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García García OR, Ortiz R, Moreno-Barbosa E, D-Kondo N, Faddegon B, Ramos-Méndez J. TOPAS-Tissue: A Framework for the Simulation of the Biological Response to Ionizing Radiation at the Multi-Cellular Level. Int J Mol Sci 2024; 25:10061. [PMID: 39337547 PMCID: PMC11431975 DOI: 10.3390/ijms251810061] [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: 07/20/2024] [Revised: 08/21/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
This work aims to develop and validate a framework for the multiscale simulation of the biological response to ionizing radiation in a population of cells forming a tissue. We present TOPAS-Tissue, a framework to allow coupling two Monte Carlo (MC) codes: TOPAS with the TOPAS-nBio extension, capable of handling the track-structure simulation and subsequent chemistry, and CompuCell3D, an agent-based model simulator for biological and environmental behavior of a population of cells. We verified the implementation by simulating the experimental conditions for a clonogenic survival assay of a 2-D PC-3 cell culture model (10 cells in 10,000 µm2) irradiated by MV X-rays at several absorbed dose values from 0-8 Gy. The simulation considered cell growth and division, irradiation, DSB induction, DNA repair, and cellular response. The survival was obtained by counting the number of colonies, defined as a surviving primary (or seeded) cell with progeny, at 2.7 simulated days after irradiation. DNA repair was simulated with an MC implementation of the two-lesion kinetic model and the cell response with a p53 protein-pulse model. The simulated survival curve followed the theoretical linear-quadratic response with dose. The fitted coefficients α = 0.280 ± 0.025/Gy and β = 0.042 ± 0.006/Gy2 agreed with published experimental data within two standard deviations. TOPAS-Tissue extends previous works by simulating in an end-to-end way the effects of radiation in a cell population, from irradiation and DNA damage leading to the cell fate. In conclusion, TOPAS-Tissue offers an extensible all-in-one simulation framework that successfully couples Compucell3D and TOPAS for multiscale simulation of the biological response to radiation.
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Affiliation(s)
- Omar Rodrigo García García
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico; (O.R.G.G.); (E.M.-B.)
| | - Ramon Ortiz
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA; (R.O.); (N.D.-K.); (B.F.)
| | - Eduardo Moreno-Barbosa
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico; (O.R.G.G.); (E.M.-B.)
| | - Naoki D-Kondo
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA; (R.O.); (N.D.-K.); (B.F.)
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA; (R.O.); (N.D.-K.); (B.F.)
| | - Jose Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA; (R.O.); (N.D.-K.); (B.F.)
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2
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Gardner LL, Thompson SJ, O'Connor JD, McMahon SJ. Modelling radiobiology. Phys Med Biol 2024; 69:18TR01. [PMID: 39159658 DOI: 10.1088/1361-6560/ad70f0] [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: 04/25/2024] [Accepted: 08/19/2024] [Indexed: 08/21/2024]
Abstract
Radiotherapy has played an essential role in cancer treatment for over a century, and remains one of the best-studied methods of cancer treatment. Because of its close links with the physical sciences, it has been the subject of extensive quantitative mathematical modelling, but a complete understanding of the mechanisms of radiotherapy has remained elusive. In part this is because of the complexity and range of scales involved in radiotherapy-from physical radiation interactions occurring over nanometres to evolution of patient responses over months and years. This review presents the current status and ongoing research in modelling radiotherapy responses across these scales, including basic physical mechanisms of DNA damage, the immediate biological responses this triggers, and genetic- and patient-level determinants of response. Finally, some of the major challenges in this field and potential avenues for future improvements are also discussed.
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Affiliation(s)
- Lydia L Gardner
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
| | - Shannon J Thompson
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
| | - John D O'Connor
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
- Ulster University School of Engineering, York Street, Belfast BT15 1AP, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
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3
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Chen X, Zhang H, Pan Y, Zhu N, Zhou L, Chen G, Wang J. Nimbolide Exhibits Potent Anticancer Activity Through ROS-Mediated ER Stress and DNA Damage in Human Non-small Cell Lung Cancer Cells. Appl Biochem Biotechnol 2024; 196:182-202. [PMID: 37103738 DOI: 10.1007/s12010-023-04507-9] [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] [Accepted: 04/11/2023] [Indexed: 04/28/2023]
Abstract
The non-small cell lung cancer (NSCLC) accounts for about 85% of all lung cancers. It is usually diagnosed at an advanced stage with poor prognosis. Nimbolide (NB), a terpenoid limonoid isolated from the flowers and leaves of neem tree, possesses anticancer properties in various cancer cell lines. However, the underlying mechanism of its anticancer effect on human NSCLC cells remains unclear. In the present study, we investigated the effect of NB on A549 human NSCLC cells. We found that NB treatment inhibits A549 cells colony formation in a dose-dependent manner. Mechanistically, NB treatment increases cellular reactive oxygen species (ROS) level, leading to endoplasmic reticulum (ER) stress, DNA damage, and eventually induction of apoptosis in NSCLC cells. Furthermore, all these effects of NB were blocked by pretreatment with antioxidant glutathione (GSH), the specific ROS inhibitor. We further knockdown CHOP protein by siRNA markedly reduced NB-induced apoptosis in A549 cells. Taken together, our findings reveal that NB is an inducer of ER stress and ROS; these findings may contribute to increasing the therapeutic efficiency of NSCLC.
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Affiliation(s)
- Xi Chen
- Department of Pharmacology, School of Medicine, Taizhou University, Jiaojiang, Taizhou, 318000, Zhejiang, China.
| | - Hangshuo Zhang
- Department of Clinical Medicine, School of Medicine, Taizhou University, Jiaojiang, Taizhou, 318000, Zhejiang, China
| | - Yuzhu Pan
- Department of Clinical Medicine, School of Medicine, Taizhou University, Jiaojiang, Taizhou, 318000, Zhejiang, China
| | - Ning Zhu
- Municipal Hospital Affiliated to Taizhou University, Jiaojiang, Taizhou, 318000, Zhejiang, China
| | - Lisha Zhou
- Department of Biochemistry, School of Medicine, Taizhou University, Jiaojiang, Taizhou, 318000, Zhejiang, China
| | - Guang Chen
- Department of Pharmacology, School of Medicine, Taizhou University, Jiaojiang, Taizhou, 318000, Zhejiang, China
| | - Jiabing Wang
- Municipal Hospital Affiliated to Taizhou University, Jiaojiang, Taizhou, 318000, Zhejiang, China.
