scholarly journals Comprehensive of N1-Methyladenosine Modifications Patterns and Immunological Characteristics in Ovarian Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinhui Liu ◽  
Can Chen ◽  
Yichun Wang ◽  
Cheng Qian ◽  
Junting Wei ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Comprehensive Evaluation ◽  
Principal Component ◽  
Rt Pcr ◽  
Immune Infiltration ◽  
Therapeutic Benefits ◽  
Small Molecule Drugs ◽  
Principal Component Analysis Algorithm ◽  
Immune Phenotypes ◽  
Essential Function

Backgroundrecently, many researches have concentrated on the relevance between N1-methyladenosine (m1A) methylation modifications and tumor progression and prognosis. However, it remains unknown whether m1A modification has an effect in the prognosis of ovarian cancer (OC) and its immune infiltration.MethodsBased on 10 m1A modulators, we comprehensively assessed m1A modification patterns in 474 OC patients and linked them to TME immune infiltration characteristics. m1Ascore computed with principal component analysis algorithm was applied to quantify m1A modification pattern in OC patients. m1A regulators protein and mRNA expression were respectively obtained by HPA website and RT-PCR in clinical OC and normal samples.ResultsWe finally identified three different m1A modification patterns. The immune infiltration features of these m1A modification patterns correspond to three tumor immune phenotypes, including immune-desert, immune-inflamed and immune-excluded phenotypes. The results demonstrate individual tumor m1A modification patterns can predict patient survival, stage and grade. The m1Ascore was calculated to quantify individual OC patient’s m1A modification pattern. A high m1Ascore is usually accompanied by a better survival advantage and a lower mutational load. Research on m1Ascore in the treatment of OC patients showed that patients with high m1Ascore showed marked therapeutic benefits and clinical outcomes in terms of chemotherapy and immunotherapy. Lastly, we obtained four small molecule drugs that may potentially ameliorate prognosis.ConclusionThis research demonstrates that m1A methylation modification makes an essential function in the prognosis of OC and in shaping the immune microenvironment. Comprehensive evaluation of m1A modifications improves our knowledge of immune infiltration profile and provides a more efficient individualized immunotherapy strategy for OC patients.

scholarly journals Identification of m6A Regulator-Associated Methylation Modification Clusters and Immune Profiles in Melanoma

2021 ◽  
Vol 9 ◽  
Author(s):  
Fengying Du ◽  
Han Li ◽  
Yan Li ◽  
Yang Liu ◽  
Xinyu Li ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Molecular Mechanisms ◽  
Nk Cell ◽  
Comprehensive Evaluation ◽  
Nonnegative Matrix ◽  
Principal Component ◽  
Gene Signature ◽  
Melanoma Tumor ◽  
Immune Infiltration ◽  
Clinical Benefits

RNA N6-methyladenosine (m6A) modification in tumorigenesis and progression has been highlighted and discovered in recent years. However, the molecular and clinical implications of m6A modification in melanoma tumor microenvironment (TME) and immune infiltration remain largely unknown. Here, we utilized consensus molecular clustering with nonnegative matrix factorization based on the melanoma transcriptomic profiles of 23 m6A regulators to determine the m6A modification clusters and m6A-related gene signature. Three distinct m6A modification patterns (m6A-C1, C2, and C3), which are characterized by specific m6A regulator expression, survival outcomes, and biological pathways, were identified in more than 1,000 melanoma samples. The immune profile analyses showed that these three m6A modification subtypes were highly consistent with the three known immune phenotypes: immune-desert (C1), immune-excluded (C2), and immune-inflamed (C3). Tumor digital cytometry (CIBERSORT, ssGSEA) algorithm revealed an upregulated infiltration of CD8+ T cell and NK cell in m6A-C3 subtype. An m6A scoring scheme calculated by principal component of m6A signatures stratified melanoma patients into high- and low-m6sig score subgroups; a high score was significantly associated with prolonged survival and enhanced immune infiltration. Furthermore, fewer somatic copy number alternations (SCNA) and PD-L1 expression were found in patients with high m6Sig score. In addition, patients with high m6Sig score demonstrated marked immune responses and durable clinical benefits in two independent immunotherapy cohorts. Overall, this study indicated that m6A modification is involved in melanoma tumor microenvironment immune regulation and contributes to formation of tumor immunogenicity. Comprehensive evaluation of the m6A modification pattern of individual tumors will provide more insights into molecular mechanisms of TME characterization and promote more effective personalized biotherapy strategies.

scholarly journals Multiplexed profiling of single-cell extracellular vesicles secretion

2019 ◽  
Vol 116 (13) ◽  
pp. 5979-5984 ◽  
Author(s):  
Yahui Ji ◽  
Dongyuan Qi ◽  
Linmei Li ◽  
Haoran Su ◽  
Xiaojie Li ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Lines ◽  
Extracellular Vesicles ◽  
Single Cell Analysis ◽  
Comprehensive Evaluation ◽  
Single Cells ◽  
Deep Understanding ◽  
Principal Component ◽  
Cell Heterogeneity ◽  
Indispensable Tool

