Journal: Nature Communications

Article Title: Uncovering minimal pathways in melanoma initiation

doi: 10.1038/s41467-025-60742-0

Figure Lengend Snippet: a Tumors derived from Braf CA/+ and Braf CA/+ ; Pten Δ/+ mouse models were passaged by transplantation onto NSG (immune deficient) mice. Created in BioRender. Shiu, J. (2025) https://BioRender.com/m4kraw3 . b Single-cell gene expression profiles were used to subcluster NC-derived cell clusters (32,611 cells), among which principal tumor, melanocyte and LNM clusters were identified. UMAP visualizations of cell-types and sample distribution are shown. rd = Round of transplantation. Tx = transplant. c Gene expression profiles of the NC-derived clusters identified in ( b ). Gene signatures shared among LNM1 and LNM2 are labeled in black. Each column in the heatmap represents a cell from the corresponding group. d 182,950 cells from Braf CA/+ and Braf CA/+ ; Pten Δ/+ primary tumors ( n = 9) and transplanted NSG tumors ( n = 6) were subjected to single-cell RNA-seq. UMAP visualization of cell-types is shown. e Ridge plots of Aqp1 and Sox2 expression. Note the high expression of Aqp1 and Sox2 in both LNM1 and LNM2, compared to other cell types present in the whole skin. Percentages on the side denote the fraction of cells expressing Aqp1 and Sox2 in each cell type, respectively. Exp.: Expression. f Conditional Sox2 deletion in melanocytic/NC-derived cells inhibits tumor development. Tumor incidence in mice of the indicated genotypes is shown, and each dot represents an individual biological replicate; error bars represent the group mean ± SD. Tumor numbers were compared using an unpaired two-tailed t -test. Asterisks denote statistical significance: p < 0.05 (*), p < 0.01 (**); ns: not significant. Source data are provided as a Source Data file.

Article Snippet: RNAscope probe , Sox2 , ACD Bio , 401041-C3 , Used for RNAscope FISH.

Techniques: Derivative Assay, Transplantation Assay, Gene Expression, Labeling, RNA Sequencing, Expressing, Two Tailed Test

Journal: Nature Communications

Article Title: Uncovering minimal pathways in melanoma initiation

doi: 10.1038/s41467-025-60742-0

Figure Lengend Snippet: Skin contains both pigmented melanocytes and rare, poorly-pigmented LNM cells. Upon Braf activation, both populations expand, but melanocytes arrest as nevi, unless loss-of-function mutation in tumor suppressor gene Pten allows them to develop rapidly into pigmented melanomas (Pathway 1). Otherwise, Braf -activated LNM cells can undergo rare, stochastic transitions to produce scantly pigmented melanomas (Pathway 2). The probability of such transitions depends on host pigmentation status, Sox2 expression, and whether both alleles of Pten have become inactivated. LNM cells persist in both types of tumor. Created in BioRender. Shiu, J. (2025) https://BioRender.com/pf330qi .

Article Snippet: RNAscope probe , Sox2 , ACD Bio , 401041-C3 , Used for RNAscope FISH.

Techniques: Activation Assay, Mutagenesis, Expressing

Journal: Oncogene

Article Title: Characterizing resistant cellular states in nasopharyngeal carcinoma during EBV lytic induction

doi: 10.1038/s41388-025-03341-z

Figure Lengend Snippet: A UMAP representation of different cell types in a published NPC dataset. B UMAPs displaying the expression levels of SOX2 and other surface markers in this published NPC dataset. C Dot plot illustrating the expression levels of SOX2 and other surface markers in malignant cells from various published NPC datasets. D Immunostaining images demonstrating the detection of SOX2 and TrkB in patient slides. E RNA-scope images revealing different abundances of SOX2 and NTRK2 in patients with long survival (over 150 weeks) or short survival (less than 50 weeks). SOX2 is labeled in red, NTRK2 is labeled in green, and nuclei are labeled in blue. F Box plots presenting the quantitative results of RNA-scope; the normalized expression levels of SOX2 and NTRK2 in long and short survival patient groups. G Scatter plot displaying the correlation between SOX2 and NTRK2 using a bulk RNA-seq dataset. Patients were separated into two groups based on SOX2 / NTRK2 co-expression. H Kaplan–Meier progression-free survival curves for the two groups of patients with high SOX2 / NTRK2 co-expression or low co-expression.

Article Snippet: For RNA-scope analysis, the 2.5 HD Duplex Reagent Kit, along with RNA-scope Probe-Hs- SOX2 and RNA-scope Probe-Hs- NTRK2 -C2, were obtained from Advanced Cell Diagnostics.

