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Notghi P, Mehranjani MS, Shariatzadeh SMA. Atorvastatin improves ovarian function and follicular reserve in rats with premature ovarian insufficiency. Reprod Biomed Online 2024; 49:104324. [PMID: 39197401 DOI: 10.1016/j.rbmo.2024.104324] [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: 03/20/2024] [Revised: 06/01/2024] [Accepted: 06/10/2024] [Indexed: 09/01/2024]
Abstract
RESEARCH QUESTION Can atorvastatin, with its antioxidant, anti-inflammatory and anti-apoptotic properties, improve ovarian function and follicular reserve in rats with cyclophosphamide-induced premature ovarian insufficiency (POI)? DESIGN In this experimental study, 24 adult female Wistar rats were divided into four groups: control; POI; POI + atorvastatin; and atorvastatin. After treatment with atorvastatin, serum concentrations of total antioxidant capacity, glutathione, malondialdehyde, FSH, oestradiol, anti-Müllerian hormone, tumour necrosis factor-alpha and interleukin-6 were evaluated. Additionally, mRNA and protein expression of Bax, Bcl-2 and VEGF-A; number of follicles; and total volume of the ovary, and volumes of the cortex and medulla were examined. RESULTS The results showed that serum concentrations of total antioxidant capacity (P < 0.001), glutathione, oestradiol and anti-Müllerian hormone (P < 0.05); mRNA and protein expression of Bcl-2 and VEGF-A (P < 0.05); number of primordial and primary follicles (P < 0.001), and preantral and antral follicles (P < 0.01); and total volume of the ovary, and volume of the cortex (P < 0.05) increased significantly in the POI + atorvastatin group compared with the POI group. Serum concentrations of malondialdehyde, FSH, tumour necrosis factor-alpha and interleukin-6; and mRNA and protein expression of Bax decreased significantly in the POI + atorvastatin group compared with the POI group (P < 0.05). CONCLUSIONS Atorvastatin reduces the detrimental effects of cyclophosphamide in the POI model significantly by reducing oxidative stress and pro-inflammatory cytokines; regulating the expression of Bax, Bcl-2 and VEGF-A; and improving ovarian function and follicular reserve.
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Affiliation(s)
- Parmis Notghi
- Department of Biology, Faculty of Science, Arak University, Arak, Iran
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Tagad A, Patwari GN. Unraveling the Significance of Mg 2+ Dependency and Nucleotide Binding Specificity of H-RAS. J Phys Chem B 2024; 128:1618-1626. [PMID: 38351706 DOI: 10.1021/acs.jpcb.3c06998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
RAS is a small GTPase and acts as a binary molecular switch; the transition from its active to inactive state plays a crucial role in various cell signaling processes. Molecular dynamics simulations at the atomistic level suggest that the absence of cofactor Mg2+ ion generally leads to pronounced structural changes in the Switch-I than Switch-II regions and assists GTP binding. The presence of the Mg2+ ion also restricts the rotation of ϒ phosphate and enhances the hydrolysis rate of GTP. Further, the simulations reveal that the stability of the protein is almost uncompromised when Mg2+ is replaced with Zn2+ and not the Ca2+ ion. The specificity of H-RAS to GTP was evaluated by substituting with ATP and CTP, which indicates that the binding pocket tolerates purine bases over pyrimidine bases. However, the D119 residue specifically interacts with the guanine base and serves as one of the primary interactions that leads to the selectivity of GTP over ATP. The ring displacement of 32Y serves as gate dynamics in H-RAS which are important for its interaction with GAP for the nucleotide exchange and is restricted in the presence of ATP. Finally, the point mutations 61, 16, and 32 influence the structural changes, specifically in the Switch-II region, which are expected to impact the GTP hydrolysis and thus are termed oncogenic mutations.
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Affiliation(s)
- Amol Tagad
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Fayez AG, Esmaiel NN, Ashaat EA, Refeat MM, Lotfy RS, Raouf HA, El Ruby MO. New drug-like small molecule antagonizes phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in patients with conotruncal heart defects. J Taibah Univ Med Sci 2023; 18:1244-1253. [PMID: 37250809 PMCID: PMC10213100 DOI: 10.1016/j.jtumed.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 02/02/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
Objectives Conotruncal heart defects (CTDs) are highly heritable, and approximately one-third of all congenital heart defects are due to CTDs. Through post-analysis of GWAS data relevant to CTDs, a new putative signal transduction pathway, called Vars2-Pic3ca-Akt, associated with CTD has been hypothesized. Here, we aimed to validate the Vars2-Pic3ca-Akt pathway experimentally by measuring Vars2 and PIP3 in patients with CTDs and controls, and to construct a PIP3 inhibitor, as one of harmful-relevant CTD pathogenesis, through an Akt-based drug design strategy. Methods rs2517582 genotype and relative Vars2 expression in 207 individuals were determined by DNA sequencing and qPCR respectively, and free plasma PIP3 in 190 individuals was quantified through ELISA. An Akt-pharmacophore feature model was used to discover PIP3 antagonists with multiple computational and drug-like estimation tools. Results CTD pathogenesis due to Vars2-Pic3ca-Akt overstimulation was confirmed by elevated Vars2 and PIP3 in patients with CTDs. We identified a new small molecule, 322PESB, that antagonizes PIP3 binding. This molecule was prioritized via virtual screening of 21 hypothetical small molecules and it showed minimal RMSD change, high binding affinity andlower dissociation constant than PIP3-Akt complex by 1.99 Kcal/Mol, thus resulting in an equilibrium shift toward 322PESB-Akt complex formation. Moreover, 322PESB exhibited acceptable pharmacokinetics and drug likeness features according to ADME and Lipinski's rule of five classifiers. This compound is the first potential drug-like molecule reported for patients with CTDs with elevated PIP3. Conclusion PIP3 is a useful diagnostic biomarker for patients with CTDs. The Akt-pharmacophore feature model is a feasible approach for discovery of PIP3 signalling antagonists. Further 322PESB development and testing are recommended.
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Affiliation(s)
- Alaaeldin G. Fayez
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Nora N. Esmaiel
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Engy A. Ashaat
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Miral M. Refeat
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Randa S. Lotfy
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Haiam Abdel Raouf
- Immunogenetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Mona O. El Ruby
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
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4
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Schnöder L, Tomic I, Schwindt L, Helm D, Rettel M, Schulz-Schaeffer W, Krause E, Rettig J, Fassbender K, Liu Y. P38α-MAPK phosphorylates Snapin and reduces Snapin-mediated BACE1 transportation in APP-transgenic mice. FASEB J 2021; 35:e21691. [PMID: 34118085 DOI: 10.1096/fj.202100017r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/18/2021] [Accepted: 05/07/2021] [Indexed: 11/11/2022]
Abstract
Amyloid β peptide (Aβ) is the major pathogenic molecule in Alzheimer's disease (AD). BACE1 enzyme is essential for the generation of Aβ. Deficiency of p38α-MAPK in neurons increases lysosomal degradation of BACE1 and decreases Aβ deposition in the brain of APP-transgenic mice. However, the mechanisms mediating effects of p38α-MAPK are largely unknown. In this study, we used APP-transgenic mice and cultured neurons and observed that deletion of p38α-MAPK specifically in neurons decreased phosphorylation of Snapin at serine, increased retrograde transportation of BACE1 in axons and reduced BACE1 at synaptic terminals, which suggests that p38α-MAPK deficiency promotes axonal transportation of BACE1 from its predominant locations, axonal terminals, to lysosomes in the cell body. In vitro kinase assay revealed that p38α-MAPK directly phosphorylates Snapin. By further performing mass spectrometry analysis and site-directed mutagenic experiments in SH-SY5Y cell lines, we identified serine residue 112 as a p38α-MAPK-phosphorylating site on Snapin. Replacement of serine 112 with alanine did abolish p38α-MAPK knockdown-induced reduction of BACE1 activity and protein level, and transportation to lysosomes in SH-SY5Y cells. Taken together, our study suggests that activation of p38α-MAPK phosphorylates Snapin and inhibits the retrograde transportation of BACE1 in axons, which might exaggerate amyloid pathology in AD brain.
