Lipid Metabolism Pathways Research Articles

Abstract 3488: Decoding splicing isoforms and adaptive evolution in melanoma brain metastases through single cell long-read RNA sequencing

Abstract Melanoma brain metastasis (MBM) is the third most common origin of metastasis to the brain, with a median overall survival of 8.9 months. Alternative splicing plays a critical role in cancer pathogenesis through altered protein coding complexity in tumor cells, which however has been poorly studied in MBM due to technical limitations. Long-read single cell RNA sequencing has the unique strength of measuring transcript isoforms and mutations simultaneously in individual cells due to its capacity of measuring full-length transcripts. In this study, we employed high throughout single cell long-read RNA sequencing (scNanoRNAseq) onto patient-matched MBM and extracranial metastasis (ECM) tumor pairs to evaluate the extent to which splicing isoforms impact adaptive clonal evolution in MBM. Our results showed that MBM tumors had distinct genetic alterations and ecological cellular compositions compared to matched ECM tumors, indicating that tumor clones were adaptively expanded in brain microenvironment. Comparative isoform analysis revealed that hundreds of genes expressed different combinations of isoforms (DCIs) involved in glucose and lipid metabolic pathways. Interestingly, our data demonstrated that ~10% of splicing related genes themselves were alternatively spliced including both spliceosome members and splicing activators. Furthermore, we calculated temporal changes of isoform usages along with tumor cell evolutionary lineages to quantify their impact on adaptive clonal expansion in MBM. Taken together, our work improves the understanding of transcriptional and splicing dynamics inherent in the adaptive evolution of MBM, providing evidence for developing new therapeutics targeting tumor cell-specific and MBM-specific splicing isoforms. Citation Format: Lina Lu, Cheng-Kai Shiau, Kazutaka Fukumura, Hsiaoyun Lin, Yueying He, Timothy Pan, Lisa Norberg, Jennifer Ritchie, Jason T. Huse, Ruli Gao. Decoding splicing isoforms and adaptive evolution in melanoma brain metastases through single cell long-read RNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3488.

Abstract 4737: The combination of the BET inhibitor JQ1 and gemcitabine induces regressions in gemcitabine resistant patient-derived xenograft models of pancreatic cancer

Abstract Efforts to develop targeted therapies for drug resistant tumors have been relatively unsuccessful. The 5-year survival for patients with advanced pancreatic cancer is ~3%. Gemcitabine is usually combined with nab-paclitaxel as a standard of care for treatment of locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC). However, no chemotherapeutic regimens thus far evaluated have been curative. We developed the first PDAC patient-derived xenograft (PDX) models in which resistance against gemcitabine was acquired in vivo. We used RNA-seq and ingenuity pathway analysis to compare expression profiles of paired parent vs gemcitabine resistant PDX models. This comparison suggested a previously unreported mechanism for gemcitabine resistance, involving aberrations of cholesterol biosynthesis and lipid metabolism pathways. We also made the unexpected observation that gemcitabine-resistant PDAC models derived from primary tumors have high levels of 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), an enzyme essential to cholesterol biosynthesis and rate limiting in ketogenesis. Notably, the BET bromodomain inhibitor JQ1 decreases HMGCS2 levels; and BET inhibitors + gemcitabine exert synergistic cytotoxicity in gemcitabine-resistant PDAC cells. We determined that the BET bromodomain inhibitor JQ1 + gemcitabine induces regressions of two in vivo gemcitabine-resistant tumor models which we developed directly from primary human tumor tissue. These mechanism-based studies suggest that inhibiting HMGCS2 represents a novel approach to therapy for PDAC. We propose that combining gemcitabine with agents that decrease levels of HMGCS2 comprises effective treatment for patients with drug resistant PDAC. Citation Format: Aubrey L. Miller, Samuel C. Fehling, Eric Josh Brown, Eric O. Heard, Tracy L. Gamblin, Rebecca B. Vance, Karina J. Yoon. The combination of the BET inhibitor JQ1 and gemcitabine induces regressions in gemcitabine resistant patient-derived xenograft models of pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4737.

Abstract 434: Understanding metabolic heterogeneity of estrogen receptor positive metastatic breast tumors using spatial transcriptomics and geographic information systems approaches