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Warmenhoven JW, Henthorn NT, McNamara AL, Ingram SP, Merchant MJ, Kirkby KJ, Schuemann J, Paganetti H, Prise KM, McMahon SJ. Effects of Differing Underlying Assumptions in In Silico Models on Predictions of DNA Damage and Repair. Radiat Res 2023; 200:509-522. [PMID: 38014593 DOI: 10.1667/rade-21-00147.1] [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: 07/20/2021] [Accepted: 10/05/2023] [Indexed: 11/29/2023]
Abstract
The induction and repair of DNA double-strand breaks (DSBs) are critical factors in the treatment of cancer by radiotherapy. To investigate the relationship between incident radiation and cell death through DSB induction many in silico models have been developed. These models produce and use custom formats of data, specific to the investigative aims of the researchers, and often focus on particular pairings of damage and repair models. In this work we use a standard format for reporting DNA damage to evaluate combinations of different, independently developed, models. We demonstrate the capacity of such inter-comparison to determine the sensitivity of models to both known and implicit assumptions. Specifically, we report on the impact of differences in assumptions regarding patterns of DNA damage induction on predicted initial DSB yield, and the subsequent effects this has on derived DNA repair models. The observed differences highlight the importance of considering initial DNA damage on the scale of nanometres rather than micrometres. We show that the differences in DNA damage models result in subsequent repair models assuming significantly different rates of random DSB end diffusion to compensate. This in turn leads to disagreement on the mechanisms responsible for different biological endpoints, particularly when different damage and repair models are combined, demonstrating the importance of inter-model comparisons to explore underlying model assumptions.
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Affiliation(s)
- John W Warmenhoven
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Nicholas T Henthorn
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Aimee L McNamara
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Samuel P Ingram
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Michael J Merchant
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Karen J Kirkby
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Jan Schuemann
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Harald Paganetti
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Kevin M Prise
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
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Gao T, Wang X, Li Y, Ren F. The Role of Probiotics in Skin Health and Related Gut-Skin Axis: A Review. Nutrients 2023; 15:3123. [PMID: 37513540 PMCID: PMC10385652 DOI: 10.3390/nu15143123] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Aging skin, wrinkles, pigmentation, and dryness are problems that plague people, and researchers are working to solve them. Recent studies have shown that intestinal microbiota homeostasis can influence skin health, demonstrating the existence of a gut-skin axis. Recently, improving skin health through probiotic interventions has been proposed, and micro-ecological skin care is becoming a popular concept. By regulating skin health and gut-skin axis interactions, probiotics can be used as potential management tools to suppress and improve skin diseases in multiple ways, including decreasing oxidative stress, suppressing inflammatory responses, and keeping immune effects. The purpose of this paper is to provide a comprehensive review of the application and mechanisms of probiotic-mediated gut microbiota homeostasis in skin care and to offer a theoretical basis for the application of probiotics in skin care.
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Affiliation(s)
- Ting Gao
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, Beijing Laboratory of Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Xiaoyu Wang
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, Beijing Laboratory of Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Yixuan Li
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, Beijing Laboratory of Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Fazheng Ren
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, Beijing Laboratory of Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
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Marvalim C, Datta A, Lee SC. Role of p53 in breast cancer progression: An insight into p53 targeted therapy. Theranostics 2023; 13:1421-1442. [PMID: 36923534 PMCID: PMC10008729 DOI: 10.7150/thno.81847] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/26/2023] [Indexed: 03/14/2023] Open
Abstract
The transcription factor p53 is an important regulator of a multitude of cellular processes. In the presence of genotoxic stress, p53 is activated to facilitate DNA repair, cell cycle arrest, and apoptosis. In breast cancer, the tumor suppressive activities of p53 are frequently inactivated by either the overexpression of its negative regulator MDM2, or mutation which is present in 30-35% of all breast cancer cases. Notably, the frequency of p53 mutation is highly subtype dependent in breast cancers, with majority of hormone receptor-positive or luminal subtypes retaining the wild-type p53 status while hormone receptor-negative patients predominantly carry p53 mutations with gain-of-function oncogenic activities that contribute to poorer prognosis. Thus, a two-pronged strategy of targeting wild-type and mutant p53 in different subtypes of breast cancer can have clinical relevance. The development of p53-based therapies has rapidly progressed in recent years, and include unique small molecule chemical inhibitors, stapled peptides, PROTACs, as well as several genetic-based approaches using vectors and engineered antibodies. In this review, we highlight the therapeutic strategies that are in pre-clinical and clinical development to overcome p53 inactivation in both wild-type and mutant p53-bearing breast tumors, and discuss their efficacies and limitations in pre-clinical and clinical settings.
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Affiliation(s)
- Charlie Marvalim
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
- ✉ Corresponding authors: C.M. E-mail: ; L.S.C. E-mail: ; Tel: (65) 6516 7282
| | - Arpita Datta
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Soo Chin Lee
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore 119228, Singapore
- ✉ Corresponding authors: C.M. E-mail: ; L.S.C. E-mail: ; Tel: (65) 6516 7282
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Modeling of DNA Damage Repair and Cell Response in Relation to p53 System Exposed to Ionizing Radiation. Int J Mol Sci 2022; 23:ijms231911323. [PMID: 36232625 PMCID: PMC9569799 DOI: 10.3390/ijms231911323] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Repair of DNA damage induced by ionizing radiation plays an important role in the cell response to ionizing radiation. Radiation-induced DNA damage also activates the p53 system, which determines the fate of cells. The kinetics of repair, which is affected by the cell itself and the complexity of DNA damage, influences the cell response and fate via affecting the p53 system. To mechanistically study the influences of the cell response to different LET radiations, we introduce a new repair module and a p53 system model with NASIC, a Monte Carlo track structure code. The factors determining the kinetics of the double-strand break (DSB) repair are modeled, including the chromosome environment and complexity of DSB. The kinetics of DSB repair is modeled considering the resection-dependent and resection-independent compartments. The p53 system is modeled by simulating the interactions among genes and proteins. With this model, the cell responses to low- and high-LET irradiation are simulated, respectively. It is found that the kinetics of DSB repair greatly affects the cell fate and later biological effects. A large number of DSBs and a slow repair process lead to severe biological consequences. High-LET radiation induces more complex DSBs, which can be repaired by slow processes, subsequently resulting in a longer cycle arrest and, furthermore, apoptosis and more secreting of TGFβ. The Monte Carlo track structure simulation with a more realistic repair module and the p53 system model developed in this study can expand the functions of the NASIC code in simulating mechanical radiobiological effects.
