RESUMO

BACKGROUND AND AIMS: Optimizing metabolomics data processing parameters is a challenging and fundamental task to obtain reliable results. Automated tools have been developed to assist this optimization for LC-MS data. GC-MS data require substantial modifications in processing parameters, as the chromatographic profiles are more robust, with more symmetrical and Gaussian peaks. This work compared an automated XCMS parameter optimization using the Isotopologue Parameter Optimization (IPO) software with manual optimization of GC-MS metabolomics data. Additionally, the results were compared to online XCMS platform. METHODS: GC-MS data from control and test groups of intracellular metabolites from Trypanosoma cruzi trypomastigotes were used. Optimizations were performed on the quality control (QC) samples. RESULTS: The results in terms of the number of molecular features extracted, repeatability, missing values, and the search for significant metabolites showed the importance of optimizing the parameters for peak detection, alignment, and grouping, especially those related to peak width (fwhm, bw) and noise ratio (snthresh). CONCLUSION: This is the first time that a systematic optimization using IPO has been performed on GC-MS data. The results demonstrate that there is no universal approach for optimization but automated tools are valuable at this stage of the metabolomics workflow. The online XCMS proves to be an interesting processing tool, helping, above all, in the choice of parameters as a starting point for adjustments and optimizations. Although the tools are easy to use, there is still a need for technical knowledge about the analytical methods and instruments used.

Assuntos

Metabolômica , Software , Cromatografia Gasosa-Espectrometria de Massas , Metabolômica/métodos , Espectrometria de Massas/métodos , Cromatografia Líquida/métodos

RESUMO

BACKGROUND: Importin 7 (IPO7) belongs to the Importin ß family and is implicated in the progression of diverse human malignancies. This work is performed to probe the role of IPO7 in pancreatic cancer development and its potential downstream mechanisms. METHODS: IPO7 expression in PC and paracancerous tissues were measured using Immunohistochemistry (IHC) staining and qRT-PCR. Western blotting was utilized to detect the expression level of IPO7 in PC cells and immortalize the pancreatic ductal epithelial cell line. After constructing the IPO7 overexpression and knockdown models, the effect of IPO7 on the proliferation of PC cells was analyzed by the CCK-8 and EdU assay. The migration and invasion of PC cells were examined by wound healing assay and Transwell experiment. The apoptosis rate of PC cells was analyzed by flow cytometry and TUNEL assay. The Gene Set Enrichment Analysis (GSEA) was used to determine the enrichment pathways of IPO7. The effect of IPO7 on the ERBB2 expression was determined using Western blotting. A xenograft mouse model was applied to investigate the carcinogenic effect of IPO7 in vivo. RESULTS: IPO7 expression was remarkably elevated in the cancer tissues of PC patients. IPO7 overexpression remarkably enhanced PC cell proliferation, migration and invasion and suppressed apoptosis, while knockdown of IPO7 exerted the opposite effect. Mechanistically, IPO7 facilitated the malignant phenotype of PC cells by up-regulating ERBB2 expression. In addition, knockdown of IPO7 inhibited tumor growth and lung metastasis in vivo. CONCLUSION: IPO7 can act as an oncogenic factor and accelerate PC progression by modulating the ERBB pathway.

Assuntos

Carioferinas , Neoplasias Pancreáticas , Receptores Citoplasmáticos e Nucleares , Animais , Linhagem Celular Tumoral , Movimento Celular , Proliferação de Células , Regulação Neoplásica da Expressão Gênica , Humanos , Carioferinas/genética , Carioferinas/metabolismo , Camundongos , Pâncreas/patologia , Neoplasias Pancreáticas/patologia , Receptor ErbB-2 , Receptores Citoplasmáticos e Nucleares/genética , Receptores Citoplasmáticos e Nucleares/metabolismo , Neoplasias Pancreáticas

RESUMO

Abstract Background Importin 7 (IPO7) belongs to the Importin β family and is implicated in the progression of diverse human malignancies. This work is performed to probe the role of IPO7 in pancreatic cancer development and its potential downstream mechanisms. Methods IPO7 expression in PC and paracancerous tissues were measured using Immunohistochemistry (IHC) staining and qRT-PCR. Western blotting was utilized to detect the expression level of IPO7 in PC cells and immortalize the pancreatic ductal epithelial cell line. After constructing the IPO7 overexpression and knockdown models, the effect of IPO7 on the proliferation of PC cells was analyzed by the CCK-8 and EdU assay. The migration and invasion of PC cells were examined by wound healing assay and Transwell experiment. The apoptosis rate of PC cells was analyzed by flow cytometry and TUNEL assay. The Gene Set Enrichment Analysis (GSEA) was used to determine the enrichment pathways of IPO7. The effect of IPO7 on the ERBB2 expression was determined using Western blotting. A xenograft mouse model was applied to investigate the carcinogenic effect of IPO7 in vivo. Results IPO7 expression was remarkably elevated in the cancer tissues of PC patients. IPO7 overexpression remarkably enhanced PC cell proliferation, migration and invasion and suppressed apoptosis, while knockdown of IPO7 exerted the opposite effect. Mechanistically, IPO7 facilitated the malignant phenotype of PC cells by up-regulating ERBB2 expression. In addition, knockdown of IPO7 inhibited tumor growth and lung metastasis in vivo. Conclusion IPO7 can act as an oncogenic factor and accelerate PC progression by modulating the ERBB pathway.