KGRACDA: A Model Based on Knowledge Graph from Recursion and Attention Aggregation for CircRNA-disease Association Prediction DOI
Ying Wang,

Maoyuan Ma,

Yanxin Xie

et al.

IEEE/ACM Transactions on Computational Biology and Bioinformatics, Journal Year: 2024, Volume and Issue: 21(6), P. 2133 - 2144

Published: Aug. 21, 2024

CircRNA is closely related to human disease, so it important predict circRNA-disease association (CDA). However, the traditional biological detection methods have high difficulty and low accuracy, computational represented by deep learning ignore ability of model explicitly extract local depth information CDA. We propose a based on knowledge graph from recursion attention aggregation for prediction (KGRACDA). This combines explicit structural features implicit embedding graphs, optimizing vectors. First, we built large-scale, multi-source heterogeneous datasets construct multiple RNAs diseases. After that, use recursive method build multi-hop subgraphs optimize mechanism gating mechanism, mining information. At same time, uses multi-head balance global generate CDA scores. KGRACDA surpasses other capturing update an interactive web platform HNRBase v2.0, which visualizes circRNA data, allows users download data using model.

Language: Английский

Regulatory mechanisms of circular RNAs during human mesenchymal stem cell osteogenic differentiation DOI Creative Commons
Chiara Mazziotta, Giada Badiale,

Christian Felice Cervellera

et al.

Theranostics, Journal Year: 2023, Volume and Issue: 14(1), P. 143 - 158

Published: Nov. 15, 2023

Human osteogenic differentiation is a complex and well-orchestrated process which involves plethora of molecular players cellular processes.A growing number studies have underlined that circular RNAs (circRNAs) play an important regulatory role during human differentiation.CircRNAs are single-stranded, covalently closed non-coding RNA molecules acquiring increased attention as epigenetic regulators gene expression.Given their intrinsic high conformational stability, abundance, specificity, circRNAs can undertake various biological activities in order to regulate multiple processes, including differentiation.The most recent evidence indicates control osteogenesis by preventing the inhibitory activity miRNAs on downstream target genes, using competitive endogenous mechanism.The aim this review draw currently known mechanisms differentiation.Specifically, we provide understanding advances research conducted mesenchymal stem cell types importance regulating osteogenesis.A comprehensive underlying circRNA will improve knowledge processes bone growth, resulting potential development novel preclinical clinical discovery diagnostic therapeutic tools for disorders.

Language: Английский

Citations

32
Biomarker potential of competing endogenous RNA networks in Polycystic Ovary Syndrome (PCOS) DOI Creative Commons
Roozbeh Heidarzadehpilehrood, Maryam Pirhoushiaran

Non-coding RNA Research, Journal Year: 2024, Volume and Issue: 9(2), P. 624 - 640

Published: Jan. 17, 2024

Polycystic ovary syndrome (PCOS) is the most common condition affecting women of reproductive age globally. PCOS continues to be largest contributing factor female infertility despite significant progress in our knowledge molecular underpinnings and treatment condition. The fact that a very diverse makes it one key reasons why we haven't been able overcome it. Non-coding RNAs (ncRNAs) are implicated development PCOS, according growing evidence. However, unclear how complex regulatory relationships between many ncRNA types contribute growth this malignancy. Competing endogenous RNA (ceRNA), recently identified mechanism world, suggests interactions various RNAs, including long non-coding (lncRNAs), microRNAs (miRNAs), transcribed pseudogenes, circular (circRNAs). Recent studies on have shown dysregulation multiple ceRNA networks (ceRNETs) these ncRNAs plays crucial roles developing defining characteristics development. And believed such finding may open new door for deeper comprehension PCOS's unexplored facets. In addition, provide fresh biomarkers effective therapy targets PCOS. This review will go over body information exists about primary ceRNETs before highlighting involvement several newly found number characteristics.

Language: Английский

Citations

12
CircPVT1 promotes periodontitis progression by regulating miR-24-3p/HIF1AN pathway DOI

Bian Yuting,

Yu Jingwen,

Yang Liu

et al.

