by age and gender. Average age-specific and age-standardized rates were calculated; 1428 children were registered, an average of 286 each year, with a mean annual rate of 117.8 per million. The world-population standardized rate was 120.7 and the male-to-female ratio was 0.98. Leukaemias, lymphomas and malignant tumours of the central nervous system were the most common childhood neoplasm groups. The majority of leukaemias were acute lymphoblastic leukaemias (ALL), and the incidence peak extended until 6 years of age. The first peak of incidence of Hodgkin's disease is found in older age-groups. Burkitt's lymphoma showed a male-to-female ratio of 0.44. Most of the hepatic tumours were carcinomas, and only one fourth were hepatoblastomas. In bone tumours, similar rates were observed for osteosarcomas and Ewing's sarcoma.
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Affiliation(s)
- A A Martín
- National Institute of Oncology, Havana, Cuba.
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Massone AR, Martín AA, Ibargoyen GS, Gimeno EJ. Immunohistochemical methods for the visualization of Mycobacterium paratuberculosis in bovine tissues. Zentralbl Veterinarmed B 1990; 37:251-3. [PMID: 2382517 DOI: 10.1111/j.1439-0450.1990.tb01054.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The peroxidase-antiperoxidase (PAP), streptavidin-biotin (SB), and avidin-biotin-complex (ABC) techniques have been evaluated for the visualization of Mycobacterium paratuberculosis (Mp) in formalin-fixed, paraffin-embedded bovine tissues. The used immunoperoxidase techniques were comparatively better than the Ziehl-Neelsen stain, specially for the demonstration of small number of mycobacteria in tissue sections.
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Affiliation(s)
- A R Massone
- Institute of Pathology, Faculty of Veterinary Sciences, La Plata, Argentina
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