Molecular profiling of clear cell adenocarcinoma of the urinary tract

Two rare cases of primary clear cell adenocarcinoma of the urethra: clinical experience, case report and literature review

Background

Primary clear cell adenocarcinoma of the urethra (CCAU) is a kind of extremely rare genitourinary cancer. Despite the similarity in the clinical manifestations of these reported cases, diagnosis and determination of standard therapy remain challenging due to the rarity of findings and similarity with other urethral tumors.

Case presentation

Herein, we reported two cases of CCAU with the same chief complaint of hematuria: a 71-year-old female and a 66-year-old male. The male patient reported concomitant symptoms of frequent and painful urination. CT scans show abnormal enhancements. After a cystoscopy examination, both patients are diagnosed with malignant urethral tumors. Surgical resections and additional pathological examinations support the diagnosis of CCAU (palliative resection for case 1 and transurethral resection for case 2). Case 1 undergone progression 6 months after initial treatment with transurethral resection and chemotherapy with a 15-month overall survival. In contrast, the prognosis of case 2 remained uneventful 10 months after surgery without recurrence. After presenting our cases, we launched a literature review that included 23 articles and 33 cases of CCAU to summarize the characteristics of the disease.

Conclusion

Primary clear cell adenocarcinoma of the urethra is a rare malignant urethral tumor with controversial histological origins. Primary symptoms include hematuria and changes in voiding habits. Middle-aged and elderly females are more susceptible to primary clear-cell adenocarcinoma of the urethra. Unfortunately, it is difficult to differentiate primary clear-cell adenocarcinoma of the urethra from other urethral tumors due to similar clinical features. However, imaging tools such as CT, MRI, and cystoscopy are adjunctive in confirming diagnoses. Even though surgical resection is the primary treatment to relieve clinical symptoms, prevent recurrence, and confirm diagnosis, no standard surgical protocol is available. The therapeutic effect of postoperative adjuvant therapies remains unclear. Future investigations on CCAU are necessary to advance clinical knowledge and to provide treatment guidance.

Primary adenocarcinoma of the urinary tract and its precursors: Diagnostic criteria and classification

Primary adenocarcinoma of the urinary bladder is a rare malignancy, comprising up to 2% of bladder cancers, predominantly in males. Its rarity and similarity to urothelial carcinoma and secondary adenocarcinomas pose diagnostic challenges. A comprehensive literature review was conducted on the diagnosis, classification, morphological and immunophenotypic characteristics, and molecular profiles of primary adenocarcinoma, urachal adenocarcinoma, and precursor lesions. Primary adenocarcinoma exhibits diverse morphological patterns, including enteric, mucinous, signet ring cell, and mixed types. Immunohistochemistry is useful in differentiating primary adenocarcinoma from metastatic adenocarcinomas and secondary involvement. Genetic studies reveal mutations common in colorectal and bladder adenocarcinomas (KRAS, TP53, PIK3CA) and novel primary adenocarcinoma-specific mutations (OR2L5). Urachal adenocarcinoma shares morphological features with primary adenocarcinoma but typically occurs in younger patients with unique genomic and distinct immunoprofile. Potential precursor lesions include villous adenoma, cystitis glandularis, and intestinal metaplasia, and warrant close clinical follow-up. Despite advances in histopathological and molecular diagnostics, primary adenocarcinoma remains challenging to diagnose due to its rarity and morphological heterogeneity. Ongoing research into its molecular characteristics is essential to refine diagnostic criteria and therapeutic approaches. Thorough clinical and pathological assessment is crucial for accurate diagnosis, classification, and clinical management.

Clear Cell Adenocarcinoma of the Urinary Tract Primary to the Renal Pelvis: A Multi-institutional Clinicopathologic and Molecular Study of Five Patients