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Jin XX, Mei YN, Shen Z, Zhu JF, Xing SH, Yang HM, Liang G, Zheng XH. A chalcone-syringaldehyde hybrid inhibits triple-negative breast cancer cell proliferation and migration by inhibiting CKAP2-mediated FAK and STAT3 phosphorylation. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 101:154087. [PMID: 35429924 DOI: 10.1016/j.phymed.2022.154087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/15/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Although triple-negative breast cancer (TNBC) accounts for only 15% of breast cancer cases, it is associated with a high relapse rate and poor outcome after standard treatment. Currently, the effective drugs and treatment strategies for TNBC remain limited, and thus, developing effective treatments for TNBC is pressing. Several studies have demonstrated that both chalcone and syringaldehyde have anticancer effect, but their potential anti-TNBC bioactivity are still unknown. PURPOSE The present study aimed to synthesize a chalcone-syringaldehyde hybrid (CSH1) and explore its potential anti-TNBC effects and the underlying molecular mechanism. METHODS Cell cytotoxicity was determined by 3-(4,5-dimethythiazol)-2,5-diphenyltetrazolium bromide (MTT). The activity of cell proliferation was measured by colony formation assay and 5-ethynyl-2'-deoxyuridine (EdU) staining assay. Cell cycle distribution and cell apoptosis were determined by fluorescence-activated cell sorter (FACS). The situation of DNA damage was observed using fluorescence microscopy. The ability of cell-matrix adhesion, migration and invasion was detected using cell adhesion assay and transwell assay. Transcriptome sequencing was performed to find out the changed genes. Levels of various signaling proteins were assessed by western blotting. RESULTS CSH1 treatment triggered DNA damage and inhibited DNA replication, cell cycle arrest, and cell apoptosis via suppressing signal transducer and activator of transcription 3 (STAT3) phosphorylation. Whole genome RNA-seq analysis suggested that 4% of changed genes were correlated to DNA damage and repair, and nearly 18% of changed genes were functionally related to cell adhesion and migration. Experimental evidence indicated that CSH1 treatment significantly affected the distribution of focal adhesion kinase (FAK) and its phosphorylation, resulting in cell-matrix-adhesion reduction and migration inhibition of TNBC cells. Further mechanistic studies indicated that CSH1 inhibited TNBC cell proliferation, adhesion, and migration by inhibiting cytoskeleton-associated protein 2 (CKAP2)-mediated FAK and STAT3 phosphorylation signaling. CONCLUSION These results suggest that CKAP2-mediated FAK and STAT3 phosphorylation signaling is a valuable target for TNBC treatment, and these findings also reveal the potential of CSH1 as a prospective TNBC drug.
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Affiliation(s)
- Xiang-Xiang Jin
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, People's Republic of China
| | - Ya-Nan Mei
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, People's Republic of China
| | - Zhe Shen
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, People's Republic of China
| | - Ju-Fan Zhu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, People's Republic of China
| | - Sun-Hui Xing
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, People's Republic of China
| | - Hua-Mao Yang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, People's Republic of China
| | - Guang Liang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, People's Republic of China.
| | - Xiao-Hui Zheng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, People's Republic of China.
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Kudlova N, De Sanctis JB, Hajduch M. Cellular Senescence: Molecular Targets, Biomarkers, and Senolytic Drugs. Int J Mol Sci 2022; 23:ijms23084168. [PMID: 35456986 PMCID: PMC9028163 DOI: 10.3390/ijms23084168] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 11/16/2022] Open
Abstract
Cellular senescence is defined as irreversible cell cycle arrest caused by various processes that render viable cells non-functional, hampering normal tissue homeostasis. It has many endogenous and exogenous inducers, and is closely connected with age, age-related pathologies, DNA damage, degenerative disorders, tumor suppression and activation, wound healing, and tissue repair. However, the literature is replete with contradictory findings concerning its triggering mechanisms, specific biomarkers, and detection protocols. This may be partly due to the wide range of cellular and in vivo animal or human models of accelerated aging that have been used to study senescence and test senolytic drugs. This review summarizes recent findings concerning senescence, presents some widely used cellular and animal senescence models, and briefly describes the best-known senolytic agents.
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Affiliation(s)
- Natalie Kudlova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 77147 Olomouc, Czech Republic; (N.K.); (J.B.D.S.)
| | - Juan Bautista De Sanctis
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 77147 Olomouc, Czech Republic; (N.K.); (J.B.D.S.)
- Institute of Molecular and Translational Medicine Czech Advanced Technologies and Research Institute, Palacky University, 77147 Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 77147 Olomouc, Czech Republic; (N.K.); (J.B.D.S.)
- Institute of Molecular and Translational Medicine Czech Advanced Technologies and Research Institute, Palacky University, 77147 Olomouc, Czech Republic
- Correspondence: ; Tel.: +42-0-585632082
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Mertins SD. Capturing Biomarkers and Molecular Targets in Cellular Landscapes From Dynamic Reaction Network Models and Machine Learning. Front Oncol 2022; 11:805592. [PMID: 35127516 PMCID: PMC8813744 DOI: 10.3389/fonc.2021.805592] [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: 10/30/2021] [Accepted: 12/31/2021] [Indexed: 12/02/2022] Open
Abstract
Computational dynamic ODE models of cell function describing biochemical reactions have been created for decades, but on a small scale. Still, they have been highly effective in describing and predicting behaviors. For example, oscillatory phospho-ERK levels were predicted and confirmed in MAPK signaling encompassing both positive and negative feedback loops. These models typically were limited and not adapted to large datasets so commonly found today. But importantly, ODE models describe reaction networks in well-mixed systems representing the cell and can be simulated with ordinary differential equations that are solved deterministically. Stochastic solutions, which can account for noisy reaction networks, in some cases, also improve predictions. Today, dynamic ODE models rarely encompass an entire cell even though it might be expected that an upload of the large genomic, transcriptomic, and proteomic datasets may allow whole cell models. It is proposed here to combine output from simulated dynamic ODE models, completed with omics data, to discover both biomarkers in cancer a priori and molecular targets in the Machine Learning setting.
