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Rahimian N, Razavi ZS, Aslanbeigi F, Mirkhabbaz AM, Piroozmand H, Shahrzad MK, Hamblin MR, Mirzaei H. Non-coding RNAs related to angiogenesis in gynecological cancer. Gynecol Oncol 2021; 161:896-912. [PMID: 33781555 DOI: 10.1016/j.ygyno.2021.03.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023]
Abstract
Gynecological cancer affects the female reproductive system, including ovarian, uterine, endometrial, cervical, vulvar, and vaginal tumors. Non-coding RNAs (ncRNAs), and in particular microRNAs, function as regulatory molecules, which can control gene expression in a post-transcriptional manner. Normal physiological processes like cellular proliferation, differentiation, and apoptosis, and pathological processes such as oncogenesis and metastasis are regulated by microRNAs. Numerous reports have shown a direct role of microRNAs in the modulation of angiogenesis in gynecological cancer, via targeting pro-angiogenic factors and signaling pathways. Understanding the molecular mechanism involved in the regulation of angiogenesis by microRNAs may lead to new treatment options. Recently the regulatory role of some long non-coding RNAs in gynecological cancer has also been explored, but the information on this function is more limited. The aim of this article is to explore the pathways responsible for angiogenesis, and to what extent ncRNAs may be employed as biomarkers or therapeutic targets in gynecological cancer.
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Affiliation(s)
- Neda Rahimian
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | | | | | | | - Haleh Piroozmand
- Faculty of Veterinary Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Karim Shahrzad
- Department of Internal Medicine and endocrinology, Shohadae Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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2
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Behravan H, Hartikainen JM, Tengström M, Kosma VM, Mannermaa A. Predicting breast cancer risk using interacting genetic and demographic factors and machine learning. Sci Rep 2020; 10:11044. [PMID: 32632202 PMCID: PMC7338351 DOI: 10.1038/s41598-020-66907-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022] Open
Abstract
Breast cancer (BC) is a multifactorial disease and the most common cancer in women worldwide. We describe a machine learning approach to identify a combination of interacting genetic variants (SNPs) and demographic risk factors for BC, especially factors related to both familial history (Group 1) and oestrogen metabolism (Group 2), for predicting BC risk. This approach identifies the best combinations of interacting genetic and demographic risk factors that yield the highest BC risk prediction accuracy. In tests on the Kuopio Breast Cancer Project (KBCP) dataset, our approach achieves a mean average precision (mAP) of 77.78 in predicting BC risk by using interacting genetic and Group 1 features, which is better than the mAPs of 74.19 and 73.65 achieved using only Group 1 features and interacting SNPs, respectively. Similarly, using interacting genetic and Group 2 features yields a mAP of 78.00, which outperforms the system based on only Group 2 features, which has a mAP of 72.57. Furthermore, the gene interaction maps built from genes associated with SNPs that interact with demographic risk factors indicate important BC-related biological entities, such as angiogenesis, apoptosis and oestrogen-related networks. The results also show that demographic risk factors are individually more important than genetic variants in predicting BC risk.
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Affiliation(s)
- Hamid Behravan
- Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland.
