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Ruengsrichaiya B, Nukoolkit C, Kalapanulak S, Saithong T. Plant-DTI: Extending the landscape of TF protein and DNA interaction in plants by a machine learning-based approach. FRONTIERS IN PLANT SCIENCE 2022; 13:970018. [PMID: 36082286 PMCID: PMC9445498 DOI: 10.3389/fpls.2022.970018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
As a sessile organism, plants hold elaborate transcriptional regulatory systems that allow them to adapt to variable surrounding environments. Current understanding of plant regulatory mechanisms is greatly constrained by limited knowledge of transcription factor (TF)-DNA interactions. To mitigate this problem, a Plant-DTI predictor (Plant DBD-TFBS Interaction) was developed here as the first machine-learning model that covered the largest experimental datasets of 30 plant TF families, including 7 plant-specific DNA binding domain (DBD) types, and their transcription factor binding sites (TFBSs). Plant-DTI introduced a novel TFBS feature construction, called TFBS base-preference, which enhanced the specificity of TFBS to DBD types. The proposed model showed better predictive performance with the TFBS base-preference than the simple binary representation. Plant-DTI was validated with 22 independent ChIP-seq datasets. It accurately predicted the measured DBD-TFBS pairs along with their TFBS motifs, and effectively predicted interactions of other TFs containing similar DBD types. Comparing to the existing state-of-art methods, Plant-DTI prediction showed a figure of merit in sensitivity and specificity with respect to the position weight matrix (PWM) and TSPTFBS methods. Finally, the proposed Plant-DTI model helped to fill the knowledge gap in the regulatory mechanisms of the cassava sucrose synthase 1 gene (MeSUS1). Plant-DTI predicted MeERF72 as a regulator of MeSUS1 in consistence with the yeast one-hybrid (Y1H) experiment. Taken together, Plant-DTI would help facilitate the prediction of TF-TFBS and TF-target gene (TG) interactions, thereby accelerating the study of transcriptional regulatory systems in plant species.
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Affiliation(s)
- Bhukrit Ruengsrichaiya
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
| | - Chakarida Nukoolkit
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
- School of Information Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
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Pasqui A, Boddi A, Campanacci DA, Scoccianti G, Bernini A, Grasso D, Gambale E, Scolari F, Palchetti I, Palomba A, Fancelli S, Caliman E, Antonuzzo L, Pillozzi S. Alteration of the Nucleotide Excision Repair (NER) Pathway in Soft Tissue Sarcoma. Int J Mol Sci 2022; 23:ijms23158360. [PMID: 35955506 PMCID: PMC9369086 DOI: 10.3390/ijms23158360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 02/02/2023] Open
Abstract
Clinical responses to anticancer therapies in advanced soft tissue sarcoma (STS) are unluckily restricted to a small subgroup of patients. Much of the inter-individual variability in treatment efficacy is as result of polymorphisms in genes encoding proteins involved in drug pharmacokinetics and pharmacodynamics. The nucleotide excision repair (NER) system is the main defense mechanism for repairing DNA damage caused by carcinogens and chemotherapy drugs. Single nucleotide polymorphisms (SNPs) of NER pathway key genes, altering mRNA expression or protein activity, can be significantly associated with response to chemotherapy, toxicities, tumor relapse or risk of developing cancer. In the present study, in a cohort of STS patients, we performed DNA extraction and genotyping by SNP assay, RNA extraction and quantitative real-time reverse transcription PCR (qPCR), a molecular dynamics simulation in order to characterize the NER pathway in STS. We observed a severe deregulation of the NER pathway and we describe for the first time the effect of SNP rs1047768 in the ERCC5 structure, suggesting a role in modulating single-stranded DNA (ssDNA) binding. Our results evidenced, for the first time, the correlation between a specific genotype profile of ERCC genes and proficiency of the NER pathway in STS.
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Affiliation(s)
- Adriano Pasqui
- Medical Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.P.); (L.A.); (S.P.)
| | - Anna Boddi
- Orthopaedic Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.B.); (D.A.C.); (G.S.); (F.S.)
| | - Domenico Andrea Campanacci
- Orthopaedic Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.B.); (D.A.C.); (G.S.); (F.S.)
- Orthopaedic Oncology Unit, Careggi University Hospital, Department of Health Sciences, University of Florence, 50134 Florence, Italy
| | - Guido Scoccianti
- Orthopaedic Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.B.); (D.A.C.); (G.S.); (F.S.)
| | - Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy;
- Correspondence:
| | - Daniela Grasso
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy;
| | - Elisabetta Gambale
- Clinical Oncology Unit, Careggi University Hospital, 50134 Florence, Italy;
| | - Federico Scolari
- Orthopaedic Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.B.); (D.A.C.); (G.S.); (F.S.)
| | - Ilaria Palchetti
- Department of Chemistry Ugo Schiff, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Annarita Palomba
- Histopathology and Molecular Diagnostic Unit, Careggi University Hospital, 50134 Florence, Italy;
| | - Sara Fancelli
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (S.F.); (E.C.)
| | - Enrico Caliman
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (S.F.); (E.C.)
| | - Lorenzo Antonuzzo
- Medical Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.P.); (L.A.); (S.P.)
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy;
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (S.F.); (E.C.)
| | - Serena Pillozzi
- Medical Oncology Unit, Careggi University Hospital, 50134 Florence, Italy; (A.P.); (L.A.); (S.P.)
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (S.F.); (E.C.)
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Wang Z, Wang Q, Gong L, Liu T, Wang P, Yuan Z, Wang W. The NF-κB-regulated miR-221/222/syndecan-1 axis restores intestinal mucosal barrier function in radiation enteritis. Int J Radiat Oncol Biol Phys 2022; 113:166-176. [PMID: 35033585 DOI: 10.1016/j.ijrobp.2022.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE Radiation enteritis (RE) is the most common complication of pelvic radiotherapy, but proven therapies are lacking. Barrier function defects are closely associated with numerous inflammatory disorders. In this study, we investigated whether barrier dysfunction contributes to RE and whether syndecan-1 (Sdc1) protects intestinal barrier function in RE. The mechanism was also elucidated. MATERIALS AND METHODS Blood, urine, and tissue samples were collected from 21 patients with cervical cancer who experienced RE during radiotherapy and used to detect inflammatory responses and barrier function. The role of Sdc1 in barrier function was examined in cultured fetal human colon (FHC) cells exposed to radiation and an induced mouse RE model. Barrier function was determined by zonula occludens (ZO)-1 and occludin expression, transepithelial electrical resistance (TEER), and FITC-dextran (FD4) flux. The role of the nuclear factor (NF)-κB-P65 pathway was detected by Western blotting and chromatin immunoprecipitation. The role of miR-221/222 was assessed by real-time PCR and luciferase reporter assays. RESULTS Patients with RE exhibited obvious pathological and ultra-microstructural inflammatory injury and barrier disruption in the intestinal mucosa, as well as higher serum lipopolysaccharide (LPS), LPS-binding protein, and cytokine levels and a higher urine lactulose/mannitol ratio. Sdc1 overexpression in irradiated FHC cells reversed TEER suppression, repressed FD4 flux, and upregulated ZO-1 and occludin expression. Exogenous low-molecular-weight heparin supplementation in RE mice ameliorated the activity of enteritis and barrier defects. Mechanistically, irradiation-activated P65 increased the transcription of miR-221/222 via direct binding to their promoter regions, and miR-221/222 then post-transcriptionally suppressed the Sdc1 gene by binding to its 3'-untranslated region. CONCLUSIONS Sdc1 protects barrier function and controls inflammation during RE under transcriptional regulation by the NF-κB pathway and miR-221/222. The network including NF-κB, miR-221/222, and Sdc1 is important in the pathogenesis of RE. Sdc1 might represent a therapeutic target for novel anti-RE strategies.
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Affiliation(s)
- Zhongqiu Wang
- Department of Radiation Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, West Huanhu Road, West River District, Tianjin 300060, China.
| | - Qingxin Wang
- Department of Radiation Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, West Huanhu Road, West River District, Tianjin 300060, China; School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Nankai District, Tianjin, 300073, China
| | - Linlin Gong
- Department of Radiation Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, West Huanhu Road, West River District, Tianjin 300060, China
| | - Tao Liu
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
| | - Peiguo Wang
- Department of Radiation Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, West Huanhu Road, West River District, Tianjin 300060, China
| | - Zhiyong Yuan
- Department of Radiation Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, West Huanhu Road, West River District, Tianjin 300060, China
| | - Wei Wang
- Department of Radiation Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, West Huanhu Road, West River District, Tianjin 300060, China.
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Han YH, Kim HJ, Lee MO. RORα regulates hepatic lipolysis by inducing transcriptional expression of PNPLA3 in mice. Mol Cell Endocrinol 2021; 522:111122. [PMID: 33347955 DOI: 10.1016/j.mce.2020.111122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/16/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022]
Abstract
Nonalcoholic fatty liver diseases (NAFLDs) are characterized by excessive triacylglycerol (TAG) accumulation in the liver which contributes to hepatocyte dysfunction, inflammation, and fibrosis. Patatin-like phospholipase domain-containing 3 (PNPLA3; also known as adiponutrin) has emerged as an important enzyme leading to hepatic TAG hydrolysis. Because the I148M substitution in the PNPLA3 gene markedly reduces hepatic TAG hydrolase activity, this genetic variation is strongly associated with increased hepatic TAG in the full spectrum of NAFLDs. The Retinoic acid-related orphan receptor α (RORα) regulates various target genes related to lipid metabolism. Here, we investigated the role of RORα on PNPLA3-mediated hepatic lipid hydrolysis. With blockade of lipid esterification and β-oxidation, RORα enhanced TAG hydrolysis, resulting in increased free glycerol levels. We found a putative RORα response element on the upstream of PNPLA3 gene that was activated by RORα. Furthermore, the inhibitory action of cJUN on the RORα/PNPLA3 axis was enhanced under lipid stress and contributed to hepatic lipid accumulation. In summary, we showed for the first time that RORα activates the transcription of PNPLA3, which suggests that RORα and its ligands represent potential precision therapeutic approaches for NAFLDs.
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Affiliation(s)
- Yong-Hyun Han
- College of Pharmacy, Seoul National University, Seoul, South Korea; Laboratory of Pathology and Physiology, College of Pharmacy, Kangwon National University, Chuncheon, South Korea
| | - Hyeon-Ji Kim
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Mi-Ock Lee
- College of Pharmacy, Seoul National University, Seoul, South Korea; Bio-MAX Institute, Seoul National University, Seoul, South Korea; Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea.
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Pellegrino R, Thavamani A, Calvisi DF, Budczies J, Neumann A, Geffers R, Kroemer J, Greule D, Schirmacher P, Nordheim A, Longerich T. Serum Response Factor (SRF) Drives the Transcriptional Upregulation of the MDM4 Oncogene in HCC. Cancers (Basel) 2021; 13:E199. [PMID: 33429878 PMCID: PMC7829828 DOI: 10.3390/cancers13020199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 01/10/2023] Open
Abstract
Different molecular mechanisms support the overexpression of the mouse double minute homolog 4 (MDM4), a functional p53 inhibitor, in human hepatocellular carcinoma (HCC). However, the transcription factors (TFs) leading to its transcriptional upregulation remain unknown. Following promoter and gene expression analyses, putative TFs were investigated using gene-specific siRNAs, cDNAs, luciferase reporter assays, chromatin immunoprecipitation, and XI-011 drug treatment in vitro. Additionally, MDM4 expression was investigated in SRF-VP16iHep transgenic mice. We observed a copy-number-independent upregulation of MDM4 in human HCCs. Serum response factor (SRF), ELK1 and ELK4 were identified as TFs activating MDM4 transcription. While SRF was constitutively detected in TF complexes at the MDM4 promoter, presence of ELK1 and ELK4 was cell-type dependent. Furthermore, MDM4 was upregulated in SRF-VP16-driven murine liver tumors. The pharmacological inhibitor XI-011 exhibited anti-MDM4 activity by downregulating the TFs driving MDM4 transcription, which decreased HCC cell viability and increased apoptosis. In conclusion, SRF drives transcriptional MDM4 upregulation in HCC, acting in concert with either ELK1 or ELK4. The transcriptional regulation of MDM4 may be a promising target for precision oncology of human HCC, as XI-011 treatment exerts anti-MDM4 activity independent from the MDM4 copy number and the p53 status.
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Affiliation(s)
- Rossella Pellegrino
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (J.B.); (A.N.); (J.K.); (D.G.); (P.S.); (T.L.)
| | - Abhishek Thavamani
- Department for Molecular Biology, Interfaculty Institute of Cell Biology, University of Tuebingen, 72074 Tuebingen, Germany; (A.T.); (A.N.)
| | - Diego F. Calvisi
- Institute of Pathology, University Hospital Regensburg, 93053 Regensburg, Germany;
| | - Jan Budczies
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (J.B.); (A.N.); (J.K.); (D.G.); (P.S.); (T.L.)
| | - Ariane Neumann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (J.B.); (A.N.); (J.K.); (D.G.); (P.S.); (T.L.)
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Jasmin Kroemer
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (J.B.); (A.N.); (J.K.); (D.G.); (P.S.); (T.L.)
| | - Damaris Greule
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (J.B.); (A.N.); (J.K.); (D.G.); (P.S.); (T.L.)
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (J.B.); (A.N.); (J.K.); (D.G.); (P.S.); (T.L.)
| | - Alfred Nordheim
- Department for Molecular Biology, Interfaculty Institute of Cell Biology, University of Tuebingen, 72074 Tuebingen, Germany; (A.T.); (A.N.)
| | - Thomas Longerich
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany; (J.B.); (A.N.); (J.K.); (D.G.); (P.S.); (T.L.)
