Cancer Genetics

Prognosis prediction and drug guidance of ovarian serous cystadenocarcinoma through mitochondria gene-based model

Mitochondrial dysregulation contributes to the chemoresistance of multiple cancer types. Yet, the functions of mitochondrial dysregulation in Ovarian serous cystadenocarcinoma (OSC) remain largely unknown. We sought to investigate the function of mitochondrial dysregulation in OSC from the bioinformatics perspective. We aimed to establish a model for prognosis prediction and chemosensitivity evaluation of the OSC patients by targeting mitochondrial dysregulation. Differentially expressed genes (DEGs) were screened from the Cancer Genome Atlas (TCGA)-OV dataset and the mitochondrial-related DEGs were identified from the Human MitoCarta 3.0 database. Prognosis-related mitochondria-related genes (MRGs) were screened to establish the MRGs-based risk score model for prognosis prediction. To validate the risk score model, the risk score model was then evaluated by IHC staining intensity and survival curves from clinical specimens of OSC patients. Migration and proliferation assays were performed to elucidate the role of carcinogenic gene ACSS3 in serous ovarian cancer cell lines. Using consensus clustering algorithm, we identified 341 MRGs and two subtypes of OSC patients. Moreover, we established a novel prognostic risk score model by combining the transcription level, intensity and extent scores of MRGs for prognosis prediction purpose. The model was established using 7 MRGs (ACOT13, ACSS3, COA6, HINT2, MRPL14, NDUFC2, and NDUFV2) significantly correlated to the prognosis of OSC. Importantly, by performing the drug sensitivity analysis, we found that the OSC patients in the low-risk group were more sensitive to cisplatin, paclitaxel and docetaxel than those in the high-risk group, while the latter ones were more sensitive to VEGFR inhibitor Axitinib and BRAF inhibitors Vemurafenib and SB590885. In addition, patients in the low-risk group were predicted to have better response in anti-PD-1 immunotherapy than those in the high-risk group. The risk score model was then validated by survival curves of high-risk and low-risk groups determined by IHC staining scores of OSC clinical samples. The carcinogenic effect of ACSS3 in OSC was confirmed through the knockdown of ACSS3 in SKOV3 and HO-8910 cells. To summarize, we established a novel 7 MRGs - based risk score model that could be utilized for prognosis prediction and chemosensitivity assessment in OSC patients.

Alcohol consumption and risk of breast and ovarian cancer: A Mendelian randomization study

Alcohol consumption has been found to increase the risk of breast cancer in observation studies, yet it remains unknown if alcohol is related to other hormone-dependent cancers such as ovarian cancer. No Mendelian randomization (MR) studies have been performed to assess a potential causal relationship between alcohol use and risk of breast and ovarian cancer. We aim to determine if alcohol consumption is causally associated with the risk of female hormone-dependent cancers, by using summary level genetic data from the hitherto largest genome-wide association studies (GWAS) conducted on alcohol consumption (N=~1.5 million individuals), breast (N We did not find any evidence to support for a causal association between alcohol consumption and risk of breast cancer [OR We do not find any compelling evidence in support for a causal relationship between genetically predicted alcohol consumption and risk of breast or ovarian cancer, consistent across three different alcohol-related exposures. Future MR studies validating our findings are needed, when large-scale alcohol consumption GWAS results become available.

Double mutation of APC and BRCA1 in an Italian family

Familial adenomatous polyposis (FAP) is a rare genetic disorder caused mainly by monoallelic mutations of APC gene. The hereditary breast and ovarian cancer (HBOC) syndrome is an autosomal dominantly inherited disease, which mostly predisposes to breast and ovarian cancers as a result of germline mutations in BRCA1 or BRCA2 genes. In a family, mutations in two cancer susceptibility genes are extremely rare. We studied a family with a case of a 46 years-old woman affected with FAP and ovarian cancer. The patient was affected with profuse FAP since the age of 18 years and a serous ovarian cancer was diagnosed at the age of 45 years. She reported other FAP cases and one case of breast cancer in maternal family. Initially, she was tested for FAP predisposition with mutational analysis of APC gene that revealed the presence of a frameshift mutation, c.3927_3931delAAAGA (p.Glu1309AspfsX4). The presence of ovarian cancer in the patient and of a breast cancer case in the maternal family, suggested an extended analysis to HBOC susceptibility genes that led to the detection of a frameshift mutation, c.3756_3759delGTCT (p.Ser1253Argfs), in BRCA1 gene. The genetic analysis was extended also to family members. The occurrence of the double mutation in APC and BRCA1 genes in the patient was responsible for the onset of FAP and ovarian cancer respectively. The genetic counselling in hereditary cancer with a careful analysis of the pedigree allows identifying the gene to be analyzed. The development of multi-gene panels testing for cancer predisposition, with next generation sequencing (NGS), may reveal mutations in genes of high and moderate penetrance for cancer, although at a low frequency and allows diagnosing a possible double heterozygosity. This enables an adjusted treatment for the affected patient and is critical as it allows initiation of early risk-reducing measures for identified mutation carriers among family members.