Journal of Stomatology Oral and Maxillofacial Surgery, Journal Year: 2025, Volume and Issue: unknown, P. 102198 - 102198

Published: Feb. 1, 2025

Language: Английский

Citations

1
Ferroptosis and circular RNAs: new horizons in cancer therapy. DOI
Asif Ahmad Bhat,

Neelima Kukreti,

Muhammad Afzal

et al.

PubMed, Journal Year: 2024, Volume and Issue: 23, P. 570 - 599

Published: Jan. 1, 2024

Cancer poses intricate challenges to treatment due its complexity and diversity. Ferroptosis circular RNAs (circRNAs) are emerging as innovative therapeutic avenues amid the evolving landscape of cancer therapy. Extensive investigations into circRNAs reveal their diverse roles, ranging from molecular regulators pivotal influencers ferroptosis in cell lines. The results underscore significance modulating pathways that impact crucial aspects development, including survival, proliferation, metastasis. A detailed analysis delineates these pathways, shedding light on mechanisms through which influence ferroptosis. Building upon recent experimental findings, study evaluates potential targeting induce By identifying specific associated with etiology cancer, this paves way for development targeted therapeutics exploit vulnerabilities cells. This review consolidates existing understanding circRNAs, emphasizing role therapy providing impetus ongoing research dynamic field. See also graphical abstract(Fig. 1).

Language: Английский

Citations

7
Exploring the theranostic potentials of miRNA and epigenetic networks in autoimmune diseases: A comprehensive review DOI Creative Commons
Sagnik Nag, Oishi Mitra, G. Tripathi

et al.

Immunity Inflammation and Disease, Journal Year: 2023, Volume and Issue: 11(12)

Published: Dec. 1, 2023

Abstract Background Autoimmune diseases (AD) are severe pathophysiological ailments that stimulated by an exaggerated immunogenic response towards self‐antigens, which can cause systemic or site‐specific organ damage. An array of complex genetic and epigenetic facets majorly contributes to the progression AD, thus providing significant insight into regulatory mechanism microRNA (miRNA). miRNAs short, non‐coding RNAs have been identified as essential contributors post‐transcriptional regulation host genome expression crucial regulators a myriad biological processes such immune homeostasis, T helper cell differentiation, central peripheral tolerance, development. Aims This article tends deliberate conceptualize brief pathogenesis pertinent well miRNA networks affecting five different ADs namely rheumatoid arthritis (RA), type 1 diabetes, multiple sclerosis (MS), lupus erythematosus (SLE) inflammatory bowel disorder (IBD) thereby novel miRNA‐based theranostic interventions. Results & Discussion Pertaining differential attributed in target tissues cellular bodies innate adaptive immunity, paradigm scientific expeditions suggests optimistic correlation between dysfunction alterations. Conclusion Therefore, it is not astonishing dysregulations patterns now recognized wide spectrum disorders, establishing themselves potential biomarkers therapeutic targets. Owing its potencies, targets widely utilized development biosensors other molecules originating from same.

Language: Английский

Citations

16
The role of ncRNAs‐mediated pyroptosis in diabetes and its vascular complications DOI
Xinyao Feng, Xiaoxu Yang,

Yancheng Zhong

et al.

Cell Biochemistry and Function, Journal Year: 2024, Volume and Issue: 42(2)

Published: March 1, 2024

Abstract Over the past decade, prevalence of diabetes has increased significantly worldwide, leading to an increase in vascular complications (VCD), such as diabetic cardiomyopathy (DCM), nephropathy (DN), and retinopathy (DR). Noncoding RNAs (ncRNAs), microRNAs (miRNAs), long (lncRNAs), circular (circRNAs), play a key role cellular processes, including pathophysiology VCD via pyroptosis. ncRNAs (e.g., miR‐17, lnc‐MEG3, lnc‐KCNQ1OT1) can regulate pyroptosis pancreatic β cells. Some are involved progression. For example, miR‐21, lnc‐KCNQ1OT1, lnc‐GAS5, lnc‐MALAT1 were reported DN DCM, lnc‐MIAT was identified DCM DR. Herein, this review aimed summarize recent research findings related ncRNAs‐mediated at onset progression VCD.

