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Concern about the Effectiveness of mRNA Vaccination Technology and Its Long-Term Safety: Potential Interference on miRNA Machinery. Int J Mol Sci 2023; 24:ijms24021404. [PMID: 36674919 PMCID: PMC9863643 DOI: 10.3390/ijms24021404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
After the outbreak of the pandemic due to COVID-19 infection, several vaccines were developed on short timelines to counteract the public health crisis. To allow the administration of mRNA vaccines through a faster-paced approval process, the Emergency Use Authorization (EUA) was applied. The Ba.5 (omicron) variant of SARS-CoV-2 is the predominant one at this moment. Its highly mutable single-stranded RNA genome, along with its high transmissivity, generated concern about the effectiveness of vaccination. The interaction between the vaccine and the host cell is finely regulated by miRNA machinery, a complex network that oversees a wide range of biological processes. The dysregulation of miRNA machinery has been associated with the development of clinical complications during COVID-19 infection and, moreover, to several human pathologies, among which is cancer disease. Now that in some areas, four doses of mRNA vaccine have been administered, it is natural to wonder about its effectiveness and long-term safety.
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Exploring regulatory network of metabolism through liver research. Diabetol Int 2021; 12:343-348. [PMID: 34567916 DOI: 10.1007/s13340-021-00536-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/20/2021] [Indexed: 10/20/2022]
Abstract
In recent years, the techniques in molecular biology have been dramatically advanced, and consequently the landscape of metabolism research has undergone a remarkable change. One of the emerging pictures as the fruits of these advancements is one depicting the regulation of systemic metabolism through inter-organ networks involving multiple tissues, either via humoral factors, which are secreted from one tissue and conveyed to their remote target tissues, or through neuronal networks which are integrated by the central nervous system. In addition, the progress in high-throughput research tools enabled detailed characterization and deeper understanding of the nature of human genome, which has attracted much attention to the importance of various non-coding RNAs species. These non-coding RNAs are often co-expressed and co-regulated with adjacent protein coding genes, adding higher levels of complexities by them functioning together as a system and often influencing biologically important pathways in a cooperative manner. Here in this review several examples of these regulatory network systems are presented, illustrating the significance of them in systemic metabolism, with a possible future research direction also being proposed.
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Ferro E, Enrico Bena C, Grigolon S, Bosia C. From Endogenous to Synthetic microRNA-Mediated Regulatory Circuits: An Overview. Cells 2019; 8:E1540. [PMID: 31795372 PMCID: PMC6952906 DOI: 10.3390/cells8121540] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs are short non-coding RNAs that are evolutionarily conserved and are pivotal post-transcriptional mediators of gene regulation. Together with transcription factors and epigenetic regulators, they form a highly interconnected network whose building blocks can be classified depending on the number of molecular species involved and the type of interactions amongst them. Depending on their topology, these molecular circuits may carry out specific functions that years of studies have related to the processing of gene expression noise. In this review, we first present the different over-represented network motifs involving microRNAs and their specific role in implementing relevant biological functions, reviewing both theoretical and experimental studies. We then illustrate the recent advances in synthetic biology, such as the construction of artificially synthesised circuits, which provide a controlled tool to test experimentally the possible microRNA regulatory tasks and constitute a starting point for clinical applications.
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Affiliation(s)
- Elsi Ferro
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Chiara Enrico Bena
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Silvia Grigolon
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Carla Bosia
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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4
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Varakantham V, Ale K, Sailoo AKK, Nagalla B, Bharatraj DK. Sex-specific role of CYP24A1 rs2762939 in the risk of essential hypertension based on the serum vitamin D and total renin concentrations. Genomics 2019; 112:764-768. [PMID: 31102703 DOI: 10.1016/j.ygeno.2019.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 11/17/2022]
Abstract
CYP24A1, Vitamin D 24-hydroxylase catabolizes 25-hydroxyvitamin D (25(OH)D) and 1,25-dihydroxyvitamin D to 24-hydroxylated vitamin D products. It is widely known that low Vitamin D can lead to increased renal renin and angiotensin II production, consequently elevating blood pressure or development of essential hypertension (EH). We have conducted an investigation on hypertensives and controls to evaluate the association of the gene variant, CYP24A1 rs2762939 and 25(OH)D in an Indian population with EH. On gender-based stratification, with multivariate logistic analysis after adjustment for covariates, the CYP24A1 rs2762939 CC variant showed a higher risk of EH in males (aOR = 3.141, CI 1.164-8.478, P = .024) while females illustrated an inverse association with EH (aOR = 0.398, CI 0.172-0.092, P = .031). The 25(OH)D levels among the three genotypes of hypertensives substantiate these results. Our results clearly suggest that gender, CYP24A1 rs2762939, and Vitamin D status may play a significant role in disease susceptibility towards EH in Indian population.
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Affiliation(s)
- Varsha Varakantham
- Food and Drug Toxicology Research Centre, National Institute of Nutrition, Hyderabad, India
| | - Kiranmayee Ale
- Food and Drug Toxicology Research Centre, National Institute of Nutrition, Hyderabad, India
| | | | - Balakrishna Nagalla
- Department of Biostatistics, National Institute of Nutrition, Hyderabad, India
| | - Dinesh Kumar Bharatraj
- Food and Drug Toxicology Research Centre, National Institute of Nutrition, Hyderabad, India.
