Journal: Science advances

Article Title: Three-dimensional histological electrophoresis enables fast automatic distinguishment of cancer margins and lymph node metastases.

doi: 10.1126/sciadv.adg2690

Figure Lengend Snippet: Fig. 2. Verification of the 3D histological electrophoresis distinguishing tumors from adjacent nonmalignant tissues. (A) Fluorescence images demonstrated the differences between the IR-780–labeled proteins in 4T1 tumor, breast, and muscle lysates following the separation using the 2D SDS-PAGE. (B) Western blotting for detecting overexpressed albumin and AKT1 in the 4T1 tumor sample. (C) Fraction 1 was selected to distinguish tumor and muscle tissues. Quantification of the Fraction 1–to–Fraction 2 (actin) ratio as annotated in (A), albumin-to-actin ratio, and AKT1-to-actin ratio as annotated in (A) (**P < 0.05). (D) IHC staining of albumin and AKT1 levels in 4T1 tumor and muscle tissues. Scale bar, 50 μm. (E) Western blotting for detecting albumin and AKT1 levels in a set of 4T1 tumor samples collected after 3, 7, 21, and 35 days of inoculation, respectively. (F) Schematic representation of the workflow of the 3D histological electrophoresis for tissue sections. (G) Two samples with either muscle&muscle or 4T1 tumor&muscle combination were subjected to the 3D histological electrophoresis. (H) The tumor-to-muscle ratios were analyzed and plotted before/after the separation by 3D histological electrophoresis (n = 3 mice per group, ****P < 0.05). (I) By collecting a set of 4T1 tumor samples after 3, 7, 21, and 35 days of inoculation, the tumor-to-muscle ratios were analyzed and plotted after the 3D histological electrophoresis (n = 3 mice per group). (J) NIR images and signal quantifi- cation of the seven fractionated layers for the muscle&muscle sample after the 3D histological electrophoresis. Scale bar, 1 cm. (K) NIR images and signal quantification of seven fractionated layers for the tumor&muscle sample following the 3D histological electrophoresis. Layers 2, 3, and 4 were observed with the maximum signal differ- ence between tumors and muscles, primed for assessing the tumor-positive margins. Scale bar, 1 cm.

Article Snippet: AKT1 was purchased from MedChemExpress.

Techniques: Electrophoresis, Fluorescence, Labeling, SDS Page, Western Blot, Immunohistochemistry, Muscles

Journal: AMB Express

Article Title: Bioactive potential of Pulicaria undulata from arid regions against multidrug-resistant pathogens and cancer cells

doi: 10.1186/s13568-026-02020-w

Figure Lengend Snippet: Antiviral features of P. undulata extract against HSV1 and CoxB4 A Cell viability; B toxicity; and C antiviral activity. Data are presented as Mean ± SE ( n = 3)

Article Snippet: The tested microbes as follow: Staphylococcus aureus ATCC 25,923, Enterococcus feacalis ATCC 29,212, Klebciella pneumonia ATCC 13,883, and Acinetobacter baumannii ATCC 17,978 and Herpes simplex type I (HSV-1) ATCC VR-1383 and Coxsackie B4 (CoxB4) ATCC VR-184 viruses were used in our manuscript.

Techniques: Activity Assay

Journal: Environment international

Article Title: Bisphenol S impairs mitochondrial function by targeting Myo19/oxidative phosphorylation pathway contributing to axonal and dendritic injury.

doi: 10.1016/j.envint.2024.108643

Figure Lengend Snippet: Fig. 3. Early-life BPS exposure regulated OXPHOS pathway in PFC. KEGG pathway enrichment bubble map of DEGs (A). GO (Cellular component) pathway enrichment bubble map of the DEGs (B). Volcano plot of the DEGs (C). Heat map of the selected DEGs related to OXPHOS pathway in PFC (D). Early-life exposure to BPS decreased the expression ATP6V1B1 (E), ATP5K (F), NDUFC1 (G), NDUFC2 (H), NDUFA3 (M), COX6B1 (O) in PFC on PND 28. Early-life exposure to BPS decreased the expression ATP6V1B1 (I), ATP5K (J), NDUFC1 (K), NDUFC2 (L), NDUFA3 (N), COX6B1 (P) in PFC on PND 56. Data are expressed as mean ± SEM, n = 4. * P < 0.05, ** P < 0.01, *** P < 0.001 compared to the control group.

Article Snippet: Primary antibody dilutions were as follows: mouse anti-MAP2 antibody (M4403, Sigma, USA; 1:1000), rabbit anti-NFL antibody (12998-1-AP, Proteintech, USA; 1:2000), rabbit anti-ATP6V1B1 antibody (14780-1-AP, Proteintech, X. Zhang et al.

Techniques: Expressing, Control

Journal: Environment international

Article Title: Bisphenol S impairs mitochondrial function by targeting Myo19/oxidative phosphorylation pathway contributing to axonal and dendritic injury.

doi: 10.1016/j.envint.2024.108643

Figure Lengend Snippet: Fig. 6. BPS exposure regulated the OXPHOS pathway in cultured neurons. Exposure to BPS decreased the expression ATP6V1B1 (A), ATP5K (B), NDUFC1 (C), NDUFC2 (D), NDUFA3 (E), COX6B1 (F) in cultured neurons. Data are expressed as mean ± SEM, n = 4. * P < 0.05, ** P < 0.01, *** P < 0.001 compared to the control group.

