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Bachus S, Akkerman N, Fulham L, Graves D, Helwer R, Rempel J, Pelka P. ARGLU1 enhances promoter-proximal pausing of RNA polymerase II and stimulates DNA damage repair. Nucleic Acids Res 2024; 52:5658-5675. [PMID: 38520408 PMCID: PMC11162773 DOI: 10.1093/nar/gkae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
Arginine and glutamate rich 1 (ARGLU1) is a poorly understood cellular protein with functions in RNA splicing and transcription. Computational prediction suggests that ARGLU1 contains intrinsically disordered regions and lacks any known structural or functional domains. We used adenovirus Early protein 1A (E1A) to probe for critical regulators of important cellular pathways and identified ARGLU1 as a significant player in transcription and the DNA damage response pathway. Transcriptional effects induced by ARGLU1 occur via enhancement of promoter-proximal RNA polymerase II pausing, likely by inhibiting the interaction between JMJD6 and BRD4. When overexpressed, ARGLU1 increases the growth rate of cancer cells, while its knockdown leads to growth arrest. Significantly, overexpression of ARGLU1 increased cancer cell resistance to genotoxic drugs and promoted DNA damage repair. These results identify new roles for ARGLU1 in cancer cell survival and the DNA damage repair pathway, with potential clinical implications for chemotherapy resistance.
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Affiliation(s)
- Scott Bachus
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Nikolas Akkerman
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Lauren Fulham
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Drayson Graves
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Rafe Helwer
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Jordan Rempel
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Peter Pelka
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
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Shi J, Yu X, Li G, Zhao X, Chen J, Fang Y, Yang Y, Wang T, Xu T, Bian L, Lyu L, He Y. DTL promotes head and neck squamous cell carcinoma progression by mediating the degradation of ARGLU1 to regulate the Notch signaling pathway. Int J Biol Macromol 2024; 259:129184. [PMID: 38218284 DOI: 10.1016/j.ijbiomac.2023.129184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 01/15/2024]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, with a high incidence in squamous epithelium. The E3 ubiquitin ligase DTL is a component of the CRL4A complex and is widely involved in tumor progression. We aimed to analyze the role of DTL in HNSCC and to explore its mechanism of action. Through clinical analysis, we found that DTL is upregulated in HNSCC tissues and is associated with the tumor microenvironment and poor survival in patients. Through gain-of-function and loss-of-function assays, we showed that DTL promotes cell proliferation and migration in vitro and tumor growth in vivo. Mass spectrometry analysis and immunoprecipitation assays showed that DTL interacts with ARGLU1 to promote K11-linked ubiquitination-mediated degradation of ARGLU1, thereby promoting the activation of the CSL-dependent Notch signaling pathway. Furthermore, siARGLU1 blocks the inhibitory effects of DTL knockdown on HNSCC cells. In this study, we showed that DTL promotes HNSCC progression through K11-linked ubiquitination of ARGLU1 to activate the CSL-dependent Notch pathway. These findings identify a promising therapeutic target for HNSCC.
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Affiliation(s)
- Jingpei Shi
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, NHC Key Laboratory of Drug Addiction Medicine, Kunming Medical University, Kunming 650106, Yunnan, China; Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Xiaonan Yu
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, NHC Key Laboratory of Drug Addiction Medicine, Kunming Medical University, Kunming 650106, Yunnan, China
| | - Guoyu Li
- Department of Colorectal Surgery, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming 650118, Yunnan, China
| | - Xiaoyu Zhao
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032,Yunnan, China
| | - Jiwen Chen
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Ying Fang
- Department of Infection and Hepatology, The First Affiliated Hospital of Kunming Medical University, 650032, Yunnan, China
| | - Yan Yang
- Department of Hepatobiliary and Pancreatic Surgery and Liver Transplantion, the First People's Hospital of Kunming, Kunming 650011, Yunnan, China
| | - Ting Wang
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Tianyong Xu
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Li Bian
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China.
| | - Lechun Lyu
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, Yunnan, China.
| | - Yongwen He
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, NHC Key Laboratory of Drug Addiction Medicine, Kunming Medical University, Kunming 650106, Yunnan, China; Qujing Medical College, Qujing 655099, Yunnan, China.
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Yao F, Huang S, Liu J, Tan C, Xu M, Wang D, Huang M, Zhu Y, Huang X, He S. Deletion of ARGLU1 causes global defects in alternative splicing in vivo and mouse cortical malformations primarily via apoptosis. Cell Death Dis 2023; 14:543. [PMID: 37612280 PMCID: PMC10447433 DOI: 10.1038/s41419-023-06071-w] [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: 02/14/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023]
Abstract
Haploinsufficient mutation in arginine and glutamine-rich protein 1 (Arglu1), a newly identified pre-mRNA splicing regulator, may be linked to neural developmental disorders associated with mental retardation and epilepsy in human patients, but the underlying causes remain elusive. Here we show that ablation of Arglu1 promotes radial glial cell (RG) detachment from the ventricular zone (VZ), leading to ectopic localized RGs in the mouse embryonic cortex. Although they remain proliferative, ectopic progenitors, as well as progenitors in the VZ, exhibit prolonged mitosis, p53 upregulation and cell apoptosis, leading to reduced neuron production, neuronal loss and microcephaly. RNA seq analysis reveals widespread changes in alternative splicing in the mutant mouse embryonic cortex, preferentially affecting genes involved in neuronal functions. Mdm2 and Mdm4 are found to be alternatively spliced at the exon 3 and exon 5 respectively, leading to absence of the p53-binding domain and nonsense-mediated mRNA decay (NMD) and thus relieve inhibition of p53. Removal of p53 largely rescues the microcephaly caused by deletion of Arglu1. Our findings provide mechanistic insights into cortical malformations of human patients with Arglu1 haploinsufficient mutation.
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Affiliation(s)
- Fenyong Yao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Shisheng Huang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
- Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiahui Liu
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Chunhua Tan
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Mengqi Xu
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Dengkui Wang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Maoqing Huang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Yiyao Zhu
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China.
| | - Shuijin He
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China.
- Shanghai Clinical Research and Trial Center, 201210, Shanghai, China.
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Li S, Qi Y, Yu J, Hao Y, Xu L, Ding X, Zhang M, Geng J. Aurora kinase A regulates cancer-associated RNA aberrant splicing in breast cancer. Heliyon 2023; 9:e17386. [PMID: 37415951 PMCID: PMC10320321 DOI: 10.1016/j.heliyon.2023.e17386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 06/03/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023] Open
Abstract
The contribution of oncogenes to tumor-associated RNA splicing and the relevant molecular mechanisms therein require further elaboration. Here, we show that oncogenic Aurora kinase A (AURKA) promotes breast cancer-related RNA aberrant splicing in a context-dependent manner. AURKA regulated pan-breast cancer-associated RNA splicing events including GOLGA4, RBM4 and UBQLN1. Aberrant splicing of GOLGA4 and RBM4 was closely related to breast cancer development. Mechanistically, AURKA interacted with the splicing factor YBX1 and promoted AURKA-YBX1 complex-mediated GOLGA4 exon inclusion. AURKA binding to the splicing factor hnRNPK promoted AURKA-hnRNPK complex-mediated RBM4 exon skipping. Analysis of clinical data identified an association between the AURKA-YBX1/hnRNPK complex and poor prognosis in breast cancer. Blocking AURKA nuclear translocation with small molecule drugs partially reversed the oncogenic splicing of RBM4 and GOLGA4 in breast cancer cells. In summary, oncogenic AURKA executes its function on modulating breast cancer-related RNA splicing, and nuclear AURKA is distinguished as a hopeful target in the case of treating breast cancer.
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Affiliation(s)
- Sisi Li
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Jiachuan Yu
- Department of Anesthesiology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yuchao Hao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Lingzhi Xu
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xudong Ding
- Department of Pathology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Minghui Zhang
- Department of Oncology, Chifeng City Hospital, Chifeng, China
| | - Jingshu Geng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
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Relationship between tumor microbiota transcriptional activity and gene expression in breast cancer. BMC Cancer 2023; 23:252. [PMID: 36927310 PMCID: PMC10018882 DOI: 10.1186/s12885-023-10726-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND A few studies have reported the distribution of the microbiota in breast cancer tissues, but few reports have compared the microbiota in different subtypes of breast cancer tissue. Moreover, no study has reported on the relationship between the microbiota and gene expression in breast tumor. METHODS Sections of formalin-fixed paraffin-embedded (FFPE) tissue were prepared from the breast tumors of 70 patients and were subjected to microarray analysis to identify gene expression profiles. The same total RNA samples were also used to analyze the microbiota activity in tumor tissues by performing 16 S rRNA sequencing and internal transcribed spacer (ITS) sequencing of reverse transcript cDNA with Illumina Miseq. Pearson's correlation coefficient was used for calculating the correlation between microbial relative activity and gene expression. RESULTS The microbiota transcriptional activity of 70 FFPE samples mainly consisted of the phyla Bacteroidetes, Firmicutes and Proteobacteria. Prevotella_9, Bacteroides and Alloprevotella were the most active genera in ER+/HER2-, ER+/HER2 + and ER-/HER2 + tumors, while triple-negative samples exhibited a higher activity of Lactobacillus. In ER-negative samples (triple-negative and ER-/HER2+), 479 genes, including the breast carcinogenesis genes phospholipase A2, histone cluster 2, Crk-like, and cyclin D1, were significantly positive associated with the activity of Lactobacillus. CONCLUSION This was the first study to clarify an association between the breast tumor microbiota transcriptional activity and the expression of carcinogenesis genes in ER-negative breast cancer. Changes in the microbiota of breast tissue induced by external factors might be one of the key causes of ER negative breast cancer.
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Chan SN, Pek JW. Distinct biogenesis pathways may have led to functional divergence of the human and Drosophila Arglu1 sisRNA. EMBO Rep 2023; 24:e54350. [PMID: 36533631 PMCID: PMC9900350 DOI: 10.15252/embr.202154350] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Stable intronic sequence RNAs (sisRNAs) are stable, long noncoding RNAs containing intronic sequences. While sisRNAs have been found across diverse species, their level of conservation remains poorly understood. Here we report that the biogenesis and functions of a sisRNA transcribed from the highly conserved Arglu1 locus are distinct in human and Drosophila melanogaster. The Arglu1 genes in both species show similar exon-intron structures where the intron 2 is orthologous and positionally conserved. In humans, Arglu1 sisRNA retains the entire intron 2 and promotes host gene splicing. Mechanistically, Arglu1 sisRNA represses the splicing-inhibitory activity of ARGLU1 protein by binding to ARGLU1 protein and promoting its localization to nuclear speckles, away from the Arglu1 gene locus. In contrast, Drosophila dArglu1 sisRNA forms via premature cleavage of intron 2 and represses host gene splicing. This repression occurs through a local accumulation of dARGLU1 protein and inhibition of telescripting by U1 snRNPs at the dArglu1 locus. We propose that distinct biogenesis of positionally conserved Arglu1 sisRNAs in both species may have led to functional divergence.
