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He J, Huo X, Pei G, Jia Z, Yan Y, Yu J, Qu H, Xie Y, Yuan J, Zheng Y, Hu Y, Shi M, You K, Li T, Ma T, Zhang MQ, Ding S, Li P, Li Y. Dual-role transcription factors stabilize intermediate expression levels. Cell 2024; 187:2746-2766.e25. [PMID: 38631355 DOI: 10.1016/j.cell.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Precise control of gene expression levels is essential for normal cell functions, yet how they are defined and tightly maintained, particularly at intermediate levels, remains elusive. Here, using a series of newly developed sequencing, imaging, and functional assays, we uncover a class of transcription factors with dual roles as activators and repressors, referred to as condensate-forming level-regulating dual-action transcription factors (TFs). They reduce high expression but increase low expression to achieve stable intermediate levels. Dual-action TFs directly exert activating and repressing functions via condensate-forming domains that compartmentalize core transcriptional unit selectively. Clinically relevant mutations in these domains, which are linked to a range of developmental disorders, impair condensate selectivity and dual-action TF activity. These results collectively address a fundamental question in expression regulation and demonstrate the potential of level-regulating dual-action TFs as powerful effectors for engineering controlled expression levels.
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Affiliation(s)
- Jinnan He
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiangru Huo
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Zeran Jia
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yiming Yan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawei Yu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Haozhi Qu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yunxin Xie
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Junsong Yuan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yuan Zheng
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yanyan Hu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Minglei Shi
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kaiqiang You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tianhua Ma
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Michael Q Zhang
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China; Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas, TX 75080-3021, USA
| | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China.
| | - Yinqing Li
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
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2
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Wang X, Li X, Niu L, Lv F, Guo T, Gao Y, Ran Y, Huang W, Wang B. FAK-LINC01089 negative regulatory loop controls chemoresistance and progression of small cell lung cancer. Oncogene 2024; 43:1669-1687. [PMID: 38594505 DOI: 10.1038/s41388-024-03027-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
The focal adhesion kinase (FAK) tyrosine kinase is activated and upregulated in multiple cancer types including small cell lung cancer (SCLC). However, FAK inhibitors have shown limited efficacy in clinical trials for cancer treatment. With the aim of identifying potential therapeutic strategies to inhibit FAK for cancer treatment, we investigated long non-coding RNAs (lncRNAs) that potentially regulate FAK in SCLC. In this study, we identified a long non-coding RNA LINC01089 that binds and inhibits FAK phosphorylation (activation). Expression analysis revealed that LINC01089 was downregulated in SCLC tissues and negatively correlated with chemoresistance and survival in SCLC patients. Functionally, LINC01089 inhibited chemoresistance and progression of SCLC in vitro and in vivo. Mechanistically, LINC01089 inhibits FAK activation by blocking binding with Src and talin kinases, while FAK negatively regulates LINC01089 transcription by activating the ERK signaling pathway to recruit the REST transcription factor. Furthermore, LINC01089-FAK axis mediates the expression of drug resist-related genes by modulating YBX1 phosphorylation, leading to drug resistance in SCLC. Intriguingly, the FAK-LINC01089 interaction depends on the co-occurrence of the novel FAK variant and the non-conserved region of LINC01089 in primates. In Conclusion, our results indicated that LINC01089 may serve as a novel high-efficiency FAK inhibitor and the FAK-LINC01089 axis represents a valuable prognostic biomarker and potential therapeutic target in SCLC.
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Affiliation(s)
- Xianteng Wang
- Department of Urology, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical school, Shenzhen, 518060, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xingkai Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Liman Niu
- Chongqing Key Laboratory of Sichuan-Chongging Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fang Lv
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Guo
- Graduate School, Guangxi University of Chinese Medicine, Nanning, China
| | - Yushun Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuliang Ran
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Weiren Huang
- Department of Urology, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical school, Shenzhen, 518060, China.
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.
| | - Bing Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Jin L, Liu Y, Wu Y, Huang Y, Zhang D. REST Is Not Resting: REST/NRSF in Health and Disease. Biomolecules 2023; 13:1477. [PMID: 37892159 PMCID: PMC10605157 DOI: 10.3390/biom13101477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Chromatin modifications play a crucial role in the regulation of gene expression. The repressor element-1 (RE1) silencing transcription factor (REST), also known as neuron-restrictive silencer factor (NRSF) and X2 box repressor (XBR), was found to regulate gene transcription by binding to chromatin and recruiting chromatin-modifying enzymes. Earlier studies revealed that REST plays an important role in the development and disease of the nervous system, mainly by repressing the transcription of neuron-specific genes. Subsequently, REST was found to be critical in other tissues, such as the heart, pancreas, skin, eye, and vascular. Dysregulation of REST was also found in nervous and non-nervous system cancers. In parallel, multiple strategies to target REST have been developed. In this paper, we provide a comprehensive summary of the research progress made over the past 28 years since the discovery of REST, encompassing both physiological and pathological aspects. These insights into the effects and mechanisms of REST contribute to an in-depth understanding of the transcriptional regulatory mechanisms of genes and their roles in the development and progression of disease, with a view to discovering potential therapeutic targets and intervention strategies for various related diseases.
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Affiliation(s)
- Lili Jin
- School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Ying Liu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yifan Wu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yi Huang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Dianbao Zhang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
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Veverka P, Brom T, Janovič T, Stojaspal M, Pinkas M, Nováček J, Hofr C. Electron microscopy reveals toroidal shape of master neuronal cell differentiator REST - RE1-silencing transcription factor. Comput Struct Biotechnol J 2022; 21:731-741. [PMID: 36698979 PMCID: PMC9860152 DOI: 10.1016/j.csbj.2022.12.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The RE1-Silencing Transcription factor (REST) is essential for neuronal differentiation. Here, we report the first 18.5-angstrom electron microscopy structure of human REST. The refined electron map suggests that REST forms a torus that can accommodate DNA double-helix in the central hole. Additionally, we quantitatively described REST binding to the canonical DNA sequence of the neuron-restrictive silencer element. We developed protocols for the expression and purification of full-length REST and the shortened variant REST-N62 produced by alternative splicing. We tested the mutual interaction of full-length REST and the splicing variant REST-N62. Revealed structure-function relationships of master neuronal repressor REST will allow finding new biological ways of prevention and treatment of neurodegenerative disorders and diseases.
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Key Words
- CD, circular dichroism
- CoIP, coimmunoprecipitation
- DLS, dynamic light scattering
- Differentiation
- EM
- EM, electron microscopy
- Electron microscopy
- IDRs, intrinsically disordered regions
- NRSE, neuron-restrictive silencer element
- NRSF
- NRSF, neuron-restrictive silencer factor
- Neuron-restrictive silencer factor
- Neuronal
- PCNA, proliferating cell nuclear antigen
- RD1/2, repressor domain 1/2
- RE1, repressor element-1
- RE1-silencing transcription factor
- REST
- REST, RE1-silencing transcription factor
- REST-FL, full-length REST
- REST-N62
- REST-N62, splicing isoform of REST, also known as REST4 or REST4-S3
- REST4
- ZF, zinc finger
- aa, amino acid(s)
- bp, base pair(s)
- kDa, kilodaltons
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Affiliation(s)
- Pavel Veverka
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, Královopolská 135, Brno 612 65, Czech Republic
| | - Tomáš Brom
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Tomáš Janovič
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Martin Stojaspal
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, Královopolská 135, Brno 612 65, Czech Republic
| | | | - Jiří Nováček
- CEITEC, Masaryk University, Brno, Czech Republic
| | - Ctirad Hofr
- LifeB, FGP – NCBR, Faculty of Science, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Corresponding author.
