pISSN 1598-2998, eISSN 2005-9256

https://doi.org/10.4143/crt.2023.577 Cancer Res Treat. 2024;56(1):280-293

Original Article

Clear Cell Adenocarcinoma of Urethra: Clinical and Pathologic Implications and

Characterization of Molecular Aberrations
Boram Song 1
, Seok Hyun Lee2, Jeong Hwan Park 2,3
, Kyung Chul Moon 2

1
Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, 2Department of Pathology,
Seoul National University College of Medicine, Seoul, 3Department of Pathology, Seoul Metropolitan Government-Seoul National University
Boramae Medical Center, Seoul, Korea

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.
Key words Clear cell adenocarcinoma of the urinary tract, Exome sequencing, Pathogenesis, Molecular targeted therapy

Introduction diverticula [3]. This neoplasm is morphologically identical

to the Müllerian-derived clear cell carcinoma of the female
The 2022, World Health Organization (WHO) classification genital tract characterized by tubulocystic or papillary archi-
of adenocarcinoma of the urinary tract, including the ure- tecture with hobnail-like cells showing abundant clear or
thra, listed uncommon Müllerian-derived carcinomas along eosinophilic cytoplasm, moderate-to-marked nuclear pleo-
with conventional adenocarcinomas not otherwise specified morphism, and frequent mitosis [1].
and enteric and mucinous types. Müllerian-type tumors are Immunohistologically tumor cells show positivity for cyto-
composed of clear cells and endometrioid adenocarcinomas kerain 7 (CK7), paired box 8 (PAX8), alpha-methylacyl-CoA
originating from benign Müllerian precursors, such as endo- racemase (AMACR), and p53 and negativity for GATA bind-
metriosis or Müllerianosis [1]. ing protein 3 (GATA3), p63, estrogen receptor (ER), and pro-
Clear cell adenocarcinoma (CCA) of the urinary tract is gesterone receptor (PR) [3]. The histogenesis of CCA in the
a rare malignancy, occurring predominantly in women. urinary tract remains controversial, although several theo-
The female-to-male sex predilection of this tumor has been ries have been proposed. Currently, the most widely accept-
reported variably, ranging from 17:1 to 4:1 of in small series, ed theory is that this tumor is derived from the Müllerian
with very few male cases [2]. CCA frequently involves the remnant of the genitourinary system, as recognized by the
lower urinary tract in women, most commonly occurring in 2022 WHO classification [1]. However, other theories insist-
the urethra, where it may arise in the paraurethral ducts or ing on a mesonephric remnant or urothelial origin have been

Correspondence: Jeong Hwan Park Co-correspondence: Kyung Chul Moon

Department of Pathology, Seoul Metropolitan Government-Seoul National Uni- Department of Pathology, Seoul National University College of Medicine,
versity Boramae Medical Center, 20 Boramae-ro 5-gil, Dongjak-gu, 103 Daehak-ro, Jongno-gu, Seoul 03080, Korea
Seoul 07061, Korea Tel: 82-2-740-8380 Fax: 82-2-740-8380 E-mail: [email protected]
Tel: 82-2-870-2644 Fax: 82-2-831-0261 E-mail: [email protected]

Received April 16, 2023 Accepted September 8, 2023

Published Online September 11, 2023

280 Copyright 2024­­by the Korean Cancer Association │ https://www.e-crt.org │

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/)
which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
 Boram Song, Clear Cell Adenocarcinoma of the Urinary Tract

reported, with supporting molecular and histological evi- 3. WES and bioinformatic analysis
dence [4,5]. Normal and cancer tissue were obtained from formalin-
Despite its aggressive behavior and poor prognosis, the fixed, paraffin embedded tissue blocks. DNA was extracted,
molecular signature of urinary CCA and the strategies for and the quality of DNA was checked. Whole exome sequenc-
improved clinical management have not been definitively ing (WES) was conducted on a HiSeq 2500 platform (Illumi-
established, owing to the paucity of cases. Previous studies na, San Diego, CA). Sequencing libraries were prepared, and
have reported mutations in ATM, SMAD4, PIK3CA (pho- adapter ligated DNA was amplified. Sequence was mapped
sphatidylinositol-4,5-bisphosphate 3-kinase catalytic subu- to NCBI b37 human reference genome sequence, and BAM
nit alpha), KRAS, ARID1A (AT-rich interaction domain files were realigned. The MuTect2 algorithm was used to
1A), SMARCA4 (SWI/SNF related, matrix associated, actin identify somatic variants which is allele depth of ≥ 10× and
dependent regulator of chromatin, subfamily A, member variant allele frequency of ≥ 10%, including single nucleotide
4) and the PI3K (phosphoinositide 3-kinase)/AKT/mTOR variants (SNVs), small insertions and deletions (Indels).
(mammalian target of rapamycin) pathway and chromatin Further filtering of pathogenicity was assessed using pub-
modeling pathway have been proposed as pathogenic path- licly available resources, cBioPortal, Catalogue Of Somatic
ways [6-8]. In this study, we analyzed five cases of CCA of Mutations In Cancer (COSMIC) and commercially available
the urinary tract, especially the urethra. We performed whole cancer panels (S2 Table) [9,10].
exome sequencing (WES) and subsequent bioinformatics The variants absent in public database were excluded. The
analyses to determine the mutational spectrum and possible alterations of cancer-related genes were identified.
pathogenic pathways of this rare neoplasm. The final list of selected SNV and Indels in the present study
was compared with additional cancer entities, such as endo-
metrial carcinoma, serous carcinoma of the ovary, urothelial
Materials and Methods carcinoma of the bladder and clear cell renal cell carcinoma,
using publicly available datasets from The Cancer Genome
1. Patient selection and clinicopathologic review Atlas (TCGA). SNVs and clinicopathological data were ret-
We collected the data of a total of five patients who were rieved from the cBioPortal platform [10] for comparison with
diagnosed with CCA of the urinary tract at Seoul National the genetic alterations identified in this study.
University Hospital between January 1999 and December Pathogenic pathways were analyzed using the method
2016. All cases were independently reviewed by two pathol- described above. Gene ontology enrichment analysis was
ogists (K.C.M. and B.S.), including a genitourinary patholo- used to identify biological processes, molecular functions,
gist, who confirmed the diagnosis. If there was a disagree- and cellular components [11]. Protein-protein interaction
ment on the microscopic evaluation, another pathologist was networks was assessed using STRING (http://string-db.org)
invited to review the slides for diagnostic consensus. Clini- to determine the putative pathogenic pathways.
cal data, including patient age, sex, and follow-up findings,
were obtained from electronic medical records. This study
was approved by the regional Institutional Review Board Results
(No. H-2207-201-1346).
1. Clinical and histopathologic features of urethral CCA
2. Immunohistochemistry The demographics, clinicopathologic characteristics, treat-
To confirm the diagnosis, representative slides of all cases ments, and outcomes of the five patients with CCA of the
were stained for CK7, PAX8, AMACR, napsin A, and HNF1 urinary tract are shown in Table 1. We found five CCA cases
homeobox B (HNF1β). Only tumors with > 50% nuclear posi- located in the urethra, out of 58 primary urethral carcinomas
tivity for PAX8 were included. Additional staining for GATA3, and 3,651 primary carcinomas of urinary tract between Janu-
p53, Ki-67, ARID1A, AMT, Smad4, β-catenin, phospho- ary 1999 and December 2016. All patients were female, and
mTOR, phospho-p44/42 mitogen-activated protein kinase the median age at diagnosis was 62 years (range, 53 to 74
(MAPK), CHD4, PBRM1, programmed death-ligand 1 (PD- years). All tumors were located in the urethra, and in three
L1) (SP142 and 22C3) was also performed. Immunohisto- cases, tumors developed in the proximal part. All patients
chemistry (IHC) was performed using an avidin-biotin-per- underwent surgical interventions (radical cystectomy with
oxidase detection system on a BenchMark ULTRA Stainer vaginectomy, pelvic extension, and transurethral resection
(Ventana, Tucson, AZ) according to the manufacturer’s rec- with pelvic lymph node dissection), and three of five pati-
ommendations. Used primary antibodies are described in S1 ents received adjuvant chemotherapy or chemoradiation
Table. therapy. In this study, aggressive behavior of CCAs was

