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Kim KK, Seung BJ, Kim D, Park HM, Lee S, Song DW, Lee G, Cheong JH, Nam H, Sur JH, Kim S. Whole-exome and whole-transcriptome sequencing of canine mammary gland tumors. Sci Data 2019; 6:147. [PMID: 31413331 PMCID: PMC6694171 DOI: 10.1038/s41597-019-0149-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/26/2019] [Indexed: 12/20/2022] Open
Abstract
Studies of naturally occurring cancers in dogs, which share many genetic and environmental factors with humans, provide valuable information as a comparative model for studying the mechanisms of human cancer pathogenesis. While individual and small-scale studies of canine cancers are underway, more generalized multi-omics studies have not been attempted due to the lack of large-scale and well-controlled genomic data. Here, we produced reliable whole-exome and whole-transcriptome sequencing data of 197 canine mammary cancers and their matched controls, annotated with rich clinical and biological features. Our dataset provides useful reference points for comparative analysis with human cancers and for developing novel diagnostic and therapeutic technologies for cancers in pet dogs.
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Affiliation(s)
- Ka-Kyung Kim
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Byung-Joon Seung
- Department of Veterinary Pathology, Small Animal Tumor Diagnostic Center, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dohyun Kim
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hee-Myung Park
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Sejoon Lee
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Doo-Won Song
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Gunho Lee
- Graduate Program for Nanomedical Science, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jae-Ho Cheong
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea.
| | - Jung-Hyang Sur
- Department of Veterinary Pathology, Small Animal Tumor Diagnostic Center, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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Amini P, Nassiri S, Ettlin J, Malbon A, Markkanen E. Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma. Dis Model Mech 2019; 12:dmm.040444. [PMID: 31308057 PMCID: PMC6737962 DOI: 10.1242/dmm.040444] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/09/2019] [Indexed: 01/05/2023] Open
Abstract
Spontaneous canine simple mammary carcinomas (mCA) are often viewed as models of human mCA. Cancer-associated stroma (CAS) is central for initiation and progression of human cancer, and is likely to play a key role in canine tumours as well. However, canine CAS lacks characterisation and it remains unclear how canine and human CAS compare. Formalin-fixed paraffin embedded (FFPE) tissue constitutes a valuable resource of patient material, but chemical crosslinking has largely precluded its analysis by next-generation RNA sequencing (RNAseq). We have recently established a protocol to isolate CAS and normal stroma from archival FFPE tumours using laser-capture microdissection followed by RNAseq. Using this approach, we have analysed stroma from 15 canine mCA. Our data reveal strong reprogramming of canine CAS. We demonstrate a high-grade molecular homology between canine and human CAS, and show that enrichment of upregulated canine CAS genes strongly correlates with the enrichment of an independently derived human stromal signature in the TCGA breast tumour dataset. Relationships between different gene signatures observed in human breast cancer are largely maintained in the canine model, suggesting a close interspecies similarity in the network of cancer signalling circuitries. Finally, we establish the prognostic potential of the canine CAS signature in human samples, emphasising the relevance of studying canine CAS as a model of the human disease. In conclusion, we provide a proof-of-principle to analyse specific subsections of FFPE tissue by RNAseq, and compare stromal gene expression between human and canine mCA to reveal molecular drivers in CAS supporting tumour growth and malignancy. Summary: This study offers proof-of-principle for a novel protocol to analyse gene expression in subsections of FFPE patient tissue, supporting the use of spontaneous canine mammary tumours as models for the human disease.
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Affiliation(s)
- Parisa Amini
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, CH-8057 Zürich, Switzerland
| | - Sina Nassiri
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Julia Ettlin
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, CH-8057 Zürich, Switzerland
| | - Alexandra Malbon
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, CH-8057 Zürich, Switzerland
| | - Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, CH-8057 Zürich, Switzerland
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53
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Pulz LH, Barra CN, Alexandre PA, Huete GC, Cadrobbi KG, Nishiya AT, de Freitas SH, Fukumasu H, Strefezzi RF. Identification of two molecular subtypes in canine mast cell tumours through gene expression profiling. PLoS One 2019; 14:e0217343. [PMID: 31216299 PMCID: PMC6583995 DOI: 10.1371/journal.pone.0217343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 05/09/2019] [Indexed: 12/16/2022] Open
Abstract
Mast cell tumours (MCTs) are common neoplasms in dogs and are usually regarded as potentially malignant. Several studies have attempted to identify biomarkers to better predict biological behaviours for this tumour. The aim of this study was to identify pathways connected to clinical and histopathological malignancies, shorter survival times, and poor prognoses associated with MCTs. We performed genome-wide gene expression analyses on tissues obtained from 15 dogs with single MCTs, and identified two distinct tumour subtypes—high-risk and low-risk—associated with differences in histological grades, survival times, Ki67 indices, and occurrence of death due the disease. Comparative analyses of RNA sequence profiles revealed 71 genes that were differentially expressed between high- and low-risk MCTs. In addition to these analyses, we also examined gene co-expression networks to explore the biological functions of the identified genes. The network construction revealed 63 gene modules, of which 4 were significantly associated with the more aggressive tumour group. Two of the gene modules positively correlated with high-risk MCTs were also associated with cell proliferation and extracellular matrix-related terms. At the top of the extracellular matrix module category, genes with functions directly related to those of cancer-associated fibroblasts (CAFs) were identified. Immunohistochemical analyses also revealed a greater number of CAFs in high-risk MCTs. This study provides a method for the molecular characterisation of canine MCTs into two distinct subtypes. Our data indicate that proliferation pathways are significantly involved in malignant tumour behaviours, which are known to be relevant for the induction and maintenance of MCTs. Finally, animals presenting high-risk MCTs overexpress genes associated with the extracellular matrix that can be robustly linked to CAF functions. We suggest that CAFs in the MCT stroma contribute to cancer progression.
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Affiliation(s)
- Lidia H. Pulz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
- Department of Pathology, Faculty of Veterinary Medicine and Animal Science- FMVZ, University of Sao Paulo, São Paulo, SP, Brazil
- * E-mail:
| | - Camila N. Barra
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
- Department of Pathology, Faculty of Veterinary Medicine and Animal Science- FMVZ, University of Sao Paulo, São Paulo, SP, Brazil
| | - Pamela A. Alexandre
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Greice C. Huete
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Karine G. Cadrobbi
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Adriana T. Nishiya
- Veterinary Hospital Anhembi Morumbi, R. Conselheiro Lafaiete, São Paulo—SP, Anhembi Morumbi University, São Paulo, SP, Brazil
| | - Silvio Henrique de Freitas
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Ricardo F. Strefezzi
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
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Timmermans-Sprang EPM, Mestemaker HM, Steenlage RR, Mol JA. Dasatinib inhibition of cSRC prevents the migration and metastasis of canine mammary cancer cells with enhanced Wnt and HER signalling. Vet Comp Oncol 2019; 17:413-426. [PMID: 31069942 DOI: 10.1111/vco.12490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/05/2018] [Accepted: 04/24/2019] [Indexed: 12/16/2022]
Abstract
Human epidermal growth factor 2 (HER2) overexpression leads to aggressive mammary tumour growth. Although the prognosis of HER2+ tumours in humans is greatly improved using biologicals, therapy resistance, which may be caused by increased phosphatidyl-3-kinase (PI3K), rous sarcoma proto-oncogene (cSRC) or wingless-type MMTV integration site family (Wnt) activity, is a major concern. A recent analysis of 12 canine mammary cell lines showed an association between HER2/3 overexpression and phosphatase and tensin homologue (PTEN) deletion with elevated Wnt-signalling. Wnt-activity appeared to be insensitive to phosphatidyl-3-kinase (PI3K) inhibitors but sensitive to Src-I1. We hypothesized that Wnt activation, was caused by HER2/3-activated cSRC activation. The role of HER2/3 on Wnt signalling was investigated by silencing HER2/3 expression using specific small interfering RNA (siRNAs). Next, the effect of an epidermal growth factor receptor (EGFR)/HER2 tyrosine kinase inhibitor on Wnt activity and migration was investigated and compared to other tyrosine kinase inhibitors (TKIs) of related signalling pathways. Finally, two TKIs, a cSRC and a PI3K inhibitor, were investigated in a zebrafish xenograft model. Silencing of HER1-3 did not inhibit the intrinsic high Wnt activity, whereas the HER kinase inhibitor afatinib showed enhanced Wnt activity. The strongest inhibition of Wnt activity and cell viability and migration was shown by cSRC inhibitors, which also showed strong inhibition of cell viability and metastasis in a zebrafish xenograft model. HER2/3 overexpression or HER2/3-induced cSRC activation is not the cause of enhanced Wnt activity. However, inhibition of cSRC resulted in a strong inhibition of Wnt activity and cell migration and metastasis. Further studies are needed to unravel the mechanism of cSRC activation and cSRC inhibition to restore sensitivity to HER-inhibitors in HER2/3-positive breast cancer.
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Affiliation(s)
| | - Helena M Mestemaker
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, The Netherlands
| | - Renske R Steenlage
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, The Netherlands
| | - Jan A Mol
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, The Netherlands
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55
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Hsieh PH, Oyang YJ, Chen CY. Effect of de novo transcriptome assembly on transcript quantification. Sci Rep 2019; 9:8304. [PMID: 31165774 PMCID: PMC6549443 DOI: 10.1038/s41598-019-44499-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 05/17/2019] [Indexed: 11/08/2022] Open
Abstract
Correct quantification of transcript expression is essential to understand the functional elements in different physiological conditions. For the organisms without the reference transcriptome, de novo transcriptome assembly must be carried out prior to quantification. However, a large number of erroneous contigs produced by the assemblers might result in unreliable estimation. In this regard, this study investigates how assembly quality affects the performance of quantification based on de novo transcriptome assembly. We examined the over-extended and incomplete contigs, and demonstrated that assembly completeness has a strong impact on the estimation of contig abundance. Then we investigated the behavior of the quantifiers with respect to sequence ambiguity which might be originally presented in the transcriptome or accidentally produced by assemblers. The results suggested that the quantifiers often over-estimate the expression of family-collapse contigs and under-estimate the expression of duplicated contigs. For organisms without reference transcriptome, it remains challenging to detect the inaccurate estimation on family-collapse contigs. On the contrary, we observed that the situation of under-estimation on duplicated contigs can be warned through analyzing the read proportion of estimated abundance (RPEA) of contigs in the connected component inferenced by the quantifiers. In addition, we suggest that the estimated quantification results on the connected component level have better accuracy over sequence level quantification. The analytic results conducted in this study provides valuable insights for future development of transcriptome assembly and quantification.
