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Ni K, Li ZL, Hu ZY, Hong L. Antitumor Effect of Apcin on Endometrial Carcinoma via p21-Mediated Cell Cycle Arrest and Apoptosis. Curr Med Sci 2024; 44:623-632. [PMID: 38853192 DOI: 10.1007/s11596-024-2877-z] [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: 10/06/2023] [Accepted: 03/27/2024] [Indexed: 06/11/2024]
Abstract
OBJECTIVE Endometrial carcinoma (EC) is a prevalent gynecological malignancy characterized by increasing incidence and mortality rates. This underscores the critical need for novel therapeutic targets. One such potential target is cell division cycle 20 (CDC20), which has been implicated in oncogenesis. This study investigated the effect of the CDC20 inhibitor Apcin on EC and elucidated the underlying mechanism involved. METHODS The effects of Apcin on EC cell proliferation, apoptosis, and the cell cycle were evaluated using CCK8 assays and flow cytometry. RNA sequencing (RNA-seq) was subsequently conducted to explore the underlying molecular mechanism, and Western blotting and coimmunoprecipitation were subsequently performed to validate the results. Animal studies were performed to evaluate the antitumor effects in vivo. Bioinformatics analysis was also conducted to identify CDC20 as a potential therapeutic target in EC. RESULTS Treatment with Apcin inhibited proliferation and induced apoptosis in EC cells, resulting in cell cycle arrest. Pathways associated with apoptosis and the cell cycle were activated following treatment with Apcin. Notably, Apcin treatment led to the upregulation of the cell cycle regulator p21, which was verified to interact with CDC20 and consequently decrease the expression of downstream cyclins in EC cells. In vivo experiments confirmed that Apcin treatment significantly impeded tumor growth. Higher CDC20 expression was observed in EC tissue than in nonmalignant tissue, and increased CDC20 expression in EC patients was associated with shorter overall survival and progress free interval. CONCLUSION CDC20 is a novel molecular target in EC, and Apcin could be developed as a candidate antitumor drug for EC treatment.
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Affiliation(s)
- Ke Ni
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Zi-Li Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhi-Yong Hu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Hong
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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Muzyka L, Goff NK, Choudhary N, Koltz MT. Systematic Review of Molecular Targeted Therapies for Adult-Type Diffuse Glioma: An Analysis of Clinical and Laboratory Studies. Int J Mol Sci 2023; 24:10456. [PMID: 37445633 DOI: 10.3390/ijms241310456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/05/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Gliomas are the most common brain tumor in adults, and molecularly targeted therapies to treat gliomas are becoming a frequent topic of investigation. The current state of molecular targeted therapy research for adult-type diffuse gliomas has yet to be characterized, particularly following the 2021 WHO guideline changes for classifying gliomas using molecular subtypes. This systematic review sought to characterize the current state of molecular target therapy research for adult-type diffuse glioma to better inform scientific progress and guide next steps in this field of study. A systematic review was conducted in accordance with PRISMA guidelines. Studies meeting inclusion criteria were queried for study design, subject (patients, human cell lines, mice, etc.), type of tumor studied, molecular target, respective molecular pathway, and details pertaining to the molecular targeted therapy-namely the modality, dose, and duration of treatment. A total of 350 studies met the inclusion criteria. A total of 52 of these were clinical studies, 190 were laboratory studies investigating existing molecular therapies, and 108 were laboratory studies investigating new molecular targets. Further, a total of 119 ongoing clinical trials are also underway, per a detailed query on clinicaltrials.gov. GBM was the predominant tumor studied in both ongoing and published clinical studies as well as in laboratory analyses. A few studies mentioned IDH-mutant astrocytomas or oligodendrogliomas. The most common molecular targets in published clinical studies and clinical trials were protein kinase pathways, followed by microenvironmental targets, immunotherapy, and cell cycle/apoptosis pathways. The most common molecular targets in laboratory studies were also protein kinase pathways; however, cell cycle/apoptosis pathways were the next most frequent target, followed by microenvironmental targets, then immunotherapy pathways, with the wnt/β-catenin pathway arising in the cohort of novel targets. In this systematic review, we examined the current evidence on molecular targeted therapy for adult-type diffuse glioma and discussed its implications for clinical practice and future research. Ultimately, published research falls broadly into three categories-clinical studies, laboratory testing of existing therapies, and laboratory identification of novel targets-and heavily centers on GBM rather than IDH-mutant astrocytoma or oligodendroglioma. Ongoing clinical trials are numerous in this area of research as well and follow a similar pattern in tumor type and targeted pathways as published clinical studies. The most common molecular targets in all study types were protein kinase pathways. Microenvironmental targets were more numerous in clinical studies, whereas cell cycle/apoptosis were more numerous in laboratory studies. Immunotherapy pathways are on the rise in all study types, and the wnt/β-catenin pathway is increasingly identified as a novel target.
