Pathway-Based Integrative Analysis of Metabolome and Microbiome Data from Hepatocellular Carcinoma and Liver Cirrhosis Patients

Kim, Boram; Cho, Eun Ju; Yoon, Jung‐Hwan; Kim, Soon Sun; Cheong, Jae Youn; Cho, Sung Won; Park, Taesung

doi:10.3390/cancers12092705

Cited by 7 publications

(2 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Tyr is produced by the dehydroxylation of Phe [ 67 ], and the correlation coefficient between the two was 0.58 ( p < 0.01, Figure 1 ). Thr is the precursor of Gly or Ser [ 68 , 69 ], and the correlation coefficients between Thr and the other two were 0.75 ( p < 0.01), 0.30 ( p = 0.04), and 0.63 ( p < 0.01), respectively (see Figure 1 ). However, the impact of increased protein synthesis on plasma concentrations must also be considered.…”

Section: Resultsmentioning

confidence: 99%

Effects of Individual Essential Amino Acids on Growth Rates of Young Rats Fed a Low-Protein Diet

Liu,

Wang,

Zhao

et al. 2024

Animals

View full text Add to dashboard Cite

To investigate the effects of individual essential amino acids (EAA) on growth and the underlying mechanisms, EAA individually supplemented a low-protein (LP) diet fed to young rats in the present study. Treatments were an LP diet that contained 6% crude protein (CP), a high-protein (HP) diet that contained 18% CP, and 10 LP diets supplemented with individual EAA to achieve an EAA supply equal to that of the HP diet. The CP concentration of the LP diet was ascertained from the results of the first experiment, which examined the effects of dietary CP concentrations on growth rates, with CP ranging from 2% to 26%. Weight gain was increased with the supplementation of His, Ile, Lys, Thr, or Trp as compared to the LP diet (p < 0.05). Feed intake was greater for the His-, Lys-, and Thr-supplemented treatments as compared to the LP group (p < 0.05). Protein utilization efficiency was lower for the HP group than other groups (p < 0.01). The supplementation of Leu, Lys, and Val led to reduced protein utilization efficiency (p < 0.05), but the supplementation of Thr and Trp led to greater efficiency than the LP group (p < 0.05). Compared to the LP group, plasma urea concentrations were elevated with individual EAA supplementation, with the exception of the Thr addition. The added EAA resulted in increased concentrations of the corresponding EAA in plasma, except for Arg and Phe supplementation. The supplementation of Arg, His, Leu, Lys, and Met individually stimulated mTORC1 pathway activity (p < 0.05), and all EAA resulted in the decreased expression of ATF4 (p < 0.05). In summary, the supplementation of His, Ile, Lys, Thr, or Trp to an LP diet improved the growth performance of young rats. Responses to His and Lys additions were related to the activated mTORC1 pathway and feed intake increases. The improved growth performance resulting from the addition of a single EAA is not solely attributed to the increased plasma availability of EAA. Rather, it may be the consequence of a confluence of factors encompassing signaling pathways, the availability of amino acids, and other associated elements. The additivity of these factors results in independent responses to several EAA with no order of limitation, as is universally encoded in growth models for all production animal species.

show abstract

Section: Resultsmentioning

confidence: 99%

Effects of Individual Essential Amino Acids on Growth Rates of Young Rats Fed a Low-Protein Diet

Liu,

Wang,

Zhao

et al. 2024

Animals

View full text Add to dashboard Cite

show abstract

“…One possible reason might be that glycerophospholipids, as components of cell membranes, might inhibit the diffusion of drugs. In addition, a combination of OXA and VC may induce a synergistic therapeutic effect through targeting the glycine, serine, and threonine metabolism, which has been reported to be closely related to the carcinogenesis and progression of HCC. , Furthermore, glycine and cysteine are precursors of glutathione (GSH), which is an important role for redox control . To further validate the performance of the iMSEA strategy, we have applied the developed method to an additional metabolomic data set.…”

Section: Resultsmentioning

confidence: 99%

iMSEA: A Novel Metabolite Set Enrichment Analysis Strategy to Decipher Drug Interactions

et al. 2023

View full text Add to dashboard Cite

Drug combinations are commonly used to treat various diseases to achieve synergistic therapeutic effects or to alleviate drug resistance. Nevertheless, some drug combinations might lead to adverse effects, and thus, it is crucial to explore the mechanisms of drug interactions before clinical treatment. Generally, drug interactions have been studied using nonclinical pharmacokinetics, toxicology, and pharmacology. Here, we propose a complementary strategy based on metabolomics, which we call interaction metabolite set enrichment analysis, or iMSEA, to decipher drug interactions. First, a digraph-based heterogeneous network model was constructed to model the biological metabolic network based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Second, treatment-specific influences on all detected metabolites were calculated and propagated across the whole network model. Third, pathway activity was defined and enriched to quantify the influence of each treatment on the predefined functional metabolite sets, i.e., metabolic pathways. Finally, drug interactions were identified by comparing the pathway activity enriched by the drug combination treatments and the single drug treatments. A data set consisting of hepatocellular carcinoma (HCC) cells that were treated with oxaliplatin (OXA) and/or vitamin C (VC) was used to illustrate the effectiveness of the iMSEA strategy for evaluation of drug interactions. Performance evaluation using synthetic noise data was also performed to evaluate sensitivities and parameter settings for the iMSEA strategy. The iMSEA strategy highlighted synergistic effects of combined OXA and VC treatments including the alterations in the glycerophospholipid metabolism pathway and glycine, serine, and threonine metabolism pathway. This work provides an alternative method to reveal the mechanisms of drug combinations from the viewpoint of metabolomics.

show abstract

A novel alternative strategy for monitoring and insight into liver fibrosis progression: The combination of surface-enhanced Raman spectroscopy (SERS) and gut microbiota

Xiang

Lan

et al. 2023

Biosensors and Bioelectronics

View full text Add to dashboard Cite

Pathway-Based Integrative Analysis of Metabolome and Microbiome Data from Hepatocellular Carcinoma and Liver Cirrhosis Patients

Cited by 7 publications

References 49 publications

Effects of Individual Essential Amino Acids on Growth Rates of Young Rats Fed a Low-Protein Diet

Effects of Individual Essential Amino Acids on Growth Rates of Young Rats Fed a Low-Protein Diet

iMSEA: A Novel Metabolite Set Enrichment Analysis Strategy to Decipher Drug Interactions

A novel alternative strategy for monitoring and insight into liver fibrosis progression: The combination of surface-enhanced Raman spectroscopy (SERS) and gut microbiota

Contact Info

Product

Resources

About