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Zhu D, Johnson HJ, Chen J, Schaffer DV. Optogenetic Application to Investigating Cell Behavior and Neurological Disease. Front Cell Neurosci 2022; 16:811493. [PMID: 35273478 PMCID: PMC8902366 DOI: 10.3389/fncel.2022.811493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Cells reside in a dynamic microenvironment that presents them with regulatory signals that vary in time, space, and amplitude. The cell, in turn, interprets these signals and accordingly initiates downstream processes including cell proliferation, differentiation, migration, and self-organization. Conventional approaches to perturb and investigate signaling pathways (e.g., agonist/antagonist addition, overexpression, silencing, knockouts) are often binary perturbations that do not offer precise control over signaling levels, and/or provide limited spatial or temporal control. In contrast, optogenetics leverages light-sensitive proteins to control cellular signaling dynamics and target gene expression and, by virtue of precise hardware control over illumination, offers the capacity to interrogate how spatiotemporally varying signals modulate gene regulatory networks and cellular behaviors. Recent studies have employed various optogenetic systems in stem cell, embryonic, and somatic cell patterning studies, which have addressed fundamental questions of how cell-cell communication, subcellular protein localization, and signal integration affect cell fate. Other efforts have explored how alteration of signaling dynamics may contribute to neurological diseases and have in the process created physiologically relevant models that could inform new therapeutic strategies. In this review, we focus on emerging applications within the expanding field of optogenetics to study gene regulation, cell signaling, neurodevelopment, and neurological disorders, and we comment on current limitations and future directions for the growth of the field.
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Affiliation(s)
- Danqing Zhu
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, United States
| | - Hunter J. Johnson
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
- Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, United States
- Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Jun Chen
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, United States
| | - David V. Schaffer
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: David V. Schaffer
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Bansal A, Shikha S, Zhang Y. Towards translational optogenetics. Nat Biomed Eng 2022; 7:349-369. [PMID: 35027688 DOI: 10.1038/s41551-021-00829-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 10/21/2021] [Indexed: 02/07/2023]
Abstract
Optogenetics is widely used to interrogate the neural circuits underlying disease and has most recently been harnessed for therapeutic applications. The optogenetic toolkit consists of light-responsive proteins that modulate specific cellular functions, vectors for the delivery of the transgenes that encode the light-responsive proteins to targeted cellular populations, and devices for the delivery of light of suitable wavelengths at effective fluence rates. A refined toolkit with a focus towards translational uses would include efficient and safer viral and non-viral gene-delivery vectors, increasingly red-shifted photoresponsive proteins, nanomaterials that efficiently transduce near-infrared light deep into tissue, and wireless implantable light-delivery devices that allow for spatiotemporally precise interventions at clinically relevant tissue depths. In this Review, we examine the current optogenetics toolkit and the most notable preclinical and translational uses of optogenetics, and discuss future methodological and translational developments and bottlenecks.
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Affiliation(s)
- Akshaya Bansal
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore
| | - Swati Shikha
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore
| | - Yong Zhang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore. .,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore. .,NUS Suzhou Research Institute, Suzhou, Jiangsu, P. R. China.
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Prestigio C, Ferrante D, Marte A, Romei A, Lignani G, Onofri F, Valente P, Benfenati F, Baldelli P. REST/NRSF drives homeostatic plasticity of inhibitory synapses in a target-dependent fashion. eLife 2021; 10:e69058. [PMID: 34855580 PMCID: PMC8639147 DOI: 10.7554/elife.69058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/22/2021] [Indexed: 12/31/2022] Open
Abstract
The repressor-element 1-silencing transcription/neuron-restrictive silencer factor (REST/NRSF) controls hundreds of neuron-specific genes. We showed that REST/NRSF downregulates glutamatergic transmission in response to hyperactivity, thus contributing to neuronal homeostasis. However, whether GABAergic transmission is also implicated in the homeostatic action of REST/NRSF is unknown. Here, we show that hyperactivity-induced REST/NRSF activation, triggers a homeostatic rearrangement of GABAergic inhibition, with increased frequency of miniature inhibitory postsynaptic currents (IPSCs) and amplitude of evoked IPSCs in mouse cultured hippocampal neurons. Notably, this effect is limited to inhibitory-onto-excitatory neuron synapses, whose density increases at somatic level and decreases in dendritic regions, demonstrating a complex target- and area-selectivity. The upscaling of perisomatic inhibition was occluded by TrkB receptor inhibition and resulted from a coordinated and sequential activation of the Npas4 and Bdnf gene programs. On the opposite, the downscaling of dendritic inhibition was REST-dependent, but BDNF-independent. The findings highlight the central role of REST/NRSF in the complex transcriptional responses aimed at rescuing physiological levels of network activity in front of the ever-changing environment.
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Affiliation(s)
- Cosimo Prestigio
- Department of Experimental Medicine, University of GenovaGenovaItaly
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di TecnologiaGenovaItaly
| | - Daniele Ferrante
- Department of Experimental Medicine, University of GenovaGenovaItaly
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di TecnologiaGenovaItaly
| | - Antonella Marte
- Department of Experimental Medicine, University of GenovaGenovaItaly
| | - Alessandra Romei
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di TecnologiaGenovaItaly
| | - Gabriele Lignani
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, Queen Square HouseLondonUnited Kingdom
| | - Franco Onofri
- Department of Experimental Medicine, University of GenovaGenovaItaly
- IRCCS, Ospedale Policlinico San MartinoGenovaItaly
| | - Pierluigi Valente
- Department of Experimental Medicine, University of GenovaGenovaItaly
- IRCCS, Ospedale Policlinico San MartinoGenovaItaly
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di TecnologiaGenovaItaly
- IRCCS, Ospedale Policlinico San MartinoGenovaItaly
| | - Pietro Baldelli
- Department of Experimental Medicine, University of GenovaGenovaItaly
- IRCCS, Ospedale Policlinico San MartinoGenovaItaly
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Manoilov KY, Verkhusha VV, Shcherbakova DM. A guide to the optogenetic regulation of endogenous molecules. Nat Methods 2021; 18:1027-1037. [PMID: 34446923 DOI: 10.1038/s41592-021-01240-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 07/09/2021] [Indexed: 12/26/2022]
Abstract
Genetically encoded tools for the regulation of endogenous molecules (RNA, DNA elements and protein) are needed to study and control biological processes with minimal interference caused by protein overexpression and overactivation of signaling pathways. Here we focus on light-controlled optogenetic tools (OTs) that allow spatiotemporally precise regulation of gene expression and protein function. To control endogenous molecules, OTs combine light-sensing modules from natural photoreceptors with specific protein or nucleic acid binders. We discuss OT designs and group OTs according to the principles of their regulation. We outline characteristics of OT performance, discuss considerations for their use in vivo and review available OTs and their applications in cells and in vivo. Finally, we provide a brief outlook on the development of OTs.
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Affiliation(s)
- Kyrylo Yu Manoilov
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA. .,Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Science Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia.