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Zhang L, Yang J, Luo Y, Liu F, Yuan Y, Zhuang S. A p53/lnc-Ip53 Negative Feedback Loop Regulates Tumor Growth and Chemoresistance. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001364. [PMID: 33173727 PMCID: PMC7610266 DOI: 10.1002/advs.202001364] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/08/2020] [Indexed: 06/03/2023]
Abstract
Acetylation is a critical mechanism to modulate tumor-suppressive activity of p53, but the causative roles of long non-coding RNAs (lncRNAs) in p53 acetylation and their biological significance remain unexplored. Here, lncRNA LOC100294145 is discovered to be transactivated by p53 and is thus designated as lnc-Ip53 for lncRNA induced by p53. Furthermore, lnc-Ip53 impedes p53 acetylation by interacting with histone deacetylase 1 (HDAC1) and E1A binding protein p300 (p300) to prevent HDAC1 degradation and attenuate p300 activity, resulting in abrogation of p53 activity and subsequent cell proliferation and apoptosis resistance. Mouse xenograft models reveal that lnc-Ip53 promotes tumor growth and chemoresistance in vivo, which is attenuated by an HDAC inhibitor. Silencing lnc-Ip53 inhibits the growth of xenografts with wild-type p53, but not those expressing acetylation-resistant p53. Consistently, lnc-Ip53 is upregulated in multiple cancer types, including hepatocellular carcinoma (HCC). High levels of lnc-Ip53 is associated with low levels of acetylated p53 in human HCC and mouse xenografts, and is also correlated with poor survival of HCC patients. These findings identify a novel p53/lnc-Ip53 negative feedback loop in cells and indicate that abnormal upregulation of lnc-Ip53 represents an important mechanism to inhibit p53 acetylation/activity and thereby promote tumor growth and chemoresistance, which may be exploited for anticancer therapy.
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Affiliation(s)
- Li‐Zhen Zhang
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
| | - Jin‐E Yang
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
| | - Yu‐Wei Luo
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
| | - Feng‐Ting Liu
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
| | - Yun‐Fei Yuan
- Department of Hepatobilliary OncologyCancer CenterSun Yat‐sen UniversityGuangzhou510060China
| | - Shi‐Mei Zhuang
- MOE Key Laboratory of Gene Function and RegulationSchool of Life SciencesCollaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhou510275China
- Key Laboratory of Liver Disease of Guangdong ProvinceThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630China
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Zhou J, Lu Q, Gui L, Xu R, Long Y, Wang H. MTTFsite: cross-cell type TF binding site prediction by using multi-task learning. Bioinformatics 2020; 35:5067-5077. [PMID: 31161194 PMCID: PMC6954652 DOI: 10.1093/bioinformatics/btz451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/19/2019] [Accepted: 05/30/2019] [Indexed: 12/30/2022] Open
Abstract
Motivation The prediction of transcription factor binding sites (TFBSs) is crucial for gene expression analysis. Supervised learning approaches for TFBS predictions require large amounts of labeled data. However, many TFs of certain cell types either do not have sufficient labeled data or do not have any labeled data. Results In this paper, a multi-task learning framework (called MTTFsite) is proposed to address the lack of labeled data problem by leveraging on labeled data available in cross-cell types. The proposed MTTFsite contains a shared CNN to learn common features for all cell types and a private CNN for each cell type to learn private features. The common features are aimed to help predicting TFBSs for all cell types especially those cell types that lack labeled data. MTTFsite is evaluated on 241 cell type TF pairs and compared with a baseline method without using any multi-task learning model and a fully shared multi-task model that uses only a shared CNN and do not use private CNNs. For cell types with insufficient labeled data, results show that MTTFsite performs better than the baseline method and the fully shared model on more than 89% pairs. For cell types without any labeled data, MTTFsite outperforms the baseline method and the fully shared model by more than 80 and 93% pairs, respectively. A novel gene expression prediction method (called TFChrome) using both MTTFsite and histone modification features is also presented. Results show that TFBSs predicted by MTTFsite alone can achieve good performance. When MTTFsite is combined with histone modification features, a significant 5.7% performance improvement is obtained. Availability and implementation The resource and executable code are freely available at http://hlt.hitsz.edu.cn/MTTFsite/ and http://www.hitsz-hlt.com:8080/MTTFsite/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiyun Zhou
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, China.,Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Qin Lu
- Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Lin Gui
- Department of Computer Science, University of Warwick, Coventry CV4 4AL, UK
| | - Ruifeng Xu
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, China
| | - Yunfei Long
- Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Hongpeng Wang
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, China
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Arai Y, Cwetsch AW, Coppola E, Cipriani S, Nishihara H, Kanki H, Saillour Y, Freret-Hodara B, Dutriaux A, Okada N, Okano H, Dehay C, Nardelli J, Gressens P, Shimogori T, D’Onofrio G, Pierani A. Evolutionary Gain of Dbx1 Expression Drives Subplate Identity in the Cerebral Cortex. Cell Rep 2019; 29:645-658.e5. [DOI: 10.1016/j.celrep.2019.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/12/2019] [Accepted: 09/04/2019] [Indexed: 10/25/2022] Open
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9
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Has2 natural antisense RNA and Hmga2 promote Has2 expression during TGFβ-induced EMT in breast cancer. Matrix Biol 2019; 80:29-45. [DOI: 10.1016/j.matbio.2018.09.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022]
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10
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Mitani T, Takaya T, Harada N, Katayama S, Yamaji R, Nakamura S, Ashida H. Theophylline suppresses interleukin-6 expression by inhibiting glucocorticoid receptor signaling in pre-adipocytes. Arch Biochem Biophys 2018; 646:98-106. [PMID: 29625124 DOI: 10.1016/j.abb.2018.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 12/19/2022]
Abstract
Adipose tissues in obese individuals are characterized by a state of chronic low-grade inflammation. Pre-adipocytes and adipocytes in this state secrete pro-inflammatory adipokines, such as interleukin 6 (IL-6), which induce insulin resistance and hyperglycemia. Theophylline (1,3-dimethylxanthine) exerts anti-inflammatory effects, but its effects on pro-inflammatory adipokine secretion by pre-adipocytes and adipocytes have not been examined. In this study, we found that theophylline decreased IL-6 secretion by 3T3-L1 pre-adipocytes and mouse-derived primary pre-adipocytes. The synthetic glucocorticoid dexamethasone (DEX) induced IL-6 expression in 3T3-L1 pre-adipocytes, and this effect was suppressed by theophylline at the mRNA level. Knockdown of CCAAT/enhancer binding protein (C/EBP) δ inhibited DEX-induced IL-6 expression, and theophylline suppressed C/EBPδ expression. Furthermore, theophylline suppressed transcriptional activity of the glucocorticoid receptor (GR) through suppression of nuclear localization of GR. In vivo, glucocorticoid corticosterone treatment (100 μg/mL) increased fasting blood glucose and plasma IL-6 levels in C57BL/6 N mice. Theophylline administration (0.1% diet) reduced corticosterone-increased fasting blood glucose, plasma IL-6 levels, and Il6 gene expression in adipose tissues. These results show that theophylline administration attenuated glucocorticoid-induced hyperglycemia and IL-6 production by inhibiting GR activity. The present findings indicate the potential of theophylline as a candidate therapeutic agent to treat insulin resistance and hyperglycemia.
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Affiliation(s)
- Takakazu Mitani
- Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, 8304 Minami-minowa Mura, Kamiina Gun, Nagano 3994598, Japan
| | - Tomohide Takaya
- Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, 8304 Minami-minowa Mura, Kamiina Gun, Nagano 3994598, Japan
| | - Naoki Harada
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 5998531, Japan
| | - Shigeru Katayama
- Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, 8304 Minami-minowa Mura, Kamiina Gun, Nagano 3994598, Japan; Division of Food Science and Technology, Graduate School of Sciences and Technology, Shinshu University, 8304 Minami-minowa Mura, Kamiina Gun, Nagano 399-4598, Japan.
| | - Ryoichi Yamaji
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 5998531, Japan
| | - Soichiro Nakamura
- Division of Food Science and Technology, Graduate School of Sciences and Technology, Shinshu University, 8304 Minami-minowa Mura, Kamiina Gun, Nagano 399-4598, Japan
| | - Hitoshi Ashida
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 6578501, Japan
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11
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Huang L, Tepaamorndech S, Kirschke CP, Newman JW, Keyes WR, Pedersen TL, Dumnil J. Aberrant fatty acid metabolism in skeletal muscle contributes to insulin resistance in zinc transporter 7 ( znt7)-knockout mice. J Biol Chem 2018; 293:7549-7563. [PMID: 29555680 DOI: 10.1074/jbc.m117.817692] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 03/12/2018] [Indexed: 12/22/2022] Open
Abstract
ZnT7 (Slc30a7) is a widely expressed zinc transporter involved in sequestration of zinc into the Golgi apparatus and vesicular compartments. znt7-knockout (KO) mice are mildly zinc-deficient and lean. Despite their lean phenotype, adult male znt7-KO mice are prone to insulin resistance. We hypothesized that fat partitioning from adipose to nonadipose tissues causes insulin resistance in znt7-KO mice. Here, we used biological and biochemical methods, including fatty acid and oxylipin profiling, EM, immunohistochemistry, quantitative RT-PCR, and Western blot analysis, to identify the underlying mechanism of insulin resistance in znt7-KO mice. We found that insulin resistance in this model was primarily associated with increased intracellular fatty acid levels in the skeletal muscle, which promoted intracellular lipid accumulation and production of bioactive lipid mediators, such as 12,13-dihydroxyoctadecanoic acid (12,13-DiHOME) and 12-hydroxyeicosatetraenoic acid (12-HETE). The expression of fatty acid-binding protein 3 (Fabp3) was dramatically up-regulated in the znt7-KO muscle cells accompanied by increased expression of Cd36, Slc27a1, and Slc27a4, the three major fatty acid transporters in the skeletal muscle. We also demonstrated that znt7-KO muscle cells had increased fatty acid oxidative capacity, indicated by enlarged mitochondria and increased mRNA or protein expression of key enzymes involved in the fatty acid mitochondrial shuttle and β-oxidation. We conclude that increased fatty acid uptake in the znt7-KO skeletal muscle is a key factor that contributes to the excessive intracellular lipid deposit and elevated production of bioactive lipid mediators. These mediators may play pivotal roles in oxidative stress and inflammation, leading to insulin resistance.
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Affiliation(s)
- Liping Huang
- From the Obesity and Metabolism Research Unit, United States Department of Agriculture/Agricultural Research Service/Western Human Nutrition Research Center, Davis, California 95616, .,Department of Nutrition and.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California 95616, and
| | - Surapun Tepaamorndech
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, California 95616, and.,Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Pathum Thani 12120, Thailand
| | - Catherine P Kirschke
- From the Obesity and Metabolism Research Unit, United States Department of Agriculture/Agricultural Research Service/Western Human Nutrition Research Center, Davis, California 95616
| | - John W Newman
- From the Obesity and Metabolism Research Unit, United States Department of Agriculture/Agricultural Research Service/Western Human Nutrition Research Center, Davis, California 95616.,Department of Nutrition and
| | - William R Keyes
- From the Obesity and Metabolism Research Unit, United States Department of Agriculture/Agricultural Research Service/Western Human Nutrition Research Center, Davis, California 95616
| | - Theresa L Pedersen
- From the Obesity and Metabolism Research Unit, United States Department of Agriculture/Agricultural Research Service/Western Human Nutrition Research Center, Davis, California 95616
| | - Jureeporn Dumnil
- Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Pathum Thani 12120, Thailand
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12
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Kfir-Elirachman K, Ortenberg R, Vizel B, Besser MJ, Barshack I, Schachter J, Nemlich Y, Markel G. Regulation of CEACAM1 Protein Expression by the Transcription Factor ETS-1 in BRAF-Mutant Human Metastatic Melanoma Cells. Neoplasia 2018; 20:401-409. [PMID: 29558679 PMCID: PMC5909674 DOI: 10.1016/j.neo.2018.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/21/2022] Open
Abstract
BRAF becomes constitutively activated in 50% to 70% of melanoma cases. CEACAM1 has a dual role in melanoma, including facilitation of cell proliferation and suppression of infiltrating lymphocytes, which are consistent with its value as a marker for poor prognosis in melanoma patients. Here we show that BRAFV600E melanoma cells treated with BRAF and MEK inhibitors (MAPKi) downregulate CEACAM1 mRNA and protein expression in a dose- and exposure time–dependent manners. Indeed, there is a significant correlation between the presence of BRAFV600E and CEACAM1 expression in melanoma specimens obtained from 45 patients. Vemurafenib-resistant cell systems reactivate the MAPK pathway and restore basal CEACAM1 mRNA and protein levels. These combined results suggest transcriptional regulation. Indeed, luciferase reporting assays show that CEACAM1 promoter (CEACAM1p) activity is significantly reduced by MAPKi. Importantly, we show that the MAPK-driven CEACAM1p activity is mediated by ETS1, a major transcription factor and downstream effector of the MAPK pathway. Phosphorylation mutant ETS1T38A shows a dominant negative effect over CEACAM1 expression. The data are consistent with independent RNAseq data from serial biopsies of melanoma patients treated with BRAF inhibitors, which demonstrate similar CEACAM1 downregulation. Finally, we show that CEACAM1 downregulation by MAPKi renders the cells more sensitive to T-cell activation. These results provide a new view on a potential immunological mechanism of action of MAPKi in melanoma, as well as on the aggressive phenotype observed in drug-resistant cells.
