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Mancarella C, Bley N, Penalva LOF. Editorial: RNA-binding proteins in cancer: advances in translational research. Front Cell Dev Biol 2024; 12:1390044. [PMID: 38523626 PMCID: PMC10957735 DOI: 10.3389/fcell.2024.1390044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Affiliation(s)
- Caterina Mancarella
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Nadine Bley
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Luiz O. F. Penalva
- Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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Oladipupo AR, Alaribe SCA, Ogunlaja AS, Beniddir MA, Gordon AT, Ogah CO, Okpuzor J, Coker HAB. Structure-based molecular networking, molecular docking, dynamics simulation and pharmacokinetic studies of Olax subscorpioidea for identification of potential inhibitors against selected cancer targets. J Biomol Struct Dyn 2024; 42:1110-1125. [PMID: 37029762 DOI: 10.1080/07391102.2023.2198032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/28/2023] [Indexed: 04/09/2023]
Abstract
The rationale at the basis of targeted approach in oncology is radically shifting-from development of highly specific agents aiming at a single target towards molecules interfering with multiple targets. This study was performed to isolate and characterize bioactive molecules from Olax subscorpioidea stem and investigate their potentials as multi-targeted inhibitors against selected non-small cell lung cancer, breast cancer and chronic myelogenous leukemia oncogenic targets. Three compounds: β-sitosterol (1), α-amyrin (2) and stigmasterol (3) were isolated. The structures of 1 - 3 were elucidated by analysis of their spectroscopic data (NMR, MS and IR). To the best of our knowledge, this is the first time these compounds were isolated from O. subscorpioidea stems. Furthermore, integrated analysis of MS/MS data using the Global Natural Products Social Molecular Networking (GNPS) workflow enabled dereplication and identification of 26 compounds, including alkaloids (remerine, boldine), terpenoids (3-hydroxy-11-ursen-28,13-olide, oleanolic acid), flavonoids (kaempferitrin, olax chalcone A) and saponins in O. subscorpioidea stem. Molecular docking studies revealed that some of the compounds, including olax chalcone A (-9.2 to -10.9 kcal/mol), 3-Hydroxy-11-ursen-28,13-olide (-6.6 to -10.2 kcal/mol), α-amyrin (-6.6 to -10.2 kcal/mol), stigmasterol (-7.7 to -10.1 kcal/mol), β-Sitosterol (-7 to -9.9 kcal/mol) and kaempferitrin (-7.7 to -9 kcal/mol) possessed good inhibitory potentials against selected cancer targets, when compared with reference inhibitors (-8.4 to -13.7 kcal/mol). A few of these compounds were shown to have considerable to favorable pharmacokinetic and drug-likeness properties. This study provides some rationale for the use of O. subscorpioidea in ethnomedicinal management of cancer and identifies some potential anticancer agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akolade R Oladipupo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Lagos, CMUL Campus, Lagos, Nigeria
| | - Stephenie C A Alaribe
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Lagos, CMUL Campus, Lagos, Nigeria
| | - Adeniyi S Ogunlaja
- Department of Chemistry, Nelson Mandela University, Port-Elizabeth, South Africa
| | - Mehdi A Beniddir
- Equipe Chimie des Substances Naturelles, BioCIS, Université Paris-Saclay, CNRS, Châtenay-Malabry, France
| | - Allen T Gordon
- Department of Chemistry, Nelson Mandela University, Port-Elizabeth, South Africa
| | - Celina O Ogah
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Lagos, CMUL Campus, Lagos, Nigeria
| | - Joy Okpuzor
- Department of Cell Biology & Genetics, Faculty of Science, University of Lagos, Yaba, Lagos, Nigeria
| | - Herbert A B Coker
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Lagos, CMUL Campus, Lagos, Nigeria
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Venugopal S, Kaur B, Verma A, Wadhwa P, Magan M, Hudda S, Kakoty V. Recent advances of benzimidazole as anticancer agents. Chem Biol Drug Des 2023; 102:357-376. [PMID: 37009821 DOI: 10.1111/cbdd.14236] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/20/2023] [Accepted: 03/14/2023] [Indexed: 04/04/2023]
Abstract
Cancer is the second leading cause of death globally, with 9.6 million deaths yearly. As a life-threatening disease, it necessitates the emergence of new therapies. Resistance to current chemotherapies drives scientists to develop new medications that will eventually be accessible. Because heterocycles are so common in biological substances, compounds play a big part in the variety of medications that have been developed. The "Master Key" is the benzimidazole nucleus, which consists of a six-membered benzene ring fused with a five-membered imidazole/imidazoline ring, which is an azapyrrole. One of the five-membered aromatic nitrogen heterocycles identified in American therapies that have been approved by the Food and Drug Administration (FDA). Our results show that benzimidazole's broad therapeutic spectrum is due to its structural isosteres with purine, which improves hydrogen bonding, electrostatic interactions with topoisomerase complexes, intercalation with DNA, and other functions. It also enhances protein and nucleic acid inhibition, tubulin microtubule degeneration, apoptosis, DNA fragmentation, and other functions. Additionally, readers for designing the more recent benzimidazole analogues as prospective cancer treatments.
