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Huang X, Ma J, Wei Y, Chen H, Chu W. Identification of biomarkers associated with diagnosis of postmenopausal osteoporosis patients based on bioinformatics and machine learning. Front Genet 2023; 14:1198417. [PMID: 37465165 PMCID: PMC10352088 DOI: 10.3389/fgene.2023.1198417] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/19/2023] [Indexed: 07/20/2023] Open
Abstract
Background: Accumulating evidence suggests that postmenopausal osteoporosis (PMOP) is a common chronic systemic metabolic bone disease, but its specific molecular pathogenesis remains unclear. This study aimed to identify novel genetic diagnostic markers for PMOP. Methods: In this paper, we combined three GEO datasets to identify differentially expressed genes (DEGs) and performed functional enrichment analysis of PMOP-related differential genes. Key genes were analyzed using two machine learning algorithms, namely, LASSO and the Gaussian mixture model, and candidate biomarkers were found after taking the intersection. After further ceRNA network construction, methylation analysis, and immune infiltration analysis, ACACB and WWP1 were finally selected as diagnostic markers. Twenty-four clinical samples were collected, and the expression levels of biomarkers in PMOP were detected by qPCR. Results: We identified 34 differential genes in PMOP. DEG enrichment was mainly related to amino acid synthesis, inflammatory response, and apoptosis. The ceRNA network construction found that XIST-hsa-miR-15a-5p/hsa-miR-15b-5p/hsa-miR-497-5p and hsa-miR-195-5p-WWP1/ACACB may be RNA regulatory pathways regulating PMOP disease progression. ACACB and WWP1 were identified as diagnostic genes for PMOP, and validated in datasets and clinical sample experiments. In addition, these two genes were also significantly associated with immune cells, such as T, B, and NK cells. Conclusion: Overall, we identified two vital diagnostic genes responsible for PMOP. The results may help provide potential immunotherapeutic targets for PMOP.
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Affiliation(s)
- Xinzhou Huang
- Department of Orthopedics, 3201 Hospital of Xi’an Jiaotong University Health Science Center, Hanzhong, China
| | - Jinliang Ma
- Department of Orthopedics, The First People’s Hospital of Jingzhou (First Affiliated Hospital of Yangtze University), Jingzhou, China
| | - Yongkun Wei
- Department of Orthopedics, 3201 Hospital of Xi’an Jiaotong University Health Science Center, Hanzhong, China
| | - Hui Chen
- Department of Clinical Laboratory, The First People’s Hospital of Jingzhou (First Affiliated Hospital of Yangtze University), Jingzhou, China
| | - Wei Chu
- Department of Orthopedics, The First People’s Hospital of Jingzhou (First Affiliated Hospital of Yangtze University), Jingzhou, China
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2
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Xiao Y, Cai G, Feng X, Li Y, Guo W, Guo Q, Huang Y, Su T, Li C, Luo X, Zheng Y, Yang M. Splicing factor YBX1 regulates bone marrow stromal cell fate during aging. EMBO J 2023; 42:e111762. [PMID: 36943004 PMCID: PMC10152142 DOI: 10.15252/embj.2022111762] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/23/2023] Open
Abstract
Senescence and altered differentiation potential of bone marrow stromal cells (BMSCs) lead to age-related bone loss. As an important posttranscriptional regulatory pathway, alternative splicing (AS) regulates the diversity of gene expression and has been linked to induction of cellular senescence. However, the role of splicing factors in BMSCs during aging remains poorly defined. Herein, we found that the expression of the splicing factor Y-box binding protein 1 (YBX1) in BMSCs decreased with aging in mice and humans. YBX1 deficiency resulted in mis-splicing in genes linked to BMSC osteogenic differentiation and senescence, such as Fn1, Nrp2, Sirt2, Sp7, and Spp1, thus contributing to BMSC senescence and differentiation shift during aging. Deletion of Ybx1 in BMSCs accelerated bone loss in mice, while its overexpression stimulated bone formation. Finally, we identified a small compound, sciadopitysin, which attenuated the degradation of YBX1 and bone loss in old mice. Our study demonstrated that YBX1 governs cell fate of BMSCs via fine control of RNA splicing and provides a potential therapeutic target for age-related osteoporosis.
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Affiliation(s)
- Ye Xiao
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Guang‐Ping Cai
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Xu Feng
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Yu‐Jue Li
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Wan‐Hui Guo
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Qi Guo
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Yan Huang
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Tian Su
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Chang‐Jun Li
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Xiang‐Hang Luo
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaChina
| | - Yong‐Jun Zheng
- Department of Burn SurgeryThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| | - Mi Yang
- Department of Endocrinology, Endocrinology Research CenterXiangya Hospital of Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaChina
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3
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Wang L, Chen Z, Chen D, Kan B, He Y, Cai H. Farnesyl diphosphate synthase promotes cell proliferation by regulating gene expression and alternative splicing profiles in HeLa cells. Oncol Lett 2023; 25:145. [PMID: 36936029 PMCID: PMC10018273 DOI: 10.3892/ol.2023.13731] [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: 09/02/2022] [Accepted: 02/10/2023] [Indexed: 03/04/2023] Open
Abstract
Farnesyl diphosphate synthase (FDPS), an essential enzyme involved in the mevalonate pathway, is implicated in various diseases, including multiple types of cancer. As an RNA-binding protein (RBP), FDPS is also involved in transcriptional and post-transcriptional regulation. However, to the best of our knowledge, transcriptome-wide targets of FDPS still remain unknown. In the present study, FDPS expression patterns in pan-cancer were analyzed. In addition, it was investigated how FDPS overexpression (FDPS-OE) regulates the transcriptome in HeLa cells. FDPS-OE increased the proliferation rate in HeLa cells by MTT assay. Using transcriptome-wide high throughput sequencing and bioinformatics analysis, it was found that FDPS upregulated the expression levels of genes enriched in cell proliferation and extracellular matrix organization, including the laminin subunit γ2, interferon-induced proteins with tetratricopeptide repeats 2 and matrix metallopeptidase 19 genes. According to alternative splicing (AS) analysis, FDPS modulated the splicing patterns of the bone morphogenic protein 1, semaphorin 4D, annexin A2 and sirtuin 2 genes, which are enriched in the cell cycle and DNA repair, and are related to cell proliferation. To corroborate the FDPS-regulated transcriptome findings, FDPS was overexpressed in human osteosarcoma cells. Differentially expressed genes and regulated AS genes in the cells were both validated by reverse transcription-quantitative PCR. The results suggested that, as an emerging RBP, FDPS may serve an important role in transcriptome profiles by altering gene expression and regulating AS. FDPS also affected the cell proliferation rate. These findings broaden the understanding of the molecular functions of FDPS, and the potential of FDPS as a target in therapy should be investigated.
