French bulldogs with high-grade oligodendroglioma, one of the most common and deadliest brain tumors in dogs, carry tumors whose gene expression differs measurably from those of two closely related breeds, the boxer and the Boston terrier. That is the central finding of a new open-access study published on 9 May 2025, in which researchers performed RNA sequencing on archived tumor tissue from 18 pet dogs and identified 45 differentially expressed genes, 31 of them protein-coding, that set French bulldog tumors apart. The work offers a molecular explanation to investigate for a puzzling clinical observation: French bulldogs enrolled in immunotherapy trials for high-grade glioma survived far shorter times than their genetic cousins.
High-grade oligodendroglioma is the most common primary intraparenchymal brain tumor in dogs, accounting for nearly 55 percent of all canine gliomas, and treatment options remain limited with poor outcomes across the board. The tumor shares striking similarities with glioblastoma in humans, including devastatingly short survival times, which has made pet dogs with spontaneous disease a valuable preclinical model for developing new human therapies. Three breeds that most frequently develop the tumor, the French bulldog, boxer, and Boston terrier, all fall within a single phylogenetic clade, yet their clinical outcomes diverge. In previous immunotherapy-based clinical trials, French bulldogs with high-grade oligodendroglioma had a median survival time of 132 days, compared with 221 days for other breeds within the same clade.
The research team, based at the University of Minnesota, hypothesized that the transcriptome of French bulldog tumors might differ from those of boxers and Boston terriers in ways that account for the survival disparity. They analyzed formalin-fixed, paraffin-embedded biopsy specimens submitted to the university’s Comparative Pathology Shared Resource over a ten-year period from 2005 to 2015. All samples had been obtained via surgical resection as part of enrollment in clinical trials for pet dogs with high-grade gliomas, and critically, all were collected before any trial treatment began, so the expression profiles reflect untreated tumor biology. A board-certified veterinary pathologist confirmed the diagnosis of high-grade oligodendroglioma in every case using World Health Organization criteria for tumors of the central nervous system.
The study population comprised 11 French bulldogs and a comparison group of 7 dogs, including 4 boxers and 3 Boston terriers. The mean age of the French bulldogs was 6.0 years, with a range of 3 to 9.5 years, while the comparison group averaged 7.4 years old, ranging from 4 to 9.5 years. Working with RNA extracted from the archived paraffin blocks, the team used specialized library preparation kits optimized for highly degraded samples, sequencing on an Illumina NovaSeq 6000 at a targeted depth of at least 40 million reads per sample. All 18 samples passed quality control, generating over 61.8 million reads per sample, with genome mapping rates exceeding 76 percent after trimming and filtering.
The sequencing effort paid off with a clear signal. Principal component analysis attributed 55 percent of the variance in gene expression to breed group, and differential expression testing with the DESeq2 pipeline revealed that 45 of the 29,993 annotated genes were expressed at significantly different levels in French bulldog tumors. Of the 31 protein-coding differentially expressed genes, 14 were significantly overexpressed in French bulldogs and 17 were significantly underexpressed relative to boxers and Boston terriers. Significance was defined using a Benjamini-Hochberg adjusted p-value below 0.05 to correct for multiple testing across thousands of genes.
The most dramatically overexpressed gene was fibroblast growth factor 4, or FGF4, with a log2 fold change of 6.43, equivalent to an 86-fold difference in expression. The finding carries an intriguing evolutionary wrinkle: French bulldogs carry one of two canine FGF4 retrogenes at an extremely high allele frequency of greater than 90 percent, whereas neither retrogene has been observed in Boston terriers and it has not been evaluated in boxers. However, the authors caution that several breeds with no elevated risk of high-grade oligodendroglioma, including beagles, dachshunds, and most spaniel breeds, also carry the retrogene at high frequency. The overexpression might therefore simply reflect a breed-associated variant unrelated to the tumor, or it might contribute to more aggressive tumor behavior in dogs that develop the disease. In human glioma, overexpression of the corresponding receptor FGFR4 is associated with poor prognosis and faster tumor recurrence.
