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Ahadi A. A systematic review of microRNAs as potential biomarkers for diagnosis and prognosis of gastric cancer. Immunogenetics 2021; 73:155-161. [PMID: 33399935 DOI: 10.1007/s00251-020-01201-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/18/2020] [Accepted: 12/10/2020] [Indexed: 02/08/2023]
Abstract
Gastric cancer (GC) is the third leading cause of global cancer morbidity and mortality. One of the significant challenges in GC treatment is that most GC patients are diagnosed with advanced-stage disease due to the lack of suitable biomarkers. Recent studies have shown that microRNAs (miRNAs) can acts as a potential biomarker in GC diagnosis and prognosis. I performed a systematic review of published miRNA studies in GC, which includes the miRNA expression profiles between GC tissues and normal tissues and also miRNA studies to evaluate their potential value in the diagnosis and prognosis of GC. Among the studies, upregulation of miR-21, miR-106b, miR-25, miR-214, miR-18a, miR-191, and miR-93 and downregulation of miR-375, miR-148a, miR-92, miR-155, and miR-564 were observed in GC tissues. In evaluating of diagnosis value of miRNAs, the study was performed on a combined miRNA include miR-21, miR-93, miR-106a, and miR-106b indicated the panel of these miRNAs have the highest AUC 0.887 to discriminate GC patients from healthy. Also, miR-940 with a sensitivity of 81.25% and specificity of 98.57% may be used for diagnostic biomarkers for GC. Finally, the pooled prognostic result of miR-21 for hazard ratios (HR) was 1.260 (95% CI 0.370-4.330, P < 0.001), showing that miR-21 could predict poor survival in GC patients. This systematic review can confirm that we need to find a miRNA or a panel of miRNAs with high sensitivity and specificity for further exploration to investigate a better diagnostic or therapeutic tool for personalized management of GC patients.
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Affiliation(s)
- Alireza Ahadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Ahadi A. The significance of microRNA deregulation in colorectal cancer development and the clinical uses as a diagnostic and prognostic biomarker and therapeutic agent. Noncoding RNA Res 2020; 5:125-134. [PMID: 32954092 PMCID: PMC7476809 DOI: 10.1016/j.ncrna.2020.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 07/16/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most widely recognized and deadly malignancies worldwide. Although death rates have declined over the previous decade, mainly because of enhanced screening or potential treatment alternatives, CRC remains the third leading cause of cancer-related mortality globally, with an estimated incidence of over 1 million new cases and approximately 600 000 deaths estimated yearly. Therefore, many scientific efforts are put into the development of new diagnostic biomarkers for CRC. MicroRNAs (miRNAs), one of the epigenetics categories, have demonstrated significant roles in carcinogenesis and progression through regulating epithelial-mesenchymal transition (EMT), oncogenic signaling pathways, and metastasis. Dysregulation of miRNAs expression has been reported in many cancers, including CRC. The expression profile of miRNAs is reproducibly altered in CRC, and their expression patterns are associated with diagnosis, prognosis, and therapeutic outcomes in CRC. Recently, many studies were conducted on the dysregulation of miRNAs as a diagnostic and prognostic biomarker in CRC. Among them, some miRNAs, which include miR-21, miR-34 family, miR-155, miR-224, and miR-378, have been more studied in CRC with more prominent roles in diagnosis, prognosis, and therapy. In the present review, we summarized the latest information regarding the dysregulated miRNAs in CRC and the advantages of using miRNAs as a biomarker for CRC diagnosis, treatment, and their function in different signaling pathways involved in CRC progression. Moreover, we described the translation of miRNA research to potential therapeutic applications in the management of CRC in clinical settings.
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Affiliation(s)
- Alireza Ahadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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3
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Ahadi A. Dysregulation of miRNAs as a signature for diagnosis and prognosis of gastric cancer and their involvement in the mechanism underlying gastric carcinogenesis and progression. IUBMB Life 2020; 72:884-898. [DOI: 10.1002/iub.2259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/08/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Alireza Ahadi
- Department of Medical Genetics, School of MedicineShahid Beheshti University of Medical Sciences Tehran Iran
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4
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Abstract
Long noncoding RNAs (lncRNAs) act as regulators of gene expression and pivotal transcriptional regulators in cancer cells via diverse mechanisms. lncRNAs involves a variety of pathological and biological activities, such as apoptosis, cell proliferation, metastasis, and invasion. By using microarray and RNA sequencing, it was identified that dysregulation of lncRNAs affects the tumorigenesis process. Taken together, these lncRNAs are putative biomarker and therapeutic target in human malignancies. In this review, I discuss the latest finding regarding the dysregulation of some important lncRNAs and their diverse mechanisms of these lncRNAs in the pathogenesis and progression of certain cancers; also, I summarize the possible roles of lncRNAs in clinical application for diagnosis and prognosis of cancer.
