Journal: Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico

Article Title: Multiple antibodies targeting tumor-specific mutations redirect immune cells to inhibit tumor growth and increase survival in experimental animal models.

doi: 10.1007/s12094-019-02235-3

Figure Lengend Snippet: Fig. 3 The effect of different treatments on B16F10 tumor growth in mice. Significant tumor growth retardations (34–49%) were observed in the mice treated with effector cells armed with the nine-antibody cocktail and PD1i, as compared to PBS control group. Two-way ANOVA analysis of the data shows significantly differ- ent curves by treatment and time. *Significantly different (P ≤ 0.05) in comparison to PBS and PD1i alone groups as determined by Tukey’s multiple comparisons test. The values represent the mean ± SEM of six mice in each group. EC effector cells, EC armed with Ab Cocktail Effector cells armed with a cocktail of all the nine rabbit antibodies against selected mutated peptides, TCT tumor cell transplantation, T1– T5 EC treatment days, DPI days post-implantation

Article Snippet: Anti-mouse PD1 inhibitor antibody (PD1i) was supplied by Bio X cell (West Lebanon, NH).

Techniques: Control, Comparison, Transplantation Assay

Journal: Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico

Article Title: Multiple antibodies targeting tumor-specific mutations redirect immune cells to inhibit tumor growth and increase survival in experimental animal models.

doi: 10.1007/s12094-019-02235-3

Figure Lengend Snippet: Fig. 4 The effect of different treatments on survival of mice implanted with B16F10 mela- noma cells. The combined treat- ment with effector cells armed with nine-antibody cocktail and PD1i increased the survival of mice. EC effector cells, EC armed with Ab Cocktail effector cells armed with a cocktail of all the nine antibodies against selected mutated peptides, TCT tumor cell transplanta- tion, T1–T5 EC treatment days, DPI days post-implantation

Article Snippet: Anti-mouse PD1 inhibitor antibody (PD1i) was supplied by Bio X cell (West Lebanon, NH).

Techniques:

Journal: Advanced Science

Article Title: Single‐Cell RNA Sequencing Reveals the Heterogeneity in Differentiation Trajectory and Tumor Microenvironment Leading to More Aggressive Phenotypes of Papillary Thyroid Cancer in Children and Young Adult Patients

doi: 10.1002/advs.202417672

Figure Lengend Snippet: Subtyping of cancer‐associated fibroblasts and their heterogeneity between CAYA and ADULT. A) UMAP plots for the four different CAF subtypes in papillary thyroid tumors (top left), and each cell colored for group (top right), tissue origin (bottom left). UMAP representations with cells colored by the expression level of marker genes of PTC. The black lines represent the spatial density of the cells expressing the given gene higher than the mean level of expression (bottom). B) Bubble plot showing top six differentially expressed genes in each CAF subtypes and patient. The size of the dot indicates the fraction of cells expressing a particular marker, and the intensity of the color represents the level of mean expression. Cellular phenotypes and age group are indicated left side the dot map. C) Bar plot showing the gene count for the most significantly upregulated GO BP pathways in each subtype, calculated through GSVA and Empirical Bayes Statistics for differential expression. D) Multiplex immunofluorescence staining showed major CAF clusters existed in PTC tissues. A pseudocolored image depicting different markers identified by mxIHC (colored as indicated in the key) and the results from histocytometry‐based cell classification (anti‐LAMP5 for emCAF_LAMP5, anti‐CD36 for lpmCAF_CD36, anti‐SMMC for myoCAF_MYH11, anti‐FBLN1 for iCAF_CFD). E) The pseudotime trajectory analysis of thyrocytes and fibroblasts inferred by Monocle 2. Each color represents one cell subtype (left), each point corresponds to one single cell (right). F) Trace plots of the EMT score along pseudotime separated by branch point. G) Shaded line plot indicating the expression levels of the EMT score (left) and TGF‐β (right) along the pseudotime in CAYA and adult patients. H) UMAP reflection of EMT scored by Ucell. I) Rank plot of TF (transcription factor) activities in the four CAF types, scored by pySCENIC. J) The binomial distribution heatmap of transcription factors of age‐specific transcription factors in CAYA and adults.

Article Snippet: A sequential application of antibodies against ANGPTL4 (NBP2‐80039, NOVUS, USA), LAMP5 (NBP1‐84246, NOVUS, USA), CD31 (BD, USA), CD36 (18836‐1‐AP, Proteintech, China), FBLN1 (NBP1‐84725, NOVUS, USA), MYH11 (21404‐1‐AP, Proteintech, China), VEGFC (22601‐1‐AP, Proteintech, China), VEGFR3 (20712‐1‐AP, Proteintech, China), and Pan‐CK (BD, USA) was performed, followed by incubation with horseradish peroxidase‐conjugated secondary antibodies and subsequent tyramide signal amplification.

