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Dakkak BE, Taneera J, El-Huneidi W, Abu-Gharbieh E, Hamoudi R, Semreen MH, Soares NC, Abu-Rish EY, Alkawareek MY, Alkilany AM, Bustanji Y. Unlocking the Therapeutic Potential of BCL-2 Associated Protein Family: Exploring BCL-2 Inhibitors in Cancer Therapy. Biomol Ther (Seoul) 2024; 32:267-280. [PMID: 38589288 PMCID: PMC11063480 DOI: 10.4062/biomolther.2023.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/05/2023] [Accepted: 12/05/2023] [Indexed: 04/10/2024] Open
Abstract
Apoptosis, programmed cell death pathway, is a vital physiological mechanism that ensures cellular homeostasis and overall cellular well-being. In the context of cancer, where evasion of apoptosis is a hallmark, the overexpression of anti-apoptotic proteins like Bcl2, Bcl-xL and Mcl-1 has been documented. Consequently, these proteins have emerged as promising targets for therapeutic interventions. The BCL-2 protein family is central to apoptosis and plays a significant importance in determining cellular fate serving as a critical determinant in this biological process. This review offers a comprehensive exploration of the BCL-2 protein family, emphasizing its dual nature. Specifically, certain members of this family promote cell survival (known as anti-apoptotic proteins), while others are involved in facilitating cell death (referred to as pro-apoptotic and BH3-only proteins). The potential of directly targeting these proteins is examined, particularly due to their involvement in conferring resistance to traditional cancer therapies. The effectiveness of such targeting strategies is also discussed, considering the tumor's propensity for anti-apoptotic pathways. Furthermore, the review highlights emerging research on combination therapies, where BCL-2 inhibitors are used synergistically with other treatments to enhance therapeutic outcomes. By understanding and manipulating the BCL-2 family and its associated pathways, we open doors to innovative and more effective cancer treatments, offering hope for resistant and aggressive cases.
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Affiliation(s)
- Bisan El Dakkak
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Jalal Taneera
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
| | - Mohammad H. Semreen
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Nelson C. Soares
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon 1649-016, Portugal
| | - Eman Y. Abu-Rish
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | | | | | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
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Ahmed M, Semreen AM, Giddey AD, Ramadan WS, El-Awady R, Soares NC, El-Huneidi W, Bustanji Y, Alqudah MAY, Alzoubi KH, Semreen MH. Proteomic and metabolomic signatures of U87 glioblastoma cells treated with cisplatin and/or paclitaxel. Ann Med 2024; 55:2305308. [PMID: 38253025 PMCID: PMC10810643 DOI: 10.1080/07853890.2024.2305308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Glioblastoma (GBM) is a primary malignancy of the central nervous system and is classified as a grade IV astrocytoma by the World Health Organization (WHO). Although GBM rarely metastasizes, its prognosis remains poor. Moreover, the standard treatment for GBM, temozolomide (TMZ), is associated with chemoresistance, which is a major factor behind GBM-related deaths. Investigating drugs with repurposing potential in the context of GBM is worthwhile to bypass lengthy bench-to-bedside research. The field of omics has garnered significant interest in scientific research because of its potential to delineate the intricate regulatory network underlying tumor development. In particular, proteomic and metabolomic analyses are powerful approaches for the investigation of metabolic enzymes and intermediate metabolites since they represent the functional end of the cancer phenotype. METHODS We chose two of the most widely prescribed anticancer drugs, cisplatin and paclitaxel. To our knowledge, the current literature lacks studies examining their effects on metabolic and proteomic alterations in GBM. We employed the mass spectrometry technological platform 'UHPLC-Q-TOF-MS/MS' to examine the changes in the proteome and metabolome profiles of the U87 cell line with defined concentrations of cisplatin and/or paclitaxel via an untargeted approach. RESULTS A total of 1,419 distinct proteins and 90 metabolites were generated, and subsequent analysis was performed. We observed that upon treatment with cisplatin (9.5 μM), U87 cells exhibited apparent efforts to cope with this exogenous stressor, understanding the effect of paclitaxel (5.3 μM) on altering the transport machinery of the cell, and how the combination of cisplatin and/or paclitaxel suggests potential interactions with promising benefits in GBM therapeutics. CONCLUSION Our research provides a detailed map of alterations in response to cisplatin and paclitaxel treatment, provides crucial insights into the molecular basis of their action, and paves the way for further research to identify molecular targets for this elusive malignancy.
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Affiliation(s)
- Munazza Ahmed
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Ahlam M. Semreen
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Alexander D. Giddey
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Wafaa S. Ramadan
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Raafat El-Awady
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Nelson C. Soares
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Laboratory of Proteomics, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Yasser Bustanji
- Department of Basic and Clinical Pharmacology, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Mohammad A. Y. Alqudah
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Karem H. Alzoubi
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad H. Semreen
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
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Ramadan WS, Saber-Ayad MM, Saleh E, Abdu-Allah HH, El-Shorbagi ANA, Menon V, Tarazi H, Semreen MH, Soares NC, Hafezi S, Venkatakhalam T, Ahmed S, Kanie O, Hamoudi R, El-Awady R. Design, synthesis and mechanistic anticancer activity of new acetylated 5-aminosalicylate-thiazolinone hybrid derivatives. iScience 2024; 27:108659. [PMID: 38235331 PMCID: PMC10792193 DOI: 10.1016/j.isci.2023.108659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/29/2023] [Accepted: 12/04/2023] [Indexed: 01/19/2024] Open
Abstract
The development of hybrid compounds has been widely considered as a promising strategy to circumvent the difficulties that emerge in cancer treatment. The well-established strategy of adding acetyl groups to certain drugs has been demonstrated to enhance their therapeutic efficacy. Based on our previous work, an approach of accommodating two chemical entities into a single structure was implemented to synthesize new acetylated hybrids (HH32 and HH33) from 5-aminosalicylic acid and 4-thiazolinone derivatives. These acetylated hybrids showed potential anticancer activities and distinct metabolomic profile with antiproliferative properties. The in-silico molecular docking predicts a strong binding of HH32 and HH33 to cell cycle regulators, and transcriptomic analysis revealed DNA repair and cell cycle as the main targets of HH33 compounds. These findings were validated using in vitro models. In conclusion, the pleiotropic biological effects of HH32 and HH33 compounds on cancer cells demonstrated a new avenue to develop more potent cancer therapies.
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Affiliation(s)
- Wafaa S. Ramadan
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Maha M. Saber-Ayad
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ekram Saleh
- Medical Biochemistry and Molecular Biology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 12613, Egypt
| | | | - Abdel-nasser A. El-Shorbagi
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Faculty of Pharmacy, Assiut University, Assiut 16122, Egypt
| | - Varsha Menon
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Hamadeh Tarazi
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammad H. Semreen
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Nelson C. Soares
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Shirin Hafezi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Thenmozhi Venkatakhalam
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Samrein Ahmed
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Biosciences and Chemistry, College of Health, Wellbeing and Life sciences, University of Sheffield Hallam, Sheffield S1 1WB, United Kingdom
| | - Osamu Kanie
- Department of Applied Biochemistry, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Division of Surgery and Interventional Science, Faculty of Medical Science, University College London, London, United Kingdom
| | - Raafat El-Awady
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
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Ibrahim Z, Khan NA, Qaisar R, Saleh MA, Siddiqui R, Al-Hroub HM, Giddey AD, Semreen MH, Soares NC, Elmoselhi AB. Serum multi-omics analysis in hindlimb unloading mice model: Insights into systemic molecular changes and potential diagnostic and therapeutic biomarkers. Heliyon 2024; 10:e23592. [PMID: 38187258 PMCID: PMC10770503 DOI: 10.1016/j.heliyon.2023.e23592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Microgravity, in space travel and prolonged bed rest conditions, induces cardiovascular deconditioning along with skeletal muscle mass loss and weakness. The findings of microgravity research may also aid in the understanding and treatment of human health conditions on Earth such as muscle atrophy, and cardiovascular diseases. Due to the paucity of biomarkers and the unknown underlying mechanisms of cardiovascular and skeletal muscle deconditioning in these environments, there are insufficient diagnostic and preventative measures. In this study, we employed hindlimb unloading (HU) mouse model, which mimics astronauts in space and bedridden patients, to first evaluate cardiovascular and skeletal muscle function, followed by proteomics and metabolomics LC-MS/MS-based analysis using serum samples. Three weeks of unloading caused changes in the function of the cardiovascular system in c57/Bl6 mice, as seen by a decrease in mean arterial pressure and heart weight. Unloading for three weeks also changed skeletal muscle function, causing a loss in grip strength in HU mice and atrophy of skeletal muscle indicated by a reduction in muscle mass. These modifications were partially reversed by a two-week recovery period of reloading condition, emphasizing the significance of the recovery process. Proteomics analysis revealed 12 dysregulated proteins among the groups, such as phospholipid transfer protein, Carbonic anhydrase 3, Parvalbumin alpha, Major urinary protein 20 (Mup20), Thrombospondin-1, and Apolipoprotein C-IV. On the other hand, metabolomics analysis showed altered metabolites among the groups such as inosine, hypoxanthine, xanthosine, sphinganine, l-valine, 3,4-Dihydroxyphenylglycol, and l-Glutamic acid. The joint data analysis revealed that HU conditions mainly impacted pathways such as ABC transporters, complement and coagulation cascades, nitrogen metabolism, and purine metabolism. Overall, our results indicate that microgravity environment induces significant alterations in the function, proteins, and metabolites of these mice. These observations suggest the potential utilization of these proteins and metabolites as novel biomarkers for assessing and mitigating cardiovascular and skeletal muscle deconditioning associated with such conditions.
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Affiliation(s)
- Zeinab Ibrahim
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Basic Medical Sciences Department, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Naveed A. Khan
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Microbiota Research Center, Istinye University, Istanbul, 34010, Turkey
| | - Rizwan Qaisar
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Basic Medical Sciences Department, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohamed A. Saleh
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Ruqaiyyah Siddiqui
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University Edinburgh, EH14 4AS UK
- Microbiota Research Center, Istinye University, Istanbul, 34010, Turkey
| | - Hamza M. Al-Hroub
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Alexander D. Giddey
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mohammad Harb Semreen
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Nelson C. Soares
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Laboratory of Proteomics, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Av. Padre Cruz, Lisbon, 1649-016, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), NOVA School/ Faculdade de Lisboa, Lisbon, Portugal
| | - Adel B. Elmoselhi
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Basic Medical Sciences Department, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
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Alhameed RA, Semreen MH, Hamad M, Giddey AD, Sulaiman A, Al Bataineh MT, Al-Hroub HM, Bustanji Y, Alzoubi KH, Soares NC. Multi-Omics Profiling of Candida albicans Grown on Solid Versus Liquid Media. Microorganisms 2023; 11:2831. [PMID: 38137975 PMCID: PMC10745582 DOI: 10.3390/microorganisms11122831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
Candida albicans is a common pathogenic fungus that presents a challenge to healthcare facilities. It can switch between a yeast cell form that diffuses through the bloodstream to colonize internal organs and a filamentous form that penetrates host mucosa. Understanding the pathogen's strategies for environmental adaptation and, ultimately, survival, is crucial. As a complementary study, herein, a multi-omics analysis was performed using high-resolution timsTOF MS to compare the proteomes and metabolomes of Wild Type (WT) Candida albicans (strain DK318) grown on agar plates versus liquid media. Proteomic analysis revealed a total of 1793 proteins and 15,013 peptides. Out of the 1403 identified proteins, 313 proteins were significantly differentially abundant with a p-value < 0.05. Of these, 156 and 157 proteins were significantly increased in liquid and solid media, respectively. Metabolomics analysis identified 192 metabolites in total. The majority (42/48) of the significantly altered metabolites (p-value 0.05 FDR, FC 1.5), mainly amino acids, were significantly higher in solid media, while only 2 metabolites were significantly higher in liquid media. The combined multi-omics analysis provides insight into adaptative morphological changes supporting Candida albicans' life cycle and identifies crucial virulence factors during biofilm formation and bloodstream infection.
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Affiliation(s)
- Rouba Abdulsalam Alhameed
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
| | - Mohammad H. Semreen
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates
| | - Mohamad Hamad
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
- College of Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates
| | - Alexander D. Giddey
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates;
| | - Ashna Sulaiman
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
| | - Mohammad T. Al Bataineh
- Center for Biotechnology, Department of Molecular Biology and Genetics, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Hamza M. Al-Hroub
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
| | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
- College of Medicine, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Karem H. Alzoubi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates
| | - Nelson C. Soares
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates
- Laboratory of Proteomics, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), Faculdade de Lisboa, NOVA School, 1169-056 Lisbon, Portugal
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El-Huneidi W, Anjum S, Mohammed AK, Bin Eshaq S, Abdrabh S, Bustanji Y, Soares NC, Semreen MH, Alzoubi KH, Abu-Gharbieh E, Taneera J. Rosemarinic acid protects β-cell from STZ-induced cell damage via modulating NF-κβ pathway. Heliyon 2023; 9:e19234. [PMID: 37662743 PMCID: PMC10472240 DOI: 10.1016/j.heliyon.2023.e19234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 07/30/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Rosmarinic acid (RA), a natural ester phenolic compound, is known to have antioxidant and anti-inflammatory properties. RA has also been reported to exhibit a hypoglycemic effect; however, the mechanisms underlying this effect have yet to be investigated. Therefore, the present study focused on the anti-diabetic effects and mechanism of RA in INS-1 cells using in vitro model. Streptozotocin (STZ) at a concentration of 3 mM was applied to INS-1 cells for 4 h to create a diabetic model. The cells were pretreated for 24 h with various concentrations (1 and 2.5 μM) of RA. The Cell viability, glucose-stimulated insulin secretion (GSIS), glucose uptake, lipid peroxidation, reactive oxygen species (ROS), apoptosis, and protein expression of Bcl-2, NF-κB, 1L-1β, and PARP were assessed. Results showed that STZ-treated INS-1 cells exhibited reduced cell viability, insulin release, insulin content, glucose uptake, and elevated MDA and ROS levels. Cells pretreated with RA maintained the function and morphology of β-cells against STZ-induced damage. Moreover, RA sustained high protein expression levels of Bcl-2 and low expression levels of NF-κB, IL-1β, and PARP. In conclusion, RA preserved β-cells function against STZ-induced damage by altering NF-κB and Bcl-2 pathways.