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Affiliation(s)
- Ping-Han Hsieh
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
| | - Yen-Jen Oyang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, 10617, Taiwan
| | - Chien-Yu Chen
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 10617, Taiwan.
- Genome and Systems Biology Program, National Taiwan University and Academia sinica, Taipei, 10617, Taiwan.
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56
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Timmermans-Sprang E, Collin R, Henkes A, Philipsen M, Mol JA. P-cadherin mutations are associated with high basal Wnt activity and stemness in canine mammary tumor cell lines. Oncotarget 2019; 10:2930-2946. [PMID: 31105876 PMCID: PMC6508207 DOI: 10.18632/oncotarget.26873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/04/2019] [Indexed: 01/16/2023] Open
Abstract
Purpose: To find underlying mutations causing highly-activated Wnt activity in mammary tumor cell lines associated with rounded morphology indicative of stemness/EMT. Methods: Stemness of high Wnt cell lines was confirmed using qPCR on selected genes and microRNA profiling, followed by whole-exome sequencing of 3 high Wnt canine mammary tumor cell lines and 5 low/absent Wnt cell lines. Candidate genes were identified and their involvement in Wnt activity investigated using siRNA silencing. Results: The high Wnt cell lines had morphological and gene expression characteristics reminiscent of stemness. All individual cell lines had about 4000 mutations in the exome in comparison to the reference canine genome. The three high basal Wnt cell lines had 167 unique exome mutations. Seven of these mutations resulted in a SIFT score <0.2 of proteins related to Wnt signaling. However, gene silencing did not change the Wnt pathway activation. Renewed analysis with respect to putative relations to Wnt signaling revealed that P-cadherin (CDH3) had three mutations in the coding region of the extracellular domain and was associated with high Wnt signaling. Silencing by siRNA not only in lowered Wnt activity, but also decreased levels of phosphorylated cSRC and sP-cad, and changed cell morphology towards spindle cell appearance. Conclusion: It is concluded that expression of mutated CDH3 is associated with activation of cSRC, stabilization of ß-catenin and a rounded morphology related to a stemness/EMT phenotype. A decreased Wnt activity can be found also by cSRC inhibition, but CDH3 silencing has an additional effect on morphology indicating reversal of EMT.
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Affiliation(s)
- Elpetra Timmermans-Sprang
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Rob Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjen Henkes
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Meike Philipsen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jan A. Mol
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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57
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Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM. Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology 2019; 16:6. [PMID: 30845962 PMCID: PMC6407205 DOI: 10.1186/s12977-019-0468-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 01/20/2023] Open
Abstract
Background Vertebrate genomes contain a record of retroviruses that invaded the germlines of ancestral hosts and are passed to offspring as endogenous retroviruses (ERVs). ERVs can impact host function since they contain the necessary sequences for expression within the host. Dogs are an important system for the study of disease and evolution, yet no substantiated reports of infectious retroviruses in dogs exist. Here, we utilized Illumina whole genome sequence data to assess the origin and evolution of a recently active gammaretroviral lineage in domestic and wild canids. Results We identified numerous recently integrated loci of a canid-specific ERV-Fc sublineage within Canis, including 58 insertions that were absent from the reference assembly. Insertions were found throughout the dog genome including within and near gene models. By comparison of orthologous occupied sites, we characterized element prevalence across 332 genomes including all nine extant canid species, revealing evolutionary patterns of ERV-Fc segregation among species as well as subpopulations. Conclusions Sequence analysis revealed common disruptive mutations, suggesting a predominant form of ERV-Fc spread by trans complementation of defective proviruses. ERV-Fc activity included multiple circulating variants that infected canid ancestors from the last 20 million to within 1.6 million years, with recent bursts of germline invasion in the sublineage leading to wolves and dogs. Electronic supplementary material The online version of this article (10.1186/s12977-019-0468-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia V Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Abigail S Jarosz
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Robert J Gifford
- Centre for Virus Research, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Malika L Day
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Ave., Ann Arbor, MI, 48109, USA
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58
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Lee KH, Shin TJ, Kim WH, Cho JY. Methylation of LINE-1 in cell-free DNA serves as a liquid biopsy biomarker for human breast cancers and dog mammary tumors. Sci Rep 2019; 9:175. [PMID: 30655558 PMCID: PMC6336845 DOI: 10.1038/s41598-018-36470-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/21/2018] [Indexed: 12/15/2022] Open
Abstract
Breast cancer (BC) is one of the most common cancers in both women and female dogs. Methylation changes of LINE-1 have been reported in human cancers. The aim of this study was to determine the hypomethylation of canine LINE-1 in liquid biopsies for canine mammary tumors (CMT) and to assess its diagnostic performance in human plasma. BC associated LINE-1 methylation was measured by methylation sensitive (HpaII) and insensitive (MspI) restriction enzyme digestion followed by real-time PCR using the cfDNA isolated from 300 µl of plasma. The relative level of methylated canine LINE-1 was less than 0.4 in the benign and malignant CMTs (0.29 ± 0.061 and 0.39 ± 0.066, respectively) when it was 0.92 ± 0.067 in the healthy controls. The area under the ROC curve (AUC) was significantly high in both benign and malignant tumors (0.97 and 0.93). Furthermore, this approach was also successfully implemented in a set of 26 human BCs with 10 healthy controls (AUC = 0.78). Altogether, our data suggest that the comparative approach using a dog model might be helpful to rapidly develop a new diagnostic biomarker and that the methylation of LINE-1 in cfDNA may be a good target as a diagnostic marker of both human BC and CMT.
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Affiliation(s)
- Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Tae-Jin Shin
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Wan-Hee Kim
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, South Korea.
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Wang J, Wang T, Sun Y, Feng Y, Kisseberth WC, Henry CJ, Mok I, Lana SE, Dobbin K, Northrup N, Howerth EW, Zhao S. Proliferative and Invasive Colorectal Tumors in Pet Dogs Provide Unique Insights into Human Colorectal Cancer. Cancers (Basel) 2018; 10:cancers10090330. [PMID: 30223484 PMCID: PMC6162437 DOI: 10.3390/cancers10090330] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 09/12/2018] [Accepted: 09/12/2018] [Indexed: 12/13/2022] Open
Abstract
Spontaneous tumors in pet dogs represent a valuable but undercharacterized cancer model. To better use this resource, we performed an initial global comparison between proliferative and invasive colorectal tumors from 20 canine cases, and evaluated their molecular homology to human colorectal cancer (CRC). First, proliferative canine tumors harbor overactivated WNT/β-catenin pathways and recurrent CTNNB1 (β-catenin) mutations S45F/P, D32Y and G34E. Invasive canine tumors harbor prominent fibroblast proliferation and overactivated stroma. Both groups have recurrent TP53 mutations. We observed three invasion patterns in canine tumors: collective, crypt-like and epithelial–mesenchymal transition (EMT). We detected enriched Helicobacter bilis and Alistipes finegoldii in proliferative and crypt-like tumors, but depleted mucosa-microbes in the EMT tumor. Second, guided by our canine findings, we classified 79% of 478 human colon cancers from The Cancer Genome Atlas into four subtypes: primarily proliferative, or with collective, crypt-like or EMT invasion features. Their molecular characteristics match those of canine tumors. We showed that consensus molecular subtype 4 (mesenchymal) of human CRC should be further divided into EMT and crypt-like subtypes, which differ in TGF-β activation and mucosa-microbe content. Our canine tumors share the same pathogenic pathway as human CRCs. Dog-human integration identifies three CRC invasion patterns and improves CRC subtyping.
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Affiliation(s)
- Jin Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | - Tianfang Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | - Yanfang Sun
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | - Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | - William C Kisseberth
- Department of Veterinary Clinical Sciences, the Ohio State University College of Veterinary Medicine, Columbus, OH 43210, USA.
| | - Carolyn J Henry
- College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA.
| | - Irene Mok
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO 80525, USA.
| | - Susan E Lana
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO 80525, USA.
| | - Kevin Dobbin
- Department of Biostatistics, University of Georgia, Athens, GA 30602, USA.
| | - Nicole Northrup
- College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Elizabeth W Howerth
- College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
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Lee KH, Park HM, Son KH, Shin TJ, Cho JY. Transcriptome Signatures of Canine Mammary Gland Tumors and Its Comparison to Human Breast Cancers. Cancers (Basel) 2018; 10:cancers10090317. [PMID: 30205506 PMCID: PMC6162473 DOI: 10.3390/cancers10090317] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/27/2018] [Accepted: 09/04/2018] [Indexed: 01/22/2023] Open
Abstract
Breast cancer (BC)/mammary gland carcinoma (MGC) is the most frequently diagnosed and leading cause of cancer-related mortality in both women and canines. To better understand both canine MGC and human BC-specific genes, we sequenced RNAs obtained from eight pairs of carcinomas and adjacent normal tissues in dogs. By comprehensive transcriptome analysis, 351 differentially expressed genes (DEGs) were identified in overall canine MGCs. Based on the DEGs, comparative analysis revealed correlation existing among the three histological subtypes of canine MGC (ductal, simple, and complex) and four molecular subtypes of human BC (HER2+, ER+, ER&HER2+, and TNBC). Eight DEGs shared by all three subtypes of canine MGCs had been previously reported as cancer-associated genes in human studies. Gene ontology and pathway analyses using the identified DEGs revealed that the biological processes of cell proliferation, adhesion, and inflammatory responses are enriched in up-regulated MGC DEGs. In contrast, fatty acid homeostasis and transcription regulation involved in cell fate commitment were down-regulated in MGC DEGs. Moreover, correlations are demonstrated between upstream promoter transcripts and DEGs. Canine MGC- and subtype-enriched gene expression allows us to better understand both human BC and canine MGC, yielding new insight into the development of biomarkers and targets for both diseases.
