Targeted hotspot profiling reveals a functionally relevant mutation in bladder cancer

Understanding the mutational landscape is critical for elucidating the molecular mechanisms driving cancer progression. This study aimed to profile somatic mutations in bladder cancer patients (N=7) from Bangladesh to provide insights into the genetic alterations underlying this malignancy.

We performed targeted sequencing of 50 oncogenes and tumor suppressor genes using the Ion AmpliSeq Cancer Hotspot Panel v2 on tumor and matched blood samples from seven bladder cancer patients. Somatic variants were identified with GATK Mutect2, annotated with ANNOVAR, and analyzed using maftools. Molecular subtypes were defined through NMF clustering, ssGSEA, and immune deconvolution on TCGA data. Structural and functional impacts of deleterious mutations were assessed through protein modeling, docking, molecular dynamics simulations, and survival analysis.

Analysis of somatic variants revealed the presence of frameshift indels (insertions-deletions) and missense SNVs (msSNVs), while T > C and C > T transitions were highly prevalent among the SNVs. The genes that were highly mutated in this series included ATM, APC, STK11, TP53, KIT, MET, ERBB4, RET, KDR, and PIK3CA in each sample. Among these genes, the tumor suppressor gene STK11 was found to be highly deleterious due to a mutation involving phenylalanine to serine substitution at the 255th amino acid position of the STK11 protein. Further, we investigated the effect of somatic mutations in the STK11 gene using different bioinformatics tools. 3D structure analyses and molecular dynamics simulation showed that the mutation occurred within the protein's kinase domain, contributing to the destabilization of the protein's structure; lowered the affinity for ATP binding, and affected the catalytic properties, which may ultimately lead to the loss of its tumor suppressive function. Additionally, mutational signature-based stratification identified 2 molecular subtypes with basal and luminal characteristics. Integrative transcriptomic analysis was performed to characterize these 2 subtypes using publicly available transcriptomic dataset. Despite a lower tumor mutational burden, the basal subtype was significantly associated with immune infiltration within the tumor microenvironment and displayed aggressive and metastatic disease traits.

Our study highlights STK11 as a key deleterious mutation in Bangladeshi bladder cancer patients, suggesting its potential role in tumor progression and patient prognosis.