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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9
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Kaberniuk AA, Baloban M, Monakhov MV, Shcherbakova DM, Verkhusha VV. Single-component near-infrared optogenetic systems for gene transcription regulation. Nat Commun 2021; 12:3859. [PMID: 34162879 PMCID: PMC8222386 DOI: 10.1038/s41467-021-24212-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 06/03/2021] [Indexed: 11/09/2022] Open
Abstract
Near-infrared (NIR) optogenetic systems for transcription regulation are in high demand because NIR light exhibits low phototoxicity, low scattering, and allows combining with probes of visible range. However, available NIR optogenetic systems consist of several protein components of large size and multidomain structure. Here, we engineer single-component NIR systems consisting of evolved photosensory core module of Idiomarina sp. bacterial phytochrome, named iLight, which are smaller and packable in adeno-associated virus. We characterize iLight in vitro and in gene transcription repression in bacterial and gene transcription activation in mammalian cells. Bacterial iLight system shows 115-fold repression of protein production. Comparing to multi-component NIR systems, mammalian iLight system exhibits higher activation of 65-fold in cells and faster 6-fold activation in deep tissues of mice. Neurons transduced with viral-encoded iLight system exhibit 50-fold induction of fluorescent reporter. NIR light-induced neuronal expression of green-light-activatable CheRiff channelrhodopsin causes 20-fold increase of photocurrent and demonstrates efficient spectral multiplexing. Current near-IR optogenetic systems to regulate transcription consist of a number of large protein components. Here the authors report a smaller single-component near-IR system, iLight, developed from a bacterial phytochrome that they use to control gene transcription in bacterial and mammalian cells.
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Affiliation(s)
- Andrii A Kaberniuk
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Mikhail Baloban
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Mikhail V Monakhov
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA. .,Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Science Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia.
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10
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Xu C, Zhang M, Zu L, Zhang P, Sun L, Liu X, Fang M. Repressor element-1 silencing transcription factor regulates glutamate receptors and immediate early genes to affect synaptic plasticity. Aging (Albany NY) 2021; 13:15569-15579. [PMID: 34106879 PMCID: PMC8221361 DOI: 10.18632/aging.203118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVE This study aimed to investigate the regulatory effects of repressor element-1 silencing transcription factor (REST) on the glutamate receptors and immediate early genes (IEGs) in the SH-SY5Y cells. METHODS The genes regulated by REST were screened by bioinformatics between AD patients and the control group. Then, SH-SY5Y cells were treated with 10 μM Aβ or REST siRNA/cDNA, and the expressions of synaptic genes and IEGs were detected. Moreover, the protein expression of synaptophysin and PSD-95 was detected by Western blotting in the primary mouse hippocampal neurons. RESULTS Firstly, 464 differentially expressed genes regulated by REST were identified between Alzheimer's disease (AD) patients and controls, and REST was closely related to the glutamatergic synapses and long-term potentiation. GRIA1, GRIN2A, GRIN1, and ARC showed significant variations with the changes of REST. Moreover, the loss of REST reduced the expression of synaptophysin and PSD-95, which was related to synaptic plasticity. CONCLUSION REST maintains synaptic plasticity by affecting both glutamate receptors and IEGs, and the imbalance between neural excitation and inhibition mediated by REST compromises neural function, contributing to cognitive impairment.
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Affiliation(s)
- Chenhaoyi Xu
- Department of Neurology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Min Zhang
- Department of Neurology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Lu Zu
- Department of Neurology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Pei Zhang
- Department of Neurology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Letao Sun
- Gordon F. Derner School of Psychology, Adelphi University, New York, NY 11530-0701, USA
| | - Xueyuan Liu
- Department of Neurology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Min Fang
- Department of Neurology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
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11
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New epigenetic players in stroke pathogenesis: From non-coding RNAs to exosomal non-coding RNAs. Biomed Pharmacother 2021; 140:111753. [PMID: 34044272 PMCID: PMC8222190 DOI: 10.1016/j.biopha.2021.111753] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/22/2021] [Accepted: 05/19/2021] [Indexed: 12/17/2022] Open
Abstract
Non-coding RNAs (ncRNAs) have critical role in the pathophysiology as well as recovery after ischemic stroke. ncRNAs, particularly microRNAs, and the long non-coding RNAs (lncRNAs) are critical for angiogenesis and neuroprotection, and they have been suggested to be therapeutic, diagnostic and prognostic tools in cerebrovascular diseases, including stroke. Moreover, exosomes have been considered as nanocarriers capable of transferring various cargos, such as lncRNAs and miRNAs to recipient cells, with prominent inter-cellular roles in the mediation of neuro-restorative events following strokes and neural injuries. In this review, we summarize the pathogenic role of ncRNAs and exosomal ncRNAs in the stroke.
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12
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Forlani G, Di Ventura B. A light way for nuclear cell biologists. J Biochem 2021; 169:273-286. [PMID: 33245128 PMCID: PMC8053400 DOI: 10.1093/jb/mvaa139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
The nucleus is a very complex organelle present in eukaryotic cells. Having the crucial task to safeguard, organize and manage the genetic information, it must tightly control its molecular constituents, its shape and its internal architecture at any given time. Despite our vast knowledge of nuclear cell biology, much is yet to be unravelled. For instance, only recently we came to appreciate the existence of a dynamic nuclear cytoskeleton made of actin filaments that regulates processes such as gene expression, DNA repair and nuclear expansion. This suggests further exciting discoveries ahead of us. Modern cell biologists embrace a new methodology relying on precise perturbations of cellular processes that require a reversible, highly spatially confinable, rapid, inexpensive and tunEable external stimulus: light. In this review, we discuss how optogenetics, the state-of-the-art technology that uses genetically encoded light-sensitive proteins to steer biological processes, can be adopted to specifically investigate nuclear cell biology.
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Affiliation(s)
- Giada Forlani
- Spemann Graduate School of Biology and Medicine (SGBM)
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
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13
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Giving names to the actors of synaptic transmission: The long journey from synaptic vesicles to neural plasticity. ADVANCES IN PHARMACOLOGY 2021; 90:19-37. [PMID: 33706933 DOI: 10.1016/bs.apha.2020.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
More than a scientific paper or a review article, this is a remembrance of a unique time of science and life that the authors spent in Paul Greengard's laboratory at the Rockefeller University in New York in the 1980s and 1990s, forming the so-called synaptic vesicle group. It was a time in which the molecular mechanisms of synaptic transmission and the nature of the organelles in charge of storing and releasing neurotransmitter were just beginning to be understood. It was an exciting time in which the protein composition of synaptic vesicles started to be identified. It turned out that the interactions of synaptic vesicle proteins with the cytoskeleton and the presynaptic membrane and their modulation by protein phosphorylation represented an essential network regulating the efficiency of neurotransmitter release and thereby synaptic strength and plasticity. This is also a description of the distinct scientific journeys that the three authors took on going back to Europe and how they were strongly influenced by the generous and outstanding mentorship of Paul Greengard, his genuine interest in their lives and careers and the life-long friendship with him.
