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Mazzone E, Aresu L. Comprehensive Analysis of Microsatellite Instability in Canine Cancers: Implications for Comparative Oncology and Personalized Veterinary Medicine. Animals (Basel) 2024; 14:2484. [PMID: 39272269 PMCID: PMC11394029 DOI: 10.3390/ani14172484] [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: 07/01/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024] Open
Abstract
Microsatellite instability (MSI) is a crucial feature in cancer biology, yet its prevalence and significance in canine cancers remain largely unexplored. This study conducted a comprehensive analysis of MSI across 10 distinct canine cancer histotypes using whole-exome sequencing data from 692 tumor-normal sample pairs. MSI was detected in 64% of tumors, with prevalence varying significantly among cancer types. B-cell lymphomas exhibited the highest MSI burden, contrasting with human studies. A novel "MSI-burden" score was developed, correlating significantly with tumor mutational burden. MSI-high (MSI-H) tumors showed elevated somatic mutation counts compared to MSI-low and microsatellite stable tumors. The study identified 3632 recurrent MSI-affected genomic regions across cancer types. Notably, seven of the ten cancer types exhibited MSI-H tumors, with prevalence ranging from 1.5% in melanomas to 37% in B-cell lymphomas. These findings highlight the potential importance of MSI in canine cancer biology and suggest opportunities for targeted therapies, particularly immunotherapies. The high prevalence of MSI in canine cancers, especially in B-cell lymphomas, warrants further investigation into its mechanistic role and potential as a biomarker for prognosis and treatment response.
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Affiliation(s)
- Eugenio Mazzone
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Italy
| | - Luca Aresu
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Italy
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2
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Cahill JA, Smith LA, Gottipati S, Torabi TS, Graim K. Bringing the Genomic Revolution to Comparative Oncology: Human and Dog Cancers. Annu Rev Biomed Data Sci 2024; 7:107-129. [PMID: 38648188 PMCID: PMC11343685 DOI: 10.1146/annurev-biodatasci-102423-111936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Dogs are humanity's oldest friend, the first species we domesticated 20,000-40,000 years ago. In this unequaled collaboration, dogs have inadvertently but serendipitously been molded into a potent human cancer model. Unlike many common model species, dogs are raised in the same environment as humans and present with spontaneous tumors with human-like comorbidities, immunocompetency, and heterogeneity. In breast, bladder, blood, and several pediatric cancers, in-depth profiling of dog and human tumors has established the benefits of the dog model. In addition to this clinical and molecular similarity, veterinary studies indicate that domestic dogs have relatively high tumor incidence rates. As a result, there are a plethora of data for analysis, the statistical power of which is bolstered by substantial breed-specific variability. As such, dog tumors provide a unique opportunity to interrogate the molecular factors underpinning cancer and facilitate the modeling of new therapeutic targets. This review discusses the emerging field of comparative oncology, how it complements human and rodent cancer studies, and where challenges remain, given the rapid proliferation of genomic resources. Increasingly, it appears that human's best friend is becoming an irreplaceable component of oncology research.
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Affiliation(s)
- James A Cahill
- University of Florida Genetics Institute, University of Florida, Gainesville, Florida, USA;
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - Leslie A Smith
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Soumya Gottipati
- Department of Computer Science, Princeton University, Princeton, New Jersey, USA
| | - Tina Salehi Torabi
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Kiley Graim
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
- University of Florida Health Cancer Center, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, Florida, USA;
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Gherman LM, Chiroi P, Nuţu A, Bica C, Berindan-Neagoe I. Profiling canine mammary tumors: A potential model for studying human breast cancer. Vet J 2024; 303:106055. [PMID: 38097103 DOI: 10.1016/j.tvjl.2023.106055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
Despite all clinical progress recorded in the last decades, human breast cancer (HBC) remains a major challenge worldwide both in terms of its incidence and its management. Canine mammary tumors (CMTs) share similarities with HBC and represent an alternative model for HBC. The utility of the canine model in studying HBC relies on their common features, include spontaneous development, subtype classification, mutational profile, alterations in gene expression profile, and incidence/prevalence. This review describes the similarities between CMTs and HBC regarding genomic landscape, microRNA expression alteration, methylation, and metabolomic changes occurring during mammary gland carcinogenesis. The primary purpose of this review is to highlight the advantages of using the canine model as a translational animal model for HBC research and to investigate the challenges and limitations of this approach.
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Affiliation(s)
- Luciana-Madalina Gherman
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; Experimental Center of Iuliu Hatieganu University of Medicine and Pharmacy Cluj-Napoca, 400349 Cluj-Napoca, Romania
| | - Paul Chiroi
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania
| | - Andreea Nuţu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania
| | - Cecilia Bica
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania
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Chen H, Shu J, Maley CC, Liu L. A Mouse-Specific Model to Detect Genes under Selection in Tumors. Cancers (Basel) 2023; 15:5156. [PMID: 37958330 PMCID: PMC10647215 DOI: 10.3390/cancers15215156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
The mouse is a widely used model organism in cancer research. However, no computational methods exist to identify cancer driver genes in mice due to a lack of labeled training data. To address this knowledge gap, we adapted the GUST (Genes Under Selection in Tumors) model, originally trained on human exomes, to mouse exomes via transfer learning. The resulting tool, called GUST-mouse, can estimate long-term and short-term evolutionary selection in mouse tumors, and distinguish between oncogenes, tumor suppressor genes, and passenger genes using high-throughput sequencing data. We applied GUST-mouse to analyze 65 exomes of mouse primary breast cancer models and 17 exomes of mouse leukemia models. Comparing the predictions between cancer types and between human and mouse tumors revealed common and unique driver genes. The GUST-mouse method is available as an open-source R package on github.
