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Cardiomyopathies: The Role of Non-Coding RNAs. 心肌病:非编码 RNA 的作用。
IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-23 DOI: 10.3390/ncrna10060053
Nicole Carabetta, Chiara Siracusa, Isabella Leo, Giuseppe Panuccio, Antonio Strangio, Jolanda Sabatino, Daniele Torella, Salvatore De Rosa

Cardiomyopathies are the structural and functional disorders of the myocardium. Etiopathogenesis is complex and involves an interplay of genetic, environmental, and lifestyle factors eventually leading to myocardial abnormalities. It is known that non-coding (Nc) RNAs, including micro (mi)-RNAs and long non-coding (lnc) RNAs, play a crucial role in regulating gene expression. Several studies have explored the role of miRNAs in the development of various pathologies, including heart diseases. In this review, we analyzed various patterns of ncRNAs expressed in the most common cardiomyopathies: dilated cardiomyopathy, hypertrophic cardiomyopathy and arrhythmogenic cardiomyopathy. Understanding the role of different ncRNAs implicated in cardiomyopathic processes may contribute to the identification of potential therapeutic targets and novel risk stratification models based on gene expression. The analysis of ncRNAs may also be helpful to unveil the molecular mechanisms subtended to these diseases.

心肌病是心肌的结构和功能紊乱。发病机制复杂,涉及遗传、环境和生活方式等因素的相互作用,最终导致心肌异常。众所周知,非编码(Nc)RNA,包括微(mi)-RNA 和长非编码(lnc)RNA,在调节基因表达方面起着至关重要的作用。一些研究探讨了 miRNA 在包括心脏病在内的各种病症的发生发展中的作用。在这篇综述中,我们分析了最常见的心肌病:扩张型心肌病、肥厚型心肌病和心律失常性心肌病中表达的各种 ncRNAs 模式。了解不同的 ncRNA 在心肌病变过程中的作用有助于确定潜在的治疗靶点和基于基因表达的新型风险分层模型。对 ncRNA 的分析还有助于揭示这些疾病的分子机制。
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引用次数: 0
MicroRNA Biogenesis, Gene Regulation Mechanisms, and Availability in Foods. MicroRNA 的生物生成、基因调控机制和食品中的可用性。
IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-11 DOI: 10.3390/ncrna10050052
Amilton S de Mello, Bradley S Ferguson, Erica L Shebs-Maurine, Francine M Giotto

MicroRNAs (miRNAs) are small, non-coding RNAs that control gene expression by degrading or repressing mRNA translation into proteins. Research recently suggested that food-derived miRNAs are bioavailable and may be absorbed in the gastrointestinal tract (GIT). Since these small RNAs may reach the circulation and organs, possible interactions with host genes will lead to epigenetic effects that alter metabolism. Therefore, from a precision nutrition standpoint, exogenous miRNAs may be essential in modulating health status. This review summarizes the process of miRNA biogenesis, the post-translational mechanisms of gene regulation, and their bioavailability in animal- and plant-derived foods.

微小核糖核酸(miRNA)是一种小型非编码核糖核酸,可通过降解或抑制 mRNA 翻译成蛋白质来控制基因表达。最近的研究表明,从食物中提取的 miRNA 具有生物可利用性,可能会被胃肠道(GIT)吸收。由于这些小核糖核酸可能进入血液循环和器官,因此可能与宿主基因发生相互作用,从而产生改变新陈代谢的表观遗传效应。因此,从精准营养的角度来看,外源 miRNA 可能是调节健康状况的关键。本综述概述了 miRNA 的生物发生过程、基因翻译后的调控机制以及它们在动物和植物源性食品中的生物利用率。
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引用次数: 0
Interplay of microRNAs and circRNAs in Epithelial Ovarian Cancer. 上皮性卵巢癌中 microRNA 与 circRNA 的相互作用
IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-30 DOI: 10.3390/ncrna10050051
Heidi Schwarzenbach