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Affiliation(s)
- Logan Muzyka
- Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, 1501 Red River Street, Austin, TX 78712, USA
| | - Nicolas K Goff
- Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, 1501 Red River Street, Austin, TX 78712, USA
| | - Nikita Choudhary
- Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, 1501 Red River Street, Austin, TX 78712, USA
| | - Michael T Koltz
- Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, 1501 Red River Street, Austin, TX 78712, USA
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Ning Z, Deng X, Li L, Feng J, Du X, Amevor FK, Tian Y, Li L, Rao Y, Yi Z, Du X, Cui Z, Zhao X. miR-128-3p regulates chicken granulosa cell function via 14-3-3β/FoxO and PPAR-γ/LPL signaling pathways. Int J Biol Macromol 2023; 241:124654. [PMID: 37119902 DOI: 10.1016/j.ijbiomac.2023.124654] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
MicroRNAs (miRNAs) are class of 22 nt short RNA sequences which inhibit protein translation through binding to the 3'UTR of its target genes. The continuous ovulatory property of chicken follicle makes it a perfect model for studying granulosa cell (GC) functions. In this study, we found that large number of miRNAs including miR-128-3p, were differentially expressed in the GCs of F1 and F5 follicles of chicken. Subsequently, the results revealed that miR-128-3p inhibited proliferation, the formation of lipid droplets, and hormone secretion in chicken primary GCs through directly targeting YWHAB and PPAR-γ genes. To determine the effects of 14-3-3β (encoded by YWHAB) protein on GCs functions, we overexpressed or inhibited the expression of YWHAB, and the results showed that YWHAB inhibited the function of FoxO proteins. Collectively, we found that miR-128-3p was highly expressed in the chicken F1 follicles compared to the F5 follicles. In addition, the results indicated that miR-128-3p promoted GC apoptosis through 14-3-3β/FoxO pathway via repressing YWHAB, and inhibited lipid synthesis by impeding the PPAR-γ/LPL pathway, as well as reduced the secretion of progesterone and estrogen. Taken together, the results showed that miR-128-3p plays a regulatory role in chicken granulosa cell function via 14-3-3β/FoxO and PPAR-γ/LPL signaling pathways.
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Affiliation(s)
- Zifan Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Xun Deng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Liang Li
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Provincial Academy of Agricultural Sciences, Guiyang, PR China
| | - Jing Feng
- Institute of Animal Husbandry and Veterinary Medicine, College of Agriculture and Animal Husbandry of Tibet Autonomous Region, Lhasa, PR China
| | - Xiaxia Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Felix Kwame Amevor
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Yaofu Tian
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Lingxiang Li
- Bazhong Academy of Agriculture and Forestry Sciences, Bazhong, PR China
| | - Yong Rao
- Bazhong Academy of Agriculture and Forestry Sciences, Bazhong, PR China
| | - Zhixin Yi
- Bazhong Academy of Agriculture and Forestry Sciences, Bazhong, PR China
| | - Xiaohui Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Zhifu Cui
- College of Animal Science and Technology, Southwest University, Chongqing, PR China.
| | - Xiaoling Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China.
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Interactions between 14-3-3 Proteins and Actin Cytoskeleton and Its Regulation by microRNAs and Long Non-Coding RNAs in Cancer. ENDOCRINES 2022. [DOI: 10.3390/endocrines3040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
14-3-3s are a family of structurally similar proteins that bind to phosphoserine or phosphothreonine residues, forming the central signaling hub that coordinates or integrates various cellular functions, thereby controlling many pathways important in cancer, cell motility, cell death, cytoskeletal remodeling, neuro-degenerative disorders and many more. Their targets are present in all cellular compartments, and when they bind to proteins they alter their subcellular localization, stability, and molecular interactions with other proteins. Changes in environmental conditions that result in altered homeostasis trigger the interaction between 14-3-3 and other proteins to retrieve or rescue homeostasis. In circumstances where these regulatory proteins are dysregulated, it leads to pathological conditions. Therefore, deeper understanding is needed on how 14-3-3 proteins bind, and how these proteins are regulated or modified. This will help to detect disease in early stages or design inhibitors to block certain pathways. Recently, more research has been devoted to identifying the role of MicroRNAs, and long non-coding RNAs, which play an important role in regulating gene expression. Although there are many reviews on the role of 14-3-3 proteins in cancer, they do not provide a holistic view of the changes in the cell, which is the focus of this review. The unique feature of the review is that it not only focuses on how the 14-3-3 subunits associate and dissociate with their binding and regulatory proteins, but also includes the role of micro-RNAs and long non-coding RNAs and how they regulate 14-3-3 isoforms. The highlight of the review is that it focuses on the role of 14-3-3, actin, actin binding proteins and Rho GTPases in cancer, and how this complex is important for cell migration and invasion. Finally, the reader is provided with super-resolution high-clarity images of each subunit of the 14-3-3 protein family, further depicting their distribution in HeLa cells to illustrate their interactions in a cancer cell.
