Journal: bioRxiv

Article Title: A Pan-Cancer Single-Cell Compendium of Intratumoural Heterogeneity

doi: 10.64898/2026.01.06.693992

Figure Lengend Snippet: a, Hematoxylin and eosin (H&E) staining of breast cancer Patient 2. b-d, spatial maps of Visium HD cells coloured by cell type ( b ), mapped cancer cell state ( c ), and CNV cluster ( d ). e, Heatmap of CNV scores in malignant cells with red and blue indicating gains and losses respectively. Leiden clusters of CNV profiles are shown on the y-axis. f-g, Mean per-gene CNV values along chromosome 11 ( f ) and chromosome 8 ( g ) for each CNV cluster (0 or 1).

Article Snippet: Visium HD data and images were directly downloaded from 10X Genomics’ datasets pages – : https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt , https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression/dataset-human-crc , https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-breast-cancer-fixed-frozen , https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-human-breast-cancer-ff-ultima .

Techniques: Staining

Journal: Frontiers in Aging Neuroscience

Article Title: Increased tau-induced inflammatory responses are associated with a greater degree of atherosclerosis in progressive supranuclear palsy

doi: 10.3389/fnagi.2025.1608631

Figure Lengend Snippet: Greater atherosclerotic burden and elevated plasma total tau, p-tau181 levels in patients with PSP. Using carotid artery Doppler ultrasound to assess the degree of carotid artery atherosclerosis by evaluating (A) max-CIMT, (B) max-CPT, (C) TPN, (D) CPS, and (E) carotid stenosis% in HCs ( n = 56) and patients with PSP ( n = 56). Using MRA to evaluate the degree of intracranial arterial atherosclerosis by recording (F) ICS vascular territory and (G) MRA GSS in HCs ( n = 56) and patients with PSP ( n = 56). (H) Heatmap of multivariable linear regression heatmap showing the association between disease duration/clinical scores H&Y staging scale, UPDRS-III, PSPRS, MMSE and atherosclerosis measures (max-CIMT, max-CPT, TPN, CPS, carotid stenosis% and MRA GSS) in patients with PSP ( n = 56). Peripheral (I–L) blood lipid, (M) glycosylated hemoglobin, (N) homocysteine parameters, and plasma levels of (O) total tau, (P) p-tau181, (Q) p-tau396 in HCs ( n = 56) and patients with PSP ( n = 56). (R) Heatmap of multivariable linear regression heatmap showing the association between tau levels (total tau, p-tau181, p-tau396) and atherosclerosis measures (max-CIMT, max-CPT, TPN, CPS, carotid stenosis% and MRA GSS) in patients with PSP ( n = 56). Results are expressed as mean and SD. Statistical approaches: (A–E, G, I–Q) covariance (ANCOVA), with age, gender, smoking status and stroke history as covariates, (F) chi-square test, (H, R) multivariable linear regression. In heatmaps, each cell represents the standardized regression coefficient (β) derived from multivariable linear regression models, where each Y -axis was regressed on X -axis while adjusting for age, gender, smoking history, hypertension, diabetes, and dyslipidemia (For MMSE, one more correction for period of education). The color intensity of heatmap indicates the strength and direction of association (β), with positive associations shown in red and negative in blue. P < 0.05 indicates statistical significance (* p < 0.05, ** p < 0.01, *** p < 0.001), and ns indicates p ≥ 0.05.

