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Feng Y, Shan L, Gong Y, Hang W, Sang Z, Sun Y, Tang K, Wang Y, Hu B, Xi X. Identification of ubiquitin markers for survival and prognosis of ovarian cancer. Heliyon 2024; 10:e37288. [PMID: 39315145 PMCID: PMC11417246 DOI: 10.1016/j.heliyon.2024.e37288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 08/11/2024] [Accepted: 08/30/2024] [Indexed: 09/25/2024] Open
Abstract
Ovarian cancer (OC) is one of the most common malignancies and a leading cause of death among women worldwide. The ubiquitin pathway plays an important role in OC development. Using the single nucleotide polymorphism data obtained using the prevalence and dominance strategies, four ubiquitin marker genes were identified according to their expression levels: BARD1, BRCA2, FANCA, and BRCA1. Based on these four genes, a consensus clustering of OC expression data was performed. The significant differences in the survival analysis, ESTIMATE, and CIBERSORT results among the clusters indicated the pivotal role of these four genes in OC development. Of the ubiquitin-representative genes in each cluster, two ubiquitin genes, TOP2A and MYLIP, were identified in the survival risk model after univariate survival, Least Absolute Shrinkage and Selection Operator regression, and multivariate survival analyses. The reliability and robustness of both the training and validation data were confirmed by comparing the significant survival difference between high- and low-risk patients. We further explored the association between our risk model and clinical outcomes as well as predicted potentially interacting drugs. The co-expression network showed clear interactions among the four marker genes and two model genes and between high- and low-risk differentially expressed genes. Significantly enriched genes were found in pathways associated with ion channels, channel activity, and neuroactive ligand-receptor interactions. Therefore, suggesting the involvement of ubiquitin genes in the survival and development of OC through neurohumoral regulation. Our results will provide valuable reference or supplementary information for studies investigating OC diagnosis and therapies.
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Affiliation(s)
- Yiwen Feng
- Departments of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, PR China
| | - Liyun Shan
- Departments of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, PR China
| | - Yanping Gong
- Departments of Oncology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, PR China
| | - Wenzhao Hang
- Departments of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, PR China
| | - Zhenyu Sang
- Departments of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, PR China
| | - Yunyan Sun
- Departments of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, PR China
| | - Kefu Tang
- Center for Reproductive Medicne, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200135, PR China
| | - Yulan Wang
- Departments of Oncology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, PR China
| | - Binjie Hu
- Departments of Oncology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, PR China
| | - Xiaowei Xi
- Departments of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, PR China
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2
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Ferreira T, da Costa RMG, Dias F, Gama A, Gaspar VM, Mano JF, Oliveira PA, Medeiros R. Exploring the role of microRNAs as diagnostic and prognostic biomarkers in canine mammary tumors. GeroScience 2024:10.1007/s11357-024-01260-7. [PMID: 38954129 DOI: 10.1007/s11357-024-01260-7] [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: 03/18/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Canine mammary tumors (CMTs) represent a significant health concern in dogs, with a high incidence among intact female dogs. CMTs are a promising comparative model for human breast cancer, due to sharing several pathophysiological features. Additionally, CMTs have a strong genetic correlation with their human counterpart, including the expression of microRNAs (miRNAs). MiRNAs are a class of non-coding RNAs that play important roles in post-translational regulation of gene expression, being implicated in carcinogenesis, tumor progression, and metastasis. Moreover, miRNAs hold promise as diagnostic, prognostic, and metastatic biomarkers. Understanding the molecular mechanisms underlying CMTs is crucial for improving diagnosis, prognosis, and monitoring of treatments. Herein, we provide a comprehensive overview of the current knowledge on miRNAs in CMTs, highlighting their roles in carcinogenesis and their potential as biomarkers. Additionally, we highlight the current limitations and critically discuss the overarching challenges in this field, emphasizing the need for future research to translate miRNA findings into veterinary clinical practice.
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Affiliation(s)
- Tiago Ferreira
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal.
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal.
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal.
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Rui M Gil da Costa
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Postgraduate Program in Adult Health (PPGSAD), Federal University of Maranhão (UFMA), São Luís, Brazil
| | - Francisca Dias
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal
| | - Adelina Gama
- Animal and Veterinary Research Centre (CECAV), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - Vítor M Gaspar
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - João F Mano
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Paula A Oliveira
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal.
- Faculty of Medicine of the University of Porto (FMUP), 4200-319, Porto, Portugal.
- Research Department of the Portuguese League against Cancer-Regional Nucleus of the North (Liga Portuguesa Contra o Cancro-Núcleo Regional do Norte), 4200-177, Porto, Portugal.
- Virology Service, Portuguese Institute of Oncology (IPO), 4200-072, Porto, Portugal.
- Biomedical Research Center (CEBIMED), Faculty of Health Sciences of the Fernando Pessoa University, 4249-004, Porto, Portugal.
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3
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Delek FSP, Tunçer ŞB, Ödemiş DA, Erciyas SK, Erdoğan ÖŞ, Saip P, Yazıcı H. miR-3653-3p Expression in PBMCs: Unveiling the Diagnostic Potential for Ovarian Cancer. Biochem Genet 2024:10.1007/s10528-024-10819-0. [PMID: 38705961 DOI: 10.1007/s10528-024-10819-0] [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: 12/02/2023] [Accepted: 04/18/2024] [Indexed: 05/07/2024]
Abstract
Ovarian cancer is typically diagnosed at an advanced stage, recurs early and often, and currently lacks effective treatment. Therefore, overall survival and progression-free survival are relatively short for this disease. Sensitive and specific biomarkers for early diagnosis and follow-up for effective treatment of the disease are currently lacking. MicroRNA (miRNA/miR) expression studies are widely used in cancer research. Disruption or malfunction of miRNAs, a class of noncoding small RNAs, has been implicated in cancer progression in several publications. Of note, the expression of a series of miRNAs is known to differ in ovarian cancer. In cancer research, it is crucial to analyze expression patterns in both cancer patients and healthy individuals to identify cancer-specific biological markers and to understand their role in cancer. In the present study, the expression levels of miR-3653-3p in the peripheral blood mononuclear cells (PBMCs) of 150 patients with high-risk ovarian cancer were determined, including those with a family history of cancer or an early-age diagnosis of ovarian cancer, as well as 100 healthy individuals. The results were then compared between the two groups. The expression level of miR-3653-3p in the PBMCs of patients with ovarian cancer was determined to be 9.49-fold higher than that in the healthy control group, and this result was statistically significant (P < 0.001). In addition, receiver-operating characteristic curve analysis of PBMC showed statistical significance of miR-3653-3p in discriminating ovarian cancer patients from healthy subjects (P < 0.001). These results suggest that miR-3653-3p detected in peripheral blood may be used as a non-invasive biomarker for ovarian cancer.
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Affiliation(s)
- Fatma Seher Pektopal Delek
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
- Division of Cancer Genetics, Department of Basic Oncology, Institute of Health Sciences, Istanbul University, Vezneciler-Fatih, 32416, Istanbul, Türkiye
| | - Şeref Buğra Tunçer
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
| | - Demet Akdeniz Ödemiş
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
| | - Seda Kılıç Erciyas
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
| | - Özge Şükrüoğlu Erdoğan
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
| | - Pınar Saip
- Department of Clinical Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
| | - Hülya Yazıcı
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye.
- Department of Medical Biology and Genetics, Faculty of Medicine, Istanbul Arel University, Cevizlibağ-Zeytinburnu, 34010, Istanbul, Türkiye.
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4
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Gherman LM, Tomuleasa D, Cismaru A, Nutu A, Berindan-Neagoe I. Exploring the contrasts: in-depth analysis of human and canine mammary tumors - discoveries at the frontier. Med Pharm Rep 2024; 97:132-142. [PMID: 38746025 PMCID: PMC11090284 DOI: 10.15386/mpr-2733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/01/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
We have examined genomic and transcriptomic abnormalities in human and canine samples to evaluate the canine model's validity for breast cancer research, emphasizing similarities and differences. Both species commonly utilize serum tumor markers and noncoding microRNAs. Immunohistochemistry and immunocytochemistry were employed to illustrate and compare results based on histological diagnoses. In addition to these factors, similarities exist in spontaneous tumor occurrence, age of onset, hormonal influences, and disease progression, including tumor size, clinical stage, and lymph node involvement. Molecular traits such as hormone receptor status, Epidermal Growth Factor Receptor (EGFR), and proliferation markers (Ki67) further endorse the canine model's utility in breast cancer studies. The advancement of technologies facilitates the identification of new cancer-associated molecules, both coding and non-coding genes, underscoring their potential as prognostic/diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Luciana Madalina Gherman
- Experimental Centre of Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Diana Tomuleasa
- MEDFUTURE - The Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andrei Cismaru
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andreea Nutu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Doctoral School, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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5
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Rezaee A, Ahmadpour S, Jafari A, Aghili S, Zadeh SST, Rajabi A, Raisi A, Hamblin MR, Mahjoubin-Tehran M, Derakhshan M. MicroRNAs, long non-coding RNAs, and circular RNAs and gynecological cancers: focus on metastasis. Front Oncol 2023; 13:1215194. [PMID: 37854681 PMCID: PMC10580988 DOI: 10.3389/fonc.2023.1215194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/28/2023] [Indexed: 10/20/2023] Open
Abstract
Gynecologic cancer is a significant cause of death in women worldwide, with cervical cancer, ovarian cancer, and endometrial cancer being among the most well-known types. The initiation and progression of gynecologic cancers involve a variety of biological functions, including angiogenesis and metastasis-given that death mostly occurs from metastatic tumors that have invaded the surrounding tissues. Therefore, understanding the molecular pathways underlying gynecologic cancer metastasis is critical for enhancing patient survival and outcomes. Recent research has revealed the contribution of numerous non-coding RNAs (ncRNAs) to metastasis and invasion of gynecologic cancer by affecting specific cellular pathways. This review focuses on three types of gynecologic cancer (ovarian, endometrial, and cervical) and three kinds of ncRNAs (long non-coding RNAs, microRNAs, and circular RNAs). We summarize the detailed role of non-coding RNAs in the different pathways and molecular interactions involved in the invasion and metastasis of these cancers.
