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Erdogan C, Suer I, Kaya M, Ozturk S, Aydin N, Kurt Z. Bioinformatics analysis of the potentially functional circRNA-miRNA-mRNA network in breast cancer. PLoS One 2024; 19:e0301995. [PMID: 38635539 PMCID: PMC11025867 DOI: 10.1371/journal.pone.0301995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
Breast cancer (BC) is the most common cancer among women with high morbidity and mortality. Therefore, new research is still needed for biomarker detection. GSE101124 and GSE182471 datasets were obtained from the Gene Expression Omnibus (GEO) database to evaluate differentially expressed circular RNAs (circRNAs). The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) databases were used to identify the significantly dysregulated microRNAs (miRNAs) and genes considering the Prediction Analysis of Microarray classification (PAM50). The circRNA-miRNA-mRNA relationship was investigated using the Cancer-Specific CircRNA, miRDB, miRTarBase, and miRWalk databases. The circRNA-miRNA-mRNA regulatory network was annotated using Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. The protein-protein interaction network was constructed by the STRING database and visualized by the Cytoscape tool. Then, raw miRNA data and genes were filtered using some selection criteria according to a specific expression level in PAM50 subgroups. A bottleneck method was utilized to obtain highly interacted hub genes using cytoHubba Cytoscape plugin. The Disease-Free Survival and Overall Survival analysis were performed for these hub genes, which are detected within the miRNA and circRNA axis in our study. We identified three circRNAs, three miRNAs, and eighteen candidate target genes that may play an important role in BC. In addition, it has been determined that these molecules can be useful in the classification of BC, especially in determining the basal-like breast cancer (BLBC) subtype. We conclude that hsa_circ_0000515/miR-486-5p/SDC1 axis may be an important biomarker candidate in distinguishing patients in the BLBC subgroup of BC.
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Affiliation(s)
- Cihat Erdogan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Ilknur Suer
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Department of Internal Medicine, Division of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Murat Kaya
- Department of Internal Medicine, Division of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Sukru Ozturk
- Department of Internal Medicine, Division of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Nizamettin Aydin
- Department of Computer Engineering, Faculty of Computer and Informatics, Istanbul Technical University, Istanbul, Turkey
| | - Zeyneb Kurt
- Information School, The University of Sheffield, Sheffield, United Kingdom
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Pham SH, Vuorinen SI, Arif KT, Griffiths LR, Okolicsanyi RK, Haupt LM. Syndecan-4 regulates the HER2-positive breast cancer cell proliferation cells via CK19/AKT signalling. Biochimie 2023; 207:49-61. [PMID: 36460206 DOI: 10.1016/j.biochi.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/27/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022]
Abstract
Despite the use of the highly specific anti-HER2 receptor (trastuzumab) therapy, HER2-positive breast cancers account for 20-30% of all breast cancer carcinomas, with HER2 status a challenge to treatment interventions. The heparan sulfate proteoglycans (HSPGs) are prominently expressed in the extracellular matrix (ECM), mediate breast cancer proliferation, development, and metastasis with most studies to date conducted in animal models. This study examined HSPGs in HER2-positive human breast cancer cell lines and their contribution to cancer cell proliferation. The study examined the cells following enhancement (via the addition of heparin) and knockdown (KD; using short interfering RNA, siRNA) of HSPG core proteins. The interaction of HSPG core proteins and AKT signalling molecules was examined to identify any influence of this signalling pathway on cancer cell proliferation. Our findings illustrated the HSPG syndecan-4 (SDC4) core protein significantly regulates cell proliferation with increased BC cell proliferation following heparin addition to cultures and decreased cell number following SDC4 KD. In addition, along with SDC4, significant changes in CK19/AKT signalling were identified as mediators of BC HER2-positive BC cell proliferation. This study provides evidence for a cell growth regulatory axis involving HSPGs/CK19 and AKT that represents a potential molecular target to prevent proliferation of HER2-positive breast cancer cells.
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Affiliation(s)
- Son H Pham
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
| | - Sofia I Vuorinen
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
| | - Km Taufiqul Arif
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
| | - Rachel K Okolicsanyi
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia; ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology (QUT), Australia.
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Scott DA, Drake RR. Glycosylation and its implications in breast cancer. Expert Rev Proteomics 2019; 16:665-680. [PMID: 31314995 PMCID: PMC6702063 DOI: 10.1080/14789450.2019.1645604] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/15/2019] [Indexed: 02/07/2023]
Abstract
Introduction: For decades, the role of glycans and glycoproteins in the progression of breast cancer and other cancers have been evaluated. Through extensive studies focused on elucidating the biological functions of glycosylation, researchers have been able to implicate alterations in these functions to tumor formation and metastasis. Areas covered: In this review, we summarize how changes in glycosylation are associated with tumorigenesis, with emphasis on breast cancers. An overview of the changes in N-linked and O-linked glycans associated with breast cancer tumors and biofluids are described. Recent advances in glycomics are emphasized in the context of continuing to decipher the glycosylation changes associated with breast cancer progression. Expert opinion: While changes in glycosylation have been studied in breast cancer for many years, the clinical relevance of these studies has been limited. This reflects the inherent biological and clinical heterogeneity of breast cancers. Glycomics analysis lags behind the advances in genomics and proteomics, but new approaches are emerging. A summary of known glycosylation changes associated with breast cancer is necessary to implement new findings in the context of clinical outcomes and therapeutic strategies. A better understanding of the dynamics of tumor and immune glycosylation is critical to improving emerging immunotherapeutic treatments.
