Identification of Candidate Genes Associated with Susceptibility to Ovarian Clear Cell Adenocarcinoma Using cis-eQTL Analysis

Kim, Jihye; Chung, Joon‐Yong; Hwang, Jae Ryoung; Lee, Yoo-Young; Kim, Tae-Joong; Lee, Jeong‐Won; Kim, Byoung-Gie; Bae, Duk-Soo; Choi, Chel Hun; Hewitt, Stephen M.

doi:10.3390/jcm9041137

Cited by 3 publications

(2 citation statements)

References 43 publications

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“…ZNF707 has recently been Kim et al (2020) identified as highly overexpressed in the Japanese population. High expression has also been shown in kidney and luminal B cancer patients Machnik et al (2019) which suggests that ZNF707 could be involved in the development of cancer in general, regardless of the tissue.…”

Section: Highly Connected Genes and Their Possible Relationship With ...mentioning

confidence: 99%

The Role of Copy Number Variants in Gene Co-Expression Patterns for Luminal B Breast Tumors

2022

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Gene co-expression networks have become a usual approach to integrate the vast amounts of information coming from gene expression studies in cancer cohorts. The reprogramming of the gene regulatory control and the molecular pathways depending on such control are central to the characterization of the disease, aiming to unveil the consequences for cancer prognosis and therapeutics. There is, however, a multitude of factors which have been associated with anomalous control of gene expression in cancer. In the particular case of co-expression patterns, we have previously documented a phenomenon of loss of long distance co-expression in several cancer types, including breast cancer. Of the many potential factors that may contribute to this phenomenology, copy number variants (CNVs) have been often discussed. However, no systematic assessment of the role that CNVs may play in shaping gene co-expression patterns in breast cancer has been performed to date. For this reason we have decided to develop such analysis. In this study, we focus on using probabilistic modeling techniques to evaluate to what extent CNVs affect the phenomenon of long/short range co-expression in Luminal B breast tumors. We analyzed the co-expression patterns in chromosome 8, since it is known to be affected by amplifications/deletions during cancer development. We found that the CNVs pattern in chromosome 8 of Luminal B network does not alter the co-expression patterns significantly, which means that the co-expression program in this cancer phenotype is not determined by CNV structure. Additionally, we found that region 8q24.3 is highly dense in interactions, as well as region p21.3. The most connected genes in this network belong to those cytobands and are associated with several manifestations of cancer in different tissues. Interestingly, among the most connected genes, we found MAF1 and POLR3D, which may constitute an axis of regulation of gene transcription, in particular for non-coding RNA species. We believe that by advancing on our knowledge of the molecular mechanisms behind gene regulation in cancer, we will be better equipped, not only to understand tumor biology, but also to broaden the scope of diagnostic, prognostic and therapeutic interventions to ultimately benefit oncologic patients.

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Section: Highly Connected Genes and Their Possible Relationship With ...mentioning

confidence: 99%

The Role of Copy Number Variants in Gene Co-Expression Patterns for Luminal B Breast Tumors

2022

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“…The high frequencies of neoantigens per somatic mutation (neoAg frequencies), rather than overall mutational load or number of predicted neoantigens per se, is an independent prognostic factor for decreased clinical outcome and low expression of immunity-associated genes 219 . Up-regulated rs4873815-TT/ZNF707, ARL4C, mitochondrial superoxide dismutase (SOD2) expression are predictive biomarkers for worse prognosis in OCCC 201 , 220 , 221 . And NAC1/FASN expression is a biomarker of poor outcome for patients treated with conventional platinum-based chemotherapy in OCCC by modulates sensitivity of ovarian cancer cells to cisplatin 203 .…”

Section: Prognosismentioning

confidence: 99%

Updates of Pathogenesis, Diagnostic and Therapeutic Perspectives for Ovarian Clear Cell Carcinoma

Zhu¹,

Xu²,

Zhang³

et al. 2021

J. Cancer

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Ovarian clear cell carcinoma (OCCC) is a special pathological type of epithelial ovarian carcinoma (EOC) and has a high prevalence in Asia without specific molecular subtype classification. Endometriosis is a recognized precancerous lesion that carries 3-fold increased risk of OCCC. Ovarian endometrioid carcinoma, which also originates from endometriosis, shares several features with OCCC, including platinum resistance and younger age at diagnosis. Patients with OCCC have about a 2.5 to 4 times greater risk of having a venous thromboembolism (VTE) compared with other EOC, and OCCC tends to metastasize through lymphatic vesicular and peritoneal spread as opposed to hematogenous metastasis. There is only mild elevation of the conventional biomarker CA125. Staging surgery or optimal cytoreduction combined with chemotherapy is a common therapeutic strategy for OCCC. However, platinum resistance commonly portends a poor prognosis, so novel treatments are urgently needed. Targeted therapy and immunotherapy are currently being studied, including PARP, EZH2, and ATR inhibitors combined with the synthetic lethality of ARID1A-dificiency, and MAPK/PI3K/HER2, VEGF/bFGF/PDGF, HNF1β, and PD-1/PD-L1 inhibitors. Advanced stage, suboptimal cytoreduction, platinum resistance, lymph node metastasis, and VTE are major prognostic predictors for OCCC. We focus on update pathogenesis, diagnostic methods and therapeutic approaches to provide future directions for clinical diagnosis and treatment of OCCC.

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Inferring DNA methylation in non-skeletal tissues of ancient specimens

Mathov,

Nissim-Rafinia,

Leibson

et al. 2024

Nat Ecol Evol

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Identification of Candidate Genes Associated with Susceptibility to Ovarian Clear Cell Adenocarcinoma Using cis-eQTL Analysis

Cited by 3 publications

References 43 publications

The Role of Copy Number Variants in Gene Co-Expression Patterns for Luminal B Breast Tumors

The Role of Copy Number Variants in Gene Co-Expression Patterns for Luminal B Breast Tumors

Updates of Pathogenesis, Diagnostic and Therapeutic Perspectives for Ovarian Clear Cell Carcinoma

Inferring DNA methylation in non-skeletal tissues of ancient specimens

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