Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies

Abstract

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.

Development of OX40 agonists for canine cancer immunotherapy

“…We also investigated whether cOX40 is expressed on tumor-infiltrating leukocytes (TILs) in the tumor samples collected from pet dogs with appendicular osteosarcoma (OSA). We analyzed our previously published data from patient-matched primary OSA and normal bone obtained from seven canine osteosarcoma patients ( Nance et al., 2022 ). Following the same bioinformatics pipeline, cOX40 expression was evaluated for differential expression using DEseq2 (v3.14).…”

“…We analyzed our previously published RNA sequencing data collected from seven pet dogs with appendicular osteosarcoma (OSA) at the Auburn University College of Veterinary Medicine in Auburn, AL ( GSE199489 ). Briefly, tumor samples and patient-matched normal bones were used to prepare RNA sequencing libraries ( Nance et al., 2022 ). Following the same bioinformatics pipeline as previously described ( Nance et al., 2022 ), we evaluated the differential expression of cOX40 in tumor samples and patient-matched normal bones using DEseq2 (v3.14).…”

“…Briefly, tumor samples and patient-matched normal bones were used to prepare RNA sequencing libraries ( Nance et al., 2022 ). Following the same bioinformatics pipeline as previously described ( Nance et al., 2022 ), we evaluated the differential expression of cOX40 in tumor samples and patient-matched normal bones using DEseq2 (v3.14).…”

Comparative Study of Colorectal Cancer Cell Lines Cultured in Two- and Three- Dimensional Models: Insights into Cellular Morphologies, Drug Responsiveness and Transcriptomics

“…Precision medicine, or personalized medicine, is a pioneering approach to tailored disease avoidance and treatment by considering the differences among people's genes, environments, and lifestyles [18]. The ultimate goal of precision medicine is to deliver the right treatments for the right patients at the right time [19]. Currently, the location of each gene in the reference genome is well known, and precise mutations can be identi ed and isolated, allowing speci c diseases to be targeted at the genetic level [20].…”

“…Consequently, transcriptome analysis not only supports bioinformation about gene function, also reveals particulars about genome plasticity, gene expression regulation, and changes in individual transcripts [21,22]. Therefore, transcriptome analysis is considered a useful approach to study the ever-changing cancer cells at the molecular level [19]. The total number of transcripts present in a cell at a given developmental stage or physiological condition is known as the transcriptome.…”