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Ncrna Regulated Pyroptosis in Liver Diseases and Traditional Chinese Medicine Intervention: A Narrative Review

JOUrnaL OF INFLAMMATION RESEARCH 2024年 17卷 2073-2088页

作者： Deng, Jiasheng Qin, Le Qin, Sulang Wu, Ruisheng Huang, Guidong Fang, Yibin Huang, Lanlan Zhou, Zhipin Guangxi Univ Chinese Med Sch Pharm Nanning 530200 Guangxi Peoples R China Youjiang Med Univ Nationalities Affiliated Hosp Dept Pharm Baise 533000 Guangxi Peoples R China Youjiang Med Univ Nationalities Sch Grad Studies Baise 533000 Guangxi Peoples R China Liuzhou Peoples Hosp Dept Pharm Liuzhou 545006 Guangxi Peoples R China Liuzhou Peoples Hosp Dept Pharm 8 Wenchang Rd Liuzhou Guangxi Peoples R China

Pyroptosis is a novel pro -inflammatory mode of programmed cell death that differs from ferroptosis, necrosis, and apoptosis in terms of its onset and regulatory mechanisms. Pyroptosis is dependent on cysteine aspartate protein hydrolase (caspase)mediated activation of GSDMD, NLRP3, and the release of pro -inflammatory cytokines, interleukin-1 (IL-1 beta), and interleukin-18 (IL18), ultimately leading to cell death. non -coding rna (ncrna) is a type of rna that does not encode proteins in gene transcription but plays an important regulatory role in other post -transcriptional links. Ncrna mediates pyroptosis by regulating various related pyroptosis factors, which we termed the pyroptosis signaling pathway. Previous researches have manifested that pyroptosis is closely related to the development of liver diseases, and is essential for liver injury, alcoholic fatty liver disease (ALD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, and liver cancer. In this review, we attempt to address the role of the ncrna-mediated pyroptosis pathway in the above liver diseases and their pathogenesis in recent years, and briefly outline that TCM (Traditional Chinese Medicine) intervene in liver diseases by modulating ncrna-mediated pyroptosis, which will provide a strategy to find new therapeutic targets for the prevention and treatment of liver diseases in the future.

关键词： non-coding rna pyroptosis liver diseases inflammasomes gasdermin traditional Chinese medicine

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pmiRScan: a LightGBM based method for prediction of animal pre-mirnas

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FUNCTIONAL & INTEGRATIVE GENOMICS 2025年第1期25卷 1-16页

作者： Venkatesan, Amrit Basak, Jolly Bahadur, Ranjit Prasad Indian Inst Technol Kharagpur Dept Biosci & Biotechnol Computat Struct Biol Lab Kharagpur 721302 West Bengal India Indian Inst Technol Kharagpur Bioinformat Ctr Dept Biosci & Biotechnol Kharagpur 721302 West Bengal India Visva Bharati Dept Biotechnol Genom Plant Stress Biol Lab Santini Ketan 731235 West Bengal India

Micrornas (mirna) are categorized as short endogenous non-coding rnas, which have a significant role in post-transcriptional gene regulation. Identifying new animal precursor mirna (pre-mirna) and mirna is crucial to understand the role of mirnas in various biological processes including the development of diseases. The present study focuses on the development of a Light Gradient Boost (LGB) based method for the classification of animal pre-mirnas using various sequence and secondary structural features. In various pre-mirna families, distinct k-mer repeat signatures with a length of three nucleotides have been identified. Out of nine different classifiers that have been trained and tested in the present study, LGB has an overall better performance with an AUROC of 0.959. In comparison with the existing methods, our method 'pmiRScan' has an overall better performance with accuracy of 0.93, sensitivity of 0.86, specificity of 0.95 and F-score of 0.82. Moreover, pmiRScan effectively classifies pre-mirnas from four distinct taxonomic groups: mammals, nematodes, molluscs and arthropods. We have used our classifier to predict genome-wide pre-mirnas in human. We find a total of 313 pre-mirna candidates using pmiRScan. A total of 180 potential mature mirnas belonging to 60 distinct mirna families are extracted from predicted pre-mirnas;of which 128 were novel and are note reported in miRBase. These discoveries may enhance our current understanding of mirnas and their targets in human. pmiRScan is freely available at http://***/applications/pmiRScan/***.