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14
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Abstract
Allosteric regulation in proteins is fundamental to many important biological processes. Allostery has been employed to control protein functions by regulating protein activity. Engineered allosteric regulation allows controlling protein activity in subsecond time scale and has a broad range of applications, from dissecting spatiotemporal dynamics in biochemical cascades to applications in biotechnology and medicine. Here, we review the concept of allostery in proteins and various approaches to identify allosteric sites and pathways. We then provide an overview of strategies and tools used in allosteric protein regulation and their utility in biological applications. We highlight various classes of proteins, where regulation is achieved through allostery. Finally, we analyze the current problems, critical challenges, and future prospective in achieving allosteric regulation in proteins.
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Affiliation(s)
| | - Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
- Departments of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
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15
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Photoreaction Mechanisms of Flavoprotein Photoreceptors and Their Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:189-206. [PMID: 33398814 DOI: 10.1007/978-981-15-8763-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Three classes of flavoprotein photoreceptors, cryptochromes (CRYs), light-oxygen-voltage (LOV)-domain proteins, and blue light using FAD (BLUF)-domain proteins, have been identified that control various physiological processes in multiple organisms. Accordingly, signaling activities of photoreceptors have been intensively studied and the related mechanisms have been exploited in numerous optogenetic tools. Herein, we summarize the current understanding of photoactivation mechanisms of the flavoprotein photoreceptors and review their applications.
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16
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Mathony J, Niopek D. Enlightening Allostery: Designing Switchable Proteins by Photoreceptor Fusion. Adv Biol (Weinh) 2020; 5:e2000181. [PMID: 33107225 DOI: 10.1002/adbi.202000181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/01/2020] [Indexed: 11/05/2022]
Abstract
Optogenetics harnesses natural photoreceptors to non-invasively control selected processes in cells with previously unmet spatiotemporal precision. Linking the activity of a protein of choice to the conformational state of a photosensor domain through allosteric coupling represents a powerful method for engineering light-responsive proteins. It enables the design of compact and highly potent single-component optogenetic systems with fast on- and off-switching kinetics. However, designing protein-photoreceptor chimeras, in which structural changes of the photoreceptor are effectively propagated to the fused effector protein, is a challenging engineering problem and often relies on trial and error. Here, recent advances in the design and application of optogenetic allosteric switches are reviewed. First, an overview of existing optogenetic tools based on inducible allostery is provided and their utility for cell biology applications is highlighted. Focusing on light-oxygen-voltage domains, a widely applied class of small blue light sensors, the available strategies for engineering light-dependent allostery are presented and their individual advantages and limitations are highlighted. Finally, high-throughput screening technologies based on comprehensive insertion libraries, which could accelerate the creation of stimulus-responsive receptor-protein chimeras for use in optogenetics and beyond, are discussed.
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Affiliation(s)
- Jan Mathony
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstrasse 12, Darmstadt, 64287, Germany.,BZH graduate school, Heidelberg University, Im Neuheimer Feld 328, Heidelberg, 69120, Germany
| | - Dominik Niopek
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstrasse 12, Darmstadt, 64287, Germany
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17
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A β-Induced Repressor Element 1-Silencing Transcription Factor (REST) Gene Delivery Suppresses Activation of Microglia-Like BV-2 Cells. Neural Plast 2020; 2020:8888871. [PMID: 33029126 PMCID: PMC7528025 DOI: 10.1155/2020/8888871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 12/28/2022] Open
Abstract
Compelling evidence from basic molecular biology has demonstrated the crucial role of microglia in the pathogenesis of Alzheimer's disease (AD). Microglia were believed to play a dual role in both promoting and inhibiting Alzheimer's disease progression. It is of great significance to regulate the function of microglia and make them develop in a favorable way. In the present study, we investigated the function of repressor element 1-silencing transcription factor (REST) in Aβ 1-42-induced BV-2 cell dysfunction. We concluded that Aβ 1-42 could promote type I activation of BV-2 cells and induce cell proliferation, migration, and proinflammation cytokine TNF-α, IL-1β, and IL-6 expression. Meanwhile, REST was upregulated, and nuclear translocalization took place due to Aβ 1-42 stimulation. When REST was knocked down by a specific short hairpin RNA (sh-RNA), BV-2 cell proliferation, migration, and proinflammation cytokine expression and secretion induced by Aβ 1-42 were increased, demonstrating that REST may act as a repressor of microglia-like BV-2 cell activation.
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18
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Lv D, Wang G, Xiong LR, Sun JX, Chen Y, Guo CL, Yu Y, He HL, Cai R, Pan JS. Genome-Wide Identification and Characterization of Lectin Receptor-Like Kinase Gene Family in Cucumber and Expression Profiling Analysis under Different Treatments. Genes (Basel) 2020; 11:genes11091032. [PMID: 32887423 PMCID: PMC7564967 DOI: 10.3390/genes11091032] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber (Cucumis sativus L.). In this study, 46 putative LecRLK genes were identified in the cucumber genome, including 23 G-type and 22 L-type, and one C-type LecRLK gene. They were unequally distributed on all seven chromosomes, with a clustering tendency. Most of the genes in the cucumber LecRLK (CsLecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormones and stress on these genes’ promoters. Transcriptome data demonstrated distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real-time PCR (qRT-PCR) analysis. This study provides a better understanding of the character and function of the LecRLK gene family in cucumber and opens up the possibility to exploring the roles that LecRLKs might play in the life cycle of cucumber.
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19
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Criscuolo S, Gatti Iou M, Merolla A, Maragliano L, Cesca F, Benfenati F. Engineering REST-Specific Synthetic PUF Proteins to Control Neuronal Gene Expression: A Combined Experimental and Computational Study. ACS Synth Biol 2020; 9:2039-2054. [PMID: 32678979 DOI: 10.1021/acssynbio.0c00119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Regulation of gene transcription is an essential mechanism for differentiation and adaptation of organisms. A key actor in this regulation process is the repressor element 1 (RE1)-silencing transcription factor (REST), a transcriptional repressor that controls more than 2000 putative target genes, most of which are neuron-specific. With the purpose of modulating REST expression, we exploited synthetic, ad hoc designed, RNA binding proteins (RBPs) able to specifically target and dock to REST mRNA. Among the various families of RBPs, we focused on the Pumilio and FBF (PUF) proteins, present in all eukaryotic organisms and controlling a variety of cellular functions. Here, a combined experimental and computational approach was used to design and test 8- and 16-repeat PUF proteins specific for REST mRNA. We explored the conformational properties and atomic features of the PUF-RNA recognition code by Molecular Dynamics simulations. Biochemical assays revealed that the 8- and 16-repeat PUF-based variants specifically bind the endogenous REST mRNA without affecting its translational regulation. The data also indicate a key role of stacking residues in determining the binding specificity. The newly characterized REST-specific PUF-based constructs act as excellent RNA-binding modules and represent a versatile and functional platform to specifically target REST mRNA and modulate its endogenous expression.
