Downregulation of ARFGEF1 and CAMK2B by promoter hypermethylation in breast cancer cells

Identification of hub genes to determine drug-disease correlation in breast carcinomas

The exact molecular mechanism underlying the heterogeneous drug response against breast carcinoma remains to be fully understood. It is urgently required to identify key genes that are intricately associated with varied clinical response of standard anti-cancer drugs, clinically used to treat breast cancer patients. In the present study, the utility of transcriptomic data of breast cancer patients in discerning the clinical drug response using machine learning-based approaches were evaluated. Here, a computational framework has been developed which can be used to identify key genes that can be linked with clinical drug response and progression of cancer, offering an immense opportunity to predict potential prognostic biomarkers and therapeutic targets. The framework concerned utilizes DeSeq2, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cytoscape, and machine learning techniques to find these crucial genes. Total RNA extraction and qRT-PCR were performed to quantify relative expression of few hub genes selected from the networks. In our study, we have experimentally checked the expression of few key hub genes like APOA2, DLX5, APOC3, CAMK2B, and PAK6 that were predicted to play an immense role in breast cancer tumorigenesis and progression in response to anti-cancer drug Paclitaxel. However, further experimental validations will be required to get mechanistic insights of these genes in regulating the drug response and cancer progression which will likely to play pivotal role in cancer treatment and precision oncology.

A novel artificial intelligence approach to detect the breast cancer using KNNet technique with EPM gene profiling

Women's most frequent type of cancer is breast cancer, second only to lung cancer. This paper summarizes changes in genomics and epigenetics and incremental biological activities. A tumour develops through a series of phases involving a separate abnormal gene. Even though many diseases cause DNA mutations, most treatments are designed to relieve symptoms rather than change the DNA. Clustering short palindromic repeats (CRISPR) or Cas9 is the primary approach for discovering and confirming tumorigenic genomic targets. A Kohonen neural network with an expression programming model was developed for gene selection. The main problem in genetic selection is reducing the number of features chosen while maintaining accuracy. This purpose is accomplished systematically. In the end, the approach method performed better than the existing quantum squirrel-inspired algorithm and the recurrent neural network oppositional call search algorithm for genetic selection. The KNNet-EPM model used an expression programming approach to identify gene biomarkers for breast cancer. This method was achieved with RAE of 42%, sensitivity of 93%, f1 score of 88%, accuracy of 98%, kappa score of 83%, specificity of 92% and MAE of 30%.

The Impact of YRNAs on HNSCC and HPV Infection

HPV infection is one of the most important risk factors for head and neck squamous cell carcinoma among younger patients. YRNAs are short non-coding RNAs involved in DNA replication. YRNAs have been found to be dysregulated in many cancers, including head and neck squamous cell carcinoma (HNSCC). In this study, we investigated the role of YRNAs in HPV-positive HNSCC using publicly available gene expression datasets from HNSCC tissue, where expression patterns of YRNAs in HPV(+) and HPV(−) HNSCC samples significantly differed. Additionally, HNSCC cell lines were treated with YRNA1-overexpressing plasmid and RNA derived from these cell lines was used to perform a NGS analysis. Additionally, a deconvolution analysis was performed to determine YRNA1’s impact on immune cells. YRNA expression levels varied according to cancer pathological and clinical stages, and correlated with more aggressive subtypes. YRNAs were mostly associated with more advanced cancer stages in the HPV(+) group, and YRNA3 and YRNA1 expression levels were found to be correlated with more advanced clinical stages despite HPV infection status, showing that they may function as potential biomarkers of more advanced stages of the disease. YRNA5 was associated with less-advanced cancer stages in the HPV(−) group. Overall survival and progression-free survival analyses showed opposite results between the HPV groups. The expression of YRNAs, especially YRNA1, correlated with a vast number of proteins and cellular processes associated with viral infections and immunologic responses to viruses. HNSCC-derived cell lines overexpressing YRNA1 were then used to determine the correlation of YRNA1 and the expression of genes associated with HPV infections. Taken together, our results highlight the potential of YRNAs as possible HNSCC biomarkers and new molecular targets.