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Affiliation(s)
- Aryan Rezaee
- Student Research Committee, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Ahmadpour
- Biotechnology Department, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Ameneh Jafari
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sarehnaz Aghili
- Department of Gynecology and Obstetrics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Ali Rajabi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Arash Raisi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Maryam Mahjoubin-Tehran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marzieh Derakhshan
- Shahid Beheshti Fertility Clinic, Department of Gynecology and Obsteterics, Isfahan University of Medical Sciences, Isfahan, Iran
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6
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Ruiz-Manriquez LM, Villarreal-Garza C, Benavides-Aguilar JA, Torres-Copado A, Isidoro-Sánchez J, Estrada-Meza C, Arvizu-Espinosa MG, Paul S, Cuevas-Diaz Duran R. Exploring the Potential Role of Circulating microRNAs as Biomarkers for Predicting Clinical Response to Neoadjuvant Therapy in Breast Cancer. Int J Mol Sci 2023; 24:9984. [PMID: 37373139 PMCID: PMC10297903 DOI: 10.3390/ijms24129984] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is a leading cause of cancer-related deaths among women worldwide. Neoadjuvant therapy (NAT) is increasingly being used to reduce tumor burden prior to surgical resection. However, current techniques for assessing tumor response have significant limitations. Additionally, drug resistance is commonly observed, raising a need to identify biomarkers that can predict treatment sensitivity and survival outcomes. Circulating microRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and have been shown to play a significant role in cancer progression as tumor inducers or suppressors. The expression of circulating miRNAs has been found to be significantly altered in breast cancer patients. Moreover, recent studies have suggested that circulating miRNAs can serve as non-invasive biomarkers for predicting response to NAT. Therefore, this review provides a brief overview of recent studies that have demonstrated the potential of circulating miRNAs as biomarkers for predicting the clinical response to NAT in BC patients. The findings of this review will strengthen future research on developing miRNA-based biomarkers and their translation into medical practice, which could significantly improve the clinical management of BC patients undergoing NAT.
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Affiliation(s)
- Luis M. Ruiz-Manriquez
- School of Medicine and Health Sciences, Tecnologico de Monterrey, Monterrey 64700, Mexico;
- School of Engineering and Sciences, Tecnologico de Monterrey, Queretaro 76130, Mexico
| | - Cynthia Villarreal-Garza
- Breast Cancer Center, Hospital Zambrano Hellion TecSalud, Tecnologico de Monterrey, Monterrey 64700, Mexico;
| | | | - Andrea Torres-Copado
- School of Engineering and Sciences, Tecnologico de Monterrey, Queretaro 76130, Mexico
| | - José Isidoro-Sánchez
- School of Engineering and Sciences, Tecnologico de Monterrey, Queretaro 76130, Mexico
| | - Carolina Estrada-Meza
- School of Engineering and Sciences, Tecnologico de Monterrey, Queretaro 76130, Mexico
| | | | - Sujay Paul
- School of Engineering and Sciences, Tecnologico de Monterrey, Queretaro 76130, Mexico
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Martins I, Neves-Silva D, Ascensão-Ferreira M, Dias AF, Ribeiro D, Isidro AF, Quitéria R, Paramos-de-Carvalho D, Barbosa-Morais NL, Saúde L. Mouse Spinal Cord Vascular Transcriptome Analysis Identifies CD9 and MYLIP as Injury-Induced Players. Int J Mol Sci 2023; 24:6433. [PMID: 37047406 PMCID: PMC10094762 DOI: 10.3390/ijms24076433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Traumatic spinal cord injury (SCI) initiates a cascade of cellular events, culminating in irreversible tissue loss and neuroinflammation. After the trauma, the blood vessels are destroyed. The blood-spinal cord barrier (BSCB), a physical barrier between the blood and spinal cord parenchyma, is disrupted, facilitating the infiltration of immune cells, and contributing to a toxic spinal microenvironment, affecting axonal regeneration. Understanding how the vascular constituents of the BSCB respond to injury is crucial to prevent BSCB impairment and to improve spinal cord repair. Here, we focus our attention on the vascular transcriptome at 3- and 7-days post-injury (dpi), during which BSCB is abnormally leaky, to identify potential molecular players that are injury-specific. Using the mouse contusion model, we identified Cd9 and Mylip genes as differentially expressed at 3 and 7 dpi. CD9 and MYLIP expression were injury-induced on vascular cells, endothelial cells and pericytes, at the injury epicentre at 7 dpi, with a spatial expression predominantly at the caudal region of the lesion. These results establish CD9 and MYLIP as two new potential players after SCI, and future studies targeting their expression might bring promising results for spinal cord repair.
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Affiliation(s)
- Isaura Martins
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Dalila Neves-Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Mariana Ascensão-Ferreira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana Filipa Dias
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Daniel Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana Filipa Isidro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Raquel Quitéria
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Diogo Paramos-de-Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Nuno L. Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Leonor Saúde
- Instituto de Medicina Molecular João Lobo Antunes e Instituto de Histologia e Biologia do Desenvolvimento, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
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Chen J, Han G, Xu A, Akutsu T, Cai H. Identifying miRNA-Gene Common and Specific Regulatory Modules for Cancer Subtyping by a High-Order Graph Matching Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:421-431. [PMID: 35320104 DOI: 10.1109/tcbb.2022.3161635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Identifying regulatory modules between miRNAs and genes is crucial in cancer research. It promotes a comprehensive understanding of the molecular mechanisms of cancer. The genomic data collected from subjects usually relate to different cancer statuses, such as different TNM Classifications of Malignant Tumors (TNM) or histological subtypes. Simple integrated analyses generally identify the core of the tumorigenesis (common modules) but miss the subtype-specific regulatory mechanisms (specific modules). In contrast, separate analyses can only report the differences and ignore important common modules. Therefore, there is an urgent need to develop a novel method to jointly analyze miRNA and gene data of different cancer statuses to identify common and specific modules. To that end, we developed a High-Order Graph Matching model to identify Common and Specific modules (HOGMCS) between miRNA and gene data of different cancer statuses. We first demonstrate the superiority of HOGMCS through a comparison with four state-of-the-art techniques using a set of simulated data. Then, we apply HOGMCS on stomach adenocarcinoma data with four TNM stages and two histological types, and breast invasive carcinoma data with four PAM50 subtypes. The experimental results demonstrate that HOGMCS can accurately extract common and subtype-specific miRNA-gene regulatory modules, where many identified miRNA-gene interactions have been confirmed in several public databases.
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9
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Zhang R, Zhang D, Sun X, Song X, Yan KC, Liang H. Polyvinyl alcohol/gelatin hydrogels regulate cell adhesion and chromatin accessibility. Int J Biol Macromol 2022; 219:672-684. [PMID: 35952815 DOI: 10.1016/j.ijbiomac.2022.08.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 12/24/2022]
Abstract
Cell adhesion has a critical influence on various processes such as cancer metastasis and wound healing. Many substrates have been used for studying cell adhesion and its related biological processes, it is still highly desirable to have a simply prepared and low-cost substrate suitable for regulating cell adhesion. In this study, we produced a series of polyvinyl alcohol/gelatin hydrogels with different gelatin concentrations via dry-annealing method. Our data showed that the protein adsorbing capability was enhanced and cell adhesion area and the ratio of non-spherical cells were increased with the increment of gelatin concentration. We also observed that varying cell adhesion conditions induced by polyvinyl alcohol /gelatin hydrogels resulted in expression level changes of genes involved in mechanotransduction from extracellular matrices (ECM) to the nucleus. In particular, we detected a widespread increase in chromatin accessibility under poor cell adhesion condition. This work provides a useful hydrogel system for regulating cell adhesion and opens up new possibilities for the design of biomaterials for cell adhesion study.
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Affiliation(s)
- Ran Zhang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China
| | - Duo Zhang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China
| | - Xingyue Sun
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China
| | - Xiaoyuan Song
- MOE Key Laboratory for Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Karen Chang Yan
- Mechanical Engineering and Biomedical Engineering, The College of New Jersey, Ewing, NJ, USA.
| | - Haiyi Liang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China; School of Civil Engineering, Anhui Jianzhu University, Hefei, China; IAT-Chungu Joint Laboratory for Additive Manufacturing, Anhui Chungu 3D printing Institute of Intelligent Equipment and Industrial Technology, Wuhu, China.
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10
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Li ZL, Li D, Yin GQ. MiR-19b-3p promotes tumor progression of non-small cell lung cancer via downregulating HOXA9 and predicts poor prognosis in patients. Histol Histopathol 2022; 37:779-789. [PMID: 35274735 DOI: 10.14670/hh-18-448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
MiR-19b-3p has been reported in several types of human cancer. Nevertheless, the expression profile and biological functions of miR-19b-3p remain unclear in non-small cell lung cancer (NSCLC). The expression level of miR-19b-3p was evaluated in NSCLC tissues and cell lines using qRT-PCR. Survival analysis was performed using Kaplan-Meier curves, while the prognostic significance of miR-19b-3p was analyzed using Cox regression analysis in 80 NSCLC patients. The effects of miR-19b-3p on cell proliferation and invasion capacities were analyzed using CCK-8, crystal violet, and transwell assays. Target genes of miR-19b-3p were assessed using luciferase reporter assay, qRT-PCR, Western blot and rescue experiments. MiR-19b-3p was found to be upregulated in human NSCLC tissues and cell lines. The expression of miR-19b-3p was observed to be closely associated with TNM stage and metastasis. High expression of miR-19b-3p was found to be capable of predicting poor clinical prognosis in NSCLC patients. Whilst overexpression of miR-19b-3p was demonstrated to promote the proliferation and invasion of NSCLC cells, knockdown of miR-19b-3p showed an opposite inhibitory effect. Bioinformatics analysis and luciferase reporter assays confirmed that HOXA9 is a direct target of miR-19b-3p. Functional assays demonstrated that NSCLC cell proliferation and invasion were promoted by miR-19b-3p via negative regulation of HOXA9. Finally, overexpression of HOXA9 was shown to partially reverse the tumor promoting effect of miR-19b-3p. This study indicates that miR-19b-3p is a crucial prognostic biomarker of NSCLC, and that targeting of the miR-19b-3p/HOXA9 axis may be a promising strategy in NSCLC therapy.
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Affiliation(s)
- Zu-Lei Li
- Department of Thoracic Surgery, Zibo Central Hospital, Zibo, Shandong Province, PR China
| | - Dong Li
- Department of Thoracic Surgery, Zibo Central Hospital, Zibo, Shandong Province, PR China
| | - Guo-Qiang Yin
- Department of Thoracic Surgery, Zibo Central Hospital, Zibo, Shandong Province, PR China.
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Siegl F, Vecera M, Roskova I, Smrcka M, Jancalek R, Kazda T, Slaby O, Sana J. The Significance of MicroRNAs in the Molecular Pathology of Brain Metastases. Cancers (Basel) 2022; 14:cancers14143386. [PMID: 35884446 PMCID: PMC9322877 DOI: 10.3390/cancers14143386] [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: 05/26/2022] [Revised: 07/07/2022] [Accepted: 07/10/2022] [Indexed: 12/07/2022] Open
Abstract
Brain metastases are the most frequent intracranial tumors in adults and the cause of death in almost one-fourth of cases. The incidence of brain metastases is steadily increasing. The main reason for this increase could be the introduction of new and more efficient therapeutic strategies that lead to longer survival but, at the same time, cause a higher risk of brain parenchyma infiltration. In addition, the advances in imaging methodology, which provide earlier identification of brain metastases, may also be a reason for the higher recorded number of patients with these tumors. Metastasis is a complex biological process that is still largely unexplored, influenced by many factors and involving many molecules. A deeper understanding of the process will allow the discovery of more effective diagnostic and therapeutic approaches that could improve the quality and length of patient survival. Recent studies have shown that microRNAs (miRNAs) are essential molecules that are involved in specific steps of the metastatic cascade. MiRNAs are endogenously expressed small non-coding RNAs that act as post-transcriptional regulators of gene expression and thus regulate most cellular processes. The dysregulation of these molecules has been implicated in many cancers, including brain metastases. Therefore, miRNAs represent promising diagnostic molecules and therapeutic targets in brain metastases. This review summarizes the current knowledge on the importance of miRNAs in brain metastasis, focusing on their involvement in the metastatic cascade and their potential clinical implications.
