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Chen C, Gao L, Ge H, Huang W, Zhao R, Gu R, Li Z, Wang X. A neural network model was constructed by screening the potential biomarkers of aortic dissection based on genes associated with pyroptosis. Aging (Albany NY) 2023; 15:12388-12399. [PMID: 37938149 PMCID: PMC10683593 DOI: 10.18632/aging.205187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/08/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Aortic dissection (AD) is one of the crucial and common cardiovascular diseases, and pyroptosis is a novel cell delivery mechanism that is probably involved in the pathogenesis of various cardiovascular diseases. However, no study has investigated the role of pyroptosis in AD. METHODS We obtained two AD datasets, GSE153434 and GSE190635, from the Gene Expression Omnibus database. The differential expression of AD-related genes was determined by differential analysis, and their enrichment analysis was performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Additionally, a protein-protein interaction network was established. Next, potential biomarkers were screened by Lasso regression analysis, and a neural network model was constructed. Finally, the potential biomarkers were validated by constructing a mouse model of AD. RESULTS A total of 1033 differentially expressed related genes were distinguished and these genes were mainly associated with the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) and mitogen-activated protein kinase signaling pathways. The Lasso regression results showed five potential biomarkers, namely platelet endothelial cell adhesion molecule-1 (PECAM1), caspase 4 (CASP4), mixed lineage kinase domain-like pseudokinase (MLKL), APAF1-interacting protein (APIP), and histone deacetylase 6 (HDAC6) and successfully constructed a neural network model to predict AD occurrence. The results showed that CASP4 and MLKL were highly expressed, whereas PECAM1 and HDAC6 were lowly expressed in AD samples, and no statistically significant difference was observed in APIP expression in AD samples. CONCLUSION Pyroptosis plays a crucial role in AD occurrence and development. Moreover, the five potential biomarkers identified in the present study can act as targets for the early diagnosis of AD in patients.
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Affiliation(s)
- Cheng Chen
- Department of Vascular Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213000, China
| | - Lulu Gao
- Department of Anesthesiology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213000, China
| | - Hongwei Ge
- Department of Vascular Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213000, China
| | - Weibin Huang
- Department of Vascular Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213000, China
| | - Rong Zhao
- Department of Cardiology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213000, China
| | - Renjun Gu
- School of Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Ziyun Li
- School of Acupuncture and Tuina, School of Regimen and Rehabilitation, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xin Wang
- Department of Vascular Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213000, China
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2
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Srivastava A, Singla DK. PTEN-AKT pathway attenuates apoptosis and adverse remodeling in ponatinib-induced skeletal muscle toxicity following BMP-7 treatment. Physiol Rep 2023; 11:e15629. [PMID: 36945866 PMCID: PMC10031244 DOI: 10.14814/phy2.15629] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 03/23/2023] Open
Abstract
Tyrosine kinase inhibitors (TKIs) including ponatinib are commonly used to treat cancer patients. Unfortunately, TKIs induce cardiac as well as skeletal muscle dysfunction as a side effect. Therefore, detailed mechanistic studies are required to understand its pathogenesis and to develop a therapeutic treatment. The current study was undertaken to examine whether ponatinib induces apoptosis and apoptotic mechanisms both in vitro and in vivo models and furthermore to test the potential of bone morphogenetic protein 7 (BMP-7) as a possible treatment option for its attenuation. Sol8 cells, a mouse myogenic cell line was exposed to ponatinib to generate an apoptotic cell culture model and were subsequently treated with BMP-7 to understand its protective effects. For the in vivo model, C57BL/6J mice were administered with ponatinib to understand apoptosis, cell signaling apoptotic mechanisms, and adverse muscle remodeling and its attenuation with BMP-7. TUNEL staining, immunohistochemistry (IHC), and real-time polymerase chain reaction (RT-PCR) methods were used. Our data show significantly (p < 0.05) increased TUNEL staining, caspase-3, BAX/Bcl2 ratio in the in vitro model. Furthermore, our in vivo muscle data show ponatinib-induced muscle myopathy, and loss in muscle function. The observed muscle myopathy was associated with increased apoptosis, caspase-3 staining, and BAX/Bcl-2 ratio as confirmed with IHC and RT-PCR. Furthermore, our data show a significant (p < 0.05) increase in the involvement of cell signaling apoptotic regulator protein PTEN and a decrease in cell survival protein AKT. These results suggest that increased apoptosis following ponatinib treatment showed an increase in skeletal muscle remodeling, sarcopenia, and fibrosis. Furthermore, BMP-7 treatment significantly (p < 0.05) attenuated ponatinib-induced apoptosis, BAX/Bcl2 ratio, decreased PTEN, and increased cell survival protein AKT, decreased adverse muscle remodeling, and improved muscle function. Overall, we provide evidence that ponatinib-induces apoptosis leading to sarcopenia and muscle myopathy with decreased function which was attenuated by BMP-7.
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Affiliation(s)
- Ayushi Srivastava
- Division of Metabolic and Cardiovascular Sciences, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Dinender K Singla
- Division of Metabolic and Cardiovascular Sciences, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
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3
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Caro-Consuegra R, Nieves-Colón MA, Rawls E, Rubin-de-Celis V, Lizárraga B, Vidaurre T, Sandoval K, Fejerman L, Stone AC, Moreno-Estrada A, Bosch E. Uncovering signals of positive selection in Peruvian populations from three ecological regions. Mol Biol Evol 2022; 39:6647595. [PMID: 35860855 PMCID: PMC9356722 DOI: 10.1093/molbev/msac158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Perú hosts extremely diverse ecosystems which can be broadly classified into three major ecoregions: the Pacific desert coast, the Andean highlands, and the Amazon rainforest. Since its initial peopling approximately 12,000 years ago, the populations inhabiting such ecoregions might have differentially adapted to their contrasting environmental pressures. Previous studies have described several candidate genes underlying adaptation to hypobaric hypoxia among Andean highlanders. However, the adaptive genetic diversity of coastal and rainforest populations has been less studied. Here, we gathered genome-wide SNP-array data from 286 Peruvians living across the three ecoregions and analysed signals of recent positive selection through population differentiation and haplotype-based selection scans. Among highland populations, we identify candidate genes related to cardiovascular function (TLL1, DUSP27, TBX5, PLXNA4, SGCD), to the Hypoxia-Inducible Factor pathway (TGFA, APIP), to skin pigmentation (MITF), as well as to glucose (GLIS3) and glycogen metabolism (PPP1R3C, GANC). In contrast, most signatures of adaptation in coastal and rainforest populations comprise candidate genes related to the immune system (including SIGLEC8, TRIM21, CD44 and ICAM1 in the coast; CBLB and PRDM1 in rainforest and the BRD2- HLA-DOA- HLA-DPA1 region in both), possibly as a result of strong pathogen-driven selection. This study identifies candidate genes related to human adaptation to the diverse environments of South America.
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Affiliation(s)
- Rocio Caro-Consuegra
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Maria A Nieves-Colón
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Erin Rawls
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Verónica Rubin-de-Celis
- Laboratorio de Genómica Molecular Evolutiva, Instituto de Ciencia y Tecnología, Universidad Ricardo Palma, Lima, Perú
| | - Beatriz Lizárraga
- Emeritus Professor, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | | | - Karla Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Laura Fejerman
- Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Elena Bosch
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
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4
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Tran PX, Inoue J, Harada H, Inazawa J. Potential for reversing miR-634-mediated cytoprotective processes to improve efficacy of chemotherapy against oral squamous cell carcinoma. Mol Ther Oncolytics 2022; 24:897-908. [PMID: 35571376 PMCID: PMC9073396 DOI: 10.1016/j.omto.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/11/2022] [Indexed: 01/04/2023] Open
Abstract
For advanced oral squamous cell carcinoma (OSCC), increasing sensitivity to chemotherapy is a major challenge in improving treatment outcomes, and targeting cytoprotective processes that lead to the chemotherapy resistance of cancer cells may be therapeutically promising. Tumor-suppressive microRNAs (miRNAs) can target multiple cancer-promoting genes concurrently and are thus expected to be useful seeds for cancer therapeutics. We revealed that miR-634-mediated targeting of multiple cytoprotective process-related genes, including cellular inhibitor of apoptosis protein 1 (cIAP1), can effectively increase cisplatin (CDDP)-induced cytotoxicity and overcome CDDP resistance in OSCC cells. The combination of topical treatment with miR-634 ointment and administration of CDDP was synergistically effective against OSCC tumor growth in a xenograft mouse model. Furthermore, the expression of miR-634 target genes is frequently upregulated in primary OSCC tumors. Our study suggests that reversing miR-634-mediated cytoprotective processes activated in cancer cells is a potentially useful strategy to improve CDDP efficacy against advanced OSCC.
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Affiliation(s)
- Phuong Xuan Tran
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Oral and Maxillofacial Surgery, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Jun Inoue
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hiroyuki Harada
- Department of Oral and Maxillofacial Surgery, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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5
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Wang N, Li R, Jia H, Xie H, Liu C, Jiang S, Zhang K, Lin P, Yu X. Apaf-1 interacting protein, a new target of microRNA-146a-3p, promotes prostate cancer cell development via the ERK1/2 pathway. Cell Biol Int 2022; 46:1156-1168. [PMID: 35293661 DOI: 10.1002/cbin.11796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/25/2022] [Accepted: 03/13/2022] [Indexed: 11/06/2022]
Abstract
The Apaf-1 interacting protein APIP, a ubiquitously expressed anti-apoptotic molecule, is aberrantly expressed and of great significance in various cancers. However, little is known regarding the potential value and underlying mechanisms of APIP in prostate cancer. Here, we demonstrated that APIP expression is significantly upregulated in prostate cancer cell lines. APIP overexpression promoted tumor cell proliferation and migration and induced ERK1/2 activation. Pharmacological inhibition of ERK1/2 signaling reversed APIP-induced increase in cell proliferation and migration induced by APIP overexpression. Expression of APIP was hampered by miR-146a-3p. A dual luciferase reporter gene assay identified the regulatory relationship between APIP and miR-146a-3p in prostate cancer, suggesting that APIP is a direct target of miR-146a-3p. miR-146a-3p reduced cell proliferation and migration in prostate cancer. Furthermore, miR-146a-3p inhibited ERK1/2 activation. Application of an ERK1/2 inhibitor reversed the increase in cell proliferation and migration induced by miR-146a-3p inhibition. In summary, this study focused on the role of APIP in regulating cell growth and migration, and proposes a theoretical basis for APIP as a promising biomarker in prostate cancer development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nan Wang
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, P.R. China
| | - Rou Li
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, P.R. China
| | - Huizhen Jia
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, P.R. China
| | - Hui Xie
- Teaching Experiment Center of Biotechnology, Harbin Medical University, Harbin, Heilongjiang, 150001, P.R. China
| | - Chi Liu
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, P.R. China
| | - Shan Jiang
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, P.R. China
| | - Ke Zhang
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, P.R. China
| | - Ping Lin
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, P.R. China
| | - Xiaoguang Yu
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, P.R. China
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6
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Inal Gültekin G, Timirci Kahraman Ö, Işbilen M, Durmuş S, Çakir T, Yaylim İ, Isbir T. Six potential biomarkers for bladder cancer: key proteins in cell-cycle division and apoptosis pathways. J Egypt Natl Canc Inst 2022; 34:54. [PMID: 36529823 PMCID: PMC9760318 DOI: 10.1186/s43046-022-00153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 09/23/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The bladder cancer (BC) pathology is caused by both exogenous environmental and endogenous molecular factors. Several genes have been implicated, but the molecular pathogenesis of BC and its subtypes remains debatable. The bioinformatic analysis evaluates high numbers of proteins in a single study, increasing the opportunity to identify possible biomarkers for disorders. METHODS The aim of this study is to identify biomarkers for the identification of BC using several bioinformatic analytical tools and methods. BC and normal samples were compared for each probeset with T test in GSE13507 and GSE37817 datasets, and statistical probesets were verified with GSE52519 and E-MTAB-1940 datasets. Differential gene expression, hierarchical clustering, gene ontology enrichment analysis, and heuristic online phenotype prediction algorithm methods were utilized. Statistically significant proteins were assessed in the Human Protein Atlas database. GSE13507 (6271 probesets) and GSE37817 (3267 probesets) data were significant after the extraction of probesets without gene annotation information. Common probesets in both datasets (2888) were further narrowed by analyzing the first 100 upregulated and downregulated probesets in BC samples. RESULTS Among the total 400 probesets, 68 were significant for both datasets with similar fold-change values (Pearson r: 0.995). Protein-protein interaction networks demonstrated strong interactions between CCNB1, BUB1B, and AURKB. The HPA database revealed similar protein expression levels for CKAP2L, AURKB, APIP, and LGALS3 both for BC and control samples. CONCLUSION This study disclosed six candidate biomarkers for the early diagnosis of BC. It is suggested that these candidate proteins be investigated in a wet lab to identify their functions in BC pathology and possible treatment approaches.
