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Filippo D, Guardone L, Listorti V, Elisabetta R. Microbiome in cancer: A comparative analysis between humans and dogs. Vet J 2024; 305:106145. [PMID: 38788999 DOI: 10.1016/j.tvjl.2024.106145] [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: 09/18/2023] [Revised: 04/22/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Cancer is a major cause of death in humans and animals worldwide. While cancer survival rates have increased over recent decades, further research to identify risk factors for the onset and progression of disease, and safe and highly efficacious treatments, is needed. Spontaneous tumours in pets represent an excellent model for neoplastic disease in humans. In this regard, dogs are an interesting species, as the divergence between the dog and human genome is low, humans and dogs have important similarities in the development and functioning of the immune system, and both species often share the same physical environment. There is also a higher homology between the canine and human microbiome than murine model. This review aims to describe and organize recently published information on canine microbiome assemblages and their relationship with the onset and progression of colorectal cancer, breast cancer and lymphoma, and to compare this with human disease. In both species, dysbiosis can induce variations in the gut microbiota that strongly influence shifts in status between health and disease. This can produce an inflammatory state, potentially leading to neoplasia, especially in the intestine, thus supporting canine studies in comparative oncology. Intestinal dysbiosis can also alter the efficacy and side effects of cancer treatments. Fewer published studies are available on changes in the relevant microbiomes in canine lymphoma and mammary cancer, and further research in this area could improve our understanding of the role of microbiota in the development of these cancers.
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Affiliation(s)
- Dell'Anno Filippo
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy; Department of Public Health, Experimental and Forensic Medicine, Section of Biostatistics and Clinical Epidemiology, University of Pavia, Pavia, Italy
| | - Lisa Guardone
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy
| | - Valeria Listorti
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy
| | - Razzuoli Elisabetta
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy.
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2
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Kagan VE, Straub AC, Tyurina YY, Kapralov AA, Hall R, Wenzel SE, Mallampalli RK, Bayir H. Vitamin E/Coenzyme Q-Dependent "Free Radical Reductases": Redox Regulators in Ferroptosis. Antioxid Redox Signal 2024; 40:317-328. [PMID: 37154783 PMCID: PMC10890965 DOI: 10.1089/ars.2022.0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/10/2023] [Accepted: 04/08/2023] [Indexed: 05/10/2023]
Abstract
Significance: Lipid peroxidation and its products, oxygenated polyunsaturated lipids, act as essential signals coordinating metabolism and physiology and can be deleterious to membranes when they accumulate in excessive amounts. Recent Advances: There is an emerging understanding that regulation of polyunsaturated fatty acid (PUFA) phospholipid peroxidation, particularly of PUFA-phosphatidylethanolamine, is important in a newly discovered type of regulated cell death, ferroptosis. Among the most recently described regulatory mechanisms is the ferroptosis suppressor protein, which controls the peroxidation process due to its ability to reduce coenzyme Q (CoQ). Critical Issues: In this study, we reviewed the most recent data in the context of the concept of free radical reductases formulated in the 1980-1990s and focused on enzymatic mechanisms of CoQ reduction in different membranes (e.g., mitochondrial, endoplasmic reticulum, and plasma membrane electron transporters) as well as TCA cycle components and cytosolic reductases capable of recycling the high antioxidant efficiency of the CoQ/vitamin E system. Future Directions: We highlight the importance of individual components of the free radical reductase network in regulating the ferroptotic program and defining the sensitivity/tolerance of cells to ferroptotic death. Complete deciphering of the interactive complexity of this system may be important for designing effective antiferroptotic modalities. Antioxid. Redox Signal. 40, 317-328.
