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Cai H, Chen L, Yang S, Jiang R, Guo Y, He M, Luo Y, Hong G, Li H, Song K. Personalized differential expression analysis in triple-negative breast cancer. Brief Funct Genomics 2024; 23:495-506. [PMID: 38197537 DOI: 10.1093/bfgp/elad057] [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: 01/30/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024] Open
Abstract
Identification of individual-level differentially expressed genes (DEGs) is a pre-step for the analysis of disease-specific biological mechanisms and precision medicine. Previous algorithms cannot balance accuracy and sufficient statistical power. Herein, RankCompV2, designed for identifying population-level DEGs based on relative expression orderings, was adjusted to identify individual-level DEGs. Furthermore, an optimized version of individual-level RankCompV2, named as RankCompV2.1, was designed based on the assumption that the rank positions of genes and relative rank differences of gene pairs would influence the identification of individual-level DEGs. In comparison to other individualized analysis algorithms, RankCompV2.1 performed better on statistical power, computational efficiency, and acquired coequal accuracy in both simulation and real paired cancer-normal data from ten cancer types. Besides, single sample GSEA and Gene Set Variation Analysis analysis showed that pathways enriched with up-regulated and down-regulated genes presented higher and lower enrichment scores, respectively. Furthermore, we identified 16 genes that were universally deregulated in 966 triple-negative breast cancer (TNBC) samples and interacted with Food and Drug Administration (FDA)-approved drugs or antineoplastic agents, indicating notable therapeutic targets for TNBC. In addition, we also identified genes with highly variable deregulation status and used these genes to cluster TNBC samples into three subgroups with different prognoses. The subgroup with the poorest outcome was characterized by down-regulated immune-regulated pathways, signal transduction pathways, and apoptosis-related pathways. Protein-protein interaction network analysis revealed that OAS family genes may be promising drug targets to activate tumor immunity in this subgroup. In conclusion, RankCompV2.1 is capable of identifying individual-level DEGs with high accuracy and statistical power, analyzing mechanisms of carcinogenesis and exploring therapeutic strategy.
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Affiliation(s)
- Hao Cai
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Liangbo Chen
- School of Information Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Shuxin Yang
- School of Information Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Ronghong Jiang
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - You Guo
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Ming He
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Yun Luo
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Guini Hong
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Hongdong Li
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Kai Song
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
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Balicki M, Śmiechowski M. Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations. Molecules 2024; 29:2435. [PMID: 38893311 PMCID: PMC11173572 DOI: 10.3390/molecules29112435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
N-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work is the comprehensive exploration of HU hydration. The topic is studied using ab initio molecular dynamic (AIMD) simulations that apply a first principles representation of the electron density of the system. This allows for the calculation of infrared spectra, which may be decomposed spatially to better capture the spectral signatures of solute-solvent interactions. The studied molecule is found to be strongly hydrated and tightly bound to the first shell water molecules. The analysis of the distance-dependent spectra of HU shows that the E and Z conformers spectrally affect, on average, 3.4 and 2.5 of the closest H2O molecules, respectively, in spheres of radii of 3.7 Å and 3.5 Å, respectively. The distance-dependent spectra corresponding to these cutoff radii show increased absorbance in the red-shifted part of the water OH stretching vibration band, indicating local enhancement of the solvent's hydrogen bond network. The radially resolved IR spectra also demonstrate that HU effortlessly incorporates into the hydrogen bond network of water and has an enhancing effect on this network. Metadynamics simulations based on AIMD methodology provide a picture of the conformational equilibria of HU in solution. Contrary to previous investigations of an isolated HU molecule in the gas phase, the Z conformer of HU is found here to be more stable by 17.4 kJ·mol-1 than the E conformer, pointing at the crucial role that hydration plays in determining the conformational stability of solutes. The potential energy surface for the OH group rotation in HU indicates that there is no intramolecular hydrogen bond in Z-HU in water, in stark contrast to the isolated solute in the gas phase. Instead, the preferred orientation of the hydroxyl group is perpendicular to the molecular plane of the solute. In view of the known chaotropic effect of urea and its N-alkyl-substituted derivatives, N-hydroxyurea emerges as a unique urea derivative that exhibits a kosmotropic ordering of nearby water. This property may be of crucial importance for its binding to the catalytic site of ribonucleotide reductase with a concomitant displacement of a water molecule.