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Affiliation(s)
- Alireza Ahadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 198396-3113, Iran
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6
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Fazeli Z, Faramarzi S, Ahadi A, Omrani MD, Ghaderian SM. Efficiency of mesenchymal stem cells in treatment of urinary incontinence: a systematic review on animal models. Regen Med 2018; 14:69-76. [PMID: 30560712 DOI: 10.2217/rme-2018-0040] [Citation(s) in RCA: 4] [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] [Indexed: 12/14/2022] Open
Abstract
AIM In recent years, the administration of stem cells has been considered a new option for treatment of urinary incontinence (UI). In the present study, the efficiency of mesenchymal stem cell (MSC) transplantation in the treatment of UI was evaluated. METHODS Combinations of the key words 'mesenchymal stem cells', 'MSCs', 'urinary incontinence', 'urethral sphincter' and 'involuntary urination' were searched in PubMed and Science Direct databases. Following application of exclusion criteria to the 1946 papers obtained and review and duplicate articles were removed, 23 articles were considered further. The search was limited to the animal model studies. RESULTS The data obtained from the evaluation of different studies indicated that the injected MSCs play an important role in the neovascularization and the recovery of muscle cells in UI models through the paracrine process. CONCLUSION The obtained data suggested that further trials are needed to be focused on clinical phase of MSC therapy on the patients affected by UI.
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Affiliation(s)
- Zahra Fazeli
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Sepideh Faramarzi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Alireza Ahadi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Mir D Omrani
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Sayyed Mh Ghaderian
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
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7
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LArki P, Ahadi A, Zare A, Tarighi S, Zaheri M, Souri M, Zali MR, Ghaedi H, Omrani MD. Up-Regulation of miR-21, miR-25, miR-93, and miR-106b in Gastric Cancer. Iran Biomed J 2018. [PMID: 29859516 DOI: 10.29252/ibj.22.6.367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
BACKGROUND Differential expression profile of microRNAs (miRNAs) could be a diagnosis signature for monitoring gastric cancer (GC) progression. In this study, we focus on the comparison of expression levels of miR-21, miR-25, miR-93, miR-106b, and miR-375 during the sequential pattern of GC development, including normal gastric, gastric dysplasia, and GC sample. METHODS We used SYBR Green-based quantitative-PCR to quantify miRNAs expression. RESULTS Our analysis revealed the increased expression levels of miR-21 (p = 0.034), miR-25 (p = 0.0003), miR-93 (p = 0.0406), and miR-106b (p = 0.023) in GC samples. In addition, GC patients with positive lymph node metastasis showed the up-regulation of miR-25, miR-93, and miR-106b (p < 0.05). CONCLUSION Our findings suggested that the expression of miR-21, miR-25, miR-93, and miR-106b altered in GC, and some of them may be further investigated as biomarkers for GC early detection and prognosis prediction.
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Affiliation(s)
- Pegah LArki
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Ahadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Zare
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahriar Tarighi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahrokh Zaheri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Souri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ghaedi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Zare A, Ahadi A, Larki P, Omrani MD, Zali MR, Alamdari NM, Ghaedi H. The clinical significance of miR-335, miR-124, miR-218 and miR-484 downregulation in gastric cancer. Mol Biol Rep 2018; 45:1587-1595. [PMID: 30171475 DOI: 10.1007/s11033-018-4278-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 04/29/2018] [Accepted: 07/22/2018] [Indexed: 12/15/2022]
Abstract
Gastric cancer (GC) is one of the leading types of malignancy worldwide, particularly in Asian populations. Although the exact molecular mechanism of GC development remains unknown, microRNA (miRNA) has recently been shown to be involved. The current study aims to investigate the expression levels of bioinformatically ranked miRNAs in gastric tissues. Using bioinformatics tools, we prioritized miRNAs thought to be implicated in GC. Furthermore, polyA-qPCR was used to validate bioinformatics findings in 40 GC, 31 normal gastric tissue (NG) and 45 gastric dysplasia (GD) samples. As identified by bioinformatics analysis, miR-335 was shown to be the top-ranked miRNA implicated in GC. Moreover, a significant downregulation of miR-335, miR-124, miR-218 and miR-484 was found in GC and GD compared to NG samples. We found bioinformatics to be an efficient approach to finding candidate miRNAs relevant to GC development. Finally, the findings show that downregulation of miRNAs such as miR-124 and miR-218 in gastric tissue can be a significant indicator for neoplastic transformation.
