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Sakthikumar S, Warrier M, Whitley D, Facista S, Adkins J, Aman S, Tsinajinnie D, Duran N, Siravegna G, Ahmed Z, Day K, Jenkins B, Patel N, Ryden K, Nadai J, Banovich K, Powers B, Edwards J, Steinberg J, Fielder S, Wong S, Byron SA, Izatt T, Zismann V, Boateng M, Zhu Z, Chuang HY, Trent JM, Haworth D, Chon E, Hendricks W, Wang G. Genomic analysis across 53 canine cancer types reveals novel mutations and high clinical actionability potential. Vet Comp Oncol 2024; 22:30-41. [PMID: 38053317 DOI: 10.1111/vco.12944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/27/2023] [Accepted: 11/12/2023] [Indexed: 12/07/2023]
Abstract
A genomic understanding of the oncogenic processes and individual variability of human cancer has steadily fueled improvement in patient outcomes over the past 20 years. Mutations within tumour tissues are routinely assessed through clinical genomic diagnostic assays by academic and commercial laboratories to facilitate diagnosis, prognosis and effective treatment stratification. The application of genomics has unveiled a wealth of mutation-based biomarkers in canine cancers, suggesting that the transformative principles that have revolutionized human cancer medicine can be brought to bear in veterinary oncology. To advance clinical genomics and genomics-guided medicine in canine oncology, we have developed and validated a canine cancer next-generation sequencing gene panel for the identification of multiple mutation types in clinical specimens. With this panel, we examined the genomic landscapes of 828 tumours from 813 dogs, spanning 53 cancer types. We identified 7856 alterations, encompassing copy number variants, single nucleotide variants, indels and internal tandem duplications. Additionally, we evaluated the clinical utility of these alterations by incorporating a biomarker framework from comprehensive curation of primary canine literature and inferences from human cancer genomic biomarker literature and clinical diagnostics. Remarkably, nearly 90% of the cases exhibited mutations with diagnostic, prognostic or therapeutic implications. Our work represents a thorough assessment of genomic landscapes in a large cohort of canine cancers, the first of its kind for its comprehensive inclusion of multiple mutation types and structured annotation of biomarkers, demonstrating the clinical potential of leveraging mutation-based biomarkers in veterinary oncology.
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Affiliation(s)
| | | | | | | | | | - Sara Aman
- Vidium Animal Health, Phoenix, Arizona, USA
| | | | | | | | | | | | | | | | - Kirk Ryden
- Vidium Animal Health, Phoenix, Arizona, USA
| | - Joe Nadai
- Vidium Animal Health, Phoenix, Arizona, USA
| | | | | | | | - Jennifer Steinberg
- Center for Cancer Research at the National Cancer Institute, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Shukmei Wong
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Sara A Byron
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Tyler Izatt
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Victoria Zismann
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | | | | | - Jeffrey M Trent
- Translational Genomics Research Institute, Phoenix, Arizona, USA
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2
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Chon E, Sakthikumar S, Tang M, Hamilton MJ, Vaughan A, Smith A, Sommer B, Robat C, Manley C, Mullin C, Ohashi E, Manor E, Custis J, Intile J, Shiu KB, Parshley L, Bergman N, Sheppard‐Olivares S, Hafeman S, Wright Z, Haworth D, Hendricks W, Wang G. Novel genomic prognostic biomarkers for dogs with cancer. J Vet Intern Med 2023; 37:2410-2421. [PMID: 37801037 PMCID: PMC10658597 DOI: 10.1111/jvim.16893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Growing evidence from dogs and humans supports the abundance of mutation-based biomarkers in tumors of dogs. Increasing the use of clinical genomic diagnostic testing now provides another powerful data source for biomarker discovery. HYPOTHESIS Analyzed clinical outcomes in dogs with cancer profiled using SearchLight DNA, a cancer gene panel for dogs, to identify mutations with prognostic value. ANIMALS A total of 127 cases of cancer in dogs were analyzed using SearchLight DNA and for which clinical outcome information was available. METHODS Clinical data points were collected by medical record review. Variables including mutated genes, mutations, signalment, and treatment were fitted using Cox proportional hazard models to identify factors associated with progression-free survival (PFS). The log-rank test was used to compare PFS between patients receiving and not receiving targeted treatment before first progression. RESULTS Combined genomic and outcomes analysis identified 336 unique mutations in 89 genes across 26 cancer types. Mutations in 6 genes (CCND1, CCND3, SMARCB1, FANCG, CDKN2A/B, and MSH6) were significantly associated with shorter PFS. Dogs that received targeted treatment before first progression (n = 45) experienced significantly longer PFS compared with those that did not (n = 82, P = .01). This significance held true for 29 dogs that received genomically informed targeted treatment compared with those that did not (P = .05). CONCLUSION AND CLINICAL IMPORTANCE We identified novel mutations with prognostic value and demonstrate the benefit of targeted treatment across multiple cancer types. These results provide clinical evidence of the potential for genomics and precision medicine in dogs with cancer.
