Amber Hassan¹, Badr Hafiz², Taghreed Alsinani³, Rakan Bokhari⁴, Dahlia Mirdad⁵, Awab Tayyib⁵, Alaa Alkhotani⁶, Ahmad Fallata⁷, Iman Mirza⁸, Eyad Faizo^9,10, Saleh Baeesa², Huda Alghefari¹¹, Maher Kurdi^11,*

Oncology Research, Vol.33, No.11, pp. 3293-3325, 2025, DOI:10.32604/or.2025.070031 - 22 October 2025

Abstract Background: Glioblastoma (GBM) remains the most aggressive primary brain tumour in adults, marked by pronounced cellular heterogeneity, diffuse infiltration, and resistance to conventional treatment. In recent years, transcriptomic profiling has provided valuable insights into the molecular mechanisms that govern the progression of glioblastoma. This systematic review aims to synthesise the current literature on dysregulated gene expression in GBM, focusing on gene signatures associated with stemness, immune modulation, extracellular matrix remodelling, metabolic adaptation, and therapeutic resistance. Methods: We conducted a systematic search of PubMed, The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), and the GlioVis… More >

Jing Zhang^1,#, Huifen Qiao^1,#, Shenglong Wang^1,#, Jiawei Yuan¹, Qingsong Ba¹, Gensheng Zhang^1,2,*, Guiping Li^1,*

Phyton-International Journal of Experimental Botany, Vol.94, No.9, pp. 2701-2718, 2025, DOI:10.32604/phyton.2025.070017 - 30 September 2025

Abstract Wheat stripe rust, a devastating disease caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), poses a significant threat to global wheat production. Growing resistant cultivars is a crucial strategy for wheat stripe rust management. However, the underlying molecular mechanisms of wheat resistance to Pst remain incompletely understood. To unravel these mechanisms, we employed high-throughput RNA sequencing (RNA-Seq) to analyze the transcriptome of the resistant wheat cultivar Mianmai 46 (MM46) at different time points (24, 48, and 96 h) post-inoculation with the Pst race CYR33. The analysis revealed that Pst infection significantly altered the expression of genes… More >

Hafiza Muniba Din Muhammad¹, Safina Naz¹, Zarina Bibi², Mohamed A. A. Ahmed³, Alina-Stefania Stanciu⁴, Riaz Ahmad^5,*

Phyton-International Journal of Experimental Botany, Vol.94, No.9, pp. 2631-2648, 2025, DOI:10.32604/phyton.2025.069474 - 30 September 2025

Abstract The production of crops is badly affected by climate change globally. Mitigation of adverse effects of climate change is in need of time through different management practices such as developing tolerant genetic resources, hormonal applications to boost defense systems, nanoparticles, and balanced fertilization. The nano-hormonal synergy had the potential to mitigate the adverse effects of climate change by modulation of morpho-physiological and biochemical activities. Plant growth, yield, and quality can be enhanced with the supplementation of nano-hormonal interactions. Therefore, the current study explores the synergy between nanoparticles and phytohormonal use. The nanoparticles, even in low… More >

Dandan Wang^*, Jiaxin Chen, Yanwen Zhang

Phyton-International Journal of Experimental Botany, Vol.94, No.4, pp. 1137-1158, 2025, DOI:10.32604/phyton.2025.063894 - 30 April 2025

Abstract Taxus cuspidata, a rare species of the Taxus genus, and its wild resources are under severe threat. The development of cultivated species has become an important strategy to replace wild species. The objective of this work was to elucidate the differences in secondary metabolite accumulation, particularly in the paclitaxel biosynthesis pathway, between wild and cultivated species. This study employed liquid chromatography-tandem mass spectrometry (LC-MS/MS) and RNA sequencing (RNA-Seq) technologies to conduct integrated metabolomic and transcriptomic analyses of wild and cultivated species of T. cuspidata. The results showed that the content of paclitaxel in cultivated species was significantly higher… More >

Xinxin Chen¹, Fuxin Li¹, Jingyu Jia¹, Yajing Tian¹, Xin Li^1,2,3,*

Phyton-International Journal of Experimental Botany, Vol.94, No.3, pp. 825-842, 2025, DOI:10.32604/phyton.2025.062015 - 31 March 2025

Abstract In plants, transcription factor (TF) family LATERAL ORGAN BOUNDARIES DOMAIN (LBD) has been identified to be involved in the ripening and senescence processes of fruits. However, the function of LBD in Hylocereus undatus (Haw.) Britton & Rose (H. undatus) has not been reported yet. Through transcriptomic analysis, virus-induced gene silencing (VIGS) technology, and RT-qPCR validation, we investigated the role of the LBD TFs in the senescence of H. undatus. Transcriptomic analysis revealed that HuLBD1 is a key transcription factor of the LBD family regulating H. undatus senescence. After silencing HuLBD1, 5075 differentially expressed genes (DEGs) were identified. GSEA results showed… More >

