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Sers C, Schäfer R. Silencing effects of mutant RAS signalling on transcriptomes. Adv Biol Regul 2023; 87:100936. [PMID: 36513579 DOI: 10.1016/j.jbior.2022.100936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Mutated genes of the RAS family encoding small GTP-binding proteins drive numerous cancers, including pancreatic, colon and lung tumors. Besides the numerous effects of mutant RAS gene expression on aberrant proliferation, transformed phenotypes, metabolism, and therapy resistance, the most striking consequences of chronic RAS activation are changes of the genetic program. By performing systematic gene expression studies in cellular models that allow comparisons of pre-neoplastic with RAS-transformed cells, we and others have estimated that 7 percent or more of all transcripts are altered in conjunction with the expression of the oncogene. In this context, the number of up-regulated transcripts approximates that of down-regulated transcripts. While up-regulated transcription factors such as MYC, FOSL1, and HMGA2 have been identified and characterized as RAS-responsive drivers of the altered transcriptome, the suppressed factors have been less well studied as potential regulators of the genetic program and transformed phenotype in the breadth of their occurrence. We therefore have collected information on downregulated RAS-responsive factors and discuss their potential role as tumor suppressors that are likely to antagonize active cancer drivers. To better understand the active mechanisms that entail anti-RAS function and those that lead to loss of tumor suppressor activity, we focus on the tumor suppressor HREV107 (alias PLAAT3 [Phospholipase A and acyltransferase 3], PLA2G16 [Phospholipase A2, group XVI] and HRASLS3 [HRAS-like suppressor 3]). Inactivating HREV107 mutations in tumors are extremely rare, hence epigenetic causes modulated by the RAS pathway are likely to lead to down-regulation and loss of function.
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Affiliation(s)
- Christine Sers
- Laboratory of Molecular Tumor Pathology and systems Biology, Institute of Pathology, Charité Universitätstmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Reinhold Schäfer
- Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
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2
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Liu S, Shi C, Wang X, Ma X, Gao P. Low expression of RalGAPs associates with the poorer overall survival of head and neck squamous cell carcinoma. Transl Cancer Res 2022; 10:5085-5094. [PMID: 35116360 PMCID: PMC8799020 DOI: 10.21037/tcr-21-1489] [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: 08/02/2021] [Accepted: 11/18/2021] [Indexed: 02/05/2023]
Abstract
Background The role of Ral and RalGAPs on the progression of head and neck squamous cell carcinoma (HNSC) remains unclear. Methods The predesigned siRNAs against RalGAPs were transfected into cells to evaluate the effect on RalA activation. The Data from TCGA and GTEx were combined to analyze the pan-cancer gene expression of RalA and RalGAPs in cancer and adjacent normal tissues. Kaplan-Meier analysis was used to assess the predictive value of RalA and RalGAPs expression on the overall survival of patients with HNSC. Methylation-specific PCR in vitro and next-generation bisulfite sequencing in vivo were used to evaluate the association between DNA methylation and the down-regulation of RalGAPs. Results RalGAPs negatively regulated RalA activation. HNSC patients with low level of RalGAPα2 had worse overall survival. The promoter of RalGAPα2 was widely methylated in comparison to RalGAPα1 and the DNA methylation level of RalGAPα2 promoter was increased in HNSC tissues and associated with the presence of neck lymph node metastasis. Conclusions RalA and RalGAPs could act as a specific predictor to assess the prognosis of HNSC. DNA methylation might be a potential mechanism that downregulated the RalGAPα2 expression.