When cascade testing for familial variant seems inadequate to provide clinically actionable information for blood relatives

A hereditary ovarian cancer family with rare pathogenic splicing mutation: Implications for variant interpretation

The BRCA1/2 gene is important for assessing the risk of familial/hereditary ovarian cancer (OC). This case is a patient with OC, and two of her immediate family members are cancer patients. We sequenced the coding and splicing regions of 42 OC susceptibility genes, and found a rare pathogenic splicing mutation BRCA1:c.132C > T (p.cys44 =) in 2 patients. Although the mutation is synonymous, software prediction and functional verification have shown that it affects alternative splicing and leads to frameshift mutations (c.131_134del). Chromosome microarray analysis of the tissue samples revealed the presence of a BRCA1 gene deletion with a fragment size of 1.42 Mb and an HRD score of 71. In addition, the proband showed a sensitive response to platinum treatment. This case suggests the clinical significance of OC susceptibility genes sequencing and HRD scoring in screening hereditary OC families.

Comparative analysis of a founder BRCA2 double mutation versus single mutation carriers reveals no additional clinical risk

Double mutations (DMs) in cis within the same BRCA gene are extremely rare, and their clinical significance remains uncertain, as it is unclear whether they confer an additive risk compared with single pathogenic variants (PVs). We retrospectively analyzed a cohort of 1722 patients referred for suspected Hereditary Breast and Ovarian Cancer (HBOC). Among them, 9 unrelated probands were found to carry the same BRCA2 DM: c.631G>A (p.Val211Ile) in exon 7 and c.7008-2A>T (IVS13-2A>T) at the acceptor splice site of intron 13. Both variants were confirmed to co-segregate in cis. A control group of 19 probands with a single BRCA2 PV located between exons 7 and 14 was selected for comparison. All DM families originated from the same geographic area in Southern Italy, suggesting a founder effect. The mean age at breast cancer onset was 50.7 years in the DM group and 51.4 years in the control group. Tumor spectrum and distribution among probands and relatives were comparable between groups, and BRCA2-related breast cancers were predominantly hormone receptor-positive in both cohorts. No statistically significant differences were observed regarding cancer types, stage, or receptor profile. These findings suggest that the BRCA2 double mutation c.631G>A/c.7008-2A>T may have a founder effect, and the coexistence of the two variants does not appear to confer an additive cancer risk or a more severe clinical phenotype compared with carriers of a single BRCA2 pathogenic mutation.

Influence of polymorphisms on the phenotype of TLR1, TLR4 and TLR9 genes and their association with cervical cancer: Bioinformatics prediction analysis and a case-control study

Susceptibility to cervical cancer has been associated with Toll-like receptors (TLRs), which is an important component of innate immunity. According to previous studies, polymorphisms in TLRs genes can affect immune response pathways and lead to the development of cervical cancer. The present study aims to evaluate the functionality of polymorphisms in TLR1, TLR4 and TLR9 genes and their associations with cervical cancer. To identify the functionality of polymorphisms, we used the following tools: MUpro, ChimeraX, SNP2TFBS and GTEx. A case-control study including 57 cases (11 High-grade Intraepithelial Lesion - HSIL and 46 cervical cancer) and 67 clinically healthy controls was conducted in the Brazilian population. Polymorphisms genotyping was performed by real-time PCR, using TaqMan probes, using the allelic discrimination method. Bioinformatics prediction showed that the TLR1 rs4833095 [NM_003263.4 (TLR1):c.743T>C (p.Asn248Ser)] and TLR4 rs4986790 [NM_138554.5 (TLR4):c.896A>G (p.Asp299Gly)] polymorphisms alter the structure and stability of their respective proteins. TLR9 rs187084 [NM_017442.3(TLR9):c.-1486A>G] polymorphism seems to affect the THAP1 binding site and modify gene expression. In the case-control study, the c.743TC heterozygous genotype of the rs4833095 SNP in the TLR1 gene was associated with an increased risk for HSIL/cervical cancer. No association of TLR4 rs4986790 and TLR9 rs187084 SNPs with HSIL/cervical cancer was found in the studied population. Allelic combination CAG (rs4833095/ rs4986790/ rs187084) increased the risk of cervical cancer. In conclusion, the present study identified that polymorphisms in TLRs genes can affect the phenotype of their respective genes and contribute to the development of HSIL or cervical cancer.

LncRNA SNHG29 Suppresses Epithelial Ovarian Cancer Cell Invasion and Migration via miR-20b-3p/GNAI3 Axis Regulation

