1
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Li J, Zhang D, Zhang Z, Meng S, Wang B, Li Z, Liu X, Zhang S. miR-2765 Modulates the Seasonal Polyphenism in Cacopsylla chinensis by Targeting a Novel Cold Rreceptor CcTRPC3. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:140-152. [PMID: 38118125 DOI: 10.1021/acs.jafc.3c05429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Polyphenism is a beneficial way in organisms to better cope with changing circumstances and is a hot topic in entomology, evolutionary biology, and ecology. Until now, this phenomenon has been proven to be season-, density-, and diet-dependent; however, there are very few reports on temperature regulation. Cacopsylla chinensis showed seasonal polyphenism, namely as summer- and winter-form, with obvious diversity in phenotypic characteristics in response to seasonal variation. Previous studies have found that low temperature in autumn is an extremely important element in inducing summer-form change to winter-form, but the underlying regulatory mechanism is still a mystery. Herein, we provided the initial evidence that the third instar of the summer-form is the critical period for developing to the winter-form, and 10 °C induces this transition by affecting the total pigment, chitin level, and thickness of the cuticle. Second, CcTPRC3 was proven to function as a novel cold receptor to control this seasonal polyphenism. Moreover, miR-2765 was found to mediate seasonal polyphenism by inhibiting CcTRPC3 expression. Last, we found that cuticle binding proteins CcCPR4 and CcCPR9 function as the downstream signals of CcTRPC3 to regulate the seasonal polyphenism in C. chinensis. In conclusion, our results displayed a novel signal pathway of miR-2765 and CcTRPC3 for the regulation of seasonal polyphenism in C. chinensis. These findings provide insights into the comprehensive analysis of insect polyphenism and are useful in developing potential strategies to block the phase transition for the pest control of C. chinensis.
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Affiliation(s)
- Jianying Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Dongyue Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Zhixian Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Shili Meng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Bo Wang
- Sanya Institute of China Agricultural University, 572025 Sanya City, Hainan Province, China
| | - Zhen Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Xiaoxia Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Songdou Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
- Sanya Institute of China Agricultural University, 572025 Sanya City, Hainan Province, China
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2
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Yu H, Wu Y, Zhang B, Xiong M, Yi Y, Zhang Q, Wu M. Exosomes Derived from E2F1 -/- Adipose-Derived Stem Cells Promote Skin Wound Healing via miR-130b-5p/TGFBR3 Axis. Int J Nanomedicine 2023; 18:6275-6292. [PMID: 37941530 PMCID: PMC10629453 DOI: 10.2147/ijn.s431725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/21/2023] [Indexed: 11/10/2023] Open
Abstract
Background Skin wound is a widespread health problem and brings extraordinary burdens to patients. Exosomes derived from adipose-derived stem cells (ADSC-Exos) are considered promising strategies for repairing skin wounds. E2F1 is a member of the E2F family of transcription factors involved in cell growth and apoptosis. E2F1 deficiency in mice enhances wound healing by improving collagen deposition and angiogenesis. Additionally, E2F1 can regulate the transcription and paracrine activity of multiple miRNAs, which will inevitably reshape the paracrine expression profile of ADSC-Exos. This study aimed to investigate the impact of transcription factor E2F1 deficiency on the functions of ADSC-Exos in promoting wound healing. Methods First, we obtained ADSCs from subcutaneous adipose tissues of WT and E2F1-/- C57BL/6 mice and separated their exosomes, denoted as ADSCWT-Exos and ADSCE2F1-/--Exos. The wound healing effects of ADSCWT-Exos and ADSCE2F1-/--Exos in full-thickness skin wound models were investigated by wound images, H&E staining, and immunohistochemical staining. For the in vitro study, the abilities of ADSCWT-Exos and ADSCE2F1-/--Exos to promote cell activities, collagen formation, and angiogenesis were evaluated. The potential mechanism by which ADSCE2F1-/--Exos promote wound healing was determined by miRNA sequencing, ChIP‒qPCR, and dual-luciferase assays. Results ADSCE2F1-/--Exos accelerated wound healing by promoting collagen formation and angiogenesis. As a result, compared with the lower wound healing rate of 30.5% within 7 days in the control group and 42.3% in the ADSCWT-Exo group, ADSCE2F1-/--Exos significantly increased the wound healing rate to 72.5%. In vitro, ADSCE2F1-/--Exos activated the function of fibroblasts and vascular endothelial cells. The loss of E2F1 promoted miR-130b-5p expression in ADSCE2F1-/--Exos through transcriptional regulation. MiRNA high-throughput sequencing identified 12 differently expressed miRNAs between ADSCE2F1-/- and ADSCWT. ADSCE2F1-/--Exos enhanced fibroblast activities via the miR-130b-5p/TGFBR3 axis and TGF-β activation. Conclusion Our results indicated that ADSCE2F1-/--Exos effectively promoted wound healing by regulating the miR-130b-5p/TGFBR3 axis, thus providing a novel strategy of gene-engineered stem cell exosomes for accelerating wound healing.
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Affiliation(s)
- Honghao Yu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Yiping Wu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Boyu Zhang
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Mingchen Xiong
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Yi Yi
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Qi Zhang
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Min Wu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
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3
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Pei B, Hu M, Wu X, Lu D, Zhang S, Zhang L, Wu S. Investigations into the effects of scaffold microstructure on slow-release system with bioactive factors for bone repair. Front Bioeng Biotechnol 2023; 11:1230682. [PMID: 37781533 PMCID: PMC10537235 DOI: 10.3389/fbioe.2023.1230682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023] Open
Abstract
In recent years, bone tissue engineering (BTE) has played an essential role in the repair of bone tissue defects. Although bioactive factors as one component of BTE have great potential to effectively promote cell differentiation and bone regeneration, they are usually not used alone due to their short effective half-lives, high concentrations, etc. The release rate of bioactive factors could be controlled by loading them into scaffolds, and the scaffold microstructure has been shown to significantly influence release rates of bioactive factors. Therefore, this review attempted to investigate how the scaffold microstructure affected the release rate of bioactive factors, in which the variables included pore size, pore shape and porosity. The loading nature and the releasing mechanism of bioactive factors were also summarized. The main conclusions were achieved as follows: i) The pore shapes in the scaffold may have had no apparent effect on the release of bioactive factors but significantly affected mechanical properties of the scaffolds; ii) The pore size of about 400 μm in the scaffold may be more conducive to controlling the release of bioactive factors to promote bone formation; iii) The porosity of scaffolds may be positively correlated with the release rate, and the porosity of 70%-80% may be better to control the release rate. This review indicates that a slow-release system with proper scaffold microstructure control could be a tremendous inspiration for developing new treatment strategies for bone disease. It is anticipated to eventually be developed into clinical applications to tackle treatment-related issues effectively.