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5
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Rose AB. Introns as Gene Regulators: A Brick on the Accelerator. Front Genet 2019; 9:672. [PMID: 30792737 PMCID: PMC6374622 DOI: 10.3389/fgene.2018.00672] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 01/25/2023] Open
Abstract
A picture is beginning to emerge from a variety of organisms that for a subset of genes, the most important sequences that regulate expression are situated not in the promoter but rather are located within introns in the first kilobase of transcribed sequences. The actual sequences involved are difficult to identify either by sequence comparisons or by deletion analysis because they are dispersed, additive, and poorly conserved. However, expression-controlling introns can be identified computationally in species with relatively small introns, based on genome-wide differences in oligomer composition between promoter-proximal and distal introns. The genes regulated by introns are often expressed in most tissues and are among the most highly expressed in the genome. The ability of some introns to strongly stimulate mRNA accumulation from several hundred nucleotides downstream of the transcription start site, even when the promoter has been deleted, reveals that our understanding of gene expression remains incomplete. It is unlikely that any diseases are caused by point mutations or small deletions that reduce the expression of an intron-regulated gene unless splicing is also affected. However, introns may be particularly useful in practical applications such as gene therapy because they strongly activate expression but only affect the transcription unit in which they are located.
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Affiliation(s)
- Alan B Rose
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
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Jiang D, Zhou B, Xiong Y, Cai H. miR-135 regulated breast cancer proliferation and epithelial-mesenchymal transition acts by the Wnt/β-catenin signaling pathway. Int J Mol Med 2019; 43:1623-1634. [PMID: 30720046 PMCID: PMC6414157 DOI: 10.3892/ijmm.2019.4081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/17/2019] [Indexed: 12/23/2022] Open
Abstract
Breast cancer (BC) is the most common cancer in women around the world. microRNAs (miRNAs/miRs) have been proved to be associated with the development and progression of breast cancer. In the present study, to elucidate the effects of dysregulated miR‑135 on cells and underlying mechanisms in BC, in vitro and in vivo experiments were conducted. The biological functions of miR‑135 were studied using MTT, colony formation, wound healing, transwell assays as well as tumorigenicity analysis. Gain‑ and loss‑ of function of miR‑135 studies revealed that ectopic expression of miR‑135 in MDA‑MB‑468 and MCF‑7 cells significantly inhibited cell growth, migration, invasion and EMT, at least in part through inhibiting the activation of the Wnt/β‑catenin pathway. Moreover, this was reversed in cells which were transfected with miR‑135 inhibitors. Taken together, the results of the present study provided evidence that miR‑135 acted as a tumor suppressor in BC, which may represent a novel therapeutic strategy for the diagnosis and prognosis of BC.
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Affiliation(s)
- Daqiong Jiang
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Bo Zhou
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yan Xiong
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Hongbing Cai
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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Awazawa M, Gabel P, Tsaousidou E, Nolte H, Krüger M, Schmitz J, Ackermann PJ, Brandt C, Altmüller J, Motameny S, Wunderlich FT, Kornfeld JW, Blüher M, Brüning JC. A microRNA screen reveals that elevated hepatic ectodysplasin A expression contributes to obesity-induced insulin resistance in skeletal muscle. Nat Med 2017; 23:1466-1473. [DOI: 10.1038/nm.4420] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/11/2017] [Indexed: 01/21/2023]
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Qin C, Zhao Y, Gong C, Yang Z. MicroRNA-154/ADAM9 axis inhibits the proliferation, migration and invasion of breast cancer cells. Oncol Lett 2017; 14:6969-6975. [PMID: 29163713 DOI: 10.3892/ol.2017.7021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/20/2017] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is the leading cause for cancer-associated mortality in women. Although great progress has been made in the earlier diagnosis and systemic therapy of patients with breast cancer in recent years, recurrence or distant metastasis continue to present major barriers to the successful treatment of breast cancer. Therefore, fully understanding the molecular mechanisms underlying the progression of breast cancer may be critical for the development of effective therapeutic strategies against breast cancer. The aim of the present study was to explore the expression, function and molecular mechanisms of microRNA-154 (miR-154) in human breast cancer. It was demonstrated that miR-154 was significantly downregulated in breast cancer tissue and cell lines. The restoration of miR-154 expression suppressed the proliferation, migration and invasion of breast cancer cells. ADAM metallopeptidase domain 9 (ADAM9) was identified as a novel direct target for miR-154 in breast cancer. It was demonstrated that miR-154 acted as a tumor suppressor in breast cancer by targeting ADAM9. The results of the present study suggest that the restoration of miR-154 expression may be an effective therapeutic strategy for the treatment of breast cancer in the future.
