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Fink JC, Landry D, Webb LJ. Probing the Electrostatic Effects of H-Ras Tyrosine 32 Mutations on Intrinsic GTP Hydrolysis Using Vibrational Stark Effect Spectroscopy of a Thiocyanate Probe. Biochemistry 2024. [PMID: 38967549 DOI: 10.1021/acs.biochem.4c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The wildtype H-Ras protein functions as a molecular switch in a variety of cell signaling pathways, and mutations to key residues result in a constitutively active oncoprotein. However, there is some debate regarding the mechanism of the intrinsic GTPase activity of H-Ras. It has been hypothesized that ordered water molecules are coordinated at the active site by Q61, a highly transforming amino acid site, and Y32, a position that has not previously been investigated. Here, we examine the electrostatic contribution of the Y32 position to GTP hydrolysis by comparing the rate of GTP hydrolysis of Y32X mutants to the vibrational energy shift of each mutation measured by a nearby thiocyanate vibrational probe to estimate changes in the electrostatic environment caused by changes at the Y32 position. We further compared vibrational energy shifts for each mutation to the hydration potential of the respective side chain and demonstrated that Y32 is less critical for recruiting water molecules into the active site to promote hydrolysis than Q61. Our results show a clear interplay between a steric contribution from Y32 and an electrostatic contribution from Q61 that are both critical for intrinsic GTP hydrolysis.
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Affiliation(s)
- Jackson C Fink
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Danielle Landry
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
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2
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Mendiratta G, Liarakos D, Tong M, Ito S, Ke E, Goshua G, Stites EC. Cancer research is not correlated with driver gene mutation burdens. MED 2024:S2666-6340(24)00217-4. [PMID: 38908369 DOI: 10.1016/j.medj.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/02/2024] [Accepted: 05/29/2024] [Indexed: 06/24/2024]
Abstract
BACKGROUND Cancer research is pursued with the goal of positively impacting patients with cancer. Decisions regarding how to allocate research funds reflect a complex balancing of priorities and factors. Even though these are subjective decisions, they should be made with consideration of all available objective facts. An accurate estimate of the affected cancer patient population by mutation is one variable that has only recently become available to inform funding decisions. METHODS We compared the overall incident burden of mutations within each cancer-associated gene with two measures of cancer research efforts: research grant funding amounts and numbers of academic manuscripts. We ask to what degree the aggregate set of cancer research efforts reflects the relative burdens of the different cancer genetic drivers. We thoroughly investigate the design of our queries to ensure that the presented results are robust and conclusions are well justified. FINDINGS We find cancer research is generally not correlated with the relative burden of mutation within the different genetic drivers of cancer. CONCLUSIONS We suggest that cancer research would benefit from incorporating, among other factors, an epidemiologically informed mutation-estimate baseline into a larger framework for funding and research allocation decisions. FUNDING This work was supported in part by the National Institutes of Health (NIH) P30CA014195 and NIH DP2AT011327.
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Affiliation(s)
- Gaurav Mendiratta
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - David Liarakos
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Melinda Tong
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Satoko Ito
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Eugene Ke
- Department of Surgery, Division of Surgical Oncology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - George Goshua
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA; Center for Outcomes Research and Evaluation, Yale School of Medicine, New Haven, CT 06510, USA
| | - Edward C Stites
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA.
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3
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Wang X, Breuer J, Garbe S, Giordano F, Brossart P, Feldmann G, Bisht S. Triple Blockade of Oncogenic RAS Signaling Using KRAS and MEK Inhibitors in Combination with Irradiation in Pancreatic Cancer. Int J Mol Sci 2024; 25:6249. [PMID: 38892436 PMCID: PMC11172716 DOI: 10.3390/ijms25116249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/27/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest of human malignancies and carries an exceptionally poor prognosis. It is mostly driven by multiple oncogenic alterations, with the highest mutation frequency being observed in the KRAS gene, which is a key oncogenic driver of tumorogenesis and malignant progression in PDAC. However, KRAS remained undruggable for decades until the emergence of G12C mutation specific KRAS inhibitors. Despite this development, this therapeutic approach to target KRAS directly is not routinely used for PDAC patients, with the reasons being the rare presence of G12C mutation in PDAC with only 1-2% of occurring cases, modest therapeutic efficacy, activation of compensatory pathways leading to cell resistance, and absence of effective KRASG12D or pan-KRAS inhibitors. Additionally, indirect approaches to targeting KRAS through upstream and downstream regulators or effectors were also found to be either ineffective or known to cause major toxicities. For this reason, new and more effective treatment strategies that combine different therapeutic modalities aiming at achieving synergism and minimizing intrinsic or adaptive resistance mechanisms are required. In the current work presented here, pancreatic cancer cell lines with oncogenic KRAS G12C, G12D, or wild-type KRAS were treated with specific KRAS or SOS1/2 inhibitors, and therapeutic synergisms with concomitant MEK inhibition and irradiation were systematically evaluated by means of cell viability, 2D-clonogenic, 3D-anchorage independent soft agar, and bioluminescent ATP assays. Underlying pathophysiological mechanisms were examined by using Western blot analyses, apoptosis assay, and RAS activation assay.
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Affiliation(s)
- Xuan Wang
- Department of Internal Medicine 3, Center of Integrated Oncology (CIO-ABCD) Aachen-Bonn-Cologne-Düsseldorf, University Hospital of Bonn, Venusberg Campus-1, 53127 Bonn, Germany
| | - Johanna Breuer
- Institute of Molecular Medicine and Experimental Immunology, University Hospital of Bonn, Venusberg Campus-1, 53127 Bonn, Germany
| | - Stephan Garbe
- Department of Radiology and Radiation Oncology, University Hospital of Bonn, Venusberg Campus-1, 53127 Bonn, Germany
| | - Frank Giordano
- Department of Radiology and Radiation Oncology, University Hospital of Bonn, Venusberg Campus-1, 53127 Bonn, Germany
| | - Peter Brossart
- Department of Internal Medicine 3, Center of Integrated Oncology (CIO-ABCD) Aachen-Bonn-Cologne-Düsseldorf, University Hospital of Bonn, Venusberg Campus-1, 53127 Bonn, Germany
| | - Georg Feldmann
- Department of Internal Medicine 3, Center of Integrated Oncology (CIO-ABCD) Aachen-Bonn-Cologne-Düsseldorf, University Hospital of Bonn, Venusberg Campus-1, 53127 Bonn, Germany
| | - Savita Bisht
- Department of Internal Medicine 3, Center of Integrated Oncology (CIO-ABCD) Aachen-Bonn-Cologne-Düsseldorf, University Hospital of Bonn, Venusberg Campus-1, 53127 Bonn, Germany
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Frank PH, Hong M, Higgins B, Perkins S, Taylor T, Wall VE, Drew M, Waybright T, Gillette W, Esposito D, Messing S. Adapting recombinant bacterial alkaline phosphatase for nucleotide exchange of small GTPases. Protein Expr Purif 2024; 218:106446. [PMID: 38395209 PMCID: PMC11000209 DOI: 10.1016/j.pep.2024.106446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/05/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
The small GTPase Rat sarcoma virus proteins (RAS) are key regulators of cell growth and involved in 20-30% of cancers. RAS switches between its active state and inactive state via exchange of GTP (active) and GDP (inactive). Therefore, to study active protein, it needs to undergo nucleotide exchange to a non-hydrolysable GTP analog. Calf intestine alkaline phosphatase bound to agarose beads (CIP-agarose) is regularly used in a nucleotide exchange protocol to replace GDP with a non-hydrolysable analog. Due to pandemic supply problems and product shortages, we found the need for an alternative to this commercially available product. Here we describe how we generated a bacterial alkaline phosphatase (BAP) with an affinity tag bound to an agarose bead. This BAP completely exchanges the nucleotide in our samples, thereby demonstrating an alternative to the commercially available product using generally available laboratory equipment.
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Affiliation(s)
- Peter H Frank
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Min Hong
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Brianna Higgins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Shelley Perkins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Vanessa E Wall
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Matthew Drew
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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Zhou Y, Tao L, Qiu J, Xu J, Yang X, Zhang Y, Tian X, Guan X, Cen X, Zhao Y. Tumor biomarkers for diagnosis, prognosis and targeted therapy. Signal Transduct Target Ther 2024; 9:132. [PMID: 38763973 PMCID: PMC11102923 DOI: 10.1038/s41392-024-01823-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 03/07/2024] [Accepted: 04/02/2024] [Indexed: 05/21/2024] Open
Abstract
Tumor biomarkers, the substances which are produced by tumors or the body's responses to tumors during tumorigenesis and progression, have been demonstrated to possess critical and encouraging value in screening and early diagnosis, prognosis prediction, recurrence detection, and therapeutic efficacy monitoring of cancers. Over the past decades, continuous progress has been made in exploring and discovering novel, sensitive, specific, and accurate tumor biomarkers, which has significantly promoted personalized medicine and improved the outcomes of cancer patients, especially advances in molecular biology technologies developed for the detection of tumor biomarkers. Herein, we summarize the discovery and development of tumor biomarkers, including the history of tumor biomarkers, the conventional and innovative technologies used for biomarker discovery and detection, the classification of tumor biomarkers based on tissue origins, and the application of tumor biomarkers in clinical cancer management. In particular, we highlight the recent advancements in biomarker-based anticancer-targeted therapies which are emerging as breakthroughs and promising cancer therapeutic strategies. We also discuss limitations and challenges that need to be addressed and provide insights and perspectives to turn challenges into opportunities in this field. Collectively, the discovery and application of multiple tumor biomarkers emphasized in this review may provide guidance on improved precision medicine, broaden horizons in future research directions, and expedite the clinical classification of cancer patients according to their molecular biomarkers rather than organs of origin.
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Affiliation(s)
- Yue Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lei Tao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiahao Qiu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Xu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinyu Yang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yu Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- School of Medicine, Tibet University, Lhasa, 850000, China
| | - Xinyu Tian
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinqi Guan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaobo Cen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yinglan Zhao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Han LY, Yu H, Wang S, Bao YR, Li TJ, Zheng Y, Luo X, Jia MN, Zhang Q, Meng XS. Classical prescription Floris Sophorae Powder treat colorectal cancer by regulating KRAS/MEK-ERK signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 325:117805. [PMID: 38278374 DOI: 10.1016/j.jep.2024.117805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/13/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Colorectal cancer (CRC) belongs to the category of intestinal wind, anal ulcer, abdominal mass and other diseases in traditional Chinese medicine (TCM). Floris Sophorae Powder (F.S), is a classical prescription is recorded in Puji Benshi Fang for the treatment of intestinal carbuncle. It has been incorporated into the prescriptions for the treatment of intestinal diseases and achieved remarkable results in modern medicine. However, the mechanism of F.S in the treatment of colorectal cancer remains unclear and requires further study. AIM OF THE STUDY To investigate F.S in treating CRC and clarify the underlying mechanism. MATERIALS AND METHODS This study was based on Dextran Sulfate Sodium Salt (DSS) combined with Azoxymethane (AOM) induced CRC mouse model to clarify the pharmacological effects of F.S. The serum metabolomics was used to study the mechanism of action, and the chemical composition of F.S was found by UPLC-Q-TOF-MS. The rationality of serm metabolomics results was verified through the clinical target database of network pharmacology, and the upstream and downstream targets of related pathways were found. The mechanism pathway was verified by Western blot to clarify its mechanism of action. RESULTS In vivo pharmacological experiments showed that F.S inhibited tumor growth and improved hematochezia. The vital signs of mice in the high-dose F.S group approached to those in the control group. A total of 43 differential metabolites were found to be significantly changed by serum metabolomics. F.S could modulate and recover most of the differential metabolites, which proved to be closely related to the KRAS/MEK-ERK signaling pathway. A total of 46 compounds in F.S were identified, and the rationality of serm metabolic pathway was verified by network pharmacology. Western blot results also verified that the expression of KRAS, E2F1, p-MEK and p-ERK were significantly decreased after F.S treatment. CONCLUSION Classical prescription Floris Sophorae Powder treat colorectal cancer by regulating KRAS/MEK-ERK signaling pathway.