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Table 1. Clinicopathological Features of Urinary CCAs

Case 1 Case 2 Case 3 Case 4 Case 5
Clinical feature
Age (yr) 53 74 66 62 54
Sex Female Female Female Female Female
Site Proximal urethra Proximal urethra Proximal urethra Urethra Urethra
Size (cm) 5×2×1.3 4×2.5×2.5 1.8×1.5×1 3×2×1.1 N/A
Treatment Pelvic exenteration Radical cystectomy Neoadjuvant Radical cystectomy, TUR with pelvic
and adjuvant with vaginectomy chemotherapy and urethrectomy and lymph node
chemotherapy radical cystectomy, vaginectomy dissection and
adjuvant palliative
chemotherapy chemoradiation
therapy
Outcome PD, metastasis PD, metastasis PD, local recurrence PD, metastasis to PD, metastasis
(F/U time) to lung (6 mo) to lung (37 mo) with neck and lung, peritoneal to lung (4 mo)
Death (36 mo) mediastinal LN seeding (23 mo) Death (11 mo)
metastasis (9 mo)
Pathologic feature
Tumor Tubulocystic Papillary and Tubulocystic Papillary, solid Solid and
architecture tubulocystic and tubulocystic tubulocystic
Cell Clear and Hobnail and Hobnail and Clear and Clear and
morphology eosinophilic cells eosinophilic cells eosinophilic cells hobnail cells hobnail cells
Nuclear Moderate Marked Mild Marked Moderate
pleomorphism
Mitosis 3 12 1 9 4
(per 10 HPFs)
Urethral diverticulum Present Present Present Present Absent
Tumor extension Bladder neck Bladder neck Bladder neck Bladder neck N/A
and vagina and vagina and vagina
LVI Lymphatic None None None N/A
Lymph node metastasis Present (4/6) N/A Present (23/53) Absent (0/36) Present (5/5)
Other malignancy No No No Yes, breast cancer Yes, breast cancer
CCA, clear cell adenocarcinoma; F/U, follow-up; HPF, high power field; LN, lymph node; LVI, lymphovascular invasion; N/A, not avail-
able; PD, progressive disease; TUR, transurethral resection.

observed, with rapid progression and poor prognosis. The radical surgical treatment. Lymph node metastasis was pre-
average duration of follow-up was 23 months (range, 9 to sent in three of the five patients with extensive involvement.
37 months), and all five patients experienced disease pro- This indicates that the cancer spreads to the lymph nodes
gression, namely exhibiting lung metastases (4/5), neck and and may have a higher risk of distant metastasis. All patients
mediastinal lymph node metastasis (1/5), peritoneal seeding progressed to distant metastases, mostly to the lungs (4/5) or
(1/5), and local recurrence (1/5). Two patients died, and one mediastinal lymph nodes (1/5).
died within year of diagnosis (11 months). Two patients had
a history of breast cancer. 2. IHC findings
Histopathologic findings of CCA of the urinary tract are The IHC staining results for several markers in the five
illustrated in Fig. 1. The tumors had clear and hobnail cells patients are detailed in Table 2 and Fig. 2. All tumors exhi-
in a tubulocystic pattern, characteristic of CCA. Tumor archi- bited strong nuclear positivity for PAX8, markers specific
tecture and nuclear pleomorphism varied among the cases. for tumors of the mesonephric (Wolffian) or Müllerian duct
Nuclear pleomorphism was prominent in tumors with pap- origin, and negativity for GATA3, suggesting non-urothelial
illary and solid architectures. In four patients, an accompa- origin. All tumors were positive for AMACR with variable
nying urethral diverticulum was observed. In three patients, cytoplasmic expression from focal weak positivity to strong
the tumors had invaded the adjacent vagina, necessitating positivity. In terms of markers of clear cell adenocarcinoma,

282 CANCER RESEARCH AND TREATMENT

 Boram Song, Clear Cell Adenocarcinoma of the Urinary Tract

A B C

D E F

Fig. 1. Histopathology of the clear cell adenocarcinoma of the urinary tract. (A) The tumor within urethral diverticulum (×12.5). (B)
Tubulopapillary architecture with fibrovascular cores (×40). (C) Urethral diverticulum showing atypical cell lining (×200). (D) Eosinophilic
hobnail cells (×200). (E) Tubulocystic architecture (×100). (F) Clear cells with solid growth pattern (×400).