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Affiliation(s)
- Seow Neng Chan
- Temasek Life Sciences LaboratoryNational University of SingaporeSingaporeSingapore
| | - Jun Wei Pek
- Temasek Life Sciences LaboratoryNational University of SingaporeSingaporeSingapore
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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7
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Identification of potentially functional modules and diagnostic genes related to amyotrophic lateral sclerosis based on the WGCNA and LASSO algorithms. Sci Rep 2022; 12:20144. [PMID: 36418457 PMCID: PMC9684499 DOI: 10.1038/s41598-022-24306-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a genetically and phenotypically heterogeneous disease results in the loss of motor neurons. Mounting information points to involvement of other systems including cognitive impairment. However, neither the valid biomarker for diagnosis nor effective therapeutic intervention is available for ALS. The present study is aimed at identifying potentially genetic biomarker that improves the diagnosis and treatment of ALS patients based on the data of the Gene Expression Omnibus. We retrieved datasets and conducted a weighted gene co-expression network analysis (WGCNA) to identify ALS-related co-expression genes. Functional enrichment analysis was performed to determine the features and pathways of the main modules. We then constructed an ALS-related model using the least absolute shrinkage and selection operator (LASSO) regression analysis and verified the model by the receiver operating characteristic (ROC) curve. Besides we screened the non-preserved gene modules in FTD and ALS-mimic disorders to distinct ALS-related genes from disorders with overlapping genes and features. Altogether, 4198 common genes between datasets with the most variation were analyzed and 16 distinct modules were identified through WGCNA. Blue module had the most correlation with ALS and functionally enriched in pathways of neurodegeneration-multiple diseases', 'amyotrophic lateral sclerosis', and 'endocytosis' KEGG terms. Further, some of other modules related to ALS were enriched in 'autophagy' and 'amyotrophic lateral sclerosis'. The 30 top of hub genes were recruited to a LASSO regression model and 5 genes (BCLAF1, GNA13, ARL6IP5, ARGLU1, and YPEL5) were identified as potentially diagnostic ALS biomarkers with validating of the ROC curve and AUC value.
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8
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Düster R, Ji Y, Pan KT, Urlaub H, Geyer M. Functional characterization of the human Cdk10/Cyclin Q complex. Open Biol 2022; 12:210381. [PMID: 35291876 PMCID: PMC8924752 DOI: 10.1098/rsob.210381] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) are key players in cell cycle regulation and transcription. The CDK-family member Cdk10 is important for neural development and can act as a tumour suppressor, but the underlying molecular mechanisms are largely unknown. Here, we provide an in-depth analysis of Cdk10 substrate specificity and function. Using recombinant Cdk10/CycQ protein complexes, we characterize RNA pol II CTD, c-MYC and RB1 as in vitro protein substrates. Using an analogue-sensitive mutant kinase, we identify 89 different Cdk10 phosphosites in HEK cells originating from 66 different proteins. Among these, proteins involved in cell cycle, translation, stress response, growth signalling, as well as rRNA, and mRNA transcriptional regulation, are found. Of a set of pan-selective CDK- and Cdk9-specific inhibitors tested, all inhibited Cdk10/CycQ at least five times weaker than their proposed target kinases. We also identify Cdk10 as an in vitro substrate of Cdk1 and Cdk5 at multiple sites, allowing for a potential cross-talk between these CDKs. With this functional characterization, Cdk10 adopts a hybrid position in both cell cycle and transcriptional regulation.
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Affiliation(s)
- Robert Düster
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Yanlong Ji
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, 37077 Göttingen, Germany,Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Kuan-Ting Pan
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, 37077 Göttingen, Germany,Institute of Clinical Chemistry, Bioanalytics Group, University Medical Center Göttingen, Göttingen, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
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Role of the Mediator Complex and MicroRNAs in Breast Cancer Etiology. Genes (Basel) 2022; 13:genes13020234. [PMID: 35205279 PMCID: PMC8871970 DOI: 10.3390/genes13020234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 12/16/2022] Open
Abstract
Transcriptional coactivators play a key role in RNA polymerase II transcription and gene regulation. One of the most important transcriptional coactivators is the Mediator (MED) complex, which is an evolutionary conserved large multiprotein complex. MED transduces the signal between DNA-bound transcriptional activators (gene-specific transcription factors) to the RNA polymerase II transcription machinery to activate transcription. It is known that MED plays an essential role in ER-mediated gene expression mainly through the MED1 subunit, since estrogen receptor (ER) can interact with MED1 by specific protein–protein interactions; therefore, MED1 plays a fundamental role in ER-positive breast cancer (BC) etiology. Additionally, other MED subunits also play a role in BC etiology. On the other hand, microRNAs (miRNAs) are a family of small non-coding RNAs, which can regulate gene expression at the post-transcriptional level by binding in a sequence-specific fashion at the 3′ UTR of the messenger RNA. The miRNAs are also important factors that influence oncogenic signaling in BC by acting as both tumor suppressors and oncogenes. Moreover, miRNAs are involved in endocrine therapy resistance of BC, specifically to tamoxifen, a drug that is used to target ER signaling. In metazoans, very little is known about the transcriptional regulation of miRNA by the MED complex and less about the transcriptional regulation of miRNAs involved in BC initiation and progression. Recently, it has been shown that MED1 is able to regulate the transcription of the ER-dependent miR-191/425 cluster promoting BC cell proliferation and migration. In this review, we will discuss the role of MED1 transcriptional coactivator in the etiology of BC and in endocrine therapy-resistance of BC and also the contribution of other MED subunits to BC development, progression and metastasis. Lastly, we identified miRNAs that potentially can regulate the expression of MED subunits.
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10
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miR-335-5p Inhibits Progression of Uterine Leiomyoma by Targeting ARGLU1. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2329576. [PMID: 35082911 PMCID: PMC8786540 DOI: 10.1155/2022/2329576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022]
Abstract
Studies have demonstrated that miR-335-5p exhibits an essential role in the progress of multiple tumors, including thyroid cancer, pancreatic cancer, and non-small-cell lung cancer. However, the possible expression, the detailed role, and the underlying mechanisms of miR-335-5p in uterine leiomyoma (UL) still remained unclear. Therefore, the present study was designed to investigate the mechanism and function of miR-335-5p in UL. In our study, microRNA-335-5p (miR-335-5p) is significantly downregulated in UL tissues and UL cell lines, especially in HCC1688 and SK-UT-1 cells. Functionally, overexpression of miR-335-5p notably inhibits the viability of UL cell lines by CCK-8 assay. Besides, upregulation of miR-335-5p inhibits proliferation of UL cell lines by colony formation assay and decreases the protein levels of PCNA and Ki-67 detected by western blot assay. In addition, overexpression of miR-335-5p induces UL cell cycle arrest at G1 phase. Upregulation of miR-335-5p decreases the levels of Cyclin A1, Cyclin B1, and Cyclin D2 and upregulates the expression of p27 protein. Additionally, upregulation of miR-335-5p promotes the apoptosis of UL cell lines, increases the protein levels of Bax, Cleaved caspase-3, and Cleaved caspase-9, and decreases the protein expression of Bcl-2. Moreover, Arginine and Glutamate-Rich protein 1 (ARGLU1) is predicted as a target of miR-335-5p by ENCORI and miRDB and confirmed by dual-luciferase reporter assay. ARGLU1 is negatively associated with miR-335-5p. Furthermore, overexpression of ARGLU1 partly restores the effects of miR-335-5p mimic on the viability, proliferation, cell cycle, and apoptosis of UL cell lines. To conclude, miR-335-5p may play a repressive role in UL by targeting ARGLU1 and serve as a potential therapeutic target for the treatment of UL.
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Roos K, Rooda I, Keif RS, Liivrand M, Smolander OP, Salumets A, Velthut-Meikas A. Single-cell RNA-seq analysis and cell-cluster deconvolution of the human preovulatory follicular fluid cells provide insights into the pathophysiology of ovarian hyporesponse. Front Endocrinol (Lausanne) 2022; 13:945347. [PMID: 36339426 PMCID: PMC9635625 DOI: 10.3389/fendo.2022.945347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Reduction in responsiveness to gonadotropins or hyporesponsiveness may lead to the failure of in vitro fertilization (IVF), due to a low number of retrieved oocytes. The ovarian sensitivity index (OSI) is used to reflect the ovarian responsiveness to gonadotropin stimulation before IVF. Although introduced to clinical practice already years ago, its usefulness to predict clinical outcomes requires further research. Nevertheless, pathophysiological mechanisms of ovarian hyporesponse, along with advanced maternal age and in younger women, have not been fully elucidated. Follicles consist of multiple cell types responsible for a repertoire of biological processes including responding to pituitary gonadotropins necessary for follicle growth and oocyte maturation as well as ovulation. Encouraging evidence suggests that hyporesponse could be influenced by many contributing factors, therefore, investigating the variability of ovarian follicular cell types and their gene expression in hyporesponders is highly informative for increasing their prognosis for IVF live birth. Due to advancements in single-cell analysis technologies, the role of somatic cell populations in the development of infertility of ovarian etiology can be clarified. Here, somatic cells were collected from the fluid of preovulatory ovarian follicles of patients undergoing IVF, and RNA-seq was performed to study the associations between OSI and gene expression. We identified 12 molecular pathways differentially regulated between hypo- and normoresponder patient groups (FDR<0.05) from which extracellular matrix organization, post-translational protein phosphorylation, and regulation of Insulin-like Growth Factor (IGF) transport and uptake by IGF Binding Proteins were regulated age-independently. We then generated single-cell RNA-seq data from matching follicles revealing 14 distinct cell clusters. Using cell cluster-specific deconvolution from the bulk RNA-seq data of 18 IVF patients we integrated the datasets as a novel approach and discovered that the abundance of three cell clusters significantly varied between hypo- and normoresponder groups suggesting their role in contributing to the deviations from normal ovarian response to gonadotropin stimulation. Our work uncovers new information regarding the differences in the follicular gene expression between hypo- and normoresponders. In addition, the current study fills the gap in understanding the inter-patient variability of cell types in human preovulatory follicles, as revealed by single-cell analysis of follicular fluid cells.
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Affiliation(s)
- Kristine Roos
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- Nova Vita Clinic AS, Tallinn, Estonia
| | - Ilmatar Rooda
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Robyn-Stefany Keif
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Maria Liivrand
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Olli-Pekka Smolander
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Andres Salumets
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Agne Velthut-Meikas
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- *Correspondence: Agne Velthut-Meikas,
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12
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Wang K, Wu P, Chen D, Zhou J, Yang X, Jiang A, Xiao W, Qiu X, Zeng Y, Xu X, Tang G. Detecting the selection signatures in Chinese Duroc,Landrace, Yorkshire, Liangshan, and Qingyu pigs. Funct Integr Genomics 2021; 21:655-664. [PMID: 34606016 DOI: 10.1007/s10142-021-00809-5] [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: 03/24/2020] [Revised: 10/23/2020] [Accepted: 09/18/2021] [Indexed: 10/20/2022]
Abstract
Here we used two kinds of chips data from 5 pig breeds, Chinese Duroc (DD), Landrace (LL), Yorkshire (YY), Liangshan (LS), and Qingyu pigs (QY) in China to identify genes which show evidence of selection during domestication. Four breed pairs, LS-YY, QY-YY, DD-YY, and LL-YY pair, were performed to detect selection signatures using the Fst method. Then we identified a list of genes that played key roles in domestication and artificial selection. For example, the PTPRM gene was shared in LS-YY, QY-YY, and DD-YY pairs and it regulates a variety of cellular processes including cell growth, differentiation as signaling molecules. The HACD3 gene was shared in QY-YY and DD-YY pairs, and the HACD3 protein is involved in the production of very long-chain fatty acids of different chain lengths. Besides, the MYH11 gene that related to muscle contraction was found in LS-YY and LL-YY pair. These results suggested that genes related to immunity, disease resistance, and metabolism were subjected to strong selection pressure in Chinese domestic pigs in the progress of domestication and evolution; however, genes related to appearance, production performance, and reproduction were undergone strong artificial selection in commercial pig breeds.