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Affiliation(s)
- Ali Zare
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Velenjak St., Shahid Chamran Highway, Tehran, Iran
| | - Alireza Ahadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Velenjak St., Shahid Chamran Highway, Tehran, Iran
| | - Pegah Larki
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Velenjak St., Shahid Chamran Highway, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Velenjak St., Shahid Chamran Highway, Tehran, Iran.,Urogenital Stem Cell Research, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nasser Malekpour Alamdari
- Department of General Surgery, Clinical Research and Development Unit at Modarres Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ghaedi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Velenjak St., Shahid Chamran Highway, Tehran, Iran.
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Keramatinia A, Ahadi A, Akbari ME, Mohseny M, Mosavi Jarahi A, Bahadori-Monfared A, Hashemi M, Moradi A, Mehrvar N, Kazemi E, Movafagh A. The roles of DNA epigenetics and clinical significance in Chronic Myeloid Leukemia: a review. Cell Mol Biol (Noisy-le-grand) 2018. [DOI: 10.14715/cmb/2018.64.9.9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Keramatinia A, Ahadi A, Akbari ME, Mohseny M, Mosavi Jarahi A, Bahadori-Monfared A, Hashemi M, Moradi A, Mehrvar N, Kazemi E, Movafagh A. The roles of DNA epigenetics and clinical significance in Chronic Myeloid Leukemia: a review. Cell Mol Biol (Noisy-le-grand) 2018; 64:58-63. [PMID: 30030958] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 06/08/2023]
Abstract
Chronic Myeloid Leukemia (CML) is a myeloproliferative disorder characterized by the genetic translocation t(9;22) (q34;q11.2) encoding for the BCR-ABL fusion oncogene. Growing body of evidence suggests that epigenetic abnormalities are involved in tyrosine kinase resistance in CML, leading to leukemic clone escape and disease propagation. The significant of therapeutic role in chronic myeloid leukemia (CML) depends on both genetic and epigenetic mechanisms. This article focused on the CML and epigenetic and clinical significance. An electronic search of peer-reviewed articles was systematically performed to obtain the relevant literature with the CINAHL, cancer, Google scholar, self-experience and PubMed databases. The keywords included leukemia, cancer, illness, epigenetic. The inclusion criteria for the reviews were that the documents were original quantitative research and published in English. Articles that were not directly relevant to the present objective were excluded. Current progress in molecular biology and bioinformatics offer novel promising experiments namely as next generation sequencing for new development in epigenetic figures characterization and more understanding of the epigenetic mechanisms to be successfully utilized for personalized CML therapy in the next coming years.
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MESH Headings
- DNA/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- MAP Kinase Signaling System
- MicroRNAs/metabolism
- Protein Kinase Inhibitors/therapeutic use
- Proto-Oncogene Proteins c-crk/metabolism
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Affiliation(s)
- Aliasghar Keramatinia
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Ahadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Maryam Mohseny
- Department of Social Medicine, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Mosavi Jarahi
- Department of Social Medicine, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ayad Bahadori-Monfared
- Department of Social Medicine, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Molecular Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Afshin Moradi
- Department of Pathology, Shohada Hospital, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Narjes Mehrvar
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elham Kazemi
- Department of Sexual Medicine, The Rhazes Center for Research in Family Health and Sexual Medicine; Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abolfazl Movafagh
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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LArki P, Ahadi A, Zare A, Tarighi S, Zaheri M, Souri M, Zali MR, Ghaedi H, Omrani MD. Up-Regulation of miR-21, miR-25, miR-93, and miR-106b in Gastric Cancer. Iran Biomed J 2018. [PMID: 29859516 PMCID: PMC6305817 DOI: 10.29252/.22.6.367] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: Differential expression profile of microRNAs (miRNAs) could be a diagnosis signature for monitoring gastric cancer (GC) progression. In this study, we focus on the comparison of expression levels of miR-21, miR-25, miR-93, miR-106b, and miR-375 during the sequential pattern of GC development, including normal gastric, gastric dysplasia, and GC sample. Methods: We used SYBR Green-based quantitative-PCR to quantify miRNAs expression. Results: Our analysis revealed the increased expression levels of miR-21 (p = 0.034), miR-25 (p = 0.0003), miR-93 (p = 0.0406), and miR-106b (p = 0.023) in GC samples. In addition, GC patients with positive lymph node metastasis showed the up-regulation of miR-25, miR-93, and miR-106b (p < 0.05). Conclusion: Our findings suggested that the expression of miR-21, miR-25, miR-93, and miR-106b altered in GC, and some of them may be further investigated as biomarkers for GC early detection and prognosis prediction.