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Affiliation(s)
- Hai Chen
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (H.C.); (J.S.)
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA;
| | - Jingmin Shu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (H.C.); (J.S.)
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA;
| | - Carlo C. Maley
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA;
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ 85281, USA
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (H.C.); (J.S.)
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA;
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ 85281, USA
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Yang IS, Jang I, Yang JO, Choi J, Kim MS, Kim KK, Seung BJ, Cheong JH, Sur JH, Nam H, Lee B, Kim J, Kim S. CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris). BMC Genomics 2023; 24:613. [PMID: 37828501 PMCID: PMC10571338 DOI: 10.1186/s12864-023-09655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete. RESULTS We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns. CONCLUSIONS CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/ .
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Affiliation(s)
- In Seok Yang
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Insu Jang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Jin Ok Yang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Jinhyuk Choi
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Min-Seo Kim
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Ka-Kyung Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Byung-Joon Seung
- Department of Veterinary Pathology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Korea
| | - Jae-Ho Cheong
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Jung-Hyang Sur
- Department of Veterinary Pathology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Korea
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Korea
| | - Byungwook Lee
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea.
| | - Junho Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea.
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Watson J, Wang T, Ho KL, Feng Y, Mahawan T, Dobbin KK, Zhao S. Human basal-like breast cancer is represented by one of the two mammary tumor subtypes in dogs. Breast Cancer Res 2023; 25:114. [PMID: 37789381 PMCID: PMC10546663 DOI: 10.1186/s13058-023-01705-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/31/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND About 20% of breast cancers in humans are basal-like, a subtype that is often triple-negative and difficult to treat. An effective translational model for basal-like breast cancer is currently lacking and urgently needed. To determine whether spontaneous mammary tumors in pet dogs could meet this need, we subtyped canine mammary tumors and evaluated the dog-human molecular homology at the subtype level. METHODS We subtyped 236 canine mammary tumors from 3 studies by applying various subtyping strategies on their RNA-seq data. We then performed PAM50 classification with canine tumors alone, as well as with canine tumors combined with human breast tumors. We identified feature genes for human BLBC and luminal A subtypes via machine learning and used these genes to repeat canine-alone and cross-species tumor classifications. We investigated differential gene expression, signature gene set enrichment, expression association, mutational landscape, and other features for dog-human subtype comparison. RESULTS Our independent genome-wide subtyping consistently identified two molecularly distinct subtypes among the canine tumors. One subtype is mostly basal-like and clusters with human BLBC in cross-species PAM50 and feature gene classifications, while the other subtype does not cluster with any human breast cancer subtype. Furthermore, the canine basal-like subtype recaptures key molecular features (e.g., cell cycle gene upregulation, TP53 mutation) and gene expression patterns that characterize human BLBC. It is enriched in histological subtypes that match human breast cancer, unlike the other canine subtype. However, about 33% of canine basal-like tumors are estrogen receptor negative (ER-) and progesterone receptor positive (PR+), which is rare in human breast cancer. Further analysis reveals that these ER-PR+ canine tumors harbor additional basal-like features, including upregulation of genes of interferon-γ response and of the Wnt-pluripotency pathway. Interestingly, we observed an association of PGR expression with gene silencing in all canine tumors and with the expression of T cell exhaustion markers (e.g., PDCD1) in ER-PR+ canine tumors. CONCLUSIONS We identify a canine mammary tumor subtype that molecularly resembles human BLBC overall and thus could serve as a vital translational model of this devastating breast cancer subtype. Our study also sheds light on the dog-human difference in the mammary tumor histology and the hormonal cycle.
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Affiliation(s)
- Joshua Watson
- Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA
| | - Tianfang Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA
| | - Kun-Lin Ho
- Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA
| | - Yuan Feng
- Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA
| | - Tanakamol Mahawan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Kevin K Dobbin
- Department of Biostatistics, University of Georgia, Athens, GA, 30602, USA
| | - Shaying Zhao
- Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA.
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA.
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7
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Watson J, Wang T, Ho KL, Feng Y, Dobbin KK, Zhao S. Human basal-like breast cancer is represented by one of the two mammary tumor subtypes in dogs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530622. [PMID: 37034591 PMCID: PMC10081165 DOI: 10.1101/2023.03.02.530622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background About 20% of breast cancers in humans are basal-like, a subtype that is often triple negative and difficult to treat. An effective translational model for basal-like breast cancer (BLBC) is currently lacking and urgently needed. To determine if spontaneous mammary tumors in pet dogs could meet this need, we subtyped canine mammary tumors and evaluated the dog-human molecular homology at the subtype level. Methods We subtyped 236 canine mammary tumors from 3 studies by applying various subtyping strategies on their RNA-seq data. We then performed PAM50 classification with canine tumors alone, as well as with canine tumors combined with human breast tumors. We investigated differential gene expression, signature gene set enrichment, expression association, mutational landscape, and other features for dog-human subtype comparison. Results Our independent genome-wide subtyping consistently identified two molecularly distinct subtypes among the canine tumors. One subtype is mostly basal-like and clusters with human BLBC in cross-species PAM50 classification, while the other subtype does not cluster with any human breast cancer subtype. Furthermore, the canine basal-like subtype recaptures key molecular features (e.g., cell cycle gene upregulation, TP53 mutation) and gene expression patterns that characterize human BLBC. It is enriched histological subtypes that match human breast cancer, unlike the other canine subtype. However, about 33% of canine basal-like tumors are estrogen receptor negative (ER-) and progesterone receptor positive (PR+), which is rare in human breast cancer. Further analysis reveals that these ER-PR+ canine tumors harbor additional basal-like features, including upregulation of genes of interferon-γ response and of the Wnt-pluripotency pathway. Interestingly, we observed an association of PGR expression with gene silencing in all canine tumors, and with the expression of T cell exhaustion markers (e.g., PDCD1 ) in ER-PR+ canine tumors. Conclusions We identify a canine mammary tumor subtype that molecularly resembles human BLBC overall, and thus could serve as a vital spontaneous animal model of this devastating breast cancer subtype. Our study also sheds light on the dog-human difference in the mammary tumor histology and the hormonal cycle.