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Affiliation(s)
- Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Shabana Anjum
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
- College of Engineering, Drug Delivery Research Group, American University of Sharjah, Sharjah, United Arab Emirates
| | - Abdul Khader Mohammed
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Shuhd Bin Eshaq
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Sham Abdrabh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman, 11942, Jordan
| | - Nelson C. Soares
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Mohammad H. Semreen
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Karem H. Alzoubi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Jalal Taneera
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
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Soares NC, Hussein A, Muhammad JS, Semreen MH, ElGhazali G, Hamad M. Plasma metabolomics profiling identifies new predictive biomarkers for disease severity in COVID-19 patients. PLoS One 2023; 18:e0289738. [PMID: 37561777 PMCID: PMC10414581 DOI: 10.1371/journal.pone.0289738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Recently, numerous studies have reported on different predictive models of disease severity in COVID-19 patients. Herein, we propose a highly predictive model of disease severity by integrating routine laboratory findings and plasma metabolites including cytosine as a potential biomarker of COVID-19 disease severity. One model was developed and internally validated on the basis of ROC-AUC values. The predictive accuracy of the model was 0.996 (95% CI: 0.989 to 1.000) with an optimal cut-off risk score of 3 from among 6 biomarkers including five lab findings (D-dimer, ferritin, neutrophil counts, Hp, and sTfR) and one metabolite (cytosine). The model is of high predictive power, needs a small number of variables that can be acquired at minimal cost and effort, and can be applied independent of non-empirical clinical data. The metabolomics profiling data and the modeling work stemming from it, as presented here, could further explain the cause of COVID-19 disease prognosis and patient management.
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Affiliation(s)
- Nelson C. Soares
- University of Sharjah, Research Institute of Medical and Health Sciences, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry University of Sharjah, Department of Medicinal Chemistry, College of Pharmacy, Sharjah, United Arab Emirates
| | - Amal Hussein
- Department of Family and Community Medicine & Behavioral Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Jibran Sualeh Muhammad
- University of Sharjah, Research Institute of Medical and Health Sciences, Sharjah, United Arab Emirates
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad H. Semreen
- University of Sharjah, Research Institute of Medical and Health Sciences, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry University of Sharjah, Department of Medicinal Chemistry, College of Pharmacy, Sharjah, United Arab Emirates
| | - Gehad ElGhazali
- Department of Immunology, Sheikh Khalifa Medical City- Union71- Purelab, Abu Dhabi and College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mawieh Hamad
- University of Sharjah, Research Institute of Medical and Health Sciences, Sharjah, United Arab Emirates
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
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8
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Haider M, Jagal J, Bajbouj K, Sharaf BM, Sahnoon L, Okendo J, Semreen MH, Hamda M, Soares NC. Integrated multi-omics analysis reveals unique signatures of paclitaxel-loaded poly(lactide-co-glycolide) nanoparticles treatment of head and neck cancer cells. Proteomics 2023; 23:e2200380. [PMID: 37148169 DOI: 10.1002/pmic.202200380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 05/08/2023]
Abstract
The use of poly(lactide-co-glycolide) (PLGA) nanoparticles (NPs) as carriers for chemotherapeutic drugs is regarded as an actively targeted nano-therapy for the specific delivery of anti-cancer drugs to target cells. However, the exact mechanism by which PLGA NPs boost anticancer cytotoxicity at the molecular level remains largely unclear. This study employed different molecular approaches to define the response of carcinoma FaDu cells to different types of treatment, specifically: paclitaxel (PTX) alone, drug free PLGA NPs, and PTX-loaded PTX-PLGA NPs. Functional cell assays revealed that PTX-PLGA NPs treated cells had a higher level of apoptosis than PTX alone, whereas the complementary, UHPLC-MS/MS (TIMS-TOF) based multi-omics analyses revealed that PTX-PLGA NPs treatment resulted in increased abundance of proteins associated with tubulin, as well as metabolites such as 5-thymidylic acid, PC(18:1(9Z)/18:1(9Z0), vitamin D, and sphinganine among others. The multi-omics analyses revealed new insights about the molecular mechanisms underlying the action of novel anticancer NP therapies. In particular, PTX-loaded NPs appeared to exacerbate specific changes induced by both PLGA-NPs and PTX as a free drug. Hence, the PTX-PLGA NPs' molecular mode of action, seen in greater detail, depends on this synergy that ultimately accelerates the apoptotic process, resulting in cancer cell death.
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Affiliation(s)
- Mohamed Haider
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, University of Sharjah, Sharjah, UAE
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, UAE
| | - Jayalakshmi Jagal
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, UAE
| | - Khuloud Bajbouj
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE
| | - Basma M Sharaf
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, UAE
| | - Lina Sahnoon
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, UAE
| | - Javan Okendo
- Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mohammad H Semreen
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, UAE
| | - Mawieh Hamda
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, UAE
| | - Nelson C Soares
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, UAE
- Laboratory of Proteomics, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), NOVA School/Faculdade de Lisboa, Lisbon, Portugal
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9
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Vava A, Paccez JD, Wang Y, Gu X, Bhasin MK, Myers M, Soares NC, Libermann TA, Zerbini LF. DCUN1D1 Is an Essential Regulator of Prostate Cancer Proliferation and Tumour Growth That Acts through Neddylation of Cullin 1, 3, 4A and 5 and Deregulation of Wnt/Catenin Pathway. Cells 2023; 12:1973. [PMID: 37566052 PMCID: PMC10417424 DOI: 10.3390/cells12151973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023] Open
Abstract
Defective in cullin neddylation 1 domain containing 1 (DCUN1D1) is an E3 ligase for the neddylation, a post-translational process similar to and occurring in parallel to ubiquitin proteasome pathway. Although established as an oncogene in a variety of squamous cell carcinomas, the precise role of DCUN1D1 in prostate cancer (PCa) has not been previously explored thoroughly. Here, we investigated the role of DCUN1D1 in PCa and demonstrated that DCUN1D1 is upregulated in cell lines as well as human tissue samples. Inhibition of DCUN1D1 significantly reduced PCa cell proliferation and migration and remarkably inhibited xenograft formation in mice. Applying both genomics and proteomics approaches, we provide novel information about the DCUN1D1 mechanism of action. We identified CUL3, CUL4B, RBX1, CAND1 and RPS19 proteins as DCUN1D1 binding partners. Our analysis also revealed the dysregulation of genes associated with cellular growth and proliferation, developmental, cell death and cancer pathways and the WNT/β-catenin pathway as potential mechanisms. Inhibition of DCUN1D1 leads to the inactivation of β-catenin through its phosphorylation and degradation which inhibits the downstream action of β-catenin, reducing its interaction with Lef1 in the Lef1/TCF complex that regulates Wnt target gene expression. Together our data point to an essential role of the DCUN1D1 protein in PCa which can be explored for potential targeted therapy.
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Affiliation(s)
- Akhona Vava
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town 7925, South Africa; (A.V.); (J.D.P.)
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Juliano D. Paccez
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town 7925, South Africa; (A.V.); (J.D.P.)
| | - Yihong Wang
- Department of Pathology and Laboratory Medicine, Warren Alpert School of Medicine, Brown University, Providence, RI 02912, USA;
| | - Xuesong Gu
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA; (X.G.); (T.A.L.)
| | - Manoj K. Bhasin
- Department of Pediatrics Bioinformatics, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Michael Myers
- Protein Networks Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy;
| | - Nelson C. Soares
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah P.O. Box 26666, United Arab Emirates;
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 26666, United Arab Emirates
- Laboratory of Proteomics, Department of Human Genetics, National Institute of Health, Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), NOVA/School/Faculdade de Lisboa, 1169-056 Lisbon, Portugal
| | - Towia A. Libermann
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA; (X.G.); (T.A.L.)
| | - Luiz F. Zerbini
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town 7925, South Africa; (A.V.); (J.D.P.)
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10
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Starodubtseva NL, Tokareva AO, Rodionov VV, Brzhozovskiy AG, Bugrova AE, Chagovets VV, Kometova VV, Kukaev EN, Soares NC, Kovalev GI, Kononikhin AS, Frankevich VE, Nikolaev EN, Sukhikh GT. Integrating Proteomics and Lipidomics for Evaluating the Risk of Breast Cancer Progression: A Pilot Study. Biomedicines 2023; 11:1786. [PMID: 37509426 PMCID: PMC10376786 DOI: 10.3390/biomedicines11071786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Metastasis is a serious and often life-threatening condition, representing the leading cause of death among women with breast cancer (BC). Although the current clinical classification of BC is well-established, the addition of minimally invasive laboratory tests based on peripheral blood biomarkers that reflect pathological changes in the body is of utmost importance. In the current study, the serum proteome and lipidome profiles for 50 BC patients with (25) and without (25) metastasis were studied. Targeted proteomic analysis for concertation measurements of 125 proteins in the serum was performed via liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM MS) using the BAK 125 kit (MRM Proteomics Inc., Victoria, BC, Canada). Untargeted label-free lipidomic analysis was performed using liquid chromatography coupled to tandem mass-spectrometry (LC-MS/MS), in both positive and negative ion modes. Finally, 87 serum proteins and 295 lipids were quantified and showed a moderate correlation with tumor grade, histological and biological subtypes, and the number of lymph node metastases. Two highly accurate classifiers that enabled distinguishing between metastatic and non-metastatic BC were developed based on proteomic (accuracy 90%) and lipidomic (accuracy 80%) features. The best classifier (91% sensitivity, 89% specificity, AUC = 0.92) for BC metastasis diagnostics was based on logistic regression and the serum levels of 11 proteins: alpha-2-macroglobulin, coagulation factor XII, adiponectin, leucine-rich alpha-2-glycoprotein, alpha-2-HS-glycoprotein, Ig mu chain C region, apolipoprotein C-IV, carbonic anhydrase 1, apolipoprotein A-II, apolipoprotein C-II and alpha-1-acid glycoprotein 1.
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Affiliation(s)
- Natalia L Starodubtseva
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- Department of Chemical Physics, Moscow Institute of Physics and Technology, 141700 Moscow, Russia
| | - Alisa O Tokareva
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Valeriy V Rodionov
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Alexander G Brzhozovskiy
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- Laboratory of Omics Technologies and Big Data for Personalized Medicine and Health, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Anna E Bugrova
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vitaliy V Chagovets
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Vlada V Kometova
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Evgenii N Kukaev
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Nelson C Soares
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Grigoriy I Kovalev
- Laboratory of Omics Technologies and Big Data for Personalized Medicine and Health, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Alexey S Kononikhin
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- Laboratory of Omics Technologies and Big Data for Personalized Medicine and Health, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Vladimir E Frankevich
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
- Laboratory of Translational Medicine, Siberian State Medical University, 634050 Tomsk, Russia
| | - Evgeny N Nikolaev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Gennady T Sukhikh
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, 117997 Moscow, Russia
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11
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Akbar N, Khan NA, Giddey AD, Soares NC, Alharbi AM, Alfahemi H, Siddiqui R. Selected Gut Bacteria from Water Monitor Lizard Exhibit Effects against Pathogenic Acanthamoeba castellanii Belonging to the T4 Genotype. Microorganisms 2023; 11:microorganisms11041072. [PMID: 37110494 PMCID: PMC10142573 DOI: 10.3390/microorganisms11041072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Water monitor lizards (WMLs) reside in unhygienic and challenging ecological surroundings and are routinely exposed to various pathogenic microorganisms. It is possible that their gut microbiota produces substances to counter microbial infections. Here we determine whether selected gut bacteria of water monitor lizards (WMLs) possess anti-amoebic properties using Acanthamoeba castellanii of the T4 genotype. Conditioned media (CM) were prepared from bacteria isolated from WML. The CM were tested using amoebicidal, adhesion, encystation, excystation, cell cytotoxicity and amoeba-mediated host cell cytotoxicity assays in vitro. Amoebicidal assays revealed that CM exhibited anti-amoebic effects. CM inhibited both excystation and encystation in A. castellanii. CM inhibited amoebae binding to and cytotoxicity of host cells. In contrast, CM alone showed limited toxic effects against human cells in vitro. Mass spectrometry revealed several antimicrobials, anticancer, neurotransmitters, anti-depressant and other metabolites with biological functions. Overall, these findings imply that bacteria from unusual places, such as WML gut, produce molecules with anti-acanthamoebic capabilities.
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Affiliation(s)
- Noor Akbar
- Department of Clinical Sciences, College of Medicine, University of Sharjah, University City, Sharjah 27272, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Naveed Ahmed Khan
- Department of Clinical Sciences, College of Medicine, University of Sharjah, University City, Sharjah 27272, United Arab Emirates
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul 34010, Turkey
| | - Alexander D Giddey
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ahmad M Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
| | - Hasan Alfahemi
- Department of Medical Microbiology, Faculty of Medicine, Al-Baha University, P.O. Box. 1988, Al-Baha 65799, Saudi Arabia
| | - Ruqaiyyah Siddiqui
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul 34010, Turkey
- College of Arts and Sciences, American University of Sharjah, University City, Sharjah 26666, United Arab Emirates
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12
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Bustanji Y, Shihab KHA, El-Huneidi W, Semreen MH, Abu-Gharbieh E, Alzoubi KH, Alqudah MAY, Abuhelwa AY, Abu-Rish EY, Bajes H, Obaideen K, Hamad I, Soares NC, Faris ME. Analysis and mapping of global scientific research on human monkeypox over the past 20 years. Vet World 2023; 16:693-703. [PMID: 37235145 PMCID: PMC10206959 DOI: 10.14202/vetworld.2023.693-703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 02/27/2023] [Indexed: 05/28/2023] Open
Abstract
Background and Aim Human monkeypox is an emerging global threat. Hundreds of publications were disseminated in the last few months. This study aimed to map, analyze, and evaluate the bibliometric indicators of the global monkeypox research output. Materials and Methods All documents published in the past 20 years were retrieved using the Scopus database. Papers published in English and peer-reviewed journals were included. VOSviewer was used to create density and network visualization maps. Results A total of 1725 published documents were retrieved. Of these, 53% were published in 2022. The average number of authors per document was 4.2. Authors from the USA were the most active and published about 42.1% of the total documents. International collaboration was evident between the USA and both UK and Congo. Keywords mapping identified the main research lines in this field that correlate monkeypox with public health, smallpox, vaccination, and antiviral treatment. Conclusion This study analyzed and mapped the expanding field of monkeypox research across the world. The bibliometric analysis revealed that the United States has contributed greatly in terms of both individual researchers and academic institutions. There was less cooperation on a global scale than was anticipated. Fostering international cooperation is essential for countering this worldwide danger. Additional scientific research should be conducted to investigate the link between smallpox immunization and monkeypox epidemics.