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Affiliation(s)
| | - Maciej Śmiechowski
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland;
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Witt BL, Tollefsbol TO. Molecular, Cellular, and Technical Aspects of Breast Cancer Cell Lines as a Foundational Tool in Cancer Research. Life (Basel) 2023; 13:2311. [PMID: 38137912 PMCID: PMC10744609 DOI: 10.3390/life13122311] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
Breast cancer comprises about 30% of all new female cancers each year and is the most common malignant cancer in women in the United States. Breast cancer cell lines have been harnessed for many years as a foundation for in vitro analytic studies to understand the use of cancer prevention and therapy. There has yet to be a compilation of works to analyze the pitfalls, novel discoveries, and essential techniques for breast cancer cell line studies in a scientific context. In this article, we review the history of breast cancer cell lines and their origins, as well as analyze the molecular pathways that pharmaceutical drugs apply to breast cancer cell lines in vitro and in vivo. Controversies regarding the origins of certain breast cancer cell lines, the benefits of utilizing Patient-Derived Xenograft (PDX) versus Cell-Derived Xenograft (CDX), and 2D versus 3D cell culturing techniques will be analyzed. Novel outcomes from epigenetic discovery with dietary compound usage are also discussed. This review is intended to create a foundational tool that will aid investigators when choosing a breast cancer cell line to use in multiple expanding areas such as epigenetic discovery, xenograft experimentation, and cancer prevention, among other areas.
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Affiliation(s)
- Brittany L. Witt
- Department of Biology, University of Alabama at Birmingham, 902 14th Street, Birmingham, AL 35228, USA;
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 902 14th Street, Birmingham, AL 35228, USA;
- Integrative Center for Aging Research, University of Alabama at Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA
- Nutrition Obesity Research Center, University of Alabama at Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA
- Comprehensive Diabetes Center, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
- University Wide Microbiome Center, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA
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Rajendra PKM, Nidamanuri BSS, Swaroop AK, Krishnamurali JS, Balan AP, Selvaraj J, Raman R, Shivakumar HN, Reddy MV, Jawahar N. Fabrication and in vitro evaluation of silk fibroin-folic acid decorated paclitaxel and hydroxyurea nanostructured lipid carriers for targeting ovarian cancer cells: A double sword approach. J Drug Deliv Sci Technol 2023. [DOI: 10.1016/j.jddst.2023.104270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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5
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Development of Liposomal Formulation for Controlled Delivery of Valacyclovir: an In Vitro Study. J Pharm Innov 2023. [DOI: 10.1007/s12247-022-09706-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Khanuja HK, Dureja H. Recent Patents and Potential Applications of Homogenisation Techniques in Drug Delivery Systems. RECENT PATENTS ON NANOTECHNOLOGY 2023; 17:33-50. [PMID: 34825646 DOI: 10.2174/1872210515666210719120203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/08/2021] [Accepted: 04/08/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The term homogenise means "to force or provide coalesce". Homogenisation is a process to attain homogenous particle size. The objective of the homogenisation process is to use fluid force to split the fragments or tiny particles contained in the fluids into very small dimensions and form a sustainable dispersion suitable for further production. METHODS The databases were collected through Scopus, google patent, science web, google scholar, PubMed on the concept of homogenisation. The data obtained were systematically investigated. RESULTS The present study focus on the use of the homogenisation in drug delivery system. The aim of homogenisation process is to achieve the particle size in micro-and nano- range as it affects the different parameters in the formulation and biopharmaceutical profile of the drug. The particle size reduction plays a key role in influencing drug dissolution and absorption. The reduced particle size enhances the stability and therapeutic efficacy of the drug. Homogenization technology ensures to achieve effective, clinically efficient and targeted drug delivery with the minimal side effect. CONCLUSION Homogenization technology has been shown to be an efficient and easy method of size reduction to increase solubility and bioavailability, stability of drug carriers. This article gives an overview of the process attributes affecting the homogenization process, the patenting of homogeniser types, design, the geometry of valves and nozzles and its role in drug delivery.
