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Huang Z, Chen P, Liu Y. WTAP-mediated m6A modification of circ_0032463 promotes osteosarcoma progression by sponging miR-145-5p and regulating GFRA1 expression. J Biochem Mol Toxicol 2024; 38:e23833. [PMID: 39243199 DOI: 10.1002/jbt.23833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 08/05/2024] [Accepted: 08/22/2024] [Indexed: 09/09/2024]
Abstract
Osteosarcoma (OS) is the most frequent bone malignancy in humans. Previous evidence suggest that circ_0032463 is an oncogenic circular RNA (circRNA) in various cancers, including OS. However, the molecular mechanism of circ_0032463 involved in OS is still unclear. Circ_0032463, microRNA-145-5p (miR-145-5p), GDNF receptor alpha 1 (GFRA1), and Wilms tumor 1-associated protein (WTAP) levels were determined using real-time quantitative polymerase chain reaction (RT-qPCR). Cell proliferation, apoptosis, migration, invasion, and angiogenesis were analyzed using 5-ethynyl-2'-deoxyuridine (EdU), flow cytometry, transwell, and tube formation assays. Western blot analysis was performed to measure matrix metalloproteinase 2 (MMP2), MMP9, GFRA1, and WTAP protein levels. Binding between miR-145-5p and circ_0032463 or GFRA1 was confirmed using a dual-luciferase reporter and pull-down assay. The biological role of circ_0032463 on OS cell growth was also analyzed using a xenograft tumor model in vivo. Methylated RNA immunoprecipitation assay validated the interaction between WTAP and circ_0032463. Circ_0032463, GFRA1, and WTAP levels were increased, and miR-145-5p was decreased in OS tissues and cells. Circ_0032463 deficiency might hinder OS cell proliferation, migration, invasion, angiogenesis, and promote apoptosis in vitro. Mechanically, circ_0032463 worked as a miR-145-5p sponge to increase GFRA1 expression. Repression of circ_0032463 knockdown on tumor cell growth was proved in vivo. Besides, N6-methyladenosine (m6A) modification facilitates the biogenesis of circ_0032463. Taken together, m6A-mediated biogenesis of circ_0032463 facilitates OS cell malignant biological behavior partly via regulating the miR-145-5p/GFRA1 axis, suggesting a promising molecular marker for OS treatment.
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Affiliation(s)
- Zhong Huang
- Orthopedic Center, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, China
| | - Pengcheng Chen
- Orthopedic Center, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, China
| | - Yiheng Liu
- Orthopedic Center, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, China
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2
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Li J, Xiang S, Song X. Screening Nonlinear miRNA Features of Breast Cancer by Using Ensemble Regularized Polynomial Logistic Regression. J Comput Biol 2024; 31:670-690. [PMID: 39017171 DOI: 10.1089/cmb.2023.0289] [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] [Indexed: 07/18/2024] Open
Abstract
Differentiating breast cancer subtypes based on miRNA data helps doctors provide more personalized treatment plans for patients. This paper explored the interaction between miRNA pairs and developed a novel ensemble regularized polynomial logistic regression method for screening nonlinear features of breast cancer. Three different types of second-order polynomial logistic regression with elastic network penalty (SOPLR-EN) in which each type contains 10 identical models were integrated to determine the most suitable sample set for feature screening by using bootstrap sampling strategy. A single feature and 39 nonlinear features were obtained by screening features that appeared at least 15 times in 30 integrations and were involved in the classification of at least 4 subtypes. The second-order polynomial logistic regression with ridge penalty (SOPLR-R) built on screened feature set achieved 82.30% classification accuracy for distinguishing breast cancer subtypes, surpassing the performance of other six methods. Further, 11 nonlinear miRNA biomarkers were identified, and their significant relevance to breast cancer was illustrated through six types of biological analysis.