Clear cell adenocarcinoma (CCA) of the urinary tract is a rare malignancy and tumors involving the renal pelvis are notably sparse in the literature, with only 5 other patients reported. We present 5 patients, 4 women, and 1 man, with CCA of the renal pelvis. The age at presentation ranged from 29 to 81 years. The tumor size ranged from 4.5 to 8.0 cm. Tumors exhibited shared morphologic and immunohistochemical features with CCA of the female genital tract and those originating in the bladder and urethra, including cells with large nuclei, prominent nucleoli, nuclear hobnailing, and scant clear cytoplasm. Common immunohistochemical findings included reactivity for PAX8, CK7, HNF1β, and Napsin-A. One of the tumors arose in the background of a mixed epithelial and stromal tumor. Another tumor occurred in a renal allograft and tumor cells were positive for the BK virus, demonstrated by SV40 immunohistochemistry. All tumors were negative for TFE3 and TFEB rearrangement and lacked TERT alterations. Follow-up was limited with no recurrence in 4 patients at a maximum of 20 months follow-up and 1 patient died of an unrelated cause at 25 months of follow-up. Next-generation sequencing analysis of all 5 CCAs revealed mutations within genes implicated in DNA damage repair and chromatin remodeling pathways, including ATM , BRCA1 , BRCA2, ARID1A, DICER1, SMAD4, NOTCH1 , and MYC amplification. These molecular findings underscore the dysregulation of fundamental cellular processes essential for genomic integrity maintenance.

[Rare tumors and tumor types of the urinary system in the 5th edition of the WHO classification 2022]

The 5th edition of the World Health Organization (WHO) classification of tumors of the urinary tract and male genital organs introduced both general and specific changes in structure, classification, and nomenclature. This also applies to rarer tumors and tumor subtypes of the urinary system. Knowledge of these changes is relevant for routine histopathological work. This article provides an overview of the main new features of the rarer tumors and tumor subtypes of the urinary system in the new edition of the WHO classification.

Diagnostic Approach to and Differential Diagnosis of Clear Cell and Glandular Lesions of the Lower Urinary Tract

CONTEXT.—

A variety of glandular and clear cell lesions may be seen in the urinary bladder and/or urethra, ranging from benign to malignant primary and secondary tumors. Lesions with no malignant potential include reactive processes, such as nephrogenic metaplasia, and may show similar morphologic features as an infiltrative neoplasm, particularly in small biopsies. Similarly, ectopic tissues of Müllerian origin may be seen in the lower urinary tract, and their distinction from a true glandular neoplasm is essential to avoid overtreatment. A wide variety of primary and secondary malignant tumors exist with varying degrees of glandular and clear cell features. Therefore, surgical pathologists must be aware of the full scope of possible lesions to avoid misdiagnosis.

OBJECTIVE.—

To provide a practical framework for approaching the diagnosis of clear cell and glandular lesions of the urinary bladder/urethra and prostate, highlighting the strengths and limitations of various diagnostic features and ancillary tests.

DATA SOURCES.—

A review of the current literature was performed to obtain data regarding up-to-date diagnostic features and ancillary studies.

CONCLUSIONS.—

In summary, distinct morphologic and immunohistochemical features and clinical and radiologic correlation are essential to establish an accurate diagnosis when such cases with glandular and clear features are encountered in the lower urinary tract.

Glandular Lesions of the Urinary Bladder: Diagnostic and Molecular Updates

Glandular lesions in the urinary tract or their associated pathologies can pose a diagnostic challenge. There is a variety of benign alterations and tumor types that need to be taken into account in differential diagnostic considerations. In recent times, efforts for better defining these alterations or lesions both on the histopathological and molecular levels have been undertaken. This article will provide an update on current diagnostic and molecular considerations of these lesions.

Clear Cell Adenocarcinoma of Urethra: Clinical and Pathologic Implications and Characterization of Molecular Aberrations

PURPOSE

This study aimed to evaluate the molecular features of clear cell adenocarcinoma (CCA) of the urinary tract and investigate its pathogenic pathways and possible actionable targets.

MATERIALS AND METHODS

We retrospectively collected the data of patients with CCA between January 1999 and December 2016; the data were independently reviewed by two pathologists. We selected five cases of urinary CCA, based on the clinicopathological features. We analyzed these five cases by whole exome sequencing (WES) and subsequent bioinformatics analyses to determine the mutational spectrum and possible pathogenic pathways.

RESULTS

All patients were female with a median age of 62 years. All tumors were located in the urethra and showed aggressive behavior with disease progression. WES revealed several genetic alterations, including driver gene mutations (AMER1, ARID1A, CHD4, KMT2D, KRAS, PBRM1, and PIK3R1) and mutations in other important genes with tumor-suppressive and oncogenic roles (CSMD3, KEAP1, SMARCA4, and CACNA1D). We suggest putative pathogenic pathways (chromatin remodeling pathway, mitogen-activated protein kinase signaling pathway, phosphoinositide 3-kinase/AKT/mammalian target of rapamycin pathway, and Wnt/β-catenin pathway) as candidates for targeted therapies.