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Affiliation(s)
- Güldal Inal Gültekin
- grid.444283.d0000 0004 0371 5255Department of Physiology, Faculty of Medicine, Istanbul Okan University, Tepeören Campus, Tuzla, Istanbul, Turkey ,grid.9601.e0000 0001 2166 6619Department of Molecular Medicine, Istanbul University, Aziz Sancar Experimental Research Institute, Çapa, Istanbul, Turkey
| | - Özlem Timirci Kahraman
- grid.9601.e0000 0001 2166 6619Department of Molecular Medicine, Istanbul University, Aziz Sancar Experimental Research Institute, Çapa, Istanbul, Turkey
| | - Murat Işbilen
- grid.411117.30000 0004 0369 7552Department of Biostatistics and Bioinformatics, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Saliha Durmuş
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Kocaeli, Turkey
| | - Tunahan Çakir
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Kocaeli, Turkey
| | - İlhan Yaylim
- grid.9601.e0000 0001 2166 6619Department of Molecular Medicine, Istanbul University, Aziz Sancar Experimental Research Institute, Çapa, Istanbul, Turkey
| | - Turgay Isbir
- grid.32140.340000 0001 0744 4075Department of Molecular Medicine, Faculty of Medicine, Yeditepe University, Kayışdağı, Istanbul, Turkey
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7
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Liu L, Chen Y, Diao J, Luo L, Gao Z. Identification and Characterization of Novel circRNAs Involved in Muscle Growth of Blunt Snout Bream ( Megalobrama amblycephala). Int J Mol Sci 2021; 22:ijms221810056. [PMID: 34576220 PMCID: PMC8467684 DOI: 10.3390/ijms221810056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Circular RNAs (circRNAs), a novel class of endogenous RNAs, have been recognized to play important roles in the growth of animals. However, the regulatory mechanism of circRNAs on fish muscle growth is still unclear. In this study, we performed whole transcriptome analysis of skeletal muscles from two populations with different growth rates (fast-growing and slow-growing) of blunt snout bream (Megalobrama amblycephala), an important fish species for aquaculture. The selected circRNAs were validated by qPCR and Sanger sequencing. Pairs of circRNA–miRNA–mRNA networks were constructed with the predicted differentially expressed (DE) pairs, which revealed regulatory roles in muscle myogenesis and hypertrophy. As a result, a total of 445 circRNAs were identified, including 42 DE circRNAs between fast-growing (FG) and slow-growing (SG) groups. Many of these DE circRNAs were related with aminoglycan biosynthetic and metabolic processes, cytokinetic processes, and the adherens junction pathway. The functional prediction results showed that novel_circ_0001608 and novel_circ_0002886, competing to bind with dre-miR-153b-5p and dre-miR-124-6-5p, might act as competing endogenous RNAs (ceRNAs) to control MamblycephalaGene14755 (pik3r1) and MamblycephalaGene10444 (apip) level, respectively, thus playing an important regulatory role in muscle growth. Overall, these results will not only help us to further understand the novel RNA transcripts in M. amblycephala, but also provide new clues to investigate the potential mechanism of circRNAs regulating fish growth and muscle development.
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Affiliation(s)
- Lifang Liu
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Yulong Chen
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jinghan Diao
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Lifei Luo
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
- Correspondence: (L.L.); or (Z.G.); Tel.: +86-2787282113 (Z.G.); Fax: +86-2787282114 (Z.G.)
| | - Zexia Gao
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
- Correspondence: (L.L.); or (Z.G.); Tel.: +86-2787282113 (Z.G.); Fax: +86-2787282114 (Z.G.)
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8
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Wiklund L, Sharma A, Patnaik R, Muresanu DF, Sahib S, Tian ZR, Castellani RJ, Nozari A, Lafuente JV, Sharma HS. Upregulation of hemeoxygenase enzymes HO-1 and HO-2 following ischemia-reperfusion injury in connection with experimental cardiac arrest and cardiopulmonary resuscitation: Neuroprotective effects of methylene blue. PROGRESS IN BRAIN RESEARCH 2021; 265:317-375. [PMID: 34560924 DOI: 10.1016/bs.pbr.2021.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Oxidative stress plays an important role in neuronal injuries after cardiac arrest. Increased production of carbon monoxide (CO) by the enzyme hemeoxygenase (HO) in the brain is induced by the oxidative stress. HO is present in the CNS in two isoforms, namely the inducible HO-1 and the constitutive HO-2. Elevated levels of serum HO-1 occurs in cardiac arrest patients and upregulation of HO-1 in cardiac arrest is seen in the neurons. However, the role of HO-2 in cardiac arrest is not well known. In this review involvement of HO-1 and HO-2 enzymes in the porcine brain following cardiac arrest and resuscitation is discussed based on our own observations. In addition, neuroprotective role of methylene blue- an antioxidant dye on alterations in HO under in cardiac arrest is also presented. The biochemical findings of HO-1 and HO-2 enzymes using ELISA were further confirmed by immunocytochemical approach to localize selective regional alterations in cardiac arrest. Our observations are the first to show that cardiac arrest followed by successful cardiopulmonary resuscitation results in significant alteration in cerebral concentrations of HO-1 and HO-2 levels indicating a prominent role of CO in brain pathology and methylene blue during CPR followed by induced hypothermia leading to superior neuroprotection after return of spontaneous circulation (ROSC), not reported earlier.
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Affiliation(s)
- Lars Wiklund
- International Experimental Central Nervous System Injury & Repair (IECNSIR), Department of Surgical Sciences, Anesthesiology & Intensive Care Medicine, Uppsala University Hospital, Uppsala University, Uppsala, Sweden
| | - Aruna Sharma
- International Experimental Central Nervous System Injury & Repair (IECNSIR), Department of Surgical Sciences, Anesthesiology & Intensive Care Medicine, Uppsala University Hospital, Uppsala University, Uppsala, Sweden.
| | - Ranjana Patnaik
- Department of Biomaterials, School of Biomedical Engineering, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Dafin F Muresanu
- Department of Clinical Neurosciences, University of Medicine & Pharmacy, Cluj-Napoca, Romania; "RoNeuro" Institute for Neurological Research and Diagnostic, Cluj-Napoca, Romania
| | - Seaab Sahib
- Department of Chemistry & Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Z Ryan Tian
- Department of Chemistry & Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Rudy J Castellani
- Department of Pathology, University of Maryland, Baltimore, MD, United States
| | - Ala Nozari
- Anesthesiology & Intensive Care, Massachusetts General Hospital, Boston, MA, United States
| | - José Vicente Lafuente
- LaNCE, Department of Neuroscience, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
| | - Hari Shanker Sharma
- International Experimental Central Nervous System Injury & Repair (IECNSIR), Department of Surgical Sciences, Anesthesiology & Intensive Care Medicine, Uppsala University Hospital, Uppsala University, Uppsala, Sweden.
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9
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Contribution of Apaf-1 to the pathogenesis of cancer and neurodegenerative diseases. Biochimie 2021; 190:91-110. [PMID: 34298080 DOI: 10.1016/j.biochi.2021.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/24/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023]
Abstract
Deregulation of apoptosis is associated with various pathologies, such as neurodegenerative disorders at one end of the spectrum and cancer at the other end. Generally speaking, differentiated cells like cardiomyocytes, skeletal myocytes and neurons exhibit low levels of Apaf-1 (Apoptotic protease activating factor 1) protein suggesting that down-regulation of Apaf-1 is an important event contributing to the resistance of these cells to apoptosis. Nonetheless, upregulation of Apaf-1 has not emerged as a common phenomenon in pathologies associated with enhanced neuronal cell death, i.e., neurodegenerative diseases. In cancer, on the other hand, Apaf-1 downregulation is a common phenomenon, which occurs through various mechanisms including mRNA hyper-methylation, gene methylation, Apaf-1 localization in lipid rafts, inhibition by microRNAs, phosphorylation, and interaction with specific inhibitors. Due to the diversity of these mechanisms and involvement of other factors, defining the exact contribution of Apaf-1 to the development of cancer in general and neurodegenerative disorders, in particular, is complicated. The current review is an attempt to provide a comprehensive image of Apaf-1's contribution to the pathologies observed in cancer and neurodegenerative diseases with the emphasis on the therapeutic aspects of Apaf-1 as an important target in these pathologies.
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10
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Choudhary S, Burns SC, Mirsafian H, Li W, Vo DT, Qiao M, Lei X, Smith AD, Penalva LO. Genomic analyses of early responses to radiation inglioblastoma reveal new alterations at transcription,splicing, and translation levels. Sci Rep 2020; 10:8979. [PMID: 32488114 PMCID: PMC7265345 DOI: 10.1038/s41598-020-65638-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/05/2020] [Indexed: 12/20/2022] Open
Abstract
High-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance is a common problem and a major contributor to tumor relapse. Understanding the molecular mechanisms driving response to radiation is critical for identifying regulatory routes that could be targeted to improve treatment response. We conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation. Changes at the transcriptional level were the most prevalent response. Downregulated genes are strongly associated with cell cycle and DNA replication and linked to a coordinated module of expression. Alterations in this group are likely driven by decreased expression of the transcription factor FOXM1 and members of the E2F family. Genes involved in RNA regulatory mechanisms were affected at the mRNA, splicing, and translation levels, highlighting their importance in radiation-response. We identified a number of oncogenic factors, with an increased expression upon radiation exposure, including BCL6, RRM2B, IDO1, FTH1, APIP, and LRIG2 and lncRNAs NEAT1 and FTX. Several of these targets have been previously implicated in radio-resistance. Therefore, antagonizing their effects post-radiation could increase therapeutic efficacy. Our integrated analysis provides a comprehensive view of early response to radiation in glioblastoma. We identify new biological processes involved in altered expression of various oncogenic factors and suggest new target options to increase radiation sensitivity and prevent relapse.
