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Wang X, Liu C, Wu H, Gu Y, Zhang L, Xu R, Lin Q. Basement membrane-associated gene expression as a predictor of survival in oral cancer. BMC Cancer 2024; 24:731. [PMID: 38877482 PMCID: PMC11177517 DOI: 10.1186/s12885-024-12485-2] [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: 10/17/2023] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND This study sought to investigate the prognostic value of basement membrane (BM)-associated gene expressions in oral cancer. METHODS We harvested and integrated data on BM-associated genes (BMGs), the oral cancer transcriptome, and clinical information from public repositories. After identifying differentially expressed BMGs, we used Cox and Lasso regression analyses to create a BMG-based risk score for overall survival at various intervals. We then validated this score using the GSE42743 cohort as a validation set. The prognostic potential of the risk scores and their relations to clinical features were assessed. Further, we conducted functional pathway enrichment, immune cell infiltration, and immune checkpoint analyses to elucidate the immunological implications and therapeutic potential of the BMG-based risk score and constituent genes. To confirm the expression levels of the BMG LAMA3 in clinical samples of oral cancer tissue, we performed quantitative real-time PCR (qRT-PCR) and immunohistochemical staining. RESULTS The BMGs LAMA3, MMP14, and GPC2 demonstrated notable prognostic significance, facilitating the construction of a BMG-based risk score. A higher risk score derived from BMGs correlated with a poorer survival prognosis for oral cancer patients. Moreover, the risk-associated BMGs exhibited a significant relationship with immune function variability (P < 0.05), discrepancies in infiltrating immune cell fractions, and immune checkpoint expressions (P < 0.05). The upregulated expression levels of LAMA3 in oral cancer tissues were substantiated through qRT-PCR and immunohistochemical staining. CONCLUSION The BMG-based risk score emerged as a reliable prognostic tool for oral cancer, meriting further research for validation and potential clinical application.
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Affiliation(s)
- Xu Wang
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Chaoge Liu
- Department of Oramaxillofacial - Head and Neck Surgery, School of Medicine, Tianjin Stomatological Hospital, Nankai University, Tianjin, 300041, China
- Tianjin Key Laboratory of Oral and Maxillofacial Function Reconstruction, Tianjin, 300041, China
| | - HuiFang Wu
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Yulu Gu
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Le Zhang
- Department of Oral Pathology, School of Medicine, Tianjin Stomatological Hospital, Nankai University, Tianjin, 300041, China
| | - Rongqing Xu
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Qing Lin
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China.
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Ma YY, Zhang GJ, Liu PF, Liu Y, Ding JC, Xu H, Hao L, Pan D, Wang HL, Wang JK, Xu P, Shi ZD, Pang K. Comprehensive Genomic Analysis of Puerarin in Inhibiting Bladder Urothelial Carcinoma Cell Proliferation and Migration. Recent Pat Anticancer Drug Discov 2024; 19:516-529. [PMID: 37694778 PMCID: PMC11348475 DOI: 10.2174/1574892819666230908110107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/04/2023] [Accepted: 06/19/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Bladder urothelial carcinoma (BUC) ranks second in the incidence of urogenital system tumors, and the treatment of BUC needs to be improved. Puerarin, a traditional Chinese medicine (TCM), has been shown to have various effects such as anti-cancer effects, the promotion of angiogenesis, and anti-inflammation. This study investigates the effects of puerarin on BUC and its molecular mechanisms. METHODS Through GeneChip experiments, we obtained differentially expressed genes (DEGs) and analyzed these DEGs using the Ingenuity® Pathway Analysis (IPA®), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway enrichment analyses. The Cell Counting Kit 8 (CCK8) assay was used to verify the inhibitory effect of puerarin on the proliferation of BUC T24 cells. String combined with Cytoscape® was used to create the Protein-Protein Interaction (PPI) network, and the MCC algorithm in cytoHubba plugin was used to screen key genes. Gene Set Enrichment Analysis (GSEA®) was used to verify the correlation between key genes and cell proliferation. RESULTS A total of 1617 DEGs were obtained by GeneChip. Based on the DEGs, the IPA® and pathway enrichment analysis showed they were mainly enriched in cancer cell proliferation and migration. CCK8 experiments proved that puerarin inhibited the proliferation of BUC T24 cells, and its IC50 at 48 hours was 218μmol/L. Through PPI and related algorithms, 7 key genes were obtained: ITGA1, LAMA3, LAMB3, LAMA4, PAK2, DMD, and UTRN. GSEA showed that these key genes were highly correlated with BUC cell proliferation. Survival curves showed that ITGA1 upregulation was associated with poor prognosis of BUC patients. CONCLUSION Our findings support the potential antitumor activity of puerarin in BUC. To the best of our knowledge, bioinformatics investigation suggests that puerarin demonstrates anticancer mechanisms via the upregulation of ITGA1, LAMA3 and 4, LAMB3, PAK2, DMD, and UTRN, all of which are involved in the proliferation and migration of bladder urothelial cancer cells.
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Affiliation(s)
- Yu-Yang Ma
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, No.199, South Jiefang Road, Xuzhou, Jiangsu, China
- Department of Urology, Graduate School, Bengbu Medical College, Building 1, Administration Building, 2600 Donghai Avenue, Bengbu City, Anhui Province, China
| | - Ge-jin Zhang
- Department of Urology, Suqian Zhongwu Hospital. No. 3786, Development Avenue, Suqian Economic and Technological Development Zone, Suqian, China
| | - Peng-fei Liu
- Jiangsu Provincial Key Laboratory of Educational Big Data Science and Engineering, Jiangsu Normal University, 101 Shanghai Road, Tongshan, Xuzhou, 221116, China
- School of Mathematics and Statistics and Research Institute of Mathematical Sciences (RIMS), Jiangsu Normal University, 101 Shanghai Road, Tongshan, Xuzhou, 221116, China
| | - Ying Liu
- Department of Central Laboratory, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College. No.199, South Jiefang Road, Xuzhou, Jiangsu, China
| | - Ji-cun Ding
- Department of Burn and Plastic Surgery, Xuzhou First People's Hospital, No. 269, Daxue Road, Tongshan District, Xuzhou, Jiangsu, China
| | - Hao Xu
- Department of Urology, Graduate School, Bengbu Medical College, Building 1, Administration Building, 2600 Donghai Avenue, Bengbu City, Anhui Province, China
| | - Lin Hao
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, No.199, South Jiefang Road, Xuzhou, Jiangsu, China
| | - Deng Pan
- Department of Urology, Graduate School, Bengbu Medical College, Building 1, Administration Building, 2600 Donghai Avenue, Bengbu City, Anhui Province, China
| | - Hai-luo Wang
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, No.199, South Jiefang Road, Xuzhou, Jiangsu, China
| | - Jing-kai Wang
- Graduate School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province, 212013, China
| | - Peng Xu
- Graduate School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province, 212013, China
| | - Zhen-Duo Shi
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, No.199, South Jiefang Road, Xuzhou, Jiangsu, China
- Department of Urology, Graduate School, Bengbu Medical College, Building 1, Administration Building, 2600 Donghai Avenue, Bengbu City, Anhui Province, China
| | - Kun Pang
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, No.199, South Jiefang Road, Xuzhou, Jiangsu, China
- Department of Urology, Graduate School, Bengbu Medical College, Building 1, Administration Building, 2600 Donghai Avenue, Bengbu City, Anhui Province, China
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Wu K, Sun Q, Liu D, Lu J, Wen D, Zang X, Gao L. Alternative Splicing Landscape of Head and Neck Squamous Cell Carcinoma. Technol Cancer Res Treat 2024; 23:15330338241272051. [PMID: 39113534 PMCID: PMC11307358 DOI: 10.1177/15330338241272051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/16/2024] [Accepted: 06/24/2024] [Indexed: 08/10/2024] Open
Abstract
Head and neck malignancies are a significant global health concern, with head and neck squamous cell carcinoma (HNSCC) being the sixth most common cancer worldwide accounting for > 90% of cases. In recent years, there has been growing recognition of the potential role of alternative splicing (AS) in the etiology of cancer. Increasing evidence suggests that AS is associated with various aspects of cancer progression, including tumor occurrence, invasion, metastasis, and drug resistance. Additionally, AS is involved in shaping the tumor microenvironment, which plays a crucial role in tumor development and response to therapy. AS can influence the expression of factors involved in angiogenesis, immune response, and extracellular matrix remodeling, all of which contribute to the formation of a supportive microenvironment for tumor growth. Exploring the mechanism of AS events in HNSCC could provide insights into the development and progression of this cancer, as well as its interaction with the tumor microenvironment. Understanding how AS contributes to the molecular changes in HNSCC cells and influences the tumor microenvironment could lead to the identification of new therapeutic targets. Targeted chemotherapy and immunotherapy strategies tailored to the specific AS patterns in HNSCC could potentially improve treatment outcomes and reduce side effects. This review explores the concept, types, processes, and technological advancements of AS, focusing on its role in the initiation, progression, treatment, and prognosis of HNSCC.