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Affiliation(s)
- Joshua Watson
- 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
| | - Kun-Lin Ho
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Yuan Feng
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Kevin K Dobbin
- Department of Biostatistics, University of Georgia, Athens, GA 30602, USA
| | - Shaying Zhao
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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8
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Feng Y, Hess PR, Tompkins SM, Hildebrand WH, Zhao S. A Kmer-based paired-end read de novo assembler and genotyper for canine MHC class I genotyping. iScience 2023; 26:105996. [PMID: 36798440 PMCID: PMC9926114 DOI: 10.1016/j.isci.2023.105996] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/28/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The major histocompatibility complex class I (MHC-I) genes are highly polymorphic. MHC-I genotyping is required for determining the peptide epitopes available to an individual's T-cell repertoire. Current genotyping software tools do not work for the dog, due to very limited known canine alleles. To address this, we developed a Kmer-based paired-end read (KPR) de novo assembler and genotyper, which assemble paired-end RNA-seq reads from MHC-I regions into contigs, and then genotype each contig and estimate its expression level. KPR tools outperform other popular software examined in typing new alleles. We used KPR tools to successfully genotype152 dogs from a published dataset. The study discovers 33 putative new alleles, finds dominant alleles in 4 dog breeds, and builds allele diversity and expression landscapes among the 152 dogs. Our software meets a significant need in biomedical research.
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Affiliation(s)
- Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Paul R. Hess
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, NC 27607, USA
| | - Stephen M. Tompkins
- Center for Vaccines and Immunology, University of Georgia, UGA, Athens, GA 30602, USA
| | - William H. Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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Krause C, Suwada K, Blomme EAG, Kowalkowski K, Liguori MJ, Mahalingaiah PK, Mittelstadt S, Peterson R, Rendino L, Vo A, Van Vleet TR. Preclinical species gene expression database: Development and meta-analysis. Front Genet 2023; 13:1078050. [PMID: 36733943 PMCID: PMC9887474 DOI: 10.3389/fgene.2022.1078050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/07/2022] [Indexed: 01/19/2023] Open
Abstract
The evaluation of toxicity in preclinical species is important for identifying potential safety liabilities of experimental medicines. Toxicology studies provide translational insight into potential adverse clinical findings, but data interpretation may be limited due to our understanding of cross-species biological differences. With the recent technological advances in sequencing and analyzing omics data, gene expression data can be used to predict cross species biological differences and improve experimental design and toxicology data interpretation. However, interpreting the translational significance of toxicogenomics analyses can pose a challenge due to the lack of comprehensive preclinical gene expression datasets. In this work, we performed RNA-sequencing across four preclinical species/strains widely used for safety assessment (CD1 mouse, Sprague Dawley rat, Beagle dog, and Cynomolgus monkey) in ∼50 relevant tissues/organs to establish a comprehensive preclinical gene expression body atlas for both males and females. In addition, we performed a meta-analysis across the large dataset to highlight species and tissue differences that may be relevant for drug safety analyses. Further, we made these databases available to the scientific community. This multi-species, tissue-, and sex-specific transcriptomic database should serve as a valuable resource to enable informed safety decision-making not only during drug development, but also in a variety of disciplines that use these preclinical species.
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Affiliation(s)
- Caitlin Krause
- R & D Data Solutions, AbbVie, North Chicago, IL, United States
| | - Kinga Suwada
- Development Biological Sciences, AbbVie, North Chicago, IL, United States
| | - Eric A. G. Blomme
- Development Biological Sciences, AbbVie, North Chicago, IL, United States
| | | | - Michael J. Liguori
- Development Biological Sciences, AbbVie, North Chicago, IL, United States
| | | | - Scott Mittelstadt
- Development Biological Sciences, AbbVie, North Chicago, IL, United States
| | - Richard Peterson
- Development Biological Sciences, AbbVie, North Chicago, IL, United States
| | - Lauren Rendino
- Development Biological Sciences, AbbVie, North Chicago, IL, United States
| | - Andy Vo
- Development Biological Sciences, AbbVie, North Chicago, IL, United States
| | - Terry R. Van Vleet
- Development Biological Sciences, AbbVie, North Chicago, IL, United States,*Correspondence: Terry R. Van Vleet,
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Perossi IFS, Saito MM, Varallo GR, de Godoy BLV, Colombo J, Zuccari DAPC. Protein Expression of PI3K/AKT/mTOR Pathway Targets Validated by Gene Expression and its Correlation with Prognosis in Canine Mammary Cancer. J Mammary Gland Biol Neoplasia 2022; 27:241-252. [PMID: 36323932 DOI: 10.1007/s10911-022-09527-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 12/31/2022] Open
Abstract
Mammary cancer is the main type of neoplasia in female dogs and is considered an adequate model for the biological and therapeutic study of cancer in women. The PIK3CA/AKT/mTOR pathway plays a central role in cellular homeostasis and is often dysregulated in cancer. The increased expression of PI3K protein in the literature is associated with a poor prognosis, and alterations in the PIK3CA gene can lead to changes in downstream pathways. Thus, the objective of this study was to validate the protein expression to confirm the gene expression of proteins belonging to the main pathway PI3K and PTEN, and their downstream pathways through ZEB1, ZEB2, HIF1A, VHL, CASP3 and PARP1 relating to prognosis in canine mammary cancer. For protein studies, the samples came from 58 female dogs with mammary neoplasia, immunohistochemistry was performed and its analysis by the histoscore method. For the genetic evaluation, the samples came from 13 patients, the DNA was extracted and the analysis for quantitative expression. Through immunohistochemistry, PI3K positivity was significantly associated with affected regional lymph node, distant metastasis, patients with HER2+, Triple Negative and Luminal B phenotypes, and the lowest survival rates. Through gene expression, we observed higher gene expression of ZEB2 and PARP1 both among patients who were alive and who died, which was not true for the expressions of PIK3CA and HIF1A. In conclusion, the data observed in this work are promising in the study of new molecular prognostic markers such as PI3K, ZEB2 and PARP1 for canine mammary cancer.
