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Esmaeilzadeh Aghjeh M, Hosseinpour Feizi MA, Safaralizadeh R, Hosseinpour Feizi AA, Pouladi N. The evaluation of the possibility of Li-Fraumeni syndrome in cancer patients in East Azarbaijan Province of Iran. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:417-426. [PMID: 37801337 DOI: 10.1080/15257770.2023.2264361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/23/2023] [Indexed: 10/07/2023]
Abstract
INTRODUCTION In 1969, Li-Fraumeni syndrome (LFS), which is a rare cancer predisposition syndrome, was reported for the first time. The main problem in LFS is the mutation in the TP53 gene, which is a crucial tumor suppressor gene in the cell cycle. A hereditary syndrome is inherited in an autosomal dominant pattern. There is a significant correlation between this syndrome and various cancers such as sarcoma, breast cancer, brain tumors, and different other types of malignancies. This study aimed to identify the possibility of LFS in cancer patients in the East Azarbaijan, Iran. METHODS In this experimental study, 45 children with cancer in the Northwest of Iran were investigated for LFS. DNA was extracted from the whole blood cells using the salting-out method. The region within the exons 5-8 of the TP53 gene has been replicated via Polymerase Chain Reaction (PCR) method. The PCR products were sent for Sanger sequencing, and finally, the data were analyzed by Chromas software. RESULTS In the studied probands, in 12 (26.67%) cases, polymorphisms in Exon 6 and Introns 6 and Intron 7 were identified, and no mutation was observed in exons 5-8 of the TP53 gene. CONCLUSION Our results show that there were no mutations in exons 5-8 of the TP53 gene as an indication of LFS possibility in these families. Further studies are needed to be done in a bigger population, and Next-Generation Sequencing (NGS) needs to be done to evaluate the whole genome of these patients to complete our data.
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Affiliation(s)
| | | | | | - Abbas Ali Hosseinpour Feizi
- Hematology-Oncology Research Center, Tabriz University of Medical Sciences, Tabriz Children's Hospital, Tabriz, Iran
| | - Nasser Pouladi
- Department of Biology, Azarbaijan Shahid Madani University, Tabriz, Iran
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2
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Kari S, Subramanian K, Altomonte IA, Murugesan A, Yli-Harja O, Kandhavelu M. Programmed cell death detection methods: a systematic review and a categorical comparison. Apoptosis 2022; 27:482-508. [PMID: 35713779 PMCID: PMC9308588 DOI: 10.1007/s10495-022-01735-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 01/15/2023]
Abstract
Programmed cell death is considered a key player in a variety of cellular processes that helps to regulate tissue growth, embryogenesis, cell turnover, immune response, and other biological processes. Among different types of cell death, apoptosis has been studied widely, especially in the field of cancer research to understand and analyse cellular mechanisms, and signaling pathways that control cell cycle arrest. Hallmarks of different types of cell death have been identified by following the patterns and events through microscopy. Identified biomarkers have also supported drug development to induce cell death in cancerous cells. There are various serological and microscopic techniques with advantages and limitations, that are available and are being utilized to detect and study the mechanism of cell death. The complexity of the mechanism and difficulties in distinguishing among different types of programmed cell death make it challenging to carry out the interventions and delay its progression. In this review, mechanisms of different forms of programmed cell death along with their conventional and unconventional methods of detection of have been critically reviewed systematically and categorized on the basis of morphological hallmarks and biomarkers to understand the principle, mechanism, application, advantages and disadvantages of each method. Furthermore, a very comprehensive comparative analysis has been drawn to highlight the most efficient and effective methods of detection of programmed cell death, helping researchers to make a reliable and prudent selection among the available methods of cell death assay. Conclusively, how programmed cell death detection methods can be improved and can provide information about distinctive stages of cell death detection have been discussed.