Epithelial ovarian cancer (EOC) with its high death incidence rate is generally detected at advanced stages. During its progression, EOC often develops peritoneal metastasis aggravating the outcomes of EOC patients. Studies on non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and circular RNAs (circRNAs), have analyzed the impact of miRNAs and circRNAs, along with their interaction among each other, on cancer cells. MiRNAs can act as oncogenes or tumor suppressors modulating post-transcriptional gene expression. There is accumulating evidence that circRNAs apply their stable, covalently closed, continuous circular structures to competitively inhibit miRNA function, and so act as competing endogenous RNAs (ceRNAs). This interplay between both ncRNAs participates in the malignity of a variety of cancer types, including EOC. In the current review, I describe the characteristics of miRNAs and circRNAs, and discuss their interplay with each other in the development, progression, and drug resistance of EOC. Sponging of miRNAs by circRNAs may be used as a biomarker and therapeutic target in EOC.

上皮性卵巢癌(EOC)死亡率高,一般在晚期才被发现。在发展过程中,EOC 往往会发生腹膜转移,从而加重 EOC 患者的病情。对非编码 RNA(ncRNA),如 microRNA(miRNA)和环状 RNA(circRNA)的研究分析了 miRNA 和 circRNA 对癌细胞的影响以及它们之间的相互作用。MiRNA 可作为致癌基因或肿瘤抑制因子调节转录后基因的表达。越来越多的证据表明,circRNAs 利用其稳定、共价封闭、连续的环状结构竞争性地抑制 miRNA 的功能,从而成为竞争性的内源性 RNAs(ceRNAs)。这两种 ncRNA 之间的相互作用参与了包括 EOC 在内的多种癌症类型的恶性程度。在本综述中,我将描述miRNAs和circRNAs的特点,并讨论它们在EOC的发生、发展和耐药性中的相互作用。circRNAs对miRNAs的疏导作用可作为EOC的生物标志物和治疗靶点。
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引用次数: 0
Non-Coding RNA as a Biomarker in Lung Cancer. 作为肺癌生物标志物的非编码 RNA
IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-30 DOI: 10.3390/ncrna10050050
Chahat Suri, Shashikant Swarnkar, Lvks Bhaskar, Henu Kumar Verma

Introduction: Lung cancer remains one of the most prevalent and deadly cancers globally, with high mortality rates largely due to late-stage diagnosis, aggressive progression, and frequent recurrence. Despite advancements in diagnostic techniques and therapeutic interventions, the overall prognosis for lung cancer patients continues to be dismal.

Method: Emerging research has identified non-coding RNAs (ncRNAs), including microRNAs, long non-coding RNAs, and circular RNAs, as critical regulators of gene expression, significantly influencing cancer biology. These ncRNAs play pivotal roles in various aspects of lung cancer pathogenesis, including tumor initiation, progression, metastasis, and resistance to therapy.

Results: We provide a comprehensive analysis of the current understanding of ncRNAs in lung cancer, emphasizing their potential as biomarkers for early diagnosis, prognostication, and the prediction of the therapeutic response. We explore the biological functions of ncRNAs, their involvement in key oncogenic pathways, and the molecular mechanisms by which they modulate gene expression and cellular processes in lung cancer. Furthermore, this review highlights recent advances in ncRNA-based diagnostic tools and therapeutic strategies, such as miRNA mimics and inhibitors, lncRNA-targeted therapies, and circRNA-modulating approaches, offering promising avenues for personalized medicine.

Conclusion: Finally, we discuss the challenges and future directions in ncRNA research, including the need for large-scale validation studies and the development of efficient delivery systems for ncRNA-based therapies. This review underscores the potential of ncRNAs to revolutionize lung cancer management by providing novel diagnostic and therapeutic options that could improve patient outcomes.