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Affiliation(s)
- Laura Schnöder
- Department of Neurology, Saarland University, Homburg/Saar, Germany.,German Institute for Dementia Prevention (DIDP), Saarland University, Homburg/Saar, Germany
| | - Inge Tomic
- Department of Neurology, Saarland University, Homburg/Saar, Germany.,German Institute for Dementia Prevention (DIDP), Saarland University, Homburg/Saar, Germany
| | - Laura Schwindt
- Department of Neurology, Saarland University, Homburg/Saar, Germany.,German Institute for Dementia Prevention (DIDP), Saarland University, Homburg/Saar, Germany
| | - Dominic Helm
- European Molecular Biology Laboratory, Proteomics Core Facility, Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory, Proteomics Core Facility, Heidelberg, Germany
| | | | - Elmar Krause
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg, Germany
| | - Jens Rettig
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg, Germany
| | - Klaus Fassbender
- Department of Neurology, Saarland University, Homburg/Saar, Germany.,German Institute for Dementia Prevention (DIDP), Saarland University, Homburg/Saar, Germany
| | - Yang Liu
- Department of Neurology, Saarland University, Homburg/Saar, Germany.,German Institute for Dementia Prevention (DIDP), Saarland University, Homburg/Saar, Germany
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Fujino T, Goyama S, Sugiura Y, Inoue D, Asada S, Yamasaki S, Matsumoto A, Yamaguchi K, Isobe Y, Tsuchiya A, Shikata S, Sato N, Morinaga H, Fukuyama T, Tanaka Y, Fukushima T, Takeda R, Yamamoto K, Honda H, Nishimura EK, Furukawa Y, Shibata T, Abdel-Wahab O, Suematsu M, Kitamura T. Mutant ASXL1 induces age-related expansion of phenotypic hematopoietic stem cells through activation of Akt/mTOR pathway. Nat Commun 2021; 12:1826. [PMID: 33758188 PMCID: PMC7988019 DOI: 10.1038/s41467-021-22053-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/23/2021] [Indexed: 01/31/2023] Open
Abstract
Somatic mutations of ASXL1 are frequently detected in age-related clonal hematopoiesis (CH). However, how ASXL1 mutations drive CH remains elusive. Using knockin (KI) mice expressing a C-terminally truncated form of ASXL1-mutant (ASXL1-MT), we examined the influence of ASXL1-MT on physiological aging in hematopoietic stem cells (HSCs). HSCs expressing ASXL1-MT display competitive disadvantage after transplantation. Nevertheless, in genetic mosaic mouse model, they acquire clonal advantage during aging, recapitulating CH in humans. Mechanistically, ASXL1-MT cooperates with BAP1 to deubiquitinate and activate AKT. Overactive Akt/mTOR signaling induced by ASXL1-MT results in aberrant proliferation and dysfunction of HSCs associated with age-related accumulation of DNA damage. Treatment with an mTOR inhibitor rapamycin ameliorates aberrant expansion of the HSC compartment as well as dysregulated hematopoiesis in aged ASXL1-MT KI mice. Our findings suggest that ASXL1-MT provokes dysfunction of HSCs, whereas it confers clonal advantage on HSCs over time, leading to the development of CH.
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Affiliation(s)
- Takeshi Fujino
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Susumu Goyama
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, and Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Suematsu Gas Biology Project, Shinjuku-ku, Tokyo Japan
| | - Daichi Inoue
- grid.51462.340000 0001 2171 9952Human Oncology and Pathogenesis Program, Memorial Sloan−Kettering Cancer Center and Weill Cornell Medical College, New York, USA ,grid.417982.10000 0004 0623 246XDepartment of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe City, Hyogo Japan
| | - Shuhei Asada
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan ,grid.410818.40000 0001 0720 6587Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo Japan
| | - Satoshi Yamasaki
- grid.26999.3d0000 0001 2151 536XLaboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Akiko Matsumoto
- grid.26999.3d0000 0001 2151 536XLaboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Kiyoshi Yamaguchi
- grid.26999.3d0000 0001 2151 536XDivision of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Yumiko Isobe
- grid.26999.3d0000 0001 2151 536XDivision of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Akiho Tsuchiya
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Shiori Shikata
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Naru Sato
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Hironobu Morinaga
- grid.265073.50000 0001 1014 9130Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo Japan
| | - Tomofusa Fukuyama
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Yosuke Tanaka
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Tsuyoshi Fukushima
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Reina Takeda
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Keita Yamamoto
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Hiroaki Honda
- grid.410818.40000 0001 0720 6587Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo Japan
| | - Emi K. Nishimura
- grid.265073.50000 0001 1014 9130Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo Japan
| | - Yoichi Furukawa
- grid.26999.3d0000 0001 2151 536XDivision of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Tatsuhiro Shibata
- grid.26999.3d0000 0001 2151 536XLaboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
| | - Omar Abdel-Wahab
- grid.51462.340000 0001 2171 9952Human Oncology and Pathogenesis Program, Memorial Sloan−Kettering Cancer Center and Weill Cornell Medical College, New York, USA
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, and Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Suematsu Gas Biology Project, Shinjuku-ku, Tokyo Japan
| | - Toshio Kitamura
- grid.26999.3d0000 0001 2151 536XDivision of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo Japan
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Dan Z, Xiujing H, Ting L, Xiaorong Z, Hong Z, Jiqiao Y, Yanchu L, Jing J. Long Non-coding RNA BTG3-7:1 and JUND Co-regulate C21ORF91 to Promote Triple-Negative Breast Cancer Progress. Front Mol Biosci 2021; 7:605623. [PMID: 33585557 PMCID: PMC7879452 DOI: 10.3389/fmolb.2020.605623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/04/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a type of highly invasive breast cancer with poor prognosis. Recently, massive data reveal that long non-coding RNAs (lncRNAs) play important roles in cancer progress. Recently, although the role of lncRNAs in breast cancer has been well documented, few focused on TNBC. In this study, we aimed to systematically identify functional lncRNAs and to explore its molecular mechanism on TNBC progress. METHODS The recurrence of lncRNAs and their target genes were validated with TNBC biopsies and cell lines. Total one hundred and thirteen TNBC biopsies, including nineteen patient-matched samples, were collected. The profile of TNBC-related lncRNAs and their target genes were characterized by RNA sequencing (RNA-seq) and bioinformatic analysis. Tumor specific lncRNAs, which also showed biological function correlated with TNBC, were identified as potential candidates; and the target genes, which regulated by the identified lncRNAs, were predicted by the analysis of expression correlation and chromosome colocalization. Cross bioinformatic validation was performed with TNBC independent datasets from the cancer genome atlas (TCGA). The biological functions and molecular mechanism were investigated in TNBC model cell lines by cell colony forming assay, flow cytometry assay, western-blot, RNA Fluorescence in situ Hybridization assay (RNA FISH) and chromatin immunoprecipitation-qPCR (ChIP-qPCR). RESULTS Abundant Lnc-BTG3-7:1, which targets gene C21ORF91, was specifically observed in TNBC biopsies and cell lines. Knockdown of Lnc-BTG3-7:1 or C21ORF91 strongly inhibited cell proliferation, promoted cell apoptosis and cell cycle G1-arrested. Meanwhile, investigation of molecular mechanism indicated that Lnc-BTG3-7:1, cooperated with transcription factor JUND, cis-regulated the transcription of C21ORF91 gene, and down-regulation of Lnc-BTG3-7:1/C21ORF91 suppressed GRB2-RAS-RAF-MEK-ERK and GRB2-PI3K-AKT-GSK3β-β-catenin pathways. CONCLUSIONS In this study, we identified a TNBC specific lncRNA Lnc-BTG3-7:1, which sustained tumor progress. Up-regulation of Lnc-BTG3-7:1 promoted the transcription of oncogene C21ORF91 and activated PI3K-AKT-GSK3β-β-catenin and MAPK pathways. Taken together, our results not only identified a biomarker for diagnosis but also provided a potential therapeutic target against TNBC.
