Journal: Nature Communications

Article Title: Identification of recurrent FHL2-GLI2 oncogenic fusion in sclerosing stromal tumors of the ovary

doi: 10.1038/s41467-019-13806-x

Figure Lengend Snippet: a Differential gene expression analysis of human sclerosing stromal tumors (SSTs) subjected to RNA-sequencing ( n = 8, this study) and high-grade serous ovarian carcinomas ( n = 16; The Cancer Genome Atlas) and other sex cord-stromal tumors (SCSTs, n = 11; this study). Gene expression fold-change is color-coded according to the legend. Only genes significantly differentially expressed ( P < 0.05; two-tailed unpaired t -test) are shown. CPM, count per million. b Expression levels of Sonic Hedgehog (SHH) pathway genes in human SSTs ( n = 11) and other sex-cord stromal tumors ( n = 9) as defined using NanoString. Expression levels and SHH enrichment scores are color-coded according to the legends. *** P < 0.001, Wilcoxon rank test. Hierarchical clustering was performed using complete linkage and Euclidian distance. c Quantitative assessment of the Sonic Hedgehog pathway PTCH1 and GLI1 transcripts in immortalized mesenchymal stem cells (MSCs), HEK-293 and medulloblastoma (DAOY) cells and of PTCH1 and CCND1 transcripts in human basal cell carcinoma (BCC) cells stably expressing empty vector (control), wild-type FHL2 (FHL2), wild-type GLI2 (GLI2), truncated GLI2 (tGLI2), or FHL2-GLI2. Expression levels were normalized to GAPDH expression, and comparisons of mRNA expression levels were performed relative to control. d Representative western blot analysis of PTCH1 and GLI1 protein expression in MSC, HEK-293 and DAOY cells and of PTCH1 and CCND1 in BCC cells stably expressing control, FHL2, GLI2, tGLI2, or FHL2-GLI2. Tubulin was used as protein loading control. Quantification (below) of protein levels as compared to control. In c – d , data are representative of at least three independent experiments. Error bars, s.d. of mean; n.s., not significant; * P < 0.05, ** P < 0.01, *** P < 0.001; two-tailed unpaired t -test.

Article Snippet: BCC cells were cultured in Human Basal Cell Carcinoma Cell Line Complete Media (CELPROGEN).

Techniques: Expressing, RNA Sequencing Assay, Two Tailed Test, Stable Transfection, Plasmid Preparation, Western Blot

Journal: bioRxiv

Article Title: A scalable tumor-vasculature-on-chip for CAR T cell trafficking and efficacy studies

doi: 10.64898/2026.02.05.703975

Figure Lengend Snippet: (A) Schematic representation of the concept of immune checkpoint inhibition. Interaction between PD-1 and PD-L1 is blocked by Nivolumab which restores release of cytotoxic molecules by the CAR T cell (red) (B) Heatmap showing an overview of changes in tumor area and release of Granzyme B, IL-6, sPD-L1 and TNFα in HT-29-GFP and HCT116-GFP co-cultures in response to both single and combination treatments with Nivolumab, Ipilimumab and Temozolomide. Data used to generate the heatmap can be found in supplementary figures 7 and 8. (C,D) PCA plots showing response of HT-29-GFP and HCT116-GFP co-cultures to EpCAM-CD28 CAR T cells and treatments. (E) PCA plot showing the response of HT-29-GFP and HCT116-GFP co-cultures to combination treatments. Datapoints are scaled for the initial tumor cell density at the start of the co-culture. Pink circle indicates a small cluster of replicates consisting of HCT116-GFP cultures exposed to Nivolumab, Ipilimumab and Temozolomide. (F) Contribution and directionality of the different features of the principal components. (G) Heatmap showing morphometric parameters measured in the endothelial vessels of HT-29-GFP and HCT116-GFP co-cultures exposed to EpCAM-CD28 CART cells and treatments. Shown are fold changes against untreated controls. (H) Correlation distance matrix showing similarity between treatment responses based on patterns in relative change in tumor area, cytokine release and endothelial response. Data are presented as unsquared correlation distances, with values <1 indicating similarity in response while values >1 indicate distinct responses. A value of 1 means no relation between observed responses and a value of 0 indicates an identical response.