Abstract The tumor microenvironment consists of numerous cell populations showing diverse metabolic preferences, causing metabolic heterogeneity and therapy resistance. Fulvestrant, a clinically approved selective estrogen receptor (ER) degrader, is the standard of care for ER-positive breast cancer, yet resistance has been reported among metastatic breast cancer patients. In our previous studies, we showed such resistance is attributable to metabolic heterogeneity in the tumor microenvironment. Despite metabolic heterogeneity posing a common challenge in cancer research, current methods, such as histology and Magnetic Resonance Imaging, cannot explore nutrient uptake at transcript-level resolution with spatial context, making it difficult to understand the heterogeneity that affects cellular growth and metabolism. Visium Spatial Transcriptomics, a method that shows regional gene expression, is emerging as a powerful spatial analysis tool, and we integrated this method with geographic information systems to investigate the tumor microenvironment heterogeneity and highlight the importance of cell-microenvironment interactions. We developed a computational pipeline to visualize hotspots of spatially relevant genes using breast cancer metastatic samples from xenograft models and human patients. This pipeline integrates Visium tools and geospatial methods for processing transcriptome profiling data. We analyzed the degree of local spatial association based on Local Moran’s I to estimate regions with significant co-localization of single and multiple gene expressions within a tumor. We then leveraged the co-localized areas in the process of biomarker identification and revealing biological pathways. We also used unsupervised clustering of the complete transcriptome profiles to test the resemblance between identified clusters and hotspots as well as any disruption in the spatial structure of clusters in response to therapy or metastasis. Gene set enrichment analysis of these clusters revealed several glucose or lipid metabolism pathways, and mapping of the genes corresponding to each pathway showed mutually exclusive gene expression patterns in the sample. We also observed minimal co-localization of two metabolic pathways but extensive co-localization between metabolic genes and ER target genes, suggesting distinct metabolic preferences and spatial distributions of endocrine therapy resistant cell populations. Altogether, our analysis pipeline established a computational framework for characterizing the link between tumor microenvironment, local metabolism, and changes in transcriptional response to external stimuli. Our findings support the development of strategies to target different endocrine resistant regions using a combination of ER and metabolic signaling inhibitors. Citation Format: Jin Young Yoo, Sabrina Akter, Nandana Varma, Atharva Jain, Aiman Soliman, Zeynep Madak Erdogan. Understanding metabolic heterogeneity of estrogen receptor positive metastatic breast tumors using spatial transcriptomics and geographic information systems approaches [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 434.

Abstract 3064: Unmasking the deadly tango: PKA and lipid genes in prostate cancer's bone invasion

Abstract About 88% of metastatic prostate cancer (PCa) cases involve bone metastasis. When PCa cells spread to the bone, a metabolic adaptation to the new environment takes place, partly influenced by factors secreted by the homing organ. Thus, we hypothesize that metabolic reprogramming, both in the tumor and bone niche drive PCa bone metastasis. In this work, we carried out an integrative in vitro, in vivo, and bioinformatics approach to identify key regulators governing the metabolic behavior of PCa cells. We performed an indirect co-culture between PCa (PC3) and bone progenitor (MC3T3 or Raw264.7) cells. PCa cells displayed a strong transcriptional (RNA-seq) activation of lipid metabolism, including PPAR-signaling, fat digestion, and PI3K-Akt pathway. Accordingly, treatment with the conditioned media (CM) of the co-culture promoted lipid accumulation in PC3 cells (Bodipy 493/503 staining). To assess the clinical relevance of the in vitro model, we performed an unsupervised clustering analysis using transcriptomics data from human PCa and bone metastatic samples (GSE74685). Results showed that the metabolic genes deregulated in PC3 by the co-culture, could accurately cluster samples in primary tumor or bone metastasis. We next performed a multivariable Cox regression analysis and built a prognostic model, identifying a novel signature of 5 lipid-associated genes, PPARA, VDR, SLC16A1, PAPSS2 and GPX1, associated with a 23-fold higher risk of death in PCa patients (SU2C-PCF dataset). The expression of this signature was validated in a PDX pre-clinical model (MDA PCa PDX series) when comparing MDA-PCa-183 growing intrafemorally vs. subcutaneously. In order to identify the central hubs regulating this transcriptional phenotype, we performed an Ingenuity Pathway Analysis (QIAGEN), showcasing that the lipid-related signature deregulated by the bone niche is indeed modulated by the Protein Kinase A (PKA). Accordingly, the expression of these signature was downregulated by PKA inhibition (H89; PKA inhibitor). Moreover, secretome analyses (ESI MS/MS) revealed that bone secreted type I collagen (Col1a1) and fibronectin (Fn1) regulate PKA activity in PCa cells. Further, we investigated whether PKA could modulate critical mechanisms for bone progression, focusing on osteopontin (SPP1), a secreted protein involved in the adhesion and invasion of PCa cells, whose regulatory mechanism in tumor cells is yet to be elucidated. Strikingly, we observed not only that the activation of PKA using Forskolin in PCa cells activated SPP1 expression, but also that PKA inhibition led to a significant impairment of the SPP1 induction triggered by bone soluble factors secreted during the PC3/MC3T3 co-culture. Altogether, we showcase PKA as a central hub of PCa energetic metabolism during bone progression and outline a lipid-associated gene signature that can be targeted to halt metastatic PCa. Citation Format: Pablo Sanchis, Nicolas Anselmino, Estefania Labanca, Agustina Sabater, Juan Bizzotto, Gaston Pascual, Rocio Seniuk, Sofia Lage-Vickers, Antonina Mitrofanova, Pia Valacco, Ayelen Toro, Javier Cotignola, Nora Navone, Elba Vazquez, Geraldine Gueron. Unmasking the deadly tango: PKA and lipid genes in prostate cancer's bone invasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3064.