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Affiliation(s)
- Li-Ying Han
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China; Liaoning Multi-dimensional Analysis of Traditional Chinese Medicine Technical Innovation Center, Dalian, 116600, China; Liaoning Province Modern Chinese Medicine Research Engineering Laboratory, Dalian, 116600, China.
| | - Hao Yu
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China; Liaoning Multi-dimensional Analysis of Traditional Chinese Medicine Technical Innovation Center, Dalian, 116600, China; Liaoning Province Modern Chinese Medicine Research Engineering Laboratory, Dalian, 116600, China.
| | - Shuai Wang
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China; Liaoning Multi-dimensional Analysis of Traditional Chinese Medicine Technical Innovation Center, Dalian, 116600, China; Liaoning Province Modern Chinese Medicine Research Engineering Laboratory, Dalian, 116600, China.
| | - Yong-Rui Bao
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China; Liaoning Multi-dimensional Analysis of Traditional Chinese Medicine Technical Innovation Center, Dalian, 116600, China; Liaoning Province Modern Chinese Medicine Research Engineering Laboratory, Dalian, 116600, China.
| | - Tian-Jiao Li
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China; Liaoning Multi-dimensional Analysis of Traditional Chinese Medicine Technical Innovation Center, Dalian, 116600, China; Liaoning Province Modern Chinese Medicine Research Engineering Laboratory, Dalian, 116600, China.
| | - Ying Zheng
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China; Liaoning Multi-dimensional Analysis of Traditional Chinese Medicine Technical Innovation Center, Dalian, 116600, China; Liaoning Province Modern Chinese Medicine Research Engineering Laboratory, Dalian, 116600, China.
| | - Xi Luo
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China; Liaoning Multi-dimensional Analysis of Traditional Chinese Medicine Technical Innovation Center, Dalian, 116600, China; Liaoning Province Modern Chinese Medicine Research Engineering Laboratory, Dalian, 116600, China.
| | - Meng-Nan Jia
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China; Liaoning Multi-dimensional Analysis of Traditional Chinese Medicine Technical Innovation Center, Dalian, 116600, China; Liaoning Province Modern Chinese Medicine Research Engineering Laboratory, Dalian, 116600, China.
| | - Qiang Zhang
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China; Liaoning Multi-dimensional Analysis of Traditional Chinese Medicine Technical Innovation Center, Dalian, 116600, China; Liaoning Province Modern Chinese Medicine Research Engineering Laboratory, Dalian, 116600, China.
| | - Xian-Sheng Meng
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China; Liaoning Multi-dimensional Analysis of Traditional Chinese Medicine Technical Innovation Center, Dalian, 116600, China; Liaoning Province Modern Chinese Medicine Research Engineering Laboratory, Dalian, 116600, China.
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Rahmati A, Mafi A, Vakili O, Soleymani F, Alishahi Z, Yahyazadeh S, Gholinezhad Y, Rezaee M, Johnston TP, Sahebkar A. Non-coding RNAs in leukemia drug resistance: new perspectives on molecular mechanisms and signaling pathways. Ann Hematol 2024; 103:1455-1482. [PMID: 37526673 DOI: 10.1007/s00277-023-05383-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023]
Abstract
Like almost all cancer types, timely diagnosis is needed for leukemias to be effectively cured. Drug efflux, attenuated drug uptake, altered drug metabolism, and epigenetic alterations are just several of the key mechanisms by which drug resistance develops. All of these mechanisms are orchestrated by up- and downregulators, in which non-coding RNAs (ncRNAs) do not encode specific proteins in most cases; albeit, some of them have been found to exhibit the potential for protein-coding. Notwithstanding, ncRNAs are chiefly known for their contribution to the regulation of physiological processes, as well as the pathological ones, such as cell proliferation, apoptosis, and immune responses. Specifically, in the case of leukemia chemo-resistance, ncRNAs have been recognized to be responsible for modulating the initiation and progression of drug resistance. Herein, we comprehensively reviewed the role of ncRNAs, specifically its effect on molecular mechanisms and signaling pathways, in the development of leukemia drug resistance.
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Affiliation(s)
- Atefe Rahmati
- Department of Hematology and Blood Banking, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Basic Sciences, Faculty of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, Autophagy Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Firooze Soleymani
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Alishahi
- Department of Basic Sciences, Faculty of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Sheida Yahyazadeh
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yasaman Gholinezhad
- Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Malihe Rezaee
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Thomas P Johnston
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, the, Islamic Republic of Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, the, Islamic Republic of Iran.
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, the, Islamic Republic of Iran.
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8
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Hacisuleyman A, Erman B. Synergy and anti-cooperativity in allostery: Molecular dynamics study of WT and oncogenic KRAS-RGL1. Proteins 2024; 92:665-678. [PMID: 38153169 DOI: 10.1002/prot.26657] [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: 07/28/2023] [Revised: 11/03/2023] [Accepted: 12/15/2023] [Indexed: 12/29/2023]
Abstract
This study focuses on investigating the effects of an oncogenic mutation (G12V) on the stability and interactions within the KRAS-RGL1 protein complex. The KRAS-RGL1 complex is of particular interest due to its relevance to KRAS-associated cancers and the potential for developing targeted drugs against the KRAS system. The stability of the complex and the allosteric effects of specific residues are examined to understand their roles as modulators of complex stability and function. Using molecular dynamics simulations, we calculate the mutual information, MI, between two neighboring residues at the interface of the KRAS-RGL1 complex, and employ the concept of interaction information, II, to measure the contribution of a third residue to the interaction between interface residue pairs. Negative II indicates synergy, where the presence of the third residue strengthens the interaction, while positive II suggests anti-cooperativity. Our findings reveal that MI serves as a dominant factor in determining the results, with the G12V mutation increasing the MI between interface residues, indicating enhanced correlations due to the formation of a more compact structure in the complex. Interestingly, although II plays a role in understanding three-body interactions and the impact of distant residues, it is not significant enough to outweigh the influence of MI in determining the overall stability of the complex. Nevertheless, II may nonetheless be a relevant factor to consider in future drug design efforts. This study provides valuable insights into the mechanisms of complex stability and function, highlighting the significance of three-body interactions and the impact of distant residues on the binding stability of the complex. Additionally, our findings demonstrate that constraining the fluctuations of a third residue consistently increases the stability of the G12V variant, making it challenging to weaken complex formation of the mutated species through allosteric manipulation. The novel perspective offered by this approach on protein dynamics, function, and allostery has potential implications for understanding and targeting other protein complexes involved in vital cellular processes. The results contribute to our understanding of the effects of oncogenic mutations on protein-protein interactions and provide a foundation for future therapeutic interventions in the context of KRAS-associated cancers and beyond.
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Affiliation(s)
- Aysima Hacisuleyman
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Burak Erman
- Department of Chemical and Biological Engineering Koc University, Istanbul, Turkey
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9
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Dutta D, Ray P, De A, Ghosh A, Hazra RS, Ghosh P, Banerjee S, Diaz FJ, Upadhyay SP, Quadir M, Banerjee SK. pH-responsive targeted nanoparticles release ERK-inhibitor in the hypoxic zone and sensitize free gemcitabine in mutant K-Ras-addicted pancreatic cancer cells and mouse model. PLoS One 2024; 19:e0297749. [PMID: 38687749 PMCID: PMC11060587 DOI: 10.1371/journal.pone.0297749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/12/2024] [Indexed: 05/02/2024] Open
Abstract
Therapeutic options for managing Pancreatic ductal adenocarcinoma (PDAC), one of the deadliest types of aggressive malignancies, are limited and disappointing. Therefore, despite suboptimal clinical effects, gemcitabine (GEM) remains the first-line chemotherapeutic drug in the clinic for PDAC treatment. The therapeutic limitations of GEM are primarily due to poor bioavailability and the development of chemoresistance resulting from the addiction of mutant-K-RAS/AKT/ERK signaling-mediated desmoplastic barriers with a hypoxic microenvironment. Several new therapeutic approaches, including nanoparticle-assisted drug delivery, are being investigated by us and others. This study used pH-responsive nanoparticles encapsulated ERK inhibitor (SCH772984) and surface functionalized with tumor-penetrating peptide, iRGD, to target PDAC tumors. We used a small molecule, SCH772984, to target ERK1 and ERK2 in PDAC and other cancer cells. This nanocarrier efficiently released ERKi in hypoxic and low-pH environments. We also found that the free-GEM, which is functionally weak when combined with nanoencapsulated ERKi, led to significant synergistic treatment outcomes in vitro and in vivo. In particular, the combination approaches significantly enhanced the GEM effect in PDAC growth inhibition and prolonged survival of the animals in a genetically engineered KPC (LSL-KrasG12D/+/LSL-Trp53R172H/+/Pdx-1-Cre) pancreatic cancer mouse model, which is not observed in a single therapy. Mechanistically, we anticipate that the GEM efficacy was increased as ERKi blocks desmoplasia by impairing the production of desmoplastic regulatory factors in PDAC cells and KPC mouse tumors. Therefore, 2nd generation ERKi (SCH 772984)-iRGD-pHNPs are vital for the cellular response to GEM and denote a promising therapeutic target in PDAC with mutant K-RAS.
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Affiliation(s)
- Debasmita Dutta
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, United States of America
| | - Priyanka Ray
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, United States of America
| | - Archana De
- Cancer Research Unit, VA Medical Center, Kansas City, MO, United States of America
| | - Arnab Ghosh
- Cancer Research Unit, VA Medical Center, Kansas City, MO, United States of America
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Raj Shankar Hazra
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, United States of America
| | - Pratyusha Ghosh
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, United States of America
- Cancer Research Unit, VA Medical Center, Kansas City, MO, United States of America
| | - Snigdha Banerjee
- Cancer Research Unit, VA Medical Center, Kansas City, MO, United States of America
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Francisco J. Diaz
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Sunil P. Upadhyay
- Cancer Research Unit, VA Medical Center, Kansas City, MO, United States of America
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Mohiuddin Quadir
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, United States of America
| | - Sushanta K. Banerjee
- Cancer Research Unit, VA Medical Center, Kansas City, MO, United States of America
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States of America
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10
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Huang Y, Zheng D, Zhou Z, Wang H, Li Y, Zheng H, Tan J, Wu J, Yang Q, Tian H, Lin L, Li Z, Li T. The research advances in Kirsten rat sarcoma viral oncogene homolog (KRAS)-related cancer during 2013 to 2022: a scientometric analysis. Front Oncol 2024; 14:1345737. [PMID: 38706597 PMCID: PMC11066287 DOI: 10.3389/fonc.2024.1345737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/08/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction Cancer represents a significant global public health concern. In recent years, the incidence of cancer has been on the rise worldwide due to various factors, including diet, environment, and an aging population. Simultaneously, advancements in tumor molecular biology and genomics have led to a shift from systemic chemotherapy focused on disease sites and morphopathology towards precise targeted therapy for driver gene mutations. Therefore, we propose a comprehensive review aimed at exploring the research hotspots and directions in the field of Kirsten rat sarcoma viral oncogene homolog (KRAS)-mutant cancers over the past decade, providing valuable insights for cancer treatment strategies. Specifically, we aim to present an intellectual landscape using data obtained from the Web of Science (WoS) regarding KRAS mutation. Methods Bibliometrix, VOSviewer, CiteSpace, and HistCite were employed to conduct scientometric analyses on national publications, influential authors, highly cited articles, frequent keywords, etc. Results A total of 16,609 publications met the screening criteria and exhibited a consistent annual growth trend overall. Among 102 countries/regions, the United States occupied the vast majority share of the published volume. The journal Oncotarget had the highest circulation among all scientific publications. Moreover, the most seminal articles in this field primarily focus on biology and targeted therapies, with overcoming drug resistance being identified as a future research direction. Conclusion The findings of the thematic analysis indicate that KRAS mutation in lung cancer, the prognosis following B-Raf proto-oncogene, serine/threonine kinase (BRAF) or rat sarcoma (RAS) mutations, and anti-epidermal growth factor receptor (EGFR)-related lung cancer are the significant hotspots in the given field. Considering the significant advancements made in direct targeting drugs like sotorasib, it is anticipated that interest in cancers associated with KRAS mutations will remain steadfast.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Zhiyang Li
- Department of Thyroid, Breast and Hernia Surgery, General Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Tianyu Li
- Department of Thyroid, Breast and Hernia Surgery, General Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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11
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Ash LJ, Busia-Bourdain O, Okpattah D, Kamel A, Liberchuk A, Wolfe AL. KRAS: Biology, Inhibition, and Mechanisms of Inhibitor Resistance. Curr Oncol 2024; 31:2024-2046. [PMID: 38668053 PMCID: PMC11049385 DOI: 10.3390/curroncol31040150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
KRAS is a small GTPase that is among the most commonly mutated oncogenes in cancer. Here, we discuss KRAS biology, therapeutic avenues to target it, and mechanisms of resistance that tumors employ in response to KRAS inhibition. Several strategies are under investigation for inhibiting oncogenic KRAS, including small molecule compounds targeting specific KRAS mutations, pan-KRAS inhibitors, PROTACs, siRNAs, PNAs, and mutant KRAS-specific immunostimulatory strategies. A central challenge to therapeutic effectiveness is the frequent development of resistance to these treatments. Direct resistance mechanisms can involve KRAS mutations that reduce drug efficacy or copy number alterations that increase the expression of mutant KRAS. Indirect resistance mechanisms arise from mutations that can rescue mutant KRAS-dependent cells either by reactivating the same signaling or via alternative pathways. Further, non-mutational forms of resistance can take the form of epigenetic marks, transcriptional reprogramming, or alterations within the tumor microenvironment. As the possible strategies to inhibit KRAS expand, understanding the nuances of resistance mechanisms is paramount to the development of both enhanced therapeutics and innovative drug combinations.
