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Golozar M, Motlagh AV, Mahdevar M, Peymani M, InanlooRahatloo K, Ghaedi K. TBX15 and SDHB expression changes in colorectal cancer serve as potential prognostic biomarkers. Exp Mol Pathol 2024; 136:104890. [PMID: 38378070 DOI: 10.1016/j.yexmp.2024.104890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 01/07/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
Alterations in the expression of certain genes could be associated with both patient mortality rates and drug resistance. This study aimed to identify genes in colorectal cancer (CRC) that potentially serve as hub genes influencing patient survival rates. RNA-Seq data were downloaded from the cancer genome atlas database, and differential expression analysis was performed between tumors and healthy controls. Through the utilization of univariate and multivariate Cox regression analyses, in combination with the MCODE clustering module, the genes whose expression changes were related to survival rate and the hub genes related to them were identified. The mortality risk model was computed using the hub genes. CRC samples and the RT-qPCR method were utilized to confirm the outcomes. PharmacoGx data were employed to link the expression of potential genes to medication resistance and sensitivity. The results revealed the discovery of seven hub genes, which emerged as independent prognostic markers. These included HOXC6, HOXC13, HOXC8, and TBX15, which were associated with poor prognosis and overexpression, as well as SDHB, COX5A, and UQCRC1, linked to favorable prognosis and downregulation. Applying the risk model developed with the mentioned genes revealed a markedly higher incidence of deceased patients in the high-risk group compared to the low-risk group. RT-qPCR results indicated a decrease in SDHB expression and an elevation in TBX15 levels in cancer samples relative to adjacent healthy tissue. Also, PharmacoGx data indicated that the expression level of SDHB was correlated with drug sensitivity to Crizotinib and Dovitinib. Our findings highlight the potential association between alterations in the expression of genes such as HOXC6, HOXC13, HOXC8, TBX15, SDHB, COX5A, and UQCRC1 and increased mortality rates in CRC patients. As revealed by the PPI network, these genes exhibited the most connections with other genes linked to survival.
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Affiliation(s)
- Melika Golozar
- Kish International Campus, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ali Valipour Motlagh
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan 8165131378, Iran
| | - Mohammad Mahdevar
- Genius Gene, Genetics and Biotechnology Company, Tehran, Iran; Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Kolsoum InanlooRahatloo
- Kish International Campus, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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Hassani M, Mahdevar M, Peymani M. Exploring the role of interleukin 11 in cancer progression, patient survival, and therapeutic insights. Mol Biol Rep 2024; 51:461. [PMID: 38551695 DOI: 10.1007/s11033-024-09358-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND The Interleukin (IL)-11 gene, which is one of the members of the cytokine family, has an oncogenic role in some cancers. The main goal of this study is to analyze IL-11 expression level in 14 prevalent cancers and highlights its role in patients' survival, drug resistance, and sensitivities. Also, an association of this gene with metastasis and inflammation pathways has been investigated. METHODS AND RESULTS Using the cancer genome atlas (TCGA) data, the level of IL-11 expression and its role in prognosis and survival rate were evaluated in 13 common cancers. Then, confirming the obtained in-silico outcomes, the relative expression level of this gene in colorectal cancer (CRC) samples and their adjusted tissues were assayed by the RT-qPCR method. Furthermore, to examine the association between IL-11 expression and drug resistance and sensitivity, PharmacoGX data was applied. The co-expression network was used to recognize the pathways in which IL-11 was involved. The results from the TCGA dataset indicated that the expression level of IL-11 increased significantly in 13 prevalence cancers compared to the control groups. Interestingly, this enhanced expression level is associated with a high rate of mortality in patients with bladder, stomach, colorectal, and endometrial cancers. Also, the co-expression network analysis showed a strong correlation between IL-11 and the genes of metastasis pathway and the genes related to the inflammation process. Finally, regarding drug sensitivity, IL-11 expression level can be introduced as a remarkable biomarker for cancer detection due to area under curve (AUC). CONCLUSION Altered expression of the IL-11 gene is observed in 13 common cancers and is associated with prognosis and mortality rate in patients. Moreover, this gene can be considered a prognostic biomarker in different types of cancer, such as CRC.
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Affiliation(s)
- Mahsa Hassani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Mahdevar
- Genius Gene, Genetics and Biotechnology Company, Isfahan, Iran
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
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Amiri S, Gholizadeh L, Rasti A, Peymani M, Mirjalili SAM, Vahidi SA, Kalantar SM. Comparison of SPAG11A gene expression in infertile men with grade 1 and 2 varicocele before and after treatment. JBRA Assist Reprod 2024. [PMID: 38446746 DOI: 10.5935/1518-0557.20220060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
OBJECTIVE Sperm Associated Antigen 11A (SPAG11A) protein is a family of the epididymis-specific secretory proteins implicated in sperm maturation and function. Varicocele might cause pathophysiological difficulties in the testis and epididymis, with a harmful effect on the environment for spermatogenesis and sperm maturation. The aim of this study was to evaluate the expression level of the SPAG11A gene and sperm parameters in infertile men with grade 1 and 2 varicocele before and after treatment. METHODS Semen specimens were collected from 20 infertile men with varicocele pre-and post-treatment and 10 healthy volunteers. Semen analysis was conducted according to world health organization guidelines. Real time PCR (qRT-PCR) reaction was applied for determination of SPAG11A mRNA expression. RESULTS The results showed that there was a significant difference between the concentration and normal morphology between pre- and post-treatment groups and the controls. There were significant differences between pre-treatment and control groups in terms of progressive and non-progressive mobility. SPAG11A mRNA levels were significantly lower in the pre-treatment group than in healthy control subjects (p=0.007). There was no statistically significant difference in the expression of SPAG11A as well as semen parameters in the post-treatment group compared to the pre-treatment group. CONCLUSIONS SPAG11A gene expression and semen parameters may be affected by varicocele. Whether varicocele treatment is an effective approach to reduce the adverse effect of this disease on SPAG11A expression and semen parameters needs further investigation.
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Affiliation(s)
- Sepide Amiri
- Shiraz University of Medical Sciences School of Advanced Technologies in Medicine Department of Tissue Engineering and Applied Cell Sciences Shiraz Iran Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Islamic Azad University Faculty of Basic Sciences Department of Biology Shahrekord Iran Department of Biology, Faculty of Basic Sciences, Islamic Azad University, Shahrekord Branch, Shahrekord, Iran
| | - Lida Gholizadeh
- Shahid Sadoughi University of Medical Sciences Yazd Reproductive Sciences Institute Research and Clinical Center for Infertility Yazd Iran Research and Clinical Center for Infertility, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Azam Rasti
- Shahid Sadoughi University of Medical Science Yazd Reproductive Sciences Institute Abortion Research Centre Yazd Iran Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Science, Yazd, Iran
- Tehran University of Medical Sciences School of Medicine Department of Medical Genetics Tehran Iran Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Peymani
- Islamic Azad University Faculty of Basic Sciences Department of Biology Shahrekord Iran Department of Biology, Faculty of Basic Sciences, Islamic Azad University, Shahrekord Branch, Shahrekord, Iran
| | - Seyed Ali Mohammad Mirjalili
- Shahid Sadoughi University of Medical Sciences Yazd Reproduction Sciences Institute Department of Andorology Yazd Iran Department of Andorology, Yazd Reproduction Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Seraj-Aldin Vahidi
- Shahid Sadoughi University of Medical Sciences Yazd Reproduction Sciences Institute Department of Andorology Yazd Iran Department of Andorology, Yazd Reproduction Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Seyed Mehdi Kalantar
- Shahid Sadoughi University of Medical Science Yazd Reproductive Sciences Institute Abortion Research Centre Yazd Iran Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Science, Yazd, Iran
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Morshedzadeh F, Ghanei M, Lotfi M, Ghasemi M, Ahmadi M, Najari-Hanjani P, Sharif S, Mozaffari-Jovin S, Peymani M, Abbaszadegan MR. An Update on the Application of CRISPR Technology in Clinical Practice. Mol Biotechnol 2024; 66:179-197. [PMID: 37269466 PMCID: PMC10239226 DOI: 10.1007/s12033-023-00724-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/13/2023] [Indexed: 06/05/2023]
Abstract
The CRISPR/Cas system, an innovative gene-editing tool, is emerging as a promising technique for genome modifications. This straightforward technique was created based on the prokaryotic adaptive immune defense mechanism and employed in the studies on human diseases that proved enormous therapeutic potential. A genetically unique patient mutation in the process of gene therapy can be corrected by the CRISPR method to treat diseases that traditional methods were unable to cure. However, introduction of CRISPR/Cas9 into the clinic will be challenging because we still need to improve the technology's effectiveness, precision, and applications. In this review, we first describe the function and applications of the CRISPR-Cas9 system. We next delineate how this technology could be utilized for gene therapy of various human disorders, including cancer and infectious diseases and highlight the promising examples in the field. Finally, we document current challenges and the potential solutions to overcome these obstacles for the effective use of CRISPR-Cas9 in clinical practice.
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Affiliation(s)
- Firouzeh Morshedzadeh
- Department of Genetics, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Ghanei
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Malihe Lotfi
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Morteza Ghasemi
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Mohsen Ahmadi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran
| | - Parisa Najari-Hanjani
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
| | - Samaneh Sharif
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Peymani
- Department of Genetics, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohammad Reza Abbaszadegan
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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Salimian N, Peymani M, Ghaedi K, Hashemi M, Rahimi E. Collagen 1A1 (COL1A1) and Collagen11A1(COL11A1) as diagnostic biomarkers in Breast, colorectal and gastric cancers. Gene 2024; 892:147867. [PMID: 37783295 DOI: 10.1016/j.gene.2023.147867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
PURPOSE Collagen family genes (CFGs) play a significant role in the pathogenesis of cancers. This study aimed to evaluate changes in the expression levels (Els) of CFGs related to epithelial-mesenchymal transition (EMT) and metastasis in gastric (GC), breast (BC), and colorectal (CRC) cancers to introduce these genes as potential diagnostic biomarkers for these three types of cancer. METHODS The Cancer Genome Atlas (TCGA) examined ELS changes in CFGs associated with EMT and metastasis to determine their diagnostic value for GC, BC, and CRC. InteractiVenn was used to find genes shared by these three cancers. The biomarker role of CFGs was determined using the receiver operating characteristic (ROC) analysis. GC, BC, and CRC samples were analyzed using the RT-qPCR method to verify the bioinformatics results and evaluate the EL of the selected genes as biomarkers for these cancers. RESULTS The in-silico results showed a significant increase in the EL of several CFGs involved in EMT and metastasis in GC, BC, and CRC samples compared to healthy samples. Six common genes (COL11A1, COL12A1, COL1A1, COL1A2, COL5A1, and COL5A2) showed significantly increased in these three cancers, therebysupporting their oncogenic role. Furthermore, the biomarker-related analyses indicated that COL11A1 and COL1A1 were common diagnostic biomarkers for the three cancers. The RT-qPCR method confirmed that the ELs of COL11A1 and COL1A1 in the GC, BC, and CRC samples increased significantly compared to the adjacent normal samples. CONCLUSION CFGs in EMT and metastasis of GC, BC, and CRC are strong common diagnostic biomarkers for these cancers.
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Affiliation(s)
- Niloufar Salimian
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ebrahim Rahimi
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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Ahmadi M, Morshedzadeh F, Ghaderian SMH, Mousavi P, Habibipour L, Peymani M, Abbaszadegan MR, Ghafouri-Fard S. Carcinogenic roles of MAFG-AS1 in human cancers. Clin Transl Oncol 2024; 26:52-68. [PMID: 37351806 DOI: 10.1007/s12094-023-03246-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
The MAF bZIP transcription factor G-antisense RNA 1 (MAFG-AS1) is located on chromosome 17. MAFG-AS1 was upregulated in 15 human cancers. MAFG-AS1 not only suppresses 16 miRNAs but also directly impacts 22 protein-coding genes' expression. Notably, abnormal MAFG-AS1 expression is connected to clinicopathological characteristics and a worse prognosis in a variety of cancers. Moreover, MAFG-AS1 takes its part in the tumorigenesis and progression of various human malignancies by suppressing apoptosis and promoting proliferation, migration, invasion, aerobic glycolysis, ferroptosis, angiogenesis, EMT, and metastasis. Besides, it can predict treatment effectiveness in ER + breast cancer, urothelial bladder carcinoma, and liver cancer by functioning as a trigger of resistance to tamoxifen, sorafenib, and cisplatin. This study systematically presents the functions of MAFG-AS1 in various cancers, as well as the findings of bioinformatics analyses of the MAFG-AS1, which should give clear advice for future research.