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Affiliation(s)
- Shan Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Congyu Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaoyi Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiangrui Ma
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, China
| | - Pan Gao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of General and Emergency Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Péter B, Boldizsár I, Kovács GM, Erdei A, Bajtay Z, Vörös A, Ramsden JJ, Szabó I, Bősze S, Horvath R. Natural Compounds as Target Biomolecules in Cellular Adhesion and Migration: From Biomolecular Stimulation to Label-Free Discovery and Bioactivity-Based Isolation. Biomedicines 2021; 9:1781. [PMID: 34944597 PMCID: PMC8698624 DOI: 10.3390/biomedicines9121781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 01/07/2023] Open
Abstract
Plants and fungi can be used for medical applications because of their accumulation of special bioactive metabolites. These substances might be beneficial to human health, exerting also anti-inflammatory and anticancer (antiproliferative) effects. We propose that they are mediated by influencing cellular adhesion and migration via various signaling pathways and by directly inactivating key cell adhesion surface receptor sites. The evidence for this proposition is reviewed (by summarizing the natural metabolites and their effects influencing cellular adhesion and migration), along with the classical measuring techniques used to gain such evidence. We systematize existing knowledge concerning the mechanisms of how natural metabolites affect adhesion and movement, and their role in gene expression as well. We conclude by highlighting the possibilities to screen natural compounds faster and more easily by applying new label-free methods, which also enable a far greater degree of quantification than the conventional methods used hitherto. We have systematically classified recent studies regarding the effects of natural compounds on cellular adhesion and movement, characterizing the active substances according to their organismal origin (plants, animals or fungi). Finally, we also summarize the results of recent studies and experiments on SARS-CoV-2 treatments by natural extracts affecting mainly the adhesion and entry of the virus.
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Affiliation(s)
- Beatrix Péter
- Nanobiosensorics Group, Research Centre for Energy Research, Institute for Technical Physics and Materials Science, Konkoly-Thege u 29-33, 1120 Budapest, Hungary; (A.V.); (R.H.)
| | - Imre Boldizsár
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (I.B.); (G.M.K.)
- Department of Pharmacognosy, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary
| | - Gábor M. Kovács
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (I.B.); (G.M.K.)
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, 1022 Budapest, Hungary
| | - Anna Erdei
- Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.E.); (Z.B.)
- MTA-ELTE Immunology Research Group, Eötvös Loránd Research Network (ELKH), Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zsuzsa Bajtay
- Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.E.); (Z.B.)
- MTA-ELTE Immunology Research Group, Eötvös Loránd Research Network (ELKH), Eötvös Loránd University, 1117 Budapest, Hungary
| | - Alexandra Vörös
- Nanobiosensorics Group, Research Centre for Energy Research, Institute for Technical Physics and Materials Science, Konkoly-Thege u 29-33, 1120 Budapest, Hungary; (A.V.); (R.H.)
| | - Jeremy J. Ramsden
- Clore Laboratory, University of Buckingham, Buckingham MK18 1EG, UK;
| | - Ildikó Szabó
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (I.S.); (S.B.)
- National Public Health Center, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - Szilvia Bősze
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (I.S.); (S.B.)
- National Public Health Center, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - Robert Horvath
- Nanobiosensorics Group, Research Centre for Energy Research, Institute for Technical Physics and Materials Science, Konkoly-Thege u 29-33, 1120 Budapest, Hungary; (A.V.); (R.H.)
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Rio-Vilariño A, del Puerto-Nevado L, García-Foncillas J, Cebrián A. Ras Family of Small GTPases in CRC: New Perspectives for Overcoming Drug Resistance. Cancers (Basel) 2021; 13:3757. [PMID: 34359657 PMCID: PMC8345156 DOI: 10.3390/cancers13153757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer remains among the cancers with the highest incidence, prevalence, and mortality worldwide. Although the development of targeted therapies against the EGFR and VEGFR membrane receptors has considerably improved survival in these patients, the appearance of resistance means that their success is still limited. Overactivation of several members of the Ras-GTPase family is one of the main actors in both tumour progression and the lack of response to cytotoxic and targeted therapies. This fact has led many resources to be devoted over the last decades to the development of targeted therapies against these proteins. However, they have not been as successful as expected in their move to the clinic so far. In this review, we will analyse the role of these Ras-GTPases in the emergence and development of colorectal cancer and their relationship with resistance to targeted therapies, as well as the status and new advances in the design of targeted therapies against these proteins and their possible clinical implications.
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Affiliation(s)
| | | | - Jesús García-Foncillas
- Translational Oncology Division, Hospital Universitario Fundación Jimenez Diaz, 28040 Madrid, Spain; (A.R.-V.); (L.d.P.-N.)
| | - Arancha Cebrián
- Translational Oncology Division, Hospital Universitario Fundación Jimenez Diaz, 28040 Madrid, Spain; (A.R.-V.); (L.d.P.-N.)
