Gene signature associated with neuro‐endocrine activity predicting prognosis of pancreatic carcinoma

Chen, Ke; He, Yiping; Liu, Yuan; Yang, Xunan

doi:10.1002/mgg3.729

Cited by 14 publications

(16 citation statements)

References 22 publications

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“…We normalized each gene from among the expression profiles using log2 transformation (20,31,32). We sequentially conducted univariate Cox, the least absolute shrinkage and selection operator (LASSO) regression using the R package "glmnet" (33,34), and multivariate Cox regression analyses to identify the GRGs associated with BC prognosis and to construct a GRG-based prediction model (34)(35)(36)(37).…”

Section: Construction and Evaluation Of The 11-grg Prediction Modelmentioning

confidence: 99%

Identification of a Novel Glycolysis-Related Gene Signature for Predicting Breast Cancer Survival

et al. 2021

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To identify a glycolysis-related gene signature for the evaluation of prognosis in patients with breast cancer, we analyzed the data of a training set from TCGA database and four validation cohorts from the GEO and ICGC databases which included 1,632 patients with breast cancer. We conducted GSEA, univariate Cox regression, LASSO, and multiple Cox regression analysis. Finally, an 11-gene signature related to glycolysis for predicting survival in patients with breast cancer was developed. And Kaplan–Meier analysis and ROC analyses suggested that the signature showed a good prognostic ability for BC in the TCGA, ICGC, and GEO datasets. The analyses of univariate Cox regression and multivariate Cox regression revealed that it’s an important prognostic factor independent of multiple clinical features. Moreover, a prognostic nomogram, combining the gene signature and clinical characteristics of patients, was constructed. These findings provide insights into the identification of breast cancer patients with a poor prognosis.

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Section: Construction and Evaluation Of The 11-grg Prediction Modelmentioning

confidence: 99%

Identification of a Novel Glycolysis-Related Gene Signature for Predicting Breast Cancer Survival

et al. 2021

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“…Further studies have shown that MRPS18-2 induces EMT through the TWIST2/E-cadherin signal and CXCR4 (PC3 cells express the chemokine receptor) mediates the migration of prostate cancer cells [ 67 ]. Lately, MRPS7 was detected as a key gene in the pathophysiological process of osteosarcoma and the MRPL3 content is positively correlated with the prognosis of osteosarcoma [ 6 ]. Through a bioinformatics analysis such as gene ontology, MRPS11 was found to be overexpressed in uveal melanoma and is a potential prognostic indicator for uveal melanoma [ 65 ].…”

Section: Mrps Associated With Cancersmentioning

confidence: 99%

Abnormal Expression of Mitochondrial Ribosomal Proteins and Their Encoding Genes with Cell Apoptosis and Diseases

Huang

Zhang

2020

IJMS

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Mammalian mitochondrial ribosomes translate 13 proteins encoded by mitochondrial genes, all of which play roles in the mitochondrial respiratory chain. After a long period of reconstruction, mitochondrial ribosomes are the most protein-rich ribosomes. Mitochondrial ribosomal proteins (MRPs) are encoded by nuclear genes, synthesized in the cytoplasm and then, transported to the mitochondria to be assembled into mitochondrial ribosomes. MRPs not only play a role in mitochondrial oxidative phosphorylation (OXPHOS). Moreover, they participate in the regulation of cell state as apoptosis inducing factors. Abnormal expressions of MRPs will lead to mitochondrial metabolism disorder, cell dysfunction, etc. Many researches have demonstrated the abnormal expression of MRPs in various tumors. This paper reviews the basic structure of mitochondrial ribosome, focuses on the structure and function of MRPs, and their relationships with cell apoptosis and diseases. It provides a reference for the study of the function of MRPs and the disease diagnosis and treatment.