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Affiliation(s)
- Chengwei Qin
- Department of General Surgery, Medical College of Shandong University, Jinan, Shandong 250012, P.R. China.,Department of Anesthesiology, Binzhou Medical University Hospital, Binzhou, Shandong 256603, P.R. China
| | - Yanming Zhao
- Department of Gastroenterology, Binzhou Medical University Hospital, Binzhou, Shandong 256603, P.R. China
| | - Chunzhi Gong
- Department of Anesthesiology, Binzhou Medical University Hospital, Binzhou, Shandong 256603, P.R. China
| | - Zhenlin Yang
- Department of General Surgery, Binzhou Medical University Hospital, Binzhou, Shandong 256603, P.R. China
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Li W, Li G, Fan Z, Liu T. Tumor-suppressive microRNA-452 inhibits migration and invasion of breast cancer cells by directly targeting RAB11A. Oncol Lett 2017; 14:2559-2565. [PMID: 28781694 DOI: 10.3892/ol.2017.6426] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/03/2017] [Indexed: 01/04/2023] Open
Abstract
Breast cancer is the most common type of malignant tumor in females, and metastasis is the most common cause of breast cancer-associated mortality. Previous studies have identified that abnormal expression of microRNAs is commonly observed in human cancer and may be crucial for cancer metastasis. In the present study, microRNA-452 (miR-452) was investigated for its ability to act as a tumor suppressor in breast cancer. miR-452 expression was quantified in breast cancer tissue samples and cell lines with reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Transwell migration and invasion assays were used to investigate the effect of miR-452 on the migration and invasion capabilities of breast cancer cells. Potential target genes of miR-452 were identified with miRanda and TargetScan. A luciferase reporter assay was performed to validate RAB11A as a putative target of miR-452, and was corroborated by RT-qPCR and western blot analyses. Finally, small interfering RNA (siRNA) was used to knockdown RAB11A expression and confirm whether miR-452 inhibited breast cancer cell migration and invasion via the negative regulation of RAB11A. The results revealed that miR-452 was downregulated in breast cancer tissues and cell lines, and that its downregulation may be associated with breast cancer metastasis, as miR-452 expression inhibited the migration and invasion capacities of breast cancer cells. RT-qPCR and western blot analyses indicated that miR-452 negatively regulated the expression of RAB11A mRNA and protein. The luciferase reporter assay revealed that miR-452 specifically bound to the 3'-untranslated region of RAB11A. Furthermore, inhibition of RAB11A with siRNA inhibited breast cancer cell migration and invasion. In conclusion, the present study has demonstrated that miR-452 may act as a tumor suppressor gene via inhibition of cell migration and invasion by targeting RAB11A in breast cancer.
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Affiliation(s)
- Wanjun Li
- Department of Pathology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, Shaanxi 723000, P.R. China
| | - Guoyin Li
- Department of Pathology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, Shaanxi 723000, P.R. China
| | - Zhigang Fan
- Department of Medical Oncology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, Shaanxi 723000, P.R. China
| | - Tao Liu
- Department of Pathology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, Shaanxi 723000, P.R. China
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Inflammatory gene networks in term human decidual cells define a potential signature for cytokine-mediated parturition. Am J Obstet Gynecol 2016; 214:284.e1-284.e47. [PMID: 26348374 DOI: 10.1016/j.ajog.2015.08.075] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/17/2015] [Accepted: 08/31/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND Inflammation is a proximate mediator of preterm birth and fetal injury. During inflammation several microRNAs (22 nucleotide noncoding ribonucleic acid (RNA) molecules) are up-regulated in response to cytokines such as interleukin-1β. MicroRNAs, in most cases, fine-tune gene expression, including both up-regulation and down-regulation of their target genes. However, the role of pro- and antiinflammatory microRNAs in this process is poorly understood. OBJECTIVE The principal goal of the work was to examine the inflammatory genomic profile of human decidual cells challenged with a proinflammatory cytokine known to be present in the setting of preterm parturition. We determined the coding (messenger RNA) and noncoding (microRNA) sequences to construct a network of interacting genes during inflammation using an in vitro model of decidual stromal cells. STUDY DESIGN The effects of interleukin-1β exposure on mature microRNA expression were tested in human decidual cell cultures using the multiplexed NanoString platform, whereas the global inflammatory transcriptional response was measured using oligonucleotide microarrays. Differential expression of select transcripts was confirmed by quantitative real time-polymerase chain reaction. Bioinformatics tools were used to infer transcription factor activation and regulatory interactions. RESULTS Interleukin-1β elicited up- and down-regulation of 350 and 78 nonredundant transcripts (false discovery rate < 0.1), respectively, including induction of numerous cytokines, chemokines, and other inflammatory mediators. Whereas this transcriptional response included marked changes in several microRNA gene loci, the pool of fully processed, mature microRNA was comparatively stable following a cytokine challenge. Of a total of 6 mature microRNAs identified as being differentially expressed by NanoString profiling, 2 (miR-146a and miR-155) were validated by quantitative real time-polymerase chain reaction. Using complementary bioinformatics approaches, activation of several inflammatory transcription factors could be inferred downstream of interleukin-1β based on the overall transcriptional response. Further analysis revealed that miR-146a and miR-155 both target genes involved in inflammatory signaling, including Toll-like receptor and mitogen-activated protein kinase pathways. CONCLUSION Stimulation of decidual cells with interleukin-1β alters the expression of microRNAs that function to temper proinflammatory signaling. In this setting, some microRNAs may be involved in tissue-level inflammation during the bulk of gestation and assist in pregnancy maintenance.
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Ye Z, Hao R, Cai Y, Wang X, Huang G. Knockdown of miR-221 promotes the cisplatin-inducing apoptosis by targeting the BIM-Bax/Bak axis in breast cancer. Tumour Biol 2015; 37:4509-15. [PMID: 26503209 DOI: 10.1007/s13277-015-4267-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/15/2015] [Indexed: 01/04/2023] Open
Abstract
Accumulating evidence shows that microRNAs (miRNAs) have a critical role in the initiation and progression of types of human cancer, including breast cancer. Recent research indicated that miRNAs are also related with the chemotherapy on cancers. In this study, the expression of miR-221 in breast cancer (BC) patients' serum and cancer tissues was found to be significantly up-regulated. The results of in vitro MTT assay indicated that although the anti-miR-221 oligonucleotide alone did not influence the viability of BC cell lines markedly, it significantly promoted the cytotoxicity of cisplatin (DDP) to BC cells. Mechanistic studies demonstrated that the gene of BIM (Bcl-2 interacting mediator of cell death), a pro-apoptotic Bcl-2 family protein, was up-regulated by the knockdown of miR-221. We found that the synergetic effect of anti-miR-221 on increasing the sensitivity of MDA-MB-231 was BIM dependant. Furthermore, results of immunoprecipitation showed the up-regulated BIM directly combined with the Bax and Bak, leading to mitochondrial dysfunction. Our results suggest the anti-miR-221 could promote the cisplatin-inducing apoptosis by targeting the Bim-Bax/Bak axis in breast cancer.