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Affiliation(s)
- Saket Choudhary
- Computational Biology and Bioinformatics, University of Southern California, California, USA
| | - Suzanne C Burns
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Hoda Mirsafian
- Computational Biology and Bioinformatics, University of Southern California, California, USA
| | - Wenzheng Li
- Computational Biology and Bioinformatics, University of Southern California, California, USA
| | - Dat T Vo
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Texas, USA
| | - Mei Qiao
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Xiufen Lei
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Andrew D Smith
- Computational Biology and Bioinformatics, University of Southern California, California, USA
| | - Luiz O Penalva
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA.
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, Texas, USA.
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11
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Cullin-4B E3 ubiquitin ligase mediates Apaf-1 ubiquitination to regulate caspase-9 activity. PLoS One 2019; 14:e0219782. [PMID: 31329620 PMCID: PMC6645535 DOI: 10.1371/journal.pone.0219782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/01/2019] [Indexed: 11/25/2022] Open
Abstract
Apoptotic protease-activating factor 1 (Apaf-1) is a component of apoptosome, which regulates caspase-9 activity. In addition to apoptosis, Apaf-1 plays critical roles in the intra-S-phase checkpoint; therefore, impaired expression of Apaf-1 has been demonstrated in chemotherapy-resistant malignant melanoma and nuclear translocation of Apaf-1 has represented a favorable prognosis of patients with non-small cell lung cancer. In contrast, increased levels of Apaf-1 protein are observed in the brain in Huntington’s disease. The regulation of Apaf-1 protein is not yet fully understood. In this study, we show that etoposide triggers the interaction of Apaf-1 with Cullin-4B, resulting in enhanced Apaf-1 ubiquitination. Ubiquitinated Apaf-1, which was degraded in healthy cells, binds p62 and forms aggregates in the cytosol. This complex of ubiquitinated Apaf-1 and p62 induces caspase-9 activation following MG132 treatment of HEK293T cells that stably express bcl-xl. These results show that ubiquitinated Apaf-1 may activate caspase-9 under conditions of proteasome impairment.
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12
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Cardioprotective role of APIP in myocardial infarction through ADORA2B. Cell Death Dis 2019; 10:511. [PMID: 31263105 PMCID: PMC6602929 DOI: 10.1038/s41419-019-1746-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/19/2022]
Abstract
In ischemic human hearts, the induction of adenosine receptor A2B (ADORA2B) is associated with cardioprotection against ischemic heart damage, but the mechanism underlying this association remains unclear. Apaf-1-interacting protein (APIP) and ADORA2B transcript levels in human hearts are substantially higher in patients with heart failure than in controls. Interestingly, the APIP and ADORA2B mRNA levels are highly correlated with each other (R = 0.912). APIP expression was significantly increased in primary neonatal cardiomyocytes under hypoxic conditions and this induction reduced myocardial cell death via the activation of the AKT-HIF1α pathway. Accordingly, infarct sizes of APIP transgenic mice after left anterior descending artery ligation were significantly reduced compared to those of wild-type mice. Strikingly, knockdown of APIP expression impaired the cytoprotective effects of ADORA2B during hypoxic damage. Immunoprecipitation and proximity ligation assays revealed that APIP interacts with ADORA2B, leading to the stabilization of both proteins by interfering with lysosomal degradation, and to the activation of the downstream PKA-CREB signaling pathways. ADORA2B levels in the hearts of APIPTg/Tg, APIPTg/+, and Apip+/- mice were proportionally downregulated. In addition, ADORA2B D296G derived from the rs200741295 polymorphism failed to bind to APIP and did not exert cardioprotective activity during hypoxia. Moreover, Adora2b D296G knock-in mice were more vulnerable than control mice to myocardial infarction and intentional increases in APIP levels overcame the defective protection of the ADORA2B SNP against ischemic injury. Collectively, APIP is crucial for cardioprotection against myocardial infarction by virtue of binding to and stabilizing ADORA2B, thereby dampening ischemic heart injury.
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13
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Tong H, Miyake Y, Mi-ichi F, Iwakura Y, Hara H, Yoshida H. Apaf1 plays a negative regulatory role in T cell responses by suppressing activation of antigen-stimulated T cells. PLoS One 2018; 13:e0195119. [PMID: 29596528 PMCID: PMC5875858 DOI: 10.1371/journal.pone.0195119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 03/17/2018] [Indexed: 01/10/2023] Open
Abstract
Apaf1 is a critical component of the apoptosome and initiates apoptosis downstream mitochondrial damages. Although the importance of Apaf1 in embryonic development was shown, the role of Apaf1 in immune responses, especially T cell responses, has yet to be elucidated. We generated T cell-specific Apaf1-deficient mice (Lck-Cre-Apaf1f/f mice) and examined the antigen-specific delayed-type hypersensitivity (DTH). Lck-Cre-Apaf1f/f mice exhibited exacerbation of DTH responses as compared with Apaf1-sufficient control mice. In Lck-Cre-Apaf1f/f mice, antigen-specific T cells proliferated more, and produced more inflammatory cytokines than control T cells. Apaf1-deficient T cells from antigen-immunized mice showed higher percentages of activation phenotypes upon restimulation in vitro. Apaf1-deficient T cells from naive (non-immunized) mice also showed higher proliferation activity and cytokine production over control cells. The impact of Apaf1-deficiency in T cells, however, was not restored by a pan-caspase inhibitor, suggesting that the role of Apaf1 in T cell responses was caspase-independent/non-apoptotic. These data collectively demonstrated that Apaf1 is a negative regulator of T cell responses and implicated Apaf1 as a potential target for immunosuppressive drug discovery.
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Affiliation(s)
- Honglian Tong
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Yasunobu Miyake
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Fumika Mi-ichi
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Yoichiro Iwakura
- Center for Experimental Animal Models, Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Hiromitsu Hara
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Hiroki Yoshida
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
- * E-mail:
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14
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Wang SH, Cheng CY, Chen CJ, Chan HL, Chen HH, Tang PC, Chen CF, Lee YP, Huang SY. Acute Heat Stress Changes Protein Expression in the Testes of a Broiler-Type Strain of Taiwan Country Chickens. Anim Biotechnol 2018; 30:129-145. [PMID: 29553885 DOI: 10.1080/10495398.2018.1446972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Heat stress leads to decreased fertility in roosters. This study investigated the global protein expression in response to acute heat stress in the testes of a broiler-type strain of Taiwan country chickens (TCCs). Twelve 45-week-old roosters were randomly allocated to the control group maintained at 25°C, and three groups subjected to acute heat stress at 38°C for 4 h, with 0, 2, and 6 h of recovery, respectively. Testis samples were collected for hematoxylin and eosin staining, apoptosis assay, and protein analysis. The results revealed 101 protein spots that differed significantly from the control following exposure to acute heat stress. The proteins that were differentially expressed participated mainly in protein metabolism and other metabolic processes, responses to stimuli, apoptosis, cellular organization, and spermatogenesis. Proteins that negatively regulate apoptosis were downregulated and proteins involved in autophagy and major heat shock proteins (HSP90α, HSPA5, and HSPA8) were upregulated in the testes of heat-stressed chickens. In conclusion, acute heat stress causes a change in protein expression in the testes of broiler-type B strain TCCs and may thus impair cell morphology, spermatogenesis, and apoptosis. The expression of heat shock proteins increased to attenuate the testicular injury induced by acute heat stress.
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Affiliation(s)
- Shih-Han Wang
- a Department of Animal Science , National Chung Hsing University , Taichung , Taiwan
| | - Chuen-Yu Cheng
- a Department of Animal Science , National Chung Hsing University , Taichung , Taiwan
| | - Chao-Jung Chen
- b Proteomics Core Laboratory, Department of Medical Research , China Medical University Hospital , Taichung , Taiwan.,c Graduate Institute of Integrated Medicine , China Medical University , Taichung , Taiwan
| | - Hong-Lin Chan
- d Institute of Bioinformatics and Structural Biology , National Tsing Hua University , Hsinchu , Taiwan.,e Department of Medical Sciences , National Tsing Hua University , Hsinchu , Taiwan
| | - Hsin-Hsin Chen
- a Department of Animal Science , National Chung Hsing University , Taichung , Taiwan
| | - Pin-Chi Tang
- a Department of Animal Science , National Chung Hsing University , Taichung , Taiwan.,f Agricultural Biotechnology Center , National Chung Hsing University , Taichung , Taiwan.,g Center for the Integrative and Evolutionary Galliformes Genomics, iEGG Center , National Chung Hsing University , Taichung , Taiwan
| | - Chih-Feng Chen
- a Department of Animal Science , National Chung Hsing University , Taichung , Taiwan.,f Agricultural Biotechnology Center , National Chung Hsing University , Taichung , Taiwan.,g Center for the Integrative and Evolutionary Galliformes Genomics, iEGG Center , National Chung Hsing University , Taichung , Taiwan
| | - Yen-Pai Lee
- a Department of Animal Science , National Chung Hsing University , Taichung , Taiwan
| | - San-Yuan Huang
- a Department of Animal Science , National Chung Hsing University , Taichung , Taiwan.,f Agricultural Biotechnology Center , National Chung Hsing University , Taichung , Taiwan.,g Center for the Integrative and Evolutionary Galliformes Genomics, iEGG Center , National Chung Hsing University , Taichung , Taiwan.,h Research Center for Sustainable Energy and Nanotechnology , National Chung Hsing University , Taichung , Taiwan
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15
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Hong SH, Lee WJ, Kim YD, Kim H, Jeon YJ, Lim B, Cho DH, Heo WD, Yang DH, Kim CY, Yang HK, Yang JK, Jung YK. APIP, an ERBB3-binding partner, stimulates erbB2-3 heterodimer formation to promote tumorigenesis. Oncotarget 2017; 7:21601-17. [PMID: 26942872 PMCID: PMC5008309 DOI: 10.18632/oncotarget.7802] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/20/2016] [Indexed: 01/07/2023] Open
Abstract
Despite the fact that the epidermal growth factor (EGF) family member ERBB3 (HER3) is deregulated in many cancers, the list of ERBB3-interacting partners remains limited. Here, we report that the Apaf-1-interacting protein (APIP) stimulates heregulin-β1 (HRG-β1)/ERBB3-driven cell proliferation and tumorigenesis. APIP levels are frequently increased in human gastric cancers and gastric cancer-derived cells. Cell proliferation and tumor formation are repressed by APIP downregulation and stimulated by its overexpression. APIP's role in the ERBB3 pathway is not associated with its functions within the methionine salvage pathway. In response to HRG-β1, APIP binds to the ERBB3 receptor, leading to an enhanced binding of ERBB3 and ERBB2 that results in sustained activations of ERK1/2 and AKT protein kinases. Furthermore, HRG-β1/ERBB3-dependent signaling is gained in APIP transgenic mouse embryonic fibroblasts (MEFs), but not lost in Apip−/− MEFs. Our findings offer compelling evidence that APIP plays an essential role in ERBB3 signaling as a positive regulator for tumorigenesis, warranting future development of therapeutic strategies for ERBB3-driven gastric cancer.