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Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:225. [PMID: 34233735 PMCID: PMC8265010 DOI: 10.1186/s13046-021-02025-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Genes in the Ras pathway have somatic mutations in at least 60 % of colorectal cancers. Despite activating the same pathway, the BRAF V600E mutation and the prevalent mutations in codon 12 and 13 of KRAS have all been linked to different clinical outcomes, but the molecular mechanisms behind these differences largely remain to be clarified. METHODS To characterize the similarities and differences between common activating KRAS mutations and between KRAS and BRAF mutations, we used genome editing to engineer KRAS G12C/D/V and G13D mutations in colorectal cancer cells that had their mutant BRAF V600E allele removed and subjected them to transcriptome sequencing, global proteomics and metabolomics analyses. RESULTS By intersecting differentially expressed genes, proteins and metabolites, we uncovered (i) two-fold more regulated genes and proteins when comparing KRAS to BRAF mutant cells to those lacking Ras pathway mutation, (ii) five differentially expressed proteins in KRAS mutants compared to cells lacking Ras pathway mutation (IFI16, S100A10, CD44, GLRX and AHNAK2) and 6 (CRABP2, FLNA, NXN, LCP1, S100A10 and S100A2) compared to BRAF mutant cells, (iii) 19 proteins expressed differentially in a KRAS mutation specific manner versus BRAF V600E cells, (iv) regulation of the Integrin Linked Kinase pathway by KRAS but not BRAF mutation, (v) regulation of amino acid metabolism, particularly of the tyrosine, histidine, arginine and proline pathways, the urea cycle and purine metabolism by Ras pathway mutations, (vi) increased free carnitine in KRAS and BRAF mutant RKO cells. CONCLUSIONS This comprehensive integrative -omics analysis confirms known and adds novel genes, proteins and metabolic pathways regulated by mutant KRAS and BRAF signaling in colorectal cancer. The results from the new model systems presented here can inform future development of diagnostic and therapeutic approaches targeting tumors with KRAS and BRAF mutations.
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Kuhn N, Klinger B, Uhlitz F, Sieber A, Rivera M, Klotz-Noack K, Fichtner I, Hoffmann J, Blüthgen N, Falk C, Sers C, Schäfer R. Mutation-specific effects of NRAS oncogenes in colorectal cancer cells. Adv Biol Regul 2020; 79:100778. [PMID: 33431353 DOI: 10.1016/j.jbior.2020.100778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022]
Abstract
In colorectal cancer (CRC), the prevalence of NRAS mutations (5-9%) is inferior to that of KRAS mutations (40-50%). NRAS mutations feature lately during tumour progression and drive resistance to anti-EGFR therapy in KRAS wild-type tumours. To elucidate specific functions of NRAS mutations in CRC, we expressed doxycycline-inducible G12D and Q61K mutations in the CRC cell line Caco-2. A focused phospho-proteome analysis based on the Bio-Plex platform, which interrogated the activity of MAPK, PI3K, mTOR, STAT, p38, JNK and ATF2, did not reveal significant differences between Caco-2 cells expressing NRASG12D, NRASQ61K and KRASG12V. However, phenotypic read-outs were different. The NRAS Q61K mutation promoted anchorage-independent proliferation and tumorigenicity, similar to features driven by canonical KRAS mutations. In contrast, expression of NRASG12D resulted in reduced proliferation and apoptosis. At the transcriptome level, we saw upregulation of cytokines and chemokines. IL1A, IL11, CXCL8 (IL-8) and CCL20 exhibited enhanced secretion into the culture medium. In addition, RNA sequencing results indicated activation of the IL1-, JAK/STAT-, NFκB- and TNFα signalling pathways. These results form the basis for an NRASG12D-driven inflammatory phenotype in CRC.
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Affiliation(s)
- Natalia Kuhn
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Bertram Klinger
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; Integrative Research Institute Life Sciences, Humboldt University Berlin, Philippstraße 13, Building 18, D-10115, Berlin, Germany
| | - Florian Uhlitz
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; Integrative Research Institute Life Sciences, Humboldt University Berlin, Philippstraße 13, Building 18, D-10115, Berlin, Germany
| | - Anja Sieber
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; Integrative Research Institute Life Sciences, Humboldt University Berlin, Philippstraße 13, Building 18, D-10115, Berlin, Germany
| | - Maria Rivera
- Experimental Pharmacology and Oncology GmbH, Berlin-Buch, Robert-Rössle-Str. 10, D-13125, Berlin, Buch, Germany
| | - Kathleen Klotz-Noack
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Iduna Fichtner
- Experimental Pharmacology and Oncology GmbH, Berlin-Buch, Robert-Rössle-Str. 10, D-13125, Berlin, Buch, Germany
| | - Jens Hoffmann
- Experimental Pharmacology and Oncology GmbH, Berlin-Buch, Robert-Rössle-Str. 10, D-13125, Berlin, Buch, Germany
| | - Nils Blüthgen
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; Integrative Research Institute Life Sciences, Humboldt University Berlin, Philippstraße 13, Building 18, D-10115, Berlin, Germany
| | - Christine Falk
- Institute of Transplant Immunology, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Christine Sers
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Reinhold Schäfer
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany; Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany.