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Affiliation(s)
- Sana Kari
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland
| | - Kumar Subramanian
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland
| | - Ilenia Agata Altomonte
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland
| | - Akshaya Murugesan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland.,Department of Biotechnology, Lady Doak College, Thallakulam, Madurai, 625002, India
| | - Olli Yli-Harja
- Institute for Systems Biology, 1441N 34th Street, Seattle, WA, USA.,Computational Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland. .,Department of Biotechnology, Lady Doak College, Thallakulam, Madurai, 625002, India.
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3
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Denney AS, Weems AD, McMurray MA. Selective functional inhibition of a tumor-derived p53 mutant by cytosolic chaperones identified using split-YFP in budding yeast. G3-GENES GENOMES GENETICS 2021; 11:6318398. [PMID: 34544131 PMCID: PMC8496213 DOI: 10.1093/g3journal/jkab230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/17/2021] [Indexed: 11/25/2022]
Abstract
Life requires the oligomerization of individual proteins into higher-order assemblies. In order to form functional oligomers, monomers must adopt appropriate 3D structures. Molecular chaperones transiently bind nascent or misfolded proteins to promote proper folding. Single missense mutations frequently cause disease by perturbing folding despite chaperone engagement. A misfolded mutant capable of oligomerizing with wild-type proteins can dominantly poison oligomer function. We previously found evidence that human-disease-linked mutations in Saccharomyces cerevisiae septin proteins slow folding and attract chaperones, resulting in a kinetic delay in oligomerization that prevents the mutant from interfering with wild-type function. Here, we build upon our septin studies to develop a new approach for identifying chaperone interactions in living cells, and use it to expand our understanding of chaperone involvement, kinetic folding delays, and oligomerization in the recessive behavior of tumor-derived mutants of the tumor suppressor p53. We find evidence of increased binding of several cytosolic chaperones to a recessive, misfolding-prone mutant, p53(V272M). Similar to our septin results, chaperone overexpression inhibits the function of p53(V272M) with minimal effect on the wild type. Unlike mutant septins, p53(V272M) is not kinetically delayed under conditions in which it is functional. Instead, it interacts with wild-type p53 but this interaction is temperature sensitive. At high temperatures or upon chaperone overexpression, p53(V272M) is excluded from the nucleus and cannot function or perturb wild-type function. Hsp90 inhibition liberates mutant p53 to enter the nucleus. These findings provide new insights into the effects of missense mutations.
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Affiliation(s)
- Ashley S Denney
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Andrew D Weems
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael A McMurray
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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4
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Moesslacher CS, Kohlmayr JM, Stelzl U. Exploring absent protein function in yeast: assaying post translational modification and human genetic variation. MICROBIAL CELL (GRAZ, AUSTRIA) 2021; 8:164-183. [PMID: 34395585 PMCID: PMC8329848 DOI: 10.15698/mic2021.08.756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/13/2021] [Accepted: 06/18/2021] [Indexed: 01/08/2023]
Abstract
Yeast is a valuable eukaryotic model organism that has evolved many processes conserved up to humans, yet many protein functions, including certain DNA and protein modifications, are absent. It is this absence of protein function that is fundamental to approaches using yeast as an in vivo test system to investigate human proteins. Functionality of the heterologous expressed proteins is connected to a quantitative, selectable phenotype, enabling the systematic analyses of mechanisms and specificity of DNA modification, post-translational protein modifications as well as the impact of annotated cancer mutations and coding variation on protein activity and interaction. Through continuous improvements of yeast screening systems, this is increasingly carried out on a global scale using deep mutational scanning approaches. Here we discuss the applicability of yeast systems to investigate absent human protein function with a specific focus on the impact of protein variation on protein-protein interaction modulation.