简介肺癌仍然是全球发病率最高、最致命的癌症之一,死亡率高的主要原因是诊断晚、病情恶化和频繁复发。尽管诊断技术和治疗干预取得了进步,但肺癌患者的总体预后仍然不容乐观:方法:新近研究发现,非编码 RNA(ncRNA),包括 microRNA、长非编码 RNA 和环状 RNA,是基因表达的关键调控因子,对癌症生物学有重大影响。这些 ncRNA 在肺癌发病机制的各个方面,包括肿瘤的发生、发展、转移和抗药性中发挥着关键作用:我们全面分析了目前对肺癌 ncRNA 的认识,强调了它们作为早期诊断、预后判断和治疗反应预测的生物标志物的潜力。我们探讨了 ncRNA 的生物学功能、它们参与关键致癌通路的情况,以及它们调节肺癌基因表达和细胞过程的分子机制。此外,本综述还重点介绍了基于ncRNA的诊断工具和治疗策略的最新进展,如miRNA模拟物和抑制剂、lncRNA靶向疗法和circRNA调节方法,为个性化医疗提供了前景广阔的途径:最后,我们讨论了 ncRNA 研究面临的挑战和未来发展方向,包括需要进行大规模验证研究和开发基于 ncRNA 疗法的高效传递系统。这篇综述强调了 ncRNA 通过提供可改善患者预后的新型诊断和治疗方案而彻底改变肺癌治疗的潜力。
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引用次数: 0
Back to the Origin: Mechanisms of circRNA-Directed Regulation of Host Genes in Human Disease. 回到起源:人类疾病中宿主基因的 circRNA 定向调控机制。
IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-24 DOI: 10.3390/ncrna10050049
Haomiao Yuan, Xizhou Liao, Ding Hu, Dawei Guan, Meihui Tian

Circular RNAs (circRNAs) have been shown to be pivotal regulators in various human diseases by participating in gene splicing, acting as microRNA (miRNA) sponges, interacting with RNA-binding proteins (RBPs), and translating into short peptides. As the back-splicing products of pre-mRNAs, many circRNAs can modulate the expression of their host genes through transcriptional, post-transcriptional, translational, and post-translational control via interaction with other molecules. This review provides a detailed summary of these regulatory mechanisms based on the class of molecules that they interact with, which encompass DNA, mRNA, miRNA, and RBPs. The co-expression of circRNAs with their parental gene productions (including linear counterparts and proteins) provides potential diagnostic biomarkers for multiple diseases. Meanwhile, the different regulatory mechanisms by which circRNAs act on their host genes via interaction with other molecules constitute complex regulatory networks, which also provide noticeable clues for therapeutic strategies against diseases. Future research should explore whether these proven mechanisms can play a similar role in other types of disease and clarify further details about the cross-talk between circRNAs and host genes. In addition, the regulatory relationship between circRNAs and their host genes in circRNA circularization, degradation, and cellular localization should receive further attention.

研究表明,环状 RNA(circRNA)通过参与基因剪接、充当微 RNA(miRNA)海绵、与 RNA 结合蛋白(RBPs)相互作用以及翻译成短肽等方式,成为各种人类疾病的关键调控因子。作为前 mRNA 的反向剪接产物,许多 circRNA 可通过与其他分子相互作用,通过转录、转录后、翻译和翻译后控制来调节宿主基因的表达。本综述根据与之相互作用的分子类别(包括 DNA、mRNA、miRNA 和 RBPs)详细总结了这些调控机制。circRNA 与其亲代基因产物(包括线性对应物和蛋白质)的共同表达为多种疾病提供了潜在的诊断生物标志物。同时,circRNA 通过与其他分子相互作用而作用于宿主基因的不同调控机制构成了复杂的调控网络,这也为疾病的治疗策略提供了重要线索。未来的研究应探索这些已被证实的机制是否能在其他类型的疾病中发挥类似作用,并进一步阐明 circRNA 与宿主基因之间的交叉对话细节。此外,circRNA 及其宿主基因在 circRNA 环化、降解和细胞定位过程中的调控关系也应得到进一步关注。
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引用次数: 0
Circulating miRNAs in the Plasma of Post-COVID-19 Patients with Typical Recovery and Those with Long-COVID Symptoms: Regulation of Immune Response-Associated Pathways. COVID-19后典型恢复期和长期COVID症状患者血浆中的循环miRNA:免疫反应相关通路的调控。
IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-02 DOI: 10.3390/ncrna10050048
Anna M Timofeeva, Artem O Nikitin, Georgy A Nevinsky

