Conserved genetic findings in metastatic bladder cancer: a possible utility of allelic loss of chromosomes 9p21 and 17p13 in diagnosis

Mapping cancer biology in space: applications and perspectives on spatial omics for oncology

Technologies to decipher cellular biology, such as bulk sequencing technologies and single-cell sequencing technologies, have greatly assisted novel findings in tumor biology. Recent findings in tumor biology suggest that tumors construct architectures that influence the underlying cancerous mechanisms. Increasing research has reported novel techniques to map the tissue in a spatial context or targeted sampling-based characterization and has introduced such technologies to solve oncology regarding tumor heterogeneity, tumor microenvironment, and spatially located biomarkers. In this study, we address spatial technologies that can delineate the omics profile in a spatial context, novel findings discovered via spatial technologies in oncology, and suggest perspectives regarding therapeutic approaches and further technological developments.

Fibroblast growth factor receptor (FGFR) gene: pathogenesis and treatment implications in urothelial carcinoma of the bladder

Dysregulation of fibroblast growth factor receptors (FGFRs) has been implicated in several human malignancies, including urothelial carcinoma. In urothelial carcinoma, the oncogenic role of mutated FGFR is mediated by the RAS-mitogen-activated protein kinase pathway, resembling the effects observed with activated HRAS Activating somatic mutations of FGFR3 are clustered in three hotspots in exons 7, 10 and 15, and are almost always missense mutations leading to amino acid substitution in the external, transmembrane or intracellular regions of the receptor. A fusion of FGFR3 to transforming acid coiled-coil containing protein 3, FGFR3 amplification and alternative splicing leading to aberrant FGFR3 activation are less common molecular alterations. In April 2020, the Food and Drug Administration (FDA) approved the first targeted FGFR therapy, erdafitinib, in patients with locally advanced or metastatic bladder cancer who have progressed on platinum-based chemotherapy. Herein, we reviewed the normal structure and function of FGFR We also explored its role in the development of urothelial carcinoma and major developments in the FGFR-targeted therapy.

Translational progress on tumor biomarkers

There is an urgent need to apply basic research achievements to the clinic. In particular, mechanistic studies should be developed by bench researchers, depending upon clinical demands, in order to improve the survival and quality of life of cancer patients. To date, translational medicine has been addressed in cancer biology, particularly in the identification and characterization of novel tumor biomarkers. This review focuses on the recent achievements and clinical application prospects in tumor biomarkers based on translational medicine.

Biomarkers in bladder cancer: translational and clinical implications

Bladder cancer is associated with high recurrence and mortality rates. These tumors show vast heterogeneity reflected by diverse morphologic manifestations and various molecular alterations associated with these disease phenotypes. Biomarkers that prospectively evaluate disease aggressiveness, progression risk, probability of recurrence and overall prognosis would improve patient care. Integration of molecular markers with conventional pathologic staging of bladder cancers may refine clinical decision making for the selection of adjuvant and salvage therapy. In the past decade, numerous bladder cancer biomarkers have been identified, including various tumor suppressor genes, oncogenes, growth factors, growth factor receptors, hormone receptors, proliferation and apoptosis markers, cell adhesion molecules, stromal factors, and oncoproteins. Recognition of two distinct pathways for urothelial carcinogenesis represents a major advance in the understanding and management of this disease. Nomograms for combining results from multiple biomarkers have been proposed to increase the accuracy of clinical predictions. The scope of this review is to summarize the major biomarker findings that may have translational and clinical implications.

Molecular evidence supporting field effect in urothelial carcinogenesis

PURPOSE

Human urothelial carcinoma is thought to arise from a field change that affects the entire urothelium. Multifocality of urothelial carcinoma is a common finding at endoscopy and surgery. Whether these coexisting tumors arise independently or are derived from the same tumor clone is uncertain. Molecular analysis of microsatellite alterations and X-chromosome inactivation status in the cells from each coexisting tumor may further our understanding of urothelial carcinogenesis.

