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Laurenti L, Csikasz-Nagy A, Kwiatkowska M, Cardelli L. Molecular Filters for Noise Reduction. Biophys J 2019; 114:3000-3011. [PMID: 29925035 PMCID: PMC6026371 DOI: 10.1016/j.bpj.2018.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/09/2018] [Accepted: 05/04/2018] [Indexed: 01/08/2023] Open
Abstract
Living systems are inherently stochastic and operate in a noisy environment, yet despite all these uncertainties, they perform their functions in a surprisingly reliable way. The biochemical mechanisms used by natural systems to tolerate and control noise are still not fully understood, and this issue also limits our capacity to engineer reliable, quantitative synthetic biological circuits. We study how representative models of biochemical systems propagate and attenuate noise, accounting for intrinsic as well as extrinsic noise. We investigate three molecular noise-filtering mechanisms, study their noise-reduction capabilities and limitations, and show that nonlinear dynamics such as complex formation are necessary for efficient noise reduction. We further suggest that the derived molecular filters are widespread in gene expression and regulation and, particularly, that microRNAs can serve as such noise filters. To our knowledge, our results provide new insight into how biochemical networks control noise and could be useful to build robust synthetic circuits.
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Affiliation(s)
- Luca Laurenti
- Department of Computer Science, University of Oxford, Oxford, United Kingdom.
| | - Attila Csikasz-Nagy
- Randall Division of Cell and Molecular Biophysics and Institute of Mathematical and Molecular Biomedicine, King's College London, London, United Kingdom; Pázmány Péter Catholic University, Budapest, Hungary
| | - Marta Kwiatkowska
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Luca Cardelli
- Department of Computer Science, University of Oxford, Oxford, United Kingdom; Microsoft Research, Cambridge, United Kingdom
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Zhang L, Xue Z, Yan J, Wang J, Liu Q, Jiang H. LncRNA Riken-201 and Riken-203 modulates neural development by regulating the Sox6 through sequestering miRNAs. Cell Prolif 2019; 52:e12573. [PMID: 30667104 PMCID: PMC6536386 DOI: 10.1111/cpr.12573] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/04/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022] Open
Abstract
Objectives Long non‐coding RNAs (LncRNAs) play important roles in epigenetic regulatory function during the development processes. In this study, we found that through alternative splicing, LncRNA C130071C03Riken variants Riken‐201 (Riken‐201) and Riken‐203 (Riken‐203) are both expressed highly in brain, and increase gradually during neural differentiation. However, the function of Rik‐201 and Rik‐203 is unknown. Materials and methods Embryonic stem cells (ESCs); RNA sequencing; gene expression of mRNAs, LncRNAs and miRNAs; over‐expression and RNA interference of genes; flow cytometry; real‐time quantity PCR; and Western blot were used in the studies. RNA pull‐down assay and PCR were employed to detect any miRNA that attached to Rik‐201 and Rik‐203. The binding of miRNA with mRNA of Sox6 was presented by the luciferase assay. Results Repression of Rik‐201 and Rik‐203 inhibited neural differentiation from mouse embryonic stem cells. Moreover, Rik‐201 and Rik‐203 functioned as the competing endogenous RNA (ceRNA) to repress the function of miR‐96 and miR‐467a‐3p, respectively, and modulate the expression of Sox6 to further regulate neural differentiation. Knockout of the Rik‐203 and Rik‐201 induced high ratio of brain developmental retardation. Further we found that C/EBPβ might potentially activated the transcription of Rik‐201 and Rik‐203. Conclusions These findings identify the functional role of Rik‐201 and Rik‐203 in facilitating neural differentiation and further brain development, and elucidate the underlying miRNAs‐Sox6‐associated molecular mechanisms.
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Affiliation(s)
- Lei Zhang
- Department of Anesthesiology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, China
| | - Zhenyu Xue
- Department of Anesthesiology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, China
| | - Jia Yan
- Department of Anesthesiology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, China
| | - Jie Wang
- Department of Anesthesiology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, China
| | - Qidong Liu
- Anesthesia and Brain Function Research Institute, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hong Jiang
- Department of Anesthesiology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Center for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai, China
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Magalhães M, Alvarez-Lorenzo C, Concheiro A, Figueiras A, Santos AC, Veiga F. RNAi-based therapeutics for lung cancer: biomarkers, microRNAs, and nanocarriers. Expert Opin Drug Deliv 2018; 15:965-982. [PMID: 30232915 DOI: 10.1080/17425247.2018.1517744] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Despite the current advances in the discovery of the lung cancer biomarkers and, consequently, in the diagnosis, this pathology continues to be the primary cause of cancer-related death worldwide. In most cases, the illness is diagnosed in an advanced stage, which limits the current treatment options available and reduces the survival rate. Therefore, RNAi-based therapy arises as a promising option to treat lung cancer. AREAS COVERED This review provides an overview on the exploitation of lung cancer biology to develop RNAi-based therapeutics to be applied in the treatment of lung cancer. Furthermore, the review analyzes the main nanocarriers designed to deliver RNAi molecules and induce antitumoral effects in lung cancer, and provides updated information about current RNAi-based therapeutics for lung cancer in clinical trials. EXPERT OPINION RNAi-based therapy uses nanocarriers to perform a targeted and efficient delivery of therapeutic genes into lung cancer cells, by taking advantage of the known biomarkers in lung cancer. These therapeutic genes are key regulatory molecules of crucial cellular pathways involved in cell proliferation, migration, and apoptosis. Thereby, the characteristics and functionalization of the nanocarrier and the knowledge of lung cancer biology have direct influence in improving the therapeutic effect of this therapy.
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Affiliation(s)
- Mariana Magalhães
- a Department of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal.,b REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal
| | - Carmen Alvarez-Lorenzo
- c Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, R+D Pharma Group (GI-1645), Facultad de Farmacia and Health Research Institute of Santiago de Compostela (IDIS) , Universidade de Santiago de Compostela , Santiago de Compostela , Spain
| | - Angel Concheiro
- c Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, R+D Pharma Group (GI-1645), Facultad de Farmacia and Health Research Institute of Santiago de Compostela (IDIS) , Universidade de Santiago de Compostela , Santiago de Compostela , Spain
| | - Ana Figueiras
- a Department of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal.,b REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal
| | - Ana Cláudia Santos
- a Department of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal.,b REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal
| | - Francisco Veiga
- a Department of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal.,b REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal
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