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“…It was detected in HepG2 and LNCaT cell lines by Professor Mann’s group 32 using the deep proteome coverage (8–12 thousand protein groups in the identification list) with original SPIDER technology of low-loss digest mixture separation. Information has been published about the involvement of this gene in the development head and neck cancer 40 , pancreas adenocarcinomas 41 . HSBP1L1 is involved in chemical hepatocyte injury 42 , prioritizing this target to investigate the genetic aspects of liver diseases.…”

Section: Resultsmentioning

confidence: 99%

“…The use of the EMBL-EBI's gene ExpressionAtlas 38 40 , pancreas adenocarcinomas 41 . HSBP1L1 is involved in chemical hepatocyte injury 42 , prioritizing this target to investigate the genetic aspects of liver diseases.…”

Section: Overview Of Chr18-coded Missing and Upe1 Proteinsmentioning

confidence: 99%

Human Chr18: “Stakhanovite” Genes, Missing and uPE1 Proteins in Liver Tissue and HepG2 Cells

Krasnov

Лисица

Ponomarenko

et al. 2020

Preprint

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Missing (MP) and functionally uncharacterized proteins (uPE1) comprise less than 5% of the total number of human Chr18 genes. Within half a year, since the January 2020 version of NextProt, the number of entries in the MP+uPE1 datasets has changed, mainly due to the achievements of antibody-based proteomics. Assuming that the proteome is closely related to the transcriptome scaffold, quantitative PCR, Illumina HiSeq, and Oxford Nanopore Technology were applied to characterize the liver samples of three male donors compared with the HepG2 cell line. The data mining of Expression Atlas (EMBL-EBI) and the profiling of our biospecimens using orthogonal methods of transcriptome analysis have shown that in HepG2 cells and the liver, the genes encoding functionally uncharacterized proteins (uPE1) are expressed as low as for the missing proteins (less than 1 copy per cell), except for selected cases of HSBP1L1, TMEM241, C18orf21, and KLHL14. The initial expectation that uPE1 genes might be expressed at higher levels than MP genes, was compromised by severe discrepancies in our semi-quantitative gene expression data and in public databanks. Such discrepancy forced us to revisit the transcriptome of Chr18, the target of Russian C-HPP Consortia. Tanglegram of highly expressed genes and further correlation analysis have shown the severe dependencies on the mRNA extraction method and analytical platform. Targeted gene expression analysis by quantitative PCR (qPCR) and high-throughput transcriptome profiling (Illumina HiSeq and ONT MinION) for the same set of samples from normal liver tissue and HepG2 cells revealed the detectable expression of 250+ (92%) protein-coding genes of Chr18 (at least one method). The expression of slightly more than 50% protein-coding genes was detected simultaneously by all three methods. Correlation analysis of the gene expression profiles showed that the grouping of the datasets depended almost equally on both the type of biological material and the experimental method, particularly cDNA/mRNA isolation and library preparation. The dependence on the choice of bioinformatics analysis pipeline was also noticeable but significantly less. Furthermore, the combination of Illumina HiSeq and ONT MinION sequencing to validate proteotypic peptides of missing and uPE1 proteins was performed for the heat-shock factor binding protein HSBP1L1 (missing protein, recently transferred to PE1 category) and uncharacterized protein C18orf21 (uPE1). We observed that a nonsynonymous SNP led to the loss of the site of trypsinolysis in HSBP1L1. The modified version of HSBP1L1 was included in the sequence database and searched against the MS/MS dataset from Kulak, Geyer & Mann (2017), but delivered no significant identification. Thus, HSBP1L1 is still missing for the MS-pillar of C-HPP, although its existence at the protein level has been confirmed.

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Gene signature associated with neuro‐endocrine activity predicting prognosis of pancreatic carcinoma

Cited by 14 publications

References 22 publications

Identification of a Novel Glycolysis-Related Gene Signature for Predicting Breast Cancer Survival

Identification of a Novel Glycolysis-Related Gene Signature for Predicting Breast Cancer Survival

Abnormal Expression of Mitochondrial Ribosomal Proteins and Their Encoding Genes with Cell Apoptosis and Diseases

Human Chr18: “Stakhanovite” Genes, Missing and uPE1 Proteins in Liver Tissue and HepG2 Cells

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