| | - Jaana M Hartikainen
- Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Maria Tengström
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
- Cancer Center, Kuopio University Hospital, Kuopio, P.O. Box 100, FI-70029, Kuopio, Finland
| | - Veli-Matti Kosma
- Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Arto Mannermaa
- Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
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3
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Alanazi IO, Al Shehri ZS, Ebrahimie E, Giahi H, Mohammadi-Dehcheshmeh M. Non-coding and coding genomic variants distinguish prostate cancer, castration-resistant prostate cancer, familial prostate cancer, and metastatic castration-resistant prostate cancer from each other. Mol Carcinog 2019; 58:862-874. [PMID: 30644608 DOI: 10.1002/mc.22975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 12/11/2022]
Abstract
A considerable number of deposited variants has provided new possibilities for knowledge discovery in different types of prostate cancer. Here, we analyzed variants located on 3'UTR, 5'UTR, CDs, Intergenic, and Intronic regions in castration-resistant prostate cancer (8496 variants), familial prostate cancer (3241 variants), metastatic castration-resistant prostate cancer (3693 variants), and prostate cancer (16599 variants). Chromosome regions 10p15-p14 and 2p13 were highly enriched (P < 0.00001) for variants located in 3'UTR, 5'UTR, CDs, intergenic, and intronic regions in castration-resistant prostate cancer. In contrast, 10p15-p14, 10q23.3, 12q13.11, 13q12.3, 1q25, and 8p22 regions were enriched (P < 0.001) in familial prostate cancer. In metastatic castration-resistant prostate cancer, 10p15-p14, 10q23.3, 11q22-q23, 14q21.1, and 14q32.13 were highly variant regions (P < 0.001). Chromosome 2 and chromosome 1 hosted many enriched variant regions. AKR1C3, BRCA1, BRCA2, CHGA, CYP19A1, HOXB13, KLK3, and PTEN contained the highest number of 3'UTR, 5'UTR, CDs, Intergenic, and Intronic variants. Network analysis showed that these genes are upstream of important functions including prostate gland development, tumor recurrence, prostate cancer-specific survival, tumor progression, cancer mortality, long-term survival, cancer recurrence, angiogenesis, and AR. Interestingly, all of EGFR, JAK2, NR3C1, PDZD2, and SEMA3C genes had single nucleotide polymorphisms (SNP) in castration-resistant prostate cancer, consistent with high selection pressure on these genes during drug treatment and consequent resistance. High occurrence of variants in 3'UTRs suggests the importance of regulatory variants in different types of prostate cancer; an area that has been neglected compared with coding variants. This study provides a comprehensive overview of genomic regions contributing to different types of prostate cancer.
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Affiliation(s)
- Ibrahim O Alanazi
- National Center for Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Zafer S Al Shehri
- Clinical Laboratory Department, College of Applied Medical Sciences, Shaqra University, KSA, Al dawadmi, Saudi Arabia
| | - Esmaeil Ebrahimie
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.,School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, The University of South Australia, Adelaide, SA, Australia.,Institute of Biotechnology, Shiraz University, Shiraz, Iran.,Faculty of Science and Engineering, School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Hassan Giahi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Manijeh Mohammadi-Dehcheshmeh
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, South Australia, Australia
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4
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Roles of DDX5 in the tumorigenesis, proliferation, differentiation, metastasis and pathway regulation of human malignancies. Biochim Biophys Acta Rev Cancer 2019; 1871:85-98. [DOI: 10.1016/j.bbcan.2018.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 02/07/2023]
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5
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Alanazi IO, AlYahya SA, Ebrahimie E, Mohammadi-Dehcheshmeh M. Computational systems biology analysis of biomarkers in lung cancer; unravelling genomic regions which frequently encode biomarkers, enriched pathways, and new candidates. Gene 2018; 659:29-36. [DOI: 10.1016/j.gene.2018.03.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 02/07/2018] [Accepted: 03/15/2018] [Indexed: 12/15/2022]
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6
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Sharifi S, Pakdel A, Ebrahimi M, Reecy JM, Fazeli Farsani S, Ebrahimie E. Integration of machine learning and meta-analysis identifies the transcriptomic bio-signature of mastitis disease in cattle. PLoS One 2018; 13:e0191227. [PMID: 29470489 PMCID: PMC5823400 DOI: 10.1371/journal.pone.0191227] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 12/29/2017] [Indexed: 12/14/2022] Open
Abstract
Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the main agents that cause severe mastitis disease with clinical signs in dairy cattle. Rapid detection of this disease is so important in order to prevent transmission to other cows and helps to reduce inappropriate use of antibiotics. With the rapid progress in high-throughput technologies, and accumulation of various kinds of '-omics' data in public repositories, there is an opportunity to retrieve, integrate, and reanalyze these resources to improve the diagnosis and treatment of different diseases and to provide mechanistic insights into host resistance in an efficient way. Meta-analysis is a relatively inexpensive option with good potential to increase the statistical power and generalizability of single-study analysis. In the current meta-analysis research, six microarray-based studies that investigate the transcriptome profile of mammary gland tissue after induced mastitis by E. coli infection were used. This meta-analysis not only reinforced the findings in individual studies, but also several novel terms including responses to hypoxia, response to drug, anti-apoptosis and positive regulation of transcription from RNA polymerase II promoter enriched by up-regulated genes. Finally, in order to identify the small sets of genes that are sufficiently informative in E. coli mastitis, the differentially expressed gene introduced by meta-analysis were prioritized by using ten different attribute weighting algorithms. Twelve meta-genes were detected by the majority of attribute weighting algorithms (with weight above 0.7) as most informative genes including CXCL8 (IL8), NFKBIZ, HP, ZC3H12A, PDE4B, CASP4, CXCL2, CCL20, GRO1(CXCL1), CFB, S100A9, and S100A8. Interestingly, the results have been demonstrated that all of these genes are the key genes in the immune response, inflammation or mastitis. The Decision tree models efficiently discovered the best combination of the meta-genes as bio-signature and confirmed that some of the top-ranked genes -ZC3H12A, CXCL2, GRO, CFB- as biomarkers for E. coli mastitis (with the accuracy 83% in average). This research properly indicated that by combination of two novel data mining tools, meta-analysis and machine learning, increased power to detect most informative genes that can help to improve the diagnosis and treatment strategies for E. coli associated with mastitis in cattle.