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Affiliation(s)
- Stefania Criscuolo
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
| | - Mahad Gatti Iou
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
| | - Assunta Merolla
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
- University of Genova, Genova 16132, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
- IRCCS Ospedale Policlinico San Martino, Genova 16132, Italy
| | - Fabrizia Cesca
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova 16132, Italy
- IRCCS Ospedale Policlinico San Martino, Genova 16132, Italy
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20
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Abstract
Glioma is the most malignant primary brain cancer which frequently occurred in adults. In recent years, long-non coding RNAs (lncRNAs) have been demonstrated to play pivotal roles in human cancers. However, the role of most lncRNAs in gliomagenesis has not been probed. Presently, through TCGA, a novel lncRNA LINC01198 was found to be up-regulated and associated with clinical outcomes in glioblastoma multiforme (GBM). In our study, LINC01198 was proved to be up-regulated in glioma cell lines, and silenced LINC01198 curbed glioma cell proliferation and accelerated cell apoptosis. Importantly, we corroborated that LINC01198 activated the PI3 K/AKT pathway to aggravate glioma progression by targeting PIK3 CA and PTEN. Subsequently, LINC01198 was validated to localize in both cytoplasm and nucleus of glioma cells. Through mechanistic exploration, we illustrated that LINC01198 increased PIK3CA expression by sponging miR-129-5p in the cytoplasm. Furthermore, PTEN was transcriptionally repressed by REST/RCOR1/HDAC2 complex. More importantly, LINC01198 accelerated the assembly of REST/RCOR1/HDAC2 complex and recruited such complex to PTEN promoter so as to impair PTEN expression in glioma. Finally, we further verified that LINC01198 hindered glioma tumour growth in vivo through AKT-dependent manner. Jointly, LINC01198 activates PI3 K/AKT signalling to exert oncogenic function in gliomagenesis by regulating PIK3CA and PTEN, which highlights a new approach for glioma treatment.
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Affiliation(s)
- Yuan Xie
- Department of Neurosurgery, The Second Affiliated Hospital of Chongqing Medical University , Chongqing, China
| | - Yuan Cheng
- Department of Neurosurgery, The Second Affiliated Hospital of Chongqing Medical University , Chongqing, China
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21
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Carminati E, Buffolo F, Rocchi A, Michetti C, Cesca F, Benfenati F. Mild Inactivation of RE-1 Silencing Transcription Factor (REST) Reduces Susceptibility to Kainic Acid-Induced Seizures. Front Cell Neurosci 2020; 13:580. [PMID: 31998079 PMCID: PMC6965066 DOI: 10.3389/fncel.2019.00580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/18/2019] [Indexed: 11/13/2022] Open
Abstract
RE-1 Silencing Transcription factor (REST) controls several steps in neural development by modulating the expression of a wide range of neural genes. Alterations in REST expression have been associated with the onset of epilepsy; however, whether such alterations are deleterious or represent a protective homeostatic response remains elusive. To study the impact of REST modulation on seizure propensity, we developed a tool for its negative modulation in vivo. The tool is composed of the paired-amphipathic helix 1 (PAH1) domain, a competitive inhibitor of REST activation by mSin3, fused to the light-oxygen-voltage sensing 2 (LOV2) domain of Avena sativa phototropin 1, a molecular switch to alternatively hide or expose the PAH1 inhibitor. We employed the C450A and I539E light-independent AsLOV2 variants to mimic the closed (inactive) and open (active) states of LOV2-PAH1, respectively. Recombinant AAV1/2 viral particles (rAAVs) allowed LOV2-PAH1 expression in HEK293T cells and primary neurons, and efficiently transduced hippocampal neurons in vivo. mRNA expression analysis revealed an increased expression of several neuronal genes in the hippocampi of mice expressing the open probe. AAV-transduced mice received a single dose of kainic acid (KA), a treatment known to induce a transient increase of REST levels in the hippocampus. Remarkably, mice expressing the active variant displayed a reduced number of KA-induced seizures, which were less severe compared to mice carrying the inactive probe. These data support the validity of our tool to modulate REST activity in vivo and the potential impact of REST modulation on epileptogenesis.
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Affiliation(s)
- Emanuele Carminati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Federica Buffolo
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Anna Rocchi
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Caterina Michetti
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Fabrizia Cesca
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
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22
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Matarèse BFE, Feyen PLC, de Mello JC, Benfenati F. Sub-millisecond Control of Neuronal Firing by Organic Light-Emitting Diodes. Front Bioeng Biotechnol 2019; 7:278. [PMID: 31750295 PMCID: PMC6817475 DOI: 10.3389/fbioe.2019.00278] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
Optogenetics combines optics and genetics to enable minimally invasive cell-type-specific stimulation in living tissue. For the purposes of bio-implantation, there is a need to develop soft, flexible, transparent and highly biocompatible light sources. Organic semiconducting materials have key advantages over their inorganic counterparts, including low Young's moduli, high strain resistances, and wide color tunability. However, until now it has been unclear whether organic light emitting diodes (OLEDs) are capable of providing sufficient optical power for successful neuronal stimulation, while still remaining within a biologically acceptable temperature range. Here we investigate the use of blue polyfluorene- and orange poly(p-phenylenevinylene)-based OLEDs as stimuli for blue-light-activated Sustained Step Function Opsin (SFFO) and red-light-activated ChrimsonR opsin, respectively. We show that, when biased using high frequency (multi-kHz) drive schemes, the OLEDs permit safe and controlled photostimulation of opsin-expressing neurons and were able to control neuronal firing with high temporal-resolution at operating temperatures lower than previously demonstrated.
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Affiliation(s)
- Bruno F. E. Matarèse
- Department of Chemistry, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Paul L. C. Feyen
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genoa, Italy
- Section of Physiology, Department of Experimental Medicine, University of Genova, Genoa, Italy
| | - John C. de Mello
- Department of Chemistry, Imperial College London, South Kensington Campus, London, United Kingdom
- Centre for Organic Electronic Materials, Department of Chemistry, Trondheim, Norway
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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Alishahi M, Ghaedrahmati F, Kolagar TA, Winlow W, Nikkar N, Farzaneh M, Khoshnam SE. Long non-coding RNAs and cell death following ischemic stroke. Metab Brain Dis 2019; 34:1243-1251. [PMID: 31055786 DOI: 10.1007/s11011-019-00423-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/21/2019] [Indexed: 01/02/2023]
Abstract
Stroke is a major cause of morbidity and mortality worldwide, and extensive efforts have focused on the improvement of therapeutic strategies to reduce cell death following ischemic stroke. Uncovering the cellular and molecular pathophysiological processes in ischemic stroke have been a top priority. Long noncoding RNAs (lncRNAs) are endogenous molecules that play key roles in the pathophysiology of cerebral ischemia, and involved in the neuronal cell death during ischemic stroke. In recent years, a bulk of aberrantly expressed lncRNAs have been screened out in ischemic stroke insulted animals. LncRNAs along with their targets could affect the genetic machinery at molecular levels, and exploring their functions and mechanisms may be a promising option for ischemic stroke treatment. In this review, we summarize the current knowledge for lncRNAs in ischemic stroke, focusing on the role of specific lncRNAs that may underlie cell death to find possible therapeutic targets.