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Affiliation(s)
- Kai Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Pingxian Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dejuan Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jie Zhou
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xidi Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anan Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Weihang Xiao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaotian Qiu
- National Animal Husbandry Service, BeijingBeijing, 100125, China
| | - Yangshuang Zeng
- Sichuan Animal Husbandry Station, Chengdu, 610041, Sichuan, China
| | - Xu Xu
- Sichuan Animal Husbandry Station, Chengdu, 610041, Sichuan, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China.
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13
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Li F, Li J, Yu J, Pan T, Yu B, Sang Q, Dai W, Hou J, Yan C, Zang M, Zhu Z, Su L, Li YY, Liu B. Identification of ARGLU1 as a potential therapeutic target for gastric cancer based on genome-wide functional screening data. EBioMedicine 2021; 69:103436. [PMID: 34157484 PMCID: PMC8220577 DOI: 10.1016/j.ebiom.2021.103436] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Due to the molecular mechanism complexity and heterogeneity of gastric cancer (GC), mechanistically interpretable biomarkers were required for predicting prognosis and discovering therapeutic targets for GC patients. METHODS Based on a total of 824 GC-specific fitness genes from the Project Score database, LASSOCox regression was performed in TCGA-STAD cohort to construct a GC Prognostic (GCP) model which was then evaluated on 7 independent GC datasets. Targets prioritization was performed in GC organoids. ARGLU1 was selected to further explore the biological function and molecular mechanism. We evaluated the potential of ARGLU1 serving as a promising therapeutic target for GC using patients derived xenograft (PDX) model. FINDINGS The 9-gene GCP model showed a statistically significant prognostic performance for GC patients in 7 validation cohorts. Perturbation of SSX4, DDX24, ARGLU1 and TTF2 inhibited GC organoids tumor growth. The results of tissue microarray indicated lower expression of ARGLU1 was correlated with advanced TNM stage and worse overall survival. Over-expression ARGLU1 significantly inhibited GC cells viability in vitro and in vivo. ARGLU1 could enhance the transcriptional level of mismatch repair genes including MLH3, MSH2, MSH3 and MSH6 by potentiating the recruitment of SP1 and YY1 on their promoters. Moreover, inducing ARGLU1 by LNP-formulated saRNA significantly inhibited tumor growth in PDX model. INTERPRETATION Based on genome-wide functional screening data, we constructed a 9-gene GCP model with satisfactory predictive accuracy and mechanistic interpretability. Out of nine prognostic genes, ARGLU1 was verified to be a potential therapeutic target for GC. FUNDING National Natural Science Foundation of China.
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Affiliation(s)
- Fangyuan Li
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Jianfang Li
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Junxian Yu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Tao Pan
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Beiqin Yu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Qingqing Sang
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Wentao Dai
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China; Shanghai Center for Bioinformation Technology, Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai 201203, PR China
| | - Junyi Hou
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Chao Yan
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Mingde Zang
- Department of Gastric Cancer Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, 200032 Shanghai, PR China
| | - Zhenggang Zhu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Liping Su
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Yuan-Yuan Li
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China; Shanghai Center for Bioinformation Technology, Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai 201203, PR China.
| | - Bingya Liu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China.
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14
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Systematic Identification of Survival-Associated Alternative Splicing Events in Kidney Renal Clear Cell Carcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:5576933. [PMID: 33959190 PMCID: PMC8075682 DOI: 10.1155/2021/5576933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 11/18/2022]
Abstract
There is growing evidence that aberrant alternative splicing (AS) is highly correlated with driving tumorigenesis, but its function in kidney renal clear cell carcinoma (KIRC) remains to be discovered. In this study, we obtained the level-3 RNA sequencing and clinical data of KIRC from The Cancer Genome Atlas (TGCA). Combining with the splicing event detail information from TGCA SpliceSeq database, we established the independent prognosis signatures for KIRC with the univariate and multivariate Cox regression analyses. Then, we used the Kaplan-Meier analysis and receiver operating characteristic curves (ROCs) to assess the accuracy of prognosis signatures. We also constructed the regulatory network of splicing factors (SFs) and AS events. Our results showed that a total of 12029 survival-associated AS events of 5761 genes were found in 524 KIRC patients. All types of prognosis signatures displayed a satisfactory ability to reliably predict, especially in exon skip model which the area under curve of ROC was 0.802. Moreover, 18 splicing factors (SFs) highly correlated to AS events were identified. With the construction of the SF-AS interactive network, we found that SF powerfully promotes the occurrence of abnormal AS and may have a profound role in KIRC. Collectively, we screened survival-associated AS events and established prognosis signatures for KIRC, coupling with the SF-AS interactive network, which might provide a key perspective to clarify the potential mechanism of AS in KIRC.
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15
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MiR-3613-3p inhibits hypertrophic scar formation by down-regulating arginine and glutamate-rich 1. Mol Cell Biochem 2020; 476:1025-1036. [PMID: 33165823 DOI: 10.1007/s11010-020-03968-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022]
Abstract
Hypertrophic scar (HS) is a severe skin disorder characterized by excessive extracellular matrix production and abnormal function of fibroblasts. Recent studies have demonstrated that microRNAs (miRNAs) play critical roles in HS formation. This study aims to investigate the role of miR-3613-3p in the formation of HS. The mRNA and miRNA levels were measured by quantitative RT-PCR analysis. The protein levels were examined by Western blot assay. Cell proliferation was determined by Cell Counting Kit-8 assay. The Caspase-3 and Caspase-9 activities were measured using flow cytometry assay. Dual-luciferase activity reporter assay and mRNA-miRNA pulldown assay were conducted to validate the target of miR-3613-3p. miR-3613-3p was downregulated, while arginine and glutamate-rich 1 (ARGLU1) was upregulated in HS fibroblasts (HSFs) and tissues. Overexpression of miR-3613-3p or knockdown of ARGLU1 markedly inhibited the expression of extracellular matrix (ECM) production-associated proteins and promoted Caspase-3 and Caspase-9 activations in HSFs. ARGLU1 was further identified as a direct target of miR-3613-3p. Restoration of ARGLU1 abrogated the suppressive effect of miR-3613-3p on cell proliferation and ECM protein expression of HSFs. Our results demonstrated that miR-3613-3p inhibited HS formation via targeting ARGLU1, which may provide potential therapeutic targets for the management of HS.
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16
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Genome-wide association study for circulating fibroblast growth factor 21 and 23. Sci Rep 2020; 10:14578. [PMID: 32884031 PMCID: PMC7471933 DOI: 10.1038/s41598-020-71569-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 08/06/2020] [Indexed: 11/09/2022] Open
Abstract
Fibroblast growth factors (FGFs) 21 and 23 are recently identified hormones regulating metabolism of glucose, lipid, phosphate and vitamin D. Here we conducted a genome-wide association study (GWAS) for circulating FGF21 and FGF23 concentrations to identify their genetic determinants. We enrolled 5,000 participants from Taiwan Biobank for this GWAS. After excluding participants with diabetes mellitus and quality control, association of single nucleotide polymorphisms (SNPs) with log-transformed FGF21 and FGF23 serum concentrations adjusted for age, sex and principal components of ancestry were analyzed. A second model additionally adjusted for body mass index (BMI) and a third model additionally adjusted for BMI and estimated glomerular filtration rate (eGFR) were used. A total of 4,201 participants underwent GWAS analysis. rs67327215, located within RGS6 (a gene involved in fatty acid synthesis), and two other SNPs (rs12565114 and rs9520257, located between PHC2-ZSCAN20 and ARGLU1-FAM155A respectively) showed suggestive associations with serum FGF21 level (P = 6.66 × 10–7, 6.00 × 10–7 and 6.11 × 10–7 respectively). The SNPs rs17111495 and rs17843626 were significantly associated with FGF23 level, with the former near PCSK9 gene and the latter near HLA-DQA1 gene (P = 1.04 × 10–10 and 1.80 × 10–8 respectively). SNP rs2798631, located within the TGFB2 gene, was suggestively associated with serum FGF23 level (P = 4.97 × 10–7). Additional adjustment for BMI yielded similar results. For FGF23, further adjustment for eGFR had similar results. We conducted the first GWAS of circulating FGF21 levels to date. Novel candidate genetic loci associated with circulating FGF21 or FGF23 levels were found. Further replication and functional studies are needed to support our findings.
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17
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Leonard M, Zhang X. Estrogen receptor coactivator Mediator Subunit 1 (MED1) as a tissue-specific therapeutic target in breast cancer. J Zhejiang Univ Sci B 2019; 20:381-390. [PMID: 31090264 DOI: 10.1631/jzus.b1900163] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Breast cancer, one of the most frequent cancer types, is a leading cause of death in women worldwide. Estrogen receptor (ER) α is a nuclear hormone receptor that plays key roles in mammary gland development and breast cancer. About 75% of breast cancer cases are diagnosed as ER-positive; however, nearly half of these cancers are either intrinsically or inherently resistant to the current anti-estrogen therapies. Recent studies have identified an ER coactivator, Mediator Subunit 1 (MED1), as a unique, tissue-specific cofactor that mediates breast cancer metastasis and treatment resistance. MED1 is overexpressed in over 50% of human breast cancer cases and co-amplifies with another important breast cancer gene, receptor tyrosine kinase HER2. Clinically, MED1 expression highly correlates with poor disease-free survival of breast cancer patients, and recent studies have reported an increased frequency of MED1 mutations in the circulating tumor cells of patients after treatment. In this review, we discuss the biochemical characterization of MED1 and its associated MED1/Mediator complex, its crosstalk with HER2 in anti-estrogen resistance, breast cancer stem cell formation, and metastasis both in vitro and in vivo. Furthermore, we elaborate on the current advancements in targeting MED1 using state-of-the-art RNA nanotechnology and discuss the future perspectives as well.
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Affiliation(s)
- Marissa Leonard
- Department of Cancer Biology, University of Cincinnati College of Medicine, 3125 Eden Avenue, Cincinnati, OH 45267, USA
| | - Xiaoting Zhang
- Department of Cancer Biology, University of Cincinnati College of Medicine, 3125 Eden Avenue, Cincinnati, OH 45267, USA
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18
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Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL. ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development. Nucleic Acids Res 2019; 47:2856-2870. [PMID: 30698747 PMCID: PMC6451108 DOI: 10.1093/nar/gkz010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 12/21/2018] [Accepted: 01/04/2019] [Indexed: 12/17/2022] Open
Abstract
Stress hormones bind and activate the glucocorticoid receptor (GR) in many tissues including the brain. We identified arginine and glutamate rich 1 (ARGLU1) in a screen for new modulators of glucocorticoid signaling in the CNS. Biochemical studies show that the glutamate rich C-terminus of ARGLU1 coactivates multiple nuclear receptors including the glucocorticoid receptor (GR) and the arginine rich N-terminus interacts with splicing factors and binds to RNA. RNA-seq of neural cells depleted of ARGLU1 revealed significant changes in the expression and alternative splicing of distinct genes involved in neurogenesis. Loss of ARGLU1 is embryonic lethal in mice, and knockdown in zebrafish causes neurodevelopmental and heart defects. Treatment with dexamethasone, a GR activator, also induces changes in the pattern of alternatively spliced genes, many of which were lost when ARGLU1 was absent. Importantly, the genes found to be alternatively spliced in response to glucocorticoid treatment were distinct from those under transcriptional control by GR, suggesting an additional mechanism of glucocorticoid action is present in neural cells. Our results thus show that ARGLU1 is a novel factor for embryonic development that modulates basal transcription and alternative splicing in neural cells with consequences for glucocorticoid signaling.