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Affiliation(s)
- Esther Chon
- Vidium Animal HealthA Subsidiary of The Translational Genomics Research Institute (TGen)ScottsdaleArizonaUSA
| | - Sharadha Sakthikumar
- Vidium Animal HealthA Subsidiary of The Translational Genomics Research Institute (TGen)ScottsdaleArizonaUSA
| | - Min Tang
- STATBEYOND Consulting LLCIrvineCaliforniaUSA
| | | | | | - Ashley Smith
- Department of Clinical SciencesAuburn University College of Veterinary MedicineAuburnAlabamaUSA
| | - Breann Sommer
- Wisconsin Veterinary Referral Center by EthosWaukeshaWisconsinUSA
| | - Cecilia Robat
- VCA Veterinary Emergency Service & Veterinary Specialty CenterMiddletonWisconsinUSA
| | | | | | - Emi Ohashi
- VCA Animal Specialty GroupLos AngelesCaliforniaUSA
| | - Emily Manor
- VCA Advanced Veterinary Care CenterFishersIndianaUSA
| | | | - Joanne Intile
- North Carolina State UniversityRaleighNorth CarolinaUSA
| | - Kai Biu Shiu
- VCA Veterinary Emergency Service & Veterinary Specialty CenterMiddletonWisconsinUSA
| | - Lisa Parshley
- Olympia Veterinary Specialists – The Cancer CenterOlympiaWashingtonUSA
| | - Noelle Bergman
- Department of Clinical SciencesAuburn University College of Veterinary MedicineAuburnAlabamaUSA
| | | | - Scott Hafeman
- VCA Highlands Ranch Animal Specialty and Emergency CenterHighlands RanchColoradoUSA
| | | | - David Haworth
- Vidium Animal HealthA Subsidiary of The Translational Genomics Research Institute (TGen)ScottsdaleArizonaUSA
| | - William Hendricks
- Vidium Animal HealthA Subsidiary of The Translational Genomics Research Institute (TGen)ScottsdaleArizonaUSA
| | - Guannan Wang
- Vidium Animal HealthA Subsidiary of The Translational Genomics Research Institute (TGen)ScottsdaleArizonaUSA
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3
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Sakthikumar S, Facista S, Whitley D, Byron SA, Ahmed Z, Warrier M, Zhu Z, Chon E, Banovich K, Haworth D, Hendricks WPD, Wang G. Standing in the canine precision medicine knowledge gap: Improving annotation of canine cancer genomic biomarkers through systematic comparative analysis of human cancer mutations in COSMIC. Vet Comp Oncol 2023; 21:482-491. [PMID: 37248814 DOI: 10.1111/vco.12911] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 05/31/2023]
Abstract
The accrual of cancer mutation data and related functional and clinical associations have revolutionised human oncology, enabling the advancement of precision medicine and biomarker-guided clinical management. The catalogue of cancer mutations is also growing in canine cancers. However, without direct high-powered functional data in dogs, it remains challenging to interpret and utilise them in research and clinical settings. It is well-recognised that canine and human cancers share genetic, molecular and phenotypic similarities. Therefore, leveraging the massive wealth of human mutation data may help advance canine oncology. Here, we present a structured analysis of sequence conservation and conversion of human mutations to the canine genome through a 'caninisation' process. We applied this analysis to COSMIC, the Catalogue of Somatic Mutations in Cancer, the most prominent human cancer mutation database. For the project's initial phase, we focused on the subset of the COSMIC data corresponding to Cancer Gene Census (CGC) genes. A total of 670 canine orthologs were found for 721 CGC genes. In these genes, 365 K unique mutations across 160 tumour types were converted successfully to canine coordinates. We identified shared putative cancer-driving mutations, including pathogenic and hotspot mutations and mutations bearing similar biomarker associations with diagnostic, prognostic and therapeutic utility. Thus, this structured caninisation of human cancer mutations facilitates the interpretation and annotation of canine mutations and helps bridge the knowledge gap to enable canine precision medicine.
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Affiliation(s)
| | | | - Derick Whitley
- Vidium Animal Health, a TGen Subsidiary, Phoenix, Arizona, USA
| | - Sara A Byron
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Zeeshan Ahmed
- Vidium Animal Health, a TGen Subsidiary, Phoenix, Arizona, USA
| | - Manisha Warrier
- Vidium Animal Health, a TGen Subsidiary, Phoenix, Arizona, USA
| | - Zhanyang Zhu
- Vidium Animal Health, a TGen Subsidiary, Phoenix, Arizona, USA
| | - Esther Chon
- Vidium Animal Health, a TGen Subsidiary, Phoenix, Arizona, USA
| | | | - David Haworth
- Vidium Animal Health, a TGen Subsidiary, Phoenix, Arizona, USA
| | | | - Guannan Wang
- Vidium Animal Health, a TGen Subsidiary, Phoenix, Arizona, USA
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4
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Roy A, Sakthikumar S, Kozyrev SV, Nordin J, Pensch R, Mäkeläinen S, Pettersson M, Karlsson EK, Lindblad-Toh K, Forsberg-Nilsson K. Using evolutionary constraint to define novel candidate driver genes in medulloblastoma. Proc Natl Acad Sci U S A 2023; 120:e2300984120. [PMID: 37549291 PMCID: PMC10438395 DOI: 10.1073/pnas.2300984120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/07/2023] [Indexed: 08/09/2023] Open
Abstract
Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory noncoding mutations, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end, we use whole-genome sequencing data from the International Cancer Genome Consortium and combined it with evolutionary constraint inferred from 240 mammals, to identify genes enriched in noncoding constraint mutations (NCCMs), mutations likely to be regulatory in nature. We compare medulloblastoma (MB), which is malignant, to pilocytic astrocytoma (PA), a primarily benign tumor, and find highly different NCCM frequencies between the two, in agreement with the fact that malignant cancers tend to have more mutations. In PA, a high NCCM frequency only affects the BRAF locus, which is the most commonly mutated gene in PA. In contrast, in MB, >500 genes have high levels of NCCMs. Intriguingly, several loci with NCCMs in MB are associated with different ages of onset, such as the HOXB cluster in young MB patients. In adult patients, NCCMs occurred in, e.g., the WASF-2/AHDC1/FGR locus. One of these NCCMs led to increased expression of the SRC kinase FGR and augmented responsiveness of MB cells to dasatinib, a SRC kinase inhibitor. Our analysis thus points to different molecular pathways in different patient groups. These newly identified putative candidate driver mutations may aid in patient stratification in MB and could be valuable for future selection of personalized treatment options.
