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Search Results (421)

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Keywords = LINC01426

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27 pages, 5245 KiB  
Article
The Good, the Bad, or Both? Unveiling the Molecular Functions of LINC01133 in Tumors
by Leandro Teodoro Júnior and Mari Cleide Sogayar
Non-Coding RNA 2025, 11(4), 58; https://doi.org/10.3390/ncrna11040058 (registering DOI) - 30 Jul 2025
Viewed by 236
Abstract
Background/Objectives: Increasing evidence suggests that lncRNAs are core regulators in the field of tumor progression, with context-specific functions in oncogenic tumorigenesis. LINC01133, a lncRNA that has been identified as both an oncogene and a tumor suppressor, remains largely unexplored in terms of its [...] Read more.
Background/Objectives: Increasing evidence suggests that lncRNAs are core regulators in the field of tumor progression, with context-specific functions in oncogenic tumorigenesis. LINC01133, a lncRNA that has been identified as both an oncogene and a tumor suppressor, remains largely unexplored in terms of its molecular mechanisms. The purpose of this study was to conduct an in silico analysis, incorporating literature research on various cancer types, to investigate the structural and functional duality of LINC01133. This analysis aimed to identify pathways influenced by LINC01133 and evaluate its mechanism of action as a potential therapeutic target and diagnostic biomarker. Methods: In silico analyses and a narrative review of the literature were performed to predict conserved structural elements, functional internal loops, and overall conservation of the LINC01133 sequence among different vertebrate organisms, summarizing the empirical evidence regarding its roles as a tumor suppressor and tumor-promoting roles in various types of tumors. Results: LINC01133 harbors the evolutionarily conserved structural regions that might allow for binding to relevant driver signaling pathways, substantiating its specific functionality. Its action extends beyond classical tumor mechanisms, affecting proliferation, migration, invasion, and epigenetic pathways in various types of tumors, as indicated by the in silico results and narrative review of the literature we present here. Clinical outcome associations pointed to its potential as a biomarker. Conclusions: The dual character of LINC01133 in tumor biology further demonstrates its prospective therapeutic value, but complete elucidation of its mechanisms of action requires further investigation. This study establishes LINC01133 as a multifaceted lncRNA, supporting context-specific strategies in targeting its pathways, and calls for expanded research to harness its full potential in oncology. Full article
(This article belongs to the Special Issue Non-coding RNA as Biomarker in Cancer)
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16 pages, 14493 KiB  
Article
Identification of Drug Repurposing Candidates for Coxsackievirus B3 Infection in iPSC-Derived Brain-like Endothelial Cells
by Jacob F. Wood, John M. Vergis, Ali S. Imami, William G. Ryan, Jon J. Sin, Brandon J. Kim, Isaac T. Schiefer and Robert E. McCullumsmith
Int. J. Mol. Sci. 2025, 26(15), 7041; https://doi.org/10.3390/ijms26157041 - 22 Jul 2025
Viewed by 182
Abstract
The enterovirus Coxsackievirus B3 causes a range of serious health problems, including aseptic meningitis, myocarditis, and pancreatitis. Currently, Coxsackievirus B3 has no targeted antiviral treatments or vaccines, leaving supportive care as the primary management option. Understanding how Coxsackievirus B3 interacts with and alters [...] Read more.
The enterovirus Coxsackievirus B3 causes a range of serious health problems, including aseptic meningitis, myocarditis, and pancreatitis. Currently, Coxsackievirus B3 has no targeted antiviral treatments or vaccines, leaving supportive care as the primary management option. Understanding how Coxsackievirus B3 interacts with and alters the blood–brain barrier may help identify new therapies to combat this often-devastating infection. We reanalyzed a previously published RNA sequencing dataset for Coxsackievirus B3-infected human-induced pluripotent stem-cell-derived brain endothelial cells (iBECs) to examine how Coxsackievirus B3 altered mRNA expression. By integrating GSEA, EnrichR, and iLINCs-based perturbagen analysis, we present a novel, systems-level approach to uncover potential drug repurposing candidates for CVB3 infection. We found dynamic changes in host transcriptomic response to Coxsackievirus B3 infection at 2- and 5-day infection time points. Downregulated pathways included ribosomal biogenesis and protein synthesis, while upregulated pathways included a defense response to viruses, and interferon production. Using iLINCs transcriptomic analysis, MEK, PDGFR, and VEGF inhibitors were identified as possible novel antiviral therapeutics. Our findings further elucidate Coxsackievirus B3-associated pathways in (iBECs) and highlight potential drug repurposing candidates, including pelitinib and neratinib, which may disrupt Coxsackievirus B3 pathology at the blood–brain barrier (BBB). Full article
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20 pages, 1712 KiB  
Article
APOE Genotype-Stratified Meta-Analysis of Cognitive Decline Reveals Novel Loci for Language and Global Cognitive Function in Older Adults
by Vibha Acharya, Kang-Hsien Fan, Beth E. Snitz, Mary Ganguli, Steven T. DeKosky, Oscar L. Lopez, Eleanor Feingold and M. Ilyas Kamboh
Int. J. Mol. Sci. 2025, 26(14), 6940; https://doi.org/10.3390/ijms26146940 - 19 Jul 2025
Viewed by 354
Abstract
Apolipoprotein E (APOE) allele 4 (APOE4), one of the robust genetic risk factors for AD, has also been associated with cognitive decline in terms of memory, executive function, language, and global cognitive function. APOE genotype-stratified analysis can help to [...] Read more.