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Affiliation(s)
- Se-Hoon Hong
- School of Biological Science, Seoul National University, Gwanak-gu, Seoul 151-747, Korea
| | - Won Jae Lee
- School of Biological Science, Seoul National University, Gwanak-gu, Seoul 151-747, Korea
| | - Young Doo Kim
- School of Biological Science, Seoul National University, Gwanak-gu, Seoul 151-747, Korea
| | - Hyunjoo Kim
- School of Biological Science, Seoul National University, Gwanak-gu, Seoul 151-747, Korea
| | - Young-Jun Jeon
- School of Biological Science, Seoul National University, Gwanak-gu, Seoul 151-747, Korea
| | - Bitna Lim
- School of Biological Science, Seoul National University, Gwanak-gu, Seoul 151-747, Korea
| | - Dong-Hyung Cho
- Graduate School of East-West Medical Science, Kyung Hee University, Gyeoggi-Do 446-701, Korea
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Doo-Hyun Yang
- Department of Surgery, Chonbuk National University Medical School, Jeonju 561-180, Korea
| | - Chan-Young Kim
- Department of Surgery, Chonbuk National University Medical School, Jeonju 561-180, Korea
| | - Han-Kwang Yang
- Department of Surgery, Seoul National University College of Medicine, Seoul 110-744, Korea
| | - Jin Kuk Yang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 156-743, Korea
| | - Yong-Keun Jung
- School of Biological Science, Seoul National University, Gwanak-gu, Seoul 151-747, Korea
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16
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Vaccinia Virus Encodes a Novel Inhibitor of Apoptosis That Associates with the Apoptosome. J Virol 2017; 91:JVI.01385-17. [PMID: 28904196 DOI: 10.1128/jvi.01385-17] [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] [Received: 08/11/2017] [Accepted: 09/08/2017] [Indexed: 12/29/2022] Open
Abstract
Apoptosis is an important antiviral host defense mechanism. Here we report the identification of a novel apoptosis inhibitor encoded by the vaccinia virus (VACV) M1L gene. M1L is absent in the attenuated modified vaccinia virus Ankara (MVA) strain of VACV, a strain that stimulates apoptosis in several types of immune cells. M1 expression increased the viability of MVA-infected THP-1 and Jurkat cells and reduced several biochemical hallmarks of apoptosis, such as PARP-1 and procaspase-3 cleavage. Furthermore, ectopic M1L expression decreased staurosporine-induced (intrinsic) apoptosis in HeLa cells. We then identified the molecular basis for M1 inhibitory function. M1 allowed mitochondrial depolarization but blocked procaspase-9 processing, suggesting that M1 targeted the apoptosome. In support of this model, we found that M1 promoted survival in Saccharomyces cerevisiae overexpressing human Apaf-1 and procaspase-9, critical components of the apoptosome, or overexpressing only conformationally active caspase-9. In mammalian cells, M1 coimmunoprecipitated with Apaf-1-procaspase-9 complexes. The current model is that M1 associates with and allows the formation of the apoptosome but prevents apoptotic functions of the apoptosome. The M1 protein features 14 predicted ankyrin (ANK) repeat domains, and M1 is the first ANK-containing protein reported to use this inhibitory strategy. Since ANK-containing proteins are encoded by many large DNA viruses and found in all domains of life, studies of M1 may lead to a better understanding of the roles of ANK proteins in virus-host interactions.IMPORTANCE Apoptosis selectively eliminates dangerous cells such as virus-infected cells. Poxviruses express apoptosis antagonists to neutralize this antiviral host defense. The vaccinia virus (VACV) M1 ankyrin (ANK) protein, a protein with no previously ascribed function, inhibits apoptosis. M1 interacts with the apoptosome and prevents procaspase-9 processing as well as downstream procaspase-3 cleavage in several cell types and under multiple conditions. M1 is the first poxviral protein reported to associate with and prevent the function of the apoptosome, giving a more detailed picture of the threats VACV encounters during infection. Dysregulation of apoptosis is associated with several human diseases. One potential treatment of apoptosis-related diseases is through the use of designed ANK repeat proteins (DARPins), similar to M1, as caspase inhibitors. Thus, the study of the novel antiapoptosis effects of M1 via apoptosome association will be helpful for understanding how to control apoptosis using either natural or synthetic molecules.
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17
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Stolzenburg LR, Yang R, Kerschner JL, Fossum S, Xu M, Hoffmann A, Lamar KM, Ghosh S, Wachtel S, Leir SH, Harris A. Regulatory dynamics of 11p13 suggest a role for EHF in modifying CF lung disease severity. Nucleic Acids Res 2017; 45:8773-8784. [PMID: 28549169 PMCID: PMC5587731 DOI: 10.1093/nar/gkx482] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/01/2017] [Accepted: 05/17/2017] [Indexed: 02/02/2023] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), but are not good predictors of lung phenotype. Genome-wide association studies (GWAS) previously identified additional genomic sites associated with CF lung disease severity. One of these, at chromosome 11p13, is an intergenic region between Ets homologous factor (EHF) and Apaf-1 interacting protein (APIP). Our goal was to determine the functional significance of this region, which being intergenic is probably regulatory. To identify cis-acting elements, we used DNase-seq and H3K4me1 and H3K27Ac ChIP-seq to map open and active chromatin respectively, in lung epithelial cells. Two elements showed strong enhancer activity for the promoters of EHF and the 5' adjacent gene E47 like ETS transcription factor 5 (ELF5) in reporter gene assays. No enhancers of the APIP promoter were found. Circular chromosome conformation capture (4C-seq) identified direct physical interactions of elements within 11p13. This confirmed the enhancer-promoter associations, identified additional interacting elements and defined topologically associating domain (TAD) boundaries, enriched for CCCTC-binding factor (CTCF). No strong interactions were observed with the APIP promoter, which lies outside the main TAD encompassing the GWAS signal. These results focus attention on the role of EHF in modifying CF lung disease severity.
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Affiliation(s)
- Lindsay R. Stolzenburg
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rui Yang
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jenny L. Kerschner
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, USA
| | - Sara Fossum
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Matthew Xu
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew Hoffmann
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kay-Marie Lamar
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, USA
| | - Sujana Ghosh
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sarah Wachtel
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shih-Hsing Leir
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, USA
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, USA
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18
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Ijiri M, Fujiya M, Konishi H, Tanaka H, Ueno N, Kashima S, Moriichi K, Sasajima J, Ikuta K, Okumura T. Ferrichrome identified from Lactobacillus casei ATCC334 induces apoptosis through its iron-binding site in gastric cancer cells. Tumour Biol 2017. [PMID: 28639907 DOI: 10.1177/1010428317711311] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ferrichrome is known to be a siderophore, but it was recently identified as a tumor-suppressive molecule derived from Lactobacillus casei ATCC334 ( L. casei). In the present study, we investigated the effects of ferrichrome in gastric cancer cells. Cell lines and xenograft models treated with ferrichrome demonstrated growth suppression. The expression levels of cleaved poly (adenosine diphosphate-ribose) polymerase, and cleaved caspase-9 were increased by ferrichrome treatment. Although the tumor-suppressive effects of ferrichrome were almost completely diminished by the iron chelation, the reduction in the intracellular iron by ferrichrome did not correlate with its tumor-suppressive effects. An exhaustive docking simulation indicated that iron-free ferrichrome can make stable conformations with various mammalian molecules, including transporters and receptors. In conclusion, probiotic-derived ferrichrome induced apoptosis in gastric cancer cells. The iron binding site of ferrichrome is the structure responsible for its tumor suppressive function.
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Affiliation(s)
- Masami Ijiri
- 1 Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Mikihiro Fujiya
- 1 Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Hiroaki Konishi
- 1 Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Hiroki Tanaka
- 2 Department of Legal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Nobuhiro Ueno
- 1 Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Shin Kashima
- 1 Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Kentaro Moriichi
- 1 Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Junpei Sasajima
- 1 Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Katsuya Ikuta
- 1 Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Toshikatsu Okumura
- 1 Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
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19
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Scott EY, Penedo MCT, Murray JD, Finno CJ. Defining Trends in Global Gene Expression in Arabian Horses with Cerebellar Abiotrophy. CEREBELLUM (LONDON, ENGLAND) 2017; 16:462-472. [PMID: 27709457 PMCID: PMC5336519 DOI: 10.1007/s12311-016-0823-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Equine cerebellar abiotrophy (CA) is a hereditary neurodegenerative disease that affects the Purkinje neurons of the cerebellum and causes ataxia in Arabian foals. Signs of CA are typically first recognized either at birth to any time up to 6 months of age. CA is inherited as an autosomal recessive trait and is associated with a single nucleotide polymorphism (SNP) on equine chromosome 2 (13074277G>A), located in the fourth exon of TOE1 and in proximity to MUTYH on the antisense strand. We hypothesize that unraveling the functional consequences of the CA SNP using RNA-seq will elucidate the molecular pathways underlying the CA phenotype. RNA-seq (100 bp PE strand-specific) was performed in cerebellar tissue from four CA-affected and five age-matched unaffected horses. Three pipelines for differential gene expression (DE) analysis were used (Tophat2/Cuffdiff2, Kallisto/EdgeR, and Kallisto/Sleuth) with 151 significant DE genes identified by all three pipelines in CA-affected horses. TOE1 (Log2(foldchange) = 0.92, p = 0.66) and MUTYH (Log2(foldchange) = 1.13, p = 0.66) were not differentially expressed. Among the major pathways that were differentially expressed, genes associated with calcium homeostasis and specifically expressed in Purkinje neurons, CALB1 (Log2(foldchange) = -1.7, p < 0.01) and CA8 (Log2(foldchange) = -0.97, p < 0.01), were significantly down-regulated, confirming loss of Purkinje neurons. There was also a significant up-regulation of markers for microglial phagocytosis, TYROBP (Log2(foldchange) = 1.99, p < 0.01) and TREM2 (Log2(foldchange) = 2.02, p < 0.01). These findings reaffirm a loss of Purkinje neurons in CA-affected horses along with a potential secondary loss of granular neurons and activation of microglial cells.
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Affiliation(s)
- E Y Scott
- Department of Animal Science, University of California, Davis, USA
| | - M C T Penedo
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, USA
| | - J D Murray
- Department of Animal Science, University of California, Davis, USA.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, USA.
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, USA.