Techniques: Expressing, Immunostaining, RNAscope, Labeling, RNA Sequencing

Journal: Oncogene

Article Title: Characterizing resistant cellular states in nasopharyngeal carcinoma during EBV lytic induction

doi: 10.1038/s41388-025-03341-z

Figure Lengend Snippet: A UMAP representation of the top 10% of cells expressing NTRK2 , with a bar plot quantifying the proportional distribution of cellular states. B FACS detection of TrkB signaling events under different conditions, including an unstained control (unstained), UT, T24, and T48 NPC43 cells. C NTRK2 and SOX2 expressions determined by qRT-PCR. Cells from different conditions were sorted into NTRK2-high and NTRK2-low groups to extract RNA for qRT-PCR. Significant differences ( p < 0.05) were observed between T24-high vs. T24-low and T48-high vs. T48-low groups. D Western blot showing SOX2 and TrkB abundance in TrkB-high and TrkB-low cells in UT and T48 conditions. GAPDH was used as a loading control. E qRT-PCR analysis of NTRK2, SOX2, and BZLF1 expression in FACS-sorted TrkB-high and TrkB-low populations (T48 condition). Significant differences ( p < 0.05) were detected between T48-high and T48-low groups. F Western blot showing TrkB and Zta abundance in TrkB-high and TrkB-low cells in T48 condition. GAPDH was used as a loading control. G Relative copy numbers of BZLF1 , EBER1 (2 EBV genes), and SOX2 determined by qPCR. Cells from different conditions were sorted into TrkB-high and TrkB-low groups to extract DNA for qPCR. H Expressions of NTRK2 and BZLF1 determined by qRT-PCR. Cells were sorted into TrkB-high and TrkB-low groups first (UT-high and UT-low). Then, sorted cells underwent lytic induction treatment for 48 h (UT-high-T48 and UT-low-T48). Significant differences ( p < 0.05) were observed between UT-high vs. UT-low and UT-high-T48 vs. UT-low-T48 groups.

Article Snippet: For RNA-scope analysis, the 2.5 HD Duplex Reagent Kit, along with RNA-scope Probe-Hs- SOX2 and RNA-scope Probe-Hs- NTRK2 -C2, were obtained from Advanced Cell Diagnostics.

Techniques: Expressing, Control, Quantitative RT-PCR, Western Blot

Journal: Oncogene

Article Title: Characterizing resistant cellular states in nasopharyngeal carcinoma during EBV lytic induction

doi: 10.1038/s41388-025-03341-z

Figure Lengend Snippet: A GSEA results from DEs between NR cells and Keratinized cells in the UT dataset. B Violin plots showing the expression or activity score of genes ( SOX2 and CD44 ) and gene sets (Stemness, p-EMT, EMV-IV, and Hypoxia). Wilcoxon signed-rank test was performed. C Images showing the size of tumorspheres. Cells with different TrkB abundance were seeded for this tumorsphere-forming assay. D Bar plots showing the numbers of tumorspheres (size over 10 µm). Cells with different TrkB abundance were seeded for this tumorsphere-forming assay. E Fluorescent immunostaining of tumorspheres showing the existence of the SOX2 and TrkB. F Images showing the size of tumorspheres. TrkB-high NPC43 or C17 cells undergo SOX2 or NTRK2 knockdown before seeding for the tumorsphere-forming assay. G Bar plots showing the numbers of tumorspheres (size over 10 µm). TrkB-high NPC43 or C17 cells undergo SOX2 or NTRK2 knockdown before seeding for tumorsphere-forming assay. H Heatmap showing the correlation of SOX2 , CD44 , and NTRK2 with EMT-related gene sets. Three gene sets defined from three different studies consistently show higher correlation with NTRK2 . I Images showing the wound healing assay with different cells. NPC43 cells were knocked down with a shRNA vector. NTRK2 -KD-sh shows slower migration compared to the control. J Violin plots showing ELF3 expression as a marker of differentiated cells in NPC43. K qPCR analysis showing increased expression of ELF3 and BZLF1 following NTRK2 knockdown and lytic induction treatment. Compared to NC-sh of UT, paired t -test p -values were less than 0.0383 for ELF3 and 0.00942 for BZLF1 . L FACS analysis of Zta+ cells indicating an increased proportion of cells entering the lytic activation state after NTRK2 knockdown. A two-proportion z-test showed a p -value smaller than 10⁻⁵.