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Zeng WJ, Zhang L, Cao H, Li D, Zhang H, Xia Z, Peng R. A novel inflammation-related lncRNAs prognostic signature identifies LINC00346 in promoting proliferation, migration, and immune infiltration of glioma. Front Immunol 2022; 13:810572. [PMID: 36311792 PMCID: PMC9609424 DOI: 10.3389/fimmu.2022.810572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 08/15/2022] [Indexed: 11/21/2022] Open
Abstract
In this study, a total of 13 inflammation-related lncRNAs with a high prognostic value were identified with univariate, multivariate Cox regression analysis, and LASSO analysis. LINC00346, which is one of the 13 lncRNAs identified, was positively associated with type 2 macrophage activation and the malignant degree of glioma. Fluorescence in situ hybridization (FISH) and immunohistochemical staining showed that LINC00346 was highly expressed in high-grade glioma, while type 2 macrophages key transcription factor STAT3 and surface marker CD204 were also highly expressed simultaneously. LINC00346 high-expression gliomas were more sensitive to the anti–PD-1 and anti-CTLA-4 therapy. LINC00346 was also associated with tumor proliferation and tumor migration validated by EdU, cell colony, formation CCK8, and transwell assays. These findings reveal novel biomarkers for predicting glioma prognosis and outline relationships between lncRNAs inflammation, and glioma, as well as possible immune checkpoint targets for glioma.
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Affiliation(s)
- Wen-Jing Zeng
- Department of Pharmarcy, Xiangya Hospital, Central South University, Changsha, China
| | - Lei Zhang
- Department of Neurology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Hui Cao
- Department of Psychiatry, The Second People’s Hospital of Hunan Province, The Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Dongjie Li
- Department of Geriatrics, Xiangya International Medical Center, Xiangya Hospital, Central South University, Changsha, China
| | - Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhiwei Xia
- Department of Neurology, Hunan Aerospace Hospital, Changsha Medical University, Changsha, China
- *Correspondence: Zhiwei Xia, ; Renjun Peng,
| | - Renjun Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Zhiwei Xia, ; Renjun Peng,
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6
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Lin HR, Chen YP, Chen HT, Liu XP, Zhou JY, Huang XK, Yuan L, Zhuo ZJ. CASC15 Gene Polymorphisms and Glioma Susceptibility in Chinese Children. Curr Med Sci 2022; 42:797-802. [PMID: 35819658 DOI: 10.1007/s11596-022-2613-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 12/24/2021] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Gliomas are the most common tumors in the central nervous system. The cancer susceptibility candidate 15 (CASC15) gene has been reported to be a susceptibility gene for several types of cancer. No studies have been carried out on the predisposing effect of CASC15 gene single nucleotide polymorphisms (SNPs) on glioma risk. METHODS In order to determine whether CASC15 gene SNPs are involved in glioma susceptibility, the first association study in a relatively large sample, which consisted of 171 patients and 228 healthy controls recruited from China, was performed. The contribution of SNPs (rs6939340 A>G, rs4712653 T>C and rs9295536 C>A) to the risk of glioma was evaluated by multinomial logistic regression, based on the calculation of the odds ratio (OR) and 95% confidence interval (CI). RESULTS In the single locus and combined analysis, it was revealed that the genetic risk score had no significant associations between CASC15 gene SNPs and glioma risk. However, in the stratified analysis, a significant decrease in risk of glioma was observed in subjects of <60 months old with the rs4712653 TT genotype, when compared to those with the CC/CT genotype (OR=0.12, 95% CI=0.02-0.91, P=0.041). CONCLUSION The present study provides referential evidence on the association between the genetic predisposition of the CASC15 gene and glioma risk in Chinese children. However, more well-designed case-control studies and functional experiments are needed to further explore the role of CASC15 gene SNPs.
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Affiliation(s)
- Hui-Ran Lin
- Faculty of Medicine, Macau University of Science and Technology, Macau, 999078, China
| | - Yong-Ping Chen
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Hui-Tong Chen
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Xiao-Ping Liu
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Jing-Ying Zhou
- Department of Hematology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiao-Kai Huang
- Department of Hematology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Li Yuan
- Department of Pathology, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China.
| | - Zhen-Jian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
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Yin X, Gao J, Liu Z, Han M, Ji X, Wang Z, Li Y, He D, Zhang F, Liu Q, Xin T. Mechanisms of long non-coding RNAs in biological phenotypes and ferroptosis of glioma. Front Oncol 2022; 12:941327. [PMID: 35912271 PMCID: PMC9330388 DOI: 10.3389/fonc.2022.941327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/24/2022] [Indexed: 12/15/2022] Open
Abstract
Glioma, one of the most common malignant tumors in the nervous system, is characterized by limited treatment, high mortality and poor prognosis. Numerous studies have shown that lncRNAs play an important role in the onset and progression of glioma by acting on various classical signaling pathways of tumors through signaling, trapping, guiding, scaffolding and other functions. LncRNAs contribute to the malignant progression of glioma via proliferation, apoptosis, epithelial-mesenchymal transformation, chemotherapy resistance, ferroptosis and other biological traits. In this paper, relevant lncRNA signaling pathways involved in glioma progression were systematically evaluated, with emphasis placed on the specific molecular mechanism of lncRNAs in the process of ferroptosis, in order to provide a theoretical basis for the application of lncRNAs in the anticancer treatment of glioma.