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Affiliation(s)
- Frantisek Siegl
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (F.S.); (M.V.); (O.S.)
| | - Marek Vecera
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (F.S.); (M.V.); (O.S.)
| | - Ivana Roskova
- Department of Neurosurgery, University Hospital Brno and Faculty of Medicine of Masaryk University, 625 00 Brno, Czech Republic; (I.R.); (M.S.)
| | - Martin Smrcka
- Department of Neurosurgery, University Hospital Brno and Faculty of Medicine of Masaryk University, 625 00 Brno, Czech Republic; (I.R.); (M.S.)
| | - Radim Jancalek
- Department of Neurosurgery, St. Annes University Hospital Brno and Faculty of Medicine of Masaryk University, 656 91 Brno, Czech Republic;
| | - Tomas Kazda
- Department of Radiation Oncology, Masaryk Memorial Cancer Institute and Faculty of Medicine of Masaryk University, 656 53 Brno, Czech Republic;
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (F.S.); (M.V.); (O.S.)
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Jiri Sana
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (F.S.); (M.V.); (O.S.)
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute and Faculty of Medicine of Masaryk University, 656 53 Brno, Czech Republic
- Department of Pathology, University Hospital Brno, 625 00 Brno, Czech Republic
- Correspondence: ; Tel.: +420-549-495-246
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Jin B, Li H, Zhang H, Yang J, Ma W, Lv M, Zheng X, Li X, Liu L, Wang K. Effects of carnosic acid on arsenic-induced liver injury in mice: A comparative transcriptomics analysis. J Trace Elem Med Biol 2022; 71:126953. [PMID: 35202923 DOI: 10.1016/j.jtemb.2022.126953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 02/06/2022] [Accepted: 02/14/2022] [Indexed: 01/29/2023]
Abstract
BACKGROUND Long-term chronic exposure to arsenic can cause different degrees of liver injury. Till date, its molecular mechanism has not meant fully elucidated. Evidence indicates that Carnosic acid (CA) has a protective role in arsenic-induced liver injury. This study aimed to reveal the potential targets and evaluate the potential effect of CA intervention at transcriptional level, and provide reference for the intervention of arsenic-induced liver injury. METHODS Arsenic-induced liver injury and CA intervention models were established in C57BL/6 mice. RNA sequencing technique was carried out to obtain the differentially expressed gene (DEG) profiles. The common covariant DEGs between arsenic induction and CA intervention was screened by comparative transcriptomic analysis methods. QRT-PCR was used to verify the covariant DEGs. RESULTS Transcriptome results showed that 220 DEGs were identified after arsenic induction. 267 DEGs were identified after CA intervention (|fold change| > 2.0 and adjusted P < 0.05). 42 covariant DEGs were discovered between the comparison of "AS vs Control" and "AS & CA vs AS". In addition, hub gene analysis revealed a total of 8 covariant DEGs (Ehhadh, Fgf21, Cyp2b10, Plin2, Aacs, Cyp7a1, Per2 and Mylip). The mRNA expressions of Fgf21 and Plin2 were significantly increased (P < 0.05) and the mRNA expressions of Cyp2b10, Cyp7a1, Per2 and Mylip were significantly decreased (P < 0.05) after arsenic induction. On the contrary, the changes of these DEGs were reversed after CA intervention. CONCLUSION The present study would be helpful to understand the potential health effects of arsenic-induced liver injury and identify new potential targets, and provide a reference for the intervention of CA.
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Affiliation(s)
- Baiming Jin
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health,Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China; Department of Preventive Medicine, Qiqihar Medical University, Qiqihar 161006, PR China.
| | - Haonan Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health,Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Hua Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health,Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Jie Yang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health,Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Wenjing Ma
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health,Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Man Lv
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health,Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Xiujuan Zheng
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health,Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China; Harbin Municipal Center for Disease Control and Prevention, Harbin 150056, PR China.
| | - Xuying Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health,Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Lele Liu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health,Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Kewei Wang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health,Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
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Petroušková P, Hudáková N, Maloveská M, Humeník F, Cizkova D. Non-Exosomal and Exosome-Derived miRNAs as Promising Biomarkers in Canine Mammary Cancer. Life (Basel) 2022; 12:life12040524. [PMID: 35455015 PMCID: PMC9032658 DOI: 10.3390/life12040524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023] Open
Abstract
Canine mammary cancer (CMC), similar to human breast cancer (HBC) in many aspects, is the most common neoplasm associated with significant mortality in female dogs. Due to the limited therapy options, biomarkers are highly desirable for early clinical diagnosis or cancer progression monitoring. Since the discovery of microRNAs (miRNAs or miRs) as post-transcriptional gene regulators, they have become attractive biomarkers in oncological research. Except for intracellular miRNAs and cell-free miRNAs, exosome-derived miRNAs (exomiRs) have drawn much attention in recent years as biomarkers for cancer detection. Analysis of exosomes represents a non-invasive, pain-free, time- and money-saving alternative to conventional tissue biopsy. The purpose of this review is to provide a summary of miRNAs that come from non-exosomal sources (canine mammary tumor, mammary tumor cell lines or canine blood serum) and from exosomes as promising biomarkers of CMC based on the current literature. As is discussed, some of the miRNAs postulated as diagnostic or prognostic biomarkers in CMC were also altered in HBC (such as miR-21, miR-29b, miR-141, miR-429, miR-200c, miR-497, miR-210, miR-96, miR-18a, miR19b, miR-20b, miR-93, miR-101, miR-105a, miR-130a, miR-200c, miR-340, miR-486), which may be considered as potential disease-specific biomarkers in both CMC and HBC.
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Affiliation(s)
- Patrícia Petroušková
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Nikola Hudáková
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Marcela Maloveská
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Filip Humeník
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Dasa Cizkova
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 10 Bratislava, Slovakia
- Correspondence: ; Tel.: +421-918-752-157
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Liu L, He H, Peng Y, Yang Z, Gao S. A four-gene prognostic signature for predicting the overall survival of patients with lung adenocarcinoma. PeerJ 2021; 9:e11911. [PMID: 34631307 PMCID: PMC8465999 DOI: 10.7717/peerj.11911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/14/2021] [Indexed: 01/12/2023] Open
Abstract
Background The prognosis of patients for lung adenocarcinoma (LUAD) is known to vary widely; the 5-year overall survival rate is just 63% even for the pathological IA stage. Thus, in order to identify high-risk patients and facilitate clinical decision making, it is vital that we identify new prognostic markers that can be used alongside TNM staging to facilitate risk stratification. Methods We used mRNA expression from The Cancer Genome Atlas (TCGA) cohort to identify a prognostic gene signature and combined this with clinical data to develop a predictive model for the prognosis of patients for lung adenocarcinoma. Kaplan-Meier curves, Lasso regression, and Cox regression, were used to identify specific prognostic genes. The model was assessed via the area under the receiver operating characteristic curve (AUC-ROC) and validated in an independent dataset (GSE50081) from the Gene Expression Omnibus (GEO). Results Our analyses identified a four-gene prognostic signature (CENPH, MYLIP, PITX3, and TRAF3IP3) that was associated with the overall survival of patients with T1-4N0-2M0 in the TCGA dataset. Multivariate regression suggested that the total risk score for the four genes represented an independent prognostic factor for the TCGA and GEO cohorts; the hazard ratio (HR) (high risk group vs low risk group) were 2.34 (p < 0.001) and 2.10 (p = 0.017). Immune infiltration estimations, as determined by an online tool (TIMER2.0) showed that CD4+ T cells were in relative abundance in the high risk group compared to the low risk group in both of the two cohorts (both p < 0.001). We established a composite prognostic model for predicting OS, combined with risk-grouping and clinical factors. The AUCs for 1-, 3-, 5- year OS in the training set were 0.750, 0.737, and 0.719; and were 0.645, 0.766, and 0.725 in the validation set. The calibration curves showed a good match between the predicted probabilities and the actual probabilities. Conclusions We identified a four-gene predictive signature which represents an independent prognostic factor and can be used to identify high-risk patients from different TNM stages of LUAD. A new prognostic model that combines a prognostic gene signature with clinical features exhibited better discriminatory ability for OS than traditional TNM staging.
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Affiliation(s)
- Lei Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huayu He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Peng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Kusmardi K, Wiyarta E, Rusdi NK, Maulana AM, Estuningtyas A, Sunaryo H. The potential of lunasin extract for the prevention of breast cancer progression by upregulating E-Cadherin and inhibiting ICAM-1. F1000Res 2021; 10:902. [PMID: 34691393 PMCID: PMC8506221 DOI: 10.12688/f1000research.55385.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/10/2021] [Indexed: 01/12/2023] Open
Abstract
Background: Research in natural substances for their anticancer potential has become increasingly popular. Lunasin, a soybean protein, is known to inhibit cancer progression via various pathways. The aim of this study was to investigate the effect of Lunasin Extract (LE) on the expression of Intercellular Adhesion Molecule 1 (ICAM-1) and epithelial cadherins (E-Cadherin) in breast cancer. Methods: In this true-experimental in vivo study, 24 Sprague-Dawley rats that were induced by 7,12-Dimethylbenz[a]anthracene (DMBA), were used. Based on the therapy given, the groups were divided into, normal, positive control (PC), negative control (NC), adjuvant, curative, and preventive. Lunasin was extracted from soybean seeds of the Grobogan variety in Indonesia. Tissue samples were obtained, processed, stained with anti-ICAM-1 and anti-E-Cadherin antibodies, examined under a microscope, and quantified using H-score. The data were analyzed using ANOVA, which was then followed by Duncan's test. Results: Statistically significant difference in ICAM-1 expression was observed between the following groups: adjuvant and NC, normal and NC, PC and NC, adjuvant and preventive, normal and preventive, PC and preventive, adjuvant and curative, normal and curative, PC and curative. E-Cadherin expression was significantly different between preventive and NC, adjuvant and NC, PC and NC, normal and NC, adjuvant and curative, PC and curative, normal and curative, normal and preventive. Significant negative correlation was found between ICAM-1 and E-Cadherin [-0.616 (-0.8165; -0.283)] with p = 0.001. Conclusion: Preventive dose of LE was able to reduce ICAM-1 expression while increasing E-Cadherin expression.