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Affiliation(s)
- Baoqing Pei
- Beijing Key Laboratory for Design and Evaluation Technology of Advanced Implantable and Interventional Medical Devices, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Mengyuan Hu
- Beijing Key Laboratory for Design and Evaluation Technology of Advanced Implantable and Interventional Medical Devices, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Xueqing Wu
- Beijing Key Laboratory for Design and Evaluation Technology of Advanced Implantable and Interventional Medical Devices, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Da Lu
- Beijing Key Laboratory for Design and Evaluation Technology of Advanced Implantable and Interventional Medical Devices, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Shijia Zhang
- Beijing Key Laboratory for Design and Evaluation Technology of Advanced Implantable and Interventional Medical Devices, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Le Zhang
- Beijing Key Laboratory for Design and Evaluation Technology of Advanced Implantable and Interventional Medical Devices, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Shuqin Wu
- School of Big Data and Information, Shanxi College of Technology, Taiyuan, Shanxi, China
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4
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Sun H, Sun Y, Yu X, Gao X, Wang H, Zhang L, Shi Y, He X. Analysis of Age-Related Circular RNA Expression Profiles in Mesenchymal Stem Cells of Rat Bone Marrow. Front Genet 2021; 12:600632. [PMID: 34262589 PMCID: PMC8273880 DOI: 10.3389/fgene.2021.600632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 05/21/2021] [Indexed: 01/09/2023] Open
Abstract
As multicellular organisms age, they undergo a reduction in tissue and organ function. Researchers have put forward a theory that stem cell aging is the main factor responsible for decreased tissue and organ function. The adult stem cells guarantee the maintenance and repair of adult tissues and organs. Among adult stem cells, mesenchymal stem cells (MSCs) are emerging as hopeful candidates for cell-based therapy of numerous diseases. In recent years, high-throughput sequencing technologies have evolved to identify circular RNAs (circRNAs) associated with an increasing number of diseases, such as cancer and age-related diseases. It has been reported that circRNAs can compete with microRNAs (miRNAs) to affect the stability or translation of target RNAs and further regulate gene expression at the transcriptional level. However, the role of circRNAs expressed in MSCs in aging mechanisms has not yet been deciphered. The aim of this study was to explore and analyze the expression profiles of age-related circRNAs in MSCs. In this study, bone marrow MSCs were extracted from aged and young rats and analyzed using high-throughput sequencing and bioinformatics. The reliability of high-throughput RNA sequencing was verified by quantitative real-time polymerase chain reaction. The most important circRNA functions and pathways were further selected by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) analysis. Age-related circRNAs were found in the circrNA-miRNA-mRNA interaction network. The results of high-throughput sequencing showed that 4,229 circRNAs were involved in age-related senescence of MSCs. Compared with the young group, there were 29 differentially expressed circRNAs in the aged group, of which four were upregulated and 25 were downregulated. GO analysis covered three domains: biological process (BP), cellular component (CC), and molecular function (MF). The terms assigned to the BP domain were cellular metabolic processes and cellular macromolecule metabolic processes. The identified CC terms were intracellular and intracellular part, and the identified MF terms were binding and protein binding. The top five KEGG pathways were mitophagy-animal-Rattus norvegicus, prostate cancer-Rattus norvegicus, pathways in cancer-Rattus norvegicus, lysosome-Rattus norvegicus, and autophagy-animal-Rattus norvegicus. Altogether, circRNAs may play a major role in age-related MSC senescence. This study provides new mechanistic insights into MSC senescence, possibly leading to novel therapeutic strategies for age-related diseases.
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Affiliation(s)
- Hui Sun
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Yanan Sun
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xiao Yu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xingyu Gao
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Huan Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Lin Zhang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Yingai Shi
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xu He
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
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5
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Li C, Liau ES, Lee Y, Huang Y, Liu Z, Willems A, Garside V, McGlinn E, Chen J, Hong T. MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback. Mol Syst Biol 2021; 17:e9945. [PMID: 33890404 PMCID: PMC8062999 DOI: 10.15252/msb.20209945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 11/09/2022] Open
Abstract
Positive feedback driven by transcriptional regulation has long been considered a key mechanism underlying cell lineage segregation during embryogenesis. Using the developing spinal cord as a paradigm, we found that canonical, transcription-driven feedback cannot explain robust lineage segregation of motor neuron subtypes marked by two cardinal factors, Hoxa5 and Hoxc8. We propose a feedback mechanism involving elementary microRNA-mRNA reaction circuits that differ from known feedback loop-like structures. Strikingly, we show that a wide range of biologically plausible post-transcriptional regulatory parameters are sufficient to generate bistable switches, a hallmark of positive feedback. Through mathematical analysis, we explain intuitively the hidden source of this feedback. Using embryonic stem cell differentiation and mouse genetics, we corroborate that microRNA-mRNA circuits govern tissue boundaries and hysteresis upon motor neuron differentiation with respect to transient morphogen signals. Our findings reveal a previously underappreciated feedback mechanism that may have widespread functions in cell fate decisions and tissue patterning.
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Affiliation(s)
- Chung‐Jung Li
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia Sinica and Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Ee Shan Liau
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia Sinica and Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Yi‐Han Lee
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Yang‐Zhe Huang
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Ziyi Liu
- Genome Science and Technology ProgramThe University of TennesseeKnoxvilleTNUSA
| | - Andrew Willems
- Genome Science and Technology ProgramThe University of TennesseeKnoxvilleTNUSA
| | - Victoria Garside
- EMBL AustraliaAustralian Regenerative Medicine InstituteMonash UniversityClaytonVicAustralia
| | - Edwina McGlinn
- EMBL AustraliaAustralian Regenerative Medicine InstituteMonash UniversityClaytonVicAustralia
| | - Jun‐An Chen
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia Sinica and Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
- Neuroscience Program Academia SinicaTaipeiTaiwan
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular BiologyThe University of TennesseeKnoxvilleTNUSA
- National Institute for Mathematical and Biological SynthesisKnoxvilleTNUSA
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6
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Miele E, Po A, Mastronuzzi A, Carai A, Besharat ZM, Pediconi N, Abballe L, Catanzaro G, Sabato C, De Smaele E, Canettieri G, Di Marcotullio L, Vacca A, Mai A, Levrero M, Pfister SM, Kool M, Giangaspero F, Locatelli F, Ferretti E. Downregulation of miR-326 and its host gene β-arrestin1 induces pro-survival activity of E2F1 and promotes medulloblastoma growth. Mol Oncol 2020; 15:523-542. [PMID: 32920979 PMCID: PMC7858128 DOI: 10.1002/1878-0261.12800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/17/2020] [Accepted: 09/07/2020] [Indexed: 01/01/2023] Open
Abstract
Persistent mortality rates of medulloblastoma (MB) and severe side effects of the current therapies require the definition of the molecular mechanisms that contribute to tumor progression. Using cultured MB cancer stem cells and xenograft tumors generated in mice, we show that low expression of miR-326 and its host gene β-arrestin1 (ARRB1) promotes tumor growth enhancing the E2F1 pro-survival function. Our models revealed that miR-326 and ARRB1 are controlled by a bivalent domain, since the H3K27me3 repressive mark is found at their regulatory region together with the activation-associated H3K4me3 mark. High levels of EZH2, a feature of MB, are responsible for the presence of H3K27me3. Ectopic expression of miR-326 and ARRB1 provides hints into how their low levels regulate E2F1 activity. MiR-326 targets E2F1 mRNA, thereby reducing its protein levels; ARRB1, triggering E2F1 acetylation, reverses its function into pro-apoptotic activity. Similar to miR-326 and ARRB1 overexpression, we also show that EZH2 inhibition restores miR-326/ARRB1 expression, limiting E2F1 pro-proliferative activity. Our results reveal a new regulatory molecular axis critical for MB progression.
