1
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Parkins EV, Gross C. Small Differences and Big Changes: The Many Variables of MicroRNA Expression and Function in the Brain. J Neurosci 2024; 44:e0365242024. [PMID: 39111834 PMCID: PMC11308354 DOI: 10.1523/jneurosci.0365-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 05/15/2024] [Accepted: 05/23/2024] [Indexed: 08/10/2024] Open
Abstract
MicroRNAs are emerging as crucial regulators within the complex, dynamic environment of the synapse, and they offer a promising new avenue for the treatment of neurological disease. These small noncoding RNAs modify gene expression in several ways, including posttranscriptional modulation via binding to complementary and semicomplementary sites on target mRNAs. This rapid, finely tuned regulation of gene expression is essential to meet the dynamic demands of the synapse. Here, we provide a detailed review of the multifaceted world of synaptic microRNA regulation. We discuss the many mechanisms by which microRNAs regulate gene expression at the synapse, particularly in the context of neuronal plasticity. We also describe the various factors, such as age, sex, and neurological disease, that can influence microRNA expression and activity in neurons. In summary, microRNAs play a crucial role in the intricate and quickly changing functional requirements of the synapse, and context is essential in the study of microRNAs and their potential therapeutic applications.
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Affiliation(s)
- Emma V Parkins
- University of Cincinnati Neuroscience Graduate Program, Cincinnati, Ohio 45229
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229
| | - Christina Gross
- University of Cincinnati Neuroscience Graduate Program, Cincinnati, Ohio 45229
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229
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2
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Krishnan MA, Pandit A, Sharma R, Chelvam V. Imaging of prostate cancer: optimizing affinity to prostate specific membrane antigen by spacer modifications in a tumor spheroid model. J Biomol Struct Dyn 2022; 40:9909-9930. [PMID: 34180367 DOI: 10.1080/07391102.2021.1936642] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Early diagnosis of prostate cancer (PCa) is crucial for staging, treatment and management of patients. Prostate specific membrane antigen (PSMA), highly over-expressed on PCa cells, is an excellent target for selective imaging of PCa. In recent years, various scaffolds have been explored as potential carriers to target diagnostic and therapeutic agents to PSMA+ tumour cells. Numerous fluorescent or radioisotope probes linked via a peptide linker have been developed that selectively binds to PCa cells. However, there are very few reports that examine the effects of chemical modifications in the peptide linker of an imaging probe on its affinity to PSMA protein. This report systematically investigates the impact of hydrophobic aromatic moieties in the peptide linker on PSMA affinity and in vitro performance. For this, a series of fluorescent bioconjugates 12-17 with different aromatic spacers were designed, synthesized, and their interactions within the PSMA pocket were first analysed in silico. Cell uptake studies were then performed for 12-17 in PSMA+ cell lines and 3D tumour models in vitro. Binding affinity values of 12-17 were found to be in the range of 36 to 157.9 nM, and 12 with three aromatic groups in the spacer exhibit highest affinity (KD = 36 nM) compared to 17 which is devoid of aromatic groups. These studies suggest that aromatic groups in the spacer region can significantly affect deep tissue imaging of fluorescent bioconjugates. Bioconjugate 12 can be a promising diagnostic tool, and conjugation to near-infrared agents would further its applications in deep-tissue imaging and surgery. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mena Asha Krishnan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Amit Pandit
- Department of Chemistry, Indian Institute of Technology Indore, Indore, India
| | - Rajesh Sharma
- School of Pharmacy, Devi Ahilya University, Indore, India
| | - Venkatesh Chelvam
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India.,Department of Chemistry, Indian Institute of Technology Indore, Indore, India
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3
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Dysregulated expression of microRNAs acts as prognostic and diagnostic biomarkers for glioma patients. Mol Genet Genomics 2022; 297:1389-1401. [DOI: 10.1007/s00438-022-01927-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/05/2022] [Indexed: 10/17/2022]
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4
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Gholami M, Zoughi M, Behboo R, Taslimi R, Kazemeini A, Bastami M, Hasani-Ranjbar S, Larijani B, Amoli MM. Association of miRNA targetome variants in LAMC1 and GNB3 genes with colorectal cancer and obesity. Cancer Med 2022; 11:3923-3938. [PMID: 35373932 PMCID: PMC9636511 DOI: 10.1002/cam4.4713] [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: 08/01/2021] [Revised: 01/28/2022] [Accepted: 03/04/2022] [Indexed: 11/22/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common obesity‐associated cancers. Inflammation is also considered the most important factor between obesity and CRC. This study aimed to examine miRNAs binding sites variants on inflammatory genes identified using bioinformatics and systematic approach on clinical samples that were collected from CRC patients and controls. Methods The candidate variants related to CRC inflammatory genes were obtained from genome‐wide association studies and their population‐specific haplotypes. The variants were analyzed according to their genomic position on the miRNA targetome. Targetome variants in inflammation‐related genes were selected for genetic association study by TaqMan genotyping assay. Results The GG genotype of rs7473 decreased the risk of obesity (p < 0.05). Heterozygous genotype (GA) of rs1547715 decreased the risk of CRC (p < 0.05). In the rs7473/rs1547715 genotype and haplotype, the frequencies of AA/GA and GG/AA lessened in CRC and obesity, respectively (p < 0.05). Conclusions The variants of rs7473 and rs1547715 were associated with obesity and CRC, respectively. The above‐mentioned associations could be made based on the interactions of these variants with miRNAs.
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Affiliation(s)
- Morteza Gholami
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Marziyeh Zoughi
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Roobic Behboo
- Hazrate Rasoole Akram Hospital, Iran University of Medical Science, Tehran, Iran
| | - Reza Taslimi
- Department of Gastroenterology, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Kazemeini
- Department of General Surgery, Imam Khomeini Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Milad Bastami
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shirin Hasani-Ranjbar
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa M Amoli
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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5
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Gupta D, Kumar M, Singh M, Salman M, Das U, Kaur P. Identification of polypharmacological anticancerous molecules against Aurora kinase family of proteins. J Cell Biochem 2022; 123:719-735. [PMID: 35040172 DOI: 10.1002/jcb.30214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 12/28/2022]
Abstract
The Human Aurora Kinase (AURK) protein family is the key player of cell cycle events including spindle assembly, kinetochore formation, chromosomal segregation, centrosome separation, microtubule dynamics, and cytokinesis. Their aberrant expression has been extensively linked with chromosomal instability in addition to derangement of multiple tumor suppressors and oncoprotein regulated pathways. Therefore, the AURK family of kinases is a promising target for the treatment of various types of cancer. Over the past few decades, several potential inhibitors of AURK proteins have been identified and have reached various phases of clinical trials. But very few molecules have currently crossed the safety criteria due to their various toxic side effects. In the present study, we have adopted a computational polypharmacological strategy and identified four novel molecules that can target all three AURKs. These molecules were further investigated for their binding stabilities at the ATP binding pocket using molecular dynamics based simulation studies. The molecules selected adopting a multipronged computational approach can be considered as potential AURKs inhibitors for cancer therapeutics.
