Integrated analysis of quantitative proteome and transcriptional profiles reveals abnormal gene expression and signal pathway in bladder cancer

Liao, Songbai; Ou, Minglin; Lai, Liusheng; Lin, Hua; Zou, Yaoshuang; Yu, Yonggang; Li, Xuede; Dai, Yong; Sui, Weiguo

doi:10.1007/s13258-019-00868-w

Cited by 5 publications

(2 citation statements)

References 30 publications

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“…GSEA showed that for BLCA, the CAMs signaling pathway, regulation of actin cytoskeleton signaling, ECM receptor interaction signaling, and focal adhesion pathway were mainly enriched in the high-risk group, which is consistent with the results of previous studies. [ 32 ] Tumor invasion is often associated with the inhibition of cell-cell junctions and accompanied by downregulation of E-cadherin expression. ECM receptor interactions were identified as 1 of the 5 most abundant signaling pathways in BLCA.…”

Section: Discussionmentioning

confidence: 99%

Identification of cuproptosis-related long non-coding RNA and construction of a novel prognostic signature for bladder cancer: An observational study

Ye,

Liu,

et al. 2024

Medicine

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Bladder Urothelial Carcinoma (BLCA), a prevalent and lethal cancer, lacks understanding regarding the roles and prognostic value of cuproptosis-related lncRNAs (CRLs), a novel form of cell death induced by copper. We collected RNA-seq data, clinical information, and prognostic data for 414 BLCA samples and 19 matched controls from The Cancer Genome Atlas. Using multivariate and univariate Cox regression analyses, we identified CRLs to create a prognostic signature. Patients were then divided into low- and high-risk groups based on their risk scores. We analyzed overall survival using the Kaplan–Meier method, evaluated stromal and immune scores, and explored functional differences between these risk groups with gene set enrichment analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were also conducted to understand the links between CRLs and BLCA development. We developed a prognostic signature using 4 independent CRLs: RC3H1-IT1, SPAG5-AS1, FAM13A-AS1, and GNG12-AS1. This signature independently predicted the prognosis of BLCA patients. High-risk patients had worse outcomes, with gene set enrichment analysis revealing enrichment in tumor- and immune-related pathways in the high-risk group. Notably, high-risk patients exhibited enhanced responses to immunotherapy and conventional chemotherapy drugs like sunitinib, paclitaxel, and gemcitabine. The independent prognostic signature variables RC3H1-IT1, SPAG5-AS1, FAM13A-AS1, and GNG12-AS1 predicted the prognoses of BLCA patients and provided a basis for the study of the mechanism of CRLs in BLCA development and progression, and the guidance of clinical treatments for patients with BLCA.

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Section: Discussionmentioning

confidence: 99%

Identification of cuproptosis-related long non-coding RNA and construction of a novel prognostic signature for bladder cancer: An observational study

Ye,

Liu,

et al. 2024

Medicine

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“…Various bioinformatics analyses, such as GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, have been performed on differentially expressed genes and proteins to characterize their corresponding functions. It is generally accepted that this joint analysis of gene and protein expression data can provide a complete picture of disease status and may be a valuable strategic approach for biomarker screening and prediction in disease diagnosis [5] .…”

Section: Introductionmentioning

confidence: 99%

Integrating Bioinformatics To Identify Potential Cytokines ALPL /TNAP In Children With Spastic Cerebral Palsy

Wang

Gao

Zhong

et al. 2021

Preprint

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Background: Several published studies have shown the significance of neuroinflammation in the pathophysiological development of cerebral palsy (CP). However, the underlying molecular mechanisms by which neuroinflammation is associated with brain injury in CP remain poorly understood. Spastic CP is the most common form of CP, comprising 80% of all cases. Therefore, identifying patterns of inflammatory and related biomarkers would serve to understand the etiology of spastic CP.Methods: Related clinical parameters were assessed in 18 children with spastic CP and 20 age-matched healthy individuals. Blood samples of children with spastic CP and controls were analyzed with integrated transcriptomics and proteomics profiling to detect common differentially expressed mRNAs and proteins. Hypoxic ischemic encephalopathy was induced in postnatal day 7 rat pups. Behavioral testing was performed postinjury, and then, the differentially expressed markers and inflammatory cytokines were verified in the peripheral blood and cerebral cortex of the CP model rats by ELISA and Western blot. Independent sample t-tests, one-way analysis of variance and the Pearson correlation were used for statistical analysis.Results: Through proteomic and transcriptome analysis, we identified common differentially expressed genes. Among them, ALPL, encoding tissue nonspecific alkaline phosphatase (TNAP), was downregulated in spastic CP. In addition, compared with those of the corresponding controls, significantly lower mRNA and protein levels of TNAP were found in children with CP and the CP model rats. In contrast, compared with the control rats, the model rats demonstrated a significant increase in osteopontin and proinflammatory biomarkers, such as interleukin (IL)-6, IL-17, and C-reactive protein (CRP), in both the plasma and cerebral cortex, while serum 25 hydroxyvitamin D and anti-inflammatory cytokines such as IL-10 were significantly decreased. Additionally, the level of serum TNAP was correlated with the content of serum CRP and IL-10 in model rats.Conclusion: These results suggest that TNAP, the gene expression product of ALPL, is closely related to the pathogenesis and development of spastic CP, particularly in the upregulation of proinflammatory cytokines and the downregulation of anti-inflammatory cytokines, which contribute to the occurrence of inflammation in the progression of spastic CP.

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Integrated flow cytometric and proteomics analyses reveal the regulatory network underlying sugarcane protoplast responses to fusion

Wang,

Li,

Zhu

et al. 2023

Plant Physiology and Biochemistry

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Integrated analysis of quantitative proteome and transcriptional profiles reveals abnormal gene expression and signal pathway in bladder cancer

Cited by 5 publications

References 30 publications

Identification of cuproptosis-related long non-coding RNA and construction of a novel prognostic signature for bladder cancer: An observational study

Identification of cuproptosis-related long non-coding RNA and construction of a novel prognostic signature for bladder cancer: An observational study

Integrating Bioinformatics To Identify Potential Cytokines ALPL /TNAP In Children With Spastic Cerebral Palsy

Integrated flow cytometric and proteomics analyses reveal the regulatory network underlying sugarcane protoplast responses to fusion

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