Epigenetic-modification associated hnRNPA3 acts as a prognostic biomarker and promotes malignant progression of HCC DOI Creative Commons

Xufan Cai,

Weihui Guo,

Fang Wu

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 24, 2024

Abstract Objective hnRNPA3 is highly expressed in numerous malignancies, including hepatocellular carcinoma (HCC), but its function and mechanism has not been elucidated. In this study, we performed a comprehensive bioinformatics analysis of the TCGA-LIHC dataset several experiments vitro to investigate potential mechanisms HCC. Methods Pan-cancer expression levels as well DNA methylation, associated ceRNA, immune infiltration, checkpoint genes were assessed. Logistic regression, receiver operating characteristic curve (ROC), Kaplan-Meier analysis, nomogram modeling used evaluate prognostic values level cell subtypes HCC tumor microenvironment was analysed through spatial transcriptomic. “pRRophetic” package predict chemotherapeutic drugs sensitivity. patients lines detected by qRT-PCR or WB. hnRNPA3’s impact on proliferation, migration studied SNU449 HuH7 lines. RNA-seq showed controled different important singaling passways Results significantly elevated tumors compared controls. correlated with Age, stage, histologic grade, status, may independently overall disease-specific survival. Significant associations found between methylation. hsa-miR-22-3p act regulatory factor for form ceRNA network multiple lncRNAs.Analysis infiltration revealed correlation macrophages. The similar conclusion also occurred transcriptomic detection. 5-Fluorouracil, Doxorubicin, Etoposide, et al, be sensitive therapy high-hnRNPA3 patients. Silencing cells resulted reducing proliferation migration. played an role malignant progression Conclusion represent promising biomarker within diagnosis prognosis maybe drug-target therapy.

Language: Английский

Underground communication: Long non-coding RNA signaling in the plant rhizosphere DOI Creative Commons

Muhammad Fahad,

Leeza Tariq,

Sajid Muhammad

et al.

Plant Communications, Journal Year: 2024, Volume and Issue: 5(7), P. 100927 - 100927

Published: April 27, 2024

Long non-coding RNAs (lncRNAs) have emerged as integral gene-expression regulators underlying plant growth, development, and adaptation. To adapt to the heterogeneous dynamic rhizosphere, plants use interconnected regulatory mechanisms optimally fine-tune gene-expression-governing interactions with soil biota, well nutrient acquisition heavy metal tolerance. Recently, high-throughput sequencing has enabled identification of lncRNAs responsive rhizosphere biotic abiotic cues. Here, we examine lncRNA biogenesis, classification, mode action, highlighting functions in mediating adaptation diverse factors. We then discuss studies that reveal significance target genes during developmental plasticity stress responses at rhizobium interface. A comprehensive understanding specific lncRNAs, their targets, intricacies functional interaction networks will provide crucial insights into how these transcriptomic switches shifting signals. Looking ahead, foresee single-cell dissection cell-type-specific dynamics enhance our precise modulation enable Overcoming future challenges through multi-omics genetic approaches more fully roles governing belowground environment.

Language: Английский

Citations

4
Maize transcriptome profiling reveals low temperatures affect photosynthesis during the emergence stage DOI Creative Commons
Manja Božić,

Dragana Ignjatović Micić,

Viоlеtа Аnđеlkоvić

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: Jan. 28, 2025

Introduction Earlier sowing is a promising strategy of ensuring sufficiently high maize yields in the face negative environmental factors caused by climate change. However, it leads to low temperature exposure plants during emergence, warranting better understanding their response and acclimation suboptimal temperatures. Materials Methods To achieve this goal, whole transcriptome sequencing was performed on two inbred lines – tolerant/susceptible temperatures, at 5-day-old seedling stage. Sampling after 6h 24h treatment (10/8°C). The data filtered, mapped, identified mRNAs, lncRNAs, circRNAs were quantified. Expression patterns RNAs, as well interactions between them, analyzed reveal ones important for low-temperature response. Results Discussion Genes involved different steps photosynthesis downregulated both genotypes: psa, psb, lhc , cab genes photosystem I II functioning, rca, prk, rbcx1 necessary Calvin cycle. difference tolerance genotypes appeared arise from ability mitigate damage photoinhibition: ctpa2, grx, elip, UF3GT showed higher expression tolerant genotype. Certain lncRNAs also targeted these genes, creating an interaction network induced (XLOC_016169- rca ; XLOC_002167-XLOC_006091- elip2 ). These findings shed light potential mechanisms emergence lay groundwork subsequent analyses across diverse developmental stages. As such, offers valuable guidance future research directions molecular breeding maize.