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Affiliation(s)
- Zheng Dan
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - He Xiujing
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Luo Ting
- Department of Head and Neck Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhong Xiaorong
- Department of Head and Neck Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Zheng Hong
- Department of Head and Neck Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Jiqiao
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Li Yanchu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Jing
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
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Loss of Tid1/DNAJA3 Co-Chaperone Promotes Progression and Recurrence of Hepatocellular Carcinoma after Surgical Resection: A Novel Model to Stratify Risk of Recurrence. Cancers (Basel) 2021; 13:cancers13010138. [PMID: 33406664 PMCID: PMC7795123 DOI: 10.3390/cancers13010138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Tid1 acts as a tumor suppressor in various cancer types, however, its role in hepatocellular carcinoma (HCC) remains unclear. Here, we observed a low protein level of Tid1 in poorly differentiated HCC cell lines. The expression of Tid1 affected the malignancy in human HCC cell lines; meanwhile the protein level of Nrf2 was negatively regulated by Tid1. In multivariate analysis, using immunohistochemical (IHC) assay in 210 HCC cases, we found the tumor size > 5 cm, multiple tumors, presence of vascular invasion, low Tid1 expression in the non-tumor part, and high Nrf2 expression in the non-tumor part, were independently associated with worse recurrence-free survival (RFS). A scoring system by integrating the five clinical and pathological factors predicts the RFS among HCC patients after surgical resection. In summary, Tid1 plays a prognostic role for surgically resected HCC. Abstract Tid1, a mitochondrial co-chaperone protein, acts as a tumor suppressor in various cancer types. However, the role of Tid1 in hepatocellular carcinoma (HCC) remains unclear. First, we found that a low endogenous Tid1 protein level was observed in poorly differentiated HCC cell lines. Further, upregulation/downregulation of Tid1 abrogated/promoted the malignancy of human HCC cell lines, respectively. Interestingly, Tid1 negatively modulated the protein level of Nrf2. Tissue assays from 210 surgically resected HCC patients were examined by immunohistochemistry (IHC) analyses. The protein levels of Tid1 in the normal and tumor part of liver tissues were correlated with the clinical outcome of the 210 HCC cases. In multivariate analysis, we discovered that tumor size > 5 cm, multiple tumors, presence of vascular invasion, low Tid1 expression in the non-tumor part, and high Nrf2 expression in the non-tumor part were significant factors associated with worse recurrence-free survival (RFS). A scoring system by integrating the five clinical and pathological factors predicts the RFS among HCC patients after surgical resection. Together, Tid1, serving as a tumor suppressor, has a prognostic role for surgically resected HCC to predict RFS.
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RBBP6 interactome: RBBP6 isoform 3/DWNN and Nek6 interaction is critical for cell cycle regulation and may play a role in carcinogenesis. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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9
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Jiang L, Hu LG. Serpin peptidase inhibitor clade A member 1-overexpression in gastric cancer promotes tumor progression in vitro and is associated with poor prognosis. Oncol Lett 2020; 20:278. [PMID: 33014156 PMCID: PMC7520747 DOI: 10.3892/ol.2020.12141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer is the second most common cause of cancer-associated death in Asia. The incidence and mortality rates of gastric cancer have markedly increased in the past few decades. Therefore, the identification of novel gastric cancer biomarkers are needed to determine prognosis. The role of serpin peptidase inhibitor clade A member 1 (SERPINA1) has been studied in several types of cancer; however, little is known about its mechanism in gastric cancer. The present study aimed to evaluate SERPINA1 as a potential prognostic biomarker in gastric cancer and to identify the possible mechanisms underlying its action. The expression levels of SERPINA1 in several gastric cancer datasets were assessed, and it was identified that high expression of SERPINA1 was associated to poor clinical outcomes. Furthermore, using histochemical analysis, western blotting, apoptotic analysis, gap closure and invasion assays in cell lines, it was reported that silencing of SERPINA1 inhibited the formation of cellular pseudopodia and did not affect apoptosis, but promoted cell cycle S-phase entry. In addition, overexpression of SERPINA1 increased the migration and invasion of gastric cancer cells, whereas knockdown of SERPINA1 decreased these functions. Moreover, SERPINA1 overexpression increased the protein levels of SMAD4, which is a key regulator of the transforming growth factor (TGF)-β signaling pathway. Taken together, the present data demonstrated that SERPINA1 promotes gastric cancer progression through TGF-β signaling, and suggested that SERPINA1 may be a novel prognostic biomarker from tumor tissue biopsy in gastric cancer.
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Affiliation(s)
- Longchang Jiang
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Asia Research and Development Center, Shanghai 201210, P.R. China
| | - Liangbiao George Hu
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Asia Research and Development Center, Shanghai 201210, P.R. China
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10
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Jia H, Mo W, Hong M, Jiang S, Zhang YY, He D, Yu D, Shi Y, Cao J, Xu X, Zhang S. Interferon-α inducible protein 6 (IFI6) confers protection against ionizing radiation in skin cells. J Dermatol Sci 2020; 100:139-147. [PMID: 33059972 DOI: 10.1016/j.jdermsci.2020.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/03/2020] [Accepted: 09/13/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Radiation-induced skin injury is one of the main adverse effects and a dose-limiting factor of radiotherapy without feasible treatment. The underlying mechanism of this disease is still limited. OBJECTIVE To investigate the potential molecular pathways and mechanisms of radiation-induced skin injury. METHODS mRNA expression profiles were determined by Affymetrix Human HTA2.0 microarray.IFI6 overexpression and knockdown were mediated by lentivirus. The functional changes of skin cells were measured by flow cytometry, ROS probe and Edu probe. Protein distribution was detected by immunofluorescence experiment, and IFI6-interacting proteins were detected by immunoprecipitation (IP) combined with mass spectrometry. The global gene changes in IFI6-overexpressed skin cells after irradiation were detected by RNA-seq. RESULTS mRNA expression profiling showed 50 upregulated and 13 down regulated genes and interferon alpha inducible protein 6 (IFI6) was top upregulated. Overexpression of IFI6 promoted cell proliferation and reduced cell apoptosis as well as ROS production following radiation, and conversely, increased the radiosensitivity of HaCaT and human skin fibroblast (WS1). IFI6 was translocated into nucleus in irradiated skin cells and the interacting relationship with mitochondrial single-stranded DNA-binding protein 1 (SSBP1), which could enhance the transcriptional activity of heat shock transcription factor 1 (HSF1).IFI6 augmented HSF1 activity following radiation in HaCaT and WS1 cells. RNA-seq analysis showed IFI6 modulated virus infection and cellular response to stress pathways, which may help to further explore how IFI6 regulate the transcriptional activity of HSF1. CONCLUSION This study reveals that IFI6 is induced by ionizing radiation and confers radioprotection in skin cells.
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Affiliation(s)
- Huimin Jia
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Wei Mo
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Min Hong
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Sheng Jiang
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yuan-Yuan Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Dan He
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Daojiang Yu
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yuhong Shi
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Jianping Cao
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Xiaohui Xu
- Department of General Surgery, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Taicang, China.
| | - Shuyu Zhang
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China; West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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11
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Ras assemblies and signaling at the membrane. Curr Opin Struct Biol 2020; 62:140-148. [DOI: 10.1016/j.sbi.2020.01.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
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12
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Wang Q, Zhang H, Liang Y, Jiang H, Tan S, Luo F, Yuan Z, Chen Y. A Novel Method to Efficiently Highlight Nonlinearly Expressed Genes. Front Genet 2020; 10:1410. [PMID: 32082366 PMCID: PMC7006292 DOI: 10.3389/fgene.2019.01410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/27/2019] [Indexed: 12/15/2022] Open
Abstract
For precision medicine, there is a need to identify genes that accurately distinguish the physiological state or response to a particular therapy, but this can be challenging. Many methods of analyzing differential expression have been established and applied to this problem, such as t-test, edgeR, and DEseq2. A common feature of these methods is their focus on a linear relationship (differential expression) between gene expression and phenotype. However, they may overlook nonlinear relationships due to various factors, such as the degree of disease progression, sex, age, ethnicity, and environmental factors. Maximal information coefficient (MIC) was proposed to capture a wide range of associations of two variables in both linear and nonlinear relationships. However, with MIC it is difficult to highlight genes with nonlinear expression patterns as the genes giving the most strongly supported hits are linearly expressed, especially for noisy data. It is thus important to also efficiently identify nonlinearly expressed genes in order to unravel the molecular basis of disease and to reveal new therapeutic targets. We propose a novel nonlinearity measure called normalized differential correlation (NDC) to efficiently highlight nonlinearly expressed genes in transcriptome datasets. Validation using six real-world cancer datasets revealed that the NDC method could highlight nonlinearly expressed genes that could not be highlighted by t-test, MIC, edgeR, and DEseq2, although MIC could capture nonlinear correlations. The classification accuracy indicated that analysis of these genes could adequately distinguish cancer and paracarcinoma tissue samples. Furthermore, the results of biological interpretation of the identified genes suggested that some of them were involved in key functional pathways associated with cancer progression and metastasis. All of this evidence suggests that these nonlinearly expressed genes may play a central role in regulating cancer progression.
