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  • MDPI AG  (14)
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  • Biodiversity Research  (14)
  • 1
    Online Resource
    Online Resource
    Time-Series Clustering of lncRNA-mRNA Expression during the Adipogenic Transdifferentiation of Porcine Skeletal Muscle Satellite Cells
    MDPI AG ; 2022
    In:  Current Issues in Molecular Biology Vol. 44, No. 5 ( 2022-05-06), p. 2038-2053
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 44, No. 5 ( 2022-05-06), p. 2038-2053
    Abstract: Skeletal muscle satellite cells (SMSCs), which are multifunctional muscle-derived stem cells, can differentiate into adipocytes. Long-chain non-coding RNA (lncRNA) has diverse biological functions, including the regulation of gene expression, chromosome silencing, and nuclear transport. However, the regulatory roles and mechanism of lncRNA during adipogenic transdifferentiation in muscle cells have not been thoroughly investigated. Here, porcine SMSCs were isolated, cultured, and induced for adipogenic differentiation. The expressions of lncRNA and mRNA at different time points during transdifferentiation were analysed using RNA-seq analysis. In total, 1005 lncRNAs and 7671 mRNAs showed significant changes in expression at differential differentiation stages. Time-series expression analysis showed that the differentially expressed (DE) lncRNAs and mRNAs were clustered into 5 and 11 different profiles with different changes, respectively. GO, KEGG, and REACTOME enrichment analyses revealed that DE mRNAs with increased expressions during the trans-differentiation were mainly enriched in the pathways for lipid metabolism and fat cell differentiation. The genes with decreased expressions were mainly enriched in the regulation of cell cycle and genetic information processing. In addition, 1883 DE mRNAs were regulated by 193 DE lncRNAs, and these genes were related to the controlling in cell cycle mainly. Notably, three genes in the fatty acid binding protein (FABP) family significantly and continuously increased during trans-differentiation, and 15, 13, and 11 lncRNAs may target FABP3, FABP4, and FABP5 genes by cis- or trans-regulation, respectively. In conclusion, these studies identify a set of new potential regulator for adipogenesis and cell fate and help us in better understanding the molecular mechanisms of trans-differentiation.
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb44050138
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2090836-2
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  • 2
    Online Resource
    Online Resource
    Correction: Zhang et al. Parkin, as a Regulator, Participates in Arsenic Trioxide-Triggered Mitophagy in HeLa Cells. Curr. Issues Mol. Biol. 2022, 44, 2759–2771
    MDPI AG ; 2023
    In:  Current Issues in Molecular Biology Vol. 45, No. 10 ( 2023-09-26), p. 7843-7844
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 45, No. 10 ( 2023-09-26), p. 7843-7844
    Abstract: In the published publication [...]
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb45100495
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2090836-2
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  • 3
    Online Resource
    Online Resource
    Parkin, as a Regulator, Participates in Arsenic Trioxide-Triggered Mitophagy in HeLa Cells
    MDPI AG ; 2022
    In:  Current Issues in Molecular Biology Vol. 44, No. 6 ( 2022-06-20), p. 2759-2771
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 44, No. 6 ( 2022-06-20), p. 2759-2771
    Abstract: Parkin is a well-established synergistic mediator of mitophagy in dysfunctional mitochondria. Mitochondria are the main target of arsenic trioxide (ATO) cytotoxicity, and the effect of mitophagy on ATO action remains unclear. In this study, we used stable Parkin-expressing (YFP-Parkin) and Parkin loss-of-function mutant (Parkin C431S) HeLa cell models to ascertain whether Parkin-mediated mitophagy participates in ATO-induced apoptosis/cell death. Our data showed that the overexpression of Parkin significantly sensitized HeLa cells to ATO-initiated proliferation inhibition and apoptosis; however, the mutation of Parkin C431S significantly weakened this Parkin-mediated responsiveness. Our further investigation found that ATO significantly downregulated two fusion proteins (Mfn1/2) and upregulated fission-related protein (Drp1). Autophagy was also activated as evidenced by the formation of autophagic vacuoles and mitophagosomes, increased expression of PINK1, and recruitment of Parkin to impaired mitochondria followed by their degradation, accompanied by the increased transformation of LC3-I to LC3-II, increased expression of Beclin1 and decreased expression of P62 in YFP-Parkin HeLa cells. Enhanced mitochondrial fragmentation and autophagy indicated that mitophagy was activated. Furthermore, during the process of mitophagy, the overproduction of ROS implied that ROS might represent a key factor that initiates mitophagy following Parkin recruitment to mitochondria. In conclusion, our findings indicate that Parkin is critically involved in ATO-triggered mitophagy and functions as a potential antiproliferative target in cancer cells.