The dysregulated expression and functional effect of CaMK2 in cancer

CaMK2 (calcium/calmodulin-dependent protein kinase 2), a multifunctional serine/threonine-protein kinase involved in diverse cellular processes, is vital for the transduction of the Ca²⁺ signaling cascade. Recently, research has highlighted the involvement of CaMK2 in cancer development. However, the specific effects of CaMK2 on cancer have not been fully elucidated. In this review, we summarize not only the altered expression of CaMK2 in a range of cancers, as evidenced by bioinformatics analysis, but also the significant role of CaMK2 in regulating cancer progression, such as proliferation and metastasis. In addition, we described the functional influence of CaMK2 on cancer stemness and resistance. Understanding the critical effects and mechanisms of CaMK2 in cancer would facilitate the development of a promising therapeutic strategy for cancer treatment.

Feature Selection for Breast Cancer Classification by Integrating Somatic Mutation and Gene Expression

Exploring the molecular mechanisms of breast cancer is essential for the early prediction, diagnosis, and treatment of cancer patients. The large scale of data obtained from the high-throughput sequencing technology makes it difficult to identify the driver mutations and a minimal optimal set of genes that are critical to the classification of cancer. In this study, we propose a novel method without any prior information to identify mutated genes associated with breast cancer. For the somatic mutation data, it is processed to a mutated matrix, from which the mutation frequency of each gene can be obtained. By setting a reasonable threshold for the mutation frequency, a mutated gene set is filtered from the mutated matrix. For the gene expression data, it is used to generate the gene expression matrix, while the mutated gene set is mapped onto the matrix to construct a co-expression profile. In the stage of feature selection, we propose a staged feature selection algorithm, using fold change, false discovery rate to select differentially expressed genes, mutual information to remove the irrelevant and redundant features, and the embedded method based on gradient boosting decision tree with Bayesian optimization to obtain an optimal model. In the stage of evaluation, we propose a weighted metric to modify the traditional accuracy to solve the sample imbalance problem. We apply the proposed method to The Cancer Genome Atlas breast cancer data and identify a mutated gene set, among which the implicated genes are oncogenes or tumor suppressors previously reported to be associated with carcinogenesis. As a comparison with the integrative network, we also perform the optimal model on the individual gene expression and the gold standard PMA50. The results show that the integrative network outperforms the gene expression and PMA50 in the average of most metrics, which indicate the effectiveness of our proposed method by integrating multiple data sources, and can discover the associated mutated genes in breast cancer.

Aberrant activation of hepatocyte growth factor/MET signaling promotes β-catenin-mediated prostatic tumorigenesis

Co-occurrence of aberrant hepatocyte growth factor (HGF)/MET proto-oncogene receptor tyrosine kinase (MET) and Wnt/β-catenin signaling pathways has been observed in advanced and metastatic prostate cancers. This co-occurrence positively correlates with prostate cancer progression and castration-resistant prostate cancer development. However, the biological consequences of these abnormalities in these disease processes remain largely unknown. Here, we investigated the aberrant activation of HGF/MET and Wnt/β-catenin cascades in prostate tumorigenesis by using a newly generated mouse model in which both murine Met transgene and stabilized β-catenin are conditionally co-expressed in prostatic epithelial cells. These compound mice displayed accelerated prostate tumor formation and invasion compared with their littermates that expressed only stabilized β-catenin. RNA-Seq and quantitative RT-PCR analyses revealed increased expression of genes associated with tumor cell proliferation, progression, and metastasis. Moreover, Wnt signaling pathways were robustly enriched in prostate tumor samples from the compound mice. ChIP-qPCR experiments revealed increased β-catenin recruitment within the regulatory regions of the Myc gene in tumor cells of the compound mice. Interestingly, the occupancy of MET on the Myc promoter also appeared in the compound mouse tumor samples, implicating a novel role of MET in β-catenin-mediated transcription. Results from implanting prostate graft tissues derived from the compound mice and controls into HGF-transgenic mice further uncovered that HGF induces prostatic oncogenic transformation and cell growth. These results indicate a role of HGF/MET in β-catenin-mediated prostate cancer cell growth and progression and implicate a molecular mechanism whereby nuclear MET promotes aberrant Wnt/β-catenin signaling-mediated prostate tumorigenesis.