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Affiliation(s)
- Valerian E. Kagan
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Environmental Health and Pharmacology and Chemical Biology and University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Radiation Oncology and Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adam C. Straub
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yulia Y. Tyurina
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Environmental Health and Pharmacology and Chemical Biology and University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alexandr A. Kapralov
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Environmental Health and Pharmacology and Chemical Biology and University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Robert Hall
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sally E. Wenzel
- Department of Environmental Health and Pharmacology and Chemical Biology and University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rama K. Mallampalli
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Hülya Bayir
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, Children's Hospital Neuroscience Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Pediatrics, Columbia University, New York, New York, USA
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3
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Rodrigues L, Watson J, Feng Y, Lewis B, Harvey G, Post G, Megquier K, White ME, Lambert L, Miller A, Lopes C, Zhao S. Shared hotspot mutations in oncogenes position dogs as an unparalleled comparative model for precision therapeutics. Sci Rep 2023; 13:10935. [PMID: 37414794 PMCID: PMC10325973 DOI: 10.1038/s41598-023-37505-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/22/2023] [Indexed: 07/08/2023] Open
Abstract
Naturally occurring canine cancers have remarkable similarities to their human counterparts. To better understand these similarities, we investigated 671 client-owned dogs from 96 breeds with 23 common tumor types, including those whose mutation profile are unknown (anal sac carcinoma and neuroendocrine carcinoma) or understudied (thyroid carcinoma, soft tissue sarcoma and hepatocellular carcinoma). We discovered mutations in 50 well-established oncogenes and tumor suppressors, and compared them to those reported in human cancers. As in human cancer, TP53 is the most commonly mutated gene, detected in 22.5% of canine tumors overall. Canine tumors share mutational hotspots with human tumors in oncogenes including PIK3CA, KRAS, NRAS, BRAF, KIT and EGFR. Hotspot mutations with significant association to tumor type include NRAS G61R and PIK3CA H1047R in hemangiosarcoma, ERBB2 V659E in pulmonary carcinoma, and BRAF V588E (equivalent of V600E in humans) in urothelial carcinoma. Our findings better position canines as a translational model of human cancer to investigate a wide spectrum of targeted therapies.
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Affiliation(s)
- Lucas Rodrigues
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA.
| | - Joshua Watson
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, B304B Life Sciences Building, 120 Green Street, Athens, GA, 30602-7229, USA
| | - Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, B304B Life Sciences Building, 120 Green Street, Athens, GA, 30602-7229, USA
| | - Benjamin Lewis
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Garrett Harvey
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Gerald Post
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Kate Megquier
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michelle E White
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Lindsay Lambert
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Aubrey Miller
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Christina Lopes
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, B304B Life Sciences Building, 120 Green Street, Athens, GA, 30602-7229, USA.
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4
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Xia C, Su J, Liu C, Mai Z, Yin S, Yang C, Fu L. Human microbiomes in cancer development and therapy. MedComm (Beijing) 2023; 4:e221. [PMID: 36860568 PMCID: PMC9969057 DOI: 10.1002/mco2.221] [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: 09/20/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 03/03/2023] Open
Abstract
Colonies formed by bacteria, archaea, fungi, and viral groups and their genomes, metabolites, and expressed proteins constitute complex human microbiomes. An increasing evidences showed that carcinogenesis and disease progression were link to microbiomes. Different organ sources, their microbial species, and their metabolites are different; the mechanisms of carcinogenic or procancerous are also different. Here, we summarize how microbiomes contribute to carcinogenesis and disease progression in cancers of the skin, mouth, esophagus, lung, gastrointestinal, genital, blood, and lymph malignancy. We also insight into the molecular mechanisms of triggering, promoting, or inhibiting carcinogenesis and disease progress induced by microbiomes or/and their secretions of bioactive metabolites. And then, the strategies of application of microorganisms in cancer treatment were discussed in detail. However, the mechanisms by which human microbiomes function are still poorly understood. The bidirectional interactions between microbiotas and endocrine systems need to be clarified. Probiotics and prebiotics are believed to benefit human health via a variety of mechanisms, in particular, in tumor inhibition. It is largely unknown how microbial agents cause cancer or how cancer progresses. We expect this review may open new perspectives on possible therapeutic approaches of patients with cancer.
