About

Matthew Breen is associated with the College of Veterinary Medicine at NC State University, which is dedicated to shaping the future of veterinary medicine and supporting the next generation of veterinarians. The college emphasizes a collaborative and inclusive culture, fostering student achievement, well-being, and extracurricular engagement, including research projects conducted in world-class labs. While specific details about Dr. Breen's research focus, background, or key contributions are not provided in the page text, his association with the college suggests involvement in advancing veterinary education and research.

Research topics

• Biology
• Medicine
• Ecology
• Chemistry
• Computer Science
• Environmental health
• Toxicology
• Internal medicine
• Archaeology
• Oncology
• Database
• Geography
• Computer vision
• Cancer research
• Environmental chemistry
• Computational biology
• Pharmacology
• Evolutionary biology
• Genetics

Selected publications

• Adventures in the Animal Archive: New Techniques for the Genetic Analysis of Parchment Manuscripts

  Manuscript studies · 2026-03-01

  articleOpen access

  Abstract: This article reports the findings of a recent interdisciplinary project to extract and analyze the genetic information contained in parchment manuscripts. We discuss the genetic analysis of ninety-one parchment manuscripts held by the David M. Rubenstein Rare Book & Manuscript Library at Duke University. Manuscripts tested ranged in date from the eighth through the twentieth centuries and originated in a wide geographical area spanning England, much of Europe, the Middle East, and northeast Africa. The article comprises an overview of the project and its aims, a description of methods and outcomes, and a discussion of the implications and promises of such research for a variety of humanistic and scientific fields.

  PublisherDOI

• Differences in PFAS exposure between Pacific pinnipeds: The Galapagos (Zalophus wollebaeki) and California (Zalophus californianus) sea lions

  Marine Pollution Bulletin · 2026-04-02

  articleOpen accessSenior author

  Per- and polyfluoroalkyl substances (PFAS) are a class of man-made persistent chemicals that have been detected in both terrestrial and aquatic environments and thus impact humans, household pets, agricultural species, and wildlife. PFAS exposure is linked to a variety of adverse health consequences, including cancer and immune disruption. This study investigates differences in PFAS exposure between California (CSL, n = 69) and Galapagos (GSL, n = 65) sea lion pups and juveniles across various sampling locations within each species' habitat range. Whereas the GSL were all considered healthy, 17 of the 69 CSL were classified as malnourished. Comparing the two species, significantly higher serum concentrations of summed PFAS, perfluorooctanesulfonic acid (PFOS), perfluorononanoic acid (PFNA), and perfluorodecanoic acid (PFDA) were detected in CSL than in GSL. This elevated PFAS exposure in CSL is likely related to historic pollution in their environment and close proximity to the urbanized coastline of Southern California. Within species, malnourished CSL had significantly higher PFNA than healthy CSL pups. GSL pups also tended to have higher PFAS levels than GSL juveniles. Within the Galapagos archipelago, PFAS exposure differed between rookeries, with PFOS exceeding its method reporting limit (0.5 ng/mL) in every sample, including GSL from islands uninhabited by humans. Summed PFAS, PFNA, PFDA, and perfluoroundecanoic acid (PFUnA) were all significantly higher in sea lions sampled on uninhabited than inhabited islands in the Galapagos archipelago. This study is the first comprehensive report of PFAS in CSL and the first archipelago-wide assessment of PFAS in GSL.

  PublisherDOI

• Evaluating non-destructive sampling methods of parchment for genomic sequencing

  npj Heritage Science · 2025-06-05 · 1 citations

  articleOpen access

  Abstract Parchment is a writing surface derived from animal skins. While sequencing the mitochondrial genome has been used to identify the parchment animal source, non-destructive sampling methods are pivotal because of their unique and irreplaceable nature. In this study, four different parchments were utilized to evaluate three non-destructive sampling methods: brushing, gecko tape, and forensic fibre lifts. For all methods, the impact of a 30-second eraser pre-cleaning to remove surface contaminants was assessed. After sample collection, total DNA was isolated, the mitochondrial genome enriched and sequenced using Illumina chemistry, and sequencing reads processed through a bioinformatics pipeline. Across all four documents, brushing with an eraser pre-cleaning was the optimal method, with an average of 98% of the mitochondrial genome recovered. Regardless of sampling method, collection after a 30-second eraser pre-cleaning resulted in higher source species DNA sequences. Non-destructive sampling will preserve documents with historical significance while allowing for genetic analysis.