Other notable overexpressed genes included DLA88, a highly polymorphic major histocompatibility complex class I molecule that presents antigens to cytotoxic CD8-positive T cells, along with the heat shock protein gene HSP90AB1 and PTP4A1, a phosphatase overexpressed in human glioma. DLA88 has 139 identified alleles across dog breeds, and while its allelic profile has been characterized in boxers, which carry a single dominant allele thought to result from severe genetic bottlenecking, it has not been profiled in French bulldogs or Boston terriers. Because human leukocyte antigen polymorphisms influence both cancer risk and responsiveness to immunotherapy, allelic differences in DLA88 could plausibly contribute to the poor immunotherapy response observed in French bulldogs, though this remains a hypothesis for future work. Among the underexpressed genes, some, such as the DNA repair gene PNKP and BRAT1, which interacts with the tumor suppressor BRCA1, might be protective genes contributing to the better prognosis in boxers and Boston terriers.
Beyond individual genes, gene set enrichment analysis identified 15 significantly enriched pathways in French bulldog tumors, falling into three broad categories. Cell cycle progression pathways included E2F targets, the G2-M checkpoint, and the mitotic spindle; oncogenic pathways included KRAS signaling, mTOR signaling, and Myc targets; and immune regulation pathways included IL2-STAT5 signaling, TNF-alpha signaling via NF-kB, interferon gamma and alpha responses, allograft rejection, inflammatory response, and complement. The enrichment of mTOR signaling was particularly notable because previous studies had not demonstrated elevated mTOR expression in canine glioma cell lines, and Myc has been observed to be amplified in 78 percent of canine gliomas. That a large proportion of the enriched pathways were immune-related suggests French bulldog high-grade oligodendroglioma produces a breed-specific tumor-immune interaction that may influence outcomes in dogs receiving immunotherapy, though the study did not directly test treatment response.
The authors are careful to spell out the limitations of their analysis. The mean age of French bulldogs was lower than that of the comparison group, tumor location differed between breeds, with more boxers having temporal or piriform lobe tumors, and the groups could not be matched for age, sex, or tumor location because of a limited tissue biobank. One French bulldog sample did not cluster with the others in the principal component analysis, and since breed was designated based on owner declarations, undisclosed mixed heritage remains a possible explanation, albeit entirely speculative. The researchers also note that comparing tumor transcriptomes with normal brain tissue from these breeds would help clarify which expression differences are truly tumor-related rather than ordinary breed variation. French bulldogs had been removed from future immunotherapy trial enrollment on ethical grounds once their poor outcomes became apparent, which limited sample availability. The datasets are publicly available through the University of Minnesota data repository and the NCBI Gene Expression Omnibus under accession number GSE284559, providing a foundation for studies linking these breed-specific expression patterns to patient outcomes and, ultimately, to precision-based therapies for individual canine patients.
Subject of Research: Breed-associated differences in gene expression in canine high-grade oligodendroglioma
Article Title: Differential gene expression analysis in French bulldog high grade oligodendroglioma: breed-associated differences in tumor and tumor microenvironment gene expression
Article References: Arnold, S. A., Llorens, J. E. A., Cullen, J., Furrow, E., Low, W. C., & Pluhar, G. E. (2025). Differential gene expression analysis in French bulldog high grade oligodendroglioma: breed-associated differences in tumor and tumor microenvironment gene expression. Companion Animal Health and Genetics, 12(1), Article 4. https://doi.org/10.1186/s40575-025-00141-2
Image Credits: AI Generated
DOI: 10.1186/s40575-025-00141-2
Keywords: French bulldog, high-grade oligodendroglioma, canine glioma, gene expression, RNA sequencing, FGF4, DLA88, tumor microenvironment, immunotherapy, gene set enrichment analysis, boxer, Boston terrier
News Source: Juliet Wilcox. (October 29, 2026). French Bulldog Brain Tumors Show Distinct Gene Expression From Related Breeds. Scienmag.