Apolipoprotein E (APOE) allele 4 (APOE4), one of the robust genetic risk factors for AD, has also been associated with cognitive decline in terms of memory, executive function, language, and global cognitive function. APOE genotype-stratified analysis can help to identify additional genetic loci which might be masked due to a strong effect of APOE4. We conducted a genome-wide meta-analysis in APOE2 carriers, APOE4 carriers, and APOE 3/3 homozygote groups among 2969 non-Hispanic Whites aged ≥ 65 years using slopes of decline over time across five cognitive domains (attention, language, executive function, memory, and visuospatial function) and global cognitive function. We identified novel genome-wide significant associations for decline in global cognitive function in the intergenic region between RNU7-66P/RNA5SP208 at rs116379916 (p = 1.44 × 10−9) in the APOE 3/3 group and for decline in language in the intergenic region between LINC0221/DTWD2 at rs13187183 (p = 3.79 × 10−8) in APOE4 carriers. A previously reported locus for decline in attention near RASEF at rs6559700 (p = 9.95 × 10−9) was found to be confined to the APOE 3/3 group. We also found two sub-threshold significant associations in the APOE 2 group for decline in attention (IL1RL2/rs77127114; p = 8.64 × 10−8) and decline in language (YTHDC2/KCNN2, rs116191836; p = 5.66 × 10−8). Our study points to potential biological pathways pertaining to specific domains within each APOE genotype group, and the findings suggest that immune-related pathways, plasma levels of polysaturated fatty acids, and bitter taste receptors may play roles in cognitive decline. Our findings enhance the understanding of cognitive aging and provide a framework for future studies. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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13 pages, 12136 KiB  
Article
Comparative Analysis of Differentially Expressed Long Non-Coding RNA in Pre- and Postmenopausal Fibroids
by Tsai-Der Chuang, Shawn Rysling, Nhu Ton, Daniel Baghdasarian and Omid Khorram
Int. J. Mol. Sci. 2025, 26(14), 6798; https://doi.org/10.3390/ijms26146798 - 16 Jul 2025
Viewed by 208
Abstract
Uterine fibroids (leiomyomas) are benign tumors whose growth is influenced by estrogen and progesterone. This study aimed to compare the profiles of differentially expressed long non-coding RNAs (lncRNAs) in fibroids from postmenopausal and premenopausal women to identify hormone-responsive lncRNAs. RNA sequencing was performed [...] Read more.
Uterine fibroids (leiomyomas) are benign tumors whose growth is influenced by estrogen and progesterone. This study aimed to compare the profiles of differentially expressed long non-coding RNAs (lncRNAs) in fibroids from postmenopausal and premenopausal women to identify hormone-responsive lncRNAs. RNA sequencing was performed on six pairs of fibroid (Fib) and adjacent myometrium (Myo) tissues from postmenopausal women. Out of 7876 normalized lncRNAs, 3684 were differentially expressed (≥1.5-fold), with 1702 upregulated and 1982 downregulated in Fib. Comparative analysis with a previously published premenopausal dataset identified 741 lncRNAs that were altered based on their menopausal status, including 62 lncRNAs that were uniquely dysregulated in postmenopausal samples. Overall, 9 lncRNAs were selected for validation by PCR in an expanded cohort of 31 postmenopausal and 84 premenopausal paired samples. Several lncRNAs, including LINC02433, LINC01449, SNHG12, H19, and HOTTIP, were upregulated in premenopausal Fib but not in postmenopausal ones, while ZEB2-AS1 displayed the opposite pattern. CASC15 and MIAT were elevated in Fib from both groups, although the increase was less pronounced in the postmenopausal group. LINC01117 was significantly downregulated in postmenopausal Fib, with no change observed in premenopausal samples. Additionally, analysis based on MED12 mutation status revealed that lncRNAs such as LINC01449, CASC15, and MIAT showed limited or reduced differential expression (mutation-positive vs. mutation-negative) in postmenopausal patients compared to the premenopausal group. These findings indicate that lncRNA expression in fibroids is modulated by menopausal status, likely reflecting hormonal influence. Hormone-responsive lncRNAs may play key roles in fibroid pathogenesis and represent potential targets for therapeutic intervention. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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19 pages, 2517 KiB  
Article
In Silico Analysis of Post-COVID-19 Condition (PCC) Associated SNP rs9367106 Predicts the Molecular Basis of Abnormalities in the Lungs and Brain Functions
by Amit K. Maiti
Int. J. Mol. Sci. 2025, 26(14), 6680; https://doi.org/10.3390/ijms26146680 - 11 Jul 2025
Viewed by 424
Abstract
Long- or post-COVID-19 syndrome, which is also designated by WHO as Post COVID-19 Condition (PCC), is characterized by the persistent symptoms that remain after recovery from SARS-CoV-2 infection. A worldwide consortium of Long COVID-19 Host Genetics Initiative (Long COVID-19 HGI) identified an SNP [...] Read more.