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Affiliation(s)
- Susan D. Mertins
- Department of Science, Mount St. Mary’s University, Emmitsburg, MD, United States
- Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Limited Liability Company (LLC), Frederick, MD, United States
- BioSystems Strategies, Limited Liability Company (LLC), Frederick, MD, United States
- *Correspondence: Susan D. Mertins,
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11
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Yu J, Ma X, Wang X, Cui X, Ding K, Wang S, Han C. Application and mechanism of probiotics in skin care: A review. J Cosmet Dermatol 2022; 21:886-894. [PMID: 34997993 DOI: 10.1111/jocd.14734] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/22/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Skin problems have been the focus of attention in recent years. Skin aging, wrinkles, pigmentation, dryness has been a problem that makes people feel troubled. Researchers have been devoted to find ways to solve these skin problems. Micro-ecological skin care is a popular concept these days, and improving skin health through the use of probiotics is a hot topic of discussion. OBJECTIVE Many experimental studies have shown that probiotics have a good effect on improving skin problems. This paper aims to comprehensively review the application and mechanism of probiotics in skin care and provide theoretical basis for the application of probiotics in skin care. METHODS Literatures in this review were searched in PubMed, China National Knowledge Infrastructure (CNKI), Web of Science, and Science Direct. RESULTS Probiotics have potent effects on skin whitening, moisturizing, anti-aging, anti-wrinkle and removing body odor. CONCLUSIONS The effects of probiotics on skin whitening, skin moisturizing, anti-aging, improving skin wrinkles and removing body odor were reviewed, which provided a new basis for the extensive application of probiotics in skin care.
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Affiliation(s)
- Jinyan Yu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xumin Ma
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaoyu Wang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xuetao Cui
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Kai Ding
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shiyuan Wang
- School of Nursing, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chunchao Han
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
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12
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Morozevic GE, Kozlova NI, Gevorkian NM, Berman AE. [Integrin α3β1 signaling in regulation of the SK-Mel-147 melanoma cell senescence]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:39-46. [PMID: 35221295 DOI: 10.18097/pbmc20226801039] [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: 06/14/2023]
Abstract
Using a model of the human SK-Mel-147 melanoma cell line, it was shown that blocking the expression of integrin α3β1 by transduction of cells with α3-specific shRNA did not affect their proliferation, but sharply increased the proportion of SA-β-Gal-positive cells, a phenotypic feature of cell senescence. These findings were accompanied by a significant increase in the activity of the Akt and mTOR protein kinases and the expression of p53 and p21 oncosupressors. Pharmacological inhibition of mTORC1 reduced the number SA-β-Gal-positive cells in the SK-Mel-147 cell population depleted of α3β1. Based on our recent data on a non-canonical function of Akt isomers in the regulation of SK-Mel-147 cell senescence caused by deficiency of α2β1 receptor, we investigated the role of Akt isomers in senescence induced by the α3β1 knockdown. It appeared that in the cell population with downregulated α3β1, inhibition of Akt1 reduced the number SA-β-Gal positive cells to the level of control cell population, while inhibition of Akt2 had no visible effect. Our results demonstrate that the laminin-specific integrin α3β1, like the collagen-specific receptor α2β1, is involved in tumor cell protection from senescence, and senescence induced by α3β1 depletion, like that caused by α2β1 deficiency, is based on a signaling mechanism employing a non-canonical function of the Akt1 isoform.
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Affiliation(s)
| | - N I Kozlova
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - A E Berman
- Institute of Biomedical Chemistry, Moscow, Russia
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Janelle V, Neault M, Lebel MÈ, De Sousa DM, Boulet S, Durrieu L, Carli C, Muzac C, Lemieux S, Labrecque N, Melichar HJ, Mallette FA, Delisle JS. p16 INK4a Regulates Cellular Senescence in PD-1-Expressing Human T Cells. Front Immunol 2021; 12:698565. [PMID: 34434190 PMCID: PMC8381277 DOI: 10.3389/fimmu.2021.698565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/20/2021] [Indexed: 01/30/2023] Open
Abstract
T-cell dysfunction arising upon repeated antigen exposure prevents effective immunity and immunotherapy. Using various clinically and physiologically relevant systems, we show that a prominent feature of PD-1-expressing exhausted T cells is the development of cellular senescence features both in vivo and ex vivo. This is associated with p16INK4a expression and an impaired cell cycle G1 to S-phase transition in repeatedly stimulated T cells. We show that these T cells accumulate DNA damage and activate the p38MAPK signaling pathway, which preferentially leads to p16INK4a upregulation. However, in highly dysfunctional T cells, p38MAPK inhibition does not restore functionality despite attenuating senescence features. In contrast, p16INK4a targeting can improve T-cell functionality in exhausted CAR T cells. Collectively, this work provides insights into the development of T-cell dysfunction and identifies T-cell senescence as a potential target in immunotherapy.
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Affiliation(s)
- Valérie Janelle
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Mathieu Neault
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Marie-Ève Lebel
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Dave Maurice De Sousa
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Salix Boulet
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Ludovic Durrieu
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Cédric Carli
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Chloé Muzac
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Nathalie Labrecque
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Heather J Melichar
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Frédérick A Mallette
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Jean-Sébastien Delisle
- Research Centre, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada.,Division of Hematology-Oncology, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
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14
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Implication of integrin α2β1 in senescence of SK-Mel-147 human melanoma cells. Aging (Albany NY) 2021; 13:18006-18017. [PMID: 34257160 PMCID: PMC8351665 DOI: 10.18632/aging.203309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/19/2021] [Indexed: 12/12/2022]
Abstract
This investigation addressed the impact of integrin-initiated signaling pathways on senescence of tumor cells. In a model of human SK-Mel-147 melanoma cells, the silencing of integrin α2β1 strongly reduced cell proliferation and enhanced the percentage of SA-β-Gal-positive cells, a phenotypic feature of cellular senescence. These changes were accompanied by a significant increase in the activity of Akt and mTOR protein kinases and also in the expression of p53 and p21 oncosuppressors. Pharmacological inhibition of Akt and mTORC1 and genetic inhibition of p53 and p21 reduced the senescence of α2β1-depleted SK-Mel-147 cells to the level of control cells. Based on our earlier data on the non-canonical functions of Akt isomers in the invasion and anoikis of SK-Mel-147 cells, we investigated the role of Akt isomers in senescence induced by α2β1 suppression. The inhibition of Akt1 strongly reduced the percentage of SA-β-Gal-positive cells in the α2β1-depleted cell population, while the inhibition of Akt2 did not have a noticeable effect. Our data demonstrated for the first time that α2β1 is involved in the protection of tumor cells against senescence and that senescence, which is induced by the downregulation of α2β, is based on a signaling mechanism in which Akt1 performs a non-canonical function.