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Affiliation(s)
- Masoumeh Alishahi
- Department of Biology, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, Medical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - William Winlow
- Dipartimento di Biologia, Università degli Studi di Napoli, Federico II, Via Cintia 26, 80126, Naples, Italy
- Honorary Research Fellow, Institute of Ageing and Chronic Diseases, University of Liverpool, The APEX building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Negin Nikkar
- Department of Biology, Faculty of Sciences, Alzahra University, Tehran, Iran
| | - Maryam Farzaneh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seyed Esmaeil Khoshnam
- Physiology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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24
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Rossoni AW, Weber APM. Systems Biology of Cold Adaptation in the Polyextremophilic Red Alga Galdieria sulphuraria. Front Microbiol 2019; 10:927. [PMID: 31118926 PMCID: PMC6504705 DOI: 10.3389/fmicb.2019.00927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/12/2019] [Indexed: 12/30/2022] Open
Abstract
Rapid fluctuation of environmental conditions can impose severe stress upon living organisms. Surviving such episodes of stress requires a rapid acclimation response, e.g., by transcriptional and post-transcriptional mechanisms. Persistent change of the environmental context, however, requires longer-term adaptation at the genetic level. Fast-growing unicellular aquatic eukaryotes enable analysis of adaptive responses at the genetic level in a laboratory setting. In this study, we applied continuous cold stress (28°C) to the thermoacidophile red alga G. sulphuraria, which is 14°C below its optimal growth temperature of 42°C. Cold stress was applied for more than 100 generations to identify components that are critical for conferring thermal adaptation. After cold exposure for more than 100 generations, the cold-adapted samples grew ∼30% faster than the starting population. Whole-genome sequencing revealed 757 variants located on 429 genes (6.1% of the transcriptome) encoding molecular functions involved in cell cycle regulation, gene regulation, signaling, morphogenesis, microtubule nucleation, and transmembrane transport. CpG islands located in the intergenic region accumulated a significant number of variants, which is likely a sign of epigenetic remodeling. We present 20 candidate genes and three putative cis-regulatory elements with various functions most affected by temperature. Our work shows that natural selection toward temperature tolerance is a complex systems biology problem that involves gradual reprogramming of an intricate gene network and deeply nested regulators.
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Affiliation(s)
| | - Andreas P. M. Weber
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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25
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Mampay M, Sheridan GK. REST: An epigenetic regulator of neuronal stress responses in the young and ageing brain. Front Neuroendocrinol 2019; 53:100744. [PMID: 31004616 DOI: 10.1016/j.yfrne.2019.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/03/2019] [Accepted: 04/11/2019] [Indexed: 12/27/2022]
Abstract
The transcriptional repressor REST (Repressor Element-1 Silencing Transcription factor) is a key modulator of the neuronal epigenome and targets genes involved in neuronal differentiation, axonal growth, vesicular transport, ion channel conductance and synaptic plasticity. Whilst its gene expression-modifying properties have been examined extensively in neuronal development, REST's response towards stress-induced neuronal insults has only recently been explored. Overall, REST appears to be an ideal candidate to fine-tune neuronal gene expression following different forms of cellular, neuropathological, psychological and physical stressors. Upregulation of REST is reportedly protective against premature neural stem cell depletion, neuronal hyperexcitability, oxidative stress, neuroendocrine system dysfunction and neuropathology. In contrast, neuronal REST activation has also been linked to neuronal dysfunction and neurodegeneration. Here, we highlight key findings and discrepancies surrounding our current understanding of REST's function in neuronal adaptation to stress and explore its potential role in neuronal stress resilience in the young and ageing brain.
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Affiliation(s)
- Myrthe Mampay
- Neuroimmunology & Neurotherapeutics Laboratory, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK
| | - Graham K Sheridan
- Neuroimmunology & Neurotherapeutics Laboratory, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK.
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26
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Isles AR. Epigenetics, chromatin and brain development and function. Brain Neurosci Adv 2018; 2:2398212818812011. [PMID: 32166158 PMCID: PMC7058192 DOI: 10.1177/2398212818812011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Indexed: 11/30/2022] Open
Abstract
Research investigating epigenetics and chromatin function in brain and behaviour has mushroomed over the last two decades. And yet epigenetics as a biological concept predates the discovery in the 1950s of DNA as the principle mode of inheritance by over a decade. This review explores the past, present and future research into epigenetics as it relates to understanding brain development and function
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Affiliation(s)
- Anthony R Isles
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
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27
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Abstract
In nature, a multitude of mechanisms have emerged for regulating biological processes and, specifically, protein activity. Light as a natural regulatory element is of outstanding interest for studying and modulating protein activity because it can be precisely applied with regard to a site of action, instant of time, or intensity. Naturally occurring photoresponsive proteins, predominantly those containing a light-oxygen-voltage (LOV) domain, have been characterized structurally and mechanistically and also conjugated to various proteins of interest. Immediate advantages of these new photoresponsive proteins such as genetic encoding, no requirement of chemical modification, and reversibility are paid for by difficulties in predicting the envisaged activity or type and site of domain fusion. In this article, we summarize recent advances and give a survey on currently available design concepts for engineering photoswitchable proteins.
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Affiliation(s)
- Swantje Seifert
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
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28
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Krishnamurthy VV, Zhang K. Chemical physics in living cells — Using light to visualize and control intracellular signal transduction. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1806152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Vishnu V. Krishnamurthy
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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29
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Hughes RM. A compendium of chemical and genetic approaches to light-regulated gene transcription. Crit Rev Biochem Mol Biol 2018; 53:453-474. [PMID: 30040498 DOI: 10.1080/10409238.2018.1487382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
On-cue regulation of gene transcription is an invaluable tool for the study of biological processes and the development and integration of next-generation therapeutics. Ideal reagents for the precise regulation of gene transcription should be nontoxic to the host system, highly tunable, and provide a high level of spatial and temporal control. Light, when coupled with protein or small molecule-linked photoresponsive elements, presents an attractive means of meeting the demands of an ideal system for regulating gene transcription. In this review, we cover recent developments in the burgeoning field of light-regulated gene transcription, covering both genetically encoded and small-molecule based strategies for optical regulation of transcription during the period 2012 till present.
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Affiliation(s)
- Robert M Hughes
- a Department of Chemistry , East Carolina University , Greenville , NC , USA
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30
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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31
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Ueda Y, Sato M. Induction of Signal Transduction by Using Non-Channelrhodopsin-Type Optogenetic Tools. Chembiochem 2018; 19:1217-1231. [PMID: 29577530 DOI: 10.1002/cbic.201700635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 12/24/2022]
Abstract
Signal transductions are the basis for all cellular functions. Previous studies investigating signal transductions mainly relied on pharmacological inhibition, RNA interference, and constitutive active/dominant negative protein expression systems. However, such studies do not allow the modulation of protein activity with high spatial and temporal precision in cells, tissues, and organs in animals. Recently, non-channelrhodopsin-type optogenetic tools for regulating signal transduction have emerged. These photoswitches address several disadvantages of previous techniques, and allow us to control a variety of signal transductions such as cell membrane dynamics, calcium signaling, lipid signaling, and apoptosis. In this review we summarize recent advances in the development of such photoswitches and in how these optotools are applied to signaling processes.
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Affiliation(s)
- Yoshibumi Ueda
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
- AMED-PRIME (Japan), Agency for Medical Research and Development, Tokyo, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
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32
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Polesskaya O, Baranova A, Bui S, Kondratev N, Kananykhina E, Nazarenko O, Shapiro T, Nardia FB, Kornienko V, Chandhoke V, Stadler I, Lanzafame R, Myakishev-Rempel M. Optogenetic regulation of transcription. BMC Neurosci 2018; 19:12. [PMID: 29745855 PMCID: PMC5998900 DOI: 10.1186/s12868-018-0411-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Optogenetics has become widely recognized for its success in real-time control of brain neurons by utilizing non-mammalian photosensitive proteins to open or close membrane channels. Here we review a less well known type of optogenetic constructs that employs photosensitive proteins to transduce the signal to regulate gene transcription, and its possible use in medicine. One of the problems with existing gene therapies is that they could remain active indefinitely while not allowing regulated transgene production on demand. Optogenetic regulation of transcription (ORT) could potentially be used to regulate the production of a biological drug in situ, by repeatedly applying light to the tissue, and inducing expression of therapeutic transgenes when needed. Red and near infrared wavelengths, which are capable of penetration into tissues, have potential for therapeutic applications. Existing ORT systems are reviewed herein with these considerations in mind.