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Bryant AE, Aldape MJ, Bayer CR, Katahira EJ, Bond L, Nicora CD, Fillmore TL, Clauss TRW, Metz TO, Webb-Robertson BJ, Stevens DL. Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study. PLoS One 2017; 12:e0172486. [PMID: 28245256 PMCID: PMC5330483 DOI: 10.1371/journal.pone.0172486] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Acute muscle injuries are exceedingly common and non-steroidal anti-inflammatory drugs (NSAIDs) are widely consumed to reduce the associated inflammation, swelling and pain that peak 1-2 days post-injury. While prophylactic use or early administration of NSAIDs has been shown to delay muscle regeneration and contribute to loss of muscle strength after healing, little is known about the effects of delayed NSAID use. Further, NSAID use following non-penetrating injury has been associated with increased risk and severity of infection, including that due to group A streptococcus, though the mechanisms remain to be elucidated. The present study investigated the effects of delayed NSAID administration on muscle repair and sought mechanisms supporting an injury/NSAID/infection axis. METHODS A murine model of eccentric contraction (EC)-induced injury of the tibialis anterior muscle was used to profile the cellular and molecular changes induced by ketorolac tromethamine administered 47 hr post injury. RESULTS NSAID administration inhibited several important muscle regeneration processes and down-regulated multiple cytoprotective proteins known to inhibit the intrinsic pathway of programmed cell death. These activities were associated with increased caspase activity in injured muscles but were independent of any NSAID effect on macrophage influx or phenotype switching. CONCLUSIONS These findings provide new molecular evidence supporting the notion that NSAIDs have a direct negative influence on muscle repair after acute strain injury in mice and thus add to renewed concern about the safety and benefits of NSAIDS in both children and adults, in those with progressive loss of muscle mass such as the elderly or patients with cancer or AIDS, and those at risk of secondary infection after trauma or surgery.
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Affiliation(s)
- Amy E. Bryant
- U.S. Department of Veterans Affairs, Office of Research and Development, Boise, ID, United States of America
- University of Washington School of Medicine, Seattle, WA, United States of America
| | - Michael J. Aldape
- U.S. Department of Veterans Affairs, Office of Research and Development, Boise, ID, United States of America
- Northwest Nazarene University, Nampa, ID, United States of America
| | - Clifford R. Bayer
- U.S. Department of Veterans Affairs, Office of Research and Development, Boise, ID, United States of America
| | - Eva J. Katahira
- U.S. Department of Veterans Affairs, Office of Research and Development, Boise, ID, United States of America
| | - Laura Bond
- Boise State University, Boise, ID, United States of America
| | - Carrie D. Nicora
- Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Thomas L. Fillmore
- Pacific Northwest National Laboratory, Richland, WA, United States of America
| | | | - Thomas O. Metz
- Pacific Northwest National Laboratory, Richland, WA, United States of America
| | | | - Dennis L. Stevens
- U.S. Department of Veterans Affairs, Office of Research and Development, Boise, ID, United States of America
- University of Washington School of Medicine, Seattle, WA, United States of America
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Shakeri R, Kheirollahi A, Davoodi J. Apaf-1: Regulation and function in cell death. Biochimie 2017; 135:111-125. [PMID: 28192157 DOI: 10.1016/j.biochi.2017.02.001] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 01/08/2023]
Abstract
Apoptosis, a form of programmed cell death, is responsible for eliminating damaged or unnecessary cells in multicellular organisms. Various types of intracellular stress trigger apoptosis by induction of cytochrome c release from mitochondria into the cytosol. Apoptotic protease activating factor-1 (Apaf-1) is a key molecule in the intrinsic or mitochondrial pathway of apoptosis, which oligomerizes in response to cytochrome c release and forms a large complex known as apoptosome. Procaspase-9, an initiator caspase in the mitochondrial pathway, is recruited and activated by the apoptosome leading to downstream caspase-3 processing. Various cellular proteins and small molecules can modulate apoptosome formation and function directly or indirectly. Despite recent progress in understanding the mitochondrial pathway of apoptosis, numerous questions such as the molecular mechanism of Apaf-1 oligomerization and caspase-9 activation remain poorly understood. In addition, reports have emerged showing non-apoptotic functions for Apaf-1. The current review summarizes the latest findings regarding structure-function relationship of Apaf-1 as well as its modifiers.
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Affiliation(s)
- Raheleh Shakeri
- Department of Biological Science and Biotechnology, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Asma Kheirollahi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Science, Tehran, Iran
| | - Jamshid Davoodi
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran.
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22
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Novel variation at chr11p13 associated with cystic fibrosis lung disease severity. Hum Genome Var 2016; 3:16020. [PMID: 27408752 PMCID: PMC4935763 DOI: 10.1038/hgv.2016.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 12/28/2022] Open
Abstract
Published genome-wide association studies (GWASs) identified an intergenic region with regulatory features on chr11p13 associated with cystic fibrosis (CF) lung disease severity. Targeted resequencing in n=377, followed by imputation to n=6,365 CF subjects, was used to identify unrecognized genetic variants (including indels and microsatellite repeats) associated with phenotype. Highly significant associations were in strong linkage disequilibrium and were seen only in Phe508del homozygous CF subjects, indicating a CFTR genotype-specific mechanism.
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Fujiwara N, Inoue J, Kawano T, Tanimoto K, Kozaki KI, Inazawa J. miR-634 Activates the Mitochondrial Apoptosis Pathway and Enhances Chemotherapy-Induced Cytotoxicity. Cancer Res 2015. [PMID: 26216549 DOI: 10.1158/0008-5472.can-15-0257] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Some tumor-suppressing miRNAs target multiple oncogenes concurrently and therefore may be useful as cancer therapeutic agents. Further, such miRNAs may be useful to address chemotherapeutic resistance in cancer, which remains a primary clinical challenge in need of solutions. Thus, cytoprotective processes upregulated in cancer cells that are resistant to chemotherapy are a logical target for investigation. Here, we report that overexpression of miR-634 activates the mitochondrial apoptotic pathway by direct concurrent targeting of genes associated with mitochondrial homeostasis, antiapoptosis, antioxidant ability, and autophagy. In particular, we show how enforced expression of miR-634 enhanced chemotherapy-induced cytotoxicity in a model of esophageal squamous cell carcinoma, where resistance to chemotherapy remains clinically problematic. Our findings illustrate how reversing miR-634-mediated cytoprotective processes may offer a broadly useful approach to improving cancer therapy.
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Affiliation(s)
- Naoto Fujiwara
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan. Department of Esophageal and General Surgery, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Jun Inoue
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuyuki Kawano
- Department of Esophageal and General Surgery, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kousuke Tanimoto
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken-Ichi Kozaki
- Department of Dental Pharmacology, Graduate School, Okayama University, Okayama, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan. Department of Genome Medicine, Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan. Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan.
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Oh HR, An CH, Yoo NJ, Lee SH. Somatic mutations of amino acid metabolism-related genes in gastric and colorectal cancers and their regional heterogeneity--a short report. Cell Oncol (Dordr) 2014; 37:455-61. [PMID: 25450519 DOI: 10.1007/s13402-014-0209-1] [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] [Accepted: 11/19/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Metabolic reprogramming is an emerging topic in cancer research. However, genetic alterations in genes encoding enzymes involved in amino acid metabolism are largely unknown. The aim of this study was to explore whether genes known to be involved in amino acid metabolism are mutated in gastric cancer (GC) and/or colorectal cancer (CRC). METHODS Through a public database search, we found that a number of genes known to be involved in amino acid metabolism, i.e., AGXT, ALDH2, APIP, MTR, DNMT1, ASH1L, ASPA, CAD, DDC, GCDH, DLD, LAP3, MCEE and MUT, harbor mononucleotide repeats that may serve as mutation targets in cancers exhibiting microsatellite instability (MSI). We assessed these genes for the presence of the mutations in 79 GCs and 124 CRCs using single-strand conformation polymorphism (SSCP) and direct sequencing analyses. RESULTS Using SSCP in conjunction with DNA sequencing we detected frameshift mutations in AGXT (17 cases), ALDH2 (3 cases), APIP (4 cases), MTR (5 cases), DNMT1 (1 case), ASH1L (1 case), ASPA (2 cases), CAD (2 cases), DDC (1 case), GCDH (3 cases), DLD (1 case), LAP3 (1 case), MCEE (5 cases) and MUT (1 case). These mutations were exclusively detected in MSI-high (MSI-H), and not in MSI-low or MSI-stable (MSI-L/MSS) cases. In addition, we analyzed 16 CRCs for the presence of intra-tumor heterogeneity (ITH) and found that two CRCs harbored regional ITH for GCDH frameshift mutations. CONCLUSIONS Our data indicate that genes known to be involved in amino acid metabolism recurrently acquire somatic mutations in MSH-H GCs and MSH-H CRCs and that, in addition, mutation ITH does occur in at least some of these tumors. Together, these data suggest that metabolic reprogramming may play a role in the etiology of MSI-H GCs and CRCs. Our data also suggest that ultra-regional mutation analysis is required for a more comprehensive evaluation of the mutation status in these tumors.
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Affiliation(s)
- Hye Rim Oh
- Departments of Pathology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Socho-gu, Seoul, 137-701, South Korea
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Abstract
INTRODUCTION Caspase-9 is the apoptotic initiator protease of the intrinsic or mitochondrial apoptotic pathway, which is activated at multi-protein activation platforms. Its activation is believed to involve homo-dimerization of the monomeric zymogens. It binds to the apoptosome to retain substantial catalytic activity. Variety of apoptotic stimuli can regulate caspase-9. However, the mechanism of action of various regulators of caspase-9 has not been summarized and compared yet. In this article, we elucidate the regulators of caspase-9 including microRNAs, natural compounds that are related to caspase-9 and ongoing clinical trials with caspase-9 to better understand the caspase-9 in suppressing cancer. AREAS COVERED In this study, the basic mechanism of apoptosis pathways, regulators of caspase-9 and the development of drugs to regulate caspase-9 are reviewed. Also, ongoing clinical trials for caspase-9 are discussed. EXPERT OPINION Apoptosis has crucial role in cancer, brain disease, aging and heart disease to name a few. Since caspase-9 is an initiator caspase of apoptosis, it is an important therapeutic target of various diseases related to apoptosis. Therefore, a deep understanding on the roles as well as regulators of caspase-9 is required to find more effective ways to conquer apoptosis-related diseases especially cancer.
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Affiliation(s)
- Bonglee Kim
- Kyunghee University, College of Korean Medicine, Cancer Preventive Material Development Research Center , 1 Hoegi-dong, Dongdaemun-ku, Seoul 131-701 , South Korea
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Dingerdissen H, Weaver DS, Karp PD, Pan Y, Simonyan V, Mazumder R. A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs. Biol Direct 2014; 9:9. [PMID: 24894379 PMCID: PMC4057618 DOI: 10.1186/1745-6150-9-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 05/19/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND We have previously suggested a method for proteome wide analysis of variation at functional residues wherein we identified the set of all human genes with nonsynonymous single nucleotide variation (nsSNV) in the active site residue of the corresponding proteins. 34 of these proteins were shown to have a 1:1:1 enzyme:pathway:reaction relationship, making these proteins ideal candidates for laboratory validation through creation and observation of specific yeast active site knock-outs and downstream targeted metabolomics experiments. Here we present the next step in the workflow toward using yeast metabolic modeling to predict human metabolic behavior resulting from nsSNV. RESULTS For the previously identified candidate proteins, we used the reciprocal best BLAST hits method followed by manual alignment and pathway comparison to identify 6 human proteins with yeast orthologs which were suitable for flux balance analysis (FBA). 5 of these proteins are known to be associated with diseases, including ribose 5-phosphate isomerase deficiency, myopathy with lactic acidosis and sideroblastic anaemia, anemia due to disorders of glutathione metabolism, and two porphyrias, and we suspect the sixth enzyme to have disease associations which are not yet classified or understood based on the work described herein. CONCLUSIONS Preliminary findings using the Yeast 7.0 FBA model show lack of growth for only one enzyme, but augmentation of the Yeast 7.0 biomass function to better simulate knockout of certain genes suggested physiological relevance of variations in three additional proteins. Thus, we suggest the following four proteins for laboratory validation: delta-aminolevulinic acid dehydratase, ferrochelatase, ribose-5 phosphate isomerase and mitochondrial tyrosyl-tRNA synthetase. This study indicates that the predictive ability of this method will improve as more advanced, comprehensive models are developed. Moreover, these findings will be useful in the development of simple downstream biochemical or mass-spectrometric assays to corroborate these predictions and detect presence of certain known nsSNVs with deleterious outcomes. Results may also be useful in predicting as yet unknown outcomes of active site nsSNVs for enzymes that are not yet well classified or annotated.