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Apken LH, Oeckinghaus A. The RAL signaling network: Cancer and beyond. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 361:21-105. [PMID: 34074494 DOI: 10.1016/bs.ircmb.2020.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The RAL proteins RALA and RALB belong to the superfamily of small RAS-like GTPases (guanosine triphosphatases). RAL GTPases function as molecular switches in cells by cycling through GDP- and GTP-bound states, a process which is regulated by several guanine exchange factors (GEFs) and two heterodimeric GTPase activating proteins (GAPs). Since their discovery in the 1980s, RALA and RALB have been established to exert isoform-specific functions in central cellular processes such as exocytosis, endocytosis, actin organization and gene expression. Consequently, it is not surprising that an increasing number of physiological functions are discovered to be controlled by RAL, including neuronal plasticity, immune response, and glucose and lipid homeostasis. The critical importance of RAL GTPases for oncogenic RAS-driven cellular transformation and tumorigenesis still attracts most research interest. Here, RAL proteins are key drivers of cell migration, metastasis, anchorage-independent proliferation, and survival. This chapter provides an overview of normal and pathological functions of RAL GTPases and summarizes the current knowledge on the involvement of RAL in human disease as well as current therapeutic targeting strategies. In particular, molecular mechanisms that specifically control RAL activity and RAL effector usage in different scenarios are outlined, putting a spotlight on the complexity of the RAL GTPase signaling network and the emerging theme of RAS-independent regulation and relevance of RAL.
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Affiliation(s)
- Lisa H Apken
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Münster, Münster, Germany
| | - Andrea Oeckinghaus
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Münster, Münster, Germany.
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Liu J, Zheng Y, Gao Y, Quan Z, Qiao B, Li L, Li T, Duan L, Yang J, Luo C, Wu X. Inhibitor 9 Combined With Androgen Deprivation Therapy or Chemotherapy Delays the Malignant Behavior of Castration-Resistant Prostate Cancer Through K-Ras/PLCε/PKCε Signaling Pathway. Front Oncol 2020; 10:75. [PMID: 32158687 PMCID: PMC7051985 DOI: 10.3389/fonc.2020.00075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/15/2020] [Indexed: 12/12/2022] Open
Abstract
Castration-resistant prostate cancer (CRPC) is a progressed stage of prostate cancer, which requires better understanding of the mechanisms and remains an unmet clinical need. As a common oncogene, K-Ras is associated with malignant behavior in different types of tumors but its role in CRPC is unknown. The present study aims to find the mechanism of K-Ras in CRPC and whether it can be used as a crucial molecule for the treatment of CRPC. For this purpose, tissue samples from primary prostate cancer (PPC) and CRPC patients were analyzed by immunohistochemistry and the data showed that K-Ras was elevated in CRPC. More importantly, higher K-Ras expression was related to a shorter recurrence-free survival time in patients with CRPC. In addition, K-Ras promoted the invasion, migration, and drug resistance of CRPC cells by activation of PLCε/PKCε signaling pathway. Meanwhile, the inhibitor of K-RasG12C mutants was able to inhibit malignant behavior of CRPC cells in vitro and in vivo. Inhibitors of K-RasG12C mutants have entered clinical trials. Taken together, the study shows that K-Ras may activate PKCε through PLCε, resulting in the alterations of malignant behavior of CRPC. Inhibitor 9, an inhibitor of the K-RasG12C mutant, has a strong anti-tumor effect in CRPC, which potentially suggests that inhibitors of this nature may serve as a promising treatment for CRPC.