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Affiliation(s)
- Leonard J. Ash
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
- Molecular, Cellular, and Developmental Biology Subprogram of the Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10031, USA
| | - Ottavia Busia-Bourdain
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
| | - Daniel Okpattah
- Biochemistry Ph.D. Program, Graduate Center, City University of New York, New York, NY 10031, USA
| | - Avrosina Kamel
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
- Macaulay Honors College, Hunter College, City University of New York, New York, NY 10065, USA
| | - Ariel Liberchuk
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
- Macaulay Honors College, Hunter College, City University of New York, New York, NY 10065, USA
| | - Andrew L. Wolfe
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
- Molecular, Cellular, and Developmental Biology Subprogram of the Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10031, USA
- Biochemistry Ph.D. Program, Graduate Center, City University of New York, New York, NY 10031, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
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12
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Pagba CV, Gupta AK, Dilsha K, Sadrpour P, Jakubec J, Prakash P, van der Hoeven D, Cho KJ, Gilbertson S, Gorfe AA. Biophysical and Biochemical Characterization of Structurally Diverse Small Molecule Hits for KRAS Inhibition. Chembiochem 2024; 25:e202300827. [PMID: 38349283 DOI: 10.1002/cbic.202300827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/12/2024] [Indexed: 03/08/2024]
Abstract
We describe six compounds as early hits for the development of direct inhibitors of KRAS, an important anticancer drug target. We show that these compounds bind to KRAS with affinities in the low micromolar range and exert different effects on its interactions with binding partners. Some of the compounds exhibit selective binding to the activated form of KRAS and inhibit signal transduction through both the MAPK or the phosphatidylinositide 3-kinase PI3K-protein kinase B (AKT) pathway in cells expressing mutant KRAS. Most inhibit intrinsic and/or SOS-mediated KRAS activation while others inhibit RAS-effector interaction. We propose these compounds as starting points for the development of non-covalent allosteric KRAS inhibitors.
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Affiliation(s)
- Cynthia V Pagba
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Amit K Gupta
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Kasuni Dilsha
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, TX 77204, USA
| | - Parisa Sadrpour
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Jacob Jakubec
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Priyanka Prakash
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Dharini van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge St., Houston, Texas, 77030, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Scott Gilbertson
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, TX 77204, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
- Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, UTHealth MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, 6431 Fannin St., Houston, Texas, 77030, USA
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13
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Fu X, Liu S, Cao D, Li C, Ji H, Wang G. Med23 deficiency reprograms the tumor microenvironment to promote lung tumorigenesis. Br J Cancer 2024; 130:716-727. [PMID: 38195889 PMCID: PMC10912217 DOI: 10.1038/s41416-023-02556-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related death worldwide. We previously found that Mediator complex subunit 23 (MED23) is important for the tumourigenicity of lung cancer cells with hyperactive Ras activity in vitro, although the in vivo function of MED23 in lung tumourigenesis remains to be explored. METHODS In this study, we utilized well-characterized KrasG12D-driven non-small cell lung cancer mouse model to investigate the role of MED23 in lung cancer. The lung tumour progression was evaluated by H&E and IHC analysis. Western blotting and qRT-PCR assays were performed to detect changes in gene expression. Immune cells were analyzed by FACS technology. RNA-seq and reporter assays were conducted to explore the mechanism. RESULTS We observed that lung epithelial Med23 deletion by adeno-Cre resulted in a significant increase in KrasG12D tumour number and size, which was further verified with another mouse model with Med23 specifically deleted in alveolar type II cells. Mice with lung-specific Med23 deficiency also exhibited accelerated tumourigenesis, and a higher proliferation rate for tumour cells, along with increased ERK phosphorylation. Notably, the numbers of infiltrating CD4+ T cells and CD8+ T cells were significantly reduced in the lungs of Med23-deficient mice, while the numbers of myeloid-derived suppressor cells (MDSCs) and Treg cells were significantly increased, suggesting the enhanced immune escape capability of the Med23-deficient lung tumours. Transcriptomic analysis revealed that the downregulated genes in Med23-deficient lung tumour tissues were associated with the immune response. Specifically, Med23 deficiency may compromise the MHC-I complex formation, partially through down-regulating B2m expression. CONCLUSIONS Collectively, these findings revealed that MED23 may negatively regulate Kras-induced lung tumourigenesis in vivo, which would improve the precise classification of KRAS-mutant lung cancer patients and provide new insights for clinical interventions.
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Affiliation(s)
- Xiaobo Fu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Siming Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dan Cao
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Chonghui Li
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Gang Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
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14
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Ranđelović I, Nyíri K, Koppány G, Baranyi M, Tóvári J, Kigyós A, Tímár J, Vértessy BG, Grolmusz V. Gluing GAP to RAS Mutants: A New Approach to an Old Problem in Cancer Drug Development. Int J Mol Sci 2024; 25:2572. [PMID: 38473821 DOI: 10.3390/ijms25052572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/11/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Mutated genes may lead to cancer development in numerous tissues. While more than 600 cancer-causing genes are known today, some of the most widespread mutations are connected to the RAS gene; RAS mutations are found in approximately 25% of all human tumors. Specifically, KRAS mutations are involved in the three most lethal cancers in the U.S., namely pancreatic ductal adenocarcinoma, colorectal adenocarcinoma, and lung adenocarcinoma. These cancers are among the most difficult to treat, and they are frequently excluded from chemotherapeutic attacks as hopeless cases. The mutated KRAS proteins have specific three-dimensional conformations, which perturb functional interaction with the GAP protein on the GAP-RAS complex surface, leading to a signaling cascade and uncontrolled cell growth. Here, we describe a gluing docking method for finding small molecules that bind to both the GAP and the mutated KRAS molecules. These small molecules glue together the GAP and the mutated KRAS molecules and may serve as new cancer drugs for the most lethal, most difficult-to-treat, carcinomas. As a proof of concept, we identify two new, drug-like small molecules with the new method; these compounds specifically inhibit the growth of the PANC-1 cell line with KRAS mutation G12D in vitro and in vivo. Importantly, the two new compounds show significantly lower IC50 and higher specificity against the G12D KRAS mutant human pancreatic cancer cell line PANC-1, as compared to the recently described selective G12D KRAS inhibitor MRTX-1133.
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Affiliation(s)
| | - Kinga Nyíri
- Laboratory of Genome Metabolism and Repair, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, 1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, BME Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Gergely Koppány
- Laboratory of Genome Metabolism and Repair, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, 1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, BME Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Marcell Baranyi
- KINETO Lab Ltd., 1037 Budapest, Hungary
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
| | - József Tóvári
- Department of Experimental Pharmacology and the National Tumor Biology Laboratory, National Institute of Oncology, 1122 Budapest, Hungary
| | | | - József Tímár
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
| | - Beáta G Vértessy
- Laboratory of Genome Metabolism and Repair, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, 1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, BME Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Vince Grolmusz
- Department of Computer Science, Mathematical Institute, Eötvös Loránd University, 1117 Budapest, Hungary
- Uratim Ltd., 1118 Budapest, Hungary
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15
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Sahu P, Mitra A, Ganguly A. Targeting KRAS and SHP2 signaling pathways for immunomodulation and improving treatment outcomes in solid tumors. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 386:167-222. [PMID: 38782499 DOI: 10.1016/bs.ircmb.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Historically, KRAS has been considered 'undruggable' inspite of being one of the most frequently altered oncogenic proteins in solid tumors, primarily due to the paucity of pharmacologically 'druggable' pockets within the mutant isoforms. However, pioneering developments in drug design capable of targeting the mutant KRAS isoforms especially KRASG12C-mutant cancers, have opened the doors for emergence of combination therapies comprising of a plethora of inhibitors targeting different signaling pathways. SHP2 signaling pathway, primarily known for activation of intracellular signaling pathways such as KRAS has come up as a potential target for such combination therapies as it emerged to be the signaling protein connecting KRAS and the immune signaling pathways and providing the link for understanding the overlapping regions of RAS/ERK/MAPK signaling cascade. Thus, SHP2 inhibitors having potent tumoricidal activity as well as role in immunomodulation have generated keen interest in researchers to explore its potential as combination therapy in KRAS mutant solid tumors. However, the excitement with these combination therapies need to overcome challenges thrown up by drug resistance and enhanced toxicity. In this review, we will discuss KRAS and SHP2 signaling pathways and their roles in immunomodulation and regulation of tumor microenvironment and also analyze the positive effects and drawbacks of the different combination therapies targeted at these signaling pathways along with their present and future potential to treat solid tumors.
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Affiliation(s)
- Priyanka Sahu
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, United States
| | - Ankita Mitra
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, United States
| | - Anirban Ganguly
- Department of Biochemistry, All India Institute of Medical Sciences, Deoghar, Jharkhand, India.
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16
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Columbus J, Turbyville T. Studying RAS Interactions in Live Cells with BRET. Methods Mol Biol 2024; 2797:253-260. [PMID: 38570465 DOI: 10.1007/978-1-0716-3822-4_18] [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] [Indexed: 04/05/2024]
Abstract
Bioluminescence resonance energy transfer (BRET) is a valuable technique for studying protein-protein interactions (PPIs) within live cells (Pfleger and Eidne, Nat Methods 3:165-174, 2006). Among the various BRET methodologies, a recent addition called NanoBRET has emerged, leveraging advancements in donor and acceptor technologies (Machleidt and Woodroofe, ACS Chem Biol 10:1797-1804, 2015). In this study, we present a developed methodology designed to measure PPIs involving the RAS protein family and their effectors and interactors at the plasma membrane. By utilizing the NanoLuc and HaloTag BRET pair, we provide evidence of a saturable interaction between KRAS4b-G12D and full-length RAF1. Conversely, the RAF1 R89L mutant, known to impede RAF1 binding to active RAS, exhibits nonspecific interactions. The assay exhibits remarkable signal-to-background ratios and is highly suitable for investigating the interactions of RAS with effectors, as well as for high-throughput screening assays.
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Affiliation(s)
- John Columbus
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Thomas Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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17
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Waybright T, Stephen AG. Nucleotide Exchange on RAS Proteins Using Hydrolysable and Non-hydrolysable Nucleotides. Methods Mol Biol 2024; 2797:35-46. [PMID: 38570451 DOI: 10.1007/978-1-0716-3822-4_4] [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] [Indexed: 04/05/2024]
Abstract
Biochemical and biophysical assays using recombinant RAS require the protein to be in either the active or inactive state. Here we describe methods to exchange the nucleotide present in the purified RAS protein with either GDPβS, GppNHp, or GTP depending on the assay requirement. In addition, we also describe the HPLC method used to validate the exchange process and provide information on the efficiency of the nucleotide exchange.
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Affiliation(s)
- Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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18
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Alexander P, Stephen AG. Affinity Measurement of Non-covalent Interactions of the Covalent KRAS G12C GDP Inhibitor MRTX849 to RAS Isoforms Using Surface Plasmon Resonance. Methods Mol Biol 2024; 2797:103-114. [PMID: 38570455 DOI: 10.1007/978-1-0716-3822-4_8] [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] [Indexed: 04/05/2024]
Abstract
Surface plasmon resonance (SPR) is an optical effect at an electron-rich surface that enables affinity measurements of biomolecules in real time. It is label free and versatile, not limited to proteins, nucleic acids, and small molecules. SPR is a widely accepted method to measure not only affinity of molecular interactions but also association and dissociation rates of such interactions. In this chapter, we describe a general method to measure the affinity of a small molecule drug, MRTX849, to GDP bound HRAS, KRAS, and NRAS.
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Affiliation(s)
- Patrick Alexander
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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19
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Lu H, Hu Z, Faraudo J, Martí J. In silico design of a lipid-like compound targeting KRAS4B-G12D through non-covalent bonds. NANOSCALE 2023; 15:19359-19368. [PMID: 38014474 DOI: 10.1039/d3nr04513g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
One of the most common drivers in human cancer is the peripheral membrane protein KRAS4B, able to promote oncogenic signalling. To signal, oncogenic KRAS4B not only requires a sufficient nucleotide exchange, but also needs to recruit effectors by exposing its effector-binding sites while anchoring to the phospholipid bilayer where KRAS4B-mediated signalling events occur. The enzyme phosphodiesterase-δ plays an important role in sequestering KRAS4B from the cytoplasm and targeting it to cellular membranes of different cell species. In this work, we present an in silico design of a lipid-like compound that has the remarkable feature of being able to target both an oncogenic KRAS4B-G12D mutant and the phosphodiesterase-δ enzyme. This double action is accomplished by adding a lipid tail (analogous to the farnesyl group of the KRAS4B protein) to an previously known active compound (2H-1,2,4-benzothiadiazine, 3,4-dihydro-,1,1-dioxide). The proposed lipid-like molecule was found to lock KRAS4B-G12D in its GDP-bound state by adjusting the effector-binding domain to be blocked by the interface of the lipid bilayer. Meanwhile, it can tune GTP-bound KRAS4B-G12D to shift from the active orientation state to the inactive state. The proposed compound is also observed to stably accommodate itself in the prenyl-binding pocket of phosphodiesterase-δ, which impairs KRAS4B enrichment at the lipid bilayer, potentially reducing the proliferation of KRAS4B inside the cytoplasm and its anchoring at the bilayer. In conclusion, we report a potential inhibitor of KRAS4B-G12D with a lipid tail attached to a specific warhead, a compound which has not yet been considered for drugs targeting RAS mutants. Our work provides new ways to target KRAS4B-G12D and can also foster drug discovery efforts for the targeting of oncogenes of the RAS family and beyond.
