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Chen X, Sun H, Yang C, Wang W, Lyu W, Zou K, Zhang F, Dai Z, He X, Dong H. Bioinformatic analysis and experimental validation of six cuproptosis-associated genes as a prognostic signature of breast cancer. PeerJ 2024; 12:e17419. [PMID: 38912044 PMCID: PMC11192027 DOI: 10.7717/peerj.17419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/28/2024] [Indexed: 06/25/2024] Open
Abstract
Background Breast carcinoma (BRCA) is a life-threatening malignancy in women and shows a poor prognosis. Cuproptosis is a novel mode of cell death but its relationship with BRCA is unclear. This study attempted to develop a cuproptosis-relevant prognostic gene signature for BRCA. Methods Cuproptosis-relevant subtypes of BRCA were obtained by consensus clustering. Differential expression analysis was implemented using the 'limma' package. Univariate Cox and multivariate Cox analyses were performed to determine a cuproptosis-relevant prognostic gene signature. The signature was constructed and validated in distinct datasets. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were also conducted using the prognostic signature to uncover the underlying molecular mechanisms. ESTIMATE and CIBERSORT algorithms were applied to probe the linkage between the gene signature and tumor microenvironment (TME). Immunotherapy responsiveness was assessed using the Tumor Immune Dysfunction and Exclusion (TIDE) web tool. Real-time quantitative PCR (RT-qPCR) was performed to detect the expressions of cuproptosis-relevant prognostic genes in breast cancer cell lines. Results Thirty-eight cuproptosis-associated differentially expressed genes (DEGs) in BRCA were mined by consensus clustering and differential expression analysis. Based on univariate Cox and multivariate Cox analyses, six cuproptosis-relevant prognostic genes, namely SAA1, KRT17, VAV3, IGHG1, TFF1, and CLEC3A, were mined to establish a corresponding signature. The signature was validated using external validation sets. GSVA and GSEA showed that multiple cell cycle-linked and immune-related pathways along with biological processes were associated with the signature. The results ESTIMATE and CIBERSORT analyses revealed significantly different TMEs between the two Cusig score subgroups. Finally, RT-qPCR analysis of cell lines further confirmed the expressional trends of SAA1, KRT17, IGHG1, and CLEC3A. Conclusion Taken together, we constructed a signature for projecting the overall survival of BRCA patients and our findings authenticated the cuproptosis-relevant prognostic genes, which are expected to provide a basis for developing prognostic molecular biomarkers and an in-depth understanding of the relationship between cuproptosis and BRCA.
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Affiliation(s)
- Xiang Chen
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Hening Sun
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Changcheng Yang
- Department of The First Affiliated Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Wei Wang
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Wenzhi Lyu
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Kejian Zou
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Fan Zhang
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Zhijun Dai
- Department of The First Affiliated Hospital, Zhejiang University, Hangzhou City, Zhejiang Province, China
| | - Xionghui He
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
| | - Huaying Dong
- Department of Hainan General Hospital, Hainan Medical College, Haikou City, Hainan Province, China
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Khanegheini B, Ghasemi A, Heidari MA, Aeinfar K, Firoozi S, Tamaddon M, Fereidouni Z. Role of MicroRNAs in Breast Cancer Metastasis to the Brain: A New Therapeutic Perspective. Galen Med J 2023; 12:1-4. [PMID: 38774849 PMCID: PMC11108662 DOI: 10.31661/gmj.v12i.3193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Indexed: 05/24/2024] Open
Affiliation(s)
- Baback Khanegheini
- Brain and Spinal Cord Injury Research Center, Neuroscience Institute, Tehran
University of Medical Sciences, Tehran, Iran
| | - Afsaneh Ghasemi
- Department of Public Health, School of Health, Fasa University of Medical Sciences,
Fasa, Iran
| | - Mohammad Amin Heidari
- Department of Pharmacology, Faculty of Medicine, Ilam University of Medical Science,
Ilam, Iran
| | - Kamkar Aeinfar
- Department of Neurosurgery, Shariati Hospital, Tehran University of Medical
Sciences, Tehran, Iran
| | - Sina Firoozi
- School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mona Tamaddon
- Chronic Disease Research Center, Endocrinology and Metabolism Population Sciences
Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Zhila Fereidouni
- Department of Nursing, School of Nursing, Fasa University of Medical Sciences, Fasa,
Iran