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Affiliation(s)
- Chenglai Xia
- Affiliated Foshan Maternity and Chlid Healthcare HospitalSouthern Medical University, Foshan, China; School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhouChina
| | - Jiyan Su
- Affiliated Foshan Maternity and Chlid Healthcare HospitalSouthern Medical University, Foshan, China; School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhouChina
| | - Can Liu
- Affiliated Foshan Maternity and Chlid Healthcare HospitalSouthern Medical University, Foshan, China; School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhouChina
| | - Zhikai Mai
- Affiliated Foshan Maternity and Chlid Healthcare HospitalSouthern Medical University, Foshan, China; School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhouChina
| | - Shuanghong Yin
- Affiliated Foshan Maternity and Chlid Healthcare HospitalSouthern Medical University, Foshan, China; School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhouChina
| | - Chuansheng Yang
- Department of Head‐Neck and Breast SurgeryYuebei People's Hospital of Shantou UniversityShaoguanChina
| | - Liwu Fu
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine; Guangdong Esophageal Cancer Institute; Sun Yat‐sen University Cancer CenterGuangzhouPeople's Republic of China
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5
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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,Corresponding author
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6
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Hall R, Yuan S, Wood K, Katona M, Straub AC. Cytochrome b5 reductases: Redox regulators of cell homeostasis. J Biol Chem 2022; 298:102654. [PMID: 36441026 PMCID: PMC9706631 DOI: 10.1016/j.jbc.2022.102654] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
The cytochrome-b5 reductase (CYB5R) family of flavoproteins is known to regulate reduction-oxidation (redox) balance in cells. The five enzyme members are highly compartmentalized at the subcellular level and function as "redox switches" enabling the reduction of several substrates, such as heme and coenzyme Q. Critical insight into the physiological and pathophysiological significance of CYB5R enzymes has been gleaned from several human genetic variants that cause congenital disease and a broad spectrum of chronic human diseases. Among the CYB5R genetic variants, CYB5R3 is well-characterized and deficiency in expression and activity is associated with type II methemoglobinemia, cancer, neurodegenerative disorders, diabetes, and cardiovascular disease. Importantly, pharmacological and genetic-based strategies are underway to target CYB5R3 to circumvent disease onset and mitigate severity. Despite our knowledge of CYB5R3 in human health and disease, the other reductases in the CYB5R family have been understudied, providing an opportunity to unravel critical function(s) for these enzymes in physiology and disease. In this review, we aim to provide the broad scientific community an up-to-date overview of the molecular, cellular, physiological, and pathophysiological roles of CYB5R proteins.
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Affiliation(s)
- Robert Hall
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shuai Yuan
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Katherine Wood
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mate Katona
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adam C Straub
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Center for Microvascular Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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7
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Piras IM, Sheahan K, Shiel RE, Shorten E, Jahns H. Pathology in Practice. J Am Vet Med Assoc 2022; 261:1-3. [PMID: 36315452 DOI: 10.2460/javma.22.08.0356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ilaria M Piras
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Kieran Sheahan
- St. Vincent's University Hospital, School of Medicine, University College Dublin, Elm Park, Dublin, Ireland
| | - Robert E Shiel
- Murdoch Veterinary School, Murdoch University, Perth, WA, Australia
| | - Eimear Shorten
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Hanne Jahns
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
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8
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Kumar RD, Burns BA, Vandeventer PJ, Luna PN, Shaw CA. Selection for or against escape from nonsense mediated decay is a novel signature for the detection of cancer genes. Cancer Genet 2021; 258-259:80-84. [PMID: 34592632 DOI: 10.1016/j.cancergen.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/18/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023]
Abstract
Escape from nonsense mediated mRNA decay (NMD-) can produce activated or inactivated gene products, and bias in rates of escape can identify functionally important genes in germline disease. We hypothesized that the same would be true of cancer genes, and tested for NMD- bias within The Cancer Genome Atlas pan-cancer somatic mutation dataset. We identify 29 genes that show significantly elevated or suppressed rates of NMD-. This novel approach to cancer gene discovery reveals genes not previously cataloged as potentially tumorigenic, and identifies many potential driver mutations in known cancer genes for functional characterization.
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Affiliation(s)
- Runjun D Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Briana A Burns
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Paul J Vandeventer
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States; Baylor Genetics, Houston, TX, United States; Department of Statistics, Rice University, Houston, TX, United States.
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9
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Alsaihati BA, Ho KL, Watson J, Feng Y, Wang T, Dobbin KK, Zhao S. Canine tumor mutational burden is correlated with TP53 mutation across tumor types and breeds. Nat Commun 2021; 12:4670. [PMID: 34344882 PMCID: PMC8333103 DOI: 10.1038/s41467-021-24836-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Spontaneous canine cancers are valuable but relatively understudied and underutilized models. To enhance their usage, we reanalyze whole exome and genome sequencing data published for 684 cases of >7 common tumor types and >35 breeds, with rigorous quality control and breed validation. Our results indicate that canine tumor alteration landscape is tumor type-dependent, but likely breed-independent. Each tumor type harbors major pathway alterations also found in its human counterpart (e.g., PI3K in mammary tumor and p53 in osteosarcoma). Mammary tumor and glioma have lower tumor mutational burden (TMB) (median < 0.5 mutations per Mb), whereas oral melanoma, osteosarcoma and hemangiosarcoma have higher TMB (median ≥ 1 mutations per Mb). Across tumor types and breeds, TMB is associated with mutation of TP53 but not PIK3CA, the most mutated genes. Golden Retrievers harbor a TMB-associated and osteosarcoma-enriched mutation signature. Here, we provide a snapshot of canine mutations across major tumor types and breeds.