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Affiliation(s)
- Jiayu Liu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongbo Zheng
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yingying Gao
- Department of Laboratory Diagnosis, Chongqing Medical University, Chongqing, China.,Department of Laboratory Diagnosis, Clinical Medical College, Jiamusi University, Heilongjiang, China
| | - Zhen Quan
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bo Qiao
- Department of Orthopaedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Luo Li
- Department of Laboratory Diagnosis, Chongqing Medical University, Chongqing, China.,Department of Laboratory Diagnosis, Chongqing Public Health Medical Treatment Center, Chongqing, China
| | - Ting Li
- Department of Laboratory Diagnosis, Chongqing Medical University, Chongqing, China
| | - Limei Duan
- Department of Laboratory Diagnosis, Chongqing Medical University, Chongqing, China
| | - Jinxiao Yang
- Department of Laboratory Diagnosis, Chongqing Medical University, Chongqing, China
| | - Chunli Luo
- Department of Laboratory Diagnosis, Chongqing Medical University, Chongqing, China
| | - Xiaohou Wu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Manaswiyoungkul P, de Araujo ED, Gunning PT. Targeting prenylation inhibition through the mevalonate pathway. RSC Med Chem 2020; 11:51-71. [PMID: 33479604 PMCID: PMC7485146 DOI: 10.1039/c9md00442d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/10/2019] [Indexed: 12/13/2022] Open
Abstract
Protein prenylation is a critical mediator in several diseases including cancer and acquired immunodeficiency syndrome (AIDS). Therapeutic intervention has focused primarily on directly targeting the prenyltransferase enzymes, FTase and GGTase I and II. To date, several drugs have advanced to clinical trials and while promising, they have yet to gain approval in a medical setting due to off-target effects and compensatory mechanisms activated by the body which results in drug resistance. While the development of dual inhibitors has mitigated undesirable side effects, potency remains sub-optimal for clinical development. An alternative approach involves antagonizing the upstream mevalonate pathway enzymes, FPPS and GGPPS, which mediate prenylation as well as cholesterol synthesis. The development of these inhibitors presents novel opportunities for dual inhibition of cancer-driven prenylation as well as cholesterol accumulation. Herein, we highlight progress towards the development of inhibitors against the prenylation machinery.
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Affiliation(s)
- Pimyupa Manaswiyoungkul
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences , University of Toronto Mississauga , 3359 Mississauga Rd N. , Mississauga , Ontario L5L 1C6 , Canada .
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences , University of Toronto Mississauga , 3359 Mississauga Rd N. , Mississauga , Ontario L5L 1C6 , Canada .
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
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10
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Yan C, Theodorescu D. RAL GTPases: Biology and Potential as Therapeutic Targets in Cancer. Pharmacol Rev 2017; 70:1-11. [PMID: 29196555 DOI: 10.1124/pr.117.014415] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
More than a hundred proteins comprise the RAS superfamily of small GTPases. This family can be divided into RAS, RHO, RAB, RAN, ARF, and RAD subfamilies, with each shown to play distinct roles in human cells in both health and disease. The RAS subfamily has a well-established role in human cancer with the three genes, HRAS, KRAS, and NRAS being the commonly mutated in tumors. These RAS mutations, most often functionally activating, are especially common in pancreatic, lung, and colorectal cancers. Efforts to inhibit RAS and related GTPases have produced inhibitors targeting the downstream effectors of RAS signaling, including inhibitors of the RAF-mitogen-activated protein kinase/extracellular signal-related kinase (ERK)-ERK kinase pathway and the phosphoinositide-3-kinase-AKT-mTOR kinase pathway. A third effector arm of RAS signaling, mediated by RAL (RAS like) has emerged in recent years as a critical driver of RAS oncogenic signaling and has not been targeted until recently. RAL belongs to the RAS branch of the RAS superfamily and shares a high structural similarity with RAS. In human cells, there are two genes, RALA and RALB, both of which have been shown to play roles in the proliferation, survival, and metastasis of a variety of human cancers, including lung, colon, pancreatic, prostate, skin, and bladder cancers. In this review, we summarize the latest knowledge of RAL in the context of human cancer and the recent advancements in the development of cancer therapeutics targeting RAL small GTPases.
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Affiliation(s)
- Chao Yan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (C.Y.); Departments of Surgery (Urology) and Pharmacology, University of Colorado, Aurora, Colorado (D.T.); and University of Colorado Comprehensive Cancer Center, Aurora, Colorado (D.T.)
| | - Dan Theodorescu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (C.Y.); Departments of Surgery (Urology) and Pharmacology, University of Colorado, Aurora, Colorado (D.T.); and University of Colorado Comprehensive Cancer Center, Aurora, Colorado (D.T.)