Article Snippet: Primary antibody dilutions were as follows: mouse anti-MAP2 antibody (M4403, Sigma, USA; 1:1000), rabbit anti-NFL antibody (12998-1-AP, Proteintech, USA; 1:2000), rabbit anti-ATP6V1B1 antibody (14780-1-AP, Proteintech, X. Zhang et al.

Techniques: Cell Culture, Expressing, Control

Journal: Environment international

Article Title: Bisphenol S impairs mitochondrial function by targeting Myo19/oxidative phosphorylation pathway contributing to axonal and dendritic injury.

doi: 10.1016/j.envint.2024.108643

Figure Lengend Snippet: Fig. 8. Myo19 overexpression attenuated BPS-induced inhibition of the OXPHOS pathway in cultured neurons. Representative images of cultured neurons transfected lentivirus (mCherry, red) on DIV 8 (A). Representative images of immunofluorescent staining of Myo19 (green) with DAPI counterstain (blue) in cultured neurons (B). BPS-induced down-regulation of Myo19 was resumed after transfection with LV-Myo19 in cultured neurons (C). BPS-induced down-regulation of ATP6V1B1 (D), ATP5K (E), NDUFC1 (F), NDUFC2 (G), NDUFA3 (H), and COX6B1 (I) was resumed after transfection with LV-Myo19 in cultured neurons. Data are expressed as mean ± SEM, n = 4. * P < 0.05, ** P < 0.01, *** P < 0.001 as compared with the control group (Cultured neurons in this group were not transfected with lentivirus). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: Primary antibody dilutions were as follows: mouse anti-MAP2 antibody (M4403, Sigma, USA; 1:1000), rabbit anti-NFL antibody (12998-1-AP, Proteintech, USA; 1:2000), rabbit anti-ATP6V1B1 antibody (14780-1-AP, Proteintech, X. Zhang et al.

Techniques: Over Expression, Inhibition, Cell Culture, Transfection, Staining, Control

Journal: Scientific Reports

Article Title: CREB-mediated synaptogenesis and neurogenesis is crucial for the role of 5-HT1a receptors in modulating anxiety behaviors

doi: 10.1038/srep29551

Figure Lengend Snippet: ( A ) Immunoblots of spinophilin and synapsin in the hippocampus of adult mice infected with different recombinant viruses. (n = 3–4). ( B , C ) Immunoblots of spinophilin and synapsin in the hippocampus of adult mice exposed to different treatments. Recombinant viruses were delivered into the DG. (n = 3–5 in ( B) ; n = 3–4 in ( C) ). ( D , E ) Immunoblots of spinophilin and synapsin in the cultured hippocampal neurons exposed to different treatments. (n = 3–5 in ( D) ; n = 3–4 in ( E )). Means ± SEM. * P < 0.05 ** P < 0.01, *** P < 0.001.

Article Snippet: Synapsin Ia/b shRNA(m) lentiviral particles, we named it LV-synapsin-shRNA-GFP, and its control shRNA lentiviral particles (LV) were purchased (Santa Cruz, CA.

Techniques: Western Blot, Infection, Recombinant, Cell Culture

Journal: Scientific Reports

Article Title: CREB-mediated synaptogenesis and neurogenesis is crucial for the role of 5-HT1a receptors in modulating anxiety behaviors

doi: 10.1038/srep29551

Figure Lengend Snippet: ( A ) Representative immunofluorescence of synapsin and β-III-tubulin ( A1 ) from the cultured hippocampal neurons and simulated diagram view of processes ( A2 ). A high magnified image ( A3 ) and simulated diagram view ( A4 ) from a selected area in A1 . Scale bar = 50 μm. ( B ) Simulated diagram views of β-III-tubulin and synapsin immunofluorescence from the cultured hippocampal neurons exposed to different treatments. ( C ) Summarized assay of density of synapsin in ( B ). (n = 6). ( D ) A representative simulated diagram view of sholl analysis of dendritic complexity from the hippocampal neurons. ( E ) Sholl analysis of dendritic complexity of the cultured hippocampal neurons exposed to different treatments in ( B ). (n = 7). Means ± SEM. In C , * P < 0.05 ** P < 0.01, *** P < 0.001; in E , * ( black ) P < 0.05, LV-GFP + 8-OH-DPAT vs LV-GFP + vehicle; * ( red ) P < 0.05, LV-GFP + NAN-190 vs LV-GFP + vehicle; # ( black ) P < 0.05, ## ( black ) P < 0.01, LV-CREB133-GFP + 8-OH-DPAT vs LV-GFP + 8-OH-DPAT; # ( red ) P < 0.05, LV-VP16-CREB-GFP + NAN-190 vs LV-GFP + NAN-190.

Article Snippet: Synapsin Ia/b shRNA(m) lentiviral particles, we named it LV-synapsin-shRNA-GFP, and its control shRNA lentiviral particles (LV) were purchased (Santa Cruz, CA.

Techniques: Immunofluorescence, Cell Culture

Journal: Scientific Reports

Article Title: CREB-mediated synaptogenesis and neurogenesis is crucial for the role of 5-HT1a receptors in modulating anxiety behaviors

doi: 10.1038/srep29551

Figure Lengend Snippet: ( A ) Simulated diagram views of synapsin immunofluorescence from the cultured hippocampal neurons infected by LV-synapsin-shRNA or LV-control-shRNA. ( B ) Immunoblot of synapsin in the hippocampus of adult mice exposed to LV-synapsin-shRNA at the doses indicated (n = 3). ( C ) Summarized assay of synapsin density in the cultured hippocampal neurons incubated with LV-synapsin-shRNA or its control for 10 d. (n = 14). ( D ) Immunoblot of synapsin in the hippocampus of adult mice exposed to different treatments (n = 4–5). ( E ) The latency to feed in the NSF test (left) and time spent in open arms in the EPM test (right) in the mice exposed to different treatments (n = 14–15). Means ± SEM. * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: Synapsin Ia/b shRNA(m) lentiviral particles, we named it LV-synapsin-shRNA-GFP, and its control shRNA lentiviral particles (LV) were purchased (Santa Cruz, CA.