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Affiliation(s)
- Pegah LArki
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Ahadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Zare
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahriar Tarighi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahrokh Zaheri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Souri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ghaedi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Keramatinia A, Ahadi A, Akbari ME, Mohseny M, Jarahi AM, Mehrvar N, Mansouri N, Tabatabaei SAM, Movafagh A. Genomic Profiling of Chronic Myelogenous Leukemia: Basic and Clinical Approach. J Cancer Prev 2017; 22:74-81. [PMID: 28698860 PMCID: PMC5503218 DOI: 10.15430/jcp.2017.22.2.74] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 05/17/2017] [Revised: 06/10/2017] [Accepted: 06/12/2017] [Indexed: 01/11/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a hematological stem cell cancer driven by BCR-ABL1 fusion protein. We review the previous and recent evidence on the significance of CML in diagnostic and clinic management. The technical monitoring of BCR-ABL1 with quantitative real time-PCR has been used in assessing patient outcome. The cytogenetic mark of CML is Philadelphia chromosome, that is formed by reciprocal chromosomal translocations between human chromosome 9 and 22, t(9:22) (q34:q11). It makes a BCR-ABL1 fusion protein with an anomaly tyrosine kinase activity that promotes the characteristic proliferation of progenitor cells in CML and acute lymphoblastic lymphoma. The targeting of BCR-ABL1 fusion kinase is the first novel paradigm of molecularly targeted curing.
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Affiliation(s)
- Aliasghar Keramatinia
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Ahadi
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Maryam Mohseny
- Department of Social Medicine, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Mosavi Jarahi
- Department of Social Medicine, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Narjes Mehrvar
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Mansouri
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S A Mortazavi Tabatabaei
- Proteomics Research Center, School of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abolfazl Movafagh
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Ahadi A, Sablok G, Hutvagner G. miRTar2GO: a novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA-target interaction data. Nucleic Acids Res 2017; 45:e42. [PMID: 27903911 PMCID: PMC5389546 DOI: 10.1093/nar/gkw1185] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 06/15/2016] [Revised: 11/13/2016] [Accepted: 11/16/2016] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are ∼19-22 nucleotides (nt) long regulatory RNAs that regulate gene expression by recognizing and binding to complementary sequences on mRNAs. The key step in revealing the function of a miRNA, is the identification of miRNA target genes. Recent biochemical advances including PAR-CLIP and HITS-CLIP allow for improved miRNA target predictions and are widely used to validate miRNA targets. Here, we present miRTar2GO, which is a model, trained on the common rules of miRNA-target interactions, Argonaute (Ago) CLIP-Seq data and experimentally validated miRNA target interactions. miRTar2GO is designed to predict miRNA target sites using more relaxed miRNA-target binding characteristics. More importantly, miRTar2GO allows for the prediction of cell-type specific miRNA targets. We have evaluated miRTar2GO against other widely used miRNA target prediction algorithms and demonstrated that miRTar2GO produced significantly higher F1 and G scores. Target predictions, binding specifications, results of the pathway analysis and gene ontology enrichment of miRNA targets are freely available at http://www.mirtar2go.org.