Article Snippet: For RNA-scope analysis, the 2.5 HD Duplex Reagent Kit, along with RNA-scope Probe-Hs- SOX2 and RNA-scope Probe-Hs- NTRK2 -C2, were obtained from Advanced Cell Diagnostics.

Techniques: Expressing, Activity Assay, Immunostaining, Knockdown, Wound Healing Assay, shRNA, Plasmid Preparation, Migration, Control, Marker, Activation Assay

Journal: Oncogene

Article Title: Characterizing resistant cellular states in nasopharyngeal carcinoma during EBV lytic induction

doi: 10.1038/s41388-025-03341-z

Figure Lengend Snippet: A Western blot showing TrkB, SOX2, E-cad (EMT-related marker), pERK (MAPK-related marker), and pS6 (PI3K-related marker) abundances in NPC43 cells undergoing SOX2 -KD or NTRK2 -KD. B Heatmap showing the activity of predicted TFs in different conditions. Predicted TFs were inferred from scRNA-seq data with the SENIC algorithm. C Rank plots showing the most specified TFs in NR cells at UT, T24, and T48. SOX2 or NTRK2 -related TFs were highlighted. D Network showing how SOX2 is connected with NTRK2 . TFs that are activated in NR cells were visualized in the network. E FACS plots showing the detection of SOX2 and TrkB in NP460 cells with SOX2 overexpression vector. F Western blot showing TrkB and SOX2 in NP460 cells with SOX2 overexpression.

Article Snippet: For RNA-scope analysis, the 2.5 HD Duplex Reagent Kit, along with RNA-scope Probe-Hs- SOX2 and RNA-scope Probe-Hs- NTRK2 -C2, were obtained from Advanced Cell Diagnostics.

Techniques: Western Blot, Marker, Activity Assay, Over Expression, Plasmid Preparation

Journal: Oncogene

Article Title: Characterizing resistant cellular states in nasopharyngeal carcinoma during EBV lytic induction

doi: 10.1038/s41388-025-03341-z

Figure Lengend Snippet: A Heatmap displaying the top features correlated with NTRK2 expression, including genes and pathways. Only features recurrent across multiple datasets are shown in the heatmap. B UMAP of integrated scRNA-seq data from C666-1, with cells colored by treatment conditions and cellular states. Expression levels of NTRK2 and SOX2 are also visualized on the UMAP. C UMAP illustrating representative pathway terms associated with different cellular states. Stemness terms are enriched in NR-like cells; cytolysis and response to UV-B are enriched in cytolysis cells; unfolded protein response and inhibitory synaptic assembly are enriched in Prelytic cells. D Violin plot showing scores for EMT, Adhesion-related, hypoxia, and stress pathways. Only UT and T48 samples are included to compare NR-like cells. E UMAP shows the density of EBV gene detection and the expression of the lytic activation marker BZLF1.

Article Snippet: For RNA-scope analysis, the 2.5 HD Duplex Reagent Kit, along with RNA-scope Probe-Hs- SOX2 and RNA-scope Probe-Hs- NTRK2 -C2, were obtained from Advanced Cell Diagnostics.

Techniques: Expressing, Activation Assay, Marker

Journal: Molecular Therapy. Methods & Clinical Development

Article Title: Human iPSC-derived neural stem cells engraft and improve pathophysiology of MPS I mice

doi: 10.1016/j.omtm.2024.101367

Figure Lengend Snippet: Purification and characterization of hiNSCs derived from iPSC (A) Fluorescence-activated cell sorting (FACS) analysis of hiNSCs. CD184 + /CD44 − /CD271 − sorting captured approximately 75.7% of the hiNSC population (top). After 4 months, approximately 89.44% of these previously sorted hiNSCs retained CD184 expression (bottom), indicating stability in the expression profile over time. (B) Immunocytochemistry staining for NSC markers Nestin, PAX6, SOX1, and SOX2 alongside CD184, a marker for migration capacity. Notably, the absence of OCT3/4, typically found in induced iPSCs, confirms the differentiated nature of the NSCs. Scale bar, 50 μm. (C) Cell migration assay. CD184 + hiNSCs grew and migrated primarily toward chemoattractant SDF-1α (100 ng/mL) (yellow arrow; left chamber) after 72-h incubation. Scale bar, 100 μm. (D) hiNSC transwell co-culture assay. Left graph: intracellular IDUA activity was significantly increased in MPS I-NSCs cross-corrected (light gray) with hiNSCs (dark gray), compared to uncorrected MPS I-NSCs (black). Right graph: GAG levels were significantly reduced in cross-corrected MPS I-NSCs, while GAG levels remained 2-fold higher in uncorrected MPS I-NSCs, with minimal amounts of enzyme activity as seen in the left graph. Data from biochemical assays are presented as mean ± SD. Statistical significance is denoted by asterisks (∗∗ p < 0.01; ∗∗∗∗ p < 0.0001; ns, not significant).