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Affiliation(s)
- Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
- Broad Institute, Cambridge, MA02142
| | - Sergey V. Kozyrev
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Jessika Nordin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Raphaela Pensch
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Suvi Mäkeläinen
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | | | - Elinor K. Karlsson
- Broad Institute, Cambridge, MA02142
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA01605
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA01605
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
- Broad Institute, Cambridge, MA02142
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
- Division of Cancer and Stem Cells, University of Nottingham Biodiscovery Institute, NottinghamNG72RD, United Kingdom
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5
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Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler A, Keough KC, Zheng Z, Zeng J, Wray NR, Li Y, Johnson J, Chen J, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science 2023; 380:eabn2937. [PMID: 37104612 PMCID: PMC10259825 DOI: 10.1126/science.abn2937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/09/2023] [Indexed: 04/29/2023]
Abstract
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
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Affiliation(s)
- Patrick F. Sullivan
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Steven Gazal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - BaDoi N. Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xue Li
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Diane P. Genereux
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael X. Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Jessika Nordin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Voichita D. Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Chao Wang
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - James Xue
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Center for System Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Quan Sun
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Laura M. Huckins
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alyssa Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kathleen C. Keough
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yun Li
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jessica Johnson
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | | | - Benedict Paten
- UC Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75185 Uppsala, Sweden
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Elinor K. Karlsson
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
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6
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Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wallerman O, Xue JR, Li Y, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler AJ, Keough KC, Zheng Z, Zeng J, Wray NR, Johnson J, Chen J, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease. bioRxiv 2023:2023.03.10.531987. [PMID: 36945512 PMCID: PMC10028973 DOI: 10.1101/2023.03.10.531987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of the human genome as significantly constrained, and likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionarily constrained positions are enriched for variants explaining common disease heritability (more than any other functional annotation). Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
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Affiliation(s)
- Patrick F. Sullivan
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet; Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Steven Gazal
- Keck School of Medicine, University of Southern California; Los Angeles, CA 90033, USA
| | - BaDoi N. Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine; Pittsburgh, PA 15261, USA
- Neuroscience Institute, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Xue Li
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School; Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
| | | | - Michael X. Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
| | - Jessika Nordin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; Uppsala, 751 85, Sweden
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; Uppsala, 751 85, Sweden
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Voichita D. Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - James R. Xue
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
| | - Yun Li
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet; Stockholm, Sweden
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
| | - Laura M. Huckins
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Alyssa J. Lawler
- Neuroscience Institute, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Kathleen C. Keough
- Department of Epidemiology & Biostatistics, University of California San Francisco; San Francisco, CA 94158, USA
- Fauna Bio Incorporated; Emeryville, CA 94608, USA
- Gladstone Institutes; San Francisco, CA 94158, USA
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland; Brisbane, Queensland, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, University of Queensland; Brisbane, Queensland, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland; Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland; Brisbane, Queensland, Australia
| | - Jessica Johnson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | | | - Benedict Paten
- Genomics Institute, University of California Santa Cruz; Santa Cruz, CA 95064, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine; New Haven, CT 06510, USA
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin; Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
| | - Katherine S. Pollard
- Department of Epidemiology & Biostatistics, University of California San Francisco; San Francisco, CA 94158, USA
- Gladstone Institutes; San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub; San Francisco, CA 94158, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; Uppsala, 751 85, Sweden
- Biodiscovery Institute, University of Nottingham; Nottingham, UK
| | - Elinor K. Karlsson
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
- Program in Molecular Medicine, UMass Chan Medical School; Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
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7
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Chon E, Wang G, Whitley D, Sakthikumar S, Warrier M, Wong S, Duran N, Adkins J, Boateng M, Zhu Z, Facista S, Haworth D, Hendricks W. Genomic tumor analysis provides clinical guidance for the management of diagnostically challenging cancers in dogs. J Am Vet Med Assoc 2023; 261:668-677. [PMID: 36862546 DOI: 10.2460/javma.22.11.0489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Abstract
OBJECTIVE To evaluate the diagnostic, prognostic, and therapeutic utility of a cancer genomic diagnostic assay (SearchLight DNA; Vidium Animal Health) for diagnostically ambiguous cancer cases. ANIMALS 69 privately owned dogs with ambiguous cancer diagnoses and for which the genomic assay was performed. PROCEDURES Genomic assay reports generated between September 28, 2020, and July 31, 2022, for dogs with malignancy or suspected malignancy were reviewed to determine the assay's clinical utility defined as providing diagnostic clarity, prognostic information, and/or therapeutic options. RESULTS Genomic analysis provided diagnostic clarity in 37 of 69 cases (54%; group 1) and therapeutic and/or prognostic information in 22 of the remaining 32 cases (69%; group 2) for which the diagnosis remained elusive. Overall, the genomic assay was clinically useful in 86% (59/69) of cases. CLINICAL RELEVANCE To our knowledge, this was the first study to evaluate the multifaceted clinical utility of a single cancer genomic test in veterinary medicine. Study findings supported the use of tumor genomic testing for dogs with cancer, particularly those that are diagnostically ambiguous and therefore inherently challenging to manage. This evidence-driven genomic assay provided diagnostic guidance, prognostic support, and therapeutic options for most patients with an unclear cancer diagnosis that would otherwise have an unsubstantiated clinical plan. Furthermore, 38% (26/69) of samples were easily obtained aspirates. Sample factors (sample type, percentage of tumor cells, and number of mutations) did not influence diagnostic yield. Our study demonstrated the value of genomic testing for the management of canine cancer.