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Affiliation(s)
- Harpreet Kaur Khanuja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak-124001, India
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak-124001, India
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Rethi L, Mutalik C, Anurogo D, Lu LS, Chu HY, Yougbaré S, Kuo TR, Cheng TM, Chen FL. Lipid-Based Nanomaterials for Drug Delivery Systems in Breast Cancer Therapy. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:2948. [PMID: 36079985 PMCID: PMC9458017 DOI: 10.3390/nano12172948] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/18/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Globally, breast cancer is one of the most prevalent diseases, inducing critical intimidation to human health. Lipid-based nanomaterials have been successfully demonstrated as drug carriers for breast cancer treatment. To date, the development of a better drug delivery system based on lipid nanomaterials is still urgent to make the treatment and diagnosis easily accessible to breast cancer patients. In a drug delivery system, lipid nanomaterials have revealed distinctive features, including high biocompatibility and efficient drug delivery. Specifically, a targeted drug delivery system based on lipid nanomaterials has inherited the advantage of optimum dosage and low side effects. In this review, insights on currently used potential lipid-based nanomaterials are collected and introduced. The review sheds light on conjugation, targeting, diagnosis, treatment, and clinical significance of lipid-based nanomaterials to treat breast cancer. Furthermore, a brighter side of lipid-based nanomaterials as future potential drug delivery systems for breast cancer therapy is discussed.
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Affiliation(s)
- Lekshmi Rethi
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan
| | - Chinmaya Mutalik
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan
| | - Dito Anurogo
- International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan or
- Faculty of Medicine and Health Sciences, Universitas Muhammadiyah Makassar, Makassar City 90221, South Sulawesi, Indonesia
| | - Long-Sheng Lu
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan
- Department of Radiation Oncology, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Hsiu-Yi Chu
- Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Sibidou Yougbaré
- Institut de Recherche en Sciences de la Santé/Direction Régionale du Centre Ouest (IRSS/DRCO), Nanoro BP 218, 11, Burkina Faso
| | - Tsung-Rong Kuo
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Nanomedicine and Medical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan
| | - Tsai-Mu Cheng
- Graduate Institute of Translational Medicine, College of Medicine and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Taipei Heart Institute, Taipei Medical University, Taipei 11031, Taiwan
| | - Fu-Lun Chen
- Department of Internal Medicine, Division of Infectious Diseases, Taipei Municipal Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
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Hydroxyurea-loaded Fe 3O 4/SiO 2/chitosan-g-mPEG2000 nanoparticles; pH-dependent drug release and evaluation of cell cycle arrest and altering p53 and lincRNA-p21 genes expression. Naunyn Schmiedebergs Arch Pharmacol 2021; 395:51-63. [PMID: 34661718 DOI: 10.1007/s00210-021-02168-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
Carbohydrate polymers were widely used in pharmaceuticals and drug delivery systems due to their biodegradability and biocompatibility. Among them, chitosan (Cs) has been considered in many new drug delivery systems. Poly(ethylene glycol) as a hydrophilic polymer can increase the solubility and stealth functions of nanocarriers. The Fe3O4 nanoparticles functionalized with polymers act as non-toxic drug vehicles for tumor targeting under external magnetic fields. In present study, the Fe3O4/SiO2-NH2 nanoparticles were prepared and then functionalized with methoxy-PEGylated chitosan (Cs-g-mPEG2000) and the hydroxyurea (HU) was loaded on this nanoparticles. The structure, crystallinity, and morphology of HU/Fe3O4/SiO2/Cs-g-mPEG2000 were determined using spectroscopic and electron microscopy analysis. Encapsulation efficiency of HU and the percentage of loading and release rate at different pH values at 37 °C were examined. Maximum drug release was observed at pH = 7.4. According to TEM results, the nanoparticle sizes were between 18 and 157 nm. The cytotoxicity effect of HU-loaded nanoparticles against MCF-7 human breast cancer cell was evaluated using MTT assay and cell cycle arrest analysis. The inhibitory concentration (IC50) values were 249 and 85 μg/mL on the MCF-7 cell line compared to the control group in 24 h and 96 h, respectively. In addition, the expression of p53 and lincRNA-P21 genes in treated cells and control group was assessed using real-time PCR, and the results showed that the ratio of p53 expression to lincRNA-P21 in MCF-7 cells was significantly increased (P < 0.05). The cell cycle arrested in the S-phase and the population of cells increased 1.3-fold compared to the control group.
