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Scientific Reports Aug 2021Mandibular condylar cartilage (MCC) is a multi-zonal heterogeneous fibrocartilage containing different types of cells, but the factors/mechanisms governing the...
Mandibular condylar cartilage (MCC) is a multi-zonal heterogeneous fibrocartilage containing different types of cells, but the factors/mechanisms governing the phenotypic transition across the zones have not been fully understood. The reliability of molecular studies heavily rely on the procurement of pure cell populations from the heterogeneous tissue. We used a combined laser-capture microdissection and microarray analysis approach which allowed identification of differential zone-specific gene expression profiling and altered pathways in the MCC of 5-week-old rats. The bioinformatics analysis demonstrated that the MCC cells clearly exhibited distinguishable phenotypes from the articular chondrocytes. Additionally, a set of genes has been determined as potential markers to identify each MCC zone individually; Crab1 gene showed the highest enrichment while Clec3a was the most downregulated gene at the superficial layer, which consists of fibrous (FZ) and proliferative zones (PZ). Ingenuity Pathway Analysis revealed numerous altered signaling pathways; Leukocyte extravasation signaling pathway was predicted to be activated at all MCC zones, in particular mature and hypertrophic chondrocytes zones (MZ&HZ), when compared with femoral condylar cartilage (FCC). Whereas Superpathway of Cholesterol Biosynthesis showed predicted activation in both FZ and PZ as compared with deep MCC zones and FCC. Determining novel zone-specific differences of large group of potential genes, upstream regulators and pathways in healthy MCC would improve our understanding of molecular mechanisms on regional (zonal) basis, and provide new insights for future therapeutic strategies.
Topics: Cartilage, Articular; Gene Expression Profiling; Gene Expression Regulation; Humans; Leukocytes; Mandibular Condyle; Molecular Sequence Annotation; Reproducibility of Results; Signal Transduction
PubMed: 34413358
DOI: 10.1038/s41598-021-96071-7 -
Epigenomes Sep 2022The polycomb group (PcG) proteins are a subset of transcription regulators highly conserved throughout evolution. Their principal role is to epigenetically modify... (Review)
Review
The polycomb group (PcG) proteins are a subset of transcription regulators highly conserved throughout evolution. Their principal role is to epigenetically modify chromatin landscapes and control the expression of master transcriptional programs to determine cellular identity. The two mayor PcG protein complexes that have been identified in mammals to date are Polycomb Repressive Complex 1 (PRC1) and 2 (PRC2). These protein complexes selectively repress gene expression via the induction of covalent post-translational histone modifications, promoting chromatin structure stabilization. PRC2 catalyzes the histone H3 methylation at lysine 27 (H3K27me1/2/3), inducing heterochromatin structures. This activity is controlled by the formation of a multi-subunit complex, which includes enhancer of zeste (EZH2), embryonic ectoderm development protein (EED), and suppressor of zeste 12 (SUZ12). This review will summarize the latest insights into how PRC2 in mammalian cells regulates transcription to orchestrate the temporal and tissue-specific expression of genes to determine cell identity and cell-fate decisions. We will specifically describe how PRC2 dysregulation in different cell types can promote phenotypic plasticity and/or non-mutational epigenetic reprogramming, inducing the development of highly aggressive epithelial neuroendocrine carcinomas, including prostate, small cell lung, and Merkel cell cancer. With this, EZH2 has emerged as an important actionable therapeutic target in such cancers.
PubMed: 36135315
DOI: 10.3390/epigenomes6030028 -
Molecular Microbiology Dec 2011Assimilatory and dissimilatory sulphite reductions are key reactions in the biogeochemical sulphur cycle and several distinct sirohaem-containing sulphite reductases...
Assimilatory and dissimilatory sulphite reductions are key reactions in the biogeochemical sulphur cycle and several distinct sirohaem-containing sulphite reductases have been characterized. Here, we describe that the Epsilonproteobacterium Wolinella succinogenes is able to grow by sulphite respiration (yielding sulphide) with formate as electron donor. Sulphite is reduced by MccA, a prototypical member of an emerging new class of periplasmic cytochrome c sulphite reductases that, phylogenetically, belongs to a multihaem cytochrome c superfamily whose members play crucial roles in the global sulphur and nitrogen cycles. Within this family, MccA represents an unconventional octahaem cytochrome c containing a special haem c group that is bound via two cysteine residues arranged in a unique CX(15)CH haem c binding motif. The phenotypes of numerous W.succinogenes mutants producing MccA variants underlined the structural importance of this motif. Several open reading frames of the mcc gene cluster were individually inactivated and characterization of the corresponding mutants indicated that the predicted iron-sulphur protein MccC, the putative quinol dehydrogenase MccD (a member of the NrfD/PsrC family) as well as a peptidyl-prolyl cis-trans isomerase, MccB, are essential for sulphite respiration. MccA synthesis in W. succinogenes was found to be induced by sulphite (but not by thiosulphate or sulphide) and repressed in the presence of fumarate or nitrate. Based on the results, a sophisticated model of respiratory sulphite reduction by the Mcc system is presented.