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Affiliation(s)
- Kehan Wu
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Qianhui Sun
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Dongxu Liu
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Jiayi Lu
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Deyu Wen
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Xiyan Zang
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Li Gao
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
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Islam K, Balasubramanian B, Venkatraman S, Thummarati P, Tunganuntarat J, Phueakphud N, Kanjanasirirat P, Khumpanied T, Kongpracha P, Kittirat Y, Tohtong R, Janvilisri T, Wongtrakoongate P, Borwornpinyo S, Namwat N, Suthiphongchai T. Upregulated LAMA3 modulates proliferation, adhesion, migration and epithelial‑to‑mesenchymal transition of cholangiocarcinoma cells. Sci Rep 2023; 13:22598. [PMID: 38114514 PMCID: PMC10730521 DOI: 10.1038/s41598-023-48798-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
A poor outcome for cholangiocarcinoma (CCA) patients is still a clinical challenge. CCA is typically recognized by the desmoplastic nature, which accounts for its malignancy. Among various extracellular matrix proteins, laminin is the most potent inducer for CCA migration. Herein, we accessed the expression profiles of laminin gene family and explored the significance of the key laminin subunit on CCA aggressiveness. Of all 11 laminin genes, LAMA3, LAMA5, LAMB3 and LAMC2 were concordantly upregulated based on the analysis of multiple public transcriptomic datasets and also overexpressed in Thai CCA cell lines and patient tissues in which LAMA3A upregulated in the highest frequency (97%) of the cases. Differential expression genes (DEGs) analysis of low and high laminin signature groups revealed LAMA3 as the sole common DEG in all investigated datasets. Restratifying CCA samples according to LAMA3 expression indicated the association of LAMA3 in the focal adhesion pathway. Silencing LAMA3 revealed that it plays important roles in CCA cell proliferation, adhesion, migration and epithelial-to-mesenchymal transition. Taken together, this research signifies the roles of dysregulated ECM homeostasis in CCA malignancy and highlights, for the first time, the potential usage of LAMA3 as the diagnostic biomarker and the therapeutic target to tackle the CCA stromal.
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Affiliation(s)
- Kittiya Islam
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Brinda Balasubramanian
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Simran Venkatraman
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Parichut Thummarati
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Janpen Tunganuntarat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nut Phueakphud
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Phongthon Kanjanasirirat
- Excellent Center for Drug Discovery (ECDD), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Tanawadee Khumpanied
- Excellent Center for Drug Discovery (ECDD), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Pornparn Kongpracha
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Yingpinyapat Kittirat
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
- Department of Medical Sciences, Regional Medical Sciences Center 2, Ministry of Public Health, Phitsanulok, 65000, Thailand
| | - Rutaiwan Tohtong
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
- Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Suparerk Borwornpinyo
- Excellent Center for Drug Discovery (ECDD), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nisana Namwat
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
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Chavda ND, Sari B, Asiri FM, Hamill KJ. Laminin N-terminus (LaNt) proteins, laminins and basement membrane regulation. Biochem Soc Trans 2022; 50:1541-1553. [PMID: 36355367 PMCID: PMC9788559 DOI: 10.1042/bst20210240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 10/03/2023]
Abstract
Basement membranes (BMs) are structured regions of the extracellular matrix that provide multiple functions including physical support and acting as a barrier, as a repository for nutrients and growth factors, and as biophysical signalling hubs. At the core of all BMs is the laminin (LM) family of proteins. These large heterotrimeric glycoproteins are essential for tissue integrity, and differences between LM family members represent a key nexus in dictating context and tissue-specific functions. These variations reflect genetic diversity within the family, which allows for multiple structurally and functionally distinct heterotrimers to be produced, each with different architectures and affinities for other matrix proteins and cell surface receptors. The ratios of these LM isoforms also influence the biophysical properties of a BM owing to differences in their relative ability to form polymers or networks. Intriguingly, the LM superfamily is further diversified through the related netrin family of proteins and through alternative splicing leading to the generation of non-LM short proteins known as the laminin N-terminus (LaNt) domain proteins. Both the netrins and LaNt proteins contain structural domains involved in LM-to-LM interaction and network assembly. Emerging findings indicate that one netrin and at least one LaNt protein can potently influence the structure and function of BMs, disrupting the networks, changing physical properties, and thereby influencing tissue function. These findings are altering the way that we think about LM polymerisation and, in the case of the LaNt proteins, suggest a hitherto unappreciated form of LM self-regulation.
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Affiliation(s)
- Natasha D. Chavda
- Institute of Life Course and Medical Sciences, University of Liverpool, 6 West Derby Street, Liverpool L78TX, U.K
| | - Bilge Sari
- Institute of Life Course and Medical Sciences, University of Liverpool, 6 West Derby Street, Liverpool L78TX, U.K
| | - Fawziah M. Asiri
- Institute of Life Course and Medical Sciences, University of Liverpool, 6 West Derby Street, Liverpool L78TX, U.K
| | - Kevin J. Hamill
- Institute of Life Course and Medical Sciences, University of Liverpool, 6 West Derby Street, Liverpool L78TX, U.K
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Orzechowska K, Kopij G, Paukszto L, Dobrzyn K, Kiezun M, Jastrzebski J, Kaminski T, Smolinska N. Chemerin effect on transcriptome of the porcine endometrium during implantation determined by RNA-sequencing†. Biol Reprod 2022; 107:557-573. [PMID: 35349661 DOI: 10.1093/biolre/ioac063] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/02/2022] [Accepted: 03/18/2022] [Indexed: 11/14/2022] Open
Abstract
It is well known that the body's metabolism and reproduction are closely related. Chemerin is one of many biologically active proteins secreted by the adipose tissue involved in the regulation of the energy homeostasis of the organism. In the present study, RNA-Sequencing (RNA-Seq) was performed to investigate the differentially expressed genes (DEGs), long non-coding RNAs (lncRNAs) and alternatively spliced (AS) transcripts in the cultured in vitro porcine endometrium exposed to chemerin for 24 hours (CHEM; 400 ng/ml) collected during the implantation period (15 to 16 days of gestation). High-throughput sequencing of transcriptomes was performed on the Illumina NovaSeq 6000 platform (Illumina, USA). In the current study, among all 130 DEGs, 58 were up-regulated and were 72 down-regulated in the CHEM-treated group. DEGs were assigned to 73 functional annotations. Twelve identified lncRNAs indicated a difference in the expression profile after CHEM administration. Additionally, we detected 386 differentially AS events encompassed 274 protein-coding genes and 2 lncRNAs. All AS events were divided into 5 alternative splicing types: alternative 3' splice site (A3SS), 5' splice site (A5SS), mutually exclusive exons (MXE), retention intron (RI), and skipping exon (SE). Within all AS events, we identified 42 A3SS, 43 A5SS, 53 MXE, 9 RI, and 239 SE. In summary, CHEM affects the transcriptomic profile of the porcine endometrium, controlling the expression of numerous genes, including those involved in the cell migration and adhesion, angiogenesis, inflammation, and steroidogenesis. It can be assumed that CHEM may be an important factor for a proper course of gestation and embryo development.
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Affiliation(s)
- Kinga Orzechowska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Grzegorz Kopij
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Lukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Kamil Dobrzyn
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marta Kiezun
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jan Jastrzebski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tadeusz Kaminski
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Nina Smolinska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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LAMA3 DNA methylation and transcriptome changes associated with chemotherapy resistance in ovarian cancer. J Ovarian Res 2021; 14:67. [PMID: 33992120 PMCID: PMC8126133 DOI: 10.1186/s13048-021-00807-y] [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: 12/10/2020] [Accepted: 04/13/2021] [Indexed: 12/22/2022] Open
Abstract
Objective LAMA3 is a widely studied methylated gene in multiple tumors, but the relationship between chemotherapy resistance in ovarian cancer is unclear. In this study, LAMA3 methylation was predicted by bioinformatics, and the ability of LAMA3 methylation to predict the chemotherapy resistance and prognosis of ovarian cancer was confirmed in experiments. Methods Multiple databases have performed the bioinformatics analysis of methylation and transcription factor binding site (TFBS) on the promoter region of LAMA3 gene. Pyrosequencing detected the methylation of LAMA3. QRT-PCR and immunohistochemistry detected the expression of LAMA3. Real Time Cell Analyzer (RTCA) detects changes in cell proliferation, migration and invasion ability. Flow cytometry was used to detect apoptosis. Results CPG islands of 176 bp, 134 bp, 125 bp and 531 bp were predicted in the promoter region of LAMA3 gene. The 4 prediction results are basically overlapped. 7 transcription factor binding sites were predicted, and the one with the highest score was on the predicted CpG island located in the proximal promoter region. LAMA3 hypermethylation and low expression are both associated with chemotherapy resistance and poor prognosis in ovarian cancer. LAMA3 methylation was negatively correlated with expression. After upregulation of LAMA3, the proliferation ability of chemoresistant ovarian cancer cell decreased, while the ability of apoptosis, invasion and migration increased. Conclusion LAMA3 hypermethylation is associated with chemotherapy resistance and poor prognosis. As a typical CpG island gene, LAMA3(cg20937934) and LAMA3(cg13270625) hypermethylation is negatively correlated with low expression. LAMA3 promotes the invasion, migration and apoptosis of SKOV3DDP. In the future, the mechanism of LAMA3 methylation in ovarian cancer will need to be further studied. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00807-y.
