scholarly journals ImReLnc: Identifying Immune-Related LncRNA Characteristics in Human Cancers Based on Heuristic Correlation Optimization

2022 ◽  
Vol 12 ◽  
Author(s):  
Meihong Gao ◽  
Shuhui Liu ◽  
Yang Qi ◽  
Xinpeng Guo ◽  
Xuequn Shang
Keyword(s):  
Correlation Coefficient ◽  
Enrichment Analysis ◽  
Highly Pathogenic ◽  
Prognostic Effect ◽  
Human Cancers ◽  
Cancer Pathogenesis ◽  
Specific Cancer ◽  
Cancer Types ◽  
Non Coding Rnas ◽  
The Relationship

Long non-coding RNAs (lncRNAs) play critical roles in cancer through gene expression and immune regulation. Identifying immune-related lncRNA (irlncRNA) characteristics would contribute to dissecting the mechanism of cancer pathogenesis. Some computational methods have been proposed to identify irlncRNA characteristics in human cancers, but most of them are aimed at identifying irlncRNA characteristics in specific cancer. Here, we proposed a new method, ImReLnc, to recognize irlncRNA characteristics for 33 human cancers and predict the pathogenicity levels of these irlncRNAs across cancer types. We first calculated the heuristic correlation coefficient between lncRNAs and mRNAs for immune-related enrichment analysis. Especially, we analyzed the relationship between lncRNAs and 17 immune-related pathways in 33 cancers to recognize the irlncRNA characteristics of each cancer. Then, we calculated the Pscore of the irlncRNA characteristics to evaluate their pathogenicity levels. The results showed that highly pathogenic irlncRNAs appeared in a higher proportion of known disease databases and had a significant prognostic effect on cancer. In addition, it was found that the expression of irlncRNAs in immune cells was higher than that of non-irlncRNAs, and the proportion of irlncRNAs related to the levels of immune infiltration was much higher than that of non-irlncRNAs. Overall, ImReLnc accurately identified the irlncRNA characteristics in multiple cancers based on the heuristic correlation coefficient. More importantly, ImReLnc effectively evaluated the pathogenicity levels of irlncRNAs across cancer types. ImReLnc is freely available at https://github.com/meihonggao/ImReLnc.

scholarly journals Long non-coding RNAs and their implications in cancer epigenetics

2013 ◽  
Vol 33 (4) ◽  
Author(s):  
Felipe C. Beckedorff ◽  
Murilo Sena Amaral ◽  
Carlos Deocesano-Pereira ◽  
Sergio Verjovski-Almeida
Keyword(s):  
Gene Expression ◽  
Cancer Survival ◽  
Regulation Of Gene Expression ◽  
Dna Methyltransferases ◽  
Control Of Gene Expression ◽  
Cancer Subtypes ◽  
Epigenetic Control ◽  
Specific Cancer ◽  
Cancer Types ◽  
Non Coding Rnas

LncRNAs (long non-coding RNAs) have emerged as key molecular players in the regulation of gene expression in different biological processes. Their involvement in epigenetic processes includes the recruitment of histone-modifying enzymes and DNA methyltransferases, leading to the establishment of chromatin conformation patterns that ultimately result in the fine control of genes. Some of these genes are related to tumorigenesis and it is well documented that the misregulation of epigenetic marks leads to cancer. In this review, we highlight how some of the lncRNAs implicated in cancer are involved in the epigenetic control of gene expression. While very few lncRNAs have already been identified as players in determining the cancer-survival outcome in a number of different cancer types, for most of the lncRNAs associated with epigenetic regulation only their altered pattern of expression in cancer is demonstrated. Thanks to their tissue-specificity features, lncRNAs have already been proposed as diagnostic markers in specific cancer types. We envision the discovery of a wealth of novel spliced and unspliced intronic lncRNAs involved in epigenetic networks or in highly location-specific epigenetic control, which might be predominantly altered in specific cancer subtypes. We expect that the characterization of new lncRNA (long non-coding RNA)–protein and lncRNA–DNA interactions will contribute to the discovery of potential lncRNA targets for use in therapies against cancer.

