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Silver KI, Mannheimer JD, Saba C, Hendricks WPD, Wang G, Day K, Warrier M, Beck JA, Mazcko C, LeBlanc AK. Clinical, pathologic and molecular findings in 2 Rottweiler littermates with appendicular osteosarcoma. Res Sq 2024:rs.3.rs-4223759. [PMID: 38659878 PMCID: PMC11042397 DOI: 10.21203/rs.3.rs-4223759/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Appendicular osteosarcoma was diagnosed and treated in a pair of littermate Rottweiler dogs, resulting in distinctly different clinical outcomes despite similar therapy within the context of a prospective, randomized clinical trial (NCI-COTC021/022). Histopathology, immunohistochemistry, mRNA sequencing, and targeted DNA hotspot sequencing techniques were applied to both dogs' tumors to define factors that could underpin their differential response to treatment. We describe the comparison of their clinical, histologic and molecular features, as well as those from a companion cohort of Rottweiler dogs, providing new insight into potential prognostic biomarkers for canine osteosarcoma.
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Affiliation(s)
| | | | | | - William P D Hendricks
- Vidium Animal Health, A Subsidiary of The Translational Genomics Research Institute (TGen)
| | - Guannan Wang
- Vidium Animal Health, A Subsidiary of The Translational Genomics Research Institute (TGen)
| | - Kenneth Day
- Vidium Animal Health, A Subsidiary of The Translational Genomics Research Institute (TGen)
| | - Manisha Warrier
- Vidium Animal Health, A Subsidiary of The Translational Genomics Research Institute (TGen)
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Mannheimer JD, Tawa G, Gerhold D, Braisted J, Sayers CM, McEachron TA, Meltzer P, Mazcko C, Beck JA, LeBlanc AK. Transcriptional profiling of canine osteosarcoma identifies prognostic gene expression signatures with translational value for humans. Commun Biol 2023; 6:856. [PMID: 37591946 PMCID: PMC10435536 DOI: 10.1038/s42003-023-05208-z] [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: 11/30/2022] [Accepted: 08/03/2023] [Indexed: 08/19/2023] Open
Abstract
Canine osteosarcoma is increasingly recognized as an informative model for human osteosarcoma. Here we show in one of the largest clinically annotated canine osteosarcoma transcriptional datasets that two previously reported, as well as de novo gene signatures devised through single sample Gene Set Enrichment Analysis (ssGSEA), have prognostic utility in both human and canine patients. Shared molecular pathway alterations are seen in immune cell signaling and activation including TH1 and TH2 signaling, interferon signaling, and inflammatory responses. Virtual cell sorting to estimate immune cell populations within canine and human tumors showed similar trends, predominantly for macrophages and CD8+ T cells. Immunohistochemical staining verified the increased presence of immune cells in tumors exhibiting immune gene enrichment. Collectively these findings further validate naturally occurring osteosarcoma of the pet dog as a translationally relevant patient model for humans and improve our understanding of the immunologic and genomic landscape of the disease in both species.
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Affiliation(s)
- Joshua D Mannheimer
- Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gregory Tawa
- Division of Preclinical Innovation, Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - David Gerhold
- Division of Preclinical Innovation, Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - John Braisted
- Division of Preclinical Innovation, Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Carly M Sayers
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Troy A McEachron
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christina Mazcko
- Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jessica A Beck
- Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy K LeBlanc
- Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Witta S, Collins KP, Ramirez DA, Mannheimer JD, Wittenburg LA, Gustafson DL. Vinblastine pharmacokinetics in mouse, dog, and human in the context of a physiologically based model incorporating tissue-specific drug binding, transport, and metabolism. Pharmacol Res Perspect 2023; 11:e01052. [PMID: 36631976 PMCID: PMC9834611 DOI: 10.1002/prp2.1052] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Vinblastine (VBL) is a vinca alkaloid-class cytotoxic chemotherapeutic that causes microtubule disruption and is typically used to treat hematologic malignancies. VBL is characterized by a narrow therapeutic index, with key dose-limiting toxicities being myelosuppression and neurotoxicity. Pharmacokinetics (PK) of VBL is primarily driven by ABCB1-mediated efflux and CYP3A4 metabolism, creating potential for drug-drug interaction. To characterize sources of variability in VBL PK, we developed a physiologically based pharmacokinetic (PBPK) model in Mdr1a/b(-/-) knockout and wild-type mice by incorporating key drivers of PK, including ABCB1 efflux, CYP3A4 metabolism, and tissue-specific tubulin binding, and scaled this model to accurately simulate VBL PK in humans and pet dogs. To investigate the capability of the model to capture interindividual variability in clinical data, virtual populations of humans and pet dogs were generated through Monte Carlo simulation of physiologic and biochemical parameters and compared to the clinical PK data. This model provides a foundation for predictive modeling of VBL PK. The base PBPK model can be further improved with supplemental experimental data identifying drug-drug interactions, ABCB1 polymorphisms and expression, and other sources of physiologic or metabolic variability.