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Affiliation(s)
- Qifei Wang
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha, China
| | - Haojian Zhang
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha, China
| | - Yuqing Liang
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha, China
| | - Heling Jiang
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha, China
| | - Siqiao Tan
- School of Information Science and Technology, Hunan Agricultural University, Changsha, China
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, United States
| | - Zheming Yuan
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha, China
| | - Yuan Chen
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha, China
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13
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Nussinov R, Tsai CJ, Jang H. Does Ras Activate Raf and PI3K Allosterically? Front Oncol 2019; 9:1231. [PMID: 31799192 PMCID: PMC6874141 DOI: 10.3389/fonc.2019.01231] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
The mechanism through which oncogenic Ras activates its effectors is vastly important to resolve. If allostery is at play, then targeting allosteric pathways could help in quelling activation of MAPK (Raf/MEK/ERK) and PI3K (PI3K/Akt/mTOR) cell proliferation pathways. On the face of it, allosteric activation is reasonable: Ras binding perturbs the conformational ensembles of its effectors. Here, however, we suggest that at least for Raf, PI3K, and NORE1A (RASSF5), that is unlikely. Raf's long disordered linker dampens effective allosteric activation. Instead, we suggest that the high-affinity Ras–Raf binding relieves Raf's autoinhibition, shifting Raf's ensemble from the inactive to the nanocluster-mediated dimerized active state, as Ras also does for NORE1A. PI3K is recruited and allosterically activated by RTK (e.g., EGFR) at the membrane. Ras restrains PI3K's distribution and active site orientation. It stabilizes and facilitates PIP2 binding at the active site and increases the PI3K residence time at the membrane. Thus, RTKs allosterically activate PI3Kα; however, merging their action with Ras accomplishes full activation. Here we review their activation mechanisms in this light and draw attention to implications for their pharmacology.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
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14
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Zhang M, Jang H, Nussinov R. The structural basis for Ras activation of PI3Kα lipid kinase. Phys Chem Chem Phys 2019; 21:12021-12028. [PMID: 31135801 PMCID: PMC6556208 DOI: 10.1039/c9cp00101h] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PI3Kα is a principal Ras effector that phosphorylates PIP2 to PIP3 in the PI3K/Akt/mTOR pathway. How Ras activates PI3K has been unclear: is Ras' role confined to PI3K recruitment to the membrane or does Ras activation also involve allostery? Recently, we determined the mechanism of PI3Kα activation at the atomic level. We showed the vital role and significance of conformational change in PI3Kα activation. Here, by a 'best-match for hydrogen-bonding pair' (BMHP) computational protocol and molecular dynamics (MD) simulations, we model the atomic structure of KRas4B in complex with the Ras binding domain (RBD) of PI3Kα, striving to understand the mechanism of PI3Kα activation by Ras. Point mutations T208D, K210E, and K227E disrupt the KRas4B-RBD interface in the models, in line with the experiments. We identify allosteric signaling pathways connecting Ras to RBD in the p110α subunit. However, the observed weak allosteric signals coupled with the detailed mechanism of PI3Kα activation make us conclude that the dominant mechanistic role of Ras is likely to be recruitment and restriction of the PI3Kα population at the membrane. Thus, RTK recruits the PI3Kα to the membrane and activates it by relieving its autoinhibition exerted by the nSH2 domain, leading to exposure of the kinase domain, which permits PIP2 binding. Ras recruitment can shift the PI3Kα ensemble toward a population where the kinase domain surface and the active site position and orientation favor PIP2 insertion. This work helps elucidate Ras-mediated PI3K activation and explores the structural basis for Ras-PI3Kα drug discovery.
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Affiliation(s)
- Mingzhen Zhang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
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15
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Seshacharyulu P, Rachagani S, Muniyan S, Siddiqui JA, Cruz E, Sharma S, Krishnan R, Killips BJ, Sheinin Y, Lele SM, Smith LM, Talmon GA, Ponnusamy MP, Datta K, Batra SK. FDPS cooperates with PTEN loss to promote prostate cancer progression through modulation of small GTPases/AKT axis. Oncogene 2019; 38:5265-5280. [PMID: 30914801 PMCID: PMC6597298 DOI: 10.1038/s41388-019-0791-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/15/2019] [Accepted: 03/03/2019] [Indexed: 02/07/2023]
Abstract
Farnesyl diphosphate synthase (FDPS), a mevalonate pathway enzyme, is highly expressed in several cancers, including prostate cancer (PCa). To date, the mechanistic, functional, and clinical significance of FDPS in cancer remains unexplored. We evaluated the FDPS expression and its cancer-associated phenotypes using in vitro and in vivo methods in PTEN-deficient and sufficient human and mouse PCa cells and tumors. Interestingly, FDPS overexpression synergizes with PTEN deficiency in PTEN conditionally knockout mice (P < 0.05) and expressed significantly higher in human (P < 0.001) PCa tissues, cell lines, and murine tumoroids compared to respective controls. In silico analysis revealed that FDPS is associated with increasing Gleason score, PTEN functionally deficient status, and poor survival of PCa. Ectopic overexpression of FDPS promotes oncogenic phenotypes such as colony formation (P < 0.01) and proliferation (P < 0.01) through activation of AKT and ERK signaling by prenylating Rho A, Rho G, and CDC42 small GTPases. Of interest, knockdown of FDPS in PCa cells exhibits decreased colony growth and proliferation (P < 0.001) by modulating AKT and ERK pathways. Further, genetic and pharmacological inhibition of PI3K but not AKT reduced FDPS expression. Pharmacological targeting of FDPS by zoledronic acid (ZOL), which is already in clinics, exhibit reduced growth and clonogenicity of human and murine PCa cells (P < 0.01) and 3D tumoroids (P < 0.02) by disrupting AKT and ERK signaling through direct interference of small GTPases protein prenylation. Thus, FDPS plays an oncogenic role in PTEN-deficient PCa through GTPase/AKT axis. Identifying mevalonate pathway proteins could serve as a therapeutic target in PTEN dysregulated tumors.
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Affiliation(s)
| | - Satyanarayana Rachagani
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sakthivel Muniyan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jawed A Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Eric Cruz
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sunandini Sharma
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ramakrishnan Krishnan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Brigham J Killips
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yuri Sheinin
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Subodh M Lele
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lynette M Smith
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Geoffrey A Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kaustubh Datta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA.
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA.
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA.
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16
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Zhou F, Li M, Wei Y, Lin K, Lu Y, Shen J, Johanning GL, Wang-Johanning F. Activation of HERV-K Env protein is essential for tumorigenesis and metastasis of breast cancer cells. Oncotarget 2018; 7:84093-84117. [PMID: 27557521 PMCID: PMC5356647 DOI: 10.18632/oncotarget.11455] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/11/2016] [Indexed: 12/12/2022] Open
Abstract
Human endogenous retrovirus type K (HERV-K) Env protein was previously demonstrated to be overexpressed in human breast cancer (BC) cells and tissues. However, the molecular pathways driving the specific alterations are unknown. We now show that knockdown of its expression with an shRNA (shRNAenv) blocked BC cell proliferation, migration, and invasion. shRNAenv transduction also attenuated the ability of BC cells to form tumors, and notably prevented metastasis. Mechanistically, downregulation of HERV-K blocked expression of tumor-associated genes that included Ras, p-RSK, and p-ERK. The major upstream regulators influenced by HERV-K knockdown were p53, TGF- β1, and MYC. Of interest, when the HERV-K env gene was overexpressed in shRNAenv-transduced BC cells using an HERV-K env expression vector, Ras/Raf/MEK/ERK pathway signaling was restored. CDK5, which alters p53 phosphorylation in some cancers, was upregulated and p53 was downregulated when HERV-K was overexpressed. CDK5 is also a mediator of TGF-β1-induced epithelial-mesenchymal transition and migration in cancer cells, and is involved in tumor formation. Importantly, reductions in migration, invasion, and transformation of BC cells stably transduced with shRNAenv was reversed after adding back a vector with a synonymous mutation of HERV-K env. Taken together, these results indicate that HERV-K Env protein plays an important role in tumorigenesis and metastasis of BC.
