Journal: Frontiers in Immunology

Article Title: Multi-omics analysis and experiments uncover the link between cancer intrinsic drivers, stemness, and immunotherapy in ovarian cancer with validation in a pan-cancer census

doi: 10.3389/fimmu.2025.1549656

Figure Lengend Snippet: Cancer intrinsic drivers and stemness properties to portrait the path of OV progression. (A) tSNE plot showing the composition of 5 main subtypes derived from OV malignant cells. (B) Heatmap showing expression programs derived in a representative patient using NMF. (C) Relative expression scores of meta-programs in each OV malignant cell cluster. (D) KEGG enrichment of cancer intrinsic driver and stemness associated mRNAs. (E) Venn diagram showing the overlap between intratumoral heterogeneity driven genes and cancer stemness associated genes. (F) AUCell score of selected 4 intrinsic variation driven cancer stemness associated genes in different cell types. (G) t-SNE visualizes the evolutionary trajectory of tumor cells calculated by slightshot. (H) Violin plots illustrating the expression of RAD21 and CSE1L across different malignant cell subtypes. (I) The relationship between gene expression and evolutionary time. (J) The correlation between inhibitory and RAD21, CSE1L in fifteen OV datasets.

Article Snippet: The primary antibodies used in this analysis included CSE1L (22219-1-AP, Proteintech, Wuhan, China) and Alpha Tubulin (11224-1-AP, Proteintech, Wuhan, China).

Techniques: Derivative Assay, Expressing, Gene Expression

Journal: Frontiers in Immunology

Article Title: Multi-omics analysis and experiments uncover the link between cancer intrinsic drivers, stemness, and immunotherapy in ovarian cancer with validation in a pan-cancer census

doi: 10.3389/fimmu.2025.1549656

Figure Lengend Snippet: Investigating CSE1L-related immune landscapes and providing drug therapy strategies. (A) Kaplan-Meier estimates of overall survival of patients in OV dataset ( GSE9891 ). (B) Box plots comparing the proportion of immune cells between low- and high- CSE1L groups ( GSE26712 ). (C) Heatmap of the expression of chemokines and their corresponding receptors, interferons and their corresponding receptors, and interleukins and their receptors in low- and high-CSE1L groups ( GSE26712 ). (D) Heatmap of the GSVA score of seven steps in cancer immunity cycle in low- and high- CSE1L groups ( GSE26712 ). (E) Heatmap of the expression of effector markers of tumor-infiltrating immune cells in low- and high-CSE1L groups ( GSE26712 ). (F) Box plots comparing the activity of JAK/STAT and VEGF pathway between low- and high- CSE1L groups ( GSE26712 ). (G) Dot plot showing the drug drug susceptibility of chemotherapy drugs. The x-axis represents the log2FC of IC50, where a positive value indicates that the IC50 of the low CSE1L group is greater than that of the high CSE1L group. The y-axis represents -log2 P-value ( GSE26712 ). The drugs highlighted in red are chemotherapy drugs that inhibit VEGF. (H) Box plots comparing the expression of CSE1L between low- and high- Stage groups in GSE30161 and GSE9891 . (I) Box plots comparing the expression of CSE1L between low- and high- Grade groups in GSE9891 . (Wilcoxon test; ns, no significant; *P < 0.05; ***P < 0.001).

Article Snippet: The primary antibodies used in this analysis included CSE1L (22219-1-AP, Proteintech, Wuhan, China) and Alpha Tubulin (11224-1-AP, Proteintech, Wuhan, China).

Techniques: Expressing, Activity Assay

Journal: Frontiers in Immunology

Article Title: Multi-omics analysis and experiments uncover the link between cancer intrinsic drivers, stemness, and immunotherapy in ovarian cancer with validation in a pan-cancer census

doi: 10.3389/fimmu.2025.1549656

Figure Lengend Snippet: CSE1L promotes progression of ovarian cancer in vitro . (A) Representative immunohistochemistry results showed that CSE1L expression was significantly upregulated in tumor tissues compared to adjacent non-cancerous tissues. (B) Validation of CSE1L of knockout in OVCAR-3 and A2780 cell lines by Western Blotting analysis. (C) Proliferation ability of CSE1L-knockout ovarian cancer cells detected by CCK8 assay. (D, E) Evaluation and quantitative analysis of the migration ability of CSE1L-knockout OVCAR-3 and A2780 cell lines using wound healing assays. (F) Analysis and quantitative assessment of the effect of CSE1L knockdown on the migration ability of ovarian cancer cells using Transwell assays. Scale bar, 100μm. (Wilcoxon test; *P < 0.05).

