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Frontiers in Medicine 2021Podocytes are an integral part of the glomerular filtration barrier. Many genes are already known to be essential for podocyte survival, structure and function, but...
Podocytes are an integral part of the glomerular filtration barrier. Many genes are already known to be essential for podocyte survival, structure and function, but there are more podocyte essential genes to be identified. By single-cell RNA-seq of mouse podocytes, we detected the expression of gene encoding MCC regulator of WNT signaling pathway (MCC) in majority of the podocytes and speculated that MCC is essential for podocytes. We confirmed MCC expression in mouse podocytes and further showed its expression in human podocytes. To experimentally prove the essentiality of MCC for podocytes, we knocked down MCC in cultured podocytes and found marked morphological change of cell shape, cytoskeletal F-actin stress fiber disruption, increased apoptosis, and downregulation of podocyte essential genes, CD2AP and WT1, demonstrating that MCC is essential for podocytes. Since MCC has been implicated in cell cycle and β-catenin signaling, we examined the expression of cell cycle related genes and activity of β-catenin in the MCC knockdown podocytes, but did not find significant changes. To further explore the mechanism underlying the role of MCC in podocytes, we performed RNA-sequencing and bioinformatics analysis of MCC knockdown podocytes and found a significant enrichment of the regulated genes in lamellipodia formation. Consistently, we found that MCC is present in lamellipodia and MCC knockdown resulted in loss of lamellipodia in the cells. Lastly, we found that MCC was downregulated in podocytes treated with puromycin aminonucleosides and in glomeruli of diabetic mice and FSGS patients, implicating MCC is involved in the development of podocytopathy and proteinuria. In conclusion, MCC is potentially essential for podocytes and its downregulation may be involved in podocytopathy.
PubMed: 34926519
DOI: 10.3389/fmed.2021.777563 -
Cancers Jun 2022Chemotherapy is a mainstay of colorectal cancer treatment, and often involves a combination drug regime. CpG island methylator phenotype (CIMP)-positive tumors are...
Chemotherapy is a mainstay of colorectal cancer treatment, and often involves a combination drug regime. CpG island methylator phenotype (CIMP)-positive tumors are potentially more responsive to the topoisomerase-inhibitor irinotecan. The mechanistic basis of the increased sensitivity of CIMP cancers to irinotecan is poorly understood. Mutated in Colorectal Cancer () is emerging as a multifunctional tumor suppressor gene in colorectal and liver cancers, and has been implicated in drug responsiveness. Here, we found that CIMP tumors undergo loss almost exclusively via promoter hypermethylation rather than copy number variation or mutations. A subset of cancers display hypomethylation which is also associated with low expression, particularly in rectal cancer, where CIMP is rare. knockdown or deletion was found to sensitize cells to SN38 (the active metabolite of irinotecan) or the PARP-inhibitor Olaparib. A synergistic effect on cell death was evident when these drugs were used concurrently. The improved SN38/irinotecan efficacy was accompanied by the down-regulation of DNA repair genes. Thus, differential methylation of is potentially a valuable biomarker to identify colorectal cancers suitable for irinotecan therapy, possibly in combination with PARP inhibitors.
PubMed: 35740525
DOI: 10.3390/cancers14122859 -
Journal of Medical Virology Jul 2023Limited molecular knowledge of Merkel cell polyomavirus (MCPyV)-positive and -negative Merkel cell carcinoma (MCC) subsets (MCCP/MCCN) has prevented so far the...
Limited molecular knowledge of Merkel cell polyomavirus (MCPyV)-positive and -negative Merkel cell carcinoma (MCC) subsets (MCCP/MCCN) has prevented so far the identification of the MCC origin cell type and, therefore, the development of effective therapies. The retinoic gene signature was investigated in various MCCP, MCCN, and control fibroblast/epithelial cell lines to elucidate the heterogeneous nature of MCC. Hierarchical clustering and principal component analysis indicated that MCCP and MCCN cells were clusterizable from each other and control cells, according to their retinoic gene signature. MCCP versus MCCN differentially expressed genes (n = 43) were identified. Protein-protein interaction network indicated SOX2, ISL1, PAX6, FGF8, ASCL1, OLIG2, SHH, and GLI1 as upregulated hub genes and JAG1 and MYC as downregulated hub genes in MCCP compared to MCCN. Numerous MCCP-associated hub genes were DNA-binding/-transcription factors involved in neurological and Merkel cell development and stemness. Enrichment analyses indicated that MCCP versus MCCN differentially expressed genes predominantly encode for to DNA-binding/-transcription factors involved in development, stemness, invasiveness, and cancer. Our findings suggest the neuroendocrine origin of MCCP, by which neuronal precursor cells could undergo an MCPyV-driven transformation. These overarching results might open the way to novel retinoid-based MCC therapies.