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Affiliation(s)
- Zhiqiang Ye
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, People's Republic of China, 325000
| | - Rutian Hao
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, People's Republic of China, 325000
| | - Yefeng Cai
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, People's Republic of China, 325000
| | - Xiaobo Wang
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, People's Republic of China, 325000
| | - Guanli Huang
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, People's Republic of China, 325000.
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Prindull G. Potential Gene Interactions in the Cell Cycles of Gametes, Zygotes, Embryonic Stem Cells and the Development of Cancer. Front Oncol 2015; 5:200. [PMID: 26442212 PMCID: PMC4585297 DOI: 10.3389/fonc.2015.00200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/31/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES This review is to explore whether potential gene interactions in the cell cycles of gametes, zygotes, and embryonic stem (ES) cells are associated with the development of cancer. METHODS MEDPILOT at the Central Library of the University of Cologne, Germany (Zentralbibliothek Köln) that covers 5,800 international medical journals and 4,300 E-journals was used to collect data. The initial searches were done in December 2012 and additional searches in October 2013-May 2015. The search terms included "cancer development," "gene interaction," and "ES cells," and the time period was between 1998 and 2015. A total of 147 articles in English language only were included in this review. RESULTS Transgenerational gene translation is implemented in the zygote through interactions of epigenetic isoforms of transcription factors (TFs) from parental gametes, predominantly during the first two zygote cleavages. Pluripotent transcription factors may provide interacting links with mutated genes during zygote-to-ES cell switches. Translation of post-transcriptional carcinogenic genes is implemented by abnormally spliced, tumor-specific isoforms of gene-encoded mRNA/non-coding RNA variants of TFs employing de novo gene synthesis and neofunctionalization. Post-translationally, mutated genes are preserved in pre-neoplastic ES cell subpopulations that can give rise to overt cancer stem cells. Thus, TFs operate as cell/disease-specific epigenetic messengers triggering clinical expression of neoplasms. CONCLUSION Potential gene interactions in the cell cycle of gametes, zygotes, and ES cells may play some roles in the development of cancer.
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Affiliation(s)
- Gregor Prindull
- Medical Faculty, University of Göttingen , Göttingen , Germany
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13
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Riestra P, Gebreab SY, Xu R, Khan RJ, Bidulescu A, Correa A, Tekola-Ayele F, Davis SK. Gender-specific associations between ADIPOQ gene polymorphisms and adiponectin levels and obesity in the Jackson Heart Study cohort. BMC MEDICAL GENETICS 2015; 16:65. [PMID: 26290432 PMCID: PMC4593213 DOI: 10.1186/s12881-015-0214-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 08/12/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Despite the important role of adiponectin in regulating general metabolic homeostasis, analysis of genetic determinants of adiponectin and the related cardio-metabolic traits in African American population has been limited and inconsistent. Considering the high genetic admixture of African Americans and thus the important population stratification that may confound the genetic-trait associations, the objective of this work was to perform a comprehensive analysis of the associations between ADIPOQ variants and adiponectin levels and obesity phenotypes in a large African American population from the Jackson Heart Study (JHS) cohort. METHODS Genotype data was available for 2968 JHS participants (1131men; 1837women). Single Nucleotide Polymorphisms (SNPs) were selected by a Tag-SNP Approach and literature review. The genotype imputation was performed using IMPUTE2 software and reference phased data from the 1000G project. PLINK software was used for the genetic analysis. Plasma specimens were analyzed by ELISA for adiponectin levels. All analyses were controlled for population stratification assessed by Individual Proportions of European Ancestry (PEA) estimates calculated in HAPMIX using ancestry informative markers (AIMs). RESULTS We found a gender-dependent association of some ADIPOQ variants and adiponectin levels. In women four of the studied polymorphisms (rs6444174, rs16861205, rs1403697, rs7641507) were associated with adiponectin levels after Bonferroni correction and controlling for the percentage of PEA, age, annual household income and smoking. These results were consistent with the haplotype analysis. The association between the rs12495941 variant and obesity is modulated by the PEA, so that the relationship between the G allele and a higher incidence of obesity was present in those individuals within the lower PEA group. In addition we found an effect modification of obesity on the association between the ADIPOQ rs6444174 SNP and BMI so that the presence of the T allele was negatively and significantly associated with BMI only in participants with a normal weight. CONCLUSIONS In this large African American cohort, ADIPOQ variants were associated with adiponectin levels in a gender-dependent manner and the relationship of some of these variants with obesity and BMI was modulated by the PEA and obesity status respectively. This suggests that the effects of these polymorphisms on adiponectin and obesity phenotypes are subject to a strong interaction with genetic and environmental factors in African American population.
