Kidney diseases and long non-coding RNAs in the limelight

Liu, Chenxin; Ma, Kuai; Zhang, Yunchao; He, Xiangming; Song, Linjiang; Chi, Mingxuan; Han, Zhongyu; Li, Guanhua; Zhang, Qinxiu; Liu, Chi

doi:10.3389/fphys.2022.932693

Cited by 5 publications

(2 citation statements)

References 155 publications

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“…This regulation is mediated through engagement with the mitogen-activated protein kinase (MAPK) and type I interferon (IFN) signaling pathways [33]. Over the past quinquennium, further investigations have been conducted to probe the intricate interplay between LN and lncRNAs, yielding supplementary insights into their participation in disease pathogenesis [34,35]. These studies have broadened our comprehension of the functional roles assumed by speci c lncRNAs in LN and their potential utility as diagnostic or therapeutic targets.…”

Section: Discussionmentioning

confidence: 99%

Unveiling Urinary Biomarkers, Crucial Genes, and Immune Infiltration in Lupus Nephritis Patients

Zeng,

Xie,

et al. 2023

Preprint

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Background This study was conducted to investigate the expression patterns and biological roles of urinary long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in individuals diagnosed with lupus nephritis (LN). Methods The study cohort comprised six participants: three with systemic lupus erythematosus (SLE) involving LN, three with SLE without LN, and three healthy controls (CON). Microarray technology was employed to analyze urinary mRNAs and lncRNAs, thereby exploring alterations in overall RNA expression. Functional insights into dysregulated differentially expressed mRNAs (DEMs) associated with LN were derived through gene ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and gene set enrichment analysis (GSEA). Furthermore, the construction of a protein-protein interaction (PPI) network was accomplished using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). The identification of immune-related cell types was facilitated by Single-sample Gene Set Enrichment Analysis (ssGSEA). To predict potential drug candidates based on differentially expressed genes (DEGs), Connectivity Map (CMap) analysis was conducted. Results Within the urine samples of SLE patients, a total of 247 mRNAs and 602 lncRNAs exhibited differential expression relative to the control group. Among these, 83 down-regulated and 141 up-regulated DEMs were specifically discerned in patients with LN. GO analysis of the network highlighted enrichment in processes such as transcriptional regulation, intrinsic apoptotic signaling pathways in response to DNA damage, and the regulation of mitophagy. KEGG pathway analysis primarily revealed enrichment in protein processing within the endoplasmic reticulum, apoptosis, and the P53 signaling pathway. Co-expression and PPI network analysis suggested that nodes with higher degrees of connectivity were concentrated in pathways related to apoptosis and autophagy. An assessment of immune infiltration unveiled a correlation between activated B cells and CD56dim natural killer (NK) cells with LN pathogenesis. The prediction of drugs implicated inhibition of mechanistic Aurora kinase A (AURKA) as a primary targeted intervention. The molecular docking process confirmed the robust binding activity of hub genes' components. Conclusion This study has illuminated the distinct expression profiles of urinary long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in lupus nephritis (LN) patients. These profiles, particularly in the context of apoptosis, autophagy, and immune cell involvement, provide valuable insights into LN's underlying mechanisms. The identification of potential therapeutic targets, such as mechanistic AURKA, offers promising directions for future interventions in LN management.

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Section: Discussionmentioning

confidence: 99%

Unveiling Urinary Biomarkers, Crucial Genes, and Immune Infiltration in Lupus Nephritis Patients

Zeng,

Xie,

et al. 2023

Preprint

View full text Add to dashboard Cite

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“…Long coding and noncoding (short or long >200 nt long) RNAs yield valuable information about the abundance and novelty of the transcriptome and its epigenetic regulation respectively. Noncoding RNAs are of interest for clinical research applications, as their relative stability and tissue-specific nature make them viable candidates for disease-state biomarkers (1)(2)(3)(4)(5)(6). There is currently a need to simultaneously sequence coding and non-coding RNAs from the same sample in a convenient and robust manner.…”

Section: Introductionmentioning

confidence: 99%

To make a short story long: simultaneous short and long RNA profiling on Nanopore devices