Epithelial ovarian cancer (EOC) is the deadliest gynecologic cancer in women. Long noncoding RNAs (lncRNAs) are critically involved in malignant progression by modulating proliferation, apoptosis, invasion, metastasis, and chemotherapy resistance. The long noncoding RNA small nucleolar RNA host gene 29 (SNHG29) is involved in multiple malignancies, although its role in EOC has not been elucidated. In our study, SNHG29 expression was significantly downregulated in EOC tissues and was negatively related to lymphatic invasion in EOC patients according to data from the TCGA database. Kaplan-Meier survival analysis revealed that among patients with early stage EOC, compared with patients with low SNHG29 expression levels, patients with high expression levels had markedly longer progression-free survival (PFS) and overall survival (OS) times. Further studies suggested that SNHG29 knockdown enhanced the invasive and migrative potential of EOC cells, whereas SNHG29 overexpression attenuated the invasive and migrative potential capacity. In animal experiments, SNHG29 knockdown significantly promoted lung metastasis in tail vein injection models. Mechanistically, the downregulation of SNHG29 expression inhibited its competitive endogenous RNA activity, resulting in increased miR-20b-3p availability and subsequent degradation of the downstream target gene GNAI3, as determined by RNA immunoprecipitation (RIP) and luciferase reporter gene assays. miR-20b-3p inhibition significantly reduces the invasive and metastatic capabilities of EOC cells resulting from a reduction in SNHG29 expression. Our study revealed that SNHG29 may be a promising prognostic factor and therapeutic target for EOC.

The mechanism of lncRNA SSTR5-AS1 promoting ferroptosis resistance and immune escape in ovarian cancer cells by recruiting STAT3 to regulate SLC7A11 expression

Ovarian cancer (OC) is the foremost cause of gynecological cancer-related mortality. Respecting the role of long noncoding RNAs (lncRNAs) in malignancies, we explored the mechanism of SSTR5-AS1 regulating OC cell ferroptosis resistance and immune escape via the signal transducer and activator of transcription 3 (STAT3)/solute carrier family 7a member 11 (SLC7A11) axis. OC cells were treated with si-SSTR5-AS1, oe-SSTR5-AS1 and oe-SLC7A11 plasmids. SSTR5-AS1, STAT3 and SLC7A11 mRNA levels, and cell malignant behaviors were assessed by RT-qPCR, CCK-8 and Transwell assays. Fe SSTR5-AS1 was up-regulated in OC cells. SSTR5-AS1 overexpression facilitated OC cell malignant behaviors, down-regulated Fe SSTR5-AS1 promoted SLC7A11 transcription and expression by recruiting STAT3, thereby promoting ferroptosis resistance and immune escape of OC cells.

Profiling of HER2, KRAS, and PIK3CA mutations in uterine cervical neuroendocrine carcinoma and implications for oncogenic driver targeting therapy

Dysregulated HER2-mediated RAS/MAPK and PI3K/AKT signaling drive uncontrolled cell growth and tumorigenesis. Following our prior report of frequent HER2 mutations in advanced uterine cervical neuroendocrine carcinoma (NEC), this study expands the genomic landscape by investigating KRAS and PIK3CA as potential therapeutic targets in a cohort of 12 Taiwanese women with cervical NEC. We analyzed 12 histologically confirmed cervical NEC tumor samples from Taiwanese patients. Targeted next-generation sequencing (NGS) was performed using a custom Qiagen GeneRead DNAseq Targeted Panels V2, a clinically relevant tumor panel to detect mutations in key oncogenes. DNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissues, followed by variant analysis to identify pathogenic alterations. Beyond HER2 mutations (41.67 %, 5/12), we detected pathogenic alterations in KRAS (16.67 %, 2/12) and PIK3CA (16.67 %, 2/12) within the same cohort. Concurrent mutations were observed in HER2/KRAS (8.3 %, 1/12) and HER2/PIK3CA (8.3 %, 1/12), indicating potential cooperative effects. This study identifies HER2, KRAS, and PIK3CA as potentially critical drivers in cervical NEC, with their co-occurrence highlighting the role of RAS/MAPK and PI3K/AKT pathways in pathogenesis. Dual pathway inhibition with multi-target therapies may enhance efficacy and address resistance in this aggressive, treatment-limited disease. Molecular profiling is essential for precision oncology, paving the way for validating these findings in larger cohorts and developing multi-pathway strategies to improve survival and quality of life.

BRCA1 and BRCA2 whole cDNA analysis in unsolved hereditary breast/ovarian cancer patients

Germline pathogenic variants in BRCA1 and BRCA2 genes (BRCA1/2) explain an important fraction of hereditary breast/ovarian cancer (HBOC) cases. Genetic testing generally involves examining coding regions and exon/intron boundaries, thus the frequency of deleterious variants in non-coding regions is unknown. Here we analysed BRCA1/2 whole cDNA in a large cohort of 320 unsolved high-risk HBOC cases in order to identify potential splicing alterations explained by variants in BRCA1/2 deep intronic regions. Whole RNA splicing profiles were analysed by RT-PCR using Sanger sequencing or high-resolution electrophoresis in a QIAxcel instrument. Known predominant BRCA1/2 alternative splicing events were detected, together with two novel events BRCA1 ▼21 and BRCA2 Δ18q_27p. BRCA2 exon 3 skipping was detected in one patient (male) affected with breast cancer, caused by a known Portuguese founder mutation (c.156_157insAluYa5). An altered BRCA2 splicing pattern was detected in three patients, consisting in the up-regulation of ▼20A, Δ22 and ▼20A+Δ22 transcripts. In silico analysis and semi-quantitative data identified the polymorphism BRCA2 c.8755-66T>C as a potential modifier of Δ22 levels. Our findings suggest that mRNA alterations in BRCA1/2 caused by deep intronic variants are rare in Spanish population. However, RNA analysis complements DNA-based strategies allowing the identification of alterations that could go undetected by conventional testing.