Following the acute phase of SARS-CoV-2 infection, certain individuals experience persistent symptoms referred to as long COVID. This study analyzed the patients categorized into three distinct groups: (1) individuals presenting rheumatological symptoms associated with long COVID, (2) patients who have successfully recovered from COVID-19, and (3) donors who have never contracted COVID-19. A notable decline in the expression of miR-200c-3p, miR-766-3p, and miR-142-3p was identified among patients exhibiting rheumatological symptoms of long COVID. The highest concentration of miR-142-3p was found in healthy donors. One potential way to reduce miRNA concentrations is through antibody-mediated hydrolysis. Not only can antibodies possessing RNA-hydrolyzing activity recognize the miRNA substrate specifically, but they also catalyze its hydrolysis. The analysis of the catalytic activity of plasma antibodies revealed that antibodies from patients with long COVID demonstrated lower hydrolysis activity against five fluorescently labeled oligonucleotide sequences corresponding to the Flu-miR-146b-5p, Flu-miR-766-3p, Flu-miR-4742-3p, and Flu-miR-142-3p miRNAs and increased activity against the Flu-miR-378a-3p miRNA compared to other patient groups. The changes in miRNA concentrations and antibody-mediated hydrolysis of miRNAs are assumed to have a complex regulatory mechanism that is linked to gene pathways associated with the immune system. We demonstrate that all six miRNAs under analysis are associated with a large number of signaling pathways associated with immune response-associated pathways.

在感染 SARS-CoV-2 的急性期后,某些人会出现持续性症状,称为长 COVID。本研究将患者分为三类进行分析:(1)出现与长COVID相关的风湿病症状的人;(2)从COVID-19中成功康复的患者;(3)从未感染过COVID-19的捐献者。研究发现,在出现长期 COVID 风湿症状的患者中,miR-200c-3p、miR-766-3p 和 miR-142-3p 的表达量明显下降。健康供体中的 miR-142-3p 浓度最高。降低 miRNA 浓度的一个潜在方法是通过抗体介导的水解作用。具有 RNA 水解活性的抗体不仅能特异性识别 miRNA 底物,还能催化其水解。对血浆抗体催化活性的分析表明,与其他患者组相比,长COVID患者的抗体对对应于Flu-miR-146b-5p、Flu-miR-766-3p、Flu-miR-4742-3p和Flu-miR-142-3p miRNA的五个荧光标记寡核苷酸序列的水解活性较低,而对Flu-miR-378a-3p miRNA的水解活性较高。miRNA浓度的变化和抗体介导的miRNA水解被认为具有复杂的调节机制,与免疫系统相关的基因通路有关。我们证明,所分析的所有六种 miRNA 都与大量与免疫反应相关的信号通路有关。
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引用次数: 0
The Circulating miR-107 as a Potential Biomarker Up-Regulated in Castration-Resistant Prostate Cancer. 循环 miR-107 作为阉割耐药前列腺癌的一种潜在生物标记物
IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-24 DOI: 10.3390/ncrna10050047
Jonathan Puente-Rivera, David Alejandro De la Rosa Pérez, Stephanie I Nuñez Olvera, Elisa Elvira Figueroa-Angulo, José Gadú Campos Saucedo, Omar Hernández-León, María Elizbeth Alvarez-Sánchez

Prostate cancer (PCa) is a prevalent malignancy in men globally. Current diagnostic methods like PSA testing have limitations, leading to overdiagnosis and unnecessary treatment. Castration-resistant prostate cancer (CRPC) emerges in some patients receiving androgen deprivation therapy (ADT). This study explores the potential of circulating microRNA-107 (miR-107) in liquid biopsies as a prognosis tool to differentiate CRPC from non-castration-resistant PCa (NCRPC). We designed a case-control study to evaluate circulating miR-107 in serum as a potential prognosis biomarker. We analyzed miR-107 expression in liquid biopsies and found significantly higher levels (p < 0.005) in CRPC patients, compared to NCRPC. Notably, miR-107 expression was statistically higher in the advanced stage (clinical stage IV), compared to stages I-III. Furthermore, CRPC patients exhibited significantly higher miR-107 levels (p < 0.05), compared to NCRPC. These findings suggest that miR-107 holds promise as a non-invasive diagnostic biomarker for identifying potential CRPC patients.