关键词： non-coding rna pre-mirna micro-rna Machine learning Taxonomic groups

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Mechanisms of Antitumor Activity of Low Doses of Radiation Associated with Activation of Cells' Defense System

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DOKLADY BIOCHEMISTRY AND BIOPHYSICS 2025年第1期520卷 96-100页

作者： Fomina, D. V. Rozhdestvensky, L. M. Raeva, N. F. Vorobeva, E. S. Zasukhina, G. D. Fed Med Biol Agcy State Res Ctr Burnasyan Fed Med Biophys Ctr Moscow 123098 Russia Russian Acad Sci Inst Gen Genet Moscow 119991 Russia

Background. The effects of ionizing radiation (IR) involve a highly orchestrated series of events in cells, including DNA damage and repair, cell death, and changes in the level of proliferation associated with the stage of the cell cycle. A large number of existing studies in literature have examined the activity of genes and their regulators in mammalian cells in response to high doses of ionizing radiation. Although there are many studies, the research in effect of low doses of ionizing radiation remains limited. Though much progress has been made in understanding the basic principles of effects of low doses of radiation on individual components of biological systems, less is known about how low doses affect target molecules and regulate the cellular networks (e.g., activation of the immune system, genes and their regulators in the phenomenon of hormesis, and the formation of an adaptive response). These observations determined the purpose of the work: to investigate the activity of genes and non-coding rnas (long non-coding rnas and micrornas) in various organs of mice with transplanted Lewis carcinoma after low-dose radiation. Materials and methods. Twenty-four female C57Bl/6 mice were transplanted subcutaneously with Lewis carcinoma cells (105 cells in 0.2 mL of Hanks' solution). Total 4-fold X-ray irradiation with an interval of 4 days at a dose of 0.075 Gy (0.85 Gy/min) was performed on the RUST M1 from 6 days after transplantation;the tumor size was measured daily. The mice were divided into the following groups: "Biocontrol", "Biocontrol + irradiation", "Tumor" and "Tumor + irradiation". On the 19th day from the beginning of the experiment, the mice were euthanized. The expression profiles of mrna genes, long non-coding rnas, and micrornas controlling the response to radiation were determined in the bone marrow, thymus, spleen, and tumor of mice. Results. Fractionated low-dose irradiation of mice with transplanted Lewis carcinoma caused a growth decrease o

关键词： low doses of radiation Lewis carcinoma non-coding rna oncogenes oncosuppressors mice

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Advances in Circular rna in the Pathogenesis of Epilepsy

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NEUROSCIENCE 2024年 551卷 246-253页

作者： Wang, Qin Qin, Baijun Yu, Haichun Hu, Yueqiang Yu, Han Zhong, Jie Liu, Jinwen Yao, Chunyuan Zeng, Jiawei Fan, Jingjing Diao, Limei Guangxi Univ Chinese Med Grad Sch Clin Med Coll 1 13 Wuhe Ave Nanning 530001 Guangxi Peoples R China Guangxi Univ Chinese Med Affiliated Hosp 1 Dept Neurol 89-9 Dongge Rd Nanning 530023 Guangxi Peoples R China Chongqing Hosp Tradit Chinese Med Dept Gastroenterol 6 Seventh Branch Rd Chongqing 400021 Peoples R China Guangxi Technol Coll Machinery & Elect Nanning Guangxi Peoples R China Harbin Med Univ 157 Baojian Rd Harbin 150081 Peoples R China

Recent studies evidenced the involvement of circular rna (circrna) in neuroin flammation, apoptosis, and synaptic remodeling suggesting an important role for circrna in the occurrence and development of epilepsy. This review provides an overview of circrnas considered to be playing regulatory roles in the process of epilepsy and to be involved in multiple biological epilepsy -related processes, such as hippocampal sclerosis, in flammatory response, cell apoptosis, synaptic remodeling, and cell proliferation and differentiation. This review covers the current research status of differential expression of circrna-mediated seizures, m6A methylation, demethylation-mediated seizures in post transcriptional circrna modi fication, as well as the mechanisms of m5C- and m7G-modi fied circrna. In summary, this article reviews the research progress on the relationship between circrna in non -coding rna and epilepsy.