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Affiliation(s)
- Juntao Li
- College of Mathematics and Information Science, Henan Normal University, Xinxiang, China
- Henan Engineering Laboratory for Big Data Statistical Analysis and Optimal Control, Xinxiang, China
| | - Shan Xiang
- College of Mathematics and Information Science, Henan Normal University, Xinxiang, China
- Henan Engineering Laboratory for Big Data Statistical Analysis and Optimal Control, Xinxiang, China
| | - Xuekun Song
- College of Information Technology, Henan University of Chinese Medicine, Zhengzhou, China
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3
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Girolimetti G, Pelisenco IA, Eusebi LH, Ricci C, Cavina B, Kurelac I, Verri T, Calcagnile M, Alifano P, Salvi A, Bucci C, Guerra F. Dysregulation of a Subset of Circulating and Vesicle-Associated miRNA in Pancreatic Cancer. Noncoding RNA 2024; 10:29. [PMID: 38804361 PMCID: PMC11130804 DOI: 10.3390/ncrna10030029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/14/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive neoplasia, characterized by early metastasis, low diagnostic rates at early stages, resistance to drugs, and poor prognosis. There is an urgent need to better characterize this disease in order to identify efficient diagnostic/prognostic biomarkers. Since microRNAs (miRNAs) contribute to oncogenesis and metastasis formation in PDAC, they are considered potential candidates for fulfilling this task. In this work, the levels of two miRNA subsets (involved in chemoresistance or with oncogenic/tumor suppressing functions) were investigated in a panel of PDAC cell lines and liquid biopsies of a small cohort of patients. We used RT-qPCR and droplet digital PCR (ddPCR) to measure the amounts of cellular- and vesicle-associated, and circulating miRNAs. We found that both PDAC cell lines, also after gemcitabine treatment, and patients showed low amounts of cellular-and vesicle-associated miR-155-5p, compared to controls. Interestingly, we did not find any differences when we analyzed circulating miR-155-5p. Furthermore, vesicle-related miR-27a-3p increased in cancer patients compared to the controls, while circulating let-7a-5p, miR-221-3p, miR-23b-3p and miR-193a-3p presented as dysregulated in patients compared to healthy individuals. Our results highlight the potential clinical significance of these analyzed miRNAs as non-invasive diagnostic molecular tools to characterize PDAC.
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Affiliation(s)
- Giulia Girolimetti
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Lecce-Monteroni 165, 73100 Lecce, Italy; (G.G.); (T.V.); (M.C.); (F.G.)
| | - Iulia Andreea Pelisenco
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy; (I.A.P.); (A.S.)
| | - Leonardo Henry Eusebi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy; (L.H.E.); (C.R.); (B.C.); (I.K.)
- Gastroenterology Unit, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Claudio Ricci
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy; (L.H.E.); (C.R.); (B.C.); (I.K.)
- Pancreatic Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Beatrice Cavina
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy; (L.H.E.); (C.R.); (B.C.); (I.K.)
- Centre for Applied Biomedical Research (CRBA), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Ivana Kurelac
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy; (L.H.E.); (C.R.); (B.C.); (I.K.)
- Centre for Applied Biomedical Research (CRBA), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Tiziano Verri
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Lecce-Monteroni 165, 73100 Lecce, Italy; (G.G.); (T.V.); (M.C.); (F.G.)
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Lecce-Monteroni 165, 73100 Lecce, Italy; (G.G.); (T.V.); (M.C.); (F.G.)
| | - Pietro Alifano
- Department of Experimental Medicine (DiMeS), University of Salento, Via Provinciale Lecce-Monteroni 165, 73100 Lecce, Italy;
| | - Alessandro Salvi
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy; (I.A.P.); (A.S.)
| | - Cecilia Bucci
- Department of Experimental Medicine (DiMeS), University of Salento, Via Provinciale Lecce-Monteroni 165, 73100 Lecce, Italy;
| | - Flora Guerra
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Lecce-Monteroni 165, 73100 Lecce, Italy; (G.G.); (T.V.); (M.C.); (F.G.)
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Armstrong L, Willoughby CE, McKenna DJ. The Suppression of the Epithelial to Mesenchymal Transition in Prostate Cancer through the Targeting of MYO6 Using MiR-145-5p. Int J Mol Sci 2024; 25:4301. [PMID: 38673886 PMCID: PMC11050364 DOI: 10.3390/ijms25084301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Aberrant expression of miR-145-5p has been observed in prostate cancer where is has been suggested to play a tumor suppressor role. In other cancers, miR-145-5p acts as an inhibitor of epithelial-to-mesenchymal transition (EMT), a key molecular process for tumor progression. However, the interaction between miR-145-5p and EMT remains to be elucidated in prostate cancer. In this paper the link between miR-145-5p and EMT in prostate cancer was investigated using a combination of in silico and in vitro analyses. miR-145-5p expression was significantly lower in prostate cancer cell lines compared to normal prostate cells. Bioinformatic analysis of The Cancer Genome Atlas prostate adenocarcinoma (TCGA PRAD) data showed significant downregulation of miR-145-5p in prostate cancer, correlating with disease progression. Functional enrichment analysis significantly associated miR-145-5p and its target genes with EMT. MYO6, an EMT-associated gene, was identified and validated as a novel target of miR-145-5p in prostate cancer cells. In vitro manipulation of miR-145-5p levels significantly altered cell proliferation, clonogenicity, migration and expression of EMT-associated markers. Additional TCGA PRAD analysis suggested miR-145-5p tumor expression may be useful predictor of disease recurrence. In summary, this is the first study to report that miR-145-5p may inhibit EMT by targeting MYO6 in prostate cancer cells. The findings suggest miR-145-5p could be a useful diagnostic and prognostic biomarker for prostate cancer.