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Affiliation(s)
- Somayeh Sharifi
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Abbas Pakdel
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | | | - James M. Reecy
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | | | - Esmaeil Ebrahimie
- School of Medicine, The University of Adelaide, Adelaide, Australia
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
- Division of Information Technology, Engineering and the Environment, School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, South Australia, Australia
- School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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7
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Oral mucosa tissue gene expression profiling before, during, and after radiation therapy for tonsil squamous cell carcinoma. PLoS One 2018; 13:e0190709. [PMID: 29338018 PMCID: PMC5770028 DOI: 10.1371/journal.pone.0190709] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/19/2017] [Indexed: 12/19/2022] Open
Abstract
Background Radiation-therapy (RT) induces mucositis, a clinically challenging condition with limited prophylactic interventions and no predictive tests. In this pilot study, we applied global gene-expression analysis on serial human oral mucosa tissue and blood cells from patients with tonsil squamous cell cancer (TSCC) to identify genes involved in mucositis pathogenesis. Methods and findings Eight patients with TSCC each provided consecutive buccal biopsies and blood cells before, after 7 days of RT treatment, and 20 days following RT. We monitored clinical mucositis and performed gene-expression analysis on tissue samples. We obtained control tissue from nine healthy individuals. After RT, expression was upregulated in apoptosis inducer and inhibitor genes, EDA2R and MDM2, and in POLH, a DNA-repair polymerase. Expression was downregulated in six members of the histone cluster family, e.g., HIST1H3B. Gene expression related to proliferation and differentiation was altered, including MKI67 (downregulated), which encodes the Ki-67-proliferation marker, and KRT16 (upregulated), which encodes keratin16. These alterations were not associated with the clinical mucositis grade. However, the expression of LY6G6C, which encodes a surface immunoregulatory protein, was upregulated before treatment in three cases of clinical none/mild mucositis, but not in four cases of ulcerative mucositis. Conclusion RT caused molecular changes related to apoptosis, DNA-damage, DNA-repair, and proliferation without a correlation to the severity of clinical mucositis. LY6G6C may be a potential protective biomarker for ulcerative mucositis. Based on these results, our study model of consecutive human biopsies will be useful in designing a prospective clinical validation trial to characterize molecular mucositis and identify predictive biomarkers.
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8
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Suman S, Mishra A. Network analysis revealed aurora kinase dysregulation in five gynecological types of cancer. Oncol Lett 2017; 15:1125-1132. [PMID: 29391900 DOI: 10.3892/ol.2017.7368] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/13/2017] [Indexed: 01/04/2023] Open
Abstract
Gene markers are crucial for cancer prognosis and treatment. Previous studies have placed greater emphasis on individual diagnostic genes, thereby ignoring systemic-level attributes across diseases. Female-specific cells namely, breast, endometrium, cervical, ovarian and vulvar cells are highly susceptible to cancer. To date, a limited number of molecular studies have been performed that evaluate common biological processes across gynecological types of cancer. Differentially expressed genes in breast, cervical, endometrial, vulvar and ovarian cancer were utilized to construct protein-protein interaction networks, and to identify a common module across the five cancer types. A single common module with 8 nodes and 26 edges was mined among the five cancer systems. In total, four hub genes were present across the five cancer gene sets. Genes in the common module were enriched for the common pathways and associated diseases. The aurora kinase pathway was revealed to be conserved across the five cancer types surveyed. The present study, therefore, revealed that the aurora kinase pathway has a crucial function in the pathogenesis of the five aforementioned gynecological types of cancer through cross-tumor conservation.
