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Ataş PK. A novel Harris Hawks Optimization-based clustering method for elucidating genetic associations in osteoarthritis and Diverse Cancer Types. Comput Biol Med 2025; 193:110343. [PMID: 40412087 DOI: 10.1016/j.compbiomed.2025.110343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/17/2025] [Accepted: 05/03/2025] [Indexed: 05/27/2025]
Abstract
Considering the high incidence of osteoarthritis (OA), especially of the knee and hip, this study explores the possible genetic associations between OA and cancer types, including cancers of the bladder, kidney, breast, and prostate. The objective of our study is to decipher the complex genetic connections among these common disorders, emphasizing potential correlations and underlying biological processes. However, the genetic connections between these diseases remain largely unexplored. It fills a vacuum in the literature by using a new clustering approach based on Harris Hawks Optimization (HHO-C), which is a first for applying machine learning methods to this particular set of genetic data. To address this gap, we introduce HHO-C, a novel machine learning-based clustering approach, for the first time in this specific genetic dataset. The work accomplishes three noteworthy firsts: firstly, it is the first to apply machine learning to the study of the genetic interactions between OA and these cancers. Second, it creates a flexible genetic dataset that will be very helpful for further studies in this field. Finally, it presents the novel HHO-C approach, showcasing how well it manages intricate genetic data and providing fresh perspectives on genetic data analysis. It is anticipated that the results of this investigation will clarify the genetic relationships between OA and these malignancies, which could result in novel understandings of medical genetics and the creation of fresh approaches to diagnosis and treatment.
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Affiliation(s)
- Pınar Karadayı Ataş
- Department of Software Engineering, Faculty of Engineering, Istanbul Arel University, Istanbul, Turkey.
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Zhang ZB, Ip SP, Cho WCS, Ng ACF, Hu Z, Huang YF, Luo DD, Xian YF, Lin ZX. Herb-drug interactions between androgenic Chinese herbal medicines and androgen receptor antagonist on tumor growth: Studies on two xenograft prostate cancer animal models. Phytother Res 2021; 35:2758-2772. [PMID: 33440458 DOI: 10.1002/ptr.7020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 01/25/2023]
Abstract
Our previous study revealed that Epimedii Folium (EF) and Codonopsis Radix (CNR) significantly promoted tumor growth on a subcutaneous mouse model of prostate cancer (PCa) via enhancing the mRNA and protein expressions of androgen receptor (AR), while Astragali Radix (AGR) inhibited tumor growth via suppressing the protein expression of AR. In the present study, we aimed to investigate the potential interactions between EF, CNR or AGR and AR antagonist (abiraterone acetate [ABI]) on the tumor growth using subcutaneous and orthotopic PCa mouse models. EF, CNR, AGR and ABI were intragastrically given to mice once every 2 days for 4 weeks. The pharmacokinetics of ABI were evaluated in the plasma of rats when combined with EF, CNR, or AGR. Our results demonstrated that EF or CNR could weaken the anti-tumor effects of ABI via increasing the AR expression involving activation of the PI3K/AKT and Rb/E2F pathways and decreasing the bioavailability of ABI, while AGR could enhance the anti-tumor effects of ABI through suppressing the AR expression via inhibiting the activations of PI3K/AKT and Rb/E2F pathways and increasing the bioavailability of ABI. These findings imply that cautions should be exercised when prescribing EF and CNR for PCa patients.
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Affiliation(s)
- Zhen-Biao Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Siu-Po Ip
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
- Brain Research Center, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | | | - Anthony Chi Fai Ng
- SH Ho Urology Centre, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Zhen Hu
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Yan-Feng Huang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Dan-Dan Luo
- Department of Pharmacy, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, PR China
| | - Yan-Fang Xian
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
- Brain Research Center, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Zhi-Xiu Lin
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
- Brain Research Center, The Chinese University of Hong Kong, Hong Kong SAR, PR China
- Hong Kong Institute of Integrative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
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Deregulated PTEN/PI3K/AKT/mTOR signaling in prostate cancer: Still a potential druggable target? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118731. [PMID: 32360668 DOI: 10.1016/j.bbamcr.2020.118731] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 01/13/2023]
Abstract
Although the prognosis of patients with localized prostate cancer is good after surgery, with a favorable response to androgen deprivation therapy, about one third of them invariably relapse, and progress to castration-resistant prostate cancer. Overall, prostate cancer therapies remain scarcely effective, thus it is mandatory to devise alternative treatments enhancing the efficacy of surgical castration and hormone administration. Dysregulation of the phosphoinositide 3-kinase pathway has attracted growing attention in prostate cancer due to the highly frequent association of epigenetic and post-translational modifications as well as to genetic alterations of both phosphoinositide 3-kinase and PTEN to onset and/or progression of this malignancy, and to resistance to canonical androgen-deprivation therapy. Here we provide a summary of the biological functions of the major players of this cascade and their deregulation in prostate cancer, summarizing the results of preclinical and clinical studies with PI3K signaling inhibitors and the reasons of failure independent from genomic changes.
