Invasive Urinary Bladder Cancer

2026-01-01

Characterisation of Gene Expression in Canine Invasive Urothelial Carcinoma Using a <scp>NanoString</scp>‐Based Urine Assay

Veterinary and Comparative Oncology · 2025-03-19

For human and canine invasive urothelial carcinoma (InvUC), there is growing interest in using the molecular characteristics of a tumour to guide individualised treatment strategies. The objective of this study was to use a non-invasive, urine-based method to characterise gene expression signatures in dogs with InvUC. RNA was isolated from canine InvUC tumour samples, urine sediment from dogs with InvUC, normal canine bladder mucosa, and normal canine urine sediment and queried using the nCounter Canine Immuno-Oncology Panel. Differential gene expression profiles were characterised for tissue and urine samples, and nCounter results were compared to bulk RNA-seq gene expression profiles. The effect of spiking normal urine with white blood cells (WBCs) from the same dog was also assessed. Key genes involved in antitumor immune responses and oncogenic signalling pathways, including potential small molecule inhibitor targets, were differentially expressed in tumour and urine samples from dogs with InvUC, compared to normal samples. nCounter-generated gene expression profiles for tumour tissue and urine from dogs with InvUC were highly correlated, whereas the correlation between the nCounter IO panel and bulk RNA-seq results for InvUC tissue was moderate. The addition of WBCs to normal urine affected the gene expression profiles. Analysis of canine urine using the nCounter canine IO panel has good potential for revealing gene expression patterns in InvUC. Additional studies are warranted to determine the extent to which WBC infiltration affects the results related to immune response patterns and the expression of other genes.

Abstract 4857: The role of tumor microenvironment lactic acid in the cancer cell resistance to anti-PD-L1 and anti-PD-1 blockade therapy

Cancer Research · 2025-04-21

Abstract Immune checkpoint blockade therapy targeting the PD-1/PD-L1 axis has shown remarkable clinical impact in multiple cancer types. However, despite its recent success, such impact has been shown to be limited to tumors encompassing specific tumor microenvironment characteristics. Furthermore, a significant proportion of initial responders eventually develop resistance. Combining PD-1/PD-L1 blockade with chemotherapy, radiotherapy, or targeted therapy have been suggested to overcome resistance, yet have been shown to be insufficient in fully accounting for resistance. Unlike normal, differentiated cells, most cancer cells produce large amounts of lactic acid. This metabolic property is often referred to as “aerobic glycolysis, ” a well-known metabolic reprogramming of cancer cells to sustain cell proliferation and a hallmark of cancer. Such property as well as others of the altered metabolism of cancer cells and its byproducts affect the anti-tumor immune response. Notably, glycolytic metabolites, such as lactate, regulate T cell proliferation and function. However, the mechanism behind how such metabolic alterations impact the cancer cells’ resistance to PD-1/PD-L1 blockade therapy remains unclear. Thus, we sought to decipher the role of tumor-cell derived lactic acid in PD-1/PD-L1 therapy resistance and propose new immunotherapeutic strategies to improve the efficacy of PD-1/PD-L1 blockade therapies. Here, we found that tumor cell-derived lactic acid renders the immunosuppressive tumor microenvironment in the PD-1/PD-L1 blockade-resistant tumors by inhibiting the interaction between the PD-L1 protein and anti-PD-L1 antibody. Furthermore, we showed that the combination therapy of targeting PD-L1 with our PD-L1 antibody-drug conjugate (PD-L1-ADC) and reducing lactic acid with the MCT-1 inhibitor, AZD3965, can effectively treat the PD-1/PD-L1 blockade resistant tumors. Altogether, the findings in this study uncover a new mechanism of how lactic acid induces an immunosuppressive tumor microenvironment and suggest a potential combination treatment strategy to overcome the tumor resistance to PD-1/PD-L1 blockade therapy and improve clinical outcomes. Citation Format: Alyssa Kim, Wonkyung Oh, Deepika Dhawan, Deborah W. Knapp, Seung-Oe Lim. The role of tumor microenvironment lactic acid in the cancer cell resistance to anti-PD-L1 and anti-PD-1 blockade therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4857.

