scholarly journals NSUN5 is Upregulated and Positively Correlated with Translation in Human Cancers: A Bioinformatics-based Study

2020 ◽  
Author(s):  
Xiao-wen Zhang ◽  
Yan Huang ◽  
Lu-yi Wu ◽  
Qin Qi ◽  
Rui Zhong ◽  
...  
Keyword(s):  
Methylation Level ◽  
Biological Processes ◽  
Kegg Pathways ◽  
Normal Tissues ◽  
Human Cancers ◽  
Molecular Functions ◽  
Cellular Components

Abstract The role of RNA m5C (5-methylcytosine) and RNA m5C methyltransferases (RCMTs, including NSUN1, NSUN2, NSUN3, NSUN4, NSUN5, NSUN6, NSUN7 and TRDMT1) in human cancers remains largely unknown. In this study, GEPIA2 was used to compare the expression of RCMTs in human cancers and that in associated normal tissues, and to analyze the prognosis value of NSUN5 expression. UALCAN was used to compare the methylation level of NSUN5 promoter in human cancers and that in associated normal tissues. LinkedOmics was used perform BPs (biological processes), CCs (cellular components), MFs (molecular functions) and KEGG pathways analyses of NSUN5-correlated genes in each cancer one by one. We found that six RCMTs (NSUN1-NSUN5 and TRDMT1), especially NSUN5, were generally upregulated in human cancers, that the hypomethylation of NSUN5 promoter may be responsible for its upregulation, and that overexpressed NSUN5 predicted poorer prognosis and was positively correlated with translation in human cancers. The function of NSUN5 in human cancers and its mechanism need to be validated by biological experiments.

scholarly journals The expression characteristics and prognostic roles of autophagy-related genes in gastric cancer

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10814
Author(s):  
Mengya Wang ◽  
Jingjing Jing ◽  
Hao Li ◽  
Jingwei Liu ◽  
Yuan Yuan ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Prognostic Factors ◽  
Differential Expression Analysis ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Normal Tissues ◽  
Genes Expression ◽  
Expression Characteristics ◽  
Cellular Components

Background Autophagy is an evolutionally highly conserved process, accompanied by the dynamic changes of various molecules, which is necessary for the orderly degradation and recycling of cellular components. The aim of the study was to identify the role of autophagy-related (ATG) genes in the occurrence and development of gastric cancer (GC). Methods Data from Oncomine dataset was used for the differential expression analysis between cancer and normal tissues. The association of ATG genes expression with clinicopathologic indicators was evaluated by The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database. Moreover, using the TCGA datasets, the prognostic role of ATG genes was assessed. A nomogram was further built to assess the independent prognostic factors. Results The expression of autophagy-related genes AMBRA1, ATG4B, ATG7, ATG10, ATG12, ATG16L2, GABARAPL2, GABARAPL1, ULK4 and WIPI2 showed differences between cancer and normal tissues. After verification, ATG14 and ATG4D were significantly associated with TNM stage. ATG9A, ATG2A, and ATG4D were associated with T stage. VMP1 and ATG4A were low-expressed in patients without lymph node metastasis. No gene in autophagy pathway was associated with M stage. Further multivariate analysis suggested that ATG4D and MAP1LC3C were independent prognostic factors for GC. The C-index of nomogram was 0.676 and the 95% CI was 0.628 to 0.724. Conclusion Our study provided a comprehensive illustration of ATG genes expression characteristics in GC. Abnormal expressions of the ubiquitin-like conjugated system in ATG genes plays a key role in the occurrence of GC. ATG8/LC3 sub-system may play an important role in development and clinical outcome of GC. In the future, it is necessary to further elucidate the alterations of specific ATG8/LC3 forms in order to provide insights for the discovery, diagnosis, or targeting for GC.

scholarly journals The role of NDRG1 in the pathology and potential treatment of human cancers