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Tang X, Li A, Xie C, Zhang Y, Liu X, Xie Y, Wu B, Zhou S, Huang X, Ma Y, Cao W, Xu R, Shen J, Huo Z, Cai S, Liang Y, Ma D. The PI3K/mTOR dual inhibitor BEZ235 nanoparticles improve radiosensitization of hepatoma cells through apoptosis and regulation DNA repair pathway. NANOSCALE RESEARCH LETTERS 2020; 15:63. [PMID: 32219609 PMCID: PMC7099126 DOI: 10.1186/s11671-020-3289-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/27/2020] [Indexed: 05/05/2023]
Abstract
Polymer materials encapsulating drugs have broad prospects for drug delivery. We evaluated the effectiveness of polyethylene glycol-poly (lactic-co-glycolic acid) (PLGA-PEG) encapsulation and release characteristics of PI3K/mTOR inhibitor NVP-BEZ235 (BEZ235). We proposed a strategy for targeting radiosensitization of liver cancer cells. The biocompatibility, cell interaction, and internalization of Glypican-3 (GPC3) antibody-modified, BEZ235-loaded PLGA-PEG nanoparticles (NP-BEZ235-Ab) in hepatoma cells in vitro were studied. Also, the cell killing effect of NP-BEZ235-Ab combined with γ-ray cell was evaluated. We used confocal microscopy to monitor nanoparticle-cell interactions and cellular uptake, conducted focus-formation experiments to analyze the synergistic biological effects of NP-BEZ235-Ab and priming, and studied synergy in liver cancer cells using molecular biological methods such as western blotting. We found that PLGA-PEG has good loading efficiency for BEZ235 and high selectivity to GPC3-positive HepG2 liver cancer cells, thus documenting that NP-BEZ235-Ab acts as a small-molecule drug delivery nanocarrier. At the nominal concentration, the NP-BEZ235-Ab nanoformulation synergistically kills liver cancer cells with significantly higher efficiency than does the free drug. Thus, NP-BEZ235-Ab is a potential radiosensitizer.
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Affiliation(s)
- Xiaolong Tang
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Amin Li
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Chunmei Xie
- Blood Transfusion Department, Guangzhou 8th People's Hospital, Guangzhou Medical University, Guangzhou, 510632, People's Republic of China
| | - Yinci Zhang
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Xueke Liu
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Yinghai Xie
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Binquan Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China
| | - Shuping Zhou
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Xudong Huang
- Department of Interventional, Affiliated Oriental Hospital, Anhui University of Technology, Huainan, 232003, People's Republic of China
| | - Yongfang Ma
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Weiya Cao
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Ruyue Xu
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Jing Shen
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Zhen Huo
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Shuyu Cai
- Huainan First People's Hospital and First Affiliated Hospital of Medical School, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Yong Liang
- Huai'an Hospital Affiliated of Xuzhou Medical College and Huai'an Second Hospital, Huai'an, 223002, People's Republic of China.
| | - Dong Ma
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, People's Republic of China.