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Affiliation(s)
- Karin Kfir-Elirachman
- Ella Lemelbaum Institute of Immuno-Oncology, Sheba Medical Center, Ramat-Gan, 5262620, Israel; Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rona Ortenberg
- Ella Lemelbaum Institute of Immuno-Oncology, Sheba Medical Center, Ramat-Gan, 5262620, Israel
| | - Bella Vizel
- Ella Lemelbaum Institute of Immuno-Oncology, Sheba Medical Center, Ramat-Gan, 5262620, Israel; Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal J Besser
- Ella Lemelbaum Institute of Immuno-Oncology, Sheba Medical Center, Ramat-Gan, 5262620, Israel; Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Iris Barshack
- Institute of Pathology, Sheba Medical Center, Ramat-Gan, 5262620, Israel; Talpiot Medical Leadership Program, Sheba Medical Center, Ramat-Gan, 5262620, Israel
| | - Jacob Schachter
- Ella Lemelbaum Institute of Immuno-Oncology, Sheba Medical Center, Ramat-Gan, 5262620, Israel; Talpiot Medical Leadership Program, Sheba Medical Center, Ramat-Gan, 5262620, Israel
| | - Yael Nemlich
- Ella Lemelbaum Institute of Immuno-Oncology, Sheba Medical Center, Ramat-Gan, 5262620, Israel
| | - Gal Markel
- Ella Lemelbaum Institute of Immuno-Oncology, Sheba Medical Center, Ramat-Gan, 5262620, Israel; Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; School of Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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13
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Caja L, Tzavlaki K, Dadras MS, Tan EJ, Hatem G, Maturi NP, Morén A, Wik L, Watanabe Y, Savary K, Kamali-Moghaddan M, Uhrbom L, Heldin CH, Moustakas A. Snail regulates BMP and TGFβ pathways to control the differentiation status of glioma-initiating cells. Oncogene 2018; 37:2515-2531. [PMID: 29449696 PMCID: PMC5945579 DOI: 10.1038/s41388-018-0136-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 12/12/2017] [Accepted: 12/28/2017] [Indexed: 12/31/2022]
Abstract
Glioblastoma multiforme is a brain malignancy characterized by high heterogeneity, invasiveness, and resistance to current therapies, attributes related to the occurrence of glioma stem cells (GSCs). Transforming growth factor β (TGFβ) promotes self-renewal and bone morphogenetic protein (BMP) induces differentiation of GSCs. BMP7 induces the transcription factor Snail to promote astrocytic differentiation in GSCs and suppress tumor growth in vivo. We demonstrate that Snail represses stemness in GSCs. Snail interacts with SMAD signaling mediators, generates a positive feedback loop of BMP signaling and transcriptionally represses the TGFB1 gene, decreasing TGFβ1 signaling activity. Exogenous TGFβ1 counteracts Snail function in vitro, and in vivo promotes proliferation and re-expression of Nestin, confirming the importance of TGFB1 gene repression by Snail. In conclusion, novel insight highlights mechanisms whereby Snail differentially regulates the activity of the opposing BMP and TGFβ pathways, thus promoting an astrocytic fate switch and repressing stemness in GSCs.
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Affiliation(s)
- Laia Caja
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Box 582, Biomedical Center, Uppsala University, SE-75123, Uppsala, Sweden. .,Ludwig Cancer Research, Science for Life Laboratory, Box 595, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden.
| | - Kalliopi Tzavlaki
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Box 582, Biomedical Center, Uppsala University, SE-75123, Uppsala, Sweden.,Ludwig Cancer Research, Science for Life Laboratory, Box 595, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Mahsa S Dadras
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Box 582, Biomedical Center, Uppsala University, SE-75123, Uppsala, Sweden.,Ludwig Cancer Research, Science for Life Laboratory, Box 595, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - E-Jean Tan
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-75185, Uppsala, Sweden
| | - Gad Hatem
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Box 582, Biomedical Center, Uppsala University, SE-75123, Uppsala, Sweden.,Ludwig Cancer Research, Science for Life Laboratory, Box 595, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Naga P Maturi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Box 582, Biomedical Center, Uppsala University, SE-75123, Uppsala, Sweden.,Ludwig Cancer Research, Science for Life Laboratory, Box 595, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-75185, Uppsala, Sweden
| | - Anita Morén
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Box 582, Biomedical Center, Uppsala University, SE-75123, Uppsala, Sweden.,Ludwig Cancer Research, Science for Life Laboratory, Box 595, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Lotta Wik
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Box 815, Biomedical Center, Uppsala University, SE-75108, Uppsala, Sweden
| | - Yukihide Watanabe
- Ludwig Cancer Research, Science for Life Laboratory, Box 595, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden.,Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Katia Savary
- Ludwig Cancer Research, Science for Life Laboratory, Box 595, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden.,UMR CNRS 7369 MEDyC, Université de Reims Champagne Ardenne, Reims, France
| | - Masood Kamali-Moghaddan
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Box 815, Biomedical Center, Uppsala University, SE-75108, Uppsala, Sweden
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-75185, Uppsala, Sweden
| | - Carl-Henrik Heldin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Box 582, Biomedical Center, Uppsala University, SE-75123, Uppsala, Sweden.,Ludwig Cancer Research, Science for Life Laboratory, Box 595, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Aristidis Moustakas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Box 582, Biomedical Center, Uppsala University, SE-75123, Uppsala, Sweden. .,Ludwig Cancer Research, Science for Life Laboratory, Box 595, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden.
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14
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Masuda Y, Saotome D, Takada K, Sugimoto K, Sasaki T, Ishii H. Peroxisome proliferator-activated receptor-alpha agonists repress expression of thrombin-activatable fibrinolysis inhibitor by decreasing transcript stability. Thromb Haemost 2017; 108:74-85. [DOI: 10.1160/th12-02-0101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 04/13/2012] [Indexed: 12/12/2022]
Abstract
SummaryThrombin-activatable fibrinolysis inhibitor (TAFI) (carboxypeptidase B2) is a plasma zymogen that is biosynthesised in the liver and released into the circulation. Activated TAFI is a prothrombotic factor which inhibits fibrin clot lysis. Cultured human hepatoma HepG2 cells were treated with peroxisome proliferator-activated receptor (PPAR)α, β or γ agonists, and the levels of TAFI antigen and mRNA (here, termed CPB2 mRNA) were measured. HepG2 cells treated with the PPARα agonist WY14643, but not agonists for PPARβ or PPARγ, decreased their release of TAFI antigen into the conditioned medium. In parallel, there were decreased levels of CPB2 mRNA and TAFI antigen in the cells. The WY14643-mediated decrease in CPB2 mRNA levels was accelerated by overexpression of PPARα and abolished by RNA interference of PPARA mRNA. CPB2 gene promoter activity was not influenced by treatment of the cells with WY14643. The half-life of the CPB2 transcript was shortened by treatment with WY14643 as compared with that of the control, and the decreased half-life of mRNA returned to control levels by treatment with a PPARα antagonist MK886 or transfection of PPARΑ-specific siRNA to WY14643-treated HepG2 cells. The present results suggest that PPARα agonists not only play a hypolipidaemic role, but also decrease the expression of TAFI, a prothrombotic factor, by decreasing stability of CPB2 transcripts.
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15
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Cumbo F, Vergni D, Santoni D. Investigating transcription factor synergism in humans. DNA Res 2017; 25:103-112. [PMID: 29069301 PMCID: PMC5824945 DOI: 10.1093/dnares/dsx041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 09/19/2017] [Indexed: 01/13/2023] Open
Abstract
Proteins are the core and the engine of every process in cells thus the study of mechanisms that drive the regulation of protein expression, is essential. Transcription factors play a central role in this extremely complex task and they synergically co-operate in order to provide a fine tuning of protein expressions. In the present study, we designed a mathematically well-founded procedure to investigate the mutual positioning of transcription factors binding sites related to a given couple of transcription factors in order to evaluate the possible association between them. We obtained a list of highly related transcription factors couples, whose binding site occurrences significantly group together for a given set of gene promoters, identifying the biological contexts in which the couples are involved in and the processes they should contribute to regulate.
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Affiliation(s)
- Fabio Cumbo
- Institute for Systems Analysis and Computer Science 'Antonio Ruberti', National Research Council of Italy, 00185 Rome, Italy.,Department of Engineering, Third University of Rome, 00146 Rome, Italy.,SYSBIO.IT-Centre of Systems Biology, 20126 Milan, Italy
| | - Davide Vergni
- Institute for Applied Mathematics 'Mauro Picone', National Research Council of Italy, 00185 Rome, Italy
| | - Daniele Santoni
- Institute for Systems Analysis and Computer Science 'Antonio Ruberti', National Research Council of Italy, 00185 Rome, Italy
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16
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Yu ZH, Lun SM, He R, Tian HP, Huang HJ, Wang QS, Li XQ, Feng YM. Dual function of MAZ mediated by FOXF2 in basal-like breast cancer: Promotion of proliferation and suppression of progression. Cancer Lett 2017; 402:142-152. [DOI: 10.1016/j.canlet.2017.05.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/03/2017] [Accepted: 05/24/2017] [Indexed: 11/16/2022]
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17
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Krentz Gober M, Collard JP, Thompson K, Black EP. A microRNA signature of response to erlotinib is descriptive of TGFβ behaviour in NSCLC. Sci Rep 2017. [PMID: 28646226 PMCID: PMC5482799 DOI: 10.1038/s41598-017-04097-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Our previous work identified a 13-gene miRNA signature predictive of response to the epidermal growth factor receptor (EGFR) inhibitor, erlotinib, in Non-Small Cell Lung Cancer cell lines. Bioinformatic analysis of the signature showed a functional convergence on TGFβ canonical signalling. We hypothesized that TGFβ signalling controls expression of the miRNA genes comprising an erlotinib response signature in NSCLC. Western analysis revealed that TGFβ signalling via Smad2/3/4 occurred differently between erlotinib-resistant A549 and erlotinib- sensitive PC9 cells. We showed that TGFβ induced an interaction between Smad4 and putative Smad Binding Elements in PC9. However, qRT-PCR analysis showed that endogenous miR-140/141/200c expression changes resulted from time in treatments, not the treatments themselves. Moreover, flow cytometry indicated that cells exited the cell cycle in the same manner. Taken together these data indicated that the miRNA comprising the signature are likely regulated by the cell cycle rather than by TGFβ. Importantly, this work revealed that TGFβ did not induce EMT in PC9 cells, but rather TGFβ-inhibition induced an EMT-intermediate. These data also show that growth/proliferation signals by constitutively-activated EGFR may rely on TGFβ and a possible relationship between TGFβ and EGFR signalling may prevent EMT progression in this context rather than promote it.
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Affiliation(s)
- Madeline Krentz Gober
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - James P Collard
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Katherine Thompson
- Department of Statistics, College of Arts and Sciences, University of Kentucky, Lexington, KY, 40536-0082, USA
| | - Esther P Black
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA.
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18
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Khot VV, Yadav DK, Shrestha S, Kaur L, Sundrani DP, Chavan-Gautam PM, Mehendale SS, Chandak GR, Joshi SR. Hypermethylated CpG sites in the MTR gene promoter in preterm placenta. Epigenomics 2017; 9:985-996. [PMID: 28617183 DOI: 10.2217/epi-2016-0173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Altered maternal one-carbon metabolism influences placental DNA methylation patterns and 'programs' the fetus for noncommunicable diseases in adult life. EXPERIMENTAL PROCEDURES Levels of plasma folate, vitamin B12, homocysteine, mRNA and protein levels of MTHFR and MTR enzymes in placenta were compared among women delivering preterm (n = 83) and term (n = 75). MTR promoter CpG methylation was undertaken. RESULTS MTHFR and MTR mRNA levels were higher while protein levels were lower, and MTR CpG sites were hypermethylated in the preterm group, as compared with the term group. Methylated CpG sites were negatively associated with maternal plasma vitamin B12 levels. CONCLUSION Study suggests a dysregulation of enzyme genes in remethylation arm of the one-carbon metabolism in placenta of women delivering preterm.
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Affiliation(s)
- Vinita V Khot
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Dilip K Yadav
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Lovejeet Kaur
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Deepali P Sundrani
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Preeti M Chavan-Gautam
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Savita S Mehendale
- Obstetrics & Gynecology, Bharati Medical College & Hospital, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Sadhana R Joshi
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
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19
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Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes. BIOLOGY 2017; 6:biology6020028. [PMID: 28467369 PMCID: PMC5485475 DOI: 10.3390/biology6020028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022]
Abstract
NRAMP1 (SLC11A1) is a professional phagocyte membrane importer of divalent metals that contributes to iron recycling at homeostasis and to nutritional immunity against infection. Analyses of data generated by several consortia and additional studies were integrated to hypothesize mechanisms restricting NRAMP1 expression to mature phagocytes. Results from various epigenetic and transcriptomic approaches were collected for mesodermal and hematopoietic cell types and compiled for combined analysis with results of genetic studies associating single nucleotide polymorphisms (SNPs) with variations in NRAMP1 expression (eQTLs). Analyses establish that NRAMP1 is part of an autonomous topologically associated domain delimited by ubiquitous CCCTC-binding factor (CTCF) sites. NRAMP1 locus contains five regulatory regions: a predicted super-enhancer (S-E) key to phagocyte-specific expression; the proximal promoter; two intronic areas, including 3' inhibitory elements that restrict expression during development; and a block of upstream sites possibly extending the S-E domain. Also the downstream region adjacent to the 3' CTCF locus boundary may regulate expression during hematopoiesis. Mobilization of the locus 14 predicted transcriptional regulatory elements occurs in three steps, beginning with hematopoiesis; at the onset of myelopoiesis and through myelo-monocytic differentiation. Basal expression level in mature phagocytes is further influenced by genetic variation, tissue environment, and in response to infections that induce various epigenetic memories depending on microorganism nature. Constitutively associated transcription factors (TFs) include CCAAT enhancer binding protein beta (C/EBPb), purine rich DNA binding protein (PU.1), early growth response 2 (EGR2) and signal transducer and activator of transcription 1 (STAT1) while hypoxia-inducible factors (HIFs) and interferon regulatory factor 1 (IRF1) may stimulate iron acquisition in pro-inflammatory conditions. Mouse orthologous locus is generally conserved; chromatin patterns typify a de novo myelo-monocytic gene whose expression is tightly controlled by TFs Pu.1, C/ebps and Irf8; Irf3 and nuclear factor NF-kappa-B p 65 subunit (RelA) regulate expression in inflammatory conditions. Functional differences in the determinants identified at these orthologous loci imply that species-specific mechanisms control gene expression.