前列腺癌(PCa)是全球普遍存在的男性恶性肿瘤。目前的诊断方法(如 PSA 检测)存在局限性,导致过度诊断和不必要的治疗。一些接受雄激素剥夺疗法(ADT)的患者会出现阉割抗性前列腺癌(CRPC)。本研究探讨了液体活检中循环microRNA-107(miR-107)作为预后工具的潜力,以区分CRPC和非阉割耐药PCa(NCRPC)。我们设计了一项病例对照研究,以评估血清中作为潜在预后生物标志物的循环 miR-107。我们分析了液体活检中的 miR-107 表达,发现 CRPC 患者的 miR-107 表达水平明显高于 NCRPC(P < 0.005)。值得注意的是,与I-III期相比,晚期(临床IV期)患者的miR-107表达在统计学上更高。此外,与 NCRPC 相比,CRPC 患者的 miR-107 水平明显更高(p < 0.05)。这些研究结果表明,miR-107有望成为识别潜在CRPC患者的非侵入性诊断生物标志物。
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引用次数: 0
MicroRNA Profiling as a Predictive Indicator for Time to First Treatment in Chronic Lymphocytic Leukemia: Insights from the O-CLL1 Prospective Study. 微RNA图谱分析作为慢性淋巴细胞白血病首次治疗时间的预测指标:O-CLL1前瞻性研究的启示。
IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-23 DOI: 10.3390/ncrna10050046
Ennio Nano, Francesco Reggiani, Adriana Agnese Amaro, Paola Monti, Monica Colombo, Nadia Bertola, Fabiana Ferrero, Franco Fais, Antonella Bruzzese, Enrica Antonia Martino, Ernesto Vigna, Noemi Puccio, Mariaelena Pistoni, Federica Torricelli, Graziella D'Arrigo, Gianluigi Greco, Giovanni Tripepi, Carlo Adornetto, Massimo Gentile, Manlio Ferrarini, Massimo Negrini, Fortunato Morabito, Antonino Neri, Giovanna Cutrona

A "watch and wait" strategy, delaying treatment until active disease manifests, is adopted for most CLL cases; however, prognostic models incorporating biomarkers have shown to be useful to predict treatment requirement. In our prospective O-CLL1 study including 224 patients, we investigated the predictive role of 513 microRNAs (miRNAs) on time to first treatment (TTFT). In the context of this study, six well-established variables (i.e., Rai stage, beta-2-microglobulin levels, IGVH mutational status, del11q, del17p, and NOTCH1 mutations) maintained significant associations with TTFT in a basic multivariable model, collectively yielding a Harrell's C-index of 75% and explaining 45.4% of the variance in the prediction of TTFT. Concerning miRNAs, 73 out of 513 were significantly associated with TTFT in a univariable model; of these, 16 retained an independent relationship with the outcome in a multivariable analysis. For 8 of these (i.e., miR-582-3p, miR-33a-3p, miR-516a-5p, miR-99a-5p, and miR-296-3p, miR-502-5p, miR-625-5p, and miR-29c-3p), a lower expression correlated with a shorter TTFT, whereas in the remaining eight (i.e., miR-150-5p, miR-148a-3p, miR-28-5p, miR-144-5p, miR-671-5p, miR-1-3p, miR-193a-3p, and miR-124-3p), the higher expression was associated with shorter TTFT. Integrating these miRNAs into the basic model significantly enhanced predictive accuracy, raising the Harrell's C-index to 81.1% and the explained variation in TTFT to 63.3%. Moreover, the inclusion of the miRNA scores enhanced the integrated discrimination improvement (IDI) and the net reclassification index (NRI), underscoring the potential of miRNAs to refine CLL prognostic models and providing insights for clinical decision-making. In silico analyses on the differently expressed miRNAs revealed their potential regulatory functions of several pathways, including those involved in the therapeutic responses. To add a biological context to the clinical evidence, an miRNA-mRNA correlation analysis revealed at least one significant negative correlation between 15 of the identified miRNAs and a set of 50 artificial intelligence (AI)-selected genes, previously identified by us as relevant for TTFT prediction in the same cohort of CLL patients. In conclusion, the identification of specific miRNAs as predictors of TTFT holds promise for enhancing risk stratification in CLL to predict therapeutic needs. However, further validation studies and in-depth functional analyses are required to confirm the robustness of these observations and to facilitate their translation into meaningful clinical utility.