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Affiliation(s)
- Xianyong Yin
- Department of Neurosurgery, Shandong Medicine and Health Key Laboratory of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Jiajia Gao
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zihao Liu
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Min Han
- Department of Neurosurgery, Shandong Medicine and Health Key Laboratory of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Xiaoshuai Ji
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhihai Wang
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuming Li
- Department of Neurosurgery, Shandong Medicine and Health Key Laboratory of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Dong He
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fenglin Zhang
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qian Liu
- Department of Histology and Embryology, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Tao Xin, ; Qian Liu,
| | - Tao Xin
- Department of Neurosurgery, Shandong Medicine and Health Key Laboratory of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Neurosurgery, Jiangxi Provincial People’s Hospital Affiliated to Nanchang University, Nanchang, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- *Correspondence: Tao Xin, ; Qian Liu,
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Kang CM, Zhao JJ, Yuan YS, Liao JM, Yu KW, Li WK, Jin X, Cao SW, Chen WY, Jin X, Chen L, Ke PF, Li XH, Huang RY, Hu YW, Huang XZ. Long Noncoding RNA RP11-732M18.3 Promotes Glioma Angiogenesis by Upregulating VEGFA. Front Oncol 2022; 12:873037. [PMID: 35785190 PMCID: PMC9247460 DOI: 10.3389/fonc.2022.873037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Gliomas are the most aggressive and common type of malignant brain tumor, with limited treatment options and a dismal prognosis. Angiogenesis, a hallmarks of cancer, is one of two critical events in the progression of gliomas. Accumulating evidence has demonstrated that in glioma dysregulated molecules like long noncoding RNAs (lncRNAs), are closely linked to tumorigenesis and prognosis. However, the effects of and mechanisms of action of lncRNAs during tumor angiogenesis are poorly understood. The effect of lncRNA RP11-732M18.3 on angiogenesis was elucidated through an intracranial orthotopic glioma model, immunohistochemistry, and an in vitro angiogenesis assay. Co-culture experiments and cell migration assays were performed to investigate the function of lncRNA RP11-732M18.3 in vitro. lncRNA RP11-732M18.3 increased CD31+ microvessel density, and overexpression of lncRNA RP11-732M18.3 resulted in poor mouse survival. lncRNA RP11-732M18.3 promoted endothelial cell migration and tube formation. Nomogram and Kaplan-Meier survival analyses indicated that higher VEGFA is correlated with a poor prognosis. Mechanistically, lncRNA RP11-732M18.3 promotes angiogenesis by increasing the nuclear level of EP300 and facilitating the transcription and secretion of VEGFA. Our study contributes to the latest understanding of glioma angiogenesis and prognosis. lncRNA RP11-732M18.3 may be a potential treatment target in glioma.
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Affiliation(s)
- Chun-Min Kang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Jing-Jing Zhao
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying-Shi Yuan
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jia-Min Liao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ke-Wei Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei-Kang Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xin Jin
- Department of Neurosurgery, Guangdong 999 Brain Hospital, Guangzhou, China
| | - Shun-Wang Cao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei-Ye Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xing Jin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lu Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Pei-Feng Ke
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xue-Heng Li
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rui-Ying Huang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yan-Wei Hu
- Department of Laboratory Medicine, Guangzhou Woman and Children Medical Center, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Xian-Zhang Huang, ; Yan-Wei Hu,
| | - Xian-Zhang Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- *Correspondence: Xian-Zhang Huang, ; Yan-Wei Hu,
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Wang Y, Zhu X, Yang L, Hu X, He K, Yu C, Jiao S, Chen J, Guo R, Yang S. IDDLncLoc: Subcellular Localization of LncRNAs Based on a Framework for Imbalanced Data Distributions. Interdiscip Sci 2022; 14:409-420. [PMID: 35192174 DOI: 10.1007/s12539-021-00497-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Long non-coding RNAs play a crucial role in many life processes of cell, such as genetic markers, RNA splicing, signaling, and protein regulation. Considering that identifying lncRNA's localization in the cell through experimental methods is complicated, hard to reproduce, and expensive, we propose a novel method named IDDLncLoc in this paper, which adopts an ensemble model to solve the problem of the subcellular localization. In the proposal model, dinucleotide-based auto-cross covariance features, k-mer nucleotide composition features, and composition, transition, and distribution features are introduced to encode a raw RNA sequence to vector. To screen out reliable features, feature selection through binomial distribution, and recursive feature elimination is employed. Furthermore, strategies of oversampling in mini-batch, random sampling, and stacking ensemble strategies are customized to overcome the problem of data imbalance on the benchmark dataset. Finally, compared with the latest methods, IDDLncLoc achieves an accuracy of 94.96% on the benchmark dataset, which is 2.59% higher than the best method, and the results further demonstrate IDDLncLoc is excellent on the subcellular localization of lncRNA. Besides, a user-friendly web server is available at http://lncloc.club .
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Affiliation(s)
- Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- School of Artificial Intelligence, Jilin University, Changchun, China
| | - Xiaopeng Zhu
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Lili Yang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Obstetrics, The First Hospital of Jilin University, Changchun, China
| | - Xuemei Hu
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Kai He
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Cuinan Yu
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Shaoqing Jiao
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Jiali Chen
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Rui Guo
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Sen Yang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China.