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11
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Xu SC, Ning P. Predicting pathogenic genes for primary myelofibrosis based on a system‑network approach. Mol Med Rep 2017; 17:186-192. [PMID: 29115418 PMCID: PMC5780125 DOI: 10.3892/mmr.2017.7847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/11/2017] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to predict pathogenic genes for primary myelofibrosis (PMF) using a system‑network approach by combining protein‑protein interaction (PPI) network and gene expression data with known pathogenic genes. PMF gene expression profiles, known pathogenic genes and protein‑protein interactions were obtained. Using these data, differentially expressed genes (DEGs) were identified between PMF and normal conditions using significance analysis of microarrays, and seed genes were determined based on the intersection of known pathogenic genes and the PMF gene expression profile. A new network was constructed using the seed genes and their adjacent DEGs within the PPI network. Subsequently, a pathogenic network was extracted from the new network, and contained genes that interacted with at least two seed genes, and the candidate pathogenic genes were predicted based on the cohesion with seed genes. Cluster analysis was performed to mine the pathogenic modules from the pathogenic network, and functional analysis was performed to identify the putative biological processes of the candidate pathogenic genes. Results from the present study identified 845 DEGs between PMF and normal conditions, and 45 seed genes in PMF were screened. Subsequently, a pathogenic network comprising 103 nodes and 265 interactions was constructed, and 4 pathogenic modules (modules A‑D) were mined from the pathogenic network. There were nine candidate pathogenic genes contained within Module A and four potential pathogenic genes, including E1A‑binding protein p300, RAS‑like proto‑oncogene A, von Willebrand factor and RAF‑1 proto‑oncogene, serine/threonine kinase, were identified that may be involved in the same biological process with the seed genes. This study predicted 10 candidate pathogenic genes and several signaling pathways that may be related to the pathogenesis of PMF using a system‑network approach. These predictions may shed light on the PMF pathogenesis and may provide guidelines for future experimental verification.
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Affiliation(s)
- Shu-Cai Xu
- Department of Oncology and Hematology, Hubei Provincial Hospital of Integrated Chinese and Western Medicine, Wuhan, Hubei 430015, P.R. China
| | - Peng Ning
- Department of Traumatic Hand and Foot Surgery, Taian City Central Hospital, Taian, Shandong 271000, P.R. China
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12
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Zeng Y, Xu Y, Shu R, Sun L, Tian Y, Shi C, Zheng Z, Wang K, Luo H. Altered expression profiles of circular RNA in colorectal cancer tissues from patients with lung metastasis. Int J Mol Med 2017; 40:1818-1828. [PMID: 29039473 PMCID: PMC5716445 DOI: 10.3892/ijmm.2017.3189] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 09/28/2017] [Indexed: 01/05/2023] Open
Abstract
The lung is the most common extra-abdominal site of metastasis in colorectal cancer (CRC), in which circular RNA (circRNA) may have a crucial role. Therefore, the present study detected circRNA expression to identify novel targets to further study lung metastasis in CRC. In the present study, total RNA was extracted from CRC tissues of patients with and without lung metastasis to perform high-throughput microarray assay in order to detect differentially expressed circRNA. Following this, gene ontology (GO) and pathway analyses of the genes producing differentially expressed circRNA were performed to predict the function of circRNA using standard enrichment computational methods. Additionally, the circRNA/microRNA (miRNA) interactions were constructed with bioinformatics methods to predict the binding of miRNA with circRNA. In the CRC tissues from patients with lung metastasis, 431 circRNA were detected to be differentially expressed, including 192 upregulated and 239 downregulated over 2-fold compared with the CRC tissues without metastasis. Furthermore, GO analysis revealed that the genes producing upregulated circRNA were involved in DNA repair, while the genes producing downregulated circRNA were enriched in signal transduction. By pathway analysis, it was identified that the genes producing downregulated circRNA were involved in the nuclear factor-κB and Wnt signaling pathway in the CRC tissues from patients with lung metastasis compared with the CRC tissues without metastasis. In addition, it was demonstrated that hsa_circRNA_105055, hsa_circRNA_086376 and hsa_circRNA_102761 could commonly bind with miR-7 regulating target genes PRKCB, EPHA3, BRCA1 and ABCC1. The findings of the present study may provide a novel perspective on circRNA and lay a foundation for future research of potential roles of circRNA in CRC with lung metastasis.