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Affiliation(s)
- Alireza Ahadi
- Faculty of Engineering and Information Technology, School of Software, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW 2007, Australia
- Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW 2007, Australia
| | - Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW 2007, Australia
| | - Gyorgy Hutvagner
- Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW 2007, Australia
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Hatoum D, Yagoub D, Ahadi A, Nassif NT, McGowan EM. Annexin/S100A Protein Family Regulation through p14ARF-p53 Activation: A Role in Cell Survival and Predicting Treatment Outcomes in Breast Cancer. PLoS One 2017; 12:e0169925. [PMID: 28068434 PMCID: PMC5222396 DOI: 10.1371/journal.pone.0169925] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 08/29/2016] [Accepted: 12/22/2016] [Indexed: 12/12/2022] Open
Abstract
The annexin family and S100A associated proteins are important regulators of diverse calcium-dependent cellular processes including cell division, growth regulation and apoptosis. Dysfunction of individual annexin and S100A proteins is associated with cancer progression, metastasis and cancer drug resistance. This manuscript describes the novel finding of differential regulation of the annexin and S100A family of proteins by activation of p53 in breast cancer cells. Additionally, the observed differential regulation is found to be beneficial to the survival of breast cancer cells and to influence treatment efficacy. We have used unbiased, quantitative proteomics to determine the proteomic changes occurring post p14ARF-p53 activation in estrogen receptor (ER) breast cancer cells. In this report we identified differential regulation of the annexin/S100A family, through unique peptide recognition at the N-terminal regions, demonstrating p14ARF-p53 is a central orchestrator of the annexin/S100A family of calcium regulators in favor of pro-survival functions in the breast cancer cell. This regulation was found to be cell-type specific. Retrospective human breast cancer studies have demonstrated that tumors with functional wild type p53 (p53wt) respond poorly to some chemotherapy agents compared to tumors with a non-functional p53. Given that modulation of calcium signaling has been demonstrated to change sensitivity of chemotherapeutic agents to apoptotic signals, in principle, we explored the paradigm of how p53 modulation of calcium regulators in ER+ breast cancer patients impacts and influences therapeutic outcomes.
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Affiliation(s)
- Diana Hatoum
- School of Life Sciences, Faculty of Science, Faculty of Engineering and IT, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Daniel Yagoub
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Alireza Ahadi
- Faculty of Engineering and IT, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Najah T. Nassif
- School of Life Sciences, Faculty of Science, Faculty of Engineering and IT, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Eileen M. McGowan
- School of Life Sciences, Faculty of Science, Faculty of Engineering and IT, University of Technology Sydney, Sydney, New South Wales, Australia
- * E-mail:
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Ahadi A, Khoury S, Losseva M, Tran N. A comparative analysis of lncRNAs in prostate cancer exosomes and their parental cell lines. Genom Data 2016; 9:7-9. [PMID: 27330995 PMCID: PMC4909828 DOI: 10.1016/j.gdata.2016.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/23/2016] [Indexed: 12/25/2022]
Abstract
Prostate cancer is the second leading cancer in men world-wide. Due to its heterogeneous nature, a considerable amount of research effort has been dedicated in identifying effective clinical biomarkers with a focus on proteins, messenger RNA and microRNAs [1]. However, there is limited data on the role and expression of long noncoding RNAs (lncRNAs) in prostate cancer exosomes [2]. This array dataset which is linked to our publication describes the profiling of human lncRNAs in prostate cancer and their exosomes from five different cell lines [3]. From this dataset, we identified a list of statistically significant prostate cancer lncRNAs which are differentially expressed in the exosomes compared to their parent cell lines. This dataset has been deposited into Gene Expression Omnibus (GSE81034).
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Affiliation(s)
- Alireza Ahadi
- Noncoding RNA Cancer Laboratory, Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney, NSW, Australia
| | - Samantha Khoury
- Noncoding RNA Cancer Laboratory, Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney, NSW, Australia
| | - Maria Losseva
- Noncoding RNA Cancer Laboratory, Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney, NSW, Australia
| | - Nham Tran
- Noncoding RNA Cancer Laboratory, Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney, NSW, Australia; The Sydney Head and Neck Cancer Institute, Sydney Cancer Centre, Royal Prince Alfred Hospital, Australia
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Ahadi A, Brennan S, Kennedy PJ, Hutvagner G, Tran N. Long non-coding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes. Sci Rep 2016; 6:24922. [PMID: 27102850 PMCID: PMC4840345 DOI: 10.1038/srep24922] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 03/21/2016] [Indexed: 12/22/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) form the largest transcript class in the human transcriptome. These lncRNA are expressed not only in the cells, but they are also present in the cell-derived extracellular vesicles such as exosomes. The function of these lncRNAs in cancer biology is not entirely clear, but they appear to be modulators of gene expression. In this study, we characterize the expression of lncRNAs in several prostate cancer exosomes and their parental cell lines. We show that certain lncRNAs are enriched in cancer exosomes with the overall expression signatures varying across cell lines. These exosomal lncRNAs are themselves enriched for miRNA seeds with a preference for let-7 family members as well as miR-17, miR-18a, miR-20a, miR-93 and miR-106b. The enrichment of miRNA seed regions in exosomal lncRNAs is matched with a concomitant high expression of the same miRNA. In addition, the exosomal lncRNAs also showed an over representation of RNA binding protein binding motifs. The two most common motifs belonged to ELAVL1 and RBMX. Given the enrichment of miRNA and RBP sites on exosomal lncRNAs, their interplay may suggest a possible function in prostate cancer carcinogenesis.
