Meta-analysis of integrated ChIP-seq and transcriptome data revealed genomic regions affected by estrogen receptor alpha in breast cancer DOI Creative Commons
Zeynab Piryaei, Zahra Salehi, Esmaeil Ebrahimie

et al.

BMC Medical Genomics, Journal Year: 2023, Volume and Issue: 16(1)

Published: Sept. 15, 2023

Abstract Background The largest group of patients with breast cancer are estrogen receptor-positive (ER + ) type. receptor acts as a transcription factor and triggers cell proliferation differentiation. Hence, investigating ER-DNA interaction genomic regions can help identify genes directly regulated by ER understand the mechanism action in progression. Methods In present study, we employed workflow to do meta-analysis ChIP-seq data lines stimulated 10 nM 100 E2. All publicly available sets were re-analyzed same platform. Then, known unknown batch effects removed. Finally, was performed obtain meta-differentially bound sites estrogen-treated MCF7 compared vehicles (as control). Also, results T47D for more precision. Enrichment analyses also find functional importance common associated among both lines. Results Remarkably, POU5F1B, ZNF662, ZNF442, KIN, ZNF410 , SGSM2 factors recognized but not individual studies. resulted candidacy pathways previously reported cancer. PCGF2, HNF1B, ZBED6 predicted through enrichment analysis genes. addition, comparing RNA-seq showed that many affected up-regulated. Conclusion line leads identification new binding have been reported. their revealed terms involved development which should be examined future vitro vivo

Language: Английский

Let-7b-5p sensitizes breast cancer cells to doxorubicin through Aurora Kinase B DOI Creative Commons
Murat Kaya, Asmaa Abuaısha, İlknur Süer

et al.

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(1), P. e0307420 - e0307420

Published: Jan. 9, 2025

MicroRNAs (miRNAs) are small, non-coding RNAs that regulate the expression level of target genes in cell. Breast cancer is responsible for majority cancer-related deaths among women globally. It has been proven deregulated miRNAs may play an essential role progression breast cancer. shown many cancers, including cancer, aberrant be associated with drug resistance. This study investigated effect let-7b-5p, detected by bioinformatics methods, on Dox resistance through Aurora Kinase B ( AURKB ) gene. In silico analysis using publicly available miRNA expression, GEO datasets revealed let-7b-5p significantly downregulated BC. Further studies potential targets was most negatively correlated and closely Expression via quantitative PCR confirmed upregulated tissue samples. Later, functional conducted MCF-10A, MCF-7, MDA-MB-231 cell lines demonstrated inhibits cells sensitizes them to conclusion, it let-7b-5p/ axis significant disruption this contribute trigger

Language: Английский

Citations

0
Elevated expression of let-7b-3p enhances aggressiveness of larynx squamous cell carcinoma cells DOI Open Access
Murat Kaya, Esra Güzel, İlknur Süer

et al.

Anatolian Current Medical Journal, Journal Year: 2025, Volume and Issue: 7(1), P. 27 - 32

Published: Jan. 10, 2025

Aims: Larynx squamous cell carcinoma (LSCC) is the second most common head and neck malignancy. While let-7b-3p has been shown to have a role in cancer progression malignancies, there no research examining association between LSCC let-7b-3p. This study aimed investigate expression status of potential roles this microRNA (miRNA) LSCC. Methods: Using quantitative real-time polymerase chain reaction (qRT-PCR), we examined let-7b3p 36 samples neighboring normal tissues. Then, miRNA mimic was transfected into Hep-2 cells via lipofectamine 2000 reagents. Cell viability determined using detection (CVDK-8) kit, migration evaluated with scratch assay. To identify differentially expressed genes (DEGs) larynx GSE137308 GSE130605 datasets were downloaded reanalyzed Gene Expression Omnibus (GEO2R) tool. Potential target investigated prediction functional annotation database (miRDB). Shared geo miRDB results identified relationship these literature. Results: We demonstrated that levels significantly upregulated tumor tissues comparison corresponding Mimic transfection enhanced proliferation migration. In vitro bioinformatics analysis showed overexpression can enhance through MYBPC1. Conclusion: It let-7b-3p/MYBPC1 axis could potentially affect process. Let-7b-3p be biomarker for LSCC, therefore, let-7b-3p/ MYBPC1/LSCC should elucidated new studies.

Language: Английский

Citations

0
Circ_0022587 Regulates Tumor Properties of Human Breast Cancer Cells by Targeting miR‐335‐5p/Phosphoglycerate Kinase 1 Pathway DOI

Dian Yin,

Yang Li, Ying Chen

et al.