2013 ◽  
Vol 66 (11) ◽  
pp. 911-917 ◽  
Author(s):  
Dong-Hun Bae ◽  
Patric J Jansson ◽  
Michael L Huang ◽  
Zaklina Kovacevic ◽  
Danuta Kalinowski ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Anticancer Agents ◽  
Tumour Progression ◽  
Antitumour Activity ◽  
Primary Tumour ◽  
Normal Tissues ◽  
Human Cancers ◽  
Physiological Processes ◽  
Cancer Pathology

N-myc downstream regulated gene 1 (NDRG1) has been well characterised to act as a metastatic suppressor in a number of human cancers. It has also been implicated to have a significant function in a number of physiological processes such as cellular differentiation and cell cycle. In this review, we discuss the role of NDRG1 in cancer pathology. NDRG1 was observed to be downregulated in the majority of cancers. Moreover, the expression of NDRG1 was found to be significantly lower in neoplastic tissues as compared with normal tissues. The most important function of NDRG1 in inhibiting tumour progression is associated with its ability to suppress metastasis. However, it has also been shown to have important effects on other stages of cancer progression (primary tumour growth and angiogenesis). Recently, novel iron chelators with selective antitumour activity (ie, Dp44mT, DpC) were shown to upregulate NDRG1 in cancer cells. Moreover, Dp44mT showed its antimetastatic potential only in cells expressing NDRG1, making this protein an important therapeutic target for cancer chemotherapy. This observation has led to increased interest in the examination of these novel anticancer agents.

scholarly journals Systematic Pan-Cancer Analysis Reveals the Prognostic Value and Immunological Role of EPHX2

2021 ◽  
Author(s):  
Weiquan Hu ◽  
Qinfei Zhao ◽  
Jing Xu ◽  
Huaying Li ◽  
Longyu Zhu ◽  
...  
Keyword(s):  
Cancer Immunotherapy ◽  
Prognostic Value ◽  
Immune Cell ◽  
Systematic Evaluation ◽  
Response Patterns ◽  
Clinical Value ◽  
Immune Modulators ◽  
Normal Tissues ◽  
Human Cancers

Abstract Background: Accumulating evidence indicates the essential role of EPHX2 in tumorigenesis. However, to date, no studies have performed a systematic evaluation of EPHX2 gene in human cancers and the predictive role of EPHX2 in cancer immunotherapy response has still not been explored. Methods: In the present study, Oncomine, TIMER2, UALCAN, GEPIA2, PrognoScan, HPA and Kaplan-Meier Plotter database were utilized to comprehensively analyze the expression landscape and prognostic clinical value of EPHX2 across 33 human cancers. To gain a better understanding of the role of EPHX2 in cancer immunotherapy, the correlations between EPHX2 and tumor immune microenvironment (TME) such as immune cell infiltrations, immune modulators, and the major histocompatibility complex were demonstrated. The underlying EPHX2-associated signaling pathways in cancer were also analysed. Moreover, the correlation between EPHX2 and immunotherapeutic biomarkers such as tumor mutational burden (TMB) and microsatellite instability (MSI) was explored. At last, the potential immune checkpoint blockers (ICB) response was predicted using tumor immune dysfunction and exclusion (TIDE) algorithm. Results: Overall, the mRNA expression of EPHX2 was significantly downregulated in the majority of tumors compared with normal tissues. Despite the significant prognostic value of EPHX2 expression across cancers, EPHX2 played a protective or detrimental role in different kinds of cancers. Generally speaking, immune cell infiltrations, immune modulators and immunotherapeutic biomarkers were all strongly related to the expression of EPHX2. Besides, EPHX2 expression was significantly related to immune-relevant pathways, especially in PAAD, THYM and UVM. Furthermore, our study demonstrated diverse response patterns of ICB in response to EPHX2 expression in different tumor types. Conclusion: Our findings here suggest that EPHX2 could be a prognostic factor in multiple cancers and play an important role in tumor immunity by affecting infiltrating immune cells, TMB and MSI. This study provides further insight into the role of EPHX2 in tumor immunotherapy.