Topics: Amino Acid Sequence; Bacterial Proteins; Iron-Sulfur Proteins; Molecular Sequence Data; Multigene Family; Oxidation-Reduction; Sulfite Dehydrogenase; Sulfites; Wolinella
PubMed: 22040142
DOI: 10.1111/j.1365-2958.2011.07906.x -
Cancer Letters Dec 1998APC gene mutations have been demonstrated not only in colorectal carcinoma but also in a variety of human cancers. To define the possible role of mutations of the APC...
APC gene mutations have been demonstrated not only in colorectal carcinoma but also in a variety of human cancers. To define the possible role of mutations of the APC gene in hepatocarcinogenesis, we examined 46 pairs of hepatocellular carcinomas and corresponding non-tumorous liver tissue by polymerase chain reaction and single strand conformation polymorphism. All 46 hepatocellular carcinomas had no altered electrophoretic mobility to suggest the presence of APC gene mutation in the mutation cluster region. We also examined the possible loss of heterozygosity of APC and MCC gene loci by fragment length polymorphism analysis and by polymerase chain reaction. None of the cases showed a loss of heterozygosity at the APC and MCC gene loci. The results suggested that the possibility of APC and MCC as the gene defect in the genesis of human hepatocellular carcinoma may be very rare.
Topics: Adult; Aged; Aged, 80 and over; Carcinoma, Hepatocellular; DNA Mutational Analysis; DNA, Neoplasm; Female; Genes, APC; Humans; Liver Neoplasms; Loss of Heterozygosity; Male; Middle Aged; Mutation; Polymerase Chain Reaction; Polymorphism, Single-Stranded Conformational; Proteins; Tumor Suppressor Proteins
PubMed: 10381126
DOI: 10.1016/s0304-3835(98)00238-9 -
Chest Apr 1993Lung cancers exhibit multiple genetic lesions including mutations activating the dominant cellular proto-oncogenes as well as those inactivating the recessive or "tumor... (Review)
Review
Lung cancers exhibit multiple genetic lesions including mutations activating the dominant cellular proto-oncogenes as well as those inactivating the recessive or "tumor suppressor" genes. Candidate tumor suppressor genes include those on chromosomes 1p, 1q, 3p14, 3p21.3, 3p25 (VHL gene), 5q21 (APC/MCC gene cluster), 9p21-22 (interferon gene cluster), 11p, 13q (rb gene), 16p24, and 17p (p53 gene). Mutations in p53 inactivate its transcriptional activity, while replacement of a wild-type p53 in lung cancer cells inhibits growth and tumorigenicity suggesting that p53 acts as a master growth regulatory switch. Lung cancer cells exhibit several positive autocrine growth factor loops and express nicotine receptors which could function as tumor promoting systems. In addition, they express a negative autocrine loop involving opioids and their receptors which is reversed by nicotine acting through nicotinic acetylcholine receptors. The presence of nicotine receptors suggests nicotine or its metabolites may play a direct role in lung cancer pathogenesis.
Topics: Carcinogens; Chromosome Aberrations; Humans; Lung Neoplasms; Mutation; Narcotics; Oncogenes
PubMed: 8462339
DOI: 10.1378/chest.103.4_supplement.449s -
The Journal of Veterinary Medical... Nov 2023Merkel cell carcinoma (MCC) is a rare skin tumor that shares a similar immunophenotype with Merkel cells, although its origin is debatable. More than 80% of human MCC... (Review)
Review
Merkel cell carcinoma (MCC) is a rare skin tumor that shares a similar immunophenotype with Merkel cells, although its origin is debatable. More than 80% of human MCC cases are associated with Merkel cell polyomavirus infections and viral gene integration. Recent studies have shown that the clinical and pathological characteristics of feline MCC are comparable to those of human MCC, including its occurrence in aged individuals, aggressive behavior, histopathological findings, and the expression of Merkel cell markers. More than 90% of feline MCC are positive for the Felis catus papillomavirus type 2 (FcaPV2) gene. Molecular changes involved in papillomavirus-associated tumorigenesis, such as increased p16 and decreased retinoblastoma (Rb) and p53 protein levels, were observed in FcaPV2-positive MCC, but not in FcaPV2-negative MCC cases. These features were also confirmed in FcaPV2-positive and -negative MCC cell lines. The expression of papillomavirus E6 and E7 genes, responsible for p53 degradation and Rb inhibition, respectively, was detected in tumor cells by in situ hybridization. Whole genome sequencing revealed the integration of FcaPV2 DNA into the host feline genome. MCC cases often develop concurrent skin lesions, such as viral plaque and squamous cell carcinoma, which are also associated with papillomavirus infection. These findings suggest that FcaPV2 infection and integration of viral genes are involved in the development of MCC in cats. This review provides an overview of the comparative pathology of feline and human MCC caused by different viruses and discusses their cell of origin.