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Affiliation(s)
- Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mohd Salman
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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6
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Ghosh A, Manhas A, Jha PC. Computational studies to identify the common type-I and type-II inhibitors against the CDK8 enzyme. J Cell Biochem 2022; 123:628-643. [PMID: 34989009 DOI: 10.1002/jcb.30209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022]
Abstract
In this study, multicomplex-based pharmacophore modeling was conducted on the structural proteome of the two states of CDK8 protein, that is, DMG-in and out. Three pharmacophores having six, five, and four features were selected as the representative models to conduct the virtual screening process using the prepared drug-like natural product database. The screened candidates were subjected to molecular docking studies on DMG-in (5XS2) and out (4F6U) conformation of the CDK8 protein. Subsequently, the common four docked candidates of 5XS2 and 4F6U were selected to perform the molecular dynamics simulation studies. Apart from one of the complexes of DMG-in (5XS2-UNPD163102), all other complexes displayed stable dynamic behavior. The interaction and stability studies of the docked complexes were compared with the references selected from the two conformations (DMG-in and out) of the protein. The current work leads to the identification of three common DMG-in and out hits with diverse scaffolds which can be employed as the initial leads for the design of the novel CDK8 inhibitors.
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Affiliation(s)
- Amar Ghosh
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Anu Manhas
- Department of Chemistry, School of Technology, Pandit Deendayal Energy University (former PDPU), Gandhinagar, Gujarat, India
| | - Prakash C Jha
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
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7
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Hossain R, Ray P, Sarkar C, Islam MS, Khan RA, Khalipha ABR, Islam MT, Cho WC, Martorell M, Sharifi-Rad J, Butnariu M, Umbetova A, Calina D. Natural Compounds or Their Derivatives against Breast Cancer: A Computational Study. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5886269. [PMID: 35837379 PMCID: PMC9276515 DOI: 10.1155/2022/5886269] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/30/2022] [Accepted: 06/21/2022] [Indexed: 12/21/2022]
Abstract
BACKGROUND Breast cancer is one of the most common types of cancer diagnosed and the second leading cause of death among women. Breast cancer susceptibility proteins of type 1 and 2 are human tumor suppressor genes. Genetic variations/mutations in these two genes lead to overexpression of human breast tumor suppressor genes (e.g., BRCA1, BRCA2), which triggers uncontrolled duplication of cells in humans. In addition, multidrug resistance protein 1 (MDR1), an important cell membrane protein that pumps many foreign substances from cells, is also responsible for developing resistance to cancer chemotherapy. Aim of the Study. The aim of this study was to analyze some natural compounds or their derivatives as part of the development of strong inhibitors for breast cancer. Methodology. Molecular docking studies were performed using compounds known in the literature to be effective against BRCA1 and BRCA2 and MDR1, with positive control being 5-fluorouracil, an antineoplastic drug as a positive control. RESULTS The binding affinity of the compounds was analyzed, and it was observed that they had a better binding affinity for the target proteins than the standard drug 5-fluorouracil. Among the compounds analyzed, α-hederin, andrographolide, apigenin, asiatic acid, auricular acid, sinularin, curcumin, citrinin, hispolon, nerol, phytol, retinol palmitate, and sclareol showed the best binding affinity energy to the BRCA1, BRCA2, and MDR1 proteins, respectively. CONCLUSIONS α-Hederin, andrographolide, apigenin, asiatic acid, auricular acid, hispolon, sclareol, curcumin, citrinin, and sinularin or their derivatives can be a good source of anticancer agents in breast cancer.
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Affiliation(s)
- Rajib Hossain
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Pranta Ray
- 2Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Chandan Sarkar
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Md. Shahazul Islam
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Rasel Ahmed Khan
- 3Pharmacy Discipline, Life Science School, Khulna University, Khulna 9280, Bangladesh
| | - Abul Bashar Ripon Khalipha
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Muhammad Torequl Islam
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - William C. Cho
- 4Department of Clinical Oncology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong 999077, China
| | - Miquel Martorell
- 5Department of Nutrition and Dietetics, Faculty of Pharmacy, and Centre for Healthy Living, University of Concepción, 4070386 Concepción, Chile
| | | | - Monica Butnariu
- 7Banat's University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Romania
| | - Almagul Umbetova
- 8Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, 050040 Almaty, Kazakhstan
| | - Daniela Calina
- 9Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
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8
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Feng Z, Qu J, Liu X, Liang J, Li Y, Jiang J, Zhang H, Tian H. Integrated bioinformatics analysis of differentially expressed genes and immune cell infiltration characteristics in Esophageal Squamous cell carcinoma. Sci Rep 2021; 11:16696. [PMID: 34404882 PMCID: PMC8371051 DOI: 10.1038/s41598-021-96274-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a life-threatening thoracic tumor with a poor prognosis. The role of molecular alterations and the immune microenvironment in ESCC development has not been fully elucidated. The present study aimed to elucidate key candidate genes and immune cell infiltration characteristics in ESCC by integrated bioinformatics analysis. Nine gene expression datasets from the Gene Expression Omnibus (GEO) database were analysed to identify robust differentially expressed genes (DEGs) using the robust rank aggregation (RRA) algorithm. Functional enrichment analyses showed that the 152 robust DEGs are involved in multiple processes in the tumor microenvironment (TME). Immune cell infiltration analysis based on the 9 normalized GEO microarray datasets was conducted with the CIBERSORT algorithm. The changes in macrophages between ESCC and normal tissues were particularly obvious. In ESCC tissues, M0 and M1 macrophages were increased dramatically, while M2 macrophages were decreased. A robust DEG-based protein–protein interaction (PPI) network was used for hub gene selection with the CytoHubba plugin in Cytoscape. Nine hub genes (CDA, CXCL1, IGFBP3, MMP3, MMP11, PLAU, SERPINE1, SPP1 and VCAN) had high diagnostic efficiency for ESCC according to receiver operating characteristic (ROC) curve analysis. The expression of all hub genes except MMP3 and PLAU was significantly related to macrophage infiltration. Univariate and multivariate regression analyses showed that a 7-gene signature constructed from the robust DEGs was useful for predicting ESCC prognosis. Our results might facilitate the exploration of potential targeted TME therapies and prognostic evaluation in ESCC.