Epigenetic-dysregulated lncRNAs in Prostate Cancer Based on Multi-omics Analysis

2021 ◽  
Author(s):  
Jianxiao Zheng ◽  
Xuexiao Xiang ◽  
Zhipeng Xu ◽  
Yangjing Xu ◽  
Xiaowei Huang ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Prognostic Markers ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Functional Enrichment ◽  
Epigenetic Changes ◽  
Gene Set Enrichment ◽  
Protein Coding ◽  
Non Coding Rnas ◽  
The Relationship

Abstract Background: The purpose of this study was to investigate the relationship between Long non-coding RNAs (lncRNAs) expression and epigenetic changes, and explore the prognostic value of these findings in patients with prostate cancer. Methods: In this study, we systematically compared the histone modification and methylation regions on lncRNAs promoter and enhancer elements by multiomics. We analyzed the distribution characteristics of histone modified apparent lncRNAs promoters and enhancers in the genome. Single sample Gene Set Enrichment Analysis (ssGSEA) and Kyoto Encyclopedia of Gene and Genomes (KEGG) were used to analyze the functional enrichment of epigenetic dysregulated lncRNAs. The prostate cancer associated lncRNAs were downloaded from lnc2cancer V3.0 and survival analysis was performed. Results: We found 1124 epigenetic-dysregulated lncRNAs (epi-lncRNAs) and 9734 epigenetic-dysregulated protein coding genes (epi-PCGs) in prostate cancer, and the abnormal frequency of lncRNAs was much lower than that of PCGs. H3K4me3, H3K4me1, H3K27ac and H3K27me3 abnormally modified histones accounted for a large proportion and were mainly concentrated in the promoter region. Epigenetic abnormal lncRNAs affects the biological specific molecular function of prostate cancer by changing the abnormal modification of histone. The abnormal expression of lncRNAs caused by abnormal modification of H3K36me3 may be an important factor in the occurrence of prostate cancer. Finally, based on lncRNAs analysis of the prognosis of prostate cancer samples, three lncRNAs (HAR1A, SNHG12 and SNHG17) were identified as prognostic markers of prostate cancer.Conclusions: These findings may help to better understand the abnormal epigenetic regulation of lncRNAs expression in prostate cancer.

scholarly journals Pan-Cancer Analysis Reveals Common and Specific Relationships between Intragenic miRNAs and Their Host Genes

Biomedicines ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 1263
Author(s):  
Baohong Liu ◽  
Yu Shyr ◽  
Qi Liu
Keyword(s):  
Mirna Biogenesis ◽  
Comprehensive Investigation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Specific Cancer ◽  
Precursor Mirnas ◽  
Cancer Types ◽  
Non Coding Rnas ◽  
Pan Cancer ◽  
Host Genes

MicroRNAs (miRNAs) are small endogenous non-coding RNAs that play important roles in regulating gene expression. Most miRNAs are located within or close to genes (host). miRNAs and their host genes have either coordinated or independent transcription. We performed a comprehensive investigation on co-transcriptional patterns of miRNAs and host genes based on 4707 patients across 21 cancer types. We found that only 11.6% of miRNA-host pairs were co-transcribed consistently and strongly across cancer types. Most miRNA-host pairs showed a strong coexpression only in some specific cancer types, demonstrating a high heterogenous pattern. For two particular types of intergenic miRNAs, readthrough and divergent miRNAs, readthrough miRNAs showed higher coexpression with their host genes than divergent ones. miRNAs located within non-coding genes had tighter co-transcription with their hosts than those located within protein-coding genes, especially exonic and junction miRNAs. A few precursor miRNAs changed their dominate form between 5′ and 3′ strands in different cancer types, including miR-486, miR-99b, let-7e, miR-125a, let-7g, miR-339, miR-26a, miR-16, and miR-218, whereas only two miRNAs with multiple host genes switched their co-transcriptional partner in different cancer types (miR-219a-1 with SLC39A7/HSD17B8 and miR-3615 with RAB37/SLC9A3R1). miRNAs generated from distinct precursors (such as miR-125b from miR-125b-1 or miR-125b-2) were more likely to have cancer-dependent main contributors. miRNAs and hosts were less co-expressed in KIRC than other cancer types, possibly due to its frequent VHL mutations. Our findings shed new light on miRNA biogenesis and cancer diagnosis and treatments.