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Affiliation(s)
- Huixia Lu
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, Bellaterra, Barcelona E-08193, Spain.
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
| | - Zheyao Hu
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, Bellaterra, Barcelona E-08193, Spain.
| | - Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
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20
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Wang Y, Chen S, Wang C, Guo F. Nanocarrier-based targeting of metabolic pathways for endometrial cancer: Status and future perspectives. Biomed Pharmacother 2023; 166:115348. [PMID: 37639743 DOI: 10.1016/j.biopha.2023.115348] [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: 06/28/2023] [Revised: 08/10/2023] [Accepted: 08/19/2023] [Indexed: 08/31/2023] Open
Abstract
Cancer is the second-most lethal global disease, as per health reports, and is responsible for around 70% of deaths in low- and middle-income countries. Endometrial cancer is one of the emerging malignancies and has been predicted as a public health challenge for the future. Insulin resistance, obesity, and diabetes mellitus are the key metabolic factors that promote risks for the development of endometrial cancer. Various signaling pathways and associated genes are involved in the genesis of endometrial cancer, and any mutation or deletion in such related factors leads to the induction of endometrial cancer. The conventional way of drug delivery has been used for ages but is associated with poor management of cancer due to non-targeting of the endometrial cancer cells, low efficacy of the therapy, and toxicity issues as well. In this context, nanocarrier-based therapy for the management of endometrial cancer is an effective alternate choice that overcomes the problems associated with conventional therapy. In this review article, we highlighted the nanocarrier-based targeting of endometrial cancer, with a special focus on targeting various metabolic signaling pathways. Furthermore, the future perspectives of nanocarrier-based targeting of metabolic pathways in endometrial cancer were also underpinned. It is concluded that targeting metabolic signaling pathways in endometrial cancer via nanocarrier scaffolds is the future of pharmaceutical design for the significant management and treatment of endometrial cancer.
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Affiliation(s)
- Yichao Wang
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun 130000, China
| | - Siyao Chen
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun 130000, China
| | - Chunling Wang
- Medical Affairs Department, The Second Hospital of Jilin University, Changchun 130000, China
| | - Fengjun Guo
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun 130000, China.
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21
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Qunaj L, May MS, Neugut AI, Herzberg BO. Prognostic and therapeutic impact of the KRAS G12C mutation in colorectal cancer. Front Oncol 2023; 13:1252516. [PMID: 37790760 PMCID: PMC10543081 DOI: 10.3389/fonc.2023.1252516] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
KRAS G12C mutations are critical in the pathogenesis of multiple cancer types, including non-small cell lung (NSCLC), pancreatic ductal adenocarcinoma (PDAC), and colorectal (CRC) cancers. As such, they have increasingly become a target of novel therapies in the management of these malignancies. However, the therapeutic success of KRAS G12C inhibitors to date has been far more limited in CRC and PDAC than NSCLC. In this review, we briefly summarize the biochemistry of KRAS targeting and treatment resistance, highlight differences in the epidemiology of various G12C-mutated cancers, and provide an overview of the published data on KRAS G12C inhibitors for various indications. We conclude with a summary of ongoing clinical trials in G12C-mutant CRC and a discussion of future directions in the management of this disease. KRAS G12C mutation, targeted therapies, colorectal cancer, non-small cell lung cancer, pancreatic cancer, drug development.
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Affiliation(s)
- Lindor Qunaj
- Division of Hematology and Oncology, Department of Medicine, Columbia University, New York, NY, United States
| | - Michael S. May
- Division of Hematology and Oncology, Department of Medicine, Columbia University, New York, NY, United States
| | - Alfred I. Neugut
- Division of Hematology and Oncology, Department of Medicine, Columbia University, New York, NY, United States
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, United States
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Benjamin O. Herzberg
- Division of Hematology and Oncology, Department of Medicine, Columbia University, New York, NY, United States
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, United States
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22
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Xie X, Yu T, Li X, Zhang N, Foster LJ, Peng C, Huang W, He G. Recent advances in targeting the "undruggable" proteins: from drug discovery to clinical trials. Signal Transduct Target Ther 2023; 8:335. [PMID: 37669923 PMCID: PMC10480221 DOI: 10.1038/s41392-023-01589-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/22/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Undruggable proteins are a class of proteins that are often characterized by large, complex structures or functions that are difficult to interfere with using conventional drug design strategies. Targeting such undruggable targets has been considered also a great opportunity for treatment of human diseases and has attracted substantial efforts in the field of medicine. Therefore, in this review, we focus on the recent development of drug discovery targeting "undruggable" proteins and their application in clinic. To make this review well organized, we discuss the design strategies targeting the undruggable proteins, including covalent regulation, allosteric inhibition, protein-protein/DNA interaction inhibition, targeted proteins regulation, nucleic acid-based approach, immunotherapy and others.
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Affiliation(s)
- Xin Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Tingting Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Xiang Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Nan Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Wei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Gu He
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China.
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23
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Ghufran M, Rehman AU, Ayaz M, Ul-Haq Z, Uddin R, Azam SS, Wadood A. New lead compounds identification against KRas mediated cancers through pharmacophore-based virtual screening and in vitro assays. J Biomol Struct Dyn 2023; 41:8053-8067. [PMID: 36184737 DOI: 10.1080/07391102.2022.2128878] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/20/2022] [Indexed: 10/07/2022]
Abstract
Cancer remains the leading cause of mortality and morbidity in the world, with 19.3 million new diagnoses and 10.1 million deaths in 2020. Cancer is caused due to mutations in proto-oncogenes and tumor-suppressor genes. Genetic analyses found that Ras (Rat sarcoma) is one of the most deregulated oncogenes in human cancers. The Ras oncogene family members including NRas (Neuroblastoma ras viral oncogene homolog), HRas (Harvey rat sarcoma) and KRas are involved in different types of human cancers. The mutant KRas is considered as the most frequent oncogene implicated in the development of lung, pancreatic and colon cancers. However, there is no efficient clinical drug even though it has been identified as an oncogene for 30 years. Therefore there is an emerging need to develop potent, new anticancer drugs. In this study, computer-aided drug designing approaches as well as experimental methods were employed to find new and potential anti-cancer drugs. The pharmacophore model was developed from an already known FDA approved anti-cancer drug Bortezomib using the software MOE. The validated pharmacophore model was then used to screen the in-house and commercially available databases. The pharmacophore-based virtual screening resulted in 26 and 86 hits from in-house and commercial databases respectively. Finally, 6/13 (in-house database) and 24/64 hits (commercial databases) were selected with different scaffolds having good interactions with the significant active residues of KRasG12D protein that were predicted as potent lead compounds. Finally, the results of pharmacophore-based virtual screening were further validated by molecular dynamics simulation analysis. The 6 hits of the in-house database were further evaluated experimentally. The experimental results showed that these compounds have good anti-cancer activity which validate the protocol of our in silico studies. KRasG12D protein is a very important anti-cancer target and potent inhibitors for this target are still not available, so small lead compound inhibitors were identified to inhibit the activity of this protein by blocking the GTP-binding pocket.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehreen Ghufran
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
- Department of Pathology, Medical Teaching Institution Bacha Khan Medical College (BKMC) Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Muhammad Ayaz
- Department of Pharmacy, University of Malakand, Chakdara, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, University of Karachi, Karachi, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, University of Karachi, Karachi, Pakistan
| | - Syed Sikander Azam
- Department of Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
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24
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Smith MJ. Defining bone fide effectors of RAS GTPases. Bioessays 2023; 45:e2300088. [PMID: 37401638 DOI: 10.1002/bies.202300088] [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: 05/24/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
RAS GTPases play essential roles in normal development and are direct drivers of human cancers. Three decades of study have failed to wholly characterize pathways stimulated by activated RAS, driven by engagement with 'effector' proteins that have RAS binding domains (RBDs). Bone fide effectors must bind directly to RAS GTPases in a nucleotide-dependent manner, and this interaction must impart a clear change in effector activity. Despite this, for most proteins currently deemed effectors there is little mechanistic understanding of how binding to the GTPase alters protein function. There has also been limited effort to comprehensively resolve the specificity of effector binding to the full array of RAS superfamily GTPase proteins. This review will summarize what is known about RAS-driven activation for an array of potential effector proteins, focusing on structural and mechanistic effects and highlighting how little is still known regarding this key paradigm of cellular signal transduction.
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Affiliation(s)
- Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
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25
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Wu X, Song W, Cheng C, Liu Z, Li X, Cui Y, Gao Y, Li D. Small molecular inhibitors for KRAS-mutant cancers. Front Immunol 2023; 14:1223433. [PMID: 37662925 PMCID: PMC10470052 DOI: 10.3389/fimmu.2023.1223433] [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: 05/16/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Three rat sarcoma (RAS) gene isoforms, KRAS, NRAS, and HRAS, constitute the most mutated family of small GTPases in cancer. While the development of targeted immunotherapies has led to a substantial improvement in the overall survival of patients with non-KRAS-mutant cancer, patients with RAS-mutant cancers have an overall poorer prognosis owing to the high aggressiveness of RAS-mutant tumors. KRAS mutations are strongly implicated in lung, pancreatic, and colorectal cancers. However, RAS mutations exhibit diverse patterns of isoforms, substitutions, and positions in different types of cancers. Despite being considered "undruggable", recent advances in the use of allele-specific covalent inhibitors against the most common mutant form of RAS in non-small-cell lung cancer have led to the development of effective pharmacological interventions against RAS-mutant cancer. Sotorasib (AMG510) has been approved by the FDA as a second-line treatment for patients with KRAS-G12C mutant NSCLC who have received at least one prior systemic therapy. Other KRAS inhibitors are on the way to block KRAS-mutant cancers. In this review, we summarize the progress and promise of small-molecule inhibitors in clinical trials, including direct inhibitors of KRAS, pan-RAS inhibitors, inhibitors of RAS effector signaling, and immune checkpoint inhibitors or combinations with RAS inhibitors, to improve the prognosis of tumors with RAS mutations.
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Affiliation(s)
- Xuan Wu
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Wenping Song
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Henan Cancer Hospital, Zhengzhou, China
- Henan Provincial Key Laboratory of Anticancer Drug Research, Henan Cancer Hospital, Zhengzhou, China
| | - Cheng Cheng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Ziyang Liu
- Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Xiang Li
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yu Cui
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yao Gao
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Ding Li
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Henan Cancer Hospital, Zhengzhou, China
- Henan Provincial Key Laboratory of Anticancer Drug Research, Henan Cancer Hospital, Zhengzhou, China
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26
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Yun SD, Scott E, Moghadamchargari Z, Laganowsky A. 2'-Deoxy Guanosine Nucleotides Alter the Biochemical Properties of Ras. Biochemistry 2023; 62:2450-2460. [PMID: 37487239 PMCID: PMC11131413 DOI: 10.1021/acs.biochem.3c00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Ras proteins in the mitogen-activated protein kinase (MAPK) signaling pathway represent one of the most frequently mutated oncogenes in cancer. Ras binds guanosine nucleotides and cycles between active (GTP) and inactive (GDP) conformations to regulate the MAPK signaling pathway. Guanosine and other nucleotides exist in cells as either 2'-hydroxy or 2'-deoxy forms, and imbalances in the deoxyribonucleotide triphosphate pool have been associated with different diseases, such as diabetes, obesity, and cancer. However, the biochemical properties of Ras bound to dGNP are not well understood. Herein, we use native mass spectrometry to monitor the intrinsic GTPase activity of H-Ras and N-Ras oncogenic mutants, revealing that the rate of 2'-deoxy guanosine triphosphate (dGTP) hydrolysis differs compared to the hydroxylated form, in some cases by seven-fold. Moreover, K-Ras expressed from HEK293 cells exhibited a higher than anticipated abundance of dGNP, despite the low abundance of dGNP in cells. Additionally, the GTPase and dGTPase activity of K-RasG12C was found to be accelerated by 10.2- and 3.8-fold in the presence of small molecule covalent inhibitors, which may open opportunities for the development of Pan-Ras inhibitors. The molecular assemblies formed between H-Ras and N-Ras, including mutant forms, with the catalytic domain of SOS (SOScat) were also investigated. The results show that the different mutants of H-Ras and N-Ras not only engage SOScat differently, but these assemblies are also dependent on the form of guanosine triphosphate bound to Ras. These findings bring to the forefront a new perspective on the nucleotide-dependent biochemical properties of Ras that may have implications for the activation of the MAPK signaling pathway and Ras-driven cancers.