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Affiliation(s)
- Yasser Bustanji
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, 27272 United Arab Emirates
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, 11942, Jordan
| | - Katia H. Abu Shihab
- Department of Clinical Nutrition and Dietetics, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Waseem El-Huneidi
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, 27272 United Arab Emirates
| | - Mohammad H. Semreen
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, 27272 United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, 27272 United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Karem H. Alzoubi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, 27272 United Arab Emirates
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Mohammad A. Y. Alqudah
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, 27272 United Arab Emirates
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Ahmad Y. Abuhelwa
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, 27272 United Arab Emirates
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Eman Y. Abu-Rish
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, 11942, Jordan
| | - Hana Bajes
- Atlantic Cape Community College, Atlantic County, New Jersey, USA
| | - Khaled Obaideen
- Department of Sustainable Energy and Power Systems Research Centre, RISE, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Islam Hamad
- Department of Pharmacy, Faculty of Health Sciences, American University of Madaba, Amman, Jordan
| | - Nelson C. Soares
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, 27272 United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Laboratory of Proteomics, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Av.a Padre Cruz, Lisbon, 1649-016, Portugal
| | - MoezAlIslam E. Faris
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, 27272 United Arab Emirates
- Department of Clinical Nutrition and Dietetics, University of Sharjah, Sharjah, 27272, United Arab Emirates
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13
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Marzook H, Gupta A, Tomar D, Saleh MA, Patil K, Semreen MH, Hamoudi R, Soares NC, Qaisar R, Ahmad F. Nicotinamide riboside kinase-2 regulates metabolic adaptation in the ischemic heart. J Mol Med (Berl) 2023; 101:311-326. [PMID: 36808555 DOI: 10.1007/s00109-023-02296-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/23/2023]
Abstract
Ischemia-induced metabolic remodeling plays a critical role in the pathogenesis of adverse cardiac remodeling and heart failure however, the underlying molecular mechanism is largely unknown. Here, we assess the potential roles of nicotinamide riboside kinase-2 (NRK-2), a muscle-specific protein, in ischemia-induced metabolic switch and heart failure through employing transcriptomic and metabolomic approaches in ischemic NRK-2 knockout mice. The investigations revealed NRK-2 as a novel regulator of several metabolic processes in the ischemic heart. Cardiac metabolism and mitochondrial function and fibrosis were identified as top dysregulated cellular processes in the KO hearts post-MI. Several genes linked to mitochondrial function, metabolism, and cardiomyocyte structural proteins were severely downregulated in the ischemic NRK-2 KO hearts. Analysis revealed significantly upregulated ECM-related pathways which was accompanied by the upregulation of several key cell signaling pathways including SMAD, MAPK, cGMP, integrin, and Akt in the KO heart post-MI. Metabolomic studies identified profound upregulation of metabolites mevalonic acid, 3,4-dihydroxyphenylglycol, 2-penylbutyric acid, and uridine. However, other metabolites stearic acid, 8,11,14-eicosatrienoic acid, and 2-pyrrolidinone were significantly downregulated in the ischemic KO hearts. Taken together, these findings suggest that NRK-2 promotes metabolic adaptation in the ischemic heart. The aberrant metabolism in the ischemic NRK-2 KO heart is largely driven by dysregulated cGMP and Akt and mitochondrial pathways. KEY MESSAGES: Post-myocardial infarction metabolic switch critically regulates the pathogenesis of adverse cardiac remodeling and heart failure. Here, we report NRK-2 as a novel regulator of several cellular processes including metabolism and mitochondrial function post-MI. NRK-2 deficiency leads to downregulation of genes important for mitochondrial pathway, metabolism, and cardiomyocyte structural proteins in the ischemic heart. It was accompanied by upregulation of several key cell signaling pathways including SMAD, MAPK, cGMP, integrin, and Akt and dysregulation of numerous metabolites essential for cardiac bioenergetics. Taken together, these findings suggest that NRK-2 is critical for metabolic adaptation of the ischemic heart.
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Affiliation(s)
- Hezlin Marzook
- Research Institute of Medical and Health Sciences, University of Sharjah, P.O. 27272 , Sharjah, United Arab Emirates
| | - Anamika Gupta
- Research Institute of Medical and Health Sciences, University of Sharjah, P.O. 27272 , Sharjah, United Arab Emirates
| | - Dhanendra Tomar
- Department of Internal Medicine, Section On Cardiovascular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Mohamed A Saleh
- Research Institute of Medical and Health Sciences, University of Sharjah, P.O. 27272 , Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, UAE
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Kiran Patil
- Research Institute of Medical and Health Sciences, University of Sharjah, P.O. 27272 , Sharjah, United Arab Emirates
| | - Mohammad H Semreen
- Research Institute of Medical and Health Sciences, University of Sharjah, P.O. 27272 , Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. 27272, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, P.O. 27272 , Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, UAE
- Division of Surgery and Interventional Science, University College London, London, W1W 7EJ, UK
| | - Nelson C Soares
- Research Institute of Medical and Health Sciences, University of Sharjah, P.O. 27272 , Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. 27272, Sharjah, United Arab Emirates
- Laboratory of Proteomics, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Av.a Padre Cruz, Lisbon, 1649-016, Portugal
| | - Rizwan Qaisar
- Research Institute of Medical and Health Sciences, University of Sharjah, P.O. 27272 , Sharjah, United Arab Emirates
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, UAE
| | - Firdos Ahmad
- Research Institute of Medical and Health Sciences, University of Sharjah, P.O. 27272 , Sharjah, United Arab Emirates.
- Department of Biomedical Sciences, College of Health Sciences, Abu Dhabi University, 59911, Abu Dhabi, United Arab Emirates.
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, 37240, USA.
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14
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Aghila Rani KG, Soares NC, Rahman B, Al-Hroub HM, Semreen MH, Al Kawas S. Effects of medwakh smoking on salivary metabolomics and its association with altered oral redox homeostasis among youth. Sci Rep 2023; 13:1870. [PMID: 36725974 PMCID: PMC9891755 DOI: 10.1038/s41598-023-27958-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 01/10/2023] [Indexed: 02/03/2023] Open
Abstract
The use of alternative tobacco products, particularly medwakh, has expanded among youth in the Middle East and around the world. The present study is conducted to investigate the biochemical and pathophysiological changes caused by medwakh smoking, and to examine the salivary metabolomics profile of medwakh smokers. Saliva samples were collected from 30 non-smokers and 30 medwakh smokers and subjected to metabolomic analysis by UHPLC-ESI-QTOF-MS. The CRP and Glutathione Peroxidase 1 activity levels in the study samples were quantified by ELISA and the total antioxidant capacity (TAC) by TAC assay kits. Statistical measurements and thorough validation of data obtained from untargeted metabolomics identified 37 uniquely and differentially abundant metabolites in saliva of medwakh smokers. The levels of phthalate, L-sorbose, cytosine, uridine, alpha-hydroxy hippurate, and L-nicotine were noticeably high in medwakh smokers. Likewise, 20 metabolic pathways were differentially altered in medwakh smokers. This study identified a distinctive saliva metabolomics profile in medwakh smokers associated with altered redox homeostasis, metabolic pathways, antioxidant system, and CRP levels. The impact of the altered metabolites in medwakh smokers and their diagnostic utility require further research in large cohorts.
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Affiliation(s)
- K G Aghila Rani
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.,Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Betul Rahman
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.,Department of Preventive and Restorative Dentistry, College of Dental Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Hamza M Al-Hroub
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Mohammad H Semreen
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates. .,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.
| | - Sausan Al Kawas
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates. .,Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, United Arab Emirates.
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15
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Madkour M, Giddey AD, Soares NC, Semreen MH, Bustanji Y, Zeb F, Halwani R, Faris ME. Ramadan diurnal intermittent fasting is associated with significant plasma metabolomics changes in subjects with overweight and obesity: A prospective cohort study. Front Nutr 2023; 9:1008730. [PMID: 36698470 PMCID: PMC9868699 DOI: 10.3389/fnut.2022.1008730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction During the holy month of Ramadan, adult healthy Muslims are mandated to abstain from dawn to sunset, with free eating at night hours that may extend up to 12 h. The current work was designed to investigate the metabolomics changes incurred upon the observance of Ramadan diurnal intermittent fasting (RDIF). Methods Twenty-five metabolically healthy participants with overweight and obesity (7 females and 18 males, with a mean age of 39.48 ± 10.0 years) were recruited for the study and were followed before and at the end of RDIF month. Dietary, anthropometric, biochemical, and physical activity assessments were performed before and at the end of the fasting month. The metabolomic assay was performed using liquid chromatography-mass spectrometry for the two-time points. Results and discussion Metabolomics assay revealed a significant reduction in a few metabolites. The analysis revealed that 27 metabolites differed significantly (P < 0.05) between pre-and post-RDIF. Among the differentially abundant metabolites, 23 showed a decrease with fasting, these included several amino acids such as aspartame, tryptophan, phenylalanine, histidine, and other metabolites including valeric acid, and cortisol. On the other hand, only four metabolites showed increased levels after RDIF including traumatic acid, 2-pyrrolidinone, PC[18:1(9Z)/18:1(9Z)], and L-sorbose. The MetaboAnalyst® platform reported that the top enriched metabolic pathways included: (1) histidine metabolism; (2) folate biosynthesis (3) phenylalanine, tyrosine, and tryptophan biosynthesis; (4) aminoacyltRNA biosynthesis; (5) caffeine metabolism; (6) vitamin B6 metabolism; and several other pathways relating to lipid metabolisms such as arachidonic acid metabolism, glycerophospholipid metabolism, and linoleic acid metabolism. In conclusion, RDIF entails significant changes in various metabolic pathways that reflect different dietary and lifestyle behaviors practiced during the fasting month.
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Affiliation(s)
- Mohamed Madkour
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Alexander D. Giddey
- Research Institute of Medical and Health Sciences (RIMHS), University of Sharjah, Sharjah, United Arab Emirates
| | - Nelson C. Soares
- Research Institute of Medical and Health Sciences (RIMHS), University of Sharjah, Sharjah, United Arab Emirates,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates,Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Mohammad H. Semreen
- Research Institute of Medical and Health Sciences (RIMHS), University of Sharjah, Sharjah, United Arab Emirates,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Yasser Bustanji
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates,School of Pharmacy, Department of Biopharmaceutics and Clinical Pharmacy, The University of Jordan, Amman, Jordan
| | - Falak Zeb
- Research Institute of Medical and Health Sciences (RIMHS), University of Sharjah, Sharjah, United Arab Emirates
| | - Rabih Halwani
- Research Institute of Medical and Health Sciences (RIMHS), University of Sharjah, Sharjah, United Arab Emirates,Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - MoezAlIslam E. Faris
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates,*Correspondence: MoezAlIslam E. Faris, ,
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16
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Ahmed M, Semreen AM, El-Huneidi W, Bustanji Y, Abu-Gharbieh E, Alqudah MAY, Alhusban A, Shara M, Abuhelwa AY, Soares NC, Semreen MH, Alzoubi KH. Preclinical and Clinical Applications of Metabolomics and Proteomics in Glioblastoma Research. Int J Mol Sci 2022; 24:ijms24010348. [PMID: 36613792 PMCID: PMC9820403 DOI: 10.3390/ijms24010348] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Glioblastoma (GB) is a primary malignancy of the central nervous system that is classified by the WHO as a grade IV astrocytoma. Despite decades of research, several aspects about the biology of GB are still unclear. Its pathogenesis and resistance mechanisms are poorly understood, and methods to optimize patient diagnosis and prognosis remain a bottle neck owing to the heterogeneity of the malignancy. The field of omics has recently gained traction, as it can aid in understanding the dynamic spatiotemporal regulatory network of enzymes and metabolites that allows cancer cells to adjust to their surroundings to promote tumor development. In combination with other omics techniques, proteomic and metabolomic investigations, which are a potent means for examining a variety of metabolic enzymes as well as intermediate metabolites, might offer crucial information in this area. Therefore, this review intends to stress the major contribution these tools have made in GB clinical and preclinical research and highlights the crucial impacts made by the integrative "omics" approach in reducing some of the therapeutic challenges associated with GB research and treatment. Thus, our study can purvey the use of these powerful tools in research by serving as a hub that particularly summarizes studies employing metabolomics and proteomics in the realm of GB diagnosis, treatment, and prognosis.
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Affiliation(s)
- Munazza Ahmed
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ahlam M. Semreen
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Waseem El-Huneidi
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Yasser Bustanji
- Department of Basic and Clinical Pharmacology, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Eman Abu-Gharbieh
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammad A. Y. Alqudah
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Ahmed Alhusban
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohd Shara
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ahmad Y. Abuhelwa
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Nelson C. Soares
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammad H. Semreen
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Correspondence: (M.H.S.); (K.H.A.)
| | - Karem H. Alzoubi
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Correspondence: (M.H.S.); (K.H.A.)
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Abufares HI, Oyoun Alsoud L, Alqudah MAY, Shara M, Soares NC, Alzoubi KH, El-Huneidi W, Bustanji Y, Soliman SSM, Semreen MH. COVID-19 Vaccines, Effectiveness, and Immune Responses. Int J Mol Sci 2022; 23:15415. [PMID: 36499742 PMCID: PMC9737588 DOI: 10.3390/ijms232315415] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has captivated the globe's attention since its emergence in 2019. This highly infectious, spreadable, and dangerous pathogen has caused health, social, and economic crises. Therefore, a worldwide collaborative effort was made to find an efficient strategy to overcome and develop vaccines. The new vaccines provide an effective immune response that safeguards the community from the virus' severity. WHO has approved nine vaccines for emergency use based on safety and efficacy data collected from various conducted clinical trials. Herein, we review the safety and effectiveness of the WHO-approved COVID-19 vaccines and associated immune responses, and their impact on improving the public's health. Several immunological studies have demonstrated that vaccination dramatically enhances the immune response and reduces the likelihood of future infections in previously infected individuals. However, the type of vaccination and individual health status can significantly affect immune responses. Exposure of healthy individuals to adenovirus vectors or mRNA vaccines causes the early production of antibodies from B and T cells. On the other hand, unhealthy individuals were more likely to experience harmful events due to relapses in their existing conditions. Taken together, aligning with the proper vaccination to a patient's case can result in better outcomes.