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Affiliation(s)
- Yujian Zeng
- Department of Gastrointestinal and Hernia Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Yu Xu
- Department of Gastrointestinal and Hernia Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Ruo Shu
- Department of Gastrointestinal and Hernia Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Liang Sun
- Yunnan Institute of Digestive Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Yan Tian
- Yunnan Institute of Digestive Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Chengmin Shi
- Yunnan Institute of Digestive Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Zhibin Zheng
- Department of Gastrointestinal and Hernia Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Kunhua Wang
- Department of Gastrointestinal and Hernia Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Huayou Luo
- Department of Gastrointestinal and Hernia Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
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13
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Pongor L, Harami-Papp H, Méhes E, Czirók A, Győrffy B. Cell Dispersal Influences Tumor Heterogeneity and Introduces a Bias in NGS Data Interpretation. Sci Rep 2017; 7:7358. [PMID: 28779157 PMCID: PMC5544774 DOI: 10.1038/s41598-017-07487-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/27/2017] [Indexed: 01/09/2023] Open
Abstract
Short and long distance cell dispersal can have a marked effect on tumor structure, high cellular motility could lead to faster cell mixing and lower observable intratumor heterogeneity. Here we evaluated a model for cell mixing that investigates how short-range dispersal and cell turnover will account for mutational proportions. We show that cancer cells can penetrate neighboring and distinct areas in a matter of days. In next generation sequencing runs, higher proportions of a given cell line generated frequencies with higher precision, while mixtures with lower amounts of each cell line had lower precision manifesting in higher standard deviations. When multiple cell lines were co-cultured, cellular movement altered observed mutation frequency by up to 18.5%. We propose that some of the shared mutations detected at low allele frequencies represent highly motile clones that appear in multiple regions of a tumor owing to dispersion throughout the tumor. In brief, cell movement will lead to a significant technical (sampling) bias when using next generation sequencing to determine clonal composition. A possible solution to this drawback would be to radically decrease detection thresholds and increase coverage in NGS analyses.
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Affiliation(s)
- Lőrinc Pongor
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary.,Semmelweis University 2nd Department of Pediatrics, Budapest, Hungary
| | - Hajnalka Harami-Papp
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary.,Semmelweis University 2nd Department of Pediatrics, Budapest, Hungary
| | - Előd Méhes
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - András Czirók
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas, USA
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary. .,Semmelweis University 2nd Department of Pediatrics, Budapest, Hungary.
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14
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Sztupinszki Z, Győrffy B. Colon cancer subtypes: concordance, effect on survival and selection of the most representative preclinical models. Sci Rep 2016; 6:37169. [PMID: 27849044 PMCID: PMC5111107 DOI: 10.1038/srep37169] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022] Open
Abstract
Multiple gene-expression-based subtypes have been proposed for the molecular subdivision of colon cancer in the last decade. We aimed to cross-validate these classifiers to explore their concordance and their power to predict survival. A gene-chip-based database comprising 2,166 samples from 12 independent datasets was set up. A total of 22 different molecular subtypes were re-trained including the CCHS, CIN25, CMS, ColoGuideEx, ColoGuidePro, CRCassigner, MDA114, Meta163, ODXcolon, Oncodefender, TCA19, and V7RHS classifiers as well as subtypes established by Budinska, Chang, DeSousa, Marisa, Merlos, Popovici, Schetter, Yuen, and Watanabe (first authors). Correlation with survival was assessed by Cox proportional hazards regression for each classifier using relapse-free survival data. The highest efficacy at predicting survival in stage 2-3 patients was achieved by Yuen (p = 3.9e-05, HR = 2.9), Marisa (p = 2.6e-05, HR = 2.6) and Chang (p = 9e-09, HR = 2.35). Finally, 61 colon cancer cell lines from four independent studies were assigned to the closest molecular subtype.