Abstract 1426: Lipid-mediated epigenetic activation of PPAR-gamma signaling promotes immune-checkpoint resistance in hepatocellular carcinoma

Abstract Background: Although use of immune-checkpoint inhibitors (ICI) has yielded impressive results in cancer patients, resistance to ICI therapies has increasingly been observed, especially in hepatocellular carcinoma (HCC). Materials and Methods: We generated a novel anti-programmed death-ligand 1 (PD-L1) treatment resistant mouse hepatoma cell Hepa1-6 (PD-L1R) by 7-generation of in vivo selection. To dissect tumor cell-intrinsic resistant mechanism, we performed single-cell RNA-sequencing (scRNA-seq) from anti-PD-L1-treated tumors generated from parental or PD-L1R cells. Expression level of target genes was detected by QPCR, western blot and immunohistochemical analyses. Lipid content and fatty acid uptake was examined by Oil Red O and BIODIPY staining. Peroxisome proliferator-activated receptor gamma (PPARγ) promoter methylation level was analyzed by bisulfite pyrosequencing. To investigate the tumor cell-extrinsic factors, we profiled the myeloid and lymphoid lineages by flow cytometry. Results: ScRNA-seq revealed significant gene enrichments in lipid metabolism and PPARγ signaling pathway in PD-L1R tumors, which could be verified in both mRNA and protein levels. Moreover, we observed evident lipid accumulation in the PD-L1R tumors when compared to the parental tumors by Oil Red O staining. Consistently, PD-L1R tumor cells exhibited higher lipid content and enhanced fatty acid uptake in vitro, as demonstrated by BODIPY493/503 and BODIPY-C16 analyses. Of note, palmitic acid could dose-dependently increase Pparg mRNA expression in parental cells to a similar level with the PD-L1R cells, supporting an important role of lipids in inducing PPARγ expression. Pyrosequencing analysis indicated that PD-L1R cells exhibited lower PPARγ methylation level compared with parental cells. Notably, 5-Azacytidine treatment in parental cells significantly reduced the promoter DNA methylation and increased Pparg mRNA expression to similar extent with the PD-L1R tumor cells, thus indicating DNA hypomethylation-driven PPARγ up-regulation. Flow cytometry analysis showed that ICI resistance was associated with lower cytotoxic CD8+ T cells but higher intermediate Th17 cells, myeloid-derived suppressor cells and T regulatory cells in the tumor microenvironment (TME). Conclusions: Our study suggested that lipid exposure may epigenetically up-regulate PPARγ transcription in the development of anti-PD-L1 resistance. Detailed investigation on the crosstalk between aberrant lipid metabolism and immunosuppressive TME is ongoing. Acknowledgment: This study is supported by RGC General Research Fund (14120621 and 14119023), Li Ka Shing Foundation and CUHK Strategic Seed Funding for Collaborative Research Scheme. Citation Format: Zhewen Xiong, Stephen Lam Chan, Jingying Zhou, Xuezhen Zeng, Weiqin Yang, Haoran Wu, Jianquan Cao, Jie-Ting Low, Michael Wing-Yan Chan, Kevin Yuk-Lap Yip, Joseph Jao-Yiu Sung, Alfred Sze-Lok Cheng. Lipid-mediated epigenetic activation of PPAR-gamma signaling promotes immune-checkpoint resistance in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1426.

Abstract 5169: Circulating levels of ANGPTL3, PCSK9, apoCIII and lipoprotein (a) in high-grade serous ovarian cancer

Abstract Background: Ovarian cancers require abundant amounts of lipids for their growth. Recent years have highlighted the role of ANGPTL3, PCSK9, ApoCIII and Lp(a) as key players in lipid metabolism. But circulating levels of these factors in ovarian cancers have not been thoroughly investigated to date. Objective: We assessed the profiles of plasma ANGPTL3, PCSK9, ApoCIII and Lp(a) in ovarian high-grade serous carcinoma (HGSC). Methods: Plasma samples collected from women diagnosed with an HGSC (n=31) or a benign ovarian lesion (BOL, n=40) were analyzed for plasma lipid profile (ApoB, total cholesterol, HDL, triglycerides, Lp(a) levels) on a clinical modular platform (Roche). ApoCIII, ANGPTL3 and PCSK9 levels were measured with commercially-available ELISA kits. Differences between HGSC and BOL were assessed by two-group comparisons. Pairwise correlation strength between variables was evaluated with Spearman’s rank order tests. Logistic regression modelling was used to further examine the associations between selected variables and HGSC diagnoses. Results: ANGPTL3 levels increased in HGSC (84.1 ng/ml, SD=29.2ng/ml, n=31) compared to BOL (66.9ng/ml, SD=30.7 ng/ml, n=40; HGSC vs BOL p=0.02). Receiver operating characteristic (ROC) curve suggested that plasma ANGPTL3 levels were moderately associated with HGSC (AUC=67.7%, p=0.005 1) and did not increase predictive performance of ovarian tumor biomarkers CA125 and HE4 in multivariable model. Associations between ANGPTL3 levels and cholesterol (HDL, non-HDL, LDL and total) could be observed in the control group but not in the HGSC group. The same dissociation was observed for the inverse correlation between HDL and triglycerides in HGSC. Furthermore, moderate associations were observed between PCSK9 & CA19-9 in the entire cohort (rho=0.34, n=53, p=0.013) and Lp(a) & CA125 in HGSC cases (rho=0.51, p= 0.017). Conclusion: In this cohort of 71 women, we report increased levels of ANGPTL3 in HGSC with an effect size (Cohen’s D) of 0.57. Confirmation of this result in larger cohort studies (minimal n>50 in each group) would warrant further investigation into the roles of circulating ANGPTL3. Its inhibition may allow to tackle deregulated lipid metabolic pathways contributing to ovarian cancer progression. Citation Format: Emilie Wong Chong, France-Hélène Joncas, Pierre Douville, Dimcho Bachvarov, Frédéric Calon, Nabil Seidah, Caroline Diorio, Anne Gangloff. Circulating levels of ANGPTL3, PCSK9, apoCIII and lipoprotein (a) in high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5169.