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Affiliation(s)
- Kusmardi Kusmardi
- Department of Anatomic Pathology, Faculty of Medicine, Universitas Indonesia, Salemba Raya Street no.6, Jakarta, 10430, Indonesia
- Drug Development Research Cluster, Indonesian Medical Education and Research Institute, Universitas Indonesia, Salemba Raya Street no.6, Jakarta, 10430, Indonesia
- Human Cancer Research Cluster, Indonesian Medical Education and Research Institute, Universitas Indonesia, Salemba Raya Street no.6, Jakarta, 10430, Indonesia
| | - Elvan Wiyarta
- Faculty of Medicine, Universitas Indonesia, Salemba Raya Street no.6, Jakarta, 10430, Indonesia
| | - Numlil Khaira Rusdi
- Faculty of Pharmacy and Science, Universitas Muhammadiyah Prof. DR. Hamka, Limau II Street, Jakarta, 12130, Indonesia
- Doctoral Program for Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Salemba Raya Street no.6, Jakarta, 10430, Indonesia
| | - Andi Muh. Maulana
- Doctoral Program for Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Salemba Raya Street no.6, Jakarta, 10430, Indonesia
- Faculty of Medicine, University of Muhammadiyah Purwakarta, KH. Ahmad Dahlan Street, Central Java, 53182, Indonesia
| | - Ari Estuningtyas
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Salemba Raya Street no.6, Jakarta, 10430, Indonesia
| | - Hadi Sunaryo
- Faculty of Pharmacy and Science, Universitas Muhammadiyah Prof. DR. Hamka, Limau II Street, Jakarta, 12130, Indonesia
- Doctoral Program for Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Salemba Raya Street no.6, Jakarta, 10430, Indonesia
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Liu T, Yang C, Wang W, Liu C. LncRNA SGMS1-AS1 regulates lung adenocarcinoma cell proliferation, migration, invasion, and EMT progression via miR-106a-5p/MYLI9 axis. Thorac Cancer 2021; 12:2104-2112. [PMID: 34061466 PMCID: PMC8287014 DOI: 10.1111/1759-7714.14043] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Lung cancer mainly includes non-small cell lung cancer (NSCLC). Lung adenocarcinoma (LUAD) is the main subtype of NSCLC. Long non-coding RNAs (LncRNAs) had been found to exert numerous functions on the progressions of cancers. MicroRNAs often exist as the target of LncRNAs to regulate a series of signaling pathways in human. We explored the effects and molecular mechanism of LncRNA SGMS1-AS1 on the procedures of LUAD cells. METHODS The ENCORI and GEPIA databases were used to analyze the differences in SGMS1, miR-106a-5p, and MYLIP between LUAD and normal tissue. Their expression levels were examined by RT-PCR. CCK8, colony formation, migration, and invasion assay were conducted in LUAD cells which had silenced SGMS1-AS1. To verify the relationship between SGMS1-AS1, miR-106a-5p, and MYLIP, we overexpressed miR-106a-5p inhibitor or MYLIP in LUAD cells after decreasing SGMS1-AS1 and repeated the above assays. RESULTS SGMS1-AS1 was downregulated in LUAD tissue as well as cells, which was related to good prognosis of patients with lung adenocarcinoma. Additionally, knockdown of SGMS1-AS1 promoted proliferation, migration, invasion, and epithelial mesenchymal transition (EMT) progression of LUAD cells, which meant that SGMS1-AS1 inhibited the progression of LUAD cells. Furthermore, miR-106a-5p was the direct target of SGMS1-AS1 and transfecting miR-106a-5p inhibitor could reversed the impact induced by knockdown of SGMS1-AS1. Subsequently, we found that MYLIP was the target of miR-106a-5p, which was negatively correlated with miR-106a-5p, but had high positive correlation with SGMS1-AS1. Consistently, overexpression MYLIP partly eliminated the effects on A549 cells induced by silencing of SGMS1-AS1. CONCLUSION LncRNA SGMS1-AS1 inhibits the proliferation, invasion, migration and EMT progression of LUAD cells via targeting miR-106a-5p/MYLIP axis.
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Affiliation(s)
- Ting Liu
- Department of Plumonary and Critical Care Medicine, Weifang People's Hospital, Weifang, China
| | - Chunli Yang
- Department of Plumonary and Critical Care Medicine, Weifang People's Hospital, Weifang, China
| | - Weizhen Wang
- Department of Plumonary and Critical Care Medicine, Weifang People's Hospital, Weifang, China
| | - Chunmei Liu
- Department of Plumonary and Critical Care Medicine, Weifang People's Hospital, Weifang, China
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Han K, Zhao D, Liu Q, Liu Y, Huang X, Yang J, Zhang L, Li Y. Transcriptome analysis reveals new insight of duck Tembusu virus (DTMUV)-infected DF-1 cells. Res Vet Sci 2021; 137:150-158. [PMID: 33975194 DOI: 10.1016/j.rvsc.2021.04.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022]
Abstract
Duck Tembusu virus (DTMUV) is a newly emerging pathogenic flavivirus that has caused huge economic losses to the duck industry in China since 2010. Moreover, the infection has spread rapidly, resulted in a potential public health concern. To improve our understanding of the host cellular responses to virus infection and the pathogenesis of DTMUV infection, we used RNA-Seq to detect the gene changes in DF-1 cells infected and mock-infected with DTMUV. A total of 663 differentially-expressed genes (DEGs) were identified in DTMUV-infected compared with mock-infected DF-1 cells at 24 h post-infection (hpi), among which 590 were up regulated and 73 were down regulated. Gene Ontology analysis indicated that the DEGs were mainly involved in cellular process, immune system processes, metabolic processes, and signal-organism process. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were mainly involved in several signaling pathways such as Toll-like receptor signaling, Jak-STAT signaling, RIG-I-like receptor signaling and AGE-RAGE signaling pathway. Moreover, some selected DEGs were further confirmed by real-time PCR and the results were consistent with the sequencing data. To our knowledge, this study is the first to analyze the transcriptomic change in DF-1 cells following DTMUV infection. We believe that our research provides useful information in better understanding the host response to DTMUV infection and the inherent mechanism of DTMUV replication and pathogenicity.
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Affiliation(s)
- Kaikai Han
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China; Institute of life sciences, Jiangsu University, Zhenjiang 212013, China.
| | - Dongmin Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Qingtao Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Yuzhuo Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Xinmei Huang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Jing Yang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Lijiao Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Yin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
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18
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Genome-wide analysis of the hypoxia-related DNA methylation-driven genes in lung adenocarcinoma progression. Biosci Rep 2021; 40:222062. [PMID: 32031203 PMCID: PMC7033312 DOI: 10.1042/bsr20194200] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 12/15/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a common type of lung cancer with high incidence and poor prognosis. Hypoxia and DNA methylation play important regulatory roles in cancer progression. The purpose of the present study was to explore the relationship between hypoxia and DNA methylation, and to identify key genes for hypoxia-regulated LUAD progression. Hypoxia score (HS) was calculated using the GSVA algorithm. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and protein-protein interaction (PPI) analysis were performed using clusterProfile package, STRING database and Cytoscape software. Kaplan-Meier curves of overall survival (OS) and disease-free survival (DFS) were drawn using R software. Smoking status and cancer stages were significantly associated with LUAD hypoxia, and hypoxia is a poor prognostic factor for LUAD. Compared with HS-low group, 1803 aberrantly methylated DEGs were identified in HS-high group. KEGG analysis showed that the 1803 genes were enriched in the metabolic pathways associated with hypoxia stress, angiogenesis and cancer progression. FAM20C, MYLIP and COL7A1 were identified as the hypoxia-related key genes in LUAD progression, which were regulated by DNA methylation. Hypoxia in LUAD tumor cells led to changes in DNA methylation patterns. In-depth study of the relationship between hypoxia and DNA methylation is helpful to elucidate the mechanism of tumorigenesis, and provides new ideas for LUAD treatment.
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19
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Ni M, Yan Q, Xue H, Du Y, Zhao S, Zhao Z. Identification of MYLIP gene and miRNA-802 involved in the growth and metastasis of cervical cancer cells. Cancer Biomark 2021; 30:287-298. [PMID: 33185588 DOI: 10.3233/cbm-201523] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND The dysregulation of microRNA-802 (miR-802) has crucial roles in cancer progression. Nevertheless, the bio-function of miR-802 in cervical cancer remains unclear. OBJECTIVE Hence, we illuminated the potential roles of miR-802 in cervical cancer cell growth, migration, and invasion. METHODS The levels of miR-802 and myosin regulatory light chain interacting protein (MYLIP) were measured using qRT-PCR assay. The potential effects of miRNA-802 on cervical cancer cell proliferation and metastatic phenotypes were determined using CCK-8, colony formation, wound healing and Transwell invasion assays. MYLIP was validated as a downstream target gene of miRNA-802 using bioinformatics analysis tool and luciferase report gene assay. The impact of miR-802 on the growth of cervical cancer cell in vivo was analyzed using xenograft model. The expression of MYLIP was measured by western blotting and immunohistochemistry (IHC). RESULTS MiRNA-802 was distinctly down-regulated in cervical cancer cells as well as clinical cervical cancer samples. Upregulation of miRNA-802 significantly inhibited the growth and aggressiveness of cervical cancer cell. Additional, MYLIP was a functional target of miR-802. MYLIP was ovrerexpressed in cervical cancer and MYLIP level was negatively associated with the level of miR-802. Overexpression of MYLIP eliminated the inhibitory effects of miR-802 on growth and metastatic-related traits of cervical cancer cell. In vivo, miR-802 also markedly reduced the tumor growth of cervical cancer cell and decreased the expression of MYLIP. CONCLUSIONS MiR-802 inhibits the growth and metastatic-related phenotypes of cervical cancer cell through targeting MYLIP.
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Affiliation(s)
- Ming Ni
- Gynecological Department, Wuhan Hanyang Hospital, Wuhan, Hubei, China.,Gynecological Department, Wuhan Hanyang Hospital, Wuhan, Hubei, China
| | - Qin Yan
- Department of Oncology, Chengdu Fifth People's Hospital, Chengdu, Sichuan, China.,Gynecological Department, Wuhan Hanyang Hospital, Wuhan, Hubei, China
| | - Hui Xue
- Department of Gynecology, The Qingdao Hiser Hospital, Qingdao, Shandong, China
| | - Yanfang Du
- Department of Obstetrics and Gynecology, Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shuangdan Zhao
- Department of Obstetrics and Gynecology, Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhiming Zhao
- Department of Reproductive Medicine, the Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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20
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Nair MG, Somashekaraiah VM, Ramamurthy V, Prabhu JS, Sridhar TS. miRNAs: Critical mediators of breast cancer metastatic programming. Exp Cell Res 2021; 401:112518. [PMID: 33607102 DOI: 10.1016/j.yexcr.2021.112518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
MicroRNA mediated aberrant gene regulation has been implicated in several diseases including cancer. Recent research has highlighted the role of epigenetic modulation of the complex process of breast cancer metastasis by miRNAs. miRNAs play a crucial role in the process of metastatic evolution by facilitating alterations in the phenotype of tumor cells and the tumor microenvironment that promote this process. They act as critical determinants of the multi-step progression starting from carcinogenesis all the way to organotropism. In this review, we focus on the current understanding of the compelling role of miRNAs in breast cancer metastasis.