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Affiliation(s)
- Isabela F S Perossi
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) UNESP, São José do Rio Preto, Brazil.
| | - Mylena M Saito
- Centro Universitário de Rio Preto (UNIRP), São José do Rio Preto, Brazil
| | | | | | - Jucimara Colombo
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Debora A P C Zuccari
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
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11
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Chen L, Liao X, Jiang X, Yan J, Liang J, Hongwei L. Identification of Metastasis-Associated Genes in Cutaneous Squamous Cell Carcinoma Based on Bioinformatics Analysis and Experimental Validation. Adv Ther 2022; 39:4594-4612. [PMID: 35947350 DOI: 10.1007/s12325-022-02276-1] [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: 05/14/2022] [Accepted: 07/19/2022] [Indexed: 01/30/2023]
Abstract
INTRODUCTION Cutaneous squamous cell carcinoma (cSCC) is a global malignant tumor with a high degree of malignancy. Once metastasis occurs, it will lead to poor prognosis and even death. This study attempts to find out the central genes closely related to cSCC metastasis, so as to clarify the molecular regulatory mechanism of cSCC metastasis and open up new ideas for clinical treatment. METHODS Firstly, cSCC data set GSE98767 was used to establish a tumor metastasis model via clustering analysis. The key module and hub genes associated with cSCC metastasis were analyzed by weighted gene co-expression analysis (WGCNA). Next, the prognostic functions of hub genes were identified by functional and pathway enrichment analysis, pan-cancer analysis, and receiver operating characteristic-area under the curve (ROC-AUC) validation. Finally, the key genes were verified by clinical sample detection and biological in vitro test. RESULTS A total of 19 hub genes related to cSCC metastasis were identified. They were highly expressed in cSCC metastatic tissues and were mainly enriched in cellular material and energy metabolism pathways. Overall survival (OS) and disease-free survival (DFS) results from pan-cancer analysis showed that eight and six highly expressed genes, respectively, with PAPSS2 and SCG5 had highly reliable ROC-AUC validation values and were poor prognostic factors. Clinical and biological tests also confirmed the upregulation of PAPSS2 and SCG5 in cSCC. Deletion of PAPSS2 and SCG5 resulted in decreased viability, migration, and invasion of A-431 cells. CONCLUSION PAPSS2 and SCG5 may be important factors for cSCC metastasis, and they are involved in the regulation of cSCC cell viability, migration, and invasion.
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Affiliation(s)
- Lang Chen
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People's Republic of China.,Department of Burns and Plastic, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan, People's Republic of China.,Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, 510630, People's Republic of China
| | - Xuan Liao
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People's Republic of China.,Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, 510630, People's Republic of China
| | - Xiao Jiang
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People's Republic of China.,Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, 510630, People's Republic of China
| | - Jianxin Yan
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People's Republic of China.,Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, 510630, People's Republic of China
| | - Jiaji Liang
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People's Republic of China.,Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, 510630, People's Republic of China
| | - Liu Hongwei
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People's Republic of China. .,Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, 510630, People's Republic of China.
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12
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Kaszak I, Witkowska-Piłaszewicz O, Domrazek K, Jurka P. The Novel Diagnostic Techniques and Biomarkers of Canine Mammary Tumors. Vet Sci 2022; 9:526. [PMID: 36288138 PMCID: PMC9610006 DOI: 10.3390/vetsci9100526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 07/25/2023] Open
Abstract
Canine mammary tumors (CMTs) are considered a serious clinical problem in older bitches. Due to the high malignancy rate and poor prognosis, an early diagnosis is essential. This article is a summary of novel diagnostic techniques as well as the main biomarkers of CMTs. So far, CMTs are detected only when changes in mammary glands are clinically visible and surgical removal of the mass is the only recommended treatment. Proper diagnostics of CMT is especially important as they represent a very diverse group of tumors and therefore different treatment approaches may be required. Recently, new diagnostic options appeared, like a new cytological grading system of CMTs or B-mode ultrasound, the Doppler technique, contrast-enhanced ultrasound, and real-time elastography, which may be useful in pre-surgical evaluation. However, in order to detect malignancies before macroscopic changes are visible, evaluation of serum and tissue biomarkers should be considered. Among them, we distinguish markers of the cell cycle, proliferation, apoptosis, metastatic potential and prognosis, hormone receptors, inflammatory and more recent: metabolomic, gene expression, miRNA, and transcriptome sequencing markers. The use of a couple of the above-mentioned markers together seems to be the most useful for the early diagnosis of neoplastic diseases as well as to evaluate response to treatment, presence of tumor progression, or further prognosis. Molecular aspects of tumors seem to be crucial for proper understanding of tumorigenesis and the application of individual treatment options.
