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Dziubańska-Kusibab PJ, Nevedomskaya E, Haendler B. Preclinical Anticipation of On- and Off-Target Resistance Mechanisms to Anti-Cancer Drugs: A Systematic Review. Int J Mol Sci 2024; 25:705. [PMID: 38255778 PMCID: PMC10815614 DOI: 10.3390/ijms25020705] [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: 11/14/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
The advent of targeted therapies has led to tremendous improvements in treatment options and their outcomes in the field of oncology. Yet, many cancers outsmart precision drugs by developing on-target or off-target resistance mechanisms. Gaining the ability to resist treatment is the rule rather than the exception in tumors, and it remains a major healthcare challenge to achieve long-lasting remission in most cancer patients. Here, we discuss emerging strategies that take advantage of innovative high-throughput screening technologies to anticipate on- and off-target resistance mechanisms before they occur in treated cancer patients. We divide the methods into non-systematic approaches, such as random mutagenesis or long-term drug treatment, and systematic approaches, relying on the clustered regularly interspaced short palindromic repeats (CRISPR) system, saturated mutagenesis, or computational methods. All these new developments, especially genome-wide CRISPR-based screening platforms, have significantly accelerated the processes for identification of the mechanisms responsible for cancer drug resistance and opened up new avenues for future treatments.
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Affiliation(s)
| | | | - Bernard Haendler
- Research and Early Development Oncology, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (P.J.D.-K.); (E.N.)
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Qian F, Nettleford SK, Zhou J, Arner BE, Hall MA, Sharma A, Annageldiyev C, Rossi RM, Tukaramrao DB, Sarkar D, Hegde S, Gandhi UH, Finch ER, Goodfield L, Quickel MD, Claxton DF, Paulson RF, Prabhu KS. Activation of GPR44 decreases severity of myeloid leukemia via specific targeting of leukemia initiating stem cells. Cell Rep 2023; 42:112794. [PMID: 37459233 PMCID: PMC10428076 DOI: 10.1016/j.celrep.2023.112794] [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: 07/22/2022] [Revised: 03/25/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Relapse of acute myeloid leukemia (AML) remains a significant concern due to persistent leukemia-initiating stem cells (LICs) that are typically not targeted by most existing therapies. Using a murine AML model, human AML cell lines, and patient samples, we show that AML LICs are sensitive to endogenous and exogenous cyclopentenone prostaglandin-J (CyPG), Δ12-PGJ2, and 15d-PGJ2, which are increased upon dietary selenium supplementation via the cyclooxygenase-hematopoietic PGD synthase pathway. CyPGs are endogenous ligands for peroxisome proliferator-activated receptor gamma and GPR44 (CRTH2; PTGDR2). Deletion of GPR44 in a mouse model of AML exacerbated the disease suggesting that GPR44 activation mediates selenium-mediated apoptosis of LICs. Transcriptomic analysis of GPR44-/- LICs indicated that GPR44 activation by CyPGs suppressed KRAS-mediated MAPK and PI3K/AKT/mTOR signaling pathways, to enhance apoptosis. Our studies show the role of GPR44, providing mechanistic underpinnings of the chemopreventive and chemotherapeutic properties of selenium and CyPGs in AML.
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Affiliation(s)
- Fenghua Qian
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shaneice K Nettleford
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jiayan Zhou
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Brooke E Arner
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Molly A Hall
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Arati Sharma
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Charyguly Annageldiyev
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Randy M Rossi
- Transgenic Core Facility, Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Diwakar B Tukaramrao
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Deborpita Sarkar
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shailaja Hegde
- Hoxworth Blood Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Ujjawal H Gandhi
- Department of Hematology and Oncology, University of North Carolina Health, Cary, NC 27518, USA
| | - Emily R Finch
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura Goodfield
- Immunooncology Division, Bicycle Therapeutics, Boston, MA 02140, USA
| | - Michael D Quickel
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - David F Claxton
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Robert F Paulson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
| | - K Sandeep Prabhu
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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Tu H, Han Y, Wang Z, Li J. Clustered tree regression to learn protein energy change with mutated amino acid. Brief Bioinform 2022; 23:6702668. [PMID: 36124753 DOI: 10.1093/bib/bbac374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/31/2022] [Accepted: 08/08/2022] [Indexed: 12/14/2022] Open
Abstract
Accurate and effective prediction of mutation-induced protein energy change remains a great challenge and of great interest in computational biology. However, high resource consumption and insufficient structural information of proteins severely limit the experimental techniques and structure-based prediction methods. Here, we design a structure-independent protocol to accurately and effectively predict the mutation-induced protein folding free energy change with only sequence, physicochemical and evolutionary features. The proposed clustered tree regression protocol is capable of effectively exploiting the inherent data patterns by integrating unsupervised feature clustering by K-means and supervised tree regression using XGBoost, and thus enabling fast and accurate protein predictions with different mutations, with an average Pearson correlation coefficient of 0.83 and an average root-mean-square error of 0.94kcal/mol. The proposed sequence-based method not only eliminates the dependence on protein structures, but also has potential applications in protein predictions with rare structural information.