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Affiliation(s)
- Fuling Zhou
- Viral Oncology Program, Center for Cancer and Metabolism, SRI International, Menlo Park, California, USA.,Department of Clinical Hematology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Ming Li
- Viral Oncology Program, Center for Cancer and Metabolism, SRI International, Menlo Park, California, USA
| | - Yongchang Wei
- Viral Oncology Program, Center for Cancer and Metabolism, SRI International, Menlo Park, California, USA.,Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Gary L Johanning
- Viral Oncology Program, Center for Cancer and Metabolism, SRI International, Menlo Park, California, USA
| | - Feng Wang-Johanning
- Viral Oncology Program, Center for Cancer and Metabolism, SRI International, Menlo Park, California, USA
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17
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Asxl1 deficiency in embryonic fibroblasts leads to cellular senescence via impairment of the AKT-E2F pathway and Ezh2 inactivation. Sci Rep 2017; 7:5198. [PMID: 28701722 PMCID: PMC5507898 DOI: 10.1038/s41598-017-05564-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/30/2017] [Indexed: 12/14/2022] Open
Abstract
Although ASXL1 mutations are frequently found in human diseases, including myeloid leukemia, the cell proliferation-associated function of ASXL1 is largely unknown. Here, we explored the molecular mechanism underlying the growth defect found in Asxl1-deficient mouse embryonic fibroblasts (MEFs). We found that Asxl1, through amino acids 371 to 655, interacts with the kinase domain of AKT1. In Asxl1-null MEFs, IGF-1 was unable to induce AKT1 phosphorylation and activation; p27Kip1, which forms a ternary complex with ASXL1 and AKT1, therefore remained unphosphorylated. Hypophosphorylated p27Kip1 is able to enter the nucleus, where it prevents the phosphorylation of Rb; this ultimately leads to the down-regulation of E2F target genes as confirmed by microarray analysis. We also found that senescence-associated (SA) genes were upregulated and that SA β-gal staining was increased in Asxl1 -/- MEFs. Further, the treatment of an AKT inhibitor not only stimulated nuclear accumulation of p27Kip1 leading to E2F inactivation, but also promoted senescence. Finally, Asxl1 disruption augmented the expression of p16Ink4a as result of the defect in Asxl1-Ezh2 cooperation. Overall, our study provides the first evidence that Asxl1 both activates the AKT-E2F pathway and cooperates with Ezh2 through direct interactions at early embryonic stages, reflecting that Asxl1 disruption causes cellular senescence.
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18
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Wang T, Seah S, Loh X, Chan CW, Hartman M, Goh BC, Lee SC. Simvastatin-induced breast cancer cell death and deactivation of PI3K/Akt and MAPK/ERK signalling are reversed by metabolic products of the mevalonate pathway. Oncotarget 2016; 7:2532-44. [PMID: 26565813 PMCID: PMC4823053 DOI: 10.18632/oncotarget.6304] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/14/2015] [Indexed: 02/07/2023] Open
Abstract
Statins purportedly exert anti-tumoral effects on breast cancer. However, the biologic mechanisms for these actions are not fully elucidated. The aims of this study were 1) to explore the effects of simvastatin on apoptosis, proliferation as well as PI3K/Akt/mTOR and MAPK/ERK pathway in a window-of-opportunity breast cancer trial; 2) to further confirm findings from the clinical trial by functional studies; 3) to explore the regulatory role of mevalonate pathway on the anti-tumoral effects of simvastatin. In clinical samples, simvastatin led to increase in cleaved caspase-3 (p = 0.002) and decreased trend for Ki67 (p = 0.245). Simvastatin markedly suppressed PI3K/Akt/mTOR signalling by activating PTEN (p = 0.005) and by dephosphorylating Akt (p = 0.002) and S6RP (p = 0.033); it also inhibited MAPK/ERK pathway by dephosphorylating c-Raf (p = 0.018) and ERK1/2 (p = 0.002). In ER-positive (MCF-7, T47D) and ER-negative (MDA-MB-231, BT-549) breast cancer cells, simvastatin treatment consistently induced apoptosis and inhibited proliferation by deregulating caspase cascades and cell cycle proteins in a dose dependent manner. Concordantly, simvastatin strongly suppressed PI3K/Akt/mTOR pathway by enhancing PTEN expression and by further sequentially dephosphorylating downstream cascades including Akt, mTOR, p70S6K, S6RP and 4E-BP1. Furthermore, simvastatin significantly inhibited MAPK/ERK pathway by dephosphorylating sequential cascades such as c-Raf, MEK1/2 and ERK1/2. These simvastatin anti-tumoral effects were reversed by metabolic products of the mevalonate pathway, including mevalonate, farnesyl pyrophosphate and geranylgeranyl pyrophosphate. These findings shed light on the biological and potential anti-tumoral effects of simvastatin in breast cancer.
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Affiliation(s)
- Tingting Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Serena Seah
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xinyi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ching-Wan Chan
- Department of Surgery, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Mikael Hartman
- Department of Surgery, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Boon-Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology and Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Soo-Chin Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology and Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
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19
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Chou CH, Chuang LY, Lu CY, Guh JY. Vitamin D-binding protein is required for the protective effects of vitamin D in renal fibroblasts and is phosphorylated in diabetic rats. Mol Cell Endocrinol 2015; 411:67-74. [PMID: 25911112 DOI: 10.1016/j.mce.2015.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 03/28/2015] [Accepted: 04/13/2015] [Indexed: 01/13/2023]
Abstract
Serum vitamin D is bound to vitamin D-binding protein (DBP). We studied the roles of DBP in streptozotocin-diabetic rats and high glucose (HG)-cultured cells. In diabetic rat sera, there was one upregulated (with a lower isoelectric point [pI], phosphorylated at S268, S270, S464 and T269) and one downregulated (with a higher pI, phosphorylated at S454 and S457) DBP. DBP levels with lower pI were increased in diabetic rat kidney and liver. HG (30 mM) increased DBP protein expression in NRK-49F cells and Clone-9 hepatocytes. HG decreased pI of DBP in Clone-9 hepatocytes. Moreover, DBP short hairpin ribonucleic acid attenuated 1,25-(OH)2D3-induced attenuation of HG-induced renin (but not collagen IV and fibronectin) protein expression in NRK-49F cells. Thus, DBP level is increased whereas DBP is phosphorylated in diabetic rat serum. HG increased DBP protein expression in renal fibroblasts and hepatocytes. Moreover, DBP is required for vitamin D-induced attenuation of HG-induced renin in NRK-49F cells.
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Affiliation(s)
- Chi-Hsien Chou
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Taiwan
| | - Lea-Yea Chuang
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Taiwan.
| | - Chi-Yu Lu
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Taiwan
| | - Jinn-Yuh Guh
- Department of Internal Medicine, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Taiwan; Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Taiwan.
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20
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Genome-wide gene-gene interaction analysis for next-generation sequencing. Eur J Hum Genet 2015; 24:421-8. [PMID: 26173972 DOI: 10.1038/ejhg.2015.147] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 04/21/2015] [Accepted: 05/26/2015] [Indexed: 01/13/2023] Open
Abstract
The critical barrier in interaction analysis for next-generation sequencing (NGS) data is that the traditional pairwise interaction analysis that is suitable for common variants is difficult to apply to rare variants because of their prohibitive computational time, large number of tests and low power. The great challenges for successful detection of interactions with NGS data are (1) the demands in the paradigm of changes in interaction analysis; (2) severe multiple testing; and (3) heavy computations. To meet these challenges, we shift the paradigm of interaction analysis between two SNPs to interaction analysis between two genomic regions. In other words, we take a gene as a unit of analysis and use functional data analysis techniques as dimensional reduction tools to develop a novel statistic to collectively test interaction between all possible pairs of SNPs within two genome regions. By intensive simulations, we demonstrate that the functional logistic regression for interaction analysis has the correct type 1 error rates and higher power to detect interaction than the currently used methods. The proposed method was applied to a coronary artery disease dataset from the Wellcome Trust Case Control Consortium (WTCCC) study and the Framingham Heart Study (FHS) dataset, and the early-onset myocardial infarction (EOMI) exome sequence datasets with European origin from the NHLBI's Exome Sequencing Project. We discovered that 6 of 27 pairs of significantly interacted genes in the FHS were replicated in the independent WTCCC study and 24 pairs of significantly interacted genes after applying Bonferroni correction in the EOMI study.
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21
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Watanabe Y, Yoshida M, Yamanishi K, Yamamoto H, Okuzaki D, Nojima H, Yasunaga T, Okamura H, Matsunaga H, Yamanishi H. Genetic analysis of genes causing hypertension and stroke in spontaneously hypertensive rats: Gene expression profiles in the kidneys. Int J Mol Med 2015; 36:712-24. [PMID: 26165378 PMCID: PMC4533772 DOI: 10.3892/ijmm.2015.2281] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 06/25/2015] [Indexed: 12/15/2022] Open
Abstract
Spontaneously hypertensive rats (SHRs) and stroke-prone SHRs (SHRSP) are frequently used as models not only of essential hypertension and stroke, but also of attention-deficit hyperactivity disorder (ADHD). Normotensive Wistar-Kyoto (WKY) rats are normally used as controls in these studies. In the present study, we aimed to identify the genes causing hypertension and stroke, as well as the genes involved in ADHD using these rats. We previously analyzed gene expression profiles in the adrenal glands and brain. Since the kidneys can directly influence the functions of the cardiovascular, endocrine and sympathetic nervous systems, gene expression profiles in the kidneys of the 3 rat strains were examined using genome-wide microarray technology when the rats were 3 and 6 weeks old, a period in which rats are considered to be in a pre-hypertensive state. Gene expression profiles were compared between the SHRs and WKY rats and also between the SHRSP and SHRs. A total of 232 unique genes showing more than a 4-fold increase or less than a 4-fold decrease in expression were isolated as SHR- and SHRSP-specific genes. Candidate genes were then selected using two different web tools: the 1st tool was the Database for Annotation, Visualization and Integrated Discovery (DAVID), which was used to search for significantly enriched genes and categorized them using Gene Ontology (GO) terms, and the 2nd was Ingenuity Pathway Analysis (IPA), which was used to search for interactions among SHR- and also SHRSP‑specific genes. The analyses of SHR-specific genes using IPA revealed that B-cell CLL/lymphoma 6 (Bcl6) and SRY (sex determining region Y)-box 2 (Sox2) were possible candidate genes responsible for causing hypertension in SHRs. Similar analyses of SHRSP-specific genes revealed that angiotensinogen (Agt), angiotensin II receptor-associated protein (Agtrap) and apolipoprotein H (Apoh) were possible candidate genes responsible for triggering strokes. Since our results revealed that SHRSP-specific genes isolated from the kidneys of rats at 6 weeks of age, included 6 genes related to Huntington's disease, we discussed the genetic association between ADHD and Huntington's disease.
