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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] [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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Rosa-Fernandes L, Oba-Shinjo SM, Macedo-da-Silva J, Marie SKN, Palmisano G. Aberrant Protein Glycosylation in Brain Cancers, with Emphasis on Glioblastoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:39-70. [DOI: 10.1007/978-3-031-05460-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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Xu W, Liu Z, Ren H, Peng X, Wu A, Ma D, Liu G, Liu L. Twenty Metabolic Genes Based Signature Predicts Survival of Glioma Patients. J Cancer 2020; 11:441-449. [PMID: 31897239 PMCID: PMC6930419 DOI: 10.7150/jca.30923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 08/05/2019] [Indexed: 12/16/2022] Open
Abstract
Background: Glioma, caused by carcinogenesis of brain and spinal glial cells, is the most common primary malignant brain tumor. To find the important indicator for glioma prognosis is still a challenge and the metabolic alteration of glioma has been frequently reported recently. Methods: In our current work, a risk score model based on the expression of twenty metabolic genes was developed using the metabolic gene expressions in The Cancer Genome Atlas (TCGA) dataset, the methods of which included the cox multivariate regression and the random forest variable hunting, a kind of machine learning algorithm, and the risk score generated from this model is used to make predictions in the survival of glioma patients in the training dataset. Subsequently, the result was further verified in other three verification sets (GSE4271, GSE4412 and GSE16011). Risk score related pathways collected in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were identified using Gene Set Enrichment Analysis (GSEA). Results: The risk score generated from our model makes good predictions in the survival of glioma patients in the training dataset and other three verification sets. By assessing the relationships between clinical indicators and the risk score, we found that the risk score was an independent and significant indicator for the prognosis of glioma patients. Simultaneously, we conducted a survival analysis of the patients who received chemotherapy and who did not, finding that the risk score was equally valid in both cases. And signaling pathways related to the genesis and development of multiple cancers were also identified. Conclusions: In summary, our risk score model is predictive for 967 glioma patients' survival from four independent datasets, and the risk score is a meaningful and independent parameter of the clinicopathological information.
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Affiliation(s)
- Wenfang Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, P.R.China
| | - Zhenhao Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, P.R.China
| | - He Ren
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, P.R.China
| | - Xueqing Peng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, P.R.China
| | - Aoshen Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, P.R.China
| | - Duan Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, P.R.China
| | - Gang Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, P.R.China
| | - Lei Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, P.R.China
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Patel R, Khalifa AO, Isali I, Shukla S. Prostate cancer susceptibility and growth linked to Y chromosome genes. Front Biosci (Elite Ed) 2018; 10:423-436. [PMID: 29293466 PMCID: PMC6152832 DOI: 10.2741/e830] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The role of Y chromosome in prostate cancer progression and incidence is not well known. Among the 46 chromosomes, Y chromosome determines the male gender. The Y chromosome is smaller than the X chromosome and contains only 458 genes compared to over 2000 genes found in the X chromosome. The Y chromosome is prone to high mutation rates, created exclusively in sperm cells due to the highly oxidative environment of the testis. Y chromosome harbors epigenetic information, which affects the expression of genes associated with the incidence and progression of prostate cancer. In this review, we focus on Y chromosome related genetic abnormalities, likely to be involved in the development and progression of prostate cancer.
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Affiliation(s)
- Riddhi Patel
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA
| | - Ahmad O Khalifa
- Urology Dept. Case Western Reserve University, Cleveland, Ohio and Menofia University, Shebin Al kom, Egpt
| | - Ilaha Isali
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA
| | - Sanjeev Shukla
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA,
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Bellezza I, Scarpelli P, Pizzo SV, Grottelli S, Costanzi E, Minelli A. ROS-independent Nrf2 activation in prostate cancer. Oncotarget 2017; 8:67506-67518. [PMID: 28978049 PMCID: PMC5620189 DOI: 10.18632/oncotarget.18724] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/23/2017] [Indexed: 12/16/2022] Open
Abstract
In prostate cancer, oxidative stress and the subsequent Nrf2 activation promote the survival of cancer cells and acquired chemoresistance. Nrf2 links prostate cancer to endoplasmic reticulum stress, an event that triggers the unfolded protein response, aiming to restore cellular homeostasis as well as an adaptive survival mechanism. Glucose-regulated protein of 78 kD /immunoglobulin heavy chain binding protein (GRP78/BiP) is a key molecular chaperone in the endoplasmic reticulum that, when expressed at the cell surface, acts as a receptor for several signaling pathways enhancing antiapoptotic and proliferative signals. We showed GRP78/BiP translocation to PC3 cell surface in the presence of tunicamycin, an ER stress inductor, and demonstrated the existence of a GRP78/BiP-dependent non-canonical Nrf2 activation, responsible for increased resistance to ER-stress induced apoptosis. We found that, even in the absence of ROS production, tunicamycin causes Nrf2 activation, and activates Akt signaling, events bulnted by anti-GRP78/BiP antibody treatment. The presence of GRP78/BiP at the cell surface might be exploited for the immunotherapeutic strategy of prostate cancer since its blockage by anti-GRP78/BiP antibodies might promote cancer death by suppressing some of the several molecular protective mechanisms found in aggressive cancer cells.
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Affiliation(s)
- Ilaria Bellezza
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Paolo Scarpelli
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | | | - Silvia Grottelli
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Egidia Costanzi
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Alba Minelli
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
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