Transcriptomics and metabolomics analysis revealed the regulatory network of apical buds development in lotus (Nelumbo nucifera Gaertn.)

As a perennial ornamental plant, lotus will begin to become dormant in the face of adverse environmental conditions. The dormancy and apical buds development of lotus are of great significance in regulating the flowering period, storage and reproduction of the lotus rhizome, but the related regulatory mechanisms have not been reported. In this study, we sampled the lotus apical buds at 0 d, 12 d and 24 d after planting, and determined that the lotus could complete the dormancy releaseprocess at 12 days after planting. The monitoring of physiological indexes, hormone levels and transcriptome sequencing of 9 samples in three periods were carried out. It was found that the contents of carbohydrates and hormones changed significantly during apical buds development. Transcriptome analysis also showed that a large number of differentially expressed genes were enriched in hormone synthesis and signal transduction pathways, starch and sucrose metabolism pathways, and lipid metabolism pathways, these genes may be involved in the development of lotus apical buds. Subsequently, we analyzed the differential transcription factors during apical buds development and screened a key differential gene NnHSP18.2. NnHSP18.2 is a heat shock protein (HSP) family gene specifically expressed on apical buds, encoding a protein of 160 amino acids with a conserved α-crystallin domain (ACD) domain. Overexpression of NnHSP18.2 can inhibit Arabidopsis seed germination. These results are of great significance for exploring the molecular mechanism of lotus apical buds development and actively promoting the development of the lotus industry.

Elucidating the hepatoprotective mechanisms of cholic acid against CCl4-Induced acute liver injury: A transcriptomic and metabolomic study

Ethnopharmacological relevanceCholic acid (CA) is one of the main active ingredients in Calculus Bovis, a traditional Chinese medicine, which helps to regulate the heart and liver meridians, clearing the heart, opening the mouth, cooling the liver and calming the wind. However, the molecular mechanism of its liver protective effect is still unclear. Aim of the studyGrowing attention has been directed towards traditional Chinese medicine (TCM), particularly Calculus Bovis, as a potential solution for liver protection. Despite this interest, a comprehensive understanding of its hepatoprotective mechanisms remains lacking. This research seeks to explore the potential protective properties of cholic acid (CA) against CCl4-induced acute liver injury (ALI) in mice, while also examining the mechanisms involved. Materials and methodsIn the experiment, a mouse model was employed to ALI using CCl4, and the potential therapeutic effects of orally administered CA at varying doses (15, 30, and 60 mg/kg) were assessed. The study employed a multi-faceted approach, integrating liver transcriptomics with serum metabolomics, and conducting thorough analyses of serum biochemical markers and liver histopathological sections. ResultsOral CA administration markedly reduced the organ indices of the liver, spleen, and thymus in comparison with the model group. It also elevated the expression of superoxide dismutase (SOD) in serum while diminishing the concentrations of ALT, AST, MDA, IL-6, and TNF-α. Moreover, CA ameliorated the pathological damage induced by CCl4. Integrated metabolomic and transcriptomic analyses indicated that the hepatoprotective action of CA on ALI is mediated through the modulation of lipid metabolic pathways—specifically, metabolisms of glycerophospholipid, arachidonic acid, as well as linoleic acid—and by altering the expression of genes such as Ptgr1, PLpp1, Tbxas1, and Cyp2c37. ConclusionsThe current investigation offers insights into the hepatoprotective mechanisms by which CA mitigates ALI caused by CCl4 exposure, thus supporting the further evaluation and development of CA-based therapeutics for ALI.

Role of the fatty pancreatic infiltration in pancreatic oncogenesis

Although pancreatic precancerous lesions are known to be related to obesity and fatty pancreatic infiltration, the mechanisms remain unclear. We assessed the role of fatty infiltration in the process of pancreatic oncogenesis and obesity. A combined transcriptomic, lipidomic and pathological approach was used to explore neoplastic transformations. Intralobular (ILF) and extralobular (ELF) lipidomic profiles were analyzed to search for lipids associated with pancreatic intraepithelial neoplasia (PanINs) and obesity; the effect of ILF and ELF on acinar tissue and the histopathological aspects of pancreatic parenchyma changes in obese (OB) and non-obese patients. This study showed that the lipid composition of ILF was different from that of ELF. ILF was related to obesity and ELF-specific lipids were correlated to PanINs. Acinar cells were shown to have different phenotypes depending on the presence and proximity to ILF in OB patients. Several lipid metabolic pathways, oxidative stress and inflammatory pathways were upregulated in acinar tissue during ILF infiltration in OB patients. Early acinar transformations, called acinar nodules (AN) were linked to obesity but not ELF or ILF suggesting that they are the first reversible precancerous pancreatic lesions to occur in OB patients. On the other hand, the number of PanINs was higher in OB patients and was positively correlated to ILF and ELF scores as well as to fibrosis. Our study suggests that two types of fat infiltration must be distinguished, ELF and ILF. ILF plays a major role in acinar modifications and the development of precancerous lesions associated with obesity, while ELF may play a role in the progression of PDAC.

