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Rice SJ, Belani CP. Characterization of effective, simple, and low-cost precipitation methods for depleting abundant plasma proteins to enhance the depth and breadth of plasma proteomics. Proteomics 2024:e2400071. [PMID: 38700387 DOI: 10.1002/pmic.202400071] [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: 02/29/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/05/2024]
Abstract
Plasma is an abundant source of proteins and potential biomarkers to aid in the detection, diagnosis, and prognosis of human diseases. These proteins are often present at low levels in the blood and difficult to identify and measure due to the large dynamic range of proteins. The goal of this work was to characterize and compare various protein precipitation methods related to how they affect the depth and breadth of plasma proteomic studies. Abundant protein precipitation with perchloric acid (PerCA) can increase protein identifications and depth of plasma proteomic studies. Three acid- and four solvent-based precipitation methods were evaluated. All methods tested provided excellent plasma proteomic coverage (>600 identified protein groups) and detected protein in the low pg/mL range. Functional enrichment analysis revealed subtle differences within and larger changes between the precipitant groups. Methanol-based precipitation outperformed the other methods based on identifications and reproducibility. The methods' performance was verified using eight lung cancer patient samples, where >700 protein groups were measured and proteins with an estimated plasma concentration of ∼10 pg/mL were detected. Various protein precipitation agents are amenable to extending the depth and breadth of plasma proteomes. These data can guide investigators to implement inexpensive, high-throughput methods for their plasma proteomic workflows.
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Affiliation(s)
- Shawn J Rice
- Penn State Cancer Institute, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Chandra P Belani
- Penn State Cancer Institute, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
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2
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Naveed M, Ali I, Aziz T, Javed K, Saleem A, Hanif N, Alharbi M. Investigating the anti-cancer compounds from Calliandra harrisii for precision medicine in pancreatic cancer via in-silico drug design and GC-MS analysis. Z NATURFORSCH C 2024; 0:znc-2024-0057. [PMID: 38635803 DOI: 10.1515/znc-2024-0057] [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: 03/12/2024] [Accepted: 04/06/2024] [Indexed: 04/20/2024]
Abstract
Pancreatic cancer is a fatal illness caused by mutations in multiple genes. Pancreatic cancer damages the organ that helps in digestion, resulting in symptoms including fatigue, bloating, and nausea. The use of medicinal plants has been crucial in the treatment of numerous disorders. The medicinal plant Calliandra Harrisi has been widely exploited for its possibilities in biology and medicine. The current study aimed to assess the biopotential of biologically active substances against pancreatic cancer. The GC-MS data of these phytochemicals from Calliandra Harrisi were further subjected to computational approaches with pancreatic cancer genes to evaluate their potential as therapeutic candidates. Molecular docking analysis revealed that N-[Carboxymethyl] maleamic acid is the leading molecule responsible for protein denaturation inhibition, having the highest binding affinity of 6.8 kJ/mol among all other compounds with KRAS inflammatory proteins. Furthermore, ADMET analysis and Lipinski's rule validation were also performed revealing its higher absorption in the gastrointestinal tract. The results of the hepatotoxicity test demonstrated that phytochemicals are non-toxic, safe to use, and do not cause necrosis, fibrosis, or vacuolar degeneration even at excessive levels. Calliandra Harrisi has phytoconstituents that have a variety of pharmacological uses in consideration.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, 66901 University of Central Punjab , Lahore 54590, Pakistan
| | - Imran Ali
- Department of Biotechnology, Faculty of Science and Technology, 66901 University of Central Punjab , Lahore 54590, Pakistan
| | - Tariq Aziz
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, 37796 University of Ioannina , Arta 47132, Greece
| | - Khushbakht Javed
- Department of Biotechnology, Faculty of Science and Technology, 66901 University of Central Punjab , Lahore 54590, Pakistan
| | - Ayesha Saleem
- Department of Biotechnology, Faculty of Science and Technology, 66901 University of Central Punjab , Lahore 54590, Pakistan
| | - Nimra Hanif
- Department of Biotechnology, Faculty of Science and Technology, 66901 University of Central Punjab , Lahore 54590, Pakistan
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, 37850 King Saud University , P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Ahmed R, Zaitone SA, Abdelmaogood AKK, Atef HM, Soliman MFM, Badawy AM, Ali HS, Zaid A, Mokhtar HI, Elabbasy LM, Kandil E, Yosef AM, Mahran RI. Chemotherapeutic potential of betanin/capecitabine combination targeting colon cancer: experimental and bioinformatic studies exploring NFκB and cyclin D1 interplay. Front Pharmacol 2024; 15:1362739. [PMID: 38645563 PMCID: PMC11026609 DOI: 10.3389/fphar.2024.1362739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/13/2024] [Indexed: 04/23/2024] Open
Abstract
Introduction: Betanin (C₂₄H₂₆N₂O₁₃) is safe to use as food additives approved by the FDA with anti-inflammatory and anticancer effects in many types of cancer cell lines. The current experiment was designed to test the chemotherapeutic effect of the combination of betanin with the standard chemotherapeutic agent, capecitabine, against chemically induced colon cancer in mice. Methods: Bioinformatic approach was designed to get information about the possible mechanisms through which the drugs may control cancer development. Five groups of mice were assigned as, (i) saline, (ii) colon cancer, (iii) betanin, (iv) capecitabine and (v) betanin/capecitabine. Drugs were given orally for a period of six weeks. Colon tissues were separated and used for biological assays and histopathology. Results: In addition, the mRNA expression of TNF-α (4.58-fold), NFκB (5.33-fold), IL-1β (4.99-fold), cyclin D1 (4.07-fold), and IL-6 (3.55-fold) and protein levels showed several folds increases versus the saline group. Tumor histopathology scores in the colon cancer group (including cryptic distortion and hyperplasia) and immunostaining for NFκB (2.94-fold) were high while periodic-acid Schiff staining demonstrated poor mucin content (33% of the saline group). These pathologic manifestations were reduced remarkably in betanin/capecitabine group. Conclusion: Collectively, our findings demonstrated the usefulness of betanin/capecitabine combination in targeting colon cancer and highlighted that betanin is a promising adjuvant therapy to capecitabine in treating colon cancer patients.
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Affiliation(s)
- Rehab Ahmed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Sawsan A. Zaitone
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, University of Tabuk, Tabuk, Saudi Arabia
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | | | - Huda M. Atef
- Department of Histology and Cell Biology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Mona F. M. Soliman
- Department of Medical Histology and Cell Biology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
- Department of Medical Histology and Cell Biology, Faculty of Medicine, Horus University, New Damiettta, Egypt
| | - Alaa M. Badawy
- Department of Anatomy and Embryology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Howaida S. Ali
- Department of Pharmacology, Faculty of Medicine, University of Tabuk, Tabuk, Saudi Arabia
- Department of Pharmacology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - AbdelNaser Zaid
- Department of Surgery, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia
- Department of General Surgery, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Hatem I. Mokhtar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sinai University-Kantara Branch, Ismailia, Egypt
| | - Lamiaa M. Elabbasy
- Department of Medical Biochemistry & Molecular Biology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
- Department of Basic Medical Sciences, College of Medicine, Almaarefa University, Riyadh, Saudi Arabia
| | - Emad Kandil
- Department of Basic Medical Sciences, College of Medicine, Almaarefa University, Riyadh, Saudi Arabia
| | - Asmaa Mokhtar Yosef
- PharmD Program, Faculty of Pharmacy, University of Tabuk, Tabuk, Saudi Arabia
| | - Rama I. Mahran
- Department of Pharmacology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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Ramírez-Carracedo R, Hernández I, Moreno-Gómez-Toledano R, Díez-Mata J, Tesoro L, González-Cucharero C, Jiménez-Guirado B, Alcharani N, Botana L, Saura M, Zamorano JL, Zaragoza C. NOS3 prevents MMP-9, and MMP-13 induced extracellular matrix proteolytic degradation through specific microRNA-targeted expression of extracellular matrix metalloproteinase inducer in hypertension-related atherosclerosis. J Hypertens 2024; 42:685-693. [PMID: 38406874 PMCID: PMC10906209 DOI: 10.1097/hjh.0000000000003679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND Endothelial nitric oxide synthase (NOS3) elicits atheroprotection by preventing extracellular matrix (ECM) proteolytic degradation through inhibition of extracellular matrix metalloproteinase inducer (EMMPRIN) and collagenase MMP-13 by still unknown mechanisms. METHODS C57BL/6 mice lacking ApoE , NOS3, and/or MMP13 were fed with a high-fat diet for 6 weeks. Entire aortas were extracted and frozen to analyze protein and nucleic acid expression. Atherosclerotic plaques were detected by ultrasound imaging, Oil Red O (ORO) staining, and Western Blot. RNA-seq and RT-qPCR were performed to evaluate EMMPRIN, MMP-9, and EMMPRIN-targeting miRNAs. Mouse aortic endothelial cells (MAEC) were incubated to assess the role of active MMP-13 over MMP-9. One-way ANOVA or Kruskal-Wallis tests were performed to determine statistical differences. RESULTS Lack of NOS3 in ApoE null mice fed with a high-fat diet increased severe plaque accumulation, vessel wall widening, and high mortality, along with EMMPRIN-induced expression by upregulation of miRNAs 46a-5p and 486-5p. However, knocking out MMP-13 in ApoE/NOS3 -deficient mice was sufficient to prevent mortality (66.6 vs. 26.6%), plaque progression (23.1 vs. 8.8%), and MMP-9 expression, as confirmed in murine aortic endothelial cell (MAEC) cultures, in which MMP-9 was upregulated by incubation with active recombinant MMP-13, suggesting MMP-9 as a new target of MMP-13 in atherosclerosis. CONCLUSION We describe a novel mechanism by which the absence of NOS3 may worsen atherosclerosis through EMMPRIN-induced ECM proteolytic degradation by targeting the expression of miRNAs 146a-5p and 485-5p. Focusing on NOS3 regulation of ECM degradation could be a promising approach in the management of atherosclerosis.
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Affiliation(s)
- Rafael Ramírez-Carracedo
- Unidad Mixta de Investigación Cardiovascular, Departamento de Cardiología, Universidad Francisco de Vitoria, Hospital Ramón y Cajal (IRYCIS)
| | - Ignacio Hernández
- Unidad Mixta de Investigación Cardiovascular, Departamento de Cardiología, Universidad Francisco de Vitoria, Hospital Ramón y Cajal (IRYCIS)
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Av. Monforte de Lemos
| | - Rafael Moreno-Gómez-Toledano
- Unidad Mixta de Investigación Cardiovascular, Departamento de Cardiología, Universidad Francisco de Vitoria, Hospital Ramón y Cajal (IRYCIS)
- Universidad de Alcalá, Unidad de Fisiología, Departamento de Biología de Sistemas, Alcalá de Henares
| | - Javier Díez-Mata
- Unidad Mixta de Investigación Cardiovascular, Departamento de Cardiología, Universidad Francisco de Vitoria, Hospital Ramón y Cajal (IRYCIS)
| | - Laura Tesoro
- Unidad Mixta de Investigación Cardiovascular, Departamento de Cardiología, Universidad Francisco de Vitoria, Hospital Ramón y Cajal (IRYCIS)
| | - Claudia González-Cucharero
- Unidad Mixta de Investigación Cardiovascular, Departamento de Cardiología, Universidad Francisco de Vitoria, Hospital Ramón y Cajal (IRYCIS)
| | - Beatriz Jiménez-Guirado
- Unidad Mixta de Investigación Cardiovascular, Departamento de Cardiología, Universidad Francisco de Vitoria, Hospital Ramón y Cajal (IRYCIS)
| | - Nunzio Alcharani
- Unidad Mixta de Investigación Cardiovascular, Departamento de Cardiología, Universidad Francisco de Vitoria, Hospital Ramón y Cajal (IRYCIS)
| | - Laura Botana
- Unidad Mixta de Investigación Cardiovascular, Departamento de Cardiología, Universidad Francisco de Vitoria, Hospital Ramón y Cajal (IRYCIS)
| | - Marta Saura
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Av. Monforte de Lemos
- Universidad de Alcalá, Unidad de Fisiología, Departamento de Biología de Sistemas, Alcalá de Henares
| | - Jose L. Zamorano
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Av. Monforte de Lemos
- Departamento de Cardiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Carlos Zaragoza
- Unidad Mixta de Investigación Cardiovascular, Departamento de Cardiología, Universidad Francisco de Vitoria, Hospital Ramón y Cajal (IRYCIS)
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Av. Monforte de Lemos
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Hýžďalová M, Procházková J, Straková N, Pěnčíková K, Strapáčová S, Slováčková J, Kajabová S, Líbalová H, Topinka J, Kabátková M, Vondráček J, Mollerup S, Machala M. Transcriptional and phenotypical alterations associated with a gradual benzo[a]pyrene-induced transition of human bronchial epithelial cells into mesenchymal-like cells. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 107:104424. [PMID: 38522766 DOI: 10.1016/j.etap.2024.104424] [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: 08/22/2023] [Accepted: 03/20/2024] [Indexed: 03/26/2024]
Abstract
The role of benzo[a]pyrene (BaP), a prominent genotoxic carcinogen and aryl hydrocarbon receptor (AhR) ligand, in tumor progression remains poorly characterized. We investigated the impact of BaP on the process of epithelial-mesenchymal transition (EMT) in normal human bronchial epithelial HBEC-12KT cells. Early morphological changes after 2-week exposure were accompanied with induction of SERPINB2, IL1, CDKN1A/p21 (linked with cell cycle delay) and chemokine CXCL5. After 8-week exposure, induction of cell migration and EMT-related pattern of markers/regulators led to induction of further pro-inflammatory cytokines or non-canonical Wnt pathway ligand WNT5A. This trend of up-regulation of pro-inflammatory genes and non-canonical Wnt pathway constituents was observed also in the BaP-transformed HBEC-12KT-B1 cells. In general, transcriptional effects of BaP differed from those of TGFβ1, a prototypical EMT inducer, or a model non-genotoxic AhR ligand, TCDD. Carcinogenic polycyclic aromatic hydrocarbons could thus induce a unique set of molecular changes linked with EMT and cancer progression.
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Affiliation(s)
- Martina Hýžďalová
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 70, Brno 62100, Czech Republic
| | - Jiřina Procházková
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 70, Brno 62100, Czech Republic; Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 61200, Czech Republic
| | - Nicol Straková
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 70, Brno 62100, Czech Republic
| | - Kateřina Pěnčíková
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 70, Brno 62100, Czech Republic
| | - Simona Strapáčová
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 70, Brno 62100, Czech Republic
| | - Jana Slováčková
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 70, Brno 62100, Czech Republic; Department of Histology and Embryology, Masaryk University, Kamenice 3, Brno 62500, Czech Republic
| | - Simona Kajabová
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 70, Brno 62100, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Helena Líbalová
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, Prague 142 20, Czech Republic
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, Prague 142 20, Czech Republic
| | - Markéta Kabátková
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 61200, Czech Republic
| | - Jan Vondráček
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 61200, Czech Republic
| | - Steen Mollerup
- Research Group for Occupational Toxicology, The National Institute of Occupational Health in Norway, Oslo 0304, Norway
| | - Miroslav Machala
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 70, Brno 62100, Czech Republic.
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Gatasheh MK, Natarajan SR, Krishnamoorthy R, Alsulami TS, Rajagopal P, Palanisamy CP, Veeraraghavan VP, Jayaraman S. Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis. Mol Cell Oncol 2024; 11:2326699. [PMID: 38505173 PMCID: PMC10950290 DOI: 10.1080/23723556.2024.2326699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
Colorectal cancer (CRC) is a heterogeneous disease that requires new diagnostic and prognostic markers. Integrated bioinformatics approach to identify novel therapeutic targets associated with CRC. Using GEO2R identified DEGs in CRC, and Funrich software facilitated the visualization of DEGs through Venn diagrams. From a total of 114 enhanced DEGs, potential hub genes were further filtered based on their nodal strength and edges using STRING database. To gain insights into the functional roles of these hub genes, gene ontology and pathway enrichment were conducted thorough g: profiler web server. Subsequently, overall survival plots from GEPIA and oncogenic predictive functions like mRNA expressions for stages and nodal metastasis were employed to identify hub genes in CRC patient samples. Additionally, the cBioPortal and HPA databases also revealed genetic alterations and expression levels in these hub genes in CRC patients, further supporting their involvement in colorectal cancer. Gene expression by RT-PCR shows upregulation of hub genes in HT-29 cells. Finally, our integrated bioinformatic analysis revealed that ABCE1, AURKA, HSPD1, PHKA1, CDK4, and YWHAE as hub genes with potential oncogenic roles in CRC. These genes hold promise as diagnostic and prognostic markers for colorectal tumorigenesis, providing insights into targeted therapies for improved patient outcomes.