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20
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Gopal R, Selvarasu K, Pandian PP, Ganesan K. Integrative transcriptome analysis of liver cancer profiles identifies upstream regulators and clinical significance of ACSM3 gene expression. Cell Oncol (Dordr) 2017; 40:219-233. [PMID: 28390038 DOI: 10.1007/s13402-017-0321-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is one of the most common human malignancies. It has frequently been associated with metabolic perturbations and liver damages. Various members of the family of acyl-CoA synthetases are known to be involved in the production of bioactive fatty acids, and altered expression of its encoding genes has been found to be involved in metabolic perturbations. For the development of novel diagnostic and therapeutic HCC options, a fundamental understanding of the mechanisms associated with the deregulation of candidate genes involved in metabolic perturbation is required. METHODS A meta-analysis of multiple HCC mRNA profiles was performed to identify consistently deregulated genes. Expression of the acyl-CoA synthetase medium chain family member 3 (ACSM3) gene was subsequently assessed in different HCC tumor stages and correlated with various clinicopathological features. Transcription regulation, survival and pathway-associated features of the ACSM3 gene were investigated using integrative functional genomic and molecular cell biological methods. RESULTS We found that expression of the ACSM3 gene was significantly reduced in HCC tissues and was frequently downregulated in patients exhibiting high alpha-fetoprotein (AFP) levels, high alanine aminotransferase (ALT) levels, multiple nodules and large tumors. Loss of ACSM3 expression was found to correlate with advanced HCC stages and a poor survival. In addition, HNF4α was found to positively regulate the expression of the ACSM3 gene, while PPARγ was found to transcriptionally repress it. Downregulation of ACSM3 expression was perceived upon activation of the TGFβ, WNT, AKT and MYC signalling pathways. In addition, we found that ACSM3 expression correlates with fatty acid oxidation in HCC. CONCLUSION Our data provide evidence for a differential expression and regulation of the ACSM3 gene in HCC, and may lay a foundation for therapeutically targeting fatty acid metabolism in these tumors.
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Affiliation(s)
- Ramani Gopal
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Karthikeyan Selvarasu
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Ponmathi Panneer Pandian
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Kumaresan Ganesan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India.
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21
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Xiao X, Chang H, Li M. Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies. Mol Psychiatry 2017; 22:497-511. [PMID: 28044063 PMCID: PMC5378805 DOI: 10.1038/mp.2016.241] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/08/2016] [Accepted: 11/14/2016] [Indexed: 12/18/2022]
Abstract
Recent large-scale genetic approaches such as genome-wide association studies have allowed the identification of common genetic variations that contribute to risk architectures of psychiatric disorders. However, most of these susceptibility variants are located in noncoding genomic regions that usually span multiple genes. As a result, pinpointing the precise variant(s) and biological mechanisms accounting for the risk remains challenging. By reviewing recent progresses in genetics, functional genomics and neurobiology of psychiatric disorders, as well as gene expression analyses of brain tissues, here we propose a roadmap to characterize the roles of noncoding risk loci in the pathogenesis of psychiatric illnesses (that is, identifying the underlying molecular mechanisms explaining the genetic risk conferred by those genomic loci, and recognizing putative functional causative variants). This roadmap involves integration of transcriptomic data, epidemiological and bioinformatic methods, as well as in vitro and in vivo experimental approaches. These tools will promote the translation of genetic discoveries to physiological mechanisms, and ultimately guide the development of preventive, therapeutic and prognostic measures for psychiatric disorders.
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Affiliation(s)
- X Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - H Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - M Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
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22
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Mimoto R, Imawari Y, Hirooka S, Takeyama H, Yoshida K. Impairment of DYRK2 augments stem-like traits by promoting KLF4 expression in breast cancer. Oncogene 2017; 36:1862-1872. [PMID: 27721402 DOI: 10.1038/onc.2016.349] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 08/05/2016] [Accepted: 08/15/2016] [Indexed: 01/03/2023]
Abstract
Whereas accumulating studies have supported the cancer stem cell theory, a specific therapy targeting a cancer stem cell subpopulation has not been established. Here, we show that dual-specificity tyrosine phosphorylation-kinase 2 (DYRK2) is a novel negative regulator for formation of breast cancer stem cells. Downregulation of DYRK2 promotes cancer stem-like traits in vitro, tumourigenesis in vivo and the proportion of the cancer stem cell population in human breast cancer tissues. We found that Krupple-like factor 4 (KLF4) serves as a key mediator of DYRK2's control over the cancer stem phenotype. Reduced DYRK2 expression increases KLF4 expression, which induces cancer stem-like properties. We identified androgen receptor (AR) as a transcription factor binding to the KLF4 promoter region; this process is dependent on DYRK2 kinase activity. Our findings delineate a mechanism of cancer stem cell regulation by the DYRK2-AR-KLF4 axis in breast cancer. Targeting of this pathway may be a promising strategy against breast cancer stem cells.
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Affiliation(s)
- R Mimoto
- Department of Biochemistry, Jikei University School of Medicine, Tokyo, Japan
- Department of Surgery, Jikei University School of Medicine, Tokyo, Japan
| | - Y Imawari
- Department of Biochemistry, Jikei University School of Medicine, Tokyo, Japan
- Department of Surgery, Jikei University School of Medicine, Tokyo, Japan
| | - S Hirooka
- Department of Pathology, Jikei University School of Medicine, Tokyo, Japan
| | - H Takeyama
- Department of Surgery, Jikei University School of Medicine, Tokyo, Japan
| | - K Yoshida
- Department of Biochemistry, Jikei University School of Medicine, Tokyo, Japan
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23
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Bevilacqua V, Gioia U, Di Carlo V, Tortorelli AF, Colombo T, Bozzoni I, Laneve P, Caffarelli E. Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells. RNA Biol 2016; 12:1323-37. [PMID: 26480000 DOI: 10.1080/15476286.2015.1096488] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human genome contains some thousands of long non coding RNAs (lncRNAs). Many of these transcripts are presently considered crucial regulators of gene expression and functionally implicated in developmental processes in Eukaryotes. Notably, despite a huge number of lncRNAs are expressed in the Central Nervous System (CNS), only a few of them have been characterized in terms of molecular structure, gene expression regulation and function. In the present study, we identify linc-NeD125 as a novel cytoplasmic, neuronal-induced long intergenic non coding RNA (lincRNA). Linc-NeD125 represents the host gene for miR-125b-1, a microRNA with an established role as negative regulator of human neuroblastoma cell proliferation. Here, we demonstrate that these two overlapping non coding RNAs are coordinately induced during in vitro neuronal differentiation, and that their expression is regulated by different mechanisms. While the production of miR-125b-1 relies on transcriptional regulation, linc-NeD125 is controlled at the post-transcriptional level, through modulation of its stability. We also demonstrate that linc-NeD125 functions independently of the hosted microRNA, by reducing cell proliferation and activating the antiapoptotic factor BCL-2.
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Affiliation(s)
- Valeria Bevilacqua
- a Department of Biology and Biotechnology C. Darwin ; Sapienza University of Rome ; Rome , Italy.,f Present addresses Valeria Bevilacqua: Virology Program, INGM - Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy; Ubaldo Gioia: IFOM; the FIRC Institute of Molecular Oncology; Milan, Italy; Valerio Di Carlo: Center for Genomic Regulation and UPF ; Barcelona , Spain.,g These authors equally contributed to this work
| | - Ubaldo Gioia
- a Department of Biology and Biotechnology C. Darwin ; Sapienza University of Rome ; Rome , Italy.,f Present addresses Valeria Bevilacqua: Virology Program, INGM - Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy; Ubaldo Gioia: IFOM; the FIRC Institute of Molecular Oncology; Milan, Italy; Valerio Di Carlo: Center for Genomic Regulation and UPF ; Barcelona , Spain.,g These authors equally contributed to this work
| | - Valerio Di Carlo
- a Department of Biology and Biotechnology C. Darwin ; Sapienza University of Rome ; Rome , Italy.,f Present addresses Valeria Bevilacqua: Virology Program, INGM - Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy; Ubaldo Gioia: IFOM; the FIRC Institute of Molecular Oncology; Milan, Italy; Valerio Di Carlo: Center for Genomic Regulation and UPF ; Barcelona , Spain
| | - Anna F Tortorelli
- a Department of Biology and Biotechnology C. Darwin ; Sapienza University of Rome ; Rome , Italy
| | - Teresa Colombo
- b Institute for Computing Applications "Mauro Picone," National Research Council ; Rome , Italy
| | - Irene Bozzoni
- a Department of Biology and Biotechnology C. Darwin ; Sapienza University of Rome ; Rome , Italy.,c Institute of Molecular Biology and Pathology, National Research Council, Sapienza University of Rome ; Rome , Italy.,d Institute Pasteur Fondazione Cenci-Bolognetti, Sapienza University of Rome ; Rome , Italy.,e Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia ; Rome , Italy
| | - Pietro Laneve
- e Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia ; Rome , Italy
| | - Elisa Caffarelli
- c Institute of Molecular Biology and Pathology, National Research Council, Sapienza University of Rome ; Rome , Italy.,e Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia ; Rome , Italy
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Okada M, Lee L, Maekawa R, Sato S, Kajimura T, Shinagawa M, Tamura I, Taketani T, Asada H, Tamura H, Sugino N. Epigenetic Changes of the Cyp11a1 Promoter Region in Granulosa Cells Undergoing Luteinization During Ovulation in Female Rats. Endocrinology 2016; 157:3344-54. [PMID: 27428926 DOI: 10.1210/en.2016-1264] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The ovulatory LH surge induces rapid up-regulation of Cyp11a1 in granulosa cells (GCs) undergoing luteinization during ovulation. This study investigated in vivo whether epigenetic controls including histone modifications and DNA methylation in the promoter region are associated with the rapid increase of Cyp11a1 gene expression after LH surge. GCs were obtained from rats treated with equine chorionic gonadotropin (CG) before (0 h) and 4 h and 12 h after human (h)CG injection. Cyp11a1 mRNA levels rapidly increased after hCG injection, reached a peak at 4 hours, and then remained elevated until 12 hours. DNA methylation status in the Cyp11a1 proximal promoter region was hypomethylated and did not change at any of the observed times after hCG injection. Chromatin immunoprecipitation assays revealed that the levels of trimethylation of lysine 4 on histone H3 (H3K4me3), an active mark for transcription, increased, whereas the levels of H3K9me3 and H3K27me3, which are marks associated with repression of transcription, decreased in the Cyp11a1 proximal promoter after hCG injection. Chromatin condensation, which was analyzed using deoxyribonuclease I, decreased in the Cyp11a1 proximal promoter after hCG injection. Chromatin immunoprecipitation assays also showed that the binding activity of CAATT/enhancer-binding protein-β to the Cyp11a1 proximal promoter increased after hCG injection. Luciferase assays revealed that the CAATT/enhancer-binding protein-β-binding site had transcriptional activity and contributed to basal and cAMP-induced Cyp11a1 expression. These results suggest that changes in histone modification and chromatin structure in the Cyp11a1 proximal promoter are involved in the rapid increase of Cyp11a1 gene expression in GCs undergoing luteinization during ovulation.