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Affiliation(s)
- Sneha Venugopal
- Department of Pharmaceutical Sciences, School of Pharmacy, Lovely Professional University, Punjab, India
| | - Balwinder Kaur
- Department of Pharmaceutical Sciences, School of Pharmacy, Lovely Professional University, Punjab, India
| | - Anil Verma
- Department of Pharmaceutical Sciences, School of Pharmacy, Lovely Professional University, Punjab, India
| | - Pankaj Wadhwa
- Department of Pharmaceutical Sciences, School of Pharmacy, Lovely Professional University, Punjab, India
| | - Muskan Magan
- Department of Pharmaceutical Sciences, School of Pharmacy, Lovely Professional University, Punjab, India
| | - Sharwan Hudda
- Department of Pharmaceutical Sciences, School of Pharmacy, Lovely Professional University, Punjab, India
| | - Violina Kakoty
- Department of Pharmaceutical Sciences, School of Pharmacy, Lovely Professional University, Punjab, India
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Diebold M, Schönemann L, Eilers M, Sotriffer C, Schindelin H. Crystal structure of a covalently linked Aurora-A-MYCN complex. Acta Crystallogr D Struct Biol 2023; 79:1-9. [PMID: 36601802 PMCID: PMC9815099 DOI: 10.1107/s2059798322011433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Formation of the Aurora-A-MYCN complex increases levels of the oncogenic transcription factor MYCN in neuroblastoma cells by abrogating its degradation through the ubiquitin proteasome system. While some small-molecule inhibitors of Aurora-A were shown to destabilize MYCN, clinical trials have not been satisfactory to date. MYCN itself is considered to be `undruggable' due to its large intrinsically disordered regions. Targeting the Aurora-A-MYCN complex rather than Aurora-A or MYCN alone will open new possibilities for drug development and screening campaigns. To overcome the challenges that a ternary system composed of Aurora-A, MYCN and a small molecule entails, a covalently cross-linked construct of the Aurora-A-MYCN complex was designed, expressed and characterized, thus enabling screening and design campaigns to identify selective binders.
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Affiliation(s)
- Mathias Diebold
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lars Schönemann
- Institute of Structural Biology, Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Haus D15, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Martin Eilers
- Theodor-Boveri-Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany,Correspondence e-mail: , ,
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany,Correspondence e-mail: , ,
| | - Hermann Schindelin
- Institute of Structural Biology, Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Haus D15, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany,Correspondence e-mail: , ,
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Gunasekaran M, Ravi R, Subramanian K. Molecular docking analysis of lupeol with different cancer targets. Bioinformation 2022; 18:134-140. [PMID: 36518133 PMCID: PMC9722432 DOI: 10.6026/97320630018134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 08/15/2023] Open
Abstract
Lupeol is one of the secondary metabolite (triterpenoid) present in many medicinally effective plants. It has numerous biological and pharmacological actions. Lupeol is found to have effective herbs and has immense biological activity against several diseases including its cytotoxic effect on cancer cells. In recent drug designing, molecular study of analysis is usually used for understanding the target and the ligand interaction. Therefore, it is of interest to document the molecular docking analysis data of lupeol with different cancer targets such as Caspase- 3, BCL-2, Topoisomerase, PTK, mTOR, H-Ras, PI3K, and AKT. These molecular docking studies were carried out by using AutoDock tools 4.2 version software. Molecular docking analyses of lupeol with target protein were found to have good dock score and minimum inhibition constant. BCL-2, Topoisomerase, PTK, mTOR and PI3Kdocking studies showed the best binding energy inhibition constant and ligand efficiency. The in-silico molecular docking analysis showed that the lupeol having relatively good docking energy, affinity and efficiency towards the active macromolecule, thus it may be considered as good inhibitor of proliferating cancer cells. By this knowledge of docking results, the lupeol can be used as promising drug for anticancer activity.