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Affiliation(s)
- Mansour K. Gatasheh
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Sathan Raj Natarajan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, SaveethaUniversity, Chennai, India
| | - Rajapandiyan Krishnamoorthy
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Tawfiq S Alsulami
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Ponnulakshmi Rajagopal
- Department of Central Research Laboratory, Meenakshi Ammal Dental College and Hospital, Meenakshi Academy of Higher Education and Research (Deemed to be University), Chennai, India
| | - Chella Perumal Palanisamy
- Mini-invasive Neurosurgery and Translational Medical Center, Xi’an Central Hospital, Xi’an Jiaotong University, Xi’an, PR China
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, SaveethaUniversity, Chennai, India
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, SaveethaUniversity, Chennai, India
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Brewer A, Sathe G, Pflug BE, Clarke RG, Macartney TJ, Sapkota GP. Mapping the substrate landscape of protein phosphatase 2A catalytic subunit PPP2CA. iScience 2024; 27:109302. [PMID: 38450154 PMCID: PMC10915630 DOI: 10.1016/j.isci.2024.109302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/18/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Protein phosphatase 2A (PP2A) is an essential Ser/Thr phosphatase. The PP2A holoenzyme complex comprises a scaffolding (A), regulatory (B), and catalytic (C) subunit, with PPP2CA being the principal catalytic subunit. The full scope of PP2A substrates in cells remains to be defined. To address this, we employed dTAG proteolysis-targeting chimeras to efficiently and selectively degrade dTAG-PPP2CA in homozygous knock-in HEK293 cells. Unbiased global phospho-proteomics identified 2,204 proteins with significantly increased phosphorylation upon dTAG-PPP2CA degradation, implicating them as potential PPP2CA substrates. A vast majority of these are novel. Bioinformatic analyses revealed involvement of the potential PPP2CA substrates in spliceosome function, cell cycle, RNA transport, and ubiquitin-mediated proteolysis. We identify a pSP/pTP motif as a predominant target for PPP2CA and confirm some of our phospho-proteomic data with immunoblotting. We provide an in-depth atlas of potential PPP2CA substrates and establish targeted degradation as a robust tool to unveil phosphatase substrates in cells.
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Affiliation(s)
- Abigail Brewer
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gajanan Sathe
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Billie E. Pflug
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rosemary G. Clarke
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Thomas J. Macartney
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gopal P. Sapkota
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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Brown TJ, Rutland CS, Choi KK, Tse F, Peffers MJ, Mongan NP, Arkill KP, Ritchie A, Clarke PA, Ratan H, Allegrucci C, Grabowska AM, James V. Modulation of the pre-metastatic bone niche: molecular changes mediated by bone-homing prostate cancer extracellular vesicles. Front Cell Dev Biol 2024; 12:1354606. [PMID: 38455075 PMCID: PMC10919403 DOI: 10.3389/fcell.2024.1354606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024] Open
Abstract
Prostate cancer (PCa) is a leading male malignancy worldwide, often progressing to bone metastasis, with limited curative options. Extracellular vesicles (EVs) have emerged as key players in cancer communication and metastasis, promoting the formation of supportive microenvironments in distant sites. Our previous studies have highlighted the role of PCa EVs in modulating osteoblasts and facilitating tumor progression. However, the early pre-metastatic changes induced by PCa EVs within the bone microenvironment remain poorly understood. To investigate the early effects of repeated exposure to PCa EVs in vivo, mimicking EVs being shed from the primary tumor, PCa EVs isolated from cell line PC3MLuc2a were fluorescently labelled and repeatedly administered via tail vein injection to adult CD1 NuNu male mice for a period of 4 weeks. In vivo imagining, histological analysis and gene expression profiling were performed to assess the impact of PCa EVs on the bone microenvironment. We demonstrate for the first time that PCa EVs home to both bone and lymph nodes following repeated exposures. Furthermore, the accumulation of EVs within the bone leads to distinct molecular changes indicative of disrupted bone homeostasis (e.g., changes to signaling pathways such as Paxillin p = 0.0163, Estrogen Receptor p = 0.0271, RHOA p = 0.0287, Ribonucleotide reductase p = 0.0307 and ERK/MAPK p = 0.0299). Changes in key regulators of these pathways were confirmed in vitro on human osteoblasts. In addition, our data compares the known gene signature of osteocytes and demonstrates a high proportion of overlap (52.2%), suggesting a potential role for this cell type in response to PCa EV exposure. No changes in bone histology or immunohistochemistry were detected, indicating that PCa EV mediated changes were induced at the molecular level. This study provides novel insights into the alterations induced by PCa EVs on the bone microenvironment. The observed molecular changes indicate changes in key pathways and suggest a role for osteocytes in these EV mediated early changes to bone. Further research to understand these early events may aid in the development of targeted interventions to disrupt the metastatic cascade in PCa.
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Affiliation(s)
- Thomas J. Brown
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Catrin S. Rutland
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Katie K. Choi
- Faculty of Medicine and Health Sciences, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Feng Tse
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Mandy J. Peffers
- Institute of Ageing and Chronic Disease, Liverpool, United Kingdom
| | - Nigel P. Mongan
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, United States
| | - Kenton P. Arkill
- Faculty of Medicine and Health Sciences, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Alison Ritchie
- Faculty of Medicine and Health Sciences, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Philip A. Clarke
- Faculty of Medicine and Health Sciences, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Hari Ratan
- Faculty of Medicine and Health Sciences, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Cinzia Allegrucci
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Anna M. Grabowska
- Faculty of Medicine and Health Sciences, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Victoria James
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
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Bhuiyan P, Sun Z, Khan MA, Hossain MA, Rahman MH, Qian Y. System biology approaches to identify hub genes linked with ECM organization and inflammatory signaling pathways in schizophrenia pathogenesis. Heliyon 2024; 10:e25191. [PMID: 38322840 PMCID: PMC10844262 DOI: 10.1016/j.heliyon.2024.e25191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
Schizophrenia (SZ) is a chronic and devastating mental illness that affects around 20 million individuals worldwide. Cognitive deficits and structural and functional changes of the brain, abnormalities of brain ECM components, chronic neuroinflammation, and devastating clinical manifestation during SZ are likely etiological factors shown by affected individuals. However, the pathophysiological events associated with multiple regulatory pathways involved in the brain of this complex disorder are still unclear. This study aimed to develop a pipeline based on bioinformatics and systems biology approaches for identifying potential therapeutic targets involving possible biological mechanisms from SZ patients and healthy volunteers. About 420 overlapping differentially expressed genes (DEGs) from three RNA-seq datasets were identified. Gene ontology (GO), and pathways analysis showed several biological mechanisms enriched by the commonly shared DEGs, including extracellular matrix organization (ECM) organization, collagen fibril organization, integrin signaling pathway, inflammation mediated by chemokines and cytokines signaling pathway, and GABA-B receptor II and IL4 mediated signaling. Besides, 15 hub genes (FN1, COL1A1, COL3A1, COL1A2, COL5A1, COL2A1, COL6A2, COL6A3, MMP2, THBS1, DCN, LUM, HLA-A, HLA-C, and FBN1) were discovered by comprehensive analysis, which was mainly involved in the ECM organization and inflammatory signaling pathway. Furthermore, the miRNA target of the hub genes was analyzed with the random-forest-based approach software miRTarBase. In addition, the transcriptional factors and protein kinases regulating overlapping DEGs in SZ, namely, SUZ12, EZH2, TRIM28, TP53, EGR1, CSNK2A1, GSK3B, CDK1, and MAPK14, were also identified. The results point to a new understanding that the hub genes (fibronectin 1, collagen, matrix metalloproteinase-2, and lumican) in the ECM organization and inflammatory signaling pathways may be involved in the SZ occurrence and pathogenesis.
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Affiliation(s)
- Piplu Bhuiyan
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, People's Republic of China
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, University of Development Alternative, Dhaka, 1209, Bangladesh
| | - Zhaochu Sun
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, People's Republic of China
| | - Md Arif Khan
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, University of Development Alternative, Dhaka, 1209, Bangladesh
- Bio-Bio-1 Bioinformatics Research Foundation, Dhaka, Bangladesh
| | - Md Arju Hossain
- Department of Microbiology, Primeasia University, Banani, Dhaka 1213, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Faculty of Engineering and Technology, Islamic University, Kushtia-7003, Bangladesh
| | - Yanning Qian
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, People's Republic of China
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Karri RL, Bojji M, Rudraraju A, Mohammad AS, Kosuru V, Kalisipudi S. Unraveling the Molecular Complexity of Adenoid Cystic Carcinoma (ACC): A Comprehensive Exploration of Hub Genes, Protein-Protein Interaction (PPI) Networks, microRNA (miRNA) Involvement, and Drug-Gene Interactions (DGIs). Cureus 2024; 16:e54730. [PMID: 38524085 PMCID: PMC10961157 DOI: 10.7759/cureus.54730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Background Adenoid cystic carcinoma (ACC) poses clinical challenges with its unique histology and potential for perineural invasion, recurrence, and distant metastases. Recent genomic advancements have unveiled key genetic alterations in ACC, offering insights into its pathogenesis. Aim This study aims to unravel the intricate molecular landscape of ACC through a comprehensive analysis of gene expression patterns. By integrating data from multiple microarray datasets, the study explores differentially expressed genes (DEGs), their functional enrichment, protein-protein interactions (PPI), hub genes, microRNA (miRNA) involvement, transcription factors, and potential drug-gene interactions. Methods Three microarray datasets (GSE88804, GSE153002, and GSE36820) related to ACC were selected from the Gene Expression Omnibus (GEO) repository. DEGs were identified using GEO2R and further analyzed for commonalities and differences. Functional enrichment analysis, including Gene Set Enrichment Analysis (GSEA), provided insights into biological processes, cellular components, molecular functions, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with ACC. PPI networks and hub genes were identified using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) (STRING Consortium, Lausanne, Switzerland) database and Cytoscape (Cytoscape Consortium, California, United States). The study also explored miRNAs, transcription factors, and potential drug-gene interactions. Results The integrated analysis revealed 339 common upregulated and 643 downregulated DEGs in ACC. Functional and pathway enrichment analyses unveiled the involvement of these genes in critical cellular processes, signaling cascades, and pathways. The PPI network, comprising 904 nodes and 4139 edges, highlighted the complexity of interactions. Hub genes, including KIF11, BUB1, and DLGAP5, were identified, shedding light on their pivotal roles in cell cycle regulation. The study also identified miRNAs (e.g., hsa-mir-7-5p and hsa-mir-138-5p) and transcription factors (e.g., E2F1 and TP53) associated with ACC. Drug-gene interactions have identified potential therapeutic options, including amsacrine and rucaparib. Conclusions The ACC gene expression highlights a nuanced molecular landscape, identifying pivotal hub genes such as KIF11 and CDK1 as potential therapeutic targets for ACC, given their roles in cell cycle progression. The dysregulation of microRNAs and transcription factors adds complexity to ACC's molecular profile. Exploration of drug-gene interactions reveals promising therapeutic strategies, involving FDA-approved drugs such as amsacrine and rucaparib, providing avenues for personalized interventions.
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Affiliation(s)
- Roja L Karri
- Oral and Maxillofacial Pathology, GSL Dental College and Hospital, Rajahmundry, IND
| | - Manasa Bojji
- Oral and Maxillofacial Pathology, Malla Reddy Dental College for Women, Hyderabad, IND
| | | | - Abdul Sadik Mohammad
- Pediatric and Preventive Dentistry, GSL Dental College and Hospital, Rajahmundry, IND
| | - Vamseedhar Kosuru
- Pediatric and Preventive Dentistry, Narayana Dental College and Hospital, Nellore, IND
| | - Sandeep Kalisipudi
- Pediatric and Preventive Dentistry, Lenora Institute of Dental Sciences, Rajahmundry, IND
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11
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Golestan A, Tahmasebi A, Maghsoodi N, Faraji SN, Irajie C, Ramezani A. Unveiling promising breast cancer biomarkers: an integrative approach combining bioinformatics analysis and experimental verification. BMC Cancer 2024; 24:155. [PMID: 38291367 PMCID: PMC10829368 DOI: 10.1186/s12885-024-11913-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Breast cancer remains a significant health challenge worldwide, necessitating the identification of reliable biomarkers for early detection, accurate prognosis, and targeted therapy. MATERIALS AND METHODS Breast cancer RNA expression data from the TCGA database were analyzed to identify differentially expressed genes (DEGs). The top 500 up-regulated DEGs were selected for further investigation using random forest analysis to identify important genes. These genes were evaluated based on their potential as diagnostic biomarkers, their overexpression in breast cancer tissues, and their low median expression in normal female tissues. Various validation methods, including online tools and quantitative Real-Time PCR (qRT-PCR), were used to confirm the potential of the identified genes as breast cancer biomarkers. RESULTS The study identified four overexpressed genes (CACNG4, PKMYT1, EPYC, and CHRNA6) among 100 genes with higher importance scores. qRT-PCR analysis confirmed the significant upregulation of these genes in breast cancer patients compared to normal samples. CONCLUSIONS These findings suggest that CACNG4, PKMYT1, EPYC, and CHRNA6 may serve as valuable biomarkers for breast cancer diagnosis, and PKMYT1 may also have prognostic significance. Furthermore, CACNG4, CHRNA6, and PKMYT1 show promise as potential therapeutic targets. These findings have the potential to advance diagnostic methods and therapeutic approaches for breast cancer.
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Affiliation(s)
- Ali Golestan
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Nafiseh Maghsoodi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Nooreddin Faraji
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Cambyz Irajie
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Ramezani
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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12
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Sun H, Fu B, Qian X, Xu P, Qin W. Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction. Nat Commun 2024; 15:852. [PMID: 38286993 PMCID: PMC10825125 DOI: 10.1038/s41467-024-44987-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs display enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of Tricarboxylic acid cycle in the translocation candidate RBPs may provide insights for investigating their possible roles in ferroptosis induced metabolism dysregulation.
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Affiliation(s)
- Haofan Sun
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Bin Fu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Ping Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Weijie Qin
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
- College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
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13
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John P, Sudandiradoss C. A comprehensive integrated gene network construction to explore the essential role of Notch 1 in lung adenocarcinoma (LUAD). J Biomol Struct Dyn 2024:1-13. [PMID: 38282473 DOI: 10.1080/07391102.2024.2306501] [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: 08/16/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024]
Abstract
The heterogeneous biological landscape of non-small cell lung cancer (NSCLC) is largely attributed to the activation of Notch signalling pathway. Among the Notch family transmembrane proteins, neurogenic locus notch homolog protein1 (NOTCH1) is a putative oncogene in NSCLC which activates the pathway as negative prognostic factor. This study aims to explore integrated network approach in lung adenocarcinoma (LUAD) especially linked to the notch pathway and its receptors. Our gene set enrichment analysis reveals the key Notch pathway genes are predominantly down regulated in LUAD. There were 675 genes with a total of 6517 functional interactions and 6 densely connected clusters of 38 miRNAs, 84 transcription factors with 156 edges identified through network construction. Here we report five key genes namely NOTCH1, CDH1, ERBB2, GAPDH and COL1A1 significantly enriched in Notch pathway which are further validated through the KM plot, box plots, stage plots and TIMER analysis. In addition, the NOTCH1 receptor is strongly linked to the immune checkpoint inhibitor CD274 (PD-L1) and can be considered as prognostic marker and tumour suppressor gene in LUAD which surely provide the basis for early diagnosis and futuristic immunotherapeutic targets for LUAD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pearl John
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C Sudandiradoss
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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14
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Mondol SM, Islam I, Islam MR, Shakil SK, Rakhi NN, Mustary JF, Amiruzzaman, Gomes DJ, Shahjalal HM, Rahaman MM. Genomic landscape of NDM-1 producing multidrug-resistant Providencia stuartii causing burn wound infections in Bangladesh. Sci Rep 2024; 14:2246. [PMID: 38278862 PMCID: PMC10817959 DOI: 10.1038/s41598-024-51819-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
The increasing antimicrobial resistance in Providencia stuartii (P. stuartii) worldwide, particularly concerning for immunocompromised and burn patients, has raised concern in Bangladesh, where the significance of this infectious opportunistic pathogen had been previously overlooked, prompting a need for investigation. The two strains of P. stuartii (P. stuartii SHNIBPS63 and P. stuartii SHNIBPS71) isolated from wound swab of two critically injured burn patients were found to be multidrug-resistant and P. stuartii SHNIBPS63 showed resistance to all the 22 antibiotics tested as well as revealed the co-existence of blaVEB-6 (Class A), blaNDM-1 (Class B), blaOXA-10 (Class D) beta lactamase genes. Complete resistance to carbapenems through the production of NDM-1, is indicative of an alarming situation as carbapenems are considered to be the last line antibiotic to combat this pathogen. Both isolates displayed strong biofilm-forming abilities and exhibited resistance to copper, zinc, and iron, in addition to carrying multiple genes associated with metal resistance and the formation of biofilms. The study also encompassed a pangenome analysis utilizing a dataset of eighty-six publicly available P. stuartii genomes (n = 86), revealing evidence of an open or expanding pangenome for P. stuartii. Also, an extensive genome-wide analysis of all the P. stuartii genomes revealed a concerning global prevalence of diverse antimicrobial resistance genes, with a particular alarm raised over the abundance of carbapenem resistance gene blaNDM-1. Additionally, this study highlighted the notable genetic diversity within P. stuartii, significant informations about phylogenomic relationships and ancestry, as well as potential for cross-species transmission, raising important implications for public health and microbial adaptation across different environments.