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Affiliation(s)
- Mohsen Ahmadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Firouzeh Morshedzadeh
- Department of Genetics, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - Leila Habibipour
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Maryam Peymani
- Department of Genetics, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Reza Abbaszadegan
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Karimi B, Mokhtari K, Rozbahani H, Peymani M, Nabavi N, Entezari M, Rashidi M, Taheriazam A, Ghaedi K, Hashemi M. Pathological roles of miRNAs and pseudogene-derived lncRNAs in human cancers, and their comparison as prognosis/diagnosis biomarkers. Pathol Res Pract 2024; 253:155014. [PMID: 38128189 DOI: 10.1016/j.prp.2023.155014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
This review examines and compares the diagnostic and prognostic capabilities of miRNAs and lncRNAs derived from pseudogenes in cancer patients. Additionally, it delves into their roles in cancer pathogenesis. Both miRNAs and pseudogene-derived lncRNAs have undergone thorough investigation as remarkably sensitive and specific cancer biomarkers, offering significant potential for cancer detection and monitoring. . Extensive research is essential to gain a complete understanding of the precise roles these non-coding RNAs play in cancer, allowing the development of novel targeted therapies and biomarkers for improved cancer detection and treatment approaches.
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Affiliation(s)
- Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Khatere Mokhtari
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Hossein Rozbahani
- Department of Psychology, North Tehran Branch, Islamic Azad University, Tehran, Iran; Department of Psychology, West Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H3Z6, Canada
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Afshin Taheriazam
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Mahmoudian Esfahani M, Mostashfi M, Vaheb Hosseinabadi S, Hashemi MS, Peymani M, Zohrabi D, Angaji SA, Nasr-Esfahani MH, Ghaedi K. Unveiling the regulatory of miR-101-3p on ZNF746 in a Parkinson's disease cell model: Implications for therapeutic targeting. Neurosci Res 2023:S0168-0102(23)00216-X. [PMID: 38103579 DOI: 10.1016/j.neures.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 11/08/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
In this study, we explored the regulatory role of microRNA miR-101-3p on the zinc finger protein 746 (ZNF746), also known as PARIS, which is implicated in both sporadic and familial forms of Parkinson's disease. In a Parkinson's disease cell model, utilizing SH-SY5Y cells treated with 1-methyl-4-phenylpyridine (MPP+), we observed that miR-101-3p was downregulated, while ZNF746 was upregulated. To investigate the direct impact of miR-101-3p on ZNF746, our team conducted overexpression experiments, successfully reversing ZNF746's expression at both the mRNA and protein levels, as confirmed through quantitative PCR and western blotting. We also performed luciferase assays, providing compelling evidence that ZNF746 is a direct target of miR-101-3p. Additionally, we noted that miR-101-3p overexpression resulted in increased expression of PGC1α, a gene targeted by ZNF746. Functionally, we assessed the implications of miR-101-3p overexpression through MTS assays and flow cytometry, revealing significant promotion of cell viability, inhibition of ROS production, and reduced apoptosis in the Parkinson's disease cell model. In conclusion, this study highlights the role of miR-101-3p in regulating ZNF746 expression and suggests its potential as a therapeutic target for Parkinson's disease. These findings provide valuable molecular insights that could pave the way for innovative treatment strategies in combating this debilitating neurodegenerative disorder.
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Affiliation(s)
| | - Maryam Mostashfi
- Department of Cell and Molecular Biology, Faculty of Biosciences, Kharazmi University, Tehran, Iran
| | | | - Motahare-Sadat Hashemi
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Dina Zohrabi
- Department of Biology, Faculty of Science, NourDanesh Institute of Higher Education, Isfahan, Iran
| | - Seyed Abdolhamid Angaji
- Department of Cell and Molecular Biology, Faculty of Biosciences, Kharazmi University, Tehran, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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Nahumi A, Peymani M, Asadi A, Abdolmaleki A, Panahi Y. Decellularized tracheal scaffold as a promising 3D scaffold for tissue engineering applications. Tissue Cell 2023; 85:102258. [PMID: 37918216 DOI: 10.1016/j.tice.2023.102258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Tissue engineering is a science that uses the combination of scaffolds, cells, and active biomolecules to make tissue in order to restore or maintain its function and improve the damaged tissue or even an organ in the laboratory. The purpose of this research was to study the characteristics and biocompatibility of decellularized sheep tracheal scaffolds and also to investigate the differentiation of Adipose-derived stem cells (AD-MSCs) into tracheal cells. After the decellularization of sheep tracheas through the detergent-enzyme method, histological evaluations, measurement of biochemical factors, measurement of DNA amount, and photographing the ultrastructure of the samples by scanning electron microscopy (SEM), they were also evaluated mechanically. Further, In order to check the viability and adhesion of stem cells to the decellularized scaffolds, adipose mesenchymal stem cells were cultured on the scaffolds, and the 3-(4,5-dimethylthiazol-2-yl)- 2,5-diphenyltetrazolium bromide (MTT) assay was performed. The expression analysis of the intended genes for the differentiation of mesenchymal stem cells into tracheal cells was evaluated by the real-time PCR method. These results show that the prepared scaffolds are an ideal model for engineering applications, have high biocompatibility, and that the tracheal scaffold provides a suitable environment for the differentiation of ADMSCs. This review provides a basis for future research on tracheal decellularization scaffolds, serves as a suitable model for organ regeneration, and paves the way for their use in clinical medicine.
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Affiliation(s)
- Aida Nahumi
- Department of Biology, Faculty of Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Asadollah Asadi
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran.
| | - Arash Abdolmaleki
- Department of Biophysics, Faculty of Advanced Technologies, University of Mohaghegh Ardabili, Namin, Iran
| | - Yassin Panahi
- Department of Basic Medical Sciences, khoy University of Medical Sciences, Khoy, Iran
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Bakhtiyari A, Bakhtiyari S, Peymani M, Haghani K, Norozi S. Association of fatty acid binding protein-4 (FABP-4) T87C and rs8192688 gene polymorphisms and FABP-4 level with cardiovascular disease susceptibility in type 2 diabetic patients. Nucleosides Nucleotides Nucleic Acids 2023; 43:427-440. [PMID: 37814502 DOI: 10.1080/15257770.2023.2265943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
Type 2 Diabetes Mellitus (T2DM) is known to cause dyslipidemia and increase the risk of cardiovascular disease (CVD). Fatty acid binding protein (FABP)-4 plays a significant role in various stages of T2DM and CVD. Although it has been demonstrated that genetic variations of the FABP-4 gene can affect insulin sensitivity, the results obtained so far are controversial. The aim of this study was to investigate the possible association between T87C and rs8192688 polymorphisms and serum levels of FABP-4 with CVD susceptibility in T2DM patients. The study included 70 healthy controls, 70 individuals with T2DM, and 70 T2DM patients with CVD. Genomic DNA was extracted, and FABP-4 T87C and rs8192688 gene polymorphic sites were amplified using the ARMS-PCR method. Lipid profile and FABP-4 serum levels were significantly higher in T2DM patients with CVD compared to those with only T2DM (p < 0.05). Additionally, FABP-4 T87C gene polymorphism (TC genotypes) and dominant model (TT vs. TC + CC) were significantly associated with a decreased risk of both T2DM and T2DM with CVD patients (p < 0.05). Patients carrying TC + CC genotypes had significantly lower levels of triglyceride and FABP-4 compared to those carrying the TT genotype (p < 0.05). There was no significant association between FABP-4 rs8192688 polymorphism and either T2DM or CVD disease. It appears that FABP-4 T87C polymorphism decreases FABP-4 levels leading to decreased serum TG levels. Since both T2DM and CVD have inflammatory backgrounds, reducing inflammation can improve insulin sensitivity and lower TG levels in these patients.
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Affiliation(s)
- Amin Bakhtiyari
- Department of Biology, Islamic Azad University, Shahrekord, Iran
| | - Salar Bakhtiyari
- Department of Clinical Biochemistry, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University School of Medicine, Chicago, IL, USA
| | - Maryam Peymani
- Department of Biology, Islamic Azad University, Shahrekord, Iran
| | - Karimeh Haghani
- Department of Clinical Biochemistry, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Siros Norozi
- Department of Cardiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
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Mahdavi Niyaki Z, Salehzadeh A, Peymani M, Zaefizadeh M. Exploring the Therapeutic Potential of Fe 3O 4@Glu-Oleuropein Nanoparticles in Targeting KRAS Pathway-Regulating lncRNAs in Colorectal Cancer Cells. Biol Trace Elem Res 2023:10.1007/s12011-023-03892-w. [PMID: 37792268 DOI: 10.1007/s12011-023-03892-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
Cancer, the leading cause of death worldwide, has witnessed significant advancements in treatment through targeted therapies. Among the proto-oncogenes prevalent in human cancers, KRAS stands out, and recent research has focused on long noncoding RNAs (lncRNAs) as regulators of miRNAs targeting the KRAS oncogene. This study specifically explores lncRNAs involved in the KRAS pathway in colorectal cancer (CRC). To investigate this, researchers employed iron oxide nanoparticles coated with glucose and conjugated with Oleuropein (Fe3O4@Glu-Oleuropein NPs) to evaluate their impact on candidate lncRNAs associated with KRAS pathway deregulation. The study utilized TCGA data to identify genes affected by KRAS mutation and lncRNAs linked to KRAS in CRC. Enrichr and MsigDB databases helped identify relevant pathways. Genes with a correlation coefficient above 0.5 and a P-value less than 0.01 with candidate lncRNAs were selected. MTT and flow cytometry assays determined the anti-proliferative and apoptotic effects of Fe3O4@Glu-Oleuropein NPs on CRC cells (SW480) and normal cells (HEK293). The findings showed that increased expression of FEZF1-AS1, GAS6-AS1, and LINC00920 correlated with mutated KRAS, and co-expressed genes were significantly involved in hypoxia, KRAS signaling, DNA repair, and IL-2/STAT5 signaling pathways. Fe3O4@Glu-Oleuropein NPs exhibited higher toxicity toward cancer cells, with IC50 values of 92 μg/ml for SW480 and 281 μg/ml for HEK293. Flow cytometry analysis revealed a substantial increase in necrotic and apoptotic cells when treated with Fe3O4@Glu-Oleuropein, along with down-regulation of GAS6-AS1, LINC00920, and FEZF1-AS1 lncRNAs in treated cells. In conclusion, this study highlights the therapeutic potential of Fe3O4@Glu-Oleuropein on colon cancer cells in vitro. The identification of lncRNAs involved in the KRAS pathway provides insights into the underlying mechanisms and offers avenues for further research in targeted cancer therapies.
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Affiliation(s)
| | - Ali Salehzadeh
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran.
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohammad Zaefizadeh
- Department of Biology, Ardabil Branch, Islamic Azad University, Ardabil, Iran
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Bakhsh MR, Rouhi L, Ghaedi K, Hashemi M, Peymani M, Samarghandian S. Therapeutic effects of guanidine hydrochloride on breast cancer through targeting KCNG1 gene. Biomed Pharmacother 2023; 164:114982. [PMID: 37311278 DOI: 10.1016/j.biopha.2023.114982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/28/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is one of the subtypes of breast cancer (BC) that is associated with poor survival rates and failure to respond to hormonal and targeted therapies. OBJECTIVE The aim of this study was to identify a specific gene at the expression level for TNBC and targeting of this type of breast cancer based on it. Using TCGA database, genes that are particularly high expression in TNBC subtypes compared to other BC subtypes (in terms of receptor status) and normal samples were identified and their sensitivity and specificity were evaluated. Using PharmacoGX and Drug Bank data, drug sensitivity and drug-appropriate genes were identified, respectively. The effects of the identified drug on triple-negative cell lines (MDA-MB-468) were evaluated in comparison with the cell line of other subtypes (MCF7) by apoptosis and MTS tests. RESULTS Data analyzes showed that the expression level of KCNG1 gene in the TNBC subgroup was significantly higher compared to other BC subtypes from the KCN gene family and ROC results showed that this gene had highest sensitivity and specificity in TNBC subtype. The results of drug resistance and sensitivity showed that an increase in the expression level of KCNG1 was associated with sensitivity to Cisplatin and Oxaliplatin. Moreover, Drug Bank results showed that Guanidine hydrochloride (GuHCl) was a suitable inhibitor for KCNG1. In vitro results showed that the expression level of KCNG1 was higher in MDA-MB-468 compared to MCF7. In addition, the rate of apoptosis in response to GuHCl treatment in MDA-MB-468 cell line as TNBC cell model was higher than MCF7 in the same concentration. CONCLUSION This study revealed that GuHCl could be a suitable treatment for TNBC subtype by targeting of KCNG1.