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Affiliation(s)
- Lijuan Wang
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Zhigang Chen
- ABLife BioBigData Institute, Wuhan, Hubei 430075, P.R. China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, Hubei 430075, P.R. China
| | - Bo Kan
- Department of Clinical Laboratory, The Second Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Yangfang He
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hanqing Cai
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
- Correspondence to: Dr Hanqing Cai, Department of Endocrinology, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan, Changchun, Jilin 130021, P.R. China, E-mail:
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4
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Deng S, Yi P, Xu M, Yi Q, Feng J. Dysfunctional gene splicing in glucose metabolism may contribute to Alzheimer's disease. Chin Med J (Engl) 2023; 136:666-675. [PMID: 35830275 PMCID: PMC10129079 DOI: 10.1097/cm9.0000000000002214] [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: 12/14/2022] [Indexed: 11/26/2022] Open
Abstract
ABSTRACT The glucose metabolism is crucial for sustained brain activity as it provides energy and is a carbon source for multiple biomacromolecules; glucose metabolism decreases dramatically in Alzheimer's disease (AD) and may be a fundamental cause for its development. Recent studies reveal that the alternative splicing events of certain genes effectively regulate several processes in glucose metabolism including insulin receptor, insulin-degrading enzyme, pyruvate kinase M, receptor for advanced glycation endproducts, and others, thereby, influencing glucose uptake, glycolysis, and advanced glycation end-products-mediated signaling pathways. Indeed, the discovery of aberrant alternative splicing that changes the proteomic diversity and protein activity in glucose metabolism has been pivotal in our understanding of AD development. In this review, we summarize the alternative splicing events of the glucose metabolism-related genes in AD pathology and highlight the crucial regulatory roles of splicing factors in the alternative splicing process. We also discuss the emerging therapeutic approaches for targeting splicing factors for AD treatment.
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Affiliation(s)
- Shengfeng Deng
- Laboratory of Anesthesiology, Department of Anesthesiology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Peng Yi
- Laboratory of Anesthesiology, Department of Anesthesiology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Mingliang Xu
- Laboratory of Anesthesiology, Department of Anesthesiology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Qian Yi
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Jianguo Feng
- Laboratory of Anesthesiology, Department of Anesthesiology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Affiliated Xinhui Hospital, Southern Medical University (People's Hospital of Xinhui District), Jiangmen, Guangdong 529100, China
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5
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Heard BJ, Barton KI, Abubacker S, Chung M, Martin CR, Schmidt TA, Shrive NG, Hart DA. Synovial and cartilage responsiveness to peri-operative hyaluronic acid ± dexamethasone administration following a limited injury to the rabbit stifle joint. J Orthop Res 2022; 40:838-845. [PMID: 34061360 DOI: 10.1002/jor.25108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/03/2021] [Accepted: 05/25/2021] [Indexed: 02/04/2023]
Abstract
Posttraumatic osteoarthritis (PTOA) can develop after an injury to the knee. Previous studies have indicated that an intra-articular (IA) injection of the potent glucocorticoid dexamethasone (DEX) may significantly prevent induction of PTOA. The aim of the present study was to investigate the effectiveness of a single IA injection of hyaluronic acid (HA), alone and in combination with DEX following a localized intra-articular injury as a PTOA-preventing treatment option. An established rabbit model of surgical injury consisting of dual intra-articular (IA) drill holes in a non-cartilaginous area of the femoral notch near the origin of the anterior cruciate ligament (ACL) to allow for bleeding into the joint space was used. Immediately following surgery, subjects were treated with HA, HA + DEX, or received no treatment. An uninjured control group was used for comparison (N = 5/group). Rabbits were sacrificed and investigated at 9 weeks post-injury. At 9 weeks post-injury, there was a significant protective capacity of the single IA treatment of DEX + HA on the histological grade of the synovial tissue, and some variable location-specific effects of HA alone and HA + DEX interactions on cartilage damage. Thus, it is possible that co-treatment with HA may interfere with the effectiveness of the DEX. In vitro friction testing indicated that DEX did not interfere with the lubricating ability of HA or synovial fluid on cartilage. These results suggest that a single IA administration of HA in combination with DEX following an IA injury is not recommended for inhibition of PTOA progression in this model.