Language: Английский

Citations

0
LTR retrotransposon-derived novel lncRNA2 enhances cold tolerance in Moso bamboo by modulating antioxidant activity and photosynthetic efficiency DOI Creative Commons
Jiamin Zhao, Yiqian Ding, Muthusamy Ramakrishnan

et al.

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e19056 - e19056

Published: Feb. 26, 2025

In Moso bamboo, the mechanism of long terminal repeat (LTR) retrotransposon-derived non-coding RNA (TElncRNA) in response to cold stress remains unclear. this study, several Pe-TElncRNAs were identified from bamboo transcriptome data. qRT-PCR analysis showed that expression a novel Pe-TElncRNA2 seedlings reached its highest level at 8 hours treatment 4 °C and was significantly higher stems compared leaves, roots, buds. Furthermore, cellular localization revealed cytoplasm than nucleus. overexpression protoplasts positively regulated FZR2 , NOT3 ABCG44 AGD6 genes. Further validation lncRNA Arabidopsis thaliana enhanced antioxidant activities, as evidenced by increased superoxide dismutase (SOD) activity proline content, well maximum photochemical efficiency PS II dark-adapted leaves ( F v / m ), transgenic plants wild-type controls. Conversely, malondialdehyde (MDA) lipid peroxidation marker (a oxidative stress), reduced plants. Notably, levels both genes upregulated after two days treatment. These findings elucidate critical role LTR lncRNAs mediating responses bamboo.

Language: Английский

Citations

0
Cytosolic and Nucleosolic Calcium-Regulated Long Non-Coding RNAs and Their Target Protein-Coding Genes in Response to Hyperosmolarity and Salt Stresses in Arabidopsis thaliana DOI Open Access

Doudou Wang,

Kaifeng Zheng, William J. Long

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(5), P. 2086 - 2086

Published: Feb. 27, 2025

Long non-coding RNAs (lncRNAs) are involved in plant biotic and abiotic stress responses, which Ca2+ also plays a significant role. There is diversity the regulation of different gene expressions by cytosolic ([Ca2+]cyt) nucleosolic ([Ca2+]nuc). However, no studies have yet explored interrelationship between lncRNAs calcium signaling, nor how signaling regulates expression lncRNAs. Here, we use transgenic materials PV-NES NLS-PV, simulate [Ca2+]cyt- [Ca2+]nuc-deficient mutants, respectively, wild type (WT) response to hyperosmolarity (250 mM sorbitol) or salt stresses (125 NaCl) at time points obtain RNA-seq data, respectively. Then, proceed with screening lncRNAs, adding 688 new known Arabidopsis lncRNA database. Subsequently, through analysis differentially expressed genes, it was found that signals distinct regulatory effects on (DElncRNAs) protein-coding genes (DEPCGs) treated high-concentration NaCl sorbitol times. Furthermore, weighted correlation network (WGCNA), discovered under stresses, lncRNA-associated PCGs related cell wall structure, plasma membrane component, osmotic substances trans-regulation. In addition, for cis-regulatory target Ca2+-regulated stress, series lncRNA-PCG pairs water transport, components, lateral root formation. Therefore, expand existing database regulated [Ca2+]cyt [Ca2+]nuc providing perspective subsequent research We explore trans- cis-regulated insights further studying stress.

Language: Английский

Citations

0
Long Non-Coding RNA Osr2 Promotes Fusarium solani Keratitis Inflammation via the miR-30a-3p/ Xcr1 Axis DOI Creative Commons

Hanfeng Tang,

Yi Lin, Jianzhang Hu

et al.

Investigative Ophthalmology & Visual Science, Journal Year: 2025, Volume and Issue: 66(3), P. 27 - 27