  PublisherOA PDFDOI

• Polypoid Cystitis: A Retrospective Case-Series of 112 Dogs

  Journal of Veterinary Internal Medicine · 2025-05-01 · 2 citations

  articleOpen access

  BACKGROUND: Polypoid cystitis (PoC) in dogs is associated with chronic inflammatory bladder conditions and is discovered during evaluation for signs of lower urinary tract disease, or incidentally. OBJECTIVE: To describe PoC in dogs evaluated in an academic practice. ANIMALS: Dogs with confirmed (n = 59) or presumptive (n = 53) PoC were evaluated between January 2004 and October 2020. METHODS: For this retrospective study, medical records were searched for PoC. RESULTS: The most common presenting signs of 112 dogs with PoC were hematuria (n = 42; 38%), stranguria (n = 28; 25%), and pollakiuria (n = 25; 22%). Polyps were found incidentally (n = 13; 12%). Urinary tract infection (UTI; n = 61; 54%) or urolithiasis (n = 38; 34%) was a common presumptive cause. Escherichia coli (n = 39; 53%), Enterococcus faecalis (n = 14; 19%) and Staphylococcus pseudintermedius (n = 5; 7%) were isolated from dogs with UTI. Ultrasonographic findings (n = 101) included polypoid structures (n = 44; 44%), broad-based masses (n = 16; 26%), and bladder wall thickening (n = 25; 25%); mostly in the cranioventral bladder apex (n = 56; 80%). Of 41 specimens tested, none had evidence of the BRAF V595E mutation. Urinary tract neoplasia was not reported in any dog during follow-up (range 1 month-8.4 years; median 8 months). Interventions included antibiotic or anti-inflammatory administration, and surgical or cystoscopic ablation. During follow-up, recurrent signs of lower urinary tract disease were reported in 23 (20%) dogs. CONCLUSIONS AND CLINICAL IMPORTANCE: History of either UTI or urolithiasis, compatible imaging findings, and absence of detectable BRAF V595E mutation support the presumptive diagnosis of PoC in dogs. Affected dogs have a good prognosis, warranting differentiation from other urinary tract diseases.

  PublisherOA PDFDOI

• Genomic Evaluation of Canine Prostatic Carcinomas as a Model for the Human Disease

  UNC Libraries · 2025-12-12

  articleOpen accessSenior author

  Spontaneous canine prostate cancer (PC) is widely considered a pertinent clinical model for the human disease. While over 95% of PC in men are adenocarcinomas, arising from prostatic glandular epithelium, it is increasingly recognised that many canine PC are of urothelial origin, arising within the prostatic urethra or ducts, or through invasion from a primary urinary bladder tumour. At diagnosis, canine prostatic tumours are often poorly differentiated and widely disseminated, masking the primary site and limiting the sensitivity of cellular biomarkers. Consequently, published studies of canine PC show varying representation of glandular versus urothelial tumours, yielding conflicting observations regarding their molecular pathogenesis and clinical behaviour. We characterised DNA sequence mutations and copy number aberrations in 31 canine PC, seeking evidence supporting relevance as a disease model. Only three tumours resembled adenocarcinomas. The remainder were either histologically consistent with urothelial carcinoma (n = 15), showed mixed glandular and urothelial morphology (n = 4), or were carcinomas of undetermined cell type (n = 9). BRAF V588E mutation was detected in 87% of tumours, including all three adenocarcinomas. Urinary bladder involvement was evident in 46% of cases, but none of the adenocarcinomas. Genome-wide DNA copy number instability was apparent throughout the cohort, with chromosome 36 gain significantly associated with urothelial tumours. Hallmark alterations of human PC, such as defects within PI3K and androgen receptor signalling pathways, were not detected. Improved molecular subclassification of canine PC is needed to direct selection of relevant cases for modelling the human disease and to ensure appropriate extrapolation between canine and human studies.