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Affiliation(s)
- Zsófia Sztupinszki
- MTA TTK Lendület Cancer Biomarker Research Group, 1117, Budapest, Hungary
- 2 Dept. of Pediatrics, Semmelweis University, 1094, Budapest, Hungary
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, 1117, Budapest, Hungary
- 2 Dept. of Pediatrics, Semmelweis University, 1094, Budapest, Hungary
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15
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Menyhárt O, Harami-Papp H, Sukumar S, Schäfer R, Magnani L, de Barrios O, Győrffy B. Guidelines for the selection of functional assays to evaluate the hallmarks of cancer. Biochim Biophys Acta Rev Cancer 2016; 1866:300-319. [PMID: 27742530 DOI: 10.1016/j.bbcan.2016.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/06/2016] [Accepted: 10/08/2016] [Indexed: 01/05/2023]
Abstract
The hallmarks of cancer capture the most essential phenotypic characteristics of malignant transformation and progression. Although numerous factors involved in this multi-step process are still unknown to date, an ever-increasing number of mutated/altered candidate genes are being identified within large-scale cancer genomic projects. Therefore, investigators need to be aware of available and appropriate techniques capable of determining characteristic features of each hallmark. We review the methods tailored to experimental cancer researchers to evaluate cell proliferation, programmed cell death, replicative immortality, induction of angiogenesis, invasion and metastasis, genome instability, and reprogramming of energy metabolism. Selecting the ideal method is based on the investigator's goals, available equipment and also on financial constraints. Multiplexing strategies enable a more in-depth data collection from a single experiment - obtaining several results from a single procedure reduces variability and saves time and relative cost, leading to more robust conclusions compared to a single end point measurement. Each hallmark possesses characteristics that can be analyzed by immunoblot, RT-PCR, immunocytochemistry, immunoprecipitation, RNA microarray or RNA-seq. In general, flow cytometry, fluorescence microscopy, and multiwell readers are extremely versatile tools and, with proper sample preparation, allow the detection of a vast number of hallmark features. Finally, we also provide a list of hallmark-specific genes to be measured in transcriptome-level studies. Although our list is not exhaustive, we provide a snapshot of the most widely used methods, with an emphasis on methods enabling the simultaneous evaluation of multiple hallmark features.
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Affiliation(s)
- Otília Menyhárt
- MTA TTK Lendület Cancer Biomarker Research Group, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | | | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Reinhold Schäfer
- German Cancer Consortium (DKTK), DKFZ, Im Neuenheimer Feld 280, D-69120 Heidelberg and Charité Comprehensive Cancer Center, Invalidenstr. 80, D-10115 Berlin, Germany
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Oriol de Barrios
- Group of Transcriptional Regulation of Gene Expression, Department of Oncology and Hematology, IDIBAPS, Barcelona, Spain
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Magyar tudósok körútja 2, H-1117 Budapest, Hungary; 2nd Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary.
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16
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Rai R, Zhang F, Colavita K, Leu NA, Kurosaka S, Kumar A, Birnbaum MD, Győrffy B, Dong DW, Shtutman M, Kashina A. Arginyltransferase suppresses cell tumorigenic potential and inversely correlates with metastases in human cancers. Oncogene 2015; 35:4058-68. [PMID: 26686093 PMCID: PMC4916053 DOI: 10.1038/onc.2015.473] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 11/09/2015] [Accepted: 11/14/2015] [Indexed: 02/07/2023]
Abstract
Arginylation is an emerging post-translational modification mediated by arginyltransferase (ATE1) that is essential for mammalian embryogenesis and regulation of the cytoskeleton. Here, we discovered that Ate1-knockout (KO) embryonic fibroblasts exhibit tumorigenic properties, including abnormally rapid contact-independent growth, reduced ability to form cell-cell contacts and chromosomal aberrations. Ate1-KO fibroblasts can form large colonies in Matrigel and exhibit invasive behavior, unlike wild-type fibroblasts. Furthermore, Ate1-KO cells form tumors in subcutaneous xenograft assays in immunocompromised mice. Abnormal growth in these cells can be partially rescued by reintroduction of stably expressed specific Ate1 isoforms, which also reduce the ability of these cells to form tumors. Tumor array studies and bioinformatics analysis show that Ate1 is downregulated in several types of human cancer samples at the protein level, and that its transcription level inversely correlates with metastatic progression and patient survival. We conclude that Ate1-KO results in carcinogenic transformation of cultured fibroblasts, suggesting that in addition to its previously known activities Ate1 gene is essential for tumor suppression and also likely participates in suppression of metastatic growth.
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Affiliation(s)
- R Rai
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - F Zhang
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Molecular & Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - K Colavita
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - N A Leu
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - S Kurosaka
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - A Kumar
- Department of Molecular & Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M D Birnbaum
- Department of Molecular & Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - B Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary.,Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - D W Dong
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Shtutman
- University of South Carolina, Columbia, SC, USA
| | - A Kashina
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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