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Affiliation(s)
- Ilona Kaszak
- Laboratory of Small Animal Reproduction, Department of Small Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Olga Witkowska-Piłaszewicz
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Kinga Domrazek
- Laboratory of Small Animal Reproduction, Department of Small Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Piotr Jurka
- Laboratory of Small Animal Reproduction, Department of Small Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
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13
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Bergholtz H, Lien T, Lingaas F, Sørlie T. Comparative analysis of the molecular subtype landscape in canine and human mammary gland tumors. J Mammary Gland Biol Neoplasia 2022; 27:171-183. [PMID: 35932380 PMCID: PMC9433360 DOI: 10.1007/s10911-022-09523-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022] Open
Abstract
Breast cancers in humans belong to one of several intrinsic molecular subtypes each with different tumor biology and different clinical impact. Mammary gland tumors in dogs are proposed as a relevant comparative model for human breast cancer; however, it is still unclear whether the intrinsic molecular subtypes have the same significance in dogs and humans. Using publicly available data, we analyzed gene expression and whole-exome sequencing data from 158 canine mammary gland tumors. We performed molecular subtyping using the PAM50 method followed by subtype-specific comparisons of gene expression characteristics, mutation patterns and copy number profiles between canine tumors and human breast tumors from The Cancer Genome Atlas (TCGA) breast cancer cohort (n = 1097). We found that luminal A canine tumors greatly resemble luminal A human tumors both in gene expression characteristics, mutations and copy number profiles. Also, the basal-like canine and human tumors were relatively similar, with low expression of luminal epithelial markers and high expression of genes involved in cell proliferation. There were, however, distinct differences in immune-related gene expression patterns in basal-like tumors between the two species. Characteristic HER2-enriched and luminal B subtypes were not present in the canine cohort, and we found no tumors with high-level ERBB2 amplifications. Benign and malignant canine tumors displayed similar PAM50 subtype characteristics. Our findings indicate that deeper understanding of the different molecular subtypes in canine mammary gland tumors will further improve the value of canines as comparative models for human breast cancer.
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Affiliation(s)
- Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Tonje Lien
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Frode Lingaas
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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14
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Chen HW, Lai YC, Rahman MM, Husna AA, Hasan MN, Miura N. Micro RNA differential expression profile in canine mammary gland tumor by next generation sequencing. Gene X 2022; 818:146237. [PMID: 35077831 DOI: 10.1016/j.gene.2022.146237] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 11/26/2022] Open
Abstract
Canine mammary gland tumors are very common and represent a potential model of human breast cancer, and microRNA (miRNAs) are promising biomarkers and therapeutic targets for these tumors. Accordingly, we aimed to identify miRNAs differentially expressed in canine mammary gland tumors using next generation sequencing (NGS), with subsequent confirmatory qPCR and target gene analyses. Mammary gland tissue was collected from healthy dogs (n=7) and dogs with suspected tumors (n=80). A subset of samples was analyzed with NGS to identify differentially expressed miRNAs with CLC Genome Workbench. Normal (n=10), tumor-adjacent (n=6), and tumor-bearing (n=76) mammary gland tissue samples were analyzed for the identified miRNAs using qPCR. An in silico analysis (TargetScan) was performed to predict the miRNAs' target genes using gene ontology (GO) terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (DAVID). We identified four miRNAs (cfa-miR-1-3p, cfa-miR-133a-3p, cfa-miR-133b-3p, and cfa-miR-133c-3p) as down regulated in canine mammary gland tumor tissues relative to normal and tumor adjacent tissues. KEGG analysis revealed the potential target genes of cfa-miR-1-3p are related to the Rap1 signaling pathway, adherens junction, and Ras signaling pathway, and those of the miR-133 family are related to the TGF-beta signaling pathway, synaptic vesicle cycle, and sphingolipid signaling pathway. In combination, these target genes are related to the regulation of transcription and DNA binding transcription (GO analysis), and the Hippo signaling pathway, adherens junction, and endocytosis (KEGG analysis). Accordingly, we suggest these four miRNAs are promising potential biomarker candidates for canine mammary gland tumors warranting further investigation.
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Affiliation(s)
- Hui-Wen Chen
- Clinical Veterinary Science, Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890‑0065, Japan
| | - Yu-Chang Lai
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890‑0065, Japan
| | - Md Mahfuzur Rahman
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890‑0065, Japan
| | - Al Asmaul Husna
- Clinical Veterinary Science, The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Kagoshima 890‑0065, Japan
| | - Md Nazmul Hasan
- Clinical Veterinary Science, Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890‑0065, Japan
| | - Naoki Miura
- Clinical Veterinary Science, Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890‑0065, Japan; Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890‑0065, Japan; Clinical Veterinary Science, The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Kagoshima 890‑0065, Japan.