Mutations in BRCA-related breast and ovarian cancer in the South African Indian population: A descriptive study

Knowledge of the genetic landscape of a specific population group is vital for population-specific diagnosis and treatment of familial breast cancer. Although BRCA-related diagnostic testing has long been implemented in South Africa, the genotyping approach previously failed for the SA Indian population as it was based on other SA population groups. Because this population is uniquely admixed, the lack of population-specific data resulted in the implementation of comprehensive mutation screens for BRCA1/2. A total of 223 female patients were screened for clinically actionable variants. High-resolution melting analysis (HRMA) was used to screen 88 patients for DNA alterations in the coding and splice site boundaries of BRCA1 exons 2-9, BRCA1 exons 11-23, BRCA2 exons 2-9 and BRCA2 exons 12-27. The protein truncation test (PTT) was used to screen the three larger exons (BRCA1 exon 10 and BRCA2 exons 10 and 11) for protein termination changes. Multiplex ligation-dependent probe amplification (MLPA) was used to determine the presence of larger indels and possible copy number differences. Next Generation Sequencing (NGS) was performed on the remaining 135 samples. All potential variants were confirmed by performing Sanger DNA sequencing. The search revealed 28 different pathogenic heterozygotic variants, together with nine variants of unknown significance (VUS). The results suggested that the SA Indian population represents a different genetic admixture compared to that of mainland India, as only five pathogenic variants corresponded to those reported for mainland India. Familial breast cancer testing for SA Indian patients should therefore be performed as comprehensively as possible as the pathogenic variants seem to be family- rather than population-specific. Furthermore, predictive testing of family members will contribute to relieve the financial burden on the country's healthcare system, as increased surveillance and appropriate management could prevent disease.

Somatic tumor mutations in moderate risk cancer genes: Targets for germline confirmatory testing

Recent changes in oncology practice guidelines indicate that mutations in cancer susceptibility genes identified on tumor genomic profiling (TGP) should prompt confirmatory germline testing. Our study aimed to determine the proportion of patients with TGP-identified mutations in moderate risk breast and ovarian cancer genes who previously would not have been considered for germline testing. From January 2013 to September 2020, 7468 adult Stanford Health Care patients underwent TGP on solid tumor samples and 166 had TGP-identified mutations in moderate risk breast and ovarian cancer susceptibility genes (ATM, BRIP1, CHEK2, PALB2, RAD51C and RAD51D). Retrospective chart reviews were performed on 160 patients. Cases were analyzed to determine eligibility for germline testing using established NCCN criteria, and somatic and germline results were compared where both were available. Nearly half (45.3% [73/160]) of patients would not have been eligible for germline testing if not for a TGP-identified mutation in a moderate risk breast or ovarian cancer gene. Of the 64 cases that underwent germline testing, about half (51.5% [33/64]) had results that confirmed germline origin of the TGP finding. High rates of germline confirmation were found in PALB2 (100% [5/5]), ATM (40% [14/35]), CHEK2 (61.5% [8/13]), and BRIP1 (57.1% [4/7]). Our study shows that the presence of TGP-identified mutations in moderate risk breast and ovarian cancer genes increases eligibility for germline testing beyond those that would be eligible based largely on personal and family history criteria alone. Additionally, results of germline testing in these newly eligible cases supports that this expanded eligibility captures individuals with hereditary cancer syndromes that would not have otherwise been identified.

High incidence of PI3K pathway gene mutations in South Indian cervical cancers

Cervical cancer is the second most common cancer in India. The phosphatidylinositol-3 kinase (PI3K) signaling is one of the most commonly activated pathways in cancer and comprises key molecules commonly targeted in cancer therapy. This study analyzed six PI3K pathway gene mutations. We carried out targeted next-generation sequencing of six PI3K pathway genes (PIK3CA, PIK3R1, PTEN, AKT1, TSC2, and mTOR) in a total of 93 South Indian cervical cancer samples and confirmed them by sanger sequencing. The PI3K pathway gene mutations were observed in 54.8% (51/93) of the tumors and PIK3CA was the most mutated (34.4%, 32/93), followed by TSC2 (18.3%, 17/93), and PIK3R1 (14%, 13/93). The PIK3CA hotspot mutations E542K and E545K observed in this study were likely to disrupt the p110α-p85α interaction that could result in the PI3K pathway activation. We also found a few novel mutations in PIK3R1, PTEN, AKT1, TSC2, and mTOR genes while some of the tumors harbored multiple mutations in the genes of the PI3K pathway. The majority of the tumors were positive for high-risk HPV16/18 (60.7%). The high incidence of the PI3K pathway gene mutations observed in this study could be exploited for the therapeutic management of cervical cancers.

