Rare cancers are usually defined as an incidence of <6/100,000 persons per year. Gynecological oncology is characterized by a paradoxical high prevalence of rare cancer subtypes, especially in ovarian tumors. Ovarian germ cell tumors, clear cell ovarian cancer and gestational trophoblastic disease encompass this set of gynecologic tumors. The WHO classification distinguishes epithelial cell tumors (85% of malignant tumors) from non-epithelial tumors, sex cord stromal tumors (8% of malignant tumors), and germ cell tumors (6% of malignant tumors). The current treatment for these tumors is similar to that for ovarian cancer but advancing quickly to incorporate targeted therapy. Gestational trophoblastic tumors are usually curable, even when widely metastatic disease is present. Ovarian clear-cell carcinoma (OCCC) remains a challenging disease characterized by intrinsic chemoresistance and distinct molecular features. A more biologically aligned treatment strategy has emerged. Continued integration of molecular selection and microenvironmental modulation will likely define the next phase of therapeutic development in OCCC. The clinical features, staging, and current treatment of each of these tumors is reviewed.

To compare preoperative MRI features between ovarian clear cell carcinoma (CCC) patients with favorable versus unfavorable clinical outcomes and to identify imaging predictors associated with adverse outcomes. We retrospectively analyzed patients with pathologically confirmed CCC to compare preoperative MRI and clinical features between the recurrence-free and unfavorable-outcome groups. Quantitative variables included MRI parameters such as tumor size, T1 ratio of the cystic component, and for the solid component, maximum width and height, T2 ratio, apparent diffusion coefficient (ADC), and dynamic contrast-enhanced (DCE) metrics, as well as clinical/laboratory data (age and serum tumor marker levels). Qualitative variables included MRI findings such as number of locules, number of solid components (≤ 3 vs. ≥4 solid components or diffuse mural thickening), presence of marked T2 hyperintensity, growth pattern, presence of necrosis, and time-intensity curve (TIC) pattern, as well as FIGO stage, and surgical completeness. Seventy-two patients were included (recurrence-free, n = 45; unfavorable-outcome, n = 27). The distribution of FIGO stage differed between the groups (p < 0.001), and complete surgery was achieved significantly less often in the unfavorable-outcome group (77.8%, p = 0.002). Among the MRI parameters, only ≥ 4 solid components were significantly associated with unfavorable outcomes (p = 0.020). In stage I-II cases, the same trend was observed, although not significant (p = 0.147). No significant associations were observed for any other variables, including tumor size, T1 ratio of the cystic component, maximum width and height of the solid component, growth pattern, T2 ratio, ADC, DCE metrics, TIC pattern, or clinical and laboratory data (p = 0.050-1.000). In this cohort of CCC patients, multiparametric MRI showed that the presence of four or more solid components, together with FIGO stage and surgical completeness, was associated with unfavorable clinical outcomes, suggesting a potential role for MRI-based risk stratification that warrants external validation.

ABSTRACT Introduction Ovarian clear cell carcinoma (OCCC) is a rare gynecologic malignancy with a high mortality rate and a lack of response to standard chemotherapy. Despite the functional association between the loss of ARID1A and mitochondrial dependency, the clinical translation of mitochondria-targeted therapies in OCCC has been hindered by a substantial disconnect between biological insight and therapeutic application. There is an urgent, unmet need to identify novel, more specific and effective therapies targeting the mitochondria-related molecular vulnerabilities of ARID1A-mutant OCCC. Areas covered This critical perspective is informed by results from PubMed literature searches and recent webinars and presentations providing insight into opportunities for mass spectrometry (MS)-based proteomic approaches to enhance and accelerate the clinical translation of mitochondria-targeted therapies in OCCC. Expert opinion The MS-based proteomic analysis of clinically-relevant experimental models of OCCC will provide a unique opportunity to progress beyond simplified preclinical models and incorporate the full spectrum of patient-specific systemic and microenvironmental factors that may influence therapeutic response, including the adipocyte-related metabolic dependencies of OCCC. Targeted MS is a precise and robust approach that can be applied to verify these novel, mechanistic insights into how mitochondria-targeted therapies intersect with tumor metabolism in OCCC.