Article Snippet: The primary antibodies used in this analysis included CSE1L (22219-1-AP, Proteintech, Wuhan, China) and Alpha Tubulin (11224-1-AP, Proteintech, Wuhan, China).

Techniques: In Vitro, Immunohistochemistry, Expressing, Biomarker Discovery, Knock-Out, Western Blot, CCK-8 Assay, Migration, Knockdown

Journal: bioRxiv

Article Title: Regulation of lipid dysmetabolism and neuroinflammation linked with Alzheimer’s disease through modulation of Dgat2

doi: 10.1101/2025.02.18.638929

Figure Lengend Snippet: a, Flow chart depicting the experimental setup. Each UAS gene was crossed with the region-specific Gal-4 drivers. To explore the contribution of Dgat2 in Aβ42 and App accumulation, we performed Elav-driven Dgat2 KD and Dgat2 OE in Drosophila and used an App NLG-F mouse model with Dgat2 inhibitor . b, Negative geotaxis assay of Elav and GLaz drove A pp NLG and Aβ42 models in 3wk males and females . c-e, Memory assay of Drosophila : Original method, the difference between fly decisions, flies avoiding shock odor in Elav, GLaz and OK107 App NLG and Aβ42 models. Two-way ANOVA with multiple comparisons done with Uncorrected Fisher’s LSD test was performed for geotaxis, n=3 replicates per group and each group had 10 flies. Chi-square tests were performed for memory assay, ( App NLG N=50, Aβ42=46, W 1118 =54, GFP=45 ). *P<0.05, **P<0.01 and ***P<0.001 n.s = not significant. Exact p values are provided in the source data.

Article Snippet: To investigate whether Dgat2 contributes to AD-related phenotypes, we used PF-06424439, a Dgat2 noncompetitive (MedChemExpress, CAS No#1469284-78-3), slowly reversible inhibitor with an IC50 of 14nM.

Techniques:

Journal: bioRxiv

Article Title: Regulation of lipid dysmetabolism and neuroinflammation linked with Alzheimer’s disease through modulation of Dgat2

doi: 10.1101/2025.02.18.638929

Figure Lengend Snippet: a, Negative geotaxis assay of Elav driven Dgat2 KD and OE in AD models in 3wk male and female . b-c, Memory assay of Drosophila: original method, difference between fly decisions, flies avoiding shock odor in Elav driven Dgat2 KD and OE in App NLG and Aβ42 . d-e, Total, day and night sleep (in minutes) and sleep fragmentation in Elav driven Dgat KD and OE in APP/aβ Models. Two-way ANOVA with multiple comparisons done with Uncorrected Fisher’s LSD test was performed for geotaxis, n=3 replicates per group and each group had 10 flies. Chi-square tests were performed for memory assay, (App NLG N=50, Aβ42=46, W 1118 =54, GFP=45). Non-parametric One-way ANOVA with multiple comparisons done with Kruskal Wallis test was performed for sleep activity and sleep fragmentation. Each dot represents several flies *P<0.05, **P<0.01 and ***P<0.001 n.s = not significant. Exact p values are provided in the source data.

Article Snippet: To investigate whether Dgat2 contributes to AD-related phenotypes, we used PF-06424439, a Dgat2 noncompetitive (MedChemExpress, CAS No#1469284-78-3), slowly reversible inhibitor with an IC50 of 14nM.

Techniques: Activity Assay

Journal: bioRxiv

Article Title: Regulation of lipid dysmetabolism and neuroinflammation linked with Alzheimer’s disease through modulation of Dgat2

doi: 10.1101/2025.02.18.638929

Figure Lengend Snippet: a, Representative image showing the expression of lipid accumulation (green), synaptic loss (purple), a marker of neurodegeneration, and DAPI (white) in the brains of Elav-driven KD in AD models in flies . b-c, Quantification of the expression level of lipid counts and synapsin intensity in Elav-driven AD models. d, Relative expression of inflammatory genes. e, Relative expression of metabolic genes in flies. f, Immunofluorescence staining showing the expression level of lipid spots and Gfap in hippocampus region of the brain of WT and App NLG-F mouse model in presence of Dgat2 inhibitor. g, Quantification of the Lipid spot expression level, h, Quantification of the Gfap expression level n=3 mice per group. i, Relative expression level of inflammatory and AD risk genes WT and App knock-in mouse models in the presence of Dgat2 inhibitor. One-way ANOVA with Turkey’s multiple comparisons test was performed for Flies data. N=3 replicates per group and each group has 8-10 flies. Two-way ANOVA with multiple comparisons done with Uncorrected Fisher’s LSD test was performed. *p < .05; **p < .01; ***p < .001; ns = not significant. Exact p values are provided in the source data.