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Affiliation(s)
- Lilia Magomedova
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jens Tiefenbach
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Emma Zilberman
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Florian Le Billan
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Veronique Voisin
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Michael Saikali
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Vincent Boivin
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Melanie Robitaille
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Serge Gueroussov
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Manuel Irimia
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Debashish Ray
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Rucha Patel
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - ChangJiang Xu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Pancharatnam Jeyasuria
- Department of Obstetrics and Gynecology, Wayne State University Perinatal Initiative, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Gary D Bader
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Quaid D Morris
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michelle S Scott
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Henry Krause
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Biochemistry,University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Carolyn L Cummins
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
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19
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Mini E, Lapucci A, Perrone G, D'Aurizio R, Napoli C, Brugia M, Landini I, Tassi R, Picariello L, Simi L, Mancini I, Messerini L, Magi A, Pinzani P, Mazzei T, Tonelli F, Nobili S. RNA sequencing reveals PNN and KCNQ1OT1 as predictive biomarkers of clinical outcome in stage III colorectal cancer patients treated with adjuvant chemotherapy. Int J Cancer 2019; 145:2580-2593. [PMID: 30973654 DOI: 10.1002/ijc.32326] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/13/2019] [Accepted: 04/01/2019] [Indexed: 12/16/2022]
Abstract
Five-year overall survival of stage III colorectal cancer (CRC) patients treated with standard adjuvant chemotherapy (ACHT) is highly variable. Genomic biomarkers and/or transcriptomic profiles identified lack of adequate validation. Aim of our study was to identify and validate molecular biomarkers predictive of ACHT response in stage III CRC patients by a transcriptomic approach. From a series of CRC patients who received ACHT, two stage III extreme cohorts (unfavorable vs. favorable prognosis) were selected. RNA-sequencing was performed from fresh frozen explants. Tumors were characterized for somatic mutations. Validation was performed in stage III CRC patients extracted from two GEO datasets. According to disease-free survival (DFS), 108 differentially expressed genes (104/4 up/downregulated in the unfavorable prognosis group) were identified. Among 104 upregulated genes, 42 belonged to olfactory signaling pathways, 62 were classified as pseudogenes (n = 17), uncharacterized noncoding RNA (n = 10), immune response genes (n = 4), microRNA (n = 1), cancer-related genes (n = 14) and cancer-unrelated genes (n = 16). Three out of four down-regulated genes were cancer-related. Mutational status (i.e., RAS, BRAF, PIK3CA) did not differ among the cohorts. In the validation cohort, multivariate analysis showed high PNN and KCNQ1OT1 expression predictive of shorter DFS in ACHT treated patients (p = 0.018 and p = 0.014, respectively); no difference was observed in untreated patients. This is the first study that identifies by a transcriptomic approach and validates PNN and KCNQ1OT1 as molecular biomarkers predictive of chemotherapy response in stage III CRC patients. After a further validation in an independent cohort, PNN and KCNQ1OT1 evaluation could be proposed to prospectively identify stage III CRC patients benefiting from ACHT.
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Affiliation(s)
- Enrico Mini
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
| | - Andrea Lapucci
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
| | - Gabriele Perrone
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
| | - Romina D'Aurizio
- Institute of Informatics and Telematics (IIT), National Research Council (CNR), Pisa, Italy
| | - Cristina Napoli
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
| | - Marco Brugia
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Ida Landini
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
| | - Renato Tassi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lucia Picariello
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Lisa Simi
- Molecular and Clinical Biochemistry Laboratory, Careggi University Hospital, Florence, Italy
| | - Irene Mancini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Luca Messerini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alberto Magi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Pamela Pinzani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy.,Molecular and Clinical Biochemistry Laboratory, Careggi University Hospital, Florence, Italy
| | - Teresita Mazzei
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Francesco Tonelli
- Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Stefania Nobili
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
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20
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Chen Z, Kapus A, Khatri I, Kos O, Zhu F, Gorczynski RM. Cell membrane-bound CD200 signals both via an extracellular domain and following nuclear translocation of a cytoplasmic fragment. Leuk Res 2018; 69:72-80. [DOI: 10.1016/j.leukres.2018.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/02/2018] [Accepted: 04/06/2018] [Indexed: 12/16/2022]
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21
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Weber H, Garabedian MJ. The mediator complex in genomic and non-genomic signaling in cancer. Steroids 2018; 133:8-14. [PMID: 29157917 PMCID: PMC5864542 DOI: 10.1016/j.steroids.2017.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/04/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022]
Abstract
Mediator is a conserved, multi-subunit macromolecular machine divided structurally into head, middle, and tail modules, along with a transiently associating kinase module. Mediator functions as an integrator of transcriptional regulatory activity by interacting with DNA-bound transcription factors and with RNA polymerase II (Pol II) to both activate and repress gene expression. Mediator has been shown to affect multiple steps in transcription, including chromatin looping between enhancers and promoters, pre-initiation complex formation, transcriptional elongation, and mRNA splicing. Individual Mediator subunits participate in regulation of gene expression by the estrogen and androgen receptors and are altered in a number of endocrine cancers, including breast and prostate cancer. In addition to its role in genomic signaling, MED12 has been implicated in non-genomic signaling by interacting with and activating TGF-beta receptor 2 in the cytoplasm. Recent structural studies have revealed extensive inter-domain interactions and complex architecture of the Mediator-Pol II complex, suggesting that Mediator is capable of reorganizing its conformation and composition to fit cellular needs. We propose that alterations in Mediator subunit expression that occur in various cancers could impact the organization and function of Mediator, resulting in changes in gene expression that promote malignancy. A better understanding of the role of Mediator in cancer could reveal new approaches to the diagnosis and treatment of Mediator-dependent endocrine cancers, especially in settings of therapy resistance.
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Affiliation(s)
- Hannah Weber
- Departments of Microbiology and Urology, NYU School of Medicine, 550 First Ave, New York, NY 10012, United States
| | - Michael J Garabedian
- Departments of Microbiology and Urology, NYU School of Medicine, 550 First Ave, New York, NY 10012, United States.
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22
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Lévy J, Haye D, Marziliano N, Casu G, Guimiot F, Dupont C, Teissier N, Benzacken B, Gressens P, Pipiras E, Verloes A, Tabet AC. EFNB2haploinsufficiency causes a syndromic neurodevelopmental disorder. Clin Genet 2018; 93:1141-1147. [DOI: 10.1111/cge.13234] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 01/17/2023]
Affiliation(s)
- J. Lévy
- Genetics Department, AP-HP; Robert-Debré University Hospital; Paris France
- Sorbonne Paris-Cité University; Denis Diderot Medical School; Paris France
- INSERM UMR1141, Robert-Debré Hospital; Paris Diderot University, AP-HP; Paris France
| | - D. Haye
- Genetics Department, AP-HP; Robert-Debré University Hospital; Paris France
| | - N. Marziliano
- Unità Operatica Complessa di Cardiologia; ASSL3 Nuoro-ATS Sardegna; Italy
| | - G. Casu
- Unità Operatica Complessa di Cardiologia; ASSL3 Nuoro-ATS Sardegna; Italy
| | - F. Guimiot
- Genetics Department, AP-HP; Robert-Debré University Hospital; Paris France
- Department of Developmental Biology, AP-HP Robert-Debré University Hospital; Paris Diderot University, Sorbonne Paris-Cité University; Paris France
| | - C. Dupont
- Genetics Department, AP-HP; Robert-Debré University Hospital; Paris France
| | - N. Teissier
- Sorbonne Paris-Cité University; Denis Diderot Medical School; Paris France
- INSERM UMR1141, Robert-Debré Hospital; Paris Diderot University, AP-HP; Paris France
| | - B. Benzacken
- INSERM UMR1141, Robert-Debré Hospital; Paris Diderot University, AP-HP; Paris France
- Department of Cytogenetics, University Hospital Jean-Verdier; Embryology and Histology; Bondy France
| | - P. Gressens
- INSERM UMR1141, Robert-Debré Hospital; Paris Diderot University, AP-HP; Paris France
| | - E. Pipiras
- INSERM UMR1141, Robert-Debré Hospital; Paris Diderot University, AP-HP; Paris France
- Department of Cytogenetics, University Hospital Jean-Verdier; Embryology and Histology; Bondy France
| | - A. Verloes
- Genetics Department, AP-HP; Robert-Debré University Hospital; Paris France
- Sorbonne Paris-Cité University; Denis Diderot Medical School; Paris France
- INSERM UMR1141, Robert-Debré Hospital; Paris Diderot University, AP-HP; Paris France
| | - A.-C. Tabet
- Genetics Department, AP-HP; Robert-Debré University Hospital; Paris France
- Neuroscience Department, Human Genetics et Cognitive Function Unit; Pasteur Institute; Paris France
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23
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Brugiolo M, Botti V, Liu N, Müller-McNicoll M, Neugebauer KM. Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm. Nucleic Acids Res 2017; 45:10452-10465. [PMID: 28977534 PMCID: PMC5737842 DOI: 10.1093/nar/gkx671] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 07/20/2017] [Indexed: 01/25/2023] Open
Abstract
RNA binding proteins (RBPs) regulate the lives of all RNAs from transcription, processing, and function to decay. How RNA-protein interactions change over time and space to support these roles is poorly understood. Towards this end, we sought to determine how two SR proteins-SRSF3 and SRSF7, regulators of pre-mRNA splicing, nuclear export and translation-interact with RNA in different cellular compartments. To do so, we developed Fractionation iCLIP (Fr-iCLIP), in which chromatin, nucleoplasmic and cytoplasmic fractions are prepared from UV-crosslinked cells and then subjected to iCLIP. As expected, SRSF3 and SRSF7 targets were detected in all fractions, with intron, snoRNA and lncRNA interactions enriched in the nucleus. Cytoplasmically-bound mRNAs reflected distinct functional groupings, suggesting coordinated translation regulation. Surprisingly, hundreds of cytoplasmic intron targets were detected. These cytoplasmic introns were found to be highly conserved and introduced premature termination codons into coding regions. However, many intron-retained mRNAs were not substrates for nonsense-mediated decay (NMD), even though they were detected in polysomes. These findings suggest that intron-retained mRNAs in the cytoplasm have previously uncharacterized functions and/or escape surveillance. Hence, Fr-iCLIP detects the cellular location of RNA-protein interactions and provides insight into co-transcriptional, post-transcriptional and cytoplasmic RBP functions for coding and non-coding RNAs.