Aging induces region-specific dysregulation of hormone synthesis in the primate adrenal gland.

Adrenal glands, vital for steroid secretion and the regulation of metabolism, stress responses and immune activation, experience age-related decline, impacting systemic health. However, the regulatory mechanisms underlying adrenal aging remain largely uninvestigated. Here we established a single-nucleus transcriptomic atlas of both young and aged primate suprarenal glands, identifying lipid metabolism and steroidogenic pathways as core processes impacted by aging. We found dysregulation in centripetal adrenocortical differentiation in aged adrenal tissues and cells in the zona reticularis region, responsible for producing dehydroepiandrosterone sulfate (DHEA-S), were highly susceptible to aging, reflected by senescence, exhaustion and disturbed hormone production. Remarkably, LDLR was downregulated in all cell types of the outer cortex, and its targeted inactivation in human adrenal cells compromised cholesterol uptake and secretion of dehydroepiandrosterone sulfate, as observed in aged primate adrenal glands. Our study provides crucial insights into endocrine physiology, holding therapeutic promise for addressing aging-related adrenal insufficiency and delaying systemic aging.

Sophora japonica Extract Inhibits Ulcerative Colitis and Colitis-Associated Colon Cancer via Regulation of Lipid Metabolism

Inflammation is a well-known risk factor for tumor development. Intervening in chronic inflammation may be an effective approach to inhibit the progression of ulcerative colitis (UC) to colitis-associated colon cancer (CAC). Sophora japonica is a medicinal and food plant commonly used to treat hemorrhoids, bleeding, and inflammation, symptoms that coincide with those of patients with CAC. However, studies on using Sophora japonica to treat CAC are scarce. Therefore, this study aimed to investigate the anti-inflammatory and antitumor effects of Sophora japonica extract (SJE) using dextran sodium sulfate (DSS)-induced UC and azoxymethane (AOM)/DSS-induced CAC models. Furthermore, we employed ultraperformance liquid chromatography–quadrupole time-of-flight–tandem mass spectrometry (UPLC–QTOF–MS/MS) technology to explore the metabolomics mechanism through which SJE inhibited the progression of UC to CAC. The results demonstrated that SJE significantly inhibited UC and CAC and alleviated symptoms such as bloody stools, colon shortening, inflammation, and intestinal tissue damage in model mice. Further, 57 differential metabolites were identified by UPLC–QTOF–MS/MS, which were composed mainly of lipids (fatty acids, glycerophospholipids, sterol lipids, pregnenolone lipids, etc.) and peptides (amino acids). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that SJE might inhibit the progression of UC to CAC by regulating lipid metabolic pathways such as arachidonic acid metabolism, primary bile acid biosynthesis, and linoleic acid metabolism. This study, for the first time, substantiated the inhibitory effect of SJE on CAC. Employing metabolomics techniques, the research delved into the potential pathways through which SJE may exert its inhibitory effects on CAC by suppressing the progression of UC. These findings contribute scientific evidence to the application of Sophora japonica in functional foods and the development of natural drugs for the prevention and treatment of UC and CAC.

Metabolomic analysis to understand the mechanism of Ti3C2Tx (MXene) toxicity in Daphnia magna

Due to their potential release into the environment, the ecotoxicity of Ti3C2Tx (MXene) nanomaterials is a growing concern. Unfortunately, little is known about the toxic effects and mechanisms through which Ti3C2Tx induces toxicity in aquatic organisms. The aim of this study is thus to investigate the toxic effects and mechanisms of Daphnia magna upon exposure to Ti3C2Tx with different sheet sizes (100 nm [Ti3C2Tx-100] and 500 nm [Ti3C2Tx-500]) by employing conventional toxicology and metabolomics analysis. The results showed that exposure to both Ti3C2Tx-100 and Ti3C2Tx-500 at 10 μg/mL resulted in a significant accumulation of Ti3C2Tx in D. magna, but no effects on the mortality or growth of D. magna were observed. However, the metabolomics results revealed that Ti3C2Tx-100 and Ti3C2Tx-500 induced significant changes in up to 265 and 191 differential metabolites in D. magna, respectively, of which 116 metabolites were common for both. Ti3C2Tx-100-induced metabolites were mainly enriched in phospholipid, pyrimidine, tryptophan, and arginine metabolism, whereas Ti3C2Tx-500-induced metabolites were mainly enriched in the glycerol-ester, tryptophan, and glyoxylate metabolism and the pentose phosphate pathway. These results indicated that the toxicity of Ti3C2Tx to D. magna has a size-dependent effect at the metabolic level, and both sheet sizes of Ti3C2Tx can lead to metabolic disturbances in D. magna by interfering with lipid and amino acid metabolism pathways.