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Affiliation(s)
- Zitong Feng
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Laboratory of Basic Medical Sciences, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Jingge Qu
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiao Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Laboratory of Basic Medical Sciences, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Jinghui Liang
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Laboratory of Basic Medical Sciences, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Yongmeng Li
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Laboratory of Basic Medical Sciences, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Jin Jiang
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Laboratory of Basic Medical Sciences, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Huiying Zhang
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Hui Tian
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
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9
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The Importance of Clinical Data for the Diagnosis of Breast Tumours in North Afghanistan. Int J Breast Cancer 2021; 2021:6625239. [PMID: 34373791 PMCID: PMC8349267 DOI: 10.1155/2021/6625239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/24/2021] [Accepted: 07/14/2021] [Indexed: 12/03/2022] Open
Abstract
Background This study was performed in knowledge of the increasing gap between breast disease treatment in countries with restricted resources and developed countries with increasingly sophisticated examination methods. Methods The authors present the analysis of a breast disease register consisting of diagnostic cases from Mazar e Sharif and Herat in 2018 and 2019. The study comprises a total of 567 cases, which were presented to experts via telemedicine for final diagnosis. 62 cases (10.9%) were excluded due to inacceptable data or insufficient image quality. These data provided by daily diagnostic classification were used for the built-up of a profile for each frequent breast disease and a breast cancer register. All images and cases were seen by at least 3 independent experts. The diagnoses were made in 60% of cases by cytology of fine needle aspiration and in 40% by histological images. Results For each entity of breast diseases (e.g., fibroadenoma), a profile of context variables was constructed allowing to assist medical decisions, as “wait and see,” elective surgery or immediate surgical intervention with R0 (complete) resection. These “profiles” could be described for fibroadenoma, mastitis, galactocele, fibrous-cystic disease, and invasive breast cancer. Conclusions The presented preliminary data set could serve as a cost-effective basis for a North Afghan breast cancer registry, with option to extent to a national model. These preliminary data are transformed in profiles of breast diseases, which are used by the local physicians in charge of breast disease patients. Each new case can be compared by the local treating physician with the profile of all preceded cases with the same diagnosis.
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10
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El-Huneidi W, Eladl MA, Muhammad JS. Single nucleotide polymorphisms in microRNA binding sites on the HOX genes regulate carcinogenesis: An in-silico approach. Biochem Biophys Rep 2021; 27:101083. [PMID: 34368470 PMCID: PMC8326182 DOI: 10.1016/j.bbrep.2021.101083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
Homeobox proteins, encoded by HOX genes, are transcriptional factors playing a crucial role in the master regulatory pathway in the cells. Any mutations in HOX genes will affect the expression of its allied proteins. Such mutations were correlated to the development of different cancer types. In this study, we found 15 HOX genes with a potential target to miRNA, which regulates the translation of the protein by binding to its mRNA through the 3′UTR region. Single nucleotide polymorphisms (SNPs) in this binding region could drastically affect the protein expression by affecting the number and the stability of miRNA-mRNA complexes. We found 77 miRNAs in 15 genes which were found to have altered binding efficiency because of 26 SNPs. After which, we tried to evaluate the impact of each of these SNPs on related HOX genes. Some SNPs such as SNP 15689 on the HOXB7 gene will decrease gene expression by creating or enhancing new binding sites for miRNA to mRNA, while other SNPs such as SNP 872760 on the HOXB5 gene will overexpress the gene by breaking or decreasing existing binding sites from miRNA to mRNA. Then we conducted an expression analysis to compare the mRNA expression profiles in normal and cancer tissue. Subsequently, we did an enrichment analysis followed by a network analysis to shed light on the metabolic function of the gene that could be affected by mutation and whether these mutations may affect other genes. For the first time, this study delivers information on the possible epigenetic regulation of HOX genes via the 77 miRNAs that have predicted target binding sites on HOX mRNAs, and SNPs may regulate those. Furthermore, we show that the HOX gene misregulation may influence other HOX and non-HOX genes, based on network analysis. Genes affected by SNPs in miRNA lead to deregulation of HOX genes that will cause cancer. HOX genes have role in posttranscriptional nucleic acid and protein binding. The mutational effect of any HOX gene affects other members of HOX genes.
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Affiliation(s)
- Waseem El-Huneidi
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Mohamed Ahmed Eladl
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Jibran Sualeh Muhammad
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
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11
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Chatterjee S, Chakraborty R, Hasija Y. Polymorphisms at site 469 of B-RAF protein associated with skin melanoma may be correlated with dabrafenib resistance: An in silico study. J Biomol Struct Dyn 2021; 40:10862-10877. [PMID: 34278963 DOI: 10.1080/07391102.2021.1950571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/28/2021] [Indexed: 12/24/2022]
Abstract
Melanoma is a type of skin cancer. Numerous genes and their proteins are strongly associated with melanoma susceptibility. This study aims to use an in silico method to identify genetic variants in the melanoma susceptibility gene. The COSMIC database was queried for genes and cross-referenced with three environment-gene interaction databases (EGP, SeattleSNPs and CTD) to identify shared genes. The majority of approved skin melanoma drugs were found to act on the protein serine/threonine-protein kinase (B-RAF) encoded by the BRAF gene, which was also present in all three referenced databases. Comprehensive computational analysis was performed to predict deleterious genetic variants associated with skin melanoma, and the nsSNPs G469V and G469E were prioritized based on their predicted deleterious effects. Molecular dynamic simulation analysis of the B-RAF protein mutants G469V and G469E reveals that variations in the amino acid conformation at the drug binding site result in inconsistency in drug interaction. Additionally, this analysis showed that the G469V and G469E mutants have lower binding energy for dabrafenib than the wild type. The population with the highest frequency of each deleterious and pathogenic variant has been determined. The study's findings would support the development of more effective treatment strategies for skin melanoma. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, Delhi, India
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12
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Hofrova A, Lousa P, Kubickova M, Hritz J, Otasevic T, Repko M, Knight A, Piskacek M. Universal two-point interaction of mediator KIX with 9aaTAD activation domains. J Cell Biochem 2021; 122:1544-1555. [PMID: 34224597 DOI: 10.1002/jcb.30075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023]
Abstract
The nine-amino-acid activation domain (9aaTAD) is defined by a short amino acid pattern including two hydrophobic regions (positions p3-4 and p6-7). The KIX domain of mediator transcription CBP interacts with the 9aaTAD domains of transcription factors MLL, E2A, NF-kB, and p53. In this study, we analyzed the 9aaTADs-KIX interactions by nuclear magnetic resonance. The positions of three KIX helixes α1-α2-α3 are influenced by sterically-associated hydrophobic I611, L628, and I660 residues that are exposed to solvent. The positions of two rigid KIX helixes α1 and α2 generate conditions for structural folding in the flexible KIX-L12-G2 regions localized between them. The three KIX I611, L628, and I660 residues interact with two 9aaTAD hydrophobic residues in positions p3 and p4 and together build a hydrophobic core of five residues (5R). Numerous residues in 9aaTAD position p3 and p4 could provide this interaction. Following binding of the 9aaTAD to KIX, the hydrophobic I611, L628, and I660 residues are no longer exposed to solvent and their position changes inside the hydrophobic core together with position of KIX α1-α2-α3 helixes. The new positions of the KIX helixes α1 and α2 allow the KIX-L12-G2 enhanced formation. The second hydrophobic region of the 9aaTAD (positions p6 and p7) provides strong binding with the KIX-L12-G2 region. Similarly, multiple residues in 9aaTAD position p6 and p7 could provide this interaction. In conclusion, both 9aaTAD regions p3, p4 and p6, p7 provide co-operative and highly universal binding to mediator KIX. The hydrophobic core 5R formation allows new positions of the rigid KIX α-helixes and enables the enhanced formation of the KIX-L12-G2 region. This contributes to free energy and is the key for the KIX-9aaTAD binding. Therefore, the 9aaTAD-KIX interactions do not operate under the rigid key-and-lock mechanism what explains the 9aaTAD natural variability.