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Affiliation(s)
- Yuko Watanabe
- Hirakata General Hospital for Developmental Disorders, Hirakata, Osaka 573-0122, Japan
| | - Momoko Yoshida
- Hirakata General Hospital for Developmental Disorders, Hirakata, Osaka 573-0122, Japan
| | - Kyosuke Yamanishi
- Department of Neuropsychiatry, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Hideyuki Yamamoto
- Institute for Advanced Medical Sciences, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Daisuke Okuzaki
- DNA-Chip Development Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroshi Nojima
- DNA-Chip Development Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Teruo Yasunaga
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Haruki Okamura
- Institute for Advanced Medical Sciences, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Hisato Matsunaga
- Department of Neuropsychiatry, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Hiromichi Yamanishi
- Hirakata General Hospital for Developmental Disorders, Hirakata, Osaka 573-0122, Japan
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Li Y, Wang X, Vural S, Mishra NK, Cowan KH, Guda C. Exome analysis reveals differentially mutated gene signatures of stage, grade and subtype in breast cancers. PLoS One 2015; 10:e0119383. [PMID: 25803781 PMCID: PMC4372331 DOI: 10.1371/journal.pone.0119383] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/30/2015] [Indexed: 12/17/2022] Open
Abstract
Breast cancers exhibit highly heterogeneous molecular profiles. Although gene expression profiles have been used to predict the risks and prognostic outcomes of breast cancers, the high variability of gene expression limits its clinical application. In contrast, genetic mutation profiles would be more advantageous than gene expression profiles because genetic mutations can be stably detected and the mutational heterogeneity widely exists in breast cancer genomes. We analyzed 98 breast cancer whole exome samples that were sorted into three subtypes, two grades and two stages. The sum deleterious effect of all mutations in each gene was scored to identify differentially mutated genes (DMGs) for this case-control study. DMGs were corroborated using extensive published knowledge. Functional consequences of deleterious SNVs on protein structure and function were also investigated. Genes such as ERBB2, ESP8, PPP2R4, KIAA0922, SP4, CENPJ, PRCP and SELP that have been experimentally or clinically verified to be tightly associated with breast cancer prognosis are among the DMGs identified in this study. We also identified some genes such as ARL6IP5, RAET1E, and ANO7 that could be crucial for breast cancer development and prognosis. Further, SNVs such as rs1058808, rs2480452, rs61751507, rs79167802, rs11540666, and rs2229437 that potentially influence protein functions are observed at significantly different frequencies in different comparison groups. Protein structure modeling revealed that many non-synonymous SNVs have a deleterious effect on protein stability, structure and function. Mutational profiling at gene- and SNV-level revealed differential patterns within each breast cancer comparison group, and the gene signatures correlate with expected prognostic characteristics of breast cancer classes. Some of the genes and SNVs identified in this study show high promise and are worthy of further investigation by experimental studies.
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Affiliation(s)
- You Li
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Xiaosheng Wang
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Suleyman Vural
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Nitish K. Mishra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kenneth H. Cowan
- Fred and Pamela Buffett Cancer Center, Nebraska Medical Center, Omaha, Nebraska, United States of America
- Eppley Institute for Cancer Research, Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Fred and Pamela Buffett Cancer Center, Nebraska Medical Center, Omaha, Nebraska, United States of America
- Eppley Institute for Cancer Research, Nebraska Medical Center, Omaha, Nebraska, United States of America
- Bioinformatics and Systems Biology Core, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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23
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Chalmel F, Com E, Lavigne R, Hernio N, Teixeira-Gomes AP, Dacheux JL, Pineau C. An integrative omics strategy to assess the germ cell secretome and to decipher sertoli-germ cell crosstalk in the Mammalian testis. PLoS One 2014; 9:e104418. [PMID: 25111155 PMCID: PMC4128672 DOI: 10.1371/journal.pone.0104418] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/08/2014] [Indexed: 12/11/2022] Open
Abstract
Mammalian spermatogenesis, which takes place in complex testicular structures called seminiferous tubules, is a highly specialized process controlled by the integration of juxtacrine, paracrine and endocrine information. Within the seminiferous tubules, the germ cells and Sertoli cells are surrounded by testicular fluid (TF), which probably contains most of the secreted proteins involved in crosstalk between these cells. It has already been established that germ cells can modulate somatic Sertoli cell function through the secretion of diffusible factors. We studied the germ cell secretome, which was previously considered inaccessible, by analyzing the TF collected by microsurgery in an “integrative omics” strategy combining proteomics, transcriptomics, genomics and interactomics data. This approach identified a set of proteins preferentially secreted by Sertoli cells or germ cells. An interaction network analysis revealed complex, interlaced cell-cell dialog between the secretome and membranome of seminiferous cells, mediated via the TF. We then focused on germ cell-secreted candidate proteins, and we identified several potential interacting partners located on the surface of Sertoli cells. Two interactions, APOH/CDC42 and APP/NGFR, were validated in situ, in a proximity ligation assay (PLA). Our results provide new insight into the crosstalk between germ cells and Sertoli cells occurring during spermatogenesis. Our findings also demonstrate that this “integrative omics” strategy is powerful enough for data mining and highlighting meaningful cell-cell communication events between different types of cells in a complex tissue, via a biological fluid. This integrative strategy could be applied more widely, to gain access to secretomes that have proved difficult to study whilst avoiding the limitations of in vitro culture.
