Precision oncology in urothelial cancer

Existing trends and applications of artificial intelligence in urothelial cancer A scoping review

INTRODUCTION

The use of artificial intelligence (AI) in urology is gaining significant traction. While previous reviews of AI applications in urology exist, there have been few attempts to synthesize existing literature on urothelial cancer (UC).

METHODS

Comprehensive searches based on the concepts of "AI" and "urothelial cancer" were conducted in MEDLINE , EMBASE , Web of Science, and Scopus. Study selection and data abstraction were conducted by two independent reviewers. Two independent raters assessed study quality in a random sample of 25 studies with the prediction model risk of bias assessment tool (PROBAST) and the standardized reporting of machine learning applications in urology (STREAM-URO) framework.

RESULTS

From a database search of 4581 studies, 227 were included. By area of research, 33% focused on image analysis, 26% on genomics, 16% on radiomics, and 15% on clinicopathology. Thematic content analysis identified qualitative trends in AI models employed and variables for feature extraction. Only 19% of studies compared performance of AI models to non-AI methods. All selected studies demonstrated high risk of bias for analysis and overall concern with Cohen's kappa (k)=0.68. Selected studies met 66% of STREAM-URO items, with k=0.76.

CONCLUSIONS

The use of AI in UC is a topic of increasing importance; however, there is a need for improved standardized reporting, as evidenced by the high risk of bias and low methodologic quality identified in the included studies.

Whole exome sequencing analysis of canine urothelial carcinomas without BRAF V595E mutation: Short in-frame deletions in BRAF and MAP2K1 suggest alternative mechanisms for MAPK pathway disruption

Molecular profiling studies have shown that 85% of canine urothelial carcinomas (UC) harbor an activating BRAF V595E mutation, which is orthologous to the V600E variant found in several human cancer subtypes. In dogs, this mutation provides both a powerful diagnostic marker and a potential therapeutic target; however, due to their relative infrequency, the remaining 15% of cases remain understudied at the molecular level. We performed whole exome sequencing analysis of 28 canine urine sediments exhibiting the characteristic DNA copy number signatures of canine UC, in which the BRAF V595E mutation was undetected (UDV595E specimens). Among these we identified 13 specimens (46%) harboring short in-frame deletions within either BRAF exon 12 (7/28 cases) or MAP2K1 exons 2 or 3 (6/28 cases). Orthologous variants occur in several human cancer subtypes and confer structural changes to the protein product that are predictive of response to different classes of small molecule MAPK pathway inhibitors. DNA damage response and repair genes, and chromatin modifiers were also recurrently mutated in UDV595E specimens, as were genes that are positive predictors of immunotherapy response in human cancers. Our findings suggest that short in-frame deletions within BRAF exon 12 and MAP2K1 exons 2 and 3 in UDV595E cases are alternative MAPK-pathway activating events that may have significant therapeutic implications for selecting first-line treatment for canine UC. We developed a simple, cost-effective capillary electrophoresis genotyping assay for detection of these deletions in parallel with the BRAF V595E mutation. The identification of these deletion events in dogs offers a compelling cross-species platform in which to study the relationship between somatic alteration, protein conformation, and therapeutic sensitivity.

[Molecular diagnostics of bladder cancer-practical ramifications]

In the future, precision medicine with agents targeting specific genetic alterations will play an important role in bladder cancer. This includes both single genetic alterations (e.g. FGFR3) and gene panel analyses in patients with no further therapeutic options, rare cancer subtypes or unusual clinical courses. These molecular analyses can be carried out on formalin-fixed paraffin-embedded tumor samples and the results should be discussed in interdisciplinary molecular tumor boards in order to either recommend approved targeted therapies or suggest patients for molecular-based clinical trials, compassionate use programs or off-label use of drugs. The remuneration of molecular diagnostics is largely well-represented for the outpatient sector in Germany; however, the covering of treatment costs must currently be approved by the health insurances.