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15
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Pawge G, Khatik GL. p53 regulated senescence mechanism and role of its modulators in age-related disorders. Biochem Pharmacol 2021; 190:114651. [PMID: 34118220 DOI: 10.1016/j.bcp.2021.114651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
Multiple co-morbidities are associated with age, and there is a need for the broad-spectrum drug to prevent multiple regimens that may cause an adverse effect in the geriatric population. Cellular senescence is a primary mechanism for ageing in various tissues. p53, a tumor suppressor protein, plays a significant role in forming DNA damage foci and post different stress responses. DNA damage foci can be transient or persistent that can progress to DNA-SCARS inducing senescence. p53 also plays a role in apoptosis and negative regulation of SASP. Few upstream targets like FOXO4, MDM2, MDM4, USP7 control the availability of p53 for apoptosis. Hence, the senolytic therapies, modulating p53 upstream targets, can be a good approach for preventing age-related disorders. This review discusses the insights on the role of p53 in the formation of DNA-SCARS, various upstream target proteins, and pathways involved in p53 regulation. Further, the review aimed to include recently discovered small molecules acting on these upstream targets, and those can be modified using medicinal chemistry approaches to give successful senotherapeutics.
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Affiliation(s)
- Girija Pawge
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research- Raebareli, New Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow, Uttar Pradesh 226301, India
| | - Gopal L Khatik
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research- Raebareli, New Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow, Uttar Pradesh 226301, India.
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16
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Resnik SR, Egger A, Abdo Abujamra B, Jozic I. Clinical Implications of Cellular Senescence on Wound Healing. CURRENT DERMATOLOGY REPORTS 2020. [DOI: 10.1007/s13671-020-00320-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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17
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Mijit M, Caracciolo V, Melillo A, Amicarelli F, Giordano A. Role of p53 in the Regulation of Cellular Senescence. Biomolecules 2020; 10:biom10030420. [PMID: 32182711 PMCID: PMC7175209 DOI: 10.3390/biom10030420] [Citation(s) in RCA: 258] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
The p53 transcription factor plays a critical role in cellular responses to stress. Its activation in response to DNA damage leads to cell growth arrest, allowing for DNA repair, or directs cellular senescence or apoptosis, thereby maintaining genome integrity. Senescence is a permanent cell-cycle arrest that has a crucial role in aging, and it also represents a robust physiological antitumor response, which counteracts oncogenic insults. In addition, senescent cells can also negatively impact the surrounding tissue microenvironment and the neighboring cells by secreting pro-inflammatory cytokines, ultimately triggering tissue dysfunction and/or unfavorable outcomes. This review focuses on the characteristics of senescence and on the recent advances in the contribution of p53 to cellular senescence. Moreover, we also discuss the p53-mediated regulation of several pathophysiological microenvironments that could be associated with senescence and its development.
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Affiliation(s)
- Mahmut Mijit
- Sbarro Institute for Cancer Research and Molecular Medicine, Center of Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
- Department of Medical Biotechnologies, University of Siena, 67100 Siena, Italy
| | - Valentina Caracciolo
- Sbarro Institute for Cancer Research and Molecular Medicine, Center of Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Antonio Melillo
- Sbarro Institute for Cancer Research and Molecular Medicine, Center of Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Fernanda Amicarelli
- Department of Medical Biotechnologies, University of Siena, 67100 Siena, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center of Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 53100 L’Aquila, Italy
- Correspondence:
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18
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Cencer MM, Greenlee AJ, Moore JS. Quantifying Error Correction through a Rule-Based Model of Strand Escape from an [n]-Rung Ladder. J Am Chem Soc 2019; 142:162-168. [DOI: 10.1021/jacs.9b08958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Morgan M. Cencer
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrew J. Greenlee
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jeffrey S. Moore
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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19
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Huang S, Wang LL, Xue NN, Li C, Guo HH, Ren TK, Zhan Y, Li WB, Zhang J, Chen XG, Han YX, Zhang JL, Jiang JD. Chlorogenic acid effectively treats cancers through induction of cancer cell differentiation. Theranostics 2019; 9:6745-6763. [PMID: 31660066 PMCID: PMC6815948 DOI: 10.7150/thno.34674] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/31/2019] [Indexed: 02/06/2023] Open
Abstract
Rationale: Inducing cancer differentiation is a promising approach to treat cancer. Here, we identified chlorogenic acid (CA), a potential differentiation inducer, for cancer therapy, and elucidated the molecular mechanisms underlying its differentiation-inducing effects on cancer cells. Methods: Cancer cell differentiation was investigated by measuring malignant behavior, including growth rate, invasion/migration, morphological change, maturation, and ATP production. Gene expression was analyzed by microarray analysis, qRT-PCR, and protein measurement, and molecular biology techniques were employed for mechanistic studies. LC/MS analysis was the method of choice for chemical detection. Finally, the anticancer effect of CA was evaluated both in vitro and in vivo. Results: Cancer cells treated with CA showed reduced proliferation rate, migration/invasion ability, and mitochondrial ATP production. Treating cancer cells with CA resulted in elevated SUMO1 expression through acting on its 3'UTR and stabilizing the mRNA. The increased SUMO1 caused c-Myc sumoylation, miR-17 family downregulation, and p21 upregulation leading to G0/G1 arrest and maturation phenotype. CA altered the expression of differentiation-related genes in cancer cells but not in normal cells. It inhibited hepatoma and lung cancer growth in tumor-bearing mice and prevented new tumor development in naïve mice. In glioma cells, CA increased expression of specific differentiation biomarkers Tuj1 and GFAP inducing differentiation and reducing sphere formation. The therapeutic efficacy of CA in glioma cells was comparable to that of temozolomide. CA was detectable both in the blood and brain when administered intraperitoneally in animals. Most importantly, CA was safe even at very high doses. Conclusion: CA might be a safe and effective differentiation-inducer for cancer therapy. “Educating” cancer cells to differentiate, rather than killing them, could be a novel therapeutic strategy for cancer.
