Percorrer por autor "Soares, Nelson C."
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- Estrogen-mediated inhibition of purine metabolism and cell cycle arrest as a novel therapeutic approach in colorectal cancerPublication . Zamer, Batoul Abi; Shafarin, Jasmin; Sharaf, BasmaM.; Hroub, HamzaM. Al; Soares, Nelson C.; Semreen, Mohammad H.; Hamad, Mawieh; Muhammad, Jibran SualehPurine metabolism is upregulated in various cancers including colorectal cancer (CRC). While previous work has elucidated the role of estrogen (E2) in metabolic reprogramming and ATP production, the effect of E2 on purine metabolism remains largely unknown. Herein, the impact of E2 signalling on purine metabolism in CRC cells was investigated using metabolome and transcriptome profiling of cell extracts derived from E2-treated HCT-116 cells with intact or silenced estrogen receptor alpha (ERα). Purine metabolic pathway enrichment analysis showed that 27 genes in the de novo purine synthesis pathway were downregulated in E2-treated CRC cells. Downstream consequences of E2 treatment including the induction of DNA damage, cell cycle arrest, and apoptosis were all shown to be ERα-dependent. These findings demonstrate, for the first time, that E2 exerts a significant anti-growth and survival effect in CRC cells by targeting the purine synthesis pathway in a ERα-dependent manner, meriting further investigation of the therapeutic utility of E2 signalling in CRC.
- Impact of PPP1R1A Knockdown on the Proteomic Landscape of INS-1 Cells: A Focus on Significant Modulated PathwaysPublication . Taneera, Jalal; Giddey, Alexander D.; Soares, Nelson C.; Khalique, Anila; Mohammed, Abdul Khader; Mahgoub, Mohamed Omer; Mahgoub, EglalPPP1R1A (protein phosphatase 1 regulatory inhibitor subunit 1A) is a cAMP/PKA-responsive inhibitor of protein phosphatase 1 (PP1) with a pivotal role in pancreatic β-cell physiology. To investigate its functional impact, Ppp1r1a was silenced in INS-1 (832/13) rat β-cells, and proteomic alterations were profiled using label-free DIA mass spectrometry (Orbitrap Exploris 480) with a rat spectral library. Quantitative analysis (n = 4/group) identified ∼2846 proteins with >2-fold change, revealing extensive proteome reprogramming. Key biological processes affected included vesicle trafficking and exocytosis, insulin biosynthesis and processing, organelle organization, mRNA processing, and autophagy. Pathway enrichment highlighted disruptions in insulin secretion, insulin resistance, and mTOR signaling. Crucial β-cell proteins, including INS2, Cacna1a, CPEB2, PCSK2, SNAP25, SYT5, and VAMP7, were significantly downregulated. Validation confirmed reduced phosphorylated AKT levels and p-AKT/T-AKT ratio, consistent with impaired mTOR signaling. Collectively, these findings demonstrate that PPP1R1A is essential for maintaining β-cell function and insulin secretion, and its depletion triggers broad proteomic and signaling alterations. Thus, PPP1R1A emerges as a regulatory node with potential therapeutic relevance in modulating β-cell activity and insulin dynamics in diabetes.
- Medwakh smoking induces alterations in salivary proteins and cytokine expression: a clinical exploratory proteomics investigationPublication . Aghila Rani, K.G.; Soares, Nelson C.; Rahman, Betul; Giddey, Alexander D.; Al-Hroub, Hamza M.; Semreen, Mohammad H.; Al Kawas, SausanBackground: Medwakh smoking has radically expanded among youth in the Middle East and around the world. The rising popularity of medwakh/dokha usage is linked to the onset of several chronic illnesses including cardiovascular diseases and cancers. Medwakh smoking is reported to increase the risk of inflammation in the lower respiratory tract owing to oxidative burden. To date, there are no reported studies investigating the impact of medwakh smoking on salivary protein profile. The current study aims to elucidate alterations in the salivary proteome profile of medwakh smokers. Methods: Saliva samples collected from 33 medwakh smokers and 30 non-smokers were subjected to proteomic analysis using UHPLC-ESI-QTOF-MS. Saliva samples were further subjected to validatory experiments involving analysis of inflammatory cytokine profile using LEGENDplex™ Human Essential Immune Response Panel. Results: Statistical analysis revealed alterations in the abundance of 74 key proteins including immune mediators and inflammatory markers in medwakh smokers (Accession: PXD045901). Proteins involved in building oxidative stress, alterations in cell anchorage, and cell metabolic processes were enhanced in medwakh smokers. Salivary immune response evaluation further validated the proteome findings, revealing significantly higher levels of IL-1β, IL-12p70, IL-23, IFN-γ (Th1 cytokines), IL-6 (Th2 cytokine), and MCP-1 (chemokine) in medwakh smokers. In addition, a substantial increase in abundance of involucrin suggesting a plausible stratified squamous cell differentiation and increased cell lysis in the oral cavity of medwakh smokers akin to chronic obstructive pulmonary diseases (COPD). The protein-metabolite joint pathway analysis further showed significantly enriched differentially expressed proteins and metabolites of glycolysis/gluconeogenesis, pentose phosphate, fructose and mannose, nicotinate and nicotinamide, and glutathione metabolism pathways among medwakh smokers. Conclusions: The findings of the study provide valuable insights on potential perturbations in various key immune molecules, cytokines, and signaling pathways among medwakh smokers. Medwakh smokers displayed elevated inflammation, increased oxidative stress and defective antioxidant responses, dysregulated energy metabolism, and alterations in proteins related to cell adhesion, migration, differentiation, and proliferation. The findings of study underscore the urgent need for comprehensive public health interventions among youth by raising awareness, implementing effective smoking cessation programs, and promoting healthy lifestyle to safeguard the well-being of individuals and communities worldwide.