Techniques: Immunofluorescence, Cell Culture, Infection, shRNA, Control, Western Blot, Incubation

Journal: Cell Proliferation

Article Title: Cathepsin B regulates non‐canonical NLRP 3 inflammasome pathway by modulating activation of caspase‐11 in Kupffer cells

doi: 10.1111/cpr.12487

Figure Lengend Snippet: The effects of cathepsin B inhibition or knockdown on NLRP3 inflammasome activation and pro‐inflammatory cytokines levels in both TLR4−/− and WT Kupffer cells (KCs). Cells were isolated separately from WT and TLR4−/− mice and divided into the following 4 groups: the Control group, the LPS group and the CA‐074 + LPS group, in which cells were infected with control shRNA lentiviral particles; and the shRNA + LPS group, in which cells were transfected with cathepsin B‐shRNA lentiviral particles. When stable clones expressing the shRNAs were established, the cells in the LPS group, the CA‐074 + LPS group and the shRNA + LPS group were stimulated with large dose of lipopolysaccharide (LPS) (10 μg/mL) and the KCs of CA‐074 + LPS group were pretreated with 100 μM/L CA‐074‐Me 1 h prior to LPS stimulation. A, Immunoblot analysis of cathepsin B and inflammasome proteins NLRP3 expression in KCs 4 h after LPS stimulation. B, Enzyme‐linked immunosorbent assay analyses of interleukin 1α (IL‐1α), interleukin 18 (IL‐18) and interleukin 1β (IL‐1β) concentration changes in cells culture medium 4 h after LPS challenge. C, Cell death (% cytotoxicity) was measured by LDH release 4 h after large doses of LPS challenge. D, Cytosolic cathepsin B activity assays in KCs 4 h after large doses of LPS challenge. E, Laser confocal fluorescence detection of cathepsin B and caspase‐11 protein colocalization. The results are depicted as means ± SD (n = 3). *P < .05

Article Snippet: Cathepsin B shRNA lentiviral particles (sc‐29933‐v) and puromycin dihydrochloride (sc‐108071) were purchased from Santa Cruz Biotechnology (Dallas, TX, USA).

Techniques: Inhibition, Knockdown, Activation Assay, Isolation, Control, Infection, shRNA, Transfection, Clone Assay, Expressing, Western Blot, Enzyme-linked Immunosorbent Assay, Concentration Assay, Activity Assay, Fluorescence

Journal: Discover Oncology

Article Title: The molecular mechanism of gemcitabine in inhibiting the HIF-1α/VEGFB/FGF2/FGFR1 signaling pathway for ovarian cancer treatment

doi: 10.1007/s12672-024-01723-5

Figure Lengend Snippet: Exploration of the Impact of GEM Treatment on Other Key Genes. A PPI network of genes interacting with HIF-1α among significant DEGs; B Correlation heatmap of genes interacting with HIF-1α; C Boxplots of expression levels of VEGF-B, PROX1, SOD2 (control-OVCAR3, n = 3, GEM-OVCAR3, n = 3); D – F Boxplots of expression levels of VEGF-B ( D ), PROX1 ( E ), SOD2 ( F ) in TCGA_GTEx-OV dataset, where * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001 (TCGA_GTEx-OV dataset: Normal: n = 88, Tumor: n = 427); (G) PPI network of genes interacting with VEGF-B among significantly DEGs; (H) Boxplots of expression levels of FGF2 and FGFR1 (control-OVCAR3, n = 3, GEM-OVCAR3, n = 3)

Article Snippet: The commercial FGFR1 silencing lentivirus (sc-39840-V) was purchased from Santa Cruz Biotechnology (Shanghai) and titrated to 10 9 TU/mL.

Techniques: Expressing, Control

Journal: Discover Oncology

Article Title: The molecular mechanism of gemcitabine in inhibiting the HIF-1α/VEGFB/FGF2/FGFR1 signaling pathway for ovarian cancer treatment

doi: 10.1007/s12672-024-01723-5

Figure Lengend Snippet: Validation of the upstream–downstream relationships of HIF-1α, VEGF-B, and FGF2/FGFR1. A Overexpression of HIF-1α followed by qPCR A and Western blot analysis B to assess the expression levels of HIF-1α, VEGF-B, FGF2, and FGFR1; C Overexpression of VEGF-B followed by qPCR C and Western blot analysis D to evaluate the expression levels of HIF-1α, VEGF-B, FGF2, and FGFR1; E Overexpression of FGFR1 followed by qPCR E and Western blot analysis F to determine the expression levels of HIF-1α, VEGF-B, FGF2, and FGFR1. Cell experiments were conducted in triplicate. *P < 0.05, **P < 0.01, ***P < 0.001

Article Snippet: The commercial FGFR1 silencing lentivirus (sc-39840-V) was purchased from Santa Cruz Biotechnology (Shanghai) and titrated to 10 9 TU/mL.