关键词： Epilepsy Circular rna non-coding rna Pathogenesis

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Comprehensive circular rna profiling in various sheep tissues

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SCIENTIFIC REPORTS 2024年第1期14卷 1-17页

作者： Bakhtiarizade, Mohammad Reza Heidari, Maryam Ghanatghestani, Amir Hossein Mohammadi Univ Tehran Coll Aburaihan Dept Anim & Poultry Sci Tehran Iran Isfahan Univ Technol Dept Anim Sci Coll Agr Esfahan Iran

Despite the scientific relevance of circular rnas (circrnas), the study of these rnas in non-model organisms, especially in sheep, is still in its infancy. On the other hand, while some studies have focused on sheep circrna identification in a limited number of tissues, there is a lack of comprehensive analysis that profile circrna expression patterns across the tissues not yet investigated. In this study, 61 public rna sequencing datasets from 12 different tissues were uniformly analyzed to identify circrnas, profile their expression and investigate their various characteristics. We reported for the first time a circrna expression landscape with functional annotation in sheep tissues not yet investigated including hippocampus, BonMarrowMacrophage, left-ventricle, thymus, ileum, reticulum and 23-day-embryo. A stringent computational pipeline was employed and 8919 exon-derived circrnas with high confidence were identified, including 88 novel circrnas. Tissue-specificity analysis revealed that 3059 circrnas were tissue-specific, which were also more specific to the tissues than linear rnas. The highest number of tissue-specific circrnas was found in kidney, hippocampus and thymus, respectively. Co-expression analysis revealed that expression of circrnas may not be affected by their host genes. While most of the host genes produced more than one isoform, only one isoform had dominant expression across the tissues. The host genes of the tissue-specific circrnas were significantly enriched in biological/pathways terms linked to the important functions of their corresponding tissues, suggesting potential roles of circrnas in modulating physiological activity of those tissues. Interestingly, functional terms related to the regulation and various signaling pathways were significantly enriched in all tissues, suggesting some common regulatory mechanisms of circrnas to modulate the physiological functions of tissues. Finding of the present study provide a valuable resource fo

关键词： rna-Seq Tissue-specific non-coding rna lncrnas Functional enrichment analysis

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Advancements in small interfering rnas therapy for acute lymphoblastic leukemia: promising results and future perspectives

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MOLECULAR BIOLOGY REPORTS 2024年第1期51卷 737-737页

作者： Rastgar, Amirhossein Kheyrandish, Setare Vahidi, Mahmoud Heidari, Reza Ghorbani, Mahdi AJA Univ Med Sci Student Res Comm Fac Paramed Tehran Iran Tarbiat Modares Univ Fac Med Sci Dept Hematol & Blood Banking Tehran Iran Shahid Beheshti Univ Med Sci Student Res Comm Sch Allied Med Sci Dept Hematol & Blood Banking Tehran Iran Aja Univ Med Sci Fac Paramed Dept Med Lab Sci Tehran Iran Aja Univ Med Sci Canc Epidemiol Res Ctr Tehran Iran Aja Univ Med Sci Fac Paramed Dept Hematol Lab Sci Tehran Iran AJA Univ Med Sci Infect Dis Res Ctr Tehran Iran

Acute lymphoblastic leukemia (ALL) is the most common type of cancer among children, presenting significant healthcare challenges for some patients, including drug resistance and the need for targeted therapies. Sirna-based therapy is one potential solution, but problems can arise in administration and the need for a delivery system to protect sirna during intravenous injection. Additionally, sirna encounters instability and degradation in the reticuloendothelial system, off-target effects, and potential immune system stimulation. Despite these limitations, some promising results about sirna therapy in ALL patients have been published in recent years, showing the potential for more effective and precise treatment, reduced side effects, and personalized approaches. While sirna-based therapies demonstrate safety and efficacy, addressing the mentioned limitations is crucial for further optimization. Advancements in sirna-delivery technologies and combination therapies hold promise to improve treatment effectiveness and overcome drug resistance. Ultimately, despite its challenges, sirna therapy has the potential to revolutionize ALL treatments and improve patient outcomes.