Identification of novel gene fusions in high-grade serous ovarian carcinoma: implications for tumorigenesis and targeted therapy

High-grade serous ovarian carcinoma (HGSOC) accounts for 70% of all ovarian cancer cases and 80% of related deaths. TP53 mutations are common; however, other driving genetic factors are not well understood. In this study, we used RNA sequencing to explore the genetic background of HGSOC in patients with unclear profiles. This study included 80 patients with a pathological diagnosis of HGSOC. RNA sequencing was performed to analyze gene expression and detect fusion. We identified 18 novel potential driver fusion gene candidates, including in-frame and frameshift fusions, in 80 patients with high-grade serous ovarian cancer (HGSOC). Of these, ST7-OT4::MET, STK24::DOCK9, GAB::PAK1, HDAC1::LCK, ESR1::LATS1, ZNF157::CDK16, NEK7::RP11-85M11.2, CAMKK1::R2RX1, HNRNPUL1::AXL, DYRK1A::GART, MAPKAPK2::DYRK3, and FER::GS1421I3.2 involved fusion partners harboring protein kinase domains. Notably, TAOK1::PIPOX and PSMD11::NLK were identified in the same case, similar to SH3PXD2A::BMPR1A and EIF3H::CAMK2D in another case. In addition, SLMAP::NTRK3 involves NTRK3, a known fusion partner. The remaining fusions, SWAP70::ZNF143, WDR25::YY1, and NR2F6::MYO9B, included partners with DNA-binding domains. This study identified candidate driver fusion genes and suggested new therapeutic targets for HGSOCs.

A pilot study of evaluation of a deep-learning-based homologous recombination deficiency assay in korean patients with ovarian high-grade serous carcinoma: Diagnostic performance and clinical implications

Homologous recombination deficiency (HRD)-related genetic mutations in ovarian high-grade serous carcinoma (HGSC) are known to be ethnic specific. Here, we assessed the diagnostic performance of HRD and its clinical implication in Korean HGSC patients using the SOPHiA DDM HRD Solution. Sixty-three ovarian cancer (OC) patients were enrolled, including 53 with HGSC and 10 with other subtypes. HRD status was determined by 28 homologous recombination repair (HRR) genetic sequencing and genomic scarring (GS) measurement. The GS was measured through low-pass whole-genome sequencing and quantified using the genomic integrity index (GII). HRD status was analyzed in 53 out of 63 OC patients (84.1 %). Among the 53 with HGSC, HRD results were available for 83.0 % (n = 44). Of these HGSC patients, 72.7 % (n = 32) were HRD-positive, including 15 with BRCA1/2 mutations (34.1 %) and 27 with GI-positive (61.4 %). In HGSC, HRD-positive status was associated with solid, pseudoendometrioid or transitional (SET) pattern (P = 0.015). Patients with positive HRD and high GII (>4.2) exhibited improved disease-free survival (DFS) and overall survival (OS) compared to those with negative HRD (P = 0.003 and 0.024, respectively) and low GII (P < 0.001 and P = 0.006, respectively). Multivariate analysis revealed a high GII as a better prognostic indicator for DFS and OS (P = 0.003 and 0.032, respectively). The HRD assay offers high diagnostic performance of HRD in Korean OC patients. Furthermore, the prognostic value of high GII and HRD, as well as an association with SET pattern and HRD was evident in HGSC.

Isolated multinodular goiter and follicular adenoma associated with a novel germline DICER1 variant: A benign presentation

Acute cardiac dysfunction in patients with ovarian cancer treated with Niraparib due to TFAM mutation: A case series and functional analysis

Ovarian cancer is a leading cause of gynecological cancer mortality. Despite Niraparib's efficacy in increasing progression-free survival for recurrent ovarian cancer, its potential cardiotoxic effects are underexplored. We performed a case series analysis involving two postmenopausal sisters who developed heart failure subsequent to Niraparib therapy for recurrent ovarian cancer. Utilizing targeted next-generation sequencing (NGS), we identified a novel missense mutation c.98T>A in Mitochondrial Transcription Factor A (TFAM) gene, which was subsequently confirmed by Sanger sequencing. To investigate the cardiotoxic effects of Niraparib, we generated human induced pluripotent stem cell-derived cardiomyocytes (hiPSCCMs) carrying the identified mutation. The impact of the mutation on gene expression and protein levels was evaluated through real-time PCR and Western blot analyses. Two postmenopausal sisters treated with Niraparib suffered significant cardiac dysfunction. NGS identified a novel c.98T>A variant in TFAM gene, resulting in a missense mutation. HEK293T cells transfected with mutant plasmids demonstrated normal expression of full-length TFAM mRNA and protein. hiPSCCMs model revealed the variant alone did not induce cardiomyopathy. However, it predisposed to Niraparib-induced cardiomyopathy-like toxicity, mediated by metabolic dysregulation and increased cellular apoptosis CONCLUSION: Our study revealed a novel TFAM variant which might induce potential cardiovascular toxicity of anticancer Niraparib therapies.