scholarly journals Functional Enrichment Analysis of Deregulated Long Non-Coding RNAs in Cancer Based on their Genomic Neighbors

2020 ◽  
Author(s):  
Gulden Olgun ◽  
Oznur Tastan
Keyword(s):  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Transcriptional Regulators ◽  
Functional Enrichment ◽  
Biological Processes ◽  
Driver Genes ◽  
Cancer Driver ◽  
Cancer Types ◽  
Non Coding Rnas ◽  
The Impact

AbstractThe dysregulation of long non-coding RNAs’ (lncRNAs) expressions has been implicated in cancer. Since most of the lncRNAs’ are not functionally characterized well, investigating the set of perturbed lncRNAs are is challenging. Existing methods that inspect lncRNAs functionally rely on the co-expressed coding genes, which are far better characterized functionally. LncRNAs can be known to act as transcriptional regulators; they may activate or repress the neighborhood’s coding genes on the genome. Based on this, in this work, we aim to analyze the deregulated lncRNAs in cancer by taking into account their ability to regulate nearby loci on the genome. We perform functional analysis on differentially expressed lncRNAs for 28 different cancers considering their adjacent coding genes. We identify that some deregulated lncRNAs are cancer-specific, but a substantial number of lncRNAs are shared across cancers. Next, we assess the similarities of the cancer types based on the functional enrichment of the deregulated lncRNA sets. We find some cancers are very similar in the functions and biological processes related to the deregulated lncRNAs. We observe that some of the cancers for which we find similarity can be linked through primary, metastatic site relations. We investigate the similarity of enriched functional terms for the deregulated lncRNAs and the mRNAs. We further assess the enriched functions’ similarity to the functions and processes that the known cancer driver genes take place. We believe that our methodology help to understand the impact of the lncRNAs in cancer functionally.

scholarly journals Comprehensive Characterization And Clinical Relevance of CLEC4G Expression Across Human Cancers

2022 ◽  
Author(s):  
Yong Li ◽  
Huiqin Huang ◽  
Xiangli Ye ◽  
Xiaoping Li ◽  
Zhenghui Huang ◽  
...  
Keyword(s):  
Immune Response ◽  
Enrichment Analysis ◽  
Treg Cells ◽  
Renal Clear Cell Carcinoma ◽  
Human Cancers ◽  
Cancer Immunity ◽  
Cancer Types ◽  
Molecular Expression ◽  
Comprehensive Characterization

Abstract Liver and lymph node sinusoidal endothelial cell C-type lectin (CLEC4G) interacts with the surface glycoproteins of enveloped viruses and mediates immune evasion for viruses. Recent studies have indicated that the expression of CLEC4G affects the development and microenvironment of tumors. In the present study, we revealed comprehensive characterization of CLEC4G expression across human cancers. We first explored the effect of CLEC4G expression on overall survival (OS) across human cancers. High expression of CLEC4G was beneficial in lung adenocarcinoma (LUAD) and detrimental in kidney renal clear cell carcinoma (KIRC) and uveal melanoma (UVM) in terms of OS. Enrichment analysis of the 14 cancer-related signatures suggested that CLEC4G regulated tumor metastasis and immune response. Enrichment analysis of the immunophenotypes and cancer-immunity cycles indicated that CLEC4G was involved in regulation of macrophages and Treg cells, which affected tumor immune response. We also observed correlations between CLEC4G expression and checkpoint molecular expression in different cancer types. Taken together, the present study revealed the comprehensive characterization of CLEC4G expression across human cancers, predicting the roles of CLEC4G in the development and immune microenvironment of tumors.