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Affiliation(s)
- Haneen Imad Abufares
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Leen Oyoun Alsoud
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Mohammad A. Y. Alqudah
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Mohd Shara
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Nelson C. Soares
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Karem H. Alzoubi
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Waseem El-Huneidi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Yasser Bustanji
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Sameh S. M. Soliman
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Mohammad H. Semreen
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
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18
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Semreen AM, Alsoud LO, El-Huneidi W, Ahmed M, Bustanji Y, Abu-Gharbieh E, El-Awady R, Ramadan WS, Alqudah MA, Shara M, Abuhelwa AY, Soares NC, Semreen MH, Alzoubi KH. Metabolomics Analysis Revealed Significant Metabolic Changes in Brain Cancer Cells Treated with Paclitaxel and/or Etoposide. Int J Mol Sci 2022; 23:ijms232213940. [PMID: 36430415 PMCID: PMC9693830 DOI: 10.3390/ijms232213940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer of the central nervous system (CNS) is ranked as the 19th most prevalent form of the disease in 2020. This study aims to identify candidate biomarkers and metabolic pathways affected by paclitaxel and etoposide, which serve as potential treatments for glioblastoma, and are linked to the pathogenesis of glioblastoma. We utilized an untargeted metabolomics approach using the highly sensitive ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS) for identification. In this study, 92 and 94 metabolites in U87 and U373 cell lines were profiled, respectively. The produced metabolites were then analyzed utilizing t-tests, volcano plots, and enrichment analysis modules. Our analysis revealed distinct metabolites to be significantly dysregulated (nutriacholic acid, L-phenylalanine, L-arginine, guanosine, ADP, hypoxanthine, and guanine), and to a lesser extent, mevalonic acid in paclitaxel and/or etoposide treated cells. Furthermore, both urea and citric acid cycles, and metabolism of polyamines and amino acids (aspartate, arginine, and proline) were significantly enriched. These findings can be used to create a map that can be utilized to assess the antitumor effect of paclitaxel and/or etoposide within the studied cancer cells.
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Affiliation(s)
- Ahlam M. Semreen
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Leen Oyoun Alsoud
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Waseem El-Huneidi
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Munazza Ahmed
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Yasser Bustanji
- Department of Basic and Clinical Pharmacology, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Eman Abu-Gharbieh
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Raafat El-Awady
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Wafaa S. Ramadan
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammad A.Y. Alqudah
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Mohd Shara
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ahmad Y. Abuhelwa
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Nelson C. Soares
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammad H. Semreen
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Correspondence: (M.H.S.); (K.H.A.)
| | - Karem H. Alzoubi
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Correspondence: (M.H.S.); (K.H.A.)
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19
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Sharaf BM, Giddey AD, Al-Hroub HM, Menon V, Okendo J, El-Awady R, Mousa M, Almehdi A, Semreen MH, Soares NC. Mass spectroscopy-based proteomics and metabolomics analysis of triple-positive breast cancer cells treated with tamoxifen and/or trastuzumab. Cancer Chemother Pharmacol 2022; 90:467-488. [PMID: 36264351 DOI: 10.1007/s00280-022-04478-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/22/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE HER2-enriched breast cancer with high levels of hormone receptor expression, known as "triple positive" breast cancer, may represent a new entity with a relatively favourable prognosis against which the combination of chemotherapy, HER-2 inhibition, and endocrine treatment may be considered overtreatment. We explored the effect of the anticancer drugs tamoxifen and trastuzumab, both separately and in combination, on the integrated proteomic and metabolic profile of "triple positive" breast cancer cells (BT-474). METHOD We employed ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry using a Bruker timsTOF to investigate changes in BT-474 cell line treated with either tamoxifen, trastuzumab or a combination. Differentially abundant metabolites were identified using the Bruker Human Metabolome Database metabolite library and proteins using the Uniprot proteome for Homo sapiens using MetaboScape and MaxQuant, respectively, for identification and quantitation. RESULTS A total of 77 proteins and 85 metabolites were found to significantly differ in abundance in BT-474 treated cells with tamoxifen 5 μM/and or trastuzumab 2.5 μM. Findings suggest that by targeting important cellular signalling pathways which regulate cell growth, apoptosis, proliferation, and chemoresistance, these medicines have a considerable anti-growth effect in BT-474 cells. Pathways enriched for dysregulation include RNA splicing, neutrophil degranulation and activation, cellular redox homeostasis, mitochondrial transmembrane transport, ferroptosis and necroptosis, ABC transporters and central carbon metabolism. CONCLUSION Our findings in protein and metabolite level research revealed that anti-cancer drug therapy had a significant impact on the key signalling pathways and molecular processes in triple positive BT-474 cell lines.
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Affiliation(s)
- Basma M Sharaf
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box. 27272, Sharjah, United Arab Emirates.,Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates
| | - Alexander D Giddey
- Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates
| | - Hamza M Al-Hroub
- Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates
| | - Varsha Menon
- Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates
| | - Javan Okendo
- Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road Observatory, Cape Town, 7925, South Africa
| | - Raafat El-Awady
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box. 27272, Sharjah, United Arab Emirates.,Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates
| | - Muath Mousa
- Research Institute of Science and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Ahmed Almehdi
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad H Semreen
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box. 27272, Sharjah, United Arab Emirates. .,Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates.
| | - Nelson C Soares
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box. 27272, Sharjah, United Arab Emirates. .,Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates.
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20
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Banimfreg BH, Shamayleh A, Alshraideh H, Semreen MH, Soares NC. Untargeted approach to investigating the metabolomics profile of type 2 diabetes emiratis. J Proteomics 2022; 269:104718. [PMID: 36100153 DOI: 10.1016/j.jprot.2022.104718] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 07/28/2022] [Accepted: 08/20/2022] [Indexed: 12/12/2022]
Abstract
Type 2 Diabetes (T2D) is expected to be the seventh most significant cause of death worldwide by 2030. Although research into its mechanism has received the attention it deserves, our understanding of T2D is still limited. This case-control study employs untargeted metabolomics to explore novel T2D plasma biomarkers in the Emirati population. Ninety-two UAE nationals were included in the cohort, with fifty T2D and forty-two non-T2D profiles. Participants were then stratified into three groups based on metabolic profiles, clinically verified diabetic status, and current HbA1c values: namely controlled diabetics, uncontrolled diabetics and prediabetics, and non-diabetics. The study identified fifteen significant differentially abundant metabolites between the uncontrolled diabetics group and the prediabetics or controlled diabetics group. Interestingly, some metabolites essential for the corticosteroid and thyroid signaling pathways were found to be significantly elevated in poorly controlled T2D, including cortisol, glycocholic acid, bile acids, thyroxine, and the tryptophan metabolite, 5-hydroxyindoleacetic acid. These findings align with those from prior western cohorts and suggest an intriguing linkage between T2D glycemic control and thyroid and adrenal signaling that may provide new diagnostic and prognostic indicators. RESEARCH SIGNIFICANCE: This study investigates the underlooked metabolomic role and correlation with T2D in the UAE population. The report indicates fifteen significant differentially abundant metabolites between on diabetics, uncontrolled diabetics and or controlled diabetics or prediabetics. This panel of metabolites such as thyroxine and corticosteroids should be considered further as potential diagnostic or prognostic biomarkers for T2D in the region.
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Affiliation(s)
- Bayan Hassan Banimfreg
- College of Engineering, Department of Industrial Engineering, American University of Sharjah, United Arab Emirates
| | - Abdulrahim Shamayleh
- College of Engineering, Department of Industrial Engineering, American University of Sharjah, United Arab Emirates
| | - Hussam Alshraideh
- College of Engineering, Department of Industrial Engineering, American University of Sharjah, United Arab Emirates
| | - Mohammad Harb Semreen
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Nelson C Soares
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.
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21
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Baros-Steyl SS, Al Heialy S, Semreen AH, Semreen MH, Blackburn JM, Soares NC. A review of mass spectrometry-based analyses to understand COVID-19 convalescent plasma mechanisms of action. Proteomics 2022; 22:e2200118. [PMID: 35809024 PMCID: PMC9349457 DOI: 10.1002/pmic.202200118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 01/08/2023]
Abstract
The spread of coronavirus disease 2019 (COVID‐19) viral pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has become a worldwide pandemic claiming several thousands of lives worldwide. During this pandemic, several studies reported the use of COVID‐19 convalescent plasma (CCP) from recovered patients to treat severely or critically ill patients. Although this historical and empirical treatment holds immense potential as a first line of response against eventual future unforeseen viral epidemics, there are several concerns regarding the efficacy and safety of this approach. This critical review aims to pinpoint the possible role of mass spectrometry‐based analysis in the identification of unique molecular component proteins, peptides, and metabolites of CCP that explains the therapeutic mechanism of action against COVID‐19. Additionally, the text critically reviews the potential application of mass spectrometry approaches in the search for novel plasma biomarkers that may enable a rapid and accurate assessment of the safety and efficacy of CCP. Considering the relative low‐cost value involved in the CCP therapy, this proposed line of research represents a tangible scientific challenge that will be translated into clinical practice and help save several thousand lives around the world, specifically in low‐ and middle‐income countries.
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Affiliation(s)
- Seanantha S Baros-Steyl
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Meakin-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Ahlam H Semreen
- College of Pharmacy-Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad H Semreen
- College of Pharmacy-Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nelson C Soares
- College of Pharmacy-Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
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22
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Torres-Sangiao E, Soares NC, Liu X. Editorial: Proteomic Approaches to Unravel Mechanisms of Resistance and Immune Evasion of Bacterial Pathogens. Front Med (Lausanne) 2022; 9:945264. [PMID: 35872756 PMCID: PMC9302473 DOI: 10.3389/fmed.2022.945264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 05/27/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Eva Torres-Sangiao
- Clinical Microbiology Lab, University Hospital Marqués de Valdecilla, Santander, Spain
- Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), Santander, Spain
- *Correspondence: Eva Torres-Sangiao
| | - Nelson C. Soares
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, University of Sarjah, Sharjah, United Arab Emirates
| | - Xiaoyun Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
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23
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Soares NC, Ali A, Srinivasulu V, Sharaf BM, Giddey AD, Okendo J, Al-Hroub HM, Semreen MH, Hamad M, Al-Tel TH. Unveiling the mechanism of action of nature-inspired anti-cancer compounds using a multi-omics approach. J Proteomics 2022; 265:104660. [PMID: 35728772 DOI: 10.1016/j.jprot.2022.104660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 10/18/2022]
Abstract
The 2020 global cancer registry has ranked breast cancer (BCa) as the most commonly diagnosed type of cancer and the most common cause of cancer-related deaths in women worldwide. Increasing resistance and significant side effects continue to limit the efficacy of anti-BCa drugs, hence the need to identify new drug targets and to develop novel compounds to overcome these limitations. Nature-inspired anti-cancer compounds are becoming increasingly popular since they often provide a relatively safe and effective alternative. In this study, we employed multi-omics techniques to gain insights into the relevant mechanism of action of two recently identified new nature-inspired anti-cancer compounds (SIMR3066 and SIMR3058). Discovery proteomics analysis combined with LC-MS/MS-based untargeted metabolomics analysis was performed on compound-treated vs DMSO-treated (control) MCF-7 cells. Downstream protein functional enrichment analysis showed that most of the responsive proteins were functionally associated with antigen processing and neutrophil degranulation, RNA catabolism and protein folding as well as cytoplasmic vesicle lumen and mitochondrial matrix formation. Consistent with the proteomics findings, metabolomic pathway analysis suggested that the differentially abundant compounds indicated altered metabolic pathways such as glycolysis, the Krebs cycle and oxidative phosphorylation. Furthermore, metabolomics-based enriched-for-action pathway analysis showed that the two compounds associate with mercaptopurine, thioguanine and azathioprine related pathways. Lastly, integrated proteomics and metabolomics analysis revealed that treatment of BCa with SIMR3066 disrupts several signaling pathways including p53-mediated apoptosis and the circadian entertainment pathway. Overall, the multi-omics approach we used in this study indicated that it is a powerful tool in probing the mechanism of action of lead drug candidates. SIGNIFICANCE: In this study we adopted a multi-omics (proteomics and metabolomics) strategy to learn more about the molecular mechanisms of action of nature-inspired potential anticancer drugs. Following treatment with SIMR3066 or SIMR3058, the integration of these multi-omics data sets revealed which biological pathways are altered in BCa cells. This study demonstrates that combining proteomics with metabolomics is a powerful method to investigate the mechanism of action of potential anticancer lead drug candidates.
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Affiliation(s)
- Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, United Arab Emirates.
| | - Amjad Ali
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Basma M Sharaf
- College of Pharmacy, University of Sharjah, United Arab Emirates
| | - Alexander D Giddey
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Javan Okendo
- Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road Observatory, Cape Town 7925, South Africa
| | - Hamza M Al-Hroub
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad H Semreen
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, United Arab Emirates
| | - Mawieh Hamad
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, United Arab Emirates.