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Yang H, Xu F, Chen Y, Tian Z. Putative N-glycoprotein markers of MCF-7/ADR cancer stem cells from N-glycoproteomics characterization of the whole cell lysate. Talanta 2021; 232:122437. [PMID: 34074422 DOI: 10.1016/j.talanta.2021.122437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/10/2021] [Accepted: 04/17/2021] [Indexed: 12/01/2022]
Abstract
Breast cancer is one of the most malignant diseases among females. N-glycoproteomics studies have shown that N-glycosylation alteration of tumor cells is the key player of cancer progression, multidrug resistance (MDR) and high mortality. Cancer stem cells (CSCs) have the remarkable potential of self-renewing and differentiation which leads to drug resistance and metastasis. To investigate the differentially expressed N-glycosylation in adriamycin-resistant breast cancer stem cells MCF-7/ADR CSCs (relative to MCF-7 CSCs) and find the putative biomarkers, 1:1 paired ZIC-HILIC-enriched and stable isotopic diethyl labelled (SIDE) intact N-glycopeptides from MCF-7/ADR CSCs and MCF-7 CSCs were analyzed with C18-RPLC-ESI-MS/MS (HCD with stepped NCE); differentially expressed intact N-glycopeptides (DEGPs) were identified and quantified via search engine GPSeeker. With control of spectrum-level FDR≤1%, 5515 intact N-glycopeptides were identified (1737 N-glycosites, 1705 peptide backbones and 1516 intact N-glycoproteins; 181 putative N-glycan linkages and 68 monosaccharide compositions). Among 5515 intact N-glycopeptide IDs, 3864 were identified with glycoform score≥1, i.e., one or more structure-diagnostic fragment ions were observed to distinguish sequence isomers. With the three technical replicates and the criteria of fold change≥1.5 and p value<0.05, 380 DEGPs (corresponding to 153 intact N-glycoproteins) were found along with 293 down-regulated and 87 up-regulated. For these 153 intact N-glycoproteins, the molecular functions and biological processes of were comprehensively discussed, and side-to-side comparison of differential expression results with other method were also made.
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Affiliation(s)
- Hailun Yang
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China.
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Farina AR, Cappabianca L, Sebastiano M, Zelli V, Guadagni S, Mackay AR. Hypoxia-induced alternative splicing: the 11th Hallmark of Cancer. J Exp Clin Cancer Res 2020; 39:110. [PMID: 32536347 PMCID: PMC7294618 DOI: 10.1186/s13046-020-01616-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Hypoxia-induced alternative splicing is a potent driving force in tumour pathogenesis and progression. In this review, we update currents concepts of hypoxia-induced alternative splicing and how it influences tumour biology. Following brief descriptions of tumour-associated hypoxia and the pre-mRNA splicing process, we review the many ways hypoxia regulates alternative splicing and how hypoxia-induced alternative splicing impacts each individual hallmark of cancer. Hypoxia-induced alternative splicing integrates chemical and cellular tumour microenvironments, underpins continuous adaptation of the tumour cellular microenvironment responsible for metastatic progression and plays clear roles in oncogene activation and autonomous tumour growth, tumor suppressor inactivation, tumour cell immortalization, angiogenesis, tumour cell evasion of programmed cell death and the anti-tumour immune response, a tumour-promoting inflammatory response, adaptive metabolic re-programming, epithelial to mesenchymal transition, invasion and genetic instability, all of which combine to promote metastatic disease. The impressive number of hypoxia-induced alternative spliced protein isoforms that characterize tumour progression, classifies hypoxia-induced alternative splicing as the 11th hallmark of cancer, and offers a fertile source of potential diagnostic/prognostic markers and therapeutic targets.
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Affiliation(s)
- Antonietta Rosella Farina
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Lucia Cappabianca
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Michela Sebastiano
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Veronica Zelli
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Stefano Guadagni
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Andrew Reay Mackay
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
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10
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Zhong F, Lu HP, Chen G, Dang YW, Li GS, Chen XY, Qin YY, Yao YX, Zhang XG, Liang Y, Li MX, Mo M, Zhang KL, Ding H, Huang ZG, Wei ZX. The clinical significance and potential molecular mechanism of integrin subunit beta 4 in laryngeal squamous cell carcinoma. Pathol Res Pract 2019; 216:152785. [PMID: 31889588 DOI: 10.1016/j.prp.2019.152785] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/21/2019] [Accepted: 12/10/2019] [Indexed: 01/10/2023]
Abstract
The relationship between integrin beta 4 (ITGB4) expression and laryngeal squamous cell carcinoma (LSCC) remains unclarified. The object of the present study was to explore the clinical significance and potential molecular mechanism of ITGB4 in LSCC. The protein level of ITGB4 was significantly higher in 46 LSCC patients than in 26 non-LSCC tissues detected by in-house immunohistochemistry. Consistently, ITGB4 mRNA level was also greatly upregulated based on microarray and RNA-seq data (standard mean difference, SMD = 1.62, 95 % CI: 1.23-2.00). And the area under curves (AUC) of summary receiver operator characteristic (SROC) was 0.87 (95 % CI: 0.84-0.90) based on 172 cases of LSCC and 59 cases of non-cancerous controls. Ninety genes were intersected by the ITGB4 related genes and LSCC differential expressed genes (DEGs) from all available microarray and RNA-seq datasets. Based on Gene Ontology (GO) analysis, the top terms of biological process (BP), cellular component (CC) and molecular function (MF) for the 90 ITGB4 related DEGs were extracellular matrix organization, basement membrane and extracellular matrix structural constituent, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that ITGB4 related DEGs mainly participated in the pathways of ECM-receptor interaction, Focal adhesion and Small cell lung cancer. Moreover, the Protein-Protein Interaction (PPI) network indicated that ITGA3, ITGA5, ITGB4, MET, LAMA3, and COL4A1 might be the core genes of LSCC development related to ITGB4. In conclusion, high ITGB4 expression may lead to the occurrence and development of LSCC via various signaling pathways.
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Affiliation(s)
- Feng Zhong
- Department of Pathology, Hengxian People's Hospital, 141 Jiaoyu Road, Hengxian County of Nanning 530300, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hui-Ping Lu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Guo-Sheng Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xiao-Yi Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yong-Ying Qin
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yu-Xuan Yao
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xiao-Guohui Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yao Liang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ming-Xuan Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Miao Mo
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Kai-Lang Zhang
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hua Ding
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zhi-Guang Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
| | - Zhu-Xin Wei
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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11
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Mishra R, Haldar S, Suchanti S, Bhowmick NA. Epigenetic changes in fibroblasts drive cancer metabolism and differentiation. Endocr Relat Cancer 2019; 26:R673-R688. [PMID: 31627186 PMCID: PMC6859444 DOI: 10.1530/erc-19-0347] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022]
Abstract
Genomic changes that drive cancer initiation and progression contribute to the co-evolution of the adjacent stroma. The nature of the stromal reprogramming involves differential DNA methylation patterns and levels that change in response to the tumor and systemic therapeutic intervention. Epigenetic reprogramming in carcinoma-associated fibroblasts are robust biomarkers for cancer progression and have a transcriptional impact that support cancer epithelial progression in a paracrine manner. For prostate cancer, promoter hypermethylation and silencing of the RasGAP, RASAL3 that resulted in the activation of Ras signaling in carcinoma-associated fibroblasts. Stromal Ras activity initiated a process of macropinocytosis that provided prostate cancer epithelia with abundant glutamine for metabolic conversion to fuel its proliferation and a signal to transdifferentiate into a neuroendocrine phenotype. This epigenetic oncogenic metabolic/signaling axis seemed to be further potentiated by androgen receptor signaling antagonists and contributed to therapeutic resistance. Intervention of stromal signaling may complement conventional therapies targeting the cancer cell.