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Affiliation(s)
- Shikha Suman
- Division of Applied Sciences, Indian Institute of Information Technology, Allahabad, Uttar Pradesh 211012, India
| | - Ashutosh Mishra
- Division of Applied Sciences, Indian Institute of Information Technology, Allahabad, Uttar Pradesh 211012, India
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9
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Ebrahimie E, Moussavi Nik SH, Newman M, Van Der Hoek M, Lardelli M. The Zebrafish Equivalent of Alzheimer's Disease-Associated PRESENILIN Isoform PS2V Regulates Inflammatory and Other Responses to Hypoxic Stress. J Alzheimers Dis 2017; 52:581-608. [PMID: 27031468 DOI: 10.3233/jad-150678] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Dominant mutations in the PRESENILIN genes PSEN1 and PSEN2 cause familial Alzheimer's disease (fAD) that usually shows onset before 65 years of age. In contrast, genetic variation at the PSEN1 and PSEN2 loci does not appear to contribute to risk for the sporadic, late onset form of the disease (sAD), leading to doubts that these genes play a role in the majority of AD cases. However, a truncated isoform of PSEN2, PS2V, is upregulated in sAD brains and is induced by hypoxia and high cholesterol intake. PS2V can increase γ-secretase activity and suppress the unfolded protein response (UPR), but detailed analysis of its function has been hindered by lack of a suitable, genetically manipulable animal model since mice and rats lack this PRESENILIN isoform. We recently showed that zebrafish possess an isoform, PS1IV, that is cognate to human PS2V. Using an antisense morpholino oligonucleotide, we can block specifically the induction of PS1IV that normally occurs under hypoxia. Here, we exploit this ability to identify gene regulatory networks that are modulated by PS1IV. When PS1IV is absent under hypoxia-like conditions, we observe changes in expression of genes controlling inflammation (particularly sAD-associated IL1B and CCR5), vascular development, the UPR, protein synthesis, calcium homeostasis, catecholamine biosynthesis, TOR signaling, and cell proliferation. Our results imply an important role for PS2V in sAD as a component of a pathological mechanism that includes hypoxia/oxidative stress and support investigation of the role of PS2V in other diseases, including schizophrenia, when these are implicated in the pathology.
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Affiliation(s)
- Esmaeil Ebrahimie
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, Australia.,School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, University of South Australia, Adelaide, Australia.,School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia
| | - Seyyed Hani Moussavi Nik
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Morgan Newman
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Mark Van Der Hoek
- Centre for Cancer Biology, SA Pathology, Frome Road, Adelaide, Australia
| | - Michael Lardelli
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, Australia
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10
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Isolation, Characterization, Cryopreservation of Human Amniotic Stem Cells and Differentiation to Osteogenic and Adipogenic Cells. PLoS One 2016; 11:e0158281. [PMID: 27434028 PMCID: PMC4951121 DOI: 10.1371/journal.pone.0158281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 06/13/2016] [Indexed: 01/27/2023] Open
Abstract
Human stem cells and progenitor cells can be used to treat cancer and replace dysfunctional cells within a tissue or organ. The objective of this study was to identify the appropriate cells type in regenerative medicine and targeted therapy. As an alternative to embryonic and bone marrow stem cells, we examined human amniotic fluid stem cells (hAFSCs), one of the potential source of multipotent stem cells isolated from both cell pellet (using single-stage method), and supernatant of human amniotic fluid. Source of isolation and unique property of the cells emphasize that these cells are one of the promising new tools in therapeutic field. Double sources for isolation and availability of the left over samples in diagnostic laboratory at the same time have less legal and ethical concerns compared with embryonic stem cell studies. Cells were isolated, cultured for 18th passage for 6 months and characterized using qPCR and flow cytometry. Cells showed good proliferative ability in culture condition. The cells successfully differentiated into the adipogenic and osteogenic lineages. Based on these findings, amniotic fluid can be considered as an appropriate and convenient source of human amniotic fluid stem cells. These cells provide potential tools for therapeutic applications in the field of regenerative medicine. To get a better understanding of crosstalk between Oct4/NANOG with osteogenesis and adipogenesis, we used network analysis based on Common Targets algorithm and Common Regulators algorithm as well as subnetwork discovery based on gene set enrichment. Network analysis highlighted the possible role of MIR 302A and MIR let-7g. We demonstrated the high expression of MIR 302A and low expression of MIR let7g in hAFSCs by qPCR.
