Journal: bioRxiv

Article Title: Lemonite: identification of regulatory metabolites through data-driven, interpretable integration of transcriptomics and metabolomics data

doi: 10.64898/2026.03.27.714373

Figure Lengend Snippet: A: Lemonite IBD network containing 86 gene modules and the most important metabolite and TF regulators (see methods). Gene modules are colored by GO enrichment (see methods). Regulators are colored based on the number of modules they regulate. B-G: Experimental validation of a prioritized set of predicted metabolite-gene regulatory interactions. B: Relative gene expression of ME1 24 h after treatment with C2_carnitine. C: Relative gene expression of BHLHE40 24 hours after treatment with C2_carnitine. D: Relative gene expression of APOBEC3B 24 hours after stimulation with C2_carnitine. E: Relative gene expression of SCD 24h after treatment with C2_carnitine. F: Relative gene expression of PER3 24 hours after stimulation with Trigonelline. G: Relative gene expression of NAAA 24h after treatment with α-glycerophosphocholine. Statistical significance was assessed using T-test compared to baseline (concentration 0) and p-values corrected using Benjamini & Hochberg procedure (p-adj < 0.1).

Article Snippet: Cells were treated with C2_carnitine (Larodan, 17-0200-7), trigonelline (Sigma-Aldrich, 1686411) or α-glycerophosphocholine (Santa Cruz, sc-301813) at concentrations ranging between 100μM and 10 nM (100 μM, 10 μM, 1 μM, 100 nM, 10 nM and 0).

Techniques: Biomarker Discovery, Gene Expression, Concentration Assay

Journal: Lipids in Health and Disease

Article Title: Dysregulated lipid metabolism is associated with kidney allograft fibrosis

doi: 10.1186/s12944-024-02021-3

Figure Lengend Snippet: Primer sequences used for RT-qPCR in rat

Article Snippet: The cells in some experiments were pretreated with the Carnitine palmitoyltransferase 1 A (CPT1A) activator C75 (10 μM, HY-12,364, MedChemExpress, USA) or the CPT1A antagonist Etomoxir sodium salt (80 μM, HY-50,202 A, MedChemExpress, USA) for 2 h [ ].

Techniques:

Journal: Lipids in Health and Disease

Article Title: Dysregulated lipid metabolism is associated with kidney allograft fibrosis

doi: 10.1186/s12944-024-02021-3

Figure Lengend Snippet: Immunohistochemical analysis of EMT and CPT1A expression in a rat model of kidney transplantation. (a) The gene expression level of α-SMA in the indicated kidney tissues was analyzed by RT-qPCR. (b) The gene expression level of vimentin in the indicated kidney tissues was analyzed by RT-qPCR. (c) The gene expression level of CPT1A in the indicated kidney tissues was analyzed by RT-qPCR. (d) Representative IHC image of α-SMA. (e) The percentages of α-SMA-positive cells were calculated. (f) Representative IHC image of E-cadherin. (g) The percentages of E-cadherin-positive cells were calculated. (h) Representative IHC image of CPT1A. (i) The intensity of CPT1A expression was calculated. * P < 0.05, ** P < 0.01, **** P < 0.0001, unpaired t test

Article Snippet: The cells in some experiments were pretreated with the Carnitine palmitoyltransferase 1 A (CPT1A) activator C75 (10 μM, HY-12,364, MedChemExpress, USA) or the CPT1A antagonist Etomoxir sodium salt (80 μM, HY-50,202 A, MedChemExpress, USA) for 2 h [ ].

Techniques: Immunohistochemical staining, Expressing, Transplantation Assay, Gene Expression, Quantitative RT-PCR

Journal: Lipids in Health and Disease

Article Title: Dysregulated lipid metabolism is associated with kidney allograft fibrosis

doi: 10.1186/s12944-024-02021-3

Figure Lengend Snippet: Pathological staining and Immunohistochemical analysis of EMT and CPT1A expression in human kidney allograft fibrosis. (a) Representative HE staining. (b) Representative Trichrome-Masson staining. (c) Representative IHC image of α-SMA. (d) Representative IHC image of E-cadherin. (e) Representative IHC image of CPT1A. (f) The percentages of α-SMA-positive cells were calculated. (g) The percentages of E-cadherin-positive cells were calculated. (h) The intensity of CPT1A expression was calculated. ** P < 0.01, unpaired t test

Article Snippet: The cells in some experiments were pretreated with the Carnitine palmitoyltransferase 1 A (CPT1A) activator C75 (10 μM, HY-12,364, MedChemExpress, USA) or the CPT1A antagonist Etomoxir sodium salt (80 μM, HY-50,202 A, MedChemExpress, USA) for 2 h [ ].

Techniques: Staining, Immunohistochemical staining, Expressing

Journal: Lipids in Health and Disease

Article Title: Dysregulated lipid metabolism is associated with kidney allograft fibrosis

doi: 10.1186/s12944-024-02021-3

Figure Lengend Snippet: In vitro model of EMT induced by TGF-β1. (a) A scratch healing assay showed that C75 could inhibit HK-2 cell migration induced by TGF-β1 at 24 h. (b) Comparison of migration indices among the four intervention groups. The migration index is defined as maximum migration distance at 24 h; *** P < 0.001, **** P < 0.0001; one-way ANOVA. (c) Changes in HK-2 cell morphology at 48 h in four intervention groups. (d) Volcano plot showing the DEGs between untreated group and TGF-β1 group. (e) GO analysis of the DEGs shown in Fig. 7D

Article Snippet: The cells in some experiments were pretreated with the Carnitine palmitoyltransferase 1 A (CPT1A) activator C75 (10 μM, HY-12,364, MedChemExpress, USA) or the CPT1A antagonist Etomoxir sodium salt (80 μM, HY-50,202 A, MedChemExpress, USA) for 2 h [ ].

Techniques: In Vitro, Migration, Comparison

Journal: Lipids in Health and Disease

Article Title: Dysregulated lipid metabolism is associated with kidney allograft fibrosis

doi: 10.1186/s12944-024-02021-3

Figure Lengend Snippet: Immunofluorescence analysis of EMT and CPT1A expression in the in vitro model. (a) Immunofluorescence analysis of fibronectin expression. (b) The relative fluorescence intensity of fibronectin in Fig. 8A was determined by ImageJ. (c) Immunofluorescence analysis of α-SMA expression. (d) The relative fluorescence intensity of α-SMA in Fig. 8C was determined by ImageJ. (e) Immunofluorescence assay of CPT1A expression. (F) The relative fluorescence intensity of α-SMA in Fig. 8E was determined by ImageJ. ** P < 0.01, *** P < 0.001, **** P < 0.0001, one-way ANOVA

Article Snippet: The cells in some experiments were pretreated with the Carnitine palmitoyltransferase 1 A (CPT1A) activator C75 (10 μM, HY-12,364, MedChemExpress, USA) or the CPT1A antagonist Etomoxir sodium salt (80 μM, HY-50,202 A, MedChemExpress, USA) for 2 h [ ].

Techniques: Immunofluorescence, Expressing, In Vitro, Fluorescence