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Kim J, Hegener K, Hagedorn C, Jamal Jameel K, Weidinger D, Seuthe IMC, Eichhorn S, Kreppel F, Knobloch J, Park JJH. Long-Term Cryopreservation of Nasal Polyp Tissue in a Biobank for the Isolation and Culture of Primary Epithelial Cells. Int J Mol Sci 2023; 24:ijms24076383. [PMID: 37047354 PMCID: PMC10094359 DOI: 10.3390/ijms24076383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/01/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023] Open
Abstract
Epithelial cells may play an important role in the pathologic process of chronic rhinosinusitis with nasal polyps. Therefore, providing epithelial cells from a biobank could greatly contribute to further research. In the present work, the isolation of epithelial cells from long-term cryopreserved tissue is demonstrated. Polyp tissues were cryopreserved in a commercially available freezing medium with dimethyl sulfoxide and stored in liquid nitrogen. The outgrowth and proliferation of epithelial cells from cryopreserved tissue were evaluated and compared to that of fresh tissue. Flow cytometric analysis with anti-cytokeratin, anti-p63, and anti-Ki-67 was performed to identify epithelial cells and determine differentiation and proliferation. A functionality test was performed by determining type 2–relevant proteins, representatively thymic stromal lymphopoietin (TSLP) and periostin, using ELISA. Primary epithelial cells could be isolated from cryopreserved tissues. Cells from cryopreserved tissues showed comparable outgrowth and proliferation to that of fresh tissue. Isolated epithelial cells showed high cytokeratin, p63, and Ki-67 expression and secreted TSLP and periostin. In the present study, a method for long-term cryopreservation of polyp tissue was established, thereby enabling the isolation and cell culture of primary cell culture at a later time. Epithelial cell availability should be greatly improved by including this method in a biobank.
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(Stămat) LRB, Dinescu S, Costache M. Regulation of Inflammasome by microRNAs in Triple-Negative Breast Cancer: New Opportunities for Therapy. Int J Mol Sci 2023; 24:ijms24043245. [PMID: 36834660 PMCID: PMC9963301 DOI: 10.3390/ijms24043245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/28/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
During the past decade, researchers have investigated the molecular mechanisms of breast cancer initiation and progression, especially triple-negative breast cancer (TNBC), in order to identify specific biomarkers that could serve as feasible targets for innovative therapeutic strategies development. TNBC is characterized by a dynamic and aggressive nature, due to the absence of estrogen, progesterone and human epidermal growth factor 2 receptors. TNBC progression is associated with the dysregulation of nucleotide-binding oligomerization domain-like receptor and pyrin domain-containing protein 3 (NLRP3) inflammasome, followed by the release of pro-inflammatory cytokines and caspase-1 dependent cell death, termed pyroptosis. The heterogeneity of the breast tumor microenvironment triggers the interest of non-coding RNAs' involvement in NLRP3 inflammasome assembly, TNBC progression and metastasis. Non-coding RNAs are paramount regulators of carcinogenesis and inflammasome pathways, which could help in the development of efficient treatments. This review aims to highlight the contribution of non-coding RNAs that support inflammasome activation and TNBC progression, pointing up their potential for clinical applications as biomarkers for diagnosis and therapy.
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Affiliation(s)
| | - Sorina Dinescu
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania
- Research Institute of the University of Bucharest, 050663 Bucharest, Romania
- Correspondence:
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania
- Research Institute of the University of Bucharest, 050663 Bucharest, Romania
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Balkrishna A, Mittal R, Arya V. Tumor Suppressive Role of MicroRNAs in Triple Negative Breast Cancer. Curr Pharm Des 2023; 29:3357-3367. [PMID: 38037837 DOI: 10.2174/0113816128272489231124095922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023]
Abstract
Triple-negative breast cancers are highly aggressive, a heterogeneous form of breast cancer with a high re-occurrence rate that further lacks an efficient treatment strategy and prognostic marker. The tumor microenvironment of the disease comprises cancer-associated fibroblasts, cancer stem cells, immunological molecules, epithelial-mesenchymal transition, and a metastatic microenvironment that contributes to disease progression and metastasis to distant sites. Emerging evidence indicated that miRNA clusters would be of clinical utility as they exert an oncogenic or tumor suppressor role in TNBC. The present review article aims to highlight the therapeutic significance of miRNA in targeting the above-mentioned signaling cascades and modulating the intracellular crosstalk in the tumor microenvironment of TNBC. Prognostic implications of miRNAs to depict disease-free survival, distant metastasis-free survival, relapse-free survival, and overall survival outcome were also unveiled.