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Affiliation(s)
- Hayley Dingerdissen
- Department of Biochemistry and Molecular Biology, The George Washington University Medical Center, Ross Hall, Room 540, 2300 Eye Street NW, Washington, DC 20037, USA
| | - Daniel S Weaver
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, Menlo Park, CA 94025, USA
| | - Peter D Karp
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, Menlo Park, CA 94025, USA
| | - Yang Pan
- Department of Biochemistry and Molecular Biology, The George Washington University Medical Center, Ross Hall, Room 540, 2300 Eye Street NW, Washington, DC 20037, USA
| | - Vahan Simonyan
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 1451 Rockville Pike, Rockville, MD 20852, USA
| | - Raja Mazumder
- Department of Biochemistry and Molecular Biology, The George Washington University Medical Center, Ross Hall, Room 540, 2300 Eye Street NW, Washington, DC 20037, USA
- McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA
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Interaction of translationally controlled tumor protein with Apaf-1 is involved in the development of chemoresistance in HeLa cells. BMC Cancer 2014; 14:165. [PMID: 24606760 PMCID: PMC4015309 DOI: 10.1186/1471-2407-14-165] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 02/27/2014] [Indexed: 11/11/2022] Open
Abstract
Background Translationally controlled tumor protein (TCTP), alternatively called fortilin, is believed to be involved in the development of the chemoresistance of tumor cells against anticancer drugs such as etoposide, taxol, and oxaliplatin, the underlying mechanisms of which still remain elusive. Methods Cell death analysis of TCTP-overexpressing HeLa cells was performed following etoposide treatment to assess the mitochondria-dependent apoptosis. Apoptotic pathway was analyzed through measuring the cleavage of epidermal growth factor receptor (EGFR) and phospholipase C-γ (PLC-γ), caspase activation, mitochondrial membrane perturbation, and cytochrome c release by flow cytometry and western blotting. To clarify the role of TCTP in the inhibition of apoptosome, in vitro apoptosome reconstitution and immunoprecipitation was used. Pull-down assay and silver staining using the variants of Apaf-1 protein was applied to identify the domain that is responsible for its interaction with TCTP. Results In the present study, we confirmed that adenoviral overexpression of TCTP protects HeLa cells from cell death induced by cytotoxic drugs such as taxol and etoposide. TCTP antagonized the mitochondria-dependent apoptotic pathway following etoposide treatment, including mitochondrial membrane damage and resultant cytochrome c release, activation of caspase-9, and -3, and eventually, the cleavage of EGFR and PLC-γ. More importantly, TCTP interacts with the caspase recruitment domain (CARD) of Apaf-1 and is incorporated into the heptameric Apaf-1 complex, and that C-terminal cleaved TCTP specifically associates with Apaf-1 of apoptosome in apoptosome-forming condition thereby inhibiting the amplification of caspase cascade. Conclusions TCTP protects the cancer cells from etoposide-induced cell death by inhibiting the mitochondria-mediated apoptotic pathway. Interaction of TCTP with Apaf-1 in apoptosome is involved in the molecular mechanism of TCTP-induced chemoresistance. These findings suggest that TCTP may serve as a therapeutic target for chemoresistance in cancer treatment.
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Structural and biochemical basis for the inhibition of cell death by APIP, a methionine salvage enzyme. Proc Natl Acad Sci U S A 2013; 111:E54-61. [PMID: 24367089 DOI: 10.1073/pnas.1308768111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
APIP, Apaf-1 interacting protein, has been known to inhibit two main types of programmed cell death, apoptosis and pyroptosis, and was recently found to be associated with cancers and inflammatory diseases. Distinct from its inhibitory role in cell death, APIP was also shown to act as a 5-methylthioribulose-1-phosphate dehydratase, or MtnB, in the methionine salvage pathway. Here we report the structural and enzymatic characterization of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39 μmol min(-1) mg(-1). The crystal structure was determined at 2.0-Å resolution, revealing an overall fold similar to members of the zinc-dependent class II aldolase family. APIP/MtnB exists as a tetramer in solution and exhibits an assembly with C4 symmetry in the crystal lattice. The pocket-shaped active site is located at the end of a long cleft between two adjacent subunits. We propose an enzymatic reaction mechanism involving Glu139* as a catalytic acid/base, as supported by enzymatic assay, substrate-docking study, and sequence conservation analysis. We explored the relationship between two distinct functions of APIP/MtnB, cell death inhibition, and methionine salvage, by measuring the ability of enzymatic mutants to inhibit cell death, and determined that APIP/MtnB functions as a cell death inhibitor independently of its MtnB enzyme activity for apoptosis induced by either hypoxia or etoposide, but dependently for caspase-1-induced pyroptosis. Our results establish the structural and biochemical groundwork for future mechanistic studies of the role of APIP/MtnB in modulating cell death and inflammation and in the development of related diseases.
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Templeton PD, Litman ES, Metzner SI, Ahn NG, Sousa MC. Structure of mediator of RhoA-dependent invasion (MRDI) explains its dual function as a metabolic enzyme and a mediator of cell invasion. Biochemistry 2013; 52:5675-84. [PMID: 23859498 DOI: 10.1021/bi400556e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metastatic melanoma is among the most intractable cancers to treat; patients show resistance to therapy and limited survival time. A critical step in the development of metastatic melanoma is the acquisition of invasion and transition from thin to thick tumors on the skin, followed by invasion to lymph nodes. Prior studies have shown that metastatic melanoma is associated with dysregulation of RhoA and enhanced expression of a protein named "mediator of RhoA-dependent invasion (MRDI)". Importantly, MRDI is a "moonlighting" enzyme, with two distinct functions in melanoma cells. First, MRDI acts as a methylthioribose-1-phosphate (MTR-1-P) isomerase, catalyzing a critical step in methionine salvage. Second, MRDI promotes and is necessary for melanoma cell invasion, independent of its catalytic activity. This paper demonstrates that MtnA, a bacterial MTR-1-P isomerase, rescues the methionine salvage function of MRDI, but is unable to rescue its role in invasion. The crystal structure of MRDI was solved to a resolution of 2.5 Å to identify structural elements important for its invasion activity. This structure and its comparison with other MTR-1-P isomerases are presented, and mutations within a region separate from the MTR-1-P binding site, which interfere with invasion, are identified. Thus, structural elements in MRDI distal from the MTR-1-P catalytic site are responsible for the invasion phenotype.
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Affiliation(s)
- Paul D Templeton
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0596, USA
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30
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Shams I, Malik A, Manov I, Joel A, Band M, Avivi A. Transcription pattern of p53-targeted DNA repair genes in the hypoxia-tolerant subterranean mole rat Spalax. J Mol Biol 2013; 425:1111-8. [PMID: 23318952 DOI: 10.1016/j.jmb.2013.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 12/31/2012] [Accepted: 01/08/2013] [Indexed: 10/27/2022]
Abstract
The tumor suppressor gene p53 induces growth arrest and/or apoptosis in response to DNA damage/hypoxia. Inactivation of p53 confers a selective advantage to tumor cells under a hypoxic microenvironment during tumor progression. The subterranean blind mole rat, Spalax, spends its life underground at low-oxygen tensions, hence developing a wide range of respiratory/molecular adaptations to hypoxic stress, including critical changes in p53 structure and signaling pathway. The highly conserved p53 Arg(R)-172 is substituted by lysine (K) in Spalax, identical with a tumor-associated mutation. Functionality assays revealed that Spalax p53 is unable to activate apoptotic target genes but is still capable of activating cell cycle arrest genes. Furthermore, we have shown that the transcription patterns of representative p53-induced genes (Apaf1 and Mdm2) in Spalax are influenced by hypoxia. Cell cycle arrest allows the cells to repair DNA damage via different DNA repair genes. We tested the transcription pattern of three p53-related DNA repair genes (p53R2, Mlh1, and Msh2) under normoxia and short-acute hypoxia in Spalax, C57BL/6 wild-type mice, and two strains of mutant C57BL/6 mice, each carrying a different mutation at the R172 position. Our results show that while wild-type/mutant mice exhibit strong hypoxia-induced reductions of repair gene transcript levels, no such inhibition is found in Spalax under hypoxia. Moreover, unlike mouse p53R2, Spalax p53R2 transcript levels are strongly elevated under hypoxia. These results suggest that critical repair functions, which are known to be inhibited under hypoxia in mice, remain active in Spalax, as part of its unique hypoxia tolerance mechanisms.
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Affiliation(s)
- Imad Shams
- Institute of Evolution, University of Haifa, Haifa 31905, Israel.
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Mary C, Duek P, Salleron L, Tienz P, Bumann D, Bairoch A, Lane L. Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway. PLoS One 2012; 7:e52877. [PMID: 23285211 PMCID: PMC3532061 DOI: 10.1371/journal.pone.0052877] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 11/22/2012] [Indexed: 02/08/2023] Open
Abstract
The methionine salvage pathway is widely distributed among some eubacteria, yeast, plants and animals and recycles the sulfur-containing metabolite 5-methylthioadenosine (MTA) to methionine. In eukaryotic cells, the methionine salvage pathway takes place in the cytosol and usually involves six enzymatic activities: MTA phosphorylase (MTAP, EC 2.4.2.28), 5′-methylthioribose-1-phosphate isomerase (mtnA, EC 5.3.1.23), 5′-methylthioribulose-1-phosphate dehydratase (mtnB, EC: 4.2.1.109), 2,3-dioxomethiopentane-1-phosphate enolase/phosphatase (mtnC, EC 3.1.3.77), aci-reductone dioxygenase (mtnD, EC 1.13.11.54) and 4-methylthio-2-oxo-butanoate (MTOB) transaminase (EC 2.6.1.-). The aim of this study was to complete the available information on the methionine salvage pathway in human by identifying the enzyme responsible for the dehydratase step. Using a bioinformatics approach, we propose that a protein called APIP could perform this role. The involvement of this protein in the methionine salvage pathway was investigated directly in HeLa cells by transient and stable short hairpin RNA interference. We show that APIP depletion specifically impaired the capacity of cells to grow in media where methionine is replaced by MTA. Using a Shigella mutant auxotroph for methionine, we confirm that the knockdown of APIP specifically affects the recycling of methionine. We also show that mutation of three potential phosphorylation sites does not affect APIP activity whereas mutation of the potential zinc binding site completely abrogates it. Finally, we show that the N-terminal region of APIP that is missing in the short isoform is required for activity. Together, these results confirm the involvement of APIP in the methionine salvage pathway, which plays a key role in many biological functions like cancer, apoptosis, microbial proliferation and inflammation.
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Affiliation(s)
- Camille Mary
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland.