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Affiliation(s)
- B J Heard
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.,Department of Surgery, University of Calgary, Calgary, Alberta, Canada
| | - K I Barton
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.,Faculty of Kinesiology, University of Calgary, Calgary, Alberta, Canada
| | - S Abubacker
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.,Faculty of Kinesiology, University of Calgary, Calgary, Alberta, Canada
| | - M Chung
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
| | - C R Martin
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.,Department of Surgery, University of Calgary, Calgary, Alberta, Canada
| | - T A Schmidt
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.,Faculty of Kinesiology, University of Calgary, Calgary, Alberta, Canada.,Sculich School of Engineering, University of Calgary, Calgary, Alberta, Canada
| | - N G Shrive
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.,Sculich School of Engineering, University of Calgary, Calgary, Alberta, Canada
| | - D A Hart
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.,Department of Surgery, University of Calgary, Calgary, Alberta, Canada.,Faculty of Kinesiology, University of Calgary, Calgary, Alberta, Canada.,Bone & Joint Health Strategic Clinical Network, Edmonton, Alberta, Canada
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6
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Liu Y, Shen H, Greenbaum J, Liu A, Su KJ, Zhang LS, Zhang L, Tian Q, Hu HG, He JS, Deng HW. Gene Expression and RNA Splicing Imputation Identifies Novel Candidate Genes Associated with Osteoporosis. J Clin Endocrinol Metab 2020; 105:5895512. [PMID: 32827035 PMCID: PMC7736639 DOI: 10.1210/clinem/dgaa572] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022]
Abstract
CONTEXT Though genome-wide association studies (GWASs) have identified hundreds of genetic variants associated with osteoporosis related traits, such as bone mineral density (BMD) and fracture, it remains a challenge to interpret their biological functions and underlying biological mechanisms. OBJECTIVE Integrate diverse expression quantitative trait loci and splicing quantitative trait loci data with several powerful GWAS datasets to identify novel candidate genes associated with osteoporosis. DESIGN, SETTING, AND PARTICIPANTS Here, we conducted a transcriptome-wide association study (TWAS) for total body BMD (TB-BMD) (n = 66 628 for discovery and 7697 for validation) and fracture (53 184 fracture cases and 373 611 controls for discovery and 37 857 cases and 227 116 controls for validation), respectively. We also conducted multi-SNP-based summarized mendelian randomization analysis to further validate our findings. RESULTS In total, we detected 88 genes significantly associated with TB-BMD or fracture through expression or ribonucleic acid splicing. Summarized mendelian randomization analysis revealed that 78 of the significant genes may have potential causal effects on TB-BMD or fracture in at least 1 specific tissue. Among them, 64 genes have been reported in previous GWASs or TWASs for osteoporosis, such as ING3, CPED1, and WNT16, as well as 14 novel genes, such as DBF4B, GRN, TMUB2, and UNC93B1. CONCLUSIONS Overall, our findings provide novel insights into the pathogenesis mechanisms of osteoporosis and highlight the power of a TWAS to identify and prioritize potential causal genes.
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Affiliation(s)
- Yong Liu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Jonathan Greenbaum
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Anqi Liu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Li-Shu Zhang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
| | - Qing Tian
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Hong-Gang Hu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Jin-Sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Hong-Wen Deng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
- Correspondence and Reprint Requests: Hong-Wen Deng, PhD, Professor, Director, Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, 1440 Canal St., Suite 2001, New Orleans, LA 70112.
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7
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Rehman SU, Ashraf S, Ahamad S, Sarwar T, Husain MA, Ahmad P, Tabish M, Jairajpuri MA. Identification of a novel alternatively spliced isoform of antithrombin containing an additional RCL-like loop. Biochem Biophys Res Commun 2019; 517:421-426. [PMID: 31378371 DOI: 10.1016/j.bbrc.2019.07.113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 07/28/2019] [Indexed: 11/22/2022]
Abstract
Antithrombin (AT3) is one of the most important inhibitors of blood coagulation proteases that belong to the serpin family of protease inhibitors. In this study, a novel alternatively spliced isoform of AT3 was identified, both at transcript and protein level. This novel transcript contains an additional region in the continuation of exon 3b that was included in the transcript due to use of an alternate 5' splice site. The existence of the novel transcript was confirmed in human brain and liver through RT-PCR. An analysis of the complete transcript indicated that the native reactive centre loop (RCL) of AT3 is maintained; however the novel amino acid sequence projects out as an additional loop as evident from MD simulation studies. A unique amino acid sequence present in the novel isoform was used for the development of polyclonal antibody. The expression of novel isoform was confirmed in human brain and liver tissue using Western blot analysis. Interestingly an alignment of RCL like domain with other inhibitory serpins showed significant similarity with the neuroserpin RCL. To the best of our knowledge, this is the first evidence of alternatively spliced AT3 sequence containing an additional loop and could have physiological relevance.
