RONG LIU^1,#, SHENG LI^2,#, SITU XIONG², FUCUN ZHENG², XIANGPENG ZHAN², JIN ZENG², BIN FU², SONGHUI XU², SHAOXING ZHU^1,*, RU CHEN^1,*

Oncology Research, Vol.32, No.11, pp. 1733-1746, 2024, DOI:10.32604/or.2024.050851 - 16 October 2024

Abstract EVI2A has emerged as a significant biomarker in various diseases; however, its biological role and mechanism in kidney renal clear cell carcinoma (KIRC) remains unexplored. We used TCGA and GEO databases to analyze EVI2A gene expression comprehensively and performed pan-cancer assessments. Clinical relevance was evaluated through Kaplan-Meier analysis and ROC curves. The gene’s immune relevance was explored through analyses of the tumor microenvironment (TME), Tumor Immune Single-cell Hub (TISCH), immune checkpoints, and immunotherapy sensitivity. Our results indicate that EVI2A expression is upregulated in KIRC, showing correlations with tumor grade and T/N/M stage. EVI2A demonstrates high… More >

Dongxue Su¹, Jiarui Zheng¹, Yuwei Yi¹, Shuyuan Zhang¹, Luxin Feng¹, Danzeng Quzhen², De Qiong³, Weiwei Zhang¹, Qijian Wang¹, Feng Xu^1,*

Phyton-International Journal of Experimental Botany, Vol.93, No.9, pp. 2317-2337, 2024, DOI:10.32604/phyton.2024.055350 - 30 September 2024

Abstract The multifaceted roles of MYB transcriptional regulators are pivotal in orchestrating the complex processes of secondary metabolism, stress tolerance mechanisms, and life cycle progression and development. This study extensively examined the JrMYB genes using whole genome and transcriptomic data, focusing on identifying putative MYB genes associated with fatty acid metabolism. 126 MYB genes were identified within the walnut genome, characterized by hydrophilic proteins spanning lengths ranging from 78 to 1890 base pairs. Analysis of cis-acting elements within the promoter regions of MYB genes revealed many elements linked to cell development, environmental stress, and phytohormones. Transcriptomic data was utilized… More > Graphic Abstract

Yolotzin Apatzingán Palomino-Hermosillo¹, Ángel Elpidio Díaz-Jasso², Rosendo Balois-Morales¹, Verónica Alhelí Ochoa-Jiménez^1,3, Pedro Ulises Bautista-Rosales¹, Guillermo Berumen-Varela^1,*

Phyton-International Journal of Experimental Botany, Vol.93, No.7, pp. 1717-1732, 2024, DOI:10.32604/phyton.2024.052216 - 30 July 2024

Abstract Soursop (Annona muricata L.) is a tropical fruit highly valued for its unique flavor, nutritional value, and health-promoting properties. The ripening process of soursop involves complex changes in gene expression and metabolite accumulation, which have been studied using various omics technologies. Transcriptome analysis has provided insights into the regulation of key genes involved in ripening, while metabolic compound analysis has revealed the presence of numerous bioactive compounds with potential health benefits. However, the integration of transcriptome and metabolite compound data has not been extensively explored in soursop. Therefore, in this paper, we present a comprehensive analysis… More >

MOHD ATHAR^1,*, ANU MANHAS², NISARG RANA², AHMAD IRFAN³

BIOCELL, Vol.48, No.6, pp. 935-944, 2024, DOI:10.32604/biocell.2024.049891 - 10 June 2024

Abstract Computational methods have significantly transformed biomedical research, offering a comprehensive exploration of disease mechanisms and molecular protein functions. This article reviews a spectrum of computational tools and network analysis databases that play a crucial role in identifying potential interactions and signaling networks contributing to the onset of disease states. The utilization of protein/gene interaction and genetic variation databases, coupled with pathway analysis can facilitate the identification of potential drug targets. By bridging the gap between molecular-level information and disease understanding, this review contributes insights into the impactful utilization of computational methods, paving the way for More >

ELHAM SHAKIBA¹, SETI BOROOMAND², SIMA KHERADMAND KIA³, MEHDI HEDAYATI^4,*

Oncology Research, Vol.32, No.6, pp. 1011-1019, 2024, DOI:10.32604/or.2024.049235 - 23 May 2024

Abstract This review aimed to describe the inculpation of microRNAs (miRNAs) in thyroid cancer (TC) and its subtypes, mainly medullary thyroid carcinoma (MTC), and to outline web-based tools and databases for bioinformatics analysis of miRNAs in TC. Additionally, the capacity of miRNAs to serve as therapeutic targets and biomarkers in TC management will be discussed. This review is based on a literature search of relevant articles on the role of miRNAs in TC and its subtypes, mainly MTC. Additionally, web-based tools and databases for bioinformatics analysis of miRNAs in TC were identified and described. MiRNAs can… More > Graphic Abstract