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Najmafshar A, Rostami M, Varshosaz J, Norouzian D, Samsam Shariat SZA. Enhanced antitumor activity of bovine lactoferrin through immobilization onto functionalized nano graphene oxide: an in vitro/ in vivo study. Drug Deliv 2021; 27:1236-1247. [PMID: 32812454 PMCID: PMC7470100 DOI: 10.1080/10717544.2020.1809558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This study aims to improve the anticancer activity of bovine lactoferrin through enhancing its stability by immobilization onto graphene oxide. Bovine lactoferrin was conjugated onto graphene oxide and the conjugation process was confirmed by FT-IR, SDS-PAGE, and UV spectrophotometry. Physical characterization was performed by DLS analysis and atomic force microscopy. The cytotoxicity and cellular uptake of the final construct (CGO-PEG-bLF) was inspected on lung cancer TC-1 cells by MTT assay and flow cytometry/confocal microscopy. The anticancer mechanism of the CGO-PEG-bLF was studied by cell cycle analysis, apoptosis assay, and western blot technique. Finally, the anticancer activity of CGO-PEG-bLF was assessed in an animal model of lung cancer. Size and zeta potential of CGO-PEG-bLF was obtained in the optimum range. Compared with free bLF, more cytotoxic activity, cellular uptake and more survival time was obtained for CGO-PEG-bLF. CGO-PEG-bLF significantly inhibited tumor growth in the animal model. Cell cycle arrest and apoptosis were more induced by CGO-PEG-bLF. Moreover, exposure to CGO-PEG-bLF decreased the phospho-AKT and pro-Caspase 3 levels and increased the amount of cleaved caspase 3 in the treated cells. This study revealed the potential of CGO-PEG as a promising nanocarrier for enhancing the therapeutic efficacy of anticancer agents.
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Affiliation(s)
- Azam Najmafshar
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahboubeh Rostami
- Department of Medicinal Chemistry, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jaleh Varshosaz
- Department of Pharmaceutics, School of Pharmacy and Novel Drug Delivery Systems Research Centre, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Dariush Norouzian
- Department of Nanobiotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Ziyae Aldin Samsam Shariat
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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Tazhbayev Y, Mukashev O, Burkeyev M, Lozinsky VI. Synthesis and Comparative Study of Nanoparticles Derived from Bovine and Human Serum Albumins. Polymers (Basel) 2020; 12:polym12061301. [PMID: 32517219 PMCID: PMC7361980 DOI: 10.3390/polym12061301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
This study describes the preparation of nanoparticles derived from bovine serum albumin (BSA) in comparison with the formation of nanoparticles composed of human serum albumin (HSA), when the same preparation procedure was used in both cases. To obtain protein nanoparticles, the method of desolvation with ethanol was employed, followed by the stabilization with urea and cysteine. It was shown that, upon transition from HSA to BSA, the particles with smaller sizes and with a narrower polydispersity were formed. The possibility of the immobilization of the antitumor drug hydroxyurea in such protein nanoparticles by adsorption and inclusion methods has been shown. The drug release profile from the polymer matrix was established.
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Affiliation(s)
- Yerkeblan Tazhbayev
- Chemical Materials Science and Nanochemistry Laboratory, Buketov Karaganda State University, Karaganda 100028, Kazakhstan; (O.M.); (M.B.)
- Correspondence: ; Tel.: +7-700-917-32-74; Fax: +7-7212-77-03-84
| | - Olzhas Mukashev
- Chemical Materials Science and Nanochemistry Laboratory, Buketov Karaganda State University, Karaganda 100028, Kazakhstan; (O.M.); (M.B.)
| | - Meiram Burkeyev
- Chemical Materials Science and Nanochemistry Laboratory, Buketov Karaganda State University, Karaganda 100028, Kazakhstan; (O.M.); (M.B.)
| | - Vladimir I. Lozinsky
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia;
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