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Affiliation(s)
- Mehdi Roshanian Bakhsh
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, the Islamic Republic of Iran
| | - Leila Rouhi
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, the Islamic Republic of Iran
| | - Kamran Ghaedi
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, the Islamic Republic of Iran; Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, the Islamic Republic of Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, the Islamic Republic of Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, the Islamic Republic of Iran.
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, the Islamic Republic of Iran.
| | - Saeed Samarghandian
- Healthy Ageing Research Centre, Neyshabur University of Medical Sciences, Neyshabur, the Islamic Republic of Iran.
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Mokhtari K, Peymani M, Rashidi M, Hushmandi K, Ghaedi K, Taheriazam A, Hashemi M. Colon cancer transcriptome. Prog Biophys Mol Biol 2023; 180-181:49-82. [PMID: 37059270 DOI: 10.1016/j.pbiomolbio.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.
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Affiliation(s)
- Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Asad Samani L, Ghaedi K, Majd A, Peymani M, Etemadifar M. Coordinated modification in expression levels of HSPA1A/B, DGKH, and NOTCH2 in Parkinson's patients' blood and substantia nigra as a diagnostic sign: the transcriptomes' relationship. Neurol Sci 2023:10.1007/s10072-023-06738-4. [PMID: 36973590 DOI: 10.1007/s10072-023-06738-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 03/05/2023] [Indexed: 03/29/2023]
Abstract
BACKGROUND Diagnosis of Parkinson's disease (PD) is associated with a vast number of challenges. This study aimed to assess the overlap of PD patients' transcriptomes in the substantia nigra (SN) with peripheral blood mononuclear cells (PBMCs) to discover potential biomarkers for diagnosis. METHODS GEO data were used to select genes with significant changes in expression level in the SN region and eligible studies. Also, transcriptome data related to blood of PD patients with other neurodegenerative diseases (ND) was considered. Differential expression genes between PD and control were evaluated in the SN and blood, and RT-qPCR was applied to validate the findings. RESULTS At the expression level, no significant similarity in long non-coding RNA was found between the patients' SN and blood. While in silico results revealed 16 common mRNAs in SN and blood with significant expression levels. Among all overexpressed mRNAs, HSPA1A/B expression level had the highest expression difference between control and PD samples. Moreover, DGKH had the highest score of down-regulated genes in both blood and SN. The NOTCH pathway had the highest score pathway among up-regulated pathways, and the expression levels of NOTCH2, H4C8, and H2BC21 associated with this pathway had the most ability to separate the control and PD populations. Furthermore, RT-qPCR results revealed that HSPA1A/B, NOTCH2, and H4C8 were overexpressed in PD PBMCs, while DGKH expression levels were lower compared to controls. CONCLUSION Our findings indicate that expression levels of HSPA1A/B, DGKH, and NOTCH2 could be applied as candidate biomarkers to diagnose PD patients in the SN region and PBMCs.
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Affiliation(s)
- Leila Asad Samani
- Department of Cellular and Molecular Biology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Azadi Sq., Hezar Jerib Ave, P.O. Code, Isfahan, 81746-73441, Iran.
| | - Ahmad Majd
- Department of Biology, North Tehran Branch, Islamic Azad University, Tehran, Iran.
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Masoud Etemadifar
- Department of Neurology and Isfahan Neurosurgery Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Hashemi M, Paskeh MDA, Orouei S, Abbasi P, Khorrami R, Dehghanpour A, Esmaeili N, Ghahremanzade A, Zandieh MA, Peymani M, Salimimoghadam S, Rashidi M, Taheriazam A, Entezari M, Hushmandi K. Towards dual function of autophagy in breast cancer: A potent regulator of tumor progression and therapy response. Biomed Pharmacother 2023; 161:114546. [PMID: 36958191 DOI: 10.1016/j.biopha.2023.114546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/25/2023] Open
Abstract
As a devastating disease, breast cancer has been responsible for decrease in life expectancy of females and its morbidity and mortality are high. Breast cancer is the most common tumor in females and its treatment has been based on employment of surgical resection, chemotherapy and radiotherapy. The changes in biological behavior of breast tumor relies on genomic and epigenetic mutations and depletions as well as dysregulation of molecular mechanisms that autophagy is among them. Autophagy function can be oncogenic in increasing tumorigenesis, and when it has pro-death function, it causes reduction in viability of tumor cells. The carcinogenic function of autophagy in breast tumor is an impediment towards effective therapy of patients, as it can cause drug resistance and radio-resistance. The important hallmarks of breast tumor such as glucose metabolism, proliferation, apoptosis and metastasis can be regulated by autophagy. Oncogenic autophagy can inhibit apoptosis, while it promotes stemness of breast tumor. Moreover, autophagy demonstrates interaction with tumor microenvironment components such as macrophages and its level can be regulated by anti-tumor compounds in breast tumor therapy. The reasons of considering autophagy in breast cancer therapy is its pleiotropic function, dual role (pro-survival and pro-death) and crosstalk with important molecular mechanisms such as apoptosis. Moreover, current review provides a pre-clinical and clinical evaluation of autophagy in breast tumor.
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Affiliation(s)
- Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mahshid Deldar Abad Paskeh
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sima Orouei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Pegah Abbasi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ramin Khorrami
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Amir Dehghanpour
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Negin Esmaeili
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Azin Ghahremanzade
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohammad Arad Zandieh
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari 4815733971, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
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Salimian N, Peymani M, Ghaedi K, Mirzaei S, Hashemi M. Diagnostic and therapeutic potential of LINC01929 as an oncogenic LncRNA in human cancers. Pathol Res Pract 2023; 244:154409. [PMID: 36931128 DOI: 10.1016/j.prp.2023.154409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/21/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
Recent findings have shown the significant role of long non-coding RNAs in the pathogenesis of various cancers. In this regard, the variation in the expression of LINC01929 was explored in various cancers to explore its impact on the development of diverse malignancies and cancers. The data of the cancer genome atlas (TCGA) were utilized to evaluate the changes in the expression of LINC01929 in various cancers, as well as its relationship with the patients' survival rate. The co-expression of the genes and data merging of TCGA were utilized to identify the LINC01929-associated pathways. The samples of colorectal, gastric, and breast cancers were also examined by the RT-qPCR to confirm the results and evaluate the expression of LINC01929 in the mentioned cancers. In silico investigations indicated a remarkable enhancement in the expression of LINC01929 within the tumor tissues compared to normal samples in 10 types of cancer. Based on the survival results, the increase in the LINC01929 expression is linked to poor prognosis of bladder, breast, colorectal, kidney, and liver cancers. The gene co-expression network showed the strong co-expression of LINC01929 with genes involved in the metastatic pathways including COL5A1. RT-qPCR findings showed a remarkable increment in the expression level of LINC01929 in the colorectal, gastric, and breast tumor tissues versus the adjacent normal tissues. A significant and strong relationship was also found between the expression of LINC01929 and COL5A1. This study indicated a significant enhancement in the expression level of LINC01929 in various cancer types, accompanied by the mortality rate. Moreover, LINC01929 exhibited a strong co-expression with the metastatic genes such as COL5A1. As an oncogene and regulator of the metastatic pathways, LINC01929 can be a proper candidate for diagnostic and therapeutic purposes.
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Affiliation(s)
- Niloufar Salimian
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Sepideh Mirzaei
- Department of Biology, Faculty of Science, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Bahmani L, Baghi M, Peymani M, Javeri A, Ghaedi K. The PBX1/miR-141-miR-200a/EGR2/SOCS3 Axis; Integrative Analysis of Interaction Networks to Discover the Possible Mechanism of MiR-141 and MiR-200a-Mediated Th17 Cell Differentiation. Iran J Biotechnol 2023; 21:e3211. [PMID: 36811100 PMCID: PMC9938929 DOI: 10.30498/ijb.2022.317078.3211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/06/2022] [Indexed: 02/24/2023]
Abstract
Background Overexpression of miR-141 and miR-200a is known to be associated with the differentiation of T helper 17 (Th17) cells, which are key players in the pathophysiology of autoimmune disorders. However, the function and governing mechanism of these two microRNAs (miRNAs) in Th17 cell skewing are poorly defined. Objectives The aim of the present study was to identify the common upstream transcription factors and downstream target genes of miR-141 and miR-200a to obtain a better insight into the possible dysregulated molecular regulatory networks driving miR-141/miR-200a-mediated Th17 cell development. Materials and Methods A consensus-based prediction strategy was applied for in-silico identification of potential transcription factors and putative gene targets of miR-141 and miR-200a. Thereafter, we analyzed the expression patterns of candidate transcription factors and target genes during human Th17 cell differentiation by quantitative real-time PCR and examined the direct interaction between both miRNAs and their potential target sequences using dual-luciferase reporter assays. Results According to our miRNA-based and gene-based interaction network analyses, pre-B cell leukemia homeobox (PBX1) and early growth response 2 (EGR2) were respectively taken into account as the potential upstream transcription factor and downstream target gene of miR-141 and miR-200a. There was a significant overexpression of the PBX1 gene during the Th17 cell induction period. Furthermore, both miRNAs could directly target EGR2 and inhibit its expression. As a downstream gene of EGR2, the suppressor of cytokine signaling 3 (SOCS3) was also downregulated during the differentiation process. Conclusions These results indicate that activation of the PBX1/miR-141-miR-200a/EGR2/SOCS3 axis may promote Th17 cell development and, therefore, trigger or exacerbate Th17-mediated autoimmunity.
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Affiliation(s)
- Leila Bahmani
- Department of Stem Cells and Regenerative Medicine, Institute for Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Masoud Baghi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran,
Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Arash Javeri
- Department of Stem Cells and Regenerative Medicine, Institute for Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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Salehitabar E, Mahdevar M, Valipour Motlagh A, Forootan FS, Feizbakhshan S, Zohrabi D, Peymani M. Identification of genes with high heterogeneity of expression as a predictor of different prognosis and therapeutic responses in colorectal cancer: a challenge and a strategy. Cancer Cell Int 2022; 22:276. [PMID: 36064367 PMCID: PMC9446546 DOI: 10.1186/s12935-022-02694-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/25/2022] [Indexed: 11/29/2022] Open
Abstract
Background Molecular heterogeneity is one of the most important concerns in colorectal cancer (CRC), which results in a wide range of therapy responses and patient prognosis. We aimed to identify the genes with high heterogeneity of expression (HHE) and their relation with prognosis and drug resistance. Methods Two cohort studies, the cancer genome atlas (TCGA) and the GSE39582, were used to discover oncogenes genes with HHE. The relationship between identified genes with clinical and genomic characteristics was evaluated based on TCGA data. Also, the GDSC and CCLE data were used for drug resistance and sensitivity. Sixty CRC samples were used to validate the obtained data by RT-qPCR. Results Findings revealed that 132 genes with HHE were found to be up-regulated in both cohorts and were enriched in pathways such as hypoxia, angiogenesis, and metastasis. Forty-nine of selected genes related to clinical and genomic variables, including stage, common mutations, the tumor site, and microsatellite state that were ignored. The expression level of CXCL1, SFTA2, SELE, and SACS as genes with HHE were predicted survival patients, and RT-qPCR results demonstrated that levels of SELE and SACS had HHE in CRC samples. The expression of many identified genes like BGN, MMP7, COL11A1, FAP, KLK10, and TNFRSE11B was associated with resistance to chemotherapy drugs. Conclusions Some genes expression, including SELE, SACS, BGN, KLK10, COL11A1, and TNFRSE11B have an oncogenic function with HHE, and their expression can be used as indicators for differing treatment responses and survival rates in CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02694-9.
