JIAN TANG¹, CHENQIANG ZHU¹, YUN CHEN¹, YUNLONG WU¹, MING HE¹, YI ZHOU², MINGHUA XIE^2,*

BIOCELL, Vol.48, No.4, pp. 639-651, 2024, DOI:10.32604/biocell.2024.047562

Abstract Background: The specific impact of sphingolipid metabolism on developing hepatocellular Carcinoma (HCC) remains unclear. This study aims to explore the relationship between sphingolipid metabolism and HCC prognosis, immune response, and drug sensitivity. Methods: Data were obtained from The Cancer Genome Atlas (TCGA)-Hepatocellular Carcinoma (LIHC) and Gene Expression Omnibus (GEO, GSE14520 datasets). 47 sphingolipid metabolism genes were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. After classifying HCC samples using the Non-negative Matrix Factorization (NMF) clustering method, differentially expressed genes were screened. Then, 8 risk genes were obtained by univariate analysis, survival random forest reduction and lasso analysis.… More > Graphic Abstract

Muhammad Farhan^1,#, Manda Sathish², Rafia Kiran¹, Aroosa Mushtaq³, Alaa Baazeem⁴, Ammarah Hasnain⁵, Fahad Hakim¹, Syed Atif Hasan Naqvi^1,#,*, Mustansar Mubeen⁶, Yasir Iftikhar^6,*, Aqleem Abbas⁷, Muhammad Zeeshan Hassan¹, Mahmoud Moustafa⁸

Phyton-International Journal of Experimental Botany, Vol.93, No.3, pp. 581-609, 2024, DOI:10.32604/phyton.2024.046857

Abstract

Plant growth and resilience to abiotic stresses, such as soil salinity and drought, depend intricately on nitrogen metabolism. This review explores nitrogen’s regulatory role in plant responses to these challenges, unveiling a dynamic interplay between nitrogen availability and abiotic stress. In the context of soil salinity, a nuanced relationship emerges, featuring both antagonistic and synergistic interactions between salinity and nitrogen levels. Salinity-induced chlorophyll depletion in plants can be alleviated by optimal nitrogen supplementation; however, excessive nitrogen can exacerbate salinity stress. We delve into the complexities of this interaction and its agricultural implications. Nitrogen, a vital element within essential plant structures… More >

Eduardo Burgos-Valencia^1,#, Federico García-Laynes^1,#, Ileana Echevarría-Machado¹, Fatima Medina-Lara¹, Miriam Monforte-González¹, José Narváez-Zapata^2,*, Manuel Martínez-Estévez^1,*

Phyton-International Journal of Experimental Botany, Vol.93, No.2, pp. 151-183, 2024, DOI:10.32604/phyton.2023.046943

Abstract Habanero pepper (Capsicum chinense Jacq.) is a crop of economic relevance in the Peninsula of Yucatan. Its fruits have a high level of capsaicinoids compared to peppers grown in other regions of the world, which gives them industrial importance. Soil is an important factor that affects pepper development, nutritional quality, and capsaicinoid content. However, the effect of soil type on fruit development and capsaicinoid metabolism has been little understood. This work aimed to compare the effect of soils with contrasting characteristics, black soil (BS) and red soil (RS), on the expression of genes related to the development of fruits, and… More >

YANG ZHANG^1,2,#, NANNAN QIN^5,#, XIJUN WANG^6,#, RUI LIANG⁷, QUAN LIU⁴, RUOYI GENG⁸, TIANXIAO JIANG⁸, YUNFEI LIU^8,*, JINWEI LI^3,4,*

Oncology Research, Vol.32, No.3, pp. 563-576, 2024, DOI:10.32604/or.2023.029697

Abstract Glycogen metabolism plays a key role in the development of hepatocellular carcinoma (HCC), but the function of glycogen metabolism genes in the tumor microenvironment (TME) is still to be elucidated. Single-cell RNA-seq data were obtained from ten HCC tumor samples totaling 64,545 cells, and 65 glycogen metabolism genes were analyzed by a nonnegative matrix factorization (NMF). The prognosis and immune response of new glycogen TME cell clusters were predicted by using HCC and immunotherapy cohorts from public databases. HCC single-cell analysis was divided into fibroblasts, NT T cells, macrophages, endothelial cells, and B cells, which were separately divided into new… More >

HENG ZHANG^1,#, WENJING CHENG^2,#, HAIBO ZHAO², WEIDONG CHEN², QIUJIE ZHANG^2,*, QING-QING YU^2,*

Oncology Research, Vol.32, No.2, pp. 297-308, 2024, DOI:10.32604/or.2023.043138

Abstract Background: Colorectal cancer (CRC) belongs to the class of significantly malignant tumors found in humans. Recently, dysregulated fatty acid metabolism (FAM) has been a topic of attention due to its modulation in cancer, specifically CRC. However, the regulatory FAM pathways in CRC require comprehensive elucidation. Methods: The clinical and gene expression data of 175 fatty acid metabolic genes (FAMGs) linked with colon adenocarcinoma (COAD) and normal cornerstone genes were gathered through The Cancer Genome Atlas (TCGA)-COAD corroborating with the Molecular Signature Database v7.2 (MSigDB). Initially, crucial prognostic genes were selected by uni- and multi-variate Cox proportional regression analyses; then, depending… More >