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Affiliation(s)
- Maki Okada
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
| | - Lifa Lee
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
| | - Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
| | - Takuya Kajimura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
| | - Masahiro Shinagawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
| | - Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
| | - Toshiaki Taketani
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
| | - Hiromi Asada
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
| | - Hiroshi Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
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Zhang X, Crawford EL, Blomquist TM, Khuder SA, Yeo J, Levin AM, Willey JC. Haplotype and diplotype analyses of variation in ERCC5 transcription cis-regulation in normal bronchial epithelial cells. Physiol Genomics 2016; 48:537-43. [PMID: 27235448 PMCID: PMC4967224 DOI: 10.1152/physiolgenomics.00021.2016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022] Open
Abstract
Excision repair cross-complementation group 5 (ERCC5) gene plays an important role in nucleotide excision repair, and dysregulation of ERCC5 is associated with increased lung cancer risk. Haplotype and diplotype analyses were conducted in normal bronchial epithelial cells (NBEC) to better understand mechanisms responsible for interindividual variation in transcript abundance regulation of ERCC5 We determined genotypes at putative ERCC5 cis-regulatory SNPs (cis-rSNP) rs751402 and rs2296147, and marker SNPs rs1047768 and rs17655. ERCC5 allele-specific transcript abundance was assessed by a recently developed targeted sequencing method. Syntenic relationships among alleles at rs751402, rs2296147, and rs1047768 were assessed by allele-specific PCR followed by Sanger sequencing. We then assessed association of ERCC5 allele-specific expression at rs1047768 with haplotype and diplotype structure at cis-rSNPs rs751402 and rs2296147. Genotype analysis revealed significantly (P < 0.005) higher interindividual variation in allelic ratios in cDNA samples relative to matched gDNA samples at both rs1047768 and rs17655. By diplotype analysis, mean expression was higher at the rs1047768 alleles syntenic with rs2296147 T allele compared with rs2296147 C allele. Furthermore, mean expression was lower at rs17655 C allele, which is syntenic with G allele at a linked SNP rs873601 (D' = 0.95). These data support the conclusions that in NBEC, T allele at SNP rs2296147 upregulates ERCC5, variation at rs751402 does not alter ERCC5 regulation, and that C allele at SNP rs17655 downregulates ERCC5 Variation in ERCC5 transcript abundance associated with allelic variation at these SNPs could result in variation in NER function in NBEC and lung cancer risk.
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Affiliation(s)
- Xiaolu Zhang
- Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio
| | - Erin L Crawford
- Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio
| | - Thomas M Blomquist
- Department of Pathology, University of Toledo Health Sciences Campus, Toledo, Ohio
| | - Sadik A Khuder
- Departments of Medicine and Public Health and Homeland Security, University of Toledo Health Science Campus, Toledo, Ohio; and
| | - Jiyoun Yeo
- Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - James C Willey
- Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio; Department of Pathology, University of Toledo Health Sciences Campus, Toledo, Ohio;
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26
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Sun X, Clermont PL, Jiao W, Helgason CD, Gout PW, Wang Y, Qu S. Elevated expression of the centromere protein-A(CENP-A)-encoding gene as a prognostic and predictive biomarker in human cancers. Int J Cancer 2016; 139:899-907. [PMID: 27062469 DOI: 10.1002/ijc.30133] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/09/2016] [Accepted: 03/23/2016] [Indexed: 01/08/2023]
Abstract
Centromere protein-A (CENP-A), a histone-H3 variant, plays an essential role in cell division by ensuring proper formation and function of centromeres and kinetochores. Elevated CENP-A expression has been associated with cancer development. This study aimed to establish whether elevated CENP-A expression can be used as a prognostic and predictive cancer biomarker. Molecular profiling of CENP-A in human cancers was investigated using genomic, transcriptomic and patient information from databases, including COSMIC, Oncomine, Kaplan-Meier plotter and cBioPortal. A network of CENP-A co-expressed genes was derived from cBioPortal and analyzed using Ingenuity Pathway Analysis (IPA) and Oncomine protocols to explore the function of CENP-A and its predictive potential. Transcriptional and post-transcriptional regulation of CENP-A expression was analyzed in silico. It was found that CENP-A expression was elevated in 20 types of solid cancer compared with normal counterparts. Elevated CENP-A expression highly correlated with cancer progression and poor patient outcome. Genomic analysis indicated that the elevated CENP-A expression was not due to alterations in the sequence or copy number of the CENP-A gene. Furthermore, CENP-A can be regulated by key oncogenic proteins and tumor-suppressive microRNAs. CENP-A co-expression network analysis indicated that CENP-A function is associated with cell cycle progression. Oncomine analysis showed a strong correlation between elevated CENP-A expression and oncolytic response of breast cancer patients to taxane-based chemotherapy. In conclusion, elevated CENP-A expression is coupled to malignant progression of numerous types of cancer. It may be useful as a biomarker of poor patient prognosis and as a predictive biomarker for taxane-based chemotherapy.
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Affiliation(s)
- Xia Sun
- Department of Pharmacology, School of Medicine, Shandong University, Jinan, Shandong, China
| | - Pier-Luc Clermont
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada.,Interdisciplinary Oncology Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Wenlin Jiao
- Department of Pharmacology, School of Medicine, Shandong University, Jinan, Shandong, China
| | - Cheryl D Helgason
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada.,Interdisciplinary Oncology Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Surgery, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Peter W Gout
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada.,Interdisciplinary Oncology Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Vancouver Prostate Center, Vancouver, BC, Canada.,Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sifeng Qu
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada.,Interdisciplinary Oncology Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Vancouver Prostate Center, Vancouver, BC, Canada
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27
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Heslop JA, Rowe C, Walsh J, Sison-Young R, Jenkins R, Kamalian L, Kia R, Hay D, Jones RP, Malik HZ, Fenwick S, Chadwick AE, Mills J, Kitteringham NR, Goldring CEP, Kevin Park B. Mechanistic evaluation of primary human hepatocyte culture using global proteomic analysis reveals a selective dedifferentiation profile. Arch Toxicol 2016; 91:439-452. [PMID: 27039104 PMCID: PMC5225178 DOI: 10.1007/s00204-016-1694-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 03/21/2016] [Indexed: 01/01/2023]
Abstract
The application of primary human hepatocytes following isolation from human tissue is well accepted to be compromised by the process of dedifferentiation. This phenomenon reduces many unique hepatocyte functions, limiting their use in drug disposition and toxicity assessment. The aetiology of dedifferentiation has not been well defined, and further understanding of the process would allow the development of novel strategies for sustaining the hepatocyte phenotype in culture or for improving protocols for maturation of hepatocytes generated from stem cells. We have therefore carried out the first proteomic comparison of primary human hepatocyte differentiation. Cells were cultured for 0, 24, 72 and 168 h as a monolayer in order to permit unrestricted hepatocyte dedifferentiation, so as to reveal the causative signalling pathways and factors in this process, by pathway analysis. A total of 3430 proteins were identified with a false detection rate of <1 %, of which 1117 were quantified at every time point. Increasing numbers of significantly differentially expressed proteins compared with the freshly isolated cells were observed at 24 h (40 proteins), 72 h (118 proteins) and 168 h (272 proteins) (p < 0.05). In particular, cytochromes P450 and mitochondrial proteins underwent major changes, confirmed by functional studies and investigated by pathway analysis. We report the key factors and pathways which underlie the loss of hepatic phenotype in vitro, particularly those driving the large-scale and selective remodelling of the mitochondrial and metabolic proteomes. In summary, these findings expand the current understanding of dedifferentiation should facilitate further development of simple and complex hepatic culture systems.
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Affiliation(s)
- James A Heslop
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK
| | - Cliff Rowe
- CN Bio, Centre for Innovation and Enterprise, Oxford University Begbroke Science Park, Begbroke, Oxfordshire, OX5 1PF, UK
| | - Joanne Walsh
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK
| | - Rowena Sison-Young
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK
| | - Roz Jenkins
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK
| | - Laleh Kamalian
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK
| | - Richard Kia
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK
| | - David Hay
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK
| | - Robert P Jones
- University Hospital Aintree, Longmoor Lane, Liverpool, L9 7AL, UK
| | - Hassan Z Malik
- University Hospital Aintree, Longmoor Lane, Liverpool, L9 7AL, UK
| | - Stephen Fenwick
- University Hospital Aintree, Longmoor Lane, Liverpool, L9 7AL, UK
| | - Amy E Chadwick
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK
| | - John Mills
- AstraZeneca, Personalised Healthcare and Biomarkers, Alderley Park, Cheshire, SK10 4TG, UK
| | - Neil R Kitteringham
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK
| | - Chris E P Goldring
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK.
| | - B Kevin Park
- Division of Molecular and Clinical Pharmacology, The Institute of Translational Medicine, MRC Centre for Drug Safety Science, The University of Liverpool, Liverpool, L69 3GE, UK
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28
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Feng Y, Tian J, Krylova I, Xu T, Xie HQ, Guo TL, Zhao B. Chronic TCDD exposure results in the dysregulation of gene expression in splenic B-lymphocytes and in the impairments in T-cell and B-cell differentiation in mouse model. J Environ Sci (China) 2016; 39:218-227. [PMID: 26899660 DOI: 10.1016/j.jes.2015.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/01/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) exposure in humans is associated with marked immune suppressions and increased incidence of lymphoblastic diseases. To elucidate mechanisms of impairments in humoral immune responses, we used a murine model. Following a 20-week administration of low doses of TCDD, we observed severely reduced antibody titers, dramatically decreased number of splenic Th1 and Th2 cells and an increase in CD19(+) B cells. Transcriptional profiling of CD19(+) B cells showed that markers of pre-B cells were significantly elevated, indicating delayed B cell maturation. These changes in B cells were accompanied by decreases of T helper cell numbers and reduced IgM and IgG titers. A transcriptome analysis of splenic B cells followed by Ingenuity Pathway Analysis (IPA) revealed a set of differentially expressed genes known to play roles in tumorigenesis, cell-proliferation and cell-migration. The most up-regulated transcript gene was Eph receptor A2 (EphA2), a known oncogene, and the most down-regulated transcript was ZBTB16 that codes for a negative transcriptional regulator important in epigenetic chromatin remodeling. IPA identified cAMP-responsive element modulator (CREM) and cAMP-responsive element binding protein 1 (CREB1) as top upstream regulators. Consistently, a MAPPER promoter database analysis showed that all top dysregulated genes had CREM and/or CREB1 binding sites in their promoter regions. In summary, our data showed that chronic TCDD exposure in mice caused suppressed humoral immunity accompanied with profound dysregulation of gene expression in splenic B-lymphocytes, likely through cAMP-dependent pathways. This dysregulation resulted in impairments in T-cell and B-cell differentiation and activation of the tumorigenic transcription program.
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Affiliation(s)
- Yu Feng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Jijing Tian
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | | | - Tuan Xu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Heidi Qunhui Xie
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Tai L Guo
- Department of Veterinary Biosciences and Diagnostic Imaging, College of Veterinary Medicine, University of Georgia, Athens, GA 30602-7382, USA
| | - Bin Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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29
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Corbera-Bellalta M, Planas-Rigol E, Lozano E, Terrades-García N, Alba MA, Prieto-González S, García-Martínez A, Albero R, Enjuanes A, Espígol-Frigolé G, Hernández-Rodríguez J, Roux-Lombard P, Ferlin WG, Dayer JM, Kosco-Vilbois MH, Cid MC. Blocking interferon γ reduces expression of chemokines CXCL9, CXCL10 and CXCL11 and decreases macrophage infiltration in ex vivo cultured arteries from patients with giant cell arteritis. Ann Rheum Dis 2015; 75:1177-86. [DOI: 10.1136/annrheumdis-2015-208371] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/06/2015] [Indexed: 01/21/2023]
Abstract
BackgroundInterferon γ (IFNγ) is considered a seminal cytokine in the pathogenesis of giant cell arteritis (GCA), but its functional role has not been investigated. We explored changes in infiltrating cells and biomarkers elicited by blocking IFNγ with a neutralising monoclonal antibody, A6, in temporal arteries from patients with GCA.MethodsTemporal arteries from 34 patients with GCA (positive histology) and 21 controls were cultured on 3D matrix (Matrigel) and exposed to A6 or recombinant IFNγ. Changes in gene/protein expression were measured by qRT-PCR/western blot or immunoassay. Changes in infiltrating cells were assessed by immunohistochemistry/immunofluorescence. Chemotaxis/adhesion assays were performed with temporal artery-derived vascular smooth muscle cells (VSMCs) and peripheral blood mononuclear cells (PBMCs).ResultsBlocking endogenous IFNγ with A6 abrogated STAT-1 phosphorylation in cultured GCA arteries. Furthermore, selective reduction in CXCL9, CXCL10 and CXCL11 chemokine expression was observed along with reduction in infiltrating CD68 macrophages. Adding IFNγ elicited consistent opposite effects. IFNγ induced CXCL9, CXCL10, CXCL11, CCL2 and intracellular adhesion molecule-1 expression by cultured VSMC, resulting in increased PBMC chemotaxis/adhesion. Spontaneous expression of chemokines was higher in VSMC isolated from GCA-involved arteries than in those obtained from controls. Incubation of IFNγ-treated control arteries with PBMC resulted in adhesion/infiltration by CD68 macrophages, which did not occur in untreated arteries.ConclusionsOur ex vivo system suggests that IFNγ may play an important role in the recruitment of macrophages in GCA by inducing production of specific chemokines and adhesion molecules. Vascular wall components (ie, VSMC) are mediators of these functions and may facilitate progression of inflammatory infiltrates through the vessel wall.
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30
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Kujundzic B, Zeljic K, Supic G, Magic M, Stanimirovic D, Ilic V, Jovanovic B, Magic Z. Association of vdr, cyp27b1, cyp24a1 and mthfr gene polymorphisms with oral lichen planus risk. Clin Oral Investig 2015; 20:781-9. [PMID: 26303648 DOI: 10.1007/s00784-015-1572-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
Abstract
OBJECTIVES The current study investigated the association between VDR EcoRV (rs4516035), FokI (rs2228570), ApaI (rs7975232) and TaqI (rs731236), CYP27B1 (rs4646536), CYP24A1 (rs2296241), and MTHFR (rs1801133) gene polymorphisms and risk of oral lichen planus (OLP) occurrence. MATERIALS AND METHODS The study group consisted of 65 oral lichen planus patients and 100 healthy blood donors in the control group. Single nucleotide polymorphisms were genotyped by real time PCR or PCR-restriction fragment length polymorphism (RFLP) method. RESULTS Heterozygous as well as mutated genotype of vitamin D receptor (VDR) FokI (rs2228570) polymorphism was associated with increased oral lichen planus risk in comparison with wild type genotype (odds ratio (OR) = 3.877, p = 0.017, OR = 38.153, p = 0.001, respectively). A significantly decreased OLP risk was observed for heterozygous genotype of rs2296241 polymorphism in CYP24A1 gene compared with the wild type form (OR = 0.314, p = 0.012). VDR gene polymorphisms ApaI and TaqI were in linkage disequilibrium (D' = 0.71, r(2) = 0.22). Identified haplotype AT was associated with decreased OLP risk (OR = 0.592, p = 0.047). CONCLUSION Our results highlight the possible important role of VDR FokI (rs2228570) and CYP24A1 rs2296241 gene polymorphisms for oral lichen planus susceptibility. CLINICAL RELEVANCE Identification of new molecular biomarkers could potentially contribute to determination of individuals with OLP predisposition.