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Affiliation(s)
- Esther Chon
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | - Guannan Wang
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | - Derick Whitley
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | | | - Manisha Warrier
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | - Shukmei Wong
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | - Natalie Duran
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | - Jonathan Adkins
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | - Martin Boateng
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | - Zhanyang Zhu
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | - Salvatore Facista
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | - David Haworth
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
| | - William Hendricks
- Vidium Animal Health, Translational Genomics Research Institute, Scottsdale, AZ
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8
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Arendt ML, Sakthikumar S, Melin M, Elvers I, Rivera P, Larsen M, Saellström S, Lingaas F, Rönnberg H, Lindblad-Toh K. PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia. Sci Rep 2023; 13:632. [PMID: 36635367 PMCID: PMC9837039 DOI: 10.1038/s41598-023-27664-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Biological features of neoplastic disease affecting mammary gland tissue are shared between canines and humans. Research performed in either species has translational value and early phase clinical trials performed in canines with spontaneous disease could be informative for human trials. The purpose of this study was to investigate the somatic genetic aberrations occurring in canine mammary neoplasia by exome capture and next generation sequencing. Based on 55 tumor-normal pairs we identified the PIK3CA gene as the most commonly mutated gene in canine mammary tumors, with 25% of samples carrying mutations in this gene. A recurrent missense mutation was identified, p.H1047R, which is homologous to the human PIK3CA hotspot mutation found in different types of breast neoplasia. Mutations homologous to other known human mutation hotspots such as the PIK3CA p.E545K and the KRAS p.G12V/D were also identified. We identified copy number aberrations affecting important tumor suppressor and oncogenic pathways including deletions affecting the PTEN tumor suppressor gene. We suggest that activation of the KRAS or PIK3CA oncogenes or loss of the PTEN suppressor gene may be important for mammary tumor development in dogs. This data endorses the conservation of cancer across species and the validity of studying cancer in non-human species.
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Affiliation(s)
- Maja Louise Arendt
- Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | | | - Malin Melin
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Uppsala University, Uppsala, Sweden
| | | | | | | | - Sara Saellström
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Frode Lingaas
- Veterinary Faculty, Norwegian University of Life Sciences, Ås, Norway
| | - Henrik Rönnberg
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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9
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Fellers JP, Sakthikumar S, He F, McRell K, Bakkeren G, Cuomo CA, Kolmer JA. Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations. G3 (Bethesda) 2021; 11:jkab219. [PMID: 34544127 PMCID: PMC8496273 DOI: 10.1093/g3journal/jkab219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/01/2021] [Indexed: 11/14/2022]
Abstract
The wheat leaf rust fungus, Puccinia triticina Erikss., is a worldwide pathogen of tetraploid durum and hexaploid wheat. Many races of P. triticina differ for virulence to specific leaf rust resistance genes and are found in most wheat-growing regions of the world. Wheat cultivars with effective leaf rust resistance exert selection pressure on P. triticina populations for virulent race types. The objectives of this study were to examine whole-genome sequence data of 121 P. triticina isolates and to gain insight into race evolution. The collection included isolates comprising of many different race phenotypes collected worldwide from common and durum wheat. One isolate from wild wheat relative Aegilops speltoides and two from Ae. cylindrica were also included for comparison. Based on 121,907 informative variants identified relative to the reference Race 1-1 genome, isolates were clustered into 11 major lineages with 100% bootstrap support. The isolates were also grouped based on variation in 1311 predicted secreted protein genes. In gene-coding regions, all groups had high ratios of nonsynonymous to synonymous mutations and nonsense to readthrough mutations. Grouping of isolates based on two main variation principle components for either genome-wide variation or variation just within the secreted protein genes, indicated similar groupings. Variants were distributed across the entire genome, not just within the secreted protein genes. Our results suggest that recurrent mutation and selection play a major role in differentiation within the clonal lineages.