Table 2. Immunohistochemical staining result

Case PAX-8 CK7 GATA3 AMACR HNF1β Napsin A Ki-67 (%)
1 P P N P N P 10
2 P P N FP P N 1
3 P P N P P P 5
4 P FP N FP P N 25
5 P P N FP P N 70
FP, focal positive; N, negative; P, positive.

all cases were positive for HNF1β (4/5) or Napsin A (2/5), D1A p.Trp1545*( c.4634G>A) variant.
with higher sensitivity for HNF1β. Ki-67, a marker of cell
proliferation, showed variable expression ranging from 1%- 4. Comparison with TCGA data of cancers of other origin
70%. We compared the SNV alterations identified in our series
of urethral CCAs with cancers of other origins, including
3. Genetic alterations of cancer genes in urethral CCA endometrial adenocarcinoma of the uterus (n=517), serous
This study identified several genetic alterations that may adenocarcinoma of the ovary (n=525), urothelial carcinoma
play roles in the development of CCA (Table 3). Twenty-one of the bladder (n=410), and clear cell renal cell carcinoma
SNVs and small Indels (< 50 bp) were identified, including (n=402) from the TCGA platform. Fig. 3 illustrates the SNVs
16 missense variants, one frameshift variant, two nonsense that showed the highest similarity between CCA and endo-
variants, one in-frame deletion, and one splice site variant. metrial cancer of the uterus, with the highest overall frequen-
No identical recurrent mutations were detected among the cy of the analyzed genes. ARID1A, PIK3R1, CSMD3, KRAS,
variants. The set of identified cancer genes included seven CHD4, and KMT2D showed specific similarities between
driver mutations, including notable genetic alterations such CCA and uterine endometrial adenocarcinoma.
as the oncogene KRAS p.Gly12Val (c.35G>T) variant, tumor
suppressor gene PIK3R1 p.Arg557Gln (c.1670G>A), and ARI-

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A B C

D E F

Fig. 2. Immunohistochemical features of the clear cell adenocarcinoma of the urinary tract. (A) CK7 positivity (membranous/cytoplasmic)
(×200). (B) PAX8 positivity (nuclear) (×200). (C) AMACR (P504S) positivity (cytoplasmic granular) (×200). (D) GATA3 negativity (×200).
(E) HNF1β positivity (nuclear) (×200). (F) Napsin A positivity (cytoplasmic) (×200).

5. Putative pathogenic pathways 2) Gene ontology analysis

1) Pathways, SNVs, and Indels Gene ontology analysis revealed that some molecular
The pathogenic pathways of urethral CCA according to the functions and biological processes were enriched by altered
identified 21 cancer gene alterations are shown in Table 4. The genes in urethral CCA (S3-S5 Tables). Altered genes were
most notable molecular pathway associated with CCA was associated with ATP-dependent chromatin remodeling acti-
the chromatin remodeling pathway, activated by ARID1A, vity (ARID1A, CHD4, and SMARCA4) and protein domain-
SMARCA4, ZNF219 (zinc finger protein 219), KMT2D (lysine specific binding (CACNA1D, KEAP1, KRAS, NKD1, PIK3R1,
methyltransferase 2D), and PBRM1 (polybromo 1) observed TCF12, and TNK2 [tyrosine kinase non receptor 2]) in mole-
in three patients (patients 3-5). Another important molecular cular function and regulation of nucleotide-excision repair
pathway was the PI3K/AKT/mTOR pathway activated by (ARID1A, PBRM1, and SMARCA4), positive regulation
LAMC2 (laminin subunit gamma 2), KRAS, PIK3R1 (phos- of cell differentiation (ACVRL1, ARID1A, KRAS, PBRM1,
phoinositide-3-kinase regulatory subunit 1), and ACVRL1 PIK3R1, SMARCA4, TCF12, and ZNF219), regulation of G0
(activin A receptor like type 1) gene alterations, observed to G1 transition (ARID1A, PBRM1, and SMARCA4), positive
in four patients (patients 2-5). In addition, the Keap1-Nrf2 regulation of nucleic acid-templated transcription (ACVRL1,
pathway, which is activated by KEAP1 (kelch like ECH ARID1A, CHD4 [chromodomain helicase DNA binding
associated protein 1) tumor suppressor gene, and the MAPK protein 4], KMT2D, PBRM1, PIK3R1, SMARCA4, TCF-12,
signaling pathway, which is activated by mutations in the and ZNF219), and chromatin remodeling (ARID1A, CHD4,
KRAS, CACNA1D (calcium voltage-gated channel subunit KMT2D, PBRM1, and SMARCA4) in biological processes.
alpha1 D), ACVRL1, and TCF12 (transcription factor 12)
gene, have been found to be associated with CCA. Other 3) Protein-protein interaction and network analysis
molecular pathways that have been implicated in the devel- We conducted protein-protein interaction and network
opment of CCA include the Wnt/β-catenin pathway (APC2 analyses based on the altered genes and their related genes
[APC regulator of WNT signaling pathway 2], AMER1 [APC (Fig. 4). To expand and assign weights to altered tumor
membrane recruitment protein 1], and NKD1 [NKD inhibi- suppressor genes (TSGs) or OGs, we included five related
tor of WNT signaling pathway 1]) and integrin-mediated cell genes for each altered TSG or OG. As mentioned previously,
adhesion pathway (CAPN2 [calpain 2]). AMER1, ARID1A, CSMD3 (CUB and Sushi multiple domains
3), KEAP1, PBRM1, PIK3R1, and SMARCA4 were regarded

284 CANCER RESEARCH AND TREATMENT

 Table 3. Pathogenic mutations in urethral clear cell adenocarcinoma
Case Gene Driver Role Effect Type Reference Alternate Chr. cDNA change Protein change VAF (%)
1 WBSCR27 - - Splice site Indel CTGTG C 7 c.389-5_389-2delCACA 30.76
2 APC2 - - Nonsense variant SNV C A 19 c.2855C>A p.Ser952* 42.85
CSMD3 - TSG Missense variant SNV C T 16 c.2972G>A p.Arg991His 14.28
LAMC2 - - Missense variant SNV C T 1 c.301C>T p.Arg101Trp 12.5
3 ZNF219 - - In-frame deletion Indel GGAGGCT G 14 c.698_703delAGCCTC p.Gln233_Pro234del 46.34
KRAS + OG Missense variant SNV C A 12 c.35G>T p.Gly12Val 11.79
4 KEAP1 - TSG Missense variant SNV C T 19 c.1085G>A p.Arg362Gln 37.5
SMARCA4 - TSG Missense variant SNV T C 19 c.3461T>C p.Leu1154Pro 25.45
CACNA1D - OG Missense variant SNV C G 3 c.4780C>G p.Arg1594Gly 24.17
AMER1 + TSG Missense variant SNV C T X c.2254G>A p.Glu752Lys 24.07
PIK3R1 + TSG Missense variant SNV G A 5 c.1670G>A p.Arg557Gln 19.17
TNK2 - - Missense variant SNV G T 3 c.1700C>A p.Ser567Tyr 17.97
5 PBRM1 + TSG Frameshift variant Indel AC A 3 c.3245delG p.Gly1082fs 31.75
ARID1A + TSG Nonsense variant SNV G A 1 c.4634G>A p.Trp1545* 45.26
NKD1 - - Missense variant SNV G A 16 c.92G>A p.Arg31Gln 40.35
ACVRL1 + - Missense variant SNV C A 12 c.532C>A p.Leu178Met 30.76
CAPN2 - - Missense variant SNV C T 1 c.1433C>T p.Pro478Leu 29.52
CC2D1B - - Missense variant SNV C G 1 c.1208G>C p.Arg403Pro 28.82
CHD4 - OG,TSG Missense variant SNV C T 12 c.4822G>A p.Val1608Ile 28.4
KMT2D + OG, TSG Missense variant SNV G T 12 c.2312C>A p.Ser771Tyr 28
TCF12 - TSG Missense variant SNV C T 15 c.280C>T p.His94Tyr 26.51
Chr., chromosome; Indel, insertion and deletion; OG, oncogene, SNV, single nucleotide variation; TSG, tumor suppressor gene, VAF, variant allele frequency.