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Affiliation(s)
- Mattia Brugiolo
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, CT 06520, USA
| | - Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, CT 06520, USA
| | - Na Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, CT 06520, USA
| | - Michaela Müller-McNicoll
- RNA Regulation Group, Cluster of Excellence 'Macromolecular Complexes', Goethe-University Frankfurt, Institute of Cell Biology and Neuroscience, Max-von-Laue-Str. 13, 60438 Frankfurt/Main, Germany
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, CT 06520, USA
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24
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Henning LM, Santos KF, Sticht J, Jehle S, Lee CT, Wittwer M, Urlaub H, Stelzl U, Wahl MC, Freund C. A new role for FBP21 as regulator of Brr2 helicase activity. Nucleic Acids Res 2017; 45:7922-7937. [PMID: 28838205 PMCID: PMC5570060 DOI: 10.1093/nar/gkx535] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/19/2017] [Indexed: 02/01/2023] Open
Abstract
Splicing of eukaryotic pre-mRNA is carried out by the spliceosome, which assembles stepwise on each splicing substrate. This requires the concerted action of snRNPs and non-snRNP accessory proteins, the functions of which are often not well understood. Of special interest are B complex factors that enter the spliceosome prior to catalytic activation and may alter splicing kinetics and splice site selection. One of these proteins is FBP21, for which we identified several spliceosomal binding partners in a yeast-two-hybrid screen, among them the RNA helicase Brr2. Biochemical and biophysical analyses revealed that an intrinsically disordered region of FBP21 binds to an extended surface of the C-terminal Sec63 unit of Brr2. Additional contacts in the C-terminal helicase cassette are required for allosteric inhibition of Brr2 helicase activity. Furthermore, the direct interaction between FBP21 and the U4/U6 di-snRNA was found to reduce the pool of unwound U4/U6 di-snRNA. Our results suggest FBP21 as a novel key player in the regulation of Brr2.
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Affiliation(s)
- Lisa M Henning
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Karine F Santos
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Jana Sticht
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany.,BioSupraMol Gerätezentrum, Freie Universität Berlin, Takustr. 3, Berlin 14195, Germany
| | - Stefanie Jehle
- Max-Planck-Insitute for Molecular Genetics, Ihnestraße 63-74, Berlin 14195, Germany
| | - Chung-Tien Lee
- Max-Planck-Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, Göttingen 37077, Germany.,University Medical Center Goettingen, Bioanalytics, Department of Clinical Chemistry, Robert Koch Strasse 40, Göttingen 37075, Germany
| | - Malte Wittwer
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Henning Urlaub
- Max-Planck-Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, Göttingen 37077, Germany.,University Medical Center Goettingen, Bioanalytics, Department of Clinical Chemistry, Robert Koch Strasse 40, Göttingen 37075, Germany
| | - Ulrich Stelzl
- Max-Planck-Insitute for Molecular Genetics, Ihnestraße 63-74, Berlin 14195, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert- Einstein-Straße 15, Berlin 12489, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
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25
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Gambin T, Yuan B, Bi W, Liu P, Rosenfeld JA, Coban-Akdemir Z, Pursley AN, Nagamani SCS, Marom R, Golla S, Dengle L, Petrie HG, Matalon R, Emrick L, Proud MB, Treadwell-Deering D, Chao HT, Koillinen H, Brown C, Urraca N, Mostafavi R, Bernes S, Roeder ER, Nugent KM, Bader PI, Bellus G, Cummings M, Northrup H, Ashfaq M, Westman R, Wildin R, Beck AE, Immken L, Elton L, Varghese S, Buchanan E, Faivre L, Lefebvre M, Schaaf CP, Walkiewicz M, Yang Y, Kang SHL, Lalani SR, Bacino CA, Beaudet AL, Breman AM, Smith JL, Cheung SW, Lupski JR, Patel A, Shaw CA, Stankiewicz P. Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med 2017; 9:83. [PMID: 28934986 PMCID: PMC5607840 DOI: 10.1186/s13073-017-0472-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. METHODS We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association. RESULTS In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses. CONCLUSIONS Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Amber N Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sailaja Golla
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lauren Dengle
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Reuben Matalon
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Lisa Emrick
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica B Proud
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diane Treadwell-Deering
- Department of Psychiatry and Behavioral Sciences, Child and Adolescent Psychiatry Division, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Hannele Koillinen
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, 00029, Finland
| | - Chester Brown
- Genetics Division, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, 38105, USA.,Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | - Nora Urraca
- Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | | | | | - Elizabeth R Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Kimberly M Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Patricia I Bader
- Northeast Indiana Genetic Counseling Center, Wayne, IN, 46804, USA
| | - Gary Bellus
- Section of Clinical Genetics & Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael Cummings
- Department of Psychiatry Erie County Medical Center, Buffalo, NY, 14215, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Myla Ashfaq
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | | | - Robert Wildin
- St. Luke's Children's Hospital, Boise, ID, 83702, USA.,The National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Anita E Beck
- Seattle Children's Hospital, Seattle, WA, 98105, USA.,Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | | | - Lindsay Elton
- Child Neurology Consultants of Austin, Austin, TX, 78731, USA
| | - Shaun Varghese
- THINK Neurology for Kids/Children's Memorial Hermann Hospital, The Woodlands, TX, 77380, USA
| | - Edward Buchanan
- Division of Plastic Surgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Mathilde Lefebvre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sung-Hae L Kang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, 77021, USA.
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26
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Han H, Braunschweig U, Gonatopoulos-Pournatzis T, Weatheritt RJ, Hirsch CL, Ha KCH, Radovani E, Nabeel-Shah S, Sterne-Weiler T, Wang J, O'Hanlon D, Pan Q, Ray D, Zheng H, Vizeacoumar F, Datti A, Magomedova L, Cummins CL, Hughes TR, Greenblatt JF, Wrana JL, Moffat J, Blencowe BJ. Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors. Mol Cell 2017; 65:539-553.e7. [PMID: 28157508 DOI: 10.1016/j.molcel.2017.01.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/16/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022]
Abstract
Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulatory events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one-third of the regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large "missing cache" of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms.
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Affiliation(s)
- Hong Han
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | | | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Calley L Hirsch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Kevin C H Ha
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ernest Radovani
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Juli Wang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Dave O'Hanlon
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Qun Pan
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frederick Vizeacoumar
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Alessandro Datti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Lilia Magomedova
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Carolyn L Cummins
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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27
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Pirnie SP, Osman A, Zhu Y, Carmichael GG. An Ultraconserved Element (UCE) controls homeostatic splicing of ARGLU1 mRNA. Nucleic Acids Res 2017; 45:3473-3486. [PMID: 27899669 PMCID: PMC5389617 DOI: 10.1093/nar/gkw1140] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 10/31/2016] [Indexed: 11/13/2022] Open
Abstract
Arginine and Glutamate-Rich protein 1 (ARGLU1) is a protein whose function is poorly understood, but may act in both transcription and pre-mRNA splicing. We demonstrate that the ARGLU1 gene expresses at least three distinct RNA splice isoforms – a fully spliced isoform coding for the protein, an isoform containing a retained intron that is detained in the nucleus, and an isoform containing an alternative exon that targets the transcript for nonsense mediated decay. Furthermore, ARGLU1 contains a long, highly evolutionarily conserved sequence known as an Ultraconserved Element (UCE) that is within the retained intron and overlaps the alternative exon. Manipulation of the UCE, in a reporter minigene or via random mutations in the genomic context using CRISPR/Cas9, changed the splicing pattern. Further, overexpression of the ARGLU1 protein shifted the splicing of endogenous ARGLU1 mRNA, resulting in an increase in the retained intron isoform and nonsense mediated decay susceptible isoform and a decrease in the fully spliced isoform. Taken together with data showing that functional protein knockout shifts splicing toward the fully spliced isoform, our data are consistent with a model in which unproductive splicing complexes assembled at the alternative exon lead to inefficient splicing and intron retention.
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Affiliation(s)
- Stephan P Pirnie
- Department of Genetics and Genome Sciences, UCONN Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA
| | - Ahmad Osman
- Department of Genetics and Genome Sciences, UCONN Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA
| | - Yinzhou Zhu
- Department of Genetics and Genome Sciences, UCONN Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA
| | - Gordon G Carmichael
- Department of Genetics and Genome Sciences, UCONN Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA
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Prasad S, Mandal I, Singh S, Paul A, Mandal B, Venkatramani R, Swaminathan R. Near UV-Visible electronic absorption originating from charged amino acids in a monomeric protein. Chem Sci 2017; 8:5416-5433. [PMID: 28970921 PMCID: PMC5609530 DOI: 10.1039/c7sc00880e] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/18/2017] [Indexed: 11/21/2022] Open
Abstract
Electronic absorption spectra of proteins are primarily characterized over the ultraviolet region (185-320 nm) of the electromagnetic spectrum. While recent studies on peptide aggregates have revealed absorption beyond 350 nm, monomeric proteins lacking aromatic amino acids, disulphide bonds, and active site prosthetic groups are expected to remain optically silent beyond 250 nm. Here, in a joint theoretical and experimental investigation, we report the distinctive UV-Vis absorption spectrum between 250 nm [ε = 7338 M-1 cm-1] and 800 nm [ε = 501 M-1 cm-1] in a synthetic 67 residue protein (α3C), in monomeric form, devoid of aromatic amino acids. Systematic control studies with high concentration non-aromatic amino acid solutions revealed significant absorption beyond 250 nm for charged amino acids which constitute over 50% of the sequence composition in α3C. Classical atomistic molecular dynamics (MD) simulations of α3C reveal dynamic interactions between multiple charged sidechains of Lys and Glu residues present in α3C. Time-dependent density functional theory calculations on charged amino acid residues sampled from the MD trajectories of α3C reveal that the distinctive absorption features of α3C may arise from two different types of charge transfer (CT) transitions involving spatially proximal Lys/Glu amino acids. Specifically, we show that the charged amino (NH3+)/carboxylate (COO-) groups of Lys/Glu sidechains act as electronic charge acceptors/donors for photoinduced electron transfer either from/to the polypeptide backbone or to each other. Further, the sensitivity of the CT spectra to close/far/intermediate range of encounters between sidechains of Lys/Glu owing to the three dimensional protein fold can create the long tail in the α3C absorption profile between 300 and 800 nm. Finally, we experimentally demonstrate the sensitivity of α3C absorption spectrum to temperature and pH-induced changes in protein structure. Taken together, our investigation significantly expands the pool of spectroscopically active biomolecular chromophores and adds an optical 250-800 nm spectral window, which we term ProCharTS (Protein Charge Transfer Spectra), for label free probes of biomolecular structure and dynamics.
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Affiliation(s)
- Saumya Prasad
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India .
| | - Imon Mandal
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba , Mumbai 400005 , India .
| | - Shubham Singh
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India .
| | - Ashim Paul
- Department of Chemistry , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India
| | - Bhubaneswar Mandal
- Department of Chemistry , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India
| | - Ravindra Venkatramani
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba , Mumbai 400005 , India .
| | - Rajaram Swaminathan
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India .
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Chen M, Gao C, Zhao H. Posterior Contraction Rates of the Phylogenetic Indian Buffet Processes. BAYESIAN ANALYSIS 2016; 11:477-497. [PMID: 27087886 PMCID: PMC4830498 DOI: 10.1214/15-ba958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
By expressing prior distributions as general stochastic processes, nonparametric Bayesian methods provide a flexible way to incorporate prior knowledge and constrain the latent structure in statistical inference. The Indian buffet process (IBP) is such an example that can be used to define a prior distribution on infinite binary features, where the exchangeability among subjects is assumed. The phylogenetic Indian buffet process (pIBP), a derivative of IBP, enables the modeling of non-exchangeability among subjects through a stochastic process on a rooted tree, which is similar to that used in phylogenetics, to describe relationships among the subjects. In this paper, we study the theoretical properties of IBP and pIBP under a binary factor model. We establish the posterior contraction rates for both IBP and pIBP and substantiate the theoretical results through simulation studies. This is the first work addressing the frequentist property of the posterior behaviors of IBP and pIBP. We also demonstrated its practical usefulness by applying pIBP prior to a real data example arising in the field of cancer genomics where the exchangeability among subjects is violated.