scholarly journals Long Noncoding RNA LIFR-AS1: A New Player in Human Cancers

2022 ◽  
Vol 2022 ◽  
pp. 1-11
Author(s):  
Zhiqun Bai ◽  
Xuemei Wang ◽  
Zhen Zhang
Keyword(s):  
Leukemia Inhibitory Factor ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Clinicopathological Characteristics ◽  
Vital Role ◽  
Tumor Proliferation ◽  
Biological Processes ◽  
Leukemia Inhibitory Factor Receptor ◽  
Human Cancers

Emerging evidence has indicated that aberrantly expressed long noncoding RNAs (lncRNAs) play a vital role in various biological processes associated with tumorigenesis. Leukemia inhibitory factor receptor antisense RNA1 (LIFR-AS1) is a recently identified lncRNA transcribed in an antisense manner from the LIFR gene located on human chromosome 5p13.1. LIFR-AS1 regulates tumor proliferation, migration, invasion, apoptosis, and drug resistance through different mechanisms. Its expression level is related to the clinicopathological characteristics of tumors and plays a key role in tumor occurrence and development. In this review, we summarize the role of LIFR-AS1 in the development and progression of different cancers and highlight the potential for LIFR-AS1 to serve as a biomarker and therapeutic target for a variety of human cancers.

scholarly journals Promising therapeutic role of miR-27b in tumor

Tumor Biology ◽  
2017 ◽  
Vol 39 (3) ◽  
pp. 101042831769165 ◽  
Author(s):  
Li Ding ◽  
Jie Ni ◽  
Fan Yang ◽  
Lingli Huang ◽  
Heng Deng ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Therapeutic Target ◽  
Biological Pathways ◽  
Molecular Targeting ◽  
Gene Clustering ◽  
Biological Processes ◽  
Targeting Therapy ◽  
Human Cancers ◽  
Promising Therapeutic Target

MicroRNAs are small nonprotein-encoding RNAs ranging from 18 to 25 nucleotides in size and regulate multiple biological pathways via directly targeting a variety of associated genes in cancers. MicroRNA-27b is a highly conserved MicroRNA throughout vertebrates and there are two homologs (hsa-miR-27a and hsa-miR-27b) in humans. MicroRNA-27b is an intragenic microRNA located on chromosome 9q22.1 within the C9orf3 gene, clustering with miR-23b and miR-24-1 in human. As a frequently dysregulated microRNA in human cancers, microRNA-27b could function as a tumor suppressor or an oncogenic microRNA. More and more studies indicate that microRNA-27b is involved in affecting various biological processes, such as angiogenesis, proliferation, metastasis, and drug resistance, and thus may act as a promising therapeutic target in human cancers. In this review, we discuss the role of microRNA-27b in detail and offer novel insights into molecular targeting therapy for cancers.

scholarly journals Systematic Pan-Cancer Analysis Reveals the Prognostic Value and Immunological Role of EPHX2

2022 ◽  
Author(s):  
Weiquan Hu ◽  
Qinfei Zhao ◽  
Jing Xu ◽  
Huaying Li ◽  
Longyu Zhu ◽  
...  
Keyword(s):  
Cancer Immunotherapy ◽  
Prognostic Value ◽  
Immune Cell ◽  
Systematic Evaluation ◽  
Response Patterns ◽  
Clinical Value ◽  
Immune Modulators ◽  
Normal Tissues ◽  
Human Cancers