EXPERIMENTAL DESIGN

We examined 58 tumors from 21 patients who underwent surgical excision for urothelial carcinoma. All patients had multiple separate foci of urothelial carcinoma (two to four) within the urinary tract. Genomic DNA samples were prepared from formalin-fixed, paraffin-embedded tissue sections using laser-capture microdissection. Loss of heterozygosity (LOH) assays for three microsatellite polymorphic markers on chromosome 9p21 (IFNA and D9S171), regions of putative tumor suppressor gene p16, and on chromosome 17p13 (TP53), the p53 tumor suppressor gene locus, were done. X-chromosome inactivation analysis was done on the urothelial tumors from 11 female patients.

RESULTS

Seventeen of 21 (81%) cases showed allelic loss in one or more of the urothelial tumors in at least one of the three polymorphic markers analyzed. Concordant allelic loss patterns between each coexisting urothelial tumor were seen in only 3 of 21 (14%) cases. A concordant pattern of nonrandom X-chromosome inactivation in the multiple coexisting urothelial tumors was seen in only 3 of 11 female patients; of these 3 cases, only one displayed an identical allelic loss pattern in all of the tumors on LOH analysis.

CONCLUSION

LOH and X-chromosome inactivation assays show that the coexisting tumors in many cases of multifocal urothelial carcinoma have a unique clonal origin and arise from independently transformed progenitor urothelial cells, supporting the "field effect" theory for urothelial carcinogenesis.

Molecular genetic evidence for a common clonal origin of urinary bladder small cell carcinoma and coexisting urothelial carcinoma

In most cases, small-cell carcinoma of the urinary bladder is admixed with other histological types of bladder carcinoma. To understand the pathogenetic relationship between the two tumor types, we analyzed histologically distinct tumor cell populations from the same patient for loss of heterozygosity (LOH) and X chromosome inactivation (in female patients). We examined five polymorphic microsatellite markers located on chromosome 3p25-26 (D3S3050), chromosome 9p21 (IFNA and D9S171), chromosome 9q32-33 (D9S177), and chromosome 17p13 (TP53) in 20 patients with small-cell carcinoma of the urinary bladder and concurrent urothelial carcinoma. DNA samples were prepared from formalin-fixed, paraffin-embedded tissue sections using laser-assisted microdissection. A nearly identical pattern of allelic loss was observed in the two tumor types in all cases, with an overall frequency of allelic loss of 90% (18 of 20 cases). Three patients showed different allelic loss patterns in the two tumor types at a single locus; however, the LOH patterns at the remaining loci were identical. Similarly, the same pattern of nonrandom X chromosome inactivation was present in both carcinoma components in the four cases analyzed. Concordant genetic alterations and X chromosome inactivation between small-cell carcinoma and coexisting urothelial carcinoma suggest that both tumor components originate from the same cells in the urothelium.

Molecular genetic evidence for different clonal origins of epithelial and stromal components of phyllodes tumor of the prostate

Phyllodes tumor of the prostate is a rare neoplasm, composed of epithelium-lined cysts and channels embedded in a variably cellular stroma. The pathogenetic relationship of the epithelium and stroma is unknown and whether each is a clonal neoplastic element is uncertain. We studied the clonality of phyllodes tumors from six patients who underwent either enucleation or transurethral resection as their initial treatment. This was followed by total prostatectomy in three of the patients. Laser-assisted microdissection was performed to extract epithelial and stromal components of phyllodes tumor from formalin-fixed, paraffin-embedded tissue. Polymerase chain reaction was used to amplify genomic DNA at specific loci on chromosome 7q31 (D7S522), 8p21.3-q11.1 (D8S133, D8S137), 8p22 (D8S261), 10q23 (D10S168, D10S571), 17p13 (TP53), 16q23.2 (D16S507), 12q11-12 (D12S264), 17q (D17S855), 18p11.22-p11 (D18S53), and 22q11.2 (D22S264). In each tumor, stroma and epithelium were analyzed separately. Gel electrophoresis with autoradiography was used to detect loss of heterozygosity. All tumors showed allelic loss in one or more loci of both the epithelial and stromal components. The frequency of allelic loss in the epithelial component was 2 of 5 (40%) at D7S522, 2 of 6 (33%) at D8S133, 1 of 5 (20%) at D8S137, 3 of 6 (50%) at D8S261, 4 of 4 (100%) at D10S168, 4 of 6 (67%) at TP53, 2 of 6 (33%) at D10S571, 6 of 6 (100%) at D16S507, 1 of 5 (20%) at D12S264, 1 of 6 (17%) at D17S855, 2 of 6 (33%) at D18S53, and 2 of 5 (40%) at D22S264. The frequency of allelic loss in the stromal component was 2 of 5 (40%) at D7S522, 1 of 6 (17%) at D8S133, 2 of 5 (40%) at D8S137, 3 of 6 (50%) at D8S261, 1 of 4 (25%) at D10S168, 3 of 6 (50%) at TP53, 2 of 6 (33%) at D10S571, 3 of 6 (50%) at D16S507, 1 of 5 (20%) at D12S264, 0 of 6 (0%) at D17S855, 1 of 6 (17%) at D18S53, and 0 of 5 (0%) at D22S264. The pattern of allelic loss is significantly different in both stroma and epithelium statistically; completely concordant allelic loss patterns were not seen in any tumor examined. Our data demonstrate that both epithelial and stromal components of phyllodes tumor of the prostate are clonal, supporting the hypothesis that both elements are neoplastic. While both epithelium and stroma are clonal proliferations, they appear to have different clonal origins.