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Affiliation(s)
- Christina S Moesslacher
- Institute of Pharmaceutical Sciences and BioTechMed-Graz, University of Graz, Graz, Austria
- Contributed equally to the writing of this review
| | - Johanna M Kohlmayr
- Institute of Pharmaceutical Sciences and BioTechMed-Graz, University of Graz, Graz, Austria
- Contributed equally to the writing of this review
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences and BioTechMed-Graz, University of Graz, Graz, Austria
- Contributed equally to the writing of this review
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Yang J, Sun Y, Xu F, Liu W, Hayashi T, Mizuno K, Hattori S, Fujisaki H, Ikejima T. Autophagy and glycolysis independently attenuate silibinin-induced apoptosis in human hepatocarcinoma HepG2 and Hep3B cells. Hum Exp Toxicol 2021; 40:2048-2062. [PMID: 34053323 DOI: 10.1177/09603271211017609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE The mechanism of cytotoxicity of silibinin on two human hepatocellular carcinoma (HCC) cell lines, HepG2 (p53 wild-type) and Hep3B cells (p53 null), is examined in relation with the induction of autophagy and phosphorylation of AMP-activated protein kinase (p-AMPK). MATERIALS AND METHODS Levels of apoptosis in relation to the levels of autophagy and those of glycolysis-related proteins, glucose transporter 1/4 (Glut1/4) and hexokinase-II (HK2), in HepG2 and Hep3B cells were examined. RESULTS Silibinin-induced apoptosis was incomplete for HCC cell death in that up-regulated autophagy and/or reduced level of glycolysis, which are induced by silibinin treatment, antagonized silibinin-induced apoptosis. Inhibition of autophagy with 3-methyl adenine (3MA) or blocking of AMP-activated protein kinase (AMPK) activation with Compound C (CC) enhanced silibinin-induced apoptosis. The results confirm that AMPK involved in autophagy as well as in glycolysis remaining with silibinin is responsible for attenuation of silibinin-induced apoptosis. Blocking of AMPK or autophagy contributes to the enhancement of silibinin's cytotoxicity to HepG2 and Hep3B cells. CONCLUSION This study shows that incomplete apoptosis of HCC by silibinin treatment becomes complete by repression of autophagy and/or glycolysis.
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Affiliation(s)
- J Yang
- Department of Pharmacy, 159411The Third People's Hospital of Chengdu, Chengdu, Sichuan, People's Republic of China.,Wuya College of Innovation, 58575Shenyang Pharmaceutical University, Shenyang, Liaoning, People's Republic of China
| | - Y Sun
- Wuya College of Innovation, 58575Shenyang Pharmaceutical University, Shenyang, Liaoning, People's Republic of China
| | - F Xu
- Wuya College of Innovation, 58575Shenyang Pharmaceutical University, Shenyang, Liaoning, People's Republic of China
| | - W Liu
- Wuya College of Innovation, 58575Shenyang Pharmaceutical University, Shenyang, Liaoning, People's Republic of China
| | - T Hayashi
- Wuya College of Innovation, 58575Shenyang Pharmaceutical University, Shenyang, Liaoning, People's Republic of China.,Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, Hachioji, Tokyo, Japan.,Nippi Research Institute of Biomatrix, Toride, Ibaraki, Japan
| | - K Mizuno
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, Japan
| | - S Hattori
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, Japan
| | - H Fujisaki
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, Japan
| | - T Ikejima
- Wuya College of Innovation, 58575Shenyang Pharmaceutical University, Shenyang, Liaoning, People's Republic of China.,Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, 58575Shenyang Pharmaceutical University, Shenyang, Liaoning, People's Republic of China
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Billant O, Friocourt G, Roux P, Voisset C. p53, A Victim of the Prion Fashion. Cancers (Basel) 2021; 13:E269. [PMID: 33450819 PMCID: PMC7828285 DOI: 10.3390/cancers13020269] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/17/2022] Open
Abstract
Identified in the late 1970s as an oncogene, a driving force leading to tumor development, p53 turned out to be a key tumor suppressor gene. Now p53 is considered a master gene regulating the transcription of over 3000 target genes and controlling a remarkable number of cellular functions. The elevated prevalence of p53 mutations in human cancers has led to a recurring questioning about the roles of mutant p53 proteins and their functional consequences. Both mutants and isoforms of p53 have been attributed dominant-negative and gain of function properties among which is the ability to form amyloid aggregates and behave in a prion-like manner. This report challenges the ongoing "prion p53" hypothesis by reviewing evidence of p53 behavior in light of our current knowledge regarding amyloid proteins, prionoids and prions.