Article Snippet: The following ELISA kits were used: Human interleukin-6 (IL-6) ELISA kit (E-HSEL-H0003, Elabscience Biotechnology, Wuhan, China), Human interleukin-1β (IL-1β) ELISA kit (E-HSEL-H0001, Elabscience Biotechnology, Wuhan, China), Human interleukin-10 (IL-10) ELISA kit (E-EL-H0005, Elabscience Biotechnology, Wuhan, China), Human interferon γ (IFN-γ) ELISA kit (E-HSEL-H0007, Elabscience Biotechnology, Wuhan, China), Human tumor necrosis factor-α (TNF-α) ELISA kit (E-HSEL-H0109c, Elabscience Biotechnology, Wuhan, China), Human total tau ELISA kit (ml057755, mlbio, Shanghai, China),and Human P-tau181 ELISA kit (ml057691, mlbio, Shanghai, China), Human P-tau396 ELISA kit (E-EL-H5314c, Elabscience Biotechnology, Wuhan, China), Mouse interleukin-6 (IL-6) ELISA kit (ml098430, mlbio, Shanghai, China), Mouse interleukin-1β (IL-1β) ELISA kit (ml098416, mlbio, Shanghai, China) and Mouse tumor necrosis factor-α (TNF-α) ELISA kit (mIC50536-1, mlbio, Shanghai, China).

Techniques: Clinical Proteomics, Derivative Assay

Journal: Frontiers in Aging Neuroscience

Article Title: Increased tau-induced inflammatory responses are associated with a greater degree of atherosclerosis in progressive supranuclear palsy

doi: 10.3389/fnagi.2025.1608631

Figure Lengend Snippet: Elevated peripheral blood macrophage ratio and plasma inflammatory cytokine levels in patients with PSP. Representative flow cytometry analysis of (A) macrophages (CD14 + CD68+), and (B) classically activated macrophages (CD86 + CD206-M1) subpopulations from peripheral blood (left) and quantifications (right) in HCs ( n = 10) and patients with PSP ( n = 10). Plasma levels of inflammatory cytokine (C) CRP, (D) IL-6, (E) IL-1β, (F) IL-10, (G) TNF-α, and (H) IFN-γ in HCs ( n = 56) and PSP with patients ( n = 56). (I) Heatmap of multivariable linear regression heatmap showing the association between inflammatory cytokine levels (CRP, IL-6, IL-1β, IL-10, TNF-α, and IFN-r) and atherosclerosis measures (max-CIMT, max-CPT, TPN, CPS, carotid stenosis% and MRA GSS) in patients with PSP ( n = 56). (J) Heatmap of multivariable linear regression heatmap showing the association between tau levels (total tau, p-tau181, p-tau396) and inflammatory cytokine levels (CRP, IL-6, IL-1β, IL-10, TNF-α, and IFN-r) in patients with PSP ( n = 56). Results are expressed as mean and SD. Statistical approaches: (A, B) unpaired non-parametric Mann-Whitney U tests, (C–H) covariance (ANCOVA), with age, gender, smoking status and stroke history as covariates, (I, J) multivariable linear regression. In heatmaps, each cell represents the standardized regression coefficient (β) derived from multivariable linear regression models, where each Y -axis was regressed on X -axis while adjusting for age, gender, smoking history, hypertension, diabetes, and dyslipidemia. The color intensity of heatmap indicates the strength and direction of association (β), with positive associations shown in red and negative in blue. P < 0.05 indicates statistical significance (* p < 0.05, ** p < 0.01, *** p < 0.001), and ns indicates p ≥ 0.05.

Article Snippet: The following ELISA kits were used: Human interleukin-6 (IL-6) ELISA kit (E-HSEL-H0003, Elabscience Biotechnology, Wuhan, China), Human interleukin-1β (IL-1β) ELISA kit (E-HSEL-H0001, Elabscience Biotechnology, Wuhan, China), Human interleukin-10 (IL-10) ELISA kit (E-EL-H0005, Elabscience Biotechnology, Wuhan, China), Human interferon γ (IFN-γ) ELISA kit (E-HSEL-H0007, Elabscience Biotechnology, Wuhan, China), Human tumor necrosis factor-α (TNF-α) ELISA kit (E-HSEL-H0109c, Elabscience Biotechnology, Wuhan, China), Human total tau ELISA kit (ml057755, mlbio, Shanghai, China),and Human P-tau181 ELISA kit (ml057691, mlbio, Shanghai, China), Human P-tau396 ELISA kit (E-EL-H5314c, Elabscience Biotechnology, Wuhan, China), Mouse interleukin-6 (IL-6) ELISA kit (ml098430, mlbio, Shanghai, China), Mouse interleukin-1β (IL-1β) ELISA kit (ml098416, mlbio, Shanghai, China) and Mouse tumor necrosis factor-α (TNF-α) ELISA kit (mIC50536-1, mlbio, Shanghai, China).