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, United Arab Emirates
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24
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Jalaleddine N, Hachim M, Al-Hroub H, Saheb Sharif-Askari N, Senok A, Elmoselhi A, Mahboub B, Samuel Kurien NM, Kandasamy RK, Semreen MH, Halwani R, Soares NC, Al Heialy S. N6-Acetyl-L-Lysine and p-Cresol as Key Metabolites in the Pathogenesis of COVID-19 in Obese Patients. Front Immunol 2022; 13:827603. [PMID: 35663953 PMCID: PMC9161728 DOI: 10.3389/fimmu.2022.827603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Despite the growing number of the vaccinated population, COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global health burden. Obesity, a metabolic syndrome affecting one-third of the population, has proven to be a major risk factor for COVID-19 severe complications. Several studies have identified metabolic signatures and disrupted metabolic pathways associated with COVID-19, however there are no reports evaluating the role of obesity in the COVID-19 metabolic regulation. In this study we highlight the involvement of obesity metabolically in affecting SARS-CoV-2 infection and the consequent health complications, mainly cardiovascular disease. We measured one hundred and forty-four (144) metabolites using ultra high-performance liquid chromatography-quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) to identify metabolic changes in response to SARS-CoV-2 infection, in lean and obese COVID-19 positive (n=82) and COVID-19 negative (n=24) patients. The identified metabolites are found to be mainly correlating with glucose, energy and steroid metabolisms. Further data analysis indicated twelve (12) significantly yet differentially abundant metabolites associated with viral infection and health complications, in COVID-19 obese patients. Two of the detected metabolites, n6-acetyl-l-lysine and p-cresol, are detected only among the COVID-19 cohort, exhibiting significantly higher levels in COVID-19 obese patients when compared to COVID-19 lean patients. These metabolites have important roles in viral entry and could explain the increased susceptibility of obese patients. On the same note, a set of six metabolites associated with antiviral and anti-inflammatory functions displayed significantly lower abundance in COVID-19 obese patients. In conclusion, this report highlights the plasma metabolome of COVID-19 obese patients as a metabolic feature and signature to help improve clinical outcomes. We propose n6-acetyl-l-lysine and p-cresol as potential metabolic markers which warrant further investigations to better understand their involvement in different metabolic pathways in COVID-19.
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Affiliation(s)
- Nour Jalaleddine
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mahmood Hachim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Hamza Al-Hroub
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Adel Elmoselhi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Bassam Mahboub
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Department of Pulmonary Medicine and Allergy and Sleep Medicine, Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Nimmi Moni Samuel Kurien
- Department of Pulmonary Medicine and Allergy and Sleep Medicine, Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Richard K Kandasamy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Mohammad H Semreen
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Rabih Halwani
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Prince Abdullah Ben Khaled Celiac Disease Research Chair, Department of Pediatrics, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, QC, Canada
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25
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Alsoud LO, Soares NC, Al-Hroub HM, Mousa M, Kasabri V, Bulatova N, Suyagh M, Alzoubi KH, El-Huneidi W, Abu-Irmaileh B, Bustanji Y, Semreen MH. Identification of Insulin Resistance Biomarkers in Metabolic Syndrome Detected by UHPLC-ESI-QTOF-MS. Metabolites 2022; 12:metabo12060508. [PMID: 35736441 PMCID: PMC9227428 DOI: 10.3390/metabo12060508] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/28/2022] [Accepted: 05/29/2022] [Indexed: 02/04/2023] Open
Abstract
Metabolic syndrome (MetS) is a disorder characterized by a group of factors that can increase the risk of chronic diseases, including cardiovascular diseases and type 2 diabetes mellitus (T2D). Metabolomics has provided new insight into disease diagnosis and biomarker identification. This cross-sectional investigation used an untargeted metabolomics-based technique to uncover metabolomic alterations and their relationship to pathways in normoglycemic and prediabetic MetS participants to improve disease diagnosis. Plasma samples were collected from drug-naive prediabetic MetS patients (n = 26), normoglycemic MetS patients (n = 30), and healthy (normoglycemic lean) subjects (n = 30) who met the inclusion criteria for the study. The plasma samples were analyzed using highly sensitive ultra-high-performance liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). One-way ANOVA analysis revealed that 59 metabolites differed significantly among the three groups (p < 0.05). Glutamine, 5-hydroxy-L-tryptophan, L-sorbose, and hippurate were highly associated with MetS. However, 9-methyluric acid, sphinganine, and threonic acid were highly associated with prediabetes/MetS. Metabolic pathway analysis showed that arginine biosynthesis and glutathione metabolism were associated with MetS/prediabetes, while phenylalanine, D-glutamine and D-glutamate, and lysine degradation were highly impacted in MetS. The current study sheds light on the potential diagnostic value of some metabolites in metabolic syndrome and the role of their alteration on some of the metabolic pathways. More studies are needed in larger cohorts in order to verify the implication of the above metabolites on MetS and their diagnostic value.
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Affiliation(s)
- Leen Oyoun Alsoud
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (L.O.A.); (N.C.S.); (K.H.A.)
| | - Nelson C. Soares
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (L.O.A.); (N.C.S.); (K.H.A.)
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (H.M.A.-H.); (W.E.-H.)
| | - Hamza M. Al-Hroub
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (H.M.A.-H.); (W.E.-H.)
| | - Muath Mousa
- Research Institute of Science and Engineering, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates;
| | - Violet Kasabri
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan; (V.K.); (N.B.); (M.S.)
| | - Nailya Bulatova
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan; (V.K.); (N.B.); (M.S.)
| | - Maysa Suyagh
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan; (V.K.); (N.B.); (M.S.)
| | - Karem H. Alzoubi
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (L.O.A.); (N.C.S.); (K.H.A.)
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (H.M.A.-H.); (W.E.-H.)
| | - Waseem El-Huneidi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (H.M.A.-H.); (W.E.-H.)
- College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Bashaer Abu-Irmaileh
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan;
| | - Yasser Bustanji
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (H.M.A.-H.); (W.E.-H.)
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan; (V.K.); (N.B.); (M.S.)
- College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Correspondence: (Y.B.); (M.H.S.)
| | - Mohammad H. Semreen
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (L.O.A.); (N.C.S.); (K.H.A.)
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates; (H.M.A.-H.); (W.E.-H.)
- Correspondence: (Y.B.); (M.H.S.)
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26
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Fortuin S, Soares NC. The Integration of Proteomics and Metabolomics Data Paving the Way for a Better Understanding of the Mechanisms Underlying Microbial Acquired Drug Resistance. Front Med (Lausanne) 2022; 9:849838. [PMID: 35602483 PMCID: PMC9120609 DOI: 10.3389/fmed.2022.849838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Due to an increase in the overuse of antimicrobials and accelerated incidence of drug resistant pathogens, antimicrobial resistance has become a global health threat. In particular, bacterial antimicrobial resistance, in both hospital and community acquired transmission, have been found to be the leading cause of death due to infectious diseases. Understanding the mechanisms of bacterial drug resistance is of clinical significance irrespective of hospital or community acquired since it plays an important role in the treatment strategy and controlling infectious diseases. Here we highlight the advances in mass spectrometry-based proteomics impact in bacterial proteomics and metabolomics analysis- focus on bacterial drug resistance. Advances in omics technologies over the last few decades now allows multi-omics studies in order to obtain a comprehensive understanding of the biochemical alterations of pathogenic bacteria in the context of antibiotic exposure, identify novel biomarkers to develop new drug targets, develop time-effectively screen for drug susceptibility or resistance using proteomics and metabolomics.
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Affiliation(s)
- Suereta Fortuin
- African Microbiome Institute, General Internal Medicine, Stellenbosch University, Cape Town, South Africa
- *Correspondence: Suereta Fortuin
| | - Nelson C. Soares
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Nelson C. Soares
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27
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Torres-Sangiao E, Giddey AD, Leal Rodriguez C, Tang Z, Liu X, Soares NC. Proteomic Approaches to Unravel Mechanisms of Antibiotic Resistance and Immune Evasion of Bacterial Pathogens. Front Med (Lausanne) 2022; 9:850374. [PMID: 35586072 PMCID: PMC9108449 DOI: 10.3389/fmed.2022.850374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
The profound effects of and distress caused by the global COVID-19 pandemic highlighted what has been known in the health sciences a long time ago: that bacteria, fungi, viruses, and parasites continue to present a major threat to human health. Infectious diseases remain the leading cause of death worldwide, with antibiotic resistance increasing exponentially due to a lack of new treatments. In addition to this, many pathogens share the common trait of having the ability to modulate, and escape from, the host immune response. The challenge in medical microbiology is to develop and apply new experimental approaches that allow for the identification of both the microbe and its drug susceptibility profile in a time-sensitive manner, as well as to elucidate their molecular mechanisms of survival and immunomodulation. Over the last three decades, proteomics has contributed to a better understanding of the underlying molecular mechanisms responsible for microbial drug resistance and pathogenicity. Proteomics has gained new momentum as a result of recent advances in mass spectrometry. Indeed, mass spectrometry-based biomedical research has been made possible thanks to technological advances in instrumentation capability and the continuous improvement of sample processing and workflows. For example, high-throughput applications such as SWATH or Trapped ion mobility enable the identification of thousands of proteins in a matter of minutes. This type of rapid, in-depth analysis, combined with other advanced, supportive applications such as data processing and artificial intelligence, presents a unique opportunity to translate knowledge-based findings into measurable impacts like new antimicrobial biomarkers and drug targets. In relation to the Research Topic “Proteomic Approaches to Unravel Mechanisms of Resistance and Immune Evasion of Bacterial Pathogens,” this review specifically seeks to highlight the synergies between the powerful fields of modern proteomics and microbiology, as well as bridging translational opportunities from biomedical research to clinical practice.
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Affiliation(s)
- Eva Torres-Sangiao
- Clinical Microbiology Lab, University Hospital Marqués de Valdecilla, Santander, Spain
- Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), Santander, Spain
- *Correspondence: Eva Torres-Sangiao,
| | - Alexander Dyason Giddey
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Cristina Leal Rodriguez
- Copenhagen Prospectives Studies on Asthma in Childhood, COPSAC, Copenhagen University Hospital, Herlev-Gentofte, Denmark
| | - Zhiheng Tang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xiaoyun Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Nelson C. Soares
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Nelson C. Soares,
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28
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Bataineh MTAL, Cacciatore S, Semreen MH, Dash NR, Soares NC, Zhu X, Mousa MK, Salam JSA, Zerbini LF, Hajjo R, Hamad M. Exploring the effect of estrogen on Candida albicans hyphal cell wall glycans and ergosterol synthesis. Front Cell Infect Microbiol 2022; 12:977157. [PMID: 36268228 PMCID: PMC9578540 DOI: 10.3389/fcimb.2022.977157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/17/2022] [Indexed: 02/05/2023] Open
Abstract
Increased levels of 17-β estradiol (E2) due to pregnancy in young women or to hormonal replacement therapy in postmenopausal women have long been associated with an increased risk of yeast infections. Nevertheless, the effect underlying the role of E2 in Candida albicans infections is not well understood. To address this issue, functional, transcriptomic, and metabolomic analyses were performed on C. albicans cells subjected to temperature and serum induction in the presence or absence of E2. Increased filament formation was observed in E2 treated cells. Surprisingly, cells treated with a combination of E2 and serum showed decreased filament formation. Furthermore, the transcriptomic analysis revealed that serum and E2 treatment is associated with downregulated expression of genes involved in filamentation, including HWP1, ECE1, IHD1, MEP1, SOD5, and ALS3, in comparison with cells treated with serum or estrogen alone. Moreover, glucose transporter genes HGT20 and GCV2 were downregulated in cells receiving both serum and E2. Functional pathway enrichment analysis of the differentially expressed genes (DEGs) suggested major involvement of E2 signaling in several metabolic pathways and the biosynthesis of secondary metabolites. The metabolomic analysis determined differential secretion of 36 metabolites based on the different treatments' conditions, including structural carbohydrates and fatty acids important for hyphal cell wall formation such as arabinonic acid, organicsugar acids, oleic acid, octadecanoic acid, 2-keto-D-gluconic acid, palmitic acid, and steriacstearic acid with an intriguing negative correlation between D-turanose and ergosterol under E2 treatment. In conclusion, these findings suggest that E2 signaling impacts the expression of several genes and the secretion of several metabolites that help regulate C. albicans morphogenesis and virulence.
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Affiliation(s)
- Mohammad Tahseen AL Bataineh
- College of Medicine and Health Sciences, Department of Genetics and Molecular Biology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Molecular Biology and Genetics, Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- *Correspondence: Mohammad Tahseen AL Bataineh, ; Mawieh Hamad,
| | - Stefano Cacciatore
- Bioinformatics Unit, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Mohammad Harb Semreen
- College of Pharmacy, Department of Medical Chemistry, University of Sharjah, Sharjah, United Arab Emirates
| | - Nihar Ranjan Dash
- College of Medicine, University of Sharjah, Abu Dhabi, United Arab Emirates
- Research Institute for Medical and Health Sciences at the University of Sharjah, Sharjah, United Arab Emirates
| | - Nelson C. Soares
- College of Pharmacy, Department of Medical Chemistry, University of Sharjah, Sharjah, United Arab Emirates
| | - Xiaolong Zhu
- Beijing Genomics Institute Genomics, Sharjah, United Arab Emirates
| | - Muath Khairi Mousa
- College of Pharmacy, Department of Medical Chemistry, University of Sharjah, Sharjah, United Arab Emirates
| | - Jasmin Shafarin Abdul Salam
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Luiz F. Zerbini
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Jordan CDC, Amman, Jordan
| | - Mawieh Hamad
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- *Correspondence: Mohammad Tahseen AL Bataineh, ; Mawieh Hamad,
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29
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Sharaf BM, Giddey AD, Alniss H, Al-Hroub HM, El-Awady R, Mousa M, Almehdi A, Soares NC, Semreen MH. Untargeted Metabolomics of Breast Cancer Cells MCF-7 and SkBr3 Treated With Tamoxifen/Trastuzumab. Cancer Genomics Proteomics 2021; 19:79-93. [PMID: 34949661 DOI: 10.21873/cgp.20305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Trastuzumab and tamoxifen are two of the most widely prescribed anti-cancer drugs for breast cancer (BC). To date, few studies have explored the impact of anticancer drugs on metabolic pathways in BC. Metabolomics is an emerging technology that can identify new biomarkers for tracking therapy response and novel therapeutic targets. MATERIALS AND METHODS We employed ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) to investigate changes in MCF-7 and SkBr3 cell lines treated with either tamoxifen, trastuzumab or a combination of both. The Bruker Human Metabolome Database (HMDB) metabolite library was used to match spectra and the MetaboScape software to assign each feature with a putative metabolite name or molecular formula for metabolite annotation. RESULTS A total of 98 metabolites were found to significantly differ in abundance in MCF-7 and SkBr3 treated cells. Moreover, the metabolic profile of the combination medication is similar to that of tamoxifen alone, according to functional enrichment analysis. CONCLUSION Tamoxifen/trastuzumab treatment had a significant effect on pathways essential for the control of energy-production, which have previously been linked to cancer progression, and aggressiveness.