Proteomics provides a systematic and high-throughput approach to comprehensively characterize protein networks, enabling insights into cellular functions and disease mechanisms. Carbamidomethylation using iodoacetamide (IAA), a common method for cysteine alkylation, is known to cause nonspecific modifications that increase spectral complexity in mass spectrometry and reduce quantitative accuracy. Here, we established a reproducibility-focused 2-mercaptoethanol (2-ME)/dimethyl sulfoxide (DMSO) workflow and systematically evaluated its quantitative performance at the proteome-wide level. Mouse liver proteomes were processed using either 2-ME/DMSO or conventional IAA treatment, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The optimized 2-ME treatment increased the number of cysteine-modified peptides by 1.6- to 1.9-fold. Although total protein identifications were comparable, 77% of proteins exhibited improved sequence coverage with the optimized 2-ME treatment. Quantitative reproducibility was also enhanced, with the peptide quantified CV ≤ 20% increasing from 61.4% with IAA treatment to 86.1% with 2-ME treatment, and protein quantified CV ≤ 20% increasing from 80.6% with IAA treatment to 93.5% with 2-ME treatment. Application of this new workflow to ovarian clear cell carcinoma reliably detected cisplatin-induced alterations. The 2-ME/DMSO workflow offers a simple and highly reproducible proteomics strategy for accurate quantitative proteomics.

Ovarian clear cell carcinoma (OCCC) is a rare aggressive, and chemo-resistant subtype of epithelial ovarian cancer. Current limitations in precisely characterizing its molecular features have resulted in restricted availability of clinical targeted therapies and significant therapeutic challenges. To address this unmet need, we conducted an integrative multi-omics study of 82 OCCC cases, incorporating whole-exome sequencing (WES), bulk RNA sequencing, and single-cell RNA sequencing (scRNA-seq). Our analysis uncovered recurrent mutations in multiple epigenetic regulators including ARID1A, EP300, and SETD2B, reinforcing chromatin remodeling as a hallmark of OCCC pathogenesis. Strikingly, FOXA2 mutations were absent in early-stage tumors but specifically enriched in advanced-stage cases (19% frequency), with functional validation demonstrating their role in driving malignant progression. Copy number alteration profiling revealed frequent amplifications in chromosomal arms such as 17q, which contains the ERBB2 oncogene that potentially regulates OCCC progression. Chromosomal translocations were detected in 35.59% of cases, including a novel FGFR2/RPAP3 fusion with therapeutic implications. Notably, scRNA-seq delineated immune-rich subsets characterized by abundant cytotoxic T-cell and B-cell infiltration, suggesting immunotherapeutic opportunities in a patient subset. Moreover, molecular subtyping identified ERBB2 amplification/overexpression as a high-risk feature strongly associated with poor survival. Patient-derived xenograft (PDX) models and a retrospective analysis of two clinical cases demonstrated that HER2-targeted antibody-drug conjugates (HER2-ADCs) significantly suppressed tumor growth and progression in OCCC patients with HER2 expression. In summary, our study establishes the comprehensive molecular atlas and a targeted therapeutic subtyping framework, revealing therapeutic vulnerabilities and providing novel insights for advancing precision oncology in OCCC management.