CONCLUSION

Our findings shed light on the molecular background of this extremely rare tumor with poor prognosis and can help improve treatment options.

Reprint of: Female Urethral Carcinoma: A contemporary review of the clinicopathologic features, with emphasis on the histo-anatomic landmarks and potential staging issues

Primary female urethral carcinoma (PUC-F) accounts for less than 1% of all genitourinary malignancies and comprises a histologically diverse group of tumors that are usually associated with poor prognosis. The carcinomas documented at this site include adenocarcinoma (clear cell adenocarcinoma, columnar cell carcinoma, and Skene gland adenocarcinoma), urothelial carcinoma (UCa), and squamous cell carcinoma (SCC). Recent studies have shown adenocarcinomas to be the most common type of primary urethral carcinoma in females. As most of the urethral carcinomas morphologically resemble carcinomas arising from surrounding pelvic organs or metastases, these should be ruled out before making the diagnosis of PUC-F. These tumors are currently staged according to the 8th edition of the American Joint Committee on Cancer (AJCC) staging system. However, the AJCC system has limitations, including the staging of tumors involving the anterior wall of the urethra. Staging systems like the recently proposed histology-based female urethral carcinoma staging system (UCS) takes into account the unique histological landmarks of the female urethra to better stratify pT2 and pT3 tumors into prognostic groups, that correlate with clinical outcomes including recurrence rates, disease-specific survival and overall survival. Further larger multi-institutional cohorts are however required to validate the results of this staging system. There is very limited information regarding the molecular profiling of PUC-F. Thirty-one percent of clear cell adenocarcinomas have been reported to show PIK3CA alterations, whereas 15% of adenocarcinomas show PTEN mutations. Higher tumor mutational burden and PD-L1 staining have been reported in UCa and SCC. Although multimodality treatment is usually recommended in locally advanced and metastatic disease, the role of immunotherapy and targeted therapy is promising in select PUC-F cases.

Urothelial Carcinoma: Divergent Differentiation and Morphologic Subtypes

Urothelial carcinoma (UC) is known to encompass a wide spectrum of morphologic features and molecular alterations. Approximately 15% to 25% of invasive UC exhibits histomorphologic features in the form of "divergent differentiation" along other epithelial lineages, or different "subtypes" of urothelial or sarcomatoid differentiation. It is recommended that the percentage of divergent differentiation and or subtype(s) be reported whenever possible. Recent advances in molecular biology have led to a better understanding of the molecular underpinning of these morphologic variations. In this review, we highlight histologic characteristics of the divergent differentiation and subtypes recognized by the latest version of WHO classification, with updates on their molecular and clinical features.

Female urethral carcinoma: a contemporary review of the clinicopathologic features, with emphasis on the histoanatomic landmarks and potential staging issues

Primary female urethral carcinoma (PUC-F) accounts for less than 1% of all genitourinary malignancies and comprises a histologically diverse group of tumors that are usually associated with poor prognosis. The carcinomas documented at this site include adenocarcinoma (clear cell adenocarcinoma, columnar cell carcinoma, and Skene gland adenocarcinoma), urothelial carcinoma (UCa), and squamous cell carcinoma (SCC). Recent studies have shown adenocarcinomas to be the most common type of primary urethral carcinoma in females. As most of the urethral carcinomas morphologically resemble carcinomas arising from surrounding pelvic organs or metastases, these should be ruled out before making the diagnosis of PUC-F. These tumors are currently staged according to the 8th edition of the American Joint Committee on Cancer (AJCC) staging system. However, the AJCC system has limitations, including the staging of tumors involving the anterior wall of the urethra. Staging systems like the recently proposed histology-based female urethral carcinoma staging system (UCS) takes into account the unique histological landmarks of the female urethra to better stratify pT2 and pT3 tumors into prognostic groups, that correlate with clinical outcomes including recurrence rates, disease-specific and overall survival. Further larger multi-institutional cohorts are however required to validate the results of this staging system. There is very limited information regarding the molecular profiling of PUC-F. Thirty-one percent of clear cell adenocarcinomas have been reported to show PIK3CA alterations, whereas 15% of adenocarcinomas show PTEN mutations. Higher tumor mutational burden and PD-L1 staining have been reported in UCa and SCC. Although multimodality treatment is usually recommended in locally advanced and metastatic disease, the role of immunotherapy and targeted therapy is promising in select PUC-F cases.