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Affiliation(s)
- Alena Hofrova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Lousa
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Monika Kubickova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Core Facility Biomolecular Interactions and Crystallization (CF BIC), Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tomas Otasevic
- Orthopaedic Clinic, University Hospital Brno and Faculty of Medicine Masaryk University Brno
| | - Martin Repko
- Orthopaedic Clinic, University Hospital Brno and Faculty of Medicine Masaryk University Brno
| | - Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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13
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Mahjabeen I, Maqsood Y, Abbasi R, Ahmed MW, Kayani MA. Polymorphism in miRNA target sites of CEP-63 and CEP-152 ring complex influences expression of CEP genes and favors tumorigenesis in glioma. Future Oncol 2021; 17:3355-3372. [PMID: 34156311 DOI: 10.2217/fon-2020-1034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Purpose: The present study was designed to screen the genetic polymorphisms and expression profiling of CEP-152 and CEP-63 genes in brain tumor patients. Methods: The amplification refractory mutation system PCR technique (ARMS-PCR) was used for mutation analysis using 300 blood samples of brain tumor patients and 300 overtly healthy controls. For expression analysis, 150 brain tumor tissue samples along with adjacent uninvolved/normal tissues (controls) were collected. Results: A significantly higher frequency of the mutant genotype of the CEP-152 single nucleotide polymorphism (rs2169757) and CEP-63 single nucleotide polymorphisms (rs9809619 and rs13060247) was observed in patients versus overtly healthy controls. The authors' results showed highly significant deregulation of CEP-152 (p < 0.0001) and CEP-63 (p < 0.0001) in glioma/meningioma tumor tissues versus adjacent normal tissue. Conclusion: The present study showed that variations in CEP-152 and CEP-63 genes were associated with an increased risk of brain tumor.
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Affiliation(s)
- Ishrat Mahjabeen
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, 44000, Pakistan
| | - Yusra Maqsood
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, 44000, Pakistan
| | - Ramsha Abbasi
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, 44000, Pakistan
| | - Malik Waqar Ahmed
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, 44000, Pakistan.,Pakistan Institute of Rehabilitation Sciences, Isra University Islamabad Campus, Islamabad, 44000, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, 44000, Pakistan
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14
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de Andrade BC, Gennari A, Renard G, Nervis BDR, Benvenutti EV, Costa TMH, Nicolodi S, da Silveira NP, Chies JM, Volpato G, Volken de Souza CF. Synthesis of magnetic nanoparticles functionalized with histidine and nickel to immobilize His-tagged enzymes using β-galactosidase as a model. Int J Biol Macromol 2021; 184:159-169. [PMID: 34126150 DOI: 10.1016/j.ijbiomac.2021.06.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 11/26/2022]
Abstract
The aim of this study was to synthesize iron magnetic nanoparticles functionalized with histidine and nickel (Fe3O4-His-Ni) to be used as support materials for oriented immobilization of His-tagged recombinant enzymes of high molecular weight, using β-galactosidase as a model. The texture, morphology, magnetism, thermal stability, pH and temperature reaction conditions, and the kinetic parameters of the biocatalyst obtained were assessed. In addition, the operational stability of the biocatalyst in the lactose hydrolysis of cheese whey and skim milk by batch processes was also assessed. The load of 600 Uenzyme/gsupport showed the highest recovered activity value (~50%). After the immobilization process, the recombinant β-galactosidase (HisGal) showed increased substrate affinity and greater thermal stability (~50×) compared to the free enzyme. The immobilized β-galactosidase was employed in batch processes for lactose hydrolysis of skim milk and cheese whey, resulting in hydrolysis rates higher than 50% after 15 cycles of reuse. The support used was obtained in the present study without modifying chemical agents. The support easily recovered from the reaction medium due to its magnetic characteristics. The iron nanoparticles functionalized with histidine and nickel were efficient in the oriented immobilization of the recombinant β-galactosidase, showing its potential application in other high-molecular-weight enzymes.
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Affiliation(s)
- Bruna Coelho de Andrade
- Food Biotechnology Laboratory, Biotechnology Graduate Program, University of Vale do Taquari - Univates, Lajeado, RS, Brazil
| | - Adriano Gennari
- Food Biotechnology Laboratory, Biotechnology Graduate Program, University of Vale do Taquari - Univates, Lajeado, RS, Brazil
| | - Gaby Renard
- National Institute of Science and Technology in Tuberculosis, Research Center for Molecular and Functional Biology, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | | | | | - Sabrina Nicolodi
- Institute of Physics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Giandra Volpato
- Biotechnology course, Federal Institute of Education, Science, and Technology of Rio Grande do Sul - IFRS, Porto Alegre Campus, Porto Alegre, RS, Brazil
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15
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Friedrich M, Vaxevanis CK, Biehl K, Mueller A, Seliger B. Targeting the coding sequence: opposing roles in regulating classical and non-classical MHC class I molecules by miR-16 and miR-744. J Immunother Cancer 2021; 8:jitc-2019-000396. [PMID: 32571994 PMCID: PMC7307530 DOI: 10.1136/jitc-2019-000396] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 01/31/2023] Open
Abstract
Background To control gene expression, microRNAs (miRNAs) are of key importance and their deregulation is associated with the development and progression of various cancer types. In this context, a discordant messenger RNA/protein expression pointing to extensive post-transcriptional regulation of major histocompatibility complex (MHC) class I molecules was already shown. However, only a very limited number of miRNAs targeting these molecules have yet been identified. Despite an increasing evidence of coding sequence (CDS)-located miRNA binding sites, there exists so far, no detailed study of the interaction of miRNAs with the CDS of MHC class I molecules. Methods Using an MS2-tethering approach in combination with small RNA sequencing, a number of putative miRNAs binding to the CDS of human leukocyte antigen (HLA)-G were identified. These candidate miRNAs were extensively screened for their effects in the HLA-G-positive JEG3 cell line. Due to the high sequence similarity between HLA-G and classical MHC class I molecules, the impact of HLA-G candidate miRNAs on HLA class I surface expression was also analyzed. The Cancer Genome Atlas data were used to correlate candidate miRNAs and HLA class I gene expression. Results Transfection of candidate miRNAs revealed that miR-744 significantly downregulates HLA-G protein levels. In contrast, overexpression of the candidate miRNAs miR-15, miR-16, and miR-424 sharing the same seed sequence resulted in an unexpected upregulation of HLA-G. Comparable results were obtained for classical MHC class I members after transfection of miRNA mimics into HEK293T cells. Analyses of The Cancer Genome Atlas data sets for miRNA and MHC class I expression further validated the results. Conclusions Our data expand the knowledge about MHC class I regulation and showed for the first time an miRNA-dependent control of MHC class I antigens mediated by the CDS. CDS-located miRNA binding sites could improve the general use of miRNA-based therapeutic approaches as these sites are highly independent of structural variations (e.g. mutations) in the gene body. Surprisingly, miR-16 family members promoted MHC class I expression potentially in a gene activation-like mechanism.