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Affiliation(s)
- Evelina Miele
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Agnese Po
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Angela Mastronuzzi
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Carai
- Neurosurgery Unit, Department of Neurological and Psychiatric Sciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Natalia Pediconi
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Luana Abballe
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | | | - Claudia Sabato
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Enrico De Smaele
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | | | | | - Alessandra Vacca
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Italy
| | - Massimo Levrero
- Cancer Research Center of Lyon (CRCL), UMR Inserm 1052 CNRS 5286 Mixte CLB, Université de Lyon 1 (UCBL1), France.,Department of Internal Medicine and Medical Specialties, Sapienza University, Rome, Italy
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University Hospital, Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ, Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Felice Giangaspero
- Department of Radiological, Oncological and Pathological Science, Sapienza University, Rome, Italy.,IRCCS Neuromed, Pozzilli, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Maternal Infantile and Urological Sciences, Sapienza University, Rome, Italy
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7
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Xu L, Hu H, Zheng LS, Wang MY, Mei Y, Peng LX, Qiang YY, Li CZ, Meng DF, Wang MD, Liu ZJ, Li XJ, Huang BJ, Qian CN. ETV4 is a theranostic target in clear cell renal cell carcinoma that promotes metastasis by activating the pro-metastatic gene FOSL1 in a PI3K-AKT dependent manner. Cancer Lett 2020; 482:74-89. [PMID: 32305558 DOI: 10.1016/j.canlet.2020.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/22/2020] [Accepted: 04/02/2020] [Indexed: 02/06/2023]
Abstract
Distant metastasis is the major cause of short survival in ccRCC patients. However, the development of effective therapies for metastatic ccRCC is limited. Herein, we reported that ETV4 was selected from among 150 relevant genes with in vivo evidence of promoting metastasis. In this study, we identified that ETV4 promoted ccRCC cell migration and metastasis in vitro and in vivo, and a positive correlation between ETV4 and FOSL1 expression was found in ccRCC tissues and cell lines. Further investigation suggested that ETV4 increase FOSL1 expression through direct binding with the FOSL1 promoter. Furthermore, ETV4/FOSL1 was proved as a novel upstream and downstream causal relationship in ccRCC in an AKT dependent manner. In addition, both ETV4 and FOSL1 serve as an independent, unfavorable ccRCC prognostic indicator, and the accumulation of the ETV4 and FOSL1 in ccRCC patients result in a worse survival outcome in ccRCC patients. Taken together, our results suggest that the ETV4/FOSL1 axis acts as a prognostic biomarker and ETV4 directly up-regulates FOSL1 by binding with its promoter in a PI3K-AKT dependent manner, leading to metastasis and disease progression of ccRCC.
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Affiliation(s)
- Liang Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, China; Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
| | - Hao Hu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China; Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, China
| | - Li-Sheng Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, China
| | - Meng-Yao Wang
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, Guangdong, China
| | - Yan Mei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, China
| | - Li-Xia Peng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, China
| | - Yuan-Yuan Qiang
- Ningxia Medical University, Ningxia Key Laboratory for Cerebrocranical Disease, Yinchuan, 750001, Ningxia, China
| | - Chang-Zhi Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, China
| | - Dong-Fang Meng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, China
| | - Ming-Dian Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, China
| | - Zhi-Jie Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, China
| | - Xin-Jian Li
- CAS Key Laboratory of Infection and Immunity, CAS Centre for Excellence in Bio-macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bi-Jun Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, China
| | - Chao-Nan Qian
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, China; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, China.
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8
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Mu F, Huang J, Xing T, Jing Y, Cui T, Guo Y, Yan X, Li H, Wang N. The Wnt/β-Catenin/LEF1 Pathway Promotes Cell Proliferation at Least in Part Through Direct Upregulation of miR-17-92 Cluster. Front Genet 2019; 10:525. [PMID: 31191623 PMCID: PMC6549003 DOI: 10.3389/fgene.2019.00525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022] Open
Abstract
The miR-17-92 cluster is involved in animal development and homeostasis, and its dysregulation leads to human diseases such as cancer. In the present study, we investigated the functional link between miR-17-92 cluster and Wnt/β-catenin signaling pathway in ICP2 and DF1 cells. We demonstrated that ectopic expression of either LEF1 or β-catenin increased the promoter activity of the miR-17-92 cluster host gene (MIR17HG) and combined ectopic expression of LEF1 and β-catenin further enhanced the promoter activity; while knockdown of either LEF1 or β-catenin reduced the MIR17HG promoter activity. Both LEF1 and β-catenin could directly bind to the MIR17HG promoter. Furthermore, we demonstrated that low doses of lithium chloride (LiCl), an activator of Wnt/β-catenin signaling pathway, increased MIR17HG promoter activity and the endogenous expression of the miR-17-92 cluster, while high doses of LiCl had the opposite effects. Treatment with XAV-939, an inactivator of the Wnt/β-catenin pathway, reduced the endogenous expression of miR-17-92 cluster. Finally, we found that low doses of LiCl promoted the proliferation of ICP2 and DF1 cells, while high doses of LiCl inhibited the proliferation of ICP2 and DF1 cells. Taken together, our results reveal that MIR17HG is a target of LEF1 and the Wnt/β-catenin pathway and suggest that the miR-17-92 cluster may, at least in part, mediate the proliferation-promoting effect of the Wnt/β-catenin pathway in cell proliferation.
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Affiliation(s)
- Fang Mu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jiaxin Huang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Tianyu Xing
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yang Jing
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Tingting Cui
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yaqi Guo
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xiaohong Yan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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9
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Lin HC, Ko CY, Lee KH, Chen IH, Kao TJ, Chang WC, Hsu TI, Lee YC. E2f1 regulates the induction of promyelocytic leukemia zinc finger transcription in neuronal differentiation of pluripotent P19 embryonal carcinoma cells. Biochem Biophys Res Commun 2019; 512:629-634. [PMID: 30914194 DOI: 10.1016/j.bbrc.2019.03.058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
Abstract
During brain development, the expression of promyelocytic leukemia zinc finger (Plzf) in neural stem cells is precisely controlled to maintain the balance between neural stem cell self-renewal and differentiation. However, the mechanism underlying transcriptional regulation of Plzf in neural stem cell is still unclear. Herein, using P19 embryonal carcinoma cells as a model, we observed that Plzf expression was induced in the P19-derived embryonic bodies, which enrich neural stem-like cell populations, as demonstrated by the expression of neural stem cell markers, Nestin and Sox2. We then characterized the Plzf promoter and identified two E2f1 binding sites (-755/-751 and -53/-49, the transcription start site was designated as +1) are important for the activation of Plzf promoter. Finally, we found that the induction of Plzf in the neural stem-like cells derived from pluripotent P19 cells is decrease by E2f1 knockdown. Taken together, we conclude that E2f1 is an important transcription factor that regulates Plzf transcription and may involve in maintaining the self-renewal ability of neural stem cells.