Language: Английский

Citations

4
Revisiting Epigenetics Fundamentals and Its Biomedical Implications DOI Open Access
Thuluz Meza‐Menchaca,

Arnulfo Albores‐Medina,

Alma Jaqueline Heredia-Mendez

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(14), P. 7927 - 7927

Published: July 19, 2024

In light of the post-genomic era, epigenetics brings about an opportunity to better understand how molecular machinery works and is led by a complex dynamic set mechanisms, often intricate complementary in many aspects. particular, links developmental biology genetics, as well other areas knowledge. The present work highlights substantial scopes relevant discoveries related development term from its first notions. To our understanding, concept needs be revisited, it one most multifaceted terms human redirect future novel experimental or theoretical efforts, crucial compile all significant issues that could impact ecological benefit precise accurate manner. this paper, reader can find widest compilations landmarks epistemic considerations knowledge across history earliest epigenetic formulation genetic determinism until present. work, we link current body earlier pre-genomic concepts order propose new definition faithful regulatory nature.

Language: Английский

Citations

4
BloodCircR: A Comprehensive Database for Human Peripheral Blood Circular RNAs DOI Creative Commons

Shaoxun Yuan,

Wanjun Gu

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 7, 2025

Abstract Background: Blood circular RNAs (circRNAs) are stable, noncoding with diverse functional roles. However, a comprehensive resource for blood-derived circRNAs is lacking. We developed BloodCircR, database of from human peripheral blood, to support research on in disease and biomarker discovery. Methods: BloodCircR integrates identified 89 blood RNA-seq datasets, comprising 5,430 samples across 58 diseases categorized into 16 groups. Full-length were using CIRI-full supplemented data public databases. The platform provides detailed annotations tools exploring circRNA expression differential expression. Results: includes approximately 2.3 million circRNAs, which over 1.7 exonic. Most full-length, substantial proportion derived infectious datasets. Functional suggest their interactions miRNAs RNA-binding proteins, while analysis supports the investigation roles disease. Conclusions: offering significant insights potential as biomarkers therapeutic targets.

Language: Английский

Citations

0
High-fat diet triggers transcriptomic changes in the olfactory bulb DOI Creative Commons
Young‐Kook Kim, Danbi Jo,

Seoyoon Choi

et al.

Heliyon, Journal Year: 2025, Volume and Issue: 11(3), P. e42196 - e42196

Published: Jan. 22, 2025

Language: Английский

Citations

0
Prediction of circRNA–Disease Associations via Graph Isomorphism Transformer and Dual-Stream Neural Predictor DOI Creative Commons
Hongchan Li,

Yuchao Qian,

Zhongchuan Sun

et al.

Biomolecules, Journal Year: 2025, Volume and Issue: 15(2), P. 234 - 234

Published: Feb. 6, 2025

Circular RNAs (circRNAs) have attracted increasing attention for their roles in human diseases, making the prediction of circRNA-disease associations (CDAs) a critical research area advancing disease diagnosis and treatment. However, traditional experimental methods exploring CDAs are time-consuming resource-intensive, while existing computational models often struggle with sparsity CDA data fail to uncover potential effectively. To address these challenges, we propose novel method named Graph Isomorphism Transformer Dual-Stream Neural Predictor (GIT-DSP), which leverages knowledge graph technology predict more Specifically, model incorporates multiple between circRNAs, other non-coding (e.g., lncRNAs, miRNAs) construct multi-source heterogeneous graph, thereby expanding scope exploration. Subsequently, is proposed fully exploit both local global association information within enabling deeper insights into CDAs. Furthermore, introduced accurately complex by integrating dual-stream predictive features. Experimental results demonstrate that GIT-DSP outperforms state-of-the-art models, offering valuable precision medicine disease-related research.

Language: Английский

Citations

0