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Affiliation(s)
- Basma M Sharaf
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Alexander D Giddey
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hasan Alniss
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Hamza M Al-Hroub
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Raafat El-Awady
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Muath Mousa
- Research Institute of Science and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Ahmed Almehdi
- Research Institute of Science and Engineering, University of Sharjah, Sharjah, United Arab Emirates.,Department of Chemistry, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Nelson C Soares
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates; .,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad H Semreen
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates; .,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
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Giddey AD, Ganief TA, Ganief N, Koch A, Warner DF, Soares NC, Blackburn JM. Cell Wall Proteomics Reveal Phenotypic Adaption of Drug-Resistant Mycobacterium smegmatis to Subinhibitory Rifampicin Exposure. Front Med (Lausanne) 2021; 8:723667. [PMID: 34676224 PMCID: PMC8525676 DOI: 10.3389/fmed.2021.723667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/24/2021] [Indexed: 01/01/2023] Open
Abstract
Despite the availability of effective drug treatment, Mycobacterium tuberculosis (Mtb), the causative agent of TB disease, kills ~1. 5 million people annually, and the rising prevalence of drug resistance increasingly threatens to worsen this plight. We previously showed that sublethal exposure to the frontline anti-TB drug, rifampicin, resulted in substantial adaptive remodeling of the proteome of the model organism, Mycobacterium smegmatis, in the drug-sensitive mc2155 strain [wild type (WT)]. In this study, we investigate whether these responses are conserved in an engineered, isogenic mutant harboring the clinically relevant S531L rifampicin resistance-conferring mutation (SL) and distinguish the responses that are specific to RNA polymerase β subunit- (RpoB-) binding activity of rifampicin from those that are dependent on the presence of rifampicin alone. We verified the drug resistance status of this strain and observed no phenotypic indications of rifampicin-induced stress upon treatment with the same concentration as used in WT (2.5 μg/ml). Thereafter, we used a cell wall-enrichment strategy to focus attention on the cell wall proteome and observed 253 proteins to be dysregulated in SL bacteria in comparison with 716 proteins in WT. We observed that decreased abundance of ATP-binding cassette (ABC) transporters and increased abundance of ribosomal machinery were conserved in the SL strain, whereas the upregulation of transcriptional machinery and the downregulation of numerous two-component systems were not. We conclude that the drug-resistant M. smegmatis strain displays some of the same proteomic responses observed in WT and suggest that this evidence supports the hypothesis that rifampicin exercises effects beyond RpoB-interaction alone and that mycobacteria recognise rifampicin as a signaling molecule in an RpoB-independent manner at sublethal doses. Taken together, our data indicates mixed RpoB-independent and RpoB-dependent proteomic remodeling in WT mycobacteria, with evidence for RpoB-independent ABC transporter downregulation, but drug activity-based transcriptional upregulation and two-component system downregulation.
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Affiliation(s)
- Alexander D Giddey
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tariq A Ganief
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Naadir Ganief
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anastasia Koch
- South African Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Digby F Warner
- South African Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nelson C Soares
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Jonathan M Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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van der Watt PJ, Okpara MO, Wishart A, Parker MI, Soares NC, Blackburn JM, Leaner VD. Nuclear transport proteins are secreted by cancer cells and identified as potential novel cancer biomarkers. Int J Cancer 2021; 150:347-361. [PMID: 34591985 DOI: 10.1002/ijc.33832] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/20/2021] [Accepted: 09/20/2021] [Indexed: 12/21/2022]
Abstract
Previous studies have identified increased expression of members of the nuclear transport protein family in cancer cells. Recently, certain nuclear transport proteins have been reported to be secreted by cells and found in the serum. The aims of our study were to investigate the levels of multiple nuclear transport proteins secreted from cancer cells, and to determine their potential as diagnostic markers for cervical and oesophageal cancer. Mass spectrometry identified 10 nuclear transport proteins in the secretome and exosomes of cultured cancer cells, and Western blot analysis confirmed increased secreted levels in cancer cells compared to normal. To investigate their presence in patient serum, enzyme-linked immunosorbent assays were performed and revealed significantly increased levels of KPNβ1, CRM1, CAS, IPO5 and TNPO1 in cervical and oesophageal cancer patient serum compared to non-cancer controls. Significantly elevated KPNα2 and RAN levels were also identified in oesophageal cancer serum samples. Logistics regression analyses revealed IPO5 and TNPO1 to be the best performing individual candidate biomarkers in discriminating between cancer cases and controls. The combination of KPNβ1, CRM1, KPNα2, CAS, RAN, IPO5 and TNPO1 as a panel of biomarkers had the highest diagnostic capacity with an area under the curve of 0.944 and 0.963, for cervical cancer and oesophageal cancer, and sensitivity of 92.5% at 86.8% specificity and 95.3% sensitivity at 87.5% specificity, respectively. These results suggest that nuclear transport proteins have potential as diagnostic biomarkers for cervical and oesophageal cancers, with a combination of protein family members being the best predictor.
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Affiliation(s)
- Pauline J van der Watt
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Michael O Okpara
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Andrew Wishart
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - M Iqbal Parker
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nelson C Soares
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jonathan M Blackburn
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Virna D Leaner
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,SAMRC Gynaecology Cancer Research Centre, University of Cape Town, Cape Town, South Africa
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32
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Fortuin S, Iradukunda J, Nel AJ, Blackburn JM, Soares NC. Liquid chromatography mass spectrometry-based proteomics of Escherichia coli single colony. MethodsX 2021; 8:101277. [PMID: 34434797 PMCID: PMC8374269 DOI: 10.1016/j.mex.2021.101277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/14/2021] [Indexed: 01/17/2023] Open
Abstract
The Escherichia coli proteome is the most extensively characterized and studied of all prokaryotic proteomes. Despite this, large scale bacterial proteomics experiments performed on E. coli cells grown in liquid cultures have failed to identify key virulence factors thought to be important determinants in establishing bacterial infections. It seems likely that many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth in biofilms, which can be crudely mimicked on solid media. This method describes a simple workflow to characterize the unique proteome signature of individual, isolated single colonies, using E. coli K12 strain grown on solid media as a model system. The workflow thus provides a means to explore the proteomes of minimally passaged clinical isolates of bacteria grown on primary culture plates and to identify both unique and differentially expressed proteins contained therein. Value of the method: - Simple mass spectrometry-based proteomics workflow to characterise the proteome of single colony forming units - Enables exploration of the proteomes of minimally passaged clinical isolates from primary culture plates - Identification of virulence factors expressed in true or mimicked biofilms that may be missed in liquid cultures Method name: E. coli single colony proteome analysis
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Affiliation(s)
- Suereta Fortuin
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Anzio, Observatory, Cape Town 7925, South Africa
| | - John Iradukunda
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Anzio, Observatory, Cape Town 7925, South Africa
| | - Andrew Jm Nel
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Anzio, Observatory, Cape Town 7925, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Anzio, Observatory, Cape Town 7925, South Africa.,Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio, Observatory, Cape Town 7925, South Africa
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah, United Arab Emirates
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Zaher DM, Ramadan WS, El-Awady R, Omar HA, Hersi F, Srinivasulu V, Hachim IY, Al-Marzooq FI, Vazhappilly CG, Merali S, Merali C, Soares NC, Schilf P, Ibrahim SM, Al-Tel TH. A Novel Benzopyrane Derivative Targeting Cancer Cell Metabolic and Survival Pathways. Cancers (Basel) 2021; 13:cancers13112840. [PMID: 34200264 PMCID: PMC8201054 DOI: 10.3390/cancers13112840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 02/03/2023] Open
Abstract
(1) Background: Today, the discovery of novel anticancer agents with multitarget effects and high safety margins represents a high challenge. Drug discovery efforts indicated that benzopyrane scaffolds possess a wide range of pharmacological activities. This spurs on building a skeletally diverse library of benzopyranes to identify an anticancer lead drug candidate. Here, we aim to characterize the anticancer effect of a novel benzopyrane derivative, aiming to develop a promising clinical anticancer candidate. (2) Methods: The anticancer effect of SIMR1281 against a panel of cancer cell lines was tested. In vitro assays were performed to determine the effect of SIMR1281 on GSHR, TrxR, mitochondrial metabolism, DNA damage, cell cycle progression, and the induction of apoptosis. Additionally, SIMR1281 was evaluated in vivo for its safety and in a xenograft mice model. (3) Results: SIMR1281 strongly inhibits GSHR while it moderately inhibits TrxR and modulates the mitochondrial metabolism. SIMR1281 inhibits the cell proliferation of various cancers. The antiproliferative activity of SIMR1281 was mediated through the induction of DNA damage, perturbations in the cell cycle, and the inactivation of Ras/ERK and PI3K/Akt pathways. Furthermore, SIMR1281 induced apoptosis and attenuated cell survival machinery. In addition, SIMR1281 reduced the tumor volume in a xenograft model while maintaining a high in vivo safety profile at a high dose. (4) Conclusions: Our findings demonstrate the anticancer multitarget effect of SIMR1281, including the dual inhibition of glutathione and thioredoxin reductases. These findings support the development of SIMR1281 in preclinical and clinical settings, as it represents a potential lead compound for the treatment of cancer.
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Affiliation(s)
- Dana M. Zaher
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Wafaa S. Ramadan
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Raafat El-Awady
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Hany A. Omar
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Fatema Hersi
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
| | - Ibrahim Y. Hachim
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Farah I. Al-Marzooq
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Cijo G. Vazhappilly
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- School of Arts and Sciences, American University of Ras Al Khaimah, P.O. Box 10021, Ras Al Khaimah 10021, United Arab Emirates
| | - Salim Merali
- School of Pharmacy, Temple University, 3307 N Broad Street, Room 552, Philadelphia, PA 19140, USA; (S.M.); (C.M.)
| | - Carmen Merali
- School of Pharmacy, Temple University, 3307 N Broad Street, Room 552, Philadelphia, PA 19140, USA; (S.M.); (C.M.)
| | - Nelson C. Soares
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Paul Schilf
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany;
| | - Saleh M. Ibrahim
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany;
| | - Taleb H. Al-Tel
- Sharjah Institute for Medical Researches, University of Sharjah, Sharjah 27272, United Arab Emirates; (D.M.Z.); (W.S.R.); (R.E.-A.); (H.A.O.); (F.H.); (V.S.); (I.Y.H.); (F.I.A.-M.); (C.G.V.); (N.C.S.); (S.M.I.)
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Correspondence: ; Tel.: +971-6505-7417
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Al-Tel TH, Srinivasulu V, Al-Marzooq F, Hamad M, Khanfar MA, Ramanathan M, Soares NC. Sequencing Groebke–Blackburn–Bienaymé and Aza-Michael Addition Reactions: A Modular Strategy for Accessing a Diverse Collection of Constrained Benzoxazepine and Imidazopyrazine Systems. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/s-0040-1706141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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35
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Al-Tel TH, Srinivasulu V, Al-Marzooq F, Hamad M, Khanfar MA, Ramanathan M, Soares NC. Sequencing Groebke–Blackburn–Bienaymé and Aza-Michael Addition Reactions: A Modular Strategy for Accessing a Diverse Collection of Constrained Benzoxazepine and Imidazopyrazine Systems. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/s-0040-1706006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractWe present a divergent strategy that permits access to diversely functionalized benzoxazepinium scaffolds fused to various heterocycles. The described strategy features a one-pot combination of the Groebke–Blackburn–Bienaymé reaction and an aza-Michael addition. Methyl (E)-4-(2-formylphenoxy)but-2-enoate and its derivatives are utilized as central elements in this cascade. These building blocks are reacted with a variety of functionalized amino-azines and tert-butyl isocyanide under ytterbium triflate [Yb(OTf)3] catalysis. The ensuing cascade represents a rapid, modular and atom-economic process that leads to the construction of a diverse collection of constrained benzoxazepinium systems from a wide substrate scope.
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Affiliation(s)
- Taleb H. Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah
- College of Pharmacy, University of Sharjah
| | | | - Farah Al-Marzooq
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, UAE University
| | - Mohamad Hamad
- Sharjah Institute for Medical Research, University of Sharjah
- College of Health Sciences, University of Sharjah
| | - Monther A. Khanfar
- Sharjah Institute for Medical Research, University of Sharjah
- Department of Chemistry, University of Jordan
| | - Mani Ramanathan
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, 26666
| | - Nelson C. Soares
- Sharjah Institute for Medical Research, University of Sharjah
- College of Pharmacy, University of Sharjah
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Abstract
Mass spectrometry-based single-cell proteomic analysis has recently gained momentum and is now an emerging area with established protocols and promising results. Traditional proteomic studies, especially involving bacteria, have been limited to suspension cultures with large protein yields. Such studies, however, remain population centered with the uniqueness of individual responses to environmental challenges becoming diluted. To enable bacterial single-colony proteomics, we describe a quantitative mass spectrometry-based protocol to isolate and analyze the proteome of a single mycobacterial colony from 7H10 media, with growth supplements for optimal growth. Following protein purification and digestion, tryptic peptides are analyzed by UHPLC coupled to a hybrid Q Exactive mass spectrometer. Raw data were analyzed using the MaxQuant Suite, and downstream statistical analysis was performed using Perseus software. A total of 7805 unique peptides and 1387 proteins were identified. Data are available via ProteomeXchange with identifier PXD018168. In this chapter, we identify steps most prone to sample loss and describe measures of alleviation that allows the preservation of protein yield and boosts quantitative power while increasing reproducibility, of "very limiting samples."
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Affiliation(s)
- John Iradukunda
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tariq Ganief
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, UCT, Cape Town, South Africa
| | - Nelson C Soares
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah, United Arab Emirates.
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.
