Fei Ren^1,#, Yansen Cai^2,#, Yang Song^1,*

Oncology Research, Vol.33, No.8, pp. 2055-2074, 2025, DOI:10.32604/or.2025.061301 - 18 July 2025

Abstract Objectives: Epigenetic changes, particularly N6-methyladenosine (m6A) modifications, play a pivotal role in cancer development. This study explored the role of ovarian tumor deubiquitinase 7B (OTUD7B) in esophageal squamous cell carcinoma (ESCC) in the context of m6A methylation and the hypoxia-inducible factor-1α (HIF-1α) pathway. Methods: The GSE179267 dataset was used to conduct differential gene expression analysis to identify key m6A-enriched genes. The Cancer Genome Atlas (TCGA), Cancer Cell Line Encyclopedia (CCLE), and Sequence-based RNA Adenosine Methylation Site Predictor (SRAMP) databases were used to evaluate the expression of OTUD7B in ESCC and its correlation with methyltransferase-like 14… More >

Isra Mohammed¹, Mohamed Elhafiz M. Musa², Murtada K. Elbashir^3,*, Ayman Mohamed Mostafa³, Amin Ibrahim Adam⁴, Mahmood A. Mahmood³, Areeg S. Faggad⁵

CMC-Computers, Materials & Continua, Vol.84, No.2, pp. 3749-3763, 2025, DOI:10.32604/cmc.2025.063880 - 03 July 2025

Abstract Sonic Hedgehog Medulloblastoma (SHH-MB) is one of the four primary molecular subgroups of Medulloblastoma. It is estimated to be responsible for nearly one-third of all MB cases. Using transcriptomic and DNA methylation profiling techniques, new developments in this field determined four molecular subtypes for SHH-MB. SHH-MB subtypes show distinct DNA methylation patterns that allow their discrimination from overlapping subtypes and predict clinical outcomes. Class overlapping occurs when two or more classes share common features, making it difficult to distinguish them as separate. Using the DNA methylation dataset, a novel classification technique is presented to address… More >

MILICA KONTIC^1,2,*, FILIP MARKOVIC¹

Oncology Research, Vol.33, No.4, pp. 781-793, 2025, DOI:10.32604/or.2024.057231 - 19 March 2025

Abstract Detecting lung cancer early is crucial for improving survival rates, yet it remains a significant challenge due to many cases being diagnosed at advanced stages. This review aims to provide advances in epigenetics which have highlighted DNA methylation patterns as promising biomarkers for early detection, prognosis, and treatment response in lung cancer. Techniques like bisulfite conversion followed by PCR, digital droplet polymerase chain reaction, and next-generation sequencing are commonly used for detecting these methylation patterns, which occur early in the cancer development process and can be detected in non-invasive samples like blood and sputum. Key… More >

XUETING HUANG¹, CHAOJIE XU², CHEN LI^3,*, ZHIXIAN PAN^1,*

BIOCELL, Vol.48, No.12, pp. 1805-1813, 2024, DOI:10.32604/biocell.2024.056431 - 30 December 2024

Abstract Background: Hyperuricemia is a metabolic disorder which is characterized by increased serum uric acid levels, which can contribute to serious health issues such as gout, cardiovascular disease, and kidney damage. Epigenetic modifications, for example, DNA methylation, exert a crucial function in gene regulation and have been implicated in various metabolic disorders. The ATP-Binding Cassette Subfamily G Member 2 (ABCG2) gene is involved in uric acid excretion, and its expression can be influenced by methylation of its promoter region. Methods: This study involved the design of three guide RNA (gRNA) sequences targeting specific CpG sites within… More >

Xin Qi^1,#, Yu Wang^1,#, Xing Zhang¹, Xiaoshuang Wei¹, Xinyang Liu¹, Zhennan Wang¹, Zhenhui Wang^1,*, Fenglou Ling^2,*

Phyton-International Journal of Experimental Botany, Vol.93, No.7, pp. 1767-1779, 2024, DOI:10.32604/phyton.2024.052844 - 30 July 2024

Abstract DNA methylation is an important epigenetic regulatory mechanism, it regulates gene expression by recruiting proteins involved in gene repression or by inhibiting the binding of transcription factor(s) to DNA. In this study, a novel methyltransferase 2a gene (Zmet2a) was cloned in maize and identified by polymerase chain reaction-base (PCR-base) using a bioinformatics strategy. The Zmet2a cDNA sequence is 2739 bp long and translates to 912 amino acid peptides. The Zmet2a protein revealed that it contains BAH and CHROMO structural domains, is a non-transmembrane protein that is hydrophilically unstable, and has no signal peptide structure. Meanwhile, we verified More >