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15
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Lee S, Seung BJ, Yang IS, Lee J, Ha T, Park HM, Cheong JH, Kim S, Sur JH, Hwang GS, Nam H. 1H NMR based urinary metabolites profiling dataset of canine mammary tumors. Sci Data 2022; 9:132. [PMID: 35361774 PMCID: PMC8971436 DOI: 10.1038/s41597-022-01229-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/23/2022] [Indexed: 11/09/2022] Open
Abstract
The identification of efficient and sensitive biomarkers for non-invasive tests is one of the major challenges in cancer diagnosis. To address this challenge, metabolomics is widely applied for identifying biomarkers that detect abnormal changes in cancer patients. Canine mammary tumors exhibit physiological characteristics identical to those in human breast cancer and serve as a useful animal model to conduct breast cancer research. Here, we aimed to provide a reliable large-scale metabolite dataset collected from dogs with mammary tumors, using proton nuclear magnetic resonance spectroscopy. We identified 55 metabolites in urine samples from 20 benign, 87 malignant, and 49 healthy control subjects. This dataset provides details of mammary tumor-specific metabolites in dogs and insights into cancer-specific metabolic alterations that share similar molecular characteristics.
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Affiliation(s)
- Songyeon Lee
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, South Korea
| | - Byung-Joon Seung
- Department of Veterinary Pathology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, South Korea
| | - In Seok Yang
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Jueun Lee
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, 03759, South Korea
| | - Taewoong Ha
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, 03759, South Korea
| | - Hee-Myung Park
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University, Seoul, 05029, South 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, South Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Jung-Hyang Sur
- Department of Veterinary Pathology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, South Korea
| | - Geum-Sook Hwang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, 03759, South Korea.
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, South Korea.
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, South Korea.
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16
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Huskey ALW, McNeely I, Merner ND. CEACAM Gene Family Mutations Associated With Inherited Breast Cancer Risk - A Comparative Oncology Approach to Discovery. Front Genet 2021; 12:702889. [PMID: 34447411 PMCID: PMC8383343 DOI: 10.3389/fgene.2021.702889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/05/2021] [Indexed: 01/11/2023] Open
Abstract
Introduction Recent studies comparing canine mammary tumors (CMTs) and human breast cancers have revealed remarkable tumor similarities, identifying shared expression profiles and acquired mutations. CMTs can also provide a model of inherited breast cancer susceptibility in humans; thus, we investigated breed-specific whole genome sequencing (WGS) data in search for novel CMT risk factors that could subsequently explain inherited breast cancer risk in humans. Methods WGS was carried out on five CMT-affected Gold Retrievers from a large pedigree of 18 CMT-affected dogs. Protein truncating variants (PTVs) detected in all five samples (within human orthlogs) were validated and then genotyped in the 13 remaining CMT-affected Golden Retrievers. Allele frequencies were compared to canine controls. Subsequently, human blood-derived exomes from The Cancer Genome Atlas breast cancer cases were analyzed and allele frequencies were compared to Exome Variant Server ethnic-matched controls. Results Carcinoembryonic Antigen-related Cell Adhesion Molecule 24 (CEACAM24) c.247dupG;p.(Val83Glyfs∗48) was the only validated variant and had a frequency of 66.7% amongst the 18 Golden Retrievers with CMT. This was significant compared to the European Variation Archive (p-value 1.52 × 10–8) and non-Golden Retriever American Kennel Club breeds (p-value 2.48 × 10–5). With no direct ortholog of CEACAM24 in humans but high homology to all CEACAM gene family proteins, all human CEACAM genes were investigated for PTVs. A total of six and sixteen rare PTVs were identified in African and European American breast cancer cases, respectively. Single variant assessment revealed five PTVs associated with breast cancer risk. Gene-based aggregation analyses revealed that rare PTVs in CEACAM6, CEACAM7, and CEACAM8 are associated with European American breast cancer risk, and rare PTVs in CEACAM7 are associated with breast cancer risk in African Americans. Ultimately, rare PTVs in the entire CEACAM gene family are associated with breast cancer risk in both European and African Americans with respective p-values of 1.75 × 10–13 and 1.87 × 10–04. Conclusion This study reports the first association of inherited CEACAM mutations and breast cancer risk, and potentially implicates the whole gene family in genetic risk. Precisely how these mutations contribute to breast cancer needs to be determined; especially considering our current knowledge on the role that the CEACAM gene family plays in tumor development, progression, and metastasis.
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Affiliation(s)
- Anna L W Huskey
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States.,Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, United States
| | - Isaac McNeely
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Nancy D Merner
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
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17
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Impact of Histological Subtype on Survival in Canine Mammary Carcinomas: a Retrospective Analysis of 155 Cases. J Comp Pathol 2021; 186:23-30. [PMID: 34340801 DOI: 10.1016/j.jcpa.2021.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/08/2021] [Accepted: 05/04/2021] [Indexed: 11/20/2022]
Abstract
Canine mammary carcinoma (CMC) is the most common type of neoplasm in intact female dogs. While a previous study in Western countries validated the 2011 classification as an independent prognostic indicator in CMC, its role in CMC prognostication in Asian countries such as Korea remains unclear. In the present study, we estimate the survival rates in CMC types defined by the 2011 classification, elucidate the prognostic significance of the histological subtype and grade and that of the lymphatic invasion status in CMC, and validate the 2011 classification as an independent prognostic indicator in a large cohort of CMCs (excluding cases of multicentric CMCs). A total of 155 CMC cases retrieved from archived formalin-fixed, paraffin-embedded tissues, along with 2-year follow-up data, were retrospectively analysed. A significant association was found between the histological subtype of the 2011 classification and the tumour-specific survival. Carcinosarcoma, adenosquamous carcinoma and anaplastic carcinoma subtypes were associated with the poorest prognosis. Dogs with comedocarcinoma and solid carcinoma followed a disease course that was more aggressive than that observed in dogs with a carcinoma arising in a benign mixed tumour. Moreover, age, histological grade and lymphatic invasion status significantly correlated with tumour-specific survival in univariate analysis. In multivariate analysis, histological subtype, age and lymphatic invasion status remained independent prognostic factors for CMC.