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Affiliation(s)
- Michael Friedrich
- Medical Immunology, Martin Luther University Halle Wittenberg, Halle, Sachsen-Anhalt, Germany
| | | | - Katharina Biehl
- Medical Immunology, Martin Luther University Halle Wittenberg, Halle, Sachsen-Anhalt, Germany
| | - Anja Mueller
- Medical Immunology, Martin Luther University Halle Wittenberg, Halle, Sachsen-Anhalt, Germany
| | - Barbara Seliger
- Medical Immunology, Martin Luther University Halle Wittenberg, Halle, Sachsen-Anhalt, Germany
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16
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Chen Q, Fang X, Yao N, Wu F, Xu B, Chen Z. Suppression of miR-330-3p alleviates DSS-induced ulcerative colitis and apoptosis by upregulating the endoplasmic reticulum stress components XBP1. Hereditas 2020; 157:18. [PMID: 32386518 PMCID: PMC7211341 DOI: 10.1186/s41065-020-00135-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/30/2020] [Indexed: 11/29/2022] Open
Abstract
Background This study aimed to explore the biological activities of miR-330-3p in dextan sulphate sodium (DSS)-induced ulcerative colitis and apoptosis and the direct target of miR-330-3p in this process. HT-29 cells and male C57BL/6 mice were used to examine the function of miR-330-3p in vitro and in vivo, respectively. Expression of miRNA and mRNA was measured using quantitative real time PCR (qRT-PCR). Western blotting was used to measure the change of protein expression. Flow cytometry was used to determine cell apoptosis and luciferase assay was used to confirm the direct target of miR-330-3p. Results miR-330-3p expression was increased by DSS in both HT-29 cells and mice. Upregulation miR-330-3p induced cell apoptosis, mice weight loss and ulcerative colitis in vivo, which could prevent by suppression of miR-330-3p. Cell apoptosis related protein expression, cleaved caspase-3 and cleaved PARP was also inhibited by miR-330-3p overexpression and elevated by miR-330-3p inhibition both in vitro and in vivo. Luciferase assay confirmed that 3′ untranslated region (3′-UTR) of XBP1 is the directed target of miR-330-3p and Western blotting results have showed that protein expression of XBP1 was decreased by miR-330-3p mimics and increased by miR-330-3p inhibitor. Conclusion miR-330-3p is upregulated by DSS in both HT-29 cells and mice and promoted ulcerative colitis and cell apoptosis by targeting of 3′-UTR of XBP1, which is a key component of ER stress. Inhibition of miR-330-3p prevent DSS-induced ulcerative colitis and cell apoptosis mediated by upregulation of XBP1 expression.
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Affiliation(s)
- Qifeng Chen
- Department of Gastroenterology Surgery, Shulan(hangzhou) Hospital, No. 848, Road Dongxin, District Xiacheng, Hangzhou City, 310000, Zhejiang Province, China.
| | - Xiaoming Fang
- Department of General Surgery, 903th hospital of PLA, Hangzhou City, 310000, Zhejiang Province, China
| | - Ning Yao
- Department of General Surgery, 903th hospital of PLA, Hangzhou City, 310000, Zhejiang Province, China
| | - Fang Wu
- Department of Gastroenterology Surgery, Shulan(hangzhou) Hospital, No. 848, Road Dongxin, District Xiacheng, Hangzhou City, 310000, Zhejiang Province, China
| | - Biao Xu
- Department of Gastroenterology Surgery, Shulan(hangzhou) Hospital, No. 848, Road Dongxin, District Xiacheng, Hangzhou City, 310000, Zhejiang Province, China
| | - Zhengguang Chen
- Department of Gastroenterology Surgery, Shulan(hangzhou) Hospital, No. 848, Road Dongxin, District Xiacheng, Hangzhou City, 310000, Zhejiang Province, China
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17
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Amourda C, Saunders TE. The mirtron miR-1010 functions in concert with its host gene SKIP to balance elevation of nAcRβ2. Sci Rep 2020; 10:1688. [PMID: 32015391 PMCID: PMC6997181 DOI: 10.1038/s41598-020-58655-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/19/2020] [Indexed: 02/02/2023] Open
Abstract
Mirtrons are non-canonical miRNAs arising by splicing and debranching from short introns. A plethora of introns have been inferred by computational analyses as potential mirtrons. Yet, few have been experimentally validated and their functions, particularly in relation to their host genes, remain poorly understood. Here, we found that Drosophila larvae lacking either the mirtron miR-1010 or its binding site in the nicotinic acetylcholine receptor β2 (nAcRβ2) 3′UTR fail to grow properly and pupariate. Increase of cortical nAcRβ2 mediated by neural activity elevates the level of intracellular Ca2+, which in turn activates CaMKII and, further downstream, the transcription factor Adf-1. We show that miR-1010 downregulates nAcRβ2. We reveal that Adf-1 initiates the expression of SKIP, the host gene of miR-1010. Preventing synaptic potentials from overshooting their optimal range requires both SKIP to temper synaptic potentials (incoherent feedforward loop) and miR-1010 to reduce nAcRβ2 mRNA levels (negative feedback loop). Our results demonstrate how a mirtron, in coordination with its host gene, contributes to maintaining appropriate receptor levels, which in turn may play a role in maintaining homeostasis.
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Affiliation(s)
- Christopher Amourda
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore. .,MRC London Institute of Medical Science, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
| | - Timothy E Saunders
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, Singapore. .,Institute of Molecular and Cell Biology, A*Star, Proteos, Singapore.
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18
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Circulating Extracellular Vesicle MicroRNA as Diagnostic Biomarkers in Early Colorectal Cancer-A Review. Cancers (Basel) 2019; 12:cancers12010052. [PMID: 31878015 PMCID: PMC7016718 DOI: 10.3390/cancers12010052] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies in the developed world, with global deaths expected to double in the next decade. Disease stage at diagnosis is the single greatest prognostic indicator for long-term survival. Unfortunately, early stage CRC is often asymptomatic and diagnosis frequently occurs at an advanced stage, where long-term survival can be as low as 14%. Circulating microRNAs encapsulated in extracellular vesicles (EVs) have recently come to prominence as novel diagnostic markers for cancer. EV-miRNAs are dysregulated in the circulation of CRC patients compared to healthy controls, and several specific miRNA candidates have been posited as diagnostic markers, including miR-21, miR-23a, miR-1246, and miR-92a. This review outlines the current landscape of EV-miRNAs as potential diagnostic markers for CRC, with a specific focus on those able to detect early stage disease.