Topics: Humans; Carcinoma, Merkel Cell; Merkel cell polyomavirus; Transcription Factors; Skin Neoplasms; DNA
PubMed: 37436928
DOI: 10.1002/jmv.28949 -
Frontiers in Endocrinology 2022Primary osteoporosis has long been underdiagnosed and undertreated. Currently, ferroptosis may be a promising research direction in the prevention and treatment of...
Primary osteoporosis has long been underdiagnosed and undertreated. Currently, ferroptosis may be a promising research direction in the prevention and treatment of primary osteoporosis. However, the specific mechanism of ferroptosis in primary osteoporosis remains a mystery. Differentially expressed genes (DEGs) were identified in bone mesenchymal stromal cells (BMSCs) of primary osteoporosis and heathy patients from the GEO databases with the help of bioinformatics analysis. Then, we intersected these DEGs with the ferroptosis dataset and obtained 80 Ferr-DEGs. Several bioinformatics algorithms (PCA, RLE, Limma, BC, MCC, etc.) were adopted to integrate the results. Additionally, we explored the potential functional roles of the Ferr-DEGs GO and KEGG. Protein-protein interactions (PPI) were used to predict potential interactive networks. Finally, 80 Ferr-DEGs and 5 key Ferr-DEGs were calculated. The 5 key Ferr-DEGs were further verified in the OVX mouse model. In conclusion, through a variety of bioinformatics methods, our research successfully identified 5 key Ferr-DEGs associated with primary osteoporosis and ferroptosis, namely, sirtuin 1(), heat shock protein family A () member 5 (), mechanistic target of rapamycin kinase (), hypoxia inducible factor 1 subunit alpha () and beclin 1 (), which were verified in an animal model.
Topics: Animals; Computational Biology; Ferroptosis; Gene Expression Profiling; Mesenchymal Stem Cells; Mice; Osteoporosis
PubMed: 36093072
DOI: 10.3389/fendo.2022.980867 -
Annual Review of Pathology Jan 2021Merkel cell carcinoma (MCC) is an aggressive neuroendocrine carcinoma of the skin with two distinct etiologies. Clonal integration of Merkel cell polyomavirus DNA into... (Review)
Review
Merkel cell carcinoma (MCC) is an aggressive neuroendocrine carcinoma of the skin with two distinct etiologies. Clonal integration of Merkel cell polyomavirus DNA into the tumor genome with persistent expression of viral T antigens causes at least 60% of all MCC. UV damage leading to highly mutated genomes causes a nonviral form of MCC. Despite these distinct etiologies, both forms of MCC are similar in presentation, prognosis, and response to therapy. At least three oncogenic transcriptional programs feature prominently in both forms of MCC driven by the virus or by mutation. Both forms of MCC have a high proliferative growth rate with increased levels of cell cycle-dependent genes due to inactivation of the tumor suppressors RB and p53, a strong MYC signature due to MYCL activation by the virus or gene amplification, and an attenuated neuroendocrine differentiation program driven by the ATOH1 transcription factor.
Topics: Carcinogenesis; Carcinoma, Merkel Cell; Humans; Merkel cell polyomavirus; Mutation; Polyomavirus Infections; Skin Neoplasms; Tumor Virus Infections
PubMed: 33228463
DOI: 10.1146/annurev-pathmechdis-012419-032817 -
Gene Jan 2023Glioblastoma (GBM) is the most common malignant brain tumor among adults. Cancer stem cells (CSCs) are known to drive treatment resistance and recurrence. However, a few...