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Affiliation(s)
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Md Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Shahriar Kabir Shakil
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | | | - Jannatul Ferdous Mustary
- Microbiology Department, Sheikh Hasina National Institute of Burn and Plastic Surgery, Dhaka, 1000, Bangladesh
| | - Amiruzzaman
- Department of Medicine, Sir Salimullah Medical College, Dhaka, 1000, Bangladesh
| | - Donald James Gomes
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Hussain Md Shahjalal
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Md Mizanur Rahaman
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
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15
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Thi HV, Hoang TN, Le NQK, Chu DT. Application of data science and bioinformatics in RNA therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:83-97. [PMID: 38360007 DOI: 10.1016/bs.pmbts.2023.12.019] [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: 02/17/2024]
Abstract
Nowadays, information technology (IT) has been holding a significant role in daily life worldwide. The trajectory of data science and bioinformatics promises pioneering personalized therapies, reshaping medical landscapes and patient care. For RNA therapy to reach more patients, a comprehensive understanding of the application of data science and bioinformatics to this therapy is essential. Thus, this chapter has summarized the application of data science and bioinformatics in RNA therapeutics. Data science applications in RNA therapy, such as data integration and analytics, machine learning, and drug development, have been discussed. In addition, aspects of bioinformatics such as RNA design and evaluation, drug delivery system simulation, and databases for personalized medicine have also been covered in this chapter. These insights have shed light on existing evidence and opened potential future directions. From there, scientists can elevate RNA-based therapeutics into an era of tailored treatments and revolutionary healthcare.
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Affiliation(s)
- Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Thanh-Nhat Hoang
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; AIBioMed Research Group, Taipei Medical University, Taipei, Taiwan
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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16
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Samarelli AV, Tonelli R, Raineri G, Bruzzi G, Andrisani D, Gozzi F, Marchioni A, Costantini M, Fabbiani L, Genovese F, Pinetti D, Manicardi L, Castaniere I, Masciale V, Aramini B, Tabbì L, Rizzato S, Bettelli S, Manfredini S, Dominici M, Clini E, Cerri S. Proteomic profiling of formalin-fixed paraffine-embedded tissue reveals key proteins related to lung dysfunction in idiopathic pulmonary fibrosis. Front Oncol 2024; 13:1275346. [PMID: 38322285 PMCID: PMC10844556 DOI: 10.3389/fonc.2023.1275346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/29/2023] [Indexed: 02/08/2024] Open
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) severely affects the lung leading to aberrant deposition of extracellular matrix and parenchymal stiffness with progressive functional derangement. The limited availability of fresh tissues represents one of the major limitations to study the molecular profiling of IPF lung tissue. The primary aim of this study was to explore the proteomic profiling yield of archived formalin-fixed paraffin-embedded (FFPE) specimens of IPF lung tissues. Methods We further determined the protein expression according to respiratory functional decline at the time of biopsy. The total proteins isolated from 11 FFPE samples of IPF patients compared to 3 FFPE samples from a non-fibrotic lung defined as controls, were subjected to label-free quantitative proteomic analysis by liquid chromatography-mass spectrometry (LC-MS/MS) and resulted in the detection of about 400 proteins. Results After the pairwise comparison between controls and IPF, functional enrichment analysis identified differentially expressed proteins that were involved in extracellular matrix signaling pathways, focal adhesion and transforming growth factor β (TGF-β) signaling pathways strongly associated with IPF onset and progression. Five proteins were significantly over- expressed in the lung of IPF patients with either advanced disease stage (Stage II) or impaired pulmonary function (FVC<75, DLCO<55) compared to controls; these were lymphocyte cytosolic protein 1 (LCP1), peroxiredoxin-2 (PRDX2), transgelin 2 (TAGLN2), lumican (LUM) and mimecan (OGN) that might play a key role in the fibrogenic processes. Discussion Our work showed that the analysis of FFPE samples was able to identify key proteins that might be crucial for the IPF pathogenesis. These proteins are correlated with lung carcinogenesis or involved in the immune landscape of lung cancer, thus making possible common mechanisms between lung carcinogenesis and fibrosis progression, two pathological conditions at risk for each other in the real life.
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Affiliation(s)
- Anna Valeria Samarelli
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Roberto Tonelli
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Giulia Raineri
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Giulia Bruzzi
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Dario Andrisani
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Filippo Gozzi
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Alessandro Marchioni
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Matteo Costantini
- Pathology Institute, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Luca Fabbiani
- Pathology Institute, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
- Immunohistochemistry Lab, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Filippo Genovese
- Centro Interdipartimentale Grandi Strumenti (C.I.G.S.), University of Modena and Reggio Emilia, Modena, Italy
| | - Diego Pinetti
- Centro Interdipartimentale Grandi Strumenti (C.I.G.S.), University of Modena and Reggio Emilia, Modena, Italy
| | - Linda Manicardi
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Ivana Castaniere
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Valentina Masciale
- Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
- Oncology Unit, University Hospital of Modena and Reggio Emilia, University of Modena and Reggio Emilia, Modena, Italy
| | - Beatrice Aramini
- Division of Thoracic Surgery, Department of Medical and Surgical Sciences-Diagnostic and Specialty Medicine (DIMEC) of the Alma Mater Studiorum, University of Bologna G.B. Morgagni-L. Pierantoni Hospital, Forlì, Italy
| | - Luca Tabbì
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Simone Rizzato
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Stefania Bettelli
- Molecular Pathology and Predictive Medicine Unit, Modena Cancer Center, University Hospital of Modena, Modena, Italy
| | - Samantha Manfredini
- Molecular Pathology and Predictive Medicine Unit, Modena Cancer Center, University Hospital of Modena, Modena, Italy
| | - Massimo Dominici
- Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
- Oncology Unit, University Hospital of Modena and Reggio Emilia, University of Modena and Reggio Emilia, Modena, Italy
| | - Enrico Clini
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Stefania Cerri
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
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17
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Vassileff N, Spiers JG, Lee JD, Woodruff TM, Ebrahimie E, Mohammadi Dehcheshmeh M, Hill AF, Cheng L. A Panel of miRNA Biomarkers Common to Serum and Brain-Derived Extracellular Vesicles Identified in Mouse Model of Amyotrophic Lateral Sclerosis. Mol Neurobiol 2024:10.1007/s12035-023-03857-z. [PMID: 38252383 DOI: 10.1007/s12035-023-03857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/05/2023] [Indexed: 01/23/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease characterised by the deposition of aggregated proteins including TAR DNA-binding protein 43 (TDP-43) in vulnerable motor neurons and the brain. Extracellular vesicles (EVs) facilitate the spread of neurodegenerative diseases and can be easily accessed in the bloodstream. This study aimed to identify a panel of EV miRNAs that can capture the pathology occurring in the brain and peripheral circulation. EVs were isolated from the cortex (BDEVs) and serum (serum EVs) of 3 month-old and 6-month-old TDP-43*Q331K and TDP-43*WT mice. Following characterisation and miRNA isolation, the EVs underwent next-generation sequencing where 24 differentially packaged miRNAs were identified in the TDP-43*Q331K BDEVs and 7 in the TDP-43*Q331K serum EVs. Several miRNAs, including miR-183-5p, were linked to ALS. Additionally, miR-122-5p and miR-486b-5p were identified in both panels, demonstrating the ability of the serum EVs to capture the dysregulation occurring in the brain. This is the first study to identify miRNAs common to both the serum EVs and BDEVs in a mouse model of ALS.
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Affiliation(s)
- Natasha Vassileff
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Jereme G Spiers
- Clear Vision Research, Eccles Institute of Neuroscience, John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
| | - John D Lee
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Australia
| | - Trent M Woodruff
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Australia
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, 3000, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, 5371, Australia
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | | | - Andrew F Hill
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Institute for Health and Sport, Victoria University, Footscray, Victoria, Australia
| | - Lesley Cheng
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia.
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Wang X, Liang C, Wang S, Ma Q, Pan X, Ran A, Qin C, Huang B, Yang F, Liu Y, Zhang Y, Ren J, Ning H, Li H, Jiang Y, Xiao B. RNA Binding Protein PTBP1 Promotes the Metastasis of Gastric Cancer by Stabilizing PGK1 mRNA. Cells 2024; 13:140. [PMID: 38247832 PMCID: PMC10814388 DOI: 10.3390/cells13020140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/31/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Gastric cancer (GC) is the most common type of malignant tumor within the gastrointestinal tract, and GC metastasis is associated with poor prognosis. Polypyrimidine tract binding protein 1 (PTBP1) is an RNA-binding protein implicated in various types of tumor development and metastasis. However, the role of PTBP1 in GC metastasis remains elusive. In this study, we verified that PTBP1 was upregulated in GC tissues and cell lines, and higher PTBP1 level was associated with poorer prognosis. It was shown that PTBP1 knockdown in vitro inhibited GC cell migration, whereas PTBP1 overexpression promoted the migration of GC cells. In vivo, the knockdown of PTBP1 notably reduced both the size and occurrence of metastatic nodules in a nude mice liver metastasis model. We identified phosphoglycerate kinase 1 (PGK1) as a downstream target of PTBP1 and found that PTBP1 increased the stability of PGK1 by directly binding to its mRNA. Furthermore, the PGK1/SNAIL axis could be required for PTBP1's function in the promotion of GC cell migration. These discoveries suggest that PTBP1 could be a promising therapeutic target for GC.
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Affiliation(s)
- Xiaolin Wang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Ce Liang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Shimin Wang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Qiang Ma
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Xiaojuan Pan
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Ai Ran
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Changhong Qin
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Bo Huang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, China
| | - Feifei Yang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Yuying Liu
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Yuying Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Junwu Ren
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Hao Ning
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Haiping Li
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Yan Jiang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
| | - Bin Xiao
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; (X.W.); (C.L.); (S.W.); (Q.M.); (X.P.); (A.R.); (C.Q.); (B.H.); (F.Y.); (Y.L.); (Y.Z.); (J.R.); (H.N.); (H.L.); (Y.J.)
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Xue B, Kadeerhan G, Sun LB, Chen YQ, Hu XF, Zhang ZK, Wang DW. Circulating exosomal miR-16-5p and let-7e-5p are associated with bladder fibrosis of diabetic cystopathy. Sci Rep 2024; 14:837. [PMID: 38191820 PMCID: PMC10774280 DOI: 10.1038/s41598-024-51451-7] [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: 08/06/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024] Open
Abstract
Diabetic cystopathy (DCP) is a prevalent etiology of bladder dysfunction in individuals with longstanding diabetes, frequently leading to bladder interstitial fibrosis. Research investigating the initial pathological alterations of DCP is notably scarce. To comprehend the development of fibrosis and find effective biomarkers for its diagnosis, we prepared streptozotocin-induced long-term diabetic SD rats exhibiting a type 1 diabetes phenotype and bladder fibrosis in histology detection. After observing myofibroblast differentiation from rats' primary bladder fibroblasts with immunofluorescence, we isolated fibroblasts derived exosomes and performed exosomal miRNA sequencing. The co-differentially expressed miRNAs (DEMis) (miR-16-5p and let-7e-5p) were screened through a joint analysis of diabetic rats and long-term patients' plasma data (GES97123) downloaded from the GEO database. Then two co-DEMis were validated by quantitative PCR on exosomes derived from diabetic rats' plasma. Following with a series of analysis, including target mRNAs and transcription factors (TFs) prediction, hubgenes identification, protein-protein interaction (PPI) network construction and gene enrichment analysis, a miRNA-mediated genetic regulatory network consisting of two miRNAs, nine TFs, and thirty target mRNAs were identified in relation to fibrotic processes. Thus, circulating exosomal miR-16-5p and let-7e-5p are associated with bladder fibrosis of DCP, and the crucial genes in regulatory network might hold immense significance in studying the pathogenesis and molecular mechanisms of fibrosis, which deserves further exploration.
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Affiliation(s)
- Bo Xue
- Shanxi Medical University, Taiyuan, 030001, China
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Gaohaer Kadeerhan
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Li-Bin Sun
- Shanxi Medical University, Taiyuan, 030001, China
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | | | - Xiao-Feng Hu
- Shanxi Medical University, Taiyuan, 030001, China
| | | | - Dong-Wen Wang
- Shanxi Medical University, Taiyuan, 030001, China.
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China.
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Chitti SV, Gummadi S, Kang T, Shahi S, Marzan AL, Nedeva C, Sanwlani R, Bramich K, Stewart S, Petrovska M, Sen B, Ozkan A, Akinfenwa M, Fonseka P, Mathivanan S. Vesiclepedia 2024: an extracellular vesicles and extracellular particles repository. Nucleic Acids Res 2024; 52:D1694-D1698. [PMID: 37953359 PMCID: PMC10767981 DOI: 10.1093/nar/gkad1007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
Vesiclepedia (http://www.microvesicles.org) is a free web-based compendium of DNA, RNA, proteins, lipids and metabolites that are detected or associated with extracellular vesicles (EVs) and extracellular particles (EPs). EVs are membranous vesicles that are secreted ubiquitously by cells from all domains of life from archaea to eukaryotes. In addition to EVs, it was reported recently that EPs like exomeres and supermeres are secreted by some mammalian cells. Both EVs and EPs contain proteins, nucleic acids, lipids and metabolites and has been proposed to be implicated in several key biological functions. Vesiclepedia catalogues proteins, DNA, RNA, lipids and metabolites from both published and unpublished studies. Currently, Vesiclepedia contains data obtained from 3533 EV studies, 50 550 RNA entries, 566 911 protein entries, 3839 lipid entries, 192 metabolite and 167 DNA entries. Quantitative data for 62 822 entries from 47 EV studies is available in Vesiclepedia. The datasets available in Vesiclepedia can be downloaded as tab-delimited files or accessible through the FunRich-based Vesiclepedia plugin.
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Affiliation(s)
- Sai V Chitti
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Sriram Gummadi
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Taeyoung Kang
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Sanjay Shahi
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Akbar L Marzan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Christina Nedeva
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Rahul Sanwlani
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Kyle Bramich
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Sarah Stewart
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Monika Petrovska
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Biswadeep Sen
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Alper Ozkan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Maria Akinfenwa
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Pamali Fonseka
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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Shih JW, Wu ATH, Mokgautsi N, Wei PL, Huang YJ. Preclinical Repurposing of Sitagliptin as a Drug Candidate for Colorectal Cancer by Targeting CD24/ CTNNB1/ SOX4-Centered Signaling Hub. Int J Mol Sci 2024; 25:609. [PMID: 38203779 PMCID: PMC10778938 DOI: 10.3390/ijms25010609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/14/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Despite significant advances in treatment modalities, colorectal cancer (CRC) remains a poorly understood and highly lethal malignancy worldwide. Cancer stem cells (CSCs) and the tumor microenvironment (TME) have been shown to play critical roles in initiating and promoting CRC progression, metastasis, and treatment resistance. Therefore, a better understanding of the underlying mechanisms contributing to the generation and maintenance of CSCs is crucial to developing CSC-specific therapeutics and improving the current standard of care for CRC patients. To this end, we used a bioinformatics approach to identify increased CD24/SOX4 expression in CRC samples associated with poor prognosis. We also discovered a novel population of tumor-infiltrating CD24+ cancer-associated fibroblasts (CAFs), suggesting that the CD24/SOX4-centered signaling hub could be a potential therapeutic target. Pathway networking analysis revealed a connection between the CD24/SOX4-centered signaling, β-catenin, and DPP4. Emerging evidence indicates that DPP4 plays a role in CRC initiation and progression, implicating its involvement in generating CSCs. Based on these bioinformatics data, we investigated whether sitagliptin, a DPP4 inhibitor and diabetic drug, could be repurposed to inhibit colon CSCs. Using a molecular docking approach, we demonstrated that sitagliptin targeted CD24/SOX4-centered signaling molecules with high affinity. In vitro experimental data showed that sitagliptin treatment suppressed CRC tumorigenic properties and worked in synergy with 5FU and this study thus provided preclinical evidence to support the alternative use of sitagliptin for treating CRC.