  PublisherDOI

• Genomic Evaluation of Canine Prostatic Carcinomas as a Model for the Human Disease: or ‘UC or not UC – that is the question’

  Veterinary and Comparative Oncology · 2025-07-23 · 4 citations

  articleOpen accessSenior authorCorresponding

  Spontaneous canine prostate cancer (PC) is widely considered a pertinent clinical model for the human disease. While over 95% of PC in men are adenocarcinomas, arising from prostatic glandular epithelium, it is increasingly recognised that many canine PC are of urothelial origin, arising within the prostatic urethra or ducts, or through invasion from a primary urinary bladder tumour. At diagnosis, canine prostatic tumours are often poorly differentiated and widely disseminated, masking the primary site and limiting the sensitivity of cellular biomarkers. Consequently, published studies of canine PC show varying representation of glandular versus urothelial tumours, yielding conflicting observations regarding their molecular pathogenesis and clinical behaviour. We characterised DNA sequence mutations and copy number aberrations in 31 canine PC, seeking evidence supporting relevance as a disease model. Only three tumours resembled adenocarcinomas. The remainder were either histologically consistent with urothelial carcinoma (n = 15), showed mixed glandular and urothelial morphology (n = 4), or were carcinomas of undetermined cell type (n = 9). BRAF V588E mutation was detected in 87% of tumours, including all three adenocarcinomas. Urinary bladder involvement was evident in 46% of cases, but none of the adenocarcinomas. Genome-wide DNA copy number instability was apparent throughout the cohort, with chromosome 36 gain significantly associated with urothelial tumours. Hallmark alterations of human PC, such as defects within PI3K and androgen receptor signalling pathways, were not detected. Improved molecular subclassification of canine PC is needed to direct selection of relevant cases for modelling the human disease and to ensure appropriate extrapolation between canine and human studies.

  PublisherOA PDFDOI

• Fecal microbiota is more stable during degradation and more diverse for ex situ cheetahs in Namibia compared to the USA

  Frontiers in Conservation Science · 2025-01-27 · 1 citations

  articleOpen access

  The relationships between gut microbiota and animal health are an important consideration increasingly influential in the management of wild and ex situ endangered species, such as the cheetah ( Acinonyx jubatus ). To better understand these relationships, fresh fecal samples are currently required as a non-invasive alternative for the gut microbiome. Unfortunately, fresh samples are challenging to collect in the wild. This study had two aims: 1) to determine the optimal collection time point for cheetah feces after deposit in their native environment of Namibia as a guide for wild cheetah fecal microbiome studies; and 2) to compare the fecal microbiota of two ex situ cheetah populations (Front Royal, VA, USA and Otjiwarongo, Namibia), which also consume different diets. We collected eight fresh fecal samples from cheetahs in Namibia and allowed them to decompose for four days, taking subsamples each day. The fresh Namibian samples (n = 8) were also used in objective two for comparison to fresh USA cheetah samples (n = 8). All samples were analyzed for bacterial community diversity and composition using 16S rRNA gene amplicon sequencing. First, over a five-day sampling period in Namibia, subsamples 1-3 days post-fresh showed no changes in bacterial diversity or composition compared to fresh subsamples. Second, fresh ex situ cheetah samples under Namibian conditions had increased bacterial taxa, more phylogenetically diverse bacterial communities, and compositionally distinct microbiomes from cheetahs managed in human care in the USA. However, when bacterial ASVs were weighted by relative abundance, both populations shared 69% of their total bacterial sequences indicating a conserved cheetah microbiota between the two populations. We also found few differences in predictive functions of the fecal microbiota between the populations, where only one disease-related pathway was higher in the USA samples. Overall, our findings suggest that in dry season conditions (no recorded rainfall) in Namibia, fecals may be usable for up to three days after defecation for microbial ecology studies. There are significant differences between ex situ Namibian and USA populations, and we suggest further investigation into the influence of diet, host demographics, and environment on the gut microbiota and health of cheetahs.