A rare case of a clear cell carcinoma in a female urethral diverticulum

Introduction

Urethral clear cell carcinoma is rare and often arises from a urethral diverticulum and rarely from the Müllerian duct. However, an explanation for this correlation remains unknown.

Case presentation

We report the case of a 46-year-old woman who presented with hypermenorrhea. Magnetic resonance imaging revealed a papillary tumor in a cystic lesion in the dorsal urethra. We performed a robot-assisted radical cystourethrectomy and created an ileal conduit. Since pathological findings revealed microvascular and lymphovascular invasions around the urethra, adjuvant radiation therapy was administered. The patient showed no signs of recurrence or metastasis after treatment.

Conclusion

We report a case of clear cell carcinoma in a female urethral diverticulum originating from a Müllerian duct cyst. While postoperative radiation therapy has been shown to produce a good outcome in carcinoma cases similar to this one, we recommend that a radical cystourethrectomy be performed.

Distinct mutational status in GATA3-Positive clear cell adenocarcinoma of the urinary tract: A CASE report

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Clear cell adenocarcinoma of the lower urinary tract is rare and poses diagnostic challenge.

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GATA3, which is frequently expressed in urothelial carcinoma, can be expressed in clear cell adenocarcinoma.

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ARID1A, PBRM1, ERBB4, and SMARCA4 mutations were identified in the current CASE.

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Molecular studies may aid in the diagnosis, and optimal treatment decision-making process.

Comprehensive genomic profiling of histologic subtypes of urethral carcinomas

BACKGROUND

Carcinoma of the urethra (UrthCa) is an uncommon Genitourinary (GU) malignancy that can progress to advanced metastatic disease.

METHODS

One hundred twenty-seven metastatic UrthCa underwent hybrid capture-based comprehensive genomic profiling to evaluate all classes of genomic alterations (GA). Tumor mutational burden was determined on up to 1.1 Mbp of sequenced DNA, and microsatellite instability was determined on 114 loci. PD-L1 expression was determined by IHC (Dako 22C3).

RESULTS

Forty-nine (39%) urothelial (UrthUC), 31 (24%) squamous (UrthSCC), 24 (19%) adenocarcinomas NOS (UrthAC), and 12 (9%) clear cell (UrthCC) were evaluated. UrthUC and UrthSCC are more common in men; UrthAC and UrthCC are more common in women. Ages were similar in all 4 groups. GA in PIK3CA were the most frequent potentially targetable GA; mTOR pathway GA in PTEN were also identified. GA in other potentially targetable genes were also identified including ERBB2 (6% in UrthUC, 3% in UrthSCC, and 12% in UrthAC), FGFR1-3 (3% in UrthSCC), BRAF (3% in UrthAC), PTCH1 (8% in UrthCC), and MET (8% in UrthCC). Possibly reflecting their higher GA/tumor status, potential for immunotherapy benefit associated with higher tumor mutational burden and PD-L1 staining levels were seen in UrthUC and UrthSCC compared to UrthAC and UrthCC. Microsatellite instability high status was absent throughout.

CONCLUSIONS

Comprehensive genomic profiling reveals GA that may be predictive of both targeted and immunotherapy benefit in patients with advanced UrthCa and that could potentially be used in future adjuvant, neoadjuvant, and metastatic disease trials.

Molecular Characterization of Muellerian Tumors of the Urinary Tract

In the 2016 WHO classification of genitourinary tumors Muellerian tumors of the urinary tract (MTUT) comprise clear cell adenocarcinomas and endometrioid carcinomas. Since these rare tumors remained understudied, we aimed to characterize their molecular background by performing DNA- and RNA-based targeted panel sequencing. All tumors (n = 11) presented single nucleotide alterations (SNVs), with ARID1A mutations being the most prevalent (5/11, 45%). Besides frequent ARID1A mutations, loss of ARID1A protein is not a suitable marker since protein expression is (partly) preserved also in mutated cases. Copy number alterations (CNVs) were found in 64% of cases (7/11), exclusively gene amplifications. Interestingly, a functionally relevant RSPO2 gene fusion/microdeletion was discovered in the endometrioid adenocarcinoma case. Comparing our findings with mutational profiles of other tumor entities, absence of TERT promoter mutations argues for a non-urothelial origin. No similarities were also found between MTUT and kidney cancers while parallels were observed for specific SNVs with endometrial carcinomas. In conclusion, immunohistochemical PAX8-positivity and lack of TERT promoter mutations could serve as key diagnostic features in difficult cases. Thus, understanding the molecular background of these tumors helps to refine treatment options and offers the possibility of targeted therapies in cases where needed.