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb44060189
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2090836-2
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  • 4
    Online Resource
    Online Resource
    Baicalein Relieves Ferroptosis-Mediated Phagocytosis Inhibition of Macrophages in Ovarian Endometriosis
    MDPI AG ; 2022
    In:  Current Issues in Molecular Biology Vol. 44, No. 12 ( 2022-12-07), p. 6189-6204
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 44, No. 12 ( 2022-12-07), p. 6189-6204
    Abstract: Iron overload and oxidative stress have been reported to contribute to ferroptosis in endometriotic lesions. However, the possible roles of iron overload on macrophages in endometriosis (EMs) remain unknown. Based on recent reports by single-cell sequencing data of endometriosis, here we found significant upregulations of ferroptosis-associated genes in the macrophage of the endometriotic lesion. Additionally, there was an elevated expression of HMOX1, FTH1, and FTL in macrophages of peritoneal fluid in EMs, as well as iron accumulation in the endometriotic lesions. Notably, cyst fluid significantly up-regulated levels of intracellular iron and ferroptosis in Phorbol-12-myristate-13-acetate (PMA)-stimulated THP-1 cells. Additionally, high iron-induced ferroptosis obviously reduced PMA-stimulated THP-1 cells’ phagocytosis and increased the expression of angiogenic cytokines, such as vascular endothelial growth factor A (VEGFA) and interleukin 8 (IL8). Baicalein, a potential anti-ferroptosis compound, increased GPX4 expression, significantly inhibited ferroptosis, and restored phagocytosis of THP-1 cells in vitro. Collectively, our study reveals that ferroptosis triggered by high iron in cyst fluid promotes the development of EMs by impairing macrophage phagocytosis and producing more angiogenic cytokines (e.g., IL8 and VEGFA). Baicalein displays the potential for the treatment of EMs, especially in patients with high ferroptosis and low phagocytosis of macrophages.
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb44120422
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2090836-2
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  • 5
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    Online Resource
    Ductal Hyperkeratinization and Acinar Renewal Abnormality: New Concepts on Pathogenesis of Meibomian Gland Dysfunction
    MDPI AG ; 2023
    In:  Current Issues in Molecular Biology Vol. 45, No. 3 ( 2023-02-27), p. 1889-1901
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 45, No. 3 ( 2023-02-27), p. 1889-1901
    Abstract: Meibomian gland dysfunction (MGD) is a functional and morphological disorder of the meibomian glands which results in qualitative or quantitative alteration in meibum secretion and is the major cause of evaporative dry eye (EDE). EDE is often characterized by tear film instability, increased evaporation, hyperosmolarity, inflammation, and ocular surface disorder. The precise pathogenesis of MGD remains elusive. It has been widely considered that MGD develops as a result of ductal epithelial hyperkeratinization, which obstructs the meibomian orifice, halts meibum secretion, and causes secondary acinar atrophy and gland dropout. Abnormal self-renewal and differentiation of the acinar cells also play a significant role in MGD. This review summarizes the latest research findings regarding the possible pathogenesis of MGD and provides further treatment strategies for MGD-EDE patients.
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb45030122
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2090836-2
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  • 6
    Online Resource
    Online Resource
    Evaluation of the Efficacy of Immune and Inflammatory Markers in the Diagnosis of Lacrimal-Gland Benign Lymphoepithelial Lesion
    MDPI AG ; 2023
    In:  Current Issues in Molecular Biology Vol. 45, No. 3 ( 2023-03-01), p. 2013-2020
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 45, No. 3 ( 2023-03-01), p. 2013-2020
    Abstract: This study retrospectively analyzes the immune and inflammatory indices of patients with lacrimal-gland benign lymphoepithelial lesion (LGBLEL) in order to screen out reference indices with higher diagnostic efficacy. The medical histories of patients whose diagnoses of LGBLEL and primary lacrimal prolapse were confirmed by pathology between August 2010 and August 2019 were collected. In the LGBLEL group, the erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) level, rheumatoid factor (RF), and immunoglobulins G, G1, G2, and G4 (IgG, IgG1, IgG2, IgG4) were higher (p 〈 0.05) and the expression level of C3 was lower (p 〈 0.05) compared to the lacrimal-gland prolapse group. Multivariate logistic regression analysis showed that IgG4, IgG, and C3 were independent risk factors for predicting LGBLEL occurrence (p 〈 0.05). The area under the receiver operating characteristic (ROC) curve of the prediction model (IgG4+IgG+C3) was 0.926, which was significantly better than that of any single factor. Therefore, serum levels of IgG4, IgG, and C3 were independent risk factors for predicting the occurrence of LGBLEL, and the combined diagnostic efficacy of IgG4+IgG+C3 was the highest.
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb45030129
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2090836-2
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  • 7
    Online Resource
    Online Resource
    Phenotypic Characterization and Comparative Genomic Analyses of Mycobacteriophage WIVsmall as A New Member Assigned to F1 Subcluster
    MDPI AG ; 2023
    In:  Current Issues in Molecular Biology Vol. 45, No. 8 ( 2023-08-03), p. 6432-6448
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 45, No. 8 ( 2023-08-03), p. 6432-6448
    Abstract: In this study, we conducted the morphological observation, biological and genomic characterization, evolutionary analysis, comparative genomics description, and proteome identification of a recently isolated mycobacteriophage, WIVsmall. Morphologically, WIVsmall is classified as a member of the Siphoviridae family, characterized by a flexible tail, measuring approximately 212 nm in length. The double-stranded phage genome DNA of WIVsmall spans 53,359 base pairs, and exhibits a G + C content of 61.01%. The genome of WIVsmall comprises 103 protein-coding genes, while no tRNA genes were detected. The genome annotation unveiled the presence of functional gene clusters responsible for mycobacteriophage assembly and maturation, replication, cell lysis, and functional protein synthesis. Based on the analysis of the phylogenetic tree, the genome of WIVsmall was classified as belonging to subgroup F1. A comparative genomics analysis indicated that the WIVsmall genome exhibited the highest similarity to the phage SG4, with a percentage of 64%. The single-step growth curve analysis of WIVsmall revealed a latent period of 120 min, and an outbreak period of 200 min.