Long- or post-COVID-19 syndrome, which is also designated by WHO as Post COVID-19 Condition (PCC), is characterized by the persistent symptoms that remain after recovery from SARS-CoV-2 infection. A worldwide consortium of Long COVID-19 Host Genetics Initiative (Long COVID-19 HGI) identified an SNP rs9367106 (G>C; chr6:41,515,652, GRCh38, p = 1.76 × 10−10, OR = 1.63, 95% CI: 1.40–1.89) that is associated with PCC. Unraveling the functional significance of this SNP is of prime importance to understanding the development of the PCC phenotypes and their therapy. Here, in Silico, I explored how the risk allele of this SNP alters the functional mechanisms and molecular pathways leading to the development of PCC phenotypes. Bioinformatic methods include physical interactions using HI-C and Chia-PET analysis, Transcription Factors (TFs) binding ability, RNA structure modeling, epigenetic, and pathway analysis. This SNP resides within two long RNA genes, LINC01276 and FOXP4-AS1, and is located at ~31 kb upstream of a transcription factor FOXP4. This DNA region, including this SNP, physically interacts with FOXP4-AS1 and FOXP4, implying that this regulatory SNP could alter the normal cellular function of FOXP4-AS1 and FOXP4. Furthermore, rs9367106 is in eQTL with the FOXP4 gene in lung tissue. rs9367106 carrying DNA sequences act as distant enhancers and bind with several transcription factors (TFs) including YY1, PPAR-α, IK-1, GR-α, and AP2αA. The G>C transition extensively modifies the RNA structure that may affect the TF bindings and enhancer functions to alter the interactions and functions of these RNA molecules. This SNP also includes an ALU/SINE sequence and alteration of which by the G>C transition may prevent IFIH1/MDA5 activation, leading to suppression of host innate immune responses. LINC01276 targets the MED20 gene that expresses mostly in brain tissues, associated with sleep disorders and basal ganglia abnormalities similar to some of the symptoms of PCC phenotypes. Taken together, G>C transition of rs9367601 may likely alter the function of all three genes to explain the molecular basis of developing the long-term symptomatic abnormalities in the lungs and brain observed after COVID-19 recovery. Full article
(This article belongs to the Special Issue Genetic Variations in Human Diseases: 2nd Edition)
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23 pages, 8434 KiB  
Article
Duodenal Adenocarcinoma Is Characterized by Acidity, High Infiltration of Macrophage, and Activated Linc01559–GRSF1 Axis
by Xinxin Huang, Ying Shi, Zekun Liu, Yihang Wu, Xiaotong Luo, Dongwen Chen, Zhengyu Wei, Chong Chen, Huaiqiang Ju, Xiaojian Wu, Xuanhui Liu, Zhanhong Chen and Peishan Hu
Biomedicines 2025, 13(7), 1611; https://doi.org/10.3390/biomedicines13071611 - 30 Jun 2025
Viewed by 439
Abstract
Background: Duodenal adenocarcinoma (DA) is often insidious due to the low rate of early diagnosis and because the mechanisms that underlie its malignant progression are poorly understood. The tumor microenvironment (TME) plays a crucial regulatory role in promoting tumor malignancy. Hence, this [...] Read more.
