Cargando…
Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies
Despite significant advances in cancer diagnosis and treatment, osteosarcoma (OSA), an aggressive primary bone tumor, has eluded attempts at improving patient survival for many decades. The difficulty in managing OSA lies in its extreme genetic complexity, drug resistance, and heterogeneity, making...
Autores principales: | , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9031617/ https://www.ncbi.nlm.nih.gov/pubmed/35456486 http://dx.doi.org/10.3390/genes13040680 |
_version_ | 1784692434731532288 |
---|---|
author | Nance, Rebecca L. Cooper, Sara J. Starenki, Dmytro Wang, Xu Matz, Brad Lindley, Stephanie Smith, Annette N. Smith, Ashley A. Bergman, Noelle Sandey, Maninder Koehler, Jey Agarwal, Payal Smith, Bruce F. |
author_facet | Nance, Rebecca L. Cooper, Sara J. Starenki, Dmytro Wang, Xu Matz, Brad Lindley, Stephanie Smith, Annette N. Smith, Ashley A. Bergman, Noelle Sandey, Maninder Koehler, Jey Agarwal, Payal Smith, Bruce F. |
author_sort | Nance, Rebecca L. |
collection | PubMed |
description | Despite significant advances in cancer diagnosis and treatment, osteosarcoma (OSA), an aggressive primary bone tumor, has eluded attempts at improving patient survival for many decades. The difficulty in managing OSA lies in its extreme genetic complexity, drug resistance, and heterogeneity, making it improbable that a single-target treatment would be beneficial for the majority of affected individuals. Precision medicine seeks to fill this gap by addressing the intra- and inter-tumoral heterogeneity to improve patient outcome and survival. The characterization of differentially expressed genes (DEGs) unique to the tumor provides insight into the phenotype and can be useful for informing appropriate therapies as well as the development of novel treatments. Traditional DEG analysis combines patient data to derive statistically inferred genes that are dysregulated in the group; however, the results from this approach are not necessarily consistent across individual patients, thus contradicting the basis of precision medicine. Spontaneously occurring OSA in the dog shares remarkably similar clinical, histological, and molecular characteristics to the human disease and therefore serves as an excellent model. In this study, we use transcriptomic sequencing of RNA isolated from primary OSA tumor and patient-matched normal bone from seven dogs prior to chemotherapy to identify DEGs in the group. We then evaluate the universality of these changes in transcript levels across patients to identify DEGs at the individual level. These results can be useful for reframing our perspective of transcriptomic analysis from a precision medicine perspective by identifying variations in DEGs among individuals. |
format | Online Article Text |
id | pubmed-9031617 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-90316172022-04-23 Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies Nance, Rebecca L. Cooper, Sara J. Starenki, Dmytro Wang, Xu Matz, Brad Lindley, Stephanie Smith, Annette N. Smith, Ashley A. Bergman, Noelle Sandey, Maninder Koehler, Jey Agarwal, Payal Smith, Bruce F. Genes (Basel) Article Despite significant advances in cancer diagnosis and treatment, osteosarcoma (OSA), an aggressive primary bone tumor, has eluded attempts at improving patient survival for many decades. The difficulty in managing OSA lies in its extreme genetic complexity, drug resistance, and heterogeneity, making it improbable that a single-target treatment would be beneficial for the majority of affected individuals. Precision medicine seeks to fill this gap by addressing the intra- and inter-tumoral heterogeneity to improve patient outcome and survival. The characterization of differentially expressed genes (DEGs) unique to the tumor provides insight into the phenotype and can be useful for informing appropriate therapies as well as the development of novel treatments. Traditional DEG analysis combines patient data to derive statistically inferred genes that are dysregulated in the group; however, the results from this approach are not necessarily consistent across individual patients, thus contradicting the basis of precision medicine. Spontaneously occurring OSA in the dog shares remarkably similar clinical, histological, and molecular characteristics to the human disease and therefore serves as an excellent model. In this study, we use transcriptomic sequencing of RNA isolated from primary OSA tumor and patient-matched normal bone from seven dogs prior to chemotherapy to identify DEGs in the group. We then evaluate the universality of these changes in transcript levels across patients to identify DEGs at the individual level. These results can be useful for reframing our perspective of transcriptomic analysis from a precision medicine perspective by identifying variations in DEGs among individuals. MDPI 2022-04-13 /pmc/articles/PMC9031617/ /pubmed/35456486 http://dx.doi.org/10.3390/genes13040680 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Nance, Rebecca L. Cooper, Sara J. Starenki, Dmytro Wang, Xu Matz, Brad Lindley, Stephanie Smith, Annette N. Smith, Ashley A. Bergman, Noelle Sandey, Maninder Koehler, Jey Agarwal, Payal Smith, Bruce F. Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies |
title | Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies |
title_full | Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies |
title_fullStr | Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies |
title_full_unstemmed | Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies |
title_short | Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies |
title_sort | transcriptomic analysis of canine osteosarcoma from a precision medicine perspective reveals limitations of differential gene expression studies |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9031617/ https://www.ncbi.nlm.nih.gov/pubmed/35456486 http://dx.doi.org/10.3390/genes13040680 |
work_keys_str_mv | AT nancerebeccal transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT coopersaraj transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT starenkidmytro transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT wangxu transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT matzbrad transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT lindleystephanie transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT smithannetten transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT smithashleya transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT bergmannoelle transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT sandeymaninder transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT koehlerjey transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT agarwalpayal transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies AT smithbrucef transcriptomicanalysisofcanineosteosarcomafromaprecisionmedicineperspectiverevealslimitationsofdifferentialgeneexpressionstudies |