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Affiliation(s)
- Sayeed Ur Rehman
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India; Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
| | - Shazia Ashraf
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India; Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shahzaib Ahamad
- Department of Biotechnology, School of Engineering & Technology, IFTM University, Lodhipur-Rajput, Delhi Road, Moradabad, India
| | - Tarique Sarwar
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | | | - Parvez Ahmad
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P, India
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8
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Huang W, Chen X, Guan Q, Zhong Z, Ma J, Yang B, Wang T, Zhu W, Tian J. Changes of alternative splicing in Arabidopsis thaliana grown under different CO2 concentrations. Gene 2019; 689:43-50. [DOI: 10.1016/j.gene.2018.11.083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 11/09/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
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9
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Xu J, Hu X, Jiang S, Wang Y, Parungao R, Zheng S, Nie Y, Liu T, Song K. The Application of Multi-Walled Carbon Nanotubes in Bone Tissue Repair Hybrid Scaffolds and the Effect on Cell Growth In Vitro. Polymers (Basel) 2019; 11:E230. [PMID: 30960214 PMCID: PMC6419040 DOI: 10.3390/polym11020230] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 01/20/2023] Open
Abstract
In this study, composite scaffolds with different multi-walled carbon nanotubes (MWCNTs) content were prepared by freeze-drying. These scaffolds were characterized by scanning electron microscope (SEM), energy dispersive spectroscopy (EDS), Fourier transform infrared spectroscopy (FTIR), porosity, hydrophilicity, mechanical strength, and degradation. The MWCNTs scaffolds were structurally sound and had porous structures that offered ample space for adherence, proliferation, and differentiation of MC3T3-E1 cells, and also supported the transport of nutrients and metabolic waste. CS/Gel/nHAp/0.3%MWCNTs scaffolds provided the best outcomes in terms of scaffold porosity, hydrophilicity, and degradation rate. However, CS/Gel/nHAp/0.6%MWCNTs scaffolds were found to support the optimal growth, homogenous distribution, and biological activity of MC3T3-E1 cells. The excellent properties of CS/Gel/nHAp/0.6%MWCNTs scaffolds for the adhesion, proliferation, and osteogenesis differentiation of MC3T3-E1 cells in vitro highlights the potential applications of this scaffold in bone tissue regeneration.
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Affiliation(s)
- Jie Xu
- State Key Laboratory of Fine Chemicals, Dalian R&D Center for Stem Cell and Tissue Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Xueyan Hu
- State Key Laboratory of Fine Chemicals, Dalian R&D Center for Stem Cell and Tissue Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Siyu Jiang
- State Key Laboratory of Fine Chemicals, Dalian R&D Center for Stem Cell and Tissue Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Yiwei Wang
- Burns Research Group, ANZAC Research Institute, Concord, University of Sydney, Sydney, NSW 2139, Australia.
| | - Roxanne Parungao
- Burns Research Group, ANZAC Research Institute, Concord, University of Sydney, Sydney, NSW 2139, Australia.
| | - Shuangshuang Zheng
- Zhengzhou Institute of Emerging Industrial Technology, Zhengzhou 450000, China.
| | - Yi Nie
- Zhengzhou Institute of Emerging Industrial Technology, Zhengzhou 450000, China.
- Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Tianqing Liu
- State Key Laboratory of Fine Chemicals, Dalian R&D Center for Stem Cell and Tissue Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Kedong Song
- State Key Laboratory of Fine Chemicals, Dalian R&D Center for Stem Cell and Tissue Engineering, Dalian University of Technology, Dalian 116024, China.
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10
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Differentially expressed novel alternatively spliced transcript variant of tumor suppressor Stk11 gene in mouse. Gene 2018; 668:146-154. [PMID: 29777910 DOI: 10.1016/j.gene.2018.05.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 04/26/2018] [Accepted: 05/15/2018] [Indexed: 11/22/2022]
Abstract
Serine/threonine kinase 11 (STK11) is a protein kinase that is encoded by Stk11 gene located on chromosome 19 and 10 in humans and mouse respectively. It acts as a master kinase of adenine monophosphate-activated protein kinase (AMPK) pathway that coordinates the regulation of cellular energy metabolism and cell division. STK11 exerts effect by activating more than 14 kinases including AMPK and AMPK-related kinases. It is also known to regulate cell polarity and acts as tumor suppressor. Alternative splicing of pre-mRNA is a mechanism which results in multiple transcript variants of a single gene. In human, two STK11 isoforms have been reported, an alternatively spliced isoform which has variation at its C-terminal and mostly expressed in testis (LKB1S). Another isoform exhibiting oncogenic properties lacks few residues at its N-terminal (ΔN-LKB1). In the present study, we report the identification of a new transcript variant Stk11N which is generated through alternative splicing. The new variant was found to have differential and tissue specific expression at Postnatal-7 and adult stages of mouse. As compared to the known variant Stk11C, the conceptually translated amino acid sequences of the new variant differ from exon-E2 onwards. In silico post translational studies of the new and published variant show similarity in some of the properties while differ in properties like nuclear export signals, phosphorylation, glycosylation, etc. Thus, alternative splicing of Stk11 gene generating new variant with heterogeneous properties suggests for complex regulation of these variants in controlling the AMPK pathway and other functions.
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11
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Li L, Feng J, Chen Y, Li S, Ou M, Sun W, Tang L. Estradiol shows anti-skin cancer activities through decreasing MDM2 expression. Oncotarget 2018; 8:8459-8474. [PMID: 28035066 PMCID: PMC5352414 DOI: 10.18632/oncotarget.14275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 11/30/2016] [Indexed: 12/19/2022] Open
Abstract
Estradiol plays important roles in many biological responses inducing tumor genesis and cancer treatment. However, the effects of estradiol on tumors were inconsistent among a lot of researches and the mechanism is not fully understood. Our previous study indicated that splicing factor hnRNPA1 could bind to the human homologue of mouse double minute (MDM2), an oncogene which has been observed to be over-expressed in numerous types of cancers. In this research, we investigated whether and how estradiol correlate to cancer cell behaviors through heterogeneous nuclear ribonucleoprotein (hnRNPA1) and MDM2. Results showed that 10×10-13Mestradiol elevated the expression of hnRNPA1 regardless ER expression in cells, and then down-regulated the expression of MDM2. At the same time, estradiol inhibited cell proliferation, migration and epithelial-mesenchymal transition progression of A375 and GLL19 cells. While, knocking down hnRNPA1 through the transfection of hnRNPA1 siRNA led to the increase of MDM2 at both protein level and gene level In vivo experiment, subcutaneous injection with estradiol every two days near the tumor at doses of 2.5mg/kg/d suppressed tumor growth and reduced MDM2 expression. In a word, via increasing hnRNPA1 level and then reducing the expression of MDM2, estradiol prevented carcinogenesis in melanomas. We confirmed therapeutic effect of estradiol, as well as a new way for estradiol to resist skin cancer.