Background: Duodenal adenocarcinoma (DA) is often insidious due to the low rate of early diagnosis and because the mechanisms that underlie its malignant progression are poorly understood. The tumor microenvironment (TME) plays a crucial regulatory role in promoting tumor malignancy. Hence, this study aimed to identify novel biomarkers for early diagnosis and potential therapeutic targets for DA. Methods: Surgical resection samples and normal tissues from DA patients were collected for RNA sequencing (RNA-seq). The characteristics of TME in DA patients were analyzed, and the differentially expressed long non-coding RNAs (lncRNA) were screened. Functional experiments were performed to verify the relationship between Linc01559, G-rich sequence binding factor 1 (GRSF1), and tumor malignant phenotype. Results: The present study revealed that DA exhibits a significantly upregulated expression of acidic environment markers and a high degree of macrophage infiltration. Further investigation revealed that macrophages upregulate the expression of the long noncoding RNA, Linc01559, in DA through the STAT3/c-MYC signaling pathway, thereby promoting malignant phenotypes such as invasion, metastasis, tumor stemness, and apoptosis. The interaction between GRSF1 and Linc01559 was subsequently confirmed using RNA pulldown-mass spectrometry. It was further revealed that Linc01559 promotes the malignant phenotype of duodenal cancer cells through its interaction with GRSF1. Conclusions: These findings demonstrate that the acidic microenvironment influences the phenotype of DA by regulating the Linc01559–GRSF1 axis. Therefore, these findings provide potential targets for the early detection and treatment of DA. Full article
(This article belongs to the Special Issue Genomic Insights and Translational Opportunities for Human Cancers)
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14 pages, 3880 KiB  
Article
Metastasis-Specific CpG Island DNA Hypermethylation of the Long Non-Coding RNA Gene 00404 in Renal Cell Carcinoma
by Pouriya Faraj Tabrizi, Inga Schimansky, Inga Peters, Jörg Hennenlotter, Hossein Tezval, Markus Antonius Kuczyk and Jürgen Serth
Cancers 2025, 17(13), 2204; https://doi.org/10.3390/cancers17132204 - 30 Jun 2025
Viewed by 267
Abstract
Background/Objectives: Alterations in long non-protein-coding RNAs (lncRNAs) are known to influence cellular proliferation, apoptosis, and metastasis in human cancers, including renal cell carcinoma (RCC). Methods: Using pyrosequencing, we analyzed DNA methylation (DNAm) at 23 loci within the LINC00404 CpG island across 28 human [...] Read more.
Background/Objectives: Alterations in long non-protein-coding RNAs (lncRNAs) are known to influence cellular proliferation, apoptosis, and metastasis in human cancers, including renal cell carcinoma (RCC). Methods: Using pyrosequencing, we analyzed DNA methylation (DNAm) at 23 loci within the LINC00404 CpG island across 28 human cancer cell line models, 181 RCC tumor tissues, 154 paired tumor-adjacent normal tissues (adNs), and 194 metastatic tissue samples. Results: Our analysis revealed that all CpG sites exhibited tumor-specific hypermethylation (all p ≤ 1.4 × 10−5). Moreover, primary RCC tissues with distant metastases (M1) and metastatic tissue samples (Mtx) showed significant hypermethylation compared to RCC without distant metastases (M0). Notably, DNAm in Mtx displayed a significant increase in 22 CpG sites, compared to 12 CpG sites in the M1/M0 comparison, suggesting that DNAm in Mtx differs both qualitatively and quantitatively. Conclusions: Given that elevated levels of DNAm were also observed in the majority of cell line models, our findings suggest that LINC00404 may play a pivotal role in the malignant development and progression of RCC metastasis, as well as in other human cancers. Full article
(This article belongs to the Section Cancer Biomarkers)
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25 pages, 937 KiB  
Review
T-Cadherin (CDH13) and Non-Coding RNAs: The Crosstalk Between Health and Disease
by Kseniya Rubina, Artem Maier, Polina Klimovich, Veronika Sysoeva, Daniil Romashin, Ekaterina Semina and Vsevolod Tkachuk
Int. J. Mol. Sci. 2025, 26(13), 6127; https://doi.org/10.3390/ijms26136127 - 26 Jun 2025
Viewed by 619
Abstract
T-cadherin (CDH13) is an atypical, glycosyl-phosphatidylinositol-anchored cadherin with functions ranging from axon guidance and vascular patterning to adipokine signaling and cell-fate specification. Originally identified as a homophilic cue for migrating neural crest cells, projecting axons, and growing blood vessels, it later [...] Read more.