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Affiliation(s)
- Jing-Wen Shih
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (J.-W.S.); (N.M.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Alexander T. H. Wu
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Ntlotlang Mokgautsi
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (J.-W.S.); (N.M.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Po-Li Wei
- Division of Colorectal Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan;
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
| | - Yan-Jiun Huang
- Division of Colorectal Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan;
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
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Kavoosi S, Shahraki A, Sheervalilou R. Identification of microRNA-mRNA Regulatory Networks with Therapeutic Values in Alzheimer's Disease by Bioinformatics Analysis. J Alzheimers Dis 2024; 98:671-689. [PMID: 38427479 DOI: 10.3233/jad-230966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Background Alzheimer's disease (AD) is the most prevalent neurological disorder worldwide, affecting approximately 24 million individuals. Despite more than a century of research on AD, its pathophysiology is still not fully understood. Objective Recently, genetic studies of AD have focused on analyzing the general expression profile by employing high-throughput genomic techniques such as microarrays. Current research has leveraged bioinformatics advancements in genetic science to build upon previous efforts. Methods Data from the GSE118553 dataset used in this investigation, and the analyses carried out using programs such as Limma and BioBase. Differentially expressed genes (DEGs) and differentially expressed microRNAs (DEmiRs) associated with AD identified in the studied areas of the brain. Target genes of the DEmiRs identified using the MultiMiR package. Gene ontology (GO) completed using the Enrichr website, and the protein-protein interaction (PPI) network for these genes drawn using STRING and Cytoscape software. Results The findings introduced DEGs including CTNNB1, PAK2, MAP2K1, PNPLA6, IGF1R, FOXL2, DKK3, LAMA4, PABPN1, and GDPD5, and DEmiRs linked to AD (miR-106A, miR-1826, miR-1253, miR-10B, miR-18B, miR-101-2, miR-761, miR-199A1, miR-379 and miR-668), (miR-720, miR-218-2, miR-25, miR-602, miR-1226, miR-548K, miR-H1, miR-410, miR-548F2, miR-181A2), (miR-1470, miR-651, miR-544, miR-1826, miR-195, miR-610, miR-599, miR-323, miR-587 and miR-340), and (miR-1282, miR-1914, miR-642, miR-1323, miR-373, miR-323, miR-1322, miR-612, miR-606 and miR-758) in cerebellum, frontal cortex, temporal cortex, and entorhinal cortex, respectively. Conclusions The majority of the genes and miRNAs identified by our findings may be employed as biomarkers for prediction, diagnosis, or therapy response monitoring.
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Affiliation(s)
- Sakine Kavoosi
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Ali Shahraki
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
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Zhang S, Fan W, He D. Constructing a personalized prognostic risk model for colorectal cancer using machine learning and multi-omics approach based on epithelial-mesenchymal transition-related genes. J Gene Med 2024; 26:e3660. [PMID: 38282145 DOI: 10.1002/jgm.3660] [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: 09/22/2023] [Revised: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 01/30/2024] Open
Abstract
The progression and the metastatic potential of colorectal cancer (CRC) are intricately linked to the epithelial-mesenchymal transition (EMT) process. The present study harnesses the power of machine learning combined with multi-omics data to develop a risk stratification model anchored on EMT-associated genes. The aim is to facilitate personalized prognostic assessments in CRC. We utilized publicly accessible gene expression datasets to pinpoint EMT-associated genes, employing a CoxBoost algorithm to sift through these genes for prognostic significance. The resultant model, predicated on gene expression levels, underwent rigorous independent validation across various datasets. Our model demonstrated a robust capacity to segregate CRC patients into distinct high- and low-risk categories, each correlating with markedly different survival probabilities. Notably, the risk score emerged as an independent prognostic indicator for CRC. High-risk patients were characterized by an immunosuppressive tumor milieu and a heightened responsiveness to certain chemotherapeutic agents, underlining the model's potential in steering tailored oncological therapies. Moreover, our research unearthed a putative repressive interaction between the long non-coding RNA PVT1 and the EMT-associated genes TIMP1 and MMP1, offering new insights into the molecular intricacies of CRC. In essence, our research introduces a sophisticated risk model, leveraging machine learning and multi-omics insights, which accurately prognosticates outcomes for CRC patients, paving the way for more individualized and effective oncological treatment paradigms.
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Affiliation(s)
- Shuze Zhang
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Wanli Fan
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Dong He
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, China
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Kumar S, Das A. A Cocktail of Natural Compounds Holds Promise for New Immunotherapeutic Potential in Head and Neck Cancer. Chin J Integr Med 2024; 30:42-51. [PMID: 37118529 DOI: 10.1007/s11655-023-3694-0] [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] [Accepted: 09/05/2022] [Indexed: 04/30/2023]
Abstract
OBJECTIVE To obtain detailed understanding on the gene regulation of natural compounds in altering prognosis of head and neck squamous cell carcinomas (HNSC). METHODS Gene expression data of HNSC samples and peripheral blood mononuclear cells (PBMCs) of HNSC patients were collected from Gene Expression Omnibus (GEO). Differential gene expression analysis of GEO datasets were achieved by the GEO2R tool. Common differentially expressed gerres (DEGs) were screened by comparing DEGs of HNSC with those of PBMCs. The combination was further analyzed for regulating pathways and biological processes that were affected. RESULTS Totally 110 DEGs were retrieved and identified to be involved in biological processes related to tumor regulation. Then 102 natural compounds were screened for a combination such that the expression of all 110 commonly DEGs was altered. A combination of salidroside, ginsenoside Rd, oridonin, britanin, and scutellarein was chosen. A multifaceted, multi-dimensional tumor regression was showed by altering autophagy, apoptosis, inhibiting cell proliferation, angiogenesis, metastasis and inflammatory cytokines production. CONCLUSIONS This study has helped develop a unique combination of natural compounds that will markedly reduce the propensity of development of drug resistance in tumors and immune evasion by tumors. The result is crucial to developing a combinatorial natural therapeutic cocktail with accentuated immunotherapeutic potential.
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Affiliation(s)
- Sunil Kumar
- Department of Biotechnology, Delhi Technological University, Delhi, 110042, India
| | - Asmita Das
- Department of Biotechnology, Delhi Technological University, Delhi, 110042, India.
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25
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Liu S, Wang K, Zhao Z, Pang Y, Liu F, Wang P, Wang Z, Yang X. miR-451a suppresses the proliferation and migration of high-grade serous ovarian cancer by targeting RAB5A through the Ras/Raf/MEK/ERK pathway. J Gene Med 2024; 26:e3649. [PMID: 38282155 DOI: 10.1002/jgm.3649] [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: 05/25/2023] [Revised: 10/20/2023] [Accepted: 11/17/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Ovarian cancer is one of the most common cancers in women. Profiles changes of microRNAs (miRNAs) are closely linked to malignant tumors. In the present study, we investigated expression of miR-451a in high-grade serous ovarian cancer (HGSOC). We also investigated the potential pathological roles and the likely mechanism of miR-451a in the development of HGSOC using animal models and cell lines. METHODS Using bioinformatics techniques and a real-time PCR, we analyzed differently expressed miRNAs in HGSOC compared to normal tissue. MTT (i.e. 3-[4, 5-dimethyl thiazol-2-yl]-2,5-diphenyl tetrazolium bromide), EDU (i.e. 5-ethynyl-2'-deoxyuridine) and transwell assays were performed to investigate the effect of miR-451a on the proliferation and migration of HGSOC SKOV-3 cells. A dual luciferase reporter assay was performed to verify the targeting relationship of miR-451 and RAB5A (one of the Rab GTPase proteins that regulates endocytosis and vesicle transport). Also, we analyzed levels of the RAB5A mRNA and protein by real-time PCR, western blotting and immunohistochemistry assays in HGSOC cells and tissues. Finally, we performed in vivo experiments using HGSOC mice. RESULTS miR-451a was substantially upregulated in HGSOC and associated with favorable clinical characteristics. miR-451a knockdown significantly increased growth and metastasis of HGSOC cell line SKOV-3 through Ras/Raf/mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling. In addition, RAB5A, an early endosome marker, was shown to be a direct target of miR-451a. Moreover, RAB5A is correlated with unfavorable clinical features and shows independent prognostic significance in HGSOC. CONCLUSIONS We found that the miR-451a/RAB5A axis is associated with tumorigenesis and progression through the Ras/Raf/MEK/ERK pathway, providing prognostic indicators and therapeutic targets for patients with HGSOC.
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Affiliation(s)
- Shujie Liu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Kun Wang
- Department of Gynecology, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Zhendan Zhao
- Department of Ultrasound Medcine, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Yu Pang
- Department of Pathology, The Afliated Taian City Central Hospital of Qingdao University, Tai'an, China
| | - Fang Liu
- Department of Gastroenterology, The Afliated Taian City Central Hospital of Qingdao University, Tai'an, China
| | - Pengling Wang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Zhiling Wang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xingsheng Yang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, China
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Chouhan U, Sahu RK, Bhatt S, Kurmi S, Choudhari JK. Emerging Trends in Big Data Analysis in Computational Biology and Bioinformatics in Health Informatics: A Case Study on Epilepsy and Seizures. Methods Mol Biol 2024; 2719:99-119. [PMID: 37803114 DOI: 10.1007/978-1-0716-3461-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
Advanced technology innovations allow cost-effective, high-throughput profiling of biological systems. It enabled genome sequencing in days using advanced technologies (e.g., next-generation sequencing, microarrays, and mass spectrometry). Since technology has been developed, massive biological data (e.g., genomics, proteomics) has been produced cheaply, allowing the "big data" era to create new opportunities to solve medical and biological complications in many disciplines-preventive medicine, biology, Personalized Medicine, gene sequencing, healthcare, and industry. Computational biology and bioinformatics are interdisciplinary fields that develop and apply computational methods (e.g., analytical methods, mathematical modeling, and simulation) to analyze large collections of biological data, such as genetic sequences, cell populations, or protein samples, to make new predictions or discover new biology. Biological data storage, mining, and analysis have challenges because data is much more heterogeneous. In this study, the big data resources of genomics, proteomics, and metabolomics have been explored to solve biological problems using big data analysis approaches. The goal is to build a network of relationship-based gene-disease associations to prioritize phenotypes common to epilepsy and seizure disease. Through network analysis, The 10 seed genes, 22 associated genes, 132 microRNAs, and 38 transcription factors have been identified that have a direct effect on all forms of epilepsy and seizures. The majority of seed genes, according to the results of a functional analysis of seed genes, are involved in the acetylcholine-gated channel complex (10%) and the heterotrimeric G-protein complex (10%) pathways related to cellular components, followed by a role in the regulation of action potential (20%) and positive regulation of vascular endothelial growth factor production (20%) in Epilepsy and Seizures pathways related to biological processes. This study might provide insight into the workings of the disease and shows the importance of continued research into epilepsy and other conditions that can trigger seizure activity.
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Affiliation(s)
- Usha Chouhan
- Department of Mathematics, Bioinformatics & Computer Applications, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh, India
| | - Rakesh Kumar Sahu
- Department of Biotechnology, Government V.Y.T. Post Graduate Autonomous College, Durg, Chhattisgarh, India
| | - Shaifali Bhatt
- Department of Mathematics, Bioinformatics & Computer Applications, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh, India
| | - Sonu Kurmi
- Department of Mathematics, Bioinformatics & Computer Applications, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh, India
| | - Jyoti Kant Choudhari
- Department of Mathematics, Bioinformatics & Computer Applications, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh, India
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Tay AHM, Cinotti R, Sze NSK, Lundqvist A. Inhibition of ERO1a and IDO1 improves dendritic cell infiltration into pancreatic ductal adenocarcinoma. Front Immunol 2023; 14:1264012. [PMID: 38187398 PMCID: PMC10766682 DOI: 10.3389/fimmu.2023.1264012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal and treatment resistant cancers. Due to its desmoplastic and hypoxic nature along with an abundance of myeloid cell infiltration and scarce T cell infiltration, PDAC is considered a cold tumor. Methods Here we sought to investigate myeloid cell infiltration and composition in PDAC spheroids by targeting the hypoxia-associated pathways endoplasmic reticulum oxidoreductase 1 alpha (ERO1a) and indoleamine 2,3-dioxygenase 1 (IDO1). Using MiaPaCa2 spheroids with hypoxic core, we assessed the roles of ERO1a and IDO1 inhibition in modulating monocyte infiltration and differentiation, followed by characterizing immunomodulatory factors secreted using LC-MS/MS. Results Inhibition of ERO1a and IDO1 significantly improved monocyte infiltration and differentiation into dendritic cells. LC-MS/MS analysis of the PDAC spheroid secretome identified downregulation of hypoxia and PDAC pathways, and upregulation of antigen presentation pathways upon inhibition of ERO1a and IDO1. Furthermore, immunomodulatory factors involved in immune infiltration and migration including interleukin-8, lymphocyte cytosolic protein 1, and transgelin-2, were upregulated upon inhibition of ERO1a and IDO1. Discussion Collectively, our results show that inhibition of ERO1a and IDO1 modulates the tumor microenvironment associated with improved monocyte infiltration and differentiation into dendritic cells to potentially influence therapeutic responses in patients with PDAC.
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Affiliation(s)
- Apple Hui Min Tay
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Riccardo Cinotti
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Newman Sui Kwan Sze
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, ON, Canada
| | - Andreas Lundqvist
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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Alotaibi N, Alotaibi MO, Alshammari N, Adnan M, Patel M. Network Pharmacology Combined with Molecular Docking, Molecular Dynamics, and In Vitro Experimental Validation Reveals the Therapeutic Potential of Thymus vulgaris L. Essential Oil (Thyme Oil) against Human Breast Cancer. ACS OMEGA 2023; 8:48344-48359. [PMID: 38144096 PMCID: PMC10734022 DOI: 10.1021/acsomega.3c07782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/26/2023]
Abstract
Breast cancer is a major global health issue for women. Thyme oil, extracted from Thymus vulgaris L., has shown promising anticancer effects. In the present study, we investigated how Thyme oil can influence breast cancer treatment using a multimethod approach. We used network pharmacology to identify the active compounds of Thyme oil, their molecular targets, and the pathways involved in breast cancer. We found that Thyme oil can modulate several key proteins (EGFR, AKT1, ESR1, HSP90AA1, STAT-3, SRC, IL-6, HIF1A, JUN, and BCL2) and pathways (EGFR tyrosine kinase inhibitor resistance, prolactin signaling pathway, HIF-1 signaling pathway, estrogen signaling pathway, ERBB signaling pathway, AGE-RAGE signaling pathway, JAK-STAT signaling pathway, FoxO signaling pathway, and PI3K-AKT signaling pathway) related to breast cancer progression. We then used molecular docking and dynamics to study the interactions and stability of the Thyme oil-compound complexes. We discovered three potent compounds (aromadendrene, α-humulene, and viridiflorene) that can bind strongly to important breast cancer proteins. We also performed in vitro experiments on MCF-7 cells to confirm the cytotoxicity and antiproliferative effects of Thyme oil. We observed that Thyme oil can inhibit cancer cell growth and proliferation at a concentration of 365.37 μg/mL. Overall, our results provide a comprehensive understanding of the pharmacological mechanism of Thyme oil in breast cancer treatment and suggest its potential as a new or adjuvant therapy. Further studies are needed to validate and optimize the therapeutic efficacy of Thyme oil and its active compounds.