Article Snippet: SOX2 (Molecular Probes Kit, A24354) , rabbit , IgG , Thermo Fisher Scientific, 48-1400 , AB_2533841 , ICC , 1:100.

Techniques: Purification, Derivative Assay, Fluorescence, FACS, Expressing, Immunocytochemistry, Staining, Marker, Migration, Cell Migration Assay, Incubation, Co-culture Assay, Activity Assay

Journal: Molecular Therapy. Methods & Clinical Development

Article Title: Human iPSC-derived neural stem cells engraft and improve pathophysiology of MPS I mice

doi: 10.1016/j.omtm.2024.101367

Figure Lengend Snippet: Summary of antibodies used in histology

Article Snippet: SOX2 (Molecular Probes Kit, A24354) , rabbit , IgG , Thermo Fisher Scientific, 48-1400 , AB_2533841 , ICC , 1:100.

Techniques:

Journal: EMBO Reports

Article Title: SorLA restricts TNFα release from microglia to shape a glioma-supportive brain microenvironment

doi: 10.1038/s44319-024-00117-6

Figure Lengend Snippet: ( A ) Sorl1 mRNA levels in primary murine microglia co-cultured with glioma cells (left) or stimulated with LPS (right) as assessed by qRT-PCR (relative to Hprt1 or β2M , respectively). n = 6–7 biological replicates. ( B ) TNFα levels as determined by ELISA in cell culture medium from primary WT and SorLA-KO microglia either untreated (ctrl) or treated with PMA for 24 h. TNFα levels were normalized to the protein content in the respective cell lysates. n = 6 biological replicates. ( C ) Tnfa mRNA levels in primary murine microglia stimulated with PMA as assessed by qRT-PCR (relative to Hprt1 ). n = 5–7 biological replicates. ( D ) Outline of the iPSC-to-microglia (iMG) differentiation protocol. ( E ) Phase contrast images of iPSCs, HPs, and iMG at different stages of the microglia differentiation. Scale bar, 1000 µm (iPSC, day 3, day 11); 200 µm (day 23, day 38). ( F ) Expression levels of marker genes for pluripotent stem cells ( SOX2 ) and microglia ( P2RY12 , TREM2 , AIF1 ) in iPSCs, HPs and iMG during microglia differentiation as assessed by qRT-PCR (relative to GAPDH ). n = 5 biological replicates. ( G ) Representative images of human iMG immunostained for microglia markers Iba1 (red) and P2RY12 (green) and counterstained with DAPI (blue). Scale bar, 10 µm. ( H ) SORL1 mRNA levels in human iMG stimulated with LPS as assessed by qRT-PCR (relative to β2M ). n = 3 biological replicates. ( I ) TNFα levels as determined by ELISA in cell culture medium from WT and SorLA-KO iMG either untreated (ctrl) or treated with LPS for 24 h. n = 4–5 biological replicates. Data information: ( A – C , F , H , I ) Data are presented as mean ± SEM. ns not significant; * P < 0.05; ** P < 0.01; *** P < 0.001 in one-sample t test compared to 1 ( A , F , H ) or in two-way ANOVA with Tukey’s multiple comparisons ( B , C , I ). .

Article Snippet: SOX2 TaqMan probe , ThermoFisher Scientific , Hs01053049_s1.

Techniques: Cell Culture, Quantitative RT-PCR, Enzyme-linked Immunosorbent Assay, Expressing, Marker

Journal: EMBO Reports

Article Title: SorLA restricts TNFα release from microglia to shape a glioma-supportive brain microenvironment

doi: 10.1038/s44319-024-00117-6

Figure Lengend Snippet: Reagents and tools table

Article Snippet: SOX2 TaqMan probe , ThermoFisher Scientific , Hs01053049_s1.

Techniques: Recombinant, Staining, Produced, Transduction, Sequencing, Modification, Saline, Fluorescence, Plasmid Preparation, Software, Expressing, Enzyme-linked Immunosorbent Assay, Biomarker Discovery, Bicinchoninic Acid Protein Assay, In Vivo, Imaging, Cell Culture