Distinct genetic alterations and luminal molecular subtype in nested variant of urothelial carcinoma

Since 2016, large nested urothelial carcinoma (LNUC) has been included within the WHO classification of urothelial tumors. Limited reports with mainly small case series have confirmed the malignant behavior of LNUC despite its bland morphological appearance. We evaluated, for the first time, markers for new immunooncological or targeted therapies including FGFR3 mutational status and PD-L1 status, the frequency of TERT-promoter mutations and the molecular subtype in a cohort of 25 LNUC using SNaPshot analysis and immunohistochemistry. Of the 25 cases, 17 were pure LNUC, with 13 showing an additional exophytic papillary/papillary-like component. Seven mixed LNUCs presented areas of classical nested variant urothelial carcinoma (NVUC) and one showed a component of conventional urothelial carcinoma. Of the 17 evaluable pure LNUCs, 16 were FGFR3-mutated with identical mutations in their concomitant papillary/papillary-like components. An FGFR3 mutation was found in 1/7 evaluable mixed LNUCs combined with NVUC. TERT-promoter mutations were detected in 86.7% pure and 83.3% mixed tumors. Immunohistochemistry revealed a luminal phenotype; PD-L1 was negative in the majority of tumor cells and tumor-associated immune cells. Pure LNUC is a prime example of a luminal, FGFR3-mutated, mostly PD-L1-negative tumor. In contrast, FGFR3 mutations seem to be rare in mixed LNUC, which may indicate a different pathway of tumor development.

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Nested Variant of Urothelial Carcinoma Is a Luminal Bladder Tumor With Distinct Coexpression of the Basal Marker Cytokeratin 5/6

American Journal of Clinical Pathology ◽

10.1093/ajcp/aqaa160 ◽

2020 ◽

Author(s):

Steven M Johnson ◽

Armen Khararjian ◽

Teklu B Legesse ◽

Francesca Khani ◽

Brian D Robinson ◽

...

Keyword(s):

Urothelial Carcinoma ◽

Expression Profiling ◽

Bladder Tumor ◽

Molecular Subtype ◽

Molecular Phenotype ◽

Bladder Tumors ◽

Basal Marker ◽

Cytokeratin 5 ◽

Nested Variant ◽

Molecular Phenotypes

Abstract Objectives The nested variant of urothelial carcinoma (NVUC) is a rare bladder tumor that may possess a luminal molecular phenotype. We sought to determine whether a small immunohistochemical (IHC) panel using common surrogates for molecular phenotypes would reliably classify a cohort of pure NVUC cases. Methods IHC staining with a panel composed of markers for basal subtypes (CK5/6, CK14) and luminal subtypes (FOXA1, GATA3) was performed on pure small NVUC cases (n = 23) and 5 large NVUC cases (n = 5). Scoring of IHC stains was performed semiquantitatively. Individual cases were analyzed using previously reported IHC-based surrogates for molecular subtype. Results The phenotype of NVUC was classified as luminal from 60.1% (FOXA1+/CK5/6−) to 100% (GATA3+/CK14−) of cases using composite phenotypes. No cases possessed a basal or squamous cell carcinoma–like phenotype. The majority of small NVUC cases (69.5%) showed subset CK5/6 expression distinctly localized to the basal layers of tumor cell nests. Intratumoral heterogeneity was also noted in CK5/6 (21.7% of small NVUC cases) but no other markers. Conclusions NVUC appears to express markers of both basal and luminal bladder tumors. Definitive gene expression profiling may be valuable to further characterize this unique histologic variant.

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Basal and Luminal Molecular Subtypes in Naturally-Occurring Canine Urothelial Carcinoma are Associated with Tumor Immune Signatures and Dog Breed

Bladder Cancer ◽

10.3233/blc-201523 ◽

2021 ◽

pp. 1-17

Author(s):

Breann C. Sommer ◽

Deepika Dhawan ◽

Audrey Ruple ◽

José A. Ramos-Vara ◽

Noah M. Hahn ◽

...

