Journal: Biology of Reproduction

Article Title: What has single-cell RNA-seq taught us about mammalian spermatogenesis?

doi: 10.1093/biolre/ioz088

Figure Lengend Snippet: Mouse spermatogenesis single-cell RNA-seq datasets.

Article Snippet: scRNA-seq Chemistry/Method , 3′ sequencing and full length sequence (SMART-seq2) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (Oliginal Drop-seq) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (SMART-seq2 and Microwell-seq) , full length sequence (Fluidigm C1), 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , full length sequence (Fluidigm C1) , full length sequence (Fluidigm C1) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , full length sequence (Fluidigm C1).

Techniques: Biomarker Discovery, Knock-Out, RNAscope, Transplantation Assay, Sequencing

Journal: Biology of Reproduction

Article Title: What has single-cell RNA-seq taught us about mammalian spermatogenesis?

doi: 10.1093/biolre/ioz088

Figure Lengend Snippet: Human spermatogenesis single-cell RNA-seq datasets.

Article Snippet: scRNA-seq Chemistry/Method , 3′ sequencing and full length sequence (SMART-seq2) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (Oliginal Drop-seq) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (SMART-seq2 and Microwell-seq) , full length sequence (Fluidigm C1), 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , full length sequence (Fluidigm C1) , full length sequence (Fluidigm C1) , 3′ sequencing and barcoding (10x Genomics) , 3′ sequencing and barcoding (10x Genomics) , full length sequence (Fluidigm C1).

Techniques: Biomarker Discovery, Sequencing

Journal: Advanced Science

Article Title: The TET3/GATA6 Axis Drives Lipid Metabolism and Therapeutic Vulnerabilities in Pancreatic Ductal Adenocarcinoma

doi: 10.1002/advs.202501774

Figure Lengend Snippet: TET3 transcriptionally represses GATA6 through histone deacetylation. A) Western blot analysis of GATA6 protein levels in wild‐type (WT) and TET3 knockout (KO) PANC‐1 cells. B) UMAP visualization showing the expression distribution of TET3 and GATA6 in epithelial cells from scRNA‐seq of 25 PDAC patients ( GSE242230 ). C) Violin plots showing the expression levels of GATA6 in type 1 and type 2 ductal cells previously identified in PDAC patients (CRA001160; n = 24). D) RT‐qPCR analysis of GATA6 mRNA in TET3 knockout PANC‐1 cells transduced with doxycycline‐inducible wild‐type TET3 (TET3 wt , unfilled bars) or catalytically inactive mutant TET3 (TET3 mut , striped bars), treated with (purple) or without (gray) doxycycline (1 µg mL −1 ) (n = 3). E) ChIP‐qPCR assay of H3K27ac levels in WT and KO PANC‐1 cells (n = 3). Primers targeted regions upstream or downstream of the GATA6 transcription start site, as indicated in Figure , Supporting Information. F) RT‐qPCR measuring GATA6 mRNA expression in wild‐type PANC‐1 cells treated with SAHA at 0, 5, or 10 µM for 24 or 48 h (n = 3). G) Western blot analysis of GATA6 protein levels in PANC‐1 cells treated with SAHA (0, 5, 10 µM) for 24 h. H) ChIP‐qPCR assay of V5 in PANC‐1 cells ectopically expressing V5‐tagged TET3 (n = 3). qPCR primers are the same as those used in (E). I) Immunoprecipitation of V5‐tagged TET3 in PANC‐1 cells, followed by immunoblotting for HDAC1 and HDAC2 using an anti‐V5 antibody. Data represent mean ± SD. Statistical significance was determined by two‐tailed Wilcoxon test (C), one‐way ANOVA (D, F) or two‐tailed unpaired t ‐test (E, H). * p < 0.05, ** p < 0.01, *** p < 0.001.

Article Snippet: GATA6 expression vector (Addgene, #120445) was packaged into a lentivirus transduction system and used to infect cancer cells.

Techniques: Western Blot, Knock-Out, Expressing, Quantitative RT-PCR, Transduction, Mutagenesis, ChIP-qPCR, Immunoprecipitation, Two Tailed Test

Journal: Advanced Science

Article Title: The TET3/GATA6 Axis Drives Lipid Metabolism and Therapeutic Vulnerabilities in Pancreatic Ductal Adenocarcinoma

doi: 10.1002/advs.202501774

Figure Lengend Snippet: GATA6 suppresses lipogenic gene expression and limits tumor growth. A) Western blot showing knockout efficiency of GATA6 in TET3 knockout (KO) PANC‐1 cells. B) RT‐qPCR analysis of lipid metabolic gene expression in PANC‐1 cells with wild‐type (WT), KO, and TET3 / GATA6 double knockout (KO‐sgGATA6) (n = 3). C) Western blot showing overexpression efficiency of GATA6 (GATA6 OE ) in wild‐type PANC‐1 cells. D) RT‐qPCR analysis of lipid metabolic gene expression in PANC‐1 cells with constitutive GATA6 overexpression (GATA6 OE ) (n = 3). E) Representative images of subcutaneous xenograft tumors (left) and tumor weight at 8 weeks post‐implantation (right) for the indicated cell lines. Nude mice were transplanted with WT (n = 5), KO (n = 5), or KO‐sgGATA6 PANC‐1 cells (n = 5). F) Cell viability of wild‐type PANC‐1 cells treated for 24 or 48 h with gemcitabine (1 µM), gemcitabine + SAHA (5 µM), gemcitabine + Erastin (1 µM), or a triple combination of gemcitabine, SAHA, and Erastin (n = 3). G) Representative images of xenografts (left) and tumor weight at 7 weeks post‐implantation (right) following treatment beginning at week 4 with the indicated agents. Nude mice were transplanted with wild‐type PANC‐1 cells. Data represent mean ± SD. Statistical significance was determined by one‐way ANOVA (B, E, F, G) or two‐tailed unpaired t ‐test