Techniques: Clinical Proteomics, Flow Cytometry, MANN-WHITNEY, Derivative Assay

Journal: Annals of Botany

Article Title: Genetic analysis of tomato root colonization by arbuscular mycorrhizal fungi

doi: 10.1093/aob/mcy240

Figure Lengend Snippet: List of QTLs that were detected by using the MQM procedure and corresponding SNPs (SolCAP SNPs named by number) at the LOD peak

Article Snippet: Genotypes from the recombinant population (130 P-RILs) at F 10 were genotyped for 7720 single nucleotide polymorphisms (SNPs) from the SolCAP tomato panel (Illumina BeadXhip WG-401–1004), and 4370 of them were segregating.

Techniques:

Journal: Acta Neuropathologica Communications

Article Title: TrkA activation sustains chemotherapy resistance in chemotolerant medulloblastoma cells

doi: 10.1186/s40478-026-02265-3

Figure Lengend Snippet: Activation of TrkA signaling protects MB cells from chemotherapy. A , B Dose response curves ( A ) and relative bar graphs ( B ) summarizing the effects of NGF, BDNF, or NT-3 neurotrophins onVECC sensitivity (GI 50 ) in MB-S cells (100ng/ml 12 h before VECC treatment). Dotted lines highlight GI 50 values. C Representative WB analysis of TrkA signaling activation during time upon stimulation of MB-S cells with 100ng/ml of NGF. Vinculin has been used as a loading control. D Growth curves of VECC-treated HD-MB03 (0.2U) and HuTuP33 cells (0.1U) when pre-treated or not with 100ng/ml of recombinant human NGF). E Bar graphs displaying the % of apoptotic/dead cells (Annexin-V + ) after 72 h from VECC treatment in HD-MB03-S (0.4U) and HuTuP33-S (0.2U) cells when pre-stimulated or not with 100ng/ml of recombinant human NGF. F Representative images (left) and relative quantification (right) of colonies formed by HD-MB03-S cells after treatment with NGF (100ng/ml), VECC (0.2U), or the combination of them. G Bar graphs displaying the % of Annexin-V + cells after 72 h from VECC treatment in shNT/shNTRK1-HD-MB03-S (0.4U VECC) and shNT/shNTRK1-HuTuP33-S (0.2U VECC) cells when pre-stimulated (12 h) or not with 100ng/ml of NGF. H Dose response curves displaying the effects of VECC in shNT and shNTRK1-HD-MB03-S cells or their resistant counterparts after #3 cycles of weekly VECC exposures. I Bar graph showing the progressive increase of VECC GI 50 values when shNT/shNTRK1-HD-MB03-S are weekly exposed to VECC-based chemotherapy. In all bar graphs, statistical analysis by one-way ANOVA with Tukey’s multiple comparison test. In ( I ), asterisks over single bars indicate a statistical difference with their relative controls (cycle 0). Differences between growth curves (panels D , H ) have been analyzed through the extra sum-of-squares test. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001; ns: not significant

Article Snippet: Human MB cell line HD-MB03 (group 3) was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI-1640 medium supplemented with 10% Foetal Bovine Serum, 1% L-glutamine (2mM) and 1% PenStrep solution (Penicillin-Streptomycin 10000 U/ml) (all from Thermo Fisher Scientific, Waltham, MA).

