QIAO ZHOU^1,2,3, JIAN LIU^2,4, LING XIN⁴, YANYAN FANG^2,4, LEI WAN^2,4, DAN HUANG^2,4, JINCHEN GUO¹, JIANTING WEN^2,4

BIOCELL, Vol.47, No.4, pp. 761-772, 2023, DOI:10.32604/biocell.2023.026698

Abstract The pathophysiology of osteoarthritis (OA) is multifactorial, with the primary risk factors being obesity, age, environmental variables, and genetic predisposition. The available evidence suggests that genetic diversity does not adequately account for all clinical characteristics and heterogeneity of OA. Genetics has emerged as a nascent and crucial area of research in OA. The epigenetic module presents a potential link between genetic and environmental risk factors and the susceptibility and pathogenesis of OA. As a critical epigenetic alteration, DNA methylation has been shown to have an important role in the etiology of OA and is a viable biomarker for predicting disease… More >

Noureldin Eissa^1,2,*, Uswah Khairuddin^1,3, Rubiyah Yusof¹, Ahmed Madani²

CMC-Computers, Materials & Continua, Vol.74, No.2, pp. 2817-2838, 2023, DOI:10.32604/cmc.2023.033632

Abstract Epigenetics is the study of phenotypic variations that do not alter DNA sequences. Cancer epigenetics has grown rapidly over the past few years as epigenetic alterations exist in all human cancers. One of these alterations is DNA methylation; an epigenetic process that regulates gene expression and often occurs at tumor suppressor gene loci in cancer. Therefore, studying this methylation process may shed light on different gene functions that cannot otherwise be interpreted using the changes that occur in DNA sequences. Currently, microarray technologies; such as Illumina Infinium BeadChip assays; are used to study DNA methylation at an extremely large number… More >

Minghui Cui, Limei Lin, Jie Zhang, Xin Song, Shuo Wang, Jing Dong, Xuelei Zhao, Yuehong Long^*, Zhaobin Xing^*

Phyton-International Journal of Experimental Botany, Vol.91, No.12, pp. 2649-2668, 2022, DOI:10.32604/phyton.2022.021631

Abstract Mevalonate pyrophosphate decarboxylase is a kind of key enzyme in the terpenoid synthesis pathway in Eleutherococcus senticosus. The results of bisulfite sequencing showed that there were three kinds of samples with a low (0.68%), medium (0.72%) and high (0.79%) DNA methylation ratio in the promoter of MDD in E. senticosus, respectively. The transcriptome sequencing results showed that the expression of MDD in E. senticosus was significantly up-regulated in the types with low DNA methylation ratios of MDD (P < 0.05). There was a significant negative correlation between the saponin content in E. senticosus and the DNA methylation ratio of MDD… More >

FEIFEI TIAN¹, HUAN HU¹, DI WANG¹, HUAN DING¹, QINGJIA CHI², HUAPING LIANG³, WENLI ZENG^4,*

BIOCELL, Vol.46, No.10, pp. 2291-2301, 2022, DOI:10.32604/biocell.2022.020198

Abstract This study used transcriptome and epigenetic data to predict the prognosis of immune-related genes (IRGs) Apelin (APLN) in patients with hepatocellular carcinoma (HCC). The TCGA database has gene expression and clinical data for HCC. And DNA methylation 450 k data for HCC was download from the University of California Santa Cruz (UCSC) Xena browser. Performing clinical and prognostic analysis of APLN expression, results show that APLN is highly expressed in tumor samples. And it has an increasing trend with the development of clinical stage and T stage. To explore the prognostic role of APLN, the Immune-related DNA methylation (DNAm) sites… More >

Yanqing Wu^1,2, Jiao Liu¹, Yuhan Tang², Daqiu Zhao², Jun Tao^1,2,*

Phyton-International Journal of Experimental Botany, Vol.91, No.9, pp. 2005-2016, 2022, DOI:10.32604/phyton.2022.021062

Abstract The ornamental and commercial values of herbaceous peony (Paeonia lactiflora Pall.) are directly related to its flower pattern. However, the molecular mechanisms underlying the type formation of P. lactiflora flowers have not been studied in great detail. Previous studies identified, using integrated multipleomics analysis, revealed that APETALA2 (AP2) is an important candidate gene that modulates type formation of P. lactiflora flowers. To further reveal the expression mechanism of AP2 in P. lactiflora petals, we examined the profile of AP2 expression in the inner and outer petals of ‘ZiFengyu’ at various developmental stages using qRT-PCR and BSP+Miseq methylation analysis. Based on… More >