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19
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Gholami M, Larijani B, Sharifi F, Hasani‐Ranjbar S, Taslimi R, Bastami M, Atlasi R, Amoli MM. MicroRNA-binding site polymorphisms and risk of colorectal cancer: A systematic review and meta-analysis. Cancer Med 2019; 8:7477-7499. [PMID: 31637880 PMCID: PMC6885874 DOI: 10.1002/cam4.2600] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Genetic variations in miRNAs binding site might participate in cancer risk. This study aimed to systematically review the association between miRNA-binding site polymorphisms and colorectal cancer (CRC). Electronic literature search was carried out on PubMed, Web of Science (WOS), Scopus, and Embase. All types of observational studies till 30 November 2018 were included. Overall 85 studies (21 SNPs) from two systematic searches were included analysis. The results showed that in the Middle East population, the minor allele of rs731236 was associated with decreased risk of CRC (heterozygote model: 0.76 [0.61-0.95]). The minor allele of rs3025039 was related to increased risk of CRC in East Asian population (allelic model: 1.25 [1.01-1.54]). Results for rs3212986 were significant in overall and subgroup analysis (P < .05). For rs1801157 in subgroup analysis the association was significant in Asian populations (including allelic model: 2.28 [1.11-4.69]). For rs712, subgroup analysis revealed a significant (allelic model: 1.41 [1.23-1.61]) and borderline (allelic model: 0.92 [0.84-1.00]) association in Chinese and Czech populations, respectively. The minor allele of rs17281995 increased risk of CRC in different genetic models (P < .05). Finally, rs5275, rs4648298, and rs61764370 did not show significant associations. In conclusion, minor allele of rs3025039, rs3212986, and rs712 polymorphisms increases the risk of CRC in the East Asian population, and heterozygote model of rs731236 polymorphism shows protective effect in the Middle East population. In Europeans, the minor allele of rs17281995 may increase the risk of CRC, while rs712 may have a protective effect. Further analysis based on population stratifications should be considered in future studies.
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Affiliation(s)
- Morteza Gholami
- Obesity and Eating Habits Research CenterEndocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
- Endocrinology and Metabolism Research CenterEndocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Bagher Larijani
- Endocrinology and Metabolism Research CenterEndocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Farshad Sharifi
- Elderly Health Research CenterEndocrinology and Metabolism Population Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Shirin Hasani‐Ranjbar
- Obesity and Eating Habits Research CenterEndocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Reza Taslimi
- Department of GastroenterologyImam Khomeini HospitalTehran University of Medical SciencesTehranIran
| | - Milad Bastami
- Department of Medical GeneticsFaculty of MedicineTabriz University of Medical SciencesTabrizIran
| | - Rasha Atlasi
- Evidence Based Practice Research CenterEndocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Mahsa M. Amoli
- Metabolic Disorders Research CenterEndocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical SciencesTehranIran
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20
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Yao Y, Liu R, Gao C, Zhang T, Qi L, Liu G, Zhang W, Wang X, Li J, Li J, Sun C. Identification of prognostic biomarkers for breast cancer based on miRNA and mRNA co-expression network. J Cell Biochem 2019; 120:15378-15388. [PMID: 31037764 DOI: 10.1002/jcb.28805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 12/31/2022]
Abstract
PURPOSE Breast cancer (BC) remains a serious health threat for women due to its high incidence and the trend of rejuvenation. Accumulating evidence has highlighted that microRNAs (miRNAs) and messenger RNAs (mRNAs) could play important roles in various biological processes involved in the pathogenesis of BC. The present study aimed to identify potential prognostic biomarkers associated with BC. METHODS Here, original gene expression profiles of patients with BC was downloaded from The Cancer Genome Atlas (TCGA) database. TargetScan, miRDB, and miRTarBase databases were used to predict the target genes of prognostic-related differentially expressed miRNAs (DEMs). Subsequently, functional enrichment analysis and topological analysis were performed on the overlaps of target genes and differentially expressed mRNAs (DEGs), and Kaplan-Meier analysis was used to predict prognosis-related target genes to identify prognostic biomarkers. RESULTS A total of 218 DEMs and 2222 DEGs were extracted in which eight miRNAs were associated with prognosis, and 278 target DEGs were screened out incorporated into functional enrichment analysis and protein-protein interaction network visualization studies. Additionally, five hub genes (CXCL12, IGF1, LEF1, MMP1, and RACGAP1) were observed as potential biomarkers for BC prognosis through survival analysis. CONCLUSION We performed a distinctive correlation analysis of miRNA-mRNA in BC patients, and identified eight miRNAs and five hub genes may be effective biomarkers for the prognosis of BC patients.
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Affiliation(s)
- Yan Yao
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Ruijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, People's Republic of China
| | - Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Tingting Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Lingyu Qi
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Gongxi Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, People's Republic of China
| | - Wenfeng Zhang
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Xue Wang
- Medical Colleges, Qingdao University, Qingdao, Shandong, People's Republic of China
| | - Jie Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Jia Li
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Changgang Sun
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, People's Republic of China.,Department of Oncology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
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21
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Zhang X, Gao C, Liu L, Zhou C, Liu C, Li J, Zhuang J, Sun C. DNA methylation‐based diagnostic and prognostic biomarkers of nonsmoking lung adenocarcinoma patients. J Cell Biochem 2019; 120:13520-13530. [PMID: 30920015 DOI: 10.1002/jcb.28627] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Xiaoming Zhang
- College of Traditional Chinese Medicine Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Chundi Gao
- College of First Clinical Medicine Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Lijuan Liu
- Department of Traditional Chinese Medicine Oncology Weifang Traditional Chinese Hospital Weifang Shandong PR China
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
| | - Chao Zhou
- Department of Traditional Chinese Medicine Oncology Weifang Traditional Chinese Hospital Weifang Shandong PR China
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
| | - Cun Liu
- College of First Clinical Medicine Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Jia Li
- School of Clinical Medicine Weifang Medical University Weifang Shandong PR China
| | - Jing Zhuang
- Department of Traditional Chinese Medicine Oncology Weifang Traditional Chinese Hospital Weifang Shandong PR China
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
| | - Changgang Sun
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
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22
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Agrahari AK, Doss GPC, Siva R, Magesh R, Zayed H. Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach. J Theor Biol 2019; 469:163-171. [PMID: 30844370 DOI: 10.1016/j.jtbi.2019.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022]
Abstract
The G2019S substitution in the Leucine-rich repeat kinase 2 (LRRK2) is significantly associated with Parkinson's disease (PD). This substitution was identified in both familial and sporadic forms of PD with a higher frequency. Few computational studies have reported the impact of G2019S substitution on inhibitors of the kinase domain of LRRK2. However, no computational study deeply investigated the possible impact of the G2019S substitution on the kinase domain in its Apo conformation. Therefore, in this study, we used 200 ns molecular dynamic simulation using the GROMACS 5.1.4 package software to investigate the impact of the G2019S substitution on the structure of the kinase domain of LRRK2. Our results indicate that the G2019S substitution affects the dynamics and stability of LRRK2 by decreasing the flexibility and increasing the compactness of the kinase domain and showing its tendency to be in an active conformation for long time interval because of the high energy barrier between active and inactive conformation. This study predicts the molecular pathogenicity mechanism of the G2019S on patients with PD and provides a potential platform for developing therapeutics for patients with PD that harbor this amino acid substitution.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - George Priya C Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India.