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Affiliation(s)
| | - Gaëlle Friocourt
- Inserm, Université de Bretagne Occidentale, EFS, UMR 1078, GGB, F-29200 Brest, France;
| | - Pierre Roux
- CRBM, CNRS, UMR5234, 34293 Montpellier, France;
| | - Cécile Voisset
- Inserm, Université de Bretagne Occidentale, EFS, UMR 1078, GGB, F-29200 Brest, France;
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7
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Park SK, Park S, Pentek C, Liebman SW. Tumor suppressor protein p53 expressed in yeast can remain diffuse, form a prion, or form unstable liquid-like droplets. iScience 2020; 24:102000. [PMID: 33490908 PMCID: PMC7811139 DOI: 10.1016/j.isci.2020.102000] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/20/2020] [Accepted: 12/23/2020] [Indexed: 01/08/2023] Open
Abstract
Mutations in the p53 tumor suppressor are frequent causes of cancer. Because p53 aggregates appear in some tumor cells, it has been suggested that p53 could also cause cancer by forming self-replicating protein aggregates (prions). Here, using yeast, we show that transient p53 overexpression induced the formation of p53 prion aggregates that were transmitted for >100 generations, found in lysate pellets, stained with Thioflavin T, and transmitted by cytoplasmic transfer, or transfection with lysates of cells carrying the prion or with p53 amyloid peptide. As predicted for a prion, transient interruption of p53 expression caused permanent p53 prion loss. Importantly, p53 transcription factor activity was reduced by prion formation suggesting that prion aggregation could cause cancer. p53 has also been found in liquid-like nuclear droplets in animal cell culture. In yeast, we found that liquid-like p53 foci appear in response to stress and disappear with stress removal. A published yeast model of functional nuclear human p53 tumor suppressor was used Upon transient overexpression p53 loses its transcription function and aggregates These p53 aggregates are cytoplasmic and behave like stable heritable prions Stress induces p53 to form liquid-like droplets that are unstable and not prion-like
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Affiliation(s)
- Sei-Kyoung Park
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Sangeun Park
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Christine Pentek
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Susan W Liebman
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
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8
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Wang XT, Li L, Kong FB, Zhong XG, Mai W. Lentivirus-Mediated Overexpression of SIVA-1 Reverses Cisplatin Resistance in Gastric Cancer in vitro. Cell Biochem Biophys 2020; 78:455-463. [PMID: 32648086 DOI: 10.1007/s12013-020-00929-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/24/2020] [Indexed: 11/26/2022]
Abstract
SIVA-1 plays a critical role in the induction of apoptosis in a number of different cell lines and participates in the mechanism of cisplatin (DDP)-mediated antitumor effects. However, the involvement of SIVA-1 in cisplatin resistance in gastric carcinoma has not been revealed. To explore the effect of SIVA-1 on DDP resistance, a recombinant pGV358-GFP-SIVA-1 lentiviral vector was constructed and transfected into human cisplatin-resistant MKN45/DDP gastric cancer cells. Subsequently, stable SIVA-1 overexpression was established in MKN45/DDP cells, which resulted in increased DDP sensitivity in MKN45/DDP cells in vitro. Flow cytometry demonstrated that SIVA-1 overexpression increased the percentage of apoptotic cells compared to that in the control. The colony formation assay clearly revealed that cell growth and proliferation were significantly suppressed following SIVA-1 overexpression. In addition, overexpression of SIVA-1 inhibited the migratory and invasive potential of MKN45/DDP cells in vitro. Western blot analysis indicated that SIVA-1 increased the expression levels of p53, p73, and p14ARF, whereas it reduced Bcl-2, MDM2, and Bcl-xL expression. In short, SIVA-1 upregulated the protein expression of p53, p73, and p14ARF and decreased that of Bcl-2, MDM2, and Bcl-xL in vitro and subsequently reversed cisplatin resistance in gastric cancer cells, suggesting that SIVA-1 serves as a valuable potential target for attenuating chemotherapy resistance.