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Affiliation(s)
- Pia Riestra
- National Human Genome Research Institute, Genomics of Metabolic, Cardiovascular and Inflammatory Disease Branch, Social Epidemiology Research Unit, National Institutes of Health, 10 Center Drive, Bethesda, MD, 20892, USA.
| | - Samson Y Gebreab
- National Human Genome Research Institute, Genomics of Metabolic, Cardiovascular and Inflammatory Disease Branch, Social Epidemiology Research Unit, National Institutes of Health, 10 Center Drive, Bethesda, MD, 20892, USA.
| | - Ruihua Xu
- National Human Genome Research Institute, Genomics of Metabolic, Cardiovascular and Inflammatory Disease Branch, Social Epidemiology Research Unit, National Institutes of Health, 10 Center Drive, Bethesda, MD, 20892, USA.
| | - Rumana J Khan
- National Human Genome Research Institute, Genomics of Metabolic, Cardiovascular and Inflammatory Disease Branch, Social Epidemiology Research Unit, National Institutes of Health, 10 Center Drive, Bethesda, MD, 20892, USA.
| | - Aurelian Bidulescu
- School of Public Health, Indiana University Bloomington, 1025 E. 7th Street, Suite 111, Bloomington, IN, 47405, USA.
| | - Adolfo Correa
- Jackson Heart Study, Jackson Medical Mall, 350 West Woodrow Wilson Av., Suite 701, Jackson, MS, 39217, USA.
| | - Fasil Tekola-Ayele
- National Human Genome Research Institute, Center for Research on Genomics and Global Health, National Institutes of Health, 12 South Drive, Bethesda, MD, 20892, USA.
| | - Sharon K Davis
- National Human Genome Research Institute, Genomics of Metabolic, Cardiovascular and Inflammatory Disease Branch, Social Epidemiology Research Unit, National Institutes of Health, 10 Center Drive, Bethesda, MD, 20892, USA.
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Williamson VS, Mamdani M, McMichael GO, Kim AH, Lee D, Bacanu S, Vladimirov VI. Expression quantitative trait loci (eQTLs) in microRNA genes are enriched for schizophrenia and bipolar disorder association signals. Psychol Med 2015; 45:2557-2569. [PMID: 25817407 PMCID: PMC4845662 DOI: 10.1017/s0033291715000483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Schizophrenia (SZ) and bipolar disorder (BD) have substantial negative impact on the quality of human life. Both, microRNA (miRNA) expression profiling in SZ and BD postmortem brains [and genome-wide association studies (GWAS)] have implicated miRNAs in disease etiology. Here, we aim to determine whether significant GWAS signals observed in the Psychiatric Genetic Consortium (PGC) are enriched for miRNAs. METHOD A two-stage approach was used to determine whether association signals from PGC affect miRNAs: (i) statistical assessment of enrichment using a Simes test and sum of squares test (SST) and (ii) biological evidence that quantitative trait loci (eQTL) mapping to known miRNA genes affect their expression in an independent sample of 78 postmortem brains from the Stanley Medical Research Institute. RESULTS A total of 2567 independent single nucleotide polymorphisms (SNPs) (R2 > 0.8) were mapped locally, within 1 Mb, to all known miRNAs (miRBase v. 21). We show robust enrichment for SZ- and BD-related SNPs with miRNAs using Simes (SZ: p ≤ 0.0023, BD: p ≤ 0.038), which remained significant after adjusting for background inflation in SZ (empirical p = 0.018) and approached significance in BD (empirical p = 0.07). At a false discovery rate of 10%, we identified a total of 32 eQTLs to influence miRNA expression; 11 of these overlapped with BD. CONCLUSIONS Our approach of integrating PGC findings with eQTL results can be used to generate specific hypotheses regarding the role of miRNAs in SZ and BD.
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Affiliation(s)
- V. S. Williamson
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, VA, USA
| | - M. Mamdani
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, VA, USA
| | - G. O. McMichael
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, VA, USA
| | - A. H. Kim
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, VA, USA
| | - D. Lee
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, VA, USA
| | - S. Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, VA, USA
- Department of Psychiatry, Virginia Commonwealth University, VA, USA
| | - V. I. Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, VA, USA
- Department of Psychiatry, Virginia Commonwealth University, VA, USA
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, VA, USA
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, USA
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15
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Anderegg A, Awatramani R. Making a mes: A transcription factor-microRNA pair governs the size of the midbrain and the dopaminergic progenitor pool. NEUROGENESIS 2015; 2:e998101. [PMID: 27502145 PMCID: PMC4973584 DOI: 10.1080/23262133.2014.998101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 12/04/2014] [Accepted: 12/10/2014] [Indexed: 02/03/2023]
Abstract
Canonical Wnt signaling is critical for midbrain dopaminergic progenitor specification, proliferation, and neurogenesis. Yet mechanisms that control Wnt signaling remain to be fully elucidated. Wnt1 is a key ligand in the embryonic midbrain, and directs proliferation, survival, specification and neurogenesis. In a recent study, we reveal that the transcription factor Lmx1b promotes Wnt1/Wnt signaling, and dopaminergic progenitor expansion, consistent with earlier studies. Additionally, Lmx1b drives expression of a non-coding RNA called Rmst, which harbors miR135a2 in its last intron. miR135a2 in turn targets Lmx1b as well as several Wnt pathway targets. Conditional overexpression of miR135a2 in the midbrain, particularly during an early time, results in a decreased dopaminergic progenitor pool, and less dopaminergic neurons, consistent with decreased Wnt signaling. We propose a model in which Lmx1b and miR135a2 influence levels of Wnt1 and Wnt signaling, and expansion of the dopaminergic progenitor pool. Further loss of function experiments and biochemical validation of targets will be critical to verify this model. Wnt agonists have recently been utilized for programming stem cells toward a dopaminergic fate in vitro, highlighting the importance of agents that modulate the Wnt pathway.