Germline APC I1307K and MITF E318K variants in a patient with high-grade serous ovarian carcinoma: A case report

We report the case of a 76‑year‑old woman with high‑grade serous ovarian carcinoma (HGSOC) who was found to carry germline variants in APC I1307K and MITF E318K. Although neither variant is an established contributor to ovarian cancer risk, their co‑occurrence raises the possibility of polygenic or modifier effects on tumor susceptibility. The APC I1307K allele is a founder variant linked to increased colorectal cancer risk through the creation of a hypermutable region that predisposes to somatic mutations rather than classical tumor‑suppressor inactivation. In contrast, MITF E318K is a gain‑of‑function variant associated with melanoma and renal cell carcinoma, acting through altered transcriptional regulation that promotes cell proliferation and survival. While these genes do not interact directly, both converge on signaling pathways-WNT/β‑catenin, MAPK/ERK, and PI3K/AKT-that are widely implicated in ovarian carcinogenesis. There is a possibility that HGSOC in this patient is sporadic and unrelated to these two variants. Nevertheless, the case underscores the importance of comprehensive germline testing and highlights potential, yet underexplored, genetic interactions that may influence ovarian cancer risk. To our knowledge, this represents the first reported case of HGSOC in a patient harboring both variants, offering a hypothesis‑generating observation for future investigation.

Ossifying low grade endometrial stromal sarcoma with PHF1-BRD8 fusion

Low-grade endometrial stromal sarcoma and ossifying fibromyxoid tumors are two types of mesenchymal tumors that share no similarities in terms of site, sex, and morphological characteristics. They are rare, low grade tumors of uncertain lineage, with no definite immunological markers. Interestingly, a common PHF1 gene- related rearrangement was observed in these two tumors. Here, we report a case of endometrial stromal sarcoma with distinct ossification. Microscopically, the tumor is composed of bland-looking ovoid cells with low cellularity in the fibromyxoid stroma. Foci of metaplastic bone formation were noted. Using a combination of FISH, transcriptome sequencing, and molecular techniques, we identified a new PHF1-BRD8 fusion transcript, which was previously described, but in its reciprocal fusion form. This case expands the current understanding of low-grade endometrial stromal sarcoma and emphasizes the importance of molecular characterization of unique fusion, which may be related to its distinct morphological features and the possibly chemosensitive target.

High-resolution copy number analysis of clear cell endometrial carcinoma

Uterine cancer is the 6th leading cause of cancer death amongst American women. Most uterine cancers are endometrial carcinomas (ECs), which are classified into histological subtypes including endometrioid, serous, and clear cell ECs. Somatic copy number alterations (SCNAs) are frequent in serous EC, infrequent in endometrioid ECs, and poorly defined in clear cell ECs. The purpose of this study was to evaluate the occurrence of SCNAs in clinically diagnosed clear cell ECs. Paired tumor-normal DNAs for 51 ECs were hybridized to Illumina Infinium HumanHap650Y or Human660W-Quad Beadchips. Copy number calls were made using the Hidden Markov Model based SNP-FASST2 segmentation algorithm within Nexus Copy Number software (v.6.1). High-level SCNAs were defined as gain of ≥5 copies or homozygous deletion, both <10Mb. GISTIC 1.0, in Nexus, was used to identify statistically significant SCNAs, corrected for multiple testing. One or more high-level SCNAs were detected in 50% of 6 clear cell ECs, 78.6% of 28 serous ECs, and 17.6% of 17 endometrioid ECs. A positive association was found between high-level SCNAs and TP53 mutation across ECs (two-tailed p value<0.0001). Classifying tumors according to POLE, MSI, and TP53 status yielded four molecular subgroups; copy number altered tumors were more frequent in the TP53-mutated subgroup (95.8%) than in the unspecified subgroup (22.2%), and absent from the POLE and MSI subgroups. In conclusion, our study provides evidence of inter-tumor heterogeneity in the extent to which SCNAs occur in clinically diagnosed clear cell EC, and across molecular subgroups of EC. The co-occurrence of high-level SCNAs and TP53 mutations in some clear cell ECs is consistent with the view that a subset of clinically diagnosed clear cell ECs have molecular similarities to serous ECs.

Genetic silencing of CDC6 via AAV2-Delivered shRNA as a novel cancer genetics–based therapy for cervical carcinoma

Cell division cycle 6 (Cdc6) is an oncogenic driver in cervical cancer, whose dysregulation accelerates S-phase entry and promotes genomic instability. As a key replication licensing factor, its overexpression creates a cancer-specific vulnerability, making it a promising therapeutic target. To evaluate whether silencing Cdc6 via an adeno-associated virus serotype 2 (AAV2)-delivered shRNA can selectively inhibit cervical cancer growth while sparing normal cells. We constructed an AAV2 vector encoding short hairpin RNA (shRNA) targeting Cdc6 and validated its efficacy in vitro using multiple cervical cancer cell lines and an immortalized epithelial cell line (HaCaT). Functional assays assessed cell cycle progression, apoptosis, and DNA damage. Antitumor efficacy was further assessed in xenograft mouse models. AAV2-shCdc6 transduction efficiently silenced Cdc6 expression, leading to G2/M phase arrest, increased γ-H2AX expression, and significant apoptosis in cervical cancer cells. In contrast, normal HaCaT cells exhibited only S-phase arrest without apoptosis. In vivo, AAV2-shCdc6 treatment significantly inhibited tumor growth in xenograft models without observable systemic toxicity. AAV2-mediated Cdc6 knockdown selectively targets cervical cancer by exploiting a defined genetic vulnerability. This cancer genetics-based strategy offers a precise and well-tolerated approach for cervical cancer therapy.