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Type
EC
60 SC
UC

Percentage
ccRCC
40

20

0
27
CS C2
LA D3
ZN C2
19

K S
A 1
CN 4
AM 1D
PIK 1
1
PB 2
AR 1
1A
AC D1
CA L1
CC N2
1B

KM 4

TC D
2
SM EAP
CA RCA

ER
3R
K
RM

F1
A

T2
VR
CR

F2
AP

TN

2D
M

ID
NK

CH
KR

P
BS
W

Gene
Fig. 3. Comparison of the genetic alterations of clear cell adenocarcinoma of urinary tract with The Cancer Genome Atlas data sets of
endometrial, ovarian, bladder, and clear cell kidney cancers. ccRCC, clear cell renal cell carcinoma; EC, endometrial carcinoma (uterus);
SC, serous carcinoma (ovary); UC, urothelial carcinoma (bladder).

as TSGs, CACNA1D, CHD4, KMT2D, and KRAS were regard- Discussion

ed as OGs. We included 76 genes to evaluate protein-protein
interactions and performed network analysis. We found that Urinary tract CCAs are rare. Owing to the rarity of the
the chromatin remodeling, PI3K/Akt/mTOR, and Wnt/β- entity, the nature and prognosis of this tumor remains un-
catenin pathways were main pathogenic pathways in CCA clear. The theory of Müllerian origin is generally accepted,
of urethra. and the tumor shows female predominance with an M:F
ratio of 1:4-6 [1,2,12]. Pathologically, CCA presents as a poly-
6. IHC validation of genetic alteration and biomarkers poid, papillary, or ulcerative mass. The tumor cells showed
IHC staining results for validation of the protein expression moderate-to-severe atypia with variable mitosis and necro-
of genetic alterations and putative pathways detected in our sis, and papillary, tubulocystic, and/or solid growth pat-
series, and previously reported mutations in urinary CCA terns. The immunophenotype of urinary CCA varies among
are detailed in Table 5, Fig. 5, and S6 Fig. Loss of ARID1A patients. Tumor cells are usually positive for PAX-2, PAX-8,
expression was reported in three out of five cases, including epithelial membrane antigen, CK (AE1/AE3), CAM 5.2,
patient 5 with ARID1A SNV alteration (p.Trp1545* [c.463- CK7, AMACR, and p53, and negative for GATA3, p63, ER,
4G>A] variant). Expression of CHD4 was identified in in two and PR, CK20, carbohydrate antigen 125 and variable lev-
out of five cases, including patient 5 with CHD4 V1608I mis- els of Ki-67 index [3]. In the majority of urinary CCA cases,
sense mutation (c.4822G>A, p.Val1608Ile). Loss of PBRM1 aggressive behaviors have been reported such as high local
expression was not observed in PBRM1 mutant-patient 5 recurrence, lymph node metastasis, distant metastasis, and
with strong nuclear positivity like overexpression, but pati- disease-related mortality, with a 5-year survival rate of 40%
ent 1 with wild type PBRM1 lacked protein expression in [13]. Treatment includes surgical resection with or without
IHC. The expressions of phospho-mTOR were found in two adjuvant chemotherapy or radiation therapy. Brachyther-
patients (patients 3 and 5) with associated cancer-related apy has been utilized as well [13]. No targeted therapies
gene alteration (KRAS and ACVRL1). Three patients (pati- have been introduced because the pathogenic alterations or
ents 3, 4 and 5) with KRAS, CACNA1D, ACVRL1, and TCF1 actionable targets have not yet been well established. Immu-
mutations reveals phospho-p44/42 MAPK positivity. Aber- notherapy with immune checkpoint inhibitors is not consid-
rant cytop-lasmic expressions (not nuclear expression; loss of ered because of the lack of known data on PD-L1 expression.
membranous expression) of β-catenin were identified in two The molecular signature of urinary CCA has not been defini-
patients, including patient 4 with AMER1 mutation. Most tively established, owing to the paucity of cases. A previous
patients (4/5) exhibited heterogenous p53 nuclear expres- genetic study of one case reported truncating mutations in
sion. Loss of ATM expression was identified in two, who also the ATM, copy number loss at the SMAD4 and ARID2 loci,
showed wild type p53 expression. The expression of SMAD4 and gene fusion candidates, including ANKRD28-FNDC3B
associated with the transforming growth factor β was reta- [8]. In another series of four cases, recurrent pathogenic PIK-
ined in most cases (4/5). PD-L1 SP142 and 22C3 were not 3CA (p.E545K) and KRAS (p.G12D) variants (3/4), an APC
expressed in any of the patients. (p.S2310X) variant (1/4), a TP53 (p.R273C) variant (1/4), and