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Affiliation(s)
- Mahalakshmi Gunasekaran
- Department of Pharmacology, College of Pharmacy, Mother Theresa Post Graduate and Research Institute of Health Science, Pondicherry University, Puducherry-605006, India
| | - Ravali Ravi
- Department of Pharmacology, College of Pharmacy, Mother Theresa Post Graduate and Research Institute of Health Science, Pondicherry University, Puducherry-605006, India
| | - Kavimani Subramanian
- Department of Pharmacology, College of Pharmacy, Mother Theresa Post Graduate and Research Institute of Health Science, Pondicherry University, Puducherry-605006, India
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6
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Röth S, Macartney TJ, Konopacka A, Chan KH, Zhou H, Queisser MA, Sapkota GP. Targeting Endogenous K-RAS for Degradation through the Affinity-Directed Protein Missile System. Cell Chem Biol 2020; 27:1151-1163.e6. [PMID: 32668202 PMCID: PMC7505679 DOI: 10.1016/j.chembiol.2020.06.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/12/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022]
Abstract
K-RAS is known as the most frequently mutated oncogene. However, the development of conventional K-RAS inhibitors has been extremely challenging, with a mutation-specific inhibitor reaching clinical trials only recently. Targeted proteolysis has emerged as a new modality in drug discovery to tackle undruggable targets. Our laboratory has developed a system for targeted proteolysis using peptidic high-affinity binders, called “AdPROM.” Here, we used CRISPR/Cas9 technology to knock in a GFP tag on the native K-RAS gene in A549 adenocarcinoma (A549GFPKRAS) cells and constructed AdPROMs containing high-affinity GFP or H/K-RAS binders. Expression of GFP-targeting AdPROM in A549GFPKRAS led to robust proteasomal degradation of endogenous GFP-K-RAS, while expression of anti-HRAS-targeting AdPROM in different cell lines resulted in the degradation of both GFP-tagged and untagged K-RAS, and untagged H-RAS. Our findings imply that endogenous RAS proteins can be targeted for proteolysis, supporting the idea of an alternative therapeutic approach to these undruggable targets. Generation of A549 cells with a homozygous knockin of GFP tag on the KRAS gene Proteasomal degradation of endogenous GFP-K-RAS using a VHL-GFP-nanobody fusion Proteasomal degradation of endogenous H/K-RAS using VHL-H/K-RAS-monobody fusion
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Affiliation(s)
- Sascha Röth
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Thomas J Macartney
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Agnieszka Konopacka
- GlaxoSmithKline, Protein Degradation Group, Medicines Research Centre, Gunnels Wood Road, Stevenage, UK
| | - Kwok-Ho Chan
- GlaxoSmithKline, Protein Degradation Group, Medicines Research Centre, Gunnels Wood Road, Stevenage, UK
| | - Houjiang Zhou
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Markus A Queisser
- GlaxoSmithKline, Protein Degradation Group, Medicines Research Centre, Gunnels Wood Road, Stevenage, UK
| | - Gopal P Sapkota
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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Hamza A, Driessen MRM, Tammpere E, O'Neil NJ, Hieter P. Cross-Species Complementation of Nonessential Yeast Genes Establishes Platforms for Testing Inhibitors of Human Proteins. Genetics 2020; 214:735-747. [PMID: 31937519 PMCID: PMC7054014 DOI: 10.1534/genetics.119.302971] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/13/2020] [Indexed: 01/09/2023] Open
Abstract
Cross-species complementation can be used to generate humanized yeast, which is a valuable resource with which to model and study human biology. Humanized yeast can be used as an in vivo platform to screen for chemical inhibition of human protein drug targets. To this end, we report the systematic complementation of nonessential yeast genes implicated in chromosome instability (CIN) with their human homologs. We identified 20 human-yeast complementation pairs that are replaceable in 44 assays that test rescue of chemical sensitivity and/or CIN defects. We selected a human-yeast pair (hFEN1/yRAD27), which is frequently overexpressed in cancer and is an anticancer therapeutic target, to perform in vivo inhibitor assays using a humanized yeast cell-based platform. In agreement with published in vitro assays, we demonstrate that HU-based PTPD is a species-specific hFEN1 inhibitor. In contrast, another reported hFEN1 inhibitor, the arylstibonic acid derivative NSC-13755, was determined to have off-target effects resulting in a synthetic lethal phenotype with yRAD27-deficient strains. Our study expands the list of human-yeast complementation pairs to nonessential genes by defining novel cell-based assays that can be utilized as a broad resource to study human drug targets.