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Affiliation(s)
- Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Hyoung-Min Park
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Keun-Hong Son
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Korea.
| | - Tae-Jin Shin
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
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Zhang M, Liu D, Tang J, Feng Y, Wang T, Dobbin KK, Schliekelman P, Zhao S. SEG - A Software Program for Finding Somatic Copy Number Alterations in Whole Genome Sequencing Data of Cancer. Comput Struct Biotechnol J 2018; 16:335-341. [PMID: 30258547 PMCID: PMC6154469 DOI: 10.1016/j.csbj.2018.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/31/2018] [Accepted: 09/01/2018] [Indexed: 01/15/2023] Open
Abstract
As next-generation sequencing technology advances and the cost decreases, whole genome sequencing (WGS) has become the preferred platform for the identification of somatic copy number alteration (CNA) events in cancer genomes. To more effectively decipher these massive sequencing data, we developed a software program named SEG, shortened from the word “segment”. SEG utilizes mapped read or fragment density for CNA discovery. To reduce CNA artifacts arisen from sequencing and mapping biases, SEG first normalizes the data by taking the log2-ratio of each tumor density against its matching normal density. SEG then uses dynamic programming to find change-points among a contiguous log2-ratio data series along a chromosome, dividing the chromosome into different segments. SEG finally identifies those segments having CNA. Our analyses with both simulated and real sequencing data indicate that SEG finds more small CNAs than other published software tools.
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Affiliation(s)
- Mucheng Zhang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
| | - Deli Liu
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
| | - Jie Tang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
| | - Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
| | - Tianfang Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
| | - Kevin K Dobbin
- Department of Biostatistics, University of Georgia, Athens, GA30602-7229, USA
| | - Paul Schliekelman
- Department of Statistics, University of Georgia, Athens, GA30602-7229, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
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Hendricks WPD, Zismann V, Sivaprakasam K, Legendre C, Poorman K, Tembe W, Perdigones N, Kiefer J, Liang W, DeLuca V, Stark M, Ruhe A, Froman R, Duesbery NS, Washington M, Aldrich J, Neff MW, Huentelman MJ, Hayward N, Brown K, Thamm D, Post G, Khanna C, Davis B, Breen M, Sekulic A, Trent JM. Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine malignant melanoma by integrated comparative genomic analysis. PLoS Genet 2018; 14:e1007589. [PMID: 30188888 PMCID: PMC6126841 DOI: 10.1371/journal.pgen.1007589] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/24/2018] [Indexed: 01/11/2023] Open
Abstract
Canine malignant melanoma, a significant cause of mortality in domestic dogs, is a powerful comparative model for human melanoma, but little is known about its genetic etiology. We mapped the genomic landscape of canine melanoma through multi-platform analysis of 37 tumors (31 mucosal, 3 acral, 2 cutaneous, and 1 uveal) and 17 matching constitutional samples including long- and short-insert whole genome sequencing, RNA sequencing, array comparative genomic hybridization, single nucleotide polymorphism array, and targeted Sanger sequencing analyses. We identified novel predominantly truncating mutations in the putative tumor suppressor gene PTPRJ in 19% of cases. No BRAF mutations were detected, but activating RAS mutations (24% of cases) occurred in conserved hotspots in all cutaneous and acral and 13% of mucosal subtypes. MDM2 amplifications (24%) and TP53 mutations (19%) were mutually exclusive. Additional low-frequency recurrent alterations were observed amidst low point mutation rates, an absence of ultraviolet light mutational signatures, and an abundance of copy number and structural alterations. Mutations that modulate cell proliferation and cell cycle control were common and highlight therapeutic axes such as MEK and MDM2 inhibition. This mutational landscape resembles that seen in BRAF wild-type and sun-shielded human melanoma subtypes. Overall, these data inform biological comparisons between canine and human melanoma while suggesting actionable targets in both species.
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Affiliation(s)
- William P. D. Hendricks
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Victoria Zismann
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Karthigayini Sivaprakasam
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- Department of Biomedical Informatics, Arizona State University, Phoenix, Arizona, United States of America
| | - Christophe Legendre
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Kelsey Poorman
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States of America
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Waibhav Tembe
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Nieves Perdigones
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Jeffrey Kiefer
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Winnie Liang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Valerie DeLuca
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- School of Life Sciences, Arizona State University, Phoenix, Arizona, United States of America
| | - Mitchell Stark
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Alison Ruhe
- Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
| | - Roe Froman
- Laboratory of Cancer and Developmental Cell Biology, Van Andel Research Institute (VARI), Grand Rapids, Michigan, United States of America
| | | | - Megan Washington
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Jessica Aldrich
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Mark W. Neff
- Program in Canine Genetics and Genomics, Van Andel Research Institute (VARI), Grand Rapids, Michigan, United States of America
| | - Matthew J. Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Nicholas Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Kevin Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Douglas Thamm
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gerald Post
- The Veterinary Cancer Center, Norwalk, Connecticut, United States of America
| | - Chand Khanna
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Barbara Davis
- Innogenics Inc., Harvard, Massachusetts, United States of America
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States of America
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States of America
| | - Alexander Sekulic
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Jeffrey M. Trent
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
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63
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Gattino F, Maniscalco L, Iussich S, Biasato I, Martano M, Morello E, Gola C, Millán Ruiz Y, Saeki N, Buracco P, Martín de las Mulas J, De Maria R. PDGFR-α, PDGFR-β, VEGFR-2 and CD117 expression in canine mammary tumours and evaluation of the in vitro effects of toceranib phosphate in neoplastic mammary cell lines. Vet Rec 2018; 183:221. [DOI: 10.1136/vr.104414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 08/21/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Selina Iussich
- Department of Veterinary Sciences; University of Turin; Turin Italy
| | - Ilaria Biasato
- Department of Veterinary Sciences; University of Turin; Turin Italy
| | - Marina Martano
- Department of Veterinary Sciences; University of Turin; Turin Italy
| | - Emanuela Morello
- Department of Veterinary Sciences; University of Turin; Turin Italy
| | - Cecilia Gola
- Department of Veterinary Sciences; University of Turin; Turin Italy
| | - Yolanda Millán Ruiz
- Department of Comparative Pathology, Veterinary Medicine Faculty; University of Córdoba; Córdoba Spain
| | - Nobuo Saeki
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo; Tokyo Japan
| | - Paolo Buracco
- Department of Veterinary Sciences; University of Turin; Turin Italy
| | - Juana Martín de las Mulas
- Department of Comparative Pathology, Veterinary Medicine Faculty; University of Córdoba; Córdoba Spain
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64
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Zhang H, Pei S, Zhou B, Wang H, Du H, Zhang D, Lin D. Establishment and characterization of a new triple-negative canine mammary cancer cell line. Tissue Cell 2018; 54:10-19. [PMID: 30309498 DOI: 10.1016/j.tice.2018.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 06/27/2018] [Accepted: 07/20/2018] [Indexed: 01/11/2023]
Abstract
Canine mammary tumor (CMT) has always been an ideal animal model for human breast cancer (HBC) research, however, there is a lack of various established CMT cell lines corresponding to HBC cell lines. This study was designed to establish a new type of CMT cell line. The primary tumor, CMT-7364, was identified as the intraductal papillary carcinoma, and showed negative immunoreactivity to estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptor-2 (HER-2) by immunohistochemistry (IHC) analysis. The CMT-7364 cell line from this primary tumor also shows a negative immunoreactivity to ER, PR, and HER-2, and was negative to epithelial cell markers and positive to mesenchymal cell markers by immunocytochemistry (ICC) analysis. This cell line, which has been stably cultured for more than 115 passages, and was characterized by epithelial origin with the expression of the epithelial antigen by ICC analysis and invasion ability by transwell analysis. In vivo, tumor mass and metastases in the lung were found after inoculating the CMT-7364 cells in the nude mice model, and the immune-complete mice model respectively. The tissues from the xenograft tumor were also negative to ER, PR, and HER-2 by IHC analysis. Thus, a novel triple negative canine mammary cancer cell line, CMT-7364, was successfully established, which could be used as a promising model for the research of immunotherapy and Epithelial-Mesenchymal Transition (EMT) mechanism of the triple-negative breast cancer both in canine and human.
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Affiliation(s)
- Hong Zhang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Shimin Pei
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Bin Zhou
- The College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang, 311300, China
| | - Huanan Wang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Hongchao Du
- The Clinical Department, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Di Zhang
- The Clinical Department, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Degui Lin
- The Clinical Department, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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65
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Collaborating genomic, transcriptomic and microbiomic alterations lead to canine extreme intestinal polyposis. Oncotarget 2018; 9:29162-29179. [PMID: 30018743 PMCID: PMC6044369 DOI: 10.18632/oncotarget.25646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/01/2018] [Indexed: 12/13/2022] Open
Abstract
Extreme intestinal polyposis in pet dogs has not yet been reported in literature. We identified a dog patient who developed numerous intestinal polyps, with the severity resembling human classic familial adenomatous polyposis (FAP), except the jejunum-ileum junction being the most polyp-dense. We investigated this dog, in comparison with 22 other dogs with spontaneous intestinal tumors but no severe polyposis, and with numerous published human cancers. We found, not APC mutation, but three other alteration pathways as likely reasons of this canine extreme polyposis. First, somatic truncation mutation W411X of FBXW7, a component of an E3 ubiquitin ligase, over-activates MYC and cell cycle-promoting network, accelerating crypt cell proliferation. Second, genes of protein trafficking and localization are downregulated, likely associated with germline mutation G406D of STAMBPL1, a K63-deubiquitinase, and MYC network activation. This inhibits epithelial apical-basolateral polarity establishment, preventing crypt cell differentiation. Third, Bacteroides uniformis, a commensal gut anaerobe, thrives and expresses abundantly thioredoxin and nitroreductase. These bacterial products could reduce oxidative stress linked to host germline mutation R51X of CYB5RL, a cytochrome b5 reductase homologue, decreasing cell death. Our work emphasizes the close collaboration of alterations across the genome, transcriptome and microbiome in promoting tumorigenesis.