Keyword(s):

Urothelial Carcinoma ◽

Cancer Progression ◽

Molecular Subtypes ◽

Molecular Subtype ◽

Clinical Stage ◽

Tumor Characteristics ◽

Rna Seq ◽

Advanced Clinical Stage ◽

Naturally Occurring ◽

Immune Signatures

BACKGROUND: Improved therapies are needed for patients with invasive urothelial carcinoma (InvUC). Tailoring treatment to molecular subtypes holds promise, but requires further study, including studies in pre-clinical animal models. Naturally-occurring canine InvUC harbors luminal and basal subtypes, mimicking those observed in humans, and could offer a relevant model for the disease in people. OBJECTIVE: To further validate the canine InvUC model, clinical and tumor characteristics associated with luminal and basal subtypes in dogs were determined, with comparison to findings from humans. METHODS: RNA sequencing (RNA-seq) analyses were performed on 56 canine InvUC tissues and bladder mucosa from four normal dogs. Data were aligned to CanFam 3.1, and differentially expressed genes identified. Data were interrogated with panels of genes defining luminal and basal subtypes, immune signatures, and other tumor features. Subject and tumor characteristics, and outcome data were obtained from medical records. RESULTS: Twenty-nine tumors were classified as luminal and 27 tumors as basal subtype. Basal tumors were strongly associated with immune infiltration (OR 52.22, 95%CI 4.68–582.38, P = 0.001) and cancer progression signatures in RNA-seq analyses, more advanced clinical stage, and earlier onset of distant metastases in exploratory analyses (P = 0.0113). Luminal tumors were strongly associated with breeds at high risk for InvUC (OR 0.06, 95%CI 0.01 –0.37, P = 0.002), non-immune infiltrative signatures, and less advanced clinical stage. CONCLUSIONS: Dogs with InvUC could provide a valuable model for testing new treatment strategies in the context of molecular subtype and immune status, and the search for germline variants impacting InvUC onset and subtype.

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Nested variant of urothelial carcinoma of the urinary bladder

Rare Tumors ◽

10.4081/rt.2011.e42 ◽

2011 ◽

Vol 3 (4) ◽

pp. 132-134 ◽

Cited By ~ 6

Author(s):

Tadashi Terada

Keyword(s):

Urothelial Carcinoma ◽

Lamina Propria ◽

Bladder Tumor ◽

Clinical Course ◽

Carcinoma Cells ◽

Ki 67 ◽

Atypical Cells ◽

Nested Variant ◽

Aggressive Clinical Course ◽

Nephrogenic Metaplasia

The nested variant of urothelial carcinoma (NVUC) is characterized by the presence of benign-appearing urothelial carcinoma cells in the lamina propria, sparing the surface urothelial involvement. NVUC shows aggressive clinical course despite of benign-looking histology. Herein reported are two cases of NVUC. One is 80-year-old woman, and another is 78-year-old man. In both cases, atypical cells forming nests and tubules were seen in the lamina propria without surface urothelial involvement. One case resembled nephrogenic metaplasia and another proliferated Brunn's nest or inverted papilloma. Immunohistochemically, both cases showed positive p53 and high Ki67 labeling, suggesting that both cases are malignant. Immunohistochemically, one case was characterized by positive cytokeratins, EMA, p53, Ki-67 (labeling=15%), α-methylacyl CoA racemase, CA19-9, and MUC1, and another case by positive cytokeratins, EMA, p63, p53, Ki-67 (lebeling=30%), CD10, CEA, and MUC1. Cyto keratin immunoprofiles were described and other antigens’ expressions were shown. The patients are now free of tumor 6 and 15 months after the resection of the bladder tumor.

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Epigenetic regulation of mammalian Hedgehog signaling to the stroma determines the molecular subtype of bladder cancer

eLife ◽

10.7554/elife.43024 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 5

Author(s):

SungEun Kim ◽

Yubin Kim ◽

JungHo Kong ◽

Eunjee Kim ◽

Jae Hyeok Choi ◽

...

Keyword(s):

Bladder Cancer ◽

Urothelial Carcinoma ◽

Sonic Hedgehog ◽

Hedgehog Signaling ◽

Molecular Mechanisms ◽

Molecular Subtype ◽

Early Stage ◽

Human Bladder Cancer ◽

Human Bladder ◽

Stromal Response

In bladder, loss of mammalian Sonic Hedgehog (Shh) accompanies progression to invasive urothelial carcinoma, but the molecular mechanisms underlying this cancer-initiating event are poorly defined. Here, we show that loss of Shh results from hypermethylation of the CpG shore of the Shh gene, and that inhibition of DNA methylation increases Shh expression to halt the initiation of murine urothelial carcinoma at the early stage of progression. In full-fledged tumors, pharmacologic augmentation of Hedgehog (Hh) pathway activity impedes tumor growth, and this cancer-restraining effect of Hh signaling is mediated by the stromal response to Shh signals, which stimulates subtype conversion of basal to luminal-like urothelial carcinoma. Our findings thus provide a basis to develop subtype-specific strategies for the management of human bladder cancer.

