Shuye Lin^*†, Bonan Lin^*, Xiaoyue Wang^*, Yuanming Pan^‡, Qing Xu^*, Jin-Shen He^*, Wanghua Gong^§, Rui Xing^‡, Yuqi He^¶, Lihua Guo^*, Youyong Lu^‡, Ji Ming Wang^†, Jiaqiang Huang^*†

Oncology Research, Vol.25, No.3, pp. 317-329, 2017, DOI:10.3727/096504016X14734735156265

Abstract The ATPase H⁺/K⁺ Transporting Beta Subunit (ATP4B) encodes the b subunit of the gastric H⁺, K⁺ -ATPase, which controls gastric acid secretion and is therefore a target for acid reduction. Downregulation of ATP4B was recently observed in human gastric cancer (GC) without known mechanisms. In the present study, we demonstrated that ATP4B expression was decreased in human GC tissues and cell lines associated with DNA hypermethylation and histone hypoacetylation of histone H3 lysine 9 at its intragenic region close to the transcriptional start site. The expression of ATP4B was restored in GC cell lines by treatment with… More >

Shuliang Xia^1,2,3,#, Huikang Tao^2,#, Shixin Su⁴, Xinxin Chen², Li Ma², Jianru Li⁵, Bei Gao⁶, Xumei Liu⁵, Lei Pi⁷, Jinqing Feng⁴, Fengxiang Li², Jia Li^4,*, Zhiwei Zhang^1,3,*

Congenital Heart Disease, Vol.19, No.2, pp. 247-256, 2024, DOI:10.32604/chd.2024.052583

Abstract Aims: Multiple genes and environmental factors are known to be involved in congenital heart disease (CHD), but epigenetic variation has received little attention. Monozygotic (MZ) twins with CHD provide a unique model for exploring this phenomenon. In order to investigate the potential role of Deoxyribonucleic Acid (DNA) methylation in CHD pathogenesis, the present study examined DNA methylation variation in MZ twins discordant for CHD, especially ventricular septal defect (VSD). Methods and Results: Using genome-wide DNA methylation profiles, we identified 4004 differentially methylated regions (DMRs) in 18 MZ twin pairs discordant for CHD, and 2826 genes were… More > Graphic Abstract

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 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… 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 promoter (P… 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… 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 our data,… 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… 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… 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… More >