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Affiliation(s)
- Li Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Jianguo Feng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.,Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Sichuan, China
| | - Ying Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Shun Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Mengting Ou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Weichao Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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12
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da Costa PJ, Menezes J, Romão L. The role of alternative splicing coupled to nonsense-mediated mRNA decay in human disease. Int J Biochem Cell Biol 2017; 91:168-175. [PMID: 28743674 DOI: 10.1016/j.biocel.2017.07.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/15/2017] [Accepted: 07/18/2017] [Indexed: 12/29/2022]
Abstract
Alternative pre-mRNA splicing (AS) affects gene expression as it generates proteome diversity. Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that recognizes and selectively degrades mRNAs carrying premature translation-termination codons (PTCs), preventing the production of truncated proteins that could result in disease. Several studies have also implicated NMD in the regulation of steady-state levels of physiological mRNAs. In addition, it is known that several regulated AS events do not lead to generation of protein products, as they lead to transcripts that carry PTCs and thus, they are committed to NMD. Indeed, an estimated one-third of naturally occurring, alternatively spliced mRNAs is targeted for NMD, being AS coupled to NMD (AS-NMD) an efficient strategy to regulate gene expression. In this review, we will focus on how AS mechanism operates and how can be coupled to NMD to fine-tune gene expression levels. Furthermore, we will demonstrate the physiological significance of the interplay among AS and NMD in human disease, such as cancer and neurological disorders. The understanding of how AS-NMD orchestrates expression of vital genes is of utmost importance for the advance in diagnosis, prognosis and treatment of many human disorders.
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Affiliation(s)
- Paulo J da Costa
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Juliane Menezes
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
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13
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Villegas-Ruiz V, Hendlmeier F, Buentello-Volante B, Rodríguez-Loaiza JL, Miranda-Duarte A, Zenteno JC. Genome-wide mRNA analysis reveals a TUBD1 isoform profile as a potential biomarker for diabetic retinopathy development. Exp Eye Res 2017; 155:99-106. [DOI: 10.1016/j.exer.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 12/23/2016] [Accepted: 01/21/2017] [Indexed: 01/23/2023]
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14
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Martin G, Selcuklu SD, Schouest K, Nembaware V, McKeown PC, Seoighe C, Spillane C. Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells. Gene 2017; 598:107-112. [PMID: 27826023 DOI: 10.1016/j.gene.2016.11.004] [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: 07/09/2016] [Revised: 10/16/2016] [Accepted: 11/03/2016] [Indexed: 10/20/2022]
Abstract
Allele-specific splicing is the production of different RNA isoforms from different alleles of a gene. Altered splicing patterns such as exon skipping can have a dramatic effect on the final protein product yet have traditionally proven difficult to predict. We investigated the splicing effects of a set of nine single nucleotide polymorphisms (SNPs) which are predicted to have a direct impact on mRNA splicing, each in a different gene. Predictions were based on SNP location relative to splice junctions and intronic/exonic splicing elements, combined with an analysis of splice isoform expression data from public sources. Of the nine genes tested, six SNPs led to direct impacts on mRNA splicing as determined by the splicing reporter minigene assay and RT-PCR in human HeLa cells, of which four were allele-specific effects. These included previously unreported alternative splicing patterns in the genes ZNF419 and DKKL1. Notably, the SNP in ZNF419, a transcription factor, leads to the deletion of a DNA-binding domain from the protein and is associated with an expression QTL, while the SNP in DKKL1 leads to shortened transcripts predicted to produce a truncated protein. We conclude that the impact of SNP mutations on mRNA splicing, and its biological relevance, can be predicted by integrating SNP position with available data on relative isoform abundance in human cell lines.
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Affiliation(s)
- Grace Martin
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - S Duygu Selcuklu
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - Katherine Schouest
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - Victoria Nembaware
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Private Bag, Rondebosch, 7700 Cape Town, South Africa
| | - Peter C McKeown
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Charles Spillane
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland.
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15
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Kim YG, Kim M, Kang JH, Kim HJ, Park JW, Lee JM, Suh JY, Kim JY, Lee JH, Lee Y. Transcriptome sequencing of gingival biopsies from chronic periodontitis patients reveals novel gene expression and splicing patterns. Hum Genomics 2016; 10:28. [PMID: 27531006 PMCID: PMC4988046 DOI: 10.1186/s40246-016-0084-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/04/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Periodontitis is the most common chronic inflammatory disease caused by complex interaction between the microbial biofilm and host immune responses. In the present study, high-throughput RNA sequencing was utilized to systemically and precisely identify gene expression profiles and alternative splicing. METHODS The pooled RNAs of 10 gingival tissues from both healthy and periodontitis patients were analyzed by deep sequencing followed by computational annotation and quantification of mRNA structures. RESULTS The differential expression analysis designated 400 up-regulated genes in periodontitis tissues especially in the pathways of defense/immunity protein, receptor, protease, and signaling molecules. The top 10 most up-regulated genes were CSF3, MAFA, CR2, GLDC, SAA1, LBP, MME, MMP3, MME-AS1, and SAA4. The 62 down-regulated genes in periodontitis were mainly cytoskeletal and structural proteins. The top 10 most down-regulated genes were SERPINA12, MT4, H19, KRT2, DSC1, PSORS1C2, KRT27, LCE3C, AQ5, and LCE6A. The differential alternative splicing analysis revealed unique transcription variants in periodontitis tissues. The EDB exon was predominantly included in FN1, while exon 2 was mostly skipped in BCL2A1. CONCLUSIONS These findings using RNA sequencing provide novel insights into the pathogenesis mechanism of periodontitis in terms of gene expression and alternative splicing.