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Affiliation(s)
- Madhumathy G Nair
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India.
| | | | - Vishakha Ramamurthy
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India
| | - Jyothi S Prabhu
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India
| | - T S Sridhar
- Division of Molecular Medicine, St. John's Research Institute, Bangalore, India
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21
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Sun Q, Li X, Xu M, Zhang L, Zuo H, Xin Y, Zhang L, Gong P. Differential Expression and Bioinformatics Analysis of circRNA in Non-small Cell Lung Cancer. Front Genet 2020; 11:586814. [PMID: 33329727 PMCID: PMC7732606 DOI: 10.3389/fgene.2020.586814] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/27/2020] [Indexed: 01/17/2023] Open
Abstract
Circular RNA (CircRNA) plays an important role in tumorigenesis and progression of non-small cell lung cancer (NSCLC), but the pathogenesis of NSCLC caused by circRNA has not been fully elucidated. This study aimed to investigate differentially expressed circRNAs and identify the underlying pathogenesis hub genes of NSCLC by comprehensive bioinformatics analysis. Data of gene expression microarrays (GSE101586, GSE101684, and GSE112214) were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed circRNAs (DECs) were obtained by the “limma” package of R programs and the overlapping operation was implemented of DECs. CircBase database and Cancer-Specific CircRNA database (CSCD) were used to find miRNAs binding to DECs. Target genes of the found miRNAs were identified utilizing Perl programs based on miRDB, miRTarBase, and TargetScan databases. Functional and enrichment analyses of selected target genes were performing using the “cluster profiler” package. Protein-protein interaction (PPI) network was constructed by the Search Tool for the STRING database and module analysis of selected hub genes was performed by Cytoscape 3.7.1. Survival analysis of hub genes were performed by Gene Expression Profiling Interactive Analysis (GEPIA). Respectively, 1 DEC, 249 DECs, and 101 DECs were identified in GSE101586, GSE101684, and GSE112214. A total of eight overlapped circRNAs, 43 miRNAs and 427 target genes were identified. Gene Ontology (GO) enrichment analysis showed these target genes were enriched in biological processes of regulation of histone methylation, Ras protein signal transduction and covalent chromatin modification etc. Pathway enrichment analysis showed these target genes are mainly involved in AMPK signaling pathway, signaling pathways regulating pluripotency of stem cells and insulin signaling pathway etc. A PPI network was constructed based on 427 target genes of the 43 miRNAs. Ten hub genes were found, of which the expression of MYLIP, GAN, and CDC27 were significantly related to NSCLC patient prognosis. Our study provide a deeper understanding the circRNAs-miRNAs-target genes by bioinformatics analysis, which may provide novel insights for unraveling pathogenesis of NSCLC. MYLIP, GAN, and CDC27 genes might serve as novel biomarker for precise treatment and prognosis of NSCLC in the future.
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Affiliation(s)
- Qiuwen Sun
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China
| | - Xia Li
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Muchen Xu
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Li Zhang
- School of Information and Control Engineering, University of Mining and Technology, Xuzhou, China
| | - Haiwei Zuo
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Yong Xin
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Cancer Institute of Xuzhou Medical University, Xuzhou, China
| | - Longzhen Zhang
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Cancer Institute of Xuzhou Medical University, Xuzhou, China
| | - Ping Gong
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
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22
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Kondrotienė A, Daukša A, Pamedytytė D, Kazokaitė M, Žvirblienė A, Daukšienė D, Simanavičienė V, Klimaitė R, Golubickaitė I, Stakaitis R, Šarauskas V, Verkauskienė R, Žilaitienė B. Plasma-Derived miRNA-222 as a Candidate Marker for Papillary Thyroid Cancer. Int J Mol Sci 2020; 21:ijms21176445. [PMID: 32899424 PMCID: PMC7503340 DOI: 10.3390/ijms21176445] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
We analyzed five miRNA molecules (miR-221; miR-222; miR-146b; miR-21; miR-181b) in the plasma of patients with papillary thyroid cancer (PTC), nodular goiter (NG) and healthy controls (HC) and evaluated their diagnostic value for differentiation of PTC from NG and HC. Preoperative PTC plasma miRNA expression (n = 49) was compared with plasma miRNA in the HC group (n = 57) and patients with NG (n = 23). It was demonstrated that miR-221; miR-222; miR-146b; miR-21 and miR-181b were overexpressed in preoperative PTC plasma samples compared to HC (p < 0.0001; p < 0.0001; p < 0.0001; p < 0.0001; p < 0.002; respectively). The upregulation in tumor tissue of these miRNAs was consistent with The Cancer Genome Atlas Thyroid Carcinoma dataset. A significant decrease in miR-21; miR-221; miR-146b and miR-181b expression was observed in the plasma of PTC patients after total thyroidectomy (p = 0.004; p = 0.001; p = 0.03; p = 0.036; respectively). The levels of miR-222 were significantly higher in the preoperative PTC compared to the NG group (p = 0.004). ROC curve (receiver operating characteristic curve) analysis revealed miR-222 as a potential marker in distinguishing PTC from NG (AUC 0.711; p = 0.004). In conclusion; circulating miR-222 profiles might be useful in discriminating PTC from NG.
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Affiliation(s)
- Aistė Kondrotienė
- Institute of Endocrinology, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (A.K.); (M.K.); (D.D.); (R.K.); (R.V.)
| | - Albertas Daukša
- Institute of Digestive Research, Medical Academy, Faculty of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania;
| | - Daina Pamedytytė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (D.P.); (A.Ž.); (V.S.)
| | - Mintautė Kazokaitė
- Institute of Endocrinology, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (A.K.); (M.K.); (D.D.); (R.K.); (R.V.)
| | - Aurelija Žvirblienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (D.P.); (A.Ž.); (V.S.)
| | - Dalia Daukšienė
- Institute of Endocrinology, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (A.K.); (M.K.); (D.D.); (R.K.); (R.V.)
| | - Vaida Simanavičienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (D.P.); (A.Ž.); (V.S.)
| | - Raimonda Klimaitė
- Institute of Endocrinology, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (A.K.); (M.K.); (D.D.); (R.K.); (R.V.)
| | - Ieva Golubickaitė
- Institute of Biology systems and genetic research, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania;
| | - Rytis Stakaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania;
| | - Valdas Šarauskas
- Department of Pathology, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania;
| | - Rasa Verkauskienė
- Institute of Endocrinology, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (A.K.); (M.K.); (D.D.); (R.K.); (R.V.)
| | - Birutė Žilaitienė
- Institute of Endocrinology, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (A.K.); (M.K.); (D.D.); (R.K.); (R.V.)
- Correspondence: ; Tel.: +370-68649882
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23
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Sereno M, Videira M, Wilhelm I, Krizbai IA, Brito MA. miRNAs in Health and Disease: A Focus on the Breast Cancer Metastatic Cascade towards the Brain. Cells 2020; 9:E1790. [PMID: 32731349 PMCID: PMC7463742 DOI: 10.3390/cells9081790] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that mainly act by binding to target genes to regulate their expression. Due to the multitude of genes regulated by miRNAs they have been subject of extensive research in the past few years. This state-of-the-art review summarizes the current knowledge about miRNAs and illustrates their role as powerful regulators of physiological processes. Moreover, it highlights their aberrant expression in disease, including specific cancer types and the differential hosting-metastases preferences that influence several steps of tumorigenesis. Considering the incidence of breast cancer and that the metastatic disease is presently the major cause of death in women, emphasis is put in the role of miRNAs in breast cancer and in the regulation of the different steps of the metastatic cascade. Furthermore, we depict their involvement in the cascade of events underlying breast cancer brain metastasis formation and development. Collectively, this review shall contribute to a better understanding of the uniqueness of the biologic roles of miRNAs in these processes, to the awareness of miRNAs as new and reliable biomarkers and/or of therapeutic targets, which can change the landscape of a poor prognosis and low survival rates condition of advanced breast cancer patients.
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Affiliation(s)
- Marta Sereno
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (M.S.); (M.V.)
| | - Mafalda Videira
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (M.S.); (M.V.)
- Department of Galenic Pharmacy and Pharmaceutical Technology, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Imola Wilhelm
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary, Temesvári krt. 62, 6726 Szeged, Hungary; (I.W.); (I.A.K.)
- Institute of Life Sciences, Vasile Goldiş Western University of Arad, Arad, Romania, Str. Liviu Rebreanu 86, 310414 Arad, Romania
| | - István A. Krizbai
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary, Temesvári krt. 62, 6726 Szeged, Hungary; (I.W.); (I.A.K.)
- Institute of Life Sciences, Vasile Goldiş Western University of Arad, Arad, Romania, Str. Liviu Rebreanu 86, 310414 Arad, Romania
| | - Maria Alexandra Brito
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (M.S.); (M.V.)
- Department of Biochemistry and Human Biology, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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24
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Wong JS, Cheah YK. Potential miRNAs for miRNA-Based Therapeutics in Breast Cancer. Noncoding RNA 2020; 6:E29. [PMID: 32668603 PMCID: PMC7549352 DOI: 10.3390/ncrna6030029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that can post-transcriptionally regulate the genes involved in critical cellular processes. The aberrant expressions of oncogenic or tumor suppressor miRNAs have been associated with cancer progression and malignancies. This resulted in the dysregulation of signaling pathways involved in cell proliferation, apoptosis and survival, metastasis, cancer recurrence and chemoresistance. In this review, we will first (i) provide an overview of the miRNA biogenesis pathways, and in vitro and in vivo models for research, (ii) summarize the most recent findings on the roles of microRNAs (miRNAs) that could potentially be used for miRNA-based therapy in the treatment of breast cancer and (iii) discuss the various therapeutic applications.