IMPROVEMENT OF SPRING DURUM WHEAT SELECTION METHODOLOGIES UNDER CLIMATE CHANGE CONDITIONS

1970 ◽  
pp. 33-36
Author(s):  
А. I. Grabovets ◽  
V. P. Kadushkina ◽  
S. А. Kovalenko
Keyword(s):  
Grain Yield ◽  
Durum Wheat ◽  
Correlation Coefficient ◽  
Harvest Index ◽  
Unit Area ◽  
Correlation Coefficients ◽  
Chemical Mutagenesis ◽  
Main Method ◽  
The Relationship ◽  
Selection Of

With the growing aridity of the climate on the Don, it became necessary to improve the methodology for conducting the  breeding of spring durum wheat. The main method of obtaining the source material remains intraspecific step hybridization. Crossings were performed between genetically distant forms, differing in origin and required traits and properties. The use of chemical mutagenesis was a productive way to change the heredity of genotypes in terms of drought tolerance. When breeding for productivity, both in dry years of research and in favorable years, the most objective markers were identified — the size of the aerial mass, the mass of grain per plant, spike, and harvest index. The magnitude of the correlation coefficients between the yield per unit area and the elements of its structure is established. It was most closely associated with them in dry years, while in wet years it decreased. Power the correlation of the characteristics of the pair - the grain yield per square meter - the aboveground biomass averaged r = 0.73, and in dry years it was higher (0.91) than in favorable ones (0.61 - 0.70) , between the harvest and the harvest index - r = 0.81 (on average). In dry years, the correlation coefficient increased to 0.92. Research data confirms the greatest importance of the mass of grain from one ear and the plant in the formation of grain yield per unit area in both dry and wet years. In dry years, the correlation coefficient between yield and grain mass per plant was on average r = 0.80; in favorable years, r = 0.69. The relationship between yield and grain mass from the ear was greater — r = 0.84 and r = 0.82, respectively. Consequently, the breeding significance of the aboveground mass and the productivity of the ear, as a criterion for the selection of the crop, especially increases in the dry years. They were basic in the selection.

Cancer in agricultural populations

2020 ◽  
pp. 837-837
Author(s):  
K. . Togawa
Keyword(s):  
Risk Factors ◽  
General Population ◽  
Cohort Studies ◽  
Health Effects ◽  
Cancer Incidence ◽  
Lower Prevalence ◽  
International Consortium ◽  
Adverse Health Effects ◽  
Specific Cancer ◽  
Cancer Types

Agricultural workers can be exposed to a wide variety of agents (e.g. pesticides), some of which may have adverse health effects, such as cancer. To study the health effects of agricultural exposures, an international consortium of agricultural cohort studies, AGRICOH, was established. The present analysis compared cancer incidence between the AGRICOH cohorts and the general population and found lower overall cancer incidence in the AGRICOH cohorts, with some variation across cohorts for specific cancer types. The observed lower cancer incidence may be due to healthy worker bias or lower prevalence of risk factors in the agricultural populations. Further analysis is underway.