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Affiliation(s)
- Ebrahim Salehitabar
- Department of Biology, Faculty of Science, NourDanesh Institute of Higher Education, Isfahan, Iran
| | - Mohammad Mahdevar
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.,Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Valipour Motlagh
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Farzad Seyed Forootan
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran.,Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Sara Feizbakhshan
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.,Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Dina Zohrabi
- Department of Biology, Faculty of Science, NourDanesh Institute of Higher Education, Isfahan, Iran.
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
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Hajipour M, Mokhtari K, Mahdevar M, Esmaeili M, Peymani M, Nasr-Esfahani MH, Mirzaei S, Hasehmi M, Hushmandi K, Ghaedi K. Identification of a novel interplaying loop of PPARγ and respective lncRNAs are involved in colorectal cancer progress. Int J Biol Macromol 2022; 219:779-787. [PMID: 35940433 DOI: 10.1016/j.ijbiomac.2022.07.247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) as regulatory molecules play important roles in early treatment and diagnosis of cancers. Considering the role of PPARγ in colorectal cancer (CRC) as a tumor suppressor, the GEO database was used to identify candidate genes that affect the activation of PPARγ protein in CRC cell lines. Then were selected 5 genes containing PPARγ response element (PPRE) in up to 4000 bp upstream and were affected by PPARγ protein activation in HT-29 colon cancer cell line using UCSC database. Expression meta-analysis was applied to map the expression network between candidate genes and all known lncRNAs through expression correlation and lncRNAs that correlated with a greater number of candidate genes (R > 0.5, P.value < 0.001). Moreover, were selected 3 lncRNAs as lncRNAs affected by PPARγ protein activation. Next, the expression levels of candidate genes and lncRNAs were evaluated using RT-qPCR in HT-29 cell line. Results showed a significant increase (FDR <0.05) in the expression level of 5 candidate genes and lncRNAs LINC01133, MBNL1-AS, LOC100288911 after treatment with pioglitazone as PPARγ ligand compared to the untreated group in HT-29 cells. Although additional tests are needed to confirm bioinformatics predictions, it can be concluded that increased expression of PPARγ may increase genes and lncRNAs expression. In summary, this study could be suggested identifying lncRNAs affected by PPARγ activation could be a new strategy in understanding the function and activity of PPARγ in colon cancer.
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Affiliation(s)
- Maral Hajipour
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran; Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Khatereh Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran; Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Mahdevar
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maryam Esmaeili
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Sepideh Mirzaei
- Department of Biology, Faculty of Science, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Mehrdad Hasehmi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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20
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Azad MH, Niktab I, Dastjerdi S, Abedpoor N, Rahimi G, Safaeinejad Z, Peymani M, Forootan FS, Asadi-Shekaari M, Esfahani MHN, Ghaedi K. Correction: The combination of endurance exercise and SGTC (Salvia-Ginseng-Trigonella-Cinnamon) ameliorate mitochondrial markers' overexpression with sufficient ATP production in the skeletal muscle of mice fed AGEs-rich high-fat diet. Nutr Metab (Lond) 2022; 19:44. [PMID: 35804414 PMCID: PMC9264501 DOI: 10.1186/s12986-022-00676-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Maryam Haghparast Azad
- ACECR Institute of Higher Education, Isfahan, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Iman Niktab
- ACECR Institute of Higher Education, Isfahan, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Shaghayegh Dastjerdi
- ACECR Institute of Higher Education, Isfahan, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Navid Abedpoor
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Golbarg Rahimi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., P.O. Code 81746-73441, Isfahan, Iran
| | - Zahra Safaeinejad
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Farzad Seyed Forootan
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. .,Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran.
| | - Majid Asadi-Shekaari
- Neuroscience Research Center, Neuropharmacology Institute, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hossein Nasr Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., P.O. Code 81746-73441, Isfahan, Iran.
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21
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Mokhtari K, Mahdevar M, Hajipour M, Esmaeili M, Peymani M, Mirzaei S, Nasr-Esfahani MH, Hashemi M, Hushmandi K, Ghaedi K. Title: Involvement of unsaturated fatty acid biosynthesis in CRC progression based on in vitro and in silico studies. Biomed Pharmacother 2022; 153:113338. [PMID: 35779418 DOI: 10.1016/j.biopha.2022.113338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 12/11/2022] Open
Abstract
Obesity is one of the risk factors concerns of colorectal cancer (CRC), the most common type of gastrointestinal cancer, due to the changing lifestyle and especially diet. There are various molecular pathways associated with obesity and the risk of CRC incidence, such as insulin resistance or elevated plasma free fatty acids, which alter the signaling pathways of intestinal epithelial cells. The aim of this study was to better understand the significance of unsaturated fatty acid biosynthesis on pathogenesis of colon cancer in obese. Based on GSE20931 dataset, obese individuals affected by CRC had higher increased gene expression than non-obese individuals. The analysis showed that in obese individuals, the 16 signaling pathway genes were activated and increased (FDR <0.05) significantly. The biosynthetic pathway of unsaturated fatty acids showed a cross-talk with the arachidonic acid metabolism pathway and the PPAR signaling pathway is influenced and regulated via these pathways. The biosynthetic pathway of unsaturated fatty acids consisting of 22 genes, were analyzed using GEO data and revealed that 4 genes (HSD17B12, TECR, FADS2, ELOVL5) from this pathway were significantly increased (FDR <0.05). These data were validated based on TCGA data (Adj.p.value <0.001). The expression level of candidate genes in HT-29 cells decreased significantly (P.value <0.01), and PPARγ expression increased under linoleic acid treatment (200 μM) compared to control cells. Moreover, in presence of linoleic acid treatment, migration, colony formation, and proliferation decreased (P.value <0.01) in presence of treatment. In summary, the Biosynthesis pathway of unsaturated fatty acids is an interesting and critical pathway in CRC.
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Affiliation(s)
- Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran; Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Mahdevar
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maral Hajipour
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran; Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maryam Esmaeili
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Sepideh Mirzaei
- Department of Biology, Faculty of Science, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran.
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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22
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Karimi B, Dehghani Firoozabadi A, Peymani M, Ghaedi K. Circulating long noncoding RNAs as novel bio-tools: Focus on autoimmune diseases. Hum Immunol 2022; 83:618-627. [PMID: 35717260 DOI: 10.1016/j.humimm.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/04/2022]
Abstract
Long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs that do not encode proteins. These RNAs have various essential regulatory functions. Irregular expression of lncRNAs has been related to the pathological process of varied diseases, and are considered promising diagnostic biomarkers. LncRNAs can release into the circulation and be stable in body fluids as circulating lncRNAs. A subset of circulating lncRNAs that exist in exosomes are referred to as exosomal lncRNA molecules. These lncRNAs are highly stable and resist RNases. Exosomes have captured a great deal of attention due to their involvement in regulating communications between cells. In conditions of autoimmune disease, exosomes play critical roles in the pathological processes. In this context, circulating lncRNAs have been shown to modulate the immune response and indicated as prognosis and diagnostic biomarkers for autoimmune diseases. This review highlights the role of circulating lncRNAs (particularly exosomal) as diagnostic biomarkers for autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis, psoriasis, and Sjögren's syndrome.
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Affiliation(s)
- Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Kamran Ghaedi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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23
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Pakravan G, Peymani M, Abedpoor N, Safaeinejad Z, Yadegari M, Derakhshan M, Nasr Esfahani MH, Ghaedi K. Antiapoptotic and anti-inflammatory effects of Pparγ agonist, pioglitazone, reversed Dox-induced cardiotoxicity through mediating of miR-130a downregulation in C57BL/6 mice. J Biochem Mol Toxicol 2022; 36:e23041. [PMID: 35343021 DOI: 10.1002/jbt.23041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 01/18/2022] [Accepted: 03/02/2022] [Indexed: 11/08/2022]
Abstract
Doxorubicin (Dox) is an antitumor agent widely used in cancer therapy, with notable side effects of cardiac toxicity. Peroxisome proliferator-activated receptor γ (PPARγ), is a transcriptional factor with antiapoptotic and anti-inflammatory properties. Recently we indicated that cardiac toxicity of Dox was due to upregulation of miR-130a and further suppressive effect on cardiac Pparγ in vitro. In this study, we extended our proposed hypothesis in vivo. To achieve this, pioglitazone (Pio) and GW9662 were used as the specific agonist and antagonist of Pparγ to treat Dox-injected mice. Heart function, apoptosis, and inflammation in heart tissue were studied. Pretreatment of Dox-injected mice with Pio resulted in elevated expression of Pparγ and suppression of miR-130a. However, GW9662 pretreatment was unable to increase miR-130a expression. Pio pretreatment led to partially cardiac toxicity limitation of Dox whereas GW9662 caused heart damage. Finally, our observation determined that activation of Pparγ was not adequate to reverse the Dox-induced toxicity completely.
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Affiliation(s)
- Golnaz Pakravan
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Navid Abedpoor
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Zahra Safaeinejad
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mehrdad Yadegari
- Department of Diagnostic Imaging, Faculty of Veterinary Medicine, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Derakhshan
- Department of Pathology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hossein Nasr Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kamran Ghaedi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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24
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Dana S, Ghaedi K, Peymani M, Esfahani MHN. MiR-141-3p Expression Profiling in MPP Treated Differentiated SH-SY5Y Cells: A Model of Parkinson’s Disease. NEUROCHEM J+ 2022. [DOI: 10.1134/s1819712422010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Haghparast Azad M, Niktab I, Dastjerdi S, Abedpoor N, Rahimi G, Safaeinejad Z, Peymani M, Forootan FS, Asadi-Shekaari M, Nasr Esfahani MH, Ghaedi K. The combination of endurance exercise and SGTC (Salvia-Ginseng-Trigonella-Cinnamon) ameliorate mitochondrial markers' overexpression with sufficient ATP production in the skeletal muscle of mice fed AGEs-rich high-fat diet. Nutr Metab (Lond) 2022; 19:17. [PMID: 35248109 PMCID: PMC8897771 DOI: 10.1186/s12986-022-00652-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/17/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Skeletal muscle mitochondria is one of the most important affected sites of T2DM and its molecular mechanism is yet to be elucidated. Some recent theories believed that mitochondrial markers are upregulated in response to high fat induced T2DM; however, the reasons and the affected factors are still uncertain. In this regard, we aimed to investigate the effect of high fat induced T2DM on mitochondrial markers of skeletal muscle, and an herbal component along with endurance exercise, as probable treatments, in AGE-rich high-fat diet (AGEs-HFD) induced T2DM mice. METHODS T2DM was induced by 16 weeks of AGEs-HFD consumption in male C57BL/6 mice, followed by 8 weeks of drugs ingestion and endurance exercise treatments (n = 6 in each group and total number of 42 mice). The herbal component was an aquatic extract of Salvia officinalis, Trigonella foenum-graecum, Panax ginseng, and Cinnamomum zeylanicum, termed "SGTC". We then examined the relative expression of several mitochondrial markers, including Ppargc1α, Tfam, and electron transport chain genes and ATP levels, in skeletal muscle samples. RESULTS T2DM was successfully induced according to morphological, biochemical, and molecular observations. All mitochondrial markers, including Ppargc1a, Tfam, Cpt2, and electron transport chain genes, were upregulated in T2DM group compared to controls with no significant changes in the ATP levels. Most mitochondrial markers were downregulated by drug treatment compared to T2DM, but the ATP level was not significantly altered. All mitochondrial markers were upregulated in exercised group compared to T2DM with mild increase in the ATP level. The Ex + SGTC group had moderate level of mitochondrial markers compared to T2DM, but the highest ATP production. CONCLUSION The highly significant overexpression of mitochondrial markers may be in response to free fatty acid overload. However, the lack of significant change in the ATP level may be a result of ROS generation due to electron leakage in the AGEsRAGE axis and electron transport chain. Almost all treatments ameliorate mitochondrial markers' overexpression. The SGTC appears to regulate this with its antioxidant properties. Instead, exercise upregulated mitochondrial markers efficiently; however, the most efficient results, i.e. the most ATP production among the treatments, were observed in the Ex + SGTC group.