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10
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Yin X, Lin H, Lin L, Miao L, He J, Zhuo Z. LncRNAs and CircRNAs in cancer. MedComm (Beijing) 2022; 3:e141. [PMID: 35592755 PMCID: PMC9099016 DOI: 10.1002/mco2.141] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
- Xin Yin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
- College of Pharmacy Jinan University Guangzhou Guangdong China
| | - Huiran Lin
- Faculty of Medicine Macau University of Science and Technology Macau China
| | - Lei Lin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
| | - Lei Miao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
| | - Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
- Laboratory Animal Center, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen China
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11
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Feng YH, Lim SW, Lin HY, Wang SA, Hsu SP, Kao TJ, Ko CY, Hsu TI. Allopregnanolone suppresses glioblastoma survival through decreasing DPYSL3 and S100A11 expression. J Steroid Biochem Mol Biol 2022; 219:106067. [PMID: 35114375 DOI: 10.1016/j.jsbmb.2022.106067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/15/2022] [Accepted: 01/28/2022] [Indexed: 12/14/2022]
Abstract
Allopregnanolone (allo) is a physiological regulator of neuronal activity that treats multiple neurological disorders. Allo penetrates the blood-brain barrier with very high efficiency, implying that allo can treat CNS-related diseases, including glioblastoma (GBM), which always recurs after standard therapy. Hence, this study aimed to determine whether allo has a therapeutic effect on GBM. We found that allo enhanced temozolomide (TMZ)-suppressed cell survival and proliferation of TMZ-resistant cells. In particular, allo enhanced TMZ-inhibited cell migration and TMZ-induced apoptosis. Additionally, allo strongly induced DNA damage characterized by γH2Ax. Furthermore, quantitative proteomic analysis, iTRAQ, showed that allo significantly decreased the levels of DPYSL3, S100A11, and S100A4, reflecting the poor prognosis of patients with GBM confirmed by differential gene expression and survival analysis. Moreover, single-cell RNA-Seq revealed that S100A11, expressed in malignant cells, oligodendrocytes, and macrophages, was significantly associated with immune cell infiltration. Furthermore, overexpression of DPYSL3 or S100A11 prevented allo-induced cell death. In conclusion, allo suppresses GBM cell survival by decreasing DPYSL3/S100A11 expression and inducing DNA damage.
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Affiliation(s)
| | - Sher-Wei Lim
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan; Department of Neurosurgery, Chi-Mei Medical Center, Tainan 722, Taiwan; Department of Nursing, Min-Hwei College of Health Care Management, Tainan 736, Taiwan
| | - Hong-Yi Lin
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan
| | - Shao-An Wang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Sung-Po Hsu
- Department of Physiology, School of Medicine, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Tzu-Jen Kao
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan; Ph.D. Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan; International Master Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan; TMU Research Center of Neuroscience, Taipei Medical University, Taipei 110, Taiwan
| | - Chiung-Yuan Ko
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan; Ph.D. Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan; International Master Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan; TMU Research Center of Neuroscience, Taipei Medical University, Taipei 110, Taiwan.
| | - Tsung-I Hsu
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan; Ph.D. Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan; International Master Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 110, Taiwan; TMU Research Center of Neuroscience, Taipei Medical University, Taipei 110, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei 110, Taiwan.
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12
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Liu K, Chen H, Wang Y, Jiang L, Li Y. Evolving Insights Into the Biological Function and Clinical Significance of Long Noncoding RNA in Glioblastoma. Front Cell Dev Biol 2022; 10:846864. [PMID: 35531099 PMCID: PMC9068894 DOI: 10.3389/fcell.2022.846864] [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: 12/31/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma (GBM) is one of the most prevalent and aggressive cancers worldwide. The overall survival period of GBM patients is only 15 months even with standard combination therapy. The absence of validated biomarkers for early diagnosis mainly accounts for worse clinical outcomes of GBM patients. Thus, there is an urgent requirement to characterize more biomarkers for the early diagnosis of GBM patients. In addition, the detailed molecular basis during GBM pathogenesis and oncogenesis is not fully understood, highlighting that it is of great significance to elucidate the molecular mechanisms of GBM initiation and development. Recently, accumulated pieces of evidence have revealed the central roles of long noncoding RNAs (lncRNAs) in the tumorigenesis and progression of GBM by binding with DNA, RNA, or protein. Targeting those oncogenic lncRNAs in GBM may be promising to develop more effective therapeutics. Furthermore, a better understanding of the biological function and underlying molecular basis of dysregulated lncRNAs in GBM initiation and development will offer new insights into GBM early diagnosis and develop novel treatments for GBM patients. Herein, this review builds on previous studies to summarize the dysregulated lncRNAs in GBM and their unique biological functions during GBM tumorigenesis and progression. In addition, new insights and challenges of lncRNA-based diagnostic and therapeutic potentials for GBM patients were also introduced.