Techniques: Biomarker Discovery, Over Expression, Western Blot, Expressing

Journal: Discover Oncology

Article Title: The molecular mechanism of gemcitabine in inhibiting the HIF-1α/VEGFB/FGF2/FGFR1 signaling pathway for ovarian cancer treatment

doi: 10.1007/s12672-024-01723-5

Figure Lengend Snippet: Exploring the molecular mechanisms of Dioscorea nipponica Makino extract on inhibiting the proliferation, migration, invasion capabilities, and angiogenesis of ovarian cancer cells. A , B qPCR and WB analysis of HIF-1α, VEGF-B, FGF2, and FGFR1 expression levels in ISsh-80, SK-OV-3, and SK-OV-3/GEM cells; C , D qPCR and WB analysis of HIF-1α, VEGF-B, FGF2, and FGFR1 expression levels in the control (SK-OV-3), GEM, oe-NC + GEM, oe-HIF-1α + GEM, and oe-HIF-1α + sh-FGFR1 + GEM groups; E CCK-8 assay measuring the differences in proliferation across groups; F Scratch assay measuring the differences in migration across groups; G Transwell assay measuring the differences in invasion across groups; H Angiogenesis assay measuring the formation of tubular structures across groups. All experiments were repeated three times. Cell experiments were repeated three times. **P < 0.01, ***P < 0.001

Article Snippet: The commercial FGFR1 silencing lentivirus (sc-39840-V) was purchased from Santa Cruz Biotechnology (Shanghai) and titrated to 10 9 TU/mL.

Techniques: Migration, Expressing, Control, CCK-8 Assay, Wound Healing Assay, Transwell Assay, Angiogenesis Assay

Journal: bioRxiv

Article Title: Innate Immune Remodeling Drives Therapy Resistance via Macrophage–NK Cell Crosstalk

doi: 10.1101/2025.07.22.666055

Figure Lengend Snippet: (A) Dot plots comparing pre-therapy and on-therapy CD45 (PTPRC) mRNA levels in melanoma patients treated with BRAFi or BRAF/MEKi. Matched patient sample size of n = 6. Statistics were calculated using a two-tailed paired t-test. (B) Average tumor volume curves in response to daily BRAF/MEKi in YUMM1.7 melanoma-bearing NSG mice. Tumor volumes were measured daily. (n = 5-6 tumors, mean ± SEM) (C) Schematic illustrating the different phases of syngeneic melanoma C57BL6/J mouse models. BRAF/MEKi was administered by daily oral gavage when tumors reached ∼700mm3 in size. Growing tumor: 3-day vehicle control treatment. Regressing tumor: 3-day BRAF/MEKi treatment. Residual disease: 14-day BRAF/MEKi treatment. Resistant tumor: BRAF/MEKi treatment until the rebounding tumor reaches its initial size. Created with BioRender.com. (D) Average tumor volume curves in response to daily BRAF/MEKi in different melanoma C57BL6/J models. Tumor volumes were measured daily. (n = 3-5 tumors, mean ± SEM) (E) Representative flow cytometry plots of CD45+ cells gated on live cells in different phases in BRAF/MEKi-treated C57BL/6J mice bearing YUMM1.7 (growing tumors were treated with vehicle control). The numbers in the plots represent the percentage of cells within each gate. (F-H) Quantification of CD45+ cell infiltration in different phases in BRAF/MEKi-treated C57BL/6J mice bearing YUMM1.7 (D), YUMMUV1.7 (E), and YUMMUV3.3 (F) (growing tumors were treated with vehicle control). YUMMUV3.3 tumors did not exhibit profound regressing phase as YUMM1.7 and YUMMUV1.7 but the collection timepoint was after 3-day BRAF/MEKi, consistent with timeline defined in (C). (n = 3-9 tumors, one-way ANOVA with Tukey’ s multiple comparisons test, mean ± SEM)

Article Snippet: Mice received BRAF/MEKi therapy at a dose of 25 mg/kg dabrafenib (Medchem Express, catalog no. HY-14660) and 0.15 mg/kg trametinib (Medchem Express, catalog no. HY-10999).

Techniques: Two Tailed Test, Control, Flow Cytometry

Journal: bioRxiv

Article Title: Innate Immune Remodeling Drives Therapy Resistance via Macrophage–NK Cell Crosstalk

doi: 10.1101/2025.07.22.666055

Figure Lengend Snippet: (A) Schematic showing immune cell types, including macrophages, CD8+ T cells, and NK cells, that may contribute to the BRAF/MEKi tumor response. Created with BioRender.com. (B and C) Depletion efficiencies of clodronate liposomes in tumors at the endpoint (full resistance). Quantification of F4/80-high macrophages (B) and F4/80-low macrophages (C). (n = 4-6 tumors, two-tailed unpaired t-test, mean ± SEM) (D) Kaplan-Meier curve for BRAF/MEKi-treated mice bearing YUMM1.7 receiving clodronate liposomes (CL) or PBS liposomes (PL). (n = 4-6 tumors, Log-rank Mantel-Cox test) (E and F) Depletion efficiencies of the anti-CD8b antibody. Quantification of circulating CD8+ T cells six days post anti-CD8b antibody injection (E) and tumor-infiltrating CD8+ T cells at the endpoint (full resistance) (F). (n = 4 tumors, two-tailed unpaired t-test, mean ± SEM) (G) Kaplan-Meier curve for BRAF/MEKi-treated mice bearing YUMM1.7 receiving anti-CD8b antibody or isotype control. (n = 4 tumors, Log-rank Mantel-Cox test) (H) Depletion efficiency of the anti-ASGM1 antibody in tumors at the endpoint (full resistance). Representative flow cytometry plots and quantification of tumor-infiltrating NK cells. (n = 4-5 tumors, two-tailed unpaired t-test, mean ± SEM) (I) Bar plot showing best response (%) of BRAF/MEKi-treated male mice bearing YUMM1.7 receiving the anti-ASGM1 antibody or rabbit serum. (n = 5 tumors, two-tailed unpaired t-test, mean ± SEM) (J and K) Kaplan-Meier curve for BRAF/MEKi-treated male and female mice bearing YUMM1.7 (J) or YUMMUV1.7 (K) tumors receiving the anti-ASGM1 antibody or rabbit serum. (n = 4-5 tumors, Log-rank Mantel-Cox test)

Article Snippet: Mice received BRAF/MEKi therapy at a dose of 25 mg/kg dabrafenib (Medchem Express, catalog no. HY-14660) and 0.15 mg/kg trametinib (Medchem Express, catalog no. HY-10999).