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32
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Kang W, Yang JK. Crystallization and preliminary X-ray crystallographic analysis of human Apaf-1-interacting protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1518-20. [PMID: 23192037 PMCID: PMC3509978 DOI: 10.1107/s1744309112042832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/13/2012] [Indexed: 01/05/2023]
Abstract
Apaf-1-interacting protein (APIP) is known to inhibit two different types of cell death: caspase-1-dependent pyroptosis and caspase-9-dependent apoptosis. APIP is also involved in the methionine-salvage pathway, where it is called 5-methylthioribulose-1-phosphate dehydratase (MtnB). The enzyme activity seems to be essential for inhibition of pyroptosis by APIP, but not for inhibition of apoptosis. In this study, human APIP was overproduced in Escherichia coli, purified and crystallized. An X-ray diffraction data set was collected to 2.40 Å resolution and the crystals belonged to space group C222(1), with unit-cell parameters a=106.61, b=107.50, c=189.76 Å. Given that four APIP molecules exist in the asymmetric unit, the Matthews coefficient is 2.70 Å3 Da(-1) and the corresponding solvent content is 54.4%.
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Affiliation(s)
- Wonchull Kang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 156-743, Republic of Korea
| | - Jin Kuk Yang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 156-743, Republic of Korea
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Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death. Proc Natl Acad Sci U S A 2012; 109:E2343-52. [PMID: 22837397 DOI: 10.1073/pnas.1206701109] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies can identify common differences that contribute to human phenotypic diversity and disease. When genome-wide association studies are combined with approaches that test how variants alter physiology, biological insights can emerge. Here, we used such an approach to reveal regulation of cell death by the methionine salvage pathway. A common SNP associated with reduced expression of a putative methionine salvage pathway dehydratase, apoptotic protease activating factor 1 (APAF1)-interacting protein (APIP), was associated with increased caspase-1-mediated cell death in response to Salmonella. The role of APIP in methionine salvage was confirmed by growth assays with methionine-deficient media and quantitation of the methionine salvage substrate, 5'-methylthioadenosine. Reducing expression of APIP or exogenous addition of 5'-methylthioadenosine increased Salmonellae-induced cell death. Consistent with APIP originally being identified as an inhibitor of caspase-9-dependent apoptosis, the same allele was also associated with increased sensitivity to the chemotherapeutic agent carboplatin. Our results show that common human variation affecting expression of a single gene can alter susceptibility to two distinct cell death programs. Furthermore, the same allele that promotes cell death is associated with improved survival of individuals with systemic inflammatory response syndrome, suggesting a possible evolutionary pressure that may explain the geographic pattern observed for the frequency of this SNP. Our study shows that in vitro association screens of disease-related traits can not only reveal human genetic differences that contribute to disease but also provide unexpected insights into cell biology.
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Kong BW, Song JJ, Lee JY, Hargis BM, Wing T, Lassiter K, Bottje W. Gene expression in breast muscle associated with feed efficiency in a single male broiler line using a chicken 44K oligo microarray. I. Top differentially expressed genes. Poult Sci 2011; 90:2535-47. [PMID: 22010239 DOI: 10.3382/ps.2011-01435] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Global RNA expression in breast muscle obtained from a male broiler line phenotyped for high or low feed efficiency (FE) was investigated. Pooled RNA samples (n = 6/phenotype) labeled with cyanine 3 or cyanine 5 fluorescent dyes to generate cRNA probes were hybridized on a 4 × 44K chicken oligo microarray. Local polynomial regression normalization was applied to background-corrected red and green intensities with a moderated t-statistic. Corresponding P-values were computed and adjusted for multiple testing by false discovery rate to identify differentially expressed genes. Microarray validation was carried out by comparing findings with quantitative reverse-transcription PCR. A 1.3-fold difference in gene expression was set as a cutoff value, which encompassed 20% (782 of 4,011) of the total number of genes that were differentially expressed between FE phenotypes. Using an online software program (Ingenuity Pathway Analysis), the top 10 upregulated genes identified by Ingenuity Pathway Analysis in the high-FE group were generally associated with anabolic processes. In contrast, 7 of the top 10 downregulated genes in the high-FE phenotype (upregulated in the low-FE phenotype) were associated with muscle fiber development, muscle function, and cytoskeletal organization, with the remaining 3 genes associated with self-recognition or stress-responding genes. The results from this study focusing on only the top differentially expressed genes suggest that the high-FE broiler phenotype is derived from the upregulation of genes associated with anabolic processes as well as a downregulation of genes associated with muscle fiber development, muscle function, cytoskeletal organization, and stress response.
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Affiliation(s)
- B-W Kong
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, USA
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Bacteria-based in vivo peptide library screening using biopanning approach. J Microbiol 2011; 49:847-51. [PMID: 22068505 DOI: 10.1007/s12275-011-1405-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 08/24/2011] [Indexed: 10/15/2022]
Abstract
Traditionally, library screening has been performed to identify biologically active agents including small molecules or peptides that inhibit target proteins or molecules with therapeutic interests. Due to its chemical nature, library screening is usually performed under in vitro environments using purified proteins and molecules. However, active agents identified from in vitro screenings often fail to exhibit biological activities in cells. To overcome this inherent limitation, we have developed an in vivo peptide library screening system that allows for the identification of dissociative inhibitors of protein interactions of interest. The screening is based on the reconstitution of the cI repressor from bacteriophage lambda with high-density expression peptide library and is entirely performed in bacteria cells. Furthermore, to enhance the efficacy and sensitivity of the screening, a multiple-round biopanning approach was employed for amplification and enrichment of positive peptides. Overall, this in vivo screening should provide a fast and efficient tool for identification of biologically active peptide molecules against target protein assembly.
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Škrlep M, Čandek-Potokar M, Mandelc S, Javornik B, Gou P, Chambon C, Santé-Lhoutellier V. Proteomic profile of dry-cured ham relative to PRKAG3 or CAST genotype, level of salt and pastiness. Meat Sci 2011; 88:657-67. [DOI: 10.1016/j.meatsci.2011.02.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 02/14/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
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Wright FA, Strug LJ, Doshi VK, Commander CW, Blackman SM, Sun L, Berthiaume Y, Cutler D, Cojocaru A, Collaco JM, Corey M, Dorfman R, Goddard K, Green D, Kent JW, Lange EM, Lee S, Li W, Luo J, Mayhew GM, Naughton KM, Pace RG, Paré P, Rommens JM, Sandford A, Stonebraker JR, Sun W, Taylor C, Vanscoy LL, Zou F, Blangero J, Zielenski J, O'Neal WK, Drumm ML, Durie PR, Knowles MR, Cutting GR. Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2. Nat Genet 2011; 43:539-46. [PMID: 21602797 PMCID: PMC3296486 DOI: 10.1038/ng.838] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/22/2011] [Indexed: 12/17/2022]
Abstract
A combined genome-wide association and linkage study was used to identify loci causing variation in cystic fibrosis lung disease severity. We identified a significant association (P = 3.34 × 10(-8)) near EHF and APIP (chr11p13) in p.Phe508del homozygotes (n = 1,978). The association replicated in p.Phe508del homozygotes (P = 0.006) from a separate family based study (n = 557), with P = 1.49 × 10(-9) for the three-study joint meta-analysis. Linkage analysis of 486 sibling pairs from the family based study identified a significant quantitative trait locus on chromosome 20q13.2 (log(10) odds = 5.03). Our findings provide insight into the causes of variation in lung disease severity in cystic fibrosis and suggest new therapeutic targets for this life-limiting disorder.
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Affiliation(s)
- Fred A Wright
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Affiliation(s)
- Shawn B Bratton
- Division of Pharmacology and Toxicology, College of Pharmacy, and Center for Molecular and Cellular Toxicology, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712-0125, USA.
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Chadwick W, Zhou Y, Park SS, Wang L, Mitchell N, Stone MD, Becker KG, Martin B, Maudsley S. Minimal peroxide exposure of neuronal cells induces multifaceted adaptive responses. PLoS One 2010; 5:e14352. [PMID: 21179406 PMCID: PMC3003681 DOI: 10.1371/journal.pone.0014352] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 11/24/2010] [Indexed: 12/20/2022] Open
Abstract
Oxidative exposure of cells occurs naturally and may be associated with cellular damage and dysfunction. Protracted low level oxidative exposure can induce accumulated cell disruption, affecting multiple cellular functions. Accumulated oxidative exposure has also been proposed as one of the potential hallmarks of the physiological/pathophysiological aging process. We investigated the multifactorial effects of long-term minimal peroxide exposure upon SH-SY5Y neural cells to understand how they respond to the continued presence of oxidative stressors. We show that minimal protracted oxidative stresses induce complex molecular and physiological alterations in cell functionality. Upon chronic exposure to minimal doses of hydrogen peroxide, SH-SY5Y cells displayed a multifactorial response to the stressor. To fully appreciate the peroxide-mediated cellular effects, we assessed these adaptive effects at the genomic, proteomic and cellular signal processing level. Combined analyses of these multiple levels of investigation revealed a complex cellular adaptive response to the protracted peroxide exposure. This adaptive response involved changes in cytoskeletal structure, energy metabolic shifts towards glycolysis and selective alterations in transmembrane receptor activity. Our analyses of the global responses to chronic stressor exposure, at multiple biological levels, revealed a viable neural phenotype in-part reminiscent of aged or damaged neural tissue. Our paradigm indicates how cellular physiology can subtly change in different contexts and potentially aid the appreciation of stress response adaptations.
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Affiliation(s)
- Wayne Chadwick
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yu Zhou
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Sung-Soo Park
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Liyun Wang
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Nicholas Mitchell
- Department of Biology, Saint Bonaventure University, Saint Bonaventure, New York, United States of America
| | - Matthew D. Stone
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kevin G. Becker
- Gene Expression and Genomics Unit, Research Resources Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Bronwen Martin
- Metabolism Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Stuart Maudsley
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
- * E-mail:
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Kao SH, Hsu TC, Yu JS, Chen JT, Li SL, Lai WX, Tzang BS. Proteomic analysis for the anti-apoptotic effects of cystamine on apoptosis-prone macrophage. J Cell Biochem 2010; 110:660-70. [PMID: 20512926 DOI: 10.1002/jcb.22577] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Increased macrophage vulnerability is associated with progression of systemic lupus erythematosus. Our previous studies have shown that cystamine, an inhibitor of transglutaminase 2 (TG2), alleviated the apoptosis of hepatocyte and brain cell in lupus-prone mice NZB/W-F1. In present study, we further investigated the effects of cystamine on apoptosis-prone macrophages (APMs) in the lupus mice. Using two-dimensional gel electrophoresis (2-DE) analysis, we found that cystamine induced a differential protein expression pattern of APM as comparing to the PBS control. The protein spots presenting differential level between cystamine and PBS treatment were then identified by peptide-mass fingerprinting (PMF). After bioinformatic analysis, these identified proteins were found involved in mitochondrial apoptotic pathway, oxidative stress, and mitogen-activated protein (MAP) kinase-mediated pathway. Further investigation revealed that cystamine significantly decreased the levels of apoptotic Bax and Apaf-1 and the activity of caspase-3, and increased the levels of anti-apoptotic Bcl-2 in APM. We also found that these apoptotic mediators were up-regulated in a correlation with the progression of lupus severity in NZB/W-F1, which were little affected in BALB/c mice. We also found that the reduced serum glutathione was restored by cystamine in NZB/W-F1. Interestingly, the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) in APM and the phagocytic ability was diminished in presence of cystamine. In conclusion, our findings indicate that cystamine significantly inhibited mitochondrial pathway, induced antioxidant proteins, and diminished phosphorylation of extracellular ERK1/2, which may alleviate the apoptosis and the phagocytic ability of APM.