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66
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Sultan F, Ganaie BA. Comparative oncology: Integrating human and veterinary medicine. Open Vet J 2018; 8:25-34. [PMID: 29445618 PMCID: PMC5806664 DOI: 10.4314/ovj.v8i1.5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 01/20/2018] [Indexed: 12/22/2022] Open
Abstract
Cancer constitutes the major health problem both in human and veterinary medicine. Comparative oncology as an integrative approach offers to learn more about naturally occurring cancers across different species. Canine models have many advantages as they experience spontaneous disease, have many genes similar to human genes, five to seven-fold accelerated ageing compared to humans, respond to treatments similarly as humans do and health care levels second only to humans. Also, the clinical trials in canines could generate more robust data, as their spontaneous nature mimics real-life situations and could be translated to humans.
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Affiliation(s)
- Faheem Sultan
- Indian Council of Medical Research, GADVASU-Ludhiana Punjab-141004, India
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67
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Nguyen F, Peña L, Ibisch C, Loussouarn D, Gama A, Rieder N, Belousov A, Campone M, Abadie J. Canine invasive mammary carcinomas as models of human breast cancer. Part 1: natural history and prognostic factors. Breast Cancer Res Treat 2017; 167:635-648. [PMID: 29086231 PMCID: PMC5807494 DOI: 10.1007/s10549-017-4548-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 11/30/2022]
Abstract
Purpose Dogs have been proposed as spontaneous animal models of human breast cancer, based on clinicopathologic similarities between canine and human mammary carcinomas. We hypothesized that a better knowledge of the natural history and prognostic factors of canine invasive mammary carcinomas would favor the design of preclinical trials using dogs as models of breast cancer. Methods The 2-year outcome of 350 female dogs with spontaneous invasive mammary carcinoma was studied. The investigated prognostic factors included age at diagnosis, pathologic tumor size, pathologic nodal stage, lymphovascular invasion, histological grade, and expression of Estrogen Receptor alpha (ERα), Progesterone Receptor, Ki-67, Human Epidermal Growth Factor Receptor 2, basal cytokeratins 5/6, and Epidermal Growth Factor Receptor. Multivariate survival analyses were performed using the Cox proportional hazards model. Results The overall survival after mastectomy was 11 months. Within 1 year post mastectomy, 41.5% of dogs (145/350) died from their mammary carcinoma. By multivariate analysis, the significant prognostic factors for overall survival included a pathologic tumor size larger than 20 mm [HR 1.47 (95% confidence interval 1.15–1.89)], a positive nodal stage [pN+, HR 1.89 (1.43–2.48)], a histological grade III [HR 1.32 (1.02–1.69)], ERα negativity [HR 1.39 (1.01–1.89)], a high Ki-67 proliferation index [HR 1.32 (1.04–1.67)], and EGFR absence [HR 1.33 (1.04–1.69)]. Conclusion The short natural history of spontaneous canine invasive mammary carcinomas and high rate of cancer-related death allow for rapid termination of preclinical investigations. The prognostic factors of invasive mammary carcinomas are remarkably similar in dogs and humans, highlighting the similarities in cancer biology between both species.
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Affiliation(s)
- Frédérique Nguyen
- Oniris, Nantes Atlantic College of Veterinary Medicine Food Science and Engineering, Animal Cancers, Models for Research in Comparative Oncology (AMaROC) Research Unit, Site de La Chantrerie, 102 Route de Gachet, CS40706, 44307, Nantes, France. .,CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.
| | - Laura Peña
- Department of Animal Medicine, Surgery and Pathology, Complutense University of Madrid, Madrid, Spain
| | - Catherine Ibisch
- Oniris, Nantes Atlantic College of Veterinary Medicine Food Science and Engineering, Animal Cancers, Models for Research in Comparative Oncology (AMaROC) Research Unit, Site de La Chantrerie, 102 Route de Gachet, CS40706, 44307, Nantes, France.,CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France
| | - Delphine Loussouarn
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,Department of Pathology, University Hospital, Nantes, France
| | - Adelina Gama
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Natascha Rieder
- Pathology and Tissue Analytics, Pharma Research & Early Development, Roche Innovation Center Munich, Munich, Germany
| | - Anton Belousov
- Pharmaceutical Sciences, Pharma Research & Early Development, Roche Innovation Center Munich, Munich, Germany
| | - Mario Campone
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,Institut de Cancérologie de l'Ouest, Angers, France
| | - Jérôme Abadie
- Oniris, Nantes Atlantic College of Veterinary Medicine Food Science and Engineering, Animal Cancers, Models for Research in Comparative Oncology (AMaROC) Research Unit, Site de La Chantrerie, 102 Route de Gachet, CS40706, 44307, Nantes, France.,CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France
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68
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Cordeiro YG, Xavier PLP, Rochetti AL, Alexandre PA, Mori CMC, Strefezzi RF, Fukumasu H. Transcriptomic profile reveals molecular events associated to focal adhesion and invasion in canine mammary gland tumour cell lines. Vet Comp Oncol 2017; 16:E89-E98. [DOI: 10.1111/vco.12339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/20/2017] [Accepted: 06/26/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Y. G. Cordeiro
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering; University of São Paulo; Pirassununga Brazil
| | - P. L. P. Xavier
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering; University of São Paulo; Pirassununga Brazil
| | - A. L. Rochetti
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering; University of São Paulo; Pirassununga Brazil
| | - P. A. Alexandre
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering; University of São Paulo; Pirassununga Brazil
| | - C. M. C. Mori
- Department of Pathology, School of Veterinary Medicine and Animal Science; University of São Paulo; São Paulo Brazil
| | - R. F. Strefezzi
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering; University of São Paulo; Pirassununga Brazil
| | - H. Fukumasu
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering; University of São Paulo; Pirassununga Brazil
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69
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Brachelente C, Cappelli K, Capomaccio S, Porcellato I, Silvestri S, Bongiovanni L, De Maria R, Verini Supplizi A, Mechelli L, Sforna M. Transcriptome Analysis of Canine Cutaneous Melanoma and Melanocytoma Reveals a Modulation of Genes Regulating Extracellular Matrix Metabolism and Cell Cycle. Sci Rep 2017; 7:6386. [PMID: 28743863 PMCID: PMC5526991 DOI: 10.1038/s41598-017-06281-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/12/2017] [Indexed: 12/16/2022] Open
Abstract
Interactions between tumor cells and tumor microenvironment are considered critical in carcinogenesis, tumor invasion and metastasis. To examine transcriptome changes and to explore the relationship with tumor microenvironment in canine cutaneous melanocytoma and melanoma, we extracted RNA from formalin-fixed, paraffin-embedded (FFPE) specimens and analyzed them by means of RNA-seq for transcriptional analysis. Melanocytoma and melanoma samples were compared to detect differential gene expressions and significant enriched pathways were explored to reveal functional relations between differentially expressed genes. The study demonstrated a differential expression of 60 genes in melanomas compared to melanocytomas. The differentially expressed genes cluster in the extracellular matrix-receptor interaction, protein digestion and absorption, focal adhesion and PI3K-Akt (phosphoinositide 3-kinase/protein kinase B) signaling pathways. Genes encoding for several collagen proteins were more commonly differentially expressed. Results of the RNA-seq were validated by qRT-PCR and protein expression of some target molecules was investigated by means of immunohistochemistry. We hypothesize that the developing melanoma actively promotes collagen metabolism and extracellular matrix remodeling as well as enhancing cell proliferation and survival contributing to disease progression and metastasis. In this study, we also detected unidentified genes in human melanoma expression studies and uncover new candidate drug targets for further testing in canine melanoma.
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Affiliation(s)
| | - Katia Cappelli
- Department of Veterinary Medicine, 06126, Perugia, Italy
| | | | | | | | - Laura Bongiovanni
- Faculty of Veterinary Medicine, 64100, Teramo, Italy
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | | | - Luca Mechelli
- Department of Veterinary Medicine, 06126, Perugia, Italy
| | - Monica Sforna
- Department of Veterinary Medicine, 06126, Perugia, Italy
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70
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Ceciliani F, Roccabianca P, Giudice C, Lecchi C. Application of post-genomic techniques in dog cancer research. MOLECULAR BIOSYSTEMS 2017; 12:2665-79. [PMID: 27345606 DOI: 10.1039/c6mb00227g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Omics techniques have been widely applied to veterinary science, although mostly on farm animal productions and infectious diseases. In canine oncology, on the contrary, the use of omics methodologies is still far behind. This review presents the most recent achievement in the application of postgenomic techniques, such as transcriptomics, proteomics, and metabolomics, to canine cancer research. The protocols to recover material suitable for omics analyses from formalin-fixed, paraffin-embedded tissues are presented, and omics applications for biomarker discovery and their potential for cancer diagnostics in veterinary medicine are highlighted.
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Affiliation(s)
- F Ceciliani
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - P Roccabianca
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - C Giudice
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - C Lecchi
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
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71
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Analysis of Gene Expression Signatures in Cancer-Associated Stroma from Canine Mammary Tumours Reveals Molecular Homology to Human Breast Carcinomas. Int J Mol Sci 2017; 18:ijms18051101. [PMID: 28531107 PMCID: PMC5455009 DOI: 10.3390/ijms18051101] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/03/2017] [Accepted: 05/17/2017] [Indexed: 12/21/2022] Open
Abstract
Cancer-associated stroma (CAS) plays a key role in cancer initiation and progression. Spontaneously occurring canine mammary carcinomas are viewed as excellent models of human breast carcinomas. Considering the importance of CAS for human cancer, it likely plays a central role in canine tumours as well. So far, however, canine CAS lacks characterisation, and it remains unclear whether the biology between CAS from canine and human tumours is comparable. In this proof-of-principle study, using laser-capture microdissection, we isolated CAS and normal stroma from 13 formalin-fixed paraffin embedded canine simple mammary carcinomas and analysed the expression of seven known human CAS markers by RT-qPCR (Reverse Transcription quantitative PCR) and validated some targets by immunohistochemistry. We found that Col1a1 (Collagen1α1), αSMA (alpha Smooth Muscle Actin), FAP (Fibroblast activation protein), PDGFRβ (Platelet-derived growth factor receptor beta), and Caveolin-1 were significantly upregulated in canine CAS, and the expression of CXCL12 (Stromal cell derived factor 1) significantly decreased, whereas MMP2 (Matrix Metalloproteinase 1) and IL6 (Interleukin 6) did not change. Our results suggest strong similarities in CAS biology in canine and human mammary carcinomas but also reveal some differences. To the best of our knowledge, this is the first report to provide a comprehensive expression analysis of the most important CAS markers in canine simple mammary carcinomas and further supports the validity of the dog as model for human cancer.