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Affiliation(s)
- Maryam Haghparast Azad
- ACECR Institute of Higher Education, Isfahan, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Iman Niktab
- ACECR Institute of Higher Education, Isfahan, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Shaghayegh Dastjerdi
- ACECR Institute of Higher Education, Isfahan, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Navid Abedpoor
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Golbarg Rahimi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., P.O. Code 81746-73441, Isfahan, Iran
| | - Zahra Safaeinejad
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Farzad Seyed Forootan
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. .,Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran.
| | - Majid Asadi-Shekaari
- Neuroscience Research Center, Neuropharmacology Institute, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hossein Nasr Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., P.O. Code 81746-73441, Isfahan, Iran.
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26
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Yousefi M, Peymani M, Ghaedi K, Irani S, Etemadifar M. Significant modulations of linc001128 and linc0938 with miR-24-3p and miR-30c-5p in Parkinson disease. Sci Rep 2022; 12:2569. [PMID: 35173238 PMCID: PMC8850599 DOI: 10.1038/s41598-022-06539-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/24/2022] [Indexed: 12/22/2022] Open
Abstract
Parkinson disease (PD) is the second most common neurodegenerative disease; the evidence suggests that lncRNAs and miRNAs play an important role in regulating the PD-related genes. The purpose of this research was to introduce two novel lncRNAs as the biomarker of PD diagnosis and treatment. We evaluated the expression profiles of six nodes of two regulatory networks in the PBMCs which had been got from 38 PD patients and 20 healthy individuals by qRT-PCR. Then, we compared the expression of these RNAs in both early and late stages of PD with the controls to determine if their expression could be related to the severity of disease. Further, this study investigated the direct interaction between one of the lncRNAs and target miRNA by using the dual luciferase assay. The results of the expression profiles of six nodes of the two ceRNA networks shown that linc01128, hsa-miR-24-3p and hsa-miR-30c-5p expression were significantly downregulated. While, the Linc00938, LRRK2 and ATP13A2 expression were up-regulated in the PBMC of the PD patients, in comparison to the controls. In addition, this study demonstrated that linc00938 directly sponged hsa-miR-30c-5p. The present study, therefore, for the first time, revealed two candidate lncRNAs as the biomarkers in the PD patients.
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Affiliation(s)
- Maryam Yousefi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Peymani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. .,Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Etemadifar
- Department of Neurology and Isfahan Neurosurgery Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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27
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Hashemi R, Peymani M, Ghaedi K, Saffar H. In silico identification of the specific pathways in each stage of colorectal cancer and the association of their top genes with drug resistance and sensitivity. Med Oncol 2022; 39:57. [PMID: 35150347 DOI: 10.1007/s12032-022-01661-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
Investigating the specific pathways and their relation with survival, mutation, sensitivity, and resistance to various drugs in different stages of colorectal cancer (CRC) could be effective in cancer treatment. In this study, identifying the specific pathways in each stage of CRC compared to other stages was considered via meta-analytic methodology. The Cancer Genome Atlas (TCGA) data with gene set enrichment analysis (GSEA) software, and CRC RNA-Seq data were used to enrich and determine specific pathways as well as to evaluate the expression level of TOP RANK genes. In addition, The Cancer Cell Line Encyclopedia (CCLE) data were used to correlate candidate genes with drug resistance. Finally, using Gene Expression Omnibus (GEO) data, drugs that could affect the expression level of these genes were identified. Three specific molecular pathways, including oxidative phosphorylation (OXPHOS), regulation of transporter activity (RTA), and negative regulation of transmembrane receptor protein serine threonine kinase (NRSTK) have been identified as hub pathways for stages II, III, and IV, respectively (P < 0.01). The expression level of TOP RANK genes in each stage increased on average twice compared to other stages (P < 0.01), and CCNB1, DKK1, NOG genes were associated with survival in stages II and IV, respectively (P < 0.01). The expression of some selected genes had a correlation with drug resistance and sensitivity (P < 0.05). GEO data revealed that gamma-tocotrienol (g-T3), NSC319726, and Casiopeina Cas-II-gly may reduce the expression of, NDUFAF1, CCNB1, DKK1 genes, respectively (P < 0.01). Specific pathways and TOP RANK genes could lead to cancer progression and malignancy, resistance to chemotherapy drugs, poor survival in patients, and metastasis. Therefore, identification and targeting these pathways at each stage could be crucial in inhibiting progression at different stages of CRC.
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Affiliation(s)
- Reza Hashemi
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Kamran Ghaedi
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.,Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Esfahän, Iran
| | - Hana Saffar
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.,Department of Pathology, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
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28
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Roshanian Bakhsh M, Peymani M, Rouhi L, Ghaedi K. PSAT1 gene as a biomarker for targeting triple negative breast cancer in presence of Rapamycin. Nucleosides Nucleotides Nucleic Acids 2022; 41:166-182. [PMID: 35038970 DOI: 10.1080/15257770.2021.2025393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
The Triple-Negative Breast Cancers (TNBCs) poor survival outcomes are related to not responding to hormonal therapy or targeting HER2 protein. The aim of this study was to introduce a drug among the conventional chemotherapy drugs based on the transcripts of the TNBC patients. The transcriptome of MDA-MB-468 cell line as a TNBC model was analyzed in the presence of 17 common drugs in fifteen GEO datasets. Then, decreased gene lists in the presence of each drug were compared in different subtypes of breast cancer based on TCGA data. The effect of selected drug on survival and apoptosis rates of MDA-MB-468 and MCF-7 cells (as ER+/PR + model) were compared. The outcomes showed that the expression of the decreased gene by Rapamycin among other drugs increased in TNBC subtype compared to the other two subtypes including triple-positive and ER+/PR+. The expression of PSAT1 in TNBC group was significant higher than normal and other subtypes (p ≤ 0.0001), and was introduced as a biomarker in TNBC that its expression was down-regulated by Rapamycin based on in silico studies. In the presence of 3000 µg/mL Rapamycin, there was a sharp decrease in MDA-MB-468 cell viability (p ≤ 0.0001) and a significant increase in apoptosis compared to MCF-7 cells treated with the same concentration of the drug. Moreover, RT-qPCR revealed PSAT1 expression more decreased under Rapamycin-treatment in TNBC cells compared to ER + PR + cells. The results of this study show that Rapamycin is a suitable drug for targeting TNBC based on its transcriptome and biomarker.Supplemental data for this article is available online at.
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Affiliation(s)
- Mehdi Roshanian Bakhsh
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Leila Rouhi
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Kamran Ghaedi
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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Akbari F, Peymani M, Salehzadeh A, Ghaedi K. Identification of modules based on integrative analysis for drug prediction in colorectal cancer. Gene Reports 2021. [DOI: 10.1016/j.genrep.2021.101403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kazemi M, Peymani M. Expression of Th17 axis as a biomarker panel in diagnosis and prognosis of colorectal cancer. Gene Reports 2021. [DOI: 10.1016/j.genrep.2021.101363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ghanizade P, Oroujalian A, Peymani M. Differential expression analysis of CCDC107 and RMRP lncRNA as potential biomarkers in colorectal cancer diagnosis. Nucleosides Nucleotides Nucleic Acids 2021; 40:1144-1158. [PMID: 34669559 DOI: 10.1080/15257770.2021.1983827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been found to be correlated with different cell biological processes and progression of various types of cancers including colorectal cancer (CRC). CRC is one of the most widespread cancers, thus, introducing new methods or biomarkers for its early diagnosis are desirable. The Crucial role of RMRP lncRNA and its nearby gene, CCDC107, has been shown in numerous types of malignancies. The current study aims to compare expression of CCDC107 and RMRP in CRC and its adjacent normal tissues. For this study, RT-qPCR was applied to evaluate the expression level of candidate gene and lncRNA in 72 CRC cases. ROC curve was plotted to examine the diagnostic capacity. Additionally, for more supporting data, The Cancer Gene Atlas (TCGA, Firehose Legacy) dataset hosted by the cBioportal server and GEPIA online database were enrolled to investigate the effect of both genes expression level on clinicopathological parameters. We observed expression of CCDC107 was significantly down-regulated in the patients group (p < 0.05) which was associated with poor disease-free survival, friction genome alteration and surgical margin status. In contrast, RMRP expression was not significantly altered in CRC versus normal tissues. ROC curve analysis revealed that the area under the curve (AUC) for CCDC107 and RMRP were 0.871 and 0.5, respectively. Additionally, expression of these two genes did not change significantly in different stages of the disease. In conclusion, CCDC107 significantly decreased in colorectal tumor samples and can be considered as a biomarker for diagnostic aims in CRC, but not RMRP.
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Affiliation(s)
- Parisa Ghanizade
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Andisheh Oroujalian
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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Nazempour N, Taleqani MH, Taheri N, Haji Ali Asgary Najafabadi AH, Shokrollahi A, Zamani A, Fattahi Dolatabadi N, Peymani M, Mahdevar M. The role of cell surface proteins gene expression in diagnosis, prognosis, and drug resistance of colorectal cancer: In silico analysis and validation. Exp Mol Pathol 2021; 123:104688. [PMID: 34592197 DOI: 10.1016/j.yexmp.2021.104688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Cell surface proteins (CSPs) are an important type of protein in different essential cell functions. This study aimed to distinguish overexpressed CSPs in colorectal cancer to investigate their biomarker, prognosis, and drug resistance potential. Raw data of three datasets including 1187 samples was downloaded then normalization and differential expression were performed. By the combination of the cancer genome atlas (TCGA) clinical data, survival analysis was carried out. Information of all CSPs was collected from cell surface protein atlas. The role of each candidate gene expression was investigated in drug resistance by CCEL and GDSC data from PharmacoGX. CRC samples including 30 tumor samples and adjacent normal were used to confirm data by RT-qPCR. Outcomes showed that 66 CSPs overexpressed in three datasets, and 146 CSPs expression associated with poor prognosis features in TCGA data that TIMP1 and QSOX2 can associate with poor patient survival independently. High-risk patients illustrated more fatality than low-risk patients based on the risk score calculated by the expression level of these genes. Receiver operating characteristic curve analysis showed that 39 CSPs as perfect biomarkers for diagnosis in CRC. Furthermore, QSOX2 and TIMP1 expression levels increased in tumor samples compared to adjacent normal samples. The Drug resistance analysis demonstrated ADAM12 and COL1A2 up-regulation among 66 overexpressed CSPs caused resistance to Venetoclax and Cyclophosphamide with a high estimate, respectively. Many CSPs are deregulated in CRC, and can be valuable candidates as biomarkers for diagnosis, prognosis, and drug resistance.
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Affiliation(s)
- Nasrin Nazempour
- Department of Chemistry, Shahreza Branch, Islamic Azad University, Shahreza, Isfahan, Iran; Gene Raz Bu Ali, Genetic and Biotechnology Academy, Isfahan, Iran
| | - Mohammad Hossein Taleqani
- Department of Biology, Faculty of Science, University of Yazd, Yazd, Iran; Gene Raz Bu Ali, Genetic and Biotechnology Academy, Isfahan, Iran
| | - Navid Taheri
- Department of Microbiology, Zanjan Branch, Islamic Azad University, Zanjan, Iran; Gene Raz Bu Ali, Genetic and Biotechnology Academy, Isfahan, Iran
| | | | - Alireza Shokrollahi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Atefeh Zamani
- Gene Raz Bu Ali, Genetic and Biotechnology Academy, Isfahan, Iran
| | | | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Sharekord, Iran.
| | - Mohammad Mahdevar
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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Zaniani NR, Oroujalian A, Valipour A, Peymani M. LAMTOR5 expression level is a biomarker for colorectal cancer and lncRNA LAMTOR5-AS1 predicting miRNA sponging effect. Mol Biol Rep 2021; 48:6093-6101. [PMID: 34374893 DOI: 10.1007/s11033-021-06623-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/03/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Strong evidence indicated that high expression of HBXIP (also known as LAMTOR5) promotes cancer cells proliferation and helps cancer progression. Long non-coding RNAs (lncRNA) have also a crucial role in developing cancer. In this study, we aimed to determine the expression of LAMTOR5 and its nearby lncRNA, LAMTOR5-AS1 and investigate their potential as a biomarker in colorectal cancer (CRC) patients. METHODS 75 tissues of colorectal tumors and non-tumor adjacent normal sampled in this study. After RNA procedure then RT-qPCR was applied for expression analysis. Moreover, in silico investigation also enrolled for predicting sponging effect of lncRNA with miRNAs. RESULTS LAMTOR5 transcription level significantly overexpressed (p value < 0.001) and has shown a diagnostic potential (AUC = 0.8) in CRC. LAMTOR5-AS1 did not indicate any remarkable expression change overall, but showed a significant overexpressed in elderly patients (> 60) with CRC (p value < 0.0097). Moreover, the correlation analysis between LAMTOR5 and LAMTOR5-AS1 revealed a significant association in CRC (p value = 0.0074) which can be partly explained by its predicting act as a mediator with sponging effect on hsa-miR-let-7b-3p and hsa-miR-20a-5p. CONCLUSION LAMTOR5 gene can be considered as prognostic biomarker for CRC. LAMTOR5-AS5 which is a nearby lncRNA of this gene could play a regulatory impact through its sponging effect on hsa-miR-let-7b-3p and hsa-miR-20a-5p which both have shown a significant impact on overall survival rate in CRC patients in high expression levels.
