High-throughput mass spectrometry and bioinformatics analysis of breast cancer proteomic data

Gomig, Talita Helen Bombardelli; Cavalli, Iglenir João; Souza, Ricardo Lehtonen Rodrigues de; Lucena, Aline Castro Rodrigues; Batista, Michel; Machado, Kelly Cavalcanti; Marchini, Fabrício Klerynton; Marchi, Fábio Albuquerque; Lima, Rubens Silveira de; Urban, Cı́cero de Andrade; Cavalli, Luciane R.; Ribeiro, Enilze Maria de Souza Fonseca

doi:10.1016/j.dib.2019.104125

Cited by 5 publications

(3 citation statements)

References 12 publications

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“…Moreover, cytofluorometric analyses suggested that breast cancer cells were driven toward late apoptosis and necrosis in a dose-and time-dependent manner. The involvement of the apoptotic pathway was further verified by IPA software [35], which showed that the most affected canonical biological pathway was apoptosis.…”

Section: Discussionmentioning

confidence: 99%

SUMOylation Protects FASN Against Proteasomal Degradation in Breast Cancer Cells Treated with Grape Leaf Extract

et al. 2020

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Existing therapeutic strategies for breast cancer are limited by tumor recurrence and drug-resistance. Antioxidant plant-derived compounds such as flavonoids reduce adverse outcomes and have been identified as a potential source of antineoplastic agent with less undesirable side effects. Here, we describe the novel regulation of fatty-acid synthase (FASN), the key enzyme in de novo fatty-acid synthesis, whereby Vitis vinifera L. cv Vermentino leaf hydroalcoholic extract lowers its protein stability that is regulated by small ubiquitin-like modifier (SUMO)ylation. The phenolic compounds characterization was performed by liquid chromatography–mass spectrometry (LC–MS), whereas mass spectrometry (LC–MS/MS), Western blotting/co-immunoprecipitation (Co-IP) and RT-PCR, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), clonogenicity assays, and FACS analysis were used to measure the expression of targets and tumorigenicity. Vermentino extract exhibits antitumorigenic effects, and we went on to determine that FASN and ubiquitin-conjugating enzyme 9 (UBC9), the sole E2 enzyme required for SUMOylation, were significantly reduced. Moreover, FASN was found SUMOylated in human breast cancer tissues and cell lines, and lack of SUMOylation caused by SUMO2 silencing reduced FASN protein stability. These results suggest that SUMOylation protects FASN against proteasomal degradation and may exert oncogenic activity through alteration of lipid metabolism, whereas Vermentino extract inhibits these effects which supports the additional validation of the therapeutic value of this compound in breast cancer.

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Section: Discussionmentioning

confidence: 99%

SUMOylation Protects FASN Against Proteasomal Degradation in Breast Cancer Cells Treated with Grape Leaf Extract

et al. 2020

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“…Tang et al studied 65 breast tumors and 53 adjacent noncancerous tissues with extensive fractionation, leading to 118 RAW files [20]. Gomig et al studied primary breast tumors, axillary metastatic lymph nodes and contralateral and adjacent breast tissues from seven patients, leading to 69 RAW files [21]. Lawrence et al studied 20 breast cancer cell lines and four primary breast tumors, leading to 450 RAW files [22].…”

Section: Evaluation Of the Protein Sequencing Depthmentioning

confidence: 99%

Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

Prakash¹,

Taylor

Varkey³

et al. 2021

Cancers

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The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.

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“…The number of proteins enriched by each pathway by the DIA method was much greater than those enriched by the DDA method (Figure 4D). Furthermore, to investigate the association between the significantly changed proteins and lung cancer disease, we used IPA software (IPA, QIAGEN, Redwood City, CA) to analyze the differential proteins from the DDA and DIA strategies, respectively [15]. Sixty-eight differ-ential proteins in lung cancer were identified using both methods.…”

Section: Summary Of Differential Proteins In Lung Cancer Clinical Tis...mentioning

confidence: 99%

A comparative study of data‐dependent acquisition and data‐independent acquisition in proteomics analysis of clinical lung cancer tissues constrained by blood contamination

Zhong

Zeng

et al. 2021

Proteomics Clinical Apps

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Proteomics analysis is often troubled by high-abundance proteins in samples such as plasma. However, many surgical tissue samples inevitably have got contaminated with blood before cryopreservation. Selection of an appropriate method to minimize the effect of high-abundance proteins is important for proteomics analysis of blood contaminated tissues. Here, we investigated and compared the abilities of dataindependent acquisition (DIA) and data-dependent acquisition (DDA) strategies for the proteomics analysis of blood contaminated clinical tissue samples. Twelve pairs of carcinoma and para-carcinoma tissue samples from lung cancer patients were used for proteomics assays separately by DIA and DDA, and the blood contamination level in samples was evaluated by contamination index (CI). Compared with the DDA strategy, DIA in whole exhibited much better analytical capabilities in proteomics analysis of these samples with more identified protein groups and a higher discovery of differential proteins. With CI value increasing, whether DIA or DDA showed decreasing analysis ability. However, for samples with high CI values, the DIA strategy still shows acceptable analytical capability and indicates better blood pollution resistance than the DDA strategy. Our results implied that for clinical tissue samples, particularly for those contaminated with blood, DIA strategy should be a preferred method in proteomics studies.

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High-throughput mass spectrometry and bioinformatics analysis of breast cancer proteomic data

Cited by 5 publications

References 12 publications

SUMOylation Protects FASN Against Proteasomal Degradation in Breast Cancer Cells Treated with Grape Leaf Extract

SUMOylation Protects FASN Against Proteasomal Degradation in Breast Cancer Cells Treated with Grape Leaf Extract

Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

A comparative study of data‐dependent acquisition and data‐independent acquisition in proteomics analysis of clinical lung cancer tissues constrained by blood contamination

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