Glioblastoma (GBM) is the most common malignant brain tumor among adults. Cancer stem cells (CSCs) are known to drive treatment resistance and recurrence. However, a few CSC markers have been identified as therapeutic targets for GBM. This study aimed to show highly coexpressed genes in GBM CSCs and TCGA GBM samples and to identify possible therapeutic targets for GBM. The gene expression profiles of GBM CSCs were obtained from Gene Expression Omnibus database. After the differentially upregulated genes were screened, functional enrichment analyses were performed using DAVID and Reactome databases. For upregulated genes, biological processes were mainly associated with the regulation of transcription. Subsequently, a protein-protein interaction network was constructed for upregulated genes through STRING, in which DUSP6, FGFR3, EGFR, SOX2, NES, and PLP1 were further identified as hub genes via MCC and MNC methods. Expression profiles of hub genes and their association with survival were examined in TCGA GBM dataset using GEPIA2 platform. The expression levels of four hub genes were found to be increased in TCGA GBM samples. Of these, DUSP6 and SOX2 had prognostic value for patients with GBM. Molecular compounds targeting DUSP6 were searched through PubChem database. (E/Z)-BCI and BCI were found to be inhibitors of DUSP6. The molecular docking was performed using Autodock vina 1.02. The compounds showed strong binding capacities by forming various interactions with the ERK2 binding domain of DUSP6. Hence, the current study unravels the potential of (E/Z)-BCI and BCI compounds as possible anti-cancer molecules for GBM treatment.
Topics: Adult; Brain Neoplasms; Computational Biology; ErbB Receptors; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Glioblastoma; Humans; Molecular Docking Simulation; Neoplastic Stem Cells
PubMed: 36122609
DOI: 10.1016/j.gene.2022.146895 -
Surgical Pathology Clinics Jun 2017Merkel cell carcinoma (MCC) encompasses neuroendocrine carcinomas primary to skin and occurs most commonly in association with clonally integrated Merkel cell... (Review)
Review
Merkel cell carcinoma (MCC) encompasses neuroendocrine carcinomas primary to skin and occurs most commonly in association with clonally integrated Merkel cell polyomavirus with related retinoblastoma protein sequestration or in association with UV radiation-induced alterations involving the TP53 gene and mutations, heterozygous deletion, and hypermethylation of the Retinoblastoma gene. Molecular genetic signatures may provide therapeutic guidance. Morphologic features, although patterned, are associated with predictable diagnostic pitfalls, usually resolvable by immunohistochemistry. Therapeutic options for MCC, traditionally limited to surgical intervention and later chemotherapy and radiation, are growing, given promising early results of immunotherapeutic regimens.
Topics: Carcinoma, Merkel Cell; Genes, Retinoblastoma; Humans; Merkel cell polyomavirus; Retinoblastoma Protein; Skin Neoplasms
PubMed: 28477888
DOI: 10.1016/j.path.2017.01.013 -
Frontiers in Immunology 2024Idiopathic pulmonary fibrosis (IPF) is characterized by progressive lung dysfunction due to excessive collagen production and tissue scarring. Despite recent...
INTRODUCTION
Idiopathic pulmonary fibrosis (IPF) is characterized by progressive lung dysfunction due to excessive collagen production and tissue scarring. Despite recent advancements, the molecular mechanisms remain unclear.
METHODS
RNA sequencing identified 475 differentially expressed genes (DEGs) in the TGF-β1-induced primary lung fibrosis model. Gene expression chips GSE101286 and GSE110147 from NCBI gene expression omnibus (GEO) database were analyzed using GEO2R, revealing 94 DEGs in IPF lung tissue samples. The gene ontology (GO) and pathway enrichment, Protein-protein interaction (PPI) network construction, and Maximal Clique Centrality (MCC) scoring were performed. Experimental validation included RT-qPCR, Immunohistochemistry (IHC), and Western Blot, with siRNA used for gene knockdown. A co-expression network was constructed by GeneMANIA.
RESULTS
GO enrichment highlighted significant enrichment of DEGs in TGF-β cellular response, connective tissue development, extracellular matrix components, and signaling pathways such as the AGE-RAGE signaling pathway and ECM-receptor interaction. PPI network analysis identified hub genes, including FN1, COL1A1, POSTN, KIF11, and ECT2. CALD1 (Caldesmon 1), CDH2 (Cadherin 2), and POSTN (Periostin) were identified as dysregulated hub genes in both the RNA sequencing and GEO datasets. Validation experiments confirmed the upregulation of CALD1, CDH2, and POSTN in TGF-β1-treated fibroblasts and IPF lung tissue samples. IHC experiments probed tissue-level expression patterns of these three molecules. Knockdown of CALD1, CDH2, and POSTN attenuated the expression of fibrotic markers (collagen I and α-SMA) in response to TGF-β1 stimulation in primary fibroblasts. Co-expression analysis revealed interactions between hub genes and predicted genes involved in actin cytoskeleton regulation and cell-cell junction organization.