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18
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Mestrinho LA, Santos RR. Translational oncotargets for immunotherapy: From pet dogs to humans. Adv Drug Deliv Rev 2021; 172:296-313. [PMID: 33705879 DOI: 10.1016/j.addr.2021.02.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/10/2021] [Accepted: 02/27/2021] [Indexed: 12/21/2022]
Abstract
Preclinical studies in rodent models have been a pivotal role in human clinical research, but many of them fail in the translational process. Spontaneous tumors in pet dogs have the potential to bridge the gap between preclinical models and human clinical trials. Their natural occurrence in an immunocompetent system overcome the limitations of preclinical rodent models. Due to its reasonable cellular, molecular, and genetic homology to humans, the pet dog represents a valuable model to accelerate the translation of preclinical studies to clinical trials in humans, actually with benefits for both species. Moreover, their unique genetic features of breeding and breed-related mutations have contributed to assess and optimize therapeutics in individuals with different genetic backgrounds. This review aims to outline four main immunotherapy approaches - cancer vaccines, adaptive T-cell transfer, antibodies, and cytokines -, under research in veterinary medicine and how they can serve the clinical application crosstalk with humans.
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19
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A domestic cat whole exome sequencing resource for trait discovery. Sci Rep 2021; 11:7159. [PMID: 33785770 PMCID: PMC8009874 DOI: 10.1038/s41598-021-86200-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
Over 94 million domestic cats are susceptible to cancers and other common and rare diseases. Whole exome sequencing (WES) is a proven strategy to study these disease-causing variants. Presented is a 35.7 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. Whole exome sequencing was conducted on 41 cats with known and unknown genetic diseases and traits, of which ten cats had matching whole genome sequence (WGS) data available, used to validate WES performance. At 80 × mean exome depth of coverage, 96.4% of on-target base coverage had a sequencing depth > 20-fold, while over 98% of single nucleotide variants (SNVs) identified by WGS were also identified by WES. Platform-specific SNVs were restricted to sex chromosomes and a small number of olfactory receptor genes. Within the 41 cats, we identified 31 previously known causal variants and discovered new gene candidate variants, including novel missense variance for polycystic kidney disease and atrichia in the Peterbald cat. These results show the utility of WES to identify novel gene candidate alleles for diseases and traits for the first time in a feline model.
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20
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Kim JH. PIK3CA mutations matter for cancer in dogs. Res Vet Sci 2020; 133:39-41. [PMID: 32932196 DOI: 10.1016/j.rvsc.2020.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/19/2020] [Accepted: 09/07/2020] [Indexed: 01/12/2023]
Abstract
Cancer is a genetic disease that arises from the accumulation of genetic mutations within a cell. Mutations in PIK3CA gene are frequently observed in human solid cancers, and also appear to occur in canine tumors. Specifically, recurrent somatic PIK3CA variants identified in canine mammary tumors and hemangiosarcomas are comparable to human hotspot mutations such as H1047R. PIK3CA mutations found in canine tumors encode functional proteins that may alter downstream PI3K/Akt/mTOR signaling pathway. Therefore, PI3K inhibitors have potential in cancer therapy for dogs. This article concisely reviews the emerging evidence concerning the genetic and molecular properties of PIK3CA mutations to discuss future perspectives in veterinary and comparative oncology.
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Affiliation(s)
- Jong Hyuk Kim
- Animal Cancer Care and Research Program, University of Minnesota, St Paul, MN, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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21
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Nam AR, Lee KH, Hwang HJ, Schabort JJ, An JH, Won SH, Cho JY. Alternative methylation of intron motifs is associated with cancer-related gene expression in both canine mammary tumor and human breast cancer. Clin Epigenetics 2020; 12:110. [PMID: 32693820 PMCID: PMC7374976 DOI: 10.1186/s13148-020-00888-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022] Open
Abstract
Background Canine mammary tumor (CMT) has long been considered as a good animal model for human breast cancer (HBC) due to their pathological and biological similarities. However, only a few aspects of the epigenome have been explored in both HBC and CMT. Moreover, DNA methylation studies have mainly been limited to the promoter regions of genes. Results Genome-wide methylation analysis was performed in CMT and adjacent normal tissues and focused on the intron regions as potential targets for epigenetic regulation. As expected, many tumor suppressors and oncogenes were identified. Of note, most cancer-associated biological processes were enriched in differentially methylated genes (DMGs) that included intron DMRs (differentially methylated regions). Interestingly, two PAX motifs, PAX5 (tumor suppressive) and PAX6 (oncogenic), were frequently found in hyper- and hypomethylated intron DMRs, respectively. Hypermethylation at the PAX5 motifs in the intron regions of CDH5 and LRIG1 genes were found to be anti-correlated with gene expression, while CDH2 and ADAM19 genes harboring hypomethylated PAX6 motifs in their intron region were upregulated. These results were validated from the specimens originally MBD-sequenced as well as additional clinical samples. We also comparatively investigated the intron methylation and downstream gene expression of these genes using human breast invasive carcinoma (BRCA) datasets in TCGA (The Cancer Genome Atlas) public database. Regional alteration of methylation was conserved in the corresponding intron regions and, consequently, gene expression was also altered in HBC. Conclusions This study provides good evidence for the conservation of epigenetic regulation in CMT and HBC, and suggests that intronic methylation can be an important factor in better understanding gene regulation in both CMT and HBC.