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Affiliation(s)
- Shao-Hsuan Kao
- Institute of Biochemistry and Biotechnology, Chung Shan Medical University, Taichung, Taiwan
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Abstract
Arthropoda is the largest of all animal phyla and includes about 90% of extant species. Our knowledge about regulation of apoptosis in this phylum is largely based on findings for the fruit fly Drosophila melanogaster. Recent work with crustaceans shows that apoptotic proteins, and presumably mechanisms of cell death regulation, are more diverse in arthropods than appreciated based solely on the excellent work with fruit flies. Crustacean homologs exist for many major proteins in the apoptotic networks of mammals and D. melanogaster, but integration of these proteins into the physiology and pathophysiology of crustaceans is far from complete. Whether apoptosis in crustaceans is mainly transcriptionally regulated as in D. melanogaster (e.g., RHG 'killer' proteins), or rather is controlled by pro- and anti-apoptotic Bcl-2 family proteins as in vertebrates needs to be clarified. Some phenomena like the calcium-induced opening of the mitochondrial permeability transition pore (MPTP) are apparently lacking in crustaceans and may represent a vertebrate invention. We speculate that differences in regulation of the intrinsic pathway of crustacean apoptosis might represent a prerequisite for some species to survive harsh environmental insults. Pro-apoptotic stimuli described for crustaceans include UV radiation, environmental toxins, and a diatom-produced chemical that promotes apoptosis in offspring of a copepod. Mechanisms that serve to depress apoptosis include the inhibition of caspase activity by high potassium in energetically healthy cells, alterations in nucleotide abundance during energy-limited states like diapause and anoxia, resistance to opening of the calcium-induced MPTP, and viral accommodation during persistent viral infection. Characterization of the players, pathways, and their significance in the core machinery of crustacean apoptosis is revealing new insights for the field of cell death.
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Pérez-Payá E, Orzáez M, Mondragón L, Wolan D, Wells JA, Messeguer A, Vicent MJ. Molecules that modulate Apaf-1 activity. Med Res Rev 2010; 31:649-75. [PMID: 20099266 DOI: 10.1002/med.20198] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Programmed cell death, apoptosis, is a highly regulated cellular pathway, responsible for the elimination of cells in the organism that are no longer needed or extensively damaged. Defects in the regulation of apoptosis could be at the molecular basis of different diseases, either when it is insufficient or excessive. The formation of the macromolecular complex, apoptosome, is a key event in this pathway, which has also been defined as the intrinsic apoptosis pathway. The apoptosome is a holoenzyme multiprotein complex formed by cytochrome c-activated apoptotic protease-activating factor (Apaf-1), dATP, and procaspase-9. Recent studies have produced a wealth of information about the regulation and functions of Apaf-1, but additional studies aimed at elucidating its role as a signaling device at the crosstalk between different signaling pathways are needed to take advantage for the development of modulators of apoptosis pathways and possible therapeutic applications.
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Affiliation(s)
- Enrique Pérez-Payá
- Peptide and Protein Laboratory, Department of Medicinal Chemistry, Centro de Investigación Príncipe Felipe, Avda Autopista del Saler, Valencia, Spain.
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Vidal C, Borg J, Xuereb-Anastasi A, Scerri CA. Variants within protectin (CD59) and CD44 genes linked to an inherited haplotype in a family with coeliac disease. TISSUE ANTIGENS 2009; 73:225-235. [PMID: 19254252 DOI: 10.1111/j.1399-0039.2008.01193.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Coeliac disease (CD) is an autoimmune disorder characterised by inflammation, villous atrophy and hyperplasia of the small intestinal mucosa that affects genetically susceptible individuals. A genome-wide scan was performed in 17 family members with high incidence of CD. Highest nonparametric linkage (NPL) and logarithm of odds (LOD) scores were of 6.21 (P = 0.0107) and 2.57, respectively, to a region on chromosome 11p13-12. Following fine mapping, NPL and LOD scores did not change, but the linkage interval on chromosome 11 was narrowed to a region that is approximately 50.94 cM from pTer. Two inherited haplotypes on chromosomes 11p13-12 and 9q21 were observed in all affected members but not in the majority of clinically normal individuals. Sequencing of genes at region 11p13-12 showed a number of sequence variants, two of which were linked with the inherited haplotype. One of these variants in the CD59 gene was found at a very low frequency in the population and could possibly affect pre-messenger RNA splicing. This study is of particular importance for the identification of novel genes that might be responsible for CD other than human leukocyte antigen.
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Affiliation(s)
- C Vidal
- Laboratory of Molecular Genetics, Department of Physiology and Biochemistry, University of Malta, Msida, Malta
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Cho DH, Jo YK, Hwang JJ, Lee YM, Roh SA, Kim JC. Caspase-mediated cleavage of ATG6/Beclin-1 links apoptosis to autophagy in HeLa cells. Cancer Lett 2009; 274:95-100. [DOI: 10.1016/j.canlet.2008.09.004] [Citation(s) in RCA: 183] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 08/13/2008] [Accepted: 09/02/2008] [Indexed: 12/20/2022]
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Kwasiborski A, Sayd T, Chambon C, Santé-Lhoutellier V, Rocha D, Terlouw C. Pig Longissimus lumborum proteome: Part I. Effects of genetic background, rearing environment and gender. Meat Sci 2008; 80:968-81. [DOI: 10.1016/j.meatsci.2008.04.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 02/14/2008] [Accepted: 04/28/2008] [Indexed: 11/26/2022]
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Sanchez-Olea R, Ortiz S, Barreto O, Yang Q, Xu CJ, Zhu H, Yuan J. Parcs is a dual regulator of cell proliferation and apaf-1 function. J Biol Chem 2008; 283:24400-5. [PMID: 18562310 PMCID: PMC2528988 DOI: 10.1074/jbc.m804664200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Indexed: 11/06/2022] Open
Abstract
Here we identify a novel protein, named Parcs for pro-apoptotic protein required for cell survival, that is involved in both cell cycle progression and apoptosis. Parcs interacted with Apaf-1 by binding to the oligomerization domain of Apaf-1. Apaf-1-mediated activation of caspase-9 and caspase-3 was markedly decreased in a cytosolic fraction isolated from HeLa cells with reduced parcs expression. Interestingly, parcs deficiency blocked cell proliferation in non-tumorigenic cells but not in multiple tumor cell lines. In MCF-10A cells, parcs deficiency led to early G1 arrest. Conditional inactivation of parcs in genetically modified primary mouse embryonic fibroblasts using the Cre-LoxP system also resulted in the inhibition of cell proliferation. We conclude that Parcs may define a molecular checkpoint in the control of cell proliferation for normal cells that is lost in tumor cells.
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Affiliation(s)
| | | | | | | | | | | | - Junying Yuan
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
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Cho DH, Lee HJ, Kim HJ, Hong SH, Pyo JO, Cho C, Jung YK. Suppression of hypoxic cell death by APIP-induced sustained activation of AKT and ERK1/2. Oncogene 2006; 26:2809-14. [PMID: 17086211 DOI: 10.1038/sj.onc.1210080] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Apaf-1-interacting protein (APIP) was previously isolated as an inhibitor of mitochondrial cell death interacting with Apaf-1. Here, we report a hypoxia-selective antiapoptotic activity of APIP that induces the activation of AKT and extracellular signal-regulated kinase (ERK)1/2. Stable expression of APIP in C2C12 (C2C12/APIP) cells suppressed cell death induced by hypoxia and etoposide. Unlike etoposide, however, APIP induces the sustained activation of AKT and ERK1/2 and the phosphorylation of caspase-9 during hypoxia. Inhibition of AKT and ERK1/2 activation by the treatments with phosphatidylinositol 3'-kinase and mitogen-activated protein kinase kinase (MEK)1/2 inhibitors sensitized C2C12/APIP cells to hypoxic cell death and abolished the hypoxia-induced phosphorylation of caspase-9. Further, overexpression of phosphorylation-mimic caspase-9 mutants (caspase-9-T125E and caspase-9-S196D), but not phosphorylation-defective caspase-9 mutants (caspase-9-T125A and caspase-9-S196A), effectively suppressed hypoxia-induced death of C2C12 cells. These results elucidate a novel Apaf-1-independent antiapoptotic activity of APIP during hypoxic cell death, inducing the sustained activation of AKT and ERK1/2 and leading to caspase-9 phosphorylation.
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Affiliation(s)
- D-H Cho
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju, Korea
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Abstract
Apoptosis, a form of programmed cell death, is executed by a family of zymogenic proteases known as caspases, which cleave an array of intracellular substrates in the dying cell. Many proapoptotic stimuli trigger cytochrome c release from mitochondria, promoting the formation of a complex between Apaf-1 and caspase-9 in a caspase-activating structure known as the apoptosome. In this review, we describe knockout and knockin studies of apoptosome components, elegant structural and biochemical experiments, and analyses of the apoptosome in various cancers and other disease states, all of which have provided new insight into this critical locus of apoptotic control.
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Affiliation(s)
- Zachary T Schafer
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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Anichini A, Mortarini R, Sensi M, Zanon M. APAF-1 signaling in human melanoma. Cancer Lett 2005; 238:168-79. [PMID: 16095810 DOI: 10.1016/j.canlet.2005.06.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2005] [Accepted: 06/18/2005] [Indexed: 01/01/2023]
Abstract
Acquired resistance to mechanisms of programmed cell death is one of the hallmarks of cancer. Human melanoma, in advanced stage, is hardly curable, due to development of several strategies that impair apoptosis induced by the death receptor and the mitochondrial pathways of apoptosis. Among these apoptosis escape strategies, one is based on inactivation of pro-apoptotic factors such as Apoptotic Protease Activating Factor-1 (APAF-1). APAF-1 couples cytochrome c release from the mitochondria to caspase-9 activation and has been considered a central adaptor in the intrinsic pathway of programmed cell death. Inactivation of APAF-1 in human melanoma may impair the mitochondrial pathway of apoptosis induced by chemotherapeutic drugs that activate the p53 pathway, thus contributing to the development of chemoresistance. In-vivo, loss of expression of APAF-1 is associated with tumor progression, suggesting that APAF-1 inactivation may provide a selective survival advantage to neoplastic cells. However, recent results have indicated the existence of APAF-1-independent pathways of caspase activation and apoptosis in normal and neoplastic cells. Moreover, it has been found that expression of APAF-1 is not necessary for the apoptotic response of melanoma cells to different pro-apoptotic drugs. The emerging picture from results obtained in melanoma and other human tumors is that the relevance of the APAF-1 pathway in programmed cell death is cell-context-dependent and related to the specificity of the pro-apoptotic-stimuli.
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Affiliation(s)
- Andrea Anichini
- Unit of Human Tumor Immunobiology, Dept. of Experimental Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori, Via Venezian 1, 20133, Milan, Italy.
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