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Affiliation(s)
- Sangho D. Yun
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | | | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843
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27
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Miyamoto-Sato E, Imanishi S, Huang L, Itakura S, Iwasaki Y, Ishizaka M. A First-Class Degrader Candidate Targeting Both KRAS G12D and G12V Mediated by CANDDY Technology Independent of Ubiquitination. Molecules 2023; 28:5600. [PMID: 37513471 PMCID: PMC10386196 DOI: 10.3390/molecules28145600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
"Undruggable" targets such as KRAS are particularly challenging in the development of drugs. We devised a novel chemical knockdown strategy, CANDDY (Chemical knockdown with Affinity aNd Degradation DYnamics) technology, which promotes protein degradation using small molecules (CANDDY molecules) that are conjugated to a degradation tag (CANDDY tag) modified from proteasome inhibitors. We demonstrated that CANDDY tags allowed for direct proteasomal target degradation independent of ubiquitination. We synthesized a KRAS-degrading CANDDY molecule, TUS-007, which induced degradation in KRAS mutants (G12D and G12V) and wild-type KRAS. We confirmed the tumor suppression effect of TUS-007 in subcutaneous xenograft models of human colon cells (KRAS G12V) with intraperitoneal administrations and in orthotopic xenograft models of human pancreatic cells (KRAS G12D) with oral administrations. Thus, CANDDY technology has the potential to therapeutically target previously undruggable proteins, providing a simpler and more practical drug targeting approach and avoiding the difficulties in matchmaking between the E3 enzyme and the target.
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Affiliation(s)
- Etsuko Miyamoto-Sato
- R&D Department, FuturedMe Inc., 2-3-11 Honcho, Nihonbashi, Chuo-ku, Tokyo 103-0023, Tokyo, Japan
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-0022, Chiba, Japan
- Graduate School of Biological Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-0022, Chiba, Japan
| | - Satoshi Imanishi
- Graduate School of Biological Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-0022, Chiba, Japan
| | - Lijuan Huang
- Graduate School of Biological Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-0022, Chiba, Japan
| | - Shoko Itakura
- Graduate School of Biological Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-0022, Chiba, Japan
| | - Yoichi Iwasaki
- R&D Department, FuturedMe Inc., 2-3-11 Honcho, Nihonbashi, Chuo-ku, Tokyo 103-0023, Tokyo, Japan
| | - Masamichi Ishizaka
- R&D Department, FuturedMe Inc., 2-3-11 Honcho, Nihonbashi, Chuo-ku, Tokyo 103-0023, Tokyo, Japan
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28
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Junk P, Kiel C. Structure-based prediction of Ras-effector binding affinities and design of "branchegetic" interface mutations. Structure 2023; 31:870-883.e5. [PMID: 37167973 DOI: 10.1016/j.str.2023.04.007] [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: 11/17/2022] [Revised: 02/28/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023]
Abstract
Ras is a central cellular hub protein controlling multiple cell fates. How Ras interacts with a variety of potential effector proteins is relatively unexplored, with only some key effectors characterized in great detail. Here, we have used homology modeling based on X-ray and AlphaFold2 templates to build structural models for 54 Ras-effector complexes. These models were used to estimate binding affinities using a supervised learning regressor. Furthermore, we systematically introduced Ras "branch-pruning" (or branchegetic) mutations to identify 200 interface mutations that affect the binding energy with at least one of the model structures. The impacts of these branchegetic mutants were integrated into a mathematical model to assess the potential for rewiring interactions at the Ras hub on a systems level. These findings have provided a quantitative understanding of Ras-effector interfaces and their impact on systems properties of a key cellular hub.
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Affiliation(s)
- Philipp Junk
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland.
| | - Christina Kiel
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland; Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
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29
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Xu LS, Zheng SX, Mei LH, Yang KX, Wang YF, Zhou Q, Kong XT, Zheng MY, Jiang HL, Xie CY. 143D, a novel selective KRAS G12C inhibitor exhibits potent antitumor activity in preclinical models. Acta Pharmacol Sin 2023; 44:1475-1486. [PMID: 36725884 PMCID: PMC10310808 DOI: 10.1038/s41401-023-01053-2] [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: 10/15/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
The KRASG12C mutant has emerged as an important therapeutic target in recent years. Covalent inhibitors have shown promising antitumor activity against KRASG12C-mutant cancers in the clinic. In this study, a structure-based and focused chemical library analysis was performed, which led to the identification of 143D as a novel, highly potent and selective KRASG12C inhibitor. The antitumor efficacy of 143D in vitro and in vivo was comparable with that of AMG510 and of MRTX849, two well-characterized KRASG12C inhibitors. At low nanomolar concentrations, 143D showed biochemical and cellular potency for inhibiting the effects of the KRASG12C mutation. 143D selectively inhibited cell proliferation and induced G1-phase cell cycle arrest and apoptosis by downregulating KRASG12C-dependent signal transduction. Compared with MRTX849, 143D exhibited a longer half-life and higher maximum concentration (Cmax) and area under the curve (AUC) values in mouse models, as determined by tissue distribution assays. Additionally, 143D crossed the blood‒brain barrier. Treatment with 143D led to the sustained inhibition of KRAS signaling and tumor regression in KRASG12C-mutant tumors. Moreover, 143D combined with EGFR/MEK/ERK signaling inhibitors showed enhanced antitumor activity both in vitro and in vivo. Taken together, our findings indicate that 143D may be a promising drug candidate with favorable pharmaceutical properties for the treatment of cancers harboring the KRASG12C mutation.
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Affiliation(s)
- Lan-Song Xu
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
- Drug Discovery and Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Su-Xin Zheng
- Suzhou AlphaMa Biotechnology Co., Ltd., Suzhou, 215123, China
| | - Liang-He Mei
- Suzhou Institute of Drug Innovation, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Ke-Xin Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ya-Fang Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Qiang Zhou
- Suzhou Institute of Drug Innovation, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Xiang-Tai Kong
- Drug Discovery and Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Ming-Yue Zheng
- Drug Discovery and Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
| | - Hua-Liang Jiang
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
- Drug Discovery and Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Lingang Laboratory, Shanghai, 200031, China
| | - Cheng-Ying Xie
- Drug Discovery and Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Lingang Laboratory, Shanghai, 200031, China.
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30
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Ren B, Geng Y, Chen S, Gao Z, Zheng K, Yang Y, Luo Q, Feng J, Luo Z, Ju Y, Huang Z. Alisertib exerts KRAS allele‑specific anticancer effects on colorectal cancer cell lines. Exp Ther Med 2023; 25:243. [PMID: 37153900 PMCID: PMC10160916 DOI: 10.3892/etm.2023.11942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/27/2023] [Indexed: 05/10/2023] Open
Abstract
The aim of the present study was to examine the effects of alisertib (ALS) on RAS signaling pathways against a panel of colorectal cancer (CRC) cell lines and engineered Flp-In stable cell lines expressing different Kirsten rat sarcoma virus (KRAS) mutants. The viability of Caco-2KRAS wild-type, Colo-678KRAS G12D, SK-CO-1KRAS G12V, HCT116KRAS G13D, CCCL-18KRAS A146T and HT29BRAF V600E cells was examined by Cell Titer-Glo assay, and that of stable cell lines was monitored by IncuCyte. The expression levels of phosphorylated (p-)Akt and p-Erk as RAS signal outputs were measured by western blotting. The results suggested that ALS exhibited different inhibitory effects on cell viability and different regulatory effects on guanosine triphosphate (GTP)-bound RAS in CRC cell lines. ALS also exhibited various regulatory effects on the PI3K/Akt and mitogen-activated protein kinase (MAPK) pathways, the two dominant RAS signaling pathways, and induced apoptosis and autophagy in a RAS allele-specific manner. Combined treatment with ALS and selumetinib enhanced the regulatory effects of ALS on apoptosis and autophagy in CRC cell lines in a RAS allele-specific manner. Notably, combined treatment exhibited a synergistic inhibitory effect on cell proliferation in Flp-In stable cell lines. The results of the present study suggested that ALS differentially regulates RAS signaling pathways. The combined approach of ALS and a MEK inhibitor may represent a new therapeutic strategy for precision therapy for CRC in a KRAS allele-specific manner; however, this effect requires further study in vivo.
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Affiliation(s)
- Baojun Ren
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), The Second School of Clinical Medicine, Southern Medical University, Foshan, Guangdong 528308, P.R. China
| | - Yan Geng
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), The Second School of Clinical Medicine, Southern Medical University, Foshan, Guangdong 528308, P.R. China
| | - Shuxiang Chen
- Department of Anesthesiology and Operating Theatre, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), The Second School of Clinical Medicine, Southern Medical University, Foshan, Guangdong 528308, P.R. China
| | - Zhuowei Gao
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), The Second School of Clinical Medicine, Southern Medical University, Foshan, Guangdong 528308, P.R. China
| | - Kehong Zheng
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Yong Yang
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing 100144, P.R. China
| | - Qimei Luo
- Department of Nephrology, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), The Second School of Clinical Medicine, Southern Medical University, Foshan, Guangdong 528308, P.R. China
| | - Jing Feng
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), The Second School of Clinical Medicine, Southern Medical University, Foshan, Guangdong 528308, P.R. China
| | - Zhentao Luo
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), The Second School of Clinical Medicine, Southern Medical University, Foshan, Guangdong 528308, P.R. China
| | - Yongle Ju
- Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), The Second School of Clinical Medicine, Southern Medical University, Foshan, Guangdong 528308, P.R. China
- Correspondence to: Dr Yongle Ju, Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), The Second School of Clinical Medicine, Southern Medical University, 1 Jiazi Road, Lunjiao Shunde, Foshan, Guangdong 528308, P.R. China
| | - Zonghai Huang
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
- Correspondence to: Dr Yongle Ju, Department of Gastrointestinal Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), The Second School of Clinical Medicine, Southern Medical University, 1 Jiazi Road, Lunjiao Shunde, Foshan, Guangdong 528308, P.R. China
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31
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Ai Q, Li F, Zou S, Zhang Z, Jin Y, Jiang L, Chen H, Deng X, Peng C, Mou N, Wen C, Shen B, Zhan Q. Targeting KRAS G12V mutations with HLA class II-restricted TCR for the immunotherapy in solid tumors. Front Immunol 2023; 14:1161538. [PMID: 37287989 PMCID: PMC10243368 DOI: 10.3389/fimmu.2023.1161538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/08/2023] [Indexed: 06/09/2023] Open
Abstract
KRAS mutation is a significant driving factor of tumor, and KRASG12V mutation has the highest incidence in solid tumors such as pancreatic cancer and colorectal cancer. Thus, KRASG12V neoantigen-specific TCR-engineered T cells could be a promising cancer treatment approach for pancreatic cancer. Previous studies had reported that KRASG12V-reactive TCRs originated from patients' TILs could recognized KRASG12V neoantigen presented by specific HLA subtypes and remove tumor persistently in vitro and in vivo. However, TCR drugs are different from antibody drugs in that they are HLA-restricted. The different ethnic distribution of HLA greatly limits the applicability of TCR drugs in Chinese population. In this study, we have identified a KRASG12V-specific TCR which recognized classII MHC from a colorectal cancer patient. Interestingly, we observed that KRASG12V-specific TCR-engineered CD4+ T cells, not CD8+ T cells, demonstrated significant efficacy in vitro and in xenograft mouse model, exhibiting stable expression and targeting specificity of TCR when co-cultured with APCs presenting KRASG12V peptides. TCR-engineered CD4+ T cells were co-cultured with APCs loaded with neoantigen, and then HLA subtypes were identified by the secretion of IFN-γ. Collectively, our data suggest that TCR-engineered CD4+ T cells can be used to target KRASG12V mutation presented by HLA-DPB1*03:01 and DPB1*14:01, which provide a high population coverage and are more suitable for the clinical transformation for Chinese, and mediate tumor killing effect like CD8+ T cells. This TCR hold promise for precision therapy in immunotherapy of solid tumors as an attractive candidate.
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Affiliation(s)
- Qi Ai
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fanlu Li
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Siyi Zou
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zehui Zhang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yangbing Jin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chenghong Peng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nan Mou
- Department of Cell Therapy, Shanghai Genbase Biotechnology Co., Ltd, Shanghai, China
| | - Chenlei Wen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Zhan
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
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Entrialgo-Cadierno R, Cueto-Ureña C, Welch C, Feliu I, Macaya I, Vera L, Morales X, Michelina SV, Scaparone P, Lopez I, Darbo E, Erice O, Vallejo A, Moreno H, Goñi-Salaverri A, Lara-Astiaso D, Halberg N, Cortes-Dominguez I, Guruceaga E, Ambrogio C, Lecanda F, Vicent S. The phospholipid transporter PITPNC1 links KRAS to MYC to prevent autophagy in lung and pancreatic cancer. Mol Cancer 2023; 22:86. [PMID: 37210549 DOI: 10.1186/s12943-023-01788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/11/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND The discovery of functionally relevant KRAS effectors in lung and pancreatic ductal adenocarcinoma (LUAD and PDAC) may yield novel molecular targets or mechanisms amenable to inhibition strategies. Phospholipids availability has been appreciated as a mechanism to modulate KRAS oncogenic potential. Thus, phospholipid transporters may play a functional role in KRAS-driven oncogenesis. Here, we identified and systematically studied the phospholipid transporter PITPNC1 and its controlled network in LUAD and PDAC. METHODS Genetic modulation of KRAS expression as well as pharmacological inhibition of canonical effectors was completed. PITPNC1 genetic depletion was performed in in vitro and in vivo LUAD and PDAC models. PITPNC1-deficient cells were RNA sequenced, and Gene Ontology and enrichment analyses were applied to the output data. Protein-based biochemical and subcellular localization assays were run to investigate PITPNC1-regulated pathways. A drug repurposing approach was used to predict surrogate PITPNC1 inhibitors that were tested in combination with KRASG12C inhibitors in 2D, 3D, and in vivo models. RESULTS PITPNC1 was increased in human LUAD and PDAC, and associated with poor patients' survival. PITPNC1 was regulated by KRAS through MEK1/2 and JNK1/2. Functional experiments showed PITPNC1 requirement for cell proliferation, cell cycle progression and tumour growth. Furthermore, PITPNC1 overexpression enhanced lung colonization and liver metastasis. PITPNC1 regulated a transcriptional signature which highly overlapped with that of KRAS, and controlled mTOR localization via enhanced MYC protein stability to prevent autophagy. JAK2 inhibitors were predicted as putative PITPNC1 inhibitors with antiproliferative effect and their combination with KRASG12C inhibitors elicited a substantial anti-tumour effect in LUAD and PDAC. CONCLUSIONS Our data highlight the functional and clinical relevance of PITPNC1 in LUAD and PDAC. Moreover, PITPNC1 constitutes a new mechanism linking KRAS to MYC, and controls a druggable transcriptional network for combinatorial treatments.