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Affiliation(s)
- John P Fellers
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | | | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Katie McRell
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Guus Bakkeren
- Agriculture and Agri Food Canada, Summerland, BC V0H1Z0, USA
| | | | - James A Kolmer
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN 55108, USA
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10
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Sakthikumar S, Roy A, Haseeb L, Pettersson ME, Sundström E, Marinescu VD, Lindblad-Toh K, Forsberg-Nilsson K. Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes. Genome Biol 2020; 21:127. [PMID: 32513296 PMCID: PMC7281935 DOI: 10.1186/s13059-020-02035-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) has one of the worst 5-year survival rates of all cancers. While genomic studies of the disease have been performed, alterations in the non-coding regulatory regions of GBM have largely remained unexplored. We apply whole-genome sequencing (WGS) to identify non-coding mutations, with regulatory potential in GBM, under the hypothesis that regions of evolutionary constraint are likely to be functional, and somatic mutations are likely more damaging than in unconstrained regions. RESULTS We validate our GBM cohort, finding similar copy number aberrations and mutated genes based on coding mutations as previous studies. Performing analysis on non-coding constraint mutations and their position relative to nearby genes, we find a significant enrichment of non-coding constraint mutations in the neighborhood of 78 genes that have previously been implicated in GBM. Among them, SEMA3C and DYNC1I1 show the highest frequencies of alterations, with multiple mutations overlapping transcription factor binding sites. We find that a non-coding constraint mutation in the SEMA3C promoter reduces the DNA binding capacity of the region. We also identify 1776 other genes enriched for non-coding constraint mutations with likely regulatory potential, providing additional candidate GBM genes. The mutations in the top four genes, DLX5, DLX6, FOXA1, and ISL1, are distributed over promoters, UTRs, and multiple transcription factor binding sites. CONCLUSIONS These results suggest that non-coding constraint mutations could play an essential role in GBM, underscoring the need to connect non-coding genomic variation to biological function and disease pathology.
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Affiliation(s)
- Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
- Broad Institute, Cambridge, MA, 02142, USA
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Lulu Haseeb
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Elisabeth Sundström
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Voichita D Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
- Broad Institute, Cambridge, MA, 02142, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden.
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11
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Megquier K, Turner-Maier J, Swofford R, Kim JH, Sarver AL, Wang C, Sakthikumar S, Johnson J, Koltookian M, Lewellen M, Scott MC, Schulte AJ, Borst L, Tonomura N, Alfoldi J, Painter C, Thomas R, Karlsson EK, Breen M, Modiano JF, Elvers I, Lindblad-Toh K. Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma. Mol Cancer Res 2019; 17:2410-2421. [PMID: 31570656 PMCID: PMC7067513 DOI: 10.1158/1541-7786.mcr-19-0221] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 07/12/2019] [Accepted: 09/25/2019] [Indexed: 12/23/2022]
Abstract
Angiosarcoma is a highly aggressive cancer of blood vessel-forming cells with few effective treatment options and high patient mortality. It is both rare and heterogenous, making large, well-powered genomic studies nearly impossible. Dogs commonly suffer from a similar cancer, called hemangiosarcoma, with breeds like the golden retriever carrying heritable genetic factors that put them at high risk. If the clinical similarity of canine hemangiosarcoma and human angiosarcoma reflects shared genomic etiology, dogs could be a critically needed model for advancing angiosarcoma research. We assessed the genomic landscape of canine hemangiosarcoma via whole-exome sequencing (47 golden retriever hemangiosarcomas) and RNA sequencing (74 hemangiosarcomas from multiple breeds). Somatic coding mutations occurred most frequently in the tumor suppressor TP53 (59.6% of cases) as well as two genes in the PI3K pathway: the oncogene PIK3CA (29.8%) and its regulatory subunit PIK3R1 (8.5%). The predominant mutational signature was the age-associated deamination of cytosine to thymine. As reported in human angiosarcoma, CDKN2A/B was recurrently deleted and VEGFA, KDR, and KIT recurrently gained. We compared the canine data to human data recently released by The Angiosarcoma Project, and found many of the same genes and pathways significantly enriched for somatic mutations, particularly in breast and visceral angiosarcomas. Canine hemangiosarcoma closely models the genomic landscape of human angiosarcoma of the breast and viscera, and is a powerful tool for investigating the pathogenesis of this devastating disease. IMPLICATIONS: We characterize the genomic landscape of canine hemangiosarcoma and demonstrate its similarity to human angiosarcoma.