286 CANCER RESEARCH AND TREATMENT

 Table 4. Putative pathogenic pathways in clear cell adenocarcinoma of urinary tract
Case Gene Driver Role Pathway Biologic function Tumor
1 WBSCR27 - - - Methyltransferase Colorectal ADC; malignant melanoma
2 APC2 - - Wnt/β-catenin pathway Cell proliferation, apoptosis Thyroid PTC, malignant melanoma, colorectal ADC,
epithelial-mesenchymal transition, bladder urothelial carcinoma; HCC
invasion, metastasis
CSMD3 - TSG - Tumor mutation burden, Ovarian serous carcinoma; breast IDC;
tumor-promoting inflammation colorectal ADC; uterine endometrial carcinoma
LAMC2 - - PI3K/AKT/mTOR pathway Cell junction organization; increase HCC; malignant melanoma; uterine endometrial
aggressiveness; focal adhesion; carcinoma, lung ADC
inflammatory response pathway
3 ZNF219 - - Chromatin remodeling Transcription factor Colorectal ADC; thyroid PTC; malignant melanoma;
stomach cancer; uterine endometrial carcinoma
KRAS + OG MAPK signaling pathway; Cell proliferation, differentiation Lung ADC; pancreas ADC; colorectal ADC;
PI3K/AKT/mTOR pathway; and migration uterine endometrial carcinoma
RAS signaling pathway
4 KEAP1 - TSG Keap1-Nrf2 pathway Detoxification or antioxidation Lung ADC, SqCC; endometrial carcinoma; uterine
carcinomsarcoma; tonsil SqCC; biliary tract ADC
SMARCA4 - TSG Chromatin remodeling Gene expression regulation Lung ADC; colorectal ADC; uterine endometrial
carcinoma; bladder urothelial carcinoma; breast IDC
CACNA1D - OG MAPK signaling pathway Cell proliferation, differentiation Uterine endometrial carcinoma;
and migration malignant melanoma; stomach ADC; lung SqCC
AMER1 + TSG Wnt/β-catenin pathway - Lung cancer; malignant melanoma;
uterine endometrial carcinoma; Wilms tumor
PIK3R1 + TSG PI3K/AKT/mTOR pathway; Cell proliferation; apoptosis; Uterine endometrial carcinoma; colorectal ADC;
JAK/STAT pathway; protein synthesis; metabolism; breast IDC; glioblastoma; lung ADC
RAS signaling pathway; cell cycle; apoptosis
Cell cycle pathway
TNK2 - . ACK1 signaling Cell proliferation; apoptosis Prostate cancer, breast IDC, pancreas ADC
5 PBRM1 + TSG Chromatin remodeling - Renal cell carcinoma, clear cell type; lung ADC;
colorectal ADC; breast IDC
ARID1A + TSG Chromatin remodeling Cell cycle progression; invasiveness; Uterine endometrial carcinoma; lung ADC; colorectal
stemness; differentiation ADC; bladder urothelial carcinoma; breast IDC
NKD1 - - Wnt/β-catenin pathway Cell proliferation; cell adhesion HCC; head and neck SqCC
and motility; cell cycle
progression; invasiveness
(Continued to the next page)

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Table 4. Continued
Cancer Res Treat. 2024;56(1):280-293

Case Gene Driver Role Pathway Biologic function Tumor

ACVRL1 + - TGF-beta receptor signaling Angiogenesis; invasion; migration; Breast IDC
pathway; PI3K/AKT/mTOR cell proliferation and growth;
pathway; MAPK pathway cell-cell interaction and
differentiation; epithelial-
mesenchymal transition; invasion;
dissemination to distant organ sites
CAPN2 - - Integrin-mediated cell Cellular shape; mobility; Breast IDC, uterine endometrial carcinoma; HCC
adhesion pathway cell cycle regulation
CC2D1B - - EGFR signaling; TLR4 signaling Transcription factor; cell proliferation Uterine endometrial carcinoma
CHD4 - OG, TSG Chromatin remodeling Genome instability and mutations Uterine endometrial cancer; brain diffuse glioma;
lung ADC; colorectal ADC
KMT2D + OG, TSG Chromatin remodeling - Lung adenocarcinoma; colorectal ADC;
bladder urothelial carcinoma; breast IDC;
uterine endometrial carcinoma
TCF12 - TSG Transcriptional regulation; - Extraskeletal myxoid chondrosarcoma;
MAPK pathway hepatocellular carcinoma
ACK1, activated Cdc42-associated tyrosine kinase 1; ADC, adenocarcinoma; EGFR, epidermal growth factor receptors; HCC, hepatocellular carcinoma; IDC, invasive ductal
carcinoma; JAK, Janus kinase; MAPK, mitogen-activated protein kinase; mTOR, mammalian target of rapamycin; OG, oncogene; PI3K, phosphatidylinositol-3-kinase; PTC, papil-
lary thyroid carcinoma; SqCC, squamous cell carcinoma; STAT, signal transducer and activator of transcription; TGF, transforming growth factor; TRL4, Toll-like receptor 4; TSG,
tumor suppressor gene.
 Boram Song, Clear Cell Adenocarcinoma of the Urinary Tract

TCF12 Driver gene (tumor suppressor gene)

MTA2 Driver gene (oncogene)
GATAD2A
CHD4 SMARCE1 Tumor suppressor gene
TRPS1 ANXA13
SMARCC2 DPH6 Oncogene
Altered gene
ZNF219 SMARCC1 Related gene
RBBP4 SMARCD3 OTOA
SMARCD1 SMARCA2
RBBP7
SMARCB1
WDR5 CSMD3
PBRM1
KDM6A HDAC1
PAXIP1 BTBD11
ARID2
RBBP5 SMARCA4
ASH2L ARID1A TERT CAPN2
KMT2D
PIK3R1
APC
BTRC CTNNB1 LAMC2
PIK3CA
RBX1 ERBB3
NFE2L2 KRAS
AXIN1 WBSCR27

EGFR IRS1 PIK3CB

APC2 CUL3
AMER1 CC2D1B
KEAP1
SOS1
RAF1 CACNB3
NKD1
CBL BRAF CACNA1D
CACNA1C
LRP5 PALB2 ACVRL1
SQSTM1 CACNA2D1
CACNB1
TNK2 CACNB2

Fig. 4. Protein-protein interaction and network analysis.

MYC amplification (1/4) were identified; the authors sug- INDEL variants of these mutations on WES, but some pati-
gested that the activation of the PI3K/AKT/mTOR pathway ents showed mutant-type expressions on IHC. These findings
was a possible underlying oncogenic events [7]. In recent suggest the possibility of genetic alterations affecting protein
studies, mutations in KRAS and chromatin modeling genes, expression, such as CNVs, in addition to the point mutations,
such as ARID1A, ARD1B, and SMARCA4, were reported to SNVs or Indels, that we examined. ATM and TP53 function
be common finding of female patients with genital tract CCA together in the DNA damage response pathway, and there is
[6]. a negative correlation between ATM and TP53 mutations in
In this study, we examined the data of five patients with lung adenocarcinoma [14]. Loss of ATM expression with the
urinary CCA, all of which occurred in the urethra, not only wild-type p53 pattern was observed in two patients in our
in terms of the clinical and pathological features but also series. PD-L1 SP142 and 22C3 expressions, which should be
in terms of the molecular biological features to explore the considered before starting immunotherapy, were negative in
nature of this rare entity. In our case series of single center all cases.
for 18 years, CCA was a rare histologic type, accounting for WES and bioinformatics analyses were performed to
8% of primary urethral carcinomas and 0.1% of all urinary determine the genetic and possible pathogenic alterations.
tract malignancies. CCA showed an advanced stage from the On comparing the identified mutation spectrum of urethral
time of diagnosis and aggressive behavior with rapid clini- CCA to the TCGA data of endometrial, ovarian, bladder, and
cal progression despite the combination of surgical resection kidney tumors, which are differential diagnoses owing to
and brachytherapy in most cases, indicating the need for similarities in location and histologic findings, CCA showed
careful monitoring of patients with urethral CCA as well as the highest similarity to endometrial adenocarcinoma. Gene-
the increased use of aggressive treatment measures such as tic variants reported in previous studies, such as PIKC3CA
chemotherapy and chemoradiation. and ARID1A [6,7,15], show a particularly high frequency in
IHC for p53, ATM, and SMAD4 was performed to assess endometrial cancer, and driver genes such as CSMD3, CHD4,
the protein expression of previously reported mutations in and KMT2D also show significant similarity to endometrial
urinary CCA [6-8]. Our series of CCA showed no SNV or cancer. Although CSMD3 and ARID1A are also frequently