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Affiliation(s)
- Rodrigo Entrialgo-Cadierno
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Cristina Cueto-Ureña
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Connor Welch
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Iker Feliu
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Irati Macaya
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Laura Vera
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Xabier Morales
- Imaging Unit and Cancer Imaging Laboratory, University of Navarra, CIMA, Pamplona, Spain
| | - Sandra Vietti Michelina
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Turin, Italy
| | - Pietro Scaparone
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Turin, Italy
| | - Ines Lopez
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Elodie Darbo
- University of Bordeaux, INSERM, BRIC, U 1312, F-33000, Bordeaux, France
| | - Oihane Erice
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Adrian Vallejo
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Haritz Moreno
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | | | - David Lara-Astiaso
- Molecular Therapies Program, University of Navarra, CIMA, Pamplona, Spain
- Wellcome - MRC Cambridge Stem Cell Institute (CSCI), Cambridge, UK
| | - Nils Halberg
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ivan Cortes-Dominguez
- Imaging Unit and Cancer Imaging Laboratory, University of Navarra, CIMA, Pamplona, Spain
- Bioinformatics Platform, University of Navarra, CIMA, Pamplona, Spain
| | - Elizabeth Guruceaga
- Bioinformatics Platform, University of Navarra, CIMA, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Chiara Ambrogio
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Turin, Italy
| | - Fernando Lecanda
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Department of Pathology, Anatomy and Physiology, University of Navarra, Pamplona, Spain
| | - Silve Vicent
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
- Department of Pathology, Anatomy and Physiology, University of Navarra, Pamplona, Spain.
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Omar FA, Brown TC, Gillanders WE, Fleming TP, Smith MA, Bremner RM, Sankpal NV. Cytosolic EpCAM cooperates with H-Ras to regulate epithelial to mesenchymal transition through ZEB1. PLoS One 2023; 18:e0285707. [PMID: 37192201 PMCID: PMC10187930 DOI: 10.1371/journal.pone.0285707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/30/2023] [Indexed: 05/18/2023] Open
Abstract
Next generation sequencing of human cancer mutations has identified novel therapeutic targets. Activating Ras oncogene mutations play a central role in oncogenesis, and Ras-driven tumorigenesis upregulates an array of genes and signaling cascades that can transform normal cells into tumor cells. In this study, we investigated the role of altered localization of epithelial cell adhesion molecule (EpCAM) in Ras-expressing cells. Analysis of microarray data demonstrated that Ras expression induced EpCAM expression in normal breast epithelial cells. Fluorescent and confocal microscopy showed that H-Ras mediated transformation also promoted epithelial-to-mesenchymal transition (EMT) together with EpCAM. To consistently localize EpCAM in the cytosol, we generated a cancer-associated EpCAM mutant (EpCAM-L240A) that is retained in the cytosol compartment. Normal MCF-10A cells were transduced with H-Ras together with EpCAM wild-type (WT) or EpCAM-L240A. WT-EpCAM marginally effected invasion, proliferation, and soft agar growth. EpCAM-L240A, however, markedly altered cells and transformed to mesenchymal phenotype. Ras-EpCAM-L240A expression also promoted expression of EMT factors FRA1, ZEB1 with inflammatory cytokines IL-6, IL-8, and IL1. This altered morphology was reversed using MEK-specific inhibitors and to some extent JNK inhibition. Furthermore, these transformed cells were sensitized to apoptosis using paclitaxel and quercetin, but not other therapies. For the first time, we have demonstrated that EpCAM mutations can cooperate with H-Ras and promote EMT. Collectively, our results highlight future therapeutic opportunities in EpCAM and Ras mutated cancers.
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Affiliation(s)
- Fatma A. Omar
- Norton Thoracic Institute, St. Joseph’s Hospital and Medical Center, Phoenix, Arizona, United States of America
| | - Taylor C. Brown
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - William E. Gillanders
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Timothy P. Fleming
- Norton Thoracic Institute, St. Joseph’s Hospital and Medical Center, Phoenix, Arizona, United States of America
| | - Michael A. Smith
- Norton Thoracic Institute, St. Joseph’s Hospital and Medical Center, Phoenix, Arizona, United States of America
| | - Ross M. Bremner
- Norton Thoracic Institute, St. Joseph’s Hospital and Medical Center, Phoenix, Arizona, United States of America
| | - Narendra V. Sankpal
- Norton Thoracic Institute, St. Joseph’s Hospital and Medical Center, Phoenix, Arizona, United States of America
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34
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Luo G, Wang B, Hou Q, Wu X. Development of Son of Sevenless Homologue 1 (SOS1) Modulators To Treat Cancers by Regulating RAS Signaling. J Med Chem 2023; 66:4324-4341. [PMID: 36987571 DOI: 10.1021/acs.jmedchem.2c01729] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Son of sevenless homologue 1 (SOS1) protein is universally expressed in cells and plays an important role in the RAS signaling pathway. Specifically, this protein interacts with RAS in response to upstream stimuli to promote guanine nucleotide exchange in RAS and activates the downstream signaling pathways. Thus, targeting SOS1 is a new approach for treating RAS-driven cancers. In this Perspective, we briefly summarize the structural and functional aspects of SOS1 and focus on recent advances in the discovery of activators, inhibitors, and PROTACs that target SOS1. This review aims to provide a timely and updated overview on the strategies for targeting SOS1 in cancer therapy.
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Affiliation(s)
- Guangmei Luo
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Bingrui Wang
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Qiangqiang Hou
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
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35
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Lam KK, Low YS, Lo M, Wong M, Leong Tang C, Tan E, Chok AY, Seow-En I, Wong SH, Cheah PY. KRAS-specific antibody binds to KRAS protein inside colorectal adenocarcinoma cells and inhibits its localization to the plasma membrane. Front Oncol 2023; 13:1036871. [PMID: 37051535 PMCID: PMC10084885 DOI: 10.3389/fonc.2023.1036871] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Colorectal cancer (CRC) is the third highest incidence cancer and a leading cause of cancer mortality worldwide. To date, chemotherapeutic treatment of advanced CRC that has metastasized has a dismayed success rate of less than 30%. Further, most (80%) sporadic CRCs are microsatellite-stable and are refractory to immune checkpoint blockade therapy. KRAS is a gatekeeper gene in colorectal tumorigenesis. Nevertheless, KRAS is ‘undruggable’ due to its structure. Thus, focus has been diverted to develop small molecule inhibitors for its downstream effector such as ERK/MAPK. Despite intense research efforts for the past few decades, no small molecule inhibitor has been in clinical use for CRC. Antibody targeting KRAS itself is an attractive alternative. We developed a transient ex vivo patient-derived matched mucosa-tumor primary culture to assess whether anti-KRAS antibody can be internalized to bind and inactivate KRAS. We showed that anti-KRAS antibody can enter live mucosa-tumor cells and specifically aggregate KRAS in the cytoplasm, thus hindering its translocation to the inner plasma membrane. The mis-localization of KRAS reduces KRAS dwelling time at the site where it tethers to activate downstream effectors. We previously showed that expression of SOX9 was KRAS-mutation-dependent and possibly a better effector than ERK in CRC. Herein, we showed that anti-KRAS antibody treated tumor cells have less intense SOX9 cytoplasmic and nuclear staining compared to untreated cells. Our results demonstrated that internalized anti-KRAS antibody inhibits KRAS function in tumor. With an efficient intracellular antibody delivery system, this can be further developed as combinatorial therapeutics for CRC and other KRAS-driven cancers.
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Affiliation(s)
- Kuen Kuen Lam
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Yee Syuen Low
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Michelle Lo
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Michelle Wong
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Choong Leong Tang
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Emile Tan
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Aik Yong Chok
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Isaac Seow-En
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | | | - Peh Yean Cheah
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- *Correspondence: Peh Yean Cheah,
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36
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Spella M, Ntaliarda G, Skiadas G, Lamort AS, Vreka M, Marazioti A, Lilis I, Bouloukou E, Giotopoulou GA, Pepe MAA, Weiss SAI, Petrera A, Hauck SM, Koch I, Lindner M, Hatz RA, Behr J, Arendt KAM, Giopanou I, Brunn D, Savai R, Jenne DE, de Château M, Yull FE, Blackwell TS, Stathopoulos GT. Non-Oncogene Addiction of KRAS-Mutant Cancers to IL-1β via Versican and Mononuclear IKKβ. Cancers (Basel) 2023; 15:1866. [PMID: 36980752 PMCID: PMC10047096 DOI: 10.3390/cancers15061866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Kirsten rat sarcoma virus (KRAS)-mutant cancers are frequent, metastatic, lethal, and largely undruggable. While interleukin (IL)-1β and nuclear factor (NF)-κB inhibition hold promise against cancer, untargeted treatments are not effective. Here, we show that human KRAS-mutant cancers are addicted to IL-1β via inflammatory versican signaling to macrophage inhibitor of NF-κB kinase (IKK) β. Human pan-cancer and experimental NF-κB reporter, transcriptome, and proteome screens reveal that KRAS-mutant tumors trigger macrophage IKKβ activation and IL-1β release via secretory versican. Tumor-specific versican silencing and macrophage-restricted IKKβ deletion prevents myeloid NF-κB activation and metastasis. Versican and IKKβ are mutually addicted and/or overexpressed in human cancers and possess diagnostic and prognostic power. Non-oncogene KRAS/IL-1β addiction is abolished by IL-1β and TLR1/2 inhibition, indicating cardinal and actionable roles for versican and IKKβ in metastasis.
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Affiliation(s)
- Magda Spella
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Giannoula Ntaliarda
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Georgios Skiadas
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Anne-Sophie Lamort
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Malamati Vreka
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Antonia Marazioti
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Ioannis Lilis
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Eleni Bouloukou
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Georgia A. Giotopoulou
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Mario A. A. Pepe
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Stefanie A. I. Weiss
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Agnese Petrera
- Research Unit Protein Science-Core Facility Proteomics, Helmholtz Center Munich–German Research Center for Environmental Health, 80939 Munich, Germany
| | - Stefanie M. Hauck
- Research Unit Protein Science-Core Facility Proteomics, Helmholtz Center Munich–German Research Center for Environmental Health, 80939 Munich, Germany
| | - Ina Koch
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich and Asklepios Medical Center, 82131 Gauting, Germany
| | - Michael Lindner
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich and Asklepios Medical Center, 82131 Gauting, Germany
| | - Rudolph A. Hatz
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich and Asklepios Medical Center, 82131 Gauting, Germany
| | - Juergen Behr
- Department of Internal Medicine V, Ludwig-Maximilian-University of Munich, 81377 Munich, Germany
| | - Kristina A. M. Arendt
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Ioanna Giopanou
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - David Brunn
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- Frankfurt Cancer Institute (FCI), Goethe University, 60596 Frankfurt am Main, Germany
- Department of Internal Medicine and Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
| | - Dieter E. Jenne
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
- Max-Planck-Institute of Neurobiology, 82152 Planegg, Germany
| | | | - Fiona E. Yull
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Timothy S. Blackwell
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Georgios T. Stathopoulos
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
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Ahmadi Y, Fard JK, Ghafoor D, Eid AH, Sahebkar A. Paradoxical effects of statins on endothelial and cancer cells: the impact of concentrations. Cancer Cell Int 2023; 23:43. [PMID: 36899388 PMCID: PMC9999585 DOI: 10.1186/s12935-023-02890-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/04/2023] [Indexed: 03/12/2023] Open
Abstract
In addition to their lipid-lowering functions, statins elicit additional pleiotropic effects on apoptosis, angiogenesis, inflammation, senescence, and oxidative stress. Many of these effects have been reported in cancerous and noncancerous cells like endothelial cells (ECs), endothelial progenitor cells (EPCs) and human umbilical vein cells (HUVCs). Not surprisingly, statins' effects appear to vary largely depending on the cell context, especially as pertains to modulation of cell cycle, senescence, and apoptotic processes. Perhaps the most critical reason for this discordance is the bias in selecting the applied doses in various cells. While lower (nanomolar) concentrations of statins impose anti-senescence, and antiapoptotic effects, higher concentrations (micromolar) appear to precipitate opposite effects. Indeed, most studies performed in cancer cells utilized high concentrations, where statin-induced cytotoxic and cytostatic effects were noted. Some studies report that even at low concentrations, statins induce senescence or cytostatic impacts but not cytotoxic effects. However, the literature appears to be relatively consistent that in cancer cells, statins, in both low or higher concentrations, induce apoptosis or cell cycle arrest, anti-proliferative effects, and cause senescence. However, statins' effects on ECs depend on the concentrations; at micromolar concentrations statins cause cell senescence and apoptosis, while at nonomolar concentrations statins act reversely.