Nephroblastoma Arising in a Germ Cell Tumor of Testicular Origin

We report a nephroblastoma arising in a germ cell tumor of testicular origin occurring in a 22-year-old man. Orchiectomy demonstrated a malignant mixed germ cell tumor composed of mature and immature teratoma with nephroblastoma and rhabdomyosarcoma. Following chemotherapy, the patient developed supraclavicular and retroperitoneal lymphadenopathy. Excision demonstrated metastatic teratoma at both sites. No recurrence was noted with 21 months of additional follow-up. Using tissue microdissection and loss of heterozygosity analysis, we investigated the clonality of the mature teratoma, immature teratoma, nephroblastoma, and rhabdomyosarcoma components of the primary tumor and of the metastatic mature teratoma at the two separate distant sites. Nine microsatellite polymorphic makers were used to examine the pattern of allelic loss in both primary and metastatic tumors. Loss of heterozygosity was found in 4 DNA loci, and the same pattern of allelic loss was demonstrated at all 4 loci in all of the different components of the primary tumor and the metastatic mature teratomas, supporting the germ cell tumor origin of the nephroblastoma component. Loss of heterozygosity on chromosome 17p13 (TP53) was detected in metastatic mature teratoma, but not in the primary tumor. Loss of heterozygosity was observed at 11p13, the locus of WT1 inactivation in patients genetically predisposed to nephroblastoma, and this loss may be an important genetic mechanism in nephroblastomatous differentiation of germ cell tumors. These data support a common clonal origin for nephroblastoma and the other germ cell tumor components.

Allelic Loss of the Active X Chromosome During Bladder Carcinogenesis

Context.—Previous studies have shown that loss of the X chromosome is involved in the carcinogenesis of certain human malignancies.

Objective.—To determine whether X-linked allelic losses occur during bladder tumorigenesis and whether such losses involve the active or the inactive X chromosome.

Design.—We analyzed the deletion status of the X-linked human androgen receptor gene locus in 6 female patients who underwent radical cystectomies for muscle-invasive urothelial carcinoma of the urinary bladder. Four patients had coexisting urothelial carcinoma in situ. Analysis for inactivation of the X chromosome was carried out in parallel.

Results.—Three cases were informative. Invasive tumor samples showed loss of heterozygosity involving the active allele at the androgen receptor locus in all 3 positive cases, whereas carcinoma in situ showed nonrandom X chromosome inactivation but not allelic deletion.

Conclusions.—Our data suggest that allelic loss of the activated X chromosome is involved in bladder carcinogenesis and cancer progression.

Laser capture microdissection analysis reveals frequent allelic losses in papillary urothelial neoplasm of low malignant potential of the urinary bladder

BACKGROUND

In the 1999 World Health Organization classification system, papillary tumors of the urinary bladder were classified as papilloma, papillary urothelial neoplasm of low malignant potential (PUNLMP), and as Grade 1, Grade 2, and Grade 3 urothelial carcinoma. The biologic potential of PUNLMP of the urinary bladder is controversial. To the authors' knowledge, information regarding the genetic changes of PUNLMP tumors of the bladder is limited.