Prognostic impact of molecular profiles and molecular signatures in clear cell ovarian cancer

Ovarian Clear cell carcinomas (OCCC) are characterized by low response to chemotherapy and a poor prognosis in advanced stages. Several studies have demonstrated that OCCC are heterogenous entities. We have earlier identified four molecular profiles based on the mutational status of ARID1A and PIK3CA. In this study we aimed to examine the association between molecular profiles, Tumor Mutational Burden (TMB), and molecular signatures with the clinical outcome in OCCC METHODS: We identified 55 OCCC cases with corresponding data and biological tissue samples in the Danish Gynecological Cancer Database during 2005-2016. Mutational profiling and TMB were performed using the Oncomine Tumor Mutational Load Assay. Chi-square and Cox regression analyses were used. P-values < 0.05 were considered statistically significant. Mutations in the PIK3CA gene (p=0.04) and low TMB (p=0.05) were associated with disease progression. In multivariate analyses adjusted for stage, patients with tumor mutations in the ARID1A and/or PIK3CA genes had a significantly impaired Progression Free Survival (PFS) and Overall Survival (OS) compared to patients who were wildtype ARID1A and PIK3CA (undetermined subgroup) (HR= 5.42 and HR= 2.77, respectively). High TMB status was associated with an improved PFS (HR= 0.36) and OS (HR= 0.46). A trend towards an improved PFS in patients with APOBEC enrichment was observed (HR 0.45). TMB-High was associated with decreased risk of progression and with an improved PFS and OS. Furthermore, OCCC with mutations in either ARID1A and/or PIK3CA genes had a significantly impaired prognosis compared to the undetermined subgroup in stage adjusted analyses.

Study on the correlation between BRCA1 gene polymorphism and hrHPV infection in cervical precancerous lesions

Cervical squamous intraepithelial lesions are precancerous lesions caused by high-risk subtypes of human papillomavirus (HPV). The development and prognosis of these lesions may be impacted by host genetics. Sanger sequencing was applied to sequence the breast cancer susceptibility gene (BRCA1) exons in exfoliated cervical cells. Fifteen single nucleotide polymorphisms (SNPs) were identified in the entire exon of BRCA1. It was found that there were 8 missense mutations, 1 nonsense mutation, 4 synonymous mutations, and 2 mutations not located in the protein-coding regions. Functional prediction of BRCA1 missense and synonymous mutation sites was performed using PolyPhen-2, ESEFinder3.0, and SIFT online software. The rs39812263 alteration in the BRCA1 gene was found to be significantly different by the sequencing. A significant difference was observed in the alterations of BRCA1 gene rs398122630 between hrHPV and thin- prep cytology test (TCT) groups (p < 0.05), a negative correlation was observed with both hrHPV and TCT. The genotype and allele frequencies of the BRCA1 gene rs398122630 were significantly different from those of the control group (p < 0.05). Rs398122630 may play a protective role in the progression of cervical cancer. This site is a nonsense mutation, which may lead to the premature termination of protein translation. Subsequently, we queried the Gene Expression Omnibus (GEO) and found that the expression of BRCA1 gene RNA gradually increased in cervical normal epithelium, high-grade cervical intraepithelial neoplasia (CIN), and cervical squamous cell carcinoma (CSCC). Lentiviral vectors were used to construct stable cell lines with BRCA1 (breast cancer susceptibility gene 1) knockout and overexpression. The scratch healing rate of HeLa cells with BRCA1 knockout was significantly higher than that of the negative control group (P < 0.05), while the difference in scratch healing rate in the overexpression group was not statistically significant. Compared to the control group, the proportion of cells in the G1 phase increased in the BRCA1 downregulated group (KD1), while the proportion of cells in the G1 phase decreased in the overexpression group (P < 0.05). The percentage of cells in the S phase decreased in the downregulated group compared to the control group (P < 0.05), and the proportion of cells in the G2 phase increased in the overexpression group compared to the control group (P < 0.05), BRCA1 may be involved in the migration and cell cycle of HeLa cells.

Pathogenicity reclassification of two BRCA1/BRCA2 exonic duplications after identification of genomic breakpoints and tandem orientation

The genomic consequence and clinical interpretation of large duplications are difficult to infer without determining the location and orientation of the duplicated sequence. We aimed to characterize two intragenic duplications detected in two hereditary breast and ovarian cancer syndrome (HBOC) families, namely BRCA1 exon 4 to 6 and BRCA2 exon 17 to 18, previously detected by multiplex ligation probe amplification and initially classified as variants of unknown significance. Using long range PCR, with duplication-specific primers, we were able to ascertain the genomic breakpoints and observed that the two rearrangements occurred in tandem and in direct orientation. The BRCA1 c.134+440_441+870dup and BRCA2 c.7806-2083_8332-1512dup duplications here identified are predicted to cause frameshifts that create a premature stop codon and were reclassified as pathogenic. Furthermore, both families present phenotypic traits typical of HBOC syndrome. We also observed that the genomic breakpoints of these two duplications occurred within highly homologous Alu elements. Concluding, we characterized two in tandem BRCA1 and BRCA2 duplications that likely occurred by Alu-mediated homologous recombination, allowing identification of the underlying cause of the HBOC syndrome in these families.