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - R Magesh
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Deemed to be University (DU), Porur, Chennai, 600116, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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23
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Flowers E, Flentje A, Levine J, Olshen A, Hammer M, Paul S, Conley Y, Miaskowski C, Kober KM. A Pilot Study Using a Multistaged Integrated Analysis of Gene Expression and Methylation to Evaluate Mechanisms for Evening Fatigue in Women Who Received Chemotherapy for Breast Cancer. Biol Res Nurs 2019; 21:142-156. [PMID: 30701989 PMCID: PMC6700896 DOI: 10.1177/1099800418823286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
CONTEXT Fatigue is the most common symptom associated with cancer and its treatment. Investigation of molecular mechanisms associated with fatigue may identify new therapeutic targets. OBJECTIVE The objective of this pilot study was to evaluate the relationships between gene expression and methylation status and evening fatigue severity in women with breast cancer who received chemotherapy. METHODS Latent class analysis (LCA) was used to identify evening fatigue phenotypes. In this analysis, the lowest (i.e., moderate, n = 7) and highest (i.e., very high, n = 29) fatigue-severity classes identified using LCA were analyzed via two stages. First, a total of 32,609 transcripts from whole blood were evaluated for differences in expression levels between the classes. Next, 637 methylation sites located within the putative transcription factor binding sites for those genes demonstrating differential expression were evaluated for differential methylation state between the classes. RESULTS A total of 89 transcripts in 75 unique genes were differentially expressed between the moderate (the lowest fatigue-severity class identified) and very high evening fatigue classes. In addition, 23 differentially methylated probes and three differentially methylated regions were found between the moderate and very high evening fatigue classes. CONCLUSIONS Using a multistaged integrated analysis of gene expression and methylation, differential methylation was identified in the regulatory regions of genes associated with previously hypothesized mechanisms for fatigue, including inflammation, immune function, neurotransmission, circadian rhythm, skeletal muscle energy, carbohydrate metabolism, and renal function as well as core biological processes including gene transcription and the cell-cycle regulation.
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Affiliation(s)
- Elena Flowers
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Annesa Flentje
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Jon Levine
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Olshen
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Marilyn Hammer
- 3 Department of Nursing, Mount Sinai Hospital, New York, NY, USA
| | - Steven Paul
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Yvette Conley
- 4 School of Nursing, University of Pittsburg, Pittsburg, PA, USA
| | - Christine Miaskowski
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Kord M Kober
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
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Oskooei VK, Ghafouri-Fard S. Are long non-coding RNAs involved in the interaction circuit between estrogen receptor and vitamin D receptor? Meta Gene 2019. [DOI: 10.1016/j.mgene.2018.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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25
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Guo S, Zhang J, Wang B, Zhang B, Wang X, Huang L, Liu H, Jia B. A 5-serum miRNA panel for the early detection of colorectal cancer. Onco Targets Ther 2018; 11:2603-2614. [PMID: 29780253 PMCID: PMC5951214 DOI: 10.2147/ott.s153535] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE The study aimed to screen microRNAs (miRNAs) that can be used for the early detection of colorectal cancer (CRC) based on differential expression of miRNA in serum. MATERIALS AND METHODS A three-stage study was designed with a total of 217 CRCs, 168 colorectal adenomas (CRAs), and 190 healthy controls (HCs). A quantitative reverse transcription polymerase chain reaction was performed in three stages. We screened 528 miRNA expression profiles in the sera of 40 patients (CRC n=20, CRA n=10, and HC n=10) for candidate miRNAs, then 210 serum samples (CRC n=90, CRA n=60, and HC n=60) were used for screening of candidate miRNAs. Three hundred and twenty-five independent individual samples (CRC n=107, CRA n=98, and HC n=120) were used to validate the most differentially-expressed miRNAs in the screening stage, and binary logistic regression was used in the validation stage. A receiver operating characteristic curve was drawn to evaluate the diagnostic accuracy. RESULTS A 5-serum miRNA panel (miRNA-1246, miRNA-202-3p, miRNA-21-3p, miRNA-1229-3p, and miRNA-532-3p) effectively distinguished CRCs from HCs with 91.6% sensitivity and 91.7% specificity. The area under the curve (AUC) was 0.960 (95% confidence interval [CI]: 0.937-0.983). In addition, the panel also accurately distinguished CRCs from CRAs with 94.4% sensitivity and 84.7% specificity. The AUC was 0.951 (95% CI: 0.922-0.980). CONCLUSION Our 5-serum miRNA panel accurately distinguished CRCs from CRAs and HCs with high sensitivity and specificity. The 5-serum miRNA panel may be a promising prospect for application as a nonintrusive and inexpensive method for the early detection of CRC.
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Affiliation(s)
- Shaohua Guo
- Chinese PLA Medical School, Beijing, China
- General Surgery Department II, Chinese PLA General Hospital, Beijing, China
| | - Jiajin Zhang
- General Surgery Department II, Chinese PLA General Hospital, Beijing, China
| | - Baishi Wang
- General Surgery Department II, Chinese PLA General Hospital, Beijing, China
| | | | | | | | - Hongyi Liu
- General Surgery Department II, Chinese PLA General Hospital, Beijing, China
| | - Baoqing Jia
- Chinese PLA Medical School, Beijing, China
- General Surgery Department II, Chinese PLA General Hospital, Beijing, China
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26
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Gao C, Zhou C, Zhuang J, Liu L, Liu C, Li H, Liu G, Wei J, Sun C. MicroRNA expression in cervical cancer: Novel diagnostic and prognostic biomarkers. J Cell Biochem 2018; 119:7080-7090. [PMID: 29737570 DOI: 10.1002/jcb.27029] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/06/2018] [Indexed: 12/31/2022]
Abstract
Growing evidence has shown that a large number of miRNAs are abnormally expressed in cervical cancer (CC) tissues and play irreplaceable roles in tumorigenesis, progression, and metastasis. This study aimed to identify new biomarkers and pivotal genes associated with CC prognosis through comprehensive bioinformatics analysis. At first, the data of gene expression microarray (GSE30656) was downloaded from GEO database and differential miRNAs were obtained. Additionally, 4 miRNAs associated with the survival time of patients with CC were screened through TCGA differential data analysis, Kaplan-Meier, and Landmark analysis. Among them, the low expression of miR-188 and high expression of miR-223 correlated with the short survival of CC patients, while the down-regulation of miR-99a and miR-125b was closely related to the 5-year survival rate of patients. Then, based on the correspondence between the differentially expressed genes (DEGs) in CC from the TCGA data and the 4 miRNAs target genes, 58 target genes were screened to perform the analysis of function enrichment and the visualization of protein-protein interaction (PPI) networks. The seven pivotal genes of the PPI network as the target genes of four miRNAs related to prognosis, they were directly or indirectly involved in the development of CC. In this study, based on high-throughput data mining, differentially expressed miRNAs and related target genes were analyzed to provide an effective bioinformatics basis for further understanding of the pathogenesis and prognosis of CC. And the results may be a promising biomarker for the early screening of high-risk populations and early diagnosis of cervical cancer.