Techniques: Liposomes, Two Tailed Test, Injection, Control, Flow Cytometry

Journal: bioRxiv

Article Title: Innate Immune Remodeling Drives Therapy Resistance via Macrophage–NK Cell Crosstalk

doi: 10.1101/2025.07.22.666055

Figure Lengend Snippet: (A) Bar plot showing tumor volume change (%) of different phases in BRAF/MEKi-treated mice bearing YUMM1.7 (growing tumors were treated with vehicle control). (n = 5-8 tumors, mean ± SEM) (B) Quantification of NK cell infiltration in different phases in BRAF/MEKi-treated mice bearing YUMM1.7 (growing tumors were treated with vehicle control). (n = 4-9 tumors, one-way ANOVA with Tukey’s multiple comparisons test, mean ± SEM) (C) Correlation between NK cell infiltrate in YUMM1.7 tumors and therapy response to BRAF/MEKi. (Simple linear regression) (D) Representative immunofluorescence images of NK1.1 (red), CD3 (green) and nuclear DAPI (blue) of BRAF/MEKi-treated tumors in the indicated treatment groups. NK cells are NK1.1+CD3-. Scale bar 100 μm. (E) Scatter plot showing the NK cell signature between regressing tumors and residual disease. NK cell activation and inhibitory marker genes are shown in orange and green, respectively. (F and G) Violin plot showing the expression of activation (F) and inhibitory (G) marker genes in NK cells from regressing tumors and residual disease. (H) Quantification of CD8+ T cell infiltration in different phases in BRAF/MEKi-treated mice bearing YUMM1.7 (growing tumors were treated with vehicle control). (n = 4-9 tumors, one-way ANOVA with Tukey’s multiple comparisons test, mean ± SEM) (I) Correlation between CD8+ T cell infiltration and therapeutic response in YUMM1.7 tumors treated with BRAF/MEKi. (Simple linear regression) (J) Schematic illustrating the NK cytotoxicity assay. Created with BioRender.com. (K) Bar plot showing % NK cytotoxicity to YUMM1.7-GFP enriched from regressing tumors and residual disease at effector-to-target (E: T) ratios of 3:1 and 1:1. (n = 3 tumors, conducted in two independent experiments, multiple unpaired t-tests, mean ± SEM)

Article Snippet: Mice received BRAF/MEKi therapy at a dose of 25 mg/kg dabrafenib (Medchem Express, catalog no. HY-14660) and 0.15 mg/kg trametinib (Medchem Express, catalog no. HY-10999).

Techniques: Control, Immunofluorescence, Activation Assay, Marker, Expressing, Clinical Proteomics, Cytotoxicity Assay

Journal: bioRxiv

Article Title: Innate Immune Remodeling Drives Therapy Resistance via Macrophage–NK Cell Crosstalk

doi: 10.1101/2025.07.22.666055

Figure Lengend Snippet: (A and B) Representative immunofluorescence images of F4/80 (green), NK1.1 (red), and nuclear DAPI (blue) in regressing tumors and residual disease treated with BRAF/MEKi (A). Scale bar, 100 μm, 10 μm. Quantification of F4/80+ cells next to NK1.1+ cells (B). (n = 3 tumors with 4-11 total microscopy fields analyzed across all tissues, at least 1,600 counted NK1.1+ cells per tumor, two-tailed unpaired t-test, mean ± SEM) (C and D) Depletion efficiencies with diphtheria toxin (DT) (LysM-cre;iDTR) in tumors during tumor regression. Quantification of F4/80-high macrophages (C) and F4/80-low macrophages (D). (n = 5-6 tumors, two-tailed unpaired t-test, mean ± SEM) (E) Quantification of tumor-infiltrating NK cells in BRAF/MEKi-treated mice receiving diphtheria toxin (DT) (LysM-cre;iDTR) or control (NaCl in LysM-cre;iDTR or DT in WT mice) during tumor regression. (n = 6-7 tumors, two-tailed unpaired t-test, mean ± SEM) (F and G) Violin plot showing the expression of Lyz2 (F) and Adgre1 (G) in each macrophage cluster. Mo/Mϕ, monocyte/macrophage. (H—J) Quantification of MHC II+ (H), CCL5+ (I), or CD63+ (J) F4/80-high macrophages in BRAF/MEKi-treated mice receiving diphtheria toxin (DT) (LysM-cre;iDTR) or control (NaCl in LysM-cre;iDTR) during tumor regression. (n = 9 tumors, two-tailed unpaired t-test, mean ± SEM) (K) Heatmap depicting the CCL signaling network among different immune cell types during tumor regression, analyzed using CellChat. Mo/Mϕ, monocyte/macrophage. (L) Selected DEGs of multiple Ccl genes in macrophage Clusters 0 and 3. Mo/Mϕ, monocyte/macrophage. (M) Bubble plot showing ligand-receptor-based CellChat analysis during tumor regression, with macrophages as senders and NK cells as receivers. Mo/Mϕ, monocyte/macrophage. (N) Schematic illustrating experimental design for analysis of NK cells migrated toward macrophage-derived conditioned media. Mϕ, macrophage. Created with BioRender.com (O) Bar chart showing the migrated NK cell ratio in the transwell assay using conditioned media derived from macrophages isolated from regressing tumors or residual disease and primary splenocytes treated with a CCR2/5 inhibitor (CVC) or DMSO. CVC, cenicriviroc. (n = 5-8 tumors, conducted in two independent experiments, one-way ANOVA with Tukey’s multiple comparisons test, mean ± SEM)