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Affiliation(s)
- Akil Hamza
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Maureen R M Driessen
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Erik Tammpere
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Nigel J O'Neil
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
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Sundaravadivelu S, Raj SK, Kumar BS, Arumugamand P, Ragunathan PP. Reverse Screening Bioinformatics Approach to Identify Potential Anti Breast Cancer Targets Using Thymoquinone from Neutraceuticals Black Cumin Oil. Anticancer Agents Med Chem 2020; 19:599-609. [PMID: 30678630 DOI: 10.2174/1871520619666190124155359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/25/2018] [Accepted: 01/03/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Functional foods, neutraceuticals and natural antioxidants have established their potential roles in the protection of human health and diseases. Thymoquinone (TQ), the main bioactive component of Nigella sativa seeds (black cumin seeds), a plant derived neutraceutical was used by ancient Egyptians because of their ability to cure a variety of health conditions and used as a dietary food supplement. Owing to its multi targeting nature, TQ interferes with a wide range of tumorigenic processes and counteracts carcinogenesis, malignant growth, invasion, migration, and angiogenesis. Additionally, TQ can specifically sensitize tumor cells towards conventional cancer treatments (e.g., radiotherapy, chemotherapy, and immunotherapy) and simultaneously minimize therapy-associated toxic effects in normal cells besides being cost effective and safe. TQ was found to play a protective role when given along with chemotherapeutic agents to normal cells. METHODS In the present study, reverse in silico docking approach was used to search for potential molecular targets for cancer therapy. Various metastatic and apoptotic targets were docked with the target ligand. TQ was also tested for its anticancer activities for its ability to cause cell death, arrest cell cycle and ability to inhibit PARP gene expression. RESULTS In silico docking studies showed that TQ effectively docked metastatic targets MMPs and other apoptotic and cell proliferation targets EGFR. They were able to bring about cell death mediated by apoptosis, cell cycle arrest in the late apoptotic stage and induce DNA damage too. TQ effectively down regulated PARP gene expression which can lead to enhanced cancer cell death. CONCLUSION Thymoquinone a neutraceutical can be employed as a new therapeutic agent to target triple negative breast cancer which is otherwise difficult to treat as there are no receptors on them. Can be employed along with standard chemotherapeutic drugs to treat breast cancer as a combinatorial therapy.
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Affiliation(s)
- Sumathi Sundaravadivelu
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, TN, India
| | - Sonia K Raj
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, TN, India
| | - Banupriya S Kumar
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, TN, India
| | - Poornima Arumugamand
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, TN, India
| | - Padma P Ragunathan
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, TN, India
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Gonda A, Kabagwira J, Senthil GN, Ferguson Bennit HR, Neidigh JW, Khan S, Wall NR. Exosomal survivin facilitates vesicle internalization. Oncotarget 2018; 9:34919-34934. [PMID: 30405884 PMCID: PMC6201849 DOI: 10.18632/oncotarget.26182] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 09/15/2018] [Indexed: 12/11/2022] Open
Abstract
Survivin, a member of the inhibitor of apoptosis (IAP) protein family plays a significant role in cell fate and function. It is significantly overexpressed in tumor cells and has been identified in most cancer cell types. A novel extracellular population has recently been identified and its function is still unknown. Emerging evidence continues to shed light on the important role the tumor microenvironment (TME) has on tumor survival and progression. This new population of survivin has been seen to enhance the tumor phenotype when internalized by recipient cells. In this paper, we sought to better understand the mechanism by which survivin is taken up by cancer cells and the possible role it plays in this phenomenon. We isolated the exosomal carriers of extracellular survivin and using a lipophilic stain, PKH67, we tracked their uptake with immunofluorescence and flow cytometry. We found that by blocking exosomal survivin, exosome internalization is reduced, signifying a novel function for this protein. We also discovered that the common membrane receptors, transferrin receptor, endothelin B receptor, insulin receptor alpha, and membrane glucocorticoid receptor all facilitate exosomal internalization. This understanding further clarifies the protein-protein interactions in the TME that may influence tumor progression and identifies additional potential chemotherapeutic targets.