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Affiliation(s)
- A-Reum Nam
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Gwanak-ro1, Gwanak-gu, Seoul, Korea
| | - Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Gwanak-ro1, Gwanak-gu, Seoul, Korea
| | - Hyeon-Ji Hwang
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Gwanak-ro1, Gwanak-gu, Seoul, Korea
| | - Johannes J Schabort
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Gwanak-ro1, Gwanak-gu, Seoul, Korea
| | - Jae-Hoon An
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - Sung-Ho Won
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Gwanak-ro1, Gwanak-gu, Seoul, Korea.
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22
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Kim TM, Yang IS, Seung BJ, Lee S, Kim D, Ha YJ, Seo MK, Kim KK, Kim HS, Cheong JH, Sur JH, Nam H, Kim S. Cross-species oncogenic signatures of breast cancer in canine mammary tumors. Nat Commun 2020; 11:3616. [PMID: 32680987 PMCID: PMC7367841 DOI: 10.1038/s41467-020-17458-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023] Open
Abstract
Genomic and precision medicine research has afforded notable advances in human cancer treatment, yet applicability to other species remains uncertain. Through whole-exome and transcriptome analyses of 191 spontaneous canine mammary tumors (CMTs) that exhibit the archetypal features of human breast cancers, we found a striking resemblance of genomic characteristics including frequent PIK3CA mutations (43.1%), aberrations of the PI3K-Akt pathway (61.7%), and key genes involved in cancer initiation and progression. We also identified three gene expression-based CMT subtypes, one of which segregated with basal-like human breast cancer subtypes with activated epithelial-to-mesenchymal transition, low claudin expression, and unfavorable disease prognosis. A relative lack of ERBB2 amplification and Her2-enrichment subtype in CMT denoted species-specific molecular mechanisms. Taken together, our results elucidate cross-species oncogenic signatures for a better understanding of universal and context-dependent mechanisms in breast cancer development and provide a basis for precision diagnostics and therapeutics for domestic dogs.
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Affiliation(s)
- Tae-Min Kim
- Department of Medical Informatics and Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - In Seok Yang
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Byung-Joon Seung
- Department of Veterinary Pathology, Small Animal Tumor Diagnostic Center, College of Veterinary Medicine, Konkuk University, Seoul, 05029, South Korea
| | - Sejoon Lee
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, 13620, South Korea
| | - Dohyun Kim
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, South Korea
| | - Yoo-Jin Ha
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Mi-Kyoung Seo
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Ka-Kyung Kim
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Hyun Seok Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South 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, South Korea
| | - Jung-Hyang Sur
- Department of Veterinary Pathology, Small Animal Tumor Diagnostic Center, College of Veterinary Medicine, Konkuk University, Seoul, 05029, South Korea
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, South Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea.
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23
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Seung BJ, Cho SH, Kim SH, Lim HY, Sur JH. Quantitative analysis of HER2 mRNA expression by RNA in situ hybridization in canine mammary gland tumors: Comparison with immunohistochemistry analysis. PLoS One 2020; 15:e0229031. [PMID: 32059046 PMCID: PMC7021316 DOI: 10.1371/journal.pone.0229031] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/28/2020] [Indexed: 02/06/2023] Open
Abstract
Spontaneously occurring canine mammary gland tumors share many features with human breast cancer, including biological behavior and histologic features. Compared to transgenic murine model, canine models have advantages including naturally occurring models of human diseases and cancer. In humans, breast cancer is divided into molecular subtypes based on ER, PR, and HER2 expression. In contrast with humans, few studies have evaluated these subtypes in canine mammary gland tumors, including expression of HER2. HER2 expression in canine mammary tissues has been further complicated by controversy regarding the antibody’s specificity. This study aimed to investigate c-erbB2 mRNA expression in retrospective formalin-fixed paraffin embedded samples, using RNA in situ hybridization with a novel quantitative assay and to compare this method with immunohistochemistry. Using 48 canine mammary tumor samples and 14 non-neoplastic canine mammary tissues, RNA in situ hybridization was performed with RNAscope® using a canine-specific target gene probe (ERBB2), and quantitative measurement was performed using the housekeeping gene (POLR2A) to calculate the target gene/housekeeping gene ratio. The ratio of ERBB2/POLR2A was quantified using open-source image analysis programs and compared with the immunohistochemistry results. A significant correlation was observed between the HER2 immunohistochemistry score and ERBB2/POLR2A RNA in situ hybridization (P < 0.001). When the HER2 immunohistochemistry score was 3+, significantly higher expression of HER2 mRNA was observed by RNA in situ hybridization. Interestingly, HER2 mRNA was also observed in non-neoplastic mammary tissues by RNA in situ hybridization. This assay potentially facilitates the reliable quantification of mRNA expression levels in retrospective formalin-fixed paraffin-embedded samples. Further studies are required to elucidate the role of HER2 in canine mammary gland tumors and to implement clinical trials in dogs.
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Affiliation(s)
- Byung-Joon Seung
- Department of Veterinary Pathology, Small Animal Tumor Diagnostic Center, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Seung-Hee Cho
- Department of Veterinary Pathology, Small Animal Tumor Diagnostic Center, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Soo-Hyeon Kim
- Department of Veterinary Pathology, Small Animal Tumor Diagnostic Center, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Ha-Young Lim
- Department of Veterinary Pathology, Small Animal Tumor Diagnostic Center, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Jung-Hyang Sur
- Department of Veterinary Pathology, Small Animal Tumor Diagnostic Center, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
- * E-mail:
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