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Affiliation(s)
- Bojan Kujundzic
- Department of Dentistry-Oral Surgery, Faculty of Medicine, University of East Sarajevo, Foca, Bosnia and Herzegovina
| | - Katarina Zeljic
- Institute for Medical Research, Military Medical Academy, Crnotravska 17, Belgrade, 11002, Serbia. .,Faculty of Biology, University of Belgrade, Studentski Trg 3, Belgrade, 11000, Serbia.
| | - Gordana Supic
- Institute for Medical Research, Military Medical Academy, Crnotravska 17, Belgrade, 11002, Serbia.,Faculty of Medicine, Military Medical Academy, University of Defense, Belgrade, Serbia
| | - Marko Magic
- School of Dental Medicine, Clinic of Periodontology and Oral Medicine, University of Belgrade, Belgrade, Serbia
| | - Dragan Stanimirovic
- School of Dental Medicine, Clinic of Periodontology and Oral Medicine, University of Belgrade, Belgrade, Serbia
| | - Vesna Ilic
- Institute for Medical Research, Military Medical Academy, Crnotravska 17, Belgrade, 11002, Serbia
| | - Barbara Jovanovic
- Institute for Medical Research, Military Medical Academy, Crnotravska 17, Belgrade, 11002, Serbia
| | - Zvonko Magic
- Institute for Medical Research, Military Medical Academy, Crnotravska 17, Belgrade, 11002, Serbia.,Faculty of Medicine, Military Medical Academy, University of Defense, Belgrade, Serbia
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Syndecan-1 Acts in Synergy with Tight Junction Through Stat3 Signaling to Maintain Intestinal Mucosal Barrier and Prevent Bacterial Translocation. Inflamm Bowel Dis 2015; 21:1894-907. [PMID: 25970544 DOI: 10.1097/mib.0000000000000421] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Intestinal epithelial tight junction (TJ) is the principal determinant of mucosal permeability, defects of which have been correlated to inflammatory bowel disease. In this study, we investigated whether syndecan-1 (Sdc1), the predominant cell surface heparan sulfate proteoglycan, affects TJ proteins to protect intestinal barrier function. METHODS The role of Sdc1 in barrier function was examined in cultured colonic epithelial cells and dextran sodium sulfate-induced colitis mouse model. Barrier function was determined by transepithelial electrical resistance, bacterial translocation, and FITC-dextran flux. Canonical TJ proteins ZO-1 and occludin were measured by Western blot and immunofluoresence. Role of the Stat3 pathway was detected by Western blot and chromatin immunoprecipitation. RESULTS Overexpressed Sdc1 in Caco-2 cells attenuated transepithelial electrical resistance reduction, prevented bacterial translocation, and repressed FITC-dextran flux, whereas Sdc1 knockdown in HT29 cells resulted in a greater loss of barrier function. Supplementation of exogenous Sdc1 in colitis mice ameliorated the activity of colitis and barrier defect. Mechanistically, Sdc1 significantly modulated expressions of ZO-1 and occludin by activating Stat3, which directly bound to the promoter regions of ZO-1 and occludin. Furthermore, ZO-1 and occludin were found to bind to each other, and their repression could induce Sdc1 upregulation. CONCLUSIONS Sdc1 plays an important role in protecting the intestinal barrier function and preventing bacterial translocation, in synergy with TJ through Stat3 signaling in an Sdc1/Stat3/ZO-1 and occludin feedback loop. Sdc1 participates in the mechanism that is related to intestinal barrier function and colitis and represents a therapeutic target for novel anti-inflammatory bowel disease strategies.
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Wu H, Barik A, Lu Y, Shen C, Bowman A, Li L, Sathyamurthy A, Lin TW, Xiong WC, Mei L. Slit2 as a β-catenin/Ctnnb1-dependent retrograde signal for presynaptic differentiation. eLife 2015; 4. [PMID: 26159615 PMCID: PMC4498096 DOI: 10.7554/elife.07266] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 06/18/2015] [Indexed: 12/12/2022] Open
Abstract
Neuromuscular junction formation requires proper interaction between motoneurons and muscle cells. β-Catenin (Ctnnb1) in muscle is critical for motoneuron differentiation; however, little is known about the relevant retrograde signal. In this paper, we dissected which functions of muscle Ctnnb1 are critical by an in vivo transgenic approach. We show that Ctnnb1 mutant without the transactivation domain was unable to rescue presynaptic deficits of Ctnnb1 mutation, indicating the involvement of transcription regulation. On the other hand, the cell-adhesion function of Ctnnb1 is dispensable. We screened for proteins that may serve as a Ctnnb1-directed retrograde factor and identified Slit2. Transgenic expression of Slit2 specifically in the muscle was able to diminish presynaptic deficits by Ctnnb1 mutation in mice. Slit2 immobilized on beads was able to induce synaptophysin puncta in axons of spinal cord explants. Together, these observations suggest that Slit2 serves as a factor utilized by muscle Ctnnb1 to direct presynaptic differentiation. DOI:http://dx.doi.org/10.7554/eLife.07266.001 Motor nerves are like electrical wires that connect our spinal cord to the muscles in our body. These nerves communicate with muscles across a connection called the neuromuscular junction. To first form a neuromuscular junction, the motor nerves and muscles each produce molecular cues that tell each other to do their part to build a connection. Beta-catenin in the muscle is known to regulate motor nerve development. However, beta-catenin has two different roles: it helps to coordinate whether neighboring cells stick together, and it can regulate which genes are ‘transcribed’ to produce proteins. It was not known which of these roles is necessary for forming neuromuscular junctions. Wu, Barik et al. now investigate this question by creating mice with mutant forms of beta-catenin in their muscles. Some mice had muscle beta-catenin that could not help cells stick together, and others had beta-catenin that could not control gene transcription. Only mutations that affected the ability of beta-catenin to control transcription caused abnormalities in the neuromuscular junction. However, these problems could be fixed by adding either normal beta-catenin or the mutant form that cannot help cells stick together. Wu, Barik et al. then used molecular tools to explore which genes are turned on by beta-catenin. The experiments showed that beta-catenin causes muscle fibers to produce a protein called Slit2—a developmental cue that controls where neurons grow. Furthermore, the neuromuscular junction defects found in mice without beta-catenin in their muscles could be reduced by making the muscle fibers produce more Slit2. However, not all defects in beta-catenin mutant mice are rescued by Slit2. Future research is needed to identify other beta-catenin-controlled signals and to determine whether such a pathway is altered in neuromuscular disorders. DOI:http://dx.doi.org/10.7554/eLife.07266.002
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Affiliation(s)
- Haitao Wu
- Department of Neurobiology, Institute of Basic Medical Sciences, Beijing, China
| | - Arnab Barik
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, United States
| | - Yisheng Lu
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, United States
| | - Chengyong Shen
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, United States
| | - Andrew Bowman
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, United States
| | - Lei Li
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, United States
| | - Anupama Sathyamurthy
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, United States
| | - Thiri W Lin
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, United States
| | - Wen-Cheng Xiong
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, United States
| | - Lin Mei
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, United States
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Gomez JC, Yamada M, Martin JR, Dang H, Brickey WJ, Bergmeier W, Dinauer MC, Doerschuk CM. Mechanisms of interferon-γ production by neutrophils and its function during Streptococcus pneumoniae pneumonia. Am J Respir Cell Mol Biol 2015; 52:349-64. [PMID: 25100610 DOI: 10.1165/rcmb.2013-0316oc] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bacterial pneumonia is a common public health problem associated with significant mortality, morbidity, and cost. Neutrophils are usually the earliest leukocytes to respond to bacteria in the lungs. Neutrophils rapidly sequester in the pulmonary microvasculature and migrate into the lung parenchyma and alveolar spaces, where they perform numerous effector functions for host defense. Previous studies showed that migrated neutrophils produce IFN-γ early during pneumonia induced by Streptococcus pneumoniae and that early production of IFN-γ regulates bacterial clearance. IFN-γ production by neutrophils requires Rac2, Hck/Lyn/Fgr Src family tyrosine kinases, and NADPH oxidase. Our current studies examined the mechanisms that regulate IFN-γ production by lung neutrophils during acute S. pneumoniae pneumonia in mice and its function. We demonstrate that IFN-γ production by neutrophils is a tightly regulated process that does not require IL-12. The adaptor molecule MyD88 is critical for IFN-γ production by neutrophils. The guanine nucleotide exchange factor CalDAG-GEFI modulates IFN-γ production. The CD11/CD18 complex, CD44, Toll-like receptors 2 and 4, TRIF, and Nrf2 are not required for IFN-γ production by neutrophils. The recently described neutrophil-dendritic cell hybrid cell, identified by its expression of Ly6G and CD11c, is present at low numbers in pneumonic lungs and is not a source of IFN-γ. IFN-γ produced by neutrophils early during acute S. pneumoniae pneumonia induces transcription of target genes in the lungs, which are critical for host defense. These studies underline the complexity of the neutrophil responses during pneumonia in the acute inflammatory response and in subsequent resolution or initiation of immune responses.
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Affiliation(s)
- John C Gomez
- 1 Center for Airways Disease, Department of Medicine
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Salces-Ortiz J, Ramón M, González C, Pérez-Guzmán MD, Garde JJ, García-Álvarez O, Maroto-Morales A, Calvo JH, Serrano MM. Differences in the ovine HSP90AA1 gene expression rates caused by two linked polymorphisms at its promoter affect rams sperm DNA fragmentation under environmental heat stress conditions. PLoS One 2015; 10:e0116360. [PMID: 25671615 PMCID: PMC4324765 DOI: 10.1371/journal.pone.0116360] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/28/2014] [Indexed: 12/11/2022] Open
Abstract
Heat shock (HS) is one of the best-studied exogenous cellular stresses. Almost all tissues, cell types, metabolic pathways and biochemical reactions are affected in greater or lesser extent by HS. However, there are some especially thermo sensible cellular types such as the mammalian male germ cells. The present study examined the role of three INDELs in conjunction with the -660G/C polymorphism located at the HSP90AA1 promoter region over the gene expression rate under HS. Specially, the -668insC INDEL, which is very close to the -660G/C transversion, is a good candidate to be implied in the transcriptional regulation of the gene by itself or in a cooperative way with this SNP. Animals carrying the genotype II-668 showed higher transcription rates than those with ID-668 (FC = 3.07) and DD-668 (FC = 3.40) genotypes for samples collected under HS. A linkage between gene expression and sperm DNA fragmentation was also found. When HS conditions were present along or in some stages of the spermatogenesis, alternative genotypes of the -668insC and -660G/C mutations are involved in the effect of HS over sperm DNA fragmentation. Thus, unfavorable genotypes in terms of gene expression induction (ID-668GC-660 and DD-668GG-660) do not produce enough mRNA (stored as messenger ribonucleoprotein particles) and Hsp90α protein to cope with future thermal stress which might occur in posterior stages when transcriptional activity is reduced and cell types and molecular processes are more sensible to heat (spermatocytes in pachytene and spermatids protamination). This would result in the impairment of DNA packaging and the consequent commitment of the events occurring shortly after fertilization and during embryonic development. In the short-term, the assessment of the relationship between sperm DNA fragmentation sensitivity and ram’s fertility will be of interest to a better understanding of the mechanisms of response to HS and its consequences on animal production and reproduction performance.
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Affiliation(s)
| | - Manuel Ramón
- CERSYRA, Av. Del Vino 10, 13300, Valdepeñas, Spain
- * E-mail:
| | | | | | - J. Julián Garde
- SaBio IREC (CSIC–UCLM–JCCM) Campus Universitario S.N., 02071, Albacete, Spain
| | - Olga García-Álvarez
- SaBio IREC (CSIC–UCLM–JCCM) Campus Universitario S.N., 02071, Albacete, Spain
| | | | - Jorge H. Calvo
- Unidad de Tecnología en Producción Animal, CITA, 59059, Zaragoza, Spain
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Malhotra S, Sowdhamini R. Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes. Bioinform Biol Insights 2014; 8:193-8. [PMID: 25249757 PMCID: PMC4167486 DOI: 10.4137/bbi.s16313] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 12/23/2022] Open
Abstract
Plants are simultaneously subjected to a variety of stress conditions in the field and are known to combat the hostile conditions by up/down-regulating number of genes. There exists a significant level of cross-talk between different stress responses in plants. In this study, we predict the interacting pairs of transcription factors that regulate the multiple abiotic stress-responsive genes in the plant Arabidopsis thaliana. We identified the interacting pair(s) of transcription factors (TFs) based on the spatial proximity of their binding sites. We also examined the interactions between the predicted pairs of TFs using molecular docking. Subsequent to docking, the best interaction pose was selected using our scoring scheme DockScore, which ranks the docked solutions based on several interface parameters and aims to find optimal interactions between proteins. We analyzed the selected docked pose for the interface residues and their conservation.