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72
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Timmermans-Sprang EPM, Gracanin A, Mol JA. Molecular Signaling of Progesterone, Growth Hormone, Wnt, and HER in Mammary Glands of Dogs, Rodents, and Humans: New Treatment Target Identification. Front Vet Sci 2017; 4:53. [PMID: 28451590 PMCID: PMC5389977 DOI: 10.3389/fvets.2017.00053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/28/2017] [Indexed: 12/21/2022] Open
Abstract
Mammary tumors are the most common form of neoplasia in the bitch. Female dogs are protected when they are spayed before the first estrus cycle, but this effect readily disappears and is already absent when dogs are spayed after the second heat. As the ovaries are removed during spaying, ovarian steroids are assumed to play an essential role in tumor development. The sensitivity toward tumor development is already present during early life, which may be caused by early mutations in stem cells during the first estrus cycles. Later on in life, tumors arise that are mostly steroid-receptor positive, although a small subset of tumors overexpressing human epidermal growth factor 2 (HER2) and some lacking estrogen receptor, progesterone receptor (PR), and HER2 (triple negative) are present, as is the situation in humans. Progesterone (P4), acting through PR, is the major steroid involved in outgrowth of mammary tissue. PRs are expressed in two forms, the progesterone receptor A (PRA) and progesterone receptor B (PRB) isoforms derived from splice variants from a single gene. The dog and the whole family of canids have only a functional PRA isoform, whereas the PRB isoform, if expressed at all, is devoid of intrinsic biological activity. In human breast cancer, overexpression of the PRA isoform is related to more aggressive carcinomas making the dog a unique model to study PRA-related mammary cancer. Administration of P4 to adult dogs results in local mammary expression of growth hormone (GH) and wing less-type mouse mammary tumor virus integration site family 4 (Wnt4). Both proteins play a role in activation of mammary stem cells. In this review, we summarize what is known on P4, GH, and Wnt signaling in canine mammary cancer, how the family of HER receptors could interact with this signaling, and what this means for comparative and translational oncological aspects of human breast cancer development.
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Affiliation(s)
| | - Ana Gracanin
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, Netherlands
| | - Jan A Mol
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, Netherlands
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73
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Santos M, Dias-Pereira P, Williams C, Lopes C, Breen M. Malignant canine mammary tumours: Preliminary genomic insights using oligonucleotide array comparative genomic hybridisation analysis. Vet J 2017; 222:68-71. [PMID: 28392153 DOI: 10.1016/j.tvjl.2017.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 03/24/2017] [Accepted: 03/25/2017] [Indexed: 10/19/2022]
Abstract
Neoplastic mammary disease in female dogs represents a major health concern for dog owners and veterinarians, but the genomic basis of the disease is poorly understood. In this study, we performed high resolution oligonucleotide array comparative genomic hybridisation (oaCGH) to assess genome wide DNA copy number changes in 10 malignant canine mammary tumours from seven female dogs, including multiple tumours collected at one time from each of three female dogs. In all but two tumours, genomic imbalances were detected, with losses being more common than gains. Canine chromosomes 9, 22, 26, 27, 34 and X were most frequently affected. Dissimilar oaCGH ratio profiles were observed in multiple tumours from the same dogs, providing preliminary evidence for probable independent pathogenesis. Analysis of adjacent samples of one tumour revealed regional differences in the number of genomic imbalances, suggesting heterogeneity within tumours.
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Affiliation(s)
- Marta Santos
- Department of Microscopy, Laboratory of Histology and Embryology, Institute of Biomedical Sciences Abel Salazar, ICBAS - UPorto, University of Porto, Porto, Portugal.
| | | | - Christina Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine North Carolina State University, Raleigh, NC, USA
| | - Carlos Lopes
- Department of Pathology and Molecular Immunology, ICBAS - UPorto, Porto, Portugal
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine North Carolina State University, Raleigh, NC, USA; Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA; Cancer Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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74
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Goebel K, Merner ND. A monograph proposing the use of canine mammary tumours as a model for the study of hereditary breast cancer susceptibility genes in humans. Vet Med Sci 2017; 3:51-62. [PMID: 28713573 PMCID: PMC5488221 DOI: 10.1002/vms3.61] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 12/12/2022] Open
Abstract
Canines are excellent models for cancer studies due to their similar physiology and genomic sequence to humans, companion status and limited intra‐breed heterogeneity. Due to their affliction to mammary cancers, canines can serve as powerful genetic models of hereditary breast cancers. Variants within known human breast cancer susceptibility genes only explain a fraction of familial cases. Thus, further discovery is necessary but such efforts have been thwarted by genetic heterogeneity. Reducing heterogeneity is key, and studying isolated human populations have helped in the endeavour. An alternative is to study dog pedigrees, since artificial selection has resulted in extreme homogeneity. Identifying the genetic predisposition to canine mammary tumours can translate to human discoveries – a strategy currently underutilized. To explore this potential, we reviewed published canine mammary tumour genetic studies and proposed benefits of next generation sequencing canine cohorts to facilitate moving beyond incremental advances.
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Affiliation(s)
- Katie Goebel
- Department of Drug Discovery and DevelopmentHarrison School of PharmacyAuburn UniversityAuburnAlabama.,College of Veterinary MedicineAuburn UniversityAuburnAlabama
| | - Nancy D Merner
- Department of Drug Discovery and DevelopmentHarrison School of PharmacyAuburn UniversityAuburnAlabama
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75
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Morris JS. Genomic and proteomic profiling for cancer diagnosis in dogs. Vet J 2016; 215:101-9. [DOI: 10.1016/j.tvjl.2016.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/01/2015] [Accepted: 01/01/2016] [Indexed: 11/25/2022]
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76
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van Steenbeek FG, Hytönen MK, Leegwater PAJ, Lohi H. The canine era: the rise of a biomedical model. Anim Genet 2016; 47:519-27. [PMID: 27324307 DOI: 10.1111/age.12460] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2016] [Indexed: 12/29/2022]
Abstract
Since the annotation of its genome a decade ago, the dog has proven to be an excellent model for the study of inherited diseases. A large variety of spontaneous simple and complex phenotypes occur in dogs, providing physiologically relevant models to corresponding human conditions. In addition, gene discovery is facilitated in clinically less heterogeneous purebred dogs with closed population structures because smaller study cohorts and fewer markers are often sufficient to expose causal variants. Here, we review the development of genomic resources from microsatellites to whole-genome sequencing and give examples of successful findings that have followed the technological progress. The increasing amount of whole-genome sequence data warrants better functional annotation of the canine genome to more effectively utilise this unique model to understand genetic contributions in morphological, behavioural and other complex traits.
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Affiliation(s)
- F G van Steenbeek
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3508 TD, Utrecht, the Netherlands.
| | - M K Hytönen
- Research Programs Unit, Molecular Neurology, Department of Veterinary Biosciences 00014, Folkhälsan Research Center, University of Helsinki, Helsinki, Finland
| | - P A J Leegwater
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3508 TD, Utrecht, the Netherlands
| | - H Lohi
- Research Programs Unit, Molecular Neurology, Department of Veterinary Biosciences 00014, Folkhälsan Research Center, University of Helsinki, Helsinki, Finland
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77
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Zhang W, Li Y, Kulik M, Tiedemann RL, Robertson KD, Dalton S, Zhao S. Nucleosome positioning changes during human embryonic stem cell differentiation. Epigenetics 2016; 11:426-37. [PMID: 27088311 PMCID: PMC4939925 DOI: 10.1080/15592294.2016.1176649] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/10/2016] [Accepted: 03/26/2016] [Indexed: 10/21/2022] Open
Abstract
Nucleosomes are the basic unit of chromatin. Nucleosome positioning (NP) plays a key role in transcriptional regulation and other biological processes. To better understand NP we used MNase-seq to investigate changes that occur as human embryonic stem cells (hESCs) transition to nascent mesoderm and then to smooth muscle cells (SMCs). Compared to differentiated cell derivatives, nucleosome occupancy at promoters and other notable genic sites, such as exon/intron junctions and adjacent regions, in hESCs shows a stronger correlation with transcript abundance and is less influenced by sequence content. Upon hESC differentiation, genes being silenced, but not genes being activated, display a substantial change in nucleosome occupancy at their promoters. Genome-wide, we detected a shift of NP to regions of higher G+C content as hESCs differentiate to SMCs. Notably, genomic regions with higher nucleosome occupancy harbor twice as many G↔C changes but fewer than half A↔T changes, compared to regions with lower nucleosome occupancy. Finally, our analysis indicates that the hESC genome is not rearranged and has a sequence mutation rate resembling normal human genomes. Our study reveals another unique feature of hESC chromatin, and sheds light on the relationship between nucleosome occupancy and sequence G+C content.