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Affiliation(s)
- Angela Anderegg
- Department of Neurology; Northwestern University ; Chicago, IL USA
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16
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17
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Possible role for microRNAs as inter-species mediators of epigenetic information in disease pathogenesis: Is the non-coding dark matter of the genome responsible for epigenetic interindividual or interspecies communication? Med Hypotheses 2015; 84:150-4. [DOI: 10.1016/j.mehy.2014.11.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 11/16/2014] [Accepted: 11/28/2014] [Indexed: 01/27/2023]
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18
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Gordon JAR, Montecino MA, Aqeilan RI, Stein JL, Stein GS, Lian JB. Epigenetic pathways regulating bone homeostasis: potential targeting for intervention of skeletal disorders. Curr Osteoporos Rep 2014; 12:496-506. [PMID: 25260661 PMCID: PMC4216616 DOI: 10.1007/s11914-014-0240-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic regulation utilizes different mechanisms to convey heritable traits to progeny cells that are independent of DNA sequence, including DNA silencing, post-translational modifications of histone proteins, and the post-transcriptional modulation of RNA transcript levels by non-coding RNAs. Although long non-coding RNAs have recently emerged as important regulators of gene imprinting, their functions during osteogenesis are as yet unexplored. In contrast, microRNAs (miRNAs) are well characterized for their control of osteogenic and osteoclastic pathways; thus, further defining how gene regulatory networks essential for skeleton functions are coordinated and finely tuned through the activities of miRNAs. Roles of miRNAs are constantly expanding as new studies uncover associations with skeletal disorders. The distinct functions of epigenetic regulators and evidence for integrating their activities to control normal bone gene expression and bone disease will be presented. In addition, potential for using "signature miRNAs" to identify, manage, and therapeutically treat osteosarcoma will be discussed in this review.
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Affiliation(s)
- Jonathan A. R. Gordon
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Martin A. Montecino
- Centro de Investigaciones Biomedicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Avenida Republica 239, Santiago, Chile
| | - Rami I. Aqeilan
- Lautenberg Center for Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, PO Box 12272, Ein Karem Campus, Jerusalem 91120, Israel
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
- Corresponding Author: Jane B. Lian – P: 802-656-4872, F: 802-656-8216,
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19
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Cowled C, Stewart CR, Likic VA, Friedländer MR, Tachedjian M, Jenkins KA, Tizard ML, Cottee P, Marsh GA, Zhou P, Baker ML, Bean AG, Wang LF. Characterisation of novel microRNAs in the Black flying fox (Pteropus alecto) by deep sequencing. BMC Genomics 2014; 15:682. [PMID: 25128405 PMCID: PMC4156645 DOI: 10.1186/1471-2164-15-682] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 08/07/2014] [Indexed: 12/11/2022] Open
Abstract
Background Bats are a major source of new and emerging viral diseases. Despite the fact that bats carry and shed highly pathogenic viruses including Ebola, Nipah and SARS, they rarely display clinical symptoms of infection. Host factors influencing viral replication are poorly understood in bats and are likely to include both pre- and post-transcriptional regulatory mechanisms. MicroRNAs are a major mechanism of post-transcriptional gene regulation, however very little is known about them in bats. Results This study describes 399 microRNAs identified by deep sequencing of small RNA isolated from tissues of the Black flying fox, Pteropus alecto, a confirmed natural reservoir of the human pathogens Hendra virus and Australian bat lyssavirus. Of the microRNAs identified, more than 100 are unique amongst vertebrates, including a subset containing mutations in critical seed regions. Clusters of rapidly-evolving microRNAs were identified, as well as microRNAs predicted to target genes involved in antiviral immunity, the DNA damage response, apoptosis and autophagy. Closer inspection of the predicted targets for several highly supported novel miRNA candidates suggests putative roles in host-virus interaction. Conclusions MicroRNAs are likely to play major roles in regulating virus-host interaction in bats, via dampening of inflammatory responses (limiting the effects of immunopathology), and directly limiting the extent of viral replication, either through restricting the availability of essential factors or by controlling apoptosis. Characterisation of the bat microRNA repertoire is an essential step towards understanding transcriptional regulation during viral infection, and will assist in the identification of mechanisms that enable bats to act as natural virus reservoirs. This in turn will facilitate the development of antiviral strategies for use in humans and other species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-682) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher Cowled
- CSIRO Australian Animal Health Laboratory, 5 Portarlington Rd, Geelong East, Victoria 3220, Australia.
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Abstract
Over the recent decade oligonucleotides have become an important new class of molecules, allowing therapeutic intervention through targets previously thought 'undruggable'. One of the new avenues opened up by oligonucleotide-based drugs was specific gene upregulation, which, historically, has been difficult to achieve using small-molecule drugs. This article will focus on patents covering this important development in the oligonucleotide field and highlight the different mechanisms through which the oligonucleotide-mediated gene upregulation can work, including inhibition of activity of natural antisense transcripts, interaction with promoter binding sites of noncoding regulatory RNAs, blocking of regulatory and/or miRNA binding sites in 3' UTRs, blocking splice inhibitor/enhancer sites or blocking interactions with polycomb repressive complex 2. Understanding the particular mechanism through which an oligonucleotide drug exerts its effects is highly important in drug development, as it determines the design of the drug molecule.