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Affiliation(s)
- Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, P. R. China
| | - Chao Zhou
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Jing Zhuang
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Lijuan Liu
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, P. R. China
| | - Huayao Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, P. R. China
| | - Gongxi Liu
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Junyu Wei
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Changgang Sun
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
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27
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The Pattern of microRNA Binding Site Distribution. Genes (Basel) 2017; 8:genes8110296. [PMID: 29077021 PMCID: PMC5704209 DOI: 10.3390/genes8110296] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/18/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022] Open
Abstract
Micro-RNA (miRNA or miR) regulates at least 60% of the genes in the human genome through their target sites at mRNA 3'-untranslated regions (UTR), and defects in miRNA expression regulation and target sites are frequently observed in cancers. We report here a systematic analysis of the distribution of miRNA target sites. Using the evolutionarily conserved miRNA binding sites in the TargetScan database (release 7.1), we constructed a miRNA co-regulation network by connecting genes sharing common miRNA target sites. The network possesses characteristics of the ubiquitous small-world network. Non-hub genes in the network-those sharing miRNA target sites with small numbers of genes-tend to form small cliques with their neighboring genes, while hub genes exhibit high levels of promiscuousness in their neighboring genes. Additionally, miRNA target site distribution is extremely uneven. Among the miRNAs, the distribution concentrates on a small number of miRNAs, in that their target sites occur in an extraordinarily large number of genes, that is, they have large numbers of target genes. The distribution across the genes follows a similar pattern; the mRNAs of a small proportion of the genes contain extraordinarily large numbers of miRNA binding sites. Quantitatively, the patterns fit into the P(K) ∝ K-α relationship (P(K): the number of miRNAs with K target genes or genes with K miRNA sites; α: a positive constant), the mathematical description of connection distribution among the nodes and a defining characteristic of the so-called scale-free networks-a subset of small-world networks. Notably, well-known tumor-suppressive miRNAs (Let-7, miR-15/16, 26, 29, 31, 34, 145, 200, 203-205, 223, and 375) collectively have more than expected target genes, and well-known cancer genes contain more than expected miRNA binding sites. In summary, miRNA target site distribution exhibits characteristics of the small-world network. The potential to use this pattern to better understand miRNA function and their oncological roles is discussed.
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Chang J, Huang L, Cao Q, Liu F. Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data. Onco Targets Ther 2016; 9:1787-94. [PMID: 27069368 PMCID: PMC4818051 DOI: 10.2147/ott.s93338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
To identify potential key microRNAs (miRNAs) and their target genes for colorectal cancer (CRC). High-throughput sequencing data of miRNA expression and gene expression (ID: GSE46622) were downloaded from Gene Expression Omnibus, including matched colon tumor, normal colon epithelium, and liver metastasis tissues from eight CRC patients. Paired t-test and NOISeq separately were utilized to identify differentially expressed miRNAs (DE-miRNAs) and genes. Then, target genes with differential expression and opposite expression trends were identified for DE-miRNAs. Combined with tumor suppressor gene, tumor-associated gene, and TRANSFAC databases, CRC-restricted miRNAs were screened out based on miRNA-target pairs. Compared with normal tissues, there were 56 up- and 37 downregulated miRNAs in metastasis tissues, as well as eight up- and 30 downregulated miRNAs in tumor tissues. miRNA-1 was downregulated in tumor and metastasis tissues, while its target oncogenes TWIST1 and GATA4 were upregulated. Besides, miRNA-let-7f-1-3p was downregulated in tumor tissues, which also targeted TWIST1. In addition, miRNA-133b and miRNA-4458 were downregulated in tumor tissues, while their common target gene DUSP9 was upregulated. Conversely, miRNA-450-b-3p was upregulated in metastasis tissues, while its target tumor suppressor gene CEACAM7 showed downregulation. The identified CRC-restricted miRNAs might be implicated in cancer progression via their target genes, suggesting their potential usage in CRC treatment.
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Affiliation(s)
- Jing Chang
- Department of Gerontology, Xinhua Hospital Affiliated to Jiaotong University School of Medicine, Shanghai, People’s Republic of China
| | - Liya Huang
- Department of Gerontology, Xinhua Hospital Affiliated to Jiaotong University School of Medicine, Shanghai, People’s Republic of China
| | - Qing Cao
- Department of Gerontology, Xinhua Hospital Affiliated to Jiaotong University School of Medicine, Shanghai, People’s Republic of China
| | - Fang Liu
- Department of Gerontology, Xinhua Hospital Affiliated to Jiaotong University School of Medicine, Shanghai, People’s Republic of China
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Li J, Drubay D, Michiels S, Gautheret D. Mining the coding and non-coding genome for cancer drivers. Cancer Lett 2015; 369:307-15. [PMID: 26433158 DOI: 10.1016/j.canlet.2015.09.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/24/2015] [Accepted: 09/24/2015] [Indexed: 12/20/2022]
Abstract
Progress in next-generation sequencing provides unprecedented opportunities to fully characterize the spectrum of somatic mutations of cancer genomes. Given the large number of somatic mutations identified by such technologies, the prioritization of cancer-driving events is a consistent bottleneck. Most bioinformatics tools concentrate on driver mutations in the coding fraction of the genome, those causing changes in protein products. As more non-coding pathogenic variants are identified and characterized, the development of computational approaches to effectively prioritize cancer-driving variants within the non-coding fraction of human genome is becoming critical. After a short summary of methods for coding variant prioritization, we here review the highly diverse non-coding elements that may act as cancer drivers and describe recent methods that attempt to evaluate the deleteriousness of sequence variation in these elements. With such tools, the prioritization and identification of cancer-implicated regulatory elements and non-coding RNAs is becoming a reality.
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Affiliation(s)
- Jia Li
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Damien Drubay
- Service de Biostatistique et d'Epidemiologie, Gustave Roussy, Villejuif, France; INSERM U1018, CESP, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Stefan Michiels
- Service de Biostatistique et d'Epidemiologie, Gustave Roussy, Villejuif, France; INSERM U1018, CESP, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France.
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Single nucleotide polymorphisms in microRNA binding sites: implications in colorectal cancer. ScientificWorldJournal 2014; 2014:547154. [PMID: 25654126 PMCID: PMC4310495 DOI: 10.1155/2014/547154] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 11/03/2014] [Accepted: 11/06/2014] [Indexed: 12/29/2022] Open
Abstract
Cancer is a complex genetic disorder, characterised by uncontrolled cell proliferation and caused by altered expression of oncogenes and tumour suppressor genes. When cell proliferation pertains to colon, it is called colorectal cancer. Most of colorectal cancer causing genes are potential targets for the miRNA (microRNA) that bind to 3'UTR (untranslated regions) of mRNA and inhibit translation. Mutations occurring in miRNA binding regions can alter the miRNA, mRNA combination, and can alter gene expression drastically. We hypothesized that 3'UTR mutation in miRNA binding site could alter the miRNA, mRNA interaction, thereby altering gene expression. Altered gene expression activity could promote tumorigenesis in colon. Therefore, we formulated a systematic in silico procedure that integrates data from various databases, followed rigorous selection criteria, and identified mutations that might alter the expression levels of cancer causing genes. Further we performed expression analysis to shed light on the potential tissues that might be affected by mutation, enrichment analysis to find the metabolic functions of the gene, and network analysis to highlight the important interactions of cancer causing genes with other genes to provide insight that complex network will be disturbed upon mutation. We provide in silico evidence for the effect of these mutations in colorectal cancer.
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