Article Snippet: Human colorectal cancer cell line HCT116-GFP (GeneCopoeia, SL024) was cultured in RPMI-1640 (Gibco, 11875093) supplemented with 10% Fetal Bovine Serum and 1 % Penicillin-Streptomycin.

Techniques: Inhibition, Co-Culture Assay

Journal: bioRxiv

Article Title: A scalable tumor-vasculature-on-chip for CAR T cell trafficking and efficacy studies

doi: 10.64898/2026.02.05.703975

Figure Lengend Snippet: (A) HCT116-GFP tumor cells proliferate after introduction in the lumenised ECM and cause regression of the endothelial vessel over time. The fluorescent signal could be used to create a binary mask that was used to track growth of HCT116-GFP tumor cells from day 5 until day 8. Fluorescent area at each timepoint was normalized against the area at t=1 for each individual replicate (n=15). (B) Effect of treatments on HT-29-GFP tumor area. Data was normalized against the untreated control at each timepoint (n=8-16). (C) Effect of treatments on HCT116-GFP tumor area. Data was normalized against the untreated control at each timepoint (n=8-14). Data included in the graphs are presented as mean ± SD.

Article Snippet: Human colorectal cancer cell line HCT116-GFP (GeneCopoeia, SL024) was cultured in RPMI-1640 (Gibco, 11875093) supplemented with 10% Fetal Bovine Serum and 1 % Penicillin-Streptomycin.

Techniques: Control

Journal: bioRxiv

Article Title: A scalable tumor-vasculature-on-chip for CAR T cell trafficking and efficacy studies

doi: 10.64898/2026.02.05.703975

Figure Lengend Snippet: (A) Analysis of cytokine levels (pg/mL) in media samples after 72 hours of co-culture of HT-29-GFP and HCT116-GFP tumor cells with EpCAM-CD28 CAR T cells. Co-cultures were untreated or exposed to Nivolumab, Ipilimumab and/or Temozolomide (n=8-14). (B) Cytokine levels in panel A were normalized against untreated controls per experiment resulting in fold changes that were used for principal component analysis (n=8-14). Data included in the graphs are presented as mean ± SD.

Article Snippet: Human colorectal cancer cell line HCT116-GFP (GeneCopoeia, SL024) was cultured in RPMI-1640 (Gibco, 11875093) supplemented with 10% Fetal Bovine Serum and 1 % Penicillin-Streptomycin.

Techniques: Co-Culture Assay

Journal: bioRxiv

Article Title: A scalable tumor-vasculature-on-chip for CAR T cell trafficking and efficacy studies

doi: 10.64898/2026.02.05.703975

Figure Lengend Snippet: (A) Endothelial vessels were co-cultured with either HT-29-GFP or HCT116-GFP tumor cells and stained with VE-cadherin after the 72-hour co-culture. Co-cultures were either untreated or exposed to single or combination treatments with Nivolumab, Ipilimumab and Temozolomide in the presence of EpCAM-CD28 CAR T cells (E:T = 1:1). The endothelial response was assessed by analysis of VE-cadherin objects using a range of different morphological and spatial descriptors using IN Carta® (n=7-14) and normalization against respective untreated controls containing CAR T cells for each parameter. Data are presented as mean ± SD. (B) Heatmap showing change in morphometric parameters measured in endothelial vessels, co-cultured with either HT-29-GFP or HCT116-GFP tumor cells, upon addition of EpCAM-CD28 CAR T cells (E:T = 1:1). Data is presented as fold changes against respective controls without CAR T cells.

Article Snippet: Human colorectal cancer cell line HCT116-GFP (GeneCopoeia, SL024) was cultured in RPMI-1640 (Gibco, 11875093) supplemented with 10% Fetal Bovine Serum and 1 % Penicillin-Streptomycin.