Thymine DNA glycosylase is a key regulator of CaMKIIγ expression and vascular smooth muscle phenotype

Multifunctional Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a multigene family with isoform-specific regulation of vascular smooth muscle (VSM) functions. In previous studies, we found that vascular injury resulted in VSM dedifferentiation and reduced expression of the CaMKIIγ isoform in medial wall VSM. Smooth muscle knockout of CaMKIIγ enhanced injury-induced VSM neointimal hyperplasia, whereas CaMKIIγ overexpression inhibited VSM proliferation and neointimal formation. In this study, we evaluated DNA cytosine methylation/demethylation as a mechanism for regulating CaMKII isoform expression in VSM. Inhibition of cytosine methylation with 5-Aza-2'-deoxycytidine significantly upregulated CaMKIIγ expression in cultured VSM cells and inhibited CaMKIIγ downregulation in organ-cultured aorta ex vivo. With the use of methylated cytosine immunoprecipitation, the rat Camk2g promoter was found hypomethylated in differentiated VSM, whereas injury- or cell culture-induced VSM dedifferentiation coincided with Camk2g promoter methylation and decreased expression. We report for the first time that VSM cell phenotype switching is accompanied by marked induction of thymine DNA glycosylase (TDG) protein and mRNA expression in injured arteries in vivo and in cultured VSM synthetic phenotype cells. Silencing Tdg in VSM promoted expression of CaMKIIγ and differentiation markers, including myocardin, and inhibited VSM cell proliferation and injury-induced neointima formation. This study indicates that CaMKIIγ expression in VSM is regulated by cytosine methylation/demethylation and that TDG is an important determinant of this process and, more broadly, VSM phenotype switching and function.NEW & NOTEWORTHY Expression of the calcium calmodulin-dependent protein kinase II-γ isoform (CaMKIIγ) is associated with differentiated vascular smooth muscle (VSM) and negatively regulates proliferation in VSM synthetic phenotype (VSMSyn) cells. This study demonstrates that thymine DNA glycosylase (TDG) plays a key role in regulating CaMKIIγ expression in VSM through promoter cytosine methylation/demethylation. TDG expression is strongly induced in VSMSyn cells and plays key roles in negatively regulating CaMKIIγ expression and more broadly VSM phenotype switching.

Oxidative CaMKII as a potential target for inflammatory disease (Review)

CaMKII is a calcium‑activated kinase, proved to be modulated by oxidation. Currently, the oxidative activation of CaMKII exists in several models of asthma, chronic rhinosinusitis with nasal polyps, cardiovascular disease, diabetes mellitus, acute ischemic stroke and cancer. Oxidized CaMKII (ox‑CaMKII) may be important in several of these diseases. The present review examines the mechanism underlying the oxidative activation of CaMKII and summarizes the current findings associated with the function of ox‑CaMKII in inflammatory diseases. Taken together, the findings of this review aim to improve current understanding of the function of ox‑CaMKII and provide novel insights for future research.

Activation of hepatocyte growth factor/MET signaling initiates oncogenic transformation and enhances tumor aggressiveness in the murine prostate