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Affiliation(s)
- Yasin Ahmadi
- College of Science, Department of Medical Laboratory Sciences, Komar University of Science and Technology, 46001, Sulaymania, Iraq.
| | - Javad Khalili Fard
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Dlzar Ghafoor
- College of Science, Department of Medical Laboratory Sciences, Komar University of Science and Technology, 46001, Sulaymania, Iraq
| | - Ali H Eid
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran. .,Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran. .,Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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38
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Tang X, Xue D, Zhang T, Nilsson-Payant BE, Carrau L, Duan X, Gordillo M, Tan AY, Qiu Y, Xiang J, Schwartz RE, tenOever BR, Evans T, Chen S. A multi-organoid platform identifies CIART as a key factor for SARS-CoV-2 infection. Nat Cell Biol 2023; 25:381-389. [PMID: 36918693 PMCID: PMC10014579 DOI: 10.1038/s41556-023-01095-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 01/25/2023] [Indexed: 03/16/2023]
Abstract
COVID-19 is a systemic disease involving multiple organs. We previously established a platform to derive organoids and cells from human pluripotent stem cells to model SARS-CoV-2 infection and perform drug screens1,2. This provided insight into cellular tropism and the host response, yet the molecular mechanisms regulating SARS-CoV-2 infection remain poorly defined. Here we systematically examined changes in transcript profiles caused by SARS-CoV-2 infection at different multiplicities of infection for lung airway organoids, lung alveolar organoids and cardiomyocytes, and identified several genes that are generally implicated in controlling SARS-CoV-2 infection, including CIART, the circadian-associated repressor of transcription. Lung airway organoids, lung alveolar organoids and cardiomyocytes derived from isogenic CIART-/- human pluripotent stem cells were significantly resistant to SARS-CoV-2 infection, independently of viral entry. Single-cell RNA-sequencing analysis further validated the decreased levels of SARS-CoV-2 infection in ciliated-like cells of lung airway organoids. CUT&RUN, ATAC-seq and RNA-sequencing analyses showed that CIART controls SARS-CoV-2 infection at least in part through the regulation of NR4A1, a gene also identified from the multi-organoid analysis. Finally, transcriptional profiling and pharmacological inhibition led to the discovery that the Retinoid X Receptor pathway regulates SARS-CoV-2 infection downstream of CIART and NR4A1. The multi-organoid platform identified the role of circadian-clock regulation in SARS-CoV-2 infection, which provides potential therapeutic targets for protection against COVID-19 across organ systems.
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Affiliation(s)
- Xuming Tang
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Dongxiang Xue
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin E Nilsson-Payant
- Department of Microbiology, New York University, New York, NY, USA
- TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Lucia Carrau
- Department of Microbiology, New York University, New York, NY, USA
| | - Xiaohua Duan
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Miriam Gordillo
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Adrian Y Tan
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Yunping Qiu
- Stable Isotope and Metabolomics Core Facility, The Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | | | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA.
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA.
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39
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Inhibition mechanism of MRTX1133 on KRAS G12D: a molecular dynamics simulation and Markov state model study. J Comput Aided Mol Des 2023; 37:157-166. [PMID: 36849761 DOI: 10.1007/s10822-023-00498-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/11/2023] [Indexed: 03/01/2023]
Abstract
The mutant KRAS was considered as an "undruggable" target for decades, especially KRASG12D. It is a great challenge to develop the inhibitors for KRASG12D which lacks the thiol group for covalently binding ligands. The discovery of MRTX1133 solved the dilemma. Interestingly, MRTX1133 can bind to both the inactive and active states of KRASG12D. The binding mechanism of MRTX1133 with KRASG12D, especially how MRTX1133 could bind the active state KRASG12D without triggering the active function of KRASG12D, has not been fully understood. Here, we used a combination of all-atom molecular dynamics simulations and Markov state model (MSM) to understand the inhibition mechanism of MRTX1133 and its analogs. The stationary probabilities derived from MSM show that MRTX1133 and its analogs can stabilize the inactive or active states of KRASG12D into different conformations. More remarkably, by scrutinizing the conformational differences, MRTX1133 and its analogs were hydrogen bonded to Gly60 to stabilize the switch II region and left switch I region in a dynamically inactive conformation, thus achieving an inhibitory effect. Our simulation and analysis provide detailed inhibition mechanism of KRASG12D induced by MRTX1133 and its analogs. This study will provide guidance for future design of novel small molecule inhibitors of KRASG12D.
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40
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Jung YH, Choi Y, Seo HD, Seo MH, Kim HS. A conformation-selective protein binder for a KRAS mutant inhibits the interaction between RAS and RAF. Biochem Biophys Res Commun 2023; 645:110-117. [PMID: 36682330 DOI: 10.1016/j.bbrc.2023.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Small GTPases are key signaling nodes that regulate the cellular processes and subcellular events, and their abnormal activities and dysregulations are closely linked with diverse cancers. Here, we report the development of conformation-selective protein binders for a KRAS mutant. The conformation-specific protein binders were selected from a repebody scaffold composed of LRR (Leucine-rich repeat) modules through phage display and modular engineering against constitute active conformation of KRAS. Epitope of the selected binders was mapped to be located close to switch I of KRAS. The conformation-selective protein binders were shown to effectively block the interaction between active KRAS and RAS-binding domain of BRAF, suppressing the KRAS-mediated downstream signaling.
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Affiliation(s)
- Youn Hee Jung
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea
| | - Yoonjoo Choi
- Combinatorial Tumor Immunotherapy MRC, Chonnam National University Medical School, Hwasun-gun, Jeollanam-do, 58128, South Korea
| | - Hyo-Deok Seo
- Aging and Metabolism Research Group, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, 55365, South Korea
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea.
| | - Hak-Sung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
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41
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Kung H, Yu J. Targeted therapy for pancreatic ductal adenocarcinoma: Mechanisms and clinical study. MedComm (Beijing) 2023; 4:e216. [PMID: 36814688 PMCID: PMC9939368 DOI: 10.1002/mco2.216] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 02/21/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive and lethal malignancy with a high rate of recurrence and a dismal 5-year survival rate. Contributing to the poor prognosis of PDAC is the lack of early detection, a complex network of signaling pathways and molecular mechanisms, a dense and desmoplastic stroma, and an immunosuppressive tumor microenvironment. A recent shift toward a neoadjuvant approach to treating PDAC has been sparked by the numerous benefits neoadjuvant therapy (NAT) has to offer compared with upfront surgery. However, certain aspects of NAT against PDAC, including the optimal regimen, the use of radiotherapy, and the selection of patients that would benefit from NAT, have yet to be fully elucidated. This review describes the major signaling pathways and molecular mechanisms involved in PDAC initiation and progression in addition to the immunosuppressive tumor microenvironment of PDAC. We then review current guidelines, ongoing research, and future research directions on the use of NAT based on randomized clinical trials and other studies. Finally, the current use of and research regarding targeted therapy for PDAC are examined. This review bridges the molecular understanding of PDAC with its clinical significance, development of novel therapies, and shifting directions in treatment paradigm.
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Affiliation(s)
- Heng‐Chung Kung
- Krieger School of Arts and SciencesJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Jun Yu
- Departments of Medicine and OncologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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42
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Lam KK, Wong SH, Cheah PY. Targeting the 'Undruggable' Driver Protein, KRAS, in Epithelial Cancers: Current Perspective. Cells 2023; 12:cells12040631. [PMID: 36831298 PMCID: PMC9954350 DOI: 10.3390/cells12040631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
This review summarizes recent development in synthetic drugs and biologics targeting intracellular driver genes in epithelial cancers, focusing on KRAS, and provides a current perspective and potential leads for the field. Compared to biologics, small molecule inhibitors (SMIs) readily penetrate cells, thus being able to target intracellular proteins. However, SMIs frequently suffer from pleiotropic effects, off-target cytotoxicity and invariably elicit resistance. In contrast, biologics are much larger molecules limited by cellular entry, but if this is surmounted, they may have more specific effects and less therapy-induced resistance. Exciting breakthroughs in the past two years include engineering of non-covalent KRAS G12D-specific inhibitor, probody bispecific antibodies, drug-peptide conjugate as MHC-restricted neoantigen to prompt immune response by T-cells, and success in the adoptive cell therapy front in both breast and pancreatic cancers.
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Affiliation(s)
- Kuen Kuen Lam
- Department of Colorectal Surgery, Singapore General Hospital, Singapore 169856, Singapore
| | | | - Peh Yean Cheah
- Department of Colorectal Surgery, Singapore General Hospital, Singapore 169856, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
- Correspondence:
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Ismail M, Martin SR, George R, Houghton F, Kelly G, Chaleil RAG, Anastasiou P, Wang X, O'Reilly N, Federico S, Joshi D, Nagaraj H, Cooley R, Hui NS, Molina-Arcas M, Hancock DC, Tavassoli A, Downward J. Characterisation of a cyclic peptide that binds to the RAS binding domain of phosphoinositide 3-kinase p110α. Sci Rep 2023; 13:1889. [PMID: 36732563 PMCID: PMC9894841 DOI: 10.1038/s41598-023-28756-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/24/2023] [Indexed: 02/04/2023] Open
Abstract
P110α is a member of the phosphoinositide 3-kinase (PI3K) enzyme family that functions downstream of RAS. RAS proteins contribute to the activation of p110α by interacting directly with its RAS binding domain (RBD), resulting in the promotion of many cellular functions such as cell growth, proliferation and survival. Previous work from our lab has highlighted the importance of the p110α/RAS interaction in tumour initiation and growth. Here we report the discovery and characterisation of a cyclic peptide inhibitor (cyclo-CRVLIR) that interacts with the p110α-RBD and blocks its interaction with KRAS. cyclo-CRVLIR was discovered by screening a "split-intein cyclisation of peptides and proteins" (SICLOPPS) cyclic peptide library. The primary cyclic peptide hit from the screen initially showed a weak affinity for the p110α-RBD (Kd about 360 µM). However, two rounds of amino acid substitution led to cyclo-CRVLIR, with an improved affinity for p110α-RBD in the low µM (Kd 3 µM). We show that cyclo-CRVLIR binds selectively to the p110α-RBD but not to KRAS or the structurally-related RAF-RBD. Further, using biophysical, biochemical and cellular assays, we show that cyclo-CRVLIR effectively blocks the p110α/KRAS interaction in a dose dependent manner and reduces phospho-AKT levels in several oncogenic KRAS cell lines.
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Affiliation(s)
- Mohamed Ismail
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stephen R Martin
- Structural Biology, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Roger George
- Structural Biology, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Francesca Houghton
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- Structural Biology, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Raphaël A G Chaleil
- Biomolecular Modelling Lab, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Panayiotis Anastasiou
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Xinyue Wang
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stefania Federico
- Peptide Chemistry, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Dhira Joshi
- Peptide Chemistry, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Hemavathi Nagaraj
- Peptide Chemistry, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Rachel Cooley
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ning Sze Hui
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Miriam Molina-Arcas
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David C Hancock
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ali Tavassoli
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Julian Downward
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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44
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Draetta EL, Lazarević D, Provero P, Cittaro D. The frequency of somatic mutations in cancer predicts the phenotypic relevance of germline mutations. Front Genet 2023; 13:1045301. [PMID: 36699457 PMCID: PMC9868957 DOI: 10.3389/fgene.2022.1045301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
Genomic sequence mutations can be pathogenic in both germline and somatic cells. Several authors have observed that often the same genes are involved in cancer when mutated in somatic cells and in genetic diseases when mutated in the germline. Recent advances in high-throughput sequencing techniques have provided us with large databases of both types of mutations, allowing us to investigate this issue in a systematic way. Hence, we applied a machine learning based framework to this problem, comparing multiple models. The models achieved significant predictive power as shown by both cross-validation and their application to recently discovered gene/phenotype associations not used for training. We found that genes characterized by high frequency of somatic mutations in the most common cancers and ancient evolutionary age are most likely to be involved in abnormal phenotypes and diseases. These results suggest that the combination of tolerance for mutations at the cell viability level (measured by the frequency of somatic mutations in cancer) and functional relevance (demonstrated by evolutionary conservation) are the main predictors of disease genes. Our results thus confirm the deep relationship between pathogenic mutations in somatic and germline cells, provide new insight into the common origin of cancer and genetic diseases, and can be used to improve the identification of new disease genes.