Mackenzie

Tigert

Lovato

et al. 2022

Preprint

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Sequencing of long coding RNAs informs about the abundance and the novelty in the transcriptome, while sequencing of short coding RNAs (e.g., microRNAs) or long non-coding RNAs informs about the epigenetic regulation of the transcriptome. Currently, each of these goals is addressed by separate sequencing experiments given the different physical characteristics of RNA species from biological samples. Sequencing of both short and long RNAs from the same experimental run has not been reported for long-read Nanopore sequencing to date and only recently has been achieved for short-read (Illumina) methods. We propose a library preparation method capable of simultaneously profiling short and long RNA reads in the same library on the Nanopore platform and provide the relevant bioinformatics workflows to support the goals of RNA quantification. Using a variety of synthetic samples we demonstrate that the proposed method can simultaneously detect short and long RNAs in a manner that is linear over 5 orders of magnitude for RNA abundance and three orders of magnitude for RNA length. In biological samples the proposed method is capable of profiling a wider variety of short and long non-coding RNAs when compared against the existing Smart-seq protocols for Illumina and Nanopore sequencing.

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Development of a novel disulfidptosis-related lncRNA signature for prognostic and immune response prediction in clear cell renal cell carcinoma

Wang,

Hu,

Wang

et al. 2024

Sci Rep

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Disulfidptosis, a novel form of regulated cell death, occurs due to the aberrant accumulation of intracellular cystine and other disulfides. Moreover, targeting disulfidptosis could identify promising approaches for cancer treatment. Long non-coding RNAs (lncRNAs) are known to be critically implicated in clear cell renal cell carcinoma (ccRCC) development. Currently, the involvement of disulfidptosis-related lncRNAs in ccRCC is yet to be elucidated. This study primarily dealt with identifying and validating a disulfidptosis-related lncRNAs-based signature for predicting the prognosis and immune landscape of individuals with ccRCC. Clinical and RNA sequencing data of ccRCC samples were accessed from The Cancer Genome Atlas (TCGA) database. Pearson correlation analysis was conducted for the identification of the disulfidptosis-related lncRNAs. Additionally, univariate Cox regression analysis, Least Absolute Shrinkage and Selection Operator Cox regression, and stepwise multivariate Cox analysis were executed to develop a novel risk prognostic model. The prognosis-predictive capacity of the model was then assessed using an integrated method. Variation in biological function was noted using GO, KEGG, and GSEA. Additionally, immune cell infiltration, the tumor mutational burden (TMB), and tumor immune dysfunction and exclusion (TIDE) scores were calculated to investigate differences in the immune landscape. Finally, the expression of hub disulfidptosis-related lncRNAs was validated using qPCR. We established a novel signature comprised of eight lncRNAs that were associated with disulfidptosis (SPINT1-AS1, AL121944.1, AC131009.3, AC104088.3, AL035071.1, LINC00886, AL035587.2, and AC007743.1). Kaplan–Meier and receiver operating characteristic curves demonstrated the acceptable predictive potency of the model. The nomogram and C-index confirmed the strong correlation between the risk signature and clinical decision-making. Furthermore, immune cell infiltration analysis and ssGSEA revealed significantly different immune statuses among risk groups. TMB analysis revealed the link between the high-risk group and high TMB. It is worth noting that the cumulative effect of the patients belonging to the high-risk group and having elevated TMB led to decreased patient survival times. The high-risk group depicted greater TIDE scores in contrast with the low-risk group, indicating greater potential for immune escape. Finally, qPCR validated the hub disulfidptosis-related lncRNAs in cell lines. The established novel signature holds potential regarding the prognosis prediction of individuals with ccRCC as well as predicting their responses to immunotherapy.

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Kidney diseases and long non-coding RNAs in the limelight

Cited by 5 publications

References 155 publications

Unveiling Urinary Biomarkers, Crucial Genes, and Immune Infiltration in Lupus Nephritis Patients

Unveiling Urinary Biomarkers, Crucial Genes, and Immune Infiltration in Lupus Nephritis Patients

To make a short story long: simultaneous short and long RNA profiling on Nanopore devices

Development of a novel disulfidptosis-related lncRNA signature for prognostic and immune response prediction in clear cell renal cell carcinoma

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