JIANFA WU^1,2,#, QIANYI LIAO^3,#, LI ZHANG^1,2,#, SUQIN WU^1,2,*, ZHOU LIU^1,2,*

Oncology Research, Vol.32, No.2, pp. 373-391, 2024, DOI:10.32604/or.2023.031404

Abstract The impact of different iron metabolism processes (DIMP) on ovarian cancer remains unclear. In this study, we employed various gene chips and databases to investigate the role of DIMP in the initiation and development of ovarian cancer. cBioPortal was used to determine mutations in DIMP-associated genes in ovarian cancer. Kaplan-Meier plotter was used to examine the influence of DIMP on the prognosis of ovarian cancer. By analyzing 1669 serous ovarian cancer cases, we identified a range of mutations in iron metabolism genes, notably in those coding for the transferrin receptor (19%), melanotransferrin (19%), and ceruloplasmin (10%) in the iron import… More >

QINGPAN BU, PING LI, YUNFEI XIA, XINPEI WEI, KAI SONG^*

BIOCELL, Vol.47, No.11, pp. 2535-2546, 2023, DOI:10.32604/biocell.2023.030781

Abstract Mannose, a different isomer of the hydroxyl group at the C-2 position of glucose, shares the same transport carrier protein with glucose to enter cells and participate in the regulation of glucose metabolism. It affects cell growth, differentiation, and function and plays an active role in tumor immunity and inflammatory processes. This paper provides theoretical support for expanding the clinical applications of mannose by exploring its constitution, metabolic pathways, and role in regulating immune cell function and treating immunology-related diseases. More > Graphic Abstract

MINGHONG WEI^1,#, CHENG XIAO^1,2,#, JIAN WU^1,3, LIHONG QIN^1,3, HONGLIANG LIU^1,3, YANG CAO^1,*, YUMIN ZHAO^1,3,*

BIOCELL, Vol.47, No.9, pp. 2115-2123, 2023, DOI:10.32604/biocell.2023.030364

Abstract Background: The regulatory genes related to lipid metabolism affect the intramuscular fat (IMF) content and improve meat quality traits. Mediator Complex Subunit 4 (MED4), a vitamin D receptor protein, affects vitamin D, livestock growth, carcass traits, and triglyceride deposition. However, the physiological function of the MED4 gene on bovine adipocyte differentiation remains unknown. Methods: This study explored the function of the MED4 gene in preadipocyte differentiation in Chinese Red Steppe cattle. The overexpression plasmid and the interference sequences of the MED4 gene were constructed to detect the effects of the MED4 gene on adipogenesis and biomakers using quantitative polymerase chain… More >

MENGQIN ZHU^1,2,3,4,#, TIANYI XU^5,#, HAN ZHANG^3,4, XIN FAN^3,4, YULAN WANG⁶, JIAJIA ZHANG^3,4, FEI YU^1,2,3,4,*

BIOCELL, Vol.47, No.9, pp. 1931-1945, 2023, DOI:10.32604/biocell.2023.028968

Abstract Glutamine metabolism (GM) plays an important role in tumor growth and proliferation. Skin cutaneous melanoma (SKCM) is a glutamine-dependent cancer. However, the molecular characteristics and action mechanism of GM on SKCM remain unclear. Therefore, we aimed to explore the effects of GM-related genes on survival, clinicopathological characteristics, and the tumor microenvironment in SKCM. In this study, 682 SKCM samples were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Consensus clustering was used to classify SKCM samples into distinct subtypes based on 41 GM-related genes. Differences in survival, immune infiltration, clinical characteristics, and Kyoto Encyclopedia of… More > Graphic Abstract

Shaochun Liu, Jiamin Hu, Haohua He, Junru Fu, Xu Jie, Dahu Zhou^*, Haihui Fu^*

Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2035-2049, 2023, DOI:10.32604/phyton.2023.028296

Abstract OsPLS4 encodes a β-ketoacyl carrier protein reductase (KAR). The role of OsPLS4 in rice sheath blight (Rhizoctonia solani) remains unclear. Our preliminary studies showed that premature leaf senescence mutants (pls4) were highly susceptive to sheath blight in the early stage of rice development. To explore the role of this gene in the development of rice sheath blight, the transcriptome profiles of the rice pls4 mutant and wild type were compared by RNA-seq. The results revealed 2,569 differentially expressed genes (DEGs). The down-regulated genes were significantly enriched in the defense response-related biological processes. These down-regulated genes included the chitinase genes and… More >