Genome-wide DNA copy number analysis in clonally expanded human ovarian cancer cells with distinct invasive/migratory capacities

Li, Lei; Bai, Huimin; Yang, Jiaxin; Cao, Dongyan; Shen, Keng

doi:10.18632/oncotarget.14767

Cited by 7 publications

(9 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Numerous patient cohorts have enabled the precise characterisation of CNAs that predict clinical outcomes in high-grade serous ovarian cancer 35 , 36 . Moreover, in cell model study, CNAsdiffered between matched highly and minimally invasive/migratory subclones of ovarian cancer 37 . Also, in endometrial cancer, copy number high in a tumour have shown the poorest disease-free survival 27 .…”

Section: Discussionmentioning

confidence: 99%

Massively parallel sequencing of cell-free DNA in plasma for detecting gynaecological tumour-associated copy number alteration

Nakabayashi

Kawashima

Yasuhara

et al. 2018

Sci Rep

View full text Add to dashboard Cite

The discovery of circulating tumour DNA molecules created a paradigm shift in tumour biomarkers as predictors of recurrence. Non-invasive prenatal testing (NIPT) to detect circulating cell-free foetal DNA in maternal plasma is increasingly recognised as a valuable substitute to perceive foetal copy number variation (CNV). This study aimed to determine whether the copy number detection in plasma samples using NIPT platform could be used as a prognostic biomarker in patients with gynaecological cancer. We conducted a prospective study using samples containing preoperative plasma from 100 women with gynaecological cancers. Samples were randomly rearranged and blindly sequenced using a low-coverage whole-genome sequencing plasma DNA, NIPT platform. The NIPT pipeline identified copy number alterations (CNAs) were counted in plasma as a gain or loss if they exceeded 10 Mb from the expected diploid coverage. Progression-free survival (PFS) and overall survival (OS) were analysed according to the presence of CNA in plasma using Kaplan–Meier analyses. The NIPT pipeline detected 19/100 cases of all gynaecological cancers, including 6/36 ovarian cancers, 3/11 cervical cancers, and 10/53 endometrial cancers. Patients with CNA in plasma had a significantly poorer prognosis in all stages concerning PFS and OS. Therefore, low-coverage sequencing NIPT platform could serve as a predictive marker of patient outcome.

show abstract

Section: Discussionmentioning

confidence: 99%

Massively parallel sequencing of cell-free DNA in plasma for detecting gynaecological tumour-associated copy number alteration

Nakabayashi

Kawashima

Yasuhara

et al. 2018

Sci Rep

View full text Add to dashboard Cite

show abstract

“…It is well known that ccRCC is characterized by the presence of several SCNAs, as are other cancers, including gastric, 20 colorectal, 21 and ovarian cancers 22 . Data show that multiple SCNAs may enhance tumor invasion and metastasis.…”

Section: Discussionmentioning

confidence: 99%

“…and ovarian cancers. 22 Data show that multiple SCNAs may enhance tumor invasion and metastasis. ccRCC, however, can invade and/or metastasize irrespective of the low frequency of SCNAs, suggesting that the accumulation of SCNAs might be a minor facilitator of cancer invasion/metastasis in a subset of cancers.…”

Section: Differences In the Scna Patterns Between Subgroups 1 And 2mentioning

confidence: 98%

Comprehensive analysis of somatic copy number alterations in clear cell renal cell carcinoma

Tsuyukubo

Ishida

Osakabe

et al. 2020

Molecular Carcinogenesis

View full text Add to dashboard Cite

Somatic copy number alterations (SCNAs) are important biological characteristics that can identify genome‐wide alterations in renal cell carcinoma (RCC). Recent studies have shown that SCNAs have potential value for determining the prognosis of RCC. We examined SCNAs using the Affymetrix platform to analyze samples from 59 patients with clear cell RCCs (ccRCCs) including first cohort (30 cases) and second cohort (validation cohort, 29 cases). We stratified SCNAs in the ccRCCs using a hierarchical cluster analysis based on SCNA types, including gain, loss of heterozygosity (LOH), copy neutral LOH, mosaic, and mixed types. In this way, the examined two cohorts were categorized into two subgroups (1 and 2). Although the frequency of mixed type was higher in subgroup 1 than in subgroup 2 in the two cohorts, the association did not reach statistical significance. There was a significant difference in the frequency of metachronous metastasis between subgroups 1 and 2 (subgroup 2 > 1). In addition, subgroup 2 was retained in multivariate analysis of both cohorts. We examined whether there were specific alleles differing between subgroups 1 and 2 in both cohorts. We found that there was indeed a statistically significant difference in the 3p mixed types. Among the 3p mixed type, we found that 3p24.3 mixed type was inversely correlated with the presence of metachronous metastasis in ccRCC. The association was also retained in multivariate analysis in second cohort. We suggest that the 3p24.3 mixed type may be a novel marker to predict a favorable prognosis in ccRCC.

show abstract

“…Overexpression of CXCR4 was significantly associated with cisplatin-based chemotherapy resistance and it could be a prognostic factor in epithelial OC [34]. PRPF19 was one of the seven genes with different copy number alterations between matched highly and minimally invasive/migratory OC cell subclones, which could be specifically targeted for the treatment and prognosis of advanced OC [35]. High expression of CXCL10 was associated with almost doubled overall survival and it was confirmed as an independent validation set, which supported the notion that CXCL10 exerted a tumor-suppressive function in OC [36].…”

Section: Discussionmentioning

confidence: 99%

Survival-associated transcriptome analysis in ovarian cancer

Xu¹,

Zhou²,

Wang³

et al. 2020

EJGO

View full text Add to dashboard Cite

Purpose of investigation: Ovarian Cancer (OC) is one of the most lethal gynecologic cancers worldwide. Despite the standard treatment, including radical resection, systemic chemotherapy, and targeted drugs for patients, survival rates remain low. This study provides new ideas for the diagnosis and treatment of Ovarian Cancer. Material and Methods: We performed Kaplan-Meier analysis on the transcriptome of Ovarian Cancer based on RNA-Seq data from The Cancer Genome Atlas (TCGA). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment were used for pathway and functional enrichment. Protein-protein interaction (PPI) network was constructed and visualized by SRING and Cytoscape. Results: A total of 1693 genes associated with survival were identified. The Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology enrichment analysis revealed that these selected genes were differently enriched in numerous functional pathways. The top ten hub genes (RIPK4, HSPA8, FOS, STAT1, CD40LG, FGF2, RAC1, CXCR4, PRPF19, and CXCL10) were identified in our PPI network. Three highly connected cluster modules were differently enriched in several functional pathways. Conclusion: These key biomarkers in Ovarian Cancer may have diagnostic and therapeutic value in the future.

show abstract

Genome-wide DNA copy number analysis in clonally expanded human ovarian cancer cells with distinct invasive/migratory capacities

Cited by 7 publications

References 64 publications

Massively parallel sequencing of cell-free DNA in plasma for detecting gynaecological tumour-associated copy number alteration

Massively parallel sequencing of cell-free DNA in plasma for detecting gynaecological tumour-associated copy number alteration

Comprehensive analysis of somatic copy number alterations in clear cell renal cell carcinoma

Survival-associated transcriptome analysis in ovarian cancer

Contact Info

Product

Resources

About