scholarly journals Network Properties for Ranking Predicted miRNA Targets in Breast Cancer

2009 ◽  
Vol 2009 ◽  
pp. 1-7 ◽  
Author(s):  
Jörg Linde ◽  
Björn Olsson ◽  
Zelmina Lubovac
Keyword(s):  
Breast Cancer ◽  
Target Genes ◽  
State Of The Art ◽  
Translational Repression ◽  
Prediction Methods ◽  
Biological Processes ◽  
Computer Prediction ◽  
Prediction Tools ◽  
Network Properties

MicroRNAs control the expression of their target genes by translational repression and transcriptional cleavage. They are involved in various biological processes including development and progression of cancer. To uncover the biological role of miRNAs it is important to identify their target genes. The small number of experimentally validated target genes makes computer prediction methods very important. However, state-of-the-art prediction tools result in a great number of putative targets with an unpredictable number of false positives. In this paper, we propose and evaluate two approaches for ranking the biological relevance of putative targets of miRNAs which are associated with breast cancer.

scholarly journals Emerging multifaceted roles of BAP1 complexes in biological processes

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Aileen Patricia Szczepanski ◽  
Lu Wang
Keyword(s):  
Transcriptional Repression ◽  
Target Genes ◽  
Regulatory Mechanisms ◽  
Biological Processes ◽  
Multiprotein Complex ◽  
Downstream Target ◽  
Evolutionarily Conserved ◽  
Complex Forms ◽  
Polycomb Repressive Complex 1

AbstractHistone H2AK119 mono-ubiquitination (H2AK119Ub) is a relatively abundant histone modification, mainly catalyzed by the Polycomb Repressive Complex 1 (PRC1) to regulate Polycomb-mediated transcriptional repression of downstream target genes. Consequently, H2AK119Ub can also be dynamically reversed by the BAP1 complex, an evolutionarily conserved multiprotein complex that functions as a general transcriptional activator. In previous studies, it has been reported that the BAP1 complex consists of important biological roles in development, metabolism, and cancer. However, identifying the BAP1 complex’s regulatory mechanisms remains to be elucidated due to its various complex forms and its ability to target non-histone substrates. In this review, we will summarize recent findings that have contributed to the diverse functional role of the BAP1 complex and further discuss the potential in targeting BAP1 for therapeutic use.

scholarly journals FcircSEC: An R Package for Full Length circRNA Sequence Extraction and Classification

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Md. Tofazzal Hossain ◽  
Yin Peng ◽  
Shengzhong Feng ◽  
Yanjie Wei
Keyword(s):  
State Of The Art ◽  
Gene Annotation ◽  
R Package ◽  
Full Length ◽  
Circular Rnas ◽  
Prediction Methods ◽  
Rna Molecules ◽  
Prediction Tools

Circular RNAs (circRNAs) are formed by joining the 3′ and 5′ ends of RNA molecules. Identification of circRNAs is an important part of circRNA research. The circRNA prediction methods can predict the circRNAs with start and end positions in the chromosome but cannot identify the full-length circRNA sequences. We present an R package FcircSEC (Full Length circRNA Sequence Extraction and Classification) to extract the full-length circRNA sequences based on gene annotation and the output of any circRNA prediction tools whose output has a chromosome, start and end positions, and a strand for each circRNA. To validate FcircSEC, we have used three databases, circbase, circRNAdb, and plantcircbase. With information such as the chromosome and strand of each circRNA as the input, the identified sequences by FcircSEC are consistent with the databases. The novelty of FcircSEC is that it can take the output of state-of-the-art circRNA prediction tools as input and is applicable for human and other species. We also classify the circRNAs as exonic, intronic, and others. The R package FcircSEC is freely available.

scholarly journals Hypoxia and HIF Signaling: One Axis with Divergent Effects

2020 ◽  
Vol 21 (16) ◽  
pp. 5611 ◽  
Author(s):  
Chiara Corrado ◽  
Simona Fontana
Keyword(s):  
Cellular Response ◽  
Target Genes ◽  
Hypoxia Inducible Factor ◽  
Biological Processes ◽  
Oxygen Homeostasis ◽  
Tissue Responses ◽  
Liver And Kidney ◽  
Heterodimeric Complex ◽  
Complex Activities