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Affiliation(s)
- Wenjuan Zhang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Yaping Li
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Michael Kulik
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Rochelle L. Tiedemann
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Keith D. Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
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78
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Zamani-Ahmadmahmudi M. Relationship between microRNA genes incidence and cancer-associated genomic regions in canine tumors: a comprehensive bioinformatics study. Funct Integr Genomics 2016; 16:143-52. [DOI: 10.1007/s10142-016-0473-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/18/2022]
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79
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Igase M, Hwang CC, Kambayashi S, Kubo M, Coffey M, Miyama TS, Baba K, Okuda M, Noguchi S, Mizuno T. Oncolytic reovirus synergizes with chemotherapeutic agents to promote cell death in canine mammary gland tumor. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2016; 80:21-31. [PMID: 26733729 PMCID: PMC4686031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 06/17/2015] [Indexed: 06/05/2023]
Abstract
The oncolytic effects of reovirus in various cancers have been proven in many clinical trials in human medicine. Oncolytic virotherapy using reovirus for canine cancers is being developed in our laboratory. The objective of this study was to examine the synergistic anti-cancer effects of a combination of reovirus and low doses of various chemotherapeutic agents on mammary gland tumors (MGTs) in dogs. The first part of this study demonstrated the efficacy of reovirus in canine MGTs in vitro and in vivo. Reovirus alone exerted significant cell death by means of caspase-dependent apoptosis in canine MGT cell lines. A single injection of reovirus impeded growth of canine MGT tumors in xenografted mice, but was insufficient to induce complete tumor regression. The second part of this study highlighted the anti-tumor effects of reovirus in combination with low doses of paclitaxel, carboplatin, gemcitabine, or toceranib. Enhanced synergistic activity was observed in the MGT cell line treated concomitantly with reovirus and in all the chemotherapeutic agents except toceranib. In addition, combining reovirus with paclitaxel or gemcitabine at half dosage of half maximal inhibitory concentration (IC50) enhanced cytotoxicity by activating caspase 3. Our data suggest that the combination of reovirus and low dose chemotherapeutic agents provides an attractive option in canine cancer therapy.
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Affiliation(s)
- Masaya Igase
- Laboratory of Molecular Diagnostics and Therapeutics (Igase, Noguchi, Mizuno), Laboratory of Veterinary Internal Medicine (Kambayashi, Miyama, Baba, Okuda), and Laboratory of Veterinary Pathology (Kubo), Joint Faculty of Veterinary Medicine and Laboratory of Molecular Diagnostics and Therapeutics (Hwang) and Biomedical Science Center for Translational Research (Okuda, Noguchi, Mizuno), United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan; Oncolytics Biotech Inc., Calgary, Alberta (Coffey)
| | - Chung Chew Hwang
- Laboratory of Molecular Diagnostics and Therapeutics (Igase, Noguchi, Mizuno), Laboratory of Veterinary Internal Medicine (Kambayashi, Miyama, Baba, Okuda), and Laboratory of Veterinary Pathology (Kubo), Joint Faculty of Veterinary Medicine and Laboratory of Molecular Diagnostics and Therapeutics (Hwang) and Biomedical Science Center for Translational Research (Okuda, Noguchi, Mizuno), United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan; Oncolytics Biotech Inc., Calgary, Alberta (Coffey)
| | - Satoshi Kambayashi
- Laboratory of Molecular Diagnostics and Therapeutics (Igase, Noguchi, Mizuno), Laboratory of Veterinary Internal Medicine (Kambayashi, Miyama, Baba, Okuda), and Laboratory of Veterinary Pathology (Kubo), Joint Faculty of Veterinary Medicine and Laboratory of Molecular Diagnostics and Therapeutics (Hwang) and Biomedical Science Center for Translational Research (Okuda, Noguchi, Mizuno), United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan; Oncolytics Biotech Inc., Calgary, Alberta (Coffey)
| | - Masato Kubo
- Laboratory of Molecular Diagnostics and Therapeutics (Igase, Noguchi, Mizuno), Laboratory of Veterinary Internal Medicine (Kambayashi, Miyama, Baba, Okuda), and Laboratory of Veterinary Pathology (Kubo), Joint Faculty of Veterinary Medicine and Laboratory of Molecular Diagnostics and Therapeutics (Hwang) and Biomedical Science Center for Translational Research (Okuda, Noguchi, Mizuno), United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan; Oncolytics Biotech Inc., Calgary, Alberta (Coffey)
| | - Matt Coffey
- Laboratory of Molecular Diagnostics and Therapeutics (Igase, Noguchi, Mizuno), Laboratory of Veterinary Internal Medicine (Kambayashi, Miyama, Baba, Okuda), and Laboratory of Veterinary Pathology (Kubo), Joint Faculty of Veterinary Medicine and Laboratory of Molecular Diagnostics and Therapeutics (Hwang) and Biomedical Science Center for Translational Research (Okuda, Noguchi, Mizuno), United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan; Oncolytics Biotech Inc., Calgary, Alberta (Coffey)
| | - Takako Shimokawa Miyama
- Laboratory of Molecular Diagnostics and Therapeutics (Igase, Noguchi, Mizuno), Laboratory of Veterinary Internal Medicine (Kambayashi, Miyama, Baba, Okuda), and Laboratory of Veterinary Pathology (Kubo), Joint Faculty of Veterinary Medicine and Laboratory of Molecular Diagnostics and Therapeutics (Hwang) and Biomedical Science Center for Translational Research (Okuda, Noguchi, Mizuno), United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan; Oncolytics Biotech Inc., Calgary, Alberta (Coffey)
| | - Kenji Baba
- Laboratory of Molecular Diagnostics and Therapeutics (Igase, Noguchi, Mizuno), Laboratory of Veterinary Internal Medicine (Kambayashi, Miyama, Baba, Okuda), and Laboratory of Veterinary Pathology (Kubo), Joint Faculty of Veterinary Medicine and Laboratory of Molecular Diagnostics and Therapeutics (Hwang) and Biomedical Science Center for Translational Research (Okuda, Noguchi, Mizuno), United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan; Oncolytics Biotech Inc., Calgary, Alberta (Coffey)
| | - Masaru Okuda
- Laboratory of Molecular Diagnostics and Therapeutics (Igase, Noguchi, Mizuno), Laboratory of Veterinary Internal Medicine (Kambayashi, Miyama, Baba, Okuda), and Laboratory of Veterinary Pathology (Kubo), Joint Faculty of Veterinary Medicine and Laboratory of Molecular Diagnostics and Therapeutics (Hwang) and Biomedical Science Center for Translational Research (Okuda, Noguchi, Mizuno), United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan; Oncolytics Biotech Inc., Calgary, Alberta (Coffey)
| | - Shunsuke Noguchi
- Laboratory of Molecular Diagnostics and Therapeutics (Igase, Noguchi, Mizuno), Laboratory of Veterinary Internal Medicine (Kambayashi, Miyama, Baba, Okuda), and Laboratory of Veterinary Pathology (Kubo), Joint Faculty of Veterinary Medicine and Laboratory of Molecular Diagnostics and Therapeutics (Hwang) and Biomedical Science Center for Translational Research (Okuda, Noguchi, Mizuno), United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan; Oncolytics Biotech Inc., Calgary, Alberta (Coffey)
| | - Takuya Mizuno
- Laboratory of Molecular Diagnostics and Therapeutics (Igase, Noguchi, Mizuno), Laboratory of Veterinary Internal Medicine (Kambayashi, Miyama, Baba, Okuda), and Laboratory of Veterinary Pathology (Kubo), Joint Faculty of Veterinary Medicine and Laboratory of Molecular Diagnostics and Therapeutics (Hwang) and Biomedical Science Center for Translational Research (Okuda, Noguchi, Mizuno), United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan; Oncolytics Biotech Inc., Calgary, Alberta (Coffey)
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80
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Jaillardon L, Abadie J, Godard T, Campone M, Loussouarn D, Siliart B, Nguyen F. The dog as a naturally-occurring model for insulin-like growth factor type 1 receptor-overexpressing breast cancer: an observational cohort study. BMC Cancer 2015; 15:664. [PMID: 26449867 PMCID: PMC4598970 DOI: 10.1186/s12885-015-1670-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 10/01/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Dogs spontaneously develop invasive mammary carcinoma with a high prevalence of the triple-negative (TN) subtype (lack of ER-Estrogen Receptor and PR-Progesterone Receptor expression, lack of HER2-Human Epidermal Growth Factor Receptor 2 overexpression), making this animal model relevant for investigating new therapeutic pathways. Insulin-like growth factor Type-1 receptor (IGF1R) is frequently overexpressed in primary human breast cancers, with a growing role in the TN phenotype. The purpose of this study was to investigate the Dog as a candidate model for IGF1R-overexpressing mammary carcinoma. METHODS 150 bitches with canine mammary carcinoma (CMC) and a known 2-year follow-up were retrospectively included. IGF1R expression was assessed by immunohistochemistry (IHC) using a similar scoring system as for HER2 in breast cancer. The prognostic value of the IGF1R expression was assessed in terms of overall and specific survival as well as disease-free interval (DFI). RESULTS 47 CMC (31 %) were classified as luminal and 103 (69 %) as triple-negative (TN-CMC). 41 % of CMC overexpressed IGF1R (IHC score 3+) of which 76 % were TN-CMC and 62 % grade III. IGF1R overexpression was associated with aggressive features including lymphovascular invasion, histological grade III, low ER expression and the TN phenotype. Univariate and multivariate analyses revealed that IGF1R overexpression was associated with shorter overall and specific survivals and shorter DFI in TN-CMC. CONCLUSIONS IGF1R overexpression is common and related to a poor outcome in canine invasive mammary carcinoma, particularly in the triple negative subtype, as in human breast cancer. Preclinical studies using the Dog as a spontaneous animal model could be considered to investigate new therapies targeting IGF1R in triple-negative breast cancer.