Clear cell ovarian carcinoma (CCOC) is a rare, aggressive ovarian cancer subtype, comprising approximately 12% of epithelial ovarian carcinoma (EOC) cases in Western countries yet associated with the worst prognoses due to its chemoresistance. Most CCOCs harbor activating PIK3CA mutations that drive PI3K/AKT/mTOR signaling and HIF1α expression. Despite their clinical success in some cancers, mTOR inhibitors have shown limited efficacy in CCOC, even though this pathway is highly active. Consequently, CCOC continues to be managed like other epithelial ovarian cancers. We recently uncovered cystathionine γ-lyase (CTH), a key enzyme in the transsulfuration pathway, as a metabolic vulnerability in CCOC, supporting HIF1α expression, survival and metastasis. This study aims to address whether simultaneously targeting CTH and mTOR could enhance therapeutic outcomes beyond those achieved by mTOR inhibition alone.CCOC lines were engineered with CTH knockout (KO) or treated with the CTH inhibitor Aviglycine hydrochloride (AVG; ABG-3168); mTOR was blocked with everolimus, a clinical stage mTOR inhibitor. Single and combined treatments were tested in two-dimensional cultures and three-dimensional spheroids under normoxia (21% O2) and hypoxia (1% O2). We measured viability, proliferation, colony formation, apoptosis, and protein signaling. Drug interaction was quantified with a synergy model.Everolimus reduced viability and increased apoptosis across CCOC cell lines, but activity was modest as a single agent. Adding CTH inhibition produced synergistic growth suppression at low doses, with the effect being stronger under hypoxia. The combination reduced colony formation over 14days and decreased spheroid size while increasing caspase-3/7 activity. Dual treatment decreased HIF1α protein expression more than either monotherapy while maintaining strong inhibition of mTOR/S6 kinase signaling; total mTOR and S6 kinase were unchanged. In CTH-deficient models, the synergy was maintained; however, pharmacological inhibition of CTH with AVG did not produce additional effects, indicating dependence on CTH activity and supporting an on-target mechanism. Similar antiproliferative effects with combined treatment were observed in a CTH-expressing Ewing sarcoma (EwS) model.Together, these findings support biomarker-guided strategies and rational combination therapies that achieve dual targeting of mTOR and CTH, thereby disrupting protein translation and hypoxia adaptation in CCOC and other CTH-expressing cancers.

Ovarian clear cell carcinoma (OCCC) frequently exhibits resistance to conventional chemotherapy with limited treatment options. This study reports a heavily pretreated advanced case with liver metastases to investigate the efficacy of gemcitabine combined with PD-1 inhibitor in such refractory patients. We present a case of stage IIIC OCCC that progressed after first-line platinum-based chemotherapy. The patient was treated with gemcitabine incombination with the PD-1 inhibitor toripalimab. Genetic alterations were analyzed using next-generation sequencing, and PD-L1 expression was assessed by immunohistochemistry (Combined Positive Score, CPS). Treatment response andsafety profiles were regularly monitored. The combination therapy induced a complete remission lasting over 24 months, with a manageable safety profile. Molecular profiling revealed a loss-of-function mutation in ARID1A, which may enhance tumor sensitivity to gemcitabine, while elevated PD-L1 expression (CPS = 30) may serve as a predictive biomarker for immunotherapy response in OCCC. Notably, the deep and durable clinical response observed suggests a potential synergistic effect between gemcitabine and immunotherapy, wherein ARID1A deficiency-induced chemosensitivity may prime the tumor microenvironment for enhanced immune checkpoint inhibition, offering a compelling rationale for this combination strategy in platinum-resistant OCCC. This study proposes a promising therapeutic strategy for advanced OCCC and supports the clinical value of molecular profiling-guided treatment. Both ARID1A status and PD-L1 expression warrant further validation as potential biomarkers inprospective clinical trials.

Ovarian cancer (OC) is a highly invasive disease with a poor prognosis, underscoring the importance of identifying specific biomarkers in early screening to enhance the overall survival of patients with OC. In this study, quantitative methylation-specific PCR was used to investigate the methylation levels of the nidogen-2 (NID2) and cysteine dioxygenase 1 (CDO1) gene promoters in peripheral blood samples from 72 patients with OC and 75 healthy individuals. The results revealed significantly higher methylation levels of the NID2 and CDO1 genes in patients with OC compared with those in healthy controls. NID2 methylation demonstrated a sensitivity of 70.83% and a specificity of 96.00% in predicting OC, whereas CDO1 exhibited a sensitivity of 90.28% and a specificity of 69.33%. The positivity rate of NID2 methylation was elevated in patients with stage III-IV OC compared with those with stage I-II OC and was higher in high-grade serous carcinoma compared with that in ovarian clear cell carcinoma. Additionally, the positivity rate of CDO1 methylation could reach 84.6% in patients with stage I-II OC. Furthermore, the methylation levels of NID2 and CDO1 exhibited a positive correlation with carbohydrate antigen 125 (CA125) levels. Combining the detection of NID2 and CDO1 methylation with CA125 significantly enhanced the sensitivity and specificity of OC detection compared with CA125 detection alone. In conclusion, enhanced methylation of the NID2 and CDO1 genes has emerged as an independent risk factor for OC development.