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Cancer Res Treat. 2024;56(1):280-293

altered in urothelial carcinoma or bladder cancer, the absence

C, cytoplasmic staining (in the markers with a)P: retained expression, N: loss of expression); FP, focal positive; M, membranous staining; MT, mutant type; N, negative; P, positive;
of a TERT promoter mutation, the most prevalent mutation

PD-L1
in urothelial carcinoma [16], indicates the non-urothelial ori-

22C3

N
N
N
N

N
gin of urethral CCA. Urinary CCAs are known to arise from
pre-existing Müllerian precursors within the urinary tract
[1], and our molecular data support the theory of Müllerian
PD-L1
SP142

origin.

N
N
N
N

N
We found several TSGs and OGs, some of which have been
identified in previous studies (KRAS, ARID1A, SMARCA4)
Phospho-

[6,7,15]. In patient 3, we identified KRAS G12V missense

PBRM1a)

Strong P
mutation (c.35G>T, p.Gly12Val), which is a well-known
N
P

P
P

oncogene in the colorectal, pancreatic, lung, ovarian, and bil-

iary tract cancers [9,17]. KRAS is a small GTPase that regu-
lates many cellular responses through the MAPK, PI3K/
AKT/mTOR, and RAS signaling pathways. Oncogenic acti-
CHD4

N
N

N
P

vation of KRAS results in cell proliferation or immortality,

angiogenesis, invasion, metastasis, changes in cellular ener-
getics, and escape from apoptosis [18]. In patient 4, two
ARID1Aa)

TSGs, AMER1 and PIK3R1 were observed. The AMER1

N
N

N
P
P

encodes APC membrane recruitment protein 1 and is invol-

ved in β-catenin, thus inhibiting the Wnt/β-catenin path-
way [19]. An AMER1 E752K missense variant (c.2254G>A,
p.Glu752Lys) was also identified. AMER1 competes with
MAPK
p44/42

WP
N
N
P

NRF2 for binding to KEAP1. Interestingly, patient 4 har-

bored a KEAP1 mutation (c.1085G>A, p.Arg362Gln). KEAP1

is regarded as a TSG and is thought to suppress the expres-
β -catenin

sion of survival genes by inhibiting NRF2 [20]. ML385, an

M
M

NRF2 inhibiting molecule, shows specificity and selectiv-

C
C

ity for NRF2-addicted non–small cell lung cancer cells

Table 5. Immunohistochemical validation of genetic alteration and biomarkers

with KEAP1 mutations and significant antitumor activity

Phospho-

in combination with carboplatin [21]. There was a possibil-

mTOR

WP

ity of NRF2 activation in patient 4, and targeted therapy for

N
N

N
P

NRF2 could have had a therapeutic effect. PIK3R1 is a com-

ponent of the PI3K/AKT/mTOR pathway, which regulates
cell proliferation, apoptosis, and metabolism [22]. In the
Smad4a)

present case, there was PIK3R1 R557Q missense mutation

FP
P
P
P

(c.1670G>A, p.Arg557Gln). As the inactivation of PIK3R1

could lead to mTOR pathway activity, drugs targeting the
PI3K/AKT/mTOR pathway, such as everolimus and tem-
ATMa)

sirolimus, would be beneficial. In patient 5, we identified

N

N
P
P

PBRM1 and ARID1A mutations associated with chroma-

tin remodeling, and CHD4 and KMT2D mutations associ-
WP, weak positive; WT, wild type.

ated with histone remodeling. A PBRM1 frameshift dele-

tion (c.3245delG, p.Gly1082fs) was also identified. PBRM1
p53

WT
WT
WT
WT
MT

is a subunit of the SWItch/Sucrose Non-Fermentable (SWI/

SNF) complex and is involved in chromatin remodeling, thus
affecting the expression of various genes [23]. PBRM1 muta-
tions lead to genomic instability and mutations, impaired
tumor growth suppression, tumor-promoting inflammation,
and escape from the immune response to cancer [23]. In our
Case

study, the loss of PBRM1 expression was not validated in

1
2
3
4
5

290 CANCER RESEARCH AND TREATMENT

 Boram Song, Clear Cell Adenocarcinoma of the Urinary Tract

A B

Fig. 5. ARID1A protein expression and loss in clear cell adenocarcinoma (CCA) of the urinary tract. (A) ARID1A wild type with strong
nuclear staining of ARID1A immunohistochemical staining (B) ARID1A protein loss in CCA with p.Trp1545*ARID1A mutation (case 5) (A
and B, ×400).