Abstract Background Accumulating evidence indicates the essential role of EPHX2 in tumorigenesis. However, to date, no studies have performed a systematic evaluation of EPHX2 gene in human cancers and the predictive role of EPHX2 in cancer immunotherapy response has still not been explored. Methods In the present study, Oncomine, TIMER2, UALCAN, GEPIA2, PrognoScan, HPA and Kaplan-Meier Plotter database were utilized to comprehensively analyze the expression landscape and prognostic clinical value of EPHX2 across 33 human cancers. To gain a better understanding of the role of EPHX2 in cancer immunotherapy, the correlations between EPHX2 and tumor immune microenvironment (TME) such as immune cell infiltrations, immune modulators, and the major histocompatibility complex were demonstrated. The underlying EPHX2-associated signaling pathways in cancer were also analysed. Moreover, the correlation between EPHX2 and immunotherapeutic biomarkers such as tumor mutational burden (TMB) and microsatellite instability (MSI) was explored. At last, the potential immune checkpoint blockers (ICB) response was predicted using tumor immune dysfunction and exclusion (TIDE) algorithm. Results Overall, the mRNA expression of EPHX2 was significantly downregulated in the majority of tumors compared with normal tissues. Despite the significant prognostic value of EPHX2 expression across cancers, EPHX2 played a protective or detrimental role in different kinds of cancers. Generally speaking, immune cell infiltrations, immune modulators and immunotherapeutic biomarkers were all strongly related to the expression of EPHX2. Besides, EPHX2 expression was significantly related to immune-relevant pathways, especially in PAAD, THYM and UVM. Furthermore, our study demonstrated diverse response patterns of ICB in response to EPHX2 expression in different tumor types. Conclusion Our findings here suggest that EPHX2 could be a prognostic factor in multiple cancers and play an important role in tumor immunity by affecting infiltrating immune cells, TMB and MSI. This study provides further insight into the role of EPHX2 in tumor immunotherapy.

scholarly journals Prognostic Value and Immunological Role of MORF4-Related Gene-Binding Protein in Human Cancers

2021 ◽  
Vol 9 ◽  
Author(s):  
Dongqi Chai ◽  
Lilong Zhang ◽  
Yongjun Guan ◽  
Jingping Yuan ◽  
Man Li ◽  
...  
Keyword(s):  
Prognostic Value ◽  
Binding Protein ◽  
Macrophage Infiltration ◽  
Lower Grade ◽  
Related Gene ◽  
Immune Infiltration ◽  
Normal Tissues ◽  
Human Cancers ◽  
The Relationship

MORF4-related gene-binding protein (MRGBP) is the subunit of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histones H4 and H2A. Much of the research indicated an oncogenic role of MRGBP in the development of cancers. However, it is still unknown the role MRGBP plays in human cancers, which deserves further exploration. In this research, the expression profile, prognostic value of MRGBP, and the relationship between MRGBP and immune infiltration were explored in 33 types of cancer. The differences in MRGBP expression in tumor and normal tissues were explored using data from The Cancer Genome Atlas, Gene Expression Omnibus and ONCOMINE. Analysis of the association between MRGBP and prognosis using Kaplan-Meier survival curve and COX analysis. The data of Tumor mutational burden (TMB), microsatellite instability (MSI) from TCGA. The relationship Between MRGBP expression and immunity was analyzed using the ESTIMATE algorithm and CIBERSORT. Furthermore, we explored MRGBP expression and the relationship between MRGBP expression and macrophage infiltration using immunohistochemical analysis in lower grade glioma (LGG). Our results revealed that MRGBP was highly expressed in most cancer tissues compared with normal tissues. Tumors with increased MRGBP expression had a high clinicopathologic stage and poor prognosis. The expression of MRGBP was closely related to the TMB, MSI. We also found a significant negative correlation between MRGBP expression and stromal scores and immune scores in various types of cancer. Furthermore, MRGBP expression was associated with a variety of immune cells including B cells, NK cells, T cells, and macrophages. LGG and LIHC was selected as representative cancer types for further study, the results of immunohistochemistry indicated that the protein levels of MRGBP were significantly elevated in tumor tissues. Moreover, our LIHC data analysis showed that patients with high MRGBP expression were associated with short survival rates and MRGBP was a risk factor to determine OS. Immunohistochemistry also confirmed that M0 macrophage infiltration in the MRGBP-high group significantly increased. In conclusion, these results reveal that MRGBP can serve as a potential prognostic biomarker and it plays an important role in tumor immune infiltration in various tumors, especially in LGG and LIHC.