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Affiliation(s)
- Nahaa
M. Alotaibi
- Department
of Biology, College of Science, Princess
Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Modhi O. Alotaibi
- Department
of Biology, College of Science, Princess
Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Nawaf Alshammari
- Department
of Biology, College of Science, University
of Ha’il, P.O. Box 2440, Ha’il 55473, Saudi Arabia
| | - Mohd Adnan
- Department
of Biology, College of Science, University
of Ha’il, P.O. Box 2440, Ha’il 55473, Saudi Arabia
| | - Mitesh Patel
- Research
and Development Cell, Department of Biotechnology, Parul Institute
of Applied Sciences, Parul University, Vadodara 391760, India
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Antonietti L, Mariani J, Martínez MJ, Santalla M, Vensentini N, Kyle DA, de Abreu M, Tajer C, Lacunza E, Ferrero P. Circulating microRNAs as biomarkers of Chagas cardiomyopathy. Front Cardiovasc Med 2023; 10:1250029. [PMID: 38173812 PMCID: PMC10762800 DOI: 10.3389/fcvm.2023.1250029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Background Chagas cardiomyopathy (CHCM) is the most important clinical manifestation of Chagas disease. The analysis of cardiac miRNAs may contribute to predicting the progression to CHCM in Chagas indeterminate phase and/or to the differential diagnosis for cardiomyopathy. Methods We carried out a case-control study to identify circulating miRNAs associated with CHCM. We assigned 104 participants to four groups: healthy controls (HC), Chagas non-cardiomyopathy controls, CHCM cases, and ischemic cardiomyopathy controls. We performed a clinical, echocardiographic, and laboratory evaluation and profiled circulating miRNA in the serum samples. Results Differences between groups were observed in clinical variables and in the analysis of miRNAs. Compared to HC, CHCM participants had 4 over-expressed and 6 under-expressed miRNAs; miR-95-3p and miR-130b-3p were upregulated in CHCM compared with controls, Chagas non-cardiomyopathy and ischemic cardiomyopathy participants, suggesting that might be a hallmark of CHCM. Analysis of gene targets associated with cardiac injury yielded results of genes involved in arrhythmia generation, cardiomegaly, and hypertrophy. Conclusions Our data suggest that the expression of circulating miRNAs identified by deep sequencing in CHCM could be associated with different cardiac phenotypes in CHCM subjects, compared with Chagas non-CHCM, ischemic cardiomyopathy controls, and healthy controls.
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Affiliation(s)
- Laura Antonietti
- Department of Cardiology, El Cruce Hospital, Florencio Varela, Buenos Aires, Argentina
- Health Sciences Institute, Arturo Jauretche National University, Florencio Varela, Buenos Aires, Argentina
| | - Javier Mariani
- Department of Cardiology, El Cruce Hospital, Florencio Varela, Buenos Aires, Argentina
- Health Sciences Institute, Arturo Jauretche National University, Florencio Varela, Buenos Aires, Argentina
| | - María Jose Martínez
- Department of Cardiology, El Cruce Hospital, Florencio Varela, Buenos Aires, Argentina
| | - Manuela Santalla
- Cardiovascular Research Center Dr. Horacio Cingolani, Faculty of Medical Sciences, La Plata National University, La Plata, Buenos Aires, Argentina
| | - Natalia Vensentini
- Department of Cardiology, El Cruce Hospital, Florencio Varela, Buenos Aires, Argentina
| | - Diego Alfredo Kyle
- Department of Cardiology, El Cruce Hospital, Florencio Varela, Buenos Aires, Argentina
| | - Maximiliano de Abreu
- Department of Cardiology, El Cruce Hospital, Florencio Varela, Buenos Aires, Argentina
- Health Sciences Institute, Arturo Jauretche National University, Florencio Varela, Buenos Aires, Argentina
| | - Carlos Tajer
- Department of Cardiology, El Cruce Hospital, Florencio Varela, Buenos Aires, Argentina
- Health Sciences Institute, Arturo Jauretche National University, Florencio Varela, Buenos Aires, Argentina
| | - Ezequiel Lacunza
- Basic and Applied Inmunological Research, Faculty of Medical Sciences, La Plata National University, La Plata, Buenos Aires, Argentina
| | - Paola Ferrero
- Cardiovascular Research Center Dr. Horacio Cingolani, Faculty of Medical Sciences, La Plata National University, La Plata, Buenos Aires, Argentina
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Rejali L, Nazemalhosseini-Mojarad E, Valle L, Maghsoudloo M, Asadzadeh Aghdaei H, Mohammadpoor H, Zali MR, Khanabadi B, Entezari M, Hushmandi K, Taheriazam A, Hashemi M. Identification of antisense and sense RNAs of intracrine fibroblast growth factor components as novel biomarkers in colorectal cancer and in silico studies for drug and nanodrug repurposing. ENVIRONMENTAL RESEARCH 2023; 239:117117. [PMID: 37805185 DOI: 10.1016/j.envres.2023.117117] [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: 06/04/2023] [Revised: 08/29/2023] [Accepted: 09/09/2023] [Indexed: 10/09/2023]
Abstract
INTRODUCTION Colorectal cancer (CRC) is one of the most malignant tumors and in which various efforts for screening is inconclusive.The intracrine FGF panel, the non-tyrosine kinase receptors (NTKR) FGFs and affiliated antisenses play a pivotal role in FGF signaling.The expression levels of coding and non-coding intracrine FGFs were assessed in CRC donors.Also, substantial costs and slow pace of drug discovery give high attraction to repurpose of previously discovered drugs to new opportunities. OBJECTIVES The aim of present study was to evaluate the potential role of the coding and non-coding intracrine FGFs as a new biomarkers for CRC cases and defining drug repurposing to alleviate FGF down regulation. METHODS RNA-seq data of colon adenocarcinomas (COAD) was downloaded using TCGA biolinks package in R.The DrugBank database (https://go.drugbank.com/) was used to extract interactions between drugs and candidate genes. A total of 200 CRC patients with detailed criteria were enrolled.RNAs were extracted with TRIzol-based protocol and amplified via LightCycler® instrument.FGF11 and FGF13 proteins validation was performed by used of immunohistochemistry technique in tumor and non-tumoral samples.Pearson's correlation analysis and ROC curve plotted by Prism 8.0 software. RESULTS RNA-seq data from TCGA was analyzed by normalizing with edgeR.Differentially expressed gene (DEG) analysis was generated. WCC algorithm extracted the most significant genes with a total of 47 genes. Expression elevation of iFGF antisenses (12AS,13As,14AS) compared with the normal colon tissue were observed (P = 0.0003,P = 0.042,P = 0.026, respectively). Moreover,a significant decrease in expression of the corresponding sense iFGF genes was detected (P < 0.0001).Plotted receiver operating characteristic (ROC) curves for iFGF components' expression showed an area of over 0.70 (FGF11-13: 0.71% and FGF12-14: 0.78%, P < 0.001) for sense mRNA expression, with the highest sensitivity for FGF12 (92.8%) and lowest for FGF11 (61.41%).The artificial intelligence (AI) revealed the valproic acid as a repurposing drug to relief the down regulation of FGF12 and 13 in CRC patients. CONCLUSION Intracrine FGFs panel was down regulated versus up regulation of dependent antisenses. Thus, developing novel biomarkers based on iFGF can be considered as a promising strategy for CRC screening.In advanced, valporic acid detected by AI as a repurposing drug which may be applied in clinical trials for CRC treatment.
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Affiliation(s)
- Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Mazaher Maghsoudloo
- Laboratory of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadis Mohammadpoor
- Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Binazir Khanabadi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Centre, Farhikhtegan Hospital, Islamic Azad University, Tehran Medical Sciences, Tehran, Iran
| | - Kiavash Hushmandi
- Department of Epidemiology, Faculty Of Veterinary Medicine, University Of Tehran, Tehran, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Centre, Farhikhtegan Hospital, Islamic Azad University, Tehran Medical Sciences, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Centre, Farhikhtegan Hospital, Islamic Azad University, Tehran Medical Sciences, Tehran, Iran.
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Zulian V, Fiscon G, Paci P, Garbuglia AR. Hepatitis B Virus and microRNAs: A Bioinformatics Approach. Int J Mol Sci 2023; 24:17224. [PMID: 38139051 PMCID: PMC10743825 DOI: 10.3390/ijms242417224] [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: 10/12/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In recent decades, microRNAs (miRNAs) have emerged as key regulators of gene expression, and the identification of viral miRNAs (v-miRNAs) within some viruses, including hepatitis B virus (HBV), has attracted significant attention. HBV infections often progress to chronic states (CHB) and may induce fibrosis/cirrhosis and hepatocellular carcinoma (HCC). The presence of HBV can dysregulate host miRNA expression, influencing several biological pathways, such as apoptosis, innate and immune response, viral replication, and pathogenesis. Consequently, miRNAs are considered a promising biomarker for diagnostic, prognostic, and treatment response. The dynamics of miRNAs during HBV infection are multifaceted, influenced by host variability and miRNA interactions. Given the ability of miRNAs to target multiple messenger RNA (mRNA), understanding the viral-host (human) interplay is complex but essential to develop novel clinical applications. Therefore, bioinformatics can help to analyze, identify, and interpret a vast amount of miRNA data. This review explores the bioinformatics tools available for viral and host miRNA research. Moreover, we introduce a brief overview focusing on the role of miRNAs during HBV infection. In this way, this review aims to help the selection of the most appropriate bioinformatics tools based on requirements and research goals.
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Affiliation(s)
- Verdiana Zulian
- Virology Laboratory, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
| | - Giulia Fiscon
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (P.P.)
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (P.P.)
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy
| | - Anna Rosa Garbuglia
- Virology Laboratory, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
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Barchiki F, Fracaro L, Dominguez AC, Senegaglia AC, Vaz IM, Soares P, de Moura SAB, Brofman PRS. Biocompatibility of ABS and PLA Polymers with Dental Pulp Stem Cells Enhance Their Potential Biomedical Applications. Polymers (Basel) 2023; 15:4629. [PMID: 38139880 PMCID: PMC10747830 DOI: 10.3390/polym15244629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Polylactic Acid (PLA) and Acrylonitrile-Butadiene-Styrene (ABS) are commonly used polymers in 3D printing for biomedical applications. Dental Pulp Stem Cells (DPSCs) are an accessible and proliferative source of stem cells with significant differentiation potential. Limited knowledge exists regarding the biocompatibility and genetic safety of ABS and PLA when in contact with DPSCs. This study aimed to investigate the impact of PLA and ABS on the adhesion, proliferation, osteogenic differentiation, genetic stability, proteomics, and immunophenotypic profile of DPSCs. A total of three groups, 1- DPSC-control, 2- DPSC+ABS, and 3- DPSC+PLA, were used in in vitro experiments to evaluate cell morphology, proliferation, differentiation capabilities, genetic stability, proteomics (secretome), and immunophenotypic profiles regarding the interaction between DPSCs and polymers. Both ABS and PLA supported the adhesion and proliferation of DPSCs without exhibiting significant cytotoxic effects and maintaining the capacity for osteogenic differentiation. Genetic stability, proteomics, and immunophenotypic profiles were unaltered in DPSCs post-contact with these polymers, highlighting their biosafety. Our findings suggest that ABS and PLA are biocompatible with DPSCs and demonstrate potential in dental or orthopedic applications; the choice of the polymer will depend on the properties required in treatment. These promising results stimulate further studies to explore the potential therapeutic applications in vivo using prototyped polymers in personalized medicine.
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Affiliation(s)
- Fabiane Barchiki
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba 80215-901, Brazil; (L.F.); (A.C.S.); (I.M.V.); (P.R.S.B.)
- INCT—REGENERA National Institute of Science and Technology in Regenerative Medicine, Rio de Janeiro 21941-902, Brazil
| | - Letícia Fracaro
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba 80215-901, Brazil; (L.F.); (A.C.S.); (I.M.V.); (P.R.S.B.)
- INCT—REGENERA National Institute of Science and Technology in Regenerative Medicine, Rio de Janeiro 21941-902, Brazil
| | - Alejandro Correa Dominguez
- Laboratory of Basic Biology of Stem Cells, Carlos Chagas Institute, Fiocruz-PR, Curitiba 81350-010, Brazil;
| | - Alexandra Cristina Senegaglia
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba 80215-901, Brazil; (L.F.); (A.C.S.); (I.M.V.); (P.R.S.B.)
- INCT—REGENERA National Institute of Science and Technology in Regenerative Medicine, Rio de Janeiro 21941-902, Brazil
| | - Isadora May Vaz
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba 80215-901, Brazil; (L.F.); (A.C.S.); (I.M.V.); (P.R.S.B.)
- INCT—REGENERA National Institute of Science and Technology in Regenerative Medicine, Rio de Janeiro 21941-902, Brazil
| | - Paulo Soares
- LaBES—Laboratory of Biomaterials and Surface Engineering, Polytechnic School, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba 80215-901, Brazil;
| | - Sérgio Adriane Bezerra de Moura
- Departament of Morphology, Campus Universitário Lagoa Nova, Universidade Federal do Rio Grande do Norte (UFRN), Natal 59072-970, Brazil;
| | - Paulo Roberto Slud Brofman
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba 80215-901, Brazil; (L.F.); (A.C.S.); (I.M.V.); (P.R.S.B.)
- INCT—REGENERA National Institute of Science and Technology in Regenerative Medicine, Rio de Janeiro 21941-902, Brazil
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da Silva-Januário ME, da Costa CS, Tavares LA, Oliveira AK, Januário YC, de Carvalho AN, Cassiano MHA, Rodrigues RL, Miller ME, Palameta S, Arns CW, Arruda E, Paes Leme AF, daSilva LLP. HIV-1 Nef Changes the Proteome of T Cells Extracellular Vesicles Depleting IFITMs and Other Antiviral Factors. Mol Cell Proteomics 2023; 22:100676. [PMID: 37940003 PMCID: PMC10746527 DOI: 10.1016/j.mcpro.2023.100676] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 10/19/2023] [Accepted: 11/05/2023] [Indexed: 11/10/2023] Open
Abstract
Extracellular vesicles (EVs) are biomolecule carriers for intercellular communication in health and disease. Nef is a HIV virulence factor that is released from cells within EVs and is present in plasma EVs of HIV-1 infected individuals. We performed a quantitative proteomic analysis to fully characterize the Nef-induced changes in protein composition of T cell-derived EVs and identify novel host targets of HIV. Several proteins with well-described roles in infection or not previously associated with HIV pathogenesis were specifically modulated by Nef in EVs. Among the downregulated proteins are the interferon-induced transmembrane 1, 2, and 3 (IFITM1-3) proteins, broad-spectrum antiviral factors known to be cell-to-cell transferable by EVs. We demonstrate that Nef depletes IFITM1-3 from EVs by excluding these proteins from the plasma membrane and lipid rafts, which are sites of EVs biogenesis in T cells. Our data establish Nef as a modulator of EVs' global protein content and as an HIV factor that antagonizes IFITMs.
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Affiliation(s)
- Mara E da Silva-Januário
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Cristina S da Costa
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Lucas A Tavares
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ana K Oliveira
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Yunan C Januário
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Andreia N de Carvalho
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Murilo H A Cassiano
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Roger L Rodrigues
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Michael E Miller
- Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Soledad Palameta
- Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Clarice W Arns
- Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Eurico Arruda
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Adriana F Paes Leme
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Luis L P daSilva
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil.
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Ferreira GA, Thomé CH, Izumi C, Grassi ML, Lanfredi GP, Smolka M, Faça VM, Candido Dos Reis FJ. Proteomic analysis of exosomes secreted during the epithelial-mesenchymal transition and potential biomarkers of mesenchymal high-grade serous ovarian carcinoma. J Ovarian Res 2023; 16:232. [PMID: 38031074 PMCID: PMC10685605 DOI: 10.1186/s13048-023-01304-0] [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: 08/15/2023] [Accepted: 10/28/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND The epithelial-mesenchymal transition (EMT) promotes cell signaling and morphology alterations, contributing to cancer progression. Exosomes, extracellular vesicles containing proteins involved in cell-cell communication, have emerged as a potential source of biomarkers for several diseases. METHODS Our aim was to assess the proteome content of exosomes secreted after EMT-induction to identify potential biomarkers for ovarian cancer classification. EMT was induced in the ovarian cancer cell line CAOV3 by treating it with EGF (10 ng/mL) for 96 h following 24 h of serum deprivation. Subsequently, exosomes were isolated from the supernatant using selective centrifugation after decellularization, and their characteristics were determined. The proteins present in the exosomes were extracted, identified, and quantified using Label-Free-Quantification (LFQ) via Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). To identify potential biomarkers, the obtained proteomic data was integrated with the TGGA database for mRNA expression using principal component analysis and a conditional inference tree. RESULTS The exosomes derived from CAOV3 cells exhibited similar diameter and morphology, measuring approximately 150 nm, regardless of whether they were subjected to EMT stimulation or not. The proteomic analysis of proteins from CAOV3-derived exosomes revealed significant differential regulation of 157 proteins, with 100 showing upregulation and 57 downregulation upon EMT induction. Further comparison of the upregulated proteins with the TCGA transcriptomic data identified PLAU, LAMB1, COL6A1, and TGFB1 as potential biomarkers of the mesenchymal HGSOC subtype. CONCLUSIONS The induction of EMT, the isolation of exosomes, and the subsequent proteomic analysis highlight potential biomarkers for an aggressive ovarian cancer subtype. Further investigation into the role of these proteins is warranted to enhance our understanding of ovarian cancer outcomes.