Article Snippet: Mice received BRAF/MEKi therapy at a dose of 25 mg/kg dabrafenib (Medchem Express, catalog no. HY-14660) and 0.15 mg/kg trametinib (Medchem Express, catalog no. HY-10999).

Techniques: Immunofluorescence, Microscopy, Two Tailed Test, Control, Expressing, Derivative Assay, Transwell Assay, Isolation

Journal: bioRxiv

Article Title: Innate Immune Remodeling Drives Therapy Resistance via Macrophage–NK Cell Crosstalk

doi: 10.1101/2025.07.22.666055

Figure Lengend Snippet: (A) Violin plot showing Ptpn22 expression in each immune cell type. Mo/Mϕ, monocyte/macrophage. (B) Schematic illustrating experimental design for targeting Ptpn22 in YUMM1.7-bearing mice. Created with BioRender.com. (C) Quantification of tumor-infiltrating NK cells in BRAF/MEKi-treated mice receiving L-1 or vehicle control on day 13. (n = 9 tumors, two-tailed unpaired t-test, mean ± SEM) (D) Representative immunofluorescence images of NK1.1 (red), CD3 (green) and nuclear DAPI (blue) of BRAF/MEKi-treated tumors in the indicated treatment groups on day 13. NK cells are NK1.1+CD3-. Scale bar 100 μm. (E and F) Quantification of tumor-infiltrating F4/80-high (E) or F4/80-low (F) macrophages in BRAF/MEKi-treated mice receiving L-1 or vehicle control on day 13. (n = 6-7 tumors, two-tailed unpaired t-test, mean ± SEM) (G—I) Quantification of tumor-infiltrating Ccl5+ (G), Cd63+ (H), or MHC II+ (I) F4/80-high macrophages in BRAF/MEKi-treated mice receiving L-1 or vehicle control on day 13. (n = 6-7 tumors, two-tailed unpaired t-test, mean ± SEM) (J—N) Violin plot showing the expression of Adgre1 (J), Ccl5 (K), Cd63 (L), and H2-Ab1/Eb1 (M and N) in the monocyte/macrophage population between regressing tumors and residual disease. REG, regressing; RD, residual disease. (O) Kaplan-Meier curve for BRAF/MEKi-treated mice bearing YUMM1.7 receiving L-1 or vehicle control. (n = 5-6 tumors, Log-rank Mantel-Cox test)

Article Snippet: Mice received BRAF/MEKi therapy at a dose of 25 mg/kg dabrafenib (Medchem Express, catalog no. HY-14660) and 0.15 mg/kg trametinib (Medchem Express, catalog no. HY-10999).

Techniques: Expressing, Control, Two Tailed Test, Immunofluorescence

Journal: bioRxiv

Article Title: Innate Immune Remodeling Drives Therapy Resistance via Macrophage–NK Cell Crosstalk

doi: 10.1101/2025.07.22.666055

Figure Lengend Snippet: (A) Schematic illustrating the timeline and response to BRAF/MEKi for four melanoma patients in GSE229908. Each dot represents one FNA biopsy. Grey represents baseline (before BRAF/MEKi), blue represents responding tumors, and red represents BRAF/MEKi-resistant tumors. (B) UMAP plot showing the cell populations of the four melanoma patients. (C) Bar plots showing NK cell quantification at each FNA timepoint in four melanoma patients. (D) Quantification of NK cells in FNA biopsies grouped into Baseline (before BRAF/MEKi treatment), Responding, and Resistant groups. (mean ± SEM) (E—G) Violin plots showing the expression of exhaustion markers (E), activation markers (F), or RAB27A (G) in the NK cell population in Patient 2 (Resistant), 3 (Responding) and 4 (Partial Responding). (H) Bar plot showing NK cell fractional changes across three treatment states in PRJNA591860, containing 49 lung cancer biopsies before and during TKI treatment. (I) Schematic illustrating the timeline and response to TKI treatment in three lung cancer patients with sequential biopsies in PRJNA591860. Each dot represents one FNA biopsy. Grey represents naïve (before TKI treatment), blue represents responding tumors, and red represents resistant tumors. (J) Bar plots showing NK cell fractional changes at each FNA timepoint in three lung cancer patients. (K) NK fractional changes in FNA biopsies from the three patients grouped into Naïve, Responding, and Resistant groups. (mean ± SEM)

Article Snippet: Mice received BRAF/MEKi therapy at a dose of 25 mg/kg dabrafenib (Medchem Express, catalog no. HY-14660) and 0.15 mg/kg trametinib (Medchem Express, catalog no. HY-10999).