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Affiliation(s)
- Frédéric Chalmel
- IRSET, Inserm U1085, Campus de Beaulieu, Rennes, France
- * E-mail: (CP); (FC)
| | - Emmanuelle Com
- Proteomics Core Facility Biogenouest, Inserm U1085 IRSET, Campus de Beaulieu, Rennes, France
| | - Régis Lavigne
- Proteomics Core Facility Biogenouest, Inserm U1085 IRSET, Campus de Beaulieu, Rennes, France
| | - Nolwen Hernio
- Proteomics Core Facility Biogenouest, Inserm U1085 IRSET, Campus de Beaulieu, Rennes, France
| | - Ana-Paula Teixeira-Gomes
- INRA UMR 1282, Infectiologie et Santé Publique, Nouzilly, France
- INRA Plate-forme d'Analyse Intégrative des Biomolécules (PAIB), Nouzilly, France
| | | | - Charles Pineau
- Proteomics Core Facility Biogenouest, Inserm U1085 IRSET, Campus de Beaulieu, Rennes, France
- * E-mail: (CP); (FC)
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24
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Aya-Bonilla C, Camilleri E, Haupt LM, Lea R, Gandhi MK, Griffiths LR. In silico analyses reveal common cellular pathways affected by loss of heterozygosity (LOH) events in the lymphomagenesis of Non-Hodgkin's lymphoma (NHL). BMC Genomics 2014; 15:390. [PMID: 24885312 PMCID: PMC4041994 DOI: 10.1186/1471-2164-15-390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 05/02/2014] [Indexed: 11/16/2022] Open
Abstract
Background The analysis of cellular networks and pathways involved in oncogenesis has increased our knowledge about the pathogenic mechanisms that underlie tumour biology and has unmasked new molecular targets that may lead to the design of better anti-cancer therapies. Recently, using a high resolution loss of heterozygosity (LOH) analysis, we identified a number of potential tumour suppressor genes (TSGs) within common LOH regions across cases suffering from two of the most common forms of Non-Hodgkin’s lymphoma (NHL), Follicular Lymphoma (FL) and Diffuse Large B-cell Lymphoma (DLBCL). From these studies LOH of the protein tyrosine phosphatase receptor type J (PTPRJ) gene was identified as a common event in the lymphomagenesis of these B-cell lymphomas. The present study aimed to determine the cellular pathways affected by the inactivation of these TSGs including PTPRJ in FL and DLBCL tumourigenesis. Results Pathway analytical approaches identified that candidate TSGs located within common LOH regions participate within cellular pathways, which may play a crucial role in FL and DLBCL lymphomagenesis (i.e., metabolic pathways). These analyses also identified genes within the interactome of PTPRJ (i.e. PTPN11 and B2M) that when inactivated in NHL may play an important role in tumourigenesis. We also detected genes that are differentially expressed in cases with and without LOH of PTPRJ, such as NFATC3 (nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3). Moreover, upregulation of the VEGF, MAPK and ERBB signalling pathways was also observed in NHL cases with LOH of PTPRJ, indicating that LOH-driving events causing inactivation of PTPRJ, apart from possibly inducing a constitutive activation of these pathways by reduction or abrogation of its dephosphorylation activity, may also induce upregulation of these pathways when inactivated. This finding implicates these pathways in the lymphomagenesis and progression of FL and DLBCL. Conclusions The evidence obtained in this research supports findings suggesting that FL and DLBCL share common pathogenic mechanisms. Also, it indicates that PTPRJ can play a crucial role in the pathogenesis of these B-cell tumours and suggests that activation of PTPRJ might be an interesting novel chemotherapeutic target for the treatment of these B-cell tumours. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-390) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
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25
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Knudsen S, Jensen T, Hansen A, Mazin W, Lindemann J, Kuter I, Laing N, Anderson E. Development and validation of a gene expression score that predicts response to fulvestrant in breast cancer patients. PLoS One 2014; 9:e87415. [PMID: 24505287 PMCID: PMC3914825 DOI: 10.1371/journal.pone.0087415] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/24/2013] [Indexed: 11/19/2022] Open
Abstract
Fulvestrant is a selective estrogen receptor antagonist. Based on the measured growth inhibition of 60 human cancer cell lines (NCI60) in the presence of fulvestrant, as well as the baseline gene expression of the 60 cell lines, a gene expression score that predicts response to fulvestrant was developed. The score is based on 414 genes, 103 of which show increased expression in sensitive cell lines, while 311 show increased expression in the non-responding cell lines. The sensitivity genes primarily sense signaling through estrogen receptor alpha, whereas the resistance genes modulate the PI3K signaling pathway. The latter genes suggest that resistance to fulvestrant can be overcome by drugs targeting the PI3K pathway. The level of this gene expression score and its correlation with fulvestrant response was measured in a panel of 20 breast cancer cell lines. The predicted sensitivity matched the measured sensitivity well (CC = -0.63, P = 0.003). The predictor was applied to tumor biopsies obtained from a Phase II clinical trial. The sensitivity of each patient to treatment with fulvestrant was predicted based on the RNA profile of the biopsy taken before neoadjuvant treatment and without knowledge of the subsequent response. The prediction was then compared to clinical response to show that the responders had a significantly higher sensitivity prediction than the non-responders (P = 0.01). When clinical covariates, tumor grade and estrogen receptor H-score, were included in the prediction, the difference in predicted senstivity between responders and non-responders improved (P = 0.003). Using a pre-defined cutoff to separate patients into predicted sensitive and predicted resistant yielded a positive predictive value of 88% and a negative predictive value of 100% when compared to clinical data. We conclude that pre-screening patients with the new gene expression predictor has the potential to identify those postmenopausal women with locally advanced, estrogen-receptor-positive breast cancer most likely to respond to fulvestrant.
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Affiliation(s)
| | | | | | - Wiktor Mazin
- Medical Prognosis Institute, Hørsholm, Denmark
- Now at the Department of Clinical Epidemiology at Aarhus University Hospital, Aarhus C, Denmark
| | - Justin Lindemann
- Astrazeneca UK Limited, Oncology iMED, Alderley Park, Cheshire, United Kingdom
| | - Irene Kuter
- Massachusetts General Hospital, Massachusetts, Boston, United States of America
| | - Naomi Laing
- Astrazeneca R&D Boston, Waltham, United States of America
| | - Elizabeth Anderson
- Astrazeneca UK Limited, Oncology iMED, Alderley Park, Cheshire, United Kingdom
- Now at Boehringer-Ingelheim RCV GmbH & Co KG, Vienna, Austria
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26
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Okudela K, Katayama A, Woo T, Mitsui H, Suzuki T, Tateishi Y, Umeda S, Tajiri M, Masuda M, Nagahara N, Kitamura H, Ohashi K. Proteome analysis for downstream targets of oncogenic KRAS--the potential participation of CLIC4 in carcinogenesis in the lung. PLoS One 2014; 9:e87193. [PMID: 24503901 PMCID: PMC3913595 DOI: 10.1371/journal.pone.0087193] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 12/20/2013] [Indexed: 01/27/2023] Open
Abstract
This study investigated the proteome modulated by oncogenic KRAS in immortalized airway epithelial cells. Chloride intracellular channel protein 4 (CLIC4), S100 proteins (S100A2 and S100A11), tropomyosin 2, cathepsin L1, integrinsα3, eukaryotic elongation factor 1, vimentin, and others were discriminated. We here focused on CLIC4 to investigate its potential involvement in carcinogenesis in the lung because previous studies suggested that some chloride channels and chloride channel regulators could function as tumor suppressors. CILC4 protein levels were reduced in some lung cancer cell lines. The restoration of CLIC4 in lung cancer cell lines in which CLIC4 expression was reduced attenuated their growth activity. The immunohistochemical expression of the CLIC4 protein was weaker in primary lung cancer cells than in non-tumorous airway epithelial cells and was occasionally undetectable in some tumors. CLIC4 protein levels were significantly lower in a subtype of mucinous ADC than in others, and were also significantly lower in KRAS-mutated ADC than in EGFR-mutated ADC. These results suggest that the alteration in CLIC4 could be involved in restrictedly the development of a specific fraction of lung adenocarcinomas. The potential benefit of the proteome modulated by oncogenic KRAS to lung cancer research has been demonstrated.
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Affiliation(s)
- Koji Okudela
- Department of Pathology, Yokohama City University Graduate School of Medicine, 3-9, Future, Kanazawa-ku, Yokohama, Japan
- * E-mail:
| | - Akira Katayama
- Department of Biochemistry/Cell Biology, Nippon Medical University, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, Japan
| | - Tetsukan Woo
- Department of Surgey, Yokohama City University Graduate School of Medicine, 3-9, Future, Kanazawa-ku, Yokohama, Japan
| | - Hideaki Mitsui
- Department of Pathology, Yokohama City University Graduate School of Medicine, 3-9, Future, Kanazawa-ku, Yokohama, Japan
| | - Takehisa Suzuki
- Department of Pathology, Yokohama City University Graduate School of Medicine, 3-9, Future, Kanazawa-ku, Yokohama, Japan
| | - Yoko Tateishi
- Department of Pathology, Yokohama City University Graduate School of Medicine, 3-9, Future, Kanazawa-ku, Yokohama, Japan
| | - Shigeaki Umeda
- Department of Pathology, Yokohama City University Graduate School of Medicine, 3-9, Future, Kanazawa-ku, Yokohama, Japan
| | - Michihiko Tajiri
- Division of General Thoracic Surgery, Kanagawa Prefectural Cardiovascular and Respiratory Center Hospital, 6-16-1, Tomioka-higashi, Kanazawa-ku, Yokohama, Japan
| | - Munetaka Masuda
- Department of Surgey, Yokohama City University Graduate School of Medicine, 3-9, Future, Kanazawa-ku, Yokohama, Japan
| | - Noriyuki Nagahara
- Department of Enviromental Medicine, Nippon Medical University, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, Japan
| | - Hitoshi Kitamura
- Department of Pathology, Yokohama City University Graduate School of Medicine, 3-9, Future, Kanazawa-ku, Yokohama, Japan
| | - Kenichi Ohashi
- Department of Pathology, Yokohama City University Graduate School of Medicine, 3-9, Future, Kanazawa-ku, Yokohama, Japan
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Woodsmith J, Stelzl U. Studying post-translational modifications with protein interaction networks. Curr Opin Struct Biol 2014; 24:34-44. [DOI: 10.1016/j.sbi.2013.11.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/15/2013] [Accepted: 11/22/2013] [Indexed: 12/14/2022]
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28
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Saini KS, Loi S, de Azambuja E, Metzger-Filho O, Saini ML, Ignatiadis M, Dancey JE, Piccart-Gebhart MJ. Targeting the PI3K/AKT/mTOR and Raf/MEK/ERK pathways in the treatment of breast cancer. Cancer Treat Rev 2013; 39:935-46. [PMID: 23643661 DOI: 10.1016/j.ctrv.2013.03.009] [Citation(s) in RCA: 272] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 11/24/2022]
Abstract
Alterations of signal transduction pathways leading to uncontrolled cellular proliferation, survival, invasion, and metastases are hallmarks of the carcinogenic process. The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) and the Raf/mitogen-activated and extracellular signal-regulated kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling pathways are critical for normal human physiology, and also commonly dysregulated in several human cancers, including breast cancer (BC). In vitro and in vivo data suggest that the PI3K/AKT/mTOR and Raf/MEK/ERK cascades are interconnected with multiple points of convergence, cross-talk, and feedback loops. Raf/MEK/ERK and PI3K/AKT/mTOR pathway mutations may co-exist. Inhibition of one pathway can still result in the maintenance of signaling via the other (reciprocal) pathway. The existence of such "escape" mechanisms implies that dual targeting of these pathways may lead to superior efficacy and better clinical outcome in selected patients. Several clinical trials targeting one or both pathways are already underway in BC patients. The toxicity profile of this novel approach of dual pathway inhibition needs to be closely monitored, given the important physiological role of PI3K/AKT/mTOR and Raf/MEK/ERK signaling. In this article, we present a review of the current relevant pre-clinical and clinical data and discuss the rationale for dual inhibition of these pathways in the treatment of BC patients.