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Abstract
The World Health Organization (WHO) estimates that Mycobacterium tuberculosis, the most pathogenic mycobacterium species to humans, has infected up to a quarter of the world's population, with the occurrence of multidrug-resistant strains on the rise. Research into the detailed composition of the cell envelope proteome in mycobacteria over the last 20 years has formed a key part of the efforts to understand host-pathogen interactions and to control the current tuberculosis epidemic. This is due to the great importance of the cell envelope proteome during infection and during the development of antibiotic resistance as well as the search of surface-exposed proteins that could be targeted by therapeutics and vaccines. A variety of experimental approaches and mycobacterial species have been used in proteomic studies thus far. Here we provide for the first time an extensive summary of the different approaches to isolate the mycobacterial cell envelope, highlight some of the limitations of the studies performed thus far, and comment on how the recent advances in membrane proteomics in other fields might be translated into the field of mycobacteria to provide deeper coverage.
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Affiliation(s)
- Clemens Hermann
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Leshern Karamchand
- National Research Council Canada, Nanotechnology Research Centre, Biomedical Nanotechnologies, 11421 Saskatchewan Drive NW, Edmonton, Alberta T6G 2M9, Canada
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates.,College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates
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Fortuin S, Nel AJM, Blackburn JM, Soares NC. Comparison between the proteome of Escherichia coli single colony and during liquid culture. J Proteomics 2020; 228:103929. [PMID: 32800795 DOI: 10.1016/j.jprot.2020.103929] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
Most bacterial proteomic studies done to date utilise bacterial cells harvested from liquid culture media. However, it is widely accepted that many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth on solid media, as a crude mimic of true biofilms. Here, we compare the observed proteome of Escherichia coli K12 from isolated single colonies on solid media with those observed at different growth phases in liquid culture; i.e. early-log, mid-log, early-, mid- and late-stationary growth phases. A total of 2044 protein groups covering approximately 47% of the total proteome were identified across all studied conditions, including 1650 proteins identified from single colonies and 1679 proteins from liquid cultured cells. Label-free quantitative analysis revealed that the E. coli proteome of single colonies on a solid agar differs from that observed in liquid culture. Notably, the presence of proteins in the Suf-operon that are involved in iron mobilisation and swarming motility was associated exclusively with single colony profiles, whereas proteins involved in motility such as motA, motB, fliH, flip, fliD and fliJ were associated exclusively with cells grown in liquid culture. The data presented here provide a valuable resource for understanding the role of key proteins within microenvironments surrounding E. coli single colonies. SIGNIFICANCE: To date, most proteomics studies have used E. coli cells harvested from liquid culture media even though many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth on solid media. In this study, we compare the observed proteome of E. coli K12 from isolated single colonies on solid media with those observed at different growth phases in liquid culture; i.e. early-log, mid-log, early-, mid- and late-stationary growth phases. By using label-free quantitative analysis we demonstrate that the E. coli proteome of single colonies on a solid agar differs from that observed in liquid culture with an overlap of 68% of proteins between the two culture conditions. Our analysis further reveal the presence of proteins in the Suf-operon that are involved in iron mobilisation and swarming motility was associated exclusively with single colony profiles. While those proteins involved in motility such as motA, motB, fliH, flip, fliD and fliJ were associated exclusively with cells grown in liquid culture. By comparison to E. coli proteomic data available on liquid culture and solid media, this research represents a first effort to describe the differential expression of key E. coli proteins within microenvironments surrounding single colonies.
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Affiliation(s)
- Suereta Fortuin
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town. Cape Town, South Africa
| | - Andrew J M Nel
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town. Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town. Cape Town, South Africa; Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town. Cape Town, South Africa.
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.
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Semreen MH, Alniss H, Cacciatore S, El-Awady R, Mousa M, Almehdi AM, El-Huneidi W, Zerbini L, Soares NC. GC-MS based comparative metabolomic analysis of MCF-7 and MDA-MB-231 cancer cells treated with Tamoxifen and/or Paclitaxel. J Proteomics 2020; 225:103875. [PMID: 32534214 DOI: 10.1016/j.jprot.2020.103875] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 05/31/2020] [Accepted: 06/06/2020] [Indexed: 12/16/2022]
Abstract
Breast cancer cells MCF-7 and MDA-MB-231 were treated with Tamoxifen (5 μM) or Paclitaxel (1 μM) or with a combination of the two drugs. Herein, we have employed gas chromatography coupled with mass spectroscopy to identify metabolic changes occurring as response to different drug treatments. We report the identification of sixty-one metabolites and overall the two studied cell lines showed a distinct metabolomic profile from each other. Further data analysis indicates that a total of 30 metabolites were significantly differentially abundant in MCF-7 drug-treated cells, most of the metabolic changes occurred when cells were treated with either Tamoxifen (15) or Paclitaxel (25). On the other side, a total of 31 metabolites were significantly differentially abundant in MDA-MB-31 cells with drug treatment. Similarly, to MCF-7 most of the metabolic changes occurred when cells were treated with either Tamoxifen (19) or Paclitaxel (20). In conclusion, this report demonstrates that Tamoxifen and/or Paclitaxel treatment have a pronounced effect on the main metabolic pathways in both breast cancer (BC) cell lines (MCF-7 and MDA-MB231), which could be used as a foundation for future investigations to understand the possible effect of these drugs on different metabolic pathways. SIGNIFICANCE: Metabolic profiling of cancer cells is a promising tool in tumor diagnosis, biomarker discovery and drug treatment protocols, since cancer cells exhibit altered metabolism when compared to normal cells. Although numerous studies have reported the use of various OMICs applications to investigate breast cancer cells, very few of these have performed thorough screening of metabolites in such cells. Our investigation highlights the first study to characterize MCF7 and MDA-MB-231 cancer cells treated with Tamoxifen and/or Paclitaxel and to identify the affected metabolic pathways. Such findings might play an important role in revealing the molecular bases of the underlying mechanism of action of these two frontline anti-breast cancer drugs.
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Affiliation(s)
- Mohammad H Semreen
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.
| | - Hasan Alniss
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.
| | - Stefano Cacciatore
- Cancer Genomics group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Rafat El-Awady
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Muath Mousa
- Research Institute of Science and Engineering, University of Sharjah, United Arab Emirates
| | - Ahmed M Almehdi
- Research Institute of Science and Engineering, University of Sharjah, United Arab Emirates
| | - Waseem El-Huneidi
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, United Arab Emirates
| | - Luiz Zerbini
- Cancer Genomics group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Nelson C Soares
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
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Baros SS, Blackburn JM, Soares NC. Phosphoproteomic Approaches to Discover Novel Substrates of Mycobacterial Ser/Thr Protein Kinases. Mol Cell Proteomics 2020; 19:233-244. [PMID: 31839597 PMCID: PMC7000118 DOI: 10.1074/mcp.r119.001668] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Mycobacterial Ser/Thr protein kinases (STPKs) play a critical role in signal transduction pathways that ultimately determine mycobacterial growth and metabolic adaptation. Identification of key physiological substrates of these protein kinases is, therefore, crucial to better understand how Ser/Thr phosphorylation contributes to mycobacterial environmental adaptation, including response to stress, cell division, and host-pathogen interactions. Various substrate detection methods have been employed with limited success, with direct targets of STPKs remaining elusive. Recently developed mass spectrometry (MS)-based phosphoproteomic approaches have expanded the list of potential STPK substrate identifications, yet further investigation is required to define the most functionally significant phosphosites and their physiological importance. Prior to the application of MS workflows, for instance, GarA was the only known and validated physiological substrate for protein kinase G (PknG) from pathogenic mycobacteria. A subsequent list of at least 28 candidate PknG substrates has since been reported with the use of MS-based analyses. Herein, we integrate and critically review MS-generated datasets available on novel STPK substrates and report new functional and subcellular localization enrichment analyses on novel candidate protein kinase A (PknA), protein kinase B (PknB) and PknG substrates to deduce the possible physiological roles of these kinases. In addition, we assess substrate specificity patterns across different mycobacterial STPKs by analyzing reported sets of phosphopeptides, in order to determine whether novel motifs or consensus regions exist for mycobacterial Ser/Thr phosphorylation sites. This review focuses on MS-based techniques employed for STPK substrate identification in mycobacteria, while highlighting the advantages and challenges of the various applications.
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Affiliation(s)
- Seanantha S Baros
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa; Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.
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Al-Tel TH, Srinivasulu V, Ramanathan M, Soares NC, Sebastian A, Bolognesi ML, Abu-Yousef IA, Majdalawieh A. Stereocontrolled transformations of cyclohexadienone derivatives to access stereochemically rich and natural product-inspired architectures. Org Biomol Chem 2020; 18:8526-8571. [PMID: 33043327 DOI: 10.1039/d0ob01550d] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The last two decades or so have witnessed an upsurge in defining the art of designing complex natural products and nature-inspired molecules. Throughout these decades, fundamental insights into stereocontrolled, step-economic and atom-economical synthesis principles were achieved by the numerous synthetic accomplishments particularly in diversity-oriented synthesis (DOS). This has empowered the visualization of the third dimension in synthetic design and thus has resulted in a dramatic increase with today's diversity-oriented synthesis (DOS) at the forefront enabling access to diverse scaffolds with a high degree of stereochemical and skeletal complexity. To this end, a starting material-based approach is one of the powerful tools utilized in DOS that allows rapid access to molecular architectures with a high sp3 content. Skeletal and stereochemical diversity is often paramount for the selective modulation of the biological function of a complementary protein in the biological space. In this context, stereocontrolled transformation of cyclohexadienone scaffolds has positioned itself as a powerful platform for the rapid generation of stereochemically enriched and natural product-inspired compound collections. In this review, we cover multidirectional synthetic strategies that utilized cyclohexadienone derivatives as pluripotent building blocks en route for the construction of novel chemical space.
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Affiliation(s)
- Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.
| | - Mani Ramanathan
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, Sharjah, United Arab Emirates
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.
| | - Anusha Sebastian
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, Sharjah, United Arab Emirates
| | - Maria L Bolognesi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Via Belmeloro, 6, 40126 Bologna, Italy
| | - Imad A Abu-Yousef
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, Sharjah, United Arab Emirates
| | - Amin Majdalawieh
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, Sharjah, United Arab Emirates
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Ganief N, Sjouerman J, Albeldas C, Nakedi KC, Hermann C, Calder B, Blackburn JM, Soares NC. Associating H 2O 2-and NO-related changes in the proteome of Mycobacterium smegmatis with enhanced survival in macrophage. Emerg Microbes Infect 2018; 7:212. [PMID: 30546046 PMCID: PMC6292918 DOI: 10.1038/s41426-018-0210-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/26/2018] [Accepted: 11/05/2018] [Indexed: 01/24/2023]
Abstract
Mycobacterium manages to evade the host cell immune system, partially owing to its ability to survive redox stress after macrophage engulfment. Exposure to redox stress has been linked to later replication, persistence, and latent infection. In this work, mass spectrometry was used to elucidate the cell-wide changes that occur in response to sublethal doses of hydrogen peroxide and nitric oxide over time, with Mycobacterium smegmatis being used as a model organism. A total of 3135 proteins were confidently assigned, of which 1713, 1674, and 1713 were identified under NO, H2O2, and control conditions, respectively. Both treatment conditions resulted in changes of protein expression from the DosR regulon as well as those related to lipid metabolism. Complementary to the changes in the proteome, sublethal exposure to NO and H2O2 improved the survival of the bacteria after macrophage infection. Our data indicate that pre-exposure to sublethal doses of these redox stressors causes an alteration in the expression of proteins related to lipid metabolism, suggesting a link between altered lipid metabolism and enhanced survival in macrophages.
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Affiliation(s)
- Naadir Ganief
- Division of Chemical & System Biology, Department of Integrative Biomedical Science, University of Cape Town, Cape Town, South Africa
| | - Jessica Sjouerman
- Division of Chemical & System Biology, Department of Integrative Biomedical Science, University of Cape Town, Cape Town, South Africa
| | - Claudia Albeldas
- Division of Chemical & System Biology, Department of Integrative Biomedical Science, University of Cape Town, Cape Town, South Africa
| | - Kehilwe C Nakedi
- Division of Chemical & System Biology, Department of Integrative Biomedical Science, University of Cape Town, Cape Town, South Africa
| | - Clemens Hermann
- Division of Chemical & System Biology, Department of Integrative Biomedical Science, University of Cape Town, Cape Town, South Africa
| | - Bridget Calder
- Division of Chemical & System Biology, Department of Integrative Biomedical Science, University of Cape Town, Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & System Biology, Department of Integrative Biomedical Science, University of Cape Town, Cape Town, South Africa. .,Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa.
| | - Nelson C Soares
- Division of Chemical & System Biology, Department of Integrative Biomedical Science, University of Cape Town, Cape Town, South Africa.
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Senthebane DA, Jonker T, Rowe A, Thomford NE, Munro D, Dandara C, Wonkam A, Govender D, Calder B, Soares NC, Blackburn JM, Parker MI, Dzobo K. The Role of Tumor Microenvironment in Chemoresistance: 3D Extracellular Matrices as Accomplices. Int J Mol Sci 2018; 19:E2861. [PMID: 30241395 PMCID: PMC6213202 DOI: 10.3390/ijms19102861] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The functional interplay between tumor cells and their adjacent stroma has been suggested to play crucial roles in the initiation and progression of tumors and the effectiveness of chemotherapy. The extracellular matrix (ECM), a complex network of extracellular proteins, provides both physical and chemicals cues necessary for cell proliferation, survival, and migration. Understanding how ECM composition and biomechanical properties affect cancer progression and response to chemotherapeutic drugs is vital to the development of targeted treatments. METHODS 3D cell-derived-ECMs and esophageal cancer cell lines were used as a model to investigate the effect of ECM proteins on esophageal cancer cell lines response to chemotherapeutics. Immunohistochemical and qRT-PCR evaluation of ECM proteins and integrin gene expression was done on clinical esophageal squamous cell carcinoma biopsies. Esophageal cancer cell lines (WHCO1, WHCO5, WHCO6, KYSE180, KYSE 450 and KYSE 520) were cultured on decellularised ECMs (fibroblasts-derived ECM; cancer cell-derived ECM; combinatorial-ECM) and treated with 0.1% Dimethyl sulfoxide (DMSO), 4.2 µM cisplatin, 3.5 µM 5-fluorouracil and 2.5 µM epirubicin for 24 h. Cell proliferation, cell cycle progression, colony formation, apoptosis, migration and activation of signaling pathways were used as our study endpoints. RESULTS The expression of collagens, fibronectin and laminins was significantly increased in esophageal squamous cell carcinomas (ESCC) tumor samples compared to the corresponding normal tissue. Decellularised ECMs abrogated the effect of drugs on cancer cell cycling, proliferation and reduced drug induced apoptosis by 20⁻60% that of those plated on plastic. The mitogen-activated protein kinase-extracellular signal-regulated kinase (MEK-ERK) and phosphoinositide 3-kinase-protein kinase B (PI3K/Akt) signaling pathways were upregulated in the presence of the ECMs. Furthermore, our data show that concomitant addition of chemotherapeutic drugs and the use of collagen- and fibronectin-deficient ECMs through siRNA inhibition synergistically increased cancer cell sensitivity to drugs by 30⁻50%, and reduced colony formation and cancer cell migration. CONCLUSION Our study shows that ECM proteins play a key role in the response of cancer cells to chemotherapy and suggest that targeting ECM proteins can be an effective therapeutic strategy against chemoresistant tumors.