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11
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Pashaiasl M, Ebrahimi M, Ebrahimie E. Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis. Mol Biol Rep 2016; 43:923-37. [PMID: 27324248 DOI: 10.1007/s11033-016-4025-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/30/2016] [Indexed: 11/30/2022]
Abstract
Diminished ovarian reserve (DOR) is one of the reasons for infertility that not only affects both older and young women. Ovarian reserve assessment can be used as a new prognostic tool for infertility treatment decision making. Here, up- and down-regulated gene expression profiles of granulosa cells were analysed to generate a putative interaction map of the involved genes. In addition, gene ontology (GO) analysis was used to get insight intol the biological processes and molecular functions of involved proteins in DOR. Eleven up-regulated genes and nine down-regulated genes were identified and assessed by constructing interaction networks based on their biological processes. PTGS2, CTGF, LHCGR, CITED, SOCS2, STAR and FSTL3 were the key nodes in the up-regulated networks, while the IGF2, AMH, GREM, and FOXC1 proteins were key in the down-regulated networks. MIRN101-1, MIRN153-1 and MIRN194-1 inhibited the expression of SOCS2, while CSH1 and BMP2 positively regulated IGF1 and IGF2. Ossification, ovarian follicle development, vasculogenesis, sequence-specific DNA binding transcription factor activity, and golgi apparatus are the major differential groups between up-regulated and down-regulated genes in DOR. Meta-analysis of publicly available transcriptomic data highlighted the high coexpression of CTGF, connective tissue growth factor, with the other key regulators of DOR. CTGF is involved in organ senescence and focal adhesion pathway according to GO analysis. These findings provide a comprehensive system biology based insight into the aetiology of DOR through network and gene ontology analyses.
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Affiliation(s)
- Maryam Pashaiasl
- Women's Reproductive Health Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran. .,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mansour Ebrahimi
- Bioinformatics Research Group and Department of Biology, Qom University, Qom, Iran
| | - Esmaeil Ebrahimie
- Division of Information Technology, Engineering and the Environment, School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, Australia.,Institute of Biotechnology, Shiraz University, Shiraz, Iran.,Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, Australia.,School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia
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12
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Ma D, Jing X, Shen B, Liu X, Cheng X, Wang B, Fu Z, Peng C, Qiu W. Leukemia inhibitory factor receptor negatively regulates the metastasis of pancreatic cancer cells in vitro and in vivo. Oncol Rep 2016; 36:827-36. [PMID: 27375070 DOI: 10.3892/or.2016.4865] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/22/2016] [Indexed: 11/06/2022] Open
Abstract
Pancreatic cancer (PC) is one of the leading causes of cancer-related deaths worldwide. Frequent metastasis and recurrence are the main reasons for the poor prognosis of PC patients. Thus, the discovery of new biomarkers and wider insights into the mechanisms involved in pancreatic tumorigenesis and metastasis is crucial. In the present study, we report that leukemia inhibitory factor receptor (LIFR) suppresses tumorigenesis and metastasis of PC cells both in vitro and in vivo. LIFR expression was significantly lower in PC tissues and was associated with local invasion (P=0.047), lymph node metastasis (P=0.014) and tumor-node-metastasis (TNM) stage (P=0.002). Overexpression of LIFR significantly suppressed PC cell colony formation (P=0.005), migration (P=0.003), invasion (P=0.010) and wound healing ability (P=0.013) in vitro, while opposing results were observed after LIFR was silenced. Furthermore, animal xenograft and metastasis models confirm that the in vivo results were consistent with the outcomes in vitro. Meanwhile, LIFR inhibited the expression of β-catenin, vimentin and slug and induced the expression of E-cadherin, suggesting that the epithelial-mesenchymal transition regulation pathway may underlie the mechanism. These results indicate that LIFR negatively regulates the metastasis of PC cells.