Journal of Biochemical and Molecular Toxicology, Journal Year: 2025, Volume and Issue: 39(3)

Published: March 1, 2025

ABSTRACT Increasing research indicates that circular RNAs (circRNAs) affect the development of breast cancer (BC) through specific molecular mechanisms. However, there is no data regarding role circ_0022587 in BC progression. This investigation aims to reveal mechanism regulating malignant progression BC. The study recruited 27 patients undergoing a surgical operation Nantong First People's Hospital, Affiliated Hospital 2 University. Quantitative real‐time polymerase chain reaction and RNase R degradation assay were used verify structure circ_0022587. 3‐(4,5‐Dimethylthazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide, 5‐Ethynyl‐2’‐deoxyuridine, flow cytometry analysis, transwell tube formation assays detect viability, proliferation, apoptosis, invasion tumor angiogenesis cells, respectively. Glycolysis was evaluated by glycolysis metabolism assays. associations among miR‐335‐5p, phosphoglycerate kinase 1 (PGK1) identified dual‐luciferase reporter RNA immunoprecipitation. effects knockdown on growth xenograft nude mouse model positive expression rates PGK1, nuclear proliferation marker matrix metalloprotein 9 analyzed immunohistochemistry results showed upregulated tissues cells. Downregulation inhibited cell ability, glycolysis, promoted apoptosis. Overexpression relieved effect inhibitor (2‐Deoxy‐D‐glucose, 2‐DG) glucose consumption, lactate production, ATP/ADP ratios. In addition, interacted with miR‐335‐5p inhibitors attenuated silencing‐induced bound PGK1 overexpression mimics‐induced Further, vivo. above demonstrate regulates absorbing thereby affecting development, which may provide new therapeutic strategy for study's novelty innovative potential lie its discovery regulatory involving miR‐335‐5p/PGK1 pathway clinical relevance. These aspects contribute expanding knowledge base could potentially lead improved strategies future.

Language: Английский

Citations

0
Overexpression of CDC25A, AURKB, and TOP2A Genes Could Be an Important Clue for Luminal A Breast Cancer DOI Creative Commons
Murat Kaya, Asmaa Abuaısha, İlknur Süer

et al.

Meme sağlığı dergisi/Meme sağlığı dergisi, Journal Year: 2024, Volume and Issue: unknown, P. 284 - 291

Published: Sept. 26, 2024

Breast cancer (BC) is highly heterogeneous and one of the most common cancers. Luminal A (LUM A) a subtype BC with better prognosis than other subtypes. The molecular mechanisms underlying initiation progression LUM are still unclear. Big data generated from microarray sequencing systems can be re-analyzed, especially help various

Language: Английский

Citations

2
CDR1as/miR-7-5p/IGF1R axis contributes to the suppression of cell viability in prostate cancer DOI Creative Commons
Murat Kaya, İlknur Süer, Abdulmelik Aytatli

et al.

Turkish Journal of Biochemistry, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 5, 2024

Abstract Background Prostate cancer is the most frequently diagnosed male and fifth highest cause of mortality in men. CDR1as has played an essential role growth several malignancies. However, its significance progression prostate not been investigated. We aimed to investigate mechanism development identify a new target for diagnostics treatment. Methods siRNA miR-7-5p mimic were transfected into PC3 DU145 PCa cell lines their effects on cellular processes Cell viability was measured by WST-8 assay. The and/or migration detected using scratch-wound apoptotic capacity cells evaluated Caspase-3 kit. potential targets defined via silico tools. mRNA protein expression levels IGF1R EIF4E qRT-PCR western blot assays, respectively. matching between luciferase reporter Results Inhibiting or restoring reduced proliferation while increasing apoptosis. Silencing elevated decreasing IGF1R. Conclusions functions as sponge, promoting tumor development.

Language: Английский

Citations

0
Meta-analysis of integrated ChIP-seq and transcriptome data revealed genomic regions affected by estrogen receptor alpha in breast cancer DOI Creative Commons
Zeynab Piryaei, Zahra Salehi, Esmaeil Ebrahimie

et al.

BMC Medical Genomics, Journal Year: 2023, Volume and Issue: 16(1)

Published: Sept. 15, 2023

Abstract Background The largest group of patients with breast cancer are estrogen receptor-positive (ER + ) type. receptor acts as a transcription factor and triggers cell proliferation differentiation. Hence, investigating ER-DNA interaction genomic regions can help identify genes directly regulated by ER understand the mechanism action in progression. Methods In present study, we employed workflow to do meta-analysis ChIP-seq data lines stimulated 10 nM 100 E2. All publicly available sets were re-analyzed same platform. Then, known unknown batch effects removed. Finally, was performed obtain meta-differentially bound sites estrogen-treated MCF7 compared vehicles (as control). Also, results T47D for more precision. Enrichment analyses also find functional importance common associated among both lines. Results Remarkably, POU5F1B, ZNF662, ZNF442, KIN, ZNF410 , SGSM2 factors recognized but not individual studies. resulted candidacy pathways previously reported cancer. PCGF2, HNF1B, ZBED6 predicted through enrichment analysis genes. addition, comparing RNA-seq showed that many affected up-regulated. Conclusion line leads identification new binding have been reported. their revealed terms involved development which should be examined future vitro vivo

Language: Английский

Citations

1