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Affiliation(s)
- Kate Megquier
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | - Ross Swofford
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Jong-Hyuk Kim
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
- Animal Cancer Care and Research Program, University of Minnesota, St. Paul, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Aaron L Sarver
- Animal Cancer Care and Research Program, University of Minnesota, St. Paul, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sharadha Sakthikumar
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jeremy Johnson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Mitzi Lewellen
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
- Animal Cancer Care and Research Program, University of Minnesota, St. Paul, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Milcah C Scott
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
- Animal Cancer Care and Research Program, University of Minnesota, St. Paul, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Ashley J Schulte
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
- Animal Cancer Care and Research Program, University of Minnesota, St. Paul, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Luke Borst
- Department of Clinical Sciences, North Carolina State College of Veterinary Medicine, Raleigh, North Carolina
| | - Noriko Tonomura
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts
| | - Jessica Alfoldi
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Corrie Painter
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Count Me In, Cambridge, Massachusetts
| | - Rachael Thomas
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, and Comparative Medicine Institute, Raleigh, North Carolina
| | - Elinor K Karlsson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, and Comparative Medicine Institute, Raleigh, North Carolina
| | - Jaime F Modiano
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
- Animal Cancer Care and Research Program, University of Minnesota, St. Paul, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Center for Immunology, University of Minnesota, Minneapolis, Minneapolis
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota
- Institute for Engineering in Medicine, University of Minnesota, Minneapolis, Minnesota
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Ingegerd Elvers
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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12
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Sakthikumar S, Elvers I, Kim J, Arendt ML, Thomas R, Turner-Maier J, Swofford R, Johnson J, Schumacher SE, Alföldi J, Axelsson E, Couto CG, Kisseberth WC, Pettersson ME, Getz G, Meadows JRS, Modiano JF, Breen M, Kierczak M, Forsberg-Nilsson K, Marinescu VD, Lindblad-Toh K. SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma. Cancer Res 2018; 78:3421-3431. [PMID: 29724721 DOI: 10.1158/0008-5472.can-17-3558] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/15/2018] [Accepted: 04/30/2018] [Indexed: 11/16/2022]
Abstract
Osteosarcoma is a debilitating bone cancer that affects humans, especially children and adolescents. A homologous form of osteosarcoma spontaneously occurs in dogs, and its differential incidence observed across breeds allows for the investigation of tumor mutations in the context of multiple genetic backgrounds. Using whole-exome sequencing and dogs from three susceptible breeds (22 golden retrievers, 21 Rottweilers, and 23 greyhounds), we found that osteosarcoma tumors show a high frequency of somatic copy-number alterations (SCNA), affecting key oncogenes and tumor-suppressor genes. The across-breed results are similar to what has been observed for human osteosarcoma, but the disease frequency and somatic mutation counts vary in the three breeds. For all breeds, three mutational signatures (one of which has not been previously reported) and 11 significantly mutated genes were identified. TP53 was the most frequently altered gene (83% of dogs have either mutations or SCNA in TP53), recapitulating observations in human osteosarcoma. The second most frequently mutated gene, histone methyltransferase SETD2, has known roles in multiple cancers, but has not previously been strongly implicated in osteosarcoma. This study points to the likely importance of histone modifications in osteosarcoma and highlights the strong genetic similarities between human and dog osteosarcoma, suggesting that canine osteosarcoma may serve as an excellent model for developing treatment strategies in both species.Significance: Canine osteosarcoma genomics identify SETD2 as a possible oncogenic driver of osteosarcoma, and findings establish the canine model as a useful comparative model for the corresponding human disease. Cancer Res; 78(13); 3421-31. ©2018 AACR.
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Affiliation(s)
- Sharadha Sakthikumar
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Broad Institute, Cambridge, Massachusetts
| | - Ingegerd Elvers
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute, Cambridge, Massachusetts
| | - Jaegil Kim
- Broad Institute, Cambridge, Massachusetts
| | - Maja L Arendt
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg D, Denmark
| | - Rachael Thomas
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina
| | | | | | | | | | | | - Erik Axelsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - C Guillermo Couto
- Department of Veterinary Clinical Sciences and Veterinary Medical Center, the Ohio State University, Columbus, Ohio
- Couto Veterinary Consultants, Hilliard, Ohio
| | - William C Kisseberth
- Department of Veterinary Clinical Sciences and Veterinary Medical Center, the Ohio State University, Columbus, Ohio
| | - Mats E Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gad Getz
- Broad Institute, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital, Boston, Massachusetts
| | - Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jaime F Modiano
- Animal Cancer Care and Research Program, College of Veterinary Medicine, St. Paul, Minnesota
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, St. Paul, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota
- Institute for Engineering and Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Matthew Breen
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina
| | - Marcin Kierczak
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Voichita D Marinescu
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Broad Institute, Cambridge, Massachusetts
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13
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Wu JQ, Sakthikumar S, Dong C, Zhang P, Cuomo CA, Park RF. Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia. Front Plant Sci 2017; 8:148. [PMID: 28232843 PMCID: PMC5298990 DOI: 10.3389/fpls.2017.00148] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/24/2017] [Indexed: 05/05/2023]
Abstract
Leaf rust is one of the most common and damaging diseases of wheat, and is caused by an obligate biotrophic basidiomycete, Puccinia triticina (Pt). In the present study, 20 Pt isolates from Australia, comprising 10 phenotype-matched pairs with contrasting pathogenicity for Lr20, were analyzed using whole genome sequencing. Compared to the reference genome of the American Pt isolate 1-1 BBBD Race 1, an average of 404,690 single nucleotide polymorphisms (SNPs) per isolate was found and the proportion of heterozygous SNPs was above 87% in the majority of the isolates, demonstrating a high level of polymorphism and a high rate of heterozygosity. From the genome-wide SNPs, a phylogenetic tree was inferred, which consisted of a large clade of 15 isolates representing diverse presumed clonal lineages including 14 closely related isolates and the more diverged isolate 670028, and a small clade of five isolates characterized by lower heterozygosity level. Principle component analysis detected three distinct clusters, corresponding exactly to the two major subsets of the small clade and the large clade comprising all 15 isolates without further separation of isolate 670028. While genome-wide association analysis identified 302 genes harboring at least one SNP associated with Lr20 virulence (p < 0.05), a Wilcoxon rank sum test revealed that 36 and 68 genes had significant (p < 0.05) and marginally significant (p < 0.1) differences in the counts of non-synonymous mutations between Lr20 avirulent and virulent groups, respectively. Twenty of these genes were predicted to have a signal peptide without a transmembrane segment, and hence identified as candidate effector genes corresponding to Lr20. SNP analysis also implicated the potential involvement of epigenetics and small RNA in Pt pathogenicity. Future studies are thus warranted to investigate the biological functions of the candidate effectors as well as the gene regulation mechanisms at epigenetic and post-transcription levels. Our study is the first to integrate phenotype-genotype association with effector prediction in Pt genomes, an approach that may circumvent some of the technical difficulties in working with obligate rust fungi and accelerate avirulence gene identification.