Topics: Humans; Cats; Animals; Carcinoma, Merkel Cell; Tumor Suppressor Protein p53; Papillomaviridae; Merkel Cells; Skin Neoplasms; Cat Diseases
PubMed: 37743525
DOI: 10.1292/jvms.23-0322 -
Cancer Sep 1992Tumorigenesis is thought to be a multistep process in which genetic alterations accumulate, ultimately producing the neoplastic phenotype. A model was proposed to... (Review)
Review
Tumorigenesis is thought to be a multistep process in which genetic alterations accumulate, ultimately producing the neoplastic phenotype. A model was proposed to explain the genetic basis of colorectal neoplasia that included several salient features. First, colorectal tumors appear to occur as a result of the mutational activation of oncogenes coupled with the inactivation of tumor-suppressor genes. Second, mutations in at least four or five genes are required to produce a malignant tumor. Third, although the genetic alterations often occur in a preferred sequence, the total accumulation of changes, rather than their chronologic order of appearance, is responsible for determining the tumor's biologic properties. Several different genetic alterations were identified that occur during colorectal tumorigenesis. Activational mutation of the ras oncogene was found in approximately 50% of colonic carcinomas and in a similar percentage of intermediate-stage and late-stage adenomas. Allelic deletions were discovered of specific portions of chromosomes 5, 17, and 18, which presumably harbor tumor-suppressor genes. The target of allelic loss events on chromosome 17 has been shown to be the p53 gene, which is mutated, not only in colonic cancer, but also in a large percentage of other human solid tumors. The gene dcc recently was identified; this candidate tumor-suppressor gene on chromosome 18 appears to be altered in colorectal carcinomas. The protein encoded by the dcc gene has significant sequence similarity to neural cell adhesion molecules and other related cell-surface glycoproteins. By mediating cell-cell and cell-substrate interactions, this class of molecules may have important functions in mediating cell growth and differentiation. Alterations of the dcc gene may interfere with maintenance of these controls and thus may play a role in the pathogenesis of colorectal neoplasia. Another candidate tumor-suppressor gene also was identified on chromosome 5, mcc (for mutated in colorectal cancers). The mcc genetic alterations include one tumor with somatic rearrangement of one mcc allele and several tumors with somatically acquired point mutations in the coding region. Studies currently are ongoing to (1) identify additional tumor-suppressor gene candidates, (2) increase our understanding of normal tumor-suppressor gene function, and (3) demonstrate the functional tumor-suppressor ability of these genes both in vivo and in vitro.
Topics: Adenoma; Alleles; Carcinoma; Cell Adhesion Molecules; Chromosome Deletion; Colorectal Neoplasms; Genes, Tumor Suppressor; Genes, ras; Humans; Models, Genetic; Mutation
PubMed: 1516027
DOI: 10.1002/1097-0142(19920915)70:4+<1727::aid-cncr2820701613>3.0.co;2-p -
Translational Oncology Nov 2020Merkel cell carcinoma (MCC) is a rare primary cutaneous neoplasm of neuroendocrine carcinoma of the skin. About 80% of the MCC occurs due to Merkel cell polyomavirus...
Merkel cell carcinoma (MCC) is a rare primary cutaneous neoplasm of neuroendocrine carcinoma of the skin. About 80% of the MCC occurs due to Merkel cell polyomavirus (MCPyV) and 20% of the tumors usually occur due to severe UV exposure which is a more aggressive type of MCC. It tends to have an increased incidence rate among elderly and immunosuppressed individuals. On therapeutic level, sub-classification of MCC through molecular subtyping has emerged as a promising technique for MCC prognosis. In current study, two consistent distinct molecular subtypes of MCCs were identified using gene expression profiling data. Subtypes I MCCs were associated with spliceosome, DNA replication and cellular pathways. On the other hand, genes overexpressed in subtype II were found active in TNF signalling pathway and MAPK signalling pathway. We proposed different therapeutic targets based on subtype specificity, such as PTCH1, CDKN2A, AURKA in case of subtype I and MCL1, FGFR2 for subtype II. Such findings may provide fruitful knowledge to understand the intrinsic subtypes of MCCs and the pathways involved in distinct subtype oncogenesis, and will further advance the knowledge in developing a specific therapeutic strategy for these MCC subtypes.
