Mass spectroscopy-based proteomics and metabolomics analysis of triple-positive breast cancer cells treated with tamoxifen and/or trastuzumab

Sharaf, Basma M; Giddey, Alexander D.; Al-Hroub, Hamza M.; Menon, Varsha; Okendo, Javan; El‐Awady, Raafat; Mousa, Muath; Almehdi, Ahmed M.; Semreen, Mohammad H.; Soares, Nelson C.

doi:10.1007/s00280-022-04478-4

Cited by 7 publications

(5 citation statements)

References 78 publications

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“…The CM were analyzed by Q-TOF MS as described previously [ 32 ]. Briefly, samples were separated using Elute HPG 1300 pumps and Elute Autosampler.…”

Section: Methodsmentioning

confidence: 99%

Mass Spectrometric Analysis of Bioactive Conditioned Media of Bacteria Isolated From Reptilian Gut

et al. 2023

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Aim: To determine whether selected gut bacteria of crocodile exhibit antibacterial properties. Materials & methods: Two bacteria isolated from Crocodylus porosus gut were used, namely: Pseudomonas aeruginosa and Aeromonas dhakensis. Conditioned media were tested against pathogenic bacteria and metabolites were analyzed using liquid chromatography-mass spectrometry. Results & conclusion: Antibacterial assays revealed that conditioned media showed potent effects against pathogenic Gram-positive and Gram-negative bacteria. LC–MS revealed identity of 210 metabolites. The abundant metabolites were, N-Acetyl-L-tyrosine, Acetaminophen, Trans-Ferulic acid, N, N-Dimethylformamide, Pyrocatechol, Cyclohexanone, Diphenhydramine, Melatonin, Gamma–terpinene, Cysteamine, 3-phenoxypropionic acid, Indole-3-carbinol, Benzaldehyde, Benzocaine, 2-Aminobenzoic acid, 3-Methylindole. These findings suggest that crocodile gut bacteria are potential source of novel bioactive molecules that can be utilized as pre/post/antibiotics for the benefit of human health.

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“…The CM were analyzed by Q-TOF MS as described previously [ 32 ]. Briefly, samples were separated using Elute HPG 1300 pumps and Elute Autosampler.…”

Section: Methodsmentioning

confidence: 99%

Mass Spectrometric Analysis of Bioactive Conditioned Media of Bacteria Isolated From Reptilian Gut

et al. 2023

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“…RNA splicing, redox homeostasis, mitochondrial membrane transport, ferroptosis, necroptosis transporters, neutrophil activation, and degranulation were principally detected as dysregulated pathways. 171 In another study, two cell lines treated with the same drug combination (alone and in combination) were probed through untargeted MS for identifying metabolomic profiles where 98 metabolites differed in the two cell lines representing basal and luminal cell types. Energy producing pathways like glycolysis, neoglucogenesis, cholesterol, fatty acid metabolism, and pyruvaldehyde degradation were principally affected by these drugs.…”

Section: Studies Characterizing Metabolomementioning

confidence: 99%

“…Apoptosis, cell growth, proliferation and signaling pathways were associated with the drug responses. RNA splicing, redox homeostasis, mitochondrial membrane transport, ferroptosis, necroptosis transporters, neutrophil activation, and degranulation were principally detected as dysregulated pathways …”

Section: Studies Characterizing Metabolomementioning

confidence: 99%

Recent Contributions of Mass Spectrometry-Based “Omics” in the Studies of Breast Cancer

Banerjee,

Hatimuria,

Sarkar

et al. 2023

Chem. Res. Toxicol.

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Breast cancer (BC) is one of the most heterogeneous groups of cancer. As every biotype of BC is unique and presents a particular "omic" signature, they are increasingly characterized nowadays with novel mass spectrometry (MS) strategies. BC therapeutic approaches are primarily based on the two features of human epidermal growth factor receptor 2 (HER2) and estrogen receptor (ER) positivity. Various strategic MS implementations are reported in studies of BC also involving data independent acquisitions (DIAs) of MS which report novel differential proteomic, lipidomic, proteogenomic, phosphoproteomic, and metabolomic characterizations associated with the disease and its therapeutics. Recently many "omic" studies have aimed to identify distinct subsidiary biotypes for diagnosis, prognosis, and targets of treatment. Along with these, drug-induced-resistance phenotypes are characterized by "omic" changes. These identifying aspects of the disease may influence treatment outcomes in the near future. Drug quantifications and characterizations are also done regularly and have implications in therapeutic monitoring and in drug efficacy assessments. We report these studies, mentioning their implications toward the understanding of BC. We briefly provide the MS instrumentation principles that are adopted in such studies as an overview with a brief outlook on DIA-MS strategies. In all of these, we have chosen a model cancer for its revelations through MS-based "omics".

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“…Biphasic separation techniques are used in the field of multi-omics, the motivation initially being to remove potentially interfering compounds from the downstream analytical method to improve analysis quality, and it was initially designed to extract either pure lipids or polar metabolites [ 27 ]. The most common example is the use of the chloroform-methanol extraction process, where the resulting two phases are subsequently combined to gather both liquid phases [ 15 , 28 ]. Unfortunately, the primary limitation that is associated with biphasic protocols, such as with the chloroform-based extraction, is that reproducibility is lowered because of the amorphous, solid components interphase which is located between the two immiscible layers.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Two Simultaneous Metabolomic and Proteomic Extraction Protocols Assessed by Ultra-High-Performance Liquid Chromatography Tandem Mass Spectrometry

Zenati

Giddey

Al-Hroub

et al. 2023

IJMS

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Untargeted multi-omics analysis of plasma is an emerging tool for the identification of novel biomarkers for evaluating disease prognosis, and for developing a better understanding of molecular mechanisms underlying human disease. The successful application of metabolomic and proteomic approaches relies on reproducibly quantifying a wide range of metabolites and proteins. Herein, we report the results of untargeted metabolomic and proteomic analyses from blood plasma samples following analyte extraction by two frequently-used solvent systems: chloroform/methanol and methanol-only. Whole blood samples were collected from participants (n = 6) at University Hospital Sharjah (UHS) hospital, then plasma was separated and extracted by two methods: (i) methanol precipitation and (ii) 4:3 methanol:chloroform extraction. The coverage and reproducibility of the two methods were assessed by ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). The study revealed that metabolite extraction by methanol-only showed greater reproducibility for both metabolomic and proteomic quantifications than did methanol/chloroform, while yielding similar peptide coverage. However, coverage of extracted metabolites was higher with the methanol/chloroform precipitation.

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Mass spectroscopy-based proteomics and metabolomics analysis of triple-positive breast cancer cells treated with tamoxifen and/or trastuzumab

Cited by 7 publications

References 78 publications

Mass Spectrometric Analysis of Bioactive Conditioned Media of Bacteria Isolated From Reptilian Gut

Mass Spectrometric Analysis of Bioactive Conditioned Media of Bacteria Isolated From Reptilian Gut

Recent Contributions of Mass Spectrometry-Based “Omics” in the Studies of Breast Cancer

Evaluation of Two Simultaneous Metabolomic and Proteomic Extraction Protocols Assessed by Ultra-High-Performance Liquid Chromatography Tandem Mass Spectrometry

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