SETD8 promotes ovarian clear cell carcinoma by epigenetically activating RNA metabolism genes via H4K20me1.

Endometriosis is a chronic estrogen-dependent disorder affecting approximately 10% of women of reproductive age. Increasing epidemiological and molecular evidence indicates that it may represent a precursor condition for a subset of ovarian malignancies collectively defined as endometriosis-associated ovarian cancer (EAOC), predominantly endometrioid and clear cell carcinomas. Malignant transformation is driven by the interplay between chronic inflammation, oxidative stress, and local hyperestrogenism within the endometriotic microenvironment. Recurrent hemorrhage and persistent immune activation further promote genomic instability and clonal expansion. Shared somatic mutations have been identified in both atypical endometriosis and adjacent carcinomas, supporting a model of stepwise tumorigenesis. Dysregulation of signaling pathways and epigenetic mechanisms, including microRNA alterations, further contribute to tumor development. Although the absolute risk of malignant transformation remains low, women with ovarian endometriosis and deep infiltrating disease show an increased risk of ovarian cancer. EAOC is frequently diagnosed at earlier stages and generally demonstrates a more favorable prognosis than high-grade serous carcinoma, although clear cell histotypes may exhibit chemoresistance and distinct molecular vulnerabilities. This review summarizes current evidence on the pathogenesis, molecular mechanisms, and clinical implications of EAOC, highlighting future strategies for risk stratification and personalized surveillance.

Multicellular cancer cell aggregates, termed spheroids, are anoikis-resistant, avascular, heterogeneous structures responsible for transcoelomic metastasis of ovarian clear cell carcinoma (OCCC). OCCC is a rare subtype of ovarian cancer with high ARID1A gene mutation rates, resulting in genome-wide changes to H3K27Ac levels and histone deacetylase (HDAC) function. Our study investigated the utility of HDAC inhibitor (HDACi) treatment and H3K27Ac dynamics in OCCC spheroids. By comparing KOC-7c and 105C OCCC cell lines, which have opposing abilities to proliferate as spheroids, we revealed that KOC-7c and 105C spheroids differentially regulated H3K27Ac levels, which correlated with the sensitivity of KOC-7c and the resistance of 105C spheroids to H3K27Ac-altering HDACi treatment. RNA-seq of Entinostat-treated versus vehicle-treated spheroids resulted in a dramatic change in the 105C spheroid transcriptome such that it more closely resembled the proliferative KOC-7c transcriptome over the short term. Comparative pathway analysis identified preferential de-repression of a G2/M checkpoint gene program in 105C spheroids upon Entinostat treatment when compared directly to the KOC-7c spheroids. Our results suggest that the utility of HDACi in OCCC is highly context-dependent.

Ovarian clear cell carcinomas (OCCC), particularly cases that retain wild-type AT-rich interactive domain 1 A (ARID1A) expression (approximately 50% of the OCCC cases), are chemoresistant and lack specific therapies. We identified BMAL2 as a critical OCCC oncogene that promotes tumorigenesis by preventing endogenous DNA damage. BMAL2 depletion altered the expression of genes encoding DNA damage repair proteins, including RAD51, a core enzyme of the homologous recombination (HR) pathway. This led to DNA double-stranded break accumulation, decreased cell viability and reduced tumor growth. This dependence on BMAL2 to maintain DNA integrity and cell viability can be a new route to suppress OCCC. Consistent with this idea, we found that GW833972A, a cannabinoid receptor agonist, bound BMAL2 with high affinity and facilitated its protein degradation. This in turn reduced RAD51 expression, leading to an accumulation of DNA damage, decreased cell viability and reduced OCCC tumor growth. GW833972A is effective by itself at high dose and can also be used at lower dosages to enhance the effectiveness of Poly (ADP-ribose) polymerase inhibitor (PARPi) treatments in BMAL2-expressing OCCC. Together, our findings reveal an essential oncogenic role of BMAL2 and demonstrate that it is an appealing therapeutic target, especially for ARID1A-wt OCCC.