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21
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Kozakowska M, Szade K, Dulak J, Jozkowicz A. Role of heme oxygenase-1 in postnatal differentiation of stem cells: a possible cross-talk with microRNAs. Antioxid Redox Signal 2014; 20:1827-50. [PMID: 24053682 PMCID: PMC3961774 DOI: 10.1089/ars.2013.5341] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE Heme oxygenase-1 (HO-1) converts heme to biliverdin, carbon monoxide, and ferrous ions, but its cellular functions are far beyond heme metabolism. HO-1 via heme removal and degradation products acts as a cytoprotective, anti-inflammatory, immunomodulatory, and proangiogenic protein, regulating also a cell cycle. Additionally, HO-1 can translocate to nucleus and regulate transcription factors, so it can also act independently of enzymatic function. RECENT ADVANCES Recently, a body of evidence has emerged indicating a role for HO-1 in postnatal differentiation of stem and progenitor cells. Maturation of satellite cells, skeletal myoblasts, adipocytes, and osteoclasts is inhibited by HO-1, whereas neurogenic differentiation and formation of cardiomyocytes perhaps can be enhanced. Moreover, HO-1 influences a lineage commitment in pluripotent stem cells and maturation of hematopoietic cells. It may play a role in development of osteoblasts, but descriptions of its exact effects are inconsistent. CRITICAL ISSUES In this review we discuss a role of HO-1 in cell differentiation, and possible HO-1-dependent signal transduction pathways. Among the potential mediators, we focused on microRNA (miRNA). These small, noncoding RNAs are critical for cell differentiation. Recently we have found that HO-1 not only influences expression of specific miRNAs but also regulates miRNA processing enzymes. FUTURE DIRECTIONS It seems that interplay between HO-1 and miRNAs may be important in regulating fates of stem and progenitor cells and needs further intensive studies.
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Affiliation(s)
- Magdalena Kozakowska
- 1 Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Krakow, Poland
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22
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Pelosi A, Careccia S, Sagrestani G, Nanni S, Manni I, Schinzari V, Martens JH, Farsetti A, Stunnenberg HG, Gentileschi MP, Del Bufalo D, De Maria R, Piaggio G, Rizzo MG. Dual Promoter Usage as Regulatory Mechanism of let-7c Expression in Leukemic and Solid Tumors. Mol Cancer Res 2014; 12:878-89. [DOI: 10.1158/1541-7786.mcr-13-0410] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Anderegg A, Lin HP, Chen JA, Caronia-Brown G, Cherepanova N, Yun B, Joksimovic M, Rock J, Harfe BD, Johnson R, Awatramani R. An Lmx1b-miR135a2 regulatory circuit modulates Wnt1/Wnt signaling and determines the size of the midbrain dopaminergic progenitor pool. PLoS Genet 2013; 9:e1003973. [PMID: 24348261 PMCID: PMC3861205 DOI: 10.1371/journal.pgen.1003973] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/09/2013] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs regulate gene expression in diverse physiological scenarios. Their role in the control of morphogen related signaling pathways has been less studied, particularly in the context of embryonic Central Nervous System (CNS) development. Here, we uncover a role for microRNAs in limiting the spatiotemporal range of morphogen expression and function. Wnt1 is a key morphogen in the embryonic midbrain, and directs proliferation, survival, patterning and neurogenesis. We reveal an autoregulatory negative feedback loop between the transcription factor Lmx1b and a newly characterized microRNA, miR135a2, which modulates the extent of Wnt1/Wnt signaling and the size of the dopamine progenitor domain. Conditional gain of function studies reveal that Lmx1b promotes Wnt1/Wnt signaling, and thereby increases midbrain size and dopamine progenitor allocation. Conditional removal of Lmx1b has the opposite effect, in that expansion of the dopamine progenitor domain is severely compromised. Next, we provide evidence that microRNAs are involved in restricting dopamine progenitor allocation. Conditional loss of Dicer1 in embryonic stem cells (ESCs) results in expanded Lmx1a/b+ progenitors. In contrast, forced elevation of miR135a2 during an early window in vivo phenocopies the Lmx1b conditional knockout. When En1::Cre, but not Shh::Cre or Nes::Cre, is used for recombination, the expansion of Lmx1a/b+ progenitors is selectively reduced. Bioinformatics and luciferase assay data suggests that miR135a2 targets Lmx1b and many genes in the Wnt signaling pathway, including Ccnd1, Gsk3b, and Tcf7l2. Consistent with this, we demonstrate that this mutant displays reductions in the size of the Lmx1b/Wnt1 domain and range of canonical Wnt signaling. We posit that microRNA modulation of the Lmx1b/Wnt axis in the early midbrain/isthmus could determine midbrain size and allocation of dopamine progenitors. Since canonical Wnt activity has recently been recognized as a key ingredient for programming ESCs towards a dopaminergic fate in vitro, these studies could impact the rational design of such protocols.
