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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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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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3
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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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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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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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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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7
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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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8
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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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9
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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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