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Affiliation(s)
| | | | - Declan J. McKenna
- Genomic Medicine Research Group, Ulster University, Cromore Road, Coleraine BT52 1SA, UK; (L.A.); (C.E.W.)
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Hao B, Dong H, Xiong R, Song C, Xu C, Li N, Geng Q. Identification of SLC2A1 as a predictive biomarker for survival and response to immunotherapy in lung squamous cell carcinoma. Comput Biol Med 2024; 171:108183. [PMID: 38422959 DOI: 10.1016/j.compbiomed.2024.108183] [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: 11/04/2023] [Revised: 01/20/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND As one of the common subtypes of non-small lung cancer, lung squamous cell carcinoma (LUSC) patients with advanced stage have few choices of treatment strategies. Therefore, it is urgent to discover genes that are associated with the survival and efficacy of immunotherapies. METHOD Differential gene expression analyses were conducted using TCGA LUSC bulk-sequencing and single-cell RNA-sequencing data. Prognostic genes were identified from the TCGA LUSC cohort. Protein expression validation and survival analyses were performed. Experiments were conducted to explore the underlying mechanisms. In addition, the correlation between gene expression and pathological response to adjuvant immunochemotherapy was also investigated. RESULTS After a series of bioinformatic analyses, solute carrier family 2 member 1(SLC2A1), encoding glucose transporter-1 (GLUT1), was found to be differentially expressed between tumor and normal tissues. GLUT1 was subsequently identified as an independent prognostic factor for LUSC. GSEA analysis revealed the glycolysis metabolism pathway of KEGG enriched in SLC2A1high tumor tissues. LASSO analyses revealed that tumor tissues with high expression of SLC2A1 were associated with high levels of protein lactylation. We found that SLC2A1 was preferentially expressed by SPP1+ macrophages in the tumor microenvironment, and the expression of SLC2A1 was associated with the abundance of SPP1+ macrophages. Immunofluorescence demonstrated GLUT1 and HIF1α colocalization in tumor-infiltrating macrophages. In vitro experiments showed HIF-1α-induced macrophage polarization under hypoxia, and GLUT1 inhibition blocked this polarization. In addition, SLC2A1 was negatively associated with the common immune checkpoint molecules, such as programmed cell death 1(PD-1), T cell immunoreceptor with Ig and ITIM domains (TIGIT), cytotoxic T-lymphocyte associated protein 4 (CTLA4) and lymphocyte activating 3 (LAG3), while showed a positive association with CD44. Finally, we observed that there was a significant correlation between pre-adjuvant-treatment GLUT1 expression and the pathological response. CONCLUSION SLC2A1 expression was differentially upregulated in tumor tissues, and elevated GLUT1 expression was associated with worse survival and poor pathological response to adjuvant immunochemotherapy. Upregulation of GLUT1 promoted macrophage polarization into the M2 phenotype. The findings will contribute to guiding the treatment selection for LUSC patients and providing personalized immunotherapy strategies.
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Affiliation(s)
- Bo Hao
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| | - Huixing Dong
- Department of Pulmonary and Critical Care Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai 200336, China.