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Affiliation(s)
- Rajeev Mishra
- Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Subhash Haldar
- Department of Biotechnology, Brainware University, Kolkata, India
| | - Surabhi Suchanti
- Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Neil A Bhowmick
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Research, Greater Los Angeles Veterans Administration, Los Angeles, California, USA
- Correspondence should be addressed to N A Bhowmick:
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12
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Xu SF, Zheng Y, Zhang L, Wang P, Niu CM, Wu T, Tian Q, Yin XB, Shi SS, Zheng L, Gao LM. Long Non-coding RNA LINC00628 Interacts Epigenetically with the LAMA3 Promoter and Contributes to Lung Adenocarcinoma. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:166-182. [PMID: 31557618 PMCID: PMC6796683 DOI: 10.1016/j.omtn.2019.08.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 08/01/2019] [Accepted: 08/01/2019] [Indexed: 12/29/2022]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as key regulators of cellular progress in lung adenocarcinoma. In this study, to identify cancer-related lncRNAs and genes, we screened for those lncRNAs that were differentially expressed in lung adenocarcinoma, which revealed LINC00628 overexpression and low expression of laminin subunit alpha 3 (LAMA3). This was further validated in the cancerous tissues from patients diagnosed with lung adenocarcinoma. Thereafter, we explored the functional relevance of LINC00628 and LAMA3 in lung adenocarcinoma by analyzing the recruitment of DNA methyltransferase (DNMT) and the cellular processes of lung adenocarcinoma cells following treatments that induced LINC00628 overexpression or LINC00628 silencing or with 5-azacytidine (5-Aza, a DNMT inhibitor). The results showed that LINC00628 silencing decreased cell proliferation, migration, and invasion as well as the drug resistance of lung adenocarcinoma cells to vincristine (VCR). The results were opposite in the cells with LAMA3 demethylation induced by 5-Aza treatment. Further research indicated that LINC00628 recruited DNMT1, DNMT3A, and DNMT3B to promote the methylation of LAMA3 promoter, thereby decreasing its expression. Moreover, an in vivo experiment was performed in nude mice to assess the tumor growth ability and drug resistance of human lung adenocarcinoma cells. It was observed that LINC00628 silencing or 5-Aza treatment inhibited the in vivo tumor growth ability of the human lung adenocarcinoma cells and reduced their resistance to VCR. Altogether, our results provide evidence of a mechanism by which LINC00628 silencing exerts an inhibitory role in lung adenocarcinoma by modulating the DNA methylation of LAMA3, indicative of a novel molecular target for treatment of lung adenocarcinoma patients showing resistance to VCR.
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Affiliation(s)
- Shu-Feng Xu
- Department of Respiratory, The First Hospital of Qinhuangdao, Qinhuangdao 066000, P.R. China
| | - Yue Zheng
- Department of Oncology, The First Hospital of Qinhuangdao, Qinhuangdao 066000, P.R. China
| | - Ling Zhang
- Department of Respiratory, Hebei Chest Hospital, Shijiazhuang 050021, P.R. China
| | - Ping Wang
- Department of Respiratory, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Chun-Mi Niu
- Department of Respiratory, The First Hospital of Qinhuangdao, Qinhuangdao 066000, P.R. China
| | - Tong Wu
- Medical Students, Hebei Medical University, Shijiazhuang 050017, P.R. China
| | - Qi Tian
- Department of Respiratory, The First Hospital of Qinhuangdao, Qinhuangdao 066000, P.R. China
| | - Xiao-Bo Yin
- Department of Respiratory, The First Hospital of Qinhuangdao, Qinhuangdao 066000, P.R. China
| | - Shan-Shan Shi
- Medical Students, Hebei Medical University, Shijiazhuang 050017, P.R. China
| | - Lei Zheng
- Department of Oncology, The First Hospital of Qinhuangdao, Qinhuangdao 066000, P.R. China
| | - Li-Ming Gao
- Department of Oncology, The First Hospital of Qinhuangdao, Qinhuangdao 066000, P.R. China.
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Identification of important invasion and proliferation related genes in adrenocortical carcinoma. Med Oncol 2019; 36:73. [DOI: 10.1007/s12032-019-1296-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/01/2019] [Indexed: 12/17/2022]
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14
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Yao Y, Song W, Deng Q, Zhang H, Wang J, Liu H, Zhou Y. General regulatory effects of hypoxia on human cartilage endplate‑derived stem cells: A genome‑wide analysis of differential gene expression and alternative splicing events. Mol Med Rep 2017; 16:3001-3009. [PMID: 28677762 DOI: 10.3892/mmr.2017.6907] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 05/12/2017] [Indexed: 11/06/2022] Open
Abstract
Intervertebral disc (IVD) degeneration of is considered to be initiated by the degeneration of the cartilage endplate (CEP). CEP‑derived stem cells (CESCs) with the capacity for osteochondrogenic differentiation may be responsible for CEP cartilage restoration. As CEP is avascular and hypoxic, and hypoxia can greatly influence biological activities of stem cells, physiological hypoxia may serve important roles in regulating the physiological functions of CESCs. The aim of the present study was to investigate the mechanisms of hypoxia‑regulated CESCs fate by using the Human Transcriptome Array 2.0 system to identify differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) in CESCs cultured under hypoxic and normoxic conditions. The high‑throughput analysis of both DEGs and ASGs were notably enriched in the immune response signal, which so far has not been investigated in IVD cells, due to their avascular nature and low immunogenicity. The present results provided a referential study direction of the mechanisms of hypoxia‑regulated CESC fate at the level of gene expression and alternative splicing, which may aid in our understanding of the processes of CEP degeneration.
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Affiliation(s)
- Yuan Yao
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Weilin Song
- Department of Ophthalmology, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Qiyue Deng
- Department of Neurobiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, P.R. China
| | - Huiyu Zhang
- Department of Stomatology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Jian Wang
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Huan Liu
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Yue Zhou
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
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15
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Yao Y, Deng Q, Sun C, Song W, Liu H, Zhou Y. A genome-wide analysis of the gene expression profiles and alternative splicing events during the hypoxia-regulated osteogenic differentiation of human cartilage endplate-derived stem cells. Mol Med Rep 2017; 16:1991-2001. [PMID: 28656244 PMCID: PMC5562021 DOI: 10.3892/mmr.2017.6846] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 04/25/2017] [Indexed: 12/20/2022] Open
Abstract
It has been hypothesized that intervertebral disc degeneration is initiated by degeneration of the cartilage endplate (CEP), which is characterized by cartilage ossification. CEP‑derived stem cells (CESCs), with the potential for chondro‑osteogenic differentiation, may be responsible for the balance between chondrification and ossification in the CEP. The CEP remains in an avascular and hypoxic microenvironment; the present study observed that hypoxia was able to markedly inhibit the osteogenic differentiation of CESCs. This tissue‑specific CESC differentiation in response to a hypoxic microenvironment was physiologically important for the prevention of ossification in the CEP. In order to study the hypoxia‑regulated mechanisms underlying osteogenic differentiation of CESCs, a Human Transcriptome Array 2.0 was used to detect differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) during the osteogenic differentiation of CESCs under hypoxia, compared with those induced under normoxia. High‑throughput analysis of DEGs and ASGs demonstrated that genes in the complement pathway were enriched, which may be a potential mechanism underlying hypoxia inhibition of CESCs osteogenesis. The results of the present study may provide a basis for future mechanistic studies regarding gene expression levels and alternative splicing events during the hypoxia‑regulated inhibition of osteogenesis, which may be helpful in identifying targets for CEP degeneration therapy.
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Affiliation(s)
- Yuan Yao
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Qiyue Deng
- Department of Neurobiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, P.R. China
| | - Chao Sun
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Weiling Song
- Department of Ophthalmology, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Huan Liu
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Yue Zhou
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
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16
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A saga of cancer epigenetics: linking epigenetics to alternative splicing. Biochem J 2017; 474:885-896. [PMID: 28270561 DOI: 10.1042/bcj20161047] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 12/29/2016] [Accepted: 01/05/2017] [Indexed: 12/14/2022]
Abstract
The discovery of an increasing number of alternative splicing events in the human genome highlighted that ∼94% of genes generate alternatively spliced transcripts that may produce different protein isoforms with diverse functions. It is now well known that several diseases are a direct and indirect consequence of aberrant splicing events in humans. In addition to the conventional mode of alternative splicing regulation by 'cis' RNA-binding sites and 'trans' RNA-binding proteins, recent literature provides enormous evidence for epigenetic regulation of alternative splicing. The epigenetic modifications may regulate alternative splicing by either influencing the transcription elongation rate of RNA polymerase II or by recruiting a specific splicing regulator via different chromatin adaptors. The epigenetic alterations and aberrant alternative splicing are known to be associated with various diseases individually, but this review discusses/highlights the latest literature on the role of epigenetic alterations in the regulation of alternative splicing and thereby cancer progression. This review also points out the need for further studies to understand the interplay between epigenetic modifications and aberrant alternative splicing in cancer progression.