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Affiliation(s)
- Sandra Witta
- Flint Animal Cancer CenterColorado State UniversityFort CollinsColoradoUSA
- School of Biomedical EngineeringColorado State UniversityFort CollinsColoradoUSA
| | - Keagan P. Collins
- Flint Animal Cancer CenterColorado State UniversityFort CollinsColoradoUSA
- School of Biomedical EngineeringColorado State UniversityFort CollinsColoradoUSA
| | | | - Joshua D. Mannheimer
- Flint Animal Cancer CenterColorado State UniversityFort CollinsColoradoUSA
- School of Biomedical EngineeringColorado State UniversityFort CollinsColoradoUSA
| | - Luke A. Wittenburg
- Department of Surgical and Radiological SciencesUniversity of CaliforniaDavisCaliforniaUSA
- University of CaliforniaDavis Comprehensive Cancer CenterSacramentoCaliforniaUSA
| | - Daniel L. Gustafson
- Flint Animal Cancer CenterColorado State UniversityFort CollinsColoradoUSA
- School of Biomedical EngineeringColorado State UniversityFort CollinsColoradoUSA
- Developmental Therapeutics ProgramUniversity of Colorado Cancer CenterAuroraColoradoUSA
- Department of Clinical SciencesColorado State UniversityFort CollinsColoradoUSA
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Mannheimer JD, Prasad A, Gustafson DL. Predicting chemosensitivity using drug perturbed gene dynamics. BMC Bioinformatics 2021; 22:15. [PMID: 33413081 PMCID: PMC7789515 DOI: 10.1186/s12859-020-03947-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
Background One of the current directions of precision medicine is the use of computational methods to aid in the diagnosis, prognosis, and treatment of disease based on data driven approaches. For instance, in oncology, there has been a particular focus on development of algorithms and biomarkers that can be used for pre-clinical and clinical applications. In particular large-scale omics-based models to predict drug sensitivity in in vitro cancer cell line panels have been used to explore the utility and aid in the development of these models as clinical tools. Additionally, a number of web-based interfaces have been constructed for researchers to explore the potential of drug perturbed gene expression as biomarkers including the NCI Transcriptional Pharmacodynamic Workbench. In this paper we explore the influence of drug perturbed gene dynamics of the NCI Transcriptional Pharmacodynamics Workbench in computational models to predict in vitro drug sensitivity for 15 drugs on the NCI60 cell line panel. Results This work presents three main findings. First, our models show that gene expression profiles that capture changes in gene expression after 24 h of exposure to a high concentration of drug generates the most accurate predictive models compared to the expression profiles under different dosing conditions. Second, signatures of 100 genes are developed for different gene expression profiles; furthermore, when the gene signatures are applied across gene expression profiles model performance is substantially decreased when gene signatures developed using changes in gene expression are applied to non-drugged gene expression. Lastly, we show that the gene interaction networks developed on these signatures show different network topologies and can be used to inform selection of cancer relevant genes. Conclusion Our models suggest that perturbed gene signatures are predictive of drug response, but cannot be applied to predict drug response using unperturbed gene expression. Furthermore, additional drug perturbed gene expression measurements in in vitro cell lines could generate more predictive models; but, more importantly be used in conjunction with computational methods to discover important drug disease relationships.