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Affiliation(s)
- Jing Qin Wu
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Sharadha Sakthikumar
- Genome Sequencing and Analysis Program, Broad Institute of Massachusetts Institute of Technology (MIT) and HarvardCambridge, MA, USA
| | - Chongmei Dong
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Peng Zhang
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Christina A. Cuomo
- Genome Sequencing and Analysis Program, Broad Institute of Massachusetts Institute of Technology (MIT) and HarvardCambridge, MA, USA
| | - Robert F. Park
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
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14
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Muñoz JF, Farrer RA, Desjardins CA, Gallo JE, Sykes S, Sakthikumar S, Misas E, Whiston EA, Bagagli E, Soares CMA, Teixeira MDM, Taylor JW, Clay OK, McEwen JG, Cuomo CA. Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides. mSphere 2016; 1:e00213-16. [PMID: 27704050 PMCID: PMC5040785 DOI: 10.1128/msphere.00213-16] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/06/2016] [Indexed: 12/29/2022] Open
Abstract
The Paracoccidioides genus includes two species of thermally dimorphic fungi that cause paracoccidioidomycosis, a neglected health-threatening human systemic mycosis endemic to Latin America. To examine the genome evolution and the diversity of Paracoccidioides spp., we conducted whole-genome sequencing of 31 isolates representing the phylogenetic, geographic, and ecological breadth of the genus. These samples included clinical, environmental and laboratory reference strains of the S1, PS2, PS3, and PS4 lineages of P. brasiliensis and also isolates of Paracoccidioides lutzii species. We completed the first annotated genome assemblies for the PS3 and PS4 lineages and found that gene order was highly conserved across the major lineages, with only a few chromosomal rearrangements. Comparing whole-genome assemblies of the major lineages with single-nucleotide polymorphisms (SNPs) predicted from the remaining 26 isolates, we identified a deep split of the S1 lineage into two clades we named S1a and S1b. We found evidence for greater genetic exchange between the S1b lineage and all other lineages; this may reflect the broad geographic range of S1b, which is often sympatric with the remaining, largely geographically isolated lineages. In addition, we found evidence of positive selection for the GP43 and PGA1 antigen genes and genes coding for other secreted proteins and proteases and lineage-specific loss-of-function mutations in cell wall and protease genes; these together may contribute to virulence and host immune response variation among natural isolates of Paracoccidioides spp. These insights into the recent evolutionary events highlight important differences between the lineages that could impact the distribution, pathogenicity, and ecology of Paracoccidioides. IMPORTANCE Characterization of genetic differences between lineages of the dimorphic human-pathogenic fungus Paracoccidioides can identify changes linked to important phenotypes and guide the development of new diagnostics and treatments. In this article, we compared genomes of 31 diverse isolates representing the major lineages of Paracoccidioides spp. and completed the first annotated genome sequences for the PS3 and PS4 lineages. We analyzed the population structure and characterized the genetic diversity among the lineages of Paracoccidioides, including a deep split of S1 into two lineages (S1a and S1b), and differentiated S1b, associated with most clinical cases, as the more highly recombining and diverse lineage. In addition, we found patterns of positive selection in surface proteins and secreted enzymes among the lineages, suggesting diversifying mechanisms of pathogenicity and adaptation across this species complex. These genetic differences suggest associations with the geographic range, pathogenicity, and ecological niches of Paracoccidioides lineages.