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Affiliation(s)
- Edoardo Luigi Draetta
- University of Milan, Milan, Italy,Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dejan Lazarević
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Provero
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy,Department of Neurosciences “Rita Levi Montalcini”, University of Turin, Turin, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy,*Correspondence: Davide Cittaro ,
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Tang R, Shuldiner EG, Kelly M, Murray CW, Hebert JD, Andrejka L, Tsai MK, Hughes NW, Parker MI, Cai H, Li YC, Wahl GM, Dunbrack RL, Jackson PK, Petrov DA, Winslow MM. Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth. Nat Cell Biol 2023; 25:159-169. [PMID: 36635501 PMCID: PMC10521195 DOI: 10.1038/s41556-022-01049-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/09/2022] [Indexed: 01/13/2023]
Abstract
Oncogenic KRAS mutations occur in approximately 30% of lung adenocarcinoma. Despite several decades of effort, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the regulators of RAS signalling is incomplete. Here to uncover the impact of diverse KRAS-interacting proteins on lung cancer growth, we combined multiplexed somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumour barcoding and high-throughput barcode sequencing. Through a series of CRISPR/Cas9 screens in autochthonous lung cancer models, we show that HRAS and NRAS are suppressors of KRASG12D-driven tumour growth in vivo and confirm these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, RAS paralogues interact with oncogenic KRAS, suppress KRAS-KRAS interactions, and reduce downstream ERK signalling. Furthermore, HRAS and NRAS mutations identified in oncogenic KRAS-driven human tumours partially abolished this effect. By comparing the tumour-suppressive effects of HRAS and NRAS in oncogenic KRAS- and oncogenic BRAF-driven lung cancer models, we confirm that RAS paralogues are specific suppressors of KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner in vivo and highlights the role RAS paralogue imbalance in oncogenic KRAS-driven lung cancer.
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Affiliation(s)
- Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Marcus Kelly
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Baxter Laboratories, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher W Murray
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Jess D Hebert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas W Hughes
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mitchell I Parker
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
- Molecular and Cell Biology and Genetics Program, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yao-Cheng Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Geoffrey M Wahl
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roland L Dunbrack
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Peter K Jackson
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Baxter Laboratories, Stanford University School of Medicine, Stanford, CA, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- The Chan Zuckerberg BioHub, San Francisco, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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46
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Halma MTJ, Tuszynski JA, Wuite GJL. Optical tweezers for drug discovery. Drug Discov Today 2023; 28:103443. [PMID: 36396117 DOI: 10.1016/j.drudis.2022.103443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
The time taken and the cost of producing novel therapeutic drugs presents a significant burden - a typical target-based drug discovery process involves computational screening of drug libraries, compound assays and expensive clinical trials. This review summarises the value of dynamic conformational information obtained by optical tweezers and how this information can target 'undruggable' proteins. Optical tweezers provide insights into the link between biological mechanisms and structural conformations, which can be used in drug discovery. Developing workflows including software and sample preparation will improve throughput, enabling adoption of optical tweezers in biopharma. As a complementary tool, optical tweezers increase the number of drug candidates, improve the understanding of a target's complex structural dynamics and elucidate interactions between compounds and their targets.
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Affiliation(s)
- Matthew T J Halma
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands; LUMICKS B.V, Paalbergweg 3, 1105 AG Amsterdam, The Netherlands
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, 116 St 85 Ave, Edmonton, Alberta T6G 2R3, Canada
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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47
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Pagba C, Gupta AK, Naji AK, van der Hoeven D, Churion K, Liang X, Jakubec J, Hook M, Zuo Y, Martinez de Kraatz M, Frost JA, Gorfe AA. KRAS Inhibitor that Simultaneously Inhibits Nucleotide Exchange Activity and Effector Engagement. ACS BIO & MED CHEM AU 2022; 2:617-626. [PMID: 37101428 PMCID: PMC10125367 DOI: 10.1021/acsbiomedchemau.2c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/27/2022] [Accepted: 09/12/2022] [Indexed: 04/28/2023]
Abstract
We describe a small molecule ligand ACA-14 (2-hydroxy-5-{[(2-phenylcyclopropyl) carbonyl] amino} benzoic acid) as an initial lead for the development of direct inhibitors of KRAS, a notoriously difficult anticancer drug target. We show that the compound binds to KRAS near the switch regions with affinities in the low micromolar range and exerts different effects on KRAS interactions with binding partners. Specifically, ACA-14 impedes the interaction of KRAS with its effector Raf and reduces both intrinsic and SOS-mediated nucleotide exchange rates. Likely as a result of these effects, ACA-14 inhibits signal transduction through the MAPK pathway in cells expressing mutant KRAS and inhibits the growth of pancreatic and colon cancer cells harboring mutant KRAS. We thus propose compound ACA-14 as a useful initial lead for the development of broad-acting inhibitors that target multiple KRAS mutants and simultaneously deplete the fraction of GTP-loaded KRAS while abrogating the effector-binding ability of the already GTP-loaded fraction.
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Affiliation(s)
- Cynthia
V. Pagba
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Amit K. Gupta
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Ali K. Naji
- Department
of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge Street, Houston, Texas 77030, United States
| | - Dharini van der Hoeven
- Department
of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge Street, Houston, Texas 77030, United States
| | - Kelly Churion
- Center
for Infectious and Inflammatory Diseases, Texas A&M University Health Science Center, 2121 W Holcombe Blvd, Houston, Texas 77030, United States
| | - Xiaowen Liang
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Jacob Jakubec
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Magnus Hook
- Center
for Infectious and Inflammatory Diseases, Texas A&M University Health Science Center, 2121 W Holcombe Blvd, Houston, Texas 77030, United States
| | - Yan Zuo
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Marisela Martinez de Kraatz
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Jeffrey A. Frost
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
- Biochemistry
and Cell Biology Program, UTHealth MD Anderson
Cancer Center Graduate School of Biomedical Sciences, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Alemayehu A. Gorfe
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
- Biochemistry
and Cell Biology Program & Therapeutics and Pharmacology Program, UTHealth MD Anderson Cancer Center Graduate School
of Biomedical Sciences, 6431 Fannin Street, Houston, Texas 77030, United
States
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48
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Xu C, Gao Q, Wu Z, Lou W, Li X, Wang M, Wang N, Li Q. Combined HASPIN and mTOR inhibition is synergistic against KRAS-driven carcinomas. Transl Oncol 2022; 26:101540. [PMID: 36115073 PMCID: PMC9483799 DOI: 10.1016/j.tranon.2022.101540] [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: 06/09/2022] [Revised: 08/16/2022] [Accepted: 09/07/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Oncogenic mutations in the KRAS gene are very common in human cancers, resulting in cells with well-characterized selective advantages. For more than three decades, the development of effective therapeutics to inhibit KRAS-driven tumorigenesis has proved a formidable challenge and KRAS was considered 'undruggable'. Therefore, multi-targeted therapy may provide a reasonable strategy for the effective treatment of KRAS-driven cancers. Here, we assess the efficacy and mechanistic rationale for combining HASPIN and mTOR inhibition as a potential therapy for cancers carrying KRAS mutations. METHODS We investigated the synergistic effect of a combination of mTOR and HASPIN inhibitors on cell viability, cell cycle, cell apoptosis, DNA damage, and mitotic catastrophe using a panel of human KRAS-mutant and wild-type tumor cell lines. Subsequently, the human transplant models were used to test the therapeutic efficacy and pharmacodynamic effects of the dual therapy. RESULTS We demonstrated that the combination of mTOR and HASPIN inhibitors induced potent synergistic cytotoxic effects in KRAS-mutant cell lines and delayed the growth of human tumor xenograft. Mechanistically, we showed that inhibiting of mTOR potentiates HASPIN inhibition by preventing the phosphorylation of H3 histones, exacerbating mitotic catastrophe and DNA damage in tumor cell lines with KRAS mutations, and this effect is due in part to a reduction in VRK1. CONCLUSIONS These findings indicate that increased DNA damage and mitotic catastrophe are the basis for the effective synergistic effect observed with mTOR and HASPIN inhibition, and support the clinical evaluation of this dual therapy in patients with KRAS-mutant tumors.
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Affiliation(s)
- Chenyue Xu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Qiongmei Gao
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center of Diabetes, Shanghai 200233, China
| | - Zhengming Wu
- Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Weijuan Lou
- Department of Nephrology, Shanghai Fourth People's Hospital, School of Medcine, Tongji University, Shanghai 200434, China
| | - Xiaoyan Li
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Menghui Wang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Nianhong Wang
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Qingquan Li
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China.
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49
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Yuan S, Stewart KS, Yang Y, Abdusselamoglu MD, Parigi SM, Feinberg TY, Tumaneng K, Yang H, Levorse JM, Polak L, Ng D, Fuchs E. Ras drives malignancy through stem cell crosstalk with the microenvironment. Nature 2022; 612:555-563. [PMID: 36450983 PMCID: PMC9750880 DOI: 10.1038/s41586-022-05475-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/24/2022] [Indexed: 12/05/2022]
Abstract
Squamous cell carcinomas are triggered by marked elevation of RAS-MAPK signalling and progression from benign papilloma to invasive malignancy1-4. At tumour-stromal interfaces, a subset of tumour-initiating progenitors, the cancer stem cells, obtain increased resistance to chemotherapy and immunotherapy along this pathway5,6. The distribution and changes in cancer stem cells during progression from a benign state to invasive squamous cell carcinoma remain unclear. Here we show in mice that, after oncogenic RAS activation, cancer stem cells rewire their gene expression program and trigger self-propelling, aberrant signalling crosstalk with their tissue microenvironment that drives their malignant progression. The non-genetic, dynamic cascade of intercellular exchanges involves downstream pathways that are often mutated in advanced metastatic squamous cell carcinomas with high mutational burden7. Coupling our clonal skin HRASG12V mouse model with single-cell transcriptomics, chromatin landscaping, lentiviral reporters and lineage tracing, we show that aberrant crosstalk between cancer stem cells and their microenvironment triggers angiogenesis and TGFβ signalling, creating conditions that are conducive for hijacking leptin and leptin receptor signalling, which in turn launches downstream phosphoinositide 3-kinase (PI3K)-AKT-mTOR signalling during the benign-to-malignant transition. By functionally examining each step in this pathway, we reveal how dynamic temporal crosstalk with the microenvironment orchestrated by the stem cells profoundly fuels this path to malignancy. These insights suggest broad implications for cancer therapeutics.
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Affiliation(s)
- Shaopeng Yuan
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Katherine S Stewart
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Yihao Yang
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Merve Deniz Abdusselamoglu
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - S Martina Parigi
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Tamar Y Feinberg
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Volastra Therapeutics, New York, NY, USA
| | - Karen Tumaneng
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Sanofi, Cambridge, MA, USA
| | - Hanseul Yang
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - John M Levorse
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Temple University, Philadelphia, PA, USA
| | - Lisa Polak
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - David Ng
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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50
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Badheeb M, Abdelrahim A, Esmail A, Umoru G, Abboud K, Al-Najjar E, Rasheed G, Alkhulaifawi M, Abudayyeh A, Abdelrahim M. Pancreatic Tumorigenesis: Precursors, Genetic Risk Factors and Screening. Curr Oncol 2022; 29:8693-8719. [PMID: 36421339 PMCID: PMC9689647 DOI: 10.3390/curroncol29110686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022] Open
Abstract
Pancreatic cancer (PC) is a highly malignant and aggressive tumor. Despite medical advancement, the silent nature of PC results in only 20% of all cases considered resectable at the time of diagnosis. It is projected to become the second leading cause in 2030. Most pancreatic cancer cases are diagnosed in the advanced stages. Such cases are typically unresectable and are associated with a 5-year survival of less than 10%. Although there is no guideline consensus regarding recommendations for screening for pancreatic cancer, early detection has been associated with better outcomes. In addition to continued utilization of imaging and conventional tumor markers, clinicians should be aware of novel testing modalities that may be effective for early detection of pancreatic cancer in individuals with high-risk factors. The pathogenesis of PC is not well understood; however, various modifiable and non-modifiable factors have been implicated in pancreatic oncogenesis. PC detection in the earlier stages is associated with better outcomes; nevertheless, most oncological societies do not recommend universal screening as it may result in a high false-positive rate. Therefore, targeted screening for high-risk individuals represents a reasonable option. In this review, we aimed to summarize the pathogenesis, genetic risk factors, high-risk population, and screening modalities for PC.
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Affiliation(s)
- Mohamed Badheeb
- Internal Medicine Department, College of Medicine, Hadhramout University, Mukalla 50512, Yemen
| | | | - Abdullah Esmail
- Section of GI Oncology, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX 77030, USA
- Correspondence: (A.E.); (M.A.)
| | - Godsfavour Umoru
- Department of Pharmacy, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Karen Abboud
- Department of Pharmacy, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Ebtesam Al-Najjar
- Faculty of Medicine and Health Sciences, University of Science and Technology, Sana’a 15201, Yemen
| | - Ghaith Rasheed
- Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan
| | | | - Ala Abudayyeh
- Section of Nephrology, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maen Abdelrahim
- Section of GI Oncology, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 14853, USA
- Cockrell Center for Advanced Therapeutic Phase I Program, Houston Methodist Research Institute, Houston, TX 77030, USA
- Correspondence: (A.E.); (M.A.)
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