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Affiliation(s)
- Laetitia Jaillardon
- Oniris, Université Nantes-Angers-Le Mans, Department of Human Health, Biomedical Research and Animal Models, AMaROC Unit and LDHvet laboratory, Nantes Atlantic College of Veterinary Medicine, Food Science and Engineering, Site de la Chantrerie, Route de Gachet, Nantes, F-44307, France.
| | - Jérome Abadie
- Oniris, Université Nantes-Angers-Le Mans, Department of Human Health, Biomedical Research and Animal Models, AMaROC Unit and LDHvet laboratory, Nantes Atlantic College of Veterinary Medicine, Food Science and Engineering, Site de la Chantrerie, Route de Gachet, Nantes, F-44307, France.
| | - Tiffanie Godard
- Oniris, Université Nantes-Angers-Le Mans, Department of Human Health, Biomedical Research and Animal Models, AMaROC Unit and LDHvet laboratory, Nantes Atlantic College of Veterinary Medicine, Food Science and Engineering, Site de la Chantrerie, Route de Gachet, Nantes, F-44307, France.
| | - Mario Campone
- Institut de Cancérologie de l'Ouest, Boulevard Jacques Monod Saint Herblain-Nantes cedex, Centre de Recherche du Cancer Nantes-Angers, UMR-INSERM U892/CNRS 6299, Nantes, F-44805, France.
| | - Delphine Loussouarn
- Hopital G&R Laënnec, Boulevard Jacques Monod, Saint Herblain-Nantes cedex, Nantes, F-44093, France.
| | - Brigitte Siliart
- Oniris, Université Nantes-Angers-Le Mans, Department of Human Health, Biomedical Research and Animal Models, AMaROC Unit and LDHvet laboratory, Nantes Atlantic College of Veterinary Medicine, Food Science and Engineering, Site de la Chantrerie, Route de Gachet, Nantes, F-44307, France.
| | - Frédérique Nguyen
- Oniris, Université Nantes-Angers-Le Mans, Department of Human Health, Biomedical Research and Animal Models, AMaROC Unit and LDHvet laboratory, Nantes Atlantic College of Veterinary Medicine, Food Science and Engineering, Site de la Chantrerie, Route de Gachet, Nantes, F-44307, France.
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81
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Aflatoxins ingestion and canine mammary tumors: There is an association? Food Chem Toxicol 2015; 84:74-8. [DOI: 10.1016/j.fct.2015.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 07/30/2015] [Accepted: 08/03/2015] [Indexed: 01/29/2023]
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82
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Okada S, Furuya M, Takenaka S, Fukui A, Matsubayashi M, Tani H, Sasai K. Localization of heat shock protein 110 in canine mammary gland tumors. Vet Immunol Immunopathol 2015; 167:139-46. [DOI: 10.1016/j.vetimm.2015.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 12/31/2022]
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83
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Timmermans-Sprang EPM, Gracanin A, Mol JA. High basal Wnt signaling is further induced by PI3K/mTor inhibition but sensitive to cSRC inhibition in mammary carcinoma cell lines with HER2/3 overexpression. BMC Cancer 2015. [PMID: 26205886 PMCID: PMC4513708 DOI: 10.1186/s12885-015-1544-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Elevated basal, ligand-independent, Wnt signaling in some canine breast cancer cells is not caused by classical mutations in APC, β-Catenin or GSK3β but, at least partially, by enhanced LEF1 expression. We examined the expression and function of EGFR/HER-regulated pathways on the ligand-independent Wnt signaling. Methods Twelve canine mammary tumor cell lines with previously reported differential basal Wnt activity were used. The expression levels of genes related to EGF-signaling were analyzed by cluster analysis. Cell lines with a combined overexpression of EGF-related genes and enhanced basal Wnt activity were treated with PI3K/mTor or cSRC inhibitors or transfected with a construct expressing wild-type PTEN. Subsequently, effects were measured on Wnt activity, cell proliferation, gene expression and protein level. Results High basal Wnt/LEF1 activity was associated with overexpression of HER2/3, ID1, ID2, RAC1 and HSP90 together with low to absent cMET and PTEN mRNA expression, suggesting a connection between Wnt- and HER-signaling pathways. Inhibition of the HER-regulated PI3K/mTor pathway using the dual PI3K/mTor inhibitor BEZ235 or the mTor inhibitor Everolimus® resulted in reduced cell proliferation. In the cell line with high basal Wnt activity, however, an unexpected further increased Wnt activity was found that could be greatly reduced after inhibition of the HER-regulated cSRC activity. Inhibition of the PI3K/mTor pathway was associated with enhanced expression of β-Catenin, Axin2, MUC1, cMET, EGFR and HER2 and a somewhat increased β-Catenin protein content, whereas cSRC inhibition was associated with slightly enhanced HER3 and SLUG mRNA expression. A high protein expression of HER3 was found only in a cell line with high basal Wnt activity. Conclusions High basal Wnt activity in some mammary cancer cell lines is associated with overexpression of HER-receptor related genes and HER3 protein, and the absence of PTEN. Inhibition of the PI3K/mTor pathway further stimulated, however, canonical Wnt signaling, whereas the inhibitory effect with the cSRC inhibitor Src-I1 on the Wnt activity further suggested a connection between Wnt and HER2/3-signaling.
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Affiliation(s)
- Elpetra P M Timmermans-Sprang
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584, CM, Utrecht, The Netherlands.
| | - Ana Gracanin
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584, CM, Utrecht, The Netherlands.
| | - Jan A Mol
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584, CM, Utrecht, The Netherlands.
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84
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Tierny D, Serres F, Segaoula Z, Bemelmans I, Bouchaert E, Pétain A, Brel V, Couffin S, Marchal T, Nguyen L, Thuru X, Ferré P, Guilbaud N, Gomes B. Phase I Clinical Pharmacology Study of F14512, a New Polyamine-Vectorized Anticancer Drug, in Naturally Occurring Canine Lymphoma. Clin Cancer Res 2015; 21:5314-23. [PMID: 26169968 DOI: 10.1158/1078-0432.ccr-14-3174] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 07/04/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE F14512 is a new topoisomerase II inhibitor containing a spermine moiety that facilitates selective uptake by tumor cells and increases topoisomerase II poisoning. F14512 is currently in a phase I/II clinical trial in patients with acute myeloid leukemia. The aim of this study was to investigate F14512 potential in a new clinical indication. Because of the many similarities between human and dog lymphomas, we sought to determine the tolerance, efficacy, pharmacokinetic/pharmacodynamic (PK/PD) relationship of F14512 in this indication, and potential biomarkers that could be translated into human trials. EXPERIMENTAL DESIGN Twenty-three dogs with stage III-IV naturally occurring lymphomas were enrolled in the phase I dose-escalation trial, which consisted of three cycles of F14512 i.v. injections. Endpoints included safety and therapeutic efficacy. Serial blood samples and tumor biopsies were obtained for PK/PD and biomarker studies. RESULTS Five dose levels were evaluated to determine the recommended dose. F14512 was well tolerated, with the expected dose-dependent hematologic toxicity. F14512 induced an early decrease of tumoral lymph node cells, and a high response rate of 91% (21/23) with 10 complete responses, 11 partial responses, 1 stable disease, and 1 progressive disease. Phosphorylation of histone H2AX was studied as a potential PD biomarker of F14512. CONCLUSIONS This trial demonstrated that F14512 can be safely administered to dogs with lymphoma resulting in strong therapeutic efficacy. Additional evaluation of F14512 is needed to compare its efficacy with standards of care in dogs, and to translate biomarker and efficacy findings into clinical trials in humans.
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Affiliation(s)
- Dominique Tierny
- Oncovet Clinical Research, SIRIC ONCOLille, Avenue Paul Langevin, Villeneuve d'Ascq, France
| | - François Serres
- Oncovet Clinical Research, SIRIC ONCOLille, Avenue Paul Langevin, Villeneuve d'Ascq, France
| | - Zacharie Segaoula
- Oncovet Clinical Research, SIRIC ONCOLille, Avenue Paul Langevin, Villeneuve d'Ascq, France. Inserm, UMR-S1172, Jean Pierre Aubert Research Centre, Lille, France. Université de Lille, Lille, France
| | - Ingrid Bemelmans
- Oncovet Clinical Research, SIRIC ONCOLille, Avenue Paul Langevin, Villeneuve d'Ascq, France
| | - Emmanuel Bouchaert
- Oncovet Clinical Research, SIRIC ONCOLille, Avenue Paul Langevin, Villeneuve d'Ascq, France
| | - Aurélie Pétain
- Institut de Recherche Pierre Fabre, Oncology Pharmacokinetics, Toulouse, France
| | - Viviane Brel
- Institut de Recherche Pierre Fabre, Experimental Oncology Research Center, Toulouse, France
| | - Stéphane Couffin
- Institut de Recherche Pierre Fabre, Pharmacokinetics, Bel Air de Campans, Castres, France
| | - Thierry Marchal
- UPSP 2011-03-101, Interaction Cellules Environnement, Campus Vétérinaire de VetAgro-Sup, Marcy l'Etoile, France
| | - Laurent Nguyen
- Institut de Recherche Pierre Fabre, Oncology Pharmacokinetics, Toulouse, France
| | - Xavier Thuru
- Inserm, UMR-S1172, Jean Pierre Aubert Research Centre, Lille, France. Université de Lille, Lille, France
| | - Pierre Ferré
- Institut de Recherche Pierre Fabre, Oncology Pharmacokinetics, Toulouse, France
| | - Nicolas Guilbaud
- Institut de Recherche Pierre Fabre, Experimental Oncology Research Center, Toulouse, France
| | - Bruno Gomes
- Institut de Recherche Pierre Fabre, Experimental Oncology Research Center, Toulouse, France.