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Affiliation(s)
- José F. Muñoz
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rhys A. Farrer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Juan E. Gallo
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Sean Sykes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Elizabeth Misas
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Emily A. Whiston
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Eduardo Bagagli
- Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Celia M. A. Soares
- Laboratório de Biología Molecular, Instituto de Ciências Biológicas, ICBII, Goiânia, Brazil
| | - Marcus de M. Teixeira
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
- Division of Pathogen Genomics, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Oliver K. Clay
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan G. McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
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15
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Hirakawa MP, Martinez DA, Sakthikumar S, Anderson MZ, Berlin A, Gujja S, Zeng Q, Zisson E, Wang JM, Greenberg JM, Berman J, Bennett RJ, Cuomo CA. Genetic and phenotypic intra-species variation in Candida albicans. Genome Res 2014; 25:413-25. [PMID: 25504520 PMCID: PMC4352881 DOI: 10.1101/gr.174623.114] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number variations, chromosomal inversions, subtelomeric hypervariation, loss of heterozygosity (LOH), and whole or partial chromosome aneuploidies. All 21 strains were diploid, although karyotypic changes were present in eight of the 21 isolates, with multiple strains being trisomic for Chromosome 4 or Chromosome 7. Aneuploid strains exhibited a general fitness defect relative to euploid strains when grown under replete conditions. All strains were also heterozygous, yet multiple, distinct LOH tracts were present in each isolate. Higher overall levels of genome heterozygosity correlated with faster growth rates, consistent with increased overall fitness. Genes with the highest rates of amino acid substitutions included many cell wall proteins, implicating fast evolving changes in cell adhesion and host interactions. One clinical isolate, P94015, presented several striking properties including a novel cellular phenotype, an inability to filament, drug resistance, and decreased virulence. Several of these properties were shown to be due to a homozygous nonsense mutation in the EFG1 gene. Furthermore, loss of EFG1 function resulted in increased fitness of P94015 in a commensal model of infection. Our analysis therefore reveals intra-species genetic and phenotypic differences in C. albicans and delineates a natural mutation that alters the balance between commensalism and pathogenicity.
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Affiliation(s)
- Matthew P Hirakawa
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA
| | - Diego A Martinez
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Matthew Z Anderson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA; Department of Molecular, Cellular Biology and Genetics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Aaron Berlin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sharvari Gujja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ethan Zisson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA
| | - Joshua M Wang
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA
| | - Joshua M Greenberg
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA
| | - Judith Berman
- Department of Molecular, Cellular Biology and Genetics, University of Minnesota, Minneapolis, Minnesota 55455, USA; Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA;
| | - Christina A Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;
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16
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Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963. [PMID: 25409509 PMCID: PMC4237348 DOI: 10.1371/journal.pone.0112963] [Citation(s) in RCA: 5043] [Impact Index Per Article: 504.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/16/2014] [Indexed: 02/06/2023] Open
Abstract
Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3–5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.
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Affiliation(s)
- Bruce J. Walker
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (BJW); (AME)
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Margaret Priest
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Amr Abouelliel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sharadha Sakthikumar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jennifer Wortman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sarah K. Young
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ashlee M. Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (BJW); (AME)
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17
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Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailão AM, Brigido MM, Ferreira MEDS, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, León-Narváez H, Longo LVG, Ma LJ, Malavazi I, Matsuo AL, Morais FV, Pereira M, Rodríguez-Brito S, Sakthikumar S, Salem-Izacc SM, Sykes SM, Teixeira MM, Vallejo MC, Walter MEMT, Yandava C, Young S, Zeng Q, Zucker J, Felipe MS, Goldman GH, Haas BJ, McEwen JG, Nino-Vega G, Puccia R, San-Blas G, Soares CMDA, Birren BW, Cuomo CA. Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. PLoS Genet 2011; 7:e1002345. [PMID: 22046142 PMCID: PMC3203195 DOI: 10.1371/journal.pgen.1002345] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 08/30/2011] [Indexed: 12/29/2022] Open
Abstract
Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of Onygenales to transfer from soil to animal hosts.
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Affiliation(s)
| | - Mia D. Champion
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jason W. Holder
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Jonathan Goldberg
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Alexandre M. Bailão
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | | | | | - Ana Maria Garcia
- Unidad de Biología Celular y Molecular, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Sharvari Gujja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - David I. Heiman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Matthew R. Henn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Chinnappa D. Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Henry León-Narváez
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Larissa V. G. Longo
- Departamento de Microbiologia, Imunologia, e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Li-Jun Ma
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Iran Malavazi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Alisson L. Matsuo
- Departamento de Microbiologia, Imunologia, e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Flavia V. Morais
- Departamento de Microbiologia, Imunologia, e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Instituto de Pesquisa y Desenvolvimento, Universidade do Vale do Paraíba, São José dos Campos, Brazil
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Sabrina Rodríguez-Brito
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Sharadha Sakthikumar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Silvia M. Salem-Izacc
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Sean M. Sykes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Milene C. Vallejo
- Departamento de Microbiologia, Imunologia, e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Chandri Yandava
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeremy Zucker
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Maria Sueli Felipe
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo, Ribeirão Preto, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol – CTBE, São Paulo, Brazil
| | - Brian J. Haas
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Juan G. McEwen
- Unidad de Biología Celular y Molecular, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Gustavo Nino-Vega
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia, e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gioconda San-Blas
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | | | - Bruce W. Birren
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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18
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Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RAE, Chapman S, Coulson R, Coutinho PM, Danchin EGJ, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 2010; 464:367-73. [PMID: 20237561 PMCID: PMC3048781 DOI: 10.1038/nature08850] [Citation(s) in RCA: 998] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 01/20/2010] [Indexed: 11/09/2022]
Abstract
Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.
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Affiliation(s)
- Li-Jun Ma
- The Broad Institute, Cambridge, Massachusetts 02141, USA
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