Cheng Sun^1,3, Chen Zhao^2,3, Guohua Wang^2,3, Qianwen Mao^2,3, Rong Han^2,3,*

Phyton-International Journal of Experimental Botany, Vol.94, No.2, pp. 455-479, 2025, DOI:10.32604/phyton.2025.061462 - 06 March 2025

Abstract Enhanced UV-B radiation represents a major environmental factor impacting global cereal production. Researchers have explored various approaches to reduce the detrimental impact of UV-B radiation on crops. Recently, engineered nanoparticles, particularly cerium oxide nanoparticles (CeO₂-NPs), have attracted widespread interest for their ability to boost plant tolerance to a range of abiotic stresses. This study investigates how CeO₂-NPs application affects the morphology, physiology, biochemistry, and transcriptomics profiles of wheat seedling roots subjected to enhanced UV-B stress. The findings demonstrate that CeO₂-NPs notably promoted root length, fresh and dry weights, and root activity (p < 0.05) under enhanced UV-B… More >

Enyan Chen^1,#, Jingyu Jia^1,3,#, Jiaju Sun¹, Jie Wang², Xinxin Chen¹, Xin Li^1,3,4,*

Phyton-International Journal of Experimental Botany, Vol.93, No.11, pp. 2837-2856, 2024, DOI:10.32604/phyton.2024.057932 - 30 November 2024

Abstract During post-harvest storage of Cucumis sativus fruit, the application of trypsin treatment could increase flavonoid compound levels and reduce oxidative damage. To investigate the mechanism of trypsin-induced flavonoid biosynthesis in C. sativus, we conducted a combined analysis of transcriptomics and widely targeted metabolomics. One hundred and seventy-five significantly different metabolites were obtained from metabolomics data. The kyoto encyclopedia of genes and genomes (KEGG) functional enrichment results indicated that these metabolites were mainly involved in the phenylpropanoid biosynthesis pathway. By combining the results of the weighted gene co-expression network analysis (WGCNA) with the 130 upregulated phenylpropanoid metabolites, 22… More >

TIANYUN HAN^#, ZHONG LI^#, LUONING ZHANG, LINSHEN XIE^*

BIOCELL, Vol.48, No.11, pp. 1625-1638, 2024, DOI:10.32604/biocell.2024.055029 - 07 November 2024

Abstract Objective: The study aimed to explore the protective mechanism of Ganoderic acid A (GAA) in renal fibrosis and to verify that GAA can ameliorate renal fibrosis by regulating the Niemann-pick C1-like 1 (NPC1L1) gene. Methods: Transforming growth factor beta1 (TGF-β1) was used to treat Human Kidney-2 (HK-2) cells to establish a renal fibrosis model. The differentially expressed genes in the control (CTRL) group, TGF-β1 group, and TGF-β1 + GAA group were screened via transcriptome sequencing technology and verified by qPCR and Western blot experiments. The NPC1L1 gene overexpression plasmid was constructed. The expression levels of N-cad, E-cad,… More >

Xiaodong Shi^*, Tingyu Wang, Sui Ai, Jiasi Li

Phyton-International Journal of Experimental Botany, Vol.93, No.10, pp. 2571-2581, 2024, DOI:10.32604/phyton.2024.056606 - 30 October 2024

Abstract Cotton rose (Hibiscus mutabilis) is a well-known ornamental plant that produces large flowers of vibrant colors. However, metabolites in H. mutabilis flowers with vibrant color have not been fully understood. By performing a combined analysis of metabolomics and transcriptomics data, we here explored mechanisms for the production of primary active compounds in this plant. Multivariate statistics unveiled differences in flavonoid metabolism between white and pink flowers, with pink flowers exhibiting a greater flavonoid abundance. The white-to-pink transition of cotton rose flowers may be attributed to pelargonidin-3-O-glucoside formation. On examining the expression of genes related to the structure More > Graphic Abstract

KERAN JIA¹, YANHAO ZHANG¹, MENGYU JIANG², MENGGE CUI², JIA WANG², JIAJIA ZHANG², HUIHAI ZHAO², MENGYAN LI², HUA WANG², QUANMING ZOU^1,#,*, HAO ZENG^1,#,*

BIOCELL, Vol.48, No.9, pp. 1355-1368, 2024, DOI:10.32604/biocell.2024.051383 - 04 September 2024

Abstract Objective: Candida albicans is a common fungal pathogen that triggers complex host defense mechanisms, including coordinated innate and adaptive immune responses, to neutralize invading fungi effectively. Exploring the immune microenvironment has the potential to inform the development of therapeutic strategies for fungal infections. Methods: The study analyzed individual immune cell profiles in peripheral blood mononuclear cells from Candida albicans-infected mice and healthy control mice using single-cell transcriptomics, fluorescence quantitative PCR, and Western blotting. We investigated intergroup differences in the dynamics of immune cell subpopulation infiltration, pathway enrichment, and differentiation during Candida albicans infection. Results: Our findings indicate that infiltration… More >