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Affiliation(s)
- Acharya Balkrishna
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar, India
| | - Rashmi Mittal
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar, India
| | - Vedpriya Arya
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar, India
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Zhang L, Wu X, Fan X, Ai H. MUM1L1 as a Tumor Suppressor and Potential Biomarker in Ovarian Cancer: Evidence from Bioinformatics Analysis and Basic Experiments. Comb Chem High Throughput Screen 2023; 26:2487-2501. [PMID: 36856181 DOI: 10.2174/1386207326666230301141912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/01/2022] [Accepted: 12/15/2022] [Indexed: 03/02/2023]
Abstract
BACKGROUND Ovarian cancer (OC) is the most prevalent gynecologic malignancy, with high mortality rates. However, its pathogenesis remains unclear. The current study aimed to explore potential biomarkers and suppressor genes for diagnosing and treating OC. METHODS Biochemical and bioinformatics approaches were used to detect differentially expressed genes (DEGs) in ovarian tissues via integration analysis. Kaplan-Meier plot analysis was performed to assess progression-free survival and overall survival according to DEGs. Then, we constructed a protein-protein interaction (PPI) network based on data from the STRING database to identify the related target genes of DEGs. Finally, DEGs regulating the proliferation, migration, and invasion of SKOV3 cell lines were validated via in vitro experiments. RESULTS Four DEGs (MUM1L1, KLHDC8A, CRYGD, and GREB1) with enriched expression in ovarian tissues were explicitly expressed in the ovary based on an analysis of all human proteins. MUM1L1 had high specificity, and its expression was higher in normal ovarian tissues than in OC tissues. Kaplan-Meier plot analysis showed that a high MUM1L1 expression was associated with longer progression-free survival and overall survival in OC. Based on the PPI analysis results, CBLN4, CBLN1, PTH2R, TMEM255B, and COL23A1 were associated with MUM1L1. In vitro studies revealed that MUM1L1 overexpression decreased the proliferation, migration, and invasion ability of SKOV3 cell lines. Meanwhile, MUM1L1 knockdown had contrasting results. CONCLUSION MUM1L1 is a tumor suppressor gene and is a potential biomarker for diagnosing and treating OC.
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Affiliation(s)
- Lu Zhang
- Graduate School, Jinzhou Medical University, Jinzhou, Liaoning 121000, China
| | - Xue Wu
- Graduate School, Jinzhou Medical University, Jinzhou, Liaoning 121000, China
| | - Xue Fan
- Department of Obstetrics and Gynecology, 3rd Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, China
| | - Hao Ai
- Graduate School, Jinzhou Medical University, Jinzhou, Liaoning 121000, China
- Department of Obstetrics and Gynecology, 3rd Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, China
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Hsa-let-7c-5p, hsa-miR-130b-3p, and hsa-miR-142-3p as Novel miRNA Biomarkers for Melanoma Progression. Genet Res (Camb) 2022; 2022:5671562. [PMID: 35903462 PMCID: PMC9282999 DOI: 10.1155/2022/5671562] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/31/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
This study aimed to screen miRNA biomarkers for melanoma progression. Raw melanoma data were downloaded from the Gene Expression Omnibus (GSE34460, GSE35579, GSE18509, and GSE24996) and the Cancer Genome Atlas (TCGA). Then, all differentially expressed miRNAs (DEmiRNAs) between benign vs. primary, metastatic vs. benign, and metastatic vs. primary groups were obtained in the GSE34460 and GSE35579 datasets, and the miRNAs related to disease progression were further screened. Then, the miRNA-gene network was constructed, followed by enrichment, survival, and cluster analyses. Differentially expressed genes (DEGs), tumor-infiltrating immune cells, and tumor mutation burden (TMB) between subtypes were analyzed. miRNAs were verified in the GSE18509 and GSE24996 datasets. A total of 132 and 209 DEmiRNAs were obtained in the GSE34460 and GSE35579 datasets, respectively, and 27 DEmiRNAs related to disease progression were screened. hsa-miR-106b-5p, hsa-miR-27b-3p, and hsa-miR-141-3p had a higher degree and were regulated by numerous genes in the miRNA-gene network. Moreover, four miRNAs were associated with prognosis: hsa-let-7c-5p, hsa-miR-130b-3p, hsa-miR-142-3p, and hsa-miR-509-3p. Furthermore, the bidirectional hierarchical clustering of 27 miRNAs was classified into three subtypes, and TMB and four types of immune cells, including activated dendritic cells, naïve CD4 T cells, M1 macrophages, and plasma cells, showed significant differences among the three subtypes. The expression levels of most miRNAs in the GSE18509 and GSE24996 datasets were consistent with those in the training dataset. These miRNAs, including hsa-let-7c-5p, hsa-miR-130b-3p, and hsa-miR-142-3p, and activated dendritic cells, naïve CD4 T cells, M1 macrophages, and plasma cells may play vital roles in the pathogenesis of melanoma.