PubMed: 32771971
DOI: 10.1016/j.tranon.2020.100816 -
BMC Cancer Sep 2020Multiple myeloma (MM) is an incurable hematological tumor, which is closely related to hypoxic bone marrow microenvironment. However, the underlying mechanisms are still...
BACKGROUND
Multiple myeloma (MM) is an incurable hematological tumor, which is closely related to hypoxic bone marrow microenvironment. However, the underlying mechanisms are still far from fully understood. We took integrated bioinformatics analysis with expression profile GSE110113 downloaded from National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database, and screened out major histocompatibility complex, class II, DP alpha 1 (HLA-DPA1) as a hub gene related to hypoxia in MM.
METHODS
Differentially expressed genes (DEGs) were filtrated with R package "limma". Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed using "clusterProfiler" package in R. Then, protein-protein interaction (PPI) network was established. Hub genes were screened out according to Maximal Clique Centrality (MCC). PrognoScan evaluated all the significant hub genes for survival analysis. ScanGEO was used for visualization of gene expression in different clinical studies. P and Cox p value < 0.05 was considered to be statistical significance.
RESULTS
HLA-DPA1 was finally picked out as a hub gene in MM related to hypoxia. MM patients with down-regulated expression of HLA-DPA1 has statistically significantly shorter disease specific survival (DSS) (COX p = 0.005411). Based on the clinical data of GSE47552 dataset, HLA-DPA1 expression showed significantly lower in MM patients than that in healthy donors (HDs) (p = 0.017).
CONCLUSION
We identified HLA-DPA1 as a hub gene in MM related to hypoxia. HLA-DPA1 down-regulated expression was associated with MM patients' poor outcome. Further functional and mechanistic studies are need to investigate HLA-DPA1 as potential therapeutic target.
Topics: Down-Regulation; HLA-DP alpha-Chains; Humans; Multiple Myeloma; Prognosis; Survival Analysis
PubMed: 32972413
DOI: 10.1186/s12885-020-07393-0 -
PloS One 2022Selecting the most relevant genes for sample classification is a common process in gene expression studies. Moreover, determining the smallest set of relevant genes that...
MOTIVATION
Selecting the most relevant genes for sample classification is a common process in gene expression studies. Moreover, determining the smallest set of relevant genes that can achieve the required classification performance is particularly important in diagnosing cancer and improving treatment.
RESULTS
In this study, I propose a novel method to eliminate irrelevant and redundant genes, and thus determine the smallest set of relevant genes for breast cancer diagnosis. The method is based on random forest models, gene set enrichment analysis (GSEA), and my developed Sort Difference Backward Elimination (SDBE) algorithm; hence, the method is named GSEA-SDBE. Using this method, genes are filtered according to their importance following random forest training and GSEA is used to select genes by core enrichment of Kyoto Encyclopedia of Genes and Genomes pathways that are strongly related to breast cancer. Subsequently, the SDBE algorithm is applied to eliminate redundant genes and identify the most relevant genes for breast cancer diagnosis. In the SDBE algorithm, the differences in the Matthews correlation coefficients (MCCs) of performing random forest models are computed before and after the deletion of each gene to indicate the degree of redundancy of the corresponding deleted gene on the remaining genes during backward elimination. Next, the obtained MCC difference list is divided into two parts from a set position and each part is respectively sorted. By continuously iterating and changing the set position, the most relevant genes are stably assembled on the left side of the gene list, facilitating their identification, and the redundant genes are gathered on the right side of the gene list for easy elimination. A cross-comparison of the SDBE algorithm was performed by respectively computing differences between MCCs and ROC_AUC_score and then respectively using 10-fold classification models, e.g., random forest (RF), support vector machine (SVM), k-nearest neighbor (KNN), extreme gradient boosting (XGBoost), and extremely randomized trees (ExtraTrees). Finally, the classification performance of the proposed method was compared with that of three advanced algorithms for five cancer datasets. Results showed that analyzing MCC differences and using random forest models was the optimal solution for the SDBE algorithm. Accordingly, three consistently relevant genes (i.e., VEGFD, TSLP, and PKMYT1) were selected for the diagnosis of breast cancer. The performance metrics (MCC and ROC_AUC_score, respectively) of the random forest models based on 10-fold verification reached 95.28% and 98.75%. In addition, survival analysis showed that VEGFD and TSLP could be used to predict the prognosis of patients with breast cancer. Moreover, the proposed method significantly outperformed the other methods tested as it allowed selecting a smaller number of genes while maintaining the required classification accuracy.
Topics: Algorithms; Benchmarking; Breast Neoplasms; Cluster Analysis; Female; Humans; Membrane Proteins; Protein Serine-Threonine Kinases; Protein-Tyrosine Kinases; Support Vector Machine
PubMed: 35472078
DOI: 10.1371/journal.pone.0263171