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Affiliation(s)
- Najmeh Riahi Zaniani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Andisheh Oroujalian
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Ali Valipour
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
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Miralaei N, Majd A, Ghaedi K, Peymani M, Safaei M. Integrated pan-cancer of AURKA expression and drug sensitivity analysis reveals increased expression of AURKA is responsible for drug resistance. Cancer Med 2021; 10:6428-6441. [PMID: 34337875 PMCID: PMC8446408 DOI: 10.1002/cam4.4161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
Introduction The AURKA gene encodes a protein kinase involved in cell cycle regulation and plays an oncogenic role in many cancers. The main objective of this study is to analyze AURKA expression in 13 common cancers and its role in prognostic and drug resistance. Method Using the cancer genome atlas (TCGA) as well as CCLE and GDSC data, the level of AURKA gene expression and its role in prognosis and its association with drug resistance were evaluated, respectively. In addition, the expression level of AURKA was assessed in colorectal cancer (CRC) and gastric cancer (GC) samples. Besides, using Gene Expression Omnibus (GEO) data, drugs that could affect the expression level of this gene were also identified. Results The results indicated that the expression level of AURKA gene in 13 common cancers increased significantly compared to normal samples or it survived poorly (HR >1, p < 0.01) in lung, prostate, kidney, bladder, and uterine cancers. Also, the gene expression data showed increased expression in CRC and GC samples compared to normal ones. The level of AURKA was significantly associated with the resistance to SB 505124, NU‐7441, and irinotecan drugs (p < 0.01). Eventually, GEO data showed that JQ1, actinomycin D1, and camptothecin could reduce the expression of AURKA gene in different cancer cell lines (logFC < 1, p < 0.01). Conclusion Increased expression of AURKA is observed in prevalent cancers and associated with poor prognostic and the development of drug resistance. In addition, some chemotherapy drugs can reduce the expression of this gene.
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Affiliation(s)
- Noushin Miralaei
- Department of Biology, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Ahmad Majd
- Department of Biology, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Masoomeh Safaei
- Department of Pathology, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
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Oroujalian A, Peymani M, Ghaedi K. rs73092672 allele T is significantly associated with the higher risk of breast cancer incidence. Nucleosides Nucleotides Nucleic Acids 2021; 40:779-789. [PMID: 34284702 DOI: 10.1080/15257770.2021.1944637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Breast cancer is the most common cancer in women worldwide with remarkable proportion of the patients in advanced stage. Recently the importance of genetic mutations in cancers are well established and also the role of tumor suppressor genes such as FHIT gene in both heritable and non-heritable cancer. MicroRNAs are a class of non-coding RNAs which can interfere with cellular regulation. In this study, the association of rs73092672 which is located within the FHIT gene and the 3'UTR of hsa-miR-509-5p with the susceptibility to breast cancer risk has been studied in the Iranian population. By using the PCR_RFLP, the genotype rs73092672 was determined in 90 patients and 100 control subjects. The genotypes of the individuals were analyzed statistically to find the association between rs73092672 and the breast cancer incidence. The results revealed that due to the dominance of the C allele, the frequency of CC + CT genotypes, as compared with TT, had a significant correlation with the incidence of this disease in controls and cases (p = 0.02; OR= 3.6). Moreover, Bioinformatics analysis suggests rs73092672 as a polymorphism in the 3'UTR of hsa-miR-509-5p with higher binding affinity in the presence of T allele than C allele.
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Affiliation(s)
- Andisheh Oroujalian
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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Bahmani L, Baghi M, Peymani M, Javeri A, Ghaedi K. MiR-141-3p and miR-200a-3p are involved in Th17 cell differentiation by negatively regulating RARB expression. Hum Cell 2021; 34:1375-1387. [PMID: 34086186 DOI: 10.1007/s13577-021-00558-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/24/2021] [Indexed: 01/09/2023]
Abstract
Among T helper (Th) lineages differentiated from naïve CD4+ T cells, interleukin (IL)-17-producing Th17 cells are highly correlated with the pathogenesis of autoimmune disorders. This study aimed to clarify the involvement of miR-141-3p and miR-200a-3p in Th17 cell differentiation as well as explore their potential target genes involved. For this purpose, human naïve CD4+ T cells were cultured under Th17 cell polarizing condition. The differentiation process was confirmed through measurement of IL-17 secretion using the ELISA method and assessment of Th17 cell-defining genes expression during the differentiation period. MiR-141-3p and miR-200a-3p downstream genes were identified via consensus and integration in silico approach and their expression pattern and alterations were evaluated by quantitative real-time PCR. Finally, direct interaction between both microRNAs (miRNAs) and their common predicted target sequences was approved by dual-luciferase reporter assay. Highly increased IL-17 secretion and Th17 lineage-specific genes expression confirmed Th17 cell differentiation. Our results have demonstrated that miR-141-3p and miR-200a-3p are Th17 cell-associated miRNAs and their expression level is upregulated significantly during Th17 cell induction. We have also found that retinoic acid receptor beta (RARB) gene, whose product has been reported as a negative regulator of Th17 cell generation, is a direct target of both miRNAs and its downregulation can affect the transcriptional level of JAK/STAT pathway genes. Overall, our results have identified two novel Th17 lineage-associated miRNAs and have provided evidence for the RARB-dependent mechanism of miR-141-3p and miR-200a-3p-induced Th17 cell differentiation and hence Th17-mediated autoimmunity.
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Affiliation(s)
- Leila Bahmani
- Department of Stem Cells and Regenerative Medicine, Institute for Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Pajoohesh Blvd., P.O. Code 14965-161, Tehran, Iran
| | - Masoud Baghi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., P.O. Code 81746-73441, Isfahan, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Arash Javeri
- Department of Stem Cells and Regenerative Medicine, Institute for Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Pajoohesh Blvd., P.O. Code 14965-161, Tehran, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., P.O. Code 81746-73441, Isfahan, Iran.
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Baghi M, Yadegari E, Rostamian Delavar M, Peymani M, Ganjalikhani‐Hakemi M, Salari M, Nasr‐Esfahani MH, Megraw TL, Ghaedi K. MiR-193b deregulation is associated with Parkinson's disease. J Cell Mol Med 2021; 25:6348-6360. [PMID: 34018309 PMCID: PMC8366452 DOI: 10.1111/jcmm.16612] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/12/2021] [Accepted: 04/28/2021] [Indexed: 02/05/2023] Open
Abstract
PGC-1α/FNDC5/BDNF has found to be a critical pathway in neurodegeneration. MicroRNAs (miR(NA)s) are non-coding regulatory RNAs whose dysregulation has been observed in multiple neurological disorders, and miRNA-mediated gene deregulation plays a decisive role in PD. Here, candidate miRNA was chosen based on the literature survey and in silico studies. Chronic and acute models of PD were created using MPP+-treated SH-SY5Y cells. Twenty PD patients and 20 healthy volunteers were recruited. RT-qPCR was performed to assess the expression of miRNA and genes. Severe mitochondrial dysfunction induced by acute MPP+ treatment instigated compensatory mechanisms through enhancing expression of PGC-1α/FNDC5/BDNF pathway genes, while chronic MPP+ toxicity led to down-regulated levels of the genes in SH-SY5Y cells. PD peripheral blood mononuclear cells (PBMCs) also showed decreased expression of target genes. There were significant changes in the level of miR-193b in both models, as well as PD PBMCs. Moreover, miR-193b overexpression significantly affected PGC-1α, FNDC5 and TFAM levels. Interestingly, down-regulations of PGC-1α, FNDC5, BDNF and TFAM were inversely correlated with miR-193b up-regulation in PD PBMCs. This study showed the deregulation of PGC-1α/FNDC5/BDNF pathway in PD models and PBMCs, verifying its importance in neurodegeneration. Our findings also revealed that miR-193b functions in PD development, possibly through regulating PGC-1α/FNDC5/BDNF pathway, suggesting miR-193b as a potential biomarker for PD diagnosis.
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Affiliation(s)
- Masoud Baghi
- Department of Cell and Molecular Biology and MicrobiologyFaculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
- Department of Animal BiotechnologyCell Science Research CenterRoyan Institute for BiotechnologyACECRIsfahanIran
| | - Elaheh Yadegari
- Department of Cell and Molecular Biology and MicrobiologyFaculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Mahsa Rostamian Delavar
- Department of Cell and Molecular Biology and MicrobiologyFaculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Maryam Peymani
- Department of BiologyFaculty of Basic SciencesShahrekord BranchIslamic Azad UniversityShahrekordIran
| | | | - Mehri Salari
- Functional Neurosurgery Research CenterShohada Tajrish Neurosurgical Center of ExcellenceShahid Beheshti University of Medical SciencesTehranIran
| | | | - Timothy L. Megraw
- Department of Biomedical SciencesFlorida State UniversityCollege of MedicineTallahasseeFLUSA
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and MicrobiologyFaculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
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Rahimi G, Heydari S, Rahimi B, Abedpoor N, Niktab I, Safaeinejad Z, Peymani M, Seyed Forootan F, Derakhshan Z, Esfahani MHN, Ghaedi K. Correction to: A combination of herbal compound (SPTC) along with exercise or metformin more efficiently alleviated diabetic complications through down-regulation of stress oxidative pathway upon activating Nrf2-Keap1 axis in AGE rich diet-induced type 2 diabetic mice. Nutr Metab (Lond) 2021; 18:32. [PMID: 33757524 PMCID: PMC7988918 DOI: 10.1186/s12986-021-00550-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Golbarg Rahimi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Avenue, Azadi Sq., Isfahan, 81746-73441, Iran
| | - Salime Heydari
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Avenue, Azadi Sq., Isfahan, 81746-73441, Iran
| | - Bahareh Rahimi
- Department of Medical Biotechnology, Faculty of Allied Medical Science, Iran University of Medical Science, Tehran, Iran
| | - Navid Abedpoor
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Avenue, Azadi Sq., Isfahan, 81746-73441, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan Street, Salman Street, Isfahan, 816513-1378, Iran
| | - Iman Niktab
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan Street, Salman Street, Isfahan, 816513-1378, Iran
| | - Zahra Safaeinejad
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan Street, Salman Street, Isfahan, 816513-1378, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | | | - Zahra Derakhshan
- Alzahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hossein Nasr Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan Street, Salman Street, Isfahan, 816513-1378, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Avenue, Azadi Sq., Isfahan, 81746-73441, Iran.