Techniques: Expressing, Activation Assay

Journal: Nature Communications

Article Title: Targeting Tyro3 ameliorates a model of PGRN-mutant FTLD-TDP via tau-mediated synaptic pathology

doi: 10.1038/s41467-018-02821-z

Figure Lengend Snippet: Tyro3 mediates Gas6-induced signal to tau phosphorylation. Western blot analyses of the effect of siRNA-mediated knockdown of Tyro3 on phosphorylation of Tyro3 ( a ), Shc ( b ), PLCγ ( c ), B-Raf ( d ), PKCα ( e ), and tau ( f ). SiRNA-mediated knockdown of Tyro3 exerted suppressive effects on activation of Shc ( b ) and PLCγ ( c ), as well as on phosphorylation of tau at Ser203 and Thr220 ( e ). # p < 0.05; ## p <0.01 ( N = 5, Tukey’s HSD test). Averages and s.e.m. are shown. Phosphatase treatment of the samples substantially decreased the western blot band intensities of phosphorylated Tyro3 ( a ), Shc ( b ), PLCγ ( c ) B-Raf ( d ), PKCα ( e ), and Tau ( f ). p -values are shown in Supplementary Data

Article Snippet: In KD rescue experiments, lentiviral particles (2 × 10 5 titer units in 100 μl) for Tau-shRNA (sc-430402-V, Santa Cruz Biotechnology), scrambled shRNA (SC-108080, Santa Cruz Biotechnology), B-Raf shRNA (sc-63294-V, Santa Cruz Biotechnology), or Tyro3-siRNA (iV037848, ABM, Richmond, BC, Canada) diluted 1:4 with ACSF buffer (NaCl, 125 mM; KCl, 2.5 mM; NaH 2 PO 4 , 1.25 mM; MgCl 2 , 1 mM; CaCl 2 , 1 mM; NaHCO 3 , 26 mM; glucose, 25 mM) or plasmid vectors (10 μg) for PKCα-shRNA (TG501653, OriGene, Rockville, MD, USA), scrambled shRNA (TG501653, OriGene), or Gas6-shRNA (sc-35451-SH, Santa Cruz Biotechnology) dissolved in 100 μl of in vivo-jetPEI (201–10 G, Polyplus-transfection, Illkirch, France) were injected into the subarachnoid space of the right RSD via osmotic pump (0.15 μl/h) from 8 to 12 weeks of age.

Techniques: Phospho-proteomics, Western Blot, Knockdown, Activation Assay

Journal: Nature Communications

Article Title: Targeting Tyro3 ameliorates a model of PGRN-mutant FTLD-TDP via tau-mediated synaptic pathology

doi: 10.1038/s41467-018-02821-z

Figure Lengend Snippet: Suppression of Tyro3 signal rescues decrease in spine abundance and tau mislocalization in mutant PGRN-KI mice. a Experimental protocol for knockdown vectors. AAV-Syn-EGFP was injected into the area adjacent to M2 at 6 weeks of age. Lentivirus for expression of Tau-shRNA, scrambled shRNA, B-Raf-shRNA, or Tyro3-siRNA, or plasmid vectors for expression of PKCα-shRNA, scrambled shRNA, or Gas6-shRNA dissolved in in vivo-jetPEI, were continuously injected into the subarachnoid space of the right M2 via osmotic pump from 8 to 12 weeks of age. Dendritic spines in layer 1 of M2 were observed by two-photon microscopy with three mice at 12 weeks of age. 8 to 10 images were obtained from one mice and the average of spine parameters were used for quantitative analyses ( N = 3). The protocols for vemurafenib and Gö6976 were similar to those shown in Fig. , and two-photon microscopy was performed at 12 weeks of age. b Static spine morphology was observed by two-photon microscopy. Spine protrusion number, length, head diameter, and volume were analyzed. * p < 0.05; ** p < 0.01 ( N = 3, Student’s t -test). Averages and s.e.m. are shown. c Images were obtained by two-photon microscopy at 0, 8, and 24 h on the last day of injection. Dynamic changes in spines were analyzed by serial observation. Spine formation and elimination were counted. * p < 0.05; ** p < 0.01 ( N = 3, Student’s t -test). Averages and s.e.m. are shown. d Lentivirus for expression of shRNA-Tau was injected according to the protocol. ** p < 0.01 ( N = 3, Tukey’s HSD test). Scrambled RNA was used as a control. Averages and s.e.m. are shown. e Lentivirus for expression of shRNA-B-Raf was injected according to the protocol. ** p < 0.01 ( N = 3, Tukey’s HSD test). Scrambled RNA was used as a control. Averages and s.e.m. are shown. f Plasmid for expression of shRNA-PKCα was injected according to the protocol. * p < 0.05; ** p < 0.01 ( N = 3, Tukey’s HSD test). Scrambled RNA was used as a control. Averages and s.e.m. are shown. g Lentivirus for expression of siRNA-Tyro3 was injected according to the protocol. Scrambled RNA was used as a control. ** p < 0.01 ( N = 3, Tukey’s HSD test). Scrambled RNA was used as a control. Averages and s.e.m. are shown. h Plasmid for expression of shRNA-Gas6 was injected according to the protocol. Scrambled RNA was used as a control. ** p < 0.01 ( N = 3, Tukey’s HSD test). Scrambled RNA was used as a control. Averages and s.e.m. are shown. i Mice received oral administration of vemurafenib (32 mg/kg of BW/day) from 6 to 12 weeks of age, and two-photon microscopic analysis was performed at 12 weeks. ** p < 0.01 ( N = 3, Tukey’s HSD test). Averages and s.e.m. are shown. j Gö6976 (4.4 μM) or PBS was injected via osmotic pump into the subarachnoid space of PGRN-KI and C57BL/6J mice from 10 to 12 weeks of age, and two-photon microscopic analysis was performed at 12 weeks. ** p < 0.01 ( N = 3, Tukey’s HSD test). Averages and s.e.m. are shown