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Zhang D, Park D, Lu Y, Shen J, Iyer VR, Tang DG. Deep RNA-Seq analysis reveals unexpected features of human prostate basal epithelial cells. GENOMICS DATA 2016. [DOI: 10.1016/j.gdata.2015.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer. Nat Commun 2016; 7:10798. [PMID: 26924072 PMCID: PMC4773505 DOI: 10.1038/ncomms10798] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 01/21/2016] [Indexed: 12/26/2022] Open
Abstract
The prostate gland mainly contains basal and luminal cells constructed as a pseudostratified epithelium. Annotation of prostate epithelial transcriptomes provides a foundation for discoveries that can impact disease understanding and treatment. Here we describe a genome-wide transcriptome analysis of human benign prostatic basal and luminal epithelial populations using deep RNA sequencing. Through molecular and biological characterizations, we show that the differential gene-expression profiles account for their distinct functional properties. Strikingly, basal cells preferentially express gene categories associated with stem cells, neurogenesis and ribosomal RNA (rRNA) biogenesis. Consistent with this profile, basal cells functionally exhibit intrinsic stem-like and neurogenic properties with enhanced rRNA transcription activity. Of clinical relevance, the basal cell gene-expression profile is enriched in advanced, anaplastic, castration-resistant and metastatic prostate cancers. Therefore, we link the cell-type-specific gene signatures to aggressive subtypes of prostate cancer and identify gene signatures associated with adverse clinical features. Gene-expression profiles can be used to predict the prognosis of cancer patients. Here, the authors describe gene expression profiles of human prostate epithelial lineages and show that basal cells have intrinsic stem and neurogenic properties, and molecularly resemble aggressive prostate cancer.
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Luo J, Xu L, Jiang Y, Zhuo D, Zhang S, Wu L, Xu H, Huang Y. Expression profile of long non-coding RNAs in colorectal cancer: A microarray analysis. Oncol Rep 2016; 35:2035-44. [PMID: 26847923 DOI: 10.3892/or.2016.4606] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/16/2015] [Indexed: 01/17/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignant tumors and the second cause of cancer-related mortality worldwide. Due to increased morbidity and mortality rates, there is an urgent need to understand the pathogenesis of CRC, discover strategies that can improve diagnosis, and ultimately identify therapies targeting this disease. Over the past several years, research into tumor progression mechanisms has been devoted to identifying and understanding various coding and non-coding regions of the genome and how these genetic variants may affect tumorigenesis and progression. Recently, long non-coding RNAs (lncRNAs), which are non‑protein coding transcripts longer than 200 nucleotides, have emerged as a key aspect in tumor pathogenesis. In the present study, we examined the lncRNA and mRNA expression profiles in 4 patients with colon adenocarcinoma, with paired adjacent normal tissues as controls. Microarray data showed that a total of 3,523 lncRNAs and 2,515 mRNAs were consistently differentially expressed in the CRC tissues compared to adjacent normal tissues. Upon comparison of the differentially expressed transcripts between the groups, we identified 22 pathways which were related to the upregulated transcripts and 24 pathways that corresponded to the downregulated transcripts. Gene ontology analysis revealed that the upregulated transcripts were predominantly enriched in DNA metabolic processes, and the downregulated transcripts were predominantly enriched in organic hydroxyl compound metabolic processes. Coding-non-coding gene co-expression analysis showed that these differentially expressed lncRNAs were closely correlated with 'Wnt signaling pathway' components, whose aberrant activation plays a central role in CRC, indicating that a functional correlation exists between them. In conclusion, the results of the microarray and informatic analysis strongly suggest that lncRNA dysregulation is involved in the complicated process of CRC development, and may represent a novel class of diagnostic markers or therapeutic targets for CRC.
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Affiliation(s)
- Jia Luo
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Luning Xu
- Department of Pharmacy, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Yigui Jiang
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Dexiang Zhuo
- Department of Clinical Laboratory, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Shengjun Zhang
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Lianhui Wu
- Department of Endoscopy, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Huadong Xu
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Yue Huang
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
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La Ferla M, Mercatanti A, Rocchi G, Lodovichi S, Cervelli T, Pignata L, Caligo MA, Galli A. Expression of human poly (ADP-ribose) polymerase 1 in Saccharomyces cerevisiae: Effect on survival, homologous recombination and identification of genes involved in intracellular localization. Mutat Res 2015; 774:14-24. [PMID: 25779917 DOI: 10.1016/j.mrfmmm.2015.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/03/2015] [Accepted: 02/26/2015] [Indexed: 01/31/2023]
Abstract
The poly (ADP-ribose) polymerase 1 (PARP-1) actively participates in a series of functions within the cell that include: mitosis, intracellular signaling, cell cycle regulation, transcription and DNA damage repair. Therefore, inhibition of PARP1 has a great potential for use in cancer therapy. As resistance to PARP inhibitors is starting to be observed in patients, thus the function of PARP-1 needs to be studied in depth in order to find new therapeutic targets. To gain more information on the PARP-1 activity, we expressed PARP-1 in yeast and investigated its effect on cell growth and UV induced homologous recombination. To identify candidate genes affecting PARP-1 activity and cellular localization, we also developed a yeast genome wide genetic screen. We found that PARP-1 strongly inhibited yeast growth, but when yeast was exposed to the PARP-1 inhibitor 6(5-H) phenantridinone (PHE), it recovered from the growth suppression. Moreover, we showed that PARP-1 produced PAR products in yeast and we demonstrated that PARP-1 reduced UV-induced homologous recombination. By genome wide screening, we identified 99 mutants that suppressed PARP-1 growth inhibition. Orthologues of human genes were found for 41 of these yeast genes. We determined whether the PARP-1 protein level was altered in strains which are deleted for the transcription regulator GAL3, the histone H1 gene HHO1, the HUL4 gene, the deubiquitination enzyme gene OTU1, the nuclear pore protein POM152 and the SNT1 that encodes for the Set3C subunit of the histone deacetylase complex. In these strains the PARP-1 level was roughly the same as in the wild type. PARP-1 localized in the nucleus more in the snt1Δ than in the wild type strain; after UV radiation, PARP-1 localized in the nucleus more in hho1 and pom152 deletion strains than in the wild type indicating that these functions may have a role on regulating PARP-1 level and activity in the nucleus.
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Affiliation(s)
- Marco La Ferla
- Yeast Genetics and Genomics, Institute of Clinical Physiology, National Council of Research (CNR), via Moruzzi 1, 56122 Pisa, Italy
| | - Alberto Mercatanti
- Yeast Genetics and Genomics, Institute of Clinical Physiology, National Council of Research (CNR), via Moruzzi 1, 56122 Pisa, Italy
| | - Giulia Rocchi
- Yeast Genetics and Genomics, Institute of Clinical Physiology, National Council of Research (CNR), via Moruzzi 1, 56122 Pisa, Italy
| | - Samuele Lodovichi
- Yeast Genetics and Genomics, Institute of Clinical Physiology, National Council of Research (CNR), via Moruzzi 1, 56122 Pisa, Italy
| | - Tiziana Cervelli
- Yeast Genetics and Genomics, Institute of Clinical Physiology, National Council of Research (CNR), via Moruzzi 1, 56122 Pisa, Italy
| | - Luca Pignata
- Yeast Genetics and Genomics, Institute of Clinical Physiology, National Council of Research (CNR), via Moruzzi 1, 56122 Pisa, Italy
| | - Maria Adelaide Caligo
- Section of Genetic Oncology, University Hospital and University of Pisa, via Roma 57, 56125 Pisa, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics, Institute of Clinical Physiology, National Council of Research (CNR), via Moruzzi 1, 56122 Pisa, Italy.
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Cui J, Yang Y, Li H, Leng Y, Qian K, Huang Q, Zhang C, Lu Z, Chen J, Sun T, Wu R, Sun Y, Song H, Wei X, Jing P, Yang X, Zhang C. MiR-873 regulates ERα transcriptional activity and tamoxifen resistance via targeting CDK3 in breast cancer cells. Oncogene 2014; 34:3895-907. [PMID: 25531331 DOI: 10.1038/onc.2014.430] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 11/19/2014] [Accepted: 11/21/2014] [Indexed: 12/21/2022]
Abstract
miRNAs (microRNAs) are frequently and aberrantly expressed in many cancers. MiR-873 has been revealed to be downregulated in colorectal cancer and glioblastoma. However, its function remains unclear. Here we report that miR-873 is downregulated in breast tumor compared with normal tissue. Enforced expression of miR-873 decreases the transcriptional activity of ER (estrogen receptor)-α but not ERβ through the modulation of ERα phosphorylation in ER-positive breast cancer cells. We also found that miR-873 inhibits breast cancer cell proliferation and tumor growth in nude mice. Reporter gene assays revealed cyclin-dependent kinase 3 (CDK3) as a direct target of miR-873. CDK3 was shown to be overexpressed in breast cancer and phosphorylate ERα at Ser104/116 and Ser118. Furthermore, we found that Mir-873 inhibits ER activity and cell growth via targeting CDK3. Interestingly, miR-873 was observed to be downregulated in tamoxifen-resistant MCF-7/TamR cells, while CDK3 is overexpressed in these cells. More importantly, re-expression of miR-873 reversed tamoxifen resistance in MCF-7/TamR cells. Our data demonstrate that miR-873 is a novel tumor suppressor in ER-positive breast cancer and a potential therapeutic approach for treatment of tamoxifen-resistant breast cancer.