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Affiliation(s)
- Yong-Gun Kim
- Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea.,Institute for Hard Tissue and Bone Regeneration, Kyungpook National University, Daegu, 41940, Korea
| | - Minjung Kim
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Korea
| | - Ji Hyun Kang
- Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea
| | - Hyo Jeong Kim
- Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea
| | - Jin-Woo Park
- Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea
| | - Jae-Mok Lee
- Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea
| | - Jo-Young Suh
- Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea
| | - Jae-Young Kim
- Institute for Hard Tissue and Bone Regeneration, Kyungpook National University, Daegu, 41940, Korea.,Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea
| | - Jae-Hyung Lee
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Korea. .,Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul, 02447, Korea.
| | - Youngkyun Lee
- Institute for Hard Tissue and Bone Regeneration, Kyungpook National University, Daegu, 41940, Korea. .,Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea.
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16
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Feng J, Li L, Tong L, Tang L, Wu S. The Involvement of Splicing Factor hnRNP A1 in UVB-induced Alternative Splicing of hdm2. Photochem Photobiol 2016; 92:318-324. [PMID: 26757361 DOI: 10.1111/php.12564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
Abstract
Human homolog double minute 2 (hdm2), an oncoprotein, which binds to tumor suppressor p53 to facilitate its degradation, has been known to contribute to tumorigenesis. Its splicing variants are reported to be highly expressed in many cancers and can be induced by ultraviolet B light (UVB). However, the mechanisms of how UVB radiation induces hdm2 alternative splicing still remain unclear. In this study, we investigated the roles of two common splicing factors, heterogeneous nuclear ribonucleoproteins (hnRNP) A1 and serine/arginine-rich splicing factor 1 (SRSF1), in regulating UVB-induced hdm2 splicing. Our study indicated that while the expression of both hnRNP A1 and SRSF1 are induced, only hnRNP A1 is involved in hdm2 alternative splicing upon UVB irradiation. Overexpression of hnRNP A1 resulted in decrease of full-length hdm2 (hdm2-FL) and increase of hdm2B, one of hdm2 alternate-splicing forms; while down-regulated hnRNP A1 expression led to the decrease of the hdm2-FL and hdm2B in HaCaT cells. Protein-mRNA binding assay confirmed that UVB irradiation could increase the binding of hnRNP A1 to hdm2 pre-mRNA. In conclusion, we elucidated that UVB induces alternative splicing of hdm2 by increasing the expression and the binding of hnRNP A1 to hdm2 full-length mRNA.
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Affiliation(s)
- Jianguo Feng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.,Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
| | - Li Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Lingying Tong
- Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Shiyong Wu
- Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
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17
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Steffen P, Kwiatkowski M, Robertson WD, Zarrine-Afsar A, Deterra D, Richter V, Schlüter H. Protein species as diagnostic markers. J Proteomics 2016; 134:5-18. [DOI: 10.1016/j.jprot.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/28/2015] [Accepted: 12/09/2015] [Indexed: 02/07/2023]
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18
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Escobar-García D, Mejía-Saavedra J, Jarquín-Yáñez L, Molina-Frechero N, Pozos-Guillén A. Collagenase 1A2 (COL1A2) gene A/C polymorphism in relation to severity of dental fluorosis. Community Dent Oral Epidemiol 2015; 44:162-8. [DOI: 10.1111/cdoe.12201] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 10/09/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Diana Escobar-García
- Laboratorio de Ciencias Básicas; Facultad de Estomatología; Universidad Autónoma de San Luis Potosí; San Luis Potosí México
| | - Jesús Mejía-Saavedra
- Centro de Investigación Aplicada en Ambiente y Salud (CIACYT-Facultad de Medicina) Universidad Autónoma de San Luis Potosí; San Luis Potosí México
| | - Lizet Jarquín-Yáñez
- Centro de Investigación Aplicada en Ambiente y Salud (CIACYT-Facultad de Medicina) Universidad Autónoma de San Luis Potosí; San Luis Potosí México
| | - Nelly Molina-Frechero
- División de Ciencias Biológicas y de la Salud; Universidad Autónoma Metropolitana; México D.F. México
| | - Amaury Pozos-Guillén
- Laboratorio de Ciencias Básicas; Facultad de Estomatología; Universidad Autónoma de San Luis Potosí; San Luis Potosí México
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19
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Rehman SU, Husain MA, Sarwar T, Ishqi HM, Tabish M. Modulation of alternative splicing by anticancer drugs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:369-79. [DOI: 10.1002/wrna.1283] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/20/2015] [Accepted: 03/20/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Sayeed Ur Rehman
- Department of Biochemistry, Faculty of Life Sciences; Aligarh Muslim University; Aligarh India
| | - Mohammed Amir Husain
- Department of Biochemistry, Faculty of Life Sciences; Aligarh Muslim University; Aligarh India
| | - Tarique Sarwar
- Department of Biochemistry, Faculty of Life Sciences; Aligarh Muslim University; Aligarh India
| | - Hassan Mubarak Ishqi
- Department of Biochemistry, Faculty of Life Sciences; Aligarh Muslim University; Aligarh India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences; Aligarh Muslim University; Aligarh India
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20
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Chen W, Liu Y, Li H, Chang S, Shu D, Zhang H, Chen F, Xie Q. Intronic deletions of tva receptor gene decrease the susceptibility to infection by avian sarcoma and leukosis virus subgroup A. Sci Rep 2015; 5:9900. [PMID: 25873518 PMCID: PMC4397534 DOI: 10.1038/srep09900] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/17/2015] [Indexed: 12/16/2022] Open
Abstract
The group of avian sarcoma and leukosis virus (ASLV) in chickens contains six highly related subgroups, A to E and J. Four genetic loci, tva, tvb, tvc and tvj, encode for corresponding receptors that determine the susceptibility to the ASLV subgroups. The prevalence of ASLV in hosts may have imposed strong selection pressure toward resistance to ASLV infection, and the resistant alleles in all four receptor genes have been identified. In this study, two new alleles of the tva receptor gene, tvar5 and tvar6, with similar intronic deletions were identified in Chinese commercial broilers. These natural mutations delete the deduced branch point signal within the first intron, disrupting mRNA splicing of the tva receptor gene and leading to the retention of intron 1 and introduction of premature TGA stop codons in both the longer and shorter tva isoforms. As a result, decreased susceptibility to subgroup A ASLV in vitro and in vivo was observed in the subsequent analysis. In addition, we identified two groups of heterozygous allele pairs which exhibited quantitative differences in host susceptibility to ASLV-A. This study demonstrated that defective splicing of the tva receptor gene can confer genetic resistance to ASLV subgroup A in the host.