METHODS

The authors examined loss of heterogygosity (LOH) at 5 polymorphic microsatellite markers on chromosome 9q32-33 (D9S177), 9p22 (IFNA), 17p13.1 (TP53), 12q14-24 (D12S1051), and 3p25-26 (D3S3050) from 26 patients who were diagnosed with PUNLMP tumors of the urinary bladder. Tumors were microdissected from sections prepared from formalin-fixed, paraffin-processed tissue specimens using laser capture microdissection.

RESULTS

LOH was found in 21 of 26 (81%) patients with PUNLMP. The rate of LOH was 41% with D9S177, 32% with IFNA, 29% with TP53, 26% with D12S1051, and 44% with D3S3050. Allelic loss of multiple chromosome loci was often present in patients with PUNLMP tumors.

CONCLUSIONS

Genetic changes that commonly occur in advanced bladder carcinoma (> or = pT2) are frequently found in PUNLMP of the urinary bladder.

Molecular genetic alterations in the laser-capture-microdissected stroma adjacent to bladder carcinoma

BACKGROUND

Urothelial carcinoma commonly manifested loss of heterozygosity (LOH) at different regions of chromosomes 17p, 3p, and 9q. Recent studies suggested that bladder stromal cells may be implicated in the growth and progression of urothelial carcinoma. To better understand the genetic alterations in the stromal cells in patients with bladder carcinoma, the authors evaluated the prevalence of allelic loss at three microsatellite polymorphic markers on chromosomes 17p13 (TP53), 3p25-26 (D3S3050), and 9q32-33 (D9S177). In addition, the pattern of X-chromosome inactivation of the stromal cells was evaluated by analyzing the DNA methylation pattern at a polymorphic site on the androgen receptor gene.

METHODS

The authors studied 18 female patients who underwent either transurethral resection (n = 2) or radical cystectomy (n = 16) for high-grade muscle-invasive urothelial carcinoma of the urinary bladder. Genomic DNA samples from the stromal cells immediately adjacent to the tumor and the tumor itself were prepared from formalin-fixed, paraffin-processed tissues using laser-assisted microdissection and LOH was determined.

RESULTS

The stromal cells showed a high frequency of LOH on chromosomes 17p13 (29%), 3p25-26 (61%), and 9q32-33 (47%) with no clear concordance with the adjacent tumor cells. Fourteen specimens (78%) showed LOH in the stroma in at least 1 of 3 markers examined. Nonrandom X-chromosome inactivation was frequent in the stromal cells (50% of informative specimens).

CONCLUSIONS

The current study revealed that some of the genetic changes that commonly occur with invasive urothelial carcinoma were frequently found in the adjacent stroma and suggested that the stroma of urothelial carcinoma may play an important role in bladder carcinogenesis.

Molecular evidence supporting the neoplastic nature of some epidermoid cysts of the testis

CONTEXT

Loss of heterozygosity (LOH) on chromosomes 9p and 12q is common in germ cell tumors of the testis. Loss of heterozygosity of 17p13 has also been demonstrated in germ cell tumors. The incidence of LOH in epidermoid cysts, a possible special form of teratoma, has not been previously determined.

OBJECTIVE

To determine the frequency of LOH in epidermoid cysts.

DESIGN

Eight testicular epidermoid cysts and surrounding parenchyma were microdissected from formalin-fixed, paraffin-embedded tissue, and the genomic DNA was extracted using proteinase K. Polymerase chain reaction analysis targeted regions on chromosome 9p21 (D9S177 and D9S161 loci), chromosome 12q22 (D12S1051 locus), and chromosome 17p13 (TP53 locus). Gel electrophoresis followed by autoradiography was used to detect LOH.

RESULTS

All 8 of the epidermoid cysts were informative at a minimum of 1 of 4 loci. Three demonstrated LOH. In 2 tumors, LOH occurred on chromosome 9, and the third tumor demonstrated LOH on chromosome 12. Loss of heterozygosity on chromosome 17p13 was not present in any of the tumors.

CONCLUSIONS

Epidermoid cysts harbor allelic loss at some of the same loci identified in malignant testicular germ cell tumors. Our findings support that some examples of epidermoid cysts are neoplastic, although their low frequency of LOH also supports that they are genetically different from malignant germ cell tumors.