关键词： sirna Small interfering rna non-coding rna Leukemia ALL Drug resistance

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Comparative transcriptome of normal and cancer-associated fibroblasts

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BMC CANCER 2024年第1期24卷 1231页

作者： Abikar, Apoorva Mustafa, Mohammad Mehaboob Subhani Athalye, Radhika Rajiv Nadig, Namratha Tamboli, Ninad Babu, Vinod Keshavamurthy, Ramaiah Ranganathan, Prathibha Ctr Human Genet Bengaluru India Inst Nephro Urol Bengaluru India Manipal Acad Higher Educ Manipal India

BackgroundThe characteristics of a tumor are largely determined by its interaction with the surrounding micro-environment (TME). TME consists of both cellular and non-cellular components. Cancer-associated fibroblasts (CAFs) are a major component of the TME. They are a source of many secreted factors that influence the survival and progression of tumors as well as their response to drugs. Identification of markers either overexpressed in CAFs or unique to CAFs would pave the way for novel therapeutic strategies that in combination with conventional chemotherapy are likely to have better patient *** have been derived from Benign Prostatic Hyperplasia (BPH) and prostate cancer. rna from these has been used to perform a transcriptome analysis in order to get a comparative profile of normal and cancer-associated *** study has identified 818 differentially expressed mrnas and 17 lincrnas between normal and cancer-associated fibroblasts. Also, 15 potential lincrna-mirna-mrna combinations have been identified which may be potential *** study identified differentially expressed markers between normal and cancer-associated fibroblasts that would help in targeted therapy against CAFs/derived factors, in combination with conventional therapy. However, this would in future need more experimental validation.

关键词： Tumor microenvironment Cancer-associated fibroblasts Chemoresistance non-coding rna LINCrna Prostate cancer

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Osteosarcoma in a ceRNET perspective

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JOUrnaL OF BIOMEDICAL SCIENCE 2024年第1期31卷 1页

作者： Mosca, Nicola Alessio, Nicola Di Paola, Alessandra Marrapodi, Maria Maddalena Galderisi, Umberto Russo, Aniello Rossi, Francesca Potenza, Nicoletta Univ Campania Luigi Vanvitelli Dept Environm Biol & Pharmaceut Sci & Technol Caserta Italy Univ Campania Luigi Vanvitelli Dept Expt Med Naples Italy Univ Campania Luigi Vanvitelli Dept Woman Child & Gen & Specialist Surg Naples Italy

Osteosarcoma (OS) is the most prevalent and fatal type of bone tumor. It is characterized by great heterogeneity of genomic aberrations, mutated genes, and cell types contribution, making therapy and patients management particularly challenging. A unifying picture of molecular mechanisms underlying the disease could help to transform those challenges into *** review deeply explores the occurrence in OS of large-scale rna regulatory networks, denominated "competing endogenous rna network" (ceRNET), wherein different rna biotypes, such as long non-coding rnas, circular rnas and mrnas can functionally interact each other by competitively binding to shared micrornas. Here, we discuss how the unbalancing of any network component can derail the entire circuit, driving OS onset and progression by impacting on cell proliferation, migration, invasion, tumor growth and metastasis, and even chemotherapeutic resistance, as distilled from many studies. Intriguingly, the aberrant expression of the networks components in OS cells can be triggered also by the surroundings, through cytokines and vesicles, with their bioactive cargo of proteins and non-coding rnas, highlighting the relevance of tumor microenvironment. A comprehensive picture of rna regulatory networks underlying OS could pave the way for the development of innovative rna-targeted and rna-based therapies and new diagnostic tools, also in the perspective of precision oncology.