Epoxiconazole altered hepatic metabolism in adult zebrafish based on transcriptomic analysis

Epoxiconazole (EPX) is a triazole fungicide, which has been widely used in pest control of cereal crops. However, its extensive use has led to concerning levels of residue in water bodies, posing substantial risks to aquatic life. In this study, we characterized the toxicological effects of EPX on 6-month-old male and female zebrafish at 70 and 700 μg/L, respectively. The results revealed that EPX exposure markedly increased both body length and weight in zebrafish of both sexes, consequently elevating their condition factor. Besides, EPX exposure resulted in notable alterations in hepatic histopathology. These changes included loosened hepatocyte structure, ballooning degeneration, nucleolysis, and disappearance of cell line, with male zebrafish exhibiting more severe damage. High concentration of EPX also significantly increased hepatic lipid accumulation in male zebrafish, as well as increased hepatic triglyceride (TG) levels. Correspondingly, there was a notable alteration in the transcription of genes including cyp51, hmgcr, and PPAR-γ, which associated with cholesterol and lipid metabolism. Interestingly, with the hepatic transcriptomic analysis, high concentration of EPX produced 195 upregulated and 107 downregulated differential expression genes. Both KEGG and GO analyses identified significant enrichment of these genes in lipid and amino acid metabolism pathways. Notably, some key genes involved in the steroid synthesis pathway were marked upregulated. In addition, molecular docking study confirmed that EPX could bind CYP51 protein well (△G = −7.7 kcal/mol). Taken together, these findings demonstrated the multiple toxic effects of EPX on adult zebrafish.

Radiogenomic analysis based on lipid metabolism-related subset for non-invasive prediction for prognosis of renal clear cell carcinoma

PurposeMultiple lipid metabolism pathways alterations are associated with clear cell renal cell carcinoma (ccRCC) development and aggressiveness. In this study, we aim to develop a novel radiogenomics signature based on lipid metabolism-related genes (LMRGs) that may accurately predict ccRCC patients' survival. Materials and methodsFirst, 327 ccRCC were used to screen survival-related LMRGs and construct a gene signature based on The Cancer Genome Atlas (TCGA) database. Then, 182 ccRCC were analyzed to establish radiogenomics signature linking LMRGs signature to radiomic features in The Cancer Imaging Archive (TCIA) database included enhanced CT images and transcriptome sequencing data. Lastly, we validated the prognostic power of the identified radiogenomics signature using these patients of TCIA and the Third Xiangya Hospital. ResultsWe identified the LMRGs signature, consisting of 13 genes, which could efficiently discriminate between low-risk and high-risk patients and serve as an independent and reliable predictor of overall survival (OS). Radiogenomics signature, comprised of 9 radiomic features, was created and could accurately predict the expression level of LMRGs signature (low- or high-risk) for patients. The predictive performance of this radiogenomics signature was demonstrated through AUC values of 0.75 and 0.74 for the training and validation sets (at a ratio of 7:3), respectively. Radiogenomics signature was proven to be an independent risk factor for OS by multivariable analysis (HR = 4.98, 95 % CI:1.72–14.43, P = 0.003). ConclusionsThe LMRGs radiogenomics signature could serve as a novel prognostic predictor.

Transcriptomic sequencing analysis of key long noncoding RNAs and mRNAs expression profiles in postoperative recurrence of hepatocellular carcinoma.

Recurrence is the main cause of death in hepatocellular carcinoma (HCC) patients after liver resection. The long non-coding RNAs (lncRNAs) have been reported participated in progression and prognosis of HCC, however, the vital role of lncRNA in postoperative recurrence of HCC has rarely been systematically identified. RNA-sequencing (RNA-seq) was performed between orthotopic model of HCC and hepatoma postoperative recurrent model to comprehensively analyze the integrated transcriptome expression profiles of lncRNA and mRNA. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) was then conducted to quantify the expression levels of DElncRNAs and their target mRNAs. In our study, 211 lncRNAs (P-value < 0.05) and 1125 mRNAs (P-adjust < 0.05) were significantly differentially expressed (DE) between two groups. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that DElncRNAs and DEmRNAs were mainly enriched in lipid metabolism, including Arachidonic acid metabolism, PPAR signaling pathway, Steroid hormone biosynthesis, Linoleic acid metabolism, Inflammatory mediator regulation of TRP channels, and Fatty acid degradation. Furthermore, we constructed lncRNA-mRNA interaction networks and protein-protein interaction (PPI) network, and verified by qRT-PCR, suggesting that increased DEIncRNAs (XLOC_063499 and XLOC_042016) may prevent HCC recurrence after surgery by upregulating on targeted cytochrome P450 (CYP) family genes in the lipid metabolism pathway, such as cyp3a16, cyp3a44, cyp2c39, cyp2c40 and cyp2c68. Overall, Our findings provided new insights for further investigation of biological function in lncRNA related HCC recurrence.

CYP14 family in Caenorhabditis elegans: Mitochondrial function, detoxification, and lifespan.