T-cadherin (CDH13) is an atypical, glycosyl-phosphatidylinositol-anchored cadherin with functions ranging from axon guidance and vascular patterning to adipokine signaling and cell-fate specification. Originally identified as a homophilic cue for migrating neural crest cells, projecting axons, and growing blood vessels, it later emerged as a dual metabolic receptor for cardioprotective high-molecular-weight adiponectin and atherogenic low-density lipoproteins. We recently showed that mesenchymal stem/stromal cells lacking T-cadherin are predisposed to adipogenesis, underscoring its role in lineage choice. Emerging evidence indicates that CDH13 expression and function are fine-tuned by non-coding RNAs (ncRNAs). MiR-199b-5p, miR-377-3p, miR-23a/27a/24-2, and the miR-142 family directly bind CDH13 3′-UTR or its epigenetic regulators, affecting transcription or accelerating decay. Long non-coding RNAs (lncRNAs), including antisense transcripts CDH13-AS1/AS2, brain-restricted FEDORA, and context-dependent LINC00707 and UPAT, either sponge these miRNAs or recruit DNMT/TET enzymes to the CDH13 promoter. Circular RNAs (circRNAs), i.e.circCDH13 and circ_0000119, can add a third level of complexity by sequestering miRNA repressors or boosting DNMT1. Collectively, this ncRNA circuitry regulates T-cadherin across cardiovascular, metabolic, oncogenic, and neurodegenerative conditions. This review integrates both experimentally validated data and in silico predictions to map the ncRNA-CDH13 crosstalk between health and disease, opening new avenues for biomarker discovery and RNA-based therapeutics. Full article
(This article belongs to the Special Issue Regulation by Non-Coding RNAs 2025)
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14 pages, 2823 KiB  
Article
LincRNA-MSTRG.673.2 Promotes Chicken Intramuscular Adipocyte Differentiation by Sponging miR-128-3p
by Binbin Zhang, Shuaipeng Zhu, Yuehua He, Wenjie Liang, Tingqi Zhu, Ruili Han, Donghua Li, Yanbin Wang, Yadong Tian, Guoxi Li, Xiangtao Kang, Wenting Li and Guirong Sun
Animals 2025, 15(13), 1879; https://doi.org/10.3390/ani15131879 - 25 Jun 2025
Viewed by 364
Abstract
Background: Intramuscular fat content is positively correlated with meat flavor and juiciness. Increasing the intramuscular fat (IMF) content of chickens while increasing their growth rate has become a hot topic in molecular breeding. The group’s previous studies showed that miR-128-3p inhibited chicken intramuscular [...] Read more.
Background: Intramuscular fat content is positively correlated with meat flavor and juiciness. Increasing the intramuscular fat (IMF) content of chickens while increasing their growth rate has become a hot topic in molecular breeding. The group’s previous studies showed that miR-128-3p inhibited chicken intramuscular adipocyte differentiation and lipogenesis. However, the regulatory mechanism of miR-128-3p in intramuscular preadipocytes is currently unknown. In this study, we investigated the mechanism of miR-128-3p regulation of chicken intramuscular adipocyte differentiation and deposition. Results: Transcriptome data analysis of differential LincRNAs indicated that, compared to the NC group, the mimics-treated group had seventeen significantly differentially expressed LincRNAs (p < 0.05), including six upregulated and eleven downregulated ones; the inhibitor-treated group had seventeen differentially expressed LincRNAs (p < 0.05), including eight upregulated and nine downregulated ones; and twenty-four differentially expressed LincRNAs (p < 0.05) were observed when comparing the mimics-treated group to the inhibitor-treated group, with fourteen upregulated and ten downregulated ones. Functional enrichment analysis revealed that DELincRNAs from the overexpression group (M group) and interference group (SI group) were involved in the negative regulation of metabolic processes, response to steroid hormones, and regulation of actin cytoskeleton. Furthermore, target gene prediction analysis showed that miR-128-3p can target many of the DELincRNAs, such as LincRNA-MSTRG.673.2, LincRNA-MSTRG.39.2, LincRNA-MSTRG.39.3, and LincRNA-MSTRG.14270.2. LincRNA-MSTRG.673.2 was predominantly expressed in the cytoplasm of intramuscular adipocytes. Dual luciferase reporter identified the targeting relationship between miR-128-3p and LincRNA-MSTRG.673.2. The results of subsequent functional assays demonstrated that interfering with MSTRG.673.2 has been shown to inhibit lipid deposition in intramuscular preadipocytes. Transfection experiments have shown that LincRNA-MSTRG.673.2 can affect the expression of miR-128-3p. Conclusions: This study found that LincRNA-MSTRG.673.2 promoted chicken intramuscular adipocyte differentiation by downregulating miR-128-3p. The results are noteworthy for improving chicken meat quality, molecular breeding, and lipid metabolism research. Full article
(This article belongs to the Section Poultry)
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15 pages, 577 KiB  
Article
Molecular Crosstalk Between SIRT1, Wnt/β-Catenin Signaling, and Inflammatory Pathways in Renal Transplant Rejection: Role of miRNAs, lncRNAs, IL-1, IL-6, and Tubulointerstitial Inflammation
by Nurhak Aksungur, Murat Kizilkaya, Necip Altundaş, Eda Balkan, Salih Kara, Elif Demirci and Abdullah Uyanik
Medicina 2025, 61(6), 1073; https://doi.org/10.3390/medicina61061073 - 11 Jun 2025
Viewed by 767
Abstract
Background/Objectives: This study aimed to evaluate the relationship between sirtuin family members (SIRT1, SIRT3, and SIRT6) and Wnt/β-catenin pathways with inflammation during the rejection process following kidney transplantation, as well as to explore their potential roles as candidate biomarkers. Materials and Methods [...] Read more.