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Affiliation(s)
- Weiguo Chen
- College of Animal Science, South China Agricultural University &Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P. R. China
| | - Yang Liu
- College of Animal Science, South China Agricultural University &Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P. R. China
| | - Hongxing Li
- College of Animal Science, South China Agricultural University &Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P. R. China
| | - Shuang Chang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, P. R. China
| | - Dingming Shu
- Institute of Animal Science, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, P. R. China
| | - Huanmin Zhang
- USDA, Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, U.S.A
| | - Feng Chen
- 1] College of Animal Science, South China Agricultural University &Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P. R. China [2] South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642, P. R. China
| | - Qingmei Xie
- 1] College of Animal Science, South China Agricultural University &Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P. R. China [2] Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangdong, Guangzhou, 510642, P. R. China [3] South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642, P. R. China
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21
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Chen FC. Alternative RNA structure-coupled gene regulations in tumorigenesis. Int J Mol Sci 2014; 16:452-75. [PMID: 25551597 PMCID: PMC4307256 DOI: 10.3390/ijms16010452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/16/2014] [Indexed: 12/11/2022] Open
Abstract
Alternative RNA structures (ARSs), or alternative transcript isoforms, are critical for regulating cellular phenotypes in humans. In addition to generating functionally diverse protein isoforms from a single gene, ARS can alter the sequence contents of 5'/3' untranslated regions (UTRs) and intronic regions, thus also affecting the regulatory effects of these regions. ARS may introduce premature stop codon(s) into a transcript, and render the transcript susceptible to nonsense-mediated decay, which in turn can influence the overall gene expression level. Meanwhile, ARS can regulate the presence/absence of upstream open reading frames and microRNA targeting sites in 5'UTRs and 3'UTRs, respectively, thus affecting translational efficiencies and protein expression levels. Furthermore, since ARS may alter exon-intron structures, it can influence the biogenesis of intronic microRNAs and indirectly affect the expression of the target genes of these microRNAs. The connections between ARS and multiple regulatory mechanisms underline the importance of ARS in determining cell fate. Accumulating evidence indicates that ARS-coupled regulations play important roles in tumorigenesis. Here I will review our current knowledge in this field, and discuss potential future directions.
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Affiliation(s)
- Feng-Chi Chen
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taiwan.
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22
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Lord MS, Farrugia BL, Rnjak-Kovacina J, Whitelock JM. Current serological possibilities for the diagnosis of arthritis with special focus on proteins and proteoglycans from the extracellular matrix. Expert Rev Mol Diagn 2014; 15:77-95. [DOI: 10.1586/14737159.2015.979158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Li B, Ngo S, Wu W, Xu H, Xie Z, Li Q, Pan Z. Identification and characterization of yak (Bos grunniens) b-Boule gene and its alternative splice variants. Gene 2014; 550:193-9. [PMID: 25149018 DOI: 10.1016/j.gene.2014.08.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 08/11/2014] [Accepted: 08/15/2014] [Indexed: 01/31/2023]
Abstract
Boule is responsible for meiotic arrest of sperms and male sterility during mammalian spermatogenesis. In the present study, we first identified yak b-Boule gene and its two alternative splice variants. The full length coding region of yak b-Boule is 888bp and encodes a 295-amino acid protein with a typical RNA-recognition motif (RRM) and a Deleted in Azoospermia (DAZ) repetitive sequence motif. Two alternative splice variants of yak b-Boule were generated following the consensus "GT-AG" rule and named b-Boule1 (36bp deletion in exon 3) and b-Boule2 (deletion of integral exon 7), respectively. In male yak, b-Boule, b-Boule1 and b-Boule2 were found to be exclusively expressed in the testes at a ratio of 81:0.1:1. Intriguingly, the mRNA expression levels of b-Boule and b-Boule1 in yak testis were significantly higher than those in cattle-yak, although no significant difference was observed for b-Boule2 expression between the yak and cattle-yak. These results suggest that b-Boule gene, which is partially regulated by alternative splicing, may be involved in the process of yak spermatogenesis.