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Affiliation(s)
- Jun Sheng Wong
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor 43400, Malaysia
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yoke Kqueen Cheah
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor 43400, Malaysia
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25
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Salerno AG, van Solingen C, Scotti E, Wanschel ACBA, Afonso MS, Oldebeken SR, Spiro W, Tontonoz P, Rayner KJ, Moore KJ. LDL Receptor Pathway Regulation by miR-224 and miR-520d. Front Cardiovasc Med 2020; 7:81. [PMID: 32528976 PMCID: PMC7256473 DOI: 10.3389/fcvm.2020.00081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/15/2020] [Indexed: 12/27/2022] Open
Abstract
MicroRNAs (miRNA) have emerged as important post-transcriptional regulators of metabolic pathways that contribute to cellular and systemic lipoprotein homeostasis. Here, we identify two conserved miRNAs, miR-224, and miR-520d, which target gene networks regulating hepatic expression of the low-density lipoprotein (LDL) receptor (LDLR) and LDL clearance. In silico prediction of miR-224 and miR-520d target gene networks showed that they each repress multiple genes impacting the expression of the LDLR, including the chaperone molecules PCSK9 and IDOL that limit LDLR expression at the cell surface and the rate-limiting enzyme for cholesterol synthesis HMGCR, which is the target of LDL-lowering statin drugs. Using gain- and loss-of-function studies, we tested the role of miR-224 and miR-520d in the regulation of those predicted targets and their impact on LDLR expression. We show that overexpression of miR-224 or miR-520d dose-dependently reduced the activity of PCSK9, IDOL, and HMGCR 3'-untranslated region (3'-UTR)-luciferase reporter constructs and that this repression was abrogated by mutation of the putative miR-224 or miR-520d response elements in the PCSK9, IDOL, and HMGCR 3'-UTRs. Compared to a control miRNA, overexpression of miR-224 or miR-520d in hepatocytes inhibited PCSK9, IDOL, and HMGCR mRNA and protein levels and decreased PCSK9 secretion. Furthermore, miR-224 and miR-520d repression of PCSK9, IDOL, and HMGCR was associated with an increase in LDLR protein levels and cell surface expression, as well as enhanced LDL binding. Notably, the effects of miR-224 and miR-520d were additive to the effects of statins in upregulating LDLR expression. Finally, we show that overexpression of miR-224 in the livers of Ldlr +/- mice using lipid nanoparticle-mediated delivery resulted in a 15% decrease in plasma levels of LDL cholesterol, compared to a control miRNA. Together, these findings identify roles for miR-224 and miR-520d in the posttranscriptional control of LDLR expression and function.
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Affiliation(s)
- Alessandro G Salerno
- Leon H. Charney Division of Cardiology, NYU Cardiovascular Research Center, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Coen van Solingen
- Leon H. Charney Division of Cardiology, NYU Cardiovascular Research Center, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Elena Scotti
- Howard Hughes Medical Institute and Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Amarylis C B A Wanschel
- Leon H. Charney Division of Cardiology, NYU Cardiovascular Research Center, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Milessa S Afonso
- Leon H. Charney Division of Cardiology, NYU Cardiovascular Research Center, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Scott R Oldebeken
- Leon H. Charney Division of Cardiology, NYU Cardiovascular Research Center, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Westley Spiro
- Leon H. Charney Division of Cardiology, NYU Cardiovascular Research Center, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Peter Tontonoz
- Howard Hughes Medical Institute and Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Katey J Rayner
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa Heart Institute, Ottawa, ON, Canada
| | - Kathryn J Moore
- Leon H. Charney Division of Cardiology, NYU Cardiovascular Research Center, Department of Medicine, New York University School of Medicine, New York, NY, United States.,Department of Cell Biology, New York University School of Medicine, New York, NY, United States
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26
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Zhao L, Zhou Y, Zhao Y, Li Q, Zhou J, Mao Y. Long non-coding RNA TUSC8 inhibits breast cancer growth and metastasis via miR-190b-5p/MYLIP axis. Aging (Albany NY) 2020; 12:2974-2991. [PMID: 32039833 PMCID: PMC7041739 DOI: 10.18632/aging.102791] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 01/12/2020] [Indexed: 01/23/2023]
Abstract
The lncRNA tumor suppressor candidate 8 (TUSC8) plays a critical role in the development of several cancers. However, the biological functions and underlying molecular mechanisms of TUSC8 with respect to breast cancer remain largely unclear. Here, we found that TUSC8 was significantly down-regulated in breast cancer tissues and its high expression predicted better prognosis of breast cancer patients. Functionally, knock-down of TUSC8 drastically promoted the proliferation, migration and invasion of breast cancer cells in vitro and facilitated tumorigenicity and metastasis in vivo. Mechanistically, the results of luciferase reporter, RIP and RNA pull-down assays proved that TUSC8 functioned as molecular sponge for miR-190b-5p. Furthermore, we showed that TUSC8 served as a competing endogenous RNA (ceRNA) of myosin regulatory light chain interacting protein (MYLIP) through competitively binding with miR-190b-5p and suppressed breast cancer metastasis through regulating the expression of epithelial–mesenchymal transition (EMT) related markers. Clinically, the receiver operating characteristic curve (ROC) analyses revealed that the combination usage of TUSC8 and MYLIP might become novel promising diagnostic biomarkers for breast cancer. Taken together, these results suggested that TUSC8 inhibited breast cancer growth and metastasis via miR-190b-5p/MYLIP axis, providing us new insights into developing potential therapeutic targets for breast cancer patients.
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Affiliation(s)
- Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Yangying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuelong Zhao
- School of Computer Science and Engineering, South China University of Technology, Guangzhou 510640, Guangdomg, China
| | - Qingling Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
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27
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Chen L, Kong R, Wu C, Wang S, Liu Z, Liu S, Li S, Chen T, Mao C, Liu S. Circ-MALAT1 Functions as Both an mRNA Translation Brake and a microRNA Sponge to Promote Self-Renewal of Hepatocellular Cancer Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1900949. [PMID: 32099751 PMCID: PMC7029649 DOI: 10.1002/advs.201900949] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/29/2019] [Indexed: 05/23/2023]
Abstract
Both circular RNAs (circRNAs) and cancer stem cells (CSCs) are separately known to be involved in cancer, but their interaction remains unclear. Here, the regulation of hepatocellular CSC self-renewal is discovered by a circRNA, circ-MALAT1, which is produced by back-splicing of a long noncoding RNA, MALAT1. Circ-MALAT1 is highly expressed in CSCs from clinical hepatocellular carcinoma samples under the mediation of an RNA-binding protein, AUF1. Surprisingly, circMALAT1 functions as a brake in ribosomes to retard PAX5 mRNA translation and promote CSCs' self-renewal by forming an unprecedented ternary complex with both ribosomes and mRNA. The discovered braking mechanism of a circRNA, termed mRNA braking, along with its more traditional role of miRNA sponging, uncovers a dual-faceted pattern of circRNA-mediated post-transcriptional regulation for maintaining a specific cell state.
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Affiliation(s)
- Liang Chen
- Department of Laboratory and DiagnosisChanghai HospitalNavy Medical University168 Changhai RoadShanghai200433China
- No. 904 Hospital of the PLA Joint Logistics Support ForceWuxi214000China
| | - Ruijiao Kong
- Shanghai Fourth People's HospitalTongji University School of Medicine1878 Sichuan North RoadShanghai200081China
| | - Cong Wu
- Department of Laboratory and DiagnosisChanghai HospitalNavy Medical University168 Changhai RoadShanghai200433China
| | - Shuo Wang
- Department of Laboratory and DiagnosisChanghai HospitalNavy Medical University168 Changhai RoadShanghai200433China
| | - Zixin Liu
- Department of Laboratory and DiagnosisChanghai HospitalNavy Medical University168 Changhai RoadShanghai200433China
| | - Shupeng Liu
- Department of Laboratory and DiagnosisChanghai HospitalNavy Medical University168 Changhai RoadShanghai200433China
| | - Shuiping Li
- Department of PathophysiologyShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Tian Chen
- Department of Laboratory and DiagnosisChanghai HospitalNavy Medical University168 Changhai RoadShanghai200433China
| | - Chuanbin Mao
- Department of Chemistry and BiochemistryStephenson Life Sciences Research CenterUniversity of Oklahoma101 Stephenson ParkwayNormanOK73019‐5300USA
| | - Shanrong Liu
- Shanghai Fourth People's HospitalTongji University School of Medicine1878 Sichuan North RoadShanghai200081China
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Ritter A, Hirschfeld M, Berner K, Rücker G, Jäger M, Weiss D, Medl M, Nöthling C, Gassner S, Asberger J, Erbes T. Circulating non‑coding RNA‑biomarker potential in neoadjuvant chemotherapy of triple negative breast cancer? Int J Oncol 2019; 56:47-68. [PMID: 31789396 PMCID: PMC6910196 DOI: 10.3892/ijo.2019.4920] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/26/2019] [Indexed: 12/11/2022] Open
Abstract
Due to the positive association between neoadjuvant chemotherapy (NACT) and the promising early response rates of patients with triple negative breast cancer (TNBC), including probabilities of pathological complete response, NACT is increasingly used in TNBC management. Liquid biopsy-based biomarkers with the power to diagnose the early response to NACT may support established monitoring tools, which are to a certain extent imprecise and costly. Simple serum- or urine-based analyses of non-coding RNA (ncRNA) expression may allow for fast, minimally-invasive testing and timely adjustment of the therapy regimen. The present study investigated breast cancer-related ncRNAs [microRNA (miR)-7, -9, -15a, -17, -18a, -19b, -21, -30b, -222 and -320c, PIWI-interacting RNA-36743 and GlyCCC2] in triple positive BT-474 cells and three TNBC cell lines (BT-20, HS-578T and MDA-MB-231) treated with various chemotherapeutic agents using reverse transcription-quantitative PCR. Intracellular and secreted microvesicular ncRNA expression levels were analysed using a multivariable statistical regression analysis. Chemotherapy-driven effects were investigated by analysing cell cycle determinants at the mRNA and protein levels. Serum and urine specimens from 8 patients with TNBC were compared with 10 healthy females using two-sample t-tests. Samples from the patients with TNBC were compared at two time points. Chemotherapeutic treatments induced distinct changes in ncRNA expression in TNBC cell lines and the BT-474 cell line in intra- and extracellular compartments. Serum and urine-based ncRNA expression analysis was able to discriminate between patients with TNBC and controls. Time point comparisons in the urine samples of patients with TNBC revealed a general rise in the level of ncRNA. Serum data suggested a potential association between piR-36743, miR-17, -19b and -30b expression levels and an NACT-driven complete clinical response. The present study highlighted the potential of ncRNAs as liquid biopsy-based biomarkers in TNBC chemotherapy treatment. The ncRNAs tested in the present study have been previously investigated for their involvement in BC or TNBC chemotherapy responses; however, these previous studies were restricted to patient tissue or in vitro models. The data from the present study offer novel insight into ncRNA expression in liquid samples from patients with TNBC, and the study serves as an initial step in the evaluation of ncRNAs as diagnostic biomarkers in the monitoring of TNBC therapy.