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17
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Mazaki-Tovi S, Tarca AL, Vaisbuch E, Kusanovic JP, Than NG, Chaiworapongsa T, Dong Z, Hassan SS, Romero R. Characterization of visceral and subcutaneous adipose tissue transcriptome in pregnant women with and without spontaneous labor at term: implication of alternative splicing in the metabolic adaptations of adipose tissue to parturition. J Perinat Med 2016; 44:813-835. [PMID: 26994472 PMCID: PMC5987212 DOI: 10.1515/jpm-2015-0259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/26/2015] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The aim of this study was to determine gene expression and splicing changes associated with parturition and regions (visceral vs. subcutaneous) of the adipose tissue of pregnant women. STUDY DESIGN The transcriptome of visceral and abdominal subcutaneous adipose tissue from pregnant women at term with (n=15) and without (n=25) spontaneous labor was profiled with the Affymetrix GeneChip Human Exon 1.0 ST array. Overall gene expression changes and the differential exon usage rate were compared between patient groups (unpaired analyses) and adipose tissue regions (paired analyses). Selected genes were tested by quantitative reverse transcription-polymerase chain reaction. RESULTS Four hundred and eighty-two genes were differentially expressed between visceral and subcutaneous fat of pregnant women with spontaneous labor at term (q-value <0.1; fold change >1.5). Biological processes enriched in this comparison included tissue and vasculature development as well as inflammatory and metabolic pathways. Differential splicing was found for 42 genes [q-value <0.1; differences in Finding Isoforms using Robust Multichip Analysis scores >2] between adipose tissue regions of women not in labor. Differential exon usage associated with parturition was found for three genes (LIMS1, HSPA5, and GSTK1) in subcutaneous tissues. CONCLUSION We show for the first time evidence of implication of mRNA splicing and processing machinery in the subcutaneous adipose tissue of women in labor compared to those without labor.
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Affiliation(s)
- Shali Mazaki-Tovi
- Department of Obstetrics and Gynecology, Sheba Medical Center, Tel Hashomer, Israel
- Tel Aviv University, Tel Aviv, Israel
| | - Adi L. Tarca
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Computer Science, Wayne State University, Detroit, Michigan, United States of America
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Edi Vaisbuch
- Department of Obstetrics and Gynecology, Kaplan Medical Center, Rehovot, Israel
| | - Juan Pedro Kusanovic
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Research and Innovation in Maternal-Fetal Medicine (CIMAF). Department of Obstetrics and Gynecology, Sótero del Río Hospital, Santiago, Chile
| | - Nandor Gabor Than
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Zhong Dong
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
| | - Sonia S Hassan
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Roberto Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
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18
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Yao Y, Shang J, Song W, Deng Q, Liu H, Zhou Y. Global profiling of the gene expression and alternative splicing events during hypoxia-regulated chondrogenic differentiation in human cartilage endplate-derived stem cells. Genomics 2016; 107:170-7. [PMID: 26996146 DOI: 10.1016/j.ygeno.2016.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 03/09/2016] [Accepted: 03/16/2016] [Indexed: 01/08/2023]
Abstract
The intervertebral disc (IVD) degeneration is initiated by cartilage endplate (CEP) degeneration and is characterised by reduced chondrification. Cartilage endplate-derived stem cells (CESCs) with chondrogenic differentiation abilities are responsible for the restoration of cartilage. CEP remains in an avascular and hypoxic microenvironment. In this study, we observed that the physiological hypoxia greatly promotes the chondrogenic differentiation of CESCs. This tissue specificity of the differentiation fate of CESCs in response to the hypoxic microenvironment was physiologically significant for the CEP to maintain the chondrification status. To investigate the mechanisms underlying the hypoxia-regulated chondrogenic differentiation of CESCs, we adopted a high-throughput scanning technology to detect the global profiling of gene expression and alternative splicing (AS) event changes during chondrogenic differentiation under hypoxia in CESCs compared to those induced under normoxia. An Affymetrix Human Transcriptome Array 2.0 was used to identify the differentially expressed genes (DEGs) and alternatively spliced genes (ASGs). After RT-PCR validation, GO and KEGG pathway analyses of both the DEGs and ASGs were performed. The enrichment of the GO functional terms and signalling pathways provided referential direction of the mechanism to study the gene expression and AS in the hypoxia-regulated chondrogenesis promotion, which could be helpful in understanding this physiological phenomenon, and it could also be instrumental in finding targets for CEP degeneration therapy.
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Affiliation(s)
- Yuan Yao
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Jin Shang
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Weilin Song
- Department of Ophthalmology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Qiyue Deng
- Department of Neurobiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Huan Liu
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
| | - Yue Zhou
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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19
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Mazaki-Tovi S, Vaisbuch E, Tarca AL, Kusanovic JP, Than NG, Chaiworapongsa T, Dong Z, Hassan SS, Romero R. Characterization of Visceral and Subcutaneous Adipose Tissue Transcriptome and Biological Pathways in Pregnant and Non-Pregnant Women: Evidence for Pregnancy-Related Regional-Specific Differences in Adipose Tissue. PLoS One 2015; 10:e0143779. [PMID: 26636677 PMCID: PMC4670118 DOI: 10.1371/journal.pone.0143779] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 11/08/2015] [Indexed: 12/13/2022] Open
Abstract
Objective The purpose of this study was to compare the transcriptome of visceral and subcutaneous adipose tissues between pregnant and non-pregnant women. Study Design The transcriptome of paired visceral and abdominal subcutaneous adipose tissues from pregnant women at term and matched non-pregnant women (n = 11) was profiled with the Affymetrix Human Exon 1.0 ST array. Differential expression of selected genes was validated with the use of quantitative reverse transcription–polymerase chain reaction. Results Six hundred forty-four transcripts from 633 known genes were differentially expressed (false discovery rate (FDR) <0.1; fold-change >1.5), while 42 exons from 36 genes showed differential usage (difference in FIRMA scores >2 and FDR<0.1) between the visceral and subcutaneous fat of pregnant women. Fifty-six known genes were differentially expressed between pregnant and non-pregnant subcutaneous fat and three genes in the visceral fat. Enriched biological processes in the subcutaneous adipose tissue of pregnant women were mostly related to inflammation. Conclusion The transcriptome of visceral and subcutaneous fat depots reveals pregnancy-related gene expression and splicing differences in both visceral and subcutaneous adipose tissue. Furthermore, for the first time, alternative splicing in adipose tissue has been associated with regional differences and human parturition.
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Affiliation(s)
- Shali Mazaki-Tovi
- Department of Obstetrics and Gynecology, Sheba Medical Center, Tel Hashomer, Israel
- Tel Aviv University, Tel Aviv, Israel
- * E-mail: (SMT); (RR)
| | - Edi Vaisbuch
- Department of Obstetrics and Gynecology, Kaplan Medical Center, Rehovot, Israel
| | - Adi L. Tarca
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Computer Science, Wayne State University, Detroit, Michigan, United States of America
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Juan Pedro Kusanovic
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Research and Innovation in Maternal-Fetal Medicine (CIMAF), Department of Obstetrics and Gynecology, Sótero del Río Hospital, Santiago, Chile
| | - Nandor Gabor Than
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Zhong Dong
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
| | - Sonia S. Hassan
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Roberto Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- * E-mail: (SMT); (RR)
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Graves CA, Abboodi FF, Tomar S, Wells J, Pirisi L. The translational significance of epithelial-mesenchymal transition in head and neck cancer. Clin Transl Med 2014; 3:60. [PMID: 25632320 PMCID: PMC4302251 DOI: 10.1186/s40169-014-0039-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 10/29/2014] [Indexed: 01/01/2023] Open
Abstract
Positive markers of epithelial-mesenchymal transition (EMT) in head and neck cancers complicate clinical management and are associated with reduced survival. We discuss recent translational discoveries in EMT and suggest additional actionable molecular pathways, biomarkers, and clinical agents.
