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Guo Q, Qiu P, Pan K, Lin J. Comprehensive analysis of cuproptosis-related long non-coding RNA signature and personalized therapeutic strategy of breast cancer patients. Front Oncol 2022; 12:1081089. [PMID: 36620596 PMCID: PMC9815178 DOI: 10.3389/fonc.2022.1081089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Background Breast cancer (BC) is considered to be one of the primary causes of cancer deaths in women. Cuproptosis was suggested to play an important role in tumor proliferation and tumor immune microenvironment. Therefore, an investigation was conducted to identify the relationship between cuproptosis-related long non-coding RNAs (lncRNAs) and BC prognosis. Method Based on The Cancer Genome Atlas (TCGA), nine cuproptosis-related lncRNAs were identified by Pearson's analysis and Cox regression analysis to create a cuproptosis-related lncRNA signature. Subsequently, patients with BC were divided into high-risk and low-risk groups. The Kaplan-Meier curves and a time-dependent receiver operating characteristic (ROC) analysis were employed to elucidate the predictive capability of the signature. After that, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was conducted by Gene Set Enrichment Analysis (GSEA), and the lncRNA-mRNA co-expression network was established by Cytoscape software. Furthermore, the ESTIMATE score was calculated, and the immune cell type component analysis was conducted. Eventually, immunotherapy response analysis was applied to identify the predictive power of cuproptosis-related lncRNAs to tumor immunotherapy response, including immune checkpoint gene expression levels, tumor mutational burden (TMB), and microsatellite instability (MSI). Results Patients with BC in the low-risk groups showed better clinical outcomes. The KEGG pathways in the high-risk groups were mainly enriched in immune response and immune cell activation. Furthermore, the ESTIMATE scores were higher in the low-risk groups, and their immune cell infiltrations were dramatically different from those of the high-risk groups. The low-risk groups were shown to have higher infiltration levels of CD8+ T cells and TMB-high status, resulting in better response to immunotherapies. Conclusion The findings of this study revealed that the nine-cuproptosis-related lncRNA risk score was an independent prognostic factor for BC. This signature was a potential predictor for BC immunotherapy response. What we found will provide novel insight into immunotherapeutic treatment strategies in BC.
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Alam MS, Sultana A, Wang G, Haque Mollah MN. Gene expression profile analysis to discover molecular signatures for early diagnosis and therapies of triple-negative breast cancer. Front Mol Biosci 2022; 9:1049741. [PMID: 36567949 PMCID: PMC9768339 DOI: 10.3389/fmolb.2022.1049741] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most lethal subtypes of breast cancer (BC), and it accounts for approximately 10%-20% of all invasive BCs diagnosed worldwide. The survival rate of TNBC in stages III and IV is very low, and a large number of patients are diagnosed in these stages. Therefore, the purpose of this study was to identify TNBC-causing molecular signatures and anti-TNBC drug agents for early diagnosis and therapies. Five microarray datasets that contained 304 TNBC and 109 control samples were collected from the Gene Expression Omnibus (GEO) database, and RNA-Seq data with 116 tumor and 124 normal samples were collected from TCGA database to identify differentially expressed genes (DEGs) between TNBC and control samples. A total of 64 DEGs were identified, of which 29 were upregulated and 35 were downregulated, by using the statistical limma R-package. Among them, seven key genes (KGs) were commonly selected from microarray and RNA-Seq data based on the high degree of connectivity through PPI (protein-protein interaction) and module analysis. Out of these seven KGs, six KGs (TOP2A, BIRC5, AURKB, ACTB, ASPM, and BUB1B) were upregulated and one (EGFR) was downregulated. We also investigated their differential expression patterns with different subtypes and progression stages of BC by the independent datasets of RNA-seq profiles from UALCAN database, which indicated that they may be potential biomarkers for early diagnosis. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses with the proposed DEGs were performed using the online Enrichr database to investigate the pathogenetic processes of TNBC highlighting KGs. Then, we performed gene regulatory network analysis and identified three transcriptional (SOX2, E2F4, and KDM5B) and three post-transcriptional (hsa-mir-1-3p, hsa-mir-124-3p, and hsa-mir-34a-5p) regulators of KGs. Finally, we proposed five KG-guided repurposable drug molecules (imatinib, regorafenib, pazopanib, teniposide, and dexrazoxane) for TNBC through network pharmacology and molecular docking analyses. These drug molecules also showed significant binding performance with some cancer-related PTM-sites (phosphorylation, succinylation, and ubiquitination) of top-ranked four key proteins (EGFR, AURKB, BIRC5, and TOP2A). Therefore, the findings of this computational study may play a vital role in early diagnosis and therapies against TNBC by wet-lab validation.