| | - Rui Xiong
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| | - Congkuan Song
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| | - Chenzhen Xu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| | - Ning Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
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6
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Steffens Reinhardt L, Groen K, Zhang X, Morten BC, Wawruszak A, Avery-Kiejda KA. p53 isoform expression promotes a stemness phenotype and inhibits doxorubicin sensitivity in breast cancer. Cell Death Dis 2023; 14:509. [PMID: 37553320 PMCID: PMC10409720 DOI: 10.1038/s41419-023-06031-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 08/10/2023]
Abstract
In breast cancer, dysregulated TP53 expression signatures are a better predictor of chemotherapy response and survival outcomes than TP53 mutations. Our previous studies have shown that high levels of Δ40p53 are associated with worse disease-free survival and disruption of p53-induced DNA damage response in breast cancers. Here, we further investigated the in vitro and in vivo implications of Δ40p53 expression in breast cancer. We have shown that genes associated with cell differentiation are downregulated while those associated with stem cell regulation are upregulated in invasive ductal carcinomas expressing high levels of Δ40p53. In contrast to p53, endogenous ∆40p53 co-localised with the stem cell markers Sox2, Oct4, and Nanog in MCF-7 and ZR75-1 cell lines. ∆40p53 and Sox2 co-localisation was also detected in breast cancer specimens. Further, in cells expressing a high ∆40p53:p53 ratio, increased expression of stem cell markers, greater mammosphere and colony formation capacities, and downregulation of miR-145 and miR-200 (p53-target microRNAs that repress stemness) were observed compared to the control subline. In vivo, a high ∆40p53:p53 ratio led to increased tumour growth, Ki67 and Sox2 expression, and blood microvessel areas in the vehicle-treated mice. High expression of ∆40p53 also reduced tumour sensitivity to doxorubicin compared to control tumours. Enhanced therapeutic efficacy of doxorubicin was observed when transiently targeting Δ40p53 or when treating cells with OTSSP167 with concomitant chemotherapy. Taken together, high Δ40p53 levels induce tumour growth and may promote chemoresistance by inducing a stemness phenotype in breast cancer; thus, targeting Δ40p53 in tumours that have a high Δ40p53:p53 ratio could enhance the efficacy of standard-of-care therapies such as doxorubicin.
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Affiliation(s)
- Luiza Steffens Reinhardt
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton, NSW, Australia
- Cancer Detection & Therapy Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Kira Groen
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Xiajie Zhang
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton, NSW, Australia
- Cancer Detection & Therapy Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Brianna C Morten
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Anna Wawruszak
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton, NSW, Australia
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Kelly A Avery-Kiejda
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.
- Hunter Medical Research Institute, New Lambton, NSW, Australia.
- Cancer Detection & Therapy Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia.
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7
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Li J, Peng S, Zou X, Geng X, Wang T, Zhu W, Xia T. Value of negatively correlated miR-205-5p/ HMGB3 and miR-96-5p/ FOXO1 on the diagnosis of breast cancer and benign breast diseases. CANCER PATHOGENESIS AND THERAPY 2023; 1:159-167. [PMID: 38327836 PMCID: PMC10846318 DOI: 10.1016/j.cpt.2023.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/01/2023] [Accepted: 04/20/2023] [Indexed: 02/09/2024]
Abstract
Background MicroRNA (miRNA) and mRNA levels in matching specimens were used to identify miRNA-mRNA interactions. We aimed to integrate transcriptome, immunophenotype, methylation, mutation, and survival data analyses to examine the profiles of miRNAs and target mRNAs and their associations with breast cancer (BC) diagnosis. Methods Based on the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA), differentially expressed miRNAs and targeted mRNAs were screened from experimentally verified miRNA-target interaction databases using Pearson's correlation analysis. We used real-time quantitative reverse transcription polymerase chain reaction to verify BC and benign disease samples, and logistic regression analysis was used to establish a diagnostic model based on miRNAs and target mRNAs. Receiver operating characteristic curve analysis was performed to test the ability to recognize the miRNA-mRNA pairs. Next, we investigated the complex interactions between miRNA-mRNA regulatory pairs and phenotypic hallmarks. Results We identified 27 and 359 dysregulated miRNAs and mRNAs, respectively, based on the GEO and TCGA databases. Using Pearson's correlation analysis, 10 negative miRNA-mRNA regulatory pairs were identified after screening both databases, and the related miRNA and target mRNA levels were assessed in 40 BC tissues and 40 benign breast disease tissues. Two key regulatory pairs (miR-205-5p/High mobility group box 3 (HMGB3) and miR-96-5p/Forkhead Box O1 (FOXO1)) were selected to establish the diagnostic model. They also had utility in survival and clinical analyses. Conclusions A diagnostic model including two miRNAs and their respective target mRNAs was established to distinguish between BC and benign breast diseases. These markers play essential roles in BC pathogenesis.