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Baenziger M, Pachinger W, Stauffer F, Zaugg W. Development of a Robust Synthesis of Dactolisib on a Commercial Manufacturing Scale. Org Process Res Dev 2019. [DOI: 10.1021/acs.oprd.9b00221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Markus Baenziger
- Novartis Pharmaceuticals, GDD/TRD/Chemical & Analytical Development (CHAD), 4056 Basel, Switzerland
| | - Werner Pachinger
- Novartis Pharmaceuticals, GDD/TRD/Chemical & Analytical Development (CHAD), 4056 Basel, Switzerland
| | - Frédéric Stauffer
- Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Werner Zaugg
- Novartis Pharmaceuticals, GDD/TRD/Chemical & Analytical Development (CHAD), 4056 Basel, Switzerland
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Scarano WR, Bedrat A, Alonso-Costa LG, Aquino AM, Fantinatti B, Justulin LA, Barbisan LF, Freire PP, Flaws JA, Bernardo L. Exposure to an environmentally relevant phthalate mixture during prostate development induces microRNA upregulation and transcriptome modulation in rats. Toxicol Sci 2019; 171:84-97. [PMID: 31199487 PMCID: PMC6736208 DOI: 10.1093/toxsci/kfz141] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/14/2019] [Accepted: 06/02/2019] [Indexed: 12/14/2022] Open
Abstract
Environmental exposure to phthalates during intrauterine development might increase susceptibility to neoplasms in reproductive organs such as the prostate. Although studies have suggested an increase in prostatic lesions in adult animals submitted to perinatal exposure to phthalates, the molecular pathways underlying these alterations remain unclear. Genome-wide levels of mRNAs and miRNAs were monitored with RNA-seq to determine if perinatal exposure to a phthalate mixture in pregnant rats is capable of modifying gene expression expression during prostate development of the filial generation. The mixture contains diethyl-phthalate, di-(2-ethylhexyl)-phthalate, dibutyl-phthalate, di-isononyl-phthalate, di-isobutyl-phthalate, and benzylbutyl-phthalate. Pregnant females were divided into 4 groups and orally dosed daily from GD10 to PND21 with corn oil (Control:C) or the phthalate mixture at three doses (20 μg/kg/d:T1; 200 μg/kg/d:T2; 200 mg/kg/d:T3). The phthalate mixture decreased anogenital distance, prostate weight and decreased testosterone level at the lowest exposure dose at PND22. The mixture also increased inflammatory foci and focal hyperplasia incidence at PND120. miR-184 was upregulated in all treated groups in relation to control and miR-141-3p was only upregulated at the lowest dose. In addition, 120 genes were deregulated at the lowest dose with several of these genes related to developmental, differentiation and oncogenesis. The data indicate that phthalate exposure at lower doses can cause greater gene expression modulation as well as other downstream phenotypes than exposure at higher doses. A significant fraction of the downregulated genes were predicted to be targets of miR-141-3p and miR-184, both of which were induced at the lower exposure doses.
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Affiliation(s)
- Wellerson R Scarano
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil.,Harvard T. H. Chan School of Public Health, Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Boston, MA, USA
| | - Amina Bedrat
- Harvard T. H. Chan School of Public Health, Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Boston, MA, USA
| | - Luiz G Alonso-Costa
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Ariana M Aquino
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Bruno Fantinatti
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Luis A Justulin
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Luis F Barbisan
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Paula P Freire
- São Paulo State University (UNESP), Institute of Biosciences, Department of Morphology, Botucatu, SP, Brazil
| | - Jodi A Flaws
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL
| | - Lemos Bernardo
- Harvard T. H. Chan School of Public Health, Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Boston, MA, USA
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Bloom Syndrome Protein Activates AKT and PRAS40 in Prostate Cancer Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:3685817. [PMID: 31210839 PMCID: PMC6532288 DOI: 10.1155/2019/3685817] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/07/2019] [Accepted: 03/25/2019] [Indexed: 12/16/2022]
Abstract
Purpose Prostate cancer (PC) is a common malignant tumor and a leading cause of cancer-related death in men worldwide. In order to design new therapeutic interventions for PC, an understanding of the molecular events underlying PC tumorigenesis is required. Bloom syndrome protein (BLM) is a RecQ-like helicase, which helps maintain genetic stability. BLM dysfunction has been implicated in tumor development, most recently during PC tumorigenesis. However, the molecular basis for BLM-induced PC progression remains poorly characterized. In this study, we investigated whether BLM modulates the phosphorylation of an array of prooncogenic signaling pathways to promote PC progression. Methods We analyzed differentially expressed proteins (DEPs) using iTRAQ technology. Site-directed knockout of BLM in PC-3 prostate cancer cells was performed using CRISPR/Cas9-mediated homologous recombination gene editing to confirm the effects of BLM on DEPs. PathScan® Antibody Array Kits were used to analyze the phosphorylation of nodal proteins in PC tissue. Immunohistochemistry and automated western blot (WES) analyses were used to validate these findings. Results We found that silencing BLM in PC-3 cells significantly reduced their proliferative capacity. In addition, BLM downregulation significantly reduced levels of phosphorylated protein kinase B (AKT (Ser473)) and proline-rich AKT substrate of 40 kDa (PRAS40 (Thr246)), and this was accompanied by enhanced ROS (reactive oxygen species) levels. In addition, we found that AKT and PRAS40 inhibition reduced BLM, increased ROS levels, and induced PC cell apoptosis. Conclusions We demonstrated that BLM activates AKT and PRAS40 to promote PC cell proliferation and survival. We further propose that ROS act in concert with BLM to facilitate PC oncogenesis, potentially via further enhancing AKT signaling and downregulating PTEN expression. Importantly, inhibiting the BLM-AKT-PRAS40 axis induced PC cell apoptosis. Thus, we highlight new avenues for novel anti-PC treatments.
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