Background/Objectives: This study aimed to evaluate the relationship between sirtuin family members (SIRT1, SIRT3, and SIRT6) and Wnt/β-catenin pathways with inflammation during the rejection process following kidney transplantation, as well as to explore their potential roles as candidate biomarkers. Materials and Methods: Blood samples were collected from 35 kidney transplant rejection patients and 30 healthy controls. The gene expression levels of SIRT1, SIRT3, SIRT6, and Wnt/β-catenin pathway components were measured using real-time PCR, and miRNA and lncRNA expression levels were analyzed. Statistical analyses were performed using SPSS version 23. Results: Significant alterations in SIRT1, SIRT3, and SIRT6 expression levels were observed in rejection patients, suggesting their potential role in disease pathogenesis and as therapeutic biomarkers. Key altered genes included hsa-miR-34c-1, hsa-miR-122b-5b, MALAT1, HOTAIR, LINC00473, TUG, PVT1, SIRT1, SIRT3, SIRT6, WNT1, TCF-LEF, LRP, AXIN1, IL1B, IL6, and IFNB1, all showing significant changes. However, no significant differences were found for miRNAs such as hsa-miR-21-2, hsa-miR-155-5p, and hsa-miR-200b-3p. SIRT1 expression was significantly decreased in the cellular rejection group, with a more pronounced reduction in these patients. Significant differences in SIRT1 expression were observed with interstitial inflammation and glomerulitis. Increased inflammation severity correlated with decreased SIRT1 and increased TCF-LEF, TUG, and miR-21 levels, while tubulitis severity was associated with elevated TCF-LEF and miR-155 expression. Conclusions: Along with the activation of Wnt/β-catenin pathways and increased levels of certain miRNAs and long non-coding RNAs (lncRNAs) associated with TCF-LEF transcription factors, the observed decrease in SIRT1 expression may be related to the severity of inflammation and tubulitis. These findings suggest that SIRT1, Wnt/β-catenin pathways, and non-coding RNAs play a role in the rejection process following kidney transplantation and could be considered as potential biomarkers or therapeutic target candidates for future research. Full article
(This article belongs to the Section Surgery)
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27 pages, 1665 KiB  
Review
An Emphasis on the Role of Long Non-Coding RNAs in Viral Gene Expression, Pathogenesis, and Innate Immunity in Viral Chicken Diseases
by Anindita Sarma, Parul Suri, Megan Justice, Raja Angamuthu and Samuel Pushparaj
Non-Coding RNA 2025, 11(3), 42; https://doi.org/10.3390/ncrna11030042 - 26 May 2025
Viewed by 719
Abstract
The poultry farming industry encounters considerable obstacles stemming from viral diseases, resulting in elevated mortality rates and substantial economic losses. Current research highlights the significant involvement of long non-coding RNAs (lncRNAs) in the interactions between hosts and pathogens by enhancing antiviral responses at [...] Read more.
The poultry farming industry encounters considerable obstacles stemming from viral diseases, resulting in elevated mortality rates and substantial economic losses. Current research highlights the significant involvement of long non-coding RNAs (lncRNAs) in the interactions between hosts and pathogens by enhancing antiviral responses at different levels, such as the activation of pathogen recognition receptors, as well as through epigenetic, transcriptional, and post-transcriptional modifications. Specific long non-coding RNAs (lncRNAs), including ERL lncRNA, linc-GALMD3, and loc107051710, have been recognized as significant contributors to the antiviral immune response to multiple avian viral pathogens. Understanding the mechanisms by which long non-coding RNAs (lncRNAs) act offers valuable insights into prospective diagnostic and therapeutic approaches aimed at improving disease resistance in poultry. Differentially expressed lncRNAs may also be utilized as biomarkers for both prognosis and diagnosis of avian viral diseases. This review delves into the various roles of long non-coding RNAs (lncRNAs) in the context of viral diseases in chickens, such as avian leukosis, Marek’s disease, infectious bursal disease, avian influenza, infectious bronchitis, and Newcastle disease. It highlights the pivotal role of lncRNAs in the complex dynamics between the host and viral pathogens, particularly their interactions with specific viral proteins. Understanding these interactions may provide valuable insights into the spatial and temporal regulation of lncRNAs, aid in the identification of potential drug targets, and reveal the expression patterns of lncRNA and coding gene transcripts in response to different viral infections in avian species. Full article
(This article belongs to the Section Long Non-Coding RNA)
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26 pages, 3102 KiB  
Article
Effect of Recombinant Human Growth Hormone (rhGH) Use on Genetic Methylation Patterns and Their Relationship with Body Composition in Small-for-Gestational-Age (SGA) Newborns
by Juan M. Alfaro Velásquez, Elsa Maria Vásquez Trespalacios, Rodrigo Urrego, María C. Arroyave Toro, María del Pilar Montilla Velásquez, Cecilia Maria Díaz Soto, Juan C. Zuluaga Vélez, Verónica Jaramillo Henríquez, Jorge Emilio Salazar Flórez, Fernando P. Monroy, Hernando Alirio Palacio Mosquera, Sara Vélez Gómez and Ronald Guillermo Pelaez Sánchez
Biomedicines 2025, 13(6), 1288; https://doi.org/10.3390/biomedicines13061288 - 23 May 2025
Viewed by 918
Abstract
Background: Low birth weight in newborns is of multifactorial origin (fetal, maternal, placental, and environmental factors), and in one-third of cases, the cause is of unknown origin, with high infant morbidity and mortality. The main treatment for regaining weight and height in children [...] Read more.