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Affiliation(s)
- Germano Aguiar Ferreira
- Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, Ribeirão Preto, SP, Brazil
- Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, and Center for Cell Based Therapy, University of São Paulo, Ribeirão Preto, Brazil
| | - Carolina Hassibe Thomé
- Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, Ribeirão Preto, SP, Brazil
- Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, and Center for Cell Based Therapy, University of São Paulo, Ribeirão Preto, Brazil
| | - Clarice Izumi
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Mariana Lopes Grassi
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Guilherme Pauperio Lanfredi
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Marcus Smolka
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Vitor Marcel Faça
- Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, and Center for Cell Based Therapy, University of São Paulo, Ribeirão Preto, Brazil
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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Li G, Yan X. Long non-coding RNA GAS5 promotes cisplatin-chemosensitivity of osteosarcoma cells via microRNA-26b-5p/TP53INP1 axis. J Orthop Surg Res 2023; 18:890. [PMID: 37993867 PMCID: PMC10666340 DOI: 10.1186/s13018-023-04387-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023] Open
Abstract
Osteosarcoma is a common malignant bone tumor. Cisplatin (DDP) achieves a high response rate in osteosarcoma. Here we aim to study the dysregulation of long non-coding RNA the growth arrest-specific transcript 5 (GAS5), and its roles in DDP-resistance of osteosarcoma. The expression of mRNA and microRNA in osteosarcoma tissues and osteosarcoma cell lines were detected by quantitative reverse-transcription polymerase chain reaction, and protein expression levels were measured by western blotting assay. Cell Counting Kit-8 and 5-Ethynyl-2'-deoxyuridine were used to measure cell proliferation. Flow cytometer assay was used to evaluate cell apoptosis. The interactions between miR-26b-5p and GAS5 or tumor protein p53-induced nuclear protein 1 (TP53INP1) were verified by dual luciferase reporter along with biotin RNA pull-down assays. GAS5 was identified to be significantly lowly expressed in osteosarcoma samples especially in cisplatin-resistant (DDP-resistant) tissues. GAS5 was also downregulated in DDP-resistant cells. Over-expressed GAS5 prominently increased the sensitivity of osteosarcoma cells to DDP in vitro. Furthermore, over-expression of GAS5 suppressed cell proliferation and facilitated apoptosis of DDP-resistant cells. Mechanistically, GAS5 sponged miR-26b-5p, over-expression of which reversed the effects of GAS5 on cell proliferation and apoptosis of DDP-resistant cells. In addition, miR-26b-5p targeted TP53INP1. TP53INP1 abrogated the functions of miR-26b-5p on cell proliferation and apoptosis in DDP-resistant cells. Taken together, GAS5 enhanced the sensitivity of osteosarcoma cells to DDP via GAS5/miR-26b-5p/TP53INP1 axis. Therefore, GAS5 may be a potential indicator for the management of osteosarcoma.
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Affiliation(s)
- Guowei Li
- Department of Spine Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121000, Liaoning, China
| | - Xue Yan
- Respiration Medicine, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, 121000, Liaoning, China.
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Adnan M, Siddiqui AJ, Ashraf SA, Bardakci F, Alreshidi M, Badraoui R, Noumi E, Tepe B, Sachidanandan M, Patel M. Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation to Elucidate the Molecular Targets and Potential Mechanism of Phoenix dactylifera (Ajwa Dates) against Candidiasis. Pathogens 2023; 12:1369. [PMID: 38003833 PMCID: PMC10674288 DOI: 10.3390/pathogens12111369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Candidiasis, caused by opportunistic fungal pathogens of the Candida genus, poses a significant threat to immunocompromised individuals. Natural compounds derived from medicinal plants have gained attention as potential sources of anti-fungal agents. Ajwa dates (Phoenix dactylifera L.) have been recognized for their diverse phytochemical composition and therapeutic potential. In this study, we employed a multi-faceted approach to explore the anti-candidiasis potential of Ajwa dates' phytochemicals. Utilizing network pharmacology, we constructed an interaction network to elucidate the intricate relationships between Ajwa dates phytoconstituents and the Candida-associated molecular targets of humans. Our analysis revealed key nodes in the network (STAT3, IL-2, PTPRC, STAT1, CASP1, ALB, TP53, TLR4, TNF and PPARG), suggesting the potential modulation of several crucial processes (the regulation of the response to a cytokine stimulus, regulation of the inflammatory response, positive regulation of cytokine production, cellular response to external stimulus, etc.) and fungal pathways (Th17 cell differentiation, the Toll-like receptor signaling pathway, the C-type lectin receptor signaling pathway and necroptosis). To validate these findings, molecular docking studies were conducted, revealing the binding affinities of the phytochemicals towards selected Candida protein targets of humans (ALB-rutin (-9.7 kJ/mol), STAT1-rutin (-9.2 kJ/mol), STAT3-isoquercetin (-8.7 kJ/mol), IL2-β-carotene (-8.5 kJ/mol), CASP1-β-carotene (-8.2 kJ/mol), TP53-isoquercetin (-8.8 kJ/mol), PPARG-luteolin (-8.3 kJ/mol), TNF-βcarotene (-7.7 kJ/mol), TLR4-rutin (-7.4 kJ/mol) and PTPRC-rutin (-7.0 kJ/mol)). Furthermore, molecular dynamics simulations of rutin-ALB and rutin-STAT1 complex were performed to gain insights into the stability and dynamics of the identified ligand-target complexes over time. Overall, the results not only contribute to the understanding of the molecular interactions underlying the anti-fungal potential of specific phytochemicals of Ajwa dates in humans but also provide a rational basis for the development of novel therapeutic strategies against candidiasis in humans. This study underscores the significance of network pharmacology, molecular docking and dynamics simulations in accelerating the discovery of natural products as effective anti-fungal agents. However, further experimental validation of the identified compounds is warranted to translate these findings into practical therapeutic applications.
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Affiliation(s)
- Mohd Adnan
- Department of Biology, College of Science, University of Ha’il, Ha’il 55473, Saudi Arabia; (M.A.)
- Medical and Diagnostic Research Centre, University of Ha’il, Ha’il 55473, Saudi Arabia
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha’il, Ha’il 55473, Saudi Arabia; (M.A.)
- Medical and Diagnostic Research Centre, University of Ha’il, Ha’il 55473, Saudi Arabia
| | - Syed Amir Ashraf
- Medical and Diagnostic Research Centre, University of Ha’il, Ha’il 55473, Saudi Arabia
- Department of Clinical Nutrition, College of Applied Medial Sciences, University of Ha’il, Ha’il 55473, Saudi Arabia
| | - Fevzi Bardakci
- Department of Biology, College of Science, University of Ha’il, Ha’il 55473, Saudi Arabia; (M.A.)
- Medical and Diagnostic Research Centre, University of Ha’il, Ha’il 55473, Saudi Arabia
| | - Mousa Alreshidi
- Department of Biology, College of Science, University of Ha’il, Ha’il 55473, Saudi Arabia; (M.A.)
- Medical and Diagnostic Research Centre, University of Ha’il, Ha’il 55473, Saudi Arabia
| | - Riadh Badraoui
- Department of Biology, College of Science, University of Ha’il, Ha’il 55473, Saudi Arabia; (M.A.)
- Medical and Diagnostic Research Centre, University of Ha’il, Ha’il 55473, Saudi Arabia
| | - Emira Noumi
- Department of Biology, College of Science, University of Ha’il, Ha’il 55473, Saudi Arabia; (M.A.)
- Medical and Diagnostic Research Centre, University of Ha’il, Ha’il 55473, Saudi Arabia
| | - Bektas Tepe
- Department of Molecular Biology and Genetics, Faculty of Science and Literature, Kilis 7 Aralik University, Kilis TR-79000, Turkey
| | - Manojkumar Sachidanandan
- Medical and Diagnostic Research Centre, University of Ha’il, Ha’il 55473, Saudi Arabia
- Department of Oral Radiology, College of Dentistry, University of Ha’il, Ha’il 55473, Saudi Arabia
| | - Mitesh Patel
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara 391760, India
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Su W, Tian Y, Wei Y, Hao F, Ji J. Key genes and immune infiltration in chronic spontaneous urticaria: a study of bioinformatics and systems biology. Front Immunol 2023; 14:1279139. [PMID: 38045687 PMCID: PMC10693338 DOI: 10.3389/fimmu.2023.1279139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Background Chronic spontaneous urticaria (CSU) is defined by the spontaneous occurrence of wheals and/or angioedema for >6 weeks. The pathogenesis involves skin mast cells, but the complex causes of their activation remain to be characterized in detail. Objectives To explore disease-driving genes and biological pathways in CSU. Methods Two microarray data sets, e.g., GSE57178 and GSE72540, with mRNA information of skin from CSU patients, were downloaded from the Gene Expression Omnibus (GEO) database. An integrated bioinformatics pipeline including identification of differentially expressed genes (DEGs), functional enrichment analysis, protein-protein interaction (PPI) network analysis, co-expression and drug prediction analysis, and immune and stromal cells deconvolution analyses were applied to identify hub genes and key drivers of CSU pathogenesis. Results In total, we identified 92 up-regulated and 7 down-regulated genes in CSU lesions. These were significantly enriched in CSU-related pathways such as TNF, NF-κB, and JAK-STAT signaling. Based on PPI network modeling, four genes, i.e., IL-6, TLR-4, ICAM-1, and PTGS-2, were computationally identified as key pathogenic players in CSU. Immune infiltration analyses indicated that dendritic cells, Th2 cells, mast cells, megakaryocyte-erythroid progenitor, preadipocytes, and M1 macrophages were increased in lesional CSU skin. Conclusion Our results offer new insights on the pathogenesis of CSU and suggest that TNF, NF-κB, JAK-STAT, IL-6, TLR-4, ICAM-1, and PTGS-2 may be candidate targets for novel CSU treatments.
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Affiliation(s)
- Wenxing Su
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Dermatology and Plastic Surgery Center, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yu Tian
- Department of Dermatology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yuqian Wei
- Department of Dermatology, Nantong Third People’s Hospital, Nantong, China
| | - Fei Hao
- Dermatology and Plastic Surgery Center, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiang Ji
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Sundaramurthi H, Tonelotto V, Wynne K, O'Connell F, O’Reilly E, Costa-Garcia M, Kovácsházi C, Kittel A, Marcone S, Blanco A, Pallinger E, Hambalkó S, Piulats Rodriguez JM, Ferdinandy P, O'Sullivan J, Matallanas D, Jensen LD, Giricz Z, Kennedy BN. Ergolide mediates anti-cancer effects on metastatic uveal melanoma cells and modulates their cellular and extracellular vesicle proteomes. OPEN RESEARCH EUROPE 2023; 3:88. [PMID: 37981907 PMCID: PMC10654492 DOI: 10.12688/openreseurope.15973.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
Background Uveal melanoma is a poor prognosis cancer. Ergolide, a sesquiterpene lactone isolated from Inula Brittanica, exerts anti-cancer properties. The objective of this study was to 1) evaluate whether ergolide reduced metastatic uveal melanoma (MUM) cell survival/viability in vitro and in vivo; and 2) to understand the molecular mechanism of ergolide action. Methods Ergolide bioactivity was screened via long-term proliferation assay in UM/MUM cells and in zebrafish MUM xenograft models. Mass spectrometry profiled proteins modulated by ergolide within whole cell or extracellular vesicle (EVs) lysates of the OMM2.5 MUM cell line. Protein expression was analyzed by immunoblots and correlation analyses to UM patient survival used The Cancer Genome Atlas (TCGA) data. Results Ergolide treatment resulted in significant, dose-dependent reductions (48.5 to 99.9%; p<0.0001) in OMM2.5 cell survival in vitro and of normalized primary zebrafish xenograft fluorescence (56%; p<0.0001) in vivo, compared to vehicle controls. Proteome-profiling of ergolide-treated OMM2.5 cells, identified 5023 proteins, with 52 and 55 proteins significantly altered at 4 and 24 hours, respectively ( p<0.05; fold-change >1.2). Immunoblotting of heme oxygenase 1 (HMOX1) and growth/differentiation factor 15 (GDF15) corroborated the proteomic data. Additional proteomics of EVs isolated from OMM2.5 cells treated with ergolide, detected 2931 proteins. There was a large overlap with EV proteins annotated within the Vesiclepedia compendium. Within the differentially expressed proteins, the proteasomal pathway was primarily altered. Interestingly, BRCA2 and CDKN1A Interacting Protein (BCCIP) and Chitinase Domain Containing 1 (CHID1), were the only proteins significantly differentially expressed by ergolide in both the OMM2.5 cellular and EV isolates and they displayed inverse differential expression in the cells versus the EVs. Conclusions Ergolide is a novel, promising anti-proliferative agent for UM/MUM. Proteomic profiling of OMM2.5 cellular/EV lysates identified candidate pathways elucidating the action of ergolide and putative biomarkers of UM, that require further examination.
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Affiliation(s)
- Husvinee Sundaramurthi
- UCD Conway Institute, University College Dublin, Dublin, Leinster, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Leinster, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Leinster, Ireland
- UCD School of Medicine, University College Dublin, Dublin, Leinster, Ireland
| | - Valentina Tonelotto
- UCD Conway Institute, University College Dublin, Dublin, Leinster, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Leinster, Ireland
- Xenopat S.L., Business Bioincubator, Bellvitge Health Science Campus, Barcelona, 08907 L'Hospitalet de Llobregat, Spain
| | - Kieran Wynne
- Systems Biology Ireland, University College Dublin, Dublin, Leinster, Ireland
| | - Fiona O'Connell
- Department of Surgery, Trinity Translational Medicine Institute, Trinity St. James's Cancer Institute, St. James's Hospital, Trinity College Dublin, Dublin, Ireland
| | - Eve O’Reilly
- UCD Conway Institute, University College Dublin, Dublin, Leinster, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Leinster, Ireland
| | - Marcel Costa-Garcia
- Medical Oncology Department, Catalan Institute of Cancer (ICO), IDIBELL-OncoBell, Barcelona, Spain
| | - Csenger Kovácsházi
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Agnes Kittel
- Institute of Experimental Medicine, Budapest, Hungary
| | - Simone Marcone
- Department of Surgery, Trinity Translational Medicine Institute, Trinity St. James's Cancer Institute, St. James's Hospital, Trinity College Dublin, Dublin, Ireland
| | - Alfonso Blanco
- UCD Conway Institute, University College Dublin, Dublin, Leinster, Ireland
| | - Eva Pallinger
- Department of Genetics and Immunobiology, Semmelweis University, Budapest, Hungary
| | | | | | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Jacintha O'Sullivan
- Department of Surgery, Trinity Translational Medicine Institute, Trinity St. James's Cancer Institute, St. James's Hospital, Trinity College Dublin, Dublin, Ireland
| | - David Matallanas
- Systems Biology Ireland, University College Dublin, Dublin, Leinster, Ireland
- UCD School of Medicine, University College Dublin, Dublin, Leinster, Ireland
| | | | - Zoltán Giricz
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Breandán N. Kennedy
- UCD Conway Institute, University College Dublin, Dublin, Leinster, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Leinster, Ireland
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Turner N, Abeysinghe P, Flay H, Meier S, Sadowski P, Mitchell MD. SWATH-MS Analysis of Blood Plasma and Circulating Small Extracellular Vesicles Enables Detection of Putative Protein Biomarkers of Fertility in Young and Aged Dairy Cows. J Proteome Res 2023; 22:3580-3595. [PMID: 37830897 DOI: 10.1021/acs.jproteome.3c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
The development of biomarkers of fertility could provide benefits for the genetic improvement of dairy cows. Circulating small extracellular vesicles (sEVs) show promise as diagnostic or prognostic markers since their cargo reflects the metabolic state of the cell of origin; thus, they mirror the physiological status of the host. Here, we employed data-independent acquisition mass spectrometry to survey the plasma and plasma sEV proteomes of two different cohorts of Young (Peripubertal; n = 30) and Aged (Primiparous; n = 20) dairy cows (Bos taurus) of high- and low-genetic merit of fertility and known pregnancy outcomes (ProteomeXchange data set identifier PXD042891). We established predictive models of fertility status with an area under the curve of 0.97 (sEV; p value = 3.302e-07) and 0.95 (plasma; p value = 6.405e-08). Biomarker candidates unique to high-fertility Young cattle had a sensitivity of 0.77 and specificity of 0.67 (*p = 0.0287). Low-fertility biomarker candidates uniquely identified in sEVs from Young and Aged cattle had a sensitivity and specificity of 0.69 and 1.0, respectively (***p = 0.0005). Our bioinformatics pipeline enabled quantification of plasma and circulating sEV proteins associated with fertility phenotype. Further investigations are warranted to validate this research in a larger population, which may lead to improved classification of fertility status in cattle.