Techniques: Expressing, Marker, Quantitative Proteomics, Multiplex Assay, Immunofluorescence, Staining

Journal: Advanced Science

Article Title: Single‐Cell RNA Sequencing Reveals the Heterogeneity in Differentiation Trajectory and Tumor Microenvironment Leading to More Aggressive Phenotypes of Papillary Thyroid Cancer in Children and Young Adult Patients

doi: 10.1002/advs.202417672

Figure Lengend Snippet: Complex cell–cell communication networks in the PTC TME. A) Heatmap showing the strength of incoming and outgoing events in interactions between different clusters in the PTC. Histograms separately count the overall intensity of outgoing ( y ‐axis) and incoming ( x ‐axis) events for each cluster. B) Dot plots show gene expression levels of receptor–ligand pairs involved in interactions between different clusters in PTC. C) Interaction strength of emCAF, thyrocyte State 3, lymphatic EC, and vascular EC subclusters incoming and outgoing events between CAYA and adult PTC. D) Circle and chord diagram showing predicted cell–cell interactions of ANGPTL, TGF‐β, and VEGF signaling pathway between CAYA and adult PTC. The arrow width indicates the interaction strength levels. E) Bubble heatmap showing the mean interaction strength for selected ligand–receptor pairs between CAYA and adult in various cell–cell clusters. Dot size indicates P ‐value generated by permutation test, colored by interaction strength levels. F) Box plots showing the expression level of VEGFC, ANGPTL4, and FLT4 from PTCs in TCGA cohort between CAYA and adult. Violin plot showing expression of ANGPTL4 expression among different N and T stages. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001; two‐sided t ‐test. Kaplan–Meier plots for overall survival of ANGPTL4‐high and ‐low in PTC patients. P ‐value was determined by Kaplan–Meier survival curves and log‐rank test. G) Representative micrographs from multiplexed IHC (mxIHC) labeled by ANGPTL4, LAMP5, CD31, and PANCK performed on serial sections. H) Representative images from multiplexed IHC (mxIHC) labeled by VEGGC and VEGFR3 performed on serial sections.

Article Snippet: A sequential application of antibodies against ANGPTL4 (NBP2‐80039, NOVUS, USA), LAMP5 (NBP1‐84246, NOVUS, USA), CD31 (BD, USA), CD36 (18836‐1‐AP, Proteintech, China), FBLN1 (NBP1‐84725, NOVUS, USA), MYH11 (21404‐1‐AP, Proteintech, China), VEGFC (22601‐1‐AP, Proteintech, China), VEGFR3 (20712‐1‐AP, Proteintech, China), and Pan‐CK (BD, USA) was performed, followed by incubation with horseradish peroxidase‐conjugated secondary antibodies and subsequent tyramide signal amplification.

Techniques: Gene Expression, Generated, Expressing, Labeling

Journal: Advanced Science

Article Title: Single‐Cell RNA Sequencing Reveals the Heterogeneity in Differentiation Trajectory and Tumor Microenvironment Leading to More Aggressive Phenotypes of Papillary Thyroid Cancer in Children and Young Adult Patients

doi: 10.1002/advs.202417672

Figure Lengend Snippet: Characteristics of FAP and serves as a target for PET imaging. A) Dot plot showing the correlation between FAP and LAMP5. The P value was generated by Pearson correlation. B) Violin plot of the relationship between the proportion of FAP and T stage (left) and N stage (right) in TCGA‐THCA database. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001; two‐sided t ‐test. C) Overall survival curves (left) and Kaplan–Meier progress free survival curves (right) for FAP of the patients with PTC in TCGA‐THCA cohort for stratified by subclusters’ abundance using the optimal cut‐point for dichotomization. Statistical significance P value was assessed using log‐rank test. D) Related expression of FAP in CAYA and adult patient separated by tumor and para‐tumor tissues staining registration for FAP in the tumor and para‐tumor tissue from CAYA and adult patient (n=3). Overall survival curves (left) and Kaplan–Meier progress free survival curves (right) for FAP of the patients with PTC in TCGA‐THCA cohort for stratified by subclusters’ abundance using the optimal cut‐point for dichotomization. Statistical significance P ‐value was assessed using log‐rank test. F) Comparation of 18 F‐FDG‐PET and 68 Ga‐FAPI‐PET imaging.