Background: Low birth weight in newborns is of multifactorial origin (fetal, maternal, placental, and environmental factors), and in one-third of cases, the cause is of unknown origin, with high infant morbidity and mortality. The main treatment for regaining weight and height in children with low birth weight is the application of growth hormones. However, their role as a protective factor to prevent an increase in body composition and the development of metabolic diseases is still poorly understood. Methodology: A case–control study was conducted in a cohort of patients consulted at the CES Pediatric Endocrinology Clinic, Medellín, Colombia, between 2008 and 2018. We evaluated sociodemographic and clinical variables. Additionally, the identification of differential patterns of genomic methylation between cases (treated with growth hormone) and controls (without growth hormone treatment) was performed. The groups were compared using Fisher’s exact test for qualitative variables and Student’s t-test for the difference in means in independent samples. The correlation was evaluated with the Pearson coefficient. Results: Regarding clinical manifestations, body mass index (BMI) was higher in children who did not receive growth hormone treatment, higher doses of growth hormone treatment helped reduce body mass index (R: −0.21, and p = 0.067), and the use of growth hormone was related to a decrease in triglyceride blood concentrations (p = 0.06); these results tended towards significance. Regarding genome-wide methylation patterns, the following genes were found to be hypermethylated: MDGA1, HOXA5, LINC01168, ZFYVE19, ASAH1, MYH15, DNAJC17, PAMR1, MROCKI, CNDP2, CBY2, ZADH2, HOOK2, C9orf129, NXPH2, OSCP1, ZMIZ2, RUNX1, PTPRS, TEX26, EIF2A4K, MYO1F, C2orf69, and ZSCAN1. Meanwhile, the following genes were found hypomethylated: C10orf71-AS1, ZDHHC13, RPL17, EMC4, RPRD2, OBSCN-AS1, ZNF714, MUC4, SUGT1P4, TRIM38, C3, SPON1, NGF-AS1, CCSER2, P2RX2, LOC284379, GGTA1, NLRP5, OR51A4, HLA-H, and TTLL8. Conclusions: Using growth hormone as a treatment in SGA newborns helps regain weight and height. Additionally, it could be a protective factor against the increase in adolescent body composition. Full article
(This article belongs to the Section Cell Biology and Pathology)
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17 pages, 3712 KiB  
Article
Genome-Wide Detection of Leukemia Biomarkers from lincRNA–Protein-Coding Gene Interaction Networks in the Three-Dimensional Chromatin Structure
by Yue Hou, Wei Ning, Muren Huhe and Chuanjun Shu
Curr. Issues Mol. Biol. 2025, 47(6), 384; https://doi.org/10.3390/cimb47060384 - 22 May 2025
Viewed by 604
Abstract
The human genome is widely transcribed, with part of these transcribed regions producing stably expressed protein-coding or non-coding RNAs. Long intergenic non-coding RNAs (lincRNAs) are significantly differentially expressed in various cell lines and tissues. However, the influence of their transcription events remains unclear. [...] Read more.
The human genome is widely transcribed, with part of these transcribed regions producing stably expressed protein-coding or non-coding RNAs. Long intergenic non-coding RNAs (lincRNAs) are significantly differentially expressed in various cell lines and tissues. However, the influence of their transcription events remains unclear. In this study, we constructed a human genomic interaction network and found frequent interactions between lincRNA genes and protein-coding genes that are highly related to the occupancy of RNA polymerase II on the lincRNA gene. Interestingly, in the human genome interaction networks, the degree of lincRNA genes was significantly higher than that of protein-coding genes. The promoter regions of the protein-coding genes interacting with the lincRNA genes are enriched with R-loop structures, indicating that lincRNA may influence the target genes through R-loop structures. These promoters were enriched in more transcription factor binding sites. Furthermore, the whole network and sub-network could be utilized to explore potential biomarkers of leukemia. We found that zinc finger protein 668 (ZNF668), eosinophil granule ontogeny transcript (EGOT), and glutamate metabotropic receptor 7 (GRM7) could serve as novel biomarkers for acute myeloid leukemia (LMAL). Pasireotide acetate (CAS No. 396091-76-2) represents a potential drug for LMAL patients. These results suggested that potential biomarkers and corresponding drugs for cancer could be identified based on lincRNA–promoter network/sub-network topological parameters. Full article
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29 pages, 8846 KiB  
Article
Single-Cell Transcriptomic Profiling Reveals Regional Differences in the Prefrontal and Entorhinal Cortex of Alzheimer’s Disease Brain
by Rui-Ze Niu, Wan-Qing Feng, Li Chen and Tian-Hao Bao
Int. J. Mol. Sci. 2025, 26(10), 4841; https://doi.org/10.3390/ijms26104841 - 19 May 2025
Viewed by 885
Abstract
Previous studies have largely overlooked cellular differential alterations across differentially affected brain regions in both disease mechanisms and therapeutic development of Alzheimer’s disease (AD). This study aimed to compare the differential cellular and transcriptional changes in the prefrontal cortex (PFC) and entorhinal cortex [...] Read more.