  PublisherOA PDFDOI

• Environmental Exposures and Canine Bladder Cancer: A Case Control Study Using Silicone Passive Samplers

  Environmental Science & Technology · 2025-01-09 · 3 citations

  article

  Pet dogs offer valuable models for studying environmental impacts on human health due to shared environments and a shorter latency period for cancer development. We assessed environmental chemical exposures in a case–control study involving dogs at high risk of urothelial carcinoma, identified by a BRAF V595E mutation in urinary epithelial cells. Cases (n = 25) exhibited low-level BRAF mutations, while controls (n = 76) were matched dogs without the mutation. Each dog wore a silicone sampler for five continuous days to assess environmental exposures. Silicone samplers were analyzed using targeted and suspect screening (i.e., nontargeted) methods. Of 115 targeted chemicals, 39 were detected in >50% of samplers, with cases showing significantly higher levels (2–3×) of BDE-47, BDE-99, anthracene, and benzyl butyl phthalate (p < 0.05). Suspect screening identified that cases were exposed to more chemicals, often at higher exposure levels. For example, cases had significantly higher levels of 25 chemical features compared to controls (p < 0.05). This is the largest study to date to quantify such a wide breadth of contaminant exposure levels associated with canine urothelial carcinoma and the first to assess a population with subclinical disease, highlighting pet dogs as models to study environmental contributions to cancer risk, advancing both human and veterinary health.

  PublisherDOI

• Is increased mutation driving genetic diversity in dogs within the Chornobyl exclusion zone?

  UNC Libraries · 2025-02-11

  articleOpen access

  Environmental contamination can have lasting impacts on surrounding communities, though the long-term impacts can be difficult to ascertain. The disaster at the Chornobyl Nuclear Power Plant in 1986 and subsequent remediation efforts resulted in contamination of the local environment with radioactive material, heavy metals, and additional environmental toxicants. Many of these are mutagenic in nature, and the full effect of these exposures on local flora and fauna has yet to be understood. Several hundred free-roaming dogs occupy the contaminated area surrounding the Chornobyl Nuclear Power Plant, and previous studies have highlighted a striking level of genetic differentiation between two geographically close populations of these dogs. With this work, we investigate mutation as a possible driver of this genetic differentiation. First, we consider large-scale mutation by assessing the karyotypic architecture of these dogs. We then search for evidence of mutation through short tandem repeat/microsatellite diversity analyses and by calculating the proportion of recently derived alleles in individuals in both populations. Through these analyses, we do not find evidence of differential mutation accumulation for these populations. Thus, we find no evidence that an increased mutation rate is driving the genetic differentiation between these two Chornobyl populations. The dog populations at Chornobyl present a unique opportunity for studying the genetic effects of the long-term exposures they have encountered, and this study expands and builds on previous work done in the area.

  PublisherDOI

• Supplementary Table S4 from Hemangiosarcoma Cells Promote Conserved Host-derived Hematopoietic Expansion

  2024-06-11

  supplementary-materialsOpen access

  &lt;p&gt;Supplementary Table S4&lt;/p&gt;

  PublisherDOI

Recent grants

• NIH Grant R01CA112211

  NIH · $1.4M · 2013

• NIH Grant R21NS051190

  NIH · $367k · 2008

Frequent coauthors

• Rachael Thomas

  North Carolina State University

  235 shared

• Kerstin Lindblad‐Toh

  Uppsala University

  227 shared

• Jaime F. Modiano

  185 shared

• Elaine A. Ostrander

  National Institutes of Health

  122 shared

• Catherine André

  Institut de génétique et de développement de Rennes

  118 shared

• Emmett V. Schmidt

  112 shared

• Francis Galibert

  107 shared

• Heidi G. Parker

  Somerset NHS Foundation Trust

  105 shared

Labs

• Diagnostic and Research LabsPI

Education

• Ph.D., Veterinary Science

  North Carolina State University

  2005

• M.S., Veterinary Science

  North Carolina State University

  2001

• B.S., Animal Science

  University of California, Davis

  1999

Awards & honors

• Fellow, Royal Society of Biology