Published: March 11, 2025

Purpose: Fungal keratitis (FK) is a challenging and sight-threatening corneal disease caused by fungal infections. Although long noncoding RNAs (lncRNAs) have been explored in various infectious diseases, their specific roles FK remain largely unexplored. Methods: A mouse model of was created infecting stromal cells with Fusarium solani. High-throughput lncRNA expression profiling conducted on FK-affected tissues to identify differentially expressed lncRNAs. Reverse transcription quantitative PCR (RT-qPCR) used validate the results. competing endogenous RNA (ceRNA) network constructed. Additionally, antisense oligonucleotide (ASO) targeting ENSMUST00000226838/Osr2 (Osr2) developed for therapeutic evaluation. Inflammatory markers IL-1β, IL-6, TNF-α were measured, inflammation assessed through histological analysis slit-lamp examination. Fluorescent situ hybridization (FISH) confirm Osr2 localization, whereas dual-luciferase reporter assay verified interactions between miR-30a-3p. Results: We identified 1143 lncRNAs FK, 701 upregulated 442 downregulated. The ceRNA indicated that regulates Xcr1 Treatment ASO-Osr2 significantly reduced inflammation, FISH confirmed distribution both nucleus cytoplasm. Dual-luciferase assays demonstrated interaction miR-30a-3p, highlighting potential progression FK. Conclusions: This study outlined profile established regulatory network, identifying as crucial modulator pathogenesis its These findings highlighted promising target treatment

Language: Английский

Citations

0
Neurodegenerative diseases: Epigenetic regulatory mechanisms and therapeutic potential DOI

Jifang Men,

Xinyue Wang, Yumin Zhou

et al.

Cellular Signalling, Journal Year: 2025, Volume and Issue: 131, P. 111715 - 111715

Published: March 13, 2025

Language: Английский

Citations

0
Navigating thyroid cancer complexity: the emerging role of EV-derived non-coding RNAs DOI Creative Commons
Meng Jia, Jiawen Liang, Lu Gao

et al.

Cell Death Discovery, Journal Year: 2025, Volume and Issue: 11(1)

Published: April 4, 2025

Language: Английский

Citations

0
Epigenetic-modification associated hnRNPA3 acts as a prognostic biomarker and promotes malignant progression of HCC DOI Creative Commons

Xufan Cai,

Weihui Guo,

Fang Wu

et al.

BMC Cancer, Journal Year: 2025, Volume and Issue: 25(1)

Published: April 10, 2025

hnRNPA3 is highly expressed in numerous malignancies, including hepatocellular carcinoma (HCC), but its function and mechanism has not been elucidated. In this study, we performed a comprehensive bioinformatics analysis of the TCGA-LIHC dataset several experiments vitro to investigate potential mechanisms HCC. Pan-cancer expression levels as well DNA methylation, associated ceRNA, immune infiltration, checkpoint genes were assessed. Logistic regression, receiver operating characteristic curve (ROC), Kaplan-Meier analysis, nomogram modeling used evaluate prognostic values level cell subtypes HCC tumor microenvironment was analysed through spatial transcriptomic. "pRRophetic" package predict chemotherapeutic drugs sensitivity. patients lines detected by qRT-PCR or WB. hnRNPA3's impact on proliferation, migration studied SNU449 HuH7 lines. RNA-seq showed controled different important singaling passways significantly elevated tumors compared controls. correlated with Age, stage, histologic grade, status, may independently overall disease-specific survival. Significant associations found between methylation. hsa-miR-22-3p act regulatory factor for form ceRNA network multiple lncRNAs.Analysis infiltration revealed correlation macrophages. The similar conclusion also occurred transcriptomic detection. 5-Fluorouracil, Doxorubicin, Etoposide, et al., be sensitive therapy high-hnRNPA3 patients. Silencing cells resulted reducing proliferation migration. played an role malignant progression represent promising biomarker within diagnosis prognosis maybe drug-target therapy.

Language: Английский

Citations

0
Deciphering the role of non-coding RNAs SNHG18, HOXA11-AS, MEG3, and MDC1-AS1 in glioma patients: A combined experimental and computational study DOI
Kamal Mohammadian, Arash Moradi,

Mansoureh Shabani

et al.

Gene Reports, Journal Year: 2024, Volume and Issue: 36, P. 101973 - 101973

Published: July 14, 2024

Language: Английский

Citations

2
Update on functional analysis of long non-coding RNAs in common crops DOI Creative Commons
Aijing Zhang,

Wenxuan Pi,

Yashuo Wang

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: May 30, 2024

With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes extensively investigated animals, there has considerably less research on plant lncRNAs. Nevertheless, multiple studies major crops showed lncRNAs involved crucial processes, growth and development, reproduction, stress responses. This review summarizes progress lncRNA roles several crops, presents key strategies for exploring discusses current challenges future prospects. The insights provided this will enhance our comprehension of functions with potential implications improving crop genetics breeding.

Language: Английский

Citations

1