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Rahimi G, Heydari S, Rahimi B, Abedpoor N, Niktab I, Safaeinejad Z, Peymani M, Seyed Forootan F, Derakhshan Z, Esfahani MHN, Ghaedi K. A combination of herbal compound (SPTC) along with exercise or metformin more efficiently alleviated diabetic complications through down-regulation of stress oxidative pathway upon activating Nrf2-Keap1 axis in AGE rich diet-induced type 2 diabetic mice. Nutr Metab (Lond) 2021; 18:14. [PMID: 33468193 PMCID: PMC7816367 DOI: 10.1186/s12986-021-00543-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND SPTC is a mix of four herbal components (Salvia officinalis, Panax ginseng, Trigonella foenum-graeceum, and Cinnamomum zeylanicum) which might be prevented the development of AGE rich diet-induced diabetic complication and liver injury through activated the nuclear factor erythroid-2-related-factor-2 (Nrf2) pathway. Nrf2, as a master regulator of antioxidant response elements by activating cytoprotective genes expression, is decreased oxidative stress that associated with hyperglycemia and increases insulin sensitivity. the aim of this study was to assess whether the combination therapy of SPTC along with exercise or metformin moderate oxidative stress related liver injurie with more favorable effects in the treatment of AGE rich diet-induced type 2 diabetic mice. METHODS We induced diabetes in C57BL/6 mice by AGE using a diet supplementation and limitation of physical activity. After 16 weeks of intervention, AGE fed mice were compared to control mice. Diabetic mice were assigned into seven experimental groups (each group; n = 5): diabetic mice, diabetic mice treated with SPTC (130 mg/kg), diabetic mice treated with Salvia Officinalis (65 mg/kg), diabetic mice treated with metformin (300 mg/kg), diabetic mice with endurance exercise training, diabetic mice treated with SPTC + metformin (130/300 mg/kg), diabetic mice treated with SPTC + exercise training. RESULTS SPTC + exercise and SPTC + metformin reduced diabetic complications like gain weight, water and calorie intake, blood glucose, insulin, and GLUT4 content more efficiently than each treatment. These combinations improved oxidative stress hemostasis by activating the Nrf2 signaling pathway and attenuating keap1 protein more significantly. CONCLUSION Eventually, combined treatment of SPTC with exercise or metformin as a novel approach had more beneficial effects to prevent the development of diabetes and oxidative stress associated with hyperglycemia.
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Affiliation(s)
- Golbarg Rahimi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Avenue, Azadi Sq., Isfahan, 81746-73441 Iran
| | - Salime Heydari
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Avenue, Azadi Sq., Isfahan, 81746-73441 Iran
| | - Bahareh Rahimi
- Department of Medical Biotechnology, Faculty of Allied Medical Science, Iran University of Medical Science, Tehran, Iran
| | - Navid Abedpoor
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Avenue, Azadi Sq., Isfahan, 81746-73441 Iran
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan Street, Salman Street, Isfahan, 816513-1378 Iran
| | - Iman Niktab
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan Street, Salman Street, Isfahan, 816513-1378 Iran
| | - Zahra Safaeinejad
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan Street, Salman Street, Isfahan, 816513-1378 Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | | | - Zahra Derakhshan
- Alzahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hossein Nasr Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan Street, Salman Street, Isfahan, 816513-1378 Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Avenue, Azadi Sq., Isfahan, 81746-73441 Iran
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Shirani F, Baghi M, Rostamian Delavar M, Shoaraye Nejati A, Eshaghiyan A, Nasr‐Esfahani MH, Peymani M, Ghaedi K. Cover. Mol Genet Genomic Med 2020. [DOI: 10.1002/mgg3.1596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Amir-Shahkarami M, Peymani M. The expression patterns of NBAT1 and CASC15 are associated with colorectal cancer. Gene Reports 2020. [DOI: 10.1016/j.genrep.2020.100876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Fazeli S, Motovali-Bashi M, Peymani M, Hashemi MS, Etemadifar M, Nasr-Esfahani MH, Ghaedi K. A compound downregulation of SRRM2 and miR-27a-3p with upregulation of miR-27b-3p in PBMCs of Parkinson's patients is associated with the early stage onset of disease. PLoS One 2020; 15:e0240855. [PMID: 33171483 PMCID: PMC7654768 DOI: 10.1371/journal.pone.0240855] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/03/2020] [Indexed: 02/06/2023] Open
Abstract
Parkinson’s disease (PD) is diagnosed when motor symptoms emerges, which almost 70% of dopamine neurons are lost. Therefore, early diagnosis of PD is crucial to prevent the progress of disease. Blood-based biomarkers, which are minimally invasive, potentially used for diagnosis of PD, including miRNAs. The aim of this study was to assess whether SRRM2 and miR-27a/b-3p could act as early diagnostic biomarkers for PD. Total RNAs from PBMCs of 30 PD’s patients and 14 healthy age and gender matched subjects was extracted. The expression levels of respective genes were assessed. Data were presented applying a two-tailed unpaired t-test and one-way ANOVA. We observed significant down-regulation of SRRM2 (p = 0.0002) and miR-27a-3p (p = 0.0001), and up-regulation of miR-27b-3p (p = 0.02) in PBMCs of Parkinson's patients. Down-regulation of miR-27a-3p is associated with increasing disease severity, whereas the up-regulation of miR-27b-3p was observed mostly at HY-1 and disease duration between 3–5 years. There was a negative correlation between SRRM2 and miR-27b-3p expressions, and miR-27a-3p positively was correlated with miR-27b-3p. Based on functional enrichment analysis, SRRM2 and miR-27a/b-3p acted on common functional pathways. miR-27a/b-3p could potentially predict the progression and severity of PD. Although both miRs had no similarity on expression, a positive correlation between both miRs was identified, supporting their potential role as biomarkers in clinical PD stages. Of note that SRRM2 and miR-27a-3p were able to distinguish PD patients from healthy individuals. Functional analysis of the similarity between genes associated with SRRM2 and miR-27a/b-3p indicates common functional pathways and their dysfunction correlates with molecular etiopathology mechanisms of PD onset.
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Affiliation(s)
- Soudabeh Fazeli
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Majid Motovali-Bashi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- * E-mail: (MMB); , (KG); (MP)
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Islamic Azad University, Shahrekord, Iran
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
- * E-mail: (MMB); , (KG); (MP)
| | - Motahare-Sadat Hashemi
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Masoud Etemadifar
- Department of Neurology and Isfahan Neurosurgery Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
- * E-mail: (MMB); , (KG); (MP)
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Akbari F, Peymani M, Salehzadeh A, Ghaedi K. Integrative in silico and in vitro transcriptomics analysis revealed new lncRNAs related to intrinsic apoptotic genes in colorectal cancer. Cancer Cell Int 2020; 20:546. [PMID: 33292233 PMCID: PMC7653898 DOI: 10.1186/s12935-020-01633-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022] Open
Abstract
Background Pathogenesis of colorectal cancer (CRC) is connected to deregulation of apoptosis while the effect of lncRNAs, as critical regulatory molecules, on this pathway is not clear well. The present study aimed to identify differential expression of genes and their related lncRNAs which are significantly associated with intrinsic apoptotic pathway in CRC. Methods The connection between CRC and apoptosis was investigated by literature reviews and the genes were enriched by using Enrichr. At the next step, differential expression of enriched genes were evaluated between normal and tumor populations in data sets and were downloaded from GEO. Then, meta-analysis and probe re-annotation were performed. For lncRNAs selection through the highest expression correlation with each of candidate genes, mRNA-lncRNA interaction of screened genes and all of lncRNAs were visualized using Cytoscape. Identified differential expression genes and lncRNAs were validated using TCGA-COAD and the obtained data were confirmed by in vitro studies in the presence of Ag@Glu-TSC nanoparticle as an apoptotic inducer. Cytotoxicity and apoptosis induction effect of Ag@Glu-TSC on Caco-2 cells was determined via MTT and Annexin V/PI, respectively. The expression of genes and lncRNAs were assayed in presence of mentioned nanoparticle. Finally, the expression level of desired genes and lncRNAs were proven in CRC tissues compared to adjacent normal tissues. Results After detection of 48 genes associated with intrinsic apoptosis in CRC according to literature, Enrichr screened 12 common genes involved in this pathway. Among them, 6 genes including BCL2, BCL2L11, BAD, CASP7, CASP9, and CYCS expression reduced in tumor tissue compared to normal according to meta-analysis studies and RNA-seq TCGA data. Afterwards, association of 8 lncRNAs comprising CDKN2B-AS1, LOC102724156, HAGLR, ABCC13, LOC101929340, LINC00675, FAM120AOS, PDCD4-AS1 with more than 5 candidate genes were identified. In vitro studies revealed that four selected lncRNAs including, CDKN2B-AS1, LOC102724156, HAGLR and FAM120AOS were significantly increased in the presence of in optimum concentration of Ag@Glu/TSC and decreased in tumor tissues versus adjacent normal tissues. Conclusion This study developed a new data mining method to screen differentially expressed lncRNAs which are involved in regulation of intrinsic apoptosis pathway in CRC quickly using published gene expression profiling microarrays. Moreover, we could validate a number of these regulators in the cellular and laboratory disease models.
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Affiliation(s)
- Fatemeh Akbari
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Ali Salehzadeh
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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Shirani F, Baghi M, Rostamian Delavar M, Shoaraye Nejati A, Eshaghiyan A, Nasr‐Esfahani MH, Peymani M, Ghaedi K. Upregulation of miR-9 and miR-193b over human Th17 cell differentiation. Mol Genet Genomic Med 2020; 8:e1538. [PMID: 33128433 PMCID: PMC7767567 DOI: 10.1002/mgg3.1538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Th17 cells are a newly discovered subset of CD4+ T cells known as key participants in various immune responses and inflammatory conditions including autoimmune diseases. Mi(cro)RNAs are a family of non-coding RNAs that regulate numerous critical immune functions. Immuno-miRNAs modulate cell biological processes in T cells, such as differentiation and function of Th17 cells. The aim of the present study is to investigate the expression of miR-9-5p, miR-193b-3p, and autoimmunity-related genes during human Th17 cells differentiation. METHODS Human naïve CD4+ T cells were purified from peripheral blood mononuclear cells (PBMCs) by magnetic cell sorting system (MACS) and their purity was checked by flow-cytometric analysis. Naïve CD4+ T cells were cultured under Th17-polarizing condition for 6 days. IL- 17 secretion was determined by means of enzyme-linked immunosorbent assay (ELISA). Next, the expression levels of miRNAs and putative targets genes were assessed by qRT-PCR at different time points of differentiation. RESULTS Our result showed dramatic downregulation of TCF7, MAP3K1, ENTPD1, and NT5E genes during human Th17 differentiation. Polarization also had a significant inducible effect on the expression of miR-9 and miR-193b over differentiation of human Th17 cells. According to our results, miR-9-5p and miR-193b-3p may contribute to Th17 differentiation probably by inhibiting the expression of negative regulators of Th17 differentiation. CONCLUSION This study confirmed deregulation of TCF7, MAP3K1, ENTPD1, and NT5E genes in Th17 differentiation process and introduced miR-9 and miR-193b as Th17 cell-associated miRNAs, making them good candidates for further investigations.
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Affiliation(s)
- Fahimeh Shirani
- Department of Animal BiotechnologyCell Science Research CenterRoyan Institute for BiotechnologyACECRIsfahanIran
| | - Masoud Baghi
- Department of Animal BiotechnologyCell Science Research CenterRoyan Institute for BiotechnologyACECRIsfahanIran
- Department of Cell and Molecular Biology and MicrobiologyFaculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Mahsa Rostamian Delavar
- Department of Cell and Molecular Biology and MicrobiologyFaculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Alireza Shoaraye Nejati
- Department of Animal BiotechnologyCell Science Research CenterRoyan Institute for BiotechnologyACECRIsfahanIran
| | - Amir Eshaghiyan
- Department of GeneticsArsanjan BranchIslamic Azad UniversityArsanjan, ShirazIran
| | | | - Maryam Peymani
- Department of Animal BiotechnologyCell Science Research CenterRoyan Institute for BiotechnologyACECRIsfahanIran
- Department of BiologyFaculty of Basic SciencesShahrekord BranchIslamic Azad UniversityShahrekordIran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and MicrobiologyFaculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
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Esmaeili M, Keshani M, Vakilian M, Esmaeili M, Peymani M, Seyed Forootan F, Chau TL, Göktuna SI, Zaker SR, Nasr Esfahani MH, Ghaedi K. Role of non-coding RNAs as novel biomarkers for detection of colorectal cancer progression through interaction with the cell signaling pathways. Gene 2020; 753:144796. [PMID: 32450203 DOI: 10.1016/j.gene.2020.144796] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/06/2020] [Accepted: 05/19/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is one of the most common types of cancer which affects the colon and the rectum. Approximately one third of annual CRC mortality occurs due to the late detection of this type of cancer. Therefore, there is an urgent need for more powerful diagnostic and prognostic tools for identification and treatment of colorectal tumorigenesis. Non-coding RNAs (ncRNAs) have been implicated in the pathology of CRC and also linked to metastasis, proliferation, differentiation, migration, angiogenesis and apoptosis in numerous cancers. Recently, attention has turned towards ncRNAs as specific targets for diagnosis, prognosis and treatment of various types of cancers, including CRC. In this review, we have tried to outline the roles of ncRNAs, and their involvement in signaling pathways responsible for the progression of CRC.