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Affiliation(s)
- Xiao-Tong Wang
- Department of Gastrointestinal and Peripheral Vascular Surgery, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Lei Li
- Department of Gastrointestinal and Peripheral Vascular Surgery, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Fan-Biao Kong
- Department of Surgery, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
| | - Xiao-Gang Zhong
- Department of Gastrointestinal and Peripheral Vascular Surgery, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
| | - Wei Mai
- Department of Gastrointestinal and Peripheral Vascular Surgery, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
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Roohvand F, Ehsani P, Abdollahpour-Alitappeh M, Shokri M, Kossari N. Biomedical applications of yeasts - a patent view, part two: era of humanized yeasts and expanded applications. Expert Opin Ther Pat 2020; 30:609-631. [PMID: 32529867 DOI: 10.1080/13543776.2020.1781816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Yeast humanization, ranging from a simple point mutation to substitution of yeast gene(s) or even a complete pathway by human counterparts has enormously expanded yeast biomedical applications. AREAS COVERED General and patent-oriented insights into the application of native and humanized yeasts for production of human glycoproteins (gps) and antibodies (Abs), toxicity/mutagenicity assays, treatments of gastrointestinal (GI) disorders and potential drug delivery as a probiotic (with emphasis on Saccharomyces bulardii) and studies on human diseases/cancers and screening effective drugs. EXPERT OPINION Humanized yeasts cover the classical advantageous features of a 'microbial eukaryote' together with advanced human cellular processes. These unique characteristics would permit their use in the production of functional and stable therapeutic gps and Abs in lower prices compared to mammalian (CHO) production-based systems. Availability of yeasts humanized for cytochrome P450 s will expand their application in metabolism-related chemical toxicity assays. Engineered S. bulardii for expression of human proteins might expand its application by synergistically combining the probiotic activity with the treatment of metabolic diseases such as phenylketonuria via GI-delivery. Yeast models of human diseases will facilitate rapid functional/phenotypic characterization of the disease-producing mutant genes and screening of the therapeutic compounds using yeast-based high-throughput research techniques (Yeast one/two hybrid systems) and viability assays.
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Affiliation(s)
- Farzin Roohvand
- Department of Virology, Pasteur Institute of Iran , Tehran, Iran
| | - Parastoo Ehsani
- Department of Molecular Biology, Pasteur Institute of Iran , Tehran, Iran
| | | | - Mehdi Shokri
- ; Department of Dental Biomaterials, School of Dentistry, Shahid Beheshti University of Medical Sciences , Tehran, Iran
| | - Niloufar Kossari
- ; Universite de Versailles, Service de ne 'phrologie-transplantation re'nale, Hopital Foch, 40 rue Worth, Suresnes , Paris, France
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10
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Thayer KM, Carcamo C. Homologs of the Tumor Suppressor Protein p53: A Bioinformatics Study for Drug Design. MOJ PROTEOMICS & BIOINFORMATICS 2020; 9:5-14. [PMID: 34532721 PMCID: PMC8442938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sequence and structure of proteins related to the tumor suppressor protein p53 were studied from the perspective of gaining insight for the development of therapeutic drugs. Our study addresses two major issues encumber bringing novel drugs to market: side effects and artifacts from animal models. In the first phase of our study, we performed a genome-wide search to identify potentially similar proteins to p53 that may be susceptible to off target effects. In the second phase, we chose a selection of common model organisms that could potentially be available to undergraduate researchers in the university setting to assess which ones utilize p53 most similar to humans on the basis of sequence homology and structural similarity from predicted structures. Our results confirm the proteins in the humans significantly similar to p53 are known paralogs within the p53 family. In considering model organisms, murine p53 bore great similarity to human p53 in terms of both sequence and structure, but others performed similarly well. We discuss the findings against the background of other structural benchmarks and point out potential benefits and drawbacks of various alternatives for use in future drug design pilot studies.