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Molecular Subtype-Specific Immunocompetent Models of High-Grade Urothelial Carcinoma Reveal Differential Neoantigen Expression and Response to Immunotherapy

Cancer Research ◽

10.1158/0008-5472.can-18-0173 ◽

2018 ◽

Vol 78 (14) ◽

pp. 3954-3968 ◽

Cited By ~ 25

Author(s):

Ryoichi Saito ◽

Christof C. Smith ◽

Takanobu Utsumi ◽

Lisa M. Bixby ◽

Jordan Kardos ◽

...

Keyword(s):

Urothelial Carcinoma ◽

Molecular Subtype ◽

High Grade

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Melanoma with in-frame deletion of MAP2K1: a distinct molecular subtype of cutaneous melanoma mutually exclusive from BRAF, NRAS, and NF1 mutations

Modern Pathology ◽

10.1038/s41379-020-0581-5 ◽

2020 ◽

Vol 33 (12) ◽

pp. 2397-2406 ◽

Cited By ~ 1

Author(s):

Erik A. Williams ◽

Meagan Montesion ◽

Nikunj Shah ◽

Radwa Sharaf ◽

Dean C. Pavlick ◽

...

Keyword(s):

Cutaneous Melanoma ◽

Molecular Subtype ◽

Genetic Alterations ◽

Experimental Models ◽

Genomic Profiling ◽

Missense Mutations ◽

Wild Type ◽

Single Nucleotide Variants ◽

Sequencing Platform ◽

Comprehensive Genomic Profiling

AbstractWhile the genomics of BRAF, NRAS, and other key genes influencing MAP kinase (MAPK) activity have been thoroughly characterized in melanoma, mutations in MAP2K1 (MEK1) have received significantly less attention and have consisted almost entirely of missense mutations considered secondary oncogenic drivers of melanoma. Here, we investigated melanomas with in-frame deletions of MAP2K1, alterations characterized as MAPK-activating in recent experimental models. Our case archive of clinical melanoma samples with comprehensive genomic profiling by a hybrid capture-based DNA sequencing platform was searched for MAP2K1 genetic alterations. Clinical data, pathology reports, and histopathology were reviewed for each case. From a cohort of 7119 advanced melanomas, 37 unique cases (0.5%) featured small in-frame deletions in MAP2K1. These included E102_I103del (n = 11 cases), P105_A106del (n = 8), Q58_E62del (n = 6), I103_K104del (n = 5), I99_K104del (n = 3), L98_I103del (n = 3), and E41_F53del (n = 1). All 37 were wild type for BRAF, NRAS, and NF1 genomic alterations (“triple wild-type”), representing 2.0% of triple wild-type melanomas overall (37/1882). Median age was 66 years and 49% were male. The majority arose from primary cutaneous sites (35/37; 95%) and demonstrated a UV signature when available (21/25; 84%). Tumor mutational burden was typical for cutaneous melanoma (median = 9.6 mut/Mb, range 0–35.7), and frequently mutated genes included TERTp (63%), CDKN2A (46%), TP53 (11%), PTEN (8%), APC (8%), and CTNNB1 (5%). Histopathology revealed a spectrum of appearances typical of melanoma. For comparison, we evaluated 221 cases with pathogenic missense single nucleotide variants in MAP2K1. The vast majority of melanomas with missense SNVs in MAP2K1 showed co-mutations in BRAF (58%), NF1 (23%), or NRAS (18%). In-frame deletions in MAP2K1, previously shown in experimental models to be strongly MAPK-activating, characterized a significant subset of triple wild-type melanoma (2.0%), suggesting a primary oncogenic role for these mutations. Comprehensive genomic profiling of melanomas enables detection of this alteration, which may have implications for potential therapeutic options.

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