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Affiliation(s)
- Md Shahin Alam
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Adiba Sultana
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Guanghui Wang
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China,*Correspondence: Guanghui Wang, ; Md Nurul Haque Mollah,
| | - Md Nurul Haque Mollah
- Bioinformatics Lab. (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh,*Correspondence: Guanghui Wang, ; Md Nurul Haque Mollah,
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Aini S, Bolati S, Ding W, Liu S, Su P, Aili S, Naman Y, Xuekelaiti K. LncRNA SNHG10 suppresses the development of doxorubicin resistance by downregulating miR-302b in triple-negative breast cancer. Bioengineered 2022; 13:11430-11439. [PMID: 35506202 PMCID: PMC9275935 DOI: 10.1080/21655979.2022.2063592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Unlike other types of breast cancer, triple negative breast cancer (TNBC) does not respond to therapies targeting human epidermal growth factor receptor-2 (HER2) or hormone therapy, and the prognosis of patients with TNBC is usually poor. The role of long non-coding RNA (lncRNA) small nucleolar RNA host gene 10 (SNHG10) has been investigated in many types of cancer, but its role in TNBC is unknown. This study aimed to explore the role of SNHG10 in TNBC in the context of doxorubicin treatment, a common therapy for TNBC. Analysis of the TCGA dataset revealed the downregulation of SNHG10 in TNBC. The downregulation of SNHG10 of TNBC in TNBC was further confirmed by detecting its expression in 60 patients with TNBC by qPCR. The expression of SNHG10 was further downregulated after doxorubicin treatment. In TNBC, microRNA-302b (miR-302b) was downregulated and was positively correlated with SNHG10. In TNBC cells, overexpression of SNHG10 resulted in upregulation of miR-302b, and methylation-specific PCR analysis showed that SNHG10 negatively regulates the methylation of miR-302b. In addition, doxorubicin treatment resulted in the downregulation of SNHG10 in TNBC cells, and overexpression of SNHG10 and miR-302b promoted apoptosis of doxorubicin-treated TNBC cells. Furthermore, overexpression of both SNHG10 and miR-302b had a stronger effect on apoptosis than that of overexpression of SNHG10 alone. Our study showed that SNHG10 could inhibit the development of resistance to doxorubicin by upregulating miR-302b in TNBC through methylation. Our findings suggested that SNHG10 might serve as a molecular target for intervening in TBNC metastasis.
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Affiliation(s)
| | | | - Wei Ding
- Department of Mammary Gland and Thyroid Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Siyin Liu
- Department of Mammary Gland and Thyroid Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Pengcheng Su
- Department of Mammary Gland and Thyroid Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Saiding Aili
- Department of Mammary Gland and Thyroid Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Yimin Naman
- Department of Mammary Gland and Thyroid Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Kuerban Xuekelaiti
- Department of Mammary Gland and Thyroid Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
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Li DY, Yue LX, Wang SG, Wang TX. Quercitrin restrains the growth and invasion of lung adenocarcinoma cells by regulating gap junction protein beta 2. Bioengineered 2022; 13:6126-6135. [PMID: 35196203 PMCID: PMC8973705 DOI: 10.1080/21655979.2022.2037372] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most prevalent subtype of non-small cell lung cancer (NSCLC) with high lethality, and quercitrin exhibits anticancer characteristics. Here, we attempted to uncover the anticancer activity of quercitrin in LUAD. In this work, quercitrin prohibited the cell viability and clone-formation of LUAD cells in vitro. Meanwhile, quercitrin treatment reduced the aggressive phenotypes in LUAD cells. Further, Gap Junction Protein Beta 2 (GJB2) expression was aberrantly higher in LUAD when compared within control tissue. The higher expression of GJB2 is associated with an inferior overall survival for patients with LUAD. Finally, the reintroduction of GJB2 offset the inhibiting influence of quercitrin in LUAD cells. Altogether, these findings disclosed that quercitrin suppressed the growth and metastatic-related traits of LUAD cells partly via regulating GJB2 expression.