Article Snippet: To investigate whether Dgat2 contributes to AD-related phenotypes, we used PF-06424439, a Dgat2 noncompetitive (MedChemExpress, CAS No#1469284-78-3), slowly reversible inhibitor with an IC50 of 14nM.

Techniques: Expressing, Marker, Immunofluorescence, Staining, Knock-In

Journal: bioRxiv

Article Title: Regulation of lipid dysmetabolism and neuroinflammation linked with Alzheimer’s disease through modulation of Dgat2

doi: 10.1101/2025.02.18.638929

Figure Lengend Snippet: a Relative Dgat2 transcription factors expressions level in Elav-driven App NLG and Aβ42 . b, Total, day and night sleep (minutes) and sleep fragmentation in Elav-driven Dgat2 TFs KD models. c, Representative image showing the expression of lipid accumulation (green), synaptic loss (purple), a marker of neurodegeneration, and DAPI (white) in the brains of Elav-driven Dgat2 TFs KD models . d-e, Quantification of the expression level of lipid counts and synapsin intensity in Elav-driven Dgat2 TFs KD models . f, Relative expressions level of AD risk genes in Elav driven Dgat2 TFs KD models. g-h, Relative expressions level of Dgat2 TFs and AD risk genes in App knock-in mouse model in presence of Dgat2 inhibitors. One-way ANOVA with Turkey’s multiple comparisons test was performed for Flies data. N=3 replicates per group and each group has 8-10 flies. n=3 mice per group. Two-way ANOVA with multiple comparisons done with Uncorrected Fisher’s LSD test was performed in mouse data. *p < .05; **p < .01; ***p < .001; ns = not significant. Exact p values are provided in the source data.

Article Snippet: To investigate whether Dgat2 contributes to AD-related phenotypes, we used PF-06424439, a Dgat2 noncompetitive (MedChemExpress, CAS No#1469284-78-3), slowly reversible inhibitor with an IC50 of 14nM.

Techniques: Expressing, Marker, Knock-In

Journal: bioRxiv

Article Title: Regulation of lipid dysmetabolism and neuroinflammation linked with Alzheimer’s disease through modulation of Dgat2

doi: 10.1101/2025.02.18.638929

Figure Lengend Snippet: Graphical illustration showed the impacts of panneuronal and glial specific expression of App NLG and Aβ42 without and with Dgat2 KD in Drosophila and microglial/ astrocytic activation and lipid accumulation in App NLG-F mouse model. The top panel result shows that panneuronal and glial-specific expression of App NLG and Aβ42 led to compromised locomotor and cognitive performance. It also led to enhanced lipid accumulation and reduced synapsin level, which were further rescued with Dgat2 KD (up and down arrows). The bottom panel shows the changes in Gfap, Ib1, Dgat2 stain, and Adrp protein in young/old and with Dgat2 inhibitors in APP NLG-F mouse model.

Article Snippet: To investigate whether Dgat2 contributes to AD-related phenotypes, we used PF-06424439, a Dgat2 noncompetitive (MedChemExpress, CAS No#1469284-78-3), slowly reversible inhibitor with an IC50 of 14nM.

Techniques: Expressing, Activation Assay, Staining

Journal: Technology and Health Care

Article Title: H 2 S improves doxorubicin-induced myocardial fibrosis by inhibiting oxidative stress and apoptosis via Keap1-Nrf2

doi: 10.3233/THC-218020

Figure Lengend Snippet: Expression of TNF- α , TGF- β 1, IL1 β , IL6, Bcl-2, caspase-3, caspase-9, Bax protein in myocardial tissue of each group. P * < 0.05 vs Control group; P # < 0.05 vs DOX group.

Article Snippet: Doxorubicin hydrochloride was purchased from Meilun Biotech Co., Ltd., China; TGF- β (BA0290), CSE (A04496), MMP8 (BM4427), MMP16 (A05065), TIMP1 (A00561), Collagen III (A00788), and primary antibody, anti-rabbit secondary antibody were purchased from Boster Company, China; TNF- α (17590-1-AP), Keap1 (10503-2-AP), caspase-3 (19677-1-AP), Caspase-9 (10380-1-AP), Bax (50599-2-Ig), IL1 β (16806-1-AP), IL6 (21865-1-AP), COX2 (66351-1-Ig), Nrf2 (16396-1-AP), NQO1 (11451-1-AP), HO-1 (10701-1-AP), GCLC (12601-1-AP) and Bcl-2 (12789-1-AP) were purchased from Proteintech; These antibodies are diluted 1:1000.