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Affiliation(s)
- J Cui
- Institute of Disease Control and Prevention, Chinese Academy of Military Medical Sciences, Beijing, China
| | - Y Yang
- Beijing Institute for Neuroscience, Capital Medical University, Beijing, China
| | - H Li
- Department of Molecular & Biomedical Pharmacology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Y Leng
- The Affiliated Hospital of Jiujiang University, Jiujiang, China
| | - K Qian
- The Affiliated Hospital of Jiujiang University, Jiujiang, China
| | - Q Huang
- Department of Animal Sciences and Technology, Jilin Agriculture University, Changchun, China
| | - C Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Z Lu
- Institute of Disease Control and Prevention, Chinese Academy of Military Medical Sciences, Beijing, China
| | - J Chen
- Urology Department, the First Hospital of Nanchang University, Nanchang, China
| | - T Sun
- Urology Department, the First Hospital of Nanchang University, Nanchang, China
| | - R Wu
- Institute of Disease Control and Prevention, Chinese Academy of Military Medical Sciences, Beijing, China
| | - Y Sun
- Institute of Disease Control and Prevention, Chinese Academy of Military Medical Sciences, Beijing, China
| | - H Song
- Institute of Disease Control and Prevention, Chinese Academy of Military Medical Sciences, Beijing, China
| | - X Wei
- Department of Applied Chemistry, College of Chemistry & Molecular Engineering, Peking University, Beijing, China
| | - P Jing
- Department of Chemistry, College of Arts and Sciences, Indiana University-Purdue University Fort Wayne Fort Wayne, IN, USA
| | - X Yang
- Institute of Health Sciences, Anhui University, Hefei, China
| | - C Zhang
- Institute of Disease Control and Prevention, Chinese Academy of Military Medical Sciences, Beijing, China
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Waters KM, Cummings BS, Shankaran H, Scholpa NE, Weber TJ. ERK oscillation-dependent gene expression patterns and deregulation by stress response. Chem Res Toxicol 2014; 27:1496-503. [PMID: 25068892 PMCID: PMC4163986 DOI: 10.1021/tx500085u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
Studies were undertaken to determine
whether extracellular signal
regulated kinase (ERK) oscillations regulate a unique subset of genes
in human keratinocytes and subsequently whether the p38 stress response
inhibits ERK oscillations. A DNA microarray identified many genes
that were unique to ERK oscillations, and network reconstruction predicted
an important role for the mediator complex subunit 1 (MED1) node in
mediating ERK oscillation-dependent gene expression. Increased ERK-dependent
phosphorylation of MED1 was observed in oscillating cells compared
to nonoscillating counterparts as validation. Treatment of keratinocytes
with a p38 inhibitor (SB203580) increased ERK oscillation amplitudes
and MED1 and phospho-MED1 protein levels. Bromate is a probable human
carcinogen that activates p38. Bromate inhibited ERK oscillations
in human keratinocytes and JB6 cells and induced an increase in phospho-p38
and a decrease in phospho-MED1 protein levels. Treatment of normal
rat kidney cells and primary salivary gland epithelial cells with
bromate decreased phospho-MED1 levels in a reversible fashion upon
treatment with p38 inhibitors (SB202190; SB203580). Our results indicate
that oscillatory behavior in the ERK pathway alters homeostatic gene
regulation patterns and that the cellular response to perturbation
may manifest differently in oscillating vs nonoscillating cells.
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Affiliation(s)
- Katrina M Waters
- Computational Biology and Bioinformatics, ‡Systems Toxicology and Exposure Science, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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Par-4/THAP1 complex and Notch3 competitively regulated pre-mRNA splicing of CCAR1 and affected inversely the survival of T-cell acute lymphoblastic leukemia cells. Oncogene 2013; 32:5602-13. [PMID: 23975424 PMCID: PMC3898485 DOI: 10.1038/onc.2013.349] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 06/11/2013] [Accepted: 07/01/2013] [Indexed: 12/15/2022]
Abstract
Although the intensification of therapy for children with T-cell acute lymphoblastic leukemia (T-ALL) has substantially improved clinical outcomes, T-ALL remains an important challenge in pediatric oncology. Here, we report that the cooperative synergy between prostate apoptosis response factor-4 (Par-4) and THAP1 induces cell cycle and apoptosis regulator 1 (CCAR1) gene expression and cellular apoptosis in human T-ALL cell line Jurkat cells, CEM cells and primary cultured neoplastic T lymphocytes from children with T-ALL. Par-4 and THAP1 collaborated to activate the promoter of CCAR1 gene. Mechanistic investigations revealed that Par-4 and THAP1 formed a protein complex by the interaction of their carboxyl termini, and THAP1 bound to CCAR1 promoter though its zinc-dependent DNA-binding domain at amino terminus. Par-4/THAP1 complex and Notch3 competitively bound to CCAR1 promoter and competitively modulated alternative pre-mRNA splicing of CCAR1, which resulted in two different transcripts and played an opposite role in T-ALL cell survival. Despite Notch3 induced a shift splicing from the full-length isoform toward a shorter form of CCAR1 mRNA by splicing factor SRp40 and SRp55, Par-4/THAP1 complex strongly antagonized this inductive effect. Our finding revealed a mechanistic rationale for Par-4/THAP1-induced apoptosis in T-ALL cells that would be of benefit to develop a new therapy strategy for T-ALL.
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Zhang L, Cui J, Leonard M, Nephew K, Li Y, Zhang X. Silencing MED1 sensitizes breast cancer cells to pure anti-estrogen fulvestrant in vitro and in vivo. PLoS One 2013; 8:e70641. [PMID: 23936234 PMCID: PMC3728322 DOI: 10.1371/journal.pone.0070641] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/19/2013] [Indexed: 12/21/2022] Open
Abstract
Pure anti-estrogen fulvestrant has been shown to be a promising ER antagonist for locally advanced and metastatic breast cancer. Unfortunately, a significant proportion of patients developed resistance to this type of endocrine therapy but the molecular mechanisms governing cellular responsiveness to this agent remain poorly understood. Here, we’ve reported that knockdown of estrogen receptor coactivator MED1 sensitized fulvestrant resistance breast cancer cells to fulvestrant treatment. We found that MED1 knockdown further promoted cell cycle arrest induced by fulvestrant. Using an orthotopic xenograft mouse model, we found that knockdown of MED1 significantly reduced tumor growth in mice. Importantly, knockdown of MED1 further potentiated tumor growth inhibition by fulvestrant. Mechanistic studies indicated that combination of fulvestrant treatment and MED1 knockdown is able to cooperatively inhibit the expression of ER target genes. Chromatin immunoprecipitation experiments further supported a role for MED1 in regulating the recruitment of RNA polymerase II and transcriptional corepressor HDAC1 on endogenous ER target gene promoter in the presence of fulvestrant. These results demonstrate a role for MED1 in mediating resistance to the pure anti-estrogen fulvestrant both in vitro and in vivo.
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Affiliation(s)
- Lijiang Zhang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Institute of Biochemistry, College of Life Science, Zhejiang University, Hangzhou City, China
- Center of Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou City, China
| | - Jiajun Cui
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Marissa Leonard
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Kenneth Nephew
- Department of Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Yongquan Li
- Institute of Biochemistry, College of Life Science, Zhejiang University, Hangzhou City, China
- * E-mail: (XZ); (YL)
| | - Xiaoting Zhang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail: (XZ); (YL)
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The HER2 amplicon in breast cancer: Topoisomerase IIA and beyond. Biochim Biophys Acta Rev Cancer 2013; 1836:146-57. [PMID: 23628726 DOI: 10.1016/j.bbcan.2013.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 04/17/2013] [Accepted: 04/19/2013] [Indexed: 12/20/2022]
Abstract
HER2 gene amplification is observed in about 15% of breast cancers. The subgroup of HER2-positive breast cancers appears to be heterogeneous and presents complex patterns of gene amplification at the locus on chromosome 17q12-21. The molecular variations within the chromosome 17q amplicon and their clinical implications remain largely unknown. Besides the well-known TOP2A gene encoding Topoisomerase IIA, other genes might also be amplified and could play functional roles in breast cancer development and progression. This review will focus on the current knowledge concerning the HER2 amplicon heterogeneity, its clinical and biological impact and the pitfalls associated with the evaluation of gene amplifications at this locus, with particular attention to TOP2A and the link between TOP2A and anthracycline benefit. In addition it will discuss the clinical and biological implications of the amplification of ten other genes at this locus (MED1, STARD3, GRB7, THRA, RARA, IGFPB4, CCR7, KRT20, KRT19 and GAST) in breast cancer.
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39
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Uversky VN. The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e24684. [PMID: 28516010 PMCID: PMC5424795 DOI: 10.4161/idp.24684] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 03/27/2013] [Accepted: 04/12/2013] [Indexed: 11/19/2022]
Abstract
The ability of a protein to fold into unique functional state or to stay intrinsically disordered is encoded in its amino acid sequence. Both ordered and intrinsically disordered proteins (IDPs) are natural polypeptides that use the same arsenal of 20 proteinogenic amino acid residues as their major building blocks. The exceptional structural plasticity of IDPs, their capability to exist as heterogeneous structural ensembles and their wide array of important disorder-based biological functions that complements functional repertoire of ordered proteins are all rooted within the peculiar differential usage of these building blocks by ordered proteins and IDPs. In fact, some residues (so-called disorder-promoting residues) are noticeably more common in IDPs than in sequences of ordered proteins, which, in their turn, are enriched in several order-promoting residues. Furthermore, residues can be arranged according to their “disorder promoting potencies,” which are evaluated based on the relative abundances of various amino acids in ordered and disordered proteins. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and concerns glutamic acid, which is the second most disorder-promoting residue.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow, Russia
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40
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Cao W, Ma Z, Rasenick MM, Yeh S, Yu J. N-3 poly-unsaturated fatty acids shift estrogen signaling to inhibit human breast cancer cell growth. PLoS One 2012; 7:e52838. [PMID: 23285198 PMCID: PMC3532062 DOI: 10.1371/journal.pone.0052838] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 11/23/2012] [Indexed: 11/18/2022] Open
Abstract
Although evidence has shown the regulating effect of n-3 poly-unsaturated fatty acid (n-3 PUFA) on cell signaling transduction, it remains unknown whether n-3 PUFA treatment modulates estrogen signaling. The current study showed that docosahexaenoic acid (DHA, C22:6), eicosapentaenoic acid (EPA, C20:5) shifted the pro-survival and proliferative effect of estrogen to a pro-apoptotic effect in human breast cancer (BCa) MCF-7 and T47D cells. 17 β-estradiol (E2) enhanced the inhibitory effect of n-3 PUFAs on BCa cell growth. The IC50 of DHA or EPA in MCF-7 cells decreased when combined with E2 (10 nM) treatment (from 173 µM for DHA only to 113 µM for DHA+E2, and from 187 µm for EPA only to 130 µm for EPA+E2). E2 also augmented apoptosis in n-3 PUFA-treated BCa cells. In contrast, in cells treated with stearic acid (SA, C18:0) as well as cells not treated with fatty acid, E2 promoted breast cancer cell growth. Classical (nuclear) estrogen receptors may not be involved in the pro-apoptotic effects of E2 on the n-3 PUFA-treated BCa cells because ERα agonist failed to elicit, and ERα knockdown failed to block E2 pro-apoptotic effects. Subsequent studies reveal that G protein coupled estrogen receptor 1 (GPER1) may mediate the pro-apoptotic effect of estrogen. N-3 PUFA treatment initiated the pro-apoptotic signaling of estrogen by increasing GPER1-cAMP-PKA signaling response, and blunting EGFR, Erk 1/2, and AKT activity. These findings may not only provide the evidence to link n-3 PUFAs biologic effects and the pro-apoptotic signaling of estrogen in breast cancer cells, but also shed new insight into the potential application of n-3 PUFAs in BCa treatment.