大多数 CLL 病例都采用 "观察和等待 "策略,即推迟治疗,直到出现活动性疾病;然而,结合生物标志物的预后模型已被证明有助于预测治疗需求。在我们的前瞻性 O-CLL1 研究(包括 224 例患者)中,我们研究了 513 个微小 RNA(miRNA)对首次治疗时间(TTFT)的预测作用。在这项研究中,在一个基本的多变量模型中,六个成熟的变量(即 Rai 分期、β-2-微球蛋白水平、IGVH 突变状态、del11q、del17p 和 NOTCH1 突变)与 TTFT 保持着显著的相关性,共同产生了 75% 的 Harrell's C 指数,并解释了 TTFT 预测中 45.4% 的变异。关于 miRNA,513 个 miRNA 中有 73 个在单变量模型中与 TTFT 显著相关;其中 16 个在多变量分析中与结果保持独立关系。其中 8 个(即 miR-582-3p、miR-33a-3p、miR-516a-5p、miR-99a-5p、miR-296-3p、miR-502-5p、miR-625-5p 和 miR-29c-3p)表达较低与较短的 TTFT 相关,而其余 8 个(即 miR-150-5p、miR-625-5p 和 miR-29c-3p)表达较低与较短的 TTFT 相关、miR-150-5p、miR-148a-3p、miR-28-5p、miR-144-5p、miR-671-5p、miR-1-3p、miR-193a-3p 和 miR-124-3p)中,较高的表达量与较短的 TTFT 相关。将这些 miRNA 纳入基本模型可显著提高预测准确性,使 Harrell's C 指数提高到 81.1%,TTFT 的解释变异提高到 63.3%。此外,纳入 miRNA 评分还提高了综合鉴别改善指数(IDI)和净再分类指数(NRI),这凸显了 miRNA 在完善 CLL 预后模型方面的潜力,并为临床决策提供了启示。对不同表达的 miRNA 进行的硅学分析揭示了它们对几种通路的潜在调控功能,包括那些参与治疗反应的通路。为了给临床证据增加生物学背景,miRNA-mRNA 相关性分析表明,15 个已鉴定的 miRNA 与一组 50 个人工智能(AI)选择的基因之间至少有一个显著的负相关。总之,将特定 miRNA 鉴定为 TTFT 的预测因子有望加强 CLL 的风险分层,从而预测治疗需求。然而,还需要进一步的验证研究和深入的功能分析来证实这些观察结果的可靠性,并促进它们转化为有意义的临床实用性。
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引用次数: 0
Predicting the Effect of miRNA on Gene Regulation to Foster Translational Multi-Omics Research-A Review on the Role of Super-Enhancers. 预测 miRNA 对基因调控的影响,促进多基因转化研究--超级增强子的作用综述。
IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-15 DOI: 10.3390/ncrna10040045
Sarmistha Das, Shesh N Rai

Gene regulation is crucial for cellular function and homeostasis. It involves diverse mechanisms controlling the production of specific gene products and contributing to tissue-specific variations in gene expression. The dysregulation of genes leads to disease, emphasizing the need to understand these mechanisms. Computational methods have jointly studied transcription factors (TFs), microRNA (miRNA), and messenger RNA (mRNA) to investigate gene regulatory networks. However, there remains a knowledge gap in comprehending gene regulatory networks. On the other hand, super-enhancers (SEs) have been implicated in miRNA biogenesis and function in recent experimental studies, in addition to their pivotal roles in cell identity and disease progression. However, statistical/computational methodologies harnessing the potential of SEs in deciphering gene regulation networks remain notably absent. However, to understand the effect of miRNA on mRNA, existing statistical/computational methods could be updated, or novel methods could be developed by accounting for SEs in the model. In this review, we categorize existing computational methods that utilize TF and miRNA data to understand gene regulatory networks into three broad areas and explore the challenges of integrating enhancers/SEs. The three areas include unraveling indirect regulatory networks, identifying network motifs, and enriching pathway identification by dissecting gene regulators. We hypothesize that addressing these challenges will enhance our understanding of gene regulation, aiding in the identification of therapeutic targets and disease biomarkers. We believe that constructing statistical/computational models that dissect the role of SEs in predicting the effect of miRNA on gene regulation is crucial for tackling these challenges.