A FORECAST OF PRODUCTIVE LONGEVITY OF HOLSTEIN COWS BY INDIRECT SIGNS

2020 ◽  
Author(s):  
З.С. САНОВА
Keyword(s):  
Correlation Coefficient ◽  
Aging Process ◽  
Direct Relationship ◽  
Stability Index ◽  
Age At First Calving ◽  
Group I ◽  
Predicted Values ◽  
The Stability ◽  
Relationship Of ◽  
The Relationship

В статье представлены материалы о взаимосвязи продолжительности продуктивного использования коров с характеристикой устойчивости к деградации, с возрастом отела и удоем. В исследованной, разнородной по происхождению, группе животных для прогноза продуктивного периода коров, обусловленного устойчивостью к деградации и возрастом первого отела, пригодно уравнение регрессии, аргументами в котором являются индекс устойчивости, возраст первого отела в первой и второй степенях. Коэффициент корреляции межу предсказанными значениями продуктивного периода и его фактическими величинами в I группе составляет 0,502, во II - 0,604. При этом крайние варианты прогнозируются со статистическими ошибками 5 мес при оценке индекса устойчивости по 2 лактациям и 4,1 мес по 3, а средние варианты, соответственно, 1,6 и 1,51 мес. Индекс устойчивости к процессу старения является важной характеристикой биологических особенностей коров, определяющий их продуктивное долголетие. Его оценка по первым 2 и 3 лактациям имеет прямолинейную связь с продуктивным периодом (r=0,4109 и r=0,5270), соответственно. Зависимость продуктивного периода от возраста первого отела криволинейная — с увеличением возраста первого отела сокращается срок продуктивного использования, при возрасте первого отела более 1400 дней срок продуктивного использования колеблется от 1,33 до 1,41 лактации. Коэффициент корреляции между этими характеристиками коров составляет - 0,2164 в I и - 0,2620 во II группах. The article presents materials about the relationship of the duration of productive use of cows with the characteristic of resistance to degradation, with the age of calving and milk yield. In the studied group of animals, which is heterogeneous in origin, the regression equation is suitable for predicting the productive period of cows due to resistance to degradation and the age of the first calving, the arguments of which are the stability index, the age of the first calving in the first and second degrees. The correlation coefficient between the predicted values of the productive period and its actual values in group I is 0.502, in group II - 0.604. At the same time, the extreme variants are predicted with statistical errors of 5 months when evaluating the stability index for 2 lactations and 4.1 months for 3, and the average variants, respectively, are 1.6 and 1.51 months. The index of resistance to the aging process is an important characteristic of the biological characteristics of cows, which determines their productive longevity. Its estimate for the first 2 and 3 lactations has a direct relationship with the productive period (r=0.4109 and r=0.5270), respectively. The dependence of the productive period age at first calving curvilinear with increasing age at first calving reduces the time to productive use, while age at first calving of more than 1400 days, the period of productive use ranges from 1.33 to 1.41 lactation. The correlation coefficient between these characteristics of cows is-0.2164 in I and-0.2620 in II groups.

scholarly journals The correlation between lncRNAs and Helicobacter pylori in gastric cancer

2019 ◽  
Vol 77 (9) ◽  
Author(s):  
Narges Dastmalchi ◽  
Seyed Mahdi Banan Khojasteh ◽  
Mirsaed Miri Nargesi ◽  
Reza Safaralizadeh
Keyword(s):  
Gastric Cancer ◽  
Helicobacter Pylori ◽  
Molecular Mechanisms ◽  
Gastrointestinal Diseases ◽  
Mechanisms Of Action ◽  
Molecular Pathways ◽  
Gastric Diseases ◽  
Non Coding Rnas ◽  
H Pylori ◽  
The Relationship

ABSTRACT Helicobacter pylori infection performs a key role in gastric tumorigenesis. Long non-coding RNAs (lncRNAs) have demonstrated a great potential to be regarded as effective malignancy biomarkers for various gastrointestinal diseases including gastric cancer (GC). The present review highlights the relationship between lncRNAs and H. pylori in GC. Several studies have examined not only the involvement of lncRNAs in H. pylori-associated GC progression but also their molecular mechanisms of action. Among the pertinent studies, some have addressed the effects of H. pylori infection on modulatory networks of lncRNAs, while others have evaluated the effects of changes in the expression level of lncRNAs in H. pylori-associated gastric diseases, especially GC. The relationship between lncRNAs and H. pylori was found to be modulated by various molecular pathways.

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