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Affiliation(s)
- Natalie Turner
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| | - Pevindu Abeysinghe
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| | - Holly Flay
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - Susanne Meier
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - Pawel Sadowski
- Central Analytical Research Facility (CARF), QUT, Gardens Point Campus, 2 George Street, Brisbane City, Queensland 4000, Australia
| | - Murray D Mitchell
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
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Pavithran H, Kumavath R, Ghosh P. Transcriptome Profiling of Cardiac Glycoside Treatment Reveals EGR1 and Downstream Proteins of MAPK/ERK Signaling Pathway in Human Breast Cancer Cells. Int J Mol Sci 2023; 24:15922. [PMID: 37958905 PMCID: PMC10647710 DOI: 10.3390/ijms242115922] [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: 09/28/2023] [Revised: 10/24/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
Cardiac glycosides (CGs) constitute a group of steroid-like compounds renowned for their effectiveness in treating cardiovascular ailments. In recent times, there has been growing recognition of their potential use as drug leads in cancer treatment. In our prior research, we identified three highly promising CG compounds, namely lanatoside C (LC), peruvoside (PS), and strophanthidin (STR), which exhibited significant antitumor effects in lung, liver, and breast cancer cell lines. In this study, we investigated the therapeutic response of these CGs, with a particular focus on the MCF-7 breast cancer cell line. We conducted transcriptomic profiling and further validated the gene and protein expression changes induced by treatment through qRT-PCR, immunoblotting, and immunocytochemical analysis. Additionally, we demonstrated the interactions between the ligands and target proteins using the molecular docking approach. The transcriptome analysis revealed a cluster of genes with potential therapeutic targets involved in cytotoxicity, immunomodulation, and tumor-suppressor pathways. Subsequently, we focused on cross-validating the ten most significantly expressed genes, EGR1, MAPK1, p53, CCNK, CASP9, BCL2L1, CDK7, CDK2, CDK2AP1, and CDKN1A, through qRT-PCR, and their by confirming the consistent expression pattern with RNA-Seq data. Notably, among the most variable genes, we identified EGR1, the downstream effector of the MAPK signaling pathway, which performs the regulatory function in cell proliferation, tumor invasion, and immune regulation. Furthermore, we substantiated the influence of CG compounds on translational processes, resulting in an alteration in protein expression upon treatment. An additional analysis of ligand-protein interactions provided further evidence of the robust binding affinity between LC, PS, and STR and their respective protein targets. These findings underscore the intense anticancer activity of the investigated CGs, shedding light on potential target genes and elucidating the probable mechanism of action of CGs in breast cancer.
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Affiliation(s)
- Honey Pavithran
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod 671320, India;
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod 671320, India;
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA;
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Abu Aisheh M, Kayili HM, Numanoglu Cevik Y, Kanat MA, Salih B. Composition characterization of various viperidae snake venoms using MS-based proteomics N-glycoproteomics and N-glycomics. Toxicon 2023; 235:107328. [PMID: 37884129 DOI: 10.1016/j.toxicon.2023.107328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
Viperidae snake species is widely abundant and responsible for most envenomation cases in Turkey. The structural and compositional profiles of snake venom have been investigated to study the venom component variation across different species and to profile the venom biological activity variation against prey. In this context, we used proteomics, glycoproteomics and glycomics strategies to characterize the protein, glycoproteins and glycan structural and compositional profiles of various snake venoms in the Viperidae family. Moreover, we compared these profiles using the downstream bioinformatics and machine learning classification modules. The overall mass spectrometry profiles identified 144 different proteins, 36 glycoproteins and 78 distinct N-glycan structures varying in composition across the five venoms. A high amount of the characterized proteins belongs to the glycosylated protein family Trypsin-like serine protease (Tryp_SPc), Disintegrin (DISIN), and ADAM Cysteine-Rich (ACR). Most identified N-glycans have a complex chain carrying galactosylated N-glycans abundantly. The glycan composition data obtained from glycoproteomics aligns consistently with the findings from glycomics. The clustering and principal component analyses (PCA) illustrated the composition-based similarities and differences between each snake venom species' proteome, glycoproteome and glycan profiles. Specifically, the N-glycan profiles of M. xanthina (Mx) and V. a. ammodytes (Vaa) venoms were identical and difficult to differentiate; in contrast, their proteome profiles were distinct. Interestingly, the variety of the proteins across the species highlighted the impact of glycosylation on the diversity of the glycosylated protein families. This proposed high throughput approach provides accurate and comprehensive profiles of the composition and function of various Viperidae snake venoms.
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Affiliation(s)
- Marwa Abu Aisheh
- Department of Chemistry, Faculty of Science, Hacettepe University, 06800, Ankara, Turkey
| | - Haci Mehmet Kayili
- Department of Medical Engineering, Faculty of Engineering, Karabük University, 78000, Karabük, Turkey
| | - Yasemin Numanoglu Cevik
- Microbiology Reference Laboratory, Turkish Public Health Institute, Ministery of Health, 06430, Ankara, Turkey
| | - Mehmet Ali Kanat
- Microbiology and Reference Laboratory and Biological Products Department, General Directorate of Public Health, Minister of Health, 06430, Ankara, Turkey
| | - Bekir Salih
- Department of Chemistry, Faculty of Science, Hacettepe University, 06800, Ankara, Turkey.
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Wei B, Xiao S, Lou W. In silico whole-transcriptome analysis reveals a potential hsa_circ_0000375-miR-424-5p-TPM2/SRPX/SRGAP1 regulatory network related to liver metastasis of colorectal cancer. Heliyon 2023; 9:e21688. [PMID: 37954397 PMCID: PMC10638074 DOI: 10.1016/j.heliyon.2023.e21688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Liver metastasis is the main lethal cause of colorectal cancer (CRC). The knowledge of role and mechanism of circular RNA (circRNA) in liver metastasis of CRC is still inadequate. In this study, whole-transcriptome analysis was performed using three datasets (GSE147597, GSE147602 and GSE147603). A total of 14 potential circRNAs were identified, after which their structural patterns and binding miRNAs were obtained. Next, 45 differentially expressed miRNAs (DEmiRNAs) between CRC without and with liver metastasis were acquired, consisting 38 upregulated and 7 downregulated miRNAs. After conducting intersection analysis, expression validation and correlation analysis, miR-761 and miR-424-5p were selected as the most potential miRNAs linked to liver metastasis of CRC. Subsequently, the target genes of miR-761 or miR-424-5p were predicted and differentially expressed genes (DEGs) between CRC without and with liver metastasis were obtained. 257 genes that were commonly appeared in predicted genes and DEGs were significantly enriched in "epithelial-to-mesenchymal transition" and "signaling by Robo receptor". Among these enriched genes, only TPM2, SRPX and SRGAP1 were significantly negatively correlated with miR-424-5p and were positively linked to hsa_circ_0000375 in CRC without or with liver metastasis. Collectively, the current findings elucidated a potential hsa_circ_0000375-miR-424-5p-TPM2/SRPX/SRGAP1 network contributing to liver metastasis of CRC.
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Affiliation(s)
- Bajin Wei
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shuyuan Xiao
- Department of Anesthesiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Wang F, Su Q, Li C. Identification of cuproptosis-related asthma diagnostic genes by WGCNA analysis and machine learning. J Asthma 2023; 60:2052-2063. [PMID: 37289763 DOI: 10.1080/02770903.2023.2213334] [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: 03/26/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023]
Abstract
OBJECTIVE Cuproptosis is the latest novel form of cell death. However, the relationship between asthma and cuproptosis is not fully understood. METHODS In this study, we screened differentially expressed cuproptosis-related genes from the Gene Expression Omnibus (GEO) database and performed immune infiltration analysis. Subsequently, patients with asthma were typed and analyzed by Kyoto Encyclopedia of Genes and Genomes (KEGG). Weighted gene co-expression network analysis (WGCNA) was performed to calculate the module-trait correlations, and the hub genes of the intersection were taken to construct machine learning (XGB, SVM, RF, GLM). Finally, we used TGF-β to establish a BEAS-2B asthma model to observe the expression levels of hub genes. RESULTS Six cuproptosis-related genes were obtained. Immune-infiltration analysis shows that cuproptosis-related genes are associated with a variety of biological functions. We classified asthma patients into two subtypes based on the expression of cuproptosis-related genes and found significant Gene Ontology (GO) and immune function differences between the different subtypes. WGCNA selected 2 significant modules associated with disease features and typing. Finally, we identified TRIM25, DYSF, NCF4, ABTB1, CXCR1 as asthma biomarkers by taking the intersection of the hub genes of the 2 modules and constructing a 5-genes signature, which nomograph, decision curve analysis (DCA) and calibration curves, receiver operating characteristic curve (ROC) showed high efficiency in diagnosing the probability of survival of asthma patients. Finally, in vitro experiments have shown that DYSF and CXCR1 expression is up expressed in asthma. CONCLUSIONS Our study provides further directions for studying the molecular mechanism of asthma.
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Affiliation(s)
- Fangwei Wang
- Department of Respiratory Medicine, the First Affiliated Hospital of Guangxi Medical University, Nan'ning, China
| | - Qisheng Su
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Nan'ning, China
| | - Chaoqian Li
- Department of Respiratory Medicine, the First Affiliated Hospital of Guangxi Medical University, Nan'ning, China
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Xie J, Wu S, Liao W, Ning J, Ding K. Src is a target molecule of mannose against pancreatic cancer cells growth in vitro & in vivo. Glycobiology 2023; 33:766-783. [PMID: 37658770 DOI: 10.1093/glycob/cwad070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 09/05/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant cancer with limited treatment options. Mannose, a common monosaccharide taken up by cells through the same transporters as glucose, has been shown to induce growth retardation and enhance cell death in response to chemotherapy in several cancers, including PDAC. However, the molecular targets and mechanisms underlying mannose's action against PDAC are not well understood. In this study, we used an integrative approach of network pharmacology, bioinformatics analysis, and experimental verification to investigate the pharmacological targets and mechanisms of mannose against PDAC. Our results showed that the protein Src is a key target of mannose in PDAC. Additionally, computational analysis revealed that mannose is a highly soluble compound that meets Lipinski's rule of five and that the expression of its target molecules is correlated with survival rates and prognosis in PDAC patients. Finally, we validated our findings through in vitro and in vivo experiments. In conclusion, our study provides evidence that mannose plays a critical role in inhibiting PDAC growth by targeting Src, suggesting that it may be a promising therapeutic candidate for PDAC.
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Affiliation(s)
- Jianhao Xie
- Carbohydrate-Based Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Pudong New district, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Shengjie Wu
- Carbohydrate-Based Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Pudong New district, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Wenfeng Liao
- Carbohydrate-Based Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Pudong New district, Shanghai 201203, China
| | - Jingru Ning
- Carbohydrate-Based Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Pudong New district, Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Rd, Qixia District, Nanjing 210023, China
| | - Kan Ding
- Carbohydrate-Based Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Pudong New district, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan, Guangdong 528400, China
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Marzan AL, Chitti SV, Gummadi S, Kang T, Ang CS, Mathivanan S. Proteomics analysis of C2C12 myotubes treated with atrophy inducing cancer cell-derived factors. Proteomics 2023:e2300020. [PMID: 37882347 DOI: 10.1002/pmic.202300020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
Cancer-associated cachexia is a wasting syndrome that results in dramatic loss of whole-body weight, predominantly due to loss of skeletal muscle mass. It has been established that cachexia inducing cancer cells secrete proteins and extracellular vesicles (EVs) that can induce muscle atrophy. Though several studies examined these cancer-cell derived factors, targeting some of these components have shown little or no clinical benefit. To develop new therapies, understanding of the dysregulated proteins and signaling pathways that regulate catabolic gene expression during muscle wasting is essential. Here, we sought to examine the effect of conditioned media (CM) that contain secreted factors and EVs from cachexia inducing C26 colon cancer cells on C2C12 myotubes using mass spectrometry-based label-free quantitative proteomics. We identified significant changes in the protein profile of C2C12 cells upon exposure to C26-derived CM. Functional enrichment analysis revealed enrichment of proteins associated with inflammation, mitochondrial dysfunction, muscle catabolism, ROS production, and ER stress in CM treated myotubes. Furthermore, strong downregulation in muscle structural integrity and development and/or regenerative pathways were observed. Together, these enriched proteins in atrophied muscle could be utilized as potential muscle wasting markers and the dysregulated biological processes could be employed for therapeutic benefit in cancer-induced muscle wasting.
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Affiliation(s)
- Akbar L Marzan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sai V Chitti
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sriram Gummadi
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Taeyoung Kang
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- The Bio21 Institute of Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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Hernandez BJ, Skiba NP, Plössl K, Strain M, Liu Y, Grigsby D, Kelly U, Cady MA, Manocha V, Maminishkis A, Watkins T, Miller SS, Ashley‐Koch A, Stamer WD, Weber BHF, Bowes Rickman C, Klingeborn M. Polarized Desmosome and Hemidesmosome Shedding via Small Extracellular Vesicles is an Early Indicator of Outer Blood-Retina Barrier Dysfunction. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e116. [PMID: 38108061 PMCID: PMC10720597 DOI: 10.1002/jex2.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 12/19/2023]
Abstract
The retinal pigmented epithelium (RPE) constitutes the outer blood-retinal barrier, enables photoreceptor function of the eye, and is constantly exposed to oxidative stress. As such, dysfunction of the RPE underlies pathology leading to development of age-related macular degeneration (AMD), the leading cause of vision loss among the elderly in industrialized nations. A major responsibility of the RPE is to process photoreceptor outer segments, which relies on the proper functioning of its endocytic pathways and endosomal trafficking. Exosomes and other extracellular vesicles (EVs) from RPE are an essential part of these pathways and may be early indicators of cellular stress. To test the role of small EVs (sEVs) including exosomes, that may underlie the early stages of AMD, we used a polarized primary RPE cell culture model under chronic subtoxic oxidative stress. Unbiased proteomic analyses of highly purified basolateral sEVs from oxidatively stressed RPE cultures revealed changes in proteins involved in epithelial barrier integrity. There were also significant changes in proteins accumulating in the basal-side sub-RPE extracellular matrix during oxidative stress, that could be prevented with an inhibitor of sEV release. Thus, chronic subtoxic oxidative stress in primary RPE cultures induces changes in sEV content, including basal-side specific desmosome and hemidesmosome shedding via sEVs. These findings provide novel biomarkers of early cellular dysfunction and opportunity for therapeutic intervention in age-related retinal diseases (e.g., AMD).