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Affiliation(s)
- Alireza Ahadi
- Centre for Human Centred Technology Design, University of Technology, Sydney.,Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney
| | - Samuel Brennan
- School of Life Sciences, Faculty of Science, University of Technology, Sydney
| | - Paul J Kennedy
- Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney.,Centre for Quantum Computation and Intelligent Systems, University of Technology, Sydney
| | - Gyorgy Hutvagner
- Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney
| | - Nham Tran
- Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney.,The Sydney Head and Neck Cancer Institute, Sydney Cancer Centre, Royal Prince Alfred Hospital, Australia
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17
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Bou-Ali MM, Ahadi A, Alonso de Mezquia D, Galand Q, Gebhardt M, Khlybov O, Köhler W, Larrañaga M, Legros JC, Lyubimova T, Mialdun A, Ryzhkov I, Saghir MZ, Shevtsova V, Van Vaerenbergh S. Benchmark values for the Soret, thermodiffusion and molecular diffusion coefficients of the ternary mixture tetralin+isobutylbenzene+n-dodecane with 0.8-0.1-0.1 mass fraction. Eur Phys J E Soft Matter 2015; 38:30. [PMID: 25916233 DOI: 10.1140/epje/i2015-15030-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 11/06/2014] [Accepted: 02/17/2015] [Indexed: 06/04/2023]
Abstract
With the aim of providing reliable benchmark values, we have measured the Soret, thermodiffusion and molecular diffusion coefficients for the ternary mixture formed by 1,2,3,4-tetrahydronaphthalene, isobutylbenzene and n-dodecane for a mass fraction of 0.8-0.1-0.1 and at a temperature of 25°C. The experimental techniques used by the six participating laboratories are Optical Digital Interferometry, Taylor Dispersion technique, Open Ended Capillary, Optical Beam Deflection, Thermogravitational technique and Sliding Symmetric Tubes technique in ground conditions and Selectable Optical Diagnostic Instrument (SODI) in microgravity conditions. The measurements obtained in the SODI installation have been analyzed independently by four laboratories. Benchmark values are proposed for the thermodiffusion and Soret coefficients and for the eigenvalues of the diffusion matrix in ground conditions, and for Soret coefficients in microgravity conditions.
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Affiliation(s)
- M M Bou-Ali
- Mechanical and Industrial Manufacturing Department, MGEP Mondragon Goi Eskola Politeknikoa, Loramendi 4 Apdo 23, 20500, Mondragon, Spain,
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Abstract
This study was designed to follow patients regarding to achieving control, identify disease exacerbations and discover relation between exacerbation and risk factors. In a cross sectional-analytic study, 400 asthmatic patients in the range of 2-14 years old who were visited at the specialized outpatient clinic of Tabriz University of Medical Sciences were divided and studied on the base of disease severity. At the end (at least one year treatment), patients were categorized based on level of disease control and one year after this stage, cases of exacerbation were identified and studied. By excluding patients with poor adherence, 342 patients continued treatment as intermittent, mild persistent, moderate persistent and severe persistent asthma (38, 235, 61 and 8 patients, respectively). After a period of one year treatment, the patients were divided as well controlled, partly controlled and uncontrolled (68, 30 and 2%, respectively). Cases of disease exacerbations were more if sinusitis, familial asthma history and poor adherence were present (p < 0.01, p < 0.001 and p < 0.05, respectively). There is meaningful association between poor adherence, sinusitis and positive family history of asthma with disease exacerbation.
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Affiliation(s)
- B Nemat
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Islamic Republic of Iran
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