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Affiliation(s)
- Kamal S Saini
- Breast International Group, Brussels, Belgium; Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
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29
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Walker DM, Hayes EC, Webb LJ. Vibrational Stark effect spectroscopy reveals complementary electrostatic fields created by protein–protein binding at the interface of Ras and Ral. Phys Chem Chem Phys 2013; 15:12241-52. [DOI: 10.1039/c3cp51284c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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30
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Wang XQ, Hung BS, Kempf M, Liu PY, Dalley AJ, Saunders NA, Kimble RM. Fetuin-A promotes primary keratinocyte migration: independent of epidermal growth factor receptor signalling. Exp Dermatol 2011; 19:e289-92. [PMID: 19758338 DOI: 10.1111/j.1600-0625.2009.00978.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously, we reported that fetuin-A is a major component of ovine foetal skin and significantly enhances 'wound closure' in primary keratinocyte cultures. In this study, we found that in human newborn foreskin, a high level of fetuin-A protein is detected throughout the dermis. However, in adult skin a low level of fetuin-A is observed throughout the epidermal and dermal layers, except at regions surrounding hair follicles and at the epidermal-dermal junction where the level of fetuin-A is relatively high. Fetuin-A significantly induces actin-rich protrusions in human primary keratinocytes. Interestingly, blockade of epidermal growth factor (EGF) receptor signalling has a limited effect on fetuin-A promoted 'wound closure' on primary human keratinocytes, but significantly inhibits fetuin-A's effect on HaCaT cells. These results indicate that high levels of fetuin-A may partially contribute to less scar formation in newborn foreskin and that the effect of fetuin-A on primary keratinocyte migration is independent of EGF receptor signalling.
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31
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Elfaki I, Bayer P, Mueller JW. A potential transcriptional regulator is out-of-frame translated from the metallothionein 2A messenger RNA. Anal Biochem 2010; 409:159-61. [PMID: 20950582 DOI: 10.1016/j.ab.2010.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 10/06/2010] [Indexed: 01/20/2023]
Abstract
In a number of yeast two-hybrid screens, we have found clones that contained parts of the human metallothionein 2A (MT2A) nucleotide sequence. All of these clones were out-of-frame relative to the MT2A coding sequence and activated the yeast reporters in the presence of the Gal4 DNA binding domain but irrespective of the bait protein. Reporter gene activation was abolished when activation domain and MT2A coding sequences were brought in-frame. In light of these findings, we evaluated all recently reported interactions with metallothioneins because our out-of-frame proline-rich protein might have been the actual interaction partner in some of these studies.
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Affiliation(s)
- Imadeldin Elfaki
- Institute for Structural and Medicinal Biochemistry (ZMB), Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
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32
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Kim KH, Kamal AHM, Shin KH, Choi JS, Heo HY, Woo SH. Large-scale proteome investigation in wild relatives (A, B, and D genomes) of wheat. Acta Biochim Biophys Sin (Shanghai) 2010; 42:709-16. [PMID: 20810536 DOI: 10.1093/abbs/gmq079] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Large-scale proteomics of three wild relatives of wheat grain (A, B, and D genomes) were analyzed by using multidimensional protein identification technology coupled to liquid chromatography quadruple mass spectrometry. A total of 1568 (peptide match ≥1) and 255 (peptide match ≥2) unique proteins were detected and classified, which represents the most wide-ranging proteomic exploitation to date. The development of standard proteomes exhibiting all of the proteins involved in normal physiology will facilitate the delineation of disease/defense, metabolism, energy metabolism, and protein synthesis. A relative proteome exploration of the expression patterns indicates that proteins are involved in abiotic and biotic stress. Functional category analysis indicates that these differentially expressed proteins are mainly involved in disease/defense (15.38%, 21.26%, and 16.78%), metabolism (8.39%, 12.07%, and 14.09%), energy metabolism (11.19%, 11.49%, and 13.42%), protein synthesis (9.09%, 9.20%, and 8.72%), cell growth and division (9.09%, 4.60%, and 6.04%), cellular organization (4.20%, 5.75%, and 5.37%), development (6.29%, 2.87%, 3.36%), folding and stability (6.29%, 8.62%, and 8.05%), signal transduction (11.19%, 7.47%, and 8.05%), storage protein (4.20%, 1.72%, and 2.01%), transcription (5.59%, 5.17%, and 4.03%), and transport facilitation (1.40%, 1.15%, and 3.36%) in A, B, and D genomes, respectively. Here, we reported genome-specific protein interaction network using Cytoscape software, which provides further insight into the molecular functions and mechanism of biochemical pathways. We provide a promising understanding about the expressed proteins and protein functions. Our approach should be applicable as a marker to assist in breeding or gene transfer for quality and stress research of cultivated wheat.
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Affiliation(s)
- Ki-Hyun Kim
- Department of Crop Science, Chungbuk National University, Cheong-ju, Korea
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33
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Boellmann F, Zhang L, Clewell HJ, Schroth GP, Kenyon EM, Andersen ME, Thomas RS. Genome-wide Analysis of DNA Methylation and Gene Expression Changes in the Mouse Lung following Subchronic Arsenate Exposure. Toxicol Sci 2010; 117:404-17. [DOI: 10.1093/toxsci/kfq225] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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34
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Gao X, Zhang X, Zheng J, He F. Proteomics in China: Ready for prime time. SCIENCE CHINA-LIFE SCIENCES 2010; 53:22-33. [DOI: 10.1007/s11427-010-0027-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Accepted: 12/28/2009] [Indexed: 12/27/2022]
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35
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Tian C, Xing G, Xie P, Lu K, Nie J, Wang J, Li L, Gao M, Zhang L, He F. KRAB-type zinc-finger protein Apak specifically regulates p53-dependent apoptosis. Nat Cell Biol 2009; 11:580-91. [PMID: 19377469 DOI: 10.1038/ncb1864] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 02/09/2009] [Indexed: 12/27/2022]
Abstract
Only a few p53 regulators have been shown to participate in the selective control of p53-mediated cell cycle arrest or apoptosis. How p53-mediated apoptosis is negatively regulated remains largely unclear. Here we report that Apak (ATM and p53-associated KZNF protein), a Krüppel-associated box (KRAB)-type zinc-finger protein, binds directly to p53 in unstressed cells, specifically downregulates pro-apoptotic genes, and suppresses p53-mediated apoptosis by recruiting KRAB-box-associated protein (KAP)-1 and histone deacetylase 1 (HDAC1) to attenuate the acetylation of p53. Apak inhibits p53 activity by interacting with ATM, a previously identified p53 activator. In response to stress, Apak is phosphorylated by ATM and dissociates from p53, resulting in activation of p53 and induction of apoptosis. These findings revealed Apak to be a negative regulator of p53-mediated apoptosis and showed the dual role of ATM in p53 regulation.
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Affiliation(s)
- Chunyan Tian
- State Key Laboratory of Proteomics, Beijing Proteomics Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China
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36
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Abu-Farha M, Elisma F, Zhou H, Tian R, Zhou H, Asmer MS, Figeys D. Proteomics: From Technology Developments to Biological Applications. Anal Chem 2009; 81:4585-99. [DOI: 10.1021/ac900735j] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mohamed Abu-Farha
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Fred Elisma
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Houjiang Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ruijun Tian
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hu Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mehmet Selim Asmer
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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