MAHER KURDI^1,*, ALAA ALKHOTANI², ABDULRAHMAN SABBAGH³, EYAD FAIZO⁴, AHMED I. LARY⁵, AHMED K. BAMAGA⁶, MAJID ALMANSOURI⁷, BADR HAFIZ⁸, THAMER ALSHARIF⁹, SALEH BAEESA⁸

Oncology Research, Vol.32, No.6, pp. 1037-1045, 2024, DOI:10.32604/or.2024.051112 - 23 May 2024

Abstract Background: The dysregulation of Isocitrate dehydrogenase (IDH) and the subsequent production of 2-Hydroxyglutrate (2HG) may alter the expression of epigenetic proteins in Grade 4 astrocytoma. The interplay mechanism between IDH, O-6-methylguanine-DNA methyltransferase (MGMT)-promoter methylation, and protein methyltransferase proteins-5 (PRMT5) activity, with tumor progression has never been described. Methods: A retrospective cohort of 34 patients with G4 astrocytoma is classified into IDH-mutant and IDH-wildtype tumors. Both groups were tested for MGMT-promoter methylation and PRMT5 through methylation-specific and gene expression PCR analysis. Inter-cohort statistical significance was evaluated. Results: Both IDH-mutant WHO grade 4 astrocytomas (n = 22, 64.7%) and IDH-wildtype… More > Graphic Abstract

KIMBERLY FENECH¹, ISAAC MICALLEF^1,2, BYRON BARON^1,*

Oncology Research, Vol.32, No.6, pp. 1047-1061, 2024, DOI:10.32604/or.2024.049173 - 23 May 2024

Abstract Background: Colorectal cancer (CRC) is one of the most frequently diagnosed cancers. In many cases, the poor prognosis of advanced CRC is associated with resistance to treatment with chemotherapeutic drugs such as 5-Fluorouracil (5-FU). The epithelial-to-mesenchymal transition (EMT) and dysregulation in protein methylation are two mechanisms associated with chemoresistance in many cancers. This study looked into the effect of 5-FU dose escalation on EMT and protein methylation in CRC. Materials and Methods: HCT-116, Caco-2, and DLD-1 CRC cell lines were exposed to dose escalation treatment of 5-FU. The motility and invasive potentials of the cells before… More > Graphic Abstract

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 - 16 May 2024

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

SHIDA HOU^1,#, TIANJUN LAN^2,#, YAOCHENG YANG^3,#, PEISHENG LIANG¹, XIN LIU^4,5, JUNJIE WANG⁶, ZHIFENG CHEN⁷, RONGSHENG ZENG^1,*, ZIJING HUANG^8,*

BIOCELL, Vol.47, No.12, pp. 2641-2660, 2023, DOI:10.32604/biocell.2023.043291 - 27 December 2023

Abstract Background: 5-Methylcytosine (m5C) methylation contributes to the development and progression of various malignant tumors. This study aimed to explore the potential role of m5C methylation regulators (m5CMRs) in head and neck squamous cell carcinoma (HNSCC). Methods: The transcription data of HNSCC samples were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Subsequently, the m5C patterns in HNSCC were evaluated based on 14 m5CMRs. Then, the m5Cscore was developed to quantify m5C patterns by using principal component analysis (PCA) algorithms. Two single-cell RNA sequencing datasets and various methods were employed to… More >

SUNG HEE LIM^1,#, HEE JIN CHO^1,2,3,#, KYOUNG-MEE KIM⁴, HO YEONG LIM¹, WON KI KANG¹, JEEYUN LEE¹, YOUNG SUK PARK¹, HEE CHEOL KIM^5,*, SEUNG TAE KIM^1,*

Oncology Research, Vol.31, No.6, pp. 855-866, 2023, DOI:10.32604/or.2023.030374 - 15 September 2023

Abstract Background: Although bevacizumab is an important treatment for metastatic colorectal cancer (CRC), not all patients with CRC benefit from it; in unselected patient populations, only modest survival benefits have been reported. Methods: We evaluated clinical outcomes in 110 patients using comprehensive molecular characterization to identify biomarkers for a response to bevacizumab-containing treatment. The molecular analysis comprised whole-exome sequencing, ribonucleic acid sequencing, and a methylation array on patient tissues. Results: Genomic and molecular characterization was successfully conducted in 103 patients. Six of 103 CRC samples were hypermutated, and none of the non-hypermutant tumors were microsatellite unstable. Among… More >