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20
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Sizek H, Hamel A, Deritei D, Campbell S, Ravasz Regan E. Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K. PLoS Comput Biol 2019; 15:e1006402. [PMID: 30875364 PMCID: PMC6436762 DOI: 10.1371/journal.pcbi.1006402] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 03/27/2019] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
The PI3K/AKT signaling pathway plays a role in most cellular functions linked to cancer progression, including cell growth, proliferation, cell survival, tissue invasion and angiogenesis. It is generally recognized that hyperactive PI3K/AKT1 are oncogenic due to their boost to cell survival, cell cycle entry and growth-promoting metabolism. That said, the dynamics of PI3K and AKT1 during cell cycle progression are highly nonlinear. In addition to negative feedback that curtails their activity, protein expression of PI3K subunits has been shown to oscillate in dividing cells. The low-PI3K/low-AKT1 phase of these oscillations is required for cytokinesis, indicating that oncogenic PI3K may directly contribute to genome duplication. To explore this, we construct a Boolean model of growth factor signaling that can reproduce PI3K oscillations and link them to cell cycle progression and apoptosis. The resulting modular model reproduces hyperactive PI3K-driven cytokinesis failure and genome duplication and predicts the molecular drivers responsible for these failures by linking hyperactive PI3K to mis-regulation of Polo-like kinase 1 (Plk1) expression late in G2. To do this, our model captures the role of Plk1 in cell cycle progression and accurately reproduces multiple effects of its loss: G2 arrest, mitotic catastrophe, chromosome mis-segregation / aneuploidy due to premature anaphase, and cytokinesis failure leading to genome duplication, depending on the timing of Plk1 inhibition along the cell cycle. Finally, we offer testable predictions on the molecular drivers of PI3K oscillations, the timing of these oscillations with respect to division, and the role of altered Plk1 and FoxO activity in genome-level defects caused by hyperactive PI3K. Our model is an important starting point for the predictive modeling of cell fate decisions that include AKT1-driven senescence, as well as the non-intuitive effects of drugs that interfere with mitosis.
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Affiliation(s)
- Herbert Sizek
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
| | - Andrew Hamel
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
| | - Dávid Deritei
- Department of Physics, Pennsylvania State University, State College, PA, United States of America
- Department of Network and Data Science, Central European University, Budapest, Hungary
| | - Sarah Campbell
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
| | - Erzsébet Ravasz Regan
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
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21
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Guimera AM, Shanley DP, Proctor CJ. Modelling the role of redox-related mechanisms in musculoskeletal ageing. Free Radic Biol Med 2019; 132:11-18. [PMID: 30219703 DOI: 10.1016/j.freeradbiomed.2018.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 09/07/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023]
Abstract
The decline in the musculoskeletal system with age is driven at the cellular level by random molecular damage. Cells possess mechanisms to repair or remove damage and many of the pathways involved in this response are regulated by redox signals. However, with ageing there is an increase in oxidative stress which can lead to chronic inflammation and disruption of redox signalling pathways. The complexity of the processes involved has led to the use of computational modelling to help increase our understanding of the system, test hypotheses and make testable predictions. This paper will give a brief background of the biological systems that have been modelled, an introduction to computational modelling, a review of models that involve redox-related mechanisms that are applicable to musculoskeletal ageing, and finally a discussion of the future potential for modelling in this field.
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Affiliation(s)
- Alvaro Martinez Guimera
- Institute for Cell and Molecular Biosciences, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK
| | - Daryl P Shanley
- Institute for Cell and Molecular Biosciences, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK
| | - Carole J Proctor
- Institute of Cellular Medicine, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK.
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22
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Mechanistic Modelling of Radiation Responses. Cancers (Basel) 2019; 11:cancers11020205. [PMID: 30744204 PMCID: PMC6406300 DOI: 10.3390/cancers11020205] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 12/30/2022] Open
Abstract
Radiobiological modelling has been a key part of radiation biology and therapy for many decades, and many aspects of clinical practice are guided by tools such as the linear-quadratic model. However, most of the models in regular clinical use are abstract and empirical, and do not provide significant scope for mechanistic interpretation or making predictions in novel cell lines or therapies. In this review, we will discuss the key areas of ongoing mechanistic research in radiation biology, including physical, chemical, and biological steps, and review a range of mechanistic modelling approaches which are being applied in each area, highlighting the possible opportunities and challenges presented by these techniques.
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23
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Klec C, Gutschner T, Panzitt K, Pichler M. Involvement of long non-coding RNA HULC (highly up-regulated in liver cancer) in pathogenesis and implications for therapeutic intervention. Expert Opin Ther Targets 2019; 23:177-186. [PMID: 30678498 DOI: 10.1080/14728222.2019.1570499] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION HULC (highly upregulated in liver cancer) is a long non-coding RNA (lncRNA) which is, as its name suggests, highly upregulated in hepatocellular carcinoma and in several other cancers. Increased HULC expression levels are strongly associated with clinicopathologic features such as tumor stages and overall survival and is a driver of tumor proliferation, migration, and invasion. Areas covered: This review addresses the discovery of HULC and discusses the consequences of HULC deregulation in cancer, the underlying molecular mechanisms and the potential of HULC as a biomarker and therapeutic target. Expert opinion: HULC is a promising candidate as a therapeutic target in cancer; however, more studies are necessary to further elucidate the underlying molecular mechanism(s), especially in cancer types other than hepatocellular carcinomas. Future studies that focus on an optimized HULC-targeting approach are necessary to clarify the best strategy to target this lncRNA in vivo and in patients.