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Affiliation(s)
| | - Ancha Baranova
- Research Center for Medical Genetics RAMS, Moscow, Russia.,Center for the Study of Chronic Metabolic and Rare Diseases, School of Systems Biology, George Mason University, Fairfax, VA, USA.,Atlas Biomed Group, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sarah Bui
- Center for the Study of Chronic Metabolic and Rare Diseases, School of Systems Biology, George Mason University, Fairfax, VA, USA
| | | | | | | | | | | | | | - Vikas Chandhoke
- Center for the Study of Chronic Metabolic and Rare Diseases, School of Systems Biology, George Mason University, Fairfax, VA, USA
| | | | | | - Max Myakishev-Rempel
- Localized Therapeutics, LLC, San Diego, CA, USA. .,Vaccine Research Institute of San Diego, San Diego, CA, USA.
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33
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Bao MH, Szeto V, Yang BB, Zhu SZ, Sun HS, Feng ZP. Long non-coding RNAs in ischemic stroke. Cell Death Dis 2018; 9:281. [PMID: 29449542 PMCID: PMC5833768 DOI: 10.1038/s41419-018-0282-x] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 12/31/2022]
Abstract
Stroke is one of the leading causes of mortality and disability worldwide. Uncovering the cellular and molecular pathophysiological processes in stroke have been a top priority. Long non-coding (lnc) RNAs play critical roles in different kinds of diseases. In recent years, a bulk of aberrantly expressed lncRNAs have been screened out in ischemic stroke patients or ischemia insulted animals using new technologies such as RNA-seq, deep sequencing, and microarrays. Nine specific lncRNAs, antisense non-coding RNA in the INK4 locus (ANRIL), metastasis-associate lung adenocarcinoma transcript 1 (MALAT1), N1LR, maternally expressed gene 3 (MEG3), H19, CaMK2D-associated transcript 1 (C2dat1), Fos downstream transcript (FosDT), small nucleolar RNA host gene 14 (SNHG14), and taurine-upregulated gene 1 (TUG1), were found increased in cerebral ischemic animals and/or oxygen-glucose deprived (OGD) cells. These lncRNAs were suggested to promote cell apoptosis, angiogenesis, inflammation, and cell death. Our Gene Ontology (GO) enrichment analysis predicted that MEG3, H19, and MALAT1 might also be related to functions such as neurogenesis, angiogenesis, and inflammation through mechanisms of gene regulation (DNA transcription, RNA folding, methylation, and gene imprinting). This knowledge may provide a better understanding of the functions and mechanisms of lncRNAs in ischemic stroke. Further elucidating the functions and mechanisms of these lncRNAs in biological systems under normal and pathological conditions may lead to opportunities for identifying biomarkers and novel therapeutic targets of ischemic stroke.
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Affiliation(s)
- Mei-Hua Bao
- Department of Anatomy, Histology and Embryology, Institute of Neuroscience, Changsha Medical University, Changsha, 410219, China
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Vivian Szeto
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Burton B Yang
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathology, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Shu-Zhen Zhu
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Hong-Shuo Sun
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Zhong-Ping Feng
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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34
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Kolar K, Weber W. Synthetic biological approaches to optogenetically control cell signaling. Curr Opin Biotechnol 2017; 47:112-119. [DOI: 10.1016/j.copbio.2017.06.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/21/2017] [Indexed: 11/16/2022]
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35
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Strategies for the photo-control of endogenous protein activity. Curr Opin Struct Biol 2017; 45:53-58. [DOI: 10.1016/j.sbi.2016.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/13/2016] [Indexed: 11/21/2022]
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36
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Kamarulzaman NS, Dewadas HD, Leow CY, Yaacob NS, Mokhtar NF. The role of REST and HDAC2 in epigenetic dysregulation of Nav1.5 and nNav1.5 expression in breast cancer. Cancer Cell Int 2017; 17:74. [PMID: 28785170 PMCID: PMC5540501 DOI: 10.1186/s12935-017-0442-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 07/14/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Increased expression of voltage-gated sodium channels (VGSCs) have been implicated with strong metastatic potential of human breast cancer in vitro and in vivo where the main culprits are cardiac isoform Nav1.5 and its 'neonatal' splice variant, nNav1.5. Several factors have been associated with Nav1.5 and nNav1.5 gain of expression in breast cancer mainly hormones, and growth factors. AIM This study aimed to investigate the role of epigenetics via transcription repressor, repressor element silencing transcription factor (REST) and histone deacetylases (HDACs) in enhancing Nav1.5 and nNav1.5 expression in human breast cancer by assessing the effect of HDAC inhibitor, trichostatin A (TSA). METHODS The less aggressive human breast cancer cell line, MCF-7 cells which lack Nav1.5 and nNav1.5 expression was treated with TSA at a concentration range 10-10,000 ng/ml for 24 h whilst the aggressive MDA-MB-231 cells was used as control. The effect of TSA on Nav1.5, nNav1.5, REST, HDAC1, HDAC2, HDAC3, MMP2 and N-cadherin gene expression level was analysed by real-time PCR. Cell growth (MTT assay) and metastatic behaviors (lateral motility and migration assays) were also measured. RESULTS mRNA expression level of Nav1.5 and nNav1.5 were initially very low in MCF-7 compared to MDA-MB-231 cells. Inversely, mRNA expression level of REST, HDAC1, HDAC2, and HDAC3 were all greater in MCF-7 compared to MDA-MB-231 cells. Treatment with TSA significantly increased the mRNA expression level of Nav1.5 and nNav1.5 in MCF-7 cells. On the contrary, TSA significantly reduced the mRNA expression level of REST and HDAC2 in this cell line. Remarkably, despite cell growth inhibition by TSA, motility and migration of MCF-7 cells were enhanced after TSA treatment, confirmed with the up-regulation of metastatic markers, MMP2 and N-cadherin. CONCLUSIONS This study identified epigenetics as another factor that regulate the expression level of Nav1.5 and nNav1.5 in breast cancer where REST and HDAC2 play important role as epigenetic regulators that when lacking enhances the expression of Nav1.5 and nNav1.5 thus promotes motility and migration of breast cancer. Elucidation of the regulatory mechanisms for gain of Nav1.5 and nNav1.5 expression may be helpful for seeking effective strategies for the management of metastatic diseases.