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Affiliation(s)
- Christian A Graves
- Department of Pathology, Microbiology & Immunology, University of South Carolina School of Medicine, Bldg. 1 Room B43 6439 Garners Ferry Rd, Columbia, SC 29208 USA ; Department of Head and Neck Surgery, Wm. Jennings Dorn VA Medical Center, Columbia, SC 29208 USA
| | - Fadi F Abboodi
- Department of Pathology, Microbiology & Immunology, University of South Carolina School of Medicine, Bldg. 1 Room B43 6439 Garners Ferry Rd, Columbia, SC 29208 USA
| | - Swati Tomar
- Department of Pathology, Microbiology & Immunology, University of South Carolina School of Medicine, Bldg. 1 Room B43 6439 Garners Ferry Rd, Columbia, SC 29208 USA
| | - James Wells
- Department of Head and Neck Surgery, Wm. Jennings Dorn VA Medical Center, Columbia, SC 29208 USA
| | - Lucia Pirisi
- Department of Pathology, Microbiology & Immunology, University of South Carolina School of Medicine, Bldg. 1 Room B43 6439 Garners Ferry Rd, Columbia, SC 29208 USA
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21
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Hu X, Wu R, Shehadeh LA, Zhou Q, Jiang C, Huang X, Zhang L, Gao F, Liu X, Yu H, Webster KA, Wang J. Severe hypoxia exerts parallel and cell-specific regulation of gene expression and alternative splicing in human mesenchymal stem cells. BMC Genomics 2014; 15:303. [PMID: 24758227 PMCID: PMC4234502 DOI: 10.1186/1471-2164-15-303] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 04/16/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The endosteum of the bone marrow provides a specialized hypoxic niche that may serve to preserve the integrity, pluripotency, longevity and stemness of resident mesenchymal stem cells (MSCs). To explore the molecular genetic consequences of such a niche we subjected human (h) MSCs to a pO2 of 4 mmHg and analyzed global gene expression and alternative splicing (AS) by genome-exon microarray and RT-qPCR, and phenotype by western blot and immunostaining. RESULTS Out of 446 genes differentially regulated by >2.5-fold, down-regulated genes outnumbered up-regulated genes by 243:203. Exon analyses revealed 60 hypoxia-regulated AS events with splice indices (SI) >1.0 from 53 genes and a correlation between high SI and degree of transcript regulation. Parallel analyses of a publicly available AS study on human umbilical vein endothelial cells (HUVECs) showed that there was a strong cell-specific component with only 11 genes commonly regulated in hMSCs and HUVECs and 17 common differentially spliced genes. Only 3 genes were differentially responsive to hypoxia at the gene (>2.0) and AS levels in both cell types. Functional assignments revealed unique profiles of gene expression with complex regulation of differentiation, extracellular matrix, intermediate filament and metabolic marker genes. Antioxidant genes, striated muscle genes and insulin/IGF-1 signaling intermediates were down-regulated. There was a coordinate induction of 9 out of 12 acidic keratins that along with other epithelial and cell adhesion markers implies a partial mesenchymal to epithelial transition. CONCLUSIONS We conclude that severe hypoxia confers a quiescent phenotype in hMSCs that is reflected by both the transcriptome profile and gene-specific changes of splicosome actions. The results reveal that severe hypoxia imposes markedly different patterns of gene regulation of MSCs compared with more moderate hypoxia. This is the first study to report hypoxia-regulation of AS in stem/progenitor cells and the first molecular genetic characterization of MSC in a hypoxia-induced quiescent immobile state.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Keith A Webster
- Cardiovascular Key Lab of Zhejiang Province, Department of Cardiology, The Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, P,R, China.
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22
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Li R, Ochs MF, Ahn SM, Hennessey P, Tan M, Soudry E, Gaykalova DA, Uemura M, Brait M, Shao C, Westra W, Bishop J, Fertig EJ, Califano JA. Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma. PLoS One 2014; 9:e91263. [PMID: 24675808 PMCID: PMC3967989 DOI: 10.1371/journal.pone.0091263] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 02/11/2014] [Indexed: 12/22/2022] Open
Abstract
Purpose Prior studies have demonstrated tumor-specific alternative splicing events in various solid tumor types. The role of alternative splicing in the development and progression of head and neck squamous cell carcinoma (HNSCC) is unclear. Our study queried exon-level expression to implicate splice variants in HNSCC tumors. Experimental Design We performed a comparative genome-wide analysis of 44 HNSCC tumors and 25 uvulopalatopharyngoplasty (UPPP) tissue samples at an exon expression level. In our comparison we ranked genes based upon a novel score—the Maximum-Minimum Exon Score (MMES) – designed to predict the likelihood of an alternative splicing event occurring. We validated predicted alternative splicing events using quantitative RT-PCR on an independent cohort. Results After MMES scoring of 17,422 genes, the top 900 genes with the highest scores underwent additional manual inspection of expression patterns in a graphical analysis. The genes LAMA3, DST, VEGFC, SDHA, RASIP1, and TP63 were selected for further validation studies because of a high frequency of alternative splicing suggested in our graphical analysis, and literature review showing their biological relevance and known splicing patterns. We confirmed TP63 as having dominant expression of the short DeltaNp63 isoform in HNSCC tumor samples, consistent with prior reports. Two of the six genes (LAMA3 and DST) validated by quantitative RT-PCR for tumor-specific alternative splicing events (Student's t test, P<0.001). Conclusion Alternative splicing events of oncologically relevant proteins occur in HNSCC. The number of genes expressing tumor-specific splice variants needs further elucidation, as does the functional significance of selective isoform expression.
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Affiliation(s)
- Ryan Li
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Michael F. Ochs
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Mathematics and Statistics, The College of New Jersey, Ewing, New Jersey, United States of America
| | - Sun Mi Ahn
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Patrick Hennessey
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Marietta Tan
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Ethan Soudry
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Daria A. Gaykalova
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Mamoru Uemura
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Mariana Brait
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Chunbo Shao
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - William Westra
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Justin Bishop
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Elana J. Fertig
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Joseph A. Califano
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland, United States of America
- * E-mail:
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23
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Köstler WJ, Zeisel A, Körner C, Tsai JM, Jacob-Hirsch J, Ben-Chetrit N, Sharma K, Cohen-Dvashi H, Yitzhaky A, Lader E, Tschulena U, Rechavi G, Domany E, Wiemann S, Yarden Y. Epidermal growth-factor-induced transcript isoform variation drives mammary cell migration. PLoS One 2013; 8:e80566. [PMID: 24324612 PMCID: PMC3855657 DOI: 10.1371/journal.pone.0080566] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 10/03/2013] [Indexed: 11/28/2022] Open
Abstract
Signal-induced transcript isoform variation (TIV) includes alternative promoter usage as well as alternative splicing and alternative polyadenylation of mRNA. To assess the phenotypic relevance of signal-induced TIV, we employed exon arrays and breast epithelial cells, which migrate in response to the epidermal growth factor (EGF). We show that EGF rapidly – within one hour – induces widespread TIV in a significant fraction of the transcriptome. Importantly, TIV characterizes many genes that display no differential expression upon stimulus. In addition, similar EGF-dependent changes are shared by a panel of mammary cell lines. A functional screen, which utilized isoform-specific siRNA oligonucleotides, indicated that several isoforms play essential, non-redundant roles in EGF-induced mammary cell migration. Taken together, our findings highlight the importance of TIV in the rapid evolvement of a phenotypic response to extracellular signals.
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Affiliation(s)
- Wolfgang J. Köstler
- Departments of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Amit Zeisel
- Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Cindy Körner
- Division of Molecular Genome Analysis, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Jonathan M. Tsai
- Departments of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Jasmine Jacob-Hirsch
- Sheba Cancer Research Center, The Chaim Sheba Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nir Ben-Chetrit
- Departments of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Kirti Sharma
- Division of Molecular Genome Analysis, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Hadas Cohen-Dvashi
- Departments of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Assif Yitzhaky
- Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Eric Lader
- Qiagen, Frederick, Maryland, United States of America
| | - Ulrich Tschulena
- Division of Molecular Genome Analysis, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Gideon Rechavi
- Sheba Cancer Research Center, The Chaim Sheba Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eytan Domany
- Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (YY); (ED)
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Yosef Yarden
- Departments of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (YY); (ED)
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Bonomi S, Gallo S, Catillo M, Pignataro D, Biamonti G, Ghigna C. Oncogenic alternative splicing switches: role in cancer progression and prospects for therapy. Int J Cell Biol 2013; 2013:962038. [PMID: 24285959 PMCID: PMC3826442 DOI: 10.1155/2013/962038] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/12/2013] [Indexed: 01/30/2023] Open
Abstract
Alterations in the abundance or activities of alternative splicing regulators generate alternatively spliced variants that contribute to multiple aspects of tumor establishment, progression and resistance to therapeutic treatments. Notably, many cancer-associated genes are regulated through alternative splicing suggesting a significant role of this post-transcriptional regulatory mechanism in the production of oncogenes and tumor suppressors. Thus, the study of alternative splicing in cancer might provide a better understanding of the malignant transformation and identify novel pathways that are uniquely relevant to tumorigenesis. Understanding the molecular underpinnings of cancer-associated alternative splicing isoforms will not only help to explain many fundamental hallmarks of cancer, but will also offer unprecedented opportunities to improve the efficacy of anti-cancer treatments.