patient 5 with strong nuclear positivity. Gad et al. [24] recen- oncogenic and tumor-suppressive effects and could be a
tly reported increased PBRM1 expression with uniform and therapeutic target [27]. In this study, the CHD4 expression
strong nuclear staining in Von Hippel‑Lindau disease‑associ- was validated in patient 5 as well as another patient (patient
ated clear cell renal cell carcinoma and a PBRM1 mutant case 3) by IHC. In addition, a KMT2D S771F missense mutation
showing retained protein expression. Additionally, an ARI- (c.2312C>A, p.Ser771Tyr) was identified. KMT2D is a his-
D1A W1545* nonsense mutation (c.4634G>A, p.Trp1545*) tone-lysine N-methyltransferase that targets H3 lysine 4 and
was observed. ARID1A is the most commonly altered gene affects the epigenetic regulation of various genes. KMT2D
reported in prior genetic studies on urinary CCA [6,7,15]. has both oncogenic and tumor-suppressive roles and is
They are also found in endometrial adenocarcinomas, lung involved in invasion, metastasis, cell proliferation, immortal-
adenocarcinomas, colon cancer, bladder urothelial carci- ity, and changes in cellular energetics [28].
noma, and breast cancer [9]. In this study, the loss of ARI- Our data indicate that MAPK signaling pathway (KRAS,
D1A expression was validated in patient 5 as well as other CACNA1D, ACVRL1, and TCF12), PI3K/AKT/mTOR path-
two patients by IHC. ARID1A-deficient CCA in our series way (KRAS, LAMC2, PIK3R1, and ACVRL1), Wnt/β-catenin
(patients 1, 2 and 5) showed no distinguishable clinical or pathway (APC2, AMER1, and NKD1), and chromatin remod-
pathological characteristics in common. ARID1A is a mem- eling (ARID1A, SMARCA4, ZNF219, KMT2D, and PBRM1)
ber of the SWI/SNF and chromatin remodeling complex and could be the pathogenic pathways related to CCA of the uri-
acts as a tumor suppressor gene [23]. ARID1A mutation is nary tract, results of bioinformatics analyses supported these
associated with genome instability and mutations, growth findings. The most notable molecular pathway of urinary
suppression, metastasis, and escaping. The inactivation of the CCA was the chromatin remodeling pathway with many
SWI/SNF complex is considered a potential biomarker for significantly associated molecular functions and biological
various targeted drugs. Loss of ARID1A function sensitizes processes in gene ontology analysis, such as ATP-dependent
cells to poly(ADP-ribose) polymerase (PARP) inhibitors and chromatin remodeling activity (p=0.00000701), histone bind-
combined immunotherapy is recommended for ARID1A- ing (p=0.00301) and others. Ortiz-Bruchle et al. [6] recently
deficient carcinomas. Ongoing studies involving ATR inhi- proposed the chromatin remodeling pathway as a pathogno-
bitors have shown promising results, making ARID1A an monic pathway for urinary CCA in association with frequent
attractive candidate for targeted therapy [25]. Given that ARID1A mutations in their study. We validated the activa-
a recent clinical trial testing ATR and PARP inhibitors in tion of the suggested putative pathways by IHC, and sub-
gynecologic cancers assessed ARID1A status by IHC fol- stantial protein expression was identified in association with
lowed by retrospective mutational analysis [26], and that genetic mutations affecting the pathway (phospho-mTOR
ARID1A protein loss was observed in three out of five CCA [2/5], phospho-p44/42 MAPK [3/5], β-catenin [2/5], ARI-
cases in our study, the screening test by IHC for ARID1A in D1A [3/5], CHD4 [2/5]). As shown in Fig. 5, various mutated
urinary CCA would be a cost-effective evaluation for target- genes identified in this study were grouped into chromatin
ed therapy. In addition, a CHD4 V1608I missense mutation remodeling, PI3K/AKT/mTOR pathway, Wnt/β-catenin
(c.4822G>A, p.Val1608Ile) was identified. CHD4 is involved pathway, supported by protein expression assessed by IHC.
in histone deacetylation and dysfunction of this gene results Our results suggest that therapies targeting these pathogenic
in genomic instability and mutations. CHD4 exerts both pathways may be beneficial for patient management.

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Cancer Res Treat. 2024;56(1):280-293

Discordance between IHC and mutational status was lines, organoids, and animal models are needed to determine
noted in some cases, such as wild type with altered protein the clinical application of these targets.
expression (ARID1A in patients 1 and 2, CHD4 in patient In summary, we identified important driver gene muta-
3, PBRM1 in patient 1) and mutant with not altered protein tions (AMER1, ARID1A, CHD4, KMT2D, KRAS, PBRM1, and
expression (PBRM1 in patient 5). Altered IHC without muta- PIK3R1) and pathogenic pathways (chromatin remodeling
tion could be explained by loss of heterozygosity, mutations pathway, MAPK signaling pathway, PI3K/AKT/mTOR
in non-coding regions, and post-transcriptional and/or post- pathway and Wnt/β-catenin pathway) involved in CCA of
translational mechanisms [29]. Not altered protein expres- the urethra. Owing to the rarity of the disease, further mul-
sion in mutated cases could be explained by late truncating ticenter studies or meta-analyses are needed to validate our
mutation where mRNA is not undergoing nonsense medi- results. We hope that our results will contribute to enhance
ated decay [30]. Further evaluations were not performed due patient management.
to methodological reason.
Interestingly, we also identified cancer-related genes asso- Electronic Supplementary Material
ciated with these pathogenic pathways. Genetic alterations Supplementary materials are available at the Cancer Research and
in the MAPK signaling pathway included CACNA1D in Treatment website (https://www.e-crt.org).
patient 4 and ACVRL1, TCF12 in patient 5. CACNA1D muta-
tions have also been found in patients with malignant mela- Ethical Statement
noma, lung squamous cell carcinoma, and gastric cancer This study was approved by the Institutional Review Board of
[9,17]. Genetic alterations in the PI3K/AKT/mTOR pathway Seoul National University Hospital, in accordance with the Dec-
were identified in patient 2 (LAMC2). LAMC2 mutations laration of Helsinki (approved ID: H-2207-201-1346). The require-
been reported in ovarian, lung, and pancreatic cancers. Ge- ment for informed consent was waived by the Institutional Review
netic mutations involved in Wnt/β-catenin pathway was Board.
found in patients 2 (APC2) and 5 (NKD1). APC2 mutations
have been identified in thyroid, malignant melanoma, and Author Contributions
colorectal, bladder, and liver cancers. In addition, NKD1 Conceived and designed the analysis: Song B, Park JH, Moon KC.
mutations have been found in liver cancer and head and Collected the data: Song B, Moon KC.
neck squamous cell carcinoma. Genetic alterations in chro- Contributed data or analysis tools: Song B, Lee SH, Park JH, Moon
matin remodeling were identified in patients 3 (ZNF219) and KC.
4 (SMARCA4). ZNF219 mutations have been identified in Performed the analysis: Song B, Lee SH, Park JH, Moon KC.
patients with colorectal, thyroid, stomach, endometrial, and Wrote the paper: Song B, Lee SH, Park JH, Moon KC.
endometrial cancer [9,17]. SMARCA4 mutations have been
reported in patients with lung, colorectal, endometrial, blad- ORCID iDs
der, urothelial, and breast cancers. As shown in Fig. 5, vari- Boram Song : https://orcid.org/0000-0003-1598-8552
ous mutated genes identified in this study were grouped into Jeong Hwan Park : https://orcid.org/0000-0003-4522-9928
chromatin remodeling, PI3K/AKT/mTOR pathway, Wnt/ Kyung Chul Moon : https://orcid.org/0000-0002-1969-8360
β-catenin pathway. Our results suggest that therapies target-
ing these pathogenic pathways may be beneficial for patient Conflicts of Interest
management. Conflict of interest relevant to this article was not reported.
This study had some limitations. First, although we col-
lected data from a relatively large sample of CCA of the Acknowledgments
urinary tract, the number of cases was not sufficient for sta- This work was supported by grant 04-2022-0590 from the Seoul
tistical analysis of clinicopathologic or pathognomonic cor- National University Hospital Research Fund.
relations. In addition, in all our patients, the CCA arose in
the urethra, so our findings cannot be applied to CCA arising
from other parts of the urinary tract. Second, we performed
WES and bioinformatics studies, and proposed several path-
ogenic pathways related to the pathogenesis of CCA based
on genetic analyses. However, transcriptomic or proteomic
studies other than IHC are needed to validate the oncogenic
or tumor-suppressive roles of the driver genes. Third, we
identified the actionable targets for CCA, but studies of cell