GENOME EDITING WITH THE DNA-PK INHIBITOR AZD7648 INDUCES A LOW FREQUENCY OF COPY NUMBER VARIATIONS IN HEMATOPOIETIC STEM AND PROGENITORS CELLS

Cytotherapy · 2025-04-30

AnnotateAnyCell: Open-Source AI Framework for Efficient Annotation in Digital Pathology

bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-03

A bstract Manual annotation of histopathological whole slide images remains a critical bottleneck for computational pathology and clinical AI deployment, requiring prohibitive expert time at scale. Here we present an open-source semi-supervised framework combining active contrastive learning with iterative human-in-the-loop feedback for efficient cellular annotation and classification. The pipeline integrates Cellpose segmentation, UMAP-based latent space visualization, and contrastive learning with pseudolabel propagation, evaluated on five whole slide images of canine invasive urothelial carcinoma across low, intermediate, and high histological grades at 40× magnification. Latent space clustering-guided annotation required 47 minutes compared to 63 minutes for sequential annotation, a 25% reduction (95% CI 18–32%). Classification accuracy reached 96.3% ± 1.2% for mitotic figures and 98.3% ± 1.4% for nucleoli using 1,075 labeled samples, with nucleoli classification achieving 95.5% ± 1.5% accuracy from only 215 samples. Inter-annotator agreement was high for chromatin ( κ = 1.00) and nucleoli ( κ = 0.95) but moderate for mitotic figures ( κ = 0.58) and nuclear shape ( κ = 0.36), reflecting intrinsic morphological ambiguity in these categories. This framework substantially reduces annotation burden while achieving expert-level accuracy for well-defined morphological features, providing a scalable path toward AI-assisted diagnostics in resource-constrained pathology settings.

Hypoxia-inducible factor 1α expression does not differ between canine urothelial carcinoma and normal urinary bladder tissue

American Journal of Veterinary Research · 2025-04-28

Objective: To evaluate the RNA and protein expression of hypoxia-inducible factor (HIF-1α) in canine urothelial carcinoma (UC) compared to normal canine urinary bladder tissue. Methods: Dogs with normal urinary bladder tissue were enrolled at the time of euthanasia with the tissue obtained via necropsy within 1 hour after death. The high-grade UC tissue was collected via necropsy or cystoscopically utilizing a resectoscope. Dogs in the UC group were excluded if they were treated with chemotherapy or radiation therapy prior to tissue collection. Immunohistochemistry was performed on all tissues to evaluate intracytoplasmic and intranuclear immunoreactivity of HIF-1α using a semiquantitative immunoreactivity score (IRS). Ribonucleic acid sequencing was also performed to evaluate the expression of HIF-1α in normal urinary bladders and canine UC. Results: 10 dogs with high-grade UC and 10 dogs with normal urinary bladder tissue were enrolled. The median intracytoplasmic HIF-1α in the UC group was mild in intensity with a low percentage of positive cells (median IRS, 1; range, 0 to 2). The control dogs had similar intracytoplasmic HIF-1α expression (median IRS, 1; range, 0 to 1). The difference in RNA expression of HIF-1α between groups was not significant (1.3-fold change). Conclusions: This study did not identify any differential RNA or protein expression of HIF-1α between normal urinary bladder tissue and UC in dogs. Clinical Relevance: HIF-1α is not differentially expressed in canine UC, but further exploration is necessary to evaluate if other proteins associated with hypoxia and angiogenesis could play a role in tumor growth and chemotherapy resistance in canine UC.

Unbiased discovery of cancer pathways and therapeutics using Pathway Ensemble Tool and Benchmark

Nature Communications · 2024-08-24 · 14 citations

Correctly identifying perturbed biological pathways is a critical step in uncovering basic disease mechanisms and developing much-needed therapeutic strategies. However, whether current tools are optimal for unbiased discovery of relevant pathways remains unclear. Here, we create “Benchmark” to critically evaluate existing tools and find that most function sub-optimally. We thus develop the “Pathway Ensemble Tool” (PET), which outperforms existing methods. Deploying PET, we identify prognostic pathways across 12 cancer types. PET-identified prognostic pathways offer additional insights, with genes within these pathways serving as reliable biomarkers for clinical outcomes. Additionally, normalizing these pathways using drug repurposing strategies represents therapeutic opportunities. For example, the top predicted repurposed drug for bladder cancer, a CDK2/9 inhibitor, represses cell growth in vitro and in vivo. We anticipate that using Benchmark and PET for unbiased pathway discovery will offer additional insights into disease mechanisms across a spectrum of diseases, enabling biomarker discovery and therapeutic strategies. Multiple cellular pathways are altered in cancer and identifying them is relevant for prognosis and therapy. Here, the authors develop Benchmark and Pathway Ensemble Tool (PET), two computational approaches to optimise pathway discovery in cancer and predict related biomarkers and therapeutic avenues.

Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog and NIPAL1

npj Precision Oncology · 2024-05-22 · 2 citations

Naturally occurring canine invasive urinary carcinoma (iUC) closely resembles human muscle invasive bladder cancer in terms of histopathology, metastases, response to therapy, and low survival rate. The heterogeneous nature of the disease has led to the association of large numbers of risk loci in humans, however most are of small effect. There exists a need for new and accurate animal models of invasive bladder cancer. In dogs, distinct breeds show markedly different rates of iUC, thus presenting an opportunity to identify additional risk factors and overcome the locus heterogeneity encountered in human mapping studies. In the association study presented here, inclusive of 100 Shetland sheepdogs and 58 dogs of other breeds, we identify a homozygous protein altering point mutation within the NIPAL1 gene which increases risk by eight-fold (OR = 8.42, CI = 3.12-22.71), accounting for nearly 30% of iUC risk in the Shetland sheepdog. Inclusion of six additional loci accounts for most of the disease risk in the breed and explains nearly 75% of the phenotypes in this study. When combined with sequence data from tumors, we show that variation in the MAPK signaling pathway is an overarching cause of iUC susceptibility in dogs.

Abstract 3480: Alterations in the tumor microenvironment and key signaling pathways in naturally-occurring canine gliomas mirror those seen in human patients

Cancer Research · 2024-03-22

Abstract Background: Malignant gliomas are the most common type of primary brain tumors, with patient outcomes that are generally dismal. Recently, pet dogs have been assessed as a valuable model in which to study gliomas. Gliomas in pet dogs occur at similar rates to those seen in humans, and a recent study comparing canine and human gliomas identified high similarity in terms of mutational rates, aneuploidy, the timing of mutations, and methylation patterns. Here, we further compare naturally-occurring canine and human gliomas, focusing on the tumor microenvironment (TME) and key pathways dysregulated in human gliomas. Methods: Spontaneously occurring gliomas from adult and pediatric human, and canine patients were utilized for this study. RNA, whole genome/whole exome, and bisulfite sequencing data from adult and canine samples were downloaded from the Genomic Data Commons and the National Cancer Institute’s Integrated Canine Data Commons, respectively. Pediatric tumor RNA-seq and genomic data were obtained from the Gabriella Miller Kids First database. Normal adult human and canine brain tissue served as control tissue. Only tumors with a clear diagnosis of astrocytoma, oligodendroglioma, or oligoastrocytoma were included in this study. Results: Overall, we found that key canonical pathways that are altered in human gliomas are also altered in canine gliomas. A comparison of high-grade gliomas in pet dogs to normal canine brain tissues showed significant abnormal gene expression in 3 canonical oncogenic pathways of human GBM: the TP53, RB1, and RTK/RAS/PI3K pathways. Similarities between species included increased expression of PDGF, and receptors PDGFRA and PDGFRB. Frequent copy number alterations and mutations were also observed in PDGFRA and EGFR. Differences between species include the mutation rate of TP53, which we found to be mutated frequently in adults but not in pediatric or canine gliomas, however, expression of TP53 as assessed by RNA-seq was significantly increased in both adult and canine gliomas. IDH1, which drives methylation, was significantly overexpressed in adults but underexpressed in canine. Correspondingly, each of the promotor regions of TERT, PD1 and MGMT was hypermethylated in adults, but hypomethylated in canine. Although an analysis of the TME from RNA-seq data revealed an influx of immune cells in adult, pediatric and canine gliomas, there was a concurrent influx of immunosuppressive cells. Gene expression profiles of astrocytomas and oligodendrogliomas show differences in alterations of immune-related and TME-specific pathways. Conclusion: We found that similar TME and pathway alterations were observed between human and canine gliomas, and that TME alterations were different between canine astrocytomas and oligodendrogliomas. The canine TME, like that in humans, appears to be immunosuppressive. Citation Format: Nadia A. Lanman, Sagar Utturkar, Harish Kothandaraman, Deepika Dhawan, Danni Liu, Min Zhang, Matthew Beyers, Deborah W. Knapp, R. Timothy Bentley. Alterations in the tumor microenvironment and key signaling pathways in naturally-occurring canine gliomas mirror those seen in human patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3480.

THERAPEUTIC GENOME EDITING FOR SEVERE MONOGENIC SKIN DISORDERS

Cytotherapy · 2024-05-22