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Affiliation(s)
- Hongwei Tu
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanqiang Han
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhilong Wang
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinjin Li
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
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Ren Q, Zhang W, Li P, Zhou J, Li Z, Zhou Y, Li M. Upregulation of osteoprotegerin inhibits tert‑butyl hydroperoxide‑induced apoptosis of human chondrocytes. Exp Ther Med 2022; 24:470. [PMID: 35747145 PMCID: PMC9204554 DOI: 10.3892/etm.2022.11397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 03/31/2022] [Indexed: 11/29/2022] Open
Abstract
Necrosis of the femoral head (NFH) is an orthopedic disease characterized by a severe lack of blood supply to the femoral head and a marked increase in intraosseous pressure. NFH is associated with numerous factors, such as alcohol consumption and hormone levels. The present study focused on the expression levels of osteoprotegerin (OPG) in NFH and the effect of OPG overexpression on chondrocyte apoptosis. The results demonstrated that OPG expression was markedly decreased in the femoral head of patients with NFH compared with normal femoral heads. Lentivirus-mediated overexpression of OPG in human chondrocytes reversed the decrease in cell viability and the increase in reactive oxygen species production induced by an oxidative stress-inducing factor, tert-butyl hydroperoxide. Flow cytometry and TUNEL assays revealed that OPG overexpression inhibited the apoptosis of chondrocytes. In addition, it was revealed that OPG exerted its anti-apoptotic effect mainly by promoting Bcl-2 expression and Akt phosphorylation and inhibiting caspase-3 cleavage and Bax expression. The present study revealed that OPG may be an important regulator of NFH.
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Affiliation(s)
- Qifeng Ren
- Department of Joint Surgery, Dezhou People's Hospital, Dezhou, Shandong 253014, P.R. China
| | - Wenfei Zhang
- Department of Clinical Psychology, Dezhou People's Hospital, Dezhou, Shandong 253014, P.R. China
| | - Ping Li
- Department of Hematology, Dezhou People's Hospital, Dezhou, Shandong 253014, P.R. China
| | - Jianli Zhou
- Department of Nuclear Medicine, Dezhou People's Hospital, Dezhou, Shandong 253014, P.R. China
| | - Zhonghao Li
- Department of Joint Surgery, Dezhou People's Hospital, Dezhou, Shandong 253014, P.R. China
| | - Yang Zhou
- Central Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Ming Li
- Department of Joint Surgery, Dezhou People's Hospital, Dezhou, Shandong 253014, P.R. China
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Zhang J, Zhang J, Liu Q, Fan XX, Leung ELH, Yao XJ, Liu L. Resistance looms for KRAS G12C inhibitors and rational tackling strategies. Pharmacol Ther 2021; 229:108050. [PMID: 34864132 DOI: 10.1016/j.pharmthera.2021.108050] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022]
Abstract
KRAS mutations are one of the most frequent activating alterations in carcinoma. Recent efforts have witnessed a revolutionary strategy for KRAS G12C inhibitors with exhibiting conspicuous clinical responses across multiple tumor types, providing new impetus for renewed drug development and culminating in sotorasib with approximately 6-month median progression-free survival in KRAS G12C-driven lung cancer. However, diverse genomic and histological mechanisms conferring resistance to KRAS G12C inhibitors may limit their clinical efficacy. Herein, we first briefly discuss the recent resistance looms for KRAS G12C inhibitors, focusing on their clinical trials. We then comprehensively interrogate and underscore our current understanding of resistance mechanisms and the necessity of incorporating genomic analyses into the clinical investigation to further decipher resistance mechanisms. Finally, we highlight the future role of novel treatment strategies especially rational identification of targeted combinatorial approaches in tackling drug resistance, and propose our views on including the application of robust biomarkers to precisely guide combination medication regimens.
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Affiliation(s)
- Junmin Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China; School of Pharmacy, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Juanhong Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China; School of Pharmacy, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China; College of Life Science, Northwest Normal University, Lanzhou 730070, China
| | - Qing Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China
| | - Xing-Xing Fan
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China.
| | - Xiao-Jun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China.
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China.
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Yenerall P, Kittler R, Minna J. Structure-based classification of EGFR mutations informs inhibitor selection for lung cancer therapy. Cancer Cell 2021; 39:1455-1457. [PMID: 34752753 PMCID: PMC9241337 DOI: 10.1016/j.ccell.2021.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
EGFR oncogenic mutations predict sensitivity to EGFR inhibitors in NSCLC, but less is known about EGFR "variants of unknown significance." Using preclinical models, 3D structure analyses, and patient response data, Robichaux et al. show in Nature that mutations in structural regions of EGFR predict responses to different EGFR inhibitors.
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Affiliation(s)
- Paul Yenerall
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ralf Kittler
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - John Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
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