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Affiliation(s)
- Ding Ma
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Xiaoqian Jing
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Baiyong Shen
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Xinyu Liu
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Xi Cheng
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Bingrui Wang
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Zhiping Fu
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Chenghong Peng
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Weihua Qiu
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
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13
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Alanazi IO, Ebrahimie E. Computational Systems Biology Approach Predicts Regulators and Targets of microRNAs and Their Genomic Hotspots in Apoptosis Process. Mol Biotechnol 2016; 58:460-79. [DOI: 10.1007/s12033-016-9938-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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14
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Mehrfarjam Z, Esmaeili F, Shabani L, Ebrahimie E. Induction of pancreatic β cell gene expression in mesenchymal stem cells. Cell Biol Int 2016; 40:486-500. [DOI: 10.1002/cbin.10567] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 11/23/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Zahra Mehrfarjam
- Razi Herbal Medicines Research Center; Lorestan University of Medical Sciences; P.O. Box 681499468 Khorramabad Iran
| | - Fariba Esmaeili
- Faculty of Basic Sciences; Department of Biology; University of Isfahan; P.O. Box 8174673441 Isfahan Iran
- Research Institute of Biotechnology; Shahrekord University; P.O. Box 115 Shahrekord Iran
| | - Leila Shabani
- Research Institute of Biotechnology; Shahrekord University; P.O. Box 115 Shahrekord Iran
| | - Esmaeil Ebrahimie
- Institute of Biotechnology; Shiraz University; Shiraz Iran
- Division of Information Technology, Engineering & Environment; School of Information Technology and Mathematical Sciences; University of South Australia; Adelaide Australia
- Department of Genetics and Evolution; The University of Adelaide; Adelaide Australia
- Faculty of Science and Engineering; School of Biological Sciences; Flinders University; Adelaide Australia
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Pappa KI, Polyzos A, Jacob-Hirsch J, Amariglio N, Vlachos GD, Loutradis D, Anagnou NP. Profiling of Discrete Gynecological Cancers Reveals Novel Transcriptional Modules and Common Features Shared by Other Cancer Types and Embryonic Stem Cells. PLoS One 2015; 10:e0142229. [PMID: 26559525 PMCID: PMC4641642 DOI: 10.1371/journal.pone.0142229] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/18/2015] [Indexed: 01/07/2023] Open
Abstract
Studies on individual types of gynecological cancers (GCs), utilizing novel expression technologies, have revealed specific pathogenetic patterns and gene markers for cervical (CC), endometrial (EC) and vulvar cancer (VC). Although the clinical phenotypes of the three types of gynecological cancers are discrete, the fact they originate from a common embryological origin, has led to the hypothesis that they might share common features reflecting regression to early embryogenesis. To address this question, we performed a comprehensive comparative analysis of their profiles. Our data identified both common features (pathways and networks) and novel distinct modules controlling the same deregulated biological processes in all three types. Specifically, four novel transcriptional modules were discovered regulating cell cycle and apoptosis. Integration and comparison of our data with other databases, led to the identification of common features among cancer types, embryonic stem (ES) cells and the newly discovered cell population of squamocolumnar (SC) junction of the cervix, considered to host the early cancer events. Conclusively, these data lead us to propose the presence of common features among gynecological cancers, other types of cancers, ES cells and the pre-malignant SC junction cells, where the novel E2F/NFY and MAX/CEBP modules play an important role for the pathogenesis of gynecological carcinomas.