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Affiliation(s)
- Christiane Klec
- a Division of Oncology, Department of Internal Medicine , Medical University of Graz (MUG) , Graz , Austria.,b Research Unit for Non-coding RNAs and Genome Editing , Medical University of Graz (MUG) , Graz , Austria
| | - Tony Gutschner
- c Faculty of Medicine , Martin-Luther-University Halle-Wittenberg , Halle , Germany
| | - Katrin Panzitt
- d Department of Hepatology and Gastroenterology , Medical University of Graz (MUG) , Graz , Austria
| | - Martin Pichler
- a Division of Oncology, Department of Internal Medicine , Medical University of Graz (MUG) , Graz , Austria.,b Research Unit for Non-coding RNAs and Genome Editing , Medical University of Graz (MUG) , Graz , Austria.,e Department of Experimental Therapeutics , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
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24
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Zheng H, Huang Q, Huang S, Yang X, Zhu T, Wang W, Wang H, He S, Ji L, Wang Y, Qi X, Liu Z, Lu L. Senescence Inducer Shikonin ROS-Dependently Suppressed Lung Cancer Progression. Front Pharmacol 2018; 9:519. [PMID: 29875661 PMCID: PMC5974149 DOI: 10.3389/fphar.2018.00519] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/30/2018] [Indexed: 01/03/2023] Open
Abstract
Lung adenocarcinoma (LAC), predominant subclassfication of lung cancer, leads high incidence and mortality annually worldwide. During the premalignant transition from lung adenomas to LAC, cellular senescence is regard as a critical physiological barrier against tumor progression. Nevertheless, the role of senescence in tumorigenesis is controversial and few senescence inducers are extensively determined. In this study, we used two classical cell lines A549 and H1299 and two NSCLC xenograft models on Balb/c-nude mice to reveal the pro-senescence effects of shikonin and the corresponding underlying mechanism in LAC. Shikonin, a pure compound isolated from the herbal medicine Lithospermum erythrorhizon, remarkably stimulated cellular senescence including increased SAHF formation, enlarged cellular morphology, and induced SA-β-Gal positive staining. Further mechanism study revealed that the pro-senescence effect of shikonin was dependent on the increased intercellular ROS generation, which subsequently triggered DNA damage-p53/p21waf axis without activating oncogenes such as Ras and MEK-1. Meanwhile, Kdm2b, an H3K36me2-specific demethylase effectively suppressed ROS generation, was also notably suppressed by shikonin treatment. Moreover, shikonin at 10 mg/kg significantly inhibited tumor weights by 55.84% and 50.98% in A549 and H1299 xenograft model, respectively (P < 0.05) through activating cellular senescence. Our study suggested that shikonin, a ROS-dependent senescence inducer, could serve as a promising agent for further lung cancer treatment.
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Affiliation(s)
- Hongming Zheng
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiuju Huang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Suchao Huang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xia Yang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ting Zhu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wensheng Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haojia Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shugui He
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liyan Ji
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoxiao Qi
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau
| | - Linlin Lu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau
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25
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Systems modelling ageing: from single senescent cells to simple multi-cellular models. Essays Biochem 2017; 61:369-377. [PMID: 28698310 PMCID: PMC5869859 DOI: 10.1042/ebc20160087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/25/2017] [Accepted: 05/25/2017] [Indexed: 01/10/2023]
Abstract
Systems modelling has been successfully used to investigate several key molecular mechanisms of ageing. Modelling frameworks to allow integration of models and methods to enhance confidence in models are now well established. In this article, we discuss these issues and work through the process of building an integrated model for cellular senescence as a single cell and in a simple tissue context.
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26
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Jiang X, Liu W. Long Noncoding RNA Highly Upregulated in Liver Cancer Activates p53-p21 Pathway and Promotes Nasopharyngeal Carcinoma Cell Growth. DNA Cell Biol 2017; 36:596-602. [PMID: 28445086 DOI: 10.1089/dna.2017.3686] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Xue Jiang
- Department of Otolaryngology, Cangzhou Central Hospital, Hebei Medical University, Cangzhou, Hebei, China
| | - Weiwei Liu
- Department of Otolaryngology, Cangzhou Central Hospital, Hebei Medical University, Cangzhou, Hebei, China
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27
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Zhao H, Song L, Huang W, Liu J, Yuan D, Wang Y, Zhang C. Total flavonoids of Epimedium
reduce ageing-related oxidative DNA damage in testis of rats via p53-dependent pathway. Andrologia 2017; 49. [PMID: 28370226 DOI: 10.1111/and.12756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 12/11/2022] Open
Affiliation(s)
- H. Zhao
- Medical College of China Three Gorges University; Yichang China
| | - L. Song
- Medical College of China Three Gorges University; Yichang China
| | - W. Huang
- Medical College of China Three Gorges University; Yichang China
| | - J. Liu
- Medical College of China Three Gorges University; Yichang China
| | - D. Yuan
- Renhe Hospital of China Three Gorges University; Yichang China
| | - Y. Wang
- LONGHUA Hospital Shanghai University of Traditional Chinese Medicine; Shanghai China
| | - C. Zhang
- Medical College of China Three Gorges University; Yichang China
- LONGHUA Hospital Shanghai University of Traditional Chinese Medicine; Shanghai China
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28
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Mc Auley MT, Guimera AM, Hodgson D, Mcdonald N, Mooney KM, Morgan AE, Proctor CJ. Modelling the molecular mechanisms of aging. Biosci Rep 2017; 37:BSR20160177. [PMID: 28096317 PMCID: PMC5322748 DOI: 10.1042/bsr20160177] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/15/2016] [Accepted: 01/16/2017] [Indexed: 01/09/2023] Open
Abstract
The aging process is driven at the cellular level by random molecular damage that slowly accumulates with age. Although cells possess mechanisms to repair or remove damage, they are not 100% efficient and their efficiency declines with age. There are many molecular mechanisms involved and exogenous factors such as stress also contribute to the aging process. The complexity of the aging process has stimulated the use of computational modelling in order to increase our understanding of the system, test hypotheses and make testable predictions. As many different mechanisms are involved, a wide range of models have been developed. This paper gives an overview of the types of models that have been developed, the range of tools used, modelling standards and discusses many specific examples of models that have been grouped according to the main mechanisms that they address. We conclude by discussing the opportunities and challenges for future modelling in this field.
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Affiliation(s)
- Mark T Mc Auley
- Faculty of Science and Engineering, University of Chester, Chester, U.K
| | - Alvaro Martinez Guimera
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, U.K
| | - David Hodgson
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - Neil Mcdonald
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, U.K
| | | | - Amy E Morgan
- Faculty of Science and Engineering, University of Chester, Chester, U.K
| | - Carole J Proctor
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K.
