Biology subjects

Cook, S. R.

Publications and source records attributed to Cook, S. R..

5 recordsLinked to original sources

bioRxiv2026

A multi-modal transcriptomic atlas reveals the cellular and spatial landscape of canine gastric cancer

Gastric cancer is the fifth leading cause of cancer-related mortality in humans globally and remains a clinical challenge with limited treatment options and poor survival. Dogs develop spontaneous gastric cancer that parallels the clinical presentation and histology of human disease, supporting their value as a comparative oncology model. Here we present a comprehensive transcriptomic characterization of canine gastric cancer through single-nucleus RNA-sequencing, bulk RNA-sequencing, and Visium HD 3' spatial transcriptomics of treatment-naive tumor and normal stomach tissues from Belgian Tervuren and Belgian Sheepdogs. Across 107,085 nuclei, we identified 44 distinct cell populations, including tumor-enriched states as well as profound depletion of the normal parietal and chief cell gastric lineages. Cell-cell communication analysis revealed enhanced epithelial-fibroblast crosstalk driving epithelial-mesenchymal transition. Bulk RNA-sequencing further identified enrichment of signaling pathways implicated in H. pylori associated human gastric carcinogenesis, including Hippo, PI3K-Akt, and Wnt. Notably, we observed cell-type-specific altered expression of KLHL29, PDZRN3, and PLAU, which are among our previously identified canine gastric cancer susceptibility genes, linking germline risk to specific tumor cellular contexts. These data establish the first transcriptomic atlas of canine gastric cancer and demonstrate substantial molecular homology between canine and human disease.

genomics↗

bioRxiv2026

Characterization of pre-analytical blood collection and stabilization parameters to maintain endogenous protein levels for remote blood sampling technology

Blood biomarkers are central to monitoring disease progression and evaluating treatment responses, yet traditional venipuncture captures a single physiological snapshot in time and becomes burdensome with repeated sampling. Remote blood self-sampling offers a path toward longitudinal, decentralized monitoring, but maintaining protein integrity from draw to analysis remains a critical challenge. Here, we optimized pre-analytical blood collection and stabilization parameters to maintain protein levels at the time of collection for use with remote sampling technology. First, we optimized blood collection time with Tasso remote self-sampling devices to minimize interference from clotting, finding that a 2.5 min collection time best reduces clot formation while collecting enough blood. Next, we found that Protein Plus, a commercial protein stabilizer, limited hemolysis (a metric for stabilizer efficacy) in venous blood for up to 5 days at 25{degrees}C-35{degrees}C and for 1 day at 40{degrees}C. In addition, we optimized the stabilizer volume and acceptable blood volume range for self-sampling as the stabilizer efficacy is impacted by the stabilizer to blood ratio and collection volume can vary with remote self-sampling devices. Finally, we incubated stabilized blood samples collected via Tasso device at 25{degrees}C-35{degrees}C for 72 h, mimicking a 2-day shipping period. Using a panel of 21 inflammatory proteins, we found that Protein Plus limited intracellular protein release for various proteins (e.g., VEGF-A, CCL11, and IL-8), inhibited protein degradation for CCL2, and enabled minimal hemolysis. These results support Protein Plus as a viable stabilization strategy for remote blood collection technology targeting longitudinal inflammatory protein monitoring.

biochemistry↗

bioRxiv2025

Niemann-Pick C-like endo-lysosomal dysfunction in DHDDS patient cells, a congenital disorder of glycosylation, can be treated with miglustat

DHDDS (dehydrodolichol diphosphate synthetase) and NgBR (Nogo-B Receptor) collectively form an enzymatic complex important for the synthesis of dolichol - a key component of protein N-glycosylation. Mutations in DHDDS and the gene encoding NgBR (NUS1) are associated with neurodevelopmental disorders that clinically present with epilepsy, motor impairments, and developmental delay. Previous work has demonstrated both DHDDS and NgBR can also interact with NPC2 (Niemann-Pick C (NPC) type 2) - a protein which functions to traffic cholesterol out of the lysosome and, when mutated, can cause a lysosomal storage disorder (NPC disease) characterised by an accumulation of cholesterol and glycosphingolipids. Abnormal cholesterol accumulation has also been reported in cells from individuals and animal models with mutations in NUS1, and suspected lipid storage has been shown in biopsies from individuals with mutations in DHDDS. Our findings provide further evidence for overlap between NPC2 and DHDDS disorders, showing that DHDDS patient fibroblasts have increased lysosomal volume, store cholesterol and ganglioside GM1, and have altered lysosomal Ca2+ homeostasis. Treatment of DHDDS cells - with the approved NPC small molecule therapy miglustat - improves these disease-associated phenotypes, identifying a possible therapeutic option for DHDDS patients. These data suggest that treatment options currently approved for NPC disease may be translatable to DHDDS/NUS1 patients.

biochemistry↗

bioRxiv2024

Genomic analyses identify 15 susceptibility loci and reveal HDAC2, SOX2-OT, and IGF2BP2 in a naturally-occurring canine model of gastric cancer

Gastric cancer (GC) is the fifth most common human cancer worldwide, but the genetic etiology is largely unknown. We performed a Bayesian genome-wide association study and selection analyses in a naturally-occurring canine model of GC, the Belgian Tervuren and Sheepdog breeds, to elucidate underlying genetic risk factors. We identified 15 loci with over 90% predictive accuracy for the GC phenotype. Variant filtering revealed germline putative regulatory variants for the EPAS1 (HIF2A) and PTEN genes and a coding variant in CD101. Although closely related to Tervuren and Sheepdogs, Belgian Malinois rarely develop GC. Across-breed analyses uncovered protective haplotypes under selection in Malinois at SOX2-OT and IGF2BP2. Among Tervuren and Sheepdogs, HDAC2 putative regulatory variants were present at comparatively high frequency and were associated with GC. Here, we describe a complex genetic architecture governing GC in a dog model, including genes such as PDZRN3, that have not been associated with human GC.

genomics↗

bioRxiv2024

Multi-organ immunity on a 3D-printed multi-tissue chip with tubing-free impeller pump

Multi-organ-on-chip systems (MOOCs) have the potential to mimic communication between organ systems and reveal mechanisms of health and disease. However, many existing MOOCs are challenging for non-experts to implement, due to complex tubing, electronics, or pump mechanisms. In addition, few MOOCs have incorporated immune organs such as the lymph node (LN), limiting their applicability to critical events such as vaccination. Here we developed a 3D-printed, user-friendly device and companion tubing-free impeller pump with the capacity to co-culture two or more tissue samples, including a LN, under a recirculating common media. Native tissue structure and immune function were incorporated by maintaining slices of murine LN tissue ex vivo in 3D-printed mesh supports for at least 24 hr. In a two-compartment model of a LN and an upstream injection site in mock tissue, vaccination of the multi-compartment chip was similar to in vivo vaccination in terms of locations of antigen accumulation and acute changes in activation markers and gene expression in the LN. We anticipate that in the future, this flexible platform will enable models of multi-organ immune responses throughout the body.

bioengineering↗