基因调控对细胞功能和平衡至关重要。它涉及多种机制,控制特定基因产物的产生,并导致基因表达的组织特异性变化。基因失调会导致疾病,因此有必要了解这些机制。计算方法联合研究了转录因子(TFs)、微RNA(miRNA)和信使RNA(mRNA),以研究基因调控网络。然而,在理解基因调控网络方面仍存在知识空白。另一方面,在最近的实验研究中,超级增强子(SEs)除了在细胞特性和疾病进展中发挥关键作用外,还与 miRNA 的生物发生和功能有关。然而,利用 SEs 的潜力来破译基因调控网络的统计/计算方法仍然明显缺乏。然而,要了解 miRNA 对 mRNA 的影响,可以更新现有的统计/计算方法,或者通过在模型中考虑 SEs 来开发新的方法。在这篇综述中,我们将利用 TF 和 miRNA 数据了解基因调控网络的现有计算方法分为三大领域,并探讨了整合增强子/SEs 所面临的挑战。这三个领域包括揭示间接调控网络、识别网络母题以及通过剖析基因调控因子丰富通路识别。我们假设,应对这些挑战将加深我们对基因调控的理解,有助于确定治疗靶点和疾病生物标志物。我们相信,构建统计/计算模型,剖析 SE 在预测 miRNA 对基因调控影响方面的作用,对于应对这些挑战至关重要。
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引用次数: 0
Noncoding RNA-Mediated Epigenetic Regulation in Hepatic Stellate Cells of Liver Fibrosis. 非编码 RNA 介导的肝纤维化肝星状细胞表观遗传调控
IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-07 DOI: 10.3390/ncrna10040044
Ruoyu Gao, Jingwei Mao

Liver fibrosis is a significant contributor to liver-related disease mortality on a global scale. Despite this, there remains a dearth of effective therapeutic interventions capable of reversing this condition. Consequently, it is imperative that we gain a comprehensive understanding of the underlying mechanisms driving liver fibrosis. In this regard, the activation of hepatic stellate cells (HSCs) is recognized as a pivotal factor in the development and progression of liver fibrosis. The role of noncoding RNAs (ncRNAs) in epigenetic regulation of HSCs transdifferentiation into myofibroblasts has been established, providing new insights into gene expression changes during HSCs activation. NcRNAs play a crucial role in mediating the epigenetics of HSCs, serving as novel regulators in the pathogenesis of liver fibrosis. As research on epigenetics expands, the connection between ncRNAs involved in HSCs activation and epigenetic mechanisms becomes more evident. These changes in gene regulation have attracted considerable attention from researchers in the field. Furthermore, epigenetics has contributed valuable insights to drug discovery and the identification of therapeutic targets for individuals suffering from liver fibrosis and cirrhosis. As such, this review offers a thorough discussion on the role of ncRNAs in the HSCs activation of liver fibrosis.

在全球范围内,肝纤维化是造成肝脏相关疾病死亡的重要原因。尽管如此,能够逆转这种状况的有效治疗干预措施仍然匮乏。因此,我们必须全面了解驱动肝纤维化的潜在机制。在这方面,肝星状细胞(HSCs)的活化被认为是肝纤维化发生和发展的关键因素。非编码 RNA(ncRNA)在造血干细胞向肌成纤维细胞转分化的表观遗传调控中的作用已被证实,这为了解造血干细胞活化过程中基因表达的变化提供了新的视角。NcRNA 在介导造血干细胞表观遗传学方面发挥着关键作用,是肝纤维化发病机制中的新型调控因子。随着表观遗传学研究的深入,参与造血干细胞活化的 ncRNA 与表观遗传学机制之间的联系变得越来越明显。这些基因调控的变化引起了该领域研究人员的极大关注。此外,表观遗传学还为药物发现和确定肝纤维化和肝硬化患者的治疗靶点提供了宝贵的见解。因此,本综述深入探讨了 ncRNA 在造血干细胞激活肝纤维化过程中的作用。
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Non-Coding RNA
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