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Khadri FZ, Issac MSM, Gaboury LA. Impact of Epithelial-Mesenchymal Transition on the Immune Landscape in Breast Cancer. Cancers (Basel) 2021; 13:5099. [PMID: 34680248 PMCID: PMC8533811 DOI: 10.3390/cancers13205099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022] Open
Abstract
The impact of epithelial-mesenchymal transition (EMT) signature on the immune infiltrate present in the breast cancer tumor microenvironment (TME) is still poorly understood. Since there is mounting interest in the use of immunotherapy for the treatment of subsets of breast cancer patients, it is of major importance to understand the fundamental tumor characteristics which dictate the inter-tumor heterogeneity in immune landscapes. We aimed to assess the impact of EMT-related markers on the nature and magnitude of the inflammatory infiltrate present in breast cancer TME and their association with the clinicopathological parameters. Tissue microarrays were constructed from 144 formalin-fixed paraffin-embedded invasive breast cancer tumor samples. The protein expression patterns of Snail, Twist, ZEB1, N-cadherin, Vimentin, GRHL2, E-cadherin, and EpCAM were examined by immunohistochemistry (IHC). The inflammatory infiltrate in the TME was assessed semi-quantitatively on hematoxylin and eosin (H&E)-stained whole sections and was characterized using IHC. The inflammatory infiltrate was more intense in poorly differentiated carcinomas and triple-negative carcinomas in which the expression of E-cadherin and GRHL2 was reduced, while EpCAM was overexpressed. Most EMT-related markers correlated with plasma cell infiltration of the TME. Taken together, our findings reveal that the EMT signature might impact the immune response in the TME.
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Affiliation(s)
- Fatima-Zohra Khadri
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3T 1J4, Canada; (F.-Z.K.); (M.S.M.I.)
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Marianne Samir Makboul Issac
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3T 1J4, Canada; (F.-Z.K.); (M.S.M.I.)
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo 11956, Egypt
| | - Louis Arthur Gaboury
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3T 1J4, Canada; (F.-Z.K.); (M.S.M.I.)
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
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Yao M, Wang S, Chen L, Wei B, Fu P. Research on correlations of miR-585 expression with progression and prognosis of triple-negative breast cancer. Clin Exp Med 2021; 22:201-207. [PMID: 33826023 DOI: 10.1007/s10238-021-00704-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/16/2021] [Indexed: 11/25/2022]
Abstract
Triple-negative breast cancer is a special type of breast cancer, characterized by younger onset age, shorter survival period, higher malignant degree, higher mortality, recurrence and metastasis. Triple-negative breast cancer is more harmful to women's life and health, compared with other types of breast cancer. This paper mainly studied the role of miR-585 in triple-negative breast cancer. Real-time quantitative PCR was used to detect the expression of miR-585 in triple-negative breast cancer cell lines and tissues. Kaplan-Meier curve and Cox proportional hazards model analysis were used to investigate the prognostic value of miR-585 in triple-negative breast cancer. CCK-8 and Transwell assays were used to detect cell proliferation, invasion and migration. miR-585 was significantly down-regulated in triple-negative breast cancer cells and tissues. The low expression of miR-585 has been shown to be significantly associated with poor prognosis in triple-negative breast cancer patients. Abnormally low expression of miR-585 can promote cell proliferation, migration and invasion. Overall, abnormally low expression of miR-585 is associated with prognosis and progression of triple-negative breast cancer. miR-585 may serve as a prognostic biomarker for patients with triple-negative breast cancer and it is expected to be a new method and strategy for the treatment of triple-negative breast cancer.
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Affiliation(s)
- Minya Yao
- Department of Breast Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qinchun Road, Hangzhou, 310003, Zhejiang Province, P.R. China
| | - Shuqian Wang
- Department of Breast Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qinchun Road, Hangzhou, 310003, Zhejiang Province, P.R. China
| | - Luyan Chen
- Department of Breast Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qinchun Road, Hangzhou, 310003, Zhejiang Province, P.R. China
| | - Bajin Wei
- Department of Breast Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qinchun Road, Hangzhou, 310003, Zhejiang Province, P.R. China
| | - Peifen Fu
- Department of Breast Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qinchun Road, Hangzhou, 310003, Zhejiang Province, P.R. China.
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