Emerging evidence has shown that the hepatocyte growth factor (HGF) and its receptor, MET proto-oncogene, receptor tyrosine kinase (MET), promote cell proliferation, motility, morphogenesis, and angiogenesis. Whereas up-regulation of MET expression has been observed in aggressive and metastatic prostate cancer, a clear understanding of MET function in prostate tumorigenesis remains elusive. Here, we developed a conditional Met transgenic mouse strain, H11 ^Met/+ :PB-Cre4, to mimic human prostate cancer cells with increased MET expression in the prostatic luminal epithelium. We found that these mice develop prostatic intraepithelial neoplasia after HGF administration. To further assess the biological role of MET in prostate cancer progression, we bred H11 ^Met/+ /Pten^LoxP/LoxP:PBCre4 compound mice, in which transgenic Met expression and deletion of the tumor suppressor gene Pten occurred simultaneously only in prostatic epithelial cells. These compound mice exhibited accelerated prostate tumor formation and invasion as well as increased metastasis compared with Pten^LoxP/LoxP:PB-Cre4 mice. Moreover, prostatic sarcomatoid carcinomas and lesions resembling the epithelial-to-mesenchymal transition developed in tumor lesions of the compound mice. RNA-Seq and qRT-PCR analyses revealed a robust enrichment of known tumor progression and metastasis-promoting genes in samples isolated from H11 ^Met/+ /Pten^LoxP/LoxP:PB-Cre4 compound mice compared with those from Pten^LoxP/LoxP:PB-Cre4 littermate controls. HGF-induced cell proliferation and migration also increased in mouse embryonic fibroblasts (MEFs) from animals with both Met transgene expression and Pten deletion compared with Pten-null MEFs. The results from these newly developed mouse models indicate a role for MET in hastening tumorigenesis and metastasis when combined with the loss of tumor suppressors.

Selection and evaluation of new reference genes for RT-qPCR analysis in Epinephelus akaara based on transcriptome data

Groupers are an economically important fish species in world fishery markets. Because many studies using RT-qPCR have addressed gene expression in groupers, appropriate reference genes are required to obtain reliable and accurate results. In this study, the most suitable reference genes were identified from eleven candidate genes of one of the most valuable species, Epinephelus akaara, in a range of different experimental conditions. Using the software packages geNorm, NormFinder, BestKeeper and refFinder, three traditionally used reference genes, β-actin (β-ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and beta-2-microglobulin (B2M), were identified as not suitable for E. akaara gene expression studies, whereas two newly identified reference genes, conserved oligomeric Golgi complex subunit 5 (Cog5) and brefeldin a-inhibited guanine nucleotide-exchange protein 1 (ARFGEF1), could be universally applied under all the tested conditions. These data provide the foundation for more precise results in RT-qPCR studies of gene expression in E. akaara and other Epinephelus species.

The emerging role of CaMKII in cancer

Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a multifunctional serine/threonine kinases best known for its critical role in learning and memory. Recent studies suggested that high levels of CaMKII also expressed in variety of malignant diseases. In this review, we focus on the structure and biology properties of CaMKII, including the role of CaMKII in the regulation of cancer progression and therapy response. We also describe the role of CaMKII in the diagnosis of different kinds of cancer and recent progress in the development of CaMKII inhibitors. These data establishes CaMKII as a novel target whose modulation presents new opportunities for cancer diagnosis and treatment.

Identification and comparison of aberrant key regulatory networks in breast, colon, liver, lung, and stomach cancers through methylome database analysis

Aberrant methylation of specific CpG sites at the promoter is widely responsible for genesis and development of various cancer types. Even though the microarray-based methylome analyzing techniques have contributed to the elucidation of the methylation change at the genome-wide level, the identification of key methylation markers or top regulatory networks appearing common in highly incident cancers through comparison analysis is still limited. In this study, we in silico performed the genome-wide methylation analysis on each 10 sets of normal and cancer pairs of five tissues: breast, colon, liver, lung, and stomach. The methylation array covers 27,578 CpG sites, corresponding to 14,495 genes, and significantly hypermethylated or hypomethylated genes in the cancer were collected (FDR adjusted p-value <0.05; methylation difference >0.3). Analysis of the dataset confirmed the methylation of previously known methylation markers and further identified novel methylation markers, such as GPX2, CLDN15, and KL. Cluster analysis using the methylome dataset resulted in a diagram with a bipartite mode distinguishing cancer cells from normal cells regardless of tissue types. The analysis further revealed that breast cancer was closest with lung cancer, whereas it was farthest from colon cancer. Pathway analysis identified that either the “cancer” related network or the “cancer” related bio-function appeared as the highest confidence in all the five cancers, whereas each cancer type represents its tissue-specific gene sets. Our results contribute toward understanding the essential abnormal epigenetic pathways involved in carcinogenesis. Further, the novel methylation markers could be applied to establish markers for cancer prognosis.