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Affiliation(s)
- Joshua D Mannheimer
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA.,Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, USA
| | - Ashok Prasad
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA.,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Daniel L Gustafson
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA. .,Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, USA. .,Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA. .,University of Colorado, Cancer Center Developmental Therapeutics Program, University of Colorado, Aurora, CO, USA.
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Mannheimer JD, Duval DL, Prasad A, Gustafson DL. A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies. BMC Med Genomics 2019; 12:87. [PMID: 31208429 PMCID: PMC6580596 DOI: 10.1186/s12920-019-0519-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 09/10/2018] [Accepted: 04/29/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The availability and generation of large amounts of genomic data has led to the development of a new paradigm in cancer treatment emphasizing a precision approach at the molecular and genomic level. Statistical modeling techniques aimed at leveraging broad scale in vitro, in vivo, and clinical data for precision drug treatment has become an active area of research. As a rapidly developing discipline at the crossroads of medicine, computer science, and mathematics, techniques ranging from accepted to those on the cutting edge of artificial intelligence have been utilized. Given the diversity and complexity of these techniques a systematic understanding of fundamental modeling principles is essential to contextualize influential factors to better understand results and develop new approaches. METHODS Using data available from the Genomics of Drug Sensitivity in Cancer (GDSC) and the NCI60 we explore principle components regression, linear and non-linear support vector regression, and artificial neural networks in combination with different implementations of correlation based feature selection (CBF) on the prediction of drug response for several cytotoxic chemotherapeutic agents. RESULTS Our results indicate that the regression method and features used have marginal effects on Spearman correlation between the predicted and measured values as well as prediction error. Detailed analysis of these results reveal that the bulk relationship between tissue of origin and drug response is a major driving factor in model performance. CONCLUSION These results display one of the challenges in building predictive models for drug response in pan-cancer models. Mainly, that bulk genotypic traits where the signal to noise ratio is high is the dominant behavior captured in these models. This suggests that improved techniques of feature selection that can discriminate individual cell response from histotype response will yield more successful pan-cancer models.
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Affiliation(s)
- Joshua D. Mannheimer
- School of Biomedical Engineering, Colorado State University, Fort Collins, 80523 CO USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, 80523 CO USA
| | - Dawn L. Duval
- Flint Animal Cancer Center, Colorado State University, Fort Collins, 80523 CO USA
- Department of Clinical Sciences, Colorado State University, Fort Collins, 80523 CO USA
| | - Ashok Prasad
- School of Biomedical Engineering, Colorado State University, Fort Collins, 80523 CO USA
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, 80523 CO USA
| | - Daniel L. Gustafson
- School of Biomedical Engineering, Colorado State University, Fort Collins, 80523 CO USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, 80523 CO USA
- Department of Clinical Sciences, Colorado State University, Fort Collins, 80523 CO USA
- University of Colorado Cancer Center Developmental Therapeutics Program, University of Colorado, Aurora, 80045 CO USA
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Collins KP, Mannheimer JD, Gustafson DL. Vinca Alkaloid Pharmacokinetics in the Context of a Physiologically‐Based Murine Model. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.834.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Keagan P. Collins
- School of Biomedical EngineeringColorado State UniversityFort CollinsCO
| | | | - Daniel L. Gustafson
- School of Biomedical EngineeringColorado State UniversityFort CollinsCO
- Flint Animal Cancer CenterColorado State UniversityFort CollinsCO
- University of Colorado Cancer CenterAuroraCO
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Mannheimer JD, Prasad A, Duval DL, Gustafson DL. Assessment of Modeling Techniques and Feature Selection for Predicting Drug Response from Gene Expression Data for Cytotoxic Anticancer Agents. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.566.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Ashok Prasad
- Chemical and Biomedical EngineeringColorado State UniversityFort CollinsCO
| | - Dawn L. Duval
- Flint Animal Cancer CenterColorado State UniversityFort CollinsCO
- University of Colorado Cancer CenterAuroraCO
| | - Daniel L. Gustafson
- School of Biomedical EngineeringColorado State UniversityFort CollinsCO
- Flint Animal Cancer CenterColorado State UniversityFort CollinsCO
- University of Colorado Cancer CenterAuroraCO
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