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Affiliation(s)
- Jiaying Li
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
- Department of Anesthesiology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, China
| | - Shuang Peng
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xuan Zou
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032 China
| | - Xiangnan Geng
- Department of Clinical Engineering, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Tongshan Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Wei Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Tiansong Xia
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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Hashemi M, Hasani S, Hajimazdarany S, Ghadyani F, Olyaee Y, Khodadadi M, Ziyarani MF, Dehghanpour A, Salehi H, Kakavand A, Goharrizi MASB, Aref AR, Salimimoghadam S, Akbari ME, Taheriazam A, Hushmandi K, Entezari M. Biological functions and molecular interactions of Wnt/β-catenin in breast cancer: Revisiting signaling networks. Int J Biol Macromol 2023; 232:123377. [PMID: 36702226 DOI: 10.1016/j.ijbiomac.2023.123377] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/27/2022] [Accepted: 01/15/2023] [Indexed: 01/24/2023]
Abstract
Changes in lifestyle such as physical activity and eating habits have been one of the main reasons for development of various diseases in modern world, especially cancer. However, role of genetic factors in initiation of cancer cannot be ignored and Wnt/β-catenin signaling is such factor that can affect tumor progression. Breast tumor is the most malignant tumor in females and it causes high mortality and morbidity around the world. The survival and prognosis of patients are not still desirable, although there have been advances in introducing new kinds of therapies and diagnosis. The present review provides an update of Wnt/β-catenin function in breast cancer malignancy. The upregulation of Wnt is commonly observed during progression of breast tumor and confirms that tumor cells are dependent on this pathway Wnt/β-catenin induction prevents apoptosis that is of importance for mediating drug resistance. Furthermore, Wnt/β-catenin signaling induces DNA damage repair in ameliorating radio-resistance. Wnt/β-catenin enhances proliferation and metastasis of breast tumor. Wnt/β-catenin induces EMT and elevates MMP expression. Furthermore, Wnt/β-catenin participates in tumor microenvironment remodeling and due to its tumor-promoting factor, drugs for its suppression have been developed. Different kinds of upstream mediators Wnt/β-catenin signaling in breast cancer have been recognized that their targeting is a therapeutic approach. Finally, Wnt/β-catenin can be considered as a biomarker in clinical trials.
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Affiliation(s)
- Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sahar Hasani
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Shima Hajimazdarany
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fatemeh Ghadyani
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Yeganeh Olyaee
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Marzieh Khodadadi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maryam Fallah Ziyarani
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Amir Dehghanpour
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Hasti Salehi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Amirabbas Kakavand
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | | | - Amir Reza Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Translational Sciences, Xsphera Biosciences Inc., 6 Tide Street, Boston, MA 02210, USA
| | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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9
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Deng L, Fan Z, Xiao X, Liu H, Zhang J. Dual-Channel Heterogeneous Graph Neural Network for Predicting microRNA-Mediated Drug Sensitivity. J Chem Inf Model 2022; 62:5929-5937. [PMID: 36413746 DOI: 10.1021/acs.jcim.2c01060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Many studies have confirmed that microRNAs (miRNAs) are mediated in the sensitivity of tumor cells to anticancer drugs. MiRNAs are emerging as a type of promising therapeutic targets to overcome drug resistance. However, there is limited attention paid to the computational prediction of the associations between miRNAs and drug sensitivity. In this work, we proposed a heterogeneous network-based representation learning method to predict miRNA-drug sensitivity associations (DGNNMDA). An miRNA-drug heterogeneous network was constructed by integrating miRNA similarity network, drug similarity network, and experimentally validated miRNA-drug sensitivity associations. Next, we developed a dual-channel heterogeneous graph neural network model to perform feature propagation among the homogeneous and heterogeneous nodes so that our method can learn expressive representations for miRNA and drug nodes. On two benchmark datasets, our method outperformed other seven competitive methods. We also verified the effectiveness of the feature propagations on homogeneous and heterogeneous nodes. Moreover, we have conducted two case studies to verify the reliability of our methods and tried to reveal the regulatory mechanism of miRNAs mediated in drug sensitivity. The source code and datasets are freely available at https://github.com/19990915fzy/DGNNMDA.