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Affiliation(s)
- Amber Gonda
- Center for Health Disparities Research and Molecular Medicine, Loma Linda University, Loma Linda, California, 92350, USA
- Department of Basic Sciences, Division of Anatomy, Loma Linda University, Loma Linda, California, 92350, USA
| | - Janviere Kabagwira
- Center for Health Disparities Research and Molecular Medicine, Loma Linda University, Loma Linda, California, 92350, USA
- Department of Basic Sciences, Division of Biochemistry, Loma Linda University, Loma Linda, California, 92350, USA
| | - Girish N. Senthil
- Center for Health Disparities Research and Molecular Medicine, Loma Linda University, Loma Linda, California, 92350, USA
| | - Heather R. Ferguson Bennit
- Center for Health Disparities Research and Molecular Medicine, Loma Linda University, Loma Linda, California, 92350, USA
- Department of Basic Sciences, Division of Biochemistry, Loma Linda University, Loma Linda, California, 92350, USA
| | - Jonathan W. Neidigh
- Department of Basic Sciences, Division of Biochemistry, Loma Linda University, Loma Linda, California, 92350, USA
| | - Salma Khan
- Center for Health Disparities Research and Molecular Medicine, Loma Linda University, Loma Linda, California, 92350, USA
- Department of Basic Sciences, Division of Biochemistry, Loma Linda University, Loma Linda, California, 92350, USA
| | - Nathan R. Wall
- Center for Health Disparities Research and Molecular Medicine, Loma Linda University, Loma Linda, California, 92350, USA
- Department of Basic Sciences, Division of Biochemistry, Loma Linda University, Loma Linda, California, 92350, USA
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Shao F, Sun H, Deng CX. Potential therapeutic targets of triple-negative breast cancer based on its intrinsic subtype. Oncotarget 2017; 8:73329-73344. [PMID: 29069872 PMCID: PMC5641215 DOI: 10.18632/oncotarget.20274] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/06/2017] [Indexed: 12/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subgroup of human breast cancer, which is characterized as estrogen receptor (ER) negative, progesterone receptor (PR) negative, and human epidermal growth factor receptor 2 (HER2) negative. TNBC is the most difficult breast cancer subgroup to treat, due to its unresponsiveness to current clinical targeted therapies, high rate of recurrence, and poor prognosis. Thus, there is an urgent medical need to identify therapeutic targets and develop more effective stratified medicine for the treatment of TNBC. Here we review the potential therapeutic targets for TNBC based on its intrinsic subtype. We also review the aberrant activated signals found in different subgroups of TNBC, including androgen receptor (AR) and PI3K/AKT/mTOR, Notch, Wnt/β-catenin, Hedge-hog, and TGF-β signaling pathways, which play essential roles in multiple development stages of TNBC. The careful analysis of these signaling pathways and therapeutic targets would have significant impact on the drug development and clinical trials, leading to effective therapies for this deadly disease.
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Affiliation(s)
- Fangyuan Shao
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Heng Sun
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR, China
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Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, Gill S, Harrington WF, Pantel S, Krill-Burger JM, Meyers RM, Ali L, Goodale A, Lee Y, Jiang G, Hsiao J, Gerath WFJ, Howell S, Merkel E, Ghandi M, Garraway LA, Root DE, Golub TR, Boehm JS, Hahn WC. Defining a Cancer Dependency Map. Cell 2017; 170:564-576.e16. [PMID: 28753430 DOI: 10.1016/j.cell.2017.06.010] [Citation(s) in RCA: 1383] [Impact Index Per Article: 197.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/09/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022]
Abstract
Most human epithelial tumors harbor numerous alterations, making it difficult to predict which genes are required for tumor survival. To systematically identify cancer dependencies, we analyzed 501 genome-scale loss-of-function screens performed in diverse human cancer cell lines. We developed DEMETER, an analytical framework that segregates on- from off-target effects of RNAi. 769 genes were differentially required in subsets of these cell lines at a threshold of six SDs from the mean. We found predictive models for 426 dependencies (55%) by nonlinear regression modeling considering 66,646 molecular features. Many dependencies fall into a limited number of classes, and unexpectedly, in 82% of models, the top biomarkers were expression based. We demonstrated the basis behind one such predictive model linking hypermethylation of the UBB ubiquitin gene to a dependency on UBC. Together, these observations provide a foundation for a cancer dependency map that facilitates the prioritization of therapeutic targets.