The correct concentration of oxygen in all tissues is a hallmark of cellular wellness, and the negative regulation of oxygen homeostasis is able to affect the cells and tissues of the whole organism. The cellular response to hypoxia is characterized by the activation of multiple genes involved in many biological processes. Among them, hypoxia-inducible factor (HIF) represents the master regulator of the hypoxia response. The active heterodimeric complex HIF α/β, binding to hypoxia-responsive elements (HREs), determines the induction of at least 100 target genes to restore tissue homeostasis. A growing body of evidence demonstrates that hypoxia signaling can act by generating contrasting responses in cells and tissues. Here, this dual and controversial role of hypoxia and the HIF signaling pathway is discussed, with particular reference to the effects induced on the complex activities of the immune system and on mechanisms determining cell and tissue responses after an injury in both acute and chronic human diseases related to the heart, lung, liver, and kidney.

scholarly journals High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Md. Tariqul Islam ◽  
Ahlan Sabah Ferdous ◽  
Rifat Ara Najnin ◽  
Suprovath Kumar Sarker ◽  
Haseena Khan
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Kegg Pathway ◽  
Translational Repression ◽  
Biological Processes ◽  
Rt Pcr ◽  
Stem Loop ◽  
Evolutionarily Conserved ◽  
Pathway Analyses ◽  
Species Specific

MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.

scholarly journals Role of miR-10b-5p in the prognosis of breast cancer

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7728 ◽  
Author(s):  
Junmin Wang ◽  
Yanyun Yan ◽  
Zhiqi Zhang ◽  
Yali Li
Keyword(s):  
Breast Cancer ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cancer Development ◽  
Clinicopathological Parameters ◽  
Aberrant Expression ◽  
Expression Levels ◽  
Ppi Networks

Breast cancer is the leading cause of cancer-related death in women worldwide. Aberrant expression levels of miR-10b-5p in breast cancer has been reported while the molecular mechanism of miR-10b-5p in tumorigenesis remains elusive. Therefore, this study was aimed to investigate the role of miR-10b-5p in breast cancer and the network of its target genes using bioinformatics analysis. In this study, the expression profiles and prognostic value of miR-10b-5p in breast cancer were analyzed from public databases. Association between miR-10b-5p and clinicopathological parameters were analyzed by non-parametric test. Moreover, the optimal target genes of miR-10b-5p were obtained and their expression patterns were examined using starBase and HPA database. Additionally, the role of these target genes in cancer development were explored via Cancer Hallmarks Analytics Tool (CHAT). The protein–protein interaction (PPI) networks were constructed to further investigate the interactive relationships among these genes. Furthermore, GO, KEGG pathway and Reactome pathway analyses were carried out to decipher functions of these target genes. Results demonstrated that miR-10b-5p was down-regulated in breast cancer and low expression of miR-10b-5p was significantly correlated to worse outcome. Five genes, BIRC5, E2F2, KIF2C, FOXM1, and MCM5, were considered as potential key target genes of miR-10b-5p. As expected, higher expression levels of these genes were observed in breast cancer tissues than in normal tissues. Moreover, analysis from CHAT revealed that these genes were mainly involved in sustaining proliferative signaling in cancer development. In addition, PPI networks analysis revealed strong interactions between target genes. GO, KEGG, and Reactome pathway analysis suggested that these target genes of miR-10b-5p in breast cancer were significantly involved in cell cycle. Predicted target genes were further validated by qRT-PCR analysis in human breast cancer cell line MDA-MB-231 transfected with miR-10b mimic or antisense inhibitors. Taken together, our data suggest that miR-10b-5p functions to impede breast carcinoma progression via regulation of its key target genes and hopefully serves as a potential diagnostic and prognostic marker for breast cancer.

scholarly journals The Role of PARPs in Inflammation—and Metabolic—Related Diseases: Molecular Mechanisms and Beyond

Cells ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 1047 ◽  
Author(s):  
Ke ◽  
Wang ◽  
Zhang ◽  
Zhong ◽  
Wang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cardiovascular Disease ◽  
Ovarian Cancer ◽  
Molecular Mechanisms ◽  
Parp Inhibition ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Cancer Breast ◽  
Promising Strategy

Poly(ADP-ribosyl)ation (PARylation) is an essential post-translational modification catalyzed by poly(ADP-ribose) polymerase (PARP) enzymes. Poly(ADP-ribose) polymerase 1 (PARP1) is a well-characterized member of the PARP family. PARP1 plays a crucial role in multiple biological processes and PARP1 activation contributes to the development of various inflammatory and malignant disorders, including lung inflammatory disorders, cardiovascular disease, ovarian cancer, breast cancer, and diabetes. In this review, we will focus on the role and molecular mechanisms of PARPs enzymes in inflammation- and metabolic-related diseases. Specifically, we discuss the molecular mechanisms and signaling pathways that PARP1 is associated with in the regulation of pathogenesis. Recently, increasing evidence suggests that PARP inhibition is a promising strategy for intervention of some diseases. Thus, our in-depth understanding of the mechanism of how PARPs are activated and how their signaling downstream effecters can provide more potential therapeutic targets for the treatment of the related diseases in the future is crucial.