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85
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Prevalence of the Prefoldin Subunit 5 Gene Deletion in Canine Mammary Tumors. PLoS One 2015; 10:e0131280. [PMID: 26132936 PMCID: PMC4489437 DOI: 10.1371/journal.pone.0131280] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/01/2015] [Indexed: 01/07/2023] Open
Abstract
Background A somatic deletion at the proximal end of canine chromosome 27 (CFA27) was recently reported in 50% of malignant mammary tumors. This region harbours the tumor suppressor gene prefoldin subunit 5 (PFDN5) and the deletion correlated with a higher Ki-67 score. PFDN5 has been described to repress c-MYC and is, therefore, a candidate tumor-suppressor and cancer-driver gene in canine mammary cancer. Aim of this study was to confirm the recurrent deletion in a larger number of tumors. Methods Droplet digital PCR for PFDN5 was performed in DNA from 102 malignant, 40 benign mammary tumors/dysplasias, 11 non-neoplastic mammary tissues and each corresponding genomic DNA from leukocytes. The copy number of PFDN5 was normalized to a reference amplicon on canine chromosome 32 (CFA32). Z-scores were calculated, based on Gaussian distributed normalized PFDN5 copy numbers of the leukocyte DNA. Z-scores ≤ -3.0 in tissue were considered as being indicative of the PFDN5 deletion and called as such. The Ki-67 proliferation index was assessed in a subset of 79 tissue samples by immunohistochemistry. Results The deletion was confirmed in 24% of all malignant tumors, detected in only 7.5% of the benign tumors and was not present in any normal mammary tissue sample. The subgroup of solid carcinomas (n = 9) showed the highest frequency of the deletion (67%) and those malignomas without microscopical high fraction of benign tissue (n = 71) had a 32% frequency (p<0.01 vs. benign samples). The Ki-67 score was found to be significantly higher (p<0.05) in the PFDN5-deleted group compared to malignant tumors without the deletion. Conclusions A somatic deletion of the PFDN5 gene is recurrently present in canine mammary cancer, supporting a potential role in carcinogenesis. The association of this deletion with higher Ki-67 indicates an increased proliferation rate and thus a link to tumor aggressiveness can be hypothesized. The confirmation of earlier results warrants further studies on PFDN5 as cancer-driver gene.
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86
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Audfray A, Beldjoudi M, Breiman A, Hurbin A, Boos I, Unverzagt C, Bouras M, Lantuejoul S, Coll JL, Varrot A, Le Pendu J, Busser B, Imberty A. A recombinant fungal lectin for labeling truncated glycans on human cancer cells. PLoS One 2015; 10:e0128190. [PMID: 26042789 PMCID: PMC4456360 DOI: 10.1371/journal.pone.0128190] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/24/2015] [Indexed: 01/16/2023] Open
Abstract
Cell surface glycoconjugates present alterations of their structures in chronic diseases and distinct oligosaccharide epitopes have been associated with cancer. Among them, truncated glycans present terminal non-reducing β-N-acetylglucosamine (GlcNAc) residues that are rare on healthy tissues. Lectins from unconventional sources such as fungi or algi provide novel markers that bind specifically to such epitopes, but their availability may be challenging. A GlcNAc-binding lectin from the fruiting body of the fungus Psathyrella velutina (PVL) has been produced in good yield in bacterial culture. A strong specificity for terminal GlcNAc residues was evidenced by glycan array. Affinity values obtained by microcalorimetry and surface plasmon resonance demonstrated a micromolar affinity for GlcNAcβ1-3Gal epitopes and for biantennary N-glycans with GlcNAcβ1-2Man capped branches. Crystal structure of PVL complexed with GlcNAcβ1-3Gal established the structural basis of the specificity. Labeling of several types of cancer cells and use of inhibitors of glycan metabolism indicated that rPVL binds to terminal GlcNAc but also to sialic acid (Neu5Ac). Analysis of glycosyltransferase expression confirmed the higher amount of GlcNAc present on cancer cells. rPVL binding is specific to cancer tissue and weak or no labeling is observed for healthy ones, except for stomach glands that present unique αGlcNAc-presenting mucins. In lung, breast and colon carcinomas, a clear delineation could be observed between cancer regions and surrounding healthy tissues. PVL is therefore a useful tool for labeling agalacto-glycans in cancer or other diseases.
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Affiliation(s)
- Aymeric Audfray
- CERMAV, UPR5301, CNRS, University Grenoble Alpes, 38041 Grenoble, France
| | - Mona Beldjoudi
- IAB, University Grenoble Alpes, F-38000 Grenoble, France
- INSERM U823, IAB, F-38000 Grenoble, France
- University El Hadj Lakhdar, 05000 Batna, Algeria
| | - Adrien Breiman
- INSERM, UMR892, 44007 Nantes, France
- CNRS, UMR6299, 44007 Nantes, France
- IRS UN, University of Nantes, Nantes, France
- Nantes University Hospital, 44000 Nantes, France
| | - Amandine Hurbin
- IAB, University Grenoble Alpes, F-38000 Grenoble, France
- INSERM U823, IAB, F-38000 Grenoble, France
| | - Irene Boos
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Carlo Unverzagt
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440 Bayreuth, Germany
| | | | - Sylvie Lantuejoul
- IAB, University Grenoble Alpes, F-38000 Grenoble, France
- INSERM U823, IAB, F-38000 Grenoble, France
- Grenoble University Hospital, F-38000 Grenoble, France
| | - Jean-Luc Coll
- IAB, University Grenoble Alpes, F-38000 Grenoble, France
- INSERM U823, IAB, F-38000 Grenoble, France
| | - Annabelle Varrot
- CERMAV, UPR5301, CNRS, University Grenoble Alpes, 38041 Grenoble, France
| | | | - Benoit Busser
- IAB, University Grenoble Alpes, F-38000 Grenoble, France
- INSERM U823, IAB, F-38000 Grenoble, France
- Grenoble University Hospital, F-38000 Grenoble, France
- * E-mail: (JLP); (BB); (AI)
| | - Anne Imberty
- CERMAV, UPR5301, CNRS, University Grenoble Alpes, 38041 Grenoble, France
- * E-mail: (JLP); (BB); (AI)
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87
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Liu D, Xiong H, Ellis AE, Northrup NC, Dobbin KK, Shin DM, Zhao S. Canine spontaneous head and neck squamous cell carcinomas represent their human counterparts at the molecular level. PLoS Genet 2015; 11:e1005277. [PMID: 26030765 PMCID: PMC4452692 DOI: 10.1371/journal.pgen.1005277] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/14/2015] [Indexed: 01/15/2023] Open
Abstract
Spontaneous canine head and neck squamous cell carcinoma (HNSCC) represents an excellent model of human HNSCC but is greatly understudied. To better understand and utilize this valuable resource, we performed a pilot study that represents its first genome-wide characterization by investigating 12 canine HNSCC cases, of which 9 are oral, via high density array comparative genomic hybridization and RNA-seq. The analyses reveal that these canine cancers recapitulate many molecular features of human HNSCC. These include analogous genomic copy number abnormality landscapes and sequence mutation patterns, recurrent alteration of known HNSCC genes and pathways (e.g., cell cycle, PI3K/AKT signaling), and comparably extensive heterogeneity. Amplification or overexpression of protein kinase genes, matrix metalloproteinase genes, and epithelial-mesenchymal transition genes TWIST1 and SNAI1 are also prominent in these canine tumors. This pilot study, along with a rapidly growing body of literature on canine cancer, reemphasizes the potential value of spontaneous canine cancers in HNSCC basic and translational research.
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Affiliation(s)
- Deli Liu
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Huan Xiong
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Angela E. Ellis
- College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Nicole C. Northrup
- College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Kevin K. Dobbin
- Department of Biostatistics, University of Georgia, Athens, Georgia, United States of America
| | - Dong M. Shin
- Winship Cancer Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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88
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Chang Z, Li G, Liu J, Zhang Y, Ashby C, Liu D, Cramer CL, Huang X. Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome Biol 2015; 16:30. [PMID: 25723335 PMCID: PMC4342890 DOI: 10.1186/s13059-015-0596-2] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 01/23/2015] [Indexed: 11/24/2022] Open
Abstract
We present a new de novo transcriptome assembler, Bridger, which takes advantage of techniques employed in Cufflinks to overcome limitations of the existing de novo assemblers. When tested on dog, human, and mouse RNA-seq data, Bridger assembled more full-length reference transcripts while reporting considerably fewer candidate transcripts, hence greatly reducing false positive transcripts in comparison with the state-of-the-art assemblers. It runs substantially faster and requires much less memory space than most assemblers. More interestingly, Bridger reaches a comparable level of sensitivity and accuracy with Cufflinks. Bridger is available at https://sourceforge.net/projects/rnaseqassembly/files/?source=navbar.
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89
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Daly JA, Mortlock SA, Taylor RM, Williamson P. Cluster Analysis of Tumor Suppressor Genes in Canine Leukocytes Identifies Activation State. Bioinform Biol Insights 2015; 9:59-67. [PMID: 27478369 PMCID: PMC4955975 DOI: 10.4137/bbi.s30523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 05/23/2016] [Accepted: 05/29/2016] [Indexed: 02/07/2023] Open
Abstract
Cells of the immune system undergo activation and subsequent proliferation in the normal course of an immune response. Infrequently, the molecular and cellular events that underlie the mechanisms of proliferation are dysregulated and may lead to oncogenesis, leading to tumor formation. The most common forms of immunological cancers are lymphomas, which in dogs account for 8%–20% of all cancers, affecting up to 1.2% of the dog population. Key genes involved in negatively regulating proliferation of lymphocytes include a group classified as tumor suppressor genes (TSGs). These genes are also known to be associated with progression of lymphoma in humans, mice, and dogs and are potential candidates for pathological grading and diagnosis. The aim of the present study was to analyze TSG profiles in stimulated leukocytes from dogs to identify genes that discriminate an activated phenotype. A total of 554 TSGs and three gene set collections were analyzed from microarray data. Cluster analysis of three subsets of genes discriminated between stimulated and unstimulated cells. These included 20 most upregulated and downregulated TSGs, TSG in hallmark gene sets significantly enriched in active cells, and a selection of candidate TSGs, p15 (CDKN2B), p18 (CDKN2C), p19 (CDKN1A), p21 (CDKN2A), p27 (CDKN1B), and p53 (TP53) in the third set. Analysis of two subsets suggested that these genes or a subset of these genes may be used as a specialized PCR set for additional analysis.
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Affiliation(s)
- Julie-Anne Daly
- Faculty of Veterinary Science, The University of Sydney, Camperdown, NSW, Australia
| | - Sally-Anne Mortlock
- Faculty of Veterinary Science, The University of Sydney, Camperdown, NSW, Australia
| | - Rosanne M Taylor
- Faculty of Veterinary Science, The University of Sydney, Camperdown, NSW, Australia
| | - Peter Williamson
- Faculty of Veterinary Science, The University of Sydney, Camperdown, NSW, Australia
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