- Metabolomics insights into doxorubicin and 5-fluorouracil combination therapy in triple-negative breast cancer: a xenograft mouse model studyPublication . Hassanein, Mai M.; Hagyousif, Yousra A.; Zenati, Ruba A.; Al-Hroub, Hamza M.; Khan, Farman Matloob; Abuhelwa, Ahmad Y.; Alzoubi, Karem H.; Soares, Nelson C.; El-Huneidi, Waseem; Abu-Gharbieh, Eman; Omar, Hany; Zaher, Dana M.; Bustanji, Yasser; Semreen, Mohammad H.Background: Breast cancer is one of the most prevalent malignancies and a leading cause of death among women worldwide. Among its subtypes, triple-negative breast cancer (TNBC) poses significant clinical challenges due to its aggressive behavior and limited treatment options. This study aimed to investigate the effects of doxorubicin (DOX) and 5-fluorouracil (5-FU) as monotherapies and in combination using an established MDA-MB-231 xenograft model in female BALB/C nude mice employing advanced metabolomics analysis to identify molecular alterations induced by these treatments. Methods: We conducted comprehensive plasma and tumor tissue sample profiling using ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). Results: Each treatment group exhibited unique metabolic profiles in plasma and tumor analysis. Univariate and enrichment analyses identified alterations in metabolic pathways. The combination treatment of DOX + 5-FU induced the most extensive metabolic alterations disrupting key pathways including purine, pyrimidine, beta-alanine, and sphingolipid metabolism. It significantly reduced critical metabolites such as guanine, xanthine, inosine, L-fucose, and sphinganine, demonstrating enhanced cytotoxic effects compared to individual treatments. The DOX treatment uniquely increased ornithine levels, while 5-FU altered sphingolipid metabolism, promoting apoptosis. Significance: This in vivo study highlights TNBC's metabolic alterations to chemotherapeutics, identifying potential biomarkers like L-fucose and beta-alanine, and provides insights for improving treatment strategies.
- Molecular signatures of xenograft colorectal cancer in mice treated with topotecan: A mass spectrometry-based studyPublication . Hagyousif, Yousra A.; Zenati, Ruba A.; Soares, Nelson C.; Al-Hroub, Hamza M.; Khan, Farman Matloob; Qaisar, Rizwan; Hamoudi, Rifat; El-Awady, Raafat; Abuhelwa, Ahmad Y.; Ramadan, Wafaa; El-Huneidi, Waseem; Abu-Gharbieh, Eman; Alzoubi, Karem H.; Bustanji, Yasser; Semreen, Mohammad H.Background: Colorectal cancer (CRC) is one of the most common cancers worldwide, yet it continues to have a low survival rate, largely due to the lack of effective treatments. Metabolomics offers new insight into disease diagnosis and biomarkers discovery. The aim of the study is to identify serum biomarkers in a CRC xenograft mouse model treated with topotecan using advanced metabolomics techniques to enhance our understanding and management of the disease. Methods: The therapeutic potentials of the anticancer drug topotecan on metabolomic alterations in CRC were explored using the UHPLC-ESI-QTOF-MS platform. A comprehensive metabolomic analysis was conducted to compare four different animal groups: HCT-116 CRC xenograft mice treated with topotecan (treated group), vehicle-control HCT-116 xenograft mice (untreated CRC xenograft mice), positive controls (healthy mice injected with topotecan), and negative controls (healthy mice). Results: The study identified 53 altered metabolites across all four groups (p-value < 0.05). Independent T-test revealed that 15 metabolites were statistically significant among vehicle controls and negative controls. Additionally, 20 metabolites showed significant differences between the potential responders to topotecan and the vehicle controls. Moreover, only one metabolite was statistically significant between the positive and negative controls. Conclusion: The findings provide a detailed characterization of metabolic alterations associated with topotecan treatment in CRC. These insights contribute to a better understanding of the drug's mechanism of action, which may help predict CRC patients' response to topotecan and guide the development of personalized therapeutic strategies.