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Affiliation(s)
- Deng Yun Li
- School of Medicine, Zhengzhou University of Industrial Technology, Zhengzhou, Henan, China
| | - Li Xiao Yue
- School of Medicine, Zhengzhou University of Industrial Technology, Zhengzhou, Henan, China
| | - Shi Guang Wang
- School of Medicine, Zhengzhou University of Industrial Technology, Zhengzhou, Henan, China
| | - Tian Xiao Wang
- School of Pharmacy, Henan University, Kaifeng, Henan, China
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Wang D, Song Q, Zhao T, Wang F, Yu Y, Qi J, Lyu P, Duan X. Long non-coding RNA MRPS30 divergent transcript can be detected in the cytoplasm of triple-negative breast cancer cells and is targeted by microRNA-130b. Bioengineered 2022; 13:5954-5961. [PMID: 35191803 PMCID: PMC8973633 DOI: 10.1080/21655979.2022.2031393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNA (lncRNA) MRPS30 divergent transcript (also known as BRCAT54) is recently reported to promote lung cancer. The involvement of BRCAT54 in triple-negative breast cancer (TNBC) is unknown. This study investigated the role of BRCAT54 in TNBC. The expression of BRCAT54 and microRNA(miR)-130b was detected by RT-qPCR. The subcellular location of BRCAT54 in TNBC cells was analyzed by nuclear fractionation assay. Overexpression of BRCAT54 and miR-130b was achieved in TNBC cells to explore the interaction between then. The role of BRCAT54 and miR-130b in TNBC cell proliferation was evaluated by BrdU assay. BRCAT54 was downregulated in TNBC, while miR-130b was upregulated in TNBC tissues. BRCAT54 and miR-130b were inversely correlated across both TNBC and normal tissues. BRCAT54 was detected in cytoplasm and was predicted to be targeted by miR-130b. In TNBC cells, downregulation of BRCAT54 was observed after the overexpression of miR-130b. Moreover, BRCAT54 decreased cell proliferation and miR-130b increased cell proliferation. Besides, BRCAT54 suppressed the role of miR-130b in increasing cell proliferation. Therefore, BRCAT54 can be detected in cytoplasm and was targeted by miR-130b to increase cell proliferation.
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Affiliation(s)
- Dongtao Wang
- Department of Oncological Surgery, Central Hospital, Baotou, Inner Mongolia, P.R. China
| | - Qiang Song
- Department of General Surgery, Central Hospital, Baotou, Inner Mongolia, P.R. China
| | - Tianyong Zhao
- Department of Oncological Surgery, Central Hospital, Baotou, Inner Mongolia, P.R. China
| | - Fang Wang
- Department of Oncological Surgery, Central Hospital, Baotou, Inner Mongolia, P.R. China
| | - Yang Yu
- Department of Oncological Surgery, Central Hospital, Baotou, Inner Mongolia, P.R. China
| | - Jing Qi
- Department of Oncological Surgery, Central Hospital, Baotou, Inner Mongolia, P.R. China
| | - Pengfei Lyu
- Department of Breast Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province, PR. China
| | - Xiangyang Duan
- Central Blood Station, Baotou, Inner Mongolia, P.R. China
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