Techniques: Activation Assay, Control, Recombinant, Quantitative Proteomics, Comparison

Journal: Acta Neuropathologica Communications

Article Title: TrkA activation sustains chemotherapy resistance in chemotolerant medulloblastoma cells

doi: 10.1186/s40478-026-02265-3

Figure Lengend Snippet: NTRK1 gene silencing affects MB-R stemness and sensitivity to chemotherapy. A Limiting dilution assays comparing the self-renewal potential of shNT vs. shNTRK1-MB-R cells. Sphere initiating cell frequency (F) is reported and significance calculated by the extra sum-of-squares F test. B , C Representative images ( B ) and relative quantification ( C ) of MAP2 + and βIII-tubulin + cells (green) in shNT and shNTRK1-MB-R cells. Cell nuclei were counterstained with Dapi (blue). Original magnification 20X; scale bar, 20 μm. D Representative dose-response curve of shNT and shNTRK1-MB-R cells exposed to scalar doses of VECC for 72 h through a resazurin assay. E Bar graphs summarizing VECC GI 50 values calculated in control (shNT) or NTRK1 -silenced MB-R cells from ( D ). F Bar graphs displaying the % of apoptotic/dead cells (Annexin-V + ) after 72 h from VECC treatment in shNT and shNTRK1-MB-R cells (0.4U in HD-MB03 and 0.2U in HuTuP33). Statistical analysis in ( C ) and ( E ) by unpaired t-test; in ( F ) by one-way ANOVA with Tukey’s multiple comparison test. * p < 0.05, ** p < 0.01, **** p < 0.0001

Article Snippet: Human MB cell line HD-MB03 (group 3) was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI-1640 medium supplemented with 10% Foetal Bovine Serum, 1% L-glutamine (2mM) and 1% PenStrep solution (Penicillin-Streptomycin 10000 U/ml) (all from Thermo Fisher Scientific, Waltham, MA).

Techniques: Quantitative Proteomics, Resazurin Assay, Control, Comparison

Journal: Acta Neuropathologica Communications

Article Title: TrkA activation sustains chemotherapy resistance in chemotolerant medulloblastoma cells

doi: 10.1186/s40478-026-02265-3

Figure Lengend Snippet: Trk inhibition sensitizes resistant MB cells to chemotherapy. A Representative WB analysis of MB-R cells displaying the activation status of TrkA in response to GNF-5837 or GW-441,756 treatments (48 h) at the indicated compound concentrations. B Bar graphs summarizing the % of Ki67 + cells in MB-R cells after 24 h of treatment with the indicated concentrations of GNF-5837 and GW-441,756. C Dose-response curves displaying the viability of MB-R cells when treated for 72 h with scalar doses of VECC, GNF-5837, GW-441,756, or the VECC + GNF-5837 and VECC + GW-441,756 combinations (1:10 fixed ratio). D Graph summarizing the synergistic action (Combination Index ≤ 1) of the VECC + GNF-5837 and VECC + GW-441,756 combinations in MB-R cells. E Bar graphs displaying the viability of MB-R cells after 48 h from treatment with VECC, GNF-5837, GW-441,756, or the VECC combinations with them as measured by Annexin-V staining. In HD-MB03-R cells: VECC 1U, GNF-5837 10µM, and GW-441,756 10µM; in HuTuP33-R cells: VECC 0.5U + GNF-5837 5µM, and VECC 1U + GW-441,756 10µM. F Bar graph displaying the viability of HD-MB03-R spheroids after 120 h from treatment with the indicated concentrations of VECC, GW-441,756, or their combination (1:10 ratio) by a resazurin assay. G , H Representative brightfield images ( G ) and relative volume estimation ( H ) of HD-MB03-R spheroids after 120 h from treatment with VECC (1U), GW-441,756 (10µM), or their combination. Original magnification 4X; scale bar, 200 μm. In all bar graphs, statistical analyses by one-way Anova with Tukey’s multiple comparisons test; * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001

Article Snippet: Human MB cell line HD-MB03 (group 3) was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI-1640 medium supplemented with 10% Foetal Bovine Serum, 1% L-glutamine (2mM) and 1% PenStrep solution (Penicillin-Streptomycin 10000 U/ml) (all from Thermo Fisher Scientific, Waltham, MA).

Techniques: Inhibition, Activation Assay, Staining, Resazurin Assay