Previous studies have largely overlooked cellular differential alterations across differentially affected brain regions in both disease mechanisms and therapeutic development of Alzheimer’s disease (AD). This study aimed to compare the differential cellular and transcriptional changes in the prefrontal cortex (PFC) and entorhinal cortex (EC) of AD patients through an integrated single-cell transcriptomic analysis. We integrated three single-cell RNA sequencing (scRNA-seq) datasets comprising PFC and EC samples from AD patients and age-matched healthy controls. A total of 124,658 nuclei and 31 cell clusters were obtained and classified into eight major cell types, with EC exhibiting much more pronounced transcriptional alterations than PFC. Through network analysis, we pinpointed hub regulatory genes that form interconnected networks driving AD pathogenesis, findings validated by RT-qPCR showing more pronounced expression changes in EC versus PFC of AD mice. Moreover, dysregulation of the LINC01099-associated regulatory networks in the PFC and EC, showing correlation with AD progression, may present new therapeutic targets for AD. Together, these results suggest that effective AD biomarkers and therapeutic strategies may require simultaneous, precise targeting of specific cell populations across multiple brain regions. Full article
(This article belongs to the Section Molecular Neurobiology)
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14 pages, 638 KiB  
Systematic Review
Genetic Determinants of Colonic Diverticulosis—A Systematic Review
by Piotr Nehring and Adam Przybyłkowski
Genes 2025, 16(5), 581; https://doi.org/10.3390/genes16050581 - 15 May 2025
Viewed by 820
Abstract
Background: Colonic diverticulosis is a common condition, particularly in the elderly population. While dietary habits, obesity, smoking, and physical inactivity contribute to its pathogenesis, emerging evidence highlights a genetic predisposition affecting extracellular matrix (ECM) remodeling, inflammation, and connective tissue integrity. The aim [...] Read more.
Background: Colonic diverticulosis is a common condition, particularly in the elderly population. While dietary habits, obesity, smoking, and physical inactivity contribute to its pathogenesis, emerging evidence highlights a genetic predisposition affecting extracellular matrix (ECM) remodeling, inflammation, and connective tissue integrity. The aim of this systematic review was to summarize genetic determinants of colonic diverticulosis. Methods: The PubMed® database was searched for original studies in humans. The inclusion criteria were named genetic factor and confirmed diverticulosis. Patients with diverticulitis and diverticular diseases were excluded from this review. Results: Out of 137 publications, 10 articles met the inclusion criteria: six large association studies (GWAS) and four cross-sectional studies. The genes regulating ECM turnover, including TIMP1, MMP3, and MMP9, are involved in diverticulosis development. The TIMP1 (rs4898) T allele has been associated with increased susceptibility, potentially due to its role in ECM remodeling. Similarly, MMP3 (rs3025058) and MMP9 (rs3918242) polymorphisms contribute to altered collagen degradation. The COL3A1 (rs3134646) variant coding modified collagen type III may promote diverticular formation. Other genes, such as ARHGAP15 (rs4662344, rs6736741), affect cytoskeletal dynamics. Identified in GWAS studies, gene candidates may be grouped into blood group and immune system-related genes (ABO, HLA-DQA1, HLA-H, OAS1, TNFSF13, FADD), extracellular matrix and connective tissue genes (COL6A1, COLQ, EFEMP1, ELN, HAS2, TIMP2), signaling and cell communication (BMPR1B, WNT4, RHOU, PHGR1, PCSK5), nervous system and neurodevelopment (BDNF, CACNB2, GPR158, SIRT1, SCAPER, TRPS1), metabolism and transporters (SLC25A28, SLC35F3, RBKS, PPP1R14A, PPP1R16B), lipids and cholesterol (LDAH, LYPLAL1, STARD13), transcription and gene regulation (ZBTB4, UBTF, TNRC6B), apoptosis (FADD, PIAS1), and poorly characterized genes (C1TNF7, ENSG00000224849, ENSG00000251283, LINC01082, DISP2, SNX24, THEM4, UBL4B, UNC50, WDR70, SREK1IP1). Conclusions: There are a number of gene variants that probably predispose to colonic diverticulosis. Detailed characterization of the multigene background of diverticulosis will enable appropriate therapeutic or preventive interventions in the future. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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