Techniques: Cell Culture, Staining, Co-Culture Assay

Journal: Cancer & Metabolism

Article Title: The FGL1-LAG-3 axis attenuates melanoma-induced cachexia in mice

doi: 10.1186/s40170-025-00418-x

Figure Lengend Snippet: Fgl1 upregulation in WAT and liver in mice models of cancer cachexia. ( A ) Interventional design for B16F10 cachexia mouse model studies. ( B ) Tumor weight of B16F10 mice on day 18 after cell injection ( n = 3 per group). ( C ) Tumor-free body weight of PBS and B16F10 injected mice on day 18 ( n = 3 per group). ( D , E ) RNA-seq design and analysis ( n = 3 per group). ( F ) KEGG pathway analysis of RNA-seq data ( n = 3 per group). ( G ) mRNA expression of Fgl1 in eWAT. The expression of each gene was normalized to actin. ( n = 3 per group). ( H ) Protein expression of Fgl1 in eWAT. ( n = 3 per group). ( I ) Gene expression of FGL1 in the spleen, muscle, kidney, lung, liver, stomach, and intestine from the mice ( n = 3 per group). All values are presented as mean ± standard error of the mean (SEM). P values were determined by two-tailed Student’s t-test, with * p < 0.05, ** p < 0.01, and *** p < 0.001 indicating different levels of statistical significance compared to control. ns, not significant

Article Snippet: The B16F10 cell line was maintained in Dulbecco’s Modified Eagle Medium (DMEM, Sangon Biotech, E600003) supplemented with 10% fetal bovine serum (FBS, Sangon Biotech, E600052) and 1% penicillin-streptomycin (P/S, Sangon Biotech, E607011).

Techniques: Injection, RNA Sequencing, Expressing, Gene Expression, Two Tailed Test, Control

Journal: Cancer & Metabolism

Article Title: The FGL1-LAG-3 axis attenuates melanoma-induced cachexia in mice

doi: 10.1186/s40170-025-00418-x

Figure Lengend Snippet: Early treatment with FGL1 was effective in promoting tumor growth, while intermediate and late-stage treatment exhibited little effect. ( A ) Experimental design of FGL1 treatment time point. ( B ) FGL1-fc injection on day 7 promotes B16F10 growth ( n = 5 per group). ( C ) FGL1-Fc injection on day 14 does not impact B16F10 growth ( n = 5 per group). All values are presented as mean ± SEM. P values were determined by one-way analysis of variance (ANOVA), with * p < 0.05, ** p < 0.01, and *** p < 0.001 indicating different levels of statistical significance compared to control. ns, not significant

Article Snippet: The B16F10 cell line was maintained in Dulbecco’s Modified Eagle Medium (DMEM, Sangon Biotech, E600003) supplemented with 10% fetal bovine serum (FBS, Sangon Biotech, E600052) and 1% penicillin-streptomycin (P/S, Sangon Biotech, E607011).

Techniques: Injection, Control

Journal: Cancer & Metabolism

Article Title: The FGL1-LAG-3 axis attenuates melanoma-induced cachexia in mice

doi: 10.1186/s40170-025-00418-x

Figure Lengend Snippet: FGL1-fc treatment counteracts cancer cachexia by alleviating body weight loss and WAT and muscle wasting. ( A ) Study design for the FGL1-fc treatment. ( B ) Tumor-free body weight% change of B16F10 tumor-bearing mice treated with vehicle and FGL1-fc ( n = 5 per group). ( C ) Measurement of the food intake (the food intake of mice is calculated as the average of a cage of 5 mice). ( D ) Fat percentage of mice ( n = 5 per group). ( E ) Lean mass percentage of mice ( n = 5 per group). ( F – I ) Representative anatomical image, weight, hematoxylin and eosin ( H & E ) staining and adipocyte size of eWAT ( n = 5 per group). ( J – M ) Representative anatomical image, weight, H&E staining and cross-section area of gastrocnemius muscles ( n = 5 per group). All values are presented as mean ± SEM. P values were determined by one-way ANOVA, with * p < 0.05, ** p < 0.01, and *** p < 0.001 indicating different levels of statistical significance compared with control. ns, not significant

Article Snippet: The B16F10 cell line was maintained in Dulbecco’s Modified Eagle Medium (DMEM, Sangon Biotech, E600003) supplemented with 10% fetal bovine serum (FBS, Sangon Biotech, E600052) and 1% penicillin-streptomycin (P/S, Sangon Biotech, E607011).