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Affiliation(s)
- Burair A Alsaihati
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- National Center for Genomics Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Kun-Lin Ho
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Joshua Watson
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Tianfang Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Kevin K Dobbin
- Department of Epidemiology and Biostatistics, 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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10
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Wang T, Kwon SH, Peng X, Urdy S, Lu Z, Schmitz RJ, Dalton S, Mostov KE, Zhao S. A Qualitative Change in the Transcriptome Occurs after the First Cell Cycle and Coincides with Lumen Establishment during MDCKII Cystogenesis. iScience 2020; 23:101629. [PMID: 33089114 PMCID: PMC7567049 DOI: 10.1016/j.isci.2020.101629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/05/2020] [Accepted: 09/25/2020] [Indexed: 01/12/2023] Open
Abstract
Madin-Darby canine kidney II (MDCKII) cells are widely used to study epithelial morphogenesis. To better understand this process, we performed time course RNA-seq analysis of MDCKII 3D cystogenesis, along with polarized 2D cells for comparison. Our study reveals a biphasic change in the transcriptome that occurs after the first cell cycle and coincides with lumen establishment. This change appears to be linked to translocation of β-catenin, supported by analyses with AVL9- and DENND5A-knockdown clones, and regulation by HNF1B, supported by ATAC-seq study. These findings indicate a qualitative change model for transcriptome remodeling during epithelial morphogenesis, leading to cell proliferation decrease and cell polarity establishment. Furthermore, our study reveals that active mitochondria are retained and chromatin accessibility decreases in 3D cysts but not in 2D polarized cells. This indicates that 3D culture is a better model than 2D culture for studying epithelial morphogenesis. The transcriptome switches after the first cell cycle and during MDCKII lumenogenesis The transcriptome switch is linked to β-catenin translocation and HNF1B activation Chromatin accessibility decreases during MDCKII cystogenesis Active mitochondria are maintained in 3D, but not 2D, epithelial morphogenesis
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Affiliation(s)
- Tianfang Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Sang-Ho Kwon
- Department of Anatomy, University of California, San Francisco, CA 94143-2140, USA.,Department of Cellular Biology and Anatomy, Augusta University, Medical College of Georgia, 1460 Laney Walker Boulevard, CB2820A, Augusta, GA 30912, USA
| | - Xiao Peng
- Department of Anatomy, University of California, San Francisco, CA 94143-2140, USA
| | - Severine Urdy
- Department of Anatomy, University of California, San Francisco, CA 94143-2140, USA
| | - Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Keith E Mostov
- Department of Anatomy, University of California, San Francisco, CA 94143-2140, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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11
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Jha AR, Shmalberg J, Tanprasertsuk J, Perry L, Massey D, Honaker RW. Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach. PLoS One 2020; 15:e0227289. [PMID: 32078625 PMCID: PMC7032713 DOI: 10.1371/journal.pone.0227289] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/16/2019] [Indexed: 01/13/2023] Open
Abstract
The role of gut microbiomes as important regulators of mammalian health is increasingly recognized, although feline and canine gut microbiomes remain poorly characterized. In this proof-of-concept study, we assessed the utility of a direct-to-consumer approach to executing pet microbiome studies. We characterized the gut microbiomes of 238 pets (46 cats and 192 dogs) by generating ~11 million merged reads that were mapped to the V4 region of 16S ribosomal RNA gene at a sequencing depth of 45,806 (±22,325) reads per sample. Analyses of these reads revealed that both feline and canine gut microbiomes are dominated by three major phyla, namely Firmicutes, Proteobacteria, and Bacteroides and that alpha diversity is higher in the feline gut. In addition to interspecies differences between the feline and canine gut, we also detected appreciable intraspecies bacterial variation within the canine population. While the dogs in this dataset could be assigned to three distinct clusters based on their gut microbiome, no clustering was observed within the feline population. Integration of additional data obtained from survey questionnaires revealed that geography and body weight may be associated with canine gut microbiome composition. Furthermore, we found that both the inter and intraspecies differences are more pronounced at finer taxonomic levels, indicating that strain-level investigations may be necessary in the future. This study demonstrates that the direct-to-consumer approach overcomes existing limitations in pet microbiome research, for example, it allows collection of large numbers of pet samples. The direct-to-consumer approach has proven successful in human genomics as well as human microbiomics and this study demonstrates that by building partnerships with an engaged general public this approach can also propel the field of pet microbiomics forward.
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Affiliation(s)
- Aashish R. Jha
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
- * E-mail:
| | - Justin Shmalberg
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
- Department of Comparative, Diagnostic & Population Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Jirayu Tanprasertsuk
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
| | - LeeAnn Perry
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
| | - Dan Massey
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
| | - Ryan W. Honaker
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
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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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