Ovarian clear cell carcinoma (OCCC) is an endometriosis-associated ovarian cancer subtype. Somatic mutations in OCCC are reported in ARID1A, PIK3CA, and the TERT promoter (TERTp), as well as less commonly in KRAS and TP53 among other genes. OCCC is typically resistant to standard-of-care chemotherapy, especially after relapse. While recent studies have seen favourable responses to immunotherapy, patients with OCCC face limited therapeutic options. With the objective of discovering new drug treatments for OCCC, we screened OCCC (RMG-1, JHOC-5, OV207, OVISE, OVMANA, OVTOKO, and TOV-21G) and non-OCCC cell lines with a commercially available epigenetic drug compound library at two concentrations. Based on specified selection criteria, drugs were sought that preferentially inhibited viability of OCCC versus non-OCCC cells, with subsequent validation in 2D and 3D bioprinted models and exploration of a relevant signalling pathway. Taken together, OCCC cell lines were more sensitive to the Bruton's Tyrosine Kinase (BTK) inhibitor ibrutinib than non-OCCC cells, with some variation in response observed between cell lines in 2D and 3D bioprinted cultures. Furthermore, ibrutinib inhibited PI3K/AKT/mTOR cell survival signalling in some but not all OCCC cell lines, suggesting that this drug functions on additional pathways. Ibrutinib is used clinically to treat specific B cell disorders; however, it is not currently approved to treat solid tumours. Data presented in OCCC cell lines complements clinical observations of a therapeutic response to ibrutinib in low-grade serous ovarian cancer. Ibrutinib demonstrates potential for the treatment of certain rare subtypes of ovarian cancer and should be further investigated.

PRSS23 promotes ovarian cancer peritoneal dissemination independent of protease activity.

Recurrent ovarian clear cell carcinoma (OCCC) remains a therapeutic challenge due to intrinsic chemoresistance and paucity of targeted options. Surufatinib is a multi-target tyrosine kinase inhibitor that may enhance antitumor immunity when combined with PD-1 blockade. We report a 53-year-old female with recurrent OCCC who developed a platinum-sensitive first relapse (platinum-free interval, 9.8 months) after adjuvant platinum-based chemotherapy and achieved a 24-month progression-free survival (ongoing) on surufatinib plus toripalimab. The best response was partial response, and treatment was well tolerated except for Grade 1 hemoptysis and Grade 1–2 proteinuria. Radiologic disease control was durable. However, because biomarker assessment relevant to immune checkpoint inhibition was not performed, the biological basis of response remains uncertain. This case suggests the clinical feasibility of surufatinib plus toripalimab and its association with durable disease control in an individual patient with recurrent OCCC. However, given the platinum-sensitive nature of the relapse, treatment efficacy should be interpreted cautiously. Further prospective studies incorporating biomarker assessment are warranted.

Ovarian clear cell carcinoma (OCCC) is a rare cancer type of significant relevance to East Asian women harboring critical unmet needs for novel therapeutic options. It is a histological subtype of ovarian cancer with distinct pathological features, molecular profiles, and biological functions. Diverse heterogeneity contributing from histopathological and multiomic molecular features has yet to be translated to guide clinical care. Here, we presented a proof-of-concept study to demonstrate the feasibility of applying deep spatial transcriptomic (ST) profiling of tumor samples from an advanced OCCC patient in the real-world setting, aiming to identify therapeutic options beyond standard-of-care. Matched primary ovarian and metastatic bladder tumor sections were profiled by using GeoMx Digital Spatial Profiling and Xenium In Situ platforms. The spatial architecture and neighborhood niches were identified from GeoMx Cancer Transcriptome Atlas (CTA) and Xenium 5K Human Pan Tissue and Pathways Panel. An immunosuppressive Wnt-activating tumor microenvironment (TME) was identified by GeoMx while a tripartite spatial relationship between SLC2A1+ hypoxic cancer cells, IFIT2+ inflammatory cancer cells, and MMP12+ dendritic cells linking towards metabolism and immune responses was identified by Xenium. Our deep ST profiling findings provided significant biological insights and demonstrated feasibility to make novel discoveries, one patient at a time.