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Affiliation(s)
- Belinda J. Hernandez
- Department of Ophthalmology, Duke Eye CenterDuke UniversityDurhamNorth CarolinaUSA
| | - Nikolai P. Skiba
- Department of Ophthalmology, Duke Eye CenterDuke UniversityDurhamNorth CarolinaUSA
| | - Karolina Plössl
- Institute of Human GeneticsUniversity of RegensburgRegensburgGermany
| | - Madison Strain
- Duke Molecular Physiology Institute, Department of MedicineDuke UniversityDurhamNorth CarolinaUSA
| | - Yutao Liu
- Department of Cellular Biology and AnatomyAugusta UniversityAugustaGeorgiaUSA
| | - Daniel Grigsby
- Department of Ophthalmology, Duke Eye CenterDuke UniversityDurhamNorth CarolinaUSA
| | - Una Kelly
- Department of Ophthalmology, Duke Eye CenterDuke UniversityDurhamNorth CarolinaUSA
| | - Martha A. Cady
- Department of Ophthalmology, Duke Eye CenterDuke UniversityDurhamNorth CarolinaUSA
| | - Vikram Manocha
- Department of Ophthalmology, Duke Eye CenterDuke UniversityDurhamNorth CarolinaUSA
| | - Arvydas Maminishkis
- Ophthalmic Genetics and Visual Function Branch, Section on Epithelial and Retinal Physiology and DiseaseNational Eye Institute, National Institutes of HealthBethesdaMarylandUSA
| | - TeddiJo Watkins
- Department of Ophthalmology, Duke Eye CenterDuke UniversityDurhamNorth CarolinaUSA
- Office of Animal Welfare Assurance, Duke Animal Care and Use ProgramDuke UniversityDurhamNorth CarolinaUSA
| | - Sheldon S. Miller
- Ophthalmic Genetics and Visual Function Branch, Section on Epithelial and Retinal Physiology and DiseaseNational Eye Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Allison Ashley‐Koch
- Duke Molecular Physiology Institute, Department of MedicineDuke UniversityDurhamNorth CarolinaUSA
| | - W. Daniel Stamer
- Department of Ophthalmology, Duke Eye CenterDuke UniversityDurhamNorth CarolinaUSA
- Department of Biomedical EngineeringDuke UniversityDurhamNorth CarolinaUSA
| | - Bernhard H. F. Weber
- Institute of Human GeneticsUniversity of RegensburgRegensburgGermany
- Institute of Clinical Human GeneticsUniversity Hospital RegensburgRegensburgGermany
| | - Catherine Bowes Rickman
- Department of Ophthalmology, Duke Eye CenterDuke UniversityDurhamNorth CarolinaUSA
- Department of Cell BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Mikael Klingeborn
- Department of Ophthalmology, Duke Eye CenterDuke UniversityDurhamNorth CarolinaUSA
- McLaughlin Research InstituteGreat FallsMontanaUSA
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Arroyo E, Pérez Sayáns M, Bravo SB, de Oliveira Barbeiro C, Paravani Palaçon M, Chamorro Petronacci CM, García Vence M, Chantada Vázquez MDP, Blanco Carrión A, Suárez Peñaranda JM, García García A, Gándara Vila P, Días Almeida J, Veríssimo da Costa GC, Sousa Nogueira FC, Medeiros Evaristo JA, de Abreu Pereira D, Rintala M, Salo T, Rautava J, Padín Iruegas E, Oliveira Alves MG, Morandin Ferrisse T, Albergoni da Silveira H, Esquiche León J, Vilela Silva E, Flores IL, Bufalino A. Identification of Proteomic Biomarkers in Proliferative Verrucous Leukoplakia through Liquid Chromatography With Tandem Mass Spectrometry. J Transl Med 2023; 103:100222. [PMID: 37507024 DOI: 10.1016/j.labinv.2023.100222] [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: 03/08/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Proliferative verrucous leukoplakia (PVL) is an oral potentially malignant disorder associated with high risk of malignant transformation. Currently, there is no treatment available, and restrictive follow-up of patients is crucial for a better prognosis. Oral leukoplakia (OL) shares some clinical and microscopic features with PVL but exhibits different clinical manifestations and a lower rate of malignant transformation. This study aimed to investigate the proteomic profile of PVL in tissue and saliva samples to identify potential diagnostic biomarkers with therapeutic implications. Tissue and saliva samples obtained from patients with PVL were compared with those from patients with oral OL and controls. Label-free liquid chromatography with tandem mass spectrometry was employed, followed by qualitative and quantitative analyses, to identify differentially expressed proteins. Potential biomarkers were identified and further validated using immunohistochemistry. Staining intensity scan analyses were performed on tissue samples from patients with PVL, patients with OL, and controls from Brazil, Spain, and Finland. The study revealed differences in the immune system, cell cycle, DNA regulation, apoptosis pathways, and the whole proteome of PVL samples. In addition, liquid chromatography with tandem mass spectrometry analyses showed that calreticulin (CALR), receptor of activated protein C kinase 1 (RACK1), and 14-3-3 Tau-protein (YWHAQ) were highly expressed in PVL samples. Immunohistochemistry validation confirmed increased CARL expression in PVL compared with OL. Conversely, RACK1 and YWHA were highly expressed in oral potentially malignant disorder compared to the control group. Furthermore, significant differences in CALR and RACK1 expression were observed in the OL group when comparing samples with and without oral epithelial dysplasia, unlike the PVL. This research provides insights into the molecular mechanisms underlying these conditions and highlights potential targets for future diagnostic and therapeutic approaches.
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Affiliation(s)
- Esteban Arroyo
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Mario Pérez Sayáns
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS) (ORALRES Group), Santiago de Compostela, Spain.
| | - Susana Belen Bravo
- Proteomic Unit, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Camila de Oliveira Barbeiro
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Mariana Paravani Palaçon
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | | | - María García Vence
- Proteomic Unit, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | | | - Andrés Blanco Carrión
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain
| | - José M Suárez Peñaranda
- Servicio de Anatomia Patológica, Hospital Clinico Universitario de Santiago, Choupana s/n Santiago de Compostela, Spain
| | - Abel García García
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain
| | - Pilar Gándara Vila
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS) (ORALRES Group), Santiago de Compostela, Spain
| | - Janete Días Almeida
- Department of Bioscience and Buccal Diagnosis, São José dos Campos, Science and Technologies Institute, São Paulo State University (Unesp), São José dos Campos, São Paulo, Brazil
| | - Giovani Carlo Veríssimo da Costa
- Department of Basic Sciences, Nova Friburgo Health Institute, Univ. Federal Fluminense, Nova Friburgo, Rio de Janeiro, Brazil; Laboratory of Proteomics, Technological Development Support Laboratory (LADETEC), Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio César Sousa Nogueira
- Laboratory of Proteomics, Technological Development Support Laboratory (LADETEC), Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joseph Albert Medeiros Evaristo
- Laboratory of Proteomics, Technological Development Support Laboratory (LADETEC), Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Denise de Abreu Pereira
- Program on Cellular and Molecular Oncobiology, Research Coordination, National Institute of Cancer (INCA), Rio de Janeiro, Brazil
| | - Mirjami Rintala
- Department of Oral Pathology, University of Turku, Turku, Finland
| | - Tuula Salo
- Department of Oral and Maxillofacial Diseases, Clinicum, University of Helsinki, Helsinki, Finland; Department of Pathology, HUSLAB, Helsinki, Finland; Department of Cancer and Translational Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, Oulu, Finland
| | - Jaana Rautava
- Department of Oral Pathology, University of Turku, Turku, Finland; Department of Oral and Maxillofacial Diseases, Clinicum, University of Helsinki, Helsinki, Finland; Department of Pathology, HUSLAB, Helsinki, Finland
| | - Elena Padín Iruegas
- Human Anatomy and Embryology Area, Faculty of Physiotherapy, Department of Functional Biology and Health Sciences, Pontevedra, Spain
| | | | - Túlio Morandin Ferrisse
- Department of Dental Materials and Prosthodontics, São Paulo State University (UNESP), School of Dentistry, Araraquara, Brazil
| | - Heitor Albergoni da Silveira
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Jorge Esquiche León
- Oral Pathology, Department of Stomatology, Public Oral Health, and Forensic Dentistry, Ribeirão Preto Dental School (FORP/USP), University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Evânio Vilela Silva
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Isadora Luana Flores
- Oral Pathology Area, Conservative Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre/RS, Brazil
| | - Andreia Bufalino
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
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Wisztorski M, Aboulouard S, Roussel L, Duhamel M, Saudemont P, Cardon T, Narducci F, Robin YM, Lemaire AS, Bertin D, Hajjaji N, Kobeissy F, Leblanc E, Fournier I, Salzet M. Fallopian tube lesions as potential precursors of early ovarian cancer: a comprehensive proteomic analysis. Cell Death Dis 2023; 14:644. [PMID: 37775701 PMCID: PMC10541450 DOI: 10.1038/s41419-023-06165-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Ovarian cancer is the leading cause of death from gynecologic cancer worldwide. High-grade serous carcinoma (HGSC) is the most common and deadliest subtype of ovarian cancer. While the origin of ovarian tumors is still debated, it has been suggested that HGSC originates from cells in the fallopian tube epithelium (FTE), specifically the epithelial cells in the region of the tubal-peritoneal junction. Three main lesions, p53 signatures, STILs, and STICs, have been defined based on the immunohistochemistry (IHC) pattern of p53 and Ki67 markers and the architectural alterations of the cells, using the Sectioning and Extensively Examining the Fimbriated End Protocol. In this study, we performed an in-depth proteomic analysis of these pre-neoplastic epithelial lesions guided by mass spectrometry imaging and IHC. We evaluated specific markers related to each preneoplastic lesion. The study identified specific lesion markers, such as CAVIN1, Emilin2, and FBLN5. We also used SpiderMass technology to perform a lipidomic analysis and identified the specific presence of specific lipids signature including dietary Fatty acids precursors in lesions. Our study provides new insights into the molecular mechanisms underlying the progression of ovarian cancer and confirms the fimbria origin of HGSC.
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Affiliation(s)
- Maxence Wisztorski
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Soulaimane Aboulouard
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Lucas Roussel
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Marie Duhamel
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Philippe Saudemont
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Tristan Cardon
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Fabrice Narducci
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Yves-Marie Robin
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Anne-Sophie Lemaire
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Delphine Bertin
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Nawale Hajjaji
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Medical Oncology Department, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Firas Kobeissy
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), MorehouseSchool of Medicine, Atlanta, GA, 30310, USA
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Eric Leblanc
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France.
| | - Isabelle Fournier
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
- Institut Universitaire de France, 75000, Paris, France.
| | - Michel Salzet
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
- Institut Universitaire de France, 75000, Paris, France.
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Previtali V, Myers SH, Poppi L, Wynne K, Casamassima I, Girotto S, Di Stefano G, Farabegoli F, Roberti M, Oliviero G, Cavalli A. Preomic profile of BxPC-3 cells after treatment with BRC4. J Proteomics 2023; 288:104983. [PMID: 37536521 DOI: 10.1016/j.jprot.2023.104983] [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: 04/11/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
BRCA2 and RAD51 are two proteins that play a central role in homologous recombination (HR) and DNA double strand break (DSB) repair. BRCA2 assists RAD51 fibrillation and defibrillation through binding with its eight BRC repeats, with BRC4 being one of the most efficient and best characterized. RAD51 inactivation by small molecules has been proposed as a strategy to impair BRCA2/RAD51 binding and, ultimately, the HR pathway, with the aim of making cancer cells more sensitive to PARP inhibitors (PARPi). This strategy, which mimics a synthetic lethality (SL) approach, has been successfully performed in vitro by using the myristoylated derivative of BRC4 (myr-BRC4), designed for a more efficient cell entry. The present study applies a method to obtain a proteomic fingerprint after cellular treatment with the myr-BRC4 peptide using a mass spectroscopy (MS) proteomic approach. (Data are available via ProteomeXchange with identifier PXD042696.) We performed a comparative proteomic profiling of the myr-BRC4 treated vs. untreated BxPC-3 pancreatic cancer cells and evaluated the differential expression of proteins. Among the identified proteins, we focused our attention on proteins shared by both the RAD51 and the BRCA2 interactomes, and on those whose reduction showed high statistical significance. Three downregulated proteins were identified (FANCI, FANCD2, and RPA3), and protein downregulation was confirmed through immunoblotting analysis, validating the MS approach. Our results suggest that, being a direct consequence of myr-BRC4 treatment, the detection of FANCD2, FANCI, and RPA3 downregulation could be used as an indicator for monitoring HR impairment. SIGNIFICANCE: RAD51's inhibition has gained increasing attention because of its possible implications in personalized medicine through the SL approach. Chemical disruption of protein-protein interactions (PPIs) between RAD51 and BRCA2, or some of its partner proteins, could potentiate PARPi DNA damage-induced cell death. This could have application for difficult to treat cancers, such as BRCA-competent and olaparib (PARPi) resistant pancreatic adenocarcinoma. Despite RAD51 being a widely studied target, researchers still lack detailed mechanistic information. This has stifled progress in the field with only a few RAD51 inhibitors having been identified, none of which have gained regulatory approval. Nevertheless, the peptide BRC4 is one of the most specific and best characterized RAD51 binder and inhibitor reported to date. Our study is the first to report the proteomic fingerprint consequent to cellular treatment of myr-BRC4, to offer a reference for the discovery of specific protein/pathway alterations within DNA damage repair. Our results suggest that, being a direct consequence of myr-BRC4 treatment, and ultimately ofBRCA2/RAD51 disruption, the detection of FANCD2, FANCI, and RPA3 downregulation could be used as an indicator for monitoring DNA damage repair impairment and therefore be used to potentiate the development of new effective therapeutic strategies.
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Affiliation(s)
- Viola Previtali
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Samuel H Myers
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Laura Poppi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Irene Casamassima
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Stefania Girotto
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy; Structural Biophysics and Translational Pharmacology Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Giuseppina Di Stefano
- Department of Surgical and Medical Sciences, University of Bologna, 40126 Bologna, Italy
| | - Fulvia Farabegoli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Giorgio Oliviero
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
| | - Andrea Cavalli
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy; Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
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Elasbali AM, Al-Soud WA, Mousa Elayyan AE, Alhassan HH, Danciu C, Elfaki EM, Alharethi SH, Alharbi B, Alanazi HH, Mohtadi ME, Patel M, Adnan M. Antioxidative and ROS-dependent apoptotic effects of Cuscuta reflexa Roxb. stem against human lung cancer: network pharmacology and in vitro experimental validation. J Biomol Struct Dyn 2023:1-26. [PMID: 37776015 DOI: 10.1080/07391102.2023.2263889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/21/2023] [Indexed: 10/01/2023]
Abstract
Lung cancer remains a formidable global health challenge, necessitating the exploration of novel therapeutic approaches. This study investigates the potential of Cuscuta reflexa Roxb. stem extract as an anticancer agent against human lung cancer, focusing on its antioxidative and ROS-dependent apoptotic effects. Utilizing a combination of network pharmacology and in-vitro experimental validation, we delineate the multifaceted molecular mechanisms underlying the observed effects. The antioxidant potential of C. reflexa stem extract was evaluated by the 2,2-diphenyl-1-picrylhydrazyl (DPPH•), 2,2-azinobis (3-ethyl-benzothiazoline-6-sulfonic acid) (ABTS•+) and ferric reducing/antioxidant power (FRAP), hydroxyl free radical scavenging, reactive nitrogen oxide scavenging and super oxide anion radical scavenging assays. Furthermore, the antiproliferative and proapoptotic effect of C. reflexa stem extract was evaluated against A549 lung adenocarcinoma cell line using the consecrated sulforhodamine B (SBR) and Annexin V-PI assays. Additionally, the mitochondrial membrane potential (MMP) and the total reactive oxygen species (ROS) estimation assays were performed. As a result, network pharmacology analysis revealed a complex interaction network between the bioactive constituents of C. reflexa and key proteins implicated in lung cancer progression. The C. reflexa stem extract showed dose-dependent antioxidant activity against DPPH• (IC50 - 87.38 µg/mL), reactive nitrogen oxide (IC50 - 318.34 µg/mL), FRAP (IC50 - 359.96 µg/mL), hydroxy free radicals (IC50 - 526.12 µg/mL) than ABTS●+ (IC50 - 698.45 µg/mL) and super oxide anion (IC50 - 892.71 µg/mL) as well as cytotoxic activity against A549 cells (IC50 - 436.80 µg/mL). Observations of morphological features in treated cells have revealed hallmark of apoptosis properties. Furthermore, as a result of treatment with C. reflexa stem extract, ROS generation and mitochondrial depolarization were increased in A549 cells, suggesting that this treatment has significant apoptotic properties. . These findings highlight the potential utility of this natural extract as an innovative therapeutic strategy for lung cancer treatment. The integration of network pharmacology and experimental validation enhances our understanding of the underlying mechanisms and provide the way for further translational research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdelbaset Mohamed Elasbali
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Qurayyat, Saudi Arabia
| | - Waleed Abu Al-Soud
- Department of Clinical Laboratory Science, College of Applied Sciences-Sakaka, Jouf University, Sakaka, Saudi Arabia
| | - Afnan Elayyan Mousa Elayyan
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Qurayyat, Saudi Arabia
| | - Hassan H Alhassan
- Department of Clinical Laboratory Science, College of Applied Sciences-Sakaka, Jouf University, Sakaka, Saudi Arabia
| | - Corina Danciu
- Department of Pharmacognosy, Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
| | - Elyasa Mustafa Elfaki
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Qurayyat, Saudi Arabia
| | - Salem Hussain Alharethi
- Department of Biological Science, College of Arts and Science, Najran University, Najran, Saudi Arabia
| | - Bandar Alharbi
- Department of Clinical Laboratory, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Hamad H Alanazi
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Qurayyat, Saudi Arabia
| | | | - Mitesh Patel
- Research and Development Cell, Department of Biotechnology, Parul Institute of Applied Sciences, Parul University, Vadodara, India
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
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