scholarly journals Modulated Autophagy by MicroRNAs in Osteoarthritis Chondrocytes

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Yinghao Yu ◽  
Jijun Zhao
Keyword(s):  
Target Genes ◽  
Cartilage Degradation ◽  
Joint Disease ◽  
Future Research ◽  
Biological Processes ◽  
Small Noncoding Rnas ◽  
New Directions ◽  
Osteoarthritis Chondrocytes ◽  
Cell Signaling Pathways

Osteoarthritis (OA) is a chronic joint disease characterized by articular cartilage regression. The etiology of OA is diverse, the exact pathogenesis of which remains unclear. Autophagy is a conserved maintenance mechanism in eukaryotic cells. Dysfunction of chondrocyte autophagy is regarded as a crucial pathogenesis of cartilage degradation in OA. MircoRNAs (miRNAs) are a category of small noncoding RNAs, acting as posttranscriptional modulators that regulate biological processes and cell signaling pathways via target genes. A series of miRNAs are involved in the progression of chondrocyte autophagy and are connected with numerous factors and pathways. This article focuses on the mechanisms of chondrocyte autophagy in OA and reviews the role of miRNA in their modulation. Potentially relevant miRNAs are also discussed in order to provide new directions for future research and improve our understanding of the autophagic network of miRNAs.

scholarly journals In vivo NCL targeting affects breast cancer aggressiveness through miRNA regulation

2013 ◽  
Vol 210 (5) ◽  
pp. 951-968 ◽  
Author(s):  
Flavia Pichiorri ◽  
Dario Palmieri ◽  
Luciana De Luca ◽  
Jessica Consiglio ◽  
Jia You ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Target Genes ◽  
Human Cancer ◽  
Mirna Regulation ◽  
Altered Expression ◽  
Specific Subset ◽  
Cancer Aggressiveness

Numerous studies have described the altered expression and the causal role of microRNAs (miRNAs) in human cancer. However, to date, efforts to modulate miRNA levels for therapeutic purposes have been challenging to implement. Here we find that nucleolin (NCL), a major nucleolar protein, posttranscriptionally regulates the expression of a specific subset of miRNAs, including miR-21, miR-221, miR-222, and miR-103, that are causally involved in breast cancer initiation, progression, and drug resistance. We also show that NCL is commonly overexpressed in human breast tumors and that its expression correlates with that of NCL-dependent miRNAs. Finally, inhibition of NCL using guanosine-rich aptamers reduces the levels of NCL-dependent miRNAs and their target genes, thus reducing breast cancer cell aggressiveness both in vitro and in vivo. These findings illuminate a path to novel therapeutic approaches based on NCL-targeting aptamers for the modulation of miRNA expression in the treatment of breast cancer.

scholarly journals The Dual Regulatory Role of MiR-181a in Breast Cancer

2017 ◽  
Vol 44 (3) ◽  
pp. 843-856 ◽  
Author(s):  
Chun Yang ◽  
Seyed Nasrollah Tabatabaei ◽  
Xiangyan Ruan ◽  
Pierre Hardy
Keyword(s):  
Breast Cancer ◽  
Target Genes ◽  
Tumor Development ◽  
Biological Significance ◽  
Transcriptional Level ◽  
Rna Molecules ◽  
Breast Tumor Tissue ◽  
Transcriptional Gene Regulation ◽  
Breast Cancer Gene

MicroRNAs (miRNAs) are a family of highly conserved noncoding single˗stranded RNA molecules of 21 to 25 nucleotides. miRNAs silence their cognate target genes at the post-transcriptional level and have been shown to have important roles in oncogenesis, invasion, and metastasis via epigenetic post-transcriptional gene regulation. Recent evidence indicates that the expression of miR-181a is altered in breast tumor tissue and in the serum of patients with breast cancer. However, there are several contradicting findings that challenge the biological significance of miR-181a in tumor development and metastasis. In fact, some studies have implicated miR-181a in regulating breast cancer gene expression. Here we summarize the current literature demonstrating established links between miR-181a and human breast cancer with a focus on recently identified mechanisms of action. This review also aims to explore the potential of miR-181a as a diagnostic and/or prognostic biomarker for breast cancer and to discuss the contradicting data regarding its targeting therapeutics and the associated challenges.

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