Epithelial ovarian cancer is a heterogenous group, that includes histologic sub-types with distinct biologic behavior. Stage IC disease confers a higher risk of recurrence and death compared to stage IA. While adjuvant chemotherapy may improve outcomes of patients with high-grade serous ovarian carcinoma, its impact on the oncologic outcomes of other histologic sub-types that are more chemo-resistant, such as clear cell, mucinous, and low-grade serous ovarian carcinoma is not well-established. Retrospective studies have demonstrated that omission of adjuvant chemotherapy can be considered for patients with expansile mucinous, grade 1 endometrioid, and low-grade serous ovarian carcinoma and for those with stage IC1 clear cell ovarian carcinoma. However, in the absence of data from randomized clinical trials, shared decision-making, and careful counseling of patients should be considered. Future multicenter studies are required to further validate the safety of adjuvant chemotherapy omission in certain patient sub-groups with stage IC epithelial ovarian cancer.

High frequency of BRAF mutations and concomitant KRAS mutations in Taiwanese ovarian clear cell carcinoma.

Ovarian clear cell carcinoma (OCCC) is a rare histological subtype of ovarian cancer, often associated with endometrial lesions, and characterized by poor prognosis and a high propensity for recurrence and metastasis. This study aimed to investigate the clinical characteristics of patients with OCCC and identify prognostic factors. A retrospective analysis was conducted on patients diagnosed with OCCC at Fujian Cancer Hospital from January 2007 to December 2018. Inclusion criteria were as follows: (I) histologically confirmed pure OCCC; (II) surgical intervention; (III) standardized and completed postoperative follow-up. Exclusion criteria were as follows: (I) patients with recurrence or metastasis; (II) patients who did not receive treatment. Kaplan-Meier survival curves were used to estimate progression-free survival (PFS) and overall survival (OS). Clinical outcomes were further analyzed using Cox proportional hazards regression. The median follow-up duration for 102 patients was 89.62 months. At the time of the final follow-up, 44 patients had died, and 43 had experienced recurrence or metastasis. The 5-year OS and PFS rates were 59.2% and 50.0%, respectively. Univariate Cox regression analysis indicated that stage, concurrent endometriosis, chemotherapy, carbohydrate antigen 125 (CA-125) normalization, and CA-125 ≤20 U/mL were associated with both OS and PFS (P<0.05). Lymph node metastasis, platinum resistance, and venous thrombosis were only associated with OS (P<0.05). Multivariate analysis revealed that stage [hazard ratio (HR) =2.780, 95% confidence interval (CI): 1.265-6.110, P=0.01], chemotherapy (HR =0.211, 95% CI: 0.075-0.593, P=0.003), and platinum resistance (HR =8.233, 95% CI: 3.617-18.743, P<0.001) were independent prognostic factors for OS. Concurrent endometriosis (HR =0.385, 95% CI: 0.189-0.784, P=0.009) and stage (HR =4.507, 95% CI: 2.346-8.660, P<0.001) were independent prognostic factors for PFS. Stage, endometriosis, platinum resistance, and platinum-based chemotherapy are significant prognostic factors in OCCC. CA-125 levels, positive lymph nodes, and venous thrombosis are also associated with survival outcomes.

944 Increased Combined Density of CD8+ T cells and CD68+ Macrophages Co-Localizing LAG3 or PD-L1 is Associated with Recurrence in Ovarian Clear Cell Carcinoma: A Multiplex Immunofluorescence (mIF) and AI Based Digital Image Analysis Study