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Affiliation(s)
- Nur Sabrina Kamarulzaman
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan Malaysia
| | - Hemaniswarri Dewi Dewadas
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan Malaysia
| | - Chiuan Yee Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan Malaysia
| | - Nik Soriani Yaacob
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan Malaysia
| | - Noor Fatmawati Mokhtar
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan Malaysia
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37
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Liu Q, Tucker CL. Engineering genetically-encoded tools for optogenetic control of protein activity. Curr Opin Chem Biol 2017; 40:17-23. [PMID: 28527343 DOI: 10.1016/j.cbpa.2017.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/01/2017] [Accepted: 05/02/2017] [Indexed: 12/22/2022]
Abstract
Optogenetic tools offer fast and reversible control of protein activity with subcellular spatial precision. In the past few years, remarkable progress has been made in engineering photoactivatable systems regulating the activity of cellular proteins. In this review, we discuss general strategies in designing and optimizing such optogenetic tools and highlight recent advances in the field, with specific focus on applications regulating protein catalytic activity.
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Affiliation(s)
- Qi Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Chandra L Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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38
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Eleftheriou C, Cesca F, Maragliano L, Benfenati F, Maya-Vetencourt JF. Optogenetic Modulation of Intracellular Signalling and Transcription: Focus on Neuronal Plasticity. J Exp Neurosci 2017; 11:1179069517703354. [PMID: 28579827 PMCID: PMC5415353 DOI: 10.1177/1179069517703354] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/02/2017] [Indexed: 12/17/2022] Open
Abstract
Several fields in neuroscience have been revolutionized by the advent of optogenetics, a technique that offers the possibility to modulate neuronal physiology in response to light stimulation. This innovative and far-reaching tool provided unprecedented spatial and temporal resolution to explore the activity of neural circuits underlying cognition and behaviour. With an exponential growth in the discovery and synthesis of new photosensitive actuators capable of modulating neuronal networks function, other fields in biology are experiencing a similar re-evolution. Here, we review the various optogenetic toolboxes developed to influence cellular physiology as well as the diverse ways in which these can be engineered to precisely modulate intracellular signalling and transcription. We also explore the processes required to successfully express and stimulate these photo-actuators in vivo before discussing how such tools can enlighten our understanding of neuronal plasticity at the systems level.
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Affiliation(s)
- Cyril Eleftheriou
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Fabrizia Cesca
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Experimental Medicine, University of Genova, Genova, Italy
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39
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Selecting optimal combinations of transcription factors to promote axon regeneration: Why mechanisms matter. Neurosci Lett 2016; 652:64-73. [PMID: 28025113 DOI: 10.1016/j.neulet.2016.12.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 12/02/2016] [Accepted: 12/14/2016] [Indexed: 01/17/2023]
Abstract
Recovery from injuries to the central nervous system, including spinal cord injury, is constrained in part by the intrinsically low ability of many CNS neurons to mount an effective regenerative growth response. To improve outcomes, it is essential to understand and ultimately reverse these neuron-intrinsic constraints. Genetic manipulation of key transcription factors (TFs), which act to orchestrate production of multiple regeneration-associated genes, has emerged as a promising strategy. It is likely that no single TF will be sufficient to fully restore neuron-intrinsic growth potential, and that multiple, functionally interacting factors will be needed. An extensive literature, mostly from non-neural cell types, has identified potential mechanisms by which TFs can functionally synergize. Here we examine four potential mechanisms of TF/TF interaction; physical interaction, transcriptional cross-regulation, signaling-based cross regulation, and co-occupancy of regulatory DNA. For each mechanism, we consider how existing knowledge can be used to guide the discovery and effective use of TF combinations in the context of regenerative neuroscience. This mechanistic insight into TF interactions is needed to accelerate the design of effective TF-based interventions to relieve neuron-intrinsic constraints to regeneration and to foster recovery from CNS injury.
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40
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Delahaye-Duriez A, Srivastava P, Shkura K, Langley SR, Laaniste L, Moreno-Moral A, Danis B, Mazzuferi M, Foerch P, Gazina EV, Richards K, Petrou S, Kaminski RM, Petretto E, Johnson MR. Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery. Genome Biol 2016; 17:245. [PMID: 27955713 PMCID: PMC5154105 DOI: 10.1186/s13059-016-1097-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/02/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The relationship between monogenic and polygenic forms of epilepsy is poorly understood and the extent to which the genetic and acquired epilepsies share common pathways is unclear. Here, we use an integrated systems-level analysis of brain gene expression data to identify molecular networks disrupted in epilepsy. RESULTS We identified a co-expression network of 320 genes (M30), which is significantly enriched for non-synonymous de novo mutations ascertained from patients with monogenic epilepsy and for common variants associated with polygenic epilepsy. The genes in the M30 network are expressed widely in the human brain under tight developmental control and encode physically interacting proteins involved in synaptic processes. The most highly connected proteins within the M30 network were preferentially disrupted by deleterious de novo mutations for monogenic epilepsy, in line with the centrality-lethality hypothesis. Analysis of M30 expression revealed consistent downregulation in the epileptic brain in heterogeneous forms of epilepsy including human temporal lobe epilepsy, a mouse model of acquired temporal lobe epilepsy, and a mouse model of monogenic Dravet (SCN1A) disease. These results suggest functional disruption of M30 via gene mutation or altered expression as a convergent mechanism regulating susceptibility to epilepsy broadly. Using the large collection of drug-induced gene expression data from Connectivity Map, several drugs were predicted to preferentially restore the downregulation of M30 in epilepsy toward health, most notably valproic acid, whose effect on M30 expression was replicated in neurons. CONCLUSIONS Taken together, our results suggest targeting the expression of M30 as a potential new therapeutic strategy in epilepsy.
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Affiliation(s)
- Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.
- MRC Clinical Sciences Centre, Imperial College London, London, UK.
- Université Paris 13, Sorbonne Paris Cité, UFR de Santé, Médecine et Biologie Humaine, Paris, France.
- PROTECT, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
| | - Prashant Srivastava
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Sarah R Langley
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
- Duke-NUS Medical School, 8 College Road, 169857, Singapore, Republic of Singapore
| | - Liisi Laaniste
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Aida Moreno-Moral
- MRC Clinical Sciences Centre, Imperial College London, London, UK
- Duke-NUS Medical School, 8 College Road, 169857, Singapore, Republic of Singapore
| | - Bénédicte Danis
- Neuroscience TA, UCB Pharma, S.A, Allée de la Recherche, 60, 1070, Brussels, Belgium
| | - Manuela Mazzuferi
- Neuroscience TA, UCB Pharma, S.A, Allée de la Recherche, 60, 1070, Brussels, Belgium
| | - Patrik Foerch
- Neuroscience TA, UCB Pharma, S.A, Allée de la Recherche, 60, 1070, Brussels, Belgium
| | - Elena V Gazina
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Kay Richards
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Steven Petrou
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
- The Centre for Neural Engineering, The Department of Electrical Engineering, The University of Melbourne, Parkville, Victoria, 3052, Australia
- The Australian Research Council Centre of Excellence for Integrative Brain Function, Parkville, Victoria, 3052, Australia
| | - Rafal M Kaminski
- Neuroscience TA, UCB Pharma, S.A, Allée de la Recherche, 60, 1070, Brussels, Belgium
| | - Enrico Petretto
- MRC Clinical Sciences Centre, Imperial College London, London, UK.
- Duke-NUS Medical School, 8 College Road, 169857, Singapore, Republic of Singapore.
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.
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41
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Shining Light on the Sprout of Life: Optogenetics Applications in Stem Cell Research and Therapy. J Membr Biol 2016; 249:215-20. [DOI: 10.1007/s00232-016-9883-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/18/2016] [Indexed: 12/21/2022]
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