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Affiliation(s)
- Aviad Tsherniak
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Francisca Vazquez
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Phil G Montgomery
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Barbara A Weir
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Gregory Kryukov
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Stanley Gill
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | | | - Sasha Pantel
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | | | - Robin M Meyers
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Levi Ali
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Yenarae Lee
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Guozhi Jiang
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Jessica Hsiao
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | | | - Sara Howell
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Erin Merkel
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Mahmoud Ghandi
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Levi A Garraway
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, USA
| | - David E Root
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - Todd R Golub
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, USA
| | - Jesse S Boehm
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA, USA.
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12
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Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, Gill S, Harrington WF, Pantel S, Krill-Burger JM, Meyers RM, Ali L, Goodale A, Lee Y, Jiang G, Hsiao J, Gerath WFJ, Howell S, Merkel E, Ghandi M, Garraway LA, Root DE, Golub TR, Boehm JS, Hahn WC. Defining a Cancer Dependency Map. Cell 2017; 170:564-576.e16. [PMID: 28753430 DOI: 10.1016/j.cell.2017.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Most human epithelial tumors harbor numerous alterations, making it difficult to predict which genes are required for tumor survival. To systematically identify cancer dependencies, we analyzed 501 genome-scale loss-of-function screens performed in diverse human cancer cell lines. We developed DEMETER, an analytical framework that segregates on- from off-target effects of RNAi. 769 genes were differentially required in subsets of these cell lines at a threshold of six SDs from the mean. We found predictive models for 426 dependencies (55%) by nonlinear regression modeling considering 66,646 molecular features. Many dependencies fall into a limited number of classes, and unexpectedly, in 82% of models, the top biomarkers were expression based. We demonstrated the basis behind one such predictive model linking hypermethylation of the UBB ubiquitin gene to a dependency on UBC. Together, these observations provide a foundation for a cancer dependency map that facilitates the prioritization of therapeutic targets.
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13
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Harris DT, Wang N, Riley TP, Anderson SD, Singh NK, Procko E, Baker BM, Kranz DM. Deep Mutational Scans as a Guide to Engineering High Affinity T Cell Receptor Interactions with Peptide-bound Major Histocompatibility Complex. J Biol Chem 2016; 291:24566-24578. [PMID: 27681597 DOI: 10.1074/jbc.m116.748681] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/15/2016] [Indexed: 11/06/2022] Open
Abstract
Proteins are often engineered to have higher affinity for their ligands to achieve therapeutic benefit. For example, many studies have used phage or yeast display libraries of mutants within complementarity-determining regions to affinity mature antibodies and T cell receptors (TCRs). However, these approaches do not allow rapid assessment or evolution across the entire interface. By combining directed evolution with deep sequencing, it is now possible to generate sequence fitness landscapes that survey the impact of every amino acid substitution across the entire protein-protein interface. Here we used the results of deep mutational scans of a TCR-peptide-MHC interaction to guide mutational strategies. The approach yielded stable TCRs with affinity increases of >200-fold. The substitutions with the greatest enrichments based on the deep sequencing were validated to have higher affinity and could be combined to yield additional improvements. We also conducted in silico binding analyses for every substitution to compare them with the fitness landscape. Computational modeling did not effectively predict the impacts of mutations distal to the interface and did not account for yeast display results that depended on combinations of affinity and protein stability. However, computation accurately predicted affinity changes for mutations within or near the interface, highlighting the complementary strengths of computational modeling and yeast surface display coupled with deep mutational scanning for engineering high affinity TCRs.