Clear Cell Adenocarcinoma in Men: A Series of 15 Cases

Clear cell adenocarcinoma (CCA) is a rare tumor in the genitourinary tract with female predominance and few reports in men. We identified 15 cases of CCA in men evaluated at our institution. Five arose in the bladder, 7 in the prostate or prostatic urethra, 2 in the membranous urethra (1 multifocal in the prostatic and membranous urethra), 1 periprostatic (likely from an embryologic remnant), and 1 between rectum and bladder (likely in a prostatic utricle cyst). No cases showed associated Müllerian structures. One case showed separate foci of nephrogenic adenoma at diagnosis, and 1 case showed urothelial carcinoma in situ on a later follow-up biopsy. Four tumors extended into other organs (prostate to seminal vesicle and periprostatic soft tissue, periprostatic soft tissue to prostate, prostatic urethra to bladder and rectum, and prostate to bladder neck). One tumor showed extraprostatic extension alone. Four tumors metastasized to lymph nodes, with 3 also metastasizing to other sites (bladder, lung and adrenal, and right flank). Eleven patients underwent resection, including 3 transurethral resections. Seven underwent other treatments, including radiation (5 [1 for recurrence]), chemotherapy (3), hormonal therapy (3), immunotherapy with nivolumab (1), and targeted therapy with gefitinib (1). The mean follow-up was 35 months (range: 1 to 138 mo). At the last follow-up, 7 patients showed no evident disease and 3 were alive with disease. Four died with the cause of death unknown, with 2 cases having confirmed disease at the time of death and the remaining 2 dying less than a year after diagnosis. The mean time to death was 16 months (range: 6 to 39 mo). No follow-up was available on 1 patient. All patients who died in this series had CCA of the prostate or prostatic urethra. Pathologists need to be attuned to CCA occurring in males, given that the literature emphasizes its occurrence in females. In addition to established sites such as bladder and urethra, our series demonstrates that tumor may present in unusual adjacent sites, such as in periprostatic embryologic remnants or prostatic utricle.

Variant morphology and random chromosomal integration of BK polyomavirus in posttransplant urothelial carcinomas

BK polyomavirus (BKPyV) causes major complications in solid organ transplant recipients but little is known about its role in the development of urothelial carcinoma (UC) during immunosuppression. Immunohistochemistry (IHC) screening for polyomavirus large T antigen (LTag) was performed in 94 micropapillary UC (MPUC), 480 unselected UC, 199 muscle invasive UC (including 83 UC with variant differentiation), 76 cases of plasmocytoid, nested and large nested UC and 15 posttransplant UC. LTag expressing UC were reevaluated regarding their histomorphological features and characterized by IHC for p53 and HER2, chromogenic in situ hybridization for HER2 and SNaPshot analysis of the TERT promoter and HRAS. Real-time PCR and next generation sequencing (NGS) were performed to search for BKPyV-DNA and for variants in the tumor and viral genomes. We detected five LTag expressing UC which were diagnosed between 2 and 18 years after kidney (n = 4) or heart (n = 1) transplantation. 89 MPUC without history of organ transplantation and overall 755 UC (including cases with variant histology) were LTag negative. Of the five LTag expressing UC, three were MPUC, one showed extensive divergent differentiation with Mullerian type clear cell carcinoma, and one displayed focal villoglandular differentiation. All five tumors had aberrant nuclear p53 expression, 2/5 were HER2-amplified, and 3/5 had TERT promoter mutations. Within the 50 most common cancer related genes altered in UC we detected very few alterations and no TP53 mutations. BKPyV-DNA was present in 5/5 UC, chromosomal integration of the BKPyV genome was detectable in 4/5 UC. Two UC with BKPyV integration showed small deletions in the BKPyV noncoding control region (NCCR). The only UC without detectable BKPyV integration had a high viral load of human herpesvirus 6 (HHV-6). Our results suggest that LTag expression of integrated BKPyV genomes and resulting p53 inactivation lead to aggressive high-grade UC with unusual, often micropapillary morphology.