Extracellular vesicles (EVs) are important intercellular mediators regulating health and diseases. Conventional methods for EV surface marker profiling, which was based on population measurements, masked the cell-to-cell heterogeneity in the quantity and phenotypes of EV secretion. Herein, by using spatially patterned antibody barcodes, we realized multiplexed profiling of single-cell EV secretion from more than 1,000 single cells simultaneously. Applying this platform to profile human oral squamous cell carcinoma (OSCC) cell lines led to a deep understanding of previously undifferentiated single-cell heterogeneity underlying EV secretion. Notably, we observed that the decrement of certain EV phenotypes (e.g.,CD63+EV) was associated with the invasive feature of both OSCC cell lines and primary OSCC cells. We also realized multiplexed detection of EV secretion and cytokines secretion simultaneously from the same single cells to investigate the multidimensional spectrum of cellular communications, from which we resolved tiered functional subgroups with distinct secretion profiles by visualized clustering and principal component analysis. In particular, we found that different cell subgroups dominated EV secretion and cytokine secretion. The technology introduced here enables a comprehensive evaluation of EV secretion heterogeneity at single-cell level, which may become an indispensable tool to complement current single-cell analysis and EV research.

An Exploration of Provincial Low-Carbon Economy Evaluation System Based on Principal Component-Variable Fuzzy Evaluation

2013 ◽  
Vol 291-294 ◽  
pp. 1562-1567
Author(s):  
Ji Min Hu ◽  
Jian Long Gu ◽  
Chang Cui Hu ◽  
Hai Feng Wang
Keyword(s):  
Evaluation System ◽  
Comprehensive Evaluation ◽  
Principal Component ◽  
Fuzzy Comprehensive Evaluation ◽  
Fuzzy Evaluation ◽  
Low Carbon ◽  
Low Carbon Economy ◽  
Component Variable ◽  
The Status ◽  
Carbon Economy

According to indicators’ information repetition and subjectivity of the indicators’ weight set during the variable fuzzy comprehensive evaluation, Principal Component analysis can help solve the weight of the relative indicators and reduce comprehensive evaluation dimensions of the variable fussy comprehensive evaluation. This paper has made a comprehensive evaluation of the status quo of Yunnan’s low carbon economy development(2005-2009), which turns out to be more practical compared with the mere variable fussy theory analysis, thus, principal component-variable fuzzy evaluation is a kind of feasible way to analyze the regional low carbon development status.

Classification and Prediction of Goldfish Population and Water Quality Using a Potentiometric E-Tongue

2017 ◽  
Vol 60 (4) ◽  
pp. 1037-1044
Author(s):  
Zhenbo Wei ◽  
Yu Zhao ◽  
Jun Wang
Keyword(s):  
Neural Network ◽  
Water Quality ◽  
Pattern Recognition ◽  
Comprehensive Evaluation ◽  
Back Propagation ◽  
Correlation Coefficients ◽  
Principal Component ◽  
Quality Parameters ◽  
Water Quality Parameters ◽  
Pattern Recognition Methods

Abstract. In this study, a potentiometric E-tongue was employed for comprehensive evaluation of water quality and goldfish population with the help of pattern recognition methods. Four water quality parameters, i.e., pH and concentrations of dissolved oxygen (DO), nitrite (NO2-N), and ammonium (NH3-N), were tested by conventional analysis methods. The differences in water quality parameters between samples were revealed by two-way analysis of variance (ANOVA). The cultivation days and goldfish population were classified well by principal component analysis (PCA) and canonical discriminant analysis (CDA), and the distribution of each sample was clearer in CDA score plots than in PCA score plots. The cultivation days, goldfish population, and water parameters were predicted by a T-S fuzzy neural network (TSFNN) and back-propagation artificial neural network (BPANN). BPANN performed better than TSFNN in the prediction, and all fitting correlation coefficients were >0.90. The results indicated that the potentiometric E-tongue coupled with pattern recognition methods could be applied as a rapid method for the determination and evaluation of water quality and goldfish population. Keywords: Classify, E-tongue, Goldfish water, Prediction.

scholarly journals Increased Expression of the Pro-Protein Convertase Furin Predicts Decreased Survival in Ovarian Cancer

2007 ◽  
Vol 29 (4) ◽  
pp. 289-299
Author(s):  
Robert E. Page ◽  
Andrés J. P. Klein-Szanto ◽  
Samuel Litwin ◽  
Emmanuelle Nicolas ◽  
Raid Al-Jumaily ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Tumor Progression ◽  
Real Time ◽  
Cell Lines ◽  
Cancer Cell ◽  
Real Time Pcr ◽  
Ovarian Tumor ◽  
Cancer Cell Lines ◽  
Rt Pcr ◽  
Primary Tumors