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Affiliation(s)
- Bojiang Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Sherry Ngo
- Liggins Institute, University of Auckland, Auckland 1142, New Zealand
| | - Wangjun Wu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongtao Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhuang Xie
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zengxiang Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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24
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Brunet S, Sacher M. In Sickness and in Health: The Role of TRAPP and Associated Proteins in Disease. Traffic 2014; 15:803-18. [PMID: 24917561 DOI: 10.1111/tra.12183] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/06/2014] [Accepted: 06/06/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Stephanie Brunet
- Department of Biology; Concordia University; 7141 Sherbrooke Street West, SP-457.01 Montreal QC H4B 1R6 Canada
| | - Michael Sacher
- Department of Biology; Concordia University; 7141 Sherbrooke Street West, SP-457.01 Montreal QC H4B 1R6 Canada
- Department of Anatomy and Cell Biology; McGill University; 845 Sherbrooke Street West Montreal QC H3A 0G4 Canada
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25
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Multifunctional RNA processing protein SRm160 induces apoptosis and regulates eye and genital development in Drosophila. Genetics 2014; 197:1251-65. [PMID: 24907259 DOI: 10.1534/genetics.114.164434] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
SRm160 is an SR-like protein implicated in multiple steps of RNA processing and nucleocytoplasmic export. Although its biochemical functions have been extensively described, its genetic interactions and potential participation in signaling pathways remain largely unknown, despite the fact that it is highly phosphorylated in both mammalian cells and Drosophila. To begin elucidating the functions of the protein in signaling and its potential role in developmental processes, we characterized mutant and overexpression SRm160 phenotypes in Drosophila and their interactions with the locus encoding the LAMMER protein kinase, Doa. SRm160 mutations are recessive lethal, while its overexpression generates phenotypes including roughened eyes and highly disorganized internal eye structure, which are due at least in part to aberrantly high levels of apoptosis. SRm160 is required for normal somatic sex determination, since its alleles strongly enhance a subtle sex transformation phenotype induced by Doa kinase alleles. Moreover, modification of SRm160 by DOA kinase appears to be necessary for its activity, since Doa alleles suppress phenotypes induced by SRm160 overexpression in the eye and enhance those in genital discs. Modification of SRm160 may occur through direct interaction because DOA kinase phosphorylates it in vitro. Remarkably, SRm160 protein was concentrated in the nuclei of precellular embryos but was very rapidly excluded from nuclei or degraded coincident with cellularization. Also of interest, transcripts are restricted almost exclusively to the developing nervous system in mature embryos.
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26
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Gowrisankar S, Lebo MS. Designing algorithms for determining significance of DNA missense changes. Methods Mol Biol 2014; 1168:251-62. [PMID: 24870140 DOI: 10.1007/978-1-4939-0847-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Humans differ from each other in their genomes by <1 %. This determines the difference in susceptibility to disease, phenotypes, and traits. Predominantly, when looking for causal disease mutations, protein-coding sequences are screened first since those have the highest probability of affecting the function of a protein. Recent technological advances have seen a rise in the number of experiments being conducted to study a variety of diseases from monogenic to complex traits. Several computational approaches have been developed to extract putative functional missense variants. In this chapter we review some of these approaches and describe a standard step-by-step procedure that can be used to classify variants for the purpose of clinical care. We also provide two examples demonstrating this approach, one for a patient with a dilated cardiomyopathy diagnosis, and the other for a patient with an unknown etiology undergoing whole-genome sequencing (WGS).
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Affiliation(s)
- Sivakumar Gowrisankar
- Novartis Institutes for Biomedical Research, 500 Technology Square, 840-14, Cambridge, MA, 02139, USA,
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27
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Ulzi G, Sansone VA, Magri F, Corti S, Bresolin N, Comi GP, Lucchiari S. In vitro analysis of splice site mutations in the CLCN1 gene using the minigene assay. Mol Biol Rep 2014; 41:2865-74. [PMID: 24452722 DOI: 10.1007/s11033-014-3142-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/11/2014] [Indexed: 12/21/2022]
Abstract
Mutations in the chloride channel gene CLCN1 cause the allelic disorders Thomsen (dominant) and Becker (recessive) myotonia congenita (MC). The encoded protein, ClC-1, is the primary channel that mediates chloride (Cl-) conductance in skeletal muscle. Mutations in CLCN1 lower the channel's threshold voltage, leading to spontaneous action potentials that are not coupled to neuromuscular transmission and resulting in myotonia. Over 120 mutations in CLCN1 have been described, 10% of which are splicing defects. Biological specimens suitable for RNA extraction are not always available, but obtaining genomic DNA for analysis is easy and non-invasive. This is the first study to evaluate the pathogenic potential of novel splicing mutations using the minigene approach, which is based on genomic DNA analysis. Splicing mutations accounted for 23% of all pathogenic variants in our cohort of MC patients. Four were heterozygous mutations in four unrelated individuals, belonging to this cohort: c.563G>T in exon 5; c.1169-5T>G in intron 10; c.1251+1G>A in intron 11, and c.1931-2A>G in intron 16. These variants were expressed in HEK 293 cells, and aberrant splicing was verified by in vitro transcription and sequencing of the cDNA. Our findings confirm the need to further investigate the nature of rearrangements associated with this class of mutations and their effects on mature transcripts. In particular, splicing mutations predicted to generate in-frame transcripts may generate out-of-frame mRNA transcripts that do not produce functional ClC-1. Clinically, incomplete molecular evaluation could lead to delayed or faulty diagnosis.
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Affiliation(s)
- Gianna Ulzi
- Neurology Unit, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Via Sforza 35, 20122, Milan, Italy
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