Beyond driver mutations: exploring the landscape of mutational signatures in adenocarcinomas of the bladder†

The emergence of mutational signatures in cancer research represents a paradigm shift, offering profound insights into tumor biology, therapeutic strategies, and risk assessment. A recent article published in The Journal of Pathology delves into the significance of mutational signatures, assessing their role as molecular fingerprints that illuminate the etiology of individual cancer cases. By deciphering the diverse patterns of DNA alterations, in the context of urachal and nonurachal bladder adenocarcinomas, researchers can unravel intrinsic and environmental risk factors shaping cancer development. The study highlighted a predominance of environmental risk factors in Chinese populations affected by bladder adenocarcinomas. In this context, in this commentary, we highlight some of the potential applications of molecular signatures in differential diagnosis and therapy prediction. As the field continues to evolve, a deeper understanding of mutational signatures promises to revolutionize precision oncology by offering personalized approaches informed by comprehensive mutational patterns of tumors. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

No conflicts of interest were declared.
Accumulation of somatic DNA mutations has been demonstrated to be the hallmark of human cancers.In recent years, next-generation DNA sequencing (NGS) has become an integral part of the clinical routine.This technical improvement provides the basis for the administration of targeted treatment approaches in terms of precision medicine.Since the number of approved targeted therapies are expanding, interest in identifying driver mutations is constantly increasing.Daily oncological practice mostly focuses on the identification of single driver mutations in oncogenes and tumor suppressor genes, which are responsible for malignant transformation and tumor progression.As a consequence of the widespread use of NGS, available DNA sequencing data are rapidly growing, allowing the analysis of broader DNA sequences.Analysis of these larger DNA sequencing datasets led to the observation that, in addition to driver mutations, a larger number of passenger mutations also accumulate in tumor tissues and form global patterns, which can be recurrently recognized in various tumors.In the last few years, these recurrent mutation patterns have largely been discovered and classified into so-called mutation signatures.While over 60 mutational signatures have been described and the list is constantly growing (https://cancer.sanger.ac.uk/signatures/sbs/), there is a varying prevalence among distinct tumor entities.Each tumor may contain 3-10 mutational signatures [1].Despite this development, mutational signatures are still less commonly considered in current clinical practice; however, they hold significant potential.Mutational signatures serve as molecular fingerprints for the biological mechanisms of their origin.Consequently, the molecular mechanisms and, thus, the risk factors behind some of the mutational signatures could be revealed.Overall, this approach helps to identify the etiology of individual cancer cases.Accordingly, mutational signatures have been identified in association with extrinsic risk factors, including smoking, aflatoxin, alkylating agents, aristolochic acid, and UV exposure (Figure 1) [1].Other signatures are associated with intrinsic factors such as mismatch repair (MMR) and homologous recombinant repair deficiency (HRD) or expression of the endogenous mutagenic protein apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) (Figure 1) [1].Another potential implication of mutational signatures lies in their predictive value for therapy.For example, the HRD-related mutational signature was associated with BRCA1/2 gene and other homologous recombinant repair gene mutations, and patients with gastrointestinal cancers carrying the HRD-signature exhibited a superior response to platinum-based therapy [2].Similarly, HRD score calculated from HRD-related mutational signature was highly predictive for neoadjuvant platinum therapy response in triple-negative breast cancer [3].Furthermore, mutational signatures may help in differential diagnosis.For instance, distant metastases originating from cutaneous squamous cell carcinoma and undifferentiated melanoma, devoid of specific histopathologic features and immunohistochemical markers, may be mistakenly diagnosed as primary tumors in other organs.However, their UVrelated mutational signatures can reveal their cutaneous origin [4].Taken together, mutational signatures not only represent emerging biomarkers for differential diagnosis and therapy prediction but may also inform the etiology of a given tumor and thus can help to identify significant intrinsic or environmental risk factors responsible for geographic differences in incidences enabling the elaboration of better preventive measures.
Primary and urachal adenocarcinomas of the bladder are rare cancers with unknown hereditary clustering or environmental risk factors.A recent systematic review revealed a meaningful heterogeneity in the incidence of urachal adenocarcinomas between various countries, with the highest incidence in Japan, suggesting differential extrinsic or intrinsic risk factors in different geographical areas [5].However, the identification of these risk factors remains to be elucidated.A study by Yang, Shahatiaili, Bai, Wang et al adds interesting new data to this field by performing whole exome, genome, and transcriptome, as well as single-cell RNA, analyses [6].Their mutational signature analysis identified that the T>A substitution in association with signature 22 is dominant in bladder adenocarcinomas.This mutational signature is known to be associated with chemical carcinogens, including aristolochic acid.Thus, Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that genes that were affected by copy number variations are enriched in the so-called chemical carcinogenesis-DNA adduct pathway, which seems to be consistent with the results of mutational signature analysis.In contrast, the intrinsic mutagenic enzyme expressionrelated APOBEC signature 13 was present in only two cases.These results suggest that environmental risk factors were dominant in the Chinese population analyzed by the authors.However, a study from South Korea found only a low frequency of T>A substitutions, suggesting differences in risk factors between various regions [7].Accordingly, two studies assessing the molecular signatures of normal urothelium found a higher occurrence of aristolochic acid-related mutational signature in a Chinese sample set compared to a similar study with European samples [8].
The study by Yang, Shahatiaili, Bai, Wang et al furthermore revealed a gene expression pattern similar to the luminal infiltrated subtype of urothelial bladder carcinoma with significant infiltration by immune cells such as B-, NK-, and various T-cell populations (IL7R+ Th cells, CD8+ cytotoxic T cells, and CTLA4+

Mutational landscapes of bladder adenocarcinomas 401
Tregs) [6].However, these findings should be handled with caution, as the authors reported a tumor cellularity of 70-80% for most cases.In contrast, single-cell RNA sequencing data suggested a range of 0-35% tumor cell content but as high as 65-95% immune cell content.High immune cell infiltration may be associated with better response to immune checkpoint inhibition therapy.The efficacy of this therapy option was reported in only a few cases of urachal and nonurachal adenocarcinomas of the urinary bladder.For urachal cancer, two independent studies reported small urachal carcinoma case series in molecularly (PD-L1 status, TMB, MSI) unselected patients [9,10].In the former study, four urachal cancer patients were treated with ipilimumab and nivolumab combination; two patients experienced stable disease, one progressive disease and one partial response, while in the second study six patients received various immune checkpoint inhibitor monotherapies; here three patients had progressive disease, one stable disease and two partial response.These studies reflect a rather mixed response to immune checkpoint inhibitor therapy; however, the overall 3/10 (30%) response rate seems to be similar to that described in the metastatic setting of urothelial carcinoma.For primary bladder adenocarcinomas, of three cases treated with three different checkpoint inhibitors, in two patients, therapy was discontinued after 3-4 months because of disease progression, and in one case therapy was still ongoing after 18 months.These data reflect a similar response rate of 30% to immune checkpoint inhibitors in primary bladder adenocarcinomas compared to urachal cancers.

Figure 1 .
Figure 1.Associations between mutational signatures and extrinsic or intrinsic risk factors.