Techniques: Staining, Muscles, Control

Journal: Cancer & Metabolism

Article Title: The FGL1-LAG-3 axis attenuates melanoma-induced cachexia in mice

doi: 10.1186/s40170-025-00418-x

Figure Lengend Snippet: FGL1-fc reverses lipid and muscle metabolism alterations in B16F10 cachectic mice. ( A ) Three pathways of fatty acid metabolism. ( B ) FGL1-fc counteracts a decline in the expression of fatty acid synthesis genes FAS and SCD1 ( n = 5 per group). ( C ) Both B16F10 tumor and FGL1-fc do not impact the gene expression of lipolysis ( n = 5 per group). ( D ) FGL1-fc does not counteract the decrease in the expression of fatty acid storage gene DGAT2 ( n = 5 per group). ( E ) Levels of HSL or p-HSL in eWAT ( n = 4 or 5 per group). ( F , G ) Circulating esterified Free Fatty Acids (NEFA) and glycerol level ( n = 5 per group). ( H – J ) Skeletal muscle expression of atrophy-associated genes, Mustn1 and IGF1, is protected by FGL1-fc ( n = 5 per group). All values are presented as mean ± SEM. P values were determined by one-way ANOVA, with * p < 0.05, ** p < 0.01, and *** p < 0.001 indicating different levels of statistical significance compared with control. ns, not significant

Article Snippet: The B16F10 cell line was maintained in Dulbecco’s Modified Eagle Medium (DMEM, Sangon Biotech, E600003) supplemented with 10% fetal bovine serum (FBS, Sangon Biotech, E600052) and 1% penicillin-streptomycin (P/S, Sangon Biotech, E607011).

Techniques: Expressing, Gene Expression, Control

Journal: Cancer & Metabolism

Article Title: The FGL1-LAG-3 axis attenuates melanoma-induced cachexia in mice

doi: 10.1186/s40170-025-00418-x

Figure Lengend Snippet: Anti-cachectic effect of FGL1 via LAG-3. ( A ) Experimental design of LAG-3 antibody studies. ( B ) Intermediate and late-stage treatment with LAG3 block antibody or FGL1-fc had no effect on B16F10 tumor growth ( n = 5 per group). ( C – E ) Representative body weight, eWAT weight, and gastrocnemius muscles weight following FGL-fc or FGL1-fc + anti-LAG-3 antibody treatment ( n = 5 per group). All values are presented as mean ± SEM. P values were determined by one-way ANOVA, with * p < 0.05, ** p < 0.01, and *** p < 0.001 indicating different levels of statistical significance compared to control. ns, not significant

Article Snippet: The B16F10 cell line was maintained in Dulbecco’s Modified Eagle Medium (DMEM, Sangon Biotech, E600003) supplemented with 10% fetal bovine serum (FBS, Sangon Biotech, E600052) and 1% penicillin-streptomycin (P/S, Sangon Biotech, E607011).

Techniques: Blocking Assay, Muscles, Control

Journal: Oncology Reports

Article Title: Filamin B extensively regulates transcription and alternative splicing, and is associated with apoptosis in HeLa cells

doi: 10.3892/or.2020.7532

Figure Lengend Snippet: Knockdown of FLNB promotes proliferation and inhibits apoptosis of HeLa cells. (A) Relative mRNA expression of FLNB in HeLa cells after it was knocked down using FLNB -specific shRNA was determined by reverse transcription-qPCR. shFLNB_1 and shFLNB_2 indicate two biological repeats of HeLa cells transfected with FLNB-specific shRNA. Ctrl_1 and Ctrl_2 indicate two biological repeats of HeLa cells transfected with empty vector as controls. (B) Cell proliferation of shFLNB was measured by an MTT assay in HeLa cells. Cell apoptosis of cells transfected with shFLNB was measured by (C) flow cytometry and (D) subsequent analysis by a 7-ADD and Annexin V assay. *P<0.05 and **P<0.01 vs. respective Ctrl. FLNB , filamin B; sh, short hairpin; qPCR, quantitative PCR; Ctrl, control; 7-AAD, 7-amino actinomycin D; OD, optical density; PE, phycoerythrin.

Article Snippet: Human HeLa cells (CCTCC@GDC0009) were obtained from The China Center for Type Culture Collection.