ZHILI ZHUO^#, DONGNI ZHANG^#, WENPING LU^*, XIAOQING WU, YONGJIA CUI, WEIXUAN ZHANG, MENGFAN ZHANG

Oncology Research, Vol.32, No.6, pp. 1093-1107, 2024, DOI:10.32604/or.2024.047257 - 23 May 2024

Abstract Breast cancer is the leading cause of cancer-related deaths in women worldwide, with Hormone Receptor (HR)+ being the predominant subtype. Tamoxifen (TAM) serves as the primary treatment for HR+ breast cancer. However, drug resistance often leads to recurrence, underscoring the need to develop new therapies to enhance patient quality of life and reduce recurrence rates. Artemisinin (ART) has demonstrated efficacy in inhibiting the growth of drug-resistant cells, positioning art as a viable option for counteracting endocrine resistance. This study explored the interaction between artemisinin and tamoxifen through a combined approach of bioinformatics analysis and experimental… More > Graphic Abstract

JING HUI^1,2, NANA SUN³, YONG LIU⁴, CHUNBO YU^1,2, YONG KE⁴, YONG CAO⁴, ANXIAO YU⁴, QINGHONG KONG^1,2,*, YUN LIU^1,2,4,*

BIOCELL, Vol.48, No.5, pp. 803-815, 2024, DOI:10.32604/biocell.2024.047122 - 06 May 2024

Abstract Background: Although it has been established that the human Solute Carrier Family 22 (SLC22) functions as a cationic transporter, influencing cellular biological metabolism by modulating the uptake of various cations, its impact on cancer prognosis remains unclear. Methods: We conducted a comprehensive analysis utilizing data from The Cancer Genome Atlas (TCGA) and other databases to assess the prognostic value and functional implications across various tumors. Silence of SLC22A1 RNA in glioma U251 cells was performed to access the impact of SLC22A1 on lower-grade glioma (LGG) progression. Results: Our findings demonstrated a significant correlation between SLC22A1 expression… More >

Hala AlShamlan^*, Halah AlMazrua^*

CMC-Computers, Materials & Continua, Vol.79, No.1, pp. 675-694, 2024, DOI:10.32604/cmc.2024.048146 - 25 April 2024

Abstract In this study, our aim is to address the problem of gene selection by proposing a hybrid bio-inspired evolutionary algorithm that combines Grey Wolf Optimization (GWO) with Harris Hawks Optimization (HHO) for feature selection. The motivation for utilizing GWO and HHO stems from their bio-inspired nature and their demonstrated success in optimization problems. We aim to leverage the strengths of these algorithms to enhance the effectiveness of feature selection in microarray-based cancer classification. We selected leave-one-out cross-validation (LOOCV) to evaluate the performance of both two widely used classifiers, k-nearest neighbors (KNN) and support vector machine… More >

YAO FANG^1,2,#, FEI XIA^1,#, FEIFEI TIAN³, LEI QU¹, FANG YANG¹, JUAN FANG^1,2, ZHENHONG HU^1,*, HAICHAO LIU^1,*

BIOCELL, Vol.48, No.4, pp. 613-621, 2024, DOI:10.32604/biocell.2024.031539 - 09 April 2024

Abstract Objective: In the realm of Class I pathogens, Burkholderia pseudomallei (BP) stands out for its propensity to induce severe pathogenicity. Investigating the intricate interactions between BP and host cells is imperative for comprehending the dynamics of BP infection and discerning biomarkers indicative of the host cell response process. Methods: mRNA extraction from BP-infected mouse macrophages constituted the initial step of our study. Employing gene expression arrays, the extracted RNA underwent conversion into digital signals. The percentile shift method facilitated data processing, with the identification of genes manifesting significant differences accomplished through the application of the t-test. Subsequently,… More >

QIAN HU, MENGYAO WANG, JINJIN WANG, YALI TAO, TING NIU^*

Oncology Research, Vol.32, No.4, pp. 753-768, 2024, DOI:10.32604/or.2023.043647 - 20 March 2024

Abstract Multiple myeloma (MM) is a hematologic malignancy notorious for its high relapse rate and development of drug resistance, in which cell adhesion-mediated drug resistance plays a critical role. This study integrated four RNA sequencing datasets (CoMMpass, GSE136337, GSE9782, and GSE2658) and focused on analyzing 1706 adhesion-related genes. Rigorous univariate Cox regression analysis identified 18 key prognosis-related genes, including KIF14, TROAP, FLNA, MSN, LGALS1, PECAM1, and ALCAM, which demonstrated the strongest associations with poor overall survival (OS) in MM patients. To comprehensively evaluate the impact of cell adhesion on MM prognosis, an adhesion-related risk score (ARRS)… More >