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Affiliation(s)
- Dimakatso Alice Senthebane
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), UCT Campus, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Tina Jonker
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), UCT Campus, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Arielle Rowe
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), UCT Campus, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Nicholas Ekow Thomford
- Pharmacogenetics Research Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Daniella Munro
- Pharmacogenetics Research Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Collet Dandara
- Pharmacogenetics Research Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Ambroise Wonkam
- Pharmacogenetics Research Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Dhirendra Govender
- Division of Anatomical Pathology, Faculty of Health Sciences, University of Cape Town, NHLS-Groote Schuur Hospital, Cape Town 7925, South Africa.
| | - Bridget Calder
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.
| | - Nelson C Soares
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.
| | - Jonathan M Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.
| | - M Iqbal Parker
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Kevin Dzobo
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), UCT Campus, Anzio Road, Observatory, Cape Town 7925, South Africa.
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Bell L, Calder B, Hiller R, Klein A, Soares NC, Stoychev SH, Vorster BC, Tabb DL. Challenges and Opportunities for Biological Mass Spectrometry Core Facilities in the Developing World. J Biomol Tech 2018; 29:4-15. [PMID: 29623005 DOI: 10.7171/jbt.18-2901-003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The developing world is seeing rapid growth in the availability of biological mass spectrometry (MS), particularly through core facilities. As proteomics and metabolomics becomes locally feasible for investigators in these nations, application areas associated with high burden in these nations, such as infectious disease, will see greatly increased research output. This article evaluates the rapid growth of MS in South Africa (currently approaching 20 laboratories) as a model for establishing MS core facilities in other nations of the developing world. Facilities should emphasize new services rather than new instruments. The reduction of the delays associated with reagent and other supply acquisition would benefit both facilities and the users who make use of their services. Instrument maintenance and repair, often mediated by an in-country business for an international vendor, is also likely to operate on a slower schedule than in the wealthiest nations. A key challenge to facilities in the developing world is educating potential facility users in how best to design experiments for proteomics and metabolomics, what reagents are most likely to introduce problematic artifacts, and how to interpret results from the facility. Here, we summarize the experience of 6 different institutions to raise the level of biological MS available to researchers in South Africa.
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Affiliation(s)
- Liam Bell
- Centre for Proteomic and Genomic Research, Observatory, Cape Town 7925, South Africa
| | - Bridget Calder
- University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Reinhard Hiller
- Centre for Proteomic and Genomic Research, Observatory, Cape Town 7925, South Africa
| | - Ashwil Klein
- University of the Western Cape, Bellville, Cape Town 7925, South Africa
| | - Nelson C Soares
- University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Stoyan H Stoychev
- Council for Scientific and Industrial Research, Pretoria 0001, South Africa
| | - Barend C Vorster
- Centre for Human Metabolomics, North-West University, Potchefstroom 2520, South Africa; and
| | - David L Tabb
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
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Nakedi KC, Calder B, Banerjee M, Giddey A, Nel AJM, Garnett S, Blackburn JM, Soares NC. Identification of Novel Physiological Substrates of Mycobacterium bovis BCG Protein Kinase G (PknG) by Label-free Quantitative Phosphoproteomics. Mol Cell Proteomics 2018; 17:1365-1377. [PMID: 29549130 PMCID: PMC6030727 DOI: 10.1074/mcp.ra118.000705] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 01/09/2023] Open
Abstract
Mycobacterial Ser/Thr kinases play a critical role in bacterial physiology and pathogenesis. Linking kinases to the substrates they phosphorylate in vivo, thereby elucidating their exact functions, is still a challenge. The aim of this work was to associate protein phosphorylation in mycobacteria with important subsequent macro cellular events by identifying the physiological substrates of PknG in Mycobacterium bovis BCG. The study compared the phosphoproteome dynamics during the batch growth of M. bovis BCG versus the respective PknG knock-out mutant (ΔPknG-BCG) strains. We employed TiO2 phosphopeptide enrichment techniques combined with label-free quantitative phosphoproteomics workflow on LC-MS/MS. The comprehensive analysis of label-free data identified 603 phosphopeptides on 307 phosphoproteins with high confidence. Fifty-five phosphopeptides were differentially phosphorylated, of these, 23 phosphopeptides were phosphorylated in M. bovis BCG wild-type only and not in the mutant. These were further validated through targeted mass spectrometry assays (PRMs). Kinase-peptide docking studies based on a published crystal structure of PknG in complex with GarA revealed that the majority of identified phosphosites presented docking scores close to that seen in previously described PknG substrates, GarA, and ribosomal protein L13. Six out of the 22 phosphoproteins had higher docking scores than GarA, consistent with the proteins identified here being true PknG substrates. Based on protein functional analysis of the PknG substrates identified, this study confirms that PknG plays an important regulatory role in mycobacterial metabolism, through phosphorylation of ATP binding proteins and enzymes in the TCA cycle. This work also reinforces PknG's regulation of protein translation and folding machinery.
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Affiliation(s)
- Kehilwe C Nakedi
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Bridget Calder
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Mousumi Banerjee
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Alexander Giddey
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Andrew J M Nel
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Shaun Garnett
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Jonathan M Blackburn
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa.,§Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nelson C Soares
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa;
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Onile OS, Calder B, Soares NC, Anumudu CI, Blackburn JM. Quantitative label-free proteomic analysis of human urine to identify novel candidate protein biomarkers for schistosomiasis. PLoS Negl Trop Dis 2017; 11:e0006045. [PMID: 29117212 PMCID: PMC5695849 DOI: 10.1371/journal.pntd.0006045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 11/20/2017] [Accepted: 10/17/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Schistosomiasis is a chronic neglected tropical disease that is characterized by continued inflammatory challenges to the exposed population and it has been established as a possible risk factor in the aetiology of bladder cancer. Improved diagnosis of schistosomiasis and its associated pathology is possible through mass spectrometry to identify biomarkers among the infected population, which will influence early detection of the disease and its subtle morbidity. METHODOLOGY A high-throughput proteomic approach was used to analyse human urine samples for 49 volunteers from Eggua, a schistosomiasis endemic community in South-West, Nigeria. The individuals were previously screened for Schistosoma haematobium and structural bladder pathologies via microscopy and ultrasonography respectively. Samples were categorised into schistosomiasis, schistosomiasis with bladder pathology, bladder pathology, and a normal healthy control group. These samples were analysed to identify potential protein biomarkers. RESULTS A total of 1306 proteins and 9701 unique peptides were observed in this study (FDR = 0.01). Fifty-four human proteins were found to be potential biomarkers for schistosomiasis and bladder pathologies due to schistosomiasis by label-free quantitative comparison between groups. Thirty-six (36) parasite-derived potential biomarkers were also identified, which include some existing putative schistosomiasis biomarkers that have been previously reported. Some of these proteins include Elongation factor 1 alpha, phosphopyruvate hydratase, histone H4 and heat shock proteins (HSP 60, HSP 70). CONCLUSION These findings provide an in-depth analysis of potential schistosoma and human host protein biomarkers for diagnosis of chronic schistosomiasis caused by Schistosoma haematobium and its pathogenesis.
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Affiliation(s)
- Olugbenga Samson Onile
- Biotechnology Programme, Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
| | - Bridget Calder
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Nelson C. Soares
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Chiaka I. Anumudu
- Cellular Parasitology Programme, Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | - Jonathan M. Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Kalule JB, Fortuin S, Calder B, Robberts L, Keddy KH, Nel AJM, Garnett S, Nicol M, Warner DF, Soares NC, Blackburn JM. Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagar™STEC media. J Proteomics 2017; 180:25-35. [PMID: 28887208 DOI: 10.1016/j.jprot.2017.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 08/21/2017] [Accepted: 09/02/2017] [Indexed: 02/06/2023]
Abstract
Shiga-toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) are key diarrhoea-causing foodborne pathogens. We used proteomics to characterize the virulence and antimicrobial resistance protein profiles of three clinical pathogenic E. coli isolates (two EPEC [one resistant to ciprofloxacin] and one STEC) cultured on CHROMagar™STEC solid media after minimal laboratory passage. We identified 4767 unique peptides from 1630 protein group across all three clinical E. coli strains. Label-free proteomic analysis allowed the identification of virulence and drug resistance proteins that were unique to each of the clinical isolates compared in this study. The B subunit of Shiga toxin, ToxB, was uniquely detected in the STEC strain while several other virulence factors including SheA, OmpF, OmpC and OmpX were significantly more abundant in the STEC strain. The ciprofloxacin resistant EPEC isolate possessed reduced levels of key virulence proteins compared to the ciprofloxacin susceptible EPEC and STEC strains. Parallel reaction monitoring assays validated the presence of biologically relevant proteins across biologically-replicated cultures. Propagation of clinical isolates on a relevant solid medium followed by mass spectrometry analysis represents a convenient means to quantify virulence factors and drug resistance determinants that might otherwise be lost through extensive in vitro passage in enteropathogenic bacteria. SIGNIFICANCE Through the use of quantitative proteomics, we have characterized the virulence and antimicrobial resistance attributes of three clinically isolated, pathogenic E. coli strains cultured on solid media. Our results provide new, quantitative data on the expressed proteomes of these tellurite-resistant, diarrhoeagenic E. coli strains and reveal a subset of antimicrobial resistance and virulence proteins that are differentially abundant between these clinical strains. Our quantitative proteomics-based approach should thus have applicability in microbiological diagnostic labs for the identification of pathogenic/drug resistant E. coli in the future.
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Affiliation(s)
- John Bosco Kalule
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Suereta Fortuin
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Bridget Calder
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Lourens Robberts
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Karen H Keddy
- Bacteriology Division, Centre for Enteric Diseases, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew J M Nel
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Shaun Garnett
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark Nicol
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa
| | - Digby F Warner
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa; MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Nelson C Soares
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa.
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Gurwitz KT, Burman RJ, Murugan BD, Garnett S, Ganief T, Soares NC, Raimondo JV, Blackburn JM. Time-Dependent, HIV-Tat-Induced Perturbation of Human Neurons In Vitro: Towards a Model for the Molecular Pathology of HIV-Associated Neurocognitive Disorders. Front Mol Neurosci 2017; 10:163. [PMID: 28611588 PMCID: PMC5447036 DOI: 10.3389/fnmol.2017.00163] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 05/11/2017] [Indexed: 12/29/2022] Open
Abstract
A significant proportion of human immunodeficiency virus type 1 (HIV)-positive individuals are affected by the cognitive, motor and behavioral dysfunction that characterizes HIV-associated neurocognitive disorders (HAND). While the molecular etiology of HAND remains largely uncharacterized, HIV transactivator of transcription (HIV-Tat) is thought to be an important etiological cause. Here we have used mass spectrometry (MS)-based discovery proteomics to identify the quantitative, cell-wide changes that occur when non-transformed, differentiated human neurons are treated with HIV-Tat over time. We identified over 4000 protein groups (false discovery rate <0.01) in this system with 131, 118 and 45 protein groups differentially expressed at 6, 24 and 48 h post treatment, respectively. Alterations in the expression of proteins involved in gene expression and cytoskeletal maintenance were particularly evident. In tandem with proteomic evidence of cytoskeletal dysregulation we observed HIV-Tat induced functional alterations, including a reduction of neuronal intrinsic excitability as assessed by patch-clamp electrophysiology. Our findings may be relevant for understanding in vivo molecular mechanisms in HAND.
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Affiliation(s)
- Kim T Gurwitz
- Division of Chemical and Biological Systems, Department of Integrative Biomedical Sciences, University of Cape TownCape Town, South Africa
| | - Richard J Burman
- Division of Physiological Sciences, Department of Human Biology, University of Cape TownCape Town, South Africa.,Neurosciences Institute, University of Cape TownCape Town, South Africa
| | - Brandon D Murugan
- Division of Chemical and Biological Systems, Department of Integrative Biomedical Sciences, University of Cape TownCape Town, South Africa
| | - Shaun Garnett
- Division of Chemical and Biological Systems, Department of Integrative Biomedical Sciences, University of Cape TownCape Town, South Africa
| | - Tariq Ganief
- Division of Chemical and Biological Systems, Department of Integrative Biomedical Sciences, University of Cape TownCape Town, South Africa
| | - Nelson C Soares
- Division of Chemical and Biological Systems, Department of Integrative Biomedical Sciences, University of Cape TownCape Town, South Africa
| | - Joseph V Raimondo
- Division of Physiological Sciences, Department of Human Biology, University of Cape TownCape Town, South Africa.,Neurosciences Institute, University of Cape TownCape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical and Biological Systems, Department of Integrative Biomedical Sciences, University of Cape TownCape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town, South Africa
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49
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Affiliation(s)
- Nelson C Soares
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - German Bou
- Servicio de Microbiologia-Instituto de Investigación Biomédica, Complejo Hospitalario Universitario A Coruña A Coruña, Spain
| | - Jonathan M Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Cape Town, South Africa
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50
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Soares NC, Blackburn JM. Mass Spectrometry Targeted Assays as a Tool to Improve Our Understanding of Post-translational Modifications in Pathogenic Bacteria. Front Microbiol 2016; 7:1216. [PMID: 27540373 PMCID: PMC4972818 DOI: 10.3389/fmicb.2016.01216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/21/2016] [Indexed: 01/03/2023] Open
Affiliation(s)
- Nelson C. Soares
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape TownCape Town, South Africa
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