CYP-14 members of the Caenorhabditis elegans (C. elegans) Cytochrome P450 (CYP) enzyme family, plays important roles in mitochondrial dysfunction, detoxification, lipid metabolism, defense and lifespan regulation. The review identifies CYP-14 members: cyp-14A1, cyp-14A2, cyp-14A3, cyp-14A4, cyp-14A5 and their homology with human CYP families. Despite limited studies on C. elegans cyp-14 members, the findings unraveled their complex crosstalk between mitochondrial stress, detoxification mechanisms, and lifespan regulation, emphasizing the complexity of these interconnected pathways as well as how their regulation depends on environmental cues changes including pH, nutrients, ROS and chemical stressors. The review underscores the translational relevance to human health, shedding light on potential human homologues and their implications in age-related, metabolic and respiratory diseases. Among other genes, cyp-14A2 and cyp-14A4 predominate the mitochondrial function, heat resistance, lipid metabolism, detoxification and lifespan pathways. In conclusion, these insights pave the way for future research, offering promising avenues for therapeutic interventions targeting CYP-14 activity to address age-related diseases and promote healthy aging.

Comparing massa medicata fermentata before and after charred in terms of digestive promoting effect via metabolomics and microbiome analysis

Ethnopharmacological relevanceMassa Medicata Fermentata, a fermented Chinese medicine, is produced by the fermentation of six traditional Chinese medicines. Liu Shenqu (LSQ) and charred Liu Shenqu (CLSQ) have been used for strengthening the spleen and enhancing digestion for over a thousand years, and CLSQ is commonly used in clinical practice. However, it is unclear whether there is a difference in the spleen strengthening and digestion effects between LSQ and CLSQ, as well as their mechanisms of action. Aim of studyThis study aims to compare the effects of LSQ and CLSQ on the digestive function of functional dyspepsia (FD) rats and reveal their mechanisms of action. Materials and methodsSPF grade SD rats were randomly divided into 6 groups: control group, model group, Liu Shenqu decoction low-dosage (LSQ LD) group, Liu Shenqu decoction high-dosage (LSQ HD) group, charred Liu Shenqu decoction low-dosage (CLSQ LD) group, and charred Liu Shenqu decoction high-dosage (CLSQ HD) group. Rats were injected intraperitoneally with reserpine to create an FD model and then treated by intragastric administration. During this period, record the weight and food intake of the animals. After 18 days of treatment, specimens of the gastric antrum, spleen, and duodenum of rats were taken for pathological staining and immunohistochemical detection of Ghrelin protein expression. Enzyme linked immunosorbent assay (ELISA) was used to determine the concentration of relevant gastrointestinal hormones in serum. The 16 S rDNA sequencing method was used to evaluate the effect of cecal contents on the structure of the gut microbiota in experimental rats. Plasma metabolomics analysis was performed using ultra high performance liquid chromatography coupled with quadrupole time of flight mass spectrometry (UPLC-QTOF-MS) to further reveal their mechanism of action. ResultsLSQ and CLSQ improved the pathological tissue histological structure of FD rats and increased the levels of MTL and GAS hormones in serum and the levels of ghrelin in the gastric antrum, spleen, and duodenum, while reducing VIP, CCK, and SP hormone levels. The above results showed that the therapeutic efficacy of CLSQ is better than that of LSQ. Futhermore, the mechanism of action of LSQ and CLSQ were revealed. The 16 S rDNA sequencing results showed that both LSQ and CLSQ can improve the composition and diversity of the gut microbiota. And metabolomic analysis demonstrated that 20 metabolites changed after LSQ treatment, and 16 metabolites underwent continuous changes after CLSQ treatment. Further analysis revealed that LSQ mainly intervened in the metabolic pathways of glycerol phospholipid metabolism and arginine and proline metabolism, but CLSQ mainly intervened in the metabolic pathways of ether lipid metabolism, sphingolipid metabolism, and glycerophospholipid metabolism. ConclusionsBoth LSQ and CLSQ can improve functional dyspepsia in FD rats, but CLSQ has a stronger improvement effect on FD. Although their mechanisms of action are all related to regulating gastrointestinal hormone secretion, significantly improving intestinal microbiota disorders, and improving multiple metabolic pathways, but the specific gut microbiota and metabolic pathways they regulate are different.

3D-QSAR and Molecular Dynamics Study of Isoxazole Derivatives to Identify the Structural Requirements for Farnesoid X Receptor (FXR) Agonists.

The farnesoid X receptor (FXR) has been recognized as a potential drug target for the treatment of non-alcoholic fatty liver disease (NAFLD). FXR agonists benefit NAFLD by modulating bile acid synthesis and transport, lipid metabolism, inflammation, and fibrosis pathways. However, there are still great challenges involved in developing safe and effective FXR agonists. To investigate the critical factors contributing to their activity on the FXR, 3D-QSAR molecular modeling was applied to a series of isoxazole derivatives, using comparative molecular field analysis (CoMFA (q2 = 0.664, r2 = 0.960, r2pred = 0.872)) and comparative molecular similarity indices analysis (CoMSIA (q2 = 0.706, r2 = 0.969, r2pred = 0.866)) models, which demonstrated strong predictive ability in our study. The contour maps generated from molecular modeling showed that the presence of hydrophobicity at the R2 group and electronegativity group at the R3 group in these compounds is crucial to their agonistic activity. A molecular dynamics (MD) simulation was carried out to further understand the binding modes and interactions between the FXR and its agonists in preclinical or clinical studies. The conformational motions of loops L: H1/H2 and L: H5/H6 in FXR-ligand binding domain (LBD) were crucial to the protein stability and agonistic activity of ligands. Hydrophobic interactions were formed between residues (such as LEU287, MET290, ALA291, HIS294, and VAL297) in helix H3 and ligands. In particular, our study found that residue ARG331 participated in salt bridges, and HIS447 participated in salt bridges and hydrogen bonds with ligands; these interactions were significant to protein-ligand binding. Eight new potent FXR agonists were designed according to our results, and their activities were predicted to be better than that of the first synthetic FXR agonist, GW4064.