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Affiliation(s)
- Daniel T Harris
- From the Department of Biochemistry, University of Illinois, Urbana, Illinois 61801 and
| | - Ningyan Wang
- From the Department of Biochemistry, University of Illinois, Urbana, Illinois 61801 and
| | - Timothy P Riley
- the Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, South Bend, Indiana 46557
| | - Scott D Anderson
- From the Department of Biochemistry, University of Illinois, Urbana, Illinois 61801 and
| | - Nishant K Singh
- the Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, South Bend, Indiana 46557
| | - Erik Procko
- From the Department of Biochemistry, University of Illinois, Urbana, Illinois 61801 and
| | - Brian M Baker
- the Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, South Bend, Indiana 46557
| | - David M Kranz
- From the Department of Biochemistry, University of Illinois, Urbana, Illinois 61801 and.
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14
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Gautier M, Dhennin-Duthille I, Ay AS, Rybarczyk P, Korichneva I, Ouadid-Ahidouch H. New insights into pharmacological tools to TR(i)P cancer up. Br J Pharmacol 2014; 171:2582-92. [PMID: 24345078 DOI: 10.1111/bph.12561] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 12/09/2013] [Accepted: 12/13/2013] [Indexed: 12/25/2022] Open
Abstract
The aim of this review is to address the recent advances regarding the use of pharmacological agents to target transient receptor potential (TRP) channels in cancer and their potential application in therapeutics. Physiologically, TRP channels are responsible for cation entry (Ca(2+) , Na(+) , Mg(2+) ) in many mammalian cells and regulate a large number of cellular functions. However, dysfunction in channel expression and/or activity can be linked to human diseases like cancer. Indeed, there is growing evidence that TRP channel expression is altered in cancer tissues in comparison with normal ones. Moreover, these proteins are involved in many cancerous processes, including cell proliferation, apoptosis, migration and invasion, as well as resistance to chemotherapy. Among the TRP superfamily, TRPC, TRPV, TRPM and TRPA1 have been shown to play a role in many cancer types, including breast, digestive, gliomal, head and neck, lung and prostate cancers. Pharmacological modulators are used to characterize the functional implications of TRP channels in whole-cell membrane currents, resting membrane potential regulation and intracellular Ca(2+) signalling. Moreover, pharmacological modulation of TRP activity in cancer cells is systematically linked to the effect on cancerous processes (proliferation, survival, migration, invasion, sensitivity to chemotherapeutic drugs). Here we describe the effects of such TRP modulators on TRP activity and cancer cell phenotype. Furthermore, the potency and specificity of these agents will be discussed, as well as the development of new strategies for targeting TRP channels in cancer.
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Affiliation(s)
- M Gautier
- Laboratory of Cell and Molecular Physiology, SFR CAP-Santé (FED 4231), University of Picardie Jules Verne, UFR Sciences, EA 4667, Amiens, France
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15
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Bubici C, Papa S. JNK signalling in cancer: in need of new, smarter therapeutic targets. Br J Pharmacol 2014; 171:24-37. [PMID: 24117156 DOI: 10.1111/bph.12432] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/09/2013] [Accepted: 09/13/2013] [Indexed: 12/17/2022] Open
Abstract
The JNKs are master protein kinases that regulate many physiological processes, including inflammatory responses, morphogenesis, cell proliferation, differentiation, survival and death. It is increasingly apparent that persistent activation of JNKs is involved in cancer development and progression. Therefore, JNKs represent attractive targets for therapeutic intervention with small molecule kinase inhibitors. However, evidence supportive of a tumour suppressor role for the JNK proteins has also been documented. Recent studies showed that the two major JNK proteins, JNK1 and JNK2, have distinct or even opposing functions in different types of cancer. As such, close consideration of which JNK proteins are beneficial targets and, more importantly, what effect small molecule inhibitors of JNKs have on physiological processes, are essential. A number of ATP-competitive and ATP-non-competitive JNK inhibitors have been developed, but have several limitations such as a lack of specificity and cellular toxicity. In this review, we summarize the accumulating evidence supporting a role for the JNK proteins in the pathogenesis of different solid and haematological malignancies, and discuss many challenges and scientific opportunities in the targeting of JNKs in cancer.