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Affiliation(s)
- WenQing Cao
- Department of Pathology and Laboratory Medicine, George Whipple Laboratory for Cancer Research, University of Rochester Medical Center, Rochester, New York, United States of America
| | - ZhiFan Ma
- Department of Pathology and Laboratory Medicine, George Whipple Laboratory for Cancer Research, University of Rochester Medical Center, Rochester, New York, United States of America
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Mark M. Rasenick
- Departments of Physiology and Biophysics and Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - ShuYan Yeh
- Department of Pathology and Laboratory Medicine, George Whipple Laboratory for Cancer Research, University of Rochester Medical Center, Rochester, New York, United States of America
- Department of Urology, George Whipple Laboratory for Cancer Research, University of Rochester Medical Center, Rochester, New York, United States of America
| | - JiangZhou Yu
- Department of Pathology and Laboratory Medicine, George Whipple Laboratory for Cancer Research, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
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McEwan MV, Eccles MR, Horsfield JA. Cohesin is required for activation of MYC by estradiol. PLoS One 2012; 7:e49160. [PMID: 23145106 PMCID: PMC3493498 DOI: 10.1371/journal.pone.0049160] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 10/09/2012] [Indexed: 12/13/2022] Open
Abstract
Cohesin is best known as a multi-subunit protein complex that holds together replicated sister chromatids from S phase until G2. Cohesin also has an important role in the regulation of gene expression. We previously demonstrated that the cohesin complex positively regulates expression of the oncogene MYC. Cell proliferation driven by MYC contributes to many cancers, including breast cancer. The MYC oncogene is estrogen-responsive and a transcriptional target of estrogen receptor alpha (ERα). Estrogen-induced cohesin binding sites coincide with ERα binding at the MYC locus, raising the possibility that cohesin and ERα combine actions to regulate MYC transcription. The objective of this study was to investigate a putative role for cohesin in estrogen induction of MYC expression. We found that siRNA-targeted depletion of a cohesin subunit, RAD21, decreased MYC expression in ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231) breast cancer cell lines. In addition, RAD21 depletion blocked estradiol-mediated activation of MYC in ER-positive cell lines, and decreased ERα binding to estrogen response elements (EREs) upstream of MYC, without affecting total ERα levels. Treatment of MCF7 cells with estradiol caused enrichment of RAD21 binding at upstream enhancers and at the P2 promoter of MYC. Enriched binding at all sites, except the P2 promoter, was dependent on ERα. Since RAD21 depletion did not affect transcription driven by an exogenous reporter construct containing a naked ERE, chromatin-based mechanisms are likely to be involved in cohesin-dependent MYC transcription. This study demonstrates that ERα activation of MYC can be modulated by cohesin. Together, these results demonstrate a novel role for cohesin in estrogen-mediated regulation of MYC and the first evidence that cohesin plays a role in ERα binding.
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Affiliation(s)
- Miranda V. McEwan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Julia A. Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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Cui J, Germer K, Wu T, Wang J, Luo J, Wang SC, Wang Q, Zhang X. Cross-talk between HER2 and MED1 regulates tamoxifen resistance of human breast cancer cells. Cancer Res 2012; 72:5625-34. [PMID: 22964581 DOI: 10.1158/0008-5472.can-12-1305] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite the fact that most breast cancer patients have estrogen receptor (ER) α-positive tumors, up to 50% of the patients are or soon develop resistance to endocrine therapy. It is recognized that HER2 activation is one of the major mechanisms contributing to endocrine resistance. In this study, we report that the ER coactivator MED1 is a novel cross-talk point for the HER2 and ERα pathways. Tissue microarray analysis of human breast cancers revealed that MED1 expression positively correlates most strongly with HER2 status of the tumors. MED1 was highly phosphorylated, in a HER2-dependent manner, at the site known to be critical for its activation. Importantly, RNAi-mediated attenuation of MED1 sensitized HER2-overexpressing cells to tamoxifen treatment. MED1 and its phosphorylated form, but not the corepressors N-CoR and SMRT, were recruited to the ERα target gene promoter by tamoxifen in HER2-overexpressing cells. Significantly, MED1 attenuation or mutation of MED1 phosphorylation sites was sufficient to restore the promoter recruitment of N-CoR and SMRT. Notably, we found that MED1 is required for the expression of not only traditional E2-ERα target genes but also the newly described EGF-ERα target genes. Our results additionally indicated that MED1 is recruited to the HER2 gene and required for its expression. Taken together, these findings support a key role for MED1 in HER2-mediated tamoxifen resistance and suggest its potential usage as a therapeutic target to simultaneously block both ERα and HER2 pathways for the treatment of this type of endocrine resistant breast cancer.
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Affiliation(s)
- Jiajun Cui
- Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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McGuire TF, Sajithlal GB, Lu J, Nicholls RD, Prochownik EV. In vivo evolution of tumor-derived endothelial cells. PLoS One 2012; 7:e37138. [PMID: 22623986 PMCID: PMC3356387 DOI: 10.1371/journal.pone.0037138] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/16/2012] [Indexed: 12/21/2022] Open
Abstract
The growth of a malignant tumor beyond a certain, limited size requires that it first develop an independent blood supply. In addition to providing metabolic support, this neovasculature also allows tumor cells to access the systemic circulation, thus facilitating metastatic dissemination. The neovasculature may originate either from normal blood vessels in close physical proximity to the tumor and/or from the recruitment of bone marrow-derived endothelial cell (EC) precursors. Recent studies have shown that human tumor vasculature ECs may also arise directly from tumor cells themselves and that the two populations have highly similar or identical karyotypes. We now show that, during the course of serial in vivo passage, these tumor-derived ECs (TDECs) progressively acquire more pronounced EC-like properties. These include higher-level expression of EC-specific genes and proteins, a greater capacity for EC-like behavior in vitro, and a markedly enhanced propensity to incorporate into the tumor vasculature. In addition, both vessel density and size are significantly increased in neoplasms derived from mixtures of tumor cells and serially passaged TDECs. A comparison of early- and late-passage TDECs using whole-genome single nucleotide polymorphism profiling showed the latter cells to have apparently evolved by a process of clonal expansion of a population with a distinct pattern of interstitial chromosomal gains and losses affecting a relatively small number of genes. The majority of these have established roles in vascular development, tumor suppression or epithelial-mesenchymal transition. These studies provide direct evidence that TDECs have a strong evolutionary capacity as a result of their inherent genomic instability. Consequently such cells might be capable of escaping anti-angiogenic cancer therapies by generating resistant populations.
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Affiliation(s)
- Terence F. McGuire
- Division of Hematology/Oncology, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Gangadharan B. Sajithlal
- Division of Hematology/Oncology, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Jie Lu
- Division of Hematology/Oncology, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Robert D. Nicholls
- Birth Defect Laboratories, Division of Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- The University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - Edward V. Prochownik
- Division of Hematology/Oncology, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- The University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Kornegoor R, Moelans CB, Verschuur-Maes AHJ, Hogenes MCH, de Bruin PC, Oudejans JJ, Marchionni L, van Diest PJ. Oncogene amplification in male breast cancer: analysis by multiplex ligation-dependent probe amplification. Breast Cancer Res Treat 2012; 135:49-58. [PMID: 22527098 PMCID: PMC3413821 DOI: 10.1007/s10549-012-2051-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/26/2012] [Indexed: 10/28/2022]
Abstract
Gene amplification is an important mechanism for oncogene activation, a crucial step in carcinogenesis. Compared to female breast cancer, little is known on the genetic makeup of male breast cancer, because large series are lacking. Copy number changes of 21 breast cancer related genes were studied in 110 male breast cancers using multiplex ligation-dependent probe amplification. A ratio of >1.3 was regarded indicative for gene copy number gain and a ratio >2.0 for gene amplification. Data were correlated with clinicopathological features, prognosis and 17 genes were compared with a group of female breast cancers. Gene copy number gain of CCND1, TRAF4, CDC6 and MTDH was seen in >40 % of the male breast cancer cases, with also frequent amplification. The number of genes with copy number gain and several single genes were associated with high grade, but only CCND1 amplification was an independent predictor of adverse survival in Cox regression (p = 0.015; hazard ratio 3.0). In unsupervised hierarchical clustering a distinctive group of male breast cancer with poor prognosis (p = 0.009; hazard ratio 3.4) was identified, characterized by frequent CCND1, MTDH, CDC6, ADAM9, TRAF4 and MYC copy number gain. Compared to female breast cancers, EGFR (p = 0.005) and CCND1 (p = 0.041) copy number gain was more often seen in male breast cancer, while copy number gain of EMSY (p = 0.004) and CPD (p = 0.001) and amplification in general was less frequent. In conclusion, several female breast cancer genes also seem to be important in male breast carcinogenesis. However, there are also clear differences in copy number changes between male and female breast cancers, pointing toward differences in carcinogenesis between male and female breast cancer and emphasizing the importance of identifying biomarkers and therapeutic agents based on research in male breast cancer. In addition CCND1 amplification seems to be an independent prognosticator in male breast cancer.
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Affiliation(s)
- Robert Kornegoor
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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The Mediator complex in thyroid hormone receptor action. Biochim Biophys Acta Gen Subj 2012; 1830:3867-75. [PMID: 22402254 DOI: 10.1016/j.bbagen.2012.02.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/16/2012] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND Mediator is an evolutionarily conserved multisubunit complex that plays an essential regulatory role in eukaryotic transcription of protein-encoding genes. The human complex was first isolated as a transcriptional coactivator bound to the thyroid hormone receptor (TR) and has since been shown to play a key coregulatory role for a broad range of nuclear hormone receptors (NRs) as well as other signal-activated transcription factors. SCOPE OF REVIEW We provide a general overview of Mediator structure and function, summarize the mechanisms by which Mediator is targeted to NRs, and outline recent evidence revealing Mediator as a regulatory axis for other distinct coregulatory factors, chromatin modifying enzymes and cellular signal transduction pathways. MAJOR CONCLUSIONS Besides serving as a functional interface with the RNA polymerase II basal transcription machinery, Mediator plays a more versatile role in regulating transcription including the ability to: a) facilitate gene-specific chromatin looping events; b) coordinate chromatin modification events with preinitiation complex assembly; and c) regulate critical steps that occur during transcriptional elongation. The variably associated MED1 subunit continues to emerge as a pivotal player in Mediator function, not only as the primary interaction site for NRs, but also as a crucial interaction hub for other coregulatory factors, and as an important regulatory target for signal-activated kinases. GENERAL SIGNIFICANCE Mediator plays an integral coregulatory role at NR target genes by functionally interacting with the basal transcription apparatus and by coordinating the action of chromatin modifying enzymes and transcription elongation factors. This article is part of a Special Issue entitled Thyroid hormone signalling.
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Novaes MRCG, Valadares F, Reis MC, Gonçalves DR, Menezes MDC. The effects of dietary supplementation with Agaricales mushrooms and other medicinal fungi on breast cancer: evidence-based medicine. Clinics (Sao Paulo) 2011; 66:2133-9. [PMID: 22189741 PMCID: PMC3226611 DOI: 10.1590/s1807-59322011001200021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 06/26/2011] [Accepted: 07/18/2011] [Indexed: 12/02/2022] Open
Abstract
Breast cancer is the most prevalent cancer in women. The most frequent therapeutic approaches for the treatment of this disease are chemotherapy, radiotherapy, hormone therapy, and surgery. Conventional pharmacological treatments cause many harmful side effects in patients. To improve the quality of life of breast cancer patients, researchers have sought alternative adjuvant treatment strategies. To assess the effects of fungi and other basidiomycetes Agaricales on the co-adjuvant treatment of breast cancer, we conducted a literary review of the available scientific evidence. We selected articles published in refereed journals from 1990 to 2011 in Medline, Lilacs, CAPES, Scielo, and Pubmed. Articles written in English, Spanish, and Portuguese were reviewed. We used the following descriptors: Agaricales, medicinal mushroom/fungus, breast cancer, dietary supplementation, synonyms, and related terms. The pharmacological effects of nutritional and medicinal mushrooms have been reported in several experimental clinical studies and have shown promising results in the adjuvant treatment of breast cancer. Adjuvant treatment with mushrooms is associated with improvements in the immunological and hematologic parameters of breast cancer, as well as in the quality of life of these patients. Randomized clinical studies are needed to elucidate the possible mechanisms of action and clinical benefits of these fungi with respect to survival time, disease progression, and metastasis in breast cancer.
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