Enhancement of MDM2 inhibitory effects through blocking nuclear export mechanisms in ovarian cancer cells

Over 90% of ovarian cancer cells exhibit p53 mutations or inactivation. In addition, p53 is exported outside of the nucleus by exportin-1 (XPO1), a protein that mediates the nuclear export of several cancer suppressor proteins. Overexpression of XPO1 is associated with resistance to chemotherapy, leading to poor prognosis in various cancers. The MDM2 inhibitor, RG-7388, is a known reactivator of p53 and has been tested with high interest as a therapeutic agent for cancer treatment. In addition, Selinexor, which is a second-generation selective inhibitor of nuclear export (SINE), is known to cause an accumulation of p53 in the nucleus and is also being explored as a therapy potentiating agent in combination treatments. This study was conducted to assess the efficacy of RG-7388 in combination with Selinexor for treating ovarian cancer. A combination of Selinexor and RG-7388 treatments was able to reduce the cell viability compared to individual treatments. In addition, the combination treatment revealed significant up-regulation of several cancer suppressor proteins in the whole lysate, cytoplasm, and nucleus. Finally, our results confirm that the combination of Selinexor with RG-7388 can induce a caspase-mediated apoptotic mechanism via up-regulation of p53 and p21.

Discovery of BRCA1/BRCA2 founder variants by haplotype analysis

A significant number of hereditary breast or ovarian cancers are caused by germline variants, mostly BRCA1/BRCA2 genes. Because genetic predispositions vary by ethnicity, several studies have reported founder variants of BRCA1/BRCA2 genes. Such founder variants were reported primarily based on their relevant population frequencies. We reviewed the variant data relating to BRCA1 and BRCA2 genes from January 2012 to March 2019 at Samsung Medical Center, Seoul, Korea. Among the cases with pathogenic variants (PVs) or likely pathogenic variants (LPVs), we defined recurrent variants as those found in more than five unrelated patients. Using single nucleotide polymorphisms, we analyzed patient haplotypes. There were 14 recurrent variants in the BRCA1 gene and seven variants in the BRCA2 gene. Of note, three variants in each gene were primarily detected in Korean populations. Among them, the c.5339T>C (p.Leu1780Pro) BRCA1 variant had a long block sized 74.5 kb. In BRCA2, the c.1399A>T (p.Lys467*) variant had a long block sized 35.5 kb. We suggest that BRCA1 c.5339T>C (p.Leu1780Pro) and BRCA2 c.1399A>T (p.Lys467*) are founder variants of the Korean population. These two recurrent variants were ethnicity-prevalent, primarily found in Korean populations, and the sizes of the linkage disequilibrium blocks are longer than others.

Distinct somatic DICER1 hotspot mutations in three metachronous ovarian Sertoli-Leydig cell tumors in a patient with DICER1 syndrome

Potential role of microRNAs in the treatment and diagnosis of cervical cancer

Invasive cervical cancer is a leading cause of cancer death in women worldwide. miRNA may have roles in the pathogenesis of cervical cancer based on the increases or decreases in several specific miRNAs found in patients with this disease. The clinical outcomes of cervical cancer vary significantly and are difficult to predict. One unique challenge in cervical cancer biomarker study is the lack of large amounts of tumor tissues because most cervix biopsies are relatively small. The miRNA can affect HPV DNA replication shed more light on our understanding of the HPV life cycle and the mechanistic underpinnings of HPV induced oncogenesis. Also, miRNA processing proteins may be involved during early cervical cancer development. The E6 and E7 oncoproteins of HPV could induce the overexpression of DNA methyltransferase enzymes, which can catalyze the aberrant methylation of protein-coding and miRNA genes. Methods for diagnosis of cervical cancer include analysis of changes in the levels of specific miRNAs in serum and determination of aberrant hypermethylation of miRNAs. miRNAs are related on drug resistance and may be useful in combination therapy for cervical cancer with other drugs.

TCGA dataset screening for genes implicated in endometrial cancer using RNA-seq profiling

The molecular basis of the mechanism and the potential biomarkers of endometrial cancer (EC) remain to be studied. In the present study, we hypothesized that the comprehensive characterization of transcriptional changes in EC could help achieve this aim. By taking advantage of RNA-seq data from The Cancer Genome Atlas, we determined the profile of differently expressed genes (DEGs) between EC tumor tissues and normal samples. On this basis, we performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways enrichment analyses. The interacting partners for each of the DEGs were explored and a protein-protein interaction network was constructed. Consequently, 10 hub genes were identified and their association with mortality in EC patients was investigated. The genes, AURKA, CENPA, and KIF2C, were found to be potential biomarkers for EC with a significant prognostic effect. Our work provided a basis for EC studies in both biological and clinical settings.