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb45080406
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2090836-2
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  • 8
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    Online Resource
    Transcriptome Analysis and VIGS Identification of Key Genes Regulating Citric Acid Metabolism in Citrus
    MDPI AG ; 2023
    In:  Current Issues in Molecular Biology Vol. 45, No. 6 ( 2023-05-28), p. 4647-4664
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 45, No. 6 ( 2023-05-28), p. 4647-4664
    Abstract: Citrus (Citrus reticulata) is one of the world’s most widely planted and highest-yielding fruit trees. Citrus fruits are rich in a variety of nutrients. The content of citric acid plays a decisive role in the flavor quality of the fruit. There is a high organic acid content in early-maturing and extra-precocious citrus varieties. Reducing the amount of organic acid after fruit ripening is significant to the citrus industry. In this study, we selected a low-acid variety, “DF4”, and a high-acid variety, “WZ”, as research materials. Through WGCNA analysis, two differentially expressed genes, citrate synthase (CS) and ATP citrate-pro-S-lyase (ACL), were screened out, which related to the changing citric acid. The two differentially expressed genes were preliminarily verified by constructing a virus-induced gene-silencing (VIGS) vector. The VIGS results showed that the citric acid content was negatively correlated with CS expression and positively correlated with ACL expression, while CS and ACL oppositely control citric acid and inversely regulate each other. These results provide a theoretical basis for promoting the breeding of early-maturing and low-acid citrus varieties.
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb45060295
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2090836-2
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  • 9
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    Online Resource
    Role of Sleep Restriction in Daily Rhythms of Expression of Hypothalamic Core Clock Genes in Mice
    MDPI AG ; 2022
    In:  Current Issues in Molecular Biology Vol. 44, No. 2 ( 2022-01-25), p. 609-625
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 44, No. 2 ( 2022-01-25), p. 609-625
    Abstract: Lack of sleep time is a menace to modern people, and it leads to chronic diseases and mental illnesses. Circadian processes control sleep, but little is known about how sleep affects the circadian system. Therefore, we performed a 28-day sleep restriction (SR) treatment in mice. Sleep restriction disrupted the clock genes’ circadian rhythm. The circadian rhythms of the Cry1 and Per1/2/3 genes disappeared. The acrophase of the clock genes (Bmal1, Clock, Rev-erbα, and Rorβ) that still had a circadian rhythm was advanced, while the acrophase of negative clock gene Cry2 was delayed. Clock genes’ upstream signals ERK and EIFs also had circadian rhythm disorders. Accompanied by changes in the central oscillator, the plasma output signal (melatonin, corticosterone, IL-6, and TNF-α) had an advanced acrophase. While the melatonin mesor was decreased, the corticosterone, IL-6, and TNF-α mesor was increased. Our results indicated that chronic sleep loss could disrupt the circadian rhythm of the central clock through ERK and EIFs and affect the output signal downstream of the core biological clock.
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb44020042
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
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  • 10
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    Classical Angiogenic Signaling Pathways and Novel Anti-Angiogenic Strategies for Colorectal Cancer
    MDPI AG ; 2022
    In:  Current Issues in Molecular Biology Vol. 44, No. 10 ( 2022-09-26), p. 4447-4471
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 44, No. 10 ( 2022-09-26), p. 4447-4471
    Abstract: Although productive progress has been made in colorectal cancer (CRC) researchs, CRC is the second most frequent type of malignancy and the major cause of cancer-related death among gastrointestinal cancers. As angiogenesis constitutes an important point in the control of CRC progression and metastasis, understanding the key signaling pathways that regulate CRC angiogenesis is critical in elucidating ways to inhibit CRC. Herein, we comprehensively summarized the angiogenesis-related pathways of CRC, including vascular endothelial growth factor (VEGF), nuclear factor-kappa B (NF-κB), Janus kinase (JAK)/signal transducer and activator of transcription (STAT), Wingless and int-1 (Wnt), and Notch signaling pathways. We divided the factors influencing the specific pathway into promoters and inhibitors. Among these, some drugs or natural compounds that have antiangiogenic effects were emphasized. Furthermore, the interactions of these pathways in angiogenesis were discussed. The current review provides a comprehensive overview of the key signaling pathways that are involved in the angiogenesis of CRC and contributes to the new anti-angiogenic strategies for CRC.
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb44100305
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2090836-2
    SSG: 12
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