292 CANCER RESEARCH AND TREATMENT

 Boram Song, Clear Cell Adenocarcinoma of the Urinary Tract

References
1. Netto GJ, Amin MB, Berney DM, Comperat EM, Gill AJ, Hart- 16. Gunes C, Wezel F, Southgate J, Bolenz C. Implications of TERT
mann A, et al. The 2022 World Health Organization classifica- promoter mutations and telomerase activity in urothelial car-
tion of tumors of the urinary system and male genital organs- cinogenesis. Nat Rev Urol. 2018;15:386-93.
part B: prostate and urinary tract tumors. Eur Urol. 2022;82: 17. A ACR Project GENIE Consortium. AACR Project GENIE:
469-82. Powering Precision Medicine through an International Con-
2. Venyo AK. Clear cell adenocarcinoma of the urethra: review sortium. Cancer Discov. 2017;7:818-31.
of the literature. Int J Surg Oncol. 2015;2015:790235. 18. Saliani M, Jalal R, Ahmadian MR. From basic researches to
3. Alexiev BA, Tavora F. Histology and immunohistochemistry new achievements in therapeutic strategies of KRAS-driven
of clear cell adenocarcinoma of the urethra: histogenesis and cancers. Cancer Biol Med. 2019;16:435-61.
diagnostic problems. Virchows Arch. 2013;462:193-201. 19. T
 anneberger K, Pfister AS, Kriz V, Bryja V, Schambony A, Beh-
4. T ong GX, Weeden EM, Hamele-Bena D, Huan Y, Unger P, rens J. Structural and functional characterization of the Wnt
Memeo L, et al. Expression of PAX8 in nephrogenic adenoma inhibitor APC membrane recruitment 1 (Amer1). J Biol Chem.
and clear cell adenocarcinoma of the lower urinary tract: 2011;286:19204-14.
evidence of related histogenesis? Am J Surg Pathol. 2008;32: 20. Oh YS, Jun HS. Effects of glucagon-like peptide-1 on oxidative
1380-7. stress and Nrf2 signaling. Int J Mol Sci. 2017;19:26.
5. Sung MT, Zhang S, MacLennan GT, Lopez-Beltran A, Monti- 21. T
 aguchi K, Yamamoto M. The KEAP1-NRF2 system in cancer.
roni R, Wang M, et al. Histogenesis of clear cell adenocarci- Front Oncol. 2017;7:85.
noma in the urinary tract: evidence of urothelial origin. Clin 22. V anhaesebroeck B, Guillermet-Guibert J, Graupera M, Bilan-
Cancer Res. 2008;14:1947-55. ges B. The emerging mechanisms of isoform-specific PI3K
6. Ortiz-Bruchle N, Wucherpfennig S, Rose M, Garczyk S, Bertz signalling. Nat Rev Mol Cell Biol. 2010;11:329-41.
S, Hartmann A, et al. Molecular characterization of Muelle- 23. W ilson BG, Roberts CW. SWI/SNF nucleosome remodellers
rian tumors of the urinary tract. Genes (Basel). 2021;12:880. and cancer. Nat Rev Cancer. 2011;11:481-92.
7. L in CY, Saleem A, Stehr H, Zehnder JL, Pinsky BA, Kunder 24. Gad S, Le Teuff G, Nguyen B, Verkarre V, Duchatelle V, Molin-
CA. Molecular profiling of clear cell adenocarcinoma of the ie V, et al. Involvement of PBRM1 in VHL disease-associated
urinary tract. Virchows Arch. 2019;475:727-34. clear cell renal cell carcinoma and its putative relationship
8. Mehra R, Vats P, Kalyana-Sundaram S, Udager AM, Roh M, with the HIF pathway. Oncol Lett. 2021;22:835.
Alva A, et al. Primary urethral clear-cell adenocarcinoma: 25. Y ap TA, O’Carrigan B, Penney MS, Lim JS, Brown JS, de
comprehensive analysis by surgical pathology, cytopathology, Miguel Luken MJ, et al. Phase I trial of first-in-class ATR in-
and next-generation sequencing. Am J Pathol. 2014;184:584-91. hibitor M6620 (VX-970) as monotherapy or in combination
9. Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, with carboplatin in patients with advanced solid tumors. J
et al. COSMIC: the Catalogue Of Somatic Mutations In Can- Clin Oncol. 2020;38:3195-204.
cer. Nucleic Acids Res. 2019;47:D941-7. 26. B anerjee S, Stewart J, Porta N, Toms C, Leary A, Lheureux S, et
10. C erami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy al. ATARI trial: ATR inhibitor in combination with olaparib in
BA, et al. The cBio cancer genomics portal: an open platform gynecological cancers with ARID1A loss or no loss (ENGOT/
for exploring multidimensional cancer genomics data. Cancer GYN1/NCRI). Int J Gynecol Cancer. 2021;31:1471-5.
Discov. 2012;2:401-4. 27. Q i W, Chen H, Xiao T, Wang R, Li T, Han L, et al. Acetyltrans-
11. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry ferase p300 collaborates with chromodomain helicase DNA-
JM, et al. Gene ontology: tool for the unification of biology. binding protein 4 (CHD4) to facilitate DNA double-strand
The Gene Ontology Consortium. Nat Genet. 2000;25:25-9. break repair. Mutagenesis. 2016;31:193-203.
12. G rosser D, Matoso A, Epstein JI. Clear cell adenocarcinoma 28. Froimchuk E, Jang Y, Ge K. Histone H3 lysine 4 methyltrans-
in men: a series of 15 cases. Am J Surg Pathol. 2021;45:270-6. ferase KMT2D. Gene. 2017;627:337-42.
13. Patel M, Im J, Ivy A, Maraboyina S, Kim T. The epidemiology 29. W
 iegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T,
and role of surgery in the treatment of urethral clear cell car- et al. ARID1A mutations in endometriosis-associated ovarian
cinoma. Int Urol Nephrol. 2020;52:51-7. carcinomas. N Engl J Med. 2010;363:1532-43.
14. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, 30. Wang L, Piskorz A, Bosse T, Jimenez-Linan M, Rous B, Gilks
Cibulskis K, et al. Somatic mutations affect key pathways in CB, et al. Immunohistochemistry and next-generation sequ-
lung adenocarcinoma. Nature. 2008;455:1069-75. encing are complementary tests in identifying PTEN abnor-
15. Paner GP, Lopez-Beltran A, Amin MB. Mesonephric (Wolffi- mality in endometrial carcinoma biopsies. Int J Gynecol
an-derived) adenocarcinoma of the female urethra. Am J Surg Pathol. 2022;41:12-9.
Pathol. 2021;45:543-9.

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