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
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29
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Kuijper IA, Yang H, Van De Water B, Beltman JB. Unraveling cellular pathways contributing to drug-induced liver injury by dynamical modeling. Expert Opin Drug Metab Toxicol 2016; 13:5-17. [PMID: 27609146 DOI: 10.1080/17425255.2017.1234607] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Drug-induced liver injury (DILI) is a significant threat to human health and a major problem in drug development. It is hard to predict due to its idiosyncratic nature and which does not show up in animal trials. Hepatic adaptive stress response pathway activation is generally observed in drug-induced liver injury. Dynamical pathway modeling has the potential to foresee adverse effects of drugs before they go in trial. Ordinary differential equation modeling can offer mechanistic insight, and allows us to study the dynamical behavior of stress pathways involved in DILI. Areas covered: This review provides an overview on the progress of the dynamical modeling of stress and death pathways pertinent to DILI, i.e. pathways relevant for oxidative stress, inflammatory stress, DNA damage, unfolded proteins, heat shock and apoptosis. We also discuss the required steps for applying such modeling to the liver. Expert opinion: Despite the strong progress made since the turn of the century, models of stress pathways have only rarely been specifically applied to describe pathway dynamics for DILI. We argue that with minor changes, in some cases only to parameter values, many of these models can be repurposed for application in DILI research. Combining both dynamical models with in vitro testing might offer novel screening methods for the harmful side-effects of drugs.
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Affiliation(s)
- Isoude A Kuijper
- a Division of Toxicology, Leiden Academic Centre for Drug Research , Leiden University , Leiden , The Netherlands
| | - Huan Yang
- a Division of Toxicology, Leiden Academic Centre for Drug Research , Leiden University , Leiden , The Netherlands
| | - Bob Van De Water
- a Division of Toxicology, Leiden Academic Centre for Drug Research , Leiden University , Leiden , The Netherlands
| | - Joost B Beltman
- a Division of Toxicology, Leiden Academic Centre for Drug Research , Leiden University , Leiden , The Netherlands
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30
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van Overbeek M, Capurso D, Carter MM, Thompson MS, Frias E, Russ C, Reece-Hoyes JS, Nye C, Gradia S, Vidal B, Zheng J, Hoffman GR, Fuller CK, May AP. DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks. Mol Cell 2016; 63:633-646. [PMID: 27499295 DOI: 10.1016/j.molcel.2016.06.037] [Citation(s) in RCA: 293] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/11/2016] [Accepted: 06/27/2016] [Indexed: 12/16/2022]
Abstract
The repair outcomes at site-specific DNA double-strand breaks (DSBs) generated by the RNA-guided DNA endonuclease Cas9 determine how gene function is altered. Despite the widespread adoption of CRISPR-Cas9 technology to induce DSBs for genome engineering, the resulting repair products have not been examined in depth. Here, the DNA repair profiles of 223 sites in the human genome demonstrate that the pattern of DNA repair following Cas9 cutting at each site is nonrandom and consistent across experimental replicates, cell lines, and reagent delivery methods. Furthermore, the repair outcomes are determined by the protospacer sequence rather than genomic context, indicating that DNA repair profiling in cell lines can be used to anticipate repair outcomes in primary cells. Chemical inhibition of DNA-PK enabled dissection of the DNA repair profiles into contributions from c-NHEJ and MMEJ. Finally, this work elucidates a strategy for using "error-prone" DNA-repair machinery to generate precise edits.
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Affiliation(s)
| | | | | | | | - Elizabeth Frias
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Carsten Russ
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John S Reece-Hoyes
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Scott Gradia
- Caribou Biosciences, Inc., Berkeley, CA 94710, USA
| | | | | | - Gregory R Hoffman
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Andrew P May
- Caribou Biosciences, Inc., Berkeley, CA 94710, USA.
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31
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Jonak K, Kurpas M, Szoltysek K, Janus P, Abramowicz A, Puszynski K. A novel mathematical model of ATM/p53/NF- κB pathways points to the importance of the DDR switch-off mechanisms. BMC SYSTEMS BIOLOGY 2016; 10:75. [PMID: 27526774 PMCID: PMC4986247 DOI: 10.1186/s12918-016-0293-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 06/27/2016] [Indexed: 12/20/2022]
Abstract
Background Ataxia telangiectasia mutated (ATM) is a detector of double-strand breaks (DSBs) and a crucial component of the DNA damage response (DDR) along with p53 and NF- κB transcription factors and Wip1 phosphatase. Despite the recent advances in studying the DDR, the mechanisms of cell fate determination after DNA damage induction is still poorly understood. Results To investigate the importance of various DDR elements with particular emphasis on Wip1, we developed a novel mathematical model of ATM/p53/NF- κB pathways. Our results from in silico and in vitro experiments performed on U2-OS cells with Wip1 silenced to 25 % (Wip1-RNAi) revealed a strong dependence of cellular response to DNA damages on this phosphatase. Notably, Wip1-RNAi cells exhibited lower resistance to ionizing radiation (IR) resulting in smaller clonogenicity and higher apoptotic fraction. Conclusions In this article, we demonstrated that Wip1 plays a role as a gatekeeper of apoptosis and influences the pro-survival behaviour of cells – the level of Wip1 increases to block the apoptotic decision when DNA repair is successful. Moreover, we were able to verify the dynamics of proteins and transcripts, apoptotic fractions and cells viability obtained from stochastic simulations using in vitro approaches. Taken together, we demonstrated that the model can be successfully used in prediction of cellular behaviour after exposure to IR. Thus, our studies may provide further insights into key elements involved in the underlying mechanisms of the DDR. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0293-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katarzyna Jonak
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka, Gliwice, 16, 44-100, Poland
| | - Monika Kurpas
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka, Gliwice, 16, 44-100, Poland
| | - Katarzyna Szoltysek
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Wybrzeze Armii Krajowej, Gliwice, 15, 44-400, Poland
| | - Patryk Janus
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Wybrzeze Armii Krajowej, Gliwice, 15, 44-400, Poland
| | - Agata Abramowicz
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Wybrzeze Armii Krajowej, Gliwice, 15, 44-400, Poland
| | - Krzysztof Puszynski
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka, Gliwice, 16, 44-100, Poland.
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