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Affiliation(s)
- Serena Bonomi
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Stefania Gallo
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Morena Catillo
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Daniela Pignataro
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Claudia Ghigna
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
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25
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Lorenzato A, Biolatti M, Delogu G, Capobianco G, Farace C, Dessole S, Cossu A, Tanda F, Madeddu R, Olivero M, Di Renzo MF. AKT activation drives the nuclear localization of CSE1L and a pro-oncogenic transcriptional activation in ovarian cancer cells. Exp Cell Res 2013; 319:2627-36. [PMID: 23948303 DOI: 10.1016/j.yexcr.2013.07.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 07/27/2013] [Accepted: 07/31/2013] [Indexed: 12/28/2022]
Abstract
The human homolog of the yeast cse1 gene (CSE1L) is over-expressed in ovarian cancer. CSE1L forms complex with Ran and importin-α and has roles in nucleocytoplasmic traffic and gene expression. CSE1L accumulated in the nucleus of ovarian cancer cell lines, while it was localized also in the cytoplasm of other cancer cell lines. Nuclear localization depended on AKT, which was constitutively active in ovarian cancer cells, as the CSE1L protein translocated to the cytoplasm when AKT was inactivated. Moreover, the expression of a constitutively active AKT forced the translocation of CSE1L from the cytoplasm to the nucleus in other cancer cells. Nuclear accrual of CSE1L was associated to the nuclear accumulation of the phosphorylated Ran Binding protein 3 (RanBP3), which depended on AKT as well. Also in samples of human ovarian cancer, AKT activation was associated to nuclear accumulation of CSE1L and phosphorylation of RanBP3. Expression profiling of ovarian cancer cells after CSE1L silencing showed that CSE1L was required for the expression of genes promoting invasion and metastasis. In agreement, CSE1L silencing impaired motility and invasiveness of ovarian cancer cells. Altogether these data show that in ovarian cancer cells activated AKT by affecting RanBP3 phosphorylation determines the nuclear accumulation of CSE1L and likely the nuclear concentration of transcription factors conveying pro-oncogenic signals.
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Affiliation(s)
- Annalisa Lorenzato
- Department of Oncology, University of Torino School of Medicine, Torino, Italy; Institute for Cancer Research at Candiolo, Candiolo, Torino, Italy
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26
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ZRANB2 localizes to supraspliceosomes and influences the alternative splicing of multiple genes in the transcriptome. Mol Biol Rep 2013; 40:5381-95. [DOI: 10.1007/s11033-013-2637-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 05/01/2013] [Indexed: 11/27/2022]
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27
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Zhang Z, Pal S, Bi Y, Tchou J, Davuluri RV. Isoform level expression profiles provide better cancer signatures than gene level expression profiles. Genome Med 2013; 5:33. [PMID: 23594586 PMCID: PMC3706752 DOI: 10.1186/gm437] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/26/2013] [Accepted: 04/17/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The majority of mammalian genes generate multiple transcript variants and protein isoforms through alternative transcription and/or alternative splicing, and the dynamic changes at the transcript/isoform level between non-oncogenic and cancer cells remain largely unexplored. We hypothesized that isoform level expression profiles would be better than gene level expression profiles at discriminating between non-oncogenic and cancer cellsgene level. METHODS We analyzed 160 Affymetrix exon-array datasets, comprising cell lines of non-oncogenic or oncogenic tissue origins. We obtained the transcript-level and gene level expression estimates, and used unsupervised and supervised clustering algorithms to study the profile similarity between the samples at both gene and isoform levels. RESULTS Hierarchical clustering, based on isoform level expressions, effectively grouped the non-oncogenic and oncogenic cell lines with a virtually perfect homogeneity-grouping rate (97.5%), regardless of the tissue origin of the cell lines. However, gene levelthis rate was much lower, being 75% at best based on the gene level expressions. Statistical analyses of the difference between cancer and non-oncogenic samples identified the existence of numerous genes with differentially expressed isoforms, which otherwise were not significant at the gene level. We also found that canonical pathways of protein ubiquitination, purine metabolism, and breast-cancer regulation by stathmin1 were significantly enriched among genes thatshow differential expression at isoform level but not at gene level. CONCLUSIONS In summary, cancer cell lines, regardless of their tissue of origin, can be effectively discriminated from non-cancer cell lines at isoform level, but not at gene level. This study suggests the existence of an isoform signature, rather than a gene signature, which could be used to distinguish cancer cells from normal cells.
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Affiliation(s)
- ZhongFa Zhang
- Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Sharmistha Pal
- Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Yingtao Bi
- Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Julia Tchou
- Department of Surgery, Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Ramana V Davuluri
- Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
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28
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Jewer M, Findlay SD, Postovit LM. Post-transcriptional regulation in cancer progression : Microenvironmental control of alternative splicing and translation. J Cell Commun Signal 2012; 6:233-48. [PMID: 23054595 DOI: 10.1007/s12079-012-0179-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 09/24/2012] [Indexed: 12/28/2022] Open
Abstract
The microenvironment acts as a conduit for cellular communication, delivering signals that direct development and sustain tissue homeostasis. In pathologies such as cancer, this integral function of the microenvironment is hijacked to support tumor growth and progression. Cells sense the microenvironment via signal transduction pathways culminating in altered gene expression. In addition to induced transcriptional changes, the microenvironment exerts its effect on the cell through regulation of post-transcriptional processes including alternative splicing and translational control. Here we describe how alternative splicing and protein translation are controlled by microenvironmental parameters such as oxygen availability. We also emphasize how these pathways can be utilized to support processes that are hallmarks of cancer such as angiogenesis, proliferation, and cell migration. We stress that cancer cells respond to their microenvironment through an integrated regulation of gene expression at multiple levels that collectively contribute to disease progression.
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Affiliation(s)
- Michael Jewer
- Department of Anatomy & Cell Biology, The Schulich School of Medicine and Dentistry, Western University, 438 Medical Science Building, London, ON, N6A 5C1, Canada
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29
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Alternative transcription and alternative splicing in cancer. Pharmacol Ther 2012; 136:283-94. [PMID: 22909788 DOI: 10.1016/j.pharmthera.2012.08.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 08/01/2012] [Indexed: 01/27/2023]
Abstract
In recent years, the notion of "one gene makes one protein that functions in one signaling pathway" in mammalian cells has been shown to be overly simplistic. Recent genome-wide studies suggest that at least half of the human genes, including many therapeutic target genes, produce multiple protein isoforms through alternative splicing and alternative usage of transcription initiation and/or termination. For example, alternative splicing of the vascular endothelial growth factor gene (VEGFA) produces multiple protein isoforms, which display either pro-angiogenic or anti-angiogenic activities. Similarly, for the majority of human genes, the inclusion or exclusion of exonic sequences enhances the generation of transcript variants and/or protein isoforms that can vary in structure and functional properties. Many of the isoforms produced in this manner are tightly regulated during normal development but are misregulated in cancer cells. Altered expression of transcript variants and protein isoforms for numerous genes is linked with disease and its prognosis, and cancer cells manipulate regulatory mechanisms to express specific isoforms that confer drug resistance and survival advantages. Emerging insights indicate that modulating the expression of transcript and protein isoforms of a gene may hold the key to impeding tumor growth and act as a model for efficient targeting of disease-associated genes at the isoform level. This review highlights the role and regulation of alternative transcription and splicing mechanisms in generating the transcriptome, and the misuse and diagnostic/prognostic potential of alternative transcription and splicing in cancer.
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30
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Weigand JE, Boeckel JN, Gellert P, Dimmeler S. Hypoxia-induced alternative splicing in endothelial cells. PLoS One 2012; 7:e42697. [PMID: 22876330 PMCID: PMC3411717 DOI: 10.1371/journal.pone.0042697] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 07/11/2012] [Indexed: 01/12/2023] Open
Abstract
Background Adaptation to low oxygen by changing gene expression is vitally important for cell survival and tissue development. The sprouting of new blood vessels, initiated from endothelial cells, restores the oxygen supply of ischemic tissues. In contrast to the transcriptional response induced by hypoxia, which is mainly mediated by members of the HIF family, there are only few studies investigating alternative splicing events. Therefore, we performed an exon array for the genome-wide analysis of hypoxia-related changes of alternative splicing in endothelial cells. Methodology/Principal findings Human umbilical vein endothelial cells (HUVECs) were incubated under hypoxic conditions (1% O2) for 48 h. Genome-wide transcript and exon expression levels were assessed using the Affymetrix GeneChip Human Exon 1.0 ST Array. We found altered expression of 294 genes after hypoxia treatment. Upregulated genes are highly enriched in glucose metabolism and angiogenesis related processes, whereas downregulated genes are mainly connected to cell cycle and DNA repair. Thus, gene expression patterns recapitulate known adaptations to low oxygen supply. Alternative splicing events, until now not related to hypoxia, are shown for nine genes: six which are implicated in angiogenesis-mediated cytoskeleton remodeling (cask, itsn1, larp6, sptan1, tpm1 and robo1); one, which is involved in the synthesis of membrane-anchors (pign) and two universal regulators of gene expression (cugbp1 and max). Conclusions/Significance For the first time, this study investigates changes in splicing in the physiological response to hypoxia on a genome-wide scale. Nine alternative splicing events, until now not related to hypoxia, are reported, considerably expanding the information on splicing changes due to low oxygen supply. Therefore, this study provides further knowledge on hypoxia induced gene expression changes and presents new starting points to study the hypoxia adaptation of endothelial cells.