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Affiliation(s)
- Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha410083, China
| | - Ziyu Fan
- School of Computer Science and Engineering, Central South University, Changsha410083, China
| | - Xiaojun Xiao
- Software School, Xinjiang University, Urumqi830091, China
| | - Hui Liu
- School of Computer Science and Technology, Nanjing Tech University, Nanjing211816, China
| | - Jiaxuan Zhang
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, California92161, United States
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10
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MicroRNAs as Potential Tools for Predicting Cancer Patients’ Susceptibility to SARS-CoV-2 Infection and Vaccination Response. Cells 2022; 11:cells11152279. [PMID: 35892576 PMCID: PMC9332853 DOI: 10.3390/cells11152279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Coronavirus disease (COVID-19) is an infectious disease that is caused by a highly contagious and severe acute respiratory syndrome—coronavirus 2 (SARS-CoV-2). This infection started to spread across the world in 2019 and rapidly turned into a global pandemic, causing an urgent necessity for treatment strategies development. The mRNA vaccines against SARS-CoV-2 can trigger an immune response, providing genetic information that allows the production of spike glycoproteins. MiRNAs play a crucial role in diverse key cellular processes, including antiviral defense. Several miRNAs are described as key factors in SARS-CoV-2 human infection through the regulation of ACE2 levels and by the inhibition of SARS-CoV-2 replication and spike expression. Consequently, these molecules have been considered as highly promising biomarkers. In numerous human malignancies, it has been recognized that miRNAs expression is dysregulated. Since miRNAs can target SARS-CoV-2-associated mRNAs, in cancer patients, the deregulation of these molecules can impair the immune response to the vaccines. Therefore, in this review, we propose a miRNA profile of seven SARS-CoV-2-related miRNAs, namely miR-214, miR-98-5p, miR-7-5p, miR-24-3p, miR-145-5p, miR-223-3p and miR-15b-5p, that are deregulated in a high number of cancers and have the potential to be used as prognostic biomarkers to stratify cancer patients.
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11
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Huang Z, Yang L, Chen J, Li S, Huang J, Chen Y, Liu J, Wang H, Yu H. CCDC134 as a Prognostic-Related Biomarker in Breast Cancer Correlating With Immune Infiltrates. Front Oncol 2022; 12:858487. [PMID: 35311121 PMCID: PMC8927640 DOI: 10.3389/fonc.2022.858487] [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] [Received: 01/20/2022] [Accepted: 02/08/2022] [Indexed: 12/24/2022] Open
Abstract
Background The expression of Coiled-Coil Domain Containing 134(CCDC134) is up-regulated in different pan-cancer species. However, its prognostic value and correlation with immune infiltration in breast cancer are unclear. Therefore, we evaluated the prognostic role of CCDC134 in breast cancer and its correlation with immune invasion. Methods We downloaded the transcription profile of CCDC134 between breast cancer and normal tissues from the Cancer Genome Atlas (TCGA). CCDC134 protein expression was assessed by the Clinical Proteomic Cancer Analysis Consortium (CPTAC) and the Human Protein Atlas. Gene set enrichment analysis (GSEA) was also used for pathway analysis. Receiver operating characteristic (ROC) curve was used to differentiate breast cancer from adjacent normal tissues. Kaplan-Meier method was used to evaluate the effect of CCDC134 on survival rate. The protein-protein interaction (PPI) network is built from STRING. Function expansion analysis is performed using the ClusterProfiler package. Through tumor Immune Estimation Resource (TIMER) and tumor Immune System Interaction database (TISIDB) to determine the relationship between CCDC134 expression level and immune infiltration. CTD database is used to predict drugs that inhibit CCDC134 and PubChem database is used to determine the molecular structure of identified drugs. Results The expression of CCDC134 in breast cancer tissues was significantly higher than that of CCDC134 mRNA expression in adjacent normal tissues. ROC curve analysis showed that the AUC value of CCDC134 was 0.663. Kaplan-meier survival analysis showed that patients with high CCDC134 had a lower prognosis (57.27 months vs 36.96 months, P = 2.0E-6). Correlation analysis showed that CCDC134 mRNA expression was associated with tumor purity immune invasion. In addition, CTD database analysis identified abrine, Benzo (A) Pyrene, bisphenol A, Soman, Sunitinib, Tetrachloroethylene, Valproic Acid as seven targeted therapy drugs that may be effective treatments for seven targeted therapeutics. It may be an effective treatment for inhibiting CCDC134. Conclusion In breast cancer, upregulated CCDC134 is significantly associated with lower survival and immune infiltrates invasion. Our study suggests that CCDC134 can serve as a biomarker of poor prognosis and a potential immunotherapy target in breast cancer. Seven drugs with significant potential to inhibit CCDC134 were identified.