CONCLUSIONS
CALD1, CDH2, and POSTN, identified as potential contributors to pulmonary fibrosis, present promising therapeutic targets for IPF patients.
Topics: Humans; Antigens, CD; Cadherins; Calmodulin-Binding Proteins; Cell Adhesion Molecules; Collagen; Fibroblasts; Gene Expression; Idiopathic Pulmonary Fibrosis; Transforming Growth Factor beta1
PubMed: 38370408
DOI: 10.3389/fimmu.2024.1275064 -
Interdisciplinary Sciences,... Dec 2023DNA methylation is an epigenetic alteration that plays a fundamental part in governing gene regulatory processes. The DNA methylation mechanism affixes methyl groups to...
DNA methylation is an epigenetic alteration that plays a fundamental part in governing gene regulatory processes. The DNA methylation mechanism affixes methyl groups to distinct cytosine residues, influencing chromatin architectures. Multiple studies have demonstrated that DNA methylation's regulatory effect on genes is linked to the beginning and progression of several disorders. Researchers have recently uncovered thousands of phenotype-related methylation sites through the epigenome-wide association study (EWAS). However, combining the methylation levels of several sites within a gene and determining the gene-level DNA methylation remains challenging. In this study, we proposed the supervised UMAP Assisted Gene-level Methylation method (sUAGM) for disease prediction based on supervised UMAP (Uniform Manifold Approximation and Projection), a manifold learning-based method for reducing dimensionality. The methylation values at the gene level generated using the proposed method are evaluated by employing various feature selection and classification algorithms on three distinct DNA methylation datasets derived from blood samples. The performance has been assessed employing classification accuracy, F-1 score, Mathews Correlation Coefficient (MCC), Kappa, Classification Success Index (CSI) and Jaccard Index. The Support Vector Machine with the linear kernel (SVML) classifier with Recursive Feature Elimination (RFE) performs best across all three datasets. From comparative analysis, our method outperformed existing gene-level and site-level approaches by achieving 100% accuracy and F1-score with fewer genes. The functional analysis of the top 28 genes selected from the Parkinson's disease dataset revealed a significant association with the disease.
PubMed: 37603212
DOI: 10.1007/s12539-023-00584-w -
International Journal of Molecular... Jul 2023The MCC family of genes plays a role in colorectal cancer development through various immunological pathways, including the Th17/Treg axis. We have previously shown that...
The MCC family of genes plays a role in colorectal cancer development through various immunological pathways, including the Th17/Treg axis. We have previously shown that MCC1 but not MCC2 plays a role in Treg differentiation. Our understanding of the genetic divergence patterns and evolutionary history of the MCC family in relation to its function, in general, and the Th17/Treg axis, in particular, remains incomplete. In this investigation, we explored 12 species' genomes to study the phylogenetic origin, structure, and functional specificity of this family. In vertebrates, both MCC1 and MCC2 homologs have been discovered, while invertebrates have a single MCC homolog. We found MCC homologs as early as Cnidarians and Trichoplax, suggesting that the MCC family first appeared 741 million years ago (Ma), whereas MCC divergence into the MCC1 and MCC2 families occurred at 540 Ma. In general, we did not detect significant positive selection regulating MCC evolution. Our investigation, based on MCC1 structural similarity, suggests that they may play a role in the evolutionary changes in Tregs' emergence towards complexity, including the ability to utilize calcium for differentiation through the use of the EFH calcium-binding domain. We also found that the motif NPSTGE was highly conserved in MCC1, but not in MCC2. The NPSTGE motif binds KEAP1 with high affinity, suggesting an Nrf2-mediated function for MCC1. In the case of MCC2, we found that the "modifier of rudimentary" motif is highly conserved. This motif contributes to the regulation of alternative splicing. Overall, our study sheds light on how the evolution of the MCC family is connected to its function in regulating the Th17/Treg axis.
Topics: Animals; Humans; Kelch-Like ECH-Associated Protein 1; Phylogeny; T-Lymphocytes, Regulatory; Calcium; NF-E2-Related Factor 2; Colorectal Neoplasms; Th17 Cells
PubMed: 37569317
DOI: 10.3390/ijms241511940