Techniques: Expressing, Control

Journal: Cell reports methods

Article Title: A size-exclusion-based approach for purifying extracellular vesicles from human plasma

doi: 10.1016/j.crmeth.2021.100055

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: EXP®2 Stem Trap , Optimize Technologies , Part# 04003HNC18.

Techniques: Purification, Recombinant, Sequencing, Modification, Mass Spectrometry, Saline, Isolation, Software, Pore Size

Journal: Scientific Reports

Article Title: Proteome mapping of Plasmodium : identification of the P. yoelii remodellome

doi: 10.1038/srep31055

Figure Lengend Snippet: ( A ) Schematic representation of the subcellular fractionation workflow used to map the whole P. yoelii exportome. P: parasite, PV: parasitophorous vacuole, PPM: parasite plasma membrane, PVM: parasitophorous vacuole membrane, HCC: host-cell cytoplasm. Parasites expressing non-exported GFP chimera were treated with SLO or Saponin and then centrifuged to obtain a supernatant and a pellet fraction. The lysed RBC membrane is represented by a red dotted line. The composition of each SN/pellet sample obtained is indicated in red. ( B ) Assessment of the PVM, PPM and RBC membrane integrity following selective permeabilization using SLO and Saponin. P. yoelii infected RBC expressing a non-exported GFP tag were treated with SLO or Saponin (SAPO) and centrifuged to separate the supernatant (SN) from the pellet. Antibodies against the PVM marker EXP2 (pyEXP2), the intraerythrocytic GFP were used to evaluate the integrity of the PVM and PPM, respectively. The antibody against Rhesus blood group-associated glycoprotein (RHAG) was used to evaluate the integrity of the RBC membrane. Each lane was loaded with ~0.5 μl (pyEXP2 and GFP) or ~1 μl (RHAG) of equivalent parasites. The antibodies used and their cognate expected molecular weight is indicated on the left. The molecular weights on the right indicate the positions to which size markers had migrated.

Article Snippet: The membranes were probed using chicken anti-GFP sera (Abcam) (GFP), rabbit anti-EXP2 sera (Genscript) (EXP2) recognizing the peptide KNIESGKYEFDVD and rabbit anti-RHAG antibody (Abcam).

Techniques: Fractionation, Clinical Proteomics, Membrane, Expressing, Infection, Marker, Molecular Weight

Journal: Scientific Reports

Article Title: Proteome mapping of Plasmodium : identification of the P. yoelii remodellome

doi: 10.1038/srep31055

Figure Lengend Snippet: ( A ) The localization of each protein is represented in a schematic infected erythrocyte: either in the HCC cytoplasm (violet), periphery (orange) or the internal parasite (light blue). Each protein is represented by an oval, which provide information about the protein ID, the description available in PlasmoDB database and the fluorescence patterns observed. Overall, three fluorescence patterns can be distinguished. The chimera that displayed a smooth fluorescence pattern in the periphery (n = 5), the HCC (n = 15) and the internal parasite (n = 23) were highlighted in green ( , and ). Those, that showed a smooth fluorescence pattern with one or several reinforcements in the periphery (n = 2), the HCC (n = 4) or the internal parasite (n = 1) were highlighted in light green ( , and ). Finally, the chimera that induced a granular pattern in the periphery (n = 7) and the HCC (n = 3), compatible with localization in specialized structures, were highlighted in yellow ( and ). Finally, PYST PY17X_0920900 chimera displayed a fluorescence pattern associated with the RBC membrane and was represented by a red oval in the RBC membrane. The nine proteins mispredicted are highlighted in red. ( B ) Representative merged image of transfectants displaying the three GFP fluorescence patterns observed. The type of GFP pattern observed is represented horizontally and each group of subcellular localization (peripheral, exported or internal) is represented vertically. The name of the GFP chimera is indicated above the picture. None of the internal proteins screened displayed a punctate pattern.

Article Snippet: The membranes were probed using chicken anti-GFP sera (Abcam) (GFP), rabbit anti-EXP2 sera (Genscript) (EXP2) recognizing the peptide KNIESGKYEFDVD and rabbit anti-RHAG antibody (Abcam).

Techniques: Infection, Fluorescence, Membrane