Gastric cancer (GC) is highly heterogeneous and GC patients have low overall survival rates. It is also challenging to predict the prognosis of GC patients. This is partly because little is known about the prognosis-related metabolic pathways in this disease. Hence, our objective was to identify GC subtypes and genes related to prognosis, based on changes in the activity of core metabolic pathways in GC tumor samples. Differences in the activity of metabolic pathways in GC patients were analyzed using Gene Set Variation Analysis (GSVA), leading to the identification of three clinical subtypes by non-negative matrix factorization (NMF). Based on our analysis, subtype 1 showed the best prognosis while subtype 3 exhibited the worst prognosis. Interestingly, we observed marked differences in gene expression between the three subtypes, through which we identified a new evolutionary driver gene, CNBD1. Furthermore, we used 11 metabolism-associated genes identified by LASSO and random forest algorithms to construct a prognostic model and verified our results using qRT-PCR (five matched clinical tissues of GC patients). This model was found to be both effective and robust in the GSE84437 and GSE26253 cohorts, and the results from multivariate Cox regression analyses confirmed that the 11-gene signature was an independent prognostic predictor ( < 0.0001, HR = 2.8, 95% CI 2.1-3.7). The signature was found to be relevant to the infiltration of tumor-associated immune cells. In conclusion, our work identified significant GC prognosis-related metabolic pathways in different GC subtypes and provided new insights into GC-subtype prognostic assessment.
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http://dx.doi.org/10.3389/fgene.2023.1094838 | DOI Listing |
Eur J Med Res
December 2024
Department of Ophthalmology, Zhongshan City People's Hospital, Zhongshan, Guangdong, China.
Background: Age-related macular degeneration (AMD), is a neurodegenerative ocular disease. This study investigated the role of ferroptosis-related genes and their interaction with immune cell infiltration in AMD.
Methods: We screened differential expression genes (DEGs) of AMD from data sets in Gene Expression Omnibus.
BMC Plant Biol
December 2024
Biobreeding Institute, Xianghu Laboratory, Hangzhou, 311231, China.
This study delves into the combined effects of seasonal climate variations and MIPS1 gene mutations on the germination rates of soybean cultivars TW-1 and TW75. Through comprehensive metabolomic and transcriptomic analyses, we identified key KEGG pathways significantly affected by these factors, including starch and sucrose metabolism, lipid metabolism, and amino acid biosynthesis. These pathways were notably disrupted during the spring, leading to an imbalance in metabolic reserves critical for seedling development.
View Article and Find Full Text PDFJ Dairy Sci
December 2024
Ruminant Nutrition and Emissions, Agroscope, 1700 Posieux, Switzerland. Electronic address:
Exhaled breath offers an interesting matrix of low invasive sampling of potentially relevant information about the organism's metabolism in the form of volatile organic compounds (VOC). The VOC can be exhaled by the ructus (Islam et al., 2023) or passed the blood-lung barrier for expiration through the lungs.
View Article and Find Full Text PDFJ Dairy Sci
December 2024
Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58108, USA.
Demands for animal products are projected to increase in the future, and animal production is key to agricultural sustainability and food security; consequently, enhancing ruminant livestock production efficiencies in sustainable ways is a major goal for the livestock industry. Developmental programming is the concept that various stressors, including compromised maternal nutrition during critical developmental windows will result in both short- and long-term changes in the offspring. Ruminant models of developmental programming indicate that compromised maternal nutrition, including global under and over-nutrition, macronutrients, and specific micronutrients, including amino acids (Met and Arg), vitamins (folate, B, and choline), and minerals (sulfur, cobalt, and selenium) can alter offspring outcomes.
View Article and Find Full Text PDFDrug Discov Today
December 2024
Cell Signaling and Cancer Biology Laboratory, Department of Biochemistry, Guindy Campus, University of Madras, Chennai 600025, India. Electronic address:
Salt-inducible kinases (SIKs), a group of serine/threonine kinases in the adenosine monophosphate-activated protein kinase (AMPK) family, exist in three isoforms: SIK1, SIK2 and SIK3. These kinases are crucial in various physiological processes. Emerging evidence indicates that dysregulation of SIK expression and activation significantly contributes to carcinogenesis by promoting cellular proliferation, metabolic dysregulation, metastasis and chemoresistance through the modulation of crucial signaling pathways.
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