- A Phosphoproteomic Analysis of Mycobacterial PknG-Mediated Host Immune EvasionPublication . Baros-Steyl, Seanantha S.; Nakedi, Kehilwe C.; Ganief, Tariq A.; Soares, Nelson C.; Blackburn, Jonathan M.Pathogenic mycobacteria, such as Mycobacterium tuberculosis, modulate the host immune system to evade clearance and promote long-term persistence, leading to disease progression or latent infection. Understanding how these mycobacteria evade elimination is key to uncovering the molecular mechanisms of infection. Protein kinase G (PknG) in pathogenic mycobacteria plays a critical role in avoiding macrophage clearance by inhibiting phagosome-lysosome fusion; however, the exact mechanism is not completely understood. To investigate the role of PknG during early events of macrophage infection, RAW 264.7 macrophages were infected with Mycobacterium bovis BCG wild-type and PknG knockout mutant strains. Phosphoproteomic analysis, including TiO2-based phosphopeptide enrichment and LC-MS/MS, identified 3003 phosphosites across 1638 host proteins. Differential expression analysis revealed 143 phosphosites significantly altered between wild-type and mutant infections, with 95 exhibiting increased phosphorylation in the presence of PknG. Additionally, 34 phosphosites were exclusively phosphorylated in the presence of PknG. Functional analysis demonstrated that PknG kinase activity reprograms normal macrophage function by interfering with host cytoskeletal organization, phagosome maturation, and programmed cell death, establishing a new role for PknG in directing the fate of mycobacteria within macrophages. Differentially phosphorylated proteins in this study serve as a foundation for further validation and the assignment of PknG host substrate assignment.
- Repurposing proteomic nanoLC-MS platforms for untargeted metabolomics: evaluating DIA and polarity switching performance in human plasmaPublication . Pinto, Frederico G.; Giddey, Alexander D.; Mohamed, Nesrin; Almarri, Rauda S. B.; Murtaza, Munazza; Nassir, Nasna; Alkhnbashi, Omer S.; Uddin, Mohammed J.; Soares, Nelson C.Background: Many of the advanced MS methods applied in proteomics such as nanoflow LC-MS with data-independent acquisition have yet to be verified and/or optimized on metabolomics applications. Research design and methods: This study evaluates the feasibility of repurposing a proteomics-optimized nanoLC-MS platform for untargeted metabolomics. Using NIST SRM 1950 reference human plasma, we compared the performance of polarity switching and separate polarity modes under DIA conditions, focusing on metabolite coverage, annotation, and response linearity. Results: We observed, in the separate polarity and switching polarity runs 669 and 353 features in (+) mode and 558 and 446 features in (-) mode, respectively. A total of 233 metabolites were annotated using the (±) separate polarities and 179 using the (±) switching polarity based on MassBank of North America (MoNA) public MS library and filtered with the Human Metabolome Database (HMDB). Both switching and separate polarity methods performed well regarding response linearities which were investigated by spiking some amino acid compounds into plasma matrix. Conclusions: The polarity switching DIA approach for metabolomics reduced sample consumption and analysis time, but led to fewer detected features and annotations compared to separate polarity runs. These findings support the use of unified nanoLC-MS platforms for integrated multi-omics analysis.
- Untargeted Multiomics of LNCaP Cell Line Treated with a Novel DNA Minor Groove Binder and/or Doxorubicin Using Mass SpectrometryPublication . Zenati, Ruba A.; Soares, Nelson C.; Alniss, Hasan Y.; Al-Hroub, Hamza M.; El-Awady, Raafat; Abuhelwa, Ahmad Y.; Ramadan, Wafaa S.; Aleidi, Shereen M.; El-Huneidi, Waseem; Abu-Gharbieh, Eman; Alzoubi, Karem H.; Bustanji, Yasser; Semreen, Mohammad H.Prostate cancer (PCa) remains a major global health concern, ranking among the most prevalent cancer in men worldwide. Despite the availability of various therapeutic options, the clinical efficacy of current anti-PCa agents is often compromised by drug resistance and adverse effects. DNA minor groove binders offer a potential therapeutic alternative, owing to their selective mechanism of action and favorable safety profiles. In the present study, we utilized a multiomics strategy to investigate the molecular impact of novel compound MGB4. LNCaP cells were treated with doxorubicin, MGB4, or a combination of both, followed by LC-MS/MS-based untargeted proteomics and metabolomics analyses. One-way ANOVA (p-value <0.05) revealed 55 significantly dysregulated proteins and 57 altered metabolites across treatments. Our findings indicate that both MGB4 and doxorubicin impacted key cellular pathways, including inhibition of translation and alterations in sphingolipid and amino acid metabolism, while doxorubicin and the combination therapy also reduced spermine and spermidine metabolism. Notably, the combined treatment exhibited synergistic effects, significantly impacting purine metabolism and reducing metabolite levels more than individual therapies. This study provides key molecular insights into MGB4 and doxorubicin's mechanisms, supporting MGB4 as a potential prostate cancer drug candidate.