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Affiliation(s)
- Concetta Bubici
- Section of Inflammation and Signal Transduction, Department of Medicine, Imperial College, London, UK; Biosciences Division, School of Health Sciences and Social Care, Brunel University, London, UK
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16
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Dara A, Sangamwar AT. Anticancer patent landscape and technology assessment of Indian public-funded research institutes and organizations. Expert Opin Ther Pat 2014; 24:893-912. [PMID: 24898985 DOI: 10.1517/13543776.2014.926329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION This review discusses the various drug therapeutic targets and latest technologies of anticancer patents from 10 Indian public-funded research organizations covering more than 150 esteemed institutes. We have identified and reported the leading assignee and inventors along with their collaboration network and, thereby, have analyzed the various patent trends, geographical distributions, citation maps, Derwent World Patents Index, international patent classification analysis and the like. AREAS COVERED This article provides the insights of 1905 patent documents from 191 families and discusses in-depth anticancer technology through categorization studies at the level of drug discovery, drug development and treatment and diagnosis. In addition, various cancer targets were correlated with recent technologies so as to identify the white spaces for upcoming technologies. EXPERT OPINION Over a period of 13 years (1990 - 2013) the main focus of Indian cancer research was in the field of synthetic chemistry and natural extracts followed by the pharmaceutical compositions and combinations, whereas, the white spaces for future cancer remedy were identified from research in the areas of cancer stem cell lines, vaccines, gene therapy, nano formulations with targeted drug delivery systems as core and latest technologies.
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Affiliation(s)
- Ajay Dara
- National Institute of Pharmaceutical Education and Research (NIPER), Department of Pharmacoinformatics , S.A.S. Nagar, Mohali, Punjab 160062 , India +91 0172 2214682-2211 ;
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17
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Hasima N, Aggarwal BB. Cancer-linked targets modulated by curcumin. Int J Biochem Mol Biol 2012; 3:328-351. [PMID: 23301199 PMCID: PMC3533886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 10/21/2012] [Indexed: 06/01/2023]
Abstract
In spite of major advances in oncology, the World Health Organization predicts that cancer incidence will double within the next two decades. Although it is well understood that cancer is a hyperproliferative disorder mediated through dysregulation of multiple cell signaling pathways, most cancer drug development remains focused on modulation of specific targets, mostly one at a time, with agents referred to as "targeted therapies," "smart drugs," or "magic bullets." How many cancer targets there are is not known, and how many targets must be attacked to control cancer growth is not well understood. Although more than 90% of cancer-linked deaths are due to metastasis of the tumor to vital organs, most drug targeting is focused on killing the primary tumor. Besides lacking specificity, the targeted drugs induce toxicity and side effects that sometimes are greater problems than the disease itself. Furthermore, the cost of some of these drugs is so high that most people cannot afford them. The present report describes the potential anticancer properties of curcumin, a component of the Indian spice turmeric (Curcuma longa), known for its safety and low cost. Curcumin can selectively modulate multiple cell signaling pathways linked to inflammation and to survival, growth, invasion, angiogenesis, and metastasis of cancer cells. More clinical trials of curcumin are needed to prove its usefulness in the cancer setting.
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Affiliation(s)
- Noor Hasima
- Cytokine Research Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer CenterHouston, Texas, 77030, United States
- Institute Science Biology, Faculty of Science, University of Malaya50603 Kuala Lumpur, Malaysia
| | - Bharat B Aggarwal
- Cytokine Research Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer CenterHouston, Texas, 77030, United States
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18
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Abstract
Proteins carry out important functions as they fold themselves. Protein misfolding occurs during different biochemical processes and may lead to the development of diseases such as cancer, which is characterized by genetic instability. The cancer microenvironment exposes malignant cells to a variety of stressful conditions that may further promote protein misfolding. Tumor development and progression often arises from mutations that interfere with the appropriate function of tumor-suppressor proteins and oncogenes. These may be due to alteration of catalytic activity of the protein, loss of binding sites for effector proteins or alterations of the native folded protein conformation. Src family kinases, p53, mTOR and C-terminus of HSC70 interacting protein (CHIPs) are some examples associated with protein misfolding and tumorigenesis. Molecular chaperones, such as heat-shock protein (HSP)70 and HSP90, assist protein folding and recognize target misfolded proteins for degradation. It is likely that this misfolding in cancer is linked by common principles, and may, therefore, present an exciting possibility to identify common targets for therapeutic intervention. Here we aim to review a number of examples that show how alterations in the folding of tumor-suppressor proteins or oncogenes lead to tumorigenesis. The possibility of targeting the targets to repair or degrade protein misfolding in cancer therapy is discussed.
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Affiliation(s)
- Nagathihalli S Nagaraj
- Department of Surgery, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN-37232, USA.
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