MENGDAN WU¹, MENGYAO SUN¹, QINHUAI LAI¹, YIN LU¹, YUYIN FU¹, YUJIA PENG¹, WEIRONG LAI¹, LISHI ZENG¹, SHENGYAN ZHAO¹, YUYAN LI¹, ZHIXIONG ZHANG¹, XIAOFENG CHEN¹, FAN QIAO¹, YIWEN ZHANG^1,*, SHIJIE ZHOU^1,2,*, LANTU GOU¹, JINLIANG YANG^1,2

BIOCELL, Vol.45, No.3, pp. 589-597, 2021, DOI:10.32604/biocell.2021.013882

Abstract The chemokine ligand 13-chemokine receptor 5 (CXCL13-CXCR5) axis has been characterized as a critical tumor-promoting signaling pathway in the tumor microenvironment (TME) in multiple types of solid tumors. In this study, we analyzed the expression profile of CXCL13 in kidney clear cell carcinoma (KIRC) and its correlation with tumor-infiltrating immune cells (TIICs). A monoclonal antibody against CXCL13 with high affinity and purity was generated in our lab for western blot and immunohistochemistry (IHC). Bioinformatic analysis was performed based on bulk-seq data from the Cancer Genome Atlas (TCGA)-KIRC and single-cell RNA-seq data from scRNASeqDB and PanglaoDB. Results showed that high CXCL13… More >

Heyam H. Al-Baity^*, Nourah Al-Mutlaq

CMC-Computers, Materials & Continua, Vol.67, No.3, pp. 3089-3106, 2021, DOI:10.32604/cmc.2021.015291

Abstract Machine-learning algorithms have been widely used in breast cancer diagnosis to help pathologists and physicians in the decision-making process. However, the high dimensionality of genetic data makes the classification process a challenging task. In this paper, we propose a new optimized wrapper gene selection method that is based on a nature-inspired algorithm (simulated annealing (SA)), which will help select the most informative genes for breast cancer prediction. These optimal genes will then be used to train the classifier to improve its accuracy and efficiency. Three supervised machine-learning algorithms, namely, the support vector machine, the decision tree, and the random forest… More >

YONG LIU^1,2,#, ZHIHUA JU^1,#, QIANG JIANG¹, WENHAO LIU¹, CHUNHONG YANG¹, YARAN ZHANG¹, XIUGE WANG¹, YAPING GAO¹, XIAOCHAO WEI¹, YAN SUN¹, JINPENG WANG¹, MINGHAI HOU¹, LING YANG², JINMING HUANG^1,*

BIOCELL, Vol.45, No.1, pp. 79-87, 2021, DOI:10.32604/biocell.2021.013583

Abstract F-box and WD-40 domain protein 11 (FBXW11) is an important component of the E3 ubiquitin-ligase enzyme that plays a key role in the ubiquitin-dependent regulation of spermatogenesis. In our previous research, the mRNA expression of FBXW11 in bull sperm with high motility is significantly higher than that with low motility. In the present study, the protein expression levels of FBXW11 in bull testicular tissues with low-performance sperm quality groups were significantly higher than those in normal performance groups. The immunohistochemistry result demonstrated that FBXW11 protein was located in the periphery of Leydig cells and seminiferous tubules. Three splice variants of… More >

Andrew D. Spearman

Congenital Heart Disease, Vol.12, No.6, pp. 828-833, 2017, DOI:10.1111/chd.12543

Abstract A genetic basis of congenital heart disease (CHD) has been known for decades. In addition to the sequence of the genome, the contribution of epigenetics to pediatric cardiology is increasingly recognized. Multiple epigenetic mechanisms, including DNA methylation, histone modification, and RNA-based regulation, are known mediators of cardiovascular disease, including both development and progression of CHD and its sequelae. Basic understanding of the concepts of epigenetics will be essential to all pediatric cardiologists in order to understand mechanisms of pathophysiology, pharmacotherapeutic concepts, and to understand the role of epigenetics in precision medicine. More >