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Affiliation(s)
- Andrea Ritter
- Department of Obstetrics and Gynecology, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79106 Freiburg, Germany
| | - Marc Hirschfeld
- Department of Obstetrics and Gynecology, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79106 Freiburg, Germany
| | - Kai Berner
- Department of Obstetrics and Gynecology, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79106 Freiburg, Germany
| | - Gerta Rücker
- Institute of Medical Biometry and Statistics, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79104 Freiburg, Germany
| | - Markus Jäger
- Department of Obstetrics and Gynecology, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79106 Freiburg, Germany
| | - Daniela Weiss
- Department of Obstetrics and Gynecology, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79106 Freiburg, Germany
| | - Markus Medl
- Department of Obstetrics and Gynecology, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79106 Freiburg, Germany
| | - Claudia Nöthling
- Department of Obstetrics and Gynecology, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79106 Freiburg, Germany
| | - Sandra Gassner
- Department of Obstetrics and Gynecology, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79106 Freiburg, Germany
| | - Jasmin Asberger
- Department of Obstetrics and Gynecology, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79106 Freiburg, Germany
| | - Thalia Erbes
- Department of Obstetrics and Gynecology, Faculty of Medicine, Medical Center‑University of Freiburg, D‑79106 Freiburg, Germany
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Madadi S, Schwarzenbach H, Saidijam M, Mahjub R, Soleimani M. Potential microRNA-related targets in clearance pathways of amyloid-β: novel therapeutic approach for the treatment of Alzheimer's disease. Cell Biosci 2019; 9:91. [PMID: 31749959 PMCID: PMC6852943 DOI: 10.1186/s13578-019-0354-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/01/2019] [Indexed: 02/07/2023] Open
Abstract
Imbalance between amyloid-beta (Aβ) peptide synthesis and clearance results in Aβ deregulation. Failure to clear these peptides appears to cause the development of Alzheimer's disease (AD). In recent years, microRNAs have become established key regulators of biological processes that relate among others to the development and progression of neurodegenerative diseases, such as AD. This review article gives an overview on microRNAs that are involved in the Aβ cascade and discusses their inhibitory impact on their target mRNAs whose products participate in Aβ clearance. Understanding of the mechanism of microRNA in the associated signal pathways could identify novel therapeutic targets for the treatment of AD.
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Affiliation(s)
- Soheil Madadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Massoud Saidijam
- Department of Genetics and Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Reza Mahjub
- Department of Pharmaceutics, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Meysam Soleimani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
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Song Z, Zhang X, Lin Y, Wei Y, Liang S, Dong C. LINC01133 inhibits breast cancer invasion and metastasis by negatively regulating SOX4 expression through EZH2. J Cell Mol Med 2019; 23:7554-7565. [PMID: 31557401 PMCID: PMC6815803 DOI: 10.1111/jcmm.14625] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/04/2019] [Accepted: 05/12/2019] [Indexed: 01/01/2023] Open
Abstract
Mounting evidence highlights long non-coding RNAs (lncRNAs) as crucial regulators in multiple types of biological processes and contributing to tumourigenesis. LINC01133, located in chromosome 1q23.2, was a recently identified novel lncRNA with a length of 1154nt. It was involved in the development of colorectal cancer and non-small cell lung cancer. However, its clinical relevance, biological functions and potential molecular mechanism in breast cancer are still unclear. In this study, we found that the LINC01133 expression was significantly down-regulated in breast cancer samples and was associated with progression and poor prognosis of breast cancer. Further experiments demonstrated that overexpression of LINC01133 inhibited invasion and metastasis in breast cancer both in vitro and in vivo. Mechanistic investigations revealed that LINC01133 repressed SOX4 expression by recruiting EZH2 to SOX4 promoter. Moreover, rescue experiments further confirmed that LINC01133 functional acted as an anti-oncogene, at least partly, via repressing SOX4 in breast cancer. Taken together, these findings imply that LINC01133 could serve as a novel prognostic biomarker and potential therapeutic target for breast cancer.
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Affiliation(s)
- Zhiwang Song
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
| | - Xia Zhang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yun Lin
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Youzhen Wei
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shujing Liang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunyan Dong
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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Su L, Liu G, Wang J, Xu D. A rectified factor network based biclustering method for detecting cancer-related coding genes and miRNAs, and their interactions. Methods 2019; 166:22-30. [PMID: 31121299 PMCID: PMC6708461 DOI: 10.1016/j.ymeth.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/14/2019] [Accepted: 05/13/2019] [Indexed: 12/12/2022] Open
Abstract
Detecting cancer-related genes and their interactions is a crucial task in cancer research. For this purpose, we proposed an efficient method, to detect coding genes, microRNAs (miRNAs), and their interactions related to a particular cancer or a cancer subtype using their expression data from the same set of samples. Firstly, biclusters specific to a particular type of cancer are detected based on rectified factor networks and ranked according to their associations with general cancers. Secondly, coding genes and miRNAs in each bicluster are prioritized by considering their differential expression and differential correlation values, protein-protein interaction data, and potential cancer markers. Finally, a rank fusion process is used to obtain the final comprehensive rank by combining multiple ranking results. We applied our proposed method on breast cancer datasets. Results show that our method outperforms other methods in detecting breast cancer-related coding genes and miRNAs. Furthermore, our method is very efficient in computing time, which can handle tens of thousands genes/miRNAs and hundreds of patients in hours on a desktop. This work may aid researchers in studying the genetic architecture of complex diseases, and improving the accuracy of diagnosis.
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Affiliation(s)
- Lingtao Su
- Department of Computer Science and Technology, Jilin University, Changchun 130012, China; Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Guixia Liu
- Department of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Juexin Wang
- Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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Zhou J, Xiang AZ, Guo JF, Cui HD. miR-30b suppresses the progression of breast cancer through inhibition of the PI3K/Akt signaling pathway by targeting Derlin-1. Transl Cancer Res 2019; 8:180-190. [PMID: 35116747 PMCID: PMC8798179 DOI: 10.21037/tcr.2019.01.21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 12/21/2018] [Indexed: 11/09/2022]
Abstract
Background MicroRNAs (miRNAs) play an essential role in the initiation, progression and metastasis of breast cancer. It has been confirmed that miR-30b is involved in various cancers. However, the specific involvement of miR-30b on breast cancer metastasis remains unknown. In the current study, we aimed to investigate the role of miR-30b in the progression and metastasis of breast cancer in vitro. Methods We up-regulated the expression of miR-30b in breast cancer cell lines SKBR3 and MDA-MB-231 by transfecting pCMV-miR-30b vector. CCK8, colony formation, Transwell, and flow cytometry assays were used to examine cell proliferation, migration, invasion and apoptosis, respectively. A dual-luciferase reporter assay was performed to identify the relationship between miR-30b and the target gene. Western blot assay was used to detect related proteins. Results Our data showed that the overexpression of miR-30b significantly inhibited proliferation, migration and invasion abilities in SKBR3 and MDA-MB-231 cells. Meanwhile, overexpression of miR-30b induced cell apoptosis for both SKBR3 and MDA-MB-231 cells by regulating the expression of apoptosis-related proteins (Bcl-2, Bax, active Caspase-3, and Caspase-9). Moreover, miR-30b inhibited the activation of the PI3K/Akt signaling pathway by decreasing the phosphorylation levels of Akt and mTOR. Furthermore, we determined that miR-30b could down-regulate the expression of Derlin-1 in a post-transcriptional manner by employing the dual-luciferase reporter and western blot assays. Further analysis demonstrated that depletion of Derlin-1 inhibited Akt phosphorylation, and Derlin-1 could restore the effect of miR-30b on Akt. In addition, the CCK8 assay showed that Derlin-1 could partly reverse the inhibition of cell proliferation of SKBR3 and MDA-MB-231 cells mediated by miR-30b. Conclusions Our data demonstrated that miR-30b suppresses the progression and metastasis of breast cancer via inhibition of the PI3K/Akt signaling pathway by targeting Derlin-1 in vitro. This suggests that miR-30b might be a novel potent target for breast cancer therapy.
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Affiliation(s)
- Jun Zhou
- Department of Breast Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Ai-Zhai Xiang
- Department of Breast Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Ju-Feng Guo
- Department of Breast Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Hai-Dong Cui
- Department of Breast Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
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Zhao L, Zhao Y, He Y, Li Q, Mao Y. The functional pathway analysis and clinical significance of miR-20a and its related lncRNAs in breast cancer. Cell Signal 2018; 51:152-165. [PMID: 30092355 DOI: 10.1016/j.cellsig.2018.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/02/2018] [Accepted: 08/04/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND miR-20a is a critical molecule in various biological processes and cancer progression procedures. However, its relationships with lncRNAs and their functional pathway analysis in breast tumorigenesis are less intensively studied. METHODS The expression data from TCGA database and multiple bioinformatics resources were used to check the expression levels, survival curves, interactions and functional illustrations of miR-20a and its related lncRNAs (XIST, H19 and MALAT1) in breast cancer patients. The luciferase reporter assays and Pearson's correlation analyses were utilized to verify the direct regulatory relationship between miR-20a and three lncRNAs (XIST, H19 and MALAT1). In vitro cell proliferation, migration and invasion assays, were performed to check the biological effects of miR-20a and XIST in different breast cancer cell lines. The receiver operating characteristic curve (ROC) analyses were done for evaluating diagnostic values of serum miR-20a and XIST in breast cancer patients. RESULTS The miR-20a expression was significantly up-regulated in both breast cancer samples and serum samples, and correlated with poor survival rate in breast cancer patients. LncRNAs (XIST, H19 and MALAT1) directly bound to hsa-miR-20a and were negatively correlated with hsa-miR-20a expression in breast cancer patient samples. For functional illustrations and downstream signaling pathways analysis, XIST, H19 and MALAT1 mainly shared their regulatory functions in cell motility and interleukin signaling in breast cancer progression. Additionally, over-expression of miR-20a and inhibition of XIST promoted breast cancer cell growth, migration and invasion in vitro, and serum miR-20a and XIST served as potential diagnostic biomarkers for breast cancer with the area under ROC curve (AUC) of 0.87 (95% CI = 0.78 to 0.97), and 0.78 (95% CI = 0.67 to 0.89) respectively. CONCLUSIONS Taken together, these findings provide us novel insights and avenues for utilizing miR-20a and its related lncRNAs as potential diagnostic biomarkers and promising therapeutic targets for breast cancer treatment.