关键词： Osteosarcoma non-coding rna cerna ceRNET Tumor microenvironment

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Transcriptomic and bioinformatics analysis of the mechanism by which erythropoietin promotes recovery from traumatic brain injury in mice

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Neural Regeneration Research 2024年第1期19卷 171-179页

作者： Weilin Tan Jun Ma Jiayuanyuan Fu Biying Wu Ziyu Zhu Xuekang Huang Mengran Du Chenrui Wu Ehab Balawi Qiang Zhou Jie Zhang Zhengbu Liao Department of Neurosurgery The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina

Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain ***,the precise mechanism of action remains unclea *** this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive *** sequencing detected a total of 4065 differentially expressed rnas,including 1059 mrnas,92 micrornas,799 long non-coding rnas,and 2115circular *** Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding rnas that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK *** competing endogenous rna networks showed that regulatory relationship between the differentially expressed non-coding rnas and *** the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was ***6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro *** findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.

关键词： axon guidance bioinformatics analysis competing endogenous rna erythropoietin Gene Ontology Kyoto Encyclopedia of Genes and Genomes non-coding rna rna sequencing transcriptomics traumatic brain injury

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Micrornas Modulating Neuroinflammation in Parkinson's disease

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INFLAMMATION 2024年 1-21页

作者： Saadh, Mohamed J. Muhammad, Faris Anad Singh, Anamika Mustafa, Mohammed Ahmed Al Zuhairi, Rafil Adnan Hussein Ghildiyal, Pallavi Hashim, Ghassan Alsaikhan, Fahad Khalilollah, Shayan Akhavan-Sigari, Reza Middle East Univ Fac Pharm Amman 11831 Jordan Al Noor Univ Coll Dept Pharm Nineveh Iraq Jain Deemed Univ Dept Biotechnol & Genet Bengaluru 560069 Karnataka India Vivekananda Global Univ Dept Allied Healthcare & Sci Jaipur 303012 Rajasthan India Natl Univ Sci & Technol Dhi Qar Iraq Uttaranchal Univ Uttaranchal Inst Pharmaceut Sci Dehra Dun India Al Zahrawi Univ Coll Dept Nursing Karbala Iraq Prince Sattam Bin Abdulaziz Univ Coll Pharm Alkharj Saudi Arabia Islamic Azad Univ Fac Med Dept Neurosurg Tehran Med Sci Tehran Iran Univ Med Ctr Dept Neurosurg Tubingen Germany Univ Warsaw Coll Humanum Warsaw Management Dept Hlth Care Management & Clin Res Warsaw Poland Ibn Sina Natl Coll Med Studies Sch Pharm Jeddah Saudi Arabia Shobhit Univ Adarsh Vijendra Inst Pharmaceut Sci Sch Pharm Gangoh 247341 Uttar Pradesh India Arka Jain Univ Dept Pharm Jamshedpur 832108 Jharkhand India

Parkinson's disease (PD) is one of the most frequent age-associated neurodegenerative disorder. Presence of alpha-synuclein-containing aggregates in the substantia nigra pars compacta (SNpc) and loss of dopaminergic (DA) neurons are among the characteristic of PD. One of the hallmarks of PD pathophysiology is chronic neuroinflammation. Activation of glial cells and elevated levels of pro-inflammatory factors are confirmed as frequent features of the PD brain. Chronic secretion of pro-inflammatory cytokines by activated astrocytes and microglia exacerbates DA neuron degeneration in the SNpc. Micrornas (mirnas) are among endogenous non-coding small rna with the ability to perform post-transcriptional regulation in target genes. In that regard, the capability of mirnas for modulating inflammatory signaling is the center of attention in many investigations. Mirnas could enhance or limit inflammatory signaling, exacerbating or ameliorating the pathological consequences of extreme neuroinflammation. This review summarizes the importance of inflammation in the pathophysiology of PD. Besides, we discuss the role of mirnas in promoting or protecting neural cell injury in the PD model by controlling the inflammatory pathway. Modifying the neuroinflammation by mirnas could be considered a primary therapeutic strategy for PD.

关键词： Parkinson's disease Inflammation nondegenerative Diseases non-coding rna Mirna

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