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Affiliation(s)
- Kalliopi I. Pappa
- First Department of Obstetrics and Gynecology, University of Athens School of Medicine, Alexandra Hospital, Athens, Greece
- Laboratory of Cell and Gene Therapy, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Alexander Polyzos
- Basic Research Centre, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Jasmine Jacob-Hirsch
- Cancer Research Center, The Chaim Sheba Medical Center, Tel-Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ninette Amariglio
- Cancer Research Center, The Chaim Sheba Medical Center, Tel-Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - George D. Vlachos
- First Department of Obstetrics and Gynecology, University of Athens School of Medicine, Alexandra Hospital, Athens, Greece
| | - Dimitrios Loutradis
- First Department of Obstetrics and Gynecology, University of Athens School of Medicine, Alexandra Hospital, Athens, Greece
| | - Nicholas P. Anagnou
- Laboratory of Cell and Gene Therapy, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Laboratory of Biology, University of Athens School of Medicine, Athens, Greece
- * E-mail:
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16
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Ebrahimie E, Nurollah Z, Ebrahimi M, Hemmatzadeh F, Ignjatovic J. Unique ability of pandemic influenza to downregulate the genes involved in neuronal disorders. Mol Biol Rep 2015; 42:1377-90. [DOI: 10.1007/s11033-015-3916-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 07/22/2015] [Indexed: 01/01/2023]
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17
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Jayaram S, Gupta MK, Shivakumar BM, Ghatge M, Sharma A, Vangala RK, Sirdeshmukh R. Insights from Chromosome-Centric Mapping of Disease-Associated Genes: Chromosome 12 Perspective. J Proteome Res 2015; 14:3432-40. [PMID: 26143930 DOI: 10.1021/acs.jproteome.5b00488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In line with the aims of the Chromosome-based Human Proteome Project and the Biology/Disease-based Human Proteome Project, we have been studying differentially expressed transcripts and proteins in gliomas—the most prevalent primary brain tumors. Here, we present a perspective on important insights from this analysis in terms of their co-expression, co-regulation/de-regulation, and co-localization on chromosome 12 (Chr. 12). We observe the following: (1) Over-expression of genes mapping onto amplicon regions of chromosomes may be considered as a biological validation of mass spectrometry data. (2) Their co-localization further suggests common determinants of co-expression and co-regulation of these clusters. (3) Co-localization of "missing" protein genes of Chr. 12 in close proximity to functionally related genes may help in predicting their functions. (4) Further, integrating differentially expressed gene-protein sets and their ontologies with medical terms associated with clinical phenotypes in a chromosome-centric manner reveals a network of genes, diseases, and pathways—a diseasome network. Thus, chromosomal mapping of disease data sets can help uncover important regulatory and functional links that may offer new insights for biomarker development.
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Affiliation(s)
- Savita Jayaram
- Institute of Bioinformatics , International Tech Park, Bangalore-560066, India.,Manipal University , Madhav Nagar, Manipal-576104, India
| | - Manoj Kumar Gupta
- Institute of Bioinformatics , International Tech Park, Bangalore-560066, India.,Manipal University , Madhav Nagar, Manipal-576104, India
| | | | - Madankumar Ghatge
- Manipal University , Madhav Nagar, Manipal-576104, India.,Thrombosis Research Institute, Narayana Health , Bangalore-560099, India
| | - Ankit Sharma
- Manipal University , Madhav Nagar, Manipal-576104, India.,Thrombosis Research Institute, Narayana Health , Bangalore-560099, India
| | | | - Ravi Sirdeshmukh
- Institute of Bioinformatics , International Tech Park, Bangalore-560066, India.,Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health , Bangalore-560099, India
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18
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Alisoltani A, Fallahi H, Shiran B, Alisoltani A, Ebrahimie E. RNA-Seq SSRs and small RNA-Seq SSRs: New approaches in cancer biomarker discovery. Gene 2015; 560:34-43. [DOI: 10.1016/j.gene.2015.01.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/02/2014] [Accepted: 01/13/2015] [Indexed: 11/24/2022]
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19
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Zhang KC, Xi HQ, Cui JX, Shen WS, Li JY, Wei B, Chen L. Prognostic role of miR-200c in various malignancies: a systematic review and meta-analysis. Int J Clin Exp Med 2015; 8:1931-1943. [PMID: 25932122 PMCID: PMC4402769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/20/2015] [Indexed: 06/04/2023]
Abstract
MiR-200c expression is dysregulated in various malignancies and may predict the survival of patients with cancer, although the results of different studies conflict. Therefore, we conducted a meta-analysis to resolve this discrepancy. We queried the PubMed and Embase using multiple search strategies. Data were extracted from studies comparing overall survival and progression-free survival in patients with cancer with high and low levels of miR-200c expression. Fixed and random models were used where appropriate. A combined hazards ratio (HR) was calculated to estimate the association of high levels of miR-200c with survival. We selected 16 studies of 1485 participants for our final meta-analysis. Upregulated expression of miR-200c predicted significantly worse overall survival in patients with cancer (HR 1.51; 95% confidence interval [CI] 1.06-2.16, P = 0.023). Subgroup analysis indicated that high levels of miR-200c was associated with decreased survival of Caucasians and patients with gynecological tumors with pooled HR values of 1.82 (95% CI 1.27-2.26, P = 0.01) and 3.23 (95% CI 1.11-9.38, P = 0.032), respectively. Because of the absence of apparent heterogeneity, the combined HRs were 1.69 (95% CI 1.24-2.30, P = 0.001) for squamous cell carcinoma and 1.91 (95% CI 1.40-2.59, P < 0.001) for samples from peripheral blood. Increased expression of miR-200c significantly associated with shorter progression-free survival of patients with cancer (HR 2.37; 95% CI 1.47-3.81, P < 0.001). Our meta-analysis indicates that the level of miR-200c expression predicted survival of patients with cancer, particularly for Caucasians and patients with gynecological cancer. Increased expression of miR-200c predicted shorter survival of patients with squamous cell carcinomas. Our findings indicate that monitoring the levels of miR-200c in blood may be useful for following tumor progression as well as patients' prognosis.