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Affiliation(s)
- Sony Malhotra
- National Centre for Biological Sciences (TIFR), Bangalore, India
| | - R Sowdhamini
- National Centre for Biological Sciences (TIFR), Bangalore, India
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Hyper-inflammation and skin destruction mediated by rosiglitazone activation of macrophages in IL-6 deficiency. J Invest Dermatol 2014; 135:389-399. [PMID: 25184961 PMCID: PMC4291681 DOI: 10.1038/jid.2014.375] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 05/22/2014] [Accepted: 05/28/2014] [Indexed: 11/24/2022]
Abstract
Injury initiates recruitment of macrophages to support tissue repair; however, excessive macrophage activity may exacerbate tissue damage causing further destruction and subsequent delay in wound repair. Here we show that the peroxisome proliferation–activated receptor-γ agonist, rosiglitazone (Rosi), a medication recently reintroduced as a drug to treat diabetes and with known anti-inflammatory properties, paradoxically generates pro-inflammatory macrophages. This is observed in both IL-6-deficient mice and control wild-type mice experimentally induced to produce high titers of auto-antibodies against IL-6, mimicking IL-6 deficiency in human diseases. IL-6 deficiency when combined with Rosi-mediated upregulation of suppressor of cytokine signaling 3 leads to an altered ratio of nuclear signal transducer and activator of transcription 3/NF-κB that allows hyper-induction of inducible nitric oxide synthase (iNOS). Macrophages activated in this manner cause de novo tissue destruction, recapitulating human chronic wounds, and can be reversed in vivo by recombinant IL-6, blocking macrophage infiltration, or neutralizing iNOS. This study provides insight into an unanticipated paradoxical role of Rosi in mediating hyper-inflammatory macrophage activation significant for diseases associated with IL-6 deficiency.
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Yang Y, Boss IW, McIntyre LM, Renne R. A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells. BMC Genomics 2014; 15:668. [PMID: 25106478 PMCID: PMC4147158 DOI: 10.1186/1471-2164-15-668] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/01/2014] [Indexed: 01/01/2023] Open
Abstract
Background Kaposi’s sarcoma associated herpes virus (KSHV) is associated with tumors of endothelial and lymphoid origin. During latent infection, KSHV expresses miR-K12-11, an ortholog of the human tumor gene hsa-miR-155. Both gene products are microRNAs (miRNAs), which are important post-transcriptional regulators that contribute to tissue specific gene expression. Advances in target identification technologies and molecular interaction databases have allowed a systems biology approach to unravel the gene regulatory networks (GRNs) triggered by miR-K12-11 in endothelial and lymphoid cells. Understanding the tissue specific function of miR-K12-11 will help to elucidate underlying mechanisms of KSHV pathogenesis. Results Ectopic expression of miR-K12-11 differentially affected gene expression in BJAB cells of lymphoid origin and TIVE cells of endothelial origin. Direct miRNA targeting accounted for a small fraction of the observed transcriptome changes: only 29 genes were identified as putative direct targets of miR-K12-11 in both cell types. However, a number of commonly affected biological pathways, such as carbohydrate metabolism and interferon response related signaling, were revealed by gene ontology analysis. Integration of transcriptome profiling, bioinformatic algorithms, and databases of protein-protein interactome from the ENCODE project identified different nodes of GRNs utilized by miR-K12-11 in a tissue-specific fashion. These effector genes, including cancer associated transcription factors and signaling proteins, amplified the regulatory potential of a single miRNA, from a small set of putative direct targets to a larger set of genes. Conclusions This is the first comparative analysis of miRNA-K12-11’s effects in endothelial and B cells, from tissues infected with KSHV in vivo. MiR-K12-11 was able to broadly modulate gene expression in both cell types. Using a systems biology approach, we inferred that miR-K12-11 establishes its GRN by both repressing master TFs and influencing signaling pathways, to counter the host anti-viral response and to promote proliferation and survival of infected cells. The targeted GRNs are more reproducible and informative than target gene identification, and our approach can be applied to other regulatory factors of interest. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-668) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, 2033 Mowry Road, Gainesville, FL 32610, USA.
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Du W, Gao J, Wang T, Wang J. Single-nucleotide mutation matrix: a new model for predicting the NF-κB DNA binding sites. PLoS One 2014; 9:e101490. [PMID: 24992458 PMCID: PMC4081663 DOI: 10.1371/journal.pone.0101490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 06/09/2014] [Indexed: 11/18/2022] Open
Abstract
In this study, we established a single nucleotide mutation matrix (SNMM) model based on the relative binding affinities of NF-κB p50 homodimer to a wild-type binding site (GGGACTTTCC) and its all single-nucleotide mutants detected with the double-stranded DNA microarray. We evaluated this model by scoring different groups of 10-bp DNA sequences with this model and analyzing the correlations between the scores and the relative binding affinities detected with three wet experiments, including the electrophoresis mobility shift assay (EMSA), the protein-binding microarray (PBM) and the systematic evolution of ligands by exponential enrichment-sequencing (SELEX-Seq). The results revealed that the SNMM scores were strongly correlated with the detected binding affinities. We also scored the DNA sequences with other three models, including the principal coordinate (PC) model, the position weight matrix scoring algorithm (PWMSA) model and the Match model, and analyzed the correlations between the scores and the detected binding affinities. In comparison with these models, the SNMM model achieved reliable results. We finally determined 0.747 as the optimal threshold for predicting the NF-κB DNA-binding sites with the SNMM model. The SNMM model thus provides a new alternative model for scoring the relative binding affinities of NF-κB to the 10-bp DNA sequences and predicting the NF-κB DNA-binding sites.
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Affiliation(s)
- Wenxin Du
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Jing Gao
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Tingting Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
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Ma Q, Zhang H, Mao X, Zhou C, Liu B, Chen X, Xu Y. DMINDA: an integrated web server for DNA motif identification and analyses. Nucleic Acids Res 2014; 42:W12-9. [PMID: 24753419 PMCID: PMC4086085 DOI: 10.1093/nar/gku315] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DMINDA (DNA motif identification and
analyses) is an integrated web server for DNA motif identification
and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely
available to all users and there is no login requirement. This server provides a
suite of cis-regulatory motif analysis functions on DNA
sequences, which are important to elucidation of the mechanisms of
transcriptional regulation: (i) de novo motif finding for a
given set of promoter sequences along with statistical scores for the predicted
motifs derived based on information extracted from a control set, (ii) scanning
motif instances of a query motif in provided genomic sequences, (iii) motif
comparison and clustering of identified motifs, and (iv) co-occurrence analyses
of query motifs in given promoter sequences. The server is powered by a backend
computer cluster with over 150 computing nodes, and is particularly useful for
motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as
a new and comprehensive web server for cis-regulatory motif
finding and analyses, will benefit the genomic research community in general and
prokaryotic genome researchers in particular.
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Affiliation(s)
- Qin Ma
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Hanyuan Zhang
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens GA 30602, USA College of Computer Science and Technology, Jilin University, Changchun, China
| | - Xizeng Mao
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Chuan Zhou
- School of Mathematics, Shandong University, Jinan, Shandong, China
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, Shandong, China
| | - Xin Chen
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens GA 30602, USA College of Computer Science and Technology, Jilin University, Changchun, China
| | - Ying Xu
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA College of Computer Science and Technology, Jilin University, Changchun, China
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Vigneault F, Guérin SL. Regulation of gene expression: probing DNA–protein interactionsin vivoandin vitro. Expert Rev Proteomics 2014; 2:705-18. [PMID: 16209650 DOI: 10.1586/14789450.2.5.705] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Tremendous efforts have been put together over the last several years to complete the entire sequencing of the human genome. As we enter the proteomic era, when the major aim is understanding which gene encodes which protein, the time has also come to identify their precise function inside the astonishing signaling network required to accomplish all cellular functions. Understanding when, why and how a gene is expressed has now become a necessity toward identifying all the regulatory pathways that mediate cellular processes such as differentiation, migration, replication, DNA repair and apoptosis. Regulation of gene transcription is a process that is primarily under the influence of nuclear-located transcription factors. Consequently, identifying which protein activates or represses a specific gene is a prerequisite for understanding cell fate and function. The current state of, and recent advances in, transcriptional regulation approaches are reviewed here, with special emphasis on new technologies required when probing for DNA-protein interactions. This review explores different strategies aimed at identifying both the regulatory sequences of any given gene and the trans-acting regulatory factors that recognize these elements as their target sites in the nucleus. Ongoing developments in the fields of nanotechnology, RNA silencing and protein modeling toward the investigation of DNA-protein interactions and their relevance in the battle against cancer are discussed.
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Affiliation(s)
- Francois Vigneault
- Laboratoire d'Endocrinologie Moléculaire et Oncologique, Centre de recherche du CHUL (CHUQ), Sainte-Foy, Québec, G1V 4G2, Canada.
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Martínez-Hernández A, Gutierrez-Malacatt H, Carrillo-Sánchez K, Saldaña-Alvarez Y, Rojas-Ochoa A, Crespo-Solis E, Aguayo-González A, Rosas-López A, Ayala-Sanchez JM, Aquino-Ortega X, Orozco L, Cordova EJ. Small MAF genes variants and chronic myeloid leukemia. Eur J Haematol 2013; 92:35-41. [PMID: 24118457 DOI: 10.1111/ejh.12211] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2013] [Indexed: 12/18/2022]
Abstract
Chronic myeloid leukemia (CML) is one of the most frequent hematological neoplasia worldwide. The abnormal accumulation of reactive oxygen species may be an important factor in CML development. The transcription factor NRF2 can regulate the transcription of a battery of antioxidant and detoxificant genes after heterodimerizing with small-Maf proteins. Although the participation of NRF2 in the development of chronic degenerative diseases has been thoroughly studied, the role of small-Maf genes has not been documented. We have identified polymorphisms in the three MAF genes (F, G and K) and assessed their association with CML. Over 266 subjects with CML and 399 unrelated healthy donors have been studied. After sequencing each MAF gene by Sanger technology, we found 17 variants in MAFF gene, eight in MAFG and seven in MAFK. In the case-control study, the homozygote genotype CC for the rs9610915 SNP of MAFF was significantly associated with CML. The frequency of the ACC haplotype from MAFK was significantly lower than controls. After stratification by gender, the ACC and GTG haplotypes were associated only with males with CML. These novel data suggest an association between MAFF and MAFG and the development of CML.
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Affiliation(s)
- Angelica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, Instituto Nacional de Medicina Genómica, SS, México City, México
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Valaperti A, Nishii M, Liu Y, Naito K, Chan M, Zhang L, Skurk C, Schultheiss HP, Wells GA, Eriksson U, Liu PP. Innate immune interleukin-1 receptor-associated kinase 4 exacerbates viral myocarditis by reducing CCR5(+) CD11b(+) monocyte migration and impairing interferon production. Circulation 2013; 128:1542-54. [PMID: 24030499 DOI: 10.1161/circulationaha.113.002275] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Viral myocarditis follows a fatal course in ≈30% of patients. Interleukin-1 receptor-associated kinase 4 (IRAK4), a major nodal signal transducer in innate immunity, can play a pivotal role in host inflammatory response. We sought to determine how IRAK4 modulates inflammation and outcome in a mouse model of viral myocarditis. METHODS AND RESULTS Myocarditis was induced after intraperitoneal inoculation of coxsackievirus B3 into C57Bl/6 IRAK4-deficient mice and their littermate controls. Mortality and viral proliferation were markedly reduced in IRAK4(-/-) mice compared with their IRAK4(+/+) littermates. Disease resistance of IRAK4(-/-) mice paralleled increased amounts of protective heart-infiltrating CCR5(+) monocytes/macrophages and enhanced interferon-α and interferon-γ production 2 days after infection. Competitive bone marrow chimera demonstrated that intact IRAK4 function inhibited heart-specific migration of bone marrow-derived CCR5(+) cells. Mechanistically, lack of IRAK4 resulted in interferon regulatory factor 5 homodimerization via reduced melanoma differentiation-associated protein 5 degradation and enhanced Stat1 and Stat5 phosphorylation. Consequently, antiviral interferon-α and interferon-γ production, as well as CCR5(+) cell recruitment, increased, whereas the overall proinflammatory response was drastically reduced in the absence of IRAK4. CONCLUSIONS Innate immunity signal transducer IRAK4 exacerbates viral myocarditis through inhibition of interferon production and reduced mobilization of protective CCR5(+) monocytes/macrophages to the heart. The combination of IRAK4 inhibitors and antiviral adjuvants may become an attractive therapeutic approach against viral myocarditis in the future.
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Affiliation(s)
- Alan Valaperti
- Division of Cardiology, Heart and Stroke/Richard Lewar Centre of Excellence, Toronto General Research Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada (A.V., M.N., Y.L., K.N., M.C., L.Z., P.P.L.); University of Ottawa Heart Institute, University of Ottawa, Ottawa, Ontario, Canada (L.Z., G.A.W., P.P.L.); Department of Cardiology and Pneumology, Charité-University Medicine Berlin, Campus Benjamin Franklin, Berlin, Germany (C.S., H.S.); and Division of Cardioimmunology, Cardiovascular Research, Institute of Physiology and Center for Integrative Human Physiology, University of Zurich, Zurich, and Department of Medicine, GZO-Zurich Regional Health Centre, Wetzikon, Switzerland (U.E.)