scholarly journals Comparison of the Transcriptomic Responses of Two Chrysanthemum Morifolium Cultivars to Low Light

2021 ◽  
Author(s):  
Shuang Han ◽  
Qingchen Zhang ◽  
Xiaoqin Zhu ◽  
Dongli Pei
Keyword(s):  
Elongation Factor ◽  
Chrysanthemum Morifolium ◽  
Stem Length ◽  
Shade Avoidance ◽  
Biological Processes ◽  
Low Light ◽  
Helix Loop Helix ◽  
Molecular Functions ◽  
Upregulated Genes ◽  
Cellular Components

Abstract Low light is a primary regulator of chrysanthemum growth. Herein, we conducted a transcriptomic analysis of leaf samples from the ‘Nannonggongfen’ and ‘Nannongxuefeng’ chrysanthemum cultivars following a 5-day exposure to optimal light (70%, control [CK]) or low-light (20%, LL) conditions. Gene Ontology (GO) classification of upregulated genes revealed these genes to be associated with 11 cellular components, 9 molecular functions, and 15 biological processes, with the majority being localized to the chloroplast, highlighting the role of chloroplast proteins as regulators of shading tolerance. Downregulated genes were associated with 11 cellular components, 8 molecular functions, and 16 biological processes. Heat map analyses suggested that basic helix–loop–helix domain genes and elongation factors were markedly downregulated in ‘Nannongxuefeng’ leaves, consistent with the maintenance of normal stem length, whereas no comparable changes were observed in ‘Nanonggongfen’ leaves. Subsequent qPCR analyses revealed that phytochrome-interacting factors and dormancy-associated genes were significantly upregulated under LL conditions relative to CK conditions, while succinate dehydrogenase 1, elongated hypocotyls 5, and auxin-responsive gene of were significantly downregulated under LL conditions. These findings suggest that LL plants were significantly lower than those of the CK plants. Low-light tolerant chrysanthemum cultivars may maintain reduced indole-3-acetic acid (IAA) and elongation factor expression as a means of preventing the onset of shade-avoidance symptoms.

scholarly journals A Comprehensive Expression Profile of tRNA-Derived Fragments in Papillary Thyroid Cancer

2020 ◽  
pp. 1-7
Author(s):  
Chunfu Zhu ◽  
Shiting Shan ◽  
Yuting Wang ◽  
Chunfu Zhu
Keyword(s):  
Thyroid Cancer ◽  
Papillary Thyroid Cancer ◽  
Thyroid Tumor ◽  
Biological Processes ◽  
Papillary Thyroid ◽  
Normal Tissues ◽  
Non Coding Rna ◽  
Malignant Thyroid Tumor ◽  
Fresh Frozen

Objective: In recent years, the incidence of thyroid cancer has been increasing. Papillary thyroid cancer (PTC) is the most common type of malignant thyroid tumor, accounting for approximately 85% of thyroid cancer cases. Although the genetic background of PTC has been studied extensively, relatively little is known about the role of small non-coding RNA (sncRNA) in this disease. tRNA-derived fragments (tRFs) represent a newly discovered class of sncRNAs that exist in many species and play a role in many biological processes. Methods: In this study, we used RNA sequencing to analyse the expression of tRFs in fresh frozen specimens from PTC tissues and normal tissues adjacent to the tumors. Through this analysis, we identified 49 unique tRFs and transfer RNA halves and then performed quantitative PCR to determine the expression levels of these molecules and to make bioinformatic predictions. Conclusion: In this report, we provide a comprehensive catalog of tRFs in PTC and assess the abnormal expression of these fragments. These preliminary findings can be used as the basis for further research regarding the functional role of tRFs in patients with PTC.

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