Article Snippet: In KD rescue experiments, lentiviral particles (2 × 10 5 titer units in 100 μl) for Tau-shRNA (sc-430402-V, Santa Cruz Biotechnology), scrambled shRNA (SC-108080, Santa Cruz Biotechnology), B-Raf shRNA (sc-63294-V, Santa Cruz Biotechnology), or Tyro3-siRNA (iV037848, ABM, Richmond, BC, Canada) diluted 1:4 with ACSF buffer (NaCl, 125 mM; KCl, 2.5 mM; NaH 2 PO 4 , 1.25 mM; MgCl 2 , 1 mM; CaCl 2 , 1 mM; NaHCO 3 , 26 mM; glucose, 25 mM) or plasmid vectors (10 μg) for PKCα-shRNA (TG501653, OriGene, Rockville, MD, USA), scrambled shRNA (TG501653, OriGene), or Gas6-shRNA (sc-35451-SH, Santa Cruz Biotechnology) dissolved in 100 μl of in vivo-jetPEI (201–10 G, Polyplus-transfection, Illkirch, France) were injected into the subarachnoid space of the right RSD via osmotic pump (0.15 μl/h) from 8 to 12 weeks of age.

Techniques: Mutagenesis, Knockdown, Injection, Expressing, shRNA, Plasmid Preparation, In Vivo, Microscopy, Control

Journal: Nature Communications

Article Title: Targeting Tyro3 ameliorates a model of PGRN-mutant FTLD-TDP via tau-mediated synaptic pathology

doi: 10.1038/s41467-018-02821-z

Figure Lengend Snippet: Suppression of Tyro3 signal rescues tau mislocalization and cognitive impairment in mutant PGRN-KI mice. a Co-staining of phosphorylated tau (Ser203 or Thr220) and PSD-95. Confocal microscopic analysis of M2 regions of background (B6, C57BL/6J), PGRN-R504X-KI (PGRN-KI), vemurafenib-treated PGRN-KI, Gö6976-treated PGRN-KI, and lentivirus-tau-shRNA–infected PGRN-KI mice. All images were acquired by confocal microscopy (LSM510META, Carl Zeiss, Germany). Z-stack images were acquired with the following parameters; objective: ×63, average: line 2; filter (Cy3 ChS1: 550–679 nm; FITC Ch1: 505–530 nm; DAPI Ch2: 420–480 nm); master gain (Cy3 ChS1: 760; FITC Ch1: 741; DAPI Ch2: 615). b Quantitative analyses of PSD95-positive dots and p-tau/PSD95 double-positive spots. All bar graphs indicate averages and s.e.m. Three mice were used for each group. The number of spots was counted in 10 image fields (100 × 100 μm) for each mouse, and the average was used for calculation of mean with s.e.m. for each group. The number of p-tau/PSD95 double-positive spots increased in PGRN-KI mice. # p < 0.05, ## p < 0.01 ( N = 6, Dunnett’s test). Averages and s.e.m. are shown. c In vivo effects of KD of B-Raf, PKCα, Tyro3, Gas6, and tau on two parameters (% time spent at target region and number of target crosses) in the Morris water maze test, performed with PGRN-KI mice ( N = 6 in each experiment) at 12 weeks. # p < 0.05, ## p < 0.01 ( N = 6, Dunnett’s test). Averages and s.e.m. are shown. d In vivo effect of KD of B-Raf, PKCα, Tyro3, Gas6, and tau on % total freezing time in the fear-conditioning test, performed with PGRN-KI mice ( N = 6 in each experiment) at 12 weeks. # p < 0.05, ## p < 0.01 ( N = 6, Dunnett’s test). Averages and s.e.m. are shown. e Tau-KD with or without vemurafenib/Gö6976 had similar effects on % time spent at target region and number of target crosses in the Morris water maze test and on % total freezing time in fear-conditioning test. Both tests were performed at 12 weeks. * p < 0.05 ( N = 6, Dunnett’s test). Averages and s.e.m. are shown. f Western blot analysis confirming shRNA-mediated knockdown of B-Raf, PKCα, and tau. Lower graphs show quantitation. P -values were determined by Tukey’s HSD test ( N = 6). Averages and s.e.m. are shown. p -values are shown in Supplementary data

Article Snippet: In KD rescue experiments, lentiviral particles (2 × 10 5 titer units in 100 μl) for Tau-shRNA (sc-430402-V, Santa Cruz Biotechnology), scrambled shRNA (SC-108080, Santa Cruz Biotechnology), B-Raf shRNA (sc-63294-V, Santa Cruz Biotechnology), or Tyro3-siRNA (iV037848, ABM, Richmond, BC, Canada) diluted 1:4 with ACSF buffer (NaCl, 125 mM; KCl, 2.5 mM; NaH 2 PO 4 , 1.25 mM; MgCl 2 , 1 mM; CaCl 2 , 1 mM; NaHCO 3 , 26 mM; glucose, 25 mM) or plasmid vectors (10 μg) for PKCα-shRNA (TG501653, OriGene, Rockville, MD, USA), scrambled shRNA (TG501653, OriGene), or Gas6-shRNA (sc-35451-SH, Santa Cruz Biotechnology) dissolved in 100 μl of in vivo-jetPEI (201–10 G, Polyplus-transfection, Illkirch, France) were injected into the subarachnoid space of the right RSD via osmotic pump (0.15 μl/h) from 8 to 12 weeks of age.

Techniques: Mutagenesis, Staining, shRNA, Infection, Confocal Microscopy, In Vivo, Western Blot, Knockdown, Quantitation Assay