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Affiliation(s)
- Julia E Weigand
- Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Johann Wolfgang Goethe University Frankfurt, Frankfurt am Main, Germany.
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Zhang XZ, Yin AH, Zhu XY, Ding Q, Wang CH, Chen YX. Using an exon microarray to identify a global profile of gene expression and alternative splicing in K562 cells exposed to sodium valproate. Oncol Rep 2011; 27:1258-65. [PMID: 22200904 PMCID: PMC3583465 DOI: 10.3892/or.2011.1601] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 12/12/2011] [Indexed: 12/22/2022] Open
Abstract
To investigate the effect of valproate treatment on the K562 cell line, a model for chronic myelogenous leukaemia, the growth and survival of the K562 cell line were investigated using the Annexin-V/PI dual staining method, and global profiles of gene expression and alternative splicing in K562 cells were assessed using exon microarrays. A significant increase in cell apoptosis was observed in valproate-exposed K562 cells using flow cytometry. A total of 628 transcripts were identified as being significantly differentially expressed. The number of genes demonstrating increased expression levels was greater than the number of genes demonstrating decreased expression levels (445 genes vs. 183 genes, respectively). The significant enrichment analysis of GO terms for the differentially expressed genes revealed that these genes are involved in many important biological processes such as apoptosis. Six of the genes observed to be differentially expressed that might be involved in apoptosis were selected to undergo qRT-PCR validation. In total, 198 candidates of alternative splicing variants were identified. Among them, three alternative splicing events were selected for validation, and CBLC and TBX1 were confirmed to be alternatively spliced by semi-nested PCR. In conclusion, valproate exposure facilitated cell apoptosis, altered mRNA expression and alternative splicing events in the K562 cell line.
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Affiliation(s)
- Xiang-Zhong Zhang
- Department of Hematology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
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Lockstone HE. Exon array data analysis using Affymetrix power tools and R statistical software. Brief Bioinform 2011; 12:634-44. [PMID: 21498550 PMCID: PMC3220870 DOI: 10.1093/bib/bbq086] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 12/02/2010] [Indexed: 11/24/2022] Open
Abstract
The use of microarray technology to measure gene expression on a genome-wide scale has been well established for more than a decade. Methods to process and analyse the vast quantity of expression data generated by a typical microarray experiment are similarly well-established. The Affymetrix Exon 1.0 ST array is a relatively new type of array, which has the capability to assess expression at the individual exon level. This allows a more comprehensive analysis of the transcriptome, and in particular enables the study of alternative splicing, a gene regulation mechanism important in both normal conditions and in diseases. Some aspects of exon array data analysis are shared with those for standard gene expression data but others present new challenges that have required development of novel tools. Here, I will introduce the exon array and present a detailed example tutorial for analysis of data generated using this platform.
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Affiliation(s)
- Helen E Lockstone
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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Chen P, Lepikhova T, Hu Y, Monni O, Hautaniemi S. Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants. Nucleic Acids Res 2011; 39:e123. [PMID: 21745820 PMCID: PMC3185423 DOI: 10.1093/nar/gkr513] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing of pre-mRNA generates protein diversity. Dysfunction of splicing machinery and expression of specific transcripts has been linked to cancer progression and drug response. Exon microarray technology enables genome-wide quantification of expression levels of the majority of exons and facilitates the discovery of alternative splicing events. Analysis of exon array data is more challenging than the analysis of gene expression data and there is a need for reliable quantification of exons and alternatively spliced variants. We introduce a novel, computationally efficient methodology, Multiple Exon Array Preprocessing (MEAP), for exon array data pre-processing, analysis and visualization. We compared MEAP with existing pre-processing methods, and validation of six exons and two alternatively spliced variants with qPCR corroborated MEAP expression estimates. Analysis of exon array data from head and neck squamous cell carcinoma (HNSCC) cell lines revealed several transcripts associated with 11q13 amplification, which is related with decreased survival and metastasis in HNSCC patients. Our results demonstrate that MEAP produces reliable expression values at exon, alternatively spliced variant and gene levels, which allows generating novel experimentally testable predictions.
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Affiliation(s)
- Ping Chen
- Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, Biochemistry and Developmental Biology, 00014 University of Helsinki, Finland
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Hatakeyama K, Ohshima K, Fukuda Y, Ogura SI, Terashima M, Yamaguchi K, Mochizuki T. Identification of a novel protein isoform derived from cancer-related splicing variants using combined analysis of transcriptome and proteome. Proteomics 2011; 11:2275-82. [DOI: 10.1002/pmic.201100016] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/15/2011] [Accepted: 03/03/2011] [Indexed: 12/22/2022]
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Suzuki H, Osaki K, Sano K, Alam AHMK, Nakamura Y, Ishigaki Y, Kawahara K, Tsukahara T. Comprehensive analysis of alternative splicing and functionality in neuronal differentiation of P19 cells. PLoS One 2011; 6:e16880. [PMID: 21365003 PMCID: PMC3041816 DOI: 10.1371/journal.pone.0016880] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 01/03/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Alternative splicing, which produces multiple mRNAs from a single gene, occurs in most human genes and contributes to protein diversity. Many alternative isoforms are expressed in a spatio-temporal manner, and function in diverse processes, including in the neural system. METHODOLOGY/PRINCIPAL FINDINGS The purpose of the present study was to comprehensively investigate neural-splicing using P19 cells. GeneChip Exon Array analysis was performed using total RNAs purified from cells during neuronal cell differentiation. To efficiently and readily extract the alternative exon candidates, 9 filtering conditions were prepared, yielding 262 candidate exons (236 genes). Semiquantitative RT-PCR results in 30 randomly selected candidates suggested that 87% of the candidates were differentially alternatively spliced in neuronal cells compared to undifferentiated cells. Gene ontology and pathway analyses suggested that many of the candidate genes were associated with neural events. Together with 66 genes whose functions in neural cells or organs were reported previously, 47 candidate genes were found to be linked to 189 events in the gene-level profile of neural differentiation. By text-mining for the alternative isoform, distinct functions of the isoforms of 9 candidate genes indicated by the result of Exon Array were confirmed. CONCLUSIONS/SIGNIFICANCE Alternative exons were successfully extracted. Results from the informatics analyses suggested that neural events were primarily governed by genes whose expression was increased and whose transcripts were differentially alternatively spliced in the neuronal cells. In addition to known functions in neural cells or organs, the uninvestigated alternative splicing events of 11 genes among 47 candidate genes suggested that cell cycle events are also potentially important. These genes may help researchers to differentiate the roles of alternative splicing in cell differentiation and cell proliferation.
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Affiliation(s)
- Hitoshi Suzuki
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan.
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Langer W, Sohler F, Leder G, Beckmann G, Seidel H, Gröne J, Hummel M, Sommer A. Exon array analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer. BMC Genomics 2010; 11:676. [PMID: 21118496 PMCID: PMC3053589 DOI: 10.1186/1471-2164-11-676] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 11/30/2010] [Indexed: 12/22/2022] Open
Abstract
Background Treatment of non-small cell lung cancer with novel targeted therapies is a major unmet clinical need. Alternative splicing is a mechanism which generates diverse protein products and is of functional relevance in cancer. Results In this study, a genome-wide analysis of the alteration of splicing patterns between lung cancer and normal lung tissue was performed. We generated an exon array data set derived from matched pairs of lung cancer and normal lung tissue including both the adenocarcinoma and the squamous cell carcinoma subtypes. An enhanced workflow was developed to reliably detect differential splicing in an exon array data set. In total, 330 genes were found to be differentially spliced in non-small cell lung cancer compared to normal lung tissue. Microarray findings were validated with independent laboratory methods for CLSTN1, FN1, KIAA1217, MYO18A, NCOR2, NUMB, SLK, SYNE2, TPM1, (in total, 10 events) and ADD3, which was analysed in depth. We achieved a high validation rate of 69%. Evidence was found that the activity of FOX2, the splicing factor shown to cause cancer-specific splicing patterns in breast and ovarian cancer, is not altered at the transcript level in several cancer types including lung cancer. Conclusions This study demonstrates how alternatively spliced genes can reliably be identified in a cancer data set. Our findings underline that key processes of cancer progression in NSCLC are affected by alternative splicing, which can be exploited in the search for novel targeted therapies.
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Affiliation(s)
- Wolfram Langer
- Bayer Schering Pharma AG, Global Drug Discovery (GDD)-Target Discovery, Müllerstrasse 178, 13342 Berlin, Germany.
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