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Affiliation(s)
- Kun Liu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Hong Chen
- Department of Oncology, 920th Hospital of Joint Logistics Support Force, Teaching Hospital of Kunming Medical University, Kunming, China
| | - Yuanyuan Wang
- Department of Pathology, 920th Hospital of Joint Logistics Support Force, Teaching Hospital of Kunming Medical University, Kunming, China
| | - Liping Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, United States
- *Correspondence: Yi Li, ; Liping Jiang,
| | - Yi Li
- Department of Oncology, 920th Hospital of Joint Logistics Support Force, Teaching Hospital of Kunming Medical University, Kunming, China
- *Correspondence: Yi Li, ; Liping Jiang,
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13
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Tamtaji OR, Razavi ZS, Razzaghi N, Aschner M, Barati E, Mirzaei H. Quercetin and Glioma: Which signaling pathways are involved? Curr Mol Pharmacol 2022; 15:962-968. [DOI: 10.2174/1874467215666220211094136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/20/2021] [Accepted: 12/06/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Gliomas are the most common brain tumors. These tumors commonly exhibit continuous growth without invading surrounding brain tissues. Dominant remedial approaches suffer limited therapy and survival rates. Although some progress has been made in conventional glioma treatments, these breakthroughs have not yet proven sufficient for treating this malignancy. The remedial options are limited given gliomas' aggressive metastasis and drug resistance. Quercetin, a flavonoid, is an anti-oxidative, anti-allergic, antiviral, anti-inflammatory, and anticancer compound. Multiple lines of evidence have shown that Quercetin has anti-tumor effects, documenting this natural compound exerts its pharmacological effects by targeting a variety of cellular and molecular processes, i.e., apoptosis, metastasis, and autophagy. Herein, we summarize various cellular and molecular pathways that are affected by Quercetin in gliomas.
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Affiliation(s)
- Omid Reza Tamtaji
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Zahra Sadat Razavi
- Student Research Committee, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Nazanin Razzaghi
- Laboratory Sciences Research Centre, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, United States
| | - Erfaneh Barati
- Anatomical Sciences Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, I.R. Iran
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14
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Kang CM, Li WK, Yu KW, Li XH, Huang RY, Ke PF, Jin X, Cao SW, Yuan YS, Wang H, Yan J, Chen WY, Huang XZ, Zhao JJ. Long non‑coding RNA AL355711 promotes smooth muscle cell migration through the ABCG1/MMP3 pathway. Int J Mol Med 2021; 48:207. [PMID: 34608503 PMCID: PMC8510679 DOI: 10.3892/ijmm.2021.5040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/21/2021] [Indexed: 11/21/2022] Open
Abstract
Atherosclerosis and related cardiovascular diseases pose severe threats to human health worldwide. There is evidence to suggest that at least 50% of foam cells in atheromas are derived from vascular smooth muscle cells (VSMCs); the first step in this process involves migration to human atherosclerotic lesions. Long non‑coding RNAs (lncRNAs) have been found to play significant roles in diverse biological processes. The present study aimed to investigate the role of lncRNAs in VSMCs. The expression of lncRNAs or mRNAs was detected using reverse transcription‑quantitative polymerase chain reaction. The Gene Expression Omnibus datasets in the NCBI portal were searched using the key words 'Atherosclerosis AND tissue AND Homo sapiens' and the GSE12288 dataset. Gene expression in circulating leukocytes was measured to identify patients with coronary artery disease (CAD) or controls, and used to analyze the correlation coefficient and expression profiles. The protein level of ATP‑binding cassette sub‑family G member 1 (ABCG1) and matrix metalloproteinase (MMP)3 was determined using immunohistochemistry and western blot analysis. The analysis of mouse aortic roots was performed using Masson's and Oil Red O staining. The expression of lncRNA AL355711, ABCG1 and MMP3 was found to be higher in human atherosclerotic plaques or in patients with atherosclerotic CAD. The correlation analysis revealed that ABCG1 may be involved in the regulation between lncRNA AL355711 and MMP3 in atherosclerotic CAD. The knockdown of lncRNA AL355711 inhibited ABCG1 transcription and smooth muscle cell migration. In addition, lncRNA AL355711 was found to regulate MMP3 expression through the ABCG1 pathway. The expression of ABCG1 and MMP3 was found to be high in an animal model of atherosclerosis. The results indicated that lncRNA AL355711 promoted VSMC migration and atherosclerosis partly via the ABCG1/MMP3 pathway. On the whole, the present study demonstrates that the inhibition of lncRNA AL355711 may serve as a novel therapeutic target for atherosclerosis. lncRNA AL355711 in circulating leukocytes may be a novel biomarker for atherosclerotic CAD.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily G, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily G, Member 1/metabolism
- Animals
- Atherosclerosis/genetics
- Atherosclerosis/pathology
- Cell Movement/genetics
- Cells, Cultured
- Disease Models, Animal
- Gene Expression Regulation
- Humans
- Male
- Matrix Metalloproteinase 3/genetics
- Matrix Metalloproteinase 3/metabolism
- Metabolic Networks and Pathways/genetics
- Mice, Inbred C57BL
- Mice, Knockout, ApoE
- Myocytes, Smooth Muscle/cytology
- Myocytes, Smooth Muscle/pathology
- Myocytes, Smooth Muscle/physiology
- Plaque, Atherosclerotic/genetics
- Plaque, Atherosclerotic/metabolism
- Plaque, Atherosclerotic/pathology
- RNA, Long Noncoding/genetics
- Mice
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Affiliation(s)
- Chun-Min Kang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Wei-Kang Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Ke-Wei Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Xue-Heng Li
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Rui-Ying Huang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Pei-Feng Ke
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Xing Jin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Shun-Wang Cao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Ying-Shi Yuan
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Heng Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Jun Yan
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Wei-Ye Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Xian-Zhang Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Jing-Jing Zhao
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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15