Article Snippet: A sequential application of antibodies against ANGPTL4 (NBP2‐80039, NOVUS, USA), LAMP5 (NBP1‐84246, NOVUS, USA), CD31 (BD, USA), CD36 (18836‐1‐AP, Proteintech, China), FBLN1 (NBP1‐84725, NOVUS, USA), MYH11 (21404‐1‐AP, Proteintech, China), VEGFC (22601‐1‐AP, Proteintech, China), VEGFR3 (20712‐1‐AP, Proteintech, China), and Pan‐CK (BD, USA) was performed, followed by incubation with horseradish peroxidase‐conjugated secondary antibodies and subsequent tyramide signal amplification.

Techniques: Imaging, Generated, Expressing, Staining

Journal: bioRxiv

Article Title: Paclitaxel-induced mitotic arrest results in a convergence of apoptotic dependencies that can be safely exploited by BCL-X L degradation to overcome cancer chemoresistance

doi: 10.1101/2025.06.24.661170

Figure Lengend Snippet: (A) BH3 profiling of OvCa cell lines with BIM and BID activator peptides that inhibit all pro-survival proteins and also directly activate BAX and BAK and the PUMA BH3 sensitizer peptide that only inhibits all pro-survival proteins but does not activate BAX or BAK. Cytochrome c release, as indicated by the percentage of cells that are cytochrome c negative, signals initiation of apoptosis and indicates level of apoptotic priming. (B) BH3 profiling of OvCa cell lines with BAD, HRK and MS1 peptides that only inhibit indicated pro-survival proteins and do not activate BAX or BAK. Cytochrome c release indicates initiation of apoptosis and indicates level of dependence on pro-survival protein being inhibited. Mean ± SEM is shown for n = 3 biological replicates. (C) Annexin V/ PI staining and flow cytometry analysis of OvCa cell lines treated with agents targeting BCL-2 family proteins including ABT-199 (inhibits BCL-2 only), ABT-263 (inhibits BCL-2, BCL-X L and BCL-W), DT2216 (degrades BCL-X L ), A1331852 (inhibits BCL-X L ), or S63845 (inhibits MCL-1) for 72 hours. Mean ± SEM is shown for n = 3 biological replicates. (D) Spearman’s rho correlation analysis comparing responses to BAD BH3 peptide at 100 μM in BH3 profiling versus apoptosis induced by indicated BH3 mimetic in annexin/PI chemosensitivity analysis. (E) Immunoblotting analysis of indicated proteins in OvCa cells treated with DT2216 for indicated duration. (F) Immunoblotting analysis of indicated proteins in OVCAR3 cells treated with ABT-263 or DT2216. (G-H) BH3 profiling of KURAMOCHI cells that were treated with DT2216 or ABT-263 for 24 or 48 hours to measure apoptotic priming (G) or dependencies (H). Mean is shown for n = 3 biological replicates. (I-M) Data from the Cancer Dependency Map (DepMap) showing (I) effect of CRISPR knockout of indicated gene on fitness of OvCa cell lines, (J) mRNA expression of pro-survival BCL-2 family genes, (K) effect of siRNA knockdown of indicated gene on fitness of OvCa cell lines, (L-M) comparison of the effects of BCL2L1 knockout and expression of BCL2L1 (L) or MCL1 (M) mRNA expression levels. Data in A-C are shown from individual experiments with bars representing means ± SEM from at least n=3 independent experiments. P values compare biological replicates in a one- or two-way ANOVA with Holm-Sidak’s adjustment for multiple comparisons.

Article Snippet: The following antibodies were used: BCL-2 (CST, #3498, RRID: AB_1903907, 1:500), BCL-XL (CST, #2764, RRID: AB_2228008, 1:1000), Phospho-BCL-XL (S62) (Invitrogen, #44-428G, RRID: AB_2533650, 1:1000), MCL-1 (CST, #94296, RRID: AB_2722740, 1:1000), PUMA (CST, #98672S, RRID: AB_3096180, 1:1000), BIM (CTS, #2933, RRID: AB_1030947, 1:1000), BAX (CST, #2772, RRID: AB_10695870, 1:1000), BAK NT (Millipore 06-536, RRID: AB_310159, 1:1000), BIM (CST, #2933, RRID: AB_1030947, 1:1000); BID (CST, #2002, RRID: AB_10692485, 1:1000), BAD (ROCKLAND, #200-401-Z19, RRID: AB_2612247, 1:1000), BCL-w (CST, #2724S, RRID: AB_10691557, 1:1000), Noxa (CST, #14766S, RRID: AB_2798602, 1:1000), Phospho-Histone H3 (Ser10) (CST, #9701, RRID: AB_331535, 1:1000), GAPDH (CST, #5174, RRID: AB_10622025).

Techniques: Staining, Flow Cytometry, Western Blot, CRISPR, Knock-Out, Expressing, Knockdown, Comparison