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Affiliation(s)
- Ke-Cheng Zhang
- Department of General Surgery, Chinese People's Liberation Army General Hospital 28 Fuxing Road, Beijing 100853, China
| | - Hong-Qing Xi
- Department of General Surgery, Chinese People's Liberation Army General Hospital 28 Fuxing Road, Beijing 100853, China
| | - Jian-Xin Cui
- Department of General Surgery, Chinese People's Liberation Army General Hospital 28 Fuxing Road, Beijing 100853, China
| | - Wei-Song Shen
- Department of General Surgery, Chinese People's Liberation Army General Hospital 28 Fuxing Road, Beijing 100853, China
| | - Ji-Yang Li
- Department of General Surgery, Chinese People's Liberation Army General Hospital 28 Fuxing Road, Beijing 100853, China
| | - Bo Wei
- Department of General Surgery, Chinese People's Liberation Army General Hospital 28 Fuxing Road, Beijing 100853, China
| | - Lin Chen
- Department of General Surgery, Chinese People's Liberation Army General Hospital 28 Fuxing Road, Beijing 100853, China
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A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: application to Arabidopsis. J Theor Biol 2014; 364:364-76. [PMID: 25303887 DOI: 10.1016/j.jtbi.2014.09.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 09/27/2014] [Accepted: 09/29/2014] [Indexed: 11/22/2022]
Abstract
Cis regulatory elements (CREs), located within promoter regions, play a significant role in the blueprint for transcriptional regulation of genes. There is a growing interest to study the combinatorial nature of CREs including presence or absence of CREs, the number of occurrences of each CRE, as well as of their order and location relative to their target genes. Comparative promoter analysis has been shown to be a reliable strategy to test the significance of each component of promoter architecture. However, it remains unclear what level of difference in the number of occurrences of each CRE is of statistical significance in order to explain different expression patterns of two genes. In this study, we present a novel statistical approach for pairwise comparison of promoters of Arabidopsis genes in the context of number of occurrences of each CRE within the promoters. First, using the sample of 1000 Arabidopsis promoters, the results of the goodness of fit test and non-parametric analysis revealed that the number of occurrences of CREs in a promoter sequence is Poisson distributed. As a promoter sequence contained functional and non-functional CREs, we addressed the issue of the statistical distribution of functional CREs by analyzing the ChIP-seq datasets. The results showed that the number of occurrences of functional CREs over the genomic regions was determined as being Poisson distributed. In accordance with the obtained distribution of CREs occurrences, we suggested the Audic and Claverie (AC) test to compare two promoters based on the number of occurrences for the CREs. Superiority of the AC test over Chi-square (2×2) and Fisher's exact tests was also shown, as the AC test was able to detect a higher number of significant CREs. The two case studies on the Arabidopsis genes were performed in order to biologically verify the pairwise test for promoter comparison. Consequently, a number of CREs with significantly different occurrences was identified between the promoters. The results of the pairwise comparative analysis together with the expression data for the studied genes revealed the biological significance of the identified CREs.
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