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Affiliation(s)
- Angela Anderegg
- Northwestern University Feinberg School of Medicine, Department of Neurology and Center for Genetic Medicine, Chicago, Illinois, United States of America
| | - Hsin-Pin Lin
- Northwestern University Feinberg School of Medicine, Department of Neurology and Center for Genetic Medicine, Chicago, Illinois, United States of America
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Giuliana Caronia-Brown
- Northwestern University Feinberg School of Medicine, Department of Neurology and Center for Genetic Medicine, Chicago, Illinois, United States of America
| | - Natalya Cherepanova
- Northwestern University Feinberg School of Medicine, Department of Neurology and Center for Genetic Medicine, Chicago, Illinois, United States of America
| | - Beth Yun
- Northwestern University Feinberg School of Medicine, Department of Neurology and Center for Genetic Medicine, Chicago, Illinois, United States of America
| | - Milan Joksimovic
- Northwestern University Feinberg School of Medicine, Department of Neurology and Center for Genetic Medicine, Chicago, Illinois, United States of America
| | - Jason Rock
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Brian D. Harfe
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Randy Johnson
- Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Rajeshwar Awatramani
- Northwestern University Feinberg School of Medicine, Department of Neurology and Center for Genetic Medicine, Chicago, Illinois, United States of America
- * E-mail:
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Berillo O, Régnier M, Ivashchenko A. Binding of intronic miRNAs to the mRNAs of host genes encoding intronic miRNAs and proteins that participate in tumourigenesis. Comput Biol Med 2013; 43:1374-81. [PMID: 24034728 DOI: 10.1016/j.compbiomed.2013.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/11/2013] [Accepted: 07/12/2013] [Indexed: 12/28/2022]
Abstract
In this study, we examined 615 host genes encoding 915 in-miRNAs as possible targets for interactions with all in-miRNAs. Host genes whose proteins are involved in esophageal, gastric, small bowel, colorectal, and breast cancer development were studied. Unique in-miRNA binding sites with a significance of p<0.0005 were found in the 5'UTRs, CDSs, and 3'UTRs of the host genes encoding proteins that are key participants in tumourigenesis. These data shed light on the interactions between miRNAs and mRNAs and on the role of candidate proteins in cancer. Therefore, our findings have potential application in the development of diagnostic and treatment methods.
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Affiliation(s)
- O Berillo
- National nanotechnology laboratory, al-Farabi Kazakh National University, Almaty, Kazakhstan.
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25
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Polman JAE, de Kloet ER, Datson NA. Two populations of glucocorticoid receptor-binding sites in the male rat hippocampal genome. Endocrinology 2013; 154:1832-44. [PMID: 23525215 DOI: 10.1210/en.2012-2187] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the present study, genomic binding sites of glucocorticoid receptors (GR) were identified in vivo in the rat hippocampus applying chromatin immunoprecipitation followed by next-generation sequencing. We identified 2470 significant GR-binding sites (GBS) and were able to confirm GR binding to a random selection of these GBS covering a wide range of P values. Analysis of the genomic distribution of the significant GBS revealed a high prevalence of intragenic GBS. Gene ontology clusters involved in neuronal plasticity and other essential neuronal processes were overrepresented among the genes harboring a GBS or located in the vicinity of a GBS. Male adrenalectomized rats were challenged with increasing doses of the GR agonist corticosterone (CORT) ranging from 3 to 3000 μg/kg, resulting in clear differences in the GR-binding profile to individual GBS. Two groups of GBS could be distinguished: a low-CORT group that displayed GR binding across the full range of CORT concentrations, and a second high-CORT group that displayed significant GR binding only after administering the highest concentration of CORT. All validated GBS, in both the low-CORT and high-CORT groups, displayed mineralocorticoid receptor binding, which remained relatively constant from 30 μg/kg CORT upward. Motif analysis revealed that almost all GBS contained a glucocorticoid response element resembling the consensus motif in literature. In addition, motifs corresponding with new potential GR-interacting proteins were identified, such as zinc finger and BTB domain containing 3 (Zbtb3) and CUP (CG11181 gene product from transcript CG11181-RB), which may be involved in GR-dependent transactivation and transrepression, respectively. In conclusion, our results highlight the existence of 2 populations of GBS in the rat hippocampal genome.
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Affiliation(s)
- J Annelies E Polman
- Division of Medical Pharmacology, Leiden/Amsterdam Center for Drug Research, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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26
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Miura K, Fujibuchi W, Unno M. Splice isoforms as therapeutic targets for colorectal cancer. Carcinogenesis 2012; 33:2311-9. [PMID: 23118106 DOI: 10.1093/carcin/bgs347] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Alternative pre-mRNA splicing allows exons of pre-mRNA to be spliced in different arrangements to produce functionally distinct mRNAs. More than 95% of human genes encode splice isoforms, some of which exert antagonistic functions. Recent studies revealed that alterations of the splicing machinery can cause the development of neoplasms, and understanding the splicing machinery is crucial for developing novel therapeutic strategies for malignancies. Colorectal cancer patients need novel strategies not only to enhance the efficacy of the currently available agents but also to utilize newly identified therapeutic targets. This review summarizes the current knowledge about the splice isoforms of VEGFA, UGT1A, PXR, cyclin D1, BIRC5 (survivin), DPD, K-RAS, SOX9, SLC39A14 and other genes, which may be possible therapeutic targets for colorectal cancer. Among them, the VEGFA splice isoforms are classified into VEGFAxxx and VEGFAxxxb, which have proangiogenic and antiangiogenic properties, respectively; UGT1A is alternatively spliced into UGT1A1 and other isoforms, which are regulated by pregnane X receptor isoforms and undergo further splicing modifications. Recently, the splicing machinery has been extensively investigated and novel discoveries in this research field are being reported at a rapid pace. The information contained in this review also provides suggestions for how therapeutic strategies targeting alternative splicing can be further developed.
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Affiliation(s)
- Koh Miura
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan.
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