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Affiliation(s)
- Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Yuelong Zhao
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Yanong He
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Qingling Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
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Li C, Zhang J, Ma Z, Zhang F, Yu W. miR-19b serves as a prognostic biomarker of breast cancer and promotes tumor progression through PI3K/AKT signaling pathway. Onco Targets Ther 2018; 11:4087-4095. [PMID: 30038508 PMCID: PMC6052917 DOI: 10.2147/ott.s171043] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background MicroRNAs (miRNAs) are involved in tumor progression of various human malignancies. MicroRNA-19b (miR-19b) has been described as serving a crucial role in tumorigenesis of breast cancer. The purpose of this study was to investigate the expression patterns, clinical value, and functional role of miR-19b in breast cancer. Methods Expression of miR-19b was estimated by quantitative real time PCR. Kaplan–Meier survival analysis and Cox regression assay were performed to explore the prognostic value of miR-19b. The functional role of miR-19b was verified using cell experiments. Results Upregulated miR-19b expression was observed in breast cancer tissues and cells compared with the controls (all P<0.05). The miR-19b expression was associated with distant metastasis and TNM stage. The survival curves showed that high miR-19b was correlated with poor overall survival of the patients (log-rank P=0.002). Furthermore, miR-19b was proven to be an independent prognostic factor for patients. By using miR-19b mimic and inhibitor, cell proliferation, migration, and invasion were enhanced by miR-19b overexpression but were suppressed by reduction of miR-19b (all P<0.05). Besides, PI3K/AKT was demonstrated to be activated by miR-19b in breast cancer cells. Conclusion The overexpression of miR-19b serves as a candidate prognostic biomarker of breast cancer and may be involved in the tumor progression through PI3K/AKT pathway.
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Affiliation(s)
- Chuansheng Li
- Department of General Surgery, Shanxian Central Hospital, Heze, Shandong, China,
| | - Jingwei Zhang
- Department of General Surgery, Shanxian Central Hospital, Heze, Shandong, China,
| | - Zhongliang Ma
- Department of Breast Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Fan Zhang
- Department of General Surgery, Shanxian Central Hospital, Heze, Shandong, China,
| | - Wenlong Yu
- Department of General Surgery, Shanxian Central Hospital, Heze, Shandong, China,
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Wei YP, Wang XH, Liu G, Zhang JF, Yang YX, Zhang J, Song XL, Li ZD, Zhao LD. Matrine exerts inhibitory effects in melanoma through the regulation of miR-19b-3p/PTEN. Int J Oncol 2018; 53:791-800. [PMID: 29845233 DOI: 10.3892/ijo.2018.4414] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/30/2018] [Indexed: 11/06/2022] Open
Abstract
Matrine, one of the main alkaloid components extracted from the traditional Chinese herb, Sophora flavescens Ait, has various pharmacological effects, and has been reported to exert antitumor activity in melanoma. In the current study, the molecular mechanisms underlying the inhibitory effects of matrine were investigated in melanoma cell line. It was initially confirmed that matrine inhibited proliferation, invasion and induced apoptosis in human A375 and SK-MEL-2 melanoma cell lines in vitro. Subsequently, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis demonstrated that the expression of microRNA (miR)-19b-3p was significantly increased in melanoma cells and was downregulated by treatment with matrine. Furthermore, downregulated miR-19b-3p exerted effects similar to 500 µg/ml matrine on cell proliferation, invasion and apoptosis. Phosphatase and tensin homolog (PTEN) mRNA was identified as a direct target of miR-19b-3p through bioinformatics analysis and a dual-luciferase reporter assay. Additionally, western blotting and RT-qPCR analysis demonstrated that the expression of PTEN protein and mRNA were increased by the treatment with matrine. Furthermore, silencing of PTEN expression reversed the effects of matrine and miR-19b-3p downregulation in A375 and SK-MEL-2 cells. Taken together, the results indicated that matrine may suppress cell proliferation and invasion and induce cell apoptosis partially via miR-19b-3p targeting of PTEN.
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Affiliation(s)
- Yan Ping Wei
- Department of Dermatology, The People's Hospital of Jiaozuo City, Jiaozuo, Henan 454000, P.R. China
| | - Xiang Hua Wang
- Department of Dermatology, The People's Hospital of Jiaozuo City, Jiaozuo, Henan 454000, P.R. China
| | - Gang Liu
- Department of Dermatology, The People's Hospital of Jiaozuo City, Jiaozuo, Henan 454000, P.R. China
| | - Jin Feng Zhang
- Department of Dermatology, The People's Hospital of Jiaozuo City, Jiaozuo, Henan 454000, P.R. China
| | - Yong Xian Yang
- Department of Dermatology, The People's Hospital of Jiaozuo City, Jiaozuo, Henan 454000, P.R. China
| | - Juan Zhang
- Department of Dermatology, The People's Hospital of Jiaozuo City, Jiaozuo, Henan 454000, P.R. China
| | - Xiao Li Song
- Department of Dermatology, The People's Hospital of Jiaozuo City, Jiaozuo, Henan 454000, P.R. China
| | - Zhong Dong Li
- Department of Hematology, The People's Hospital of Jiaozuo City, Jiaozuo, Henan 454000, P.R. China
| | - Lin Dong Zhao
- Department of Dermatology, The People's Hospital of Jiaozuo City, Jiaozuo, Henan 454000, P.R. China
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Zhang Y, Fang L, Zang Y, Xu Z. Identification of Core Genes and Key Pathways via Integrated Analysis of Gene Expression and DNA Methylation Profiles in Bladder Cancer. Med Sci Monit 2018; 24:3024-3033. [PMID: 29739919 PMCID: PMC5968840 DOI: 10.12659/msm.909514] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background Bladder cancer (BC) is the most common urological malignant tumor. In BC, aberrant DNA methylation is believed to be associated with carcinogenesis. Therefore, the identification of key genes and pathways could help determine the potential molecular mechanisms of BC development. Material/Methods Microarray data on gene expression and gene methylation were downloaded from the Gene Expression Omnibus (GEO) database. Abnormal methylated/expressed genes were analyzed by GEO2R and statistical software R. Gene Ontology term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the DAVID database and KOBAS 3.0. STRING and Cytoscape software were used to construct protein–protein interaction (PPI) networks and analyze modules of the PPI network. Results A total of 71 hypomethylated/upregulated genes were significantly enriched in cell–cell adhesion and blood vessel development. KEGG pathway analysis highlighted p53 signaling and metabolic pathways. Five core genes in the PPI network were determined: CDH1, DDOST, CASP8, DHX15, and PTPRF. Additionally, 89 hypermethylated/downregulated genes were found. These genes were enriched mostly in cell adhesion and signal transduction. KEGG pathway analysis revealed enrichment in focal adhesion. The top 5 core genes in the PPI network were GNG4, ADCY9, NPY, ADRA2B, and PENK. We found most of the core genes were also significantly altered in the Cancer Genome Atlas database. Conclusions Abnormal methylated/expressed genes and key signaling pathways involved in BC were identified through integrated bioinformatics analysis. In the future, these genes may serve as biomarkers for diagnosis and therapeutic targets in BC.
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Affiliation(s)
- Yongzhen Zhang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Liang Fang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Yuanwei Zang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Zhonghua Xu
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
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Yin R, Guo L, Gu J, Li C, Zhang W. Over expressing miR-19b-1 suppress breast cancer growth by inhibiting tumor microenvironment induced angiogenesis. Int J Biochem Cell Biol 2018; 97:43-51. [DOI: 10.1016/j.biocel.2018.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/01/2018] [Accepted: 02/05/2018] [Indexed: 12/26/2022]
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Zhang X, Yin J, Zhang X. A Semi-Supervised Learning Algorithm for Predicting Four Types MiRNA-Disease Associations by Mutual Information in a Heterogeneous Network. Genes (Basel) 2018; 9:genes9030139. [PMID: 29498680 PMCID: PMC5867860 DOI: 10.3390/genes9030139] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 01/05/2023] Open
Abstract
Increasing evidence suggests that dysregulation of microRNAs (miRNAs) may lead to a variety of diseases. Therefore, identifying disease-related miRNAs is a crucial problem. Currently, many computational approaches have been proposed to predict binary miRNA-disease associations. In this study, in order to predict underlying miRNA-disease association types, a semi-supervised model called the network-based label propagation algorithm is proposed to infer multiple types of miRNA-disease associations (NLPMMDA) by mutual information derived from the heterogeneous network. The NLPMMDA method integrates disease semantic similarity, miRNA functional similarity, and Gaussian interaction profile kernel similarity information of miRNAs and diseases to construct a heterogeneous network. NLPMMDA is a semi-supervised model which does not require verified negative samples. Leave-one-out cross validation (LOOCV) was implemented for four known types of miRNA-disease associations and demonstrated the reliable performance of our method. Moreover, case studies of lung cancer and breast cancer confirmed effective performance of NLPMMDA to predict novel miRNA-disease associations and their association types.
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Affiliation(s)
- Xiaotian Zhang
- School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai 264209, China.
| | - Jian Yin
- School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai 264209, China.
| | - Xu Zhang
- School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai 264209, China.
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Nakamura K, Akiba J, Ogasawara S, Naito Y, Nakayama M, Abe Y, Kusukawa J, Yano H. SUOX is negatively associated with multistep carcinogenesis and proliferation in oral squamous cell carcinoma. Med Mol Morphol 2017; 51:102-110. [PMID: 29280012 DOI: 10.1007/s00795-017-0177-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/18/2017] [Indexed: 12/15/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is the most common malignant tumor in the head and neck region. The aim of this study was to identify the key molecules and to elucidate the molecular mechanisms of OSCC carcinogenesis through a microarray analysis of RNA extracted from normal epithelium, dysplasia, and squamous cell carcinoma components. Out of molecules that showed changes in gene expression in the microarray analysis, we focused on Sulfite oxidase (SUOX), which correlated significantly with carcinogenic process and exhibited a stepwise decrease in expression. The expression of SUOX was evaluated in detail at the protein level using samples from 58 patients with cancer of the tongue, and correlating clinicopathological factors were also comprehensively examined. SUOX expression declined significantly from normal epithelium to dysplasia to squamous cell carcinoma components in line with carcinogenic process. With regard to squamous cell carcinoma, SUOX expression was significantly lower when T classification was high. Our findings indicated that SUOX is negatively associated with the progression and proliferation of tongue cancer, and suggest that SUOX may be a key molecule in tongue tumors.
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Affiliation(s)
- Ken Nakamura
- Department of Pathology, Kurume University School of Medicine, 67 Asahimachi, Kurume, 830-0011, Japan
- Dental and Oral Medical Center, Kurume University School of Medicine, Kurume, Japan
| | - Jun Akiba
- Department of Pathology, Kurume University School of Medicine, 67 Asahimachi, Kurume, 830-0011, Japan.
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan.
| | - Sachiko Ogasawara
- Department of Pathology, Kurume University School of Medicine, 67 Asahimachi, Kurume, 830-0011, Japan
| | - Yoshiki Naito
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | - Masamichi Nakayama
- Department of Pathology, Kurume University School of Medicine, 67 Asahimachi, Kurume, 830-0011, Japan
| | - Yushi Abe
- Department of Pathology, Kurume University School of Medicine, 67 Asahimachi, Kurume, 830-0011, Japan
- Dental and Oral Medical Center, Kurume University School of Medicine, Kurume, Japan
| | - Jingo Kusukawa
- Dental and Oral Medical Center, Kurume University School of Medicine, Kurume, Japan
| | - Hirohisa Yano
- Department of Pathology, Kurume University School of Medicine, 67 Asahimachi, Kurume, 830-0011, Japan
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