Background: Proprotein convertases (PCs) are serine proteases that after restricted proteolysis activate many proteins that play a crucial role in cancer such as metalloproteinases, growth factors and growth factor receptors, adhesion molecules, and angiogenic factors. Although the expression of several PCs is increased in many tumors, their expression in primary ovarian tumors has not been studied in detail. We sought to determine if there was an association between the expression of the ubiquitously expressed PCs, furin, PACE-4, PC-5 and PC-7, and ovarian tumor progression. Methods: We assessed their expression by RT-PCR, Real-time PCR, Western blot, and immunohistochemistry using cells derived from normal human ovarian surface epithelium (HOSE) and cancer cell lines as well as ovarian epithelial cancer specimens (45 RT-PCR/Real-time PCR, and 120 archival specimens for Immunohistochemistry). Results: We found that furin expression was restricted to the cancer cell lines. In contrast, PACE-4 and PC-7 showed expression only in normal HOSE cells lines. Furthermore, furin was predominantly expressed in primary tumors from patients who survived for less than five years. The other PCs are either expressed in the group of survivors (PC-7 and PACE4) or expressed in low amounts (PC-5). Conclusions: Our studies point to a clear relationship between furin and ovarian cancer. In addition, these results show that furin exhibits the closest association with ovarian cancer among the ubiquitously expressed PCs, arguing against the redundancy of these proteases. In summary, furin may constitute a marker for ovarian tumor progression and could contribute to predict the outcome of this disease.

scholarly journals Identification of a gene set correlated with immune status in ovarian cancer by transcriptome-wide data mining

2020 ◽  
Author(s):  
Lili Fan ◽  
Han Lei ◽  
Ying Lin ◽  
Zhengwei Zhou ◽  
Guang Shu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Immune Cell ◽  
Good Prognosis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Survival Prognosis ◽  
Immune Activity ◽  
Gene Set ◽  
Immune Infiltration ◽  
Keywords Ovarian Cancer

Abstract Background : Ovarian cancer (OC) is a serious tumor disease in gynecology. Many papers have reported that high tumor mutational burden (TMB) can generate many neoantigens to result in a higher degree of tumor immune infiltration, so our study aims to predict the key molecules in OC immunotherapy by combined TMB with immunoactivity-related gene. Method: We divided OC cases into two groups: the low & high TMB group hinged on the somatic mutation data from the Cancer Genome Atlas (TCGA). We also used single-sample gene set enrichment analysis (ssGSEA) scores of immune cell types to conduct unsupervised clustering of OC patients in the TCGA cohort and some of them were defined as the low & high immunity group. Besides, to further understand the function of these genes, we conducted Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, protein-protein interaction network, survival prognosis analysis and immune infiltration analysis. Finally, the effects on prognosis and immunotherapy in OC patients were explored by the Group on Earth Observations verification the patients' responses to immunotherapy. Results: We found that the higher the TMB was associated with the higher OC grades. Moreover, both high TMB and high immunity were significantly correlated with a good prognosis of OC. Then, 14 up-regulated differential expression genes (Up-DEGs) that were closely related to the prognosis of OC patients were screened according to the high TMB group and the high immunity group. Next, pathway analysis revealed that Up-DGEs were mainly involved in immune response and T cell proliferation. Finally, four genes had a good prognosis and were validated in the GEO dataset which included CXCL13, FCRLA, PLA2G2D, and MS4A1. We also identified that four genes had a good prognosis in melanoma patients treated with anti-PD-L1 and anti-CTLA-4 in the TIDE database. Conclusion: High TMB can promote immune cell infiltration and increases immune activity. And our analysis also demonstrated that the higher the TMB, the higher the immune activity, the better the prognosis of OC. Altogether, we found that CXCL13, FCRLA, PLA2G2D, and MS4A1 may be biomarkers for OC immunotherapy. Keywords: ovarian cancer, TMB, immune cells infiltration, survival prognosis.

scholarly journals Research on Liquor Storage Based on Statistical Analysis Model

2021 ◽  
Vol 5 (3) ◽  
Author(s):  
Xuhua Xu
Keyword(s):  
Index System ◽  
Comprehensive Evaluation ◽  
Principal Component ◽  
Evaluation Index System ◽  
Classification Model ◽  
Analysis Model ◽  
The Index System ◽  
Storage Methods ◽  
Physical And Chemical

According to the physical and chemical indexes of different periods, different storage containers and different storage sites, a two overall T test was used to show that there were significant differences in physical and chemical indexes of liquor body in different detection sites. Correlation analysis of wine storage in different storage methods by Spearman correlation coefficient. By using the principal component analysis method, the comprehensive evaluation index system of the quality of the wine body was constructed, and the classification model of the detection location based on the comprehensive evaluation was established by using the index system. The detection sites were classified, and the results showed that the detection sites were divided into four grades.

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