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Cao Y, Zhu H, Tan J, Yin W, Zhou Q, Xin Z, Wu Z, Jiang Z, Guo Y, Kuang Y, Li C, Zhao M, Jiang X, Peng J, Ren C. Development of an Immune-Related LncRNA Prognostic Signature for Glioma. Front Genet 2021; 12:678436. [PMID: 34194477 PMCID: PMC8238205 DOI: 10.3389/fgene.2021.678436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/29/2021] [Indexed: 01/05/2023] Open
Abstract
Introduction Glioma is the most common primary cancer of the central nervous system with dismal prognosis. Long noncoding RNAs (lncRNAs) have been discovered to play key roles in tumorigenesis in various cancers, including glioma. Because of the relevance between immune infiltrating and clinical outcome of glioma, identifying immune-related lncRNAs is urgent for better personalized management. Materials and methods Single-sample gene set enrichment analysis (ssGSEA) was applied to estimate immune infiltration, and glioma samples were divided into high immune cell infiltration group and low immune cell infiltration group. After screening differentially expressed lncRNAs in two immune groups, least absolute shrinkage and selection operator (LASSO) Cox regression analysis was performed to construct an immune-related prognostic signature. Additionally, we explored the correlation between immune infiltration and the prognostic signature. Results A total of 653 samples were appropriate for further analyses, and 10 lncRNAs were identified as immune-related lncRNAs in glioma. After univariate Cox regression and LASSO Cox regression analysis, six lncRNAs were identified to construct a prognostic signature for glioma, which could be taken as independent prognostic factors in both univariate and multivariate Cox regression analyses. Moreover, risk score was significantly correlated with all the 29 immune-related checkpoint expression (p < 0.05) in ssGSEA except neutrophils (p = 0.43). Conclusion The study constructed an immune-related prognostic signature for glioma, which contributed to improve clinical outcome prediction and guide immunotherapy.
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Affiliation(s)
- Yudong Cao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Hecheng Zhu
- Changsha Kexin Cancer Hospital, Changsha, China
| | - Jun Tan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wen Yin
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Quanwei Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaoqi Xin
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaoping Wu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhipeng Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Youwei Guo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yirui Kuang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Can Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Ming Zhao
- Changsha Kexin Cancer Hospital, Changsha, China
| | - Xingjun Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jiahui Peng
- Department of Medical Ultrasonics, Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Caiping Ren
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China
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16
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Aillaud M, Schulte LN. Emerging Roles of Long Noncoding RNAs in the Cytoplasmic Milieu. Noncoding RNA 2020; 6:ncrna6040044. [PMID: 33182489 PMCID: PMC7711603 DOI: 10.3390/ncrna6040044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/26/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
While the important functions of long noncoding RNAs (lncRNAs) in nuclear organization are well documented, their orchestrating and architectural roles in the cytoplasmic environment have long been underestimated. However, recently developed fractionation and proximity labelling approaches have shown that a considerable proportion of cellular lncRNAs is exported into the cytoplasm and associates nonrandomly with proteins in the cytosol and organelles. The functions of these lncRNAs range from the control of translation and mitochondrial metabolism to the anchoring of cellular components on the cytoskeleton and regulation of protein degradation at the proteasome. In the present review, we provide an overview of the functions of lncRNAs in cytoplasmic structures and machineries und discuss their emerging roles in the coordination of the dense intracellular milieu. It is becoming apparent that further research into the functions of these lncRNAs will lead to an improved understanding of the spatiotemporal organization of cytoplasmic processes during homeostasis and disease.
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Affiliation(s)
- Michelle Aillaud
- Institute for Lung Research, Philipps University Marburg, 35043 Marburg, Germany;
| | - Leon N Schulte
- Institute for Lung Research, Philipps University Marburg, 35043 Marburg, Germany;
- German Center for Lung Research (DZL), 35392 Giessen, Germany
- Correspondence:
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17
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Pan YB, Zhu Y, Zhang QW, Zhang CH, Shao A, Zhang J. Prognostic and Predictive Value of a Long Non-coding RNA Signature in Glioma: A lncRNA Expression Analysis. Front Oncol 2020; 10:1057. [PMID: 32793467 PMCID: PMC7394186 DOI: 10.3389/fonc.2020.01057] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/27/2020] [Indexed: 01/16/2023] Open
Abstract
The current histologically based grading system for glioma does not accurately predict which patients will have better outcomes or benefit from adjuvant chemotherapy. We proposed that combining the expression profiles of multiple long non-coding RNAs (lncRNAs) into a single model could improve prediction accuracy. We included 1,094 glioma patients from three different datasets. Using the least absolute shrinkage and selection operator (LASSO) Cox regression model, we built a multiple-lncRNA-based classifier on the basis of a training set. The predictive and prognostic accuracy of the classifier was validated using an internal test set and two external independent sets. Using this classifier, we classified patients in the training set into high- or low-risk groups with significantly different overall survival (OS, HR = 8.42, 95% CI = 4.99–14.2, p < 0.0001). The prognostic power of the classifier was then assessed in the other sets. The classifier was an independent prognostic factor and had better prognostic value than clinicopathological risk factors. The patients in the high-risk group were found to have a favorable response to adjuvant chemotherapy (HR = 0.4, 95% CI = 0.25–0.64, p < 0.0001). We built a nomogram that integrated the 10-lncRNA-based classifier and four clinicopathological risk factors to predict 3 and 5 year OS. Gene set variation analysis (GSVA) showed that pathways related to tumorigenesis, undifferentiated cancer, and epithelial–mesenchymal transition were enriched in the high-risk groups. Our classifier built on 10-lncRNAs is a reliable prognostic and predictive tool for OS in glioma patients and could predict which patients would benefit from adjuvant chemotherapy.