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Affiliation(s)
- Kelly M Thayer
- Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Claudia Carcamo
- Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
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11
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A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity. Genes (Basel) 2019; 10:genes10100770. [PMID: 31575041 PMCID: PMC6826991 DOI: 10.3390/genes10100770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022] Open
Abstract
Knowledge about synthetic lethality can be applied to enhance the efficacy of anticancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential for high-resolution phenomic analysis in yeast to predict such genetic vulnerabilities by systematic, comprehensive, and quantitative assessment of drug–gene interaction for gemcitabine and cytarabine, substrates of deoxycytidine kinase that have similar molecular structures yet distinct antitumor efficacy. Human deoxycytidine kinase (dCK) was conditionally expressed in the Saccharomyces cerevisiae genomic library of knockout and knockdown (YKO/KD) strains, to globally and quantitatively characterize differential drug–gene interaction for gemcitabine and cytarabine. Pathway enrichment analysis revealed that autophagy, histone modification, chromatin remodeling, and apoptosis-related processes influence gemcitabine specifically, while drug–gene interaction specific to cytarabine was less enriched in gene ontology. Processes having influence over both drugs were DNA repair and integrity checkpoints and vesicle transport and fusion. Non-gene ontology (GO)-enriched genes were also informative. Yeast phenomic and cancer cell line pharmacogenomics data were integrated to identify yeast–human homologs with correlated differential gene expression and drug efficacy, thus providing a unique resource to predict whether differential gene expression observed in cancer genetic profiles are causal in tumor-specific responses to cytotoxic agents.
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12
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Coronas-Serna JM, Valenti M, Del Val E, Fernández-Acero T, Rodríguez-Escudero I, Mingo J, Luna S, Torices L, Pulido R, Molina M, Cid VJ. Modeling human disease in yeast: recreating the PI3K-PTEN-Akt signaling pathway in Saccharomyces cerevisiae. Int Microbiol 2019; 23:75-87. [PMID: 31218536 DOI: 10.1007/s10123-019-00082-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 12/11/2022]
Abstract
The yeast Saccharomyces cerevisiae is a model organism that has been thoroughly exploited to understand the universal mechanisms that govern signaling pathways. Due to its ease of manipulation, humanized yeast models that successfully reproduce the function of human genes permit the development of highly efficient genetic approaches for molecular studies. Of special interest are those pathways related to human disease that are conserved from yeast to mammals. However, it is also possible to engineer yeast cells to implement functions that are naturally absent in fungi. Along the years, we have reconstructed several aspects of the mammalian phosphatidylinositol 3-kinase (PI3K) pathway in S. cerevisiae. Here, we briefly review the use of S. cerevisiae as a tool to study human oncogenes and tumor suppressors, and we present an overview of the models applied to the study of the PI3K oncoproteins, the tumor suppressor PTEN, and the Akt protein kinase. We discuss the application of these models to study the basic functional properties of these signaling proteins, the functional assessment of their clinically relevant variants, and the design of feasible platforms for drug discovery.
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Affiliation(s)
- Julia María Coronas-Serna
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Marta Valenti
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Elba Del Val
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Teresa Fernández-Acero
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Isabel Rodríguez-Escudero
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Janire Mingo
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Sandra Luna
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Leire Torices
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, 48011, Bilbao, Spain
| | - María Molina
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Víctor J Cid
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain.
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