Development and Metabolomic Profiles of Bactrocera dorsalis (Diptera: Tephritidae) Larvae Exposed to Phytosanitary Irradiation Dose in Hypoxic Environment Using DI-SPME-GC/MS.

X-ray irradiation and modified atmospheres (MAs) provide eco-friendly, chemical-free methods for pest management. Although a low-oxygen atmospheric treatment improves the performance of some irradiated insects, its influence on the irradiation of quarantine insects and its impacts on pest control efficacy have yet to be investigated. Based on bioassay results, this study employed direct immersion solid-phase microextraction (DI-SPME) combined with gas chromatography-mass spectrometry (GC-MS) to determine metabolic profiles of late third-instar B. dorsalis larvae under normoxia (CON, Air), hypoxia (95% N2 + 5% O2, HY), super-hypoxia (99.5% N2 + 0.5% O2, Sup-HY), irradiation-alone (116 Gy, IR-alone), hypoxia + irradiation (HY + IR) and super-hypoxia + irradiation (Sup-HY + IR). Our findings reveal that, compared to the IR-alone group, the IR treatment under HY and Sup-HY (HY + IR and Sup-HY + IR) increases the larval pupation of B. dorsalis, and weakens the delaying effect of IR on the larval developmental stage. However, these 3 groups further hinder adult emergence under the phytosanitary IR dose of 116 Gy. Moreover, all IR-treated groups, including IR-alone, HY + IR, and Sup-HY + IR, lead to insect death as a coarctate larvae or pupae. Pathway analysis identified changed metabolic pathways across treatment groups. Specifically, changes in lipid metabolism-related pathways were observed: 3 in HY vs. CON, 2 in Sup-HY vs. CON, and 5 each in IR-alone vs. CON, HY + IR vs. CON, and Sup-HY + IR vs. CON. The treatments of IR-alone, HY + IR, and Sup-HY + IR induce comparable modifications in metabolic pathways. However, in the HY + IR, and Sup-HY + IR groups, the third-instar larvae of B. dorsalis demonstrate significantly fewer changes. Our research suggests that a low-oxygen environment (HY and Sup-HY) might enhance the radiation tolerance in B. dorsalis larvae by stabilizing lipid metabolism pathways at biologically feasible levels. Additionally, our findings indicate that the current phytosanitary IR dose contributes to the effective management of B. dorsalis, without being influenced by radioprotective effects. These results hold significant importance for understanding the biological effects of radiation on B. dorsalis and for developing IR-specific regulatory guidelines under MA environments.

Supplementation with Astragalus Root Powder Promotes Rumen Microbiota Density and Metabolome Interactions in Lambs.

The gut microbiota is highly symbiotic with the host, and the microbiota and its metabolites are essential for regulating host health and physiological functions. Astragalus, as a feed additive, can improve animal immunity. However, the effects of Astragalus root powder on the rumen microbiota and their metabolites in lambs are not apparent. In this study, thirty healthy Hu sheep lambs with similar body weights (17.42 ± 2.02 kg) were randomly selected for the feeding experiment. Lambs were fed diets supplemented with 0.3% Astragalus root powder, and the rumen microbiota density and metabolome were measured to determine the effects of Astragalus on the health of lambs in the rumen. The results showed that the relative abundance of Butyrivibrio fibrisolvens (Bf), Ruminococcus flavefaciens (Rf), Succiniclasticum (Su), and Prevotella (Pr) in the rumen was increased in the Astragalus group (p < 0.01), and metabolic profiling showed that the metabolites, such as L-lyrosine and L-leucine, were upregulated in the Astragalus group (p < 0.01). KEGG functional annotation revealed that upregulated metabolites were mainly enriched in the pathways of amino acid metabolism, lipid metabolism, fatty acid biosynthesis, and bile secretion in the Astragalus group, and downregulated metabolites were enriched in the pathways of methane metabolism and other pathways. Correlation analysis revealed that butyric acid was positively correlated with Roseburia and Blautia (p < 0.05) and negatively correlated with Desulfovibrio (p < 0.05). Thus, by analyzing the interactions of Astragalus root powder with the density of rumen microorganisms and their metabolites in lambs, it was shown that Astragalus root powder could improve the structure of rumen microbiota and their metabolites and then participate in the regulation of amino acid metabolism, lipid metabolism, immune metabolism, and other pathways to improve the efficiency of energy absorption of the lambs.