Techniques: Knockdown, Expressing, shRNA, Reverse Transcription, Transfection, Plasmid Preparation, MTT Assay, Flow Cytometry, Annexin V Assay, Real-time Polymerase Chain Reaction, Control

Journal: Oncology Reports

Article Title: Filamin B extensively regulates transcription and alternative splicing, and is associated with apoptosis in HeLa cells

doi: 10.3892/or.2020.7532

Figure Lengend Snippet: GO and KEGG analysis of differentially expressed genes between short hairpin FLNB-transfected and control HeLa cells. Top 10 most enriched GO terms (biological process) of (A) upregulated and (B) downregulated genes upon FLNB knockdown. Rectangles around GO terms indicate notable cancer-related and cartilage development terms. Top 10 most enriched KEGG pathways of (C) upregulated and (D) downregulated genes upon FLNB knockdown. GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; FLNB , filamin B.

Article Snippet: Human HeLa cells (CCTCC@GDC0009) were obtained from The China Center for Type Culture Collection.

Techniques: Transfection, Control, Knockdown

Journal: Oncology Reports

Article Title: Filamin B extensively regulates transcription and alternative splicing, and is associated with apoptosis in HeLa cells

doi: 10.3892/or.2020.7532

Figure Lengend Snippet: Validation of FLNB -regulated genes (DEGs). (A) Relative expression level (FPKM, up) and RT-qPCR measurement (down) of cartilage development-related DEGs. (B) Related expression level (FPKM, up) and RT-qPCR measurement (down) of apoptotic-related DEGs. (C) Western blot analysis of two apoptotic-related proteins in shFLNB and Ctrl HeLa cells. FLNB , filamin B; DEGs, differentially expressed genes; FPKM, fragments per kilobase of transcript per million fragments mapped; RT-qPCR, reverse transcription-quantitative PCR; sh, short hairpin; Ctrl, control; ATP7A, ATPase copper transporting α; BMP7, bone morphogenetic protein 7; COL2A1, collagen type II α 1 chain; MMP13, matrix metallopeptidase 13; IL23A, interleukin 23 subunit α; MALAT1, metastasis associated lung adenocarcinoma transcript 1; NAIP, NLR family apoptosis inhibitory protein; SLC25A36, solute carrier family 25 member 36; MAP2K7, mitogen-activated protein kinase kinase 7.

Article Snippet: Human HeLa cells (CCTCC@GDC0009) were obtained from The China Center for Type Culture Collection.

Techniques: Biomarker Discovery, Expressing, Quantitative RT-PCR, Western Blot, Reverse Transcription, Real-time Polymerase Chain Reaction, Control

Journal: Oncology Reports

Article Title: Filamin B extensively regulates transcription and alternative splicing, and is associated with apoptosis in HeLa cells

doi: 10.3892/or.2020.7532

Figure Lengend Snippet: Validation of FLNB -affected ASEs. Genome visualization (left panel) shows FLNB -regulated ASEs in shFLNB and control. (A) Validation of an ASE of VDR in HeLa cells. (B) Validation of an ASE of PACS2 in HeLa cells. (C) Validation of an ASE of MAP2K7 in HeLa cells. (D) Validation of an ASE of MALAT1 in HeLa cells. The number of junction reads were marked on the line representing splice junction composing ASE. The structures of ASEs are depicted in the top-right panel. The altered ratio of ASEs in RNA-sequencing and in reverse transcription-quantitative PCR were calculated and plotted (right panel, bottom). FLNB , filamin B; ASEs, alternative splicing events; sh/SH, short hairpin; NC, negative control; VDR, vitamin D receptor; PACS2, phosphofurin acidic cluster sorting protein 2; MAP2K7, mitogen-activated protein kinase kinase 7; MALAT1, metastasis associated lung adenocarcinoma transcript 1. *P<0.05 and ***P<0.001 vs. respectively NC.

Article Snippet: Human HeLa cells (CCTCC@GDC0009) were obtained from The China Center for Type Culture Collection.

Techniques: Biomarker Discovery, Control, RNA Sequencing, Reverse Transcription, Real-time Polymerase Chain Reaction, Alternative Splicing, Negative Control