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Affiliation(s)
- Mohadeseh Esmaeili
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran.
| | - Maryam Keshani
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran.
| | - Mehrdad Vakilian
- Department of Cell Regeneration and Advanced Therapies, Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Sevilla, Spain; Department of Cellular Biology, Genetics and Physiology, Faculty of Science, University of Malaga (UMA), Málaga, Spain.
| | - Maryam Esmaeili
- Department of Cellular Biotechnology, Cell Science Research Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran; Department of Cellular Biotechnology, Cell Science Research Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Farzad Seyed Forootan
- Department of Cellular Biotechnology, Cell Science Research Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; Legal Medicine Research Centre, Legal Medicine Organization, Tehran, Iran.
| | - Tieu Lan Chau
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey.
| | - Serkan Ismail Göktuna
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey; National Nanotechnology Research Institute (UNAM), Bilkent University, Ankara, Turkey.
| | - Sayed Rasoul Zaker
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mohammad Hossein Nasr Esfahani
- Department of Cellular Biotechnology, Cell Science Research Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran; Department of Cellular Biotechnology, Cell Science Research Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
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Najafi N, Peymani M. A genetic variant of pri-miR-182 may impact the risk for the onset of multiple sclerosis in the Iranian population. Am J Hum Biol 2020; 32:e23415. [PMID: 32212358 DOI: 10.1002/ajhb.23415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 03/05/2020] [Accepted: 03/11/2020] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is the most common autoimmune disease of the central nervous system affecting young adults. SNPs can be used as genetic biomarkers to identify disease-related genes such as MS. Moreover, SNPs can be considered as important determinants for an increased risk of autoimmune diseases such as MS. Studies have shown that miR-182 is of importance in Treg cell development and function as critical regulators in autoimmune disease. So far, no study has been conducted to investigate the association between rs4541843 polymorphism in pri-miR-182 and MS. In the present study, we assessed the frequency of rs4541843 different alleles and genotypes and their association with MS risk in Iranian population. METHODS The rs4541843 was genotyped in 81 patients with MS and 89 healthy subjects, using the PCR-RFLP method. The frequency of alleles and genotypes and the association of this polymorphism with MS risk and the gender of the patients was then statistically analyzed. RESULTS Statistical analysis showed the protective role of AA genotype against MS risk (P = .031, OR = 0.348) while there was no significance correlation between the frequency of rs4541843 different alleles and the other genotypes. CONCLUSION Our findings illustrated that the pri-miR-182 rs4541843 G>A polymorphism is associated with the risk of MS in Isfahan population. However, additional large-scale association studies in various ethnicities and more molecular studies are necessary to elaborate our findings.
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Affiliation(s)
- Nadia Najafi
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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47
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Mansouri M, Peymani M, Mohamadynejad P. A genetic variant in the flanking region of miR-182 could decrease the susceptibility to the breast cancer risk in the iranian population. Nucleosides Nucleotides Nucleic Acids 2020; 39:806-817. [PMID: 31994428 DOI: 10.1080/15257770.2019.1704778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Breast cancer is one of the most malignant tumors in the world. It is, in fact, the second leading cause of cancer death in women. Recent research has identified the role of miR-182 in this disease as an oncogene agent. In this study, the association of rs4541843 in the flanking region of the miR-182 sequence with the susceptibility to breast cancer risk has been studied in the Iranian population. By using the PCR_RFLP, the genotype rs4541843 was determined in 161 patients and 164 control subjects. The genotypes of the individuals were analyzed statistically to find the association between rs4541843 and the breast cancer incidence and its pathological characteristics. The results revealed that due to the dominance of the G allele, the frequency of GG + AG genotypes, as compared with AA, had a significant correlation with the incidence of this disease in controls and cases (P = 0.022; OR = 0.523). Moreover, the genotypes AG and AA could significantly decrease the susceptibility to the breast cancer risk; also in the presence of the A allele (OR, 0.565; P = 0.015), the incidence of the disease could be decreased. Our results indicated that this SNP was associated with the breast cancer risk of the Iranian population. We suppose that rs4541843 may influence the processing of the mature miRNA by affecting the cleavage of Drosha. Therefore, this SNP can be considered as a candidate genetic marker for the susceptibility to breast cancer in the Iranian women.
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Affiliation(s)
- Maryam Mansouri
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Parisa Mohamadynejad
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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48
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Baghi M, Rostamian Delavar M, Yadegari E, Peymani M, Pozo D, Hossein Nasr-Esfahani M, Ghaedi K. Modified level of miR-376a is associated with Parkinson's disease. J Cell Mol Med 2020; 24:2622-2634. [PMID: 31930701 PMCID: PMC7028860 DOI: 10.1111/jcmm.14979] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 11/02/2019] [Accepted: 12/16/2019] [Indexed: 12/02/2022] Open
Abstract
Parkinson's disease (PD) is a frequent progressive neurodegenerative disorder. Impaired mitochondrial function is a major feature of sporadic PD. Some susceptibility or causative genes detected in PD are strongly associated with mitochondrial dysfunction including PGC1α, TFAM and GSK3β. microRNAs (miRNAs) are non‐coding RNAs whose altered levels are proven in disparate PD models and human brains. Therefore, the aim of this study was to detect modulations of miRs upstream of PGC1α, TFAM and GSK3β in association with PD onset and progress. In this study, a total of 33 PD subjects and 25 healthy volunteers were recruited. Candidate miRNA (miR‐376a) was selected through target prediction tools and literature survey. Chronic and acute in vitro PD models were created by MPP+‐intoxicated SHSY5Y cells. The levels of miR‐376a and aforementioned genes were assessed by RT‐qPCR. The expression of target genes was decreased in chronic model while there were dramatically up‐regulated levels of those genes in acute model of PD. miR‐376a was strongly altered in both acute and chronic PD models as well as PBMCs of PD patients. Our results also showed overexpression of PGC1α, and TFAM in PBMCs is inversely correlated with down‐regulation of miR‐376a, suggesting that miR‐376a possibly has an impact on PD pathogenesis through regulation of these genes which are involved in mitochondrial function. miR‐376a expression in PD‐derived PBMCs was also correlated with disease severity and may serve as a potential biomarker for PD diagnosis. This is the first study showing altered levels of miR‐376a in PD models and PBMCs, suggesting the probable role of this miRNA in PD pathogenesis. The present study also proposed TFAM and PGC1α as target genes of miR‐376a for the first time, through which it possibly can exert its impact on PD pathogenesis.
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Affiliation(s)
- Masoud Baghi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.,Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, Isfahan, Iran
| | - Mahsa Rostamian Delavar
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.,Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, Isfahan, Iran
| | - Elaheh Yadegari
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Maryam Peymani
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, Isfahan, Iran.,Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - David Pozo
- CABIMER, Andalusian Center for Molecular Biology and Regenerative Medicine, Sevilla, Spain.,Department of Medical Biochemistry, Molecular Biology and Immunology, Universidad de Sevilla, Sevilla, Spain
| | | | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.,Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, Isfahan, Iran
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Koveitypour Z, Panahi F, Vakilian M, Peymani M, Seyed Forootan F, Nasr Esfahani MH, Ghaedi K. Signaling pathways involved in colorectal cancer progression. Cell Biosci 2019; 9:97. [PMID: 31827763 PMCID: PMC6889432 DOI: 10.1186/s13578-019-0361-4] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is the fourth leading cause of the worldwide cancer mortality. Different molecular mechanisms have been attributed to the development and progress of CRC. In this review, we will focus on the mitogen-activated protein kinase (MAPK) cascades downstream of the epidermal growth factor receptor (EGFR), Notch, PI3K/AKT pathway, transforming growth factor-β (TGF-β), and Wnt signaling pathways. Various mutations in the components of these signaling pathways have been linked to the development of CRC. Accordingly, numerous efforts have been carried out to target the signaling pathways to develop novel therapeutic approaches. Herein, we review the signaling pathways involved in the incidence and progression of CRC, and the strategies for the therapy targeting components of signaling pathways in CRC.
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Affiliation(s)
- Zahra Koveitypour
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Farnoush Panahi
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Mehrdad Vakilian
- 6Department of Cell Regeneration and Advanced Therapies, Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain.,7Department of Cellular Biology, Genetics and Physiology, Faculty of Science, University of Malaga (UMA), Malaga, Spain
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, P.O. Box: 88137-33395, Shahrekord, Iran.,4Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, P.O. Box: 816513-1378, Isfahan, Iran
| | - Farzad Seyed Forootan
- 4Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, P.O. Box: 816513-1378, Isfahan, Iran.,Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Mohammad Hossein Nasr Esfahani
- 4Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, P.O. Box: 816513-1378, Isfahan, Iran
| | - Kamran Ghaedi
- 3Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.,4Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, P.O. Box: 816513-1378, Isfahan, Iran
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Behbahanipour M, Peymani M, Salari M, Hashemi MS, Nasr-Esfahani MH, Ghaedi K. Expression Profiling of Blood microRNAs 885, 361, and 17 in the Patients with the Parkinson's disease: Integrating Interaction Data to Uncover the Possible Triggering Age-Related Mechanisms. Sci Rep 2019; 9:13759. [PMID: 31551498 PMCID: PMC6760236 DOI: 10.1038/s41598-019-50256-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/09/2019] [Indexed: 01/23/2023] Open
Abstract
MicroRNAs (miRNAs) have been reported to contribute to the pathophysiology of the Parkinson’s disease (PD), an age related-neurodegenerative disorder. The aim of present study was to compare the expression profiles of a new set of candidate miRNAs related to aging and cellular senescence in peripheral blood mononuclear cells (PBMCs) obtained from the PD patients with healthy controls and then in the early and advanced stages of the PD patients with their controls to clarify whether their expression was correlated with the disease severity. We have also proposed a consensus-based strategy to interpret the miRNAs expression data to gain a better insight into the molecular regulatory alterations during the incidence of PD. We evaluated the miRNA expression levels in the PBMCs obtained from 36 patients with PD and 16 healthy controls by the reverse transcription-quantitative real-time PCR and their performance to discriminate the PD patients from the healthy subjects assessed using the receiver operating characteristic curve analysis. Also, we applied our consensus and integration approach to construct a deregulated miRNA-based network in PD with the respective targets and transcription factors, and the enriched gene ontology and pathways using the enrichment analysis approach were obtained. There was a significant overexpression of miR-885 and miR-17 and the downregulation of miR-361 in the PD patients compared to the controls. The blood expression of miR-885 and miR-17 tended to increase along with the disease severity. On the other hand, the lower levels of miR-361 in the early stages of the PD patients, as compared to controls, and its higher levels in the advanced stages of PD patients, as compared to the early stages of the PD patients, were observed. Combination of all three miRNAs showed an appropriate value of AUC (0.985) to discriminate the PD patients from the healthy subjects. Also, the deregulated miRNAs were linked to the known PD pathways and the candidate related target genes were presented. We revealed 3 candidate biomarkers related to aging and cellular senescence for the first time in the patients with PD. Our in-silico analysis identified candidate target genes and TFs, including those related to neurodegeneration and PD. Overall, our findings provided novel insights into the probable age-regulatory mechanisms underlying PD and a rationale to further clarify the role of the identified miRNAs in the PD pathogenesis.
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Affiliation(s)
- Molood Behbahanipour
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran. .,Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Mehri Salari
- Functional Neurosurgery Research Center, Shohada Tajrish Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Motahare-Sadat Hashemi
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran. .,Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
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