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Affiliation(s)
- Hsin-Chuan Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chiung-Yuan Ko
- PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Kuen-Haur Lee
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - I-Han Chen
- Department of Chinese Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Tzu-Jen Kao
- PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Wen-Chang Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tsung-I Hsu
- PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Research Center of Neuroscience, Taipei Medical University, Taipei, Taiwan.
| | - Yi-Chao Lee
- PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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10
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Lin D, Shi Y, Hu Y, Du X, Tu G. miR‑329‑3p regulates neural stem cell proliferation by targeting E2F1. Mol Med Rep 2019; 19:4137-4146. [PMID: 30942449 PMCID: PMC6472110 DOI: 10.3892/mmr.2019.10096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/19/2019] [Indexed: 12/23/2022] Open
Abstract
Neural stem cells (NSCs) are a class of self‑renewing and undifferentiated progenitor cells that retain the ability to differentiate to neurons, astrocytes and oligodendrocytes. MicroRNAs (miRNAs) are small noncoding RNAs that serve crucial roles in regulating a number of cellular processes, including cell proliferation, differentiation and apoptosis. Our previous GeneChip data indicated that the expression of miR‑329‑3p was increased in neurons compared with NSCs. However, whether miRNA‑329‑3p participates in regulating NSC function remains to be elucidated. In the present study, it was identified that the expression of miR‑329‑3p was upregulated in NSCs during neuronal differentiation, whereas expression of transcription factor E2F1 (E2F1), a putative target gene of miR‑329‑3p, was downregulated. Using luciferase reporter assays, it was confirmed that miR‑329‑3p regulated E2F1 expression. As differentiation has been demonstrated to limit the proliferative capacity of NSCs, the effects of miR‑329‑3p and E2F1 modulation on NSC proliferation were examined. Forced overexpression of miR‑329‑3p or RNA‑mediated silencing of E2F1 inhibited NSC proliferation, and overexpression of miR‑329‑3p also inhibited E2F1 expression. Notably, ectopic expression of E2F1 reversed the inhibition of NSC proliferation induced by miR‑329‑3p overexpression. These results indicated that miR‑329‑3p may serve crucial roles in regulating the proliferation of NSCs, at least in part via inhibition of E2F1 expression. These data improve the understanding of the microRNA‑mRNA regulatory network that controls NSC proliferation.
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Affiliation(s)
- Dapeng Lin
- Department of Orthopaedic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yao Shi
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yiwen Hu
- Department of Orthopedic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Xiaowen Du
- Department of Orthopaedic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Guanjun Tu
- Department of Orthopaedic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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11
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Navarro-Quiroz E, Pacheco-Lugo L, Navarro-Quiroz R, Lorenzi H, España-Puccini P, Díaz-Olmos Y, Almendrales L, Olave V, Gonzalez-Torres H, Diaz-Perez A, Dominguez A, Iglesias A, García R, Aroca-Martinez G. Profiling analysis of circulating microRNA in peripheral blood of patients with class IV lupus nephritis. PLoS One 2017; 12:e0187973. [PMID: 29136041 PMCID: PMC5685598 DOI: 10.1371/journal.pone.0187973] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/30/2017] [Indexed: 12/11/2022] Open
Abstract
Renal involvement in Systemic Lupus Erythematous (SLE) patients is one of the leading causes of morbidity and a significant contributor to mortality. It’s estimated that nearly 50% of SLE individuals develop kidney disease in the first year of the diagnosis. Class IV lupus nephritis (LN-IV) is the class of lupus nephritis most common in Colombian patients with SLE. Altered miRNAs expression levels have been reported in human autoimmune diseases including lupus. Variations in the expression pattern of peripheral blood circulating miRNAs specific for this class of lupus nephritis could be correlated with the pathophysiological status of this group of individuals. The aim of this study was to evaluate the relative abundance of circulating microRNAs in peripheral blood from Colombian patients with LN-IV. Circulating miRNAs in plasma of patients with diagnosis of LN-IV were compared with individuals without renal involvement (LNN group) and healthy individuals (CTL group). Total RNA was extracted from 10 ml of venous blood and subsequently sequenced using Illumina. The sequences were processed and these were analyzed using miRBase and Ensembl databases. Differential gene expression analysis was carried out with edgeR and functional analysis were done with DIANA-miRPath. Analysis was carried out using as variables of selection fold change (≥2 o ≤-2) and false discovery rate (0.05). We identified 24 circulating microRNAs with differential abundance between LN-IV and CTL groups, fourteen of these microRNAs are described for the first time to lupus nephritis (hsa-miR-589-3p, hsa-miR-1260b, hsa-miR-4511, hsa-miR-485-5p, hsa-miR-584-5p, hsa-miR-543, hsa-miR-153-3p, hsa-miR-6087, hsa-miR-3942-5p, hsa-miR-7977, hsa-miR-323b-3p, hsa-miR-4732-3p and hsa-miR-6741-3p). These changes in the abundance of miRNAs could be interpreted as alterations in the miRNAs-mRNA regulatory network in the pathogenesis of LN, preceding the clinical onset of the disease. The findings thus contribute to understanding the disease process and are likely to pave the way towards identifying disease biomarkers for early diagnosis of LN.
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Affiliation(s)
| | | | - Roberto Navarro-Quiroz
- Centro de Investigación en Salud para el Trópico, Universidad Cooperativa de Colombia, Santa Marta, Colombia
| | - Hernan Lorenzi
- Infectious Diseases Department, J. Craig Venter Institute, Rockville Maryland, United States of America
| | | | - Yirys Díaz-Olmos
- Grupo de Nefrología, Universidad Simón Bolívar, Barranquilla,Colombia
| | | | - Valeria Olave
- Grupo de Nefrología, Universidad Simón Bolívar, Barranquilla,Colombia
| | | | | | - Alex Dominguez
- Grupo de Nefrología, Universidad Simón Bolívar, Barranquilla,Colombia
| | - Antonio Iglesias
- Unidad de Reumatología, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Gustavo Aroca-Martinez
- Grupo de Nefrología, Universidad Simón Bolívar, Barranquilla,Colombia
- Clínica de la Costa, Barranquilla, Colombia
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12
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Zheng J, Yi D, Liu Y, Wang M, Zhu Y, Shi H. Long nonding RNA UCA1 regulates neural stem cell differentiation by controlling miR-1/Hes1 expression. Am J Transl Res 2017; 9:3696-3704. [PMID: 28861160 PMCID: PMC5575183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/21/2017] [Indexed: 06/07/2023]
Abstract
Neural stem cells are able to self-renew and generate glial and neuronal lineages. Neural stem cell may serve as therapeutic method for neurological disorders including spinal cord injuries, Parkinson's disease, Huntington's disease and Alzheimer's disease. Long noncoding RNAs (lncRNAs) are longer than 200 nucleotides with limited protein-coding capacity. Recent studies have demonstreated that lncRNAs play an important role in several cellular processes including cell differentiation, cell development, proliferation, apoptosis, invasion and migration. However, the role of lncRNA human urothelial carcinoma associated 1 (UCA1) in the development of neural stem cells remains unknown. In this study, we showed that the expression of UCA1 was upregulated in the neural stem cell in a time-dependent manner. Knockdown of UCA1 suppressed the neural stem cell proliferation. Inhibition of UCA1 decreased the expression of nestin and the formation of neurosphere. Moreover, knockdown of UCA1 suppressed the neural stem cell differentiation to astrocyte and promoted the neural stem cell differentiation to neuron. Furthermore, we demonstrated that knockdown of UCA1 increased the expression of miR-1 in the neural stem cell and suppressed the expresion of Hes1, which is one target gene of miR-1. In addition, ectopic expression of Hes1 could impair siUCA1-induced neural stem cells proliferation. Overexpression of Hes1 suppressed siUCA1-induced β-tubulin expression and promoted siUCA1-inhibited GFAP expression in the neural stem cell. These results suggested that UCA1 regulated the neural stem cell proliferation and differentiation through regulating Hes1 expression.
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Affiliation(s)
- Jiaolin Zheng
- Department of Neruology, The Second Hospital of Harbin Medical UniversityHarbin 150086, Heilong Jiang, China
| | - Dan Yi
- Department of Pharmacology, Rush University Medical CenterChicago IL 60612, USA
| | - Yu Liu
- Department of Neruology, The Second Hospital of Harbin Medical UniversityHarbin 150086, Heilong Jiang, China
| | - Mingqiu Wang
- Department of Neruology, The Second Hospital of Harbin Medical UniversityHarbin 150086, Heilong Jiang, China
| | - Yulan Zhu
- Department of Neruology, The Second Hospital of Harbin Medical UniversityHarbin 150086, Heilong Jiang, China
| | - Huaizhang Shi
- Department of Neurosurgery, The First Hospital of Harbin Medical UniversityHarbin 150001, Heilong Jiang, China
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13
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Li L, Shi B, Chen J, Li C, Wang S, Wang Z, Zhu G. An E2F1/MiR-17-92 Negative Feedback Loop mediates proliferation of Mouse Palatal Mesenchymal Cells. Sci Rep 2017; 7:5148. [PMID: 28698574 PMCID: PMC5506009 DOI: 10.1038/s41598-017-05479-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/30/2017] [Indexed: 02/05/2023] Open
Abstract
Normal cell cycle progression and proliferation of palatal mesenchymal cells are important for palatal development. As targets of miR-17-92, E2F transcription factors family has been suggested to induce the transcription of miR-17-92 in several cell types. In the present study, we sought to investigate whether this negative feedback loop exists in mouse PMCs and what the function of this negative feedback loop would be in palatal mesenchymal cells. Using GeneMANIA, we revealed that the most important function of experimentally verified targets of miR-17-92 is cell cycle regulation. E2F1 and E2F3, but not E2F2, were extensively expressed in mouse palate. Over-expression of E2F1 significantly increased the expression of all the members of miR-17-92. After increased by E2F1, miR-17 and miR-20a may negatively target E2F1, and thereby prevent the cells from excessive proliferation. We suggest that the negative feedback loop between E2F1 and miR-17-92 may contribute to palatal development by regulating the proliferation and cell cycle of palatal mesenchymal cells.
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Affiliation(s)
- Ling Li
- Department of stomatology, Sichuan Cancer Hospital, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China.,Department of Head and Neck Surgery, Sichuan Cancer Hospital, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases, Department of Cleft lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Sichuan, China
| | - Jin Chen
- Department of Head and Neck Surgery, Sichuan Cancer Hospital, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China
| | - Chunhua Li
- Department of Head and Neck Surgery, Sichuan Cancer Hospital, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China
| | - Shaoxin Wang
- Department of Head and Neck Surgery, Sichuan Cancer Hospital, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China
| | - Zhaohui Wang
- Department of Head and Neck Surgery, Sichuan Cancer Hospital, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China.
| | - Guiquan Zhu
- Department of stomatology, Sichuan Cancer Hospital, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China. .,Department of Head and Neck Surgery, Sichuan Cancer Hospital, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China.
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14
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Deng M, Zeng C, Lu X, He X, Zhang R, Qiu Q, Zheng G, Jia X, Liu H, He Z. miR-218 suppresses gastric cancer cell cycle progression through the CDK6/Cyclin D1/E2F1 axis in a feedback loop. Cancer Lett 2017. [PMID: 28634044 DOI: 10.1016/j.canlet.2017.06.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Studies in several cancers have suggested that miR-218 has anti-tumor activities, but its function is yet to be elucidated. In this study, we investigated the regulation and function of miR-218 (miR-218-5p) in the cell cycle progression of gastric cancer (GC). We found that miR-218 could suppress proliferation of gastric cancer cells, induce cell cycle arrest at the G1 phase and inhibit tumor growth and metastasis in vivo. We also demonstrated that miR-218 specifically targeted the 3'-UTR regions of CDK6 and cyclin D1 and inhibited the expression of these molecules, which in turn repressed the pRb/E2F1 signaling pathway. Overexpression of CDK6 and Cyclin D1 reversed miR-218-mediated inhibition of pRB/E2F1 signaling and attenuated the miR-218-induced cell cycle arrest. More importantly, miR-218 expression was significantly reduced and inversely correlated with the levels of CDK6 and Cyclin D1 in gastric cancer tissues. Decreased miR-218 expression was also correlated with advanced clinical stage, lymph node metastasis, and poor prognosis in gastric cancer patients. Furthermore, we showed that miR-218 expression was directly activated by E2F1 through the transactivation of miR-218 host genes, SLIT2 and SLIT3, revealing a negative feedback regulation of miR-218 expression. Taken together, our results describe a regulatory loop miR-218-CDK6/CyclinD1-E2F1 whose disruption may contribute to cell cycle progression in gastric cancer and indicate the potential application of miR-218 in cancer therapy.
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Affiliation(s)
- Min Deng
- Cancer Hospital and Cancer Research Institute, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Chao Zeng
- Department of Pathology, Guangdong Medical University, Dongguan, Guangdong Province, China
| | - Xihong Lu
- Guangzhou Eighth People's Hospital, Guangzhou, Guangdong Province, China
| | - Xiusheng He
- Cancer Research Institute, University of South China, Hengyang, Hunan Province, China
| | - Ruixin Zhang
- Cancer Hospital and Cancer Research Institute, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Qinwei Qiu
- Cancer Hospital and Cancer Research Institute, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Guopei Zheng
- Cancer Hospital and Cancer Research Institute, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xiaoting Jia
- Cancer Hospital and Cancer Research Institute, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Hao Liu
- Cancer Hospital and Cancer Research Institute, Guangzhou Medical University, Guangzhou, Guangdong Province, China.
| | - Zhimin He
- Cancer Hospital and Cancer Research Institute, Guangzhou Medical University, Guangzhou, Guangdong Province, China.
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15
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Zheng J, Yi D, Shi X, Shi H. miR-1297 regulates neural stem cell differentiation and viability through controlling Hes1 expression. Cell Prolif 2017; 50. [PMID: 28464358 DOI: 10.1111/cpr.12347] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 02/25/2017] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Neural stem cells (NSCs) are self-renewing, undifferentiated and multipotent precursors that can generate neuronal and glial lineages. MicroRNAs (miRNAs) are small non-coding RNAs that act crucial roles in cell proliferation, differentiation and migration. However, the role of miR-1297 in the development of NSCs is still unknown. MATERIALS AND METHODS Primary NSCs were isolated from rat's embryos. The expression of miR-1297 and Hes1 were measured by qRT-PCR. Western blot was performed to detect the protein expression of Hes1, β-tubulin-III and GFAP. RESULTS We showed that miR-1297 expression was upregulated during NSC differentiation, while the expression of Hes1 was decreased during NSC differentiation. Elevated expression of miR-1297 promoted the NSCs viability and increased the formation of NSCs to neurospheres. Ecoptic expression of miR-1297 promoted β-tubulin-III expression in the NSCs. Overexpression of miR-1297 decreased GFAP expression in the NSCs. Furthermore, we demonstrated that miR-1297 regulated NSCs viability and differentiation by directly targeting Hes1. Overexpression of miR-1297 suppressed Hes1 expression in the NSCs. CONCLUSIONS These results suggested that miR-1297 played an important role in NSCs viability and differentiation through inhibiting Hes1 expression.
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Affiliation(s)
- Jiaolin Zheng
- Department of Neruology, The second hospital of Harbin Medical University, Harbin, Heilong Jiang, 150086, China
| | - Dan Yi
- Department of Pharmacology, Rush University Medical Center, Chicago, IL, 60607, USA
| | - Xiaodong Shi
- Department of Neruology, The second hospital of Harbin Medical University, Harbin, Heilong Jiang, 150086, China
| | - Huaizhang Shi
- Department of Neurosurgery, The first hospital of Harbin Medical University, Harbin, Heilong Jiang, 150001, China
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16
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Zhang L, Tao W, Feng H, Chen Y. Transcriptional and Genomic Targets of Neural Stem Cells for Functional Recovery after Hemorrhagic Stroke. Stem Cells Int 2017; 2017:2412890. [PMID: 28133486 PMCID: PMC5241497 DOI: 10.1155/2017/2412890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/21/2016] [Indexed: 01/27/2023] Open
Abstract
Hemorrhagic stroke is a life-threatening disease characterized by a sudden rupture of cerebral blood vessels, and it is widely believed that neural cell death occurs after exposure to blood metabolites or subsequently damaged cells. Neural stem cells (NSCs), which maintain neurogenesis and are found in subgranular zone and subventricular zone, are thought to be an endogenous neuroprotective mechanism for these brain injuries. However, due to the complexity of NSCs and their microenvironment, current strategies cannot satisfactorily enhance functional recovery after hemorrhagic stroke. It is well known that transcriptional and genomic pathways play important roles in ensuring the normal functions of NSCs, including proliferation, migration, differentiation, and neural reconnection. Recently, emerging evidence from the use of new technologies such as next-generation sequencing and transcriptome profiling has provided insight into our understanding of genomic function and regulation of NSCs. In the present article, we summarize and present the current data on the control of NSCs at both the transcriptional and genomic levels. Using bioinformatics methods, we sought to predict novel therapeutic targets of endogenous neurogenesis and exogenous NSC transplantation for functional recovery after hemorrhagic stroke, which could also advance our understanding of its pathophysiology.
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Affiliation(s)
- Le Zhang
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Wenjing Tao
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Hua Feng
- Department of Neurosurgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yujie Chen
- Department of Neurosurgery, Southwest Hospital, Third Military Medical University, Chongqing, China
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17
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Fricke IB, Viel T, Worlitzer MM, Collmann FM, Vrachimis A, Faust A, Wachsmuth L, Faber C, Dollé F, Kuhlmann MT, Schäfers K, Hermann S, Schwamborn JC, Jacobs AH. 6-hydroxydopamine-induced Parkinson's disease-like degeneration generates acute microgliosis and astrogliosis in the nigrostriatal system but no bioluminescence imaging-detectable alteration in adult neurogenesis. Eur J Neurosci 2016; 43:1352-65. [PMID: 26950181 DOI: 10.1111/ejn.13232] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 12/22/2022]
Abstract
Parkinson's disease is a slowly progressing neurodegenerative disorder caused by loss of dopaminergic neurons in the substantia nigra (SN), leading to severe impairment in motor and non-motor functions. Endogenous subventricular zone (SVZ) neural stem cells constantly give birth to new cells that might serve as a possible source for regeneration in the adult brain. However, neurodegeneration is accompanied by neuroinflammation and dopamine depletion, potentially compromising regeneration. We therefore employed in vivo imaging methods to study striatal deafferentation (N-ω-fluoropropyl-2β-carbomethoxy-3β-(4-[(123) I]iodophenyl)nortropane single photon emission computed tomography, DaTscan(™) ) and neuroinflammation in the SN and striatum (N,N-diethyl-2-(2-(4-(2-[(18) F]fluoroethoxy)phenyl)-5,7-dimethylpyrazolo[1,5-a]pyrimidin-3-yl)acetamide positron emission tomography, [(18) F]DPA-714 PET) in the intranigral 6-hydroxydopamine Parkinson's disease mouse model. Additionally, we transduced cells in the SVZ with a lentivirus encoding firefly luciferase and followed migration of progenitor cells in the SVZ-olfactory bulb axis via bioluminescence imaging under disease and control conditions. We found that activation of microglia in the SN is an acute process accompanying the degeneration of dopaminergic cell bodies in the SN. Dopaminergic deafferentation of the striatum does not influence the generation of doublecortin-positive neuroblasts in the SVZ, but generates chronic astrogliosis in the nigrostriatal system.
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Affiliation(s)
- Inga B Fricke
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstraße 15, D-48149, Münster, Germany.,ZMBE, Institute of Cell Biology, Stem Cell Biology and Regeneration Group, University of Münster, Münster, Germany
| | - Thomas Viel
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstraße 15, D-48149, Münster, Germany
| | - Maik M Worlitzer
- ZMBE, Institute of Cell Biology, Stem Cell Biology and Regeneration Group, University of Münster, Münster, Germany
| | - Franziska M Collmann
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstraße 15, D-48149, Münster, Germany
| | - Alexis Vrachimis
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstraße 15, D-48149, Münster, Germany.,Department of Nuclear Medicine, University Hospital Münster, Münster, Germany
| | - Andreas Faust
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstraße 15, D-48149, Münster, Germany
| | - Lydia Wachsmuth
- Department of Clinical Radiology, University Hospital Münster, Münster, Germany
| | - Cornelius Faber
- Department of Clinical Radiology, University Hospital Münster, Münster, Germany.,DFG EXC 1003, Cluster of Excellence 'Cells in Motion', Münster, Germany
| | - Frédéric Dollé
- CEA, I2BM, Service Hospitalier Frédéric Joliot, Orsay, France
| | - Michael T Kuhlmann
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstraße 15, D-48149, Münster, Germany
| | - Klaus Schäfers
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstraße 15, D-48149, Münster, Germany.,DFG EXC 1003, Cluster of Excellence 'Cells in Motion', Münster, Germany
| | - Sven Hermann
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstraße 15, D-48149, Münster, Germany.,DFG EXC 1003, Cluster of Excellence 'Cells in Motion', Münster, Germany
| | - Jens C Schwamborn
- ZMBE, Institute of Cell Biology, Stem Cell Biology and Regeneration Group, University of Münster, Münster, Germany.,Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg
| | - Andreas H Jacobs
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstraße 15, D-48149, Münster, Germany.,DFG EXC 1003, Cluster of Excellence 'Cells in Motion', Münster, Germany.,Department of Geriatric Medicine, Evangelische Kliniken, Johanniter Krankenhaus, Bonn, Germany
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18
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Zechel S, Zajac P, Lönnerberg P, Ibáñez CF, Linnarsson S. Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq. Genome Biol 2015; 15:486. [PMID: 25344199 PMCID: PMC4234883 DOI: 10.1186/s13059-014-0486-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cortical interneurons originating from the medial ganglionic eminence, MGE, are among the most diverse cells within the CNS. Different pools of proliferating progenitor cells are thought to exist in the ventricular zone of the MGE, but whether the underlying subventricular and mantle regions of the MGE are spatially patterned has not yet been addressed. Here, we combined laser-capture microdissection and multiplex RNA-sequencing to map the transcriptome of MGE cells at a spatial resolution of 50 μm. RESULTS Distinct groups of progenitor cells showing different stages of interneuron maturation are identified and topographically mapped based on their genome-wide transcriptional pattern. Although proliferating potential decreased rather abruptly outside the ventricular zone, a ventro-lateral gradient of increasing migratory capacity was identified, revealing heterogeneous cell populations within this neurogenic structure. CONCLUSIONS We demonstrate that spatially resolved RNA-seq is ideally suited for high resolution topographical mapping of genome-wide gene expression in heterogeneous anatomical structures such as the mammalian central nervous system.
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Affiliation(s)
- Sabrina Zechel
- Department of Neuroscience, Karolinska Institute, Stockholm SE-171 77, Sweden
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19
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Nicklas S, Okawa S, Hillje AL, González-Cano L, Del Sol A, Schwamborn JC. The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs. Nucleic Acids Res 2015; 43:2638-54. [PMID: 25722370 PMCID: PMC4357729 DOI: 10.1093/nar/gkv138] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In neural stem cells (NSCs), the balance between stem cell maintenance and neuronal differentiation depends on cell-fate determinants such as TRIM32. Previously, we have shown that TRIM32 associates with the RNA-induced silencing complex and increases the activity of microRNAs such as Let-7a. However, the exact mechanism of microRNA regulation by TRIM32 during neuronal differentiation has yet to be elucidated. Here, we used a mass spectrometry approach to identify novel protein–protein interaction partners of TRIM32 during neuronal differentiation. We found that TRIM32 associates with proteins involved in neurogenesis and RNA-related processes, such as the RNA helicase DDX6, which has been implicated in microRNA regulation. We demonstrate, that DDX6 colocalizes with TRIM32 in NSCs and neurons and that it increases the activity of Let-7a. Furthermore, we provide evidence that DDX6 is necessary and sufficient for neuronal differentiation and that it functions in cooperation with TRIM32.
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Affiliation(s)
- Sarah Nicklas
- Stem Cell Biology and Regeneration Group, Institute of Cell Biology, ZMBE, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany Developmental and Cellular Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-Belval, Luxembourg
| | - Satoshi Okawa
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-Belval, Luxembourg
| | - Anna-Lena Hillje
- Stem Cell Biology and Regeneration Group, Institute of Cell Biology, ZMBE, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany Developmental and Cellular Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-Belval, Luxembourg
| | - Laura González-Cano
- Stem Cell Biology and Regeneration Group, Institute of Cell Biology, ZMBE, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany Developmental and Cellular Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-Belval, Luxembourg
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-Belval, Luxembourg
| | - Jens C Schwamborn
- Stem Cell Biology and Regeneration Group, Institute of Cell Biology, ZMBE, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany Developmental and Cellular Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-Belval, Luxembourg
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20
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Hardwick LJA, Philpott A. Nervous decision-making: to divide or differentiate. Trends Genet 2014; 30:254-61. [PMID: 24791612 PMCID: PMC4046230 DOI: 10.1016/j.tig.2014.04.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/31/2014] [Accepted: 04/01/2014] [Indexed: 01/07/2023]
Abstract
Multiple mechanisms coordinate the cell cycle and neuronal differentiation. Lengthening of G1 phase is functionally important for differentiation. Cell cycle components can directly and independently affect neurogenesis. Differentiation factors can directly affect the cell cycle structure and machinery.
The intricate balance between proliferation and differentiation is of fundamental importance in the development of the central nervous system (CNS). The division versus differentiation decision influences both the number and identity of daughter cells produced, thus critically shaping the overall microstructure and function of the CNS. During the past decade, significant advances have been made to characterise the changes in the cell cycle during differentiation, and to uncover the multiple bidirectional links that coordinate these two processes. Here, we explore the nature and mechanistic basis of these links in the context of the developing CNS, highlighting new insights into transcriptional, post-translational, and epigenetic levels of interaction.
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Affiliation(s)
- Laura J A Hardwick
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Anna Philpott
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
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21
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Stem cell characteristics in glioblastoma are maintained by the ecto-nucleotidase E-NPP1. Cell Death Differ 2014; 21:929-40. [PMID: 24531536 DOI: 10.1038/cdd.2014.12] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 12/02/2013] [Accepted: 01/07/2014] [Indexed: 12/16/2022] Open
Abstract
Glioblastomas are highly aggressive brain tumours and are characterised by substantial cellular heterogeneity within a single tumour. A sub-population of glioblastoma stem-like cells (GSCs) that shares properties with neural precursor cells has been described, exhibiting resistance to therapy and therefore being considered responsible for the high recurrence rate in glioblastoma. To elucidate the underlying cellular processes we investigated the role of phosphatases in the GSC phenotype, using an in vitro phosphatome-wide RNA interference screen. We identified a set of genes, the knockdown of which induces a significant decrease in the glioma stem cell marker CD133, indicating a role in the glioblastoma stem-like phenotype. Among these genes, the ecto-nucleotidase ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase 1) was found to be highly expressed in GSCs compared with normal brain and neural stem cells. Knockdown of ENPP1 in cultured GSCs resulted in an overall downregulation of stem cell-associated genes, induction of differentiation into astrocytic cell lineage, impairment of sphere formation, in addition to increased cell death, accumulation of cells in G1/G0 cell cycle phase and sensitisation to chemotherapeutic treatment. Genome-wide gene expression analysis and nucleoside and nucleotide profiling revealed that knockdown of ENPP1 affects purine and pyrimidine metabolism, suggesting a link between ENPP1 expression and a balanced nucleoside-nucleotide pool in GSCs. The phenotypic changes in E-NPP1-deficient GSCs are assumed to be a consequence of decreased transcriptional function of E2F1. Together, these results reveal that E-NPP1, by acting upstream of E2F1, is indispensable for the maintenance of GSCs in vitro and hence required to keep GSCs in an undifferentiated, proliferative state.
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22
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Mao S, Li H, Sun Q, Zen K, Zhang CY, Li L. miR-17 regulates the proliferation and differentiation of the neural precursor cells during mouse corticogenesis. FEBS J 2014; 281:1144-58. [PMID: 24314167 DOI: 10.1111/febs.12680] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 11/08/2013] [Accepted: 12/02/2013] [Indexed: 01/28/2023]
Abstract
MicroRNAs (miRNAs) are endogenously expressed small, non-coding nucleotides that repress gene expression at the post-transcriptional level. In mammals, the developing brain contains a large, diverse group of miRNAs, which suggests that they play crucial roles in neural development. In the present study, we analyzed the miRNA expression patterns in the mouse cortex at various developmental stages. We found that miR-17 family miRNAs were highly expressed in the cortex during early developmental stages, and that their expression levels gradually decreased as the cortex developed. Further investigation revealed that the change in miR-17-5p expression occurred in the ventricular zone/sub-ventricular zone. In addition to promoting cell proliferation, miR-17-5p also influences the differentiation fate of neural precursor cells exposed to bone morphogenetic protein 2. Moreover, we show that these effects of miR-17-5p were mainly the result of regulating the bone morphogenetic protein signaling pathway by repressing expression of the bone morphogenetic protein type II receptor. Taken together, these findings suggest that miR-17 family members play a pivotal role in regulating cell activity during early development of the mouse cortex.
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Affiliation(s)
- Susu Mao
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University School of Life Sciences, China
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23
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Xiao X, Moreno-Moral A, Rotival M, Bottolo L, Petretto E. Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules. PLoS Genet 2014; 10:e1004006. [PMID: 24391511 PMCID: PMC3879165 DOI: 10.1371/journal.pgen.1004006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 10/22/2013] [Indexed: 12/27/2022] Open
Abstract
Recent high-throughput efforts such as ENCODE have generated a large body of genome-scale transcriptional data in multiple conditions (e.g., cell-types and disease states). Leveraging these data is especially important for network-based approaches to human disease, for instance to identify coherent transcriptional modules (subnetworks) that can inform functional disease mechanisms and pathological pathways. Yet, genome-scale network analysis across conditions is significantly hampered by the paucity of robust and computationally-efficient methods. Building on the Higher-Order Generalized Singular Value Decomposition, we introduce a new algorithmic approach for efficient, parameter-free and reproducible identification of network-modules simultaneously across multiple conditions. Our method can accommodate weighted (and unweighted) networks of any size and can similarly use co-expression or raw gene expression input data, without hinging upon the definition and stability of the correlation used to assess gene co-expression. In simulation studies, we demonstrated distinctive advantages of our method over existing methods, which was able to recover accurately both common and condition-specific network-modules without entailing ad-hoc input parameters as required by other approaches. We applied our method to genome-scale and multi-tissue transcriptomic datasets from rats (microarray-based) and humans (mRNA-sequencing-based) and identified several common and tissue-specific subnetworks with functional significance, which were not detected by other methods. In humans we recapitulated the crosstalk between cell-cycle progression and cell-extracellular matrix interactions processes in ventricular zones during neocortex expansion and further, we uncovered pathways related to development of later cognitive functions in the cortical plate of the developing brain which were previously unappreciated. Analyses of seven rat tissues identified a multi-tissue subnetwork of co-expressed heat shock protein (Hsp) and cardiomyopathy genes (Bag3, Cryab, Kras, Emd, Plec), which was significantly replicated using separate failing heart and liver gene expression datasets in humans, thus revealing a conserved functional role for Hsp genes in cardiovascular disease.
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Affiliation(s)
- Xiaolin Xiao
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Aida Moreno-Moral
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Maxime Rotival
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Leonardo Bottolo
- Department of Mathematics, Imperial College, London, United Kingdom
| | - Enrico Petretto
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
- * E-mail:
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Cui Y, Xiao Z, Chen T, Wei J, Chen L, Liu L, Chen B, Wang X, Li X, Dai J. The miR-7 identified from collagen biomaterial-based three-dimensional cultured cells regulates neural stem cell differentiation. Stem Cells Dev 2013; 23:393-405. [PMID: 24200387 DOI: 10.1089/scd.2013.0342] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Increasing evidence suggests that three-dimensional (3D) cultures provide more appropriate microenvironments to control stem cell response compared with traditional two-dimensional (2D) cultures. However, the molecular mechanism involved in 3D cultured stem cells is not well known. Several microRNAs whose target genes involved in the regulation of self-renewal and differentiation of stem cells were found to be downregulated in 3D cultured PA-1 cells. Among them, miR-7 was predicted to target Kruppel-like factor 4 (Klf4), a key gene for self-renewal of neural stem cells (NSCs). We showed that the differentiation of NSCs was inhibited in 3D collagen scaffolds compared with 2D cultured cells. The quantitative real-time PCR (qPCR) analysis indicated that the expression of miR-7 and Klf4 changed significantly in 2D cultures, whereas the expression stability of miR-7 and Klf4 was detected in 3D cultures. Using luciferase assay and western blot, Klf4 was identified as a target of miR-7 indicating that miR-7 plays a critical role in maintaining the self-renewal capacity through a Klf4-dependent mechanism in 3D cultured cells. Thus, the collagen scaffold-based 3D cell cultures may provide a platform to reveal the regulatory mechanism of cell regulators, which are difficult to find in traditional 2D cell cultures.
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Affiliation(s)
- Yi Cui
- 1 State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology , Chinese Academy of Sciences, Beijing, China
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25
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Lopez-Ramirez MA, Nicoli S. Role of miRNAs and epigenetics in neural stem cell fate determination. Epigenetics 2013; 9:90-100. [PMID: 24342893 DOI: 10.4161/epi.27536] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The regulation of gene expression that determines stem cell fate determination is tightly controlled by both epigenetic and posttranscriptional mechanisms. Indeed, small non-coding RNAs such as microRNAs (miRNAs) are able to regulate neural stem cell fate by targeting chromatin-remodeling pathways. Here, we aim to summarize the latest findings regarding the feedback network of epigenetics and miRNAs during embryonic and adult neurogenesis.
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Affiliation(s)
- Miguel Alejandro Lopez-Ramirez
- Yale Cardiovascular Research Center; Section of Cardiovascular Medicine; Yale University School of Medicine; New Haven, CT USA
| | - Stefania Nicoli
- Yale Cardiovascular Research Center; Section of Cardiovascular Medicine; Yale University School of Medicine; New Haven, CT USA
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