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Affiliation(s)
- Danielle A Scott
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics and MUSC, Proteomics Center, Medical University of South Carolina , Charleston , SC , USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics and MUSC, Proteomics Center, Medical University of South Carolina , Charleston , SC , USA
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Sayyad MR, Puchalapalli M, Vergara NG, Wangensteen SM, Moore M, Mu L, Edwards C, Anderson A, Kall S, Sullivan M, Dozmorov M, Singh J, Idowu MO, Koblinski JE. Syndecan-1 facilitates breast cancer metastasis to the brain. Breast Cancer Res Treat 2019; 178:35-49. [PMID: 31327090 DOI: 10.1007/s10549-019-05347-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/03/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE Although survival rates for patients with localized breast cancer have increased, patients with metastatic breast cancer still have poor prognosis. Understanding key factors involved in promoting breast cancer metastasis is imperative for better treatments. In this study, we investigated the role of syndecan-1 (Sdc1) in breast cancer metastasis. METHODS To assess the role of Sdc1 in breast cancer metastasis, we silenced Sdc1 expression in the triple-negative breast cancer human MDA-MB-231 cell line and overexpressed it in the mouse mammary carcinoma 4T1 cell line. Intracardiac injections were performed in an experimental mouse metastasis model using both cell lines. In vitro transwell blood-brain barrier (BBB) and brain section adhesion assays were utilized to specifically investigate how Sdc1 facilitates brain metastasis. A cytokine array was performed to evaluate differences in the breast cancer cell secretome when Sdc1 is silenced. RESULTS Silencing expression of Sdc1 in breast cancer cells significantly reduced metastasis to the brain. Conversely, overexpression of Sdc1 increased metastasis to the brain. We found that silencing of Sdc1 expression had no effect on attachment of breast cancer cells to brain endothelial cells or astrocytes, but migration across the BBB was reduced as well as adhesion to the perivascular regions of the brain. Loss of Sdc1 also led to changes in breast cancer cell-secreted cytokines/chemokines, which may influence the BBB. CONCLUSIONS Taken together, our study demonstrates a role for Sdc1 in promoting breast cancer metastasis to the brain. These findings suggest that Sdc1 supports breast cancer cell migration across the BBB through regulation of cytokines, which may modulate the BBB. Further elucidating this mechanism will allow for the development of therapeutic strategies to combat brain metastasis.
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Affiliation(s)
- Megan R Sayyad
- Department of Pathology, School of Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Madhavi Puchalapalli
- Department of Pathology, School of Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA.,Department of Pathology, Women's Cancer Research Program, Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Institute, Northwestern University, Chicago, IL, USA
| | - Natasha G Vergara
- Department of Pathology, Women's Cancer Research Program, Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Institute, Northwestern University, Chicago, IL, USA.,McCormick School of Engineering, Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Sierra Mosticone Wangensteen
- Department of Pathology, School of Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Melvin Moore
- Department of Pathology, Women's Cancer Research Program, Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Institute, Northwestern University, Chicago, IL, USA.,McCormick School of Engineering, Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Liang Mu
- Department of Pathology, Women's Cancer Research Program, Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Institute, Northwestern University, Chicago, IL, USA
| | - Chevaunne Edwards
- Department of Pathology, Women's Cancer Research Program, Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Institute, Northwestern University, Chicago, IL, USA
| | - Aubree Anderson
- Department of Pathology, Women's Cancer Research Program, Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Institute, Northwestern University, Chicago, IL, USA
| | - Stefanie Kall
- Department of Pathology, Women's Cancer Research Program, Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Institute, Northwestern University, Chicago, IL, USA.,McCormick School of Engineering, Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Megan Sullivan
- Department of Pathology, Women's Cancer Research Program, Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Institute, Northwestern University, Chicago, IL, USA
| | - Mikhail Dozmorov
- Department of Biostatistics, School of Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Jaime Singh
- Department of Pathology, School of Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Michael O Idowu
- Department of Pathology, School of Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Jennifer E Koblinski
- Department of Pathology, School of Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA. .,Department of Pathology, Women's Cancer Research Program, Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Institute, Northwestern University, Chicago, IL, USA. .,Department of Pathology, School of Medicine, Virginia Commonwealth University, Sanger Hall 4-013, 1101 E. Marshall St, Box 980662, Richmond, VA, 23298, USA.
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