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Mathelier A, Wasserman WW. The next generation of transcription factor binding site prediction. PLoS Comput Biol 2013; 9:e1003214. [PMID: 24039567 PMCID: PMC3764009 DOI: 10.1371/journal.pcbi.1003214] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 07/22/2013] [Indexed: 12/29/2022] Open
Abstract
Finding where transcription factors (TFs) bind to the DNA is of key importance to decipher gene regulation at a transcriptional level. Classically, computational prediction of TF binding sites (TFBSs) is based on basic position weight matrices (PWMs) which quantitatively score binding motifs based on the observed nucleotide patterns in a set of TFBSs for the corresponding TF. Such models make the strong assumption that each nucleotide participates independently in the corresponding DNA-protein interaction and do not account for flexible length motifs. We introduce transcription factor flexible models (TFFMs) to represent TF binding properties. Based on hidden Markov models, TFFMs are flexible, and can model both position interdependence within TFBSs and variable length motifs within a single dedicated framework. The availability of thousands of experimentally validated DNA-TF interaction sequences from ChIP-seq allows for the generation of models that perform as well as PWMs for stereotypical TFs and can improve performance for TFs with flexible binding characteristics. We present a new graphical representation of the motifs that convey properties of position interdependence. TFFMs have been assessed on ChIP-seq data sets coming from the ENCODE project, revealing that they can perform better than both PWMs and the dinucleotide weight matrix extension in discriminating ChIP-seq from background sequences. Under the assumption that ChIP-seq signal values are correlated with the affinity of the TF-DNA binding, we find that TFFM scores correlate with ChIP-seq peak signals. Moreover, using available TF-DNA affinity measurements for the Max TF, we demonstrate that TFFMs constructed from ChIP-seq data correlate with published experimentally measured DNA-binding affinities. Finally, TFFMs allow for the straightforward computation of an integrated TF occupancy score across a sequence. These results demonstrate the capacity of TFFMs to accurately model DNA-protein interactions, while providing a single unified framework suitable for the next generation of TFBS prediction.
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Affiliation(s)
- Anthony Mathelier
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wyeth W. Wasserman
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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LASAGNA-Search: an integrated web tool for transcription factor binding site search and visualization. Biotechniques 2013; 54:141-53. [PMID: 23599922 DOI: 10.2144/000113999] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The release of ChIP-seq data from the ENCyclopedia Of DNA Elements (ENCODE) and Model Organism ENCyclopedia Of DNA Elements (modENCODE) projects has significantly increased the amount of transcription factor (TF) binding affinity information available to researchers. However, scientists still routinely use TF binding site (TFBS) search tools to scan unannotated sequences for TFBSs, particularly when searching for lesser-known TFs or TFs in organisms for which ChIP-seq data are unavailable. The sequence analysis often involves multiple steps such as TF model collection, promoter sequence retrieval, and visualization; thus, several different tools are required. We have developed a novel integrated web tool named LASAGNA-Search that allows users to perform TFBS searches without leaving the web site. LASAGNA-Search uses the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm for TFBS alignment. Important features of LASAGNA-Search include (i) acceptance of unaligned variable-length TFBSs, (ii) a collection of 1726 TF models, (iii) automatic promoter sequence retrieval, (iv) visualization in the UCSC Genome Browser, and (v) gene regulatory network inference and visualization based on binding specificities. LASAGNA-Search is freely available at http://biogrid.engr.uconn.edu/lasagna_search/.
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Balko JM, Schwarz LJ, Bhola NE, Kurupi R, Owens P, Miller TW, Gómez H, Cook RS, Arteaga CL. Activation of MAPK pathways due to DUSP4 loss promotes cancer stem cell-like phenotypes in basal-like breast cancer. Cancer Res 2013; 73:6346-58. [PMID: 23966295 DOI: 10.1158/0008-5472.can-13-1385] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Basal-like breast cancer (BLBC) is an aggressive disease that lacks a clinically approved targeted therapy. Traditional chemotherapy is effective in BLBC, but it spares the cancer stem cell (CSC)-like population, which is likely to contribute to cancer recurrence after the initial treatment. Dual specificity phosphatase-4 (DUSP4) is a negative regulator of the mitogen-activated protein kinase (MAPK) pathway that is deficient in highly aggressive BLBCs treated with chemotherapy, leading to aberrant MAPK activation and resistance to taxane-induced apoptosis. Herein, we investigated how DUSP4 regulates the MAP-ERK kinase (MEK) and c-jun-NH2-kinase (JNK) pathways in modifying CSC-like behavior. DUSP4 loss increased mammosphere formation and the expression of the CSC-promoting cytokines interleukin (IL)-6 and IL-8. These effects were caused in part by loss of control of the MEK and JNK pathways and involved downstream activation of the ETS-1 and c-JUN transcription factors. Enforced expression of DUSP4 reduced the CD44(+)/CD24(-) population in multiple BLBC cell lines in a MEK-dependent manner, limiting tumor formation of claudin-low SUM159PT cells in mice. Our findings support the evaluation of MEK and JNK pathway inhibitors as therapeutic agents in BLBC to eliminate the CSC population.
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Affiliation(s)
- Justin M Balko
- Authors' Affiliations: Departments of Medicine and Cancer Biology; Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee; Instituto Nacional de Enfermedades Neoplásicas, Lima, Perú; and Department of Pharmacology and Toxicology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
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Abstract
RATIONALE MicroRNAs modestly suppress their direct mRNA targets, and these direct effects are amplified by modulation of gene transcription pathways. Consequently, indirect mRNA modulatory effects of microRNAs to increase or decrease mRNAs greatly outnumber direct target suppressions. Because microRNAs are products of transcription, the potential exists for microRNAs that regulate transcription to regulate other microRNAs. OBJECTIVE Determine whether cardiac-expressed microRNAs regulate expression of other cardiac microRNAs, and measure the impact of microRNA-mediated microRNA regulation on indirect regulation of nontarget mRNAs. METHODS AND RESULTS Transgenic expression of pre-microRNAs was used to generate mouse hearts expressing 6- to 16-fold normal levels of microRNA (miR)-143, miR-378, and miR-499. Genome-wide mRNA and microRNA signatures were established using deep sequencing; expression profiles provoked by each microRNA were defined. miR-143 suppressed its direct cardiac mRNA target hexokinase 2, but exhibited little indirect target regulation and did not regulate other cardiac microRNAs. Both miR-378 and miR-499 indirectly regulated hundreds of cardiac mRNAs and 15 to 30 cardiac microRNAs. MicroRNA overexpression did not alter normal processing of either transgenic or endogenous cardiac microRNAs, and microRNA-mediated regulation of other microRNAs encoded within parent genes occurred in tandem with parent mRNAs. MicroRNA regulation by miR-378 and miR-499 was stimulus specific, and contributed to observed mRNA downregulation. CONCLUSIONS MicroRNAs that modulate cardiac transcription can indirectly regulate other microRNAs. Transcriptional modulation by microRNAs, and microRNA-mediated microRNA regulation, help explain how small direct effects of microRNAs are amplified to generate striking phenotypes.
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Affiliation(s)
- Scot J Matkovich
- Department of Internal Medicine, Center for Pharmacogenomics, Washington University School of Medicine, St. Louis, MO 63110, USA
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Genome-wide DNA methylation analysis reveals a potential mechanism for the pathogenesis and development of uterine leiomyomas. PLoS One 2013; 8:e66632. [PMID: 23818951 PMCID: PMC3688587 DOI: 10.1371/journal.pone.0066632] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/09/2013] [Indexed: 02/03/2023] Open
Abstract
Background The pathogenesis of uterine leiomyomas, the most common benign tumor in women, remains unclear. Since acquired factors such as obesity, hypertension and early menarche place women at greater risk for uterine leiomyomas, uterine leiomyomas may be associated with epigenetic abnormalities that are caused by unfavorable environmental exposures. Principal Findings Profiles of genome-wide DNA methylation and mRNA expression were investigated in leiomyomas and in myometrium with and without leiomyomas. Profiles of DNA methylation and mRNA expression in the myometrium with and without leiomyomas were quite similar while those in leiomyomas were distinct. We identified 120 genes whose DNA methylation and mRNA expression patterns differed between leiomyomas and the adjacent myometrium. The biological relevance of the aberrantly methylated and expressed genes was cancer process, including IRS1 that is related to transformation, and collagen-related genes such as COL4A1, COL4A2 and COL6A3. We also detected 22 target genes of estrogen receptor (ER) alpha, including apoptosis-related genes, that have aberrant DNA methylation in the promoter, suggesting that the aberrant epigenetic regulation of ER alpha-target genes contributes to the aberrant response to estrogen. Conclusions Aberrant DNA methylation and its related transcriptional aberration were associated with cancer processes, which may represent a critical initial mechanism that triggers transformation of a single tumor stem cell that will eventually develop into a monoclonal leiomyoma tumor. The aberrant epigenetic regulation of ER alpha-target genes also may contribute to the aberrant response to estrogen, which is involved in the development of uterine leiomyomas after menarche.
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Patnala R, Clements J, Batra J. Candidate gene association studies: a comprehensive guide to useful in silico tools. BMC Genet 2013; 14:39. [PMID: 23656885 PMCID: PMC3655892 DOI: 10.1186/1471-2156-14-39] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 04/15/2013] [Indexed: 01/01/2023] Open
Abstract
The candidate gene approach has been a pioneer in the field of genetic epidemiology, identifying risk alleles and their association with clinical traits. With the advent of rapidly changing technology, there has been an explosion of in silico tools available to researchers, giving them fast, efficient resources and reliable strategies important to find casual gene variants for candidate or genome wide association studies (GWAS). In this review, following a description of candidate gene prioritisation, we summarise the approaches to single nucleotide polymorphism (SNP) prioritisation and discuss the tools available to assess functional relevance of the risk variant with consideration to its genomic location. The strategy and the tools discussed are applicable to any study investigating genetic risk factors associated with a particular disease. Some of the tools are also applicable for the functional validation of variants relevant to the era of GWAS and next generation sequencing (NGS).
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Affiliation(s)
- Radhika Patnala
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia
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Haider S, Pal R. Integrated analysis of transcriptomic and proteomic data. Curr Genomics 2013; 14:91-110. [PMID: 24082820 PMCID: PMC3637682 DOI: 10.2174/1389202911314020003] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 01/09/2013] [Accepted: 01/22/2013] [Indexed: 12/14/2022] Open
Abstract
Until recently, understanding the regulatory behavior of cells has been pursued through independent analysis of the transcriptome or the proteome. Based on the central dogma, it was generally assumed that there exist a direct correspondence between mRNA transcripts and generated protein expressions. However, recent studies have shown that the correlation between mRNA and Protein expressions can be low due to various factors such as different half lives and post transcription machinery. Thus, a joint analysis of the transcriptomic and proteomic data can provide useful insights that may not be deciphered from individual analysis of mRNA or protein expressions. This article reviews the existing major approaches for joint analysis of transcriptomic and proteomic data. We categorize the different approaches into eight main categories based on the initial algorithm and final analysis goal. We further present analogies with other domains and discuss the existing research problems in this area.
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Affiliation(s)
| | - Ranadip Pal
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX, 79409, USA
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Lee C, Huang CH. LASAGNA: a novel algorithm for transcription factor binding site alignment. BMC Bioinformatics 2013; 14:108. [PMID: 23522376 PMCID: PMC3747862 DOI: 10.1186/1471-2105-14-108] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 03/08/2013] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Scientists routinely scan DNA sequences for transcription factor (TF) binding sites (TFBSs). Most of the available tools rely on position-specific scoring matrices (PSSMs) constructed from aligned binding sites. Because of the resolutions of assays used to obtain TFBSs, databases such as TRANSFAC, ORegAnno and PAZAR store unaligned variable-length DNA segments containing binding sites of a TF. These DNA segments need to be aligned to build a PSSM. While the TRANSFAC database provides scoring matrices for TFs, nearly 78% of the TFs in the public release do not have matrices available. As work on TFBS alignment algorithms has been limited, it is highly desirable to have an alignment algorithm tailored to TFBSs. RESULTS We designed a novel algorithm named LASAGNA, which is aware of the lengths of input TFBSs and utilizes position dependence. Results on 189 TFs of 5 species in the TRANSFAC database showed that our method significantly outperformed ClustalW2 and MEME. We further compared a PSSM method dependent on LASAGNA to an alignment-free TFBS search method. Results on 89 TFs whose binding sites can be located in genomes showed that our method is significantly more precise at fixed recall rates. Finally, we described LASAGNA-ChIP, a more sophisticated version for ChIP (Chromatin immunoprecipitation) experiments. Under the one-per-sequence model, it showed comparable performance with MEME in discovering motifs in ChIP-seq peak sequences. CONCLUSIONS We conclude that the LASAGNA algorithm is simple and effective in aligning variable-length binding sites. It has been integrated into a user-friendly webtool for TFBS search and visualization called LASAGNA-Search. The tool currently stores precomputed PSSM models for 189 TFs and 133 TFs built from TFBSs in the TRANSFAC Public database (release 7.0) and the ORegAnno database (08Nov10 dump), respectively. The webtool is available at http://biogrid.engr.uconn.edu/lasagna_search/.
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Affiliation(s)
- Chih Lee
- Department of Computer Science and Engineering, University of Connecticut,
Fairfield Road, Storrs, CT 06269, USA
| | - Chun-Hsi Huang
- Department of Computer Science and Engineering, University of Connecticut,
Fairfield Road, Storrs, CT 06269, USA
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