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Affiliation(s)
- Zhijian Huang
- Department of Breast Surgical Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China.,The Graduate School of Fujian Medical University, Fuzhou, China
| | - Linhui Yang
- Department of Breast Surgical Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Jian Chen
- Department of Breast Surgical Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Shixiong Li
- Department of Breast Surgical Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Jing Huang
- Department of Pharmacy, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Yijie Chen
- Department of Ultrasound, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Jingbo Liu
- Pathology Department, Daqing Longnan Hospital, The Fifth Affiliated Hospital of Qiqihar Medical College, Daqing, China
| | - Hongyan Wang
- Department of Pathology, Daqing Oilfield General Hospital, Daqing, China
| | - Hui Yu
- Department of Pharmacy, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
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12
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Kaur B, Mukhlis Y, Natesh J, Penta D, Musthapa Meeran S. Identification of hub genes associated with EMT-induced chemoresistance in breast cancer using integrated bioinformatics analysis. Gene 2022; 809:146016. [PMID: 34655723 DOI: 10.1016/j.gene.2021.146016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/17/2021] [Accepted: 10/11/2021] [Indexed: 02/07/2023]
Abstract
Chemoresistance is one of the major challenges in the treatment of breast cancer. Recent evidence suggests that epithelial-to-mesenchymal transition (EMT) plays a critical role in not only metastasis but also in chemoresistance, hence causing tumor relapse. This study aimed to identify the hub genes associated with EMT and chemoresistance in breast cancer affecting patient/clinical survival. Commonly differentially expressed genes (DEGs) during EMT and chemoresistance in breast cancer cells were identified using publicly available datasets, GSE23655, GSE39359, GSE33146 and GSE76540. Hierarchical clustering analysis was utilized to determine the commonly DEGs expression pattern in chemoresistant (CR) breast cancer cells. GSEA revealed that EMT-related genes sets were enriched in the CR samples. Further, we found that EMT-induced breast cancer cells showed overexpression of drug efflux transporters along with resistance to chemotherapeutic drug. Pathway enrichment analysis revealed that the commonly DEGs were enriched in immunological pathways, early endosome, protein dimerization, and proteoglycans in cancer. Further, we identified eight hub genes from the protein-protein interaction (PPI) network. We validated the gene expression levels of the hub genes among TCGA breast cancer samples using UALCAN. Survival analysis for the hub genes was performed using KM plotter, which showed a worse relapse-free survival (RFS) of the hub genes among breast cancer patients. In conclusion, this study identified eight hub genes that play an important role in the pathways underlying EMT-induced chemoresistance in breast cancer and can be used as therapeutic targets after clinical validation.
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Affiliation(s)
- Bhavjot Kaur
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India
| | - Yahya Mukhlis
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jagadish Natesh
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Dhanamjai Penta
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Syed Musthapa Meeran
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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13
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Rajarajan D, Natesh J, Penta D, Meeran SM. Dietary Piperine Suppresses Obesity-Associated Breast Cancer Growth and Metastasis by Regulating the miR-181c-3p/ PPARα Axis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15562-15574. [PMID: 34905918 DOI: 10.1021/acs.jafc.1c05670] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Adipocyte-derived leptin activates multiple oncogenic signaling, leading to breast cancer cell progression and metastasis. Hence, finding effective strategies to inhibit the oncogenic effects of leptin would provide a novel approach for disrupting obesity-associated breast cancer. In the current study, we explored the role of piperine, a major plant alkaloid from Piper nigrum (black pepper), against leptin-induced breast cancer. Piperine treatment significantly inhibited leptin-induced breast cancer cell proliferation, colony formation, migration, and invasion. We found that piperine downregulated the expression of PPARα, a predicted target of miR-181c-3p. Mechanistically, piperine potentiates miR-181c-3p-mediated anticancer potential in leptin-induced breast cancer cells. Interestingly, the knockdown of PPARα reduced the proliferative potential of leptin-induced breast cancer cells. Further, oral administration of piperine inhibited breast tumor growth in diet-induced obese mice, accompanied by the upregulation of miR-181c-3p and downregulation of PPARα expression. Together, piperine represents a potential candidate for further development as an anticancer agent for treating obesity-associated breast cancer.
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Affiliation(s)
- Dheeran Rajarajan
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jagadish Natesh
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Dhanamjai Penta
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Syed Musthapa Meeran
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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