Upregulation of the microRNA cluster at the Dlk1-Dio3 locus in lung adenocarcinoma

Mice in which lung epithelial cells can be induced to express an oncogenic KrasG12D develop lung adenocarcinomas in a manner analogous to humans. A myriad of genetic changes accompany lung adenocarcinomas, many of which are poorly understood. To get a comprehensive understanding of both the transcriptional and post-transcriptional changes that accompany lung adenocarcinomas, we took an omics approach in profiling both the coding genes and the non-coding small RNAs in an induced mouse model of lung adenocarcinoma. RNAseq transcriptome analysis of Kras^G12D tumors from F1 hybrid mice revealed features specific to tumor samples. This includes the repression of a network of GTPase related genes (Prkg1, Gnao1 and Rgs9) in tumor samples and an enrichment of Apobec1-mediated cytosine to uridine RNA editing. Furthermore, analysis of known SNPs revealed not only a change in expression of Cd22 but also that its expression became allele-specific in tumors. The most salient finding however, came from small RNA sequencing of the tumor samples, which revealed that a cluster of ~53 microRNAs and mRNAs at the Dlk1-Dio3 locus on mouse chromosome 12qF1 was dramatically and consistently increased in tumors. Activation of this locus occurred specifically in sorted tumor-originating cancer cells. Interestingly, the 12qF1 RNAs were repressed in cultured Kras^G12D tumor cells but reactivated when transplanted in vivo. These microRNAs have been implicated in stem cell pleuripotency and proteins targeted by these microRNAs are involved in key pathways in cancer as well as embryogenesis. Taken together our results strongly imply that these microRNAs represent key targets in unraveling the mechanism of lung oncogenesis.

Identification of hypermethylation in hepatocyte cell adhesion molecule gene promoter region in bladder carcinoma

BACKGROUND

Epigenetic regulation such as aberrant hypermethylation of CpG islands in promoter plays a key role in tumorigenesis. 5-Aza-2'-deoxycytidine (5-aza-CdR) which is a potent inhibitor of DNA methylation can reverse the abnormal hypermethylation of the silenced tumor suppressor genes (TSGs). It has been reported that hepatocyte cell adhesion molecule (hepaCAM) acts as a tumor suppressor gene and expression of its mRNA and protein were down-regulated in bladder cancer. Over-expression of hepaCAM can inhibit cancer growth and arrest renal cancer cells at G0/G1 phase. In this study, we investigated the methylation status of hepaCAM gene, as well as the influence of 5-aza-CdR on expression of hepaCAM gene in bladder cancer cells.

METHODS

CpG islands in hepaCAM promoter and methprimers were predicted and designed using bioinformatics program. Methylation status of hepaCAM promoter was evaluated in bladder cancer tissues and two cell lines (T24 and BIU-87) by Methylation-specific PCR; Western blot and Immunofluorescence were used to detect expression of hepaCAM protein after 5-aza-CdR treatment; Flow cytometry assay was performed to determine effectiveness of 5-aza-CdR on cell cycle profile.

RESULTS

CpG island in promoter of hepaCAM gene was hyper-methylated both in bladder carcinoma tissues and cell lines (T24 and BIU-87). Otherwise, aberrant methylation of its promoter was associated with its decreased expression. Hypermethylation of hepaCAM gene was reversed and expression of its mRNA and protein were re-activated in two cell lines by DNA methyltransferases inhibitor 5-aza-CdR. Flow cytometry assay demonstrated that 5-aza-CdR can inhibit growth of cancer cells by arresting cancer cells at G0/G1 phase.

CONCLUSION

Abnormal hypermethylation in CpG island of hepaCAM promoter is involved in absence of hepaCAM gene expression when bladder cancer occurs. Re-activation of hepaCAM gene by 5-aza-CdR can inhibit growth of cancer cells and arrest cells at G0/G1 phase.