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Affiliation(s)
- Yuan-Bo Pan
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yiming Zhu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qing-Wei Zhang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China
| | - Chi-Hao Zhang
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Anwen Shao
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianmin Zhang
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Brain Research Institute, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Brain Science, Zhejiang University, Hangzhou, China
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18
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Bai HL, Kang CM, Sun ZQ, Li XH, Dai XY, Huang RY, Zhao JJ, Bei YR, Huang XZ, Lu ZF, Wu SG, Lu JB, Ping BH, Wang Q, Hu YW. TTDA inhibited apoptosis by regulating the p53-Bax/Bcl2 axis in glioma. Exp Neurol 2020; 331:113380. [PMID: 32540359 DOI: 10.1016/j.expneurol.2020.113380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/18/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022]
Abstract
The trichothiodystrophy group A protein (TTDA) functions in nucleotide excision repair and basal transcription. TTDA plays a role in cancers and serves as a prognostic and predictive factor in high-grade serous ovarian cancer; however, its role in human glioma remains unknown. Here, we found that TTDA was overexpressed in glioma tissues. In vitro experiments revealed that TTDA overexpression inhibited apoptosis of glioma cells and promoted cell growth, whereas knockdown of TTDA had the opposite effect. Increased TTDA expression significantly decreased the Bax/Bcl2 ratio and the level of cleaved-caspase3. TTDA interacted with the p53 gene at the -1959 bp and -1530 bp region and regulated its transcription, leading to inhibition of the p53-Bax/Bcl2 mitochondrial apoptosis pathway in glioma cells. These results indicate that TTDA is an upstream regulator of p53-mediated apoptosis and acts as an oncogene, suggesting its value as a potential molecular target for the diagnosis and treatment of glioma.
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Affiliation(s)
- Huan-Lan Bai
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chun-Min Kang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Zhen-Qing Sun
- Department of neurosurgery Ward 6, Guangdong 999 Brain Hospital, Guangzhou 510510, China
| | - Xue-Heng Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Xiao-Yan Dai
- Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 511436, China.
| | - Rui-Ying Huang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jing-Jing Zhao
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yan-Rou Bei
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Xian-Zhang Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Zhi-Feng Lu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Shao-Guo Wu
- Department of Clinical Laboratory, Guangzhou Twelfth People's Hospital, Guangzhou 510420, China
| | - Jing-Bo Lu
- Department of Vascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Bao-Hong Ping
- Hui Qiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Qian Wang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China; Laboratory Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, China.
| | - Yan-Wei Hu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China; Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510000, China.
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Du XH, Wei H, Qu GX, Tian ZC, Yao WT, Cai QQ. Gene expression regulations by long noncoding RNAs and their roles in cancer. Pathol Res Pract 2020; 216:152983. [DOI: 10.1016/j.prp.2020.152983] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/03/2020] [Accepted: 04/13/2020] [Indexed: 12/13/2022]
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Mudge JM, Jungreis I, Hunt T, Gonzalez JM, Wright JC, Kay M, Davidson C, Fitzgerald S, Seal R, Tweedie S, He L, Waterhouse RM, Li Y, Bruford E, Choudhary JS, Frankish A, Kellis M. Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. Genome Res 2019; 29:2073-2087. [PMID: 31537640 PMCID: PMC6886504 DOI: 10.1101/gr.246462.118] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify evolutionary signatures of protein-coding regions using multispecies genome alignments. Here, we present the first whole-genome PhyloCSF prediction tracks for human, mouse, chicken, fly, worm, and mosquito. We develop a workflow that uses machine learning to predict novel conserved protein-coding regions and efficiently guide their manual curation. We analyze more than 1000 high-scoring human PhyloCSF regions and confidently add 144 conserved protein-coding genes to the GENCODE gene set, as well as additional coding regions within 236 previously annotated protein-coding genes, and 169 pseudogenes, most of them disabled after primates diverged. The majority of these represent new discoveries, including 70 previously undetected protein-coding genes. The novel coding genes are additionally supported by single-nucleotide variant evidence indicative of continued purifying selection in the human lineage, coding-exon splicing evidence from new GENCODE transcripts using next-generation transcriptomic data sets, and mass spectrometry evidence of translation for several new genes. Our discoveries required simultaneous comparative annotation of other vertebrate genomes, which we show is essential to remove spurious ORFs and to distinguish coding from pseudogene regions. Our new coding regions help elucidate disease-associated regions by revealing that 118 GWAS variants previously thought to be noncoding are in fact protein altering. Altogether, our PhyloCSF data sets and algorithms will help researchers seeking to interpret these genomes, while our new annotations present exciting loci for further experimental characterization.
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Affiliation(s)
- Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Jose Manuel Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - James C Wright
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Stephen Fitzgerald
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Ruth Seal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge CB2 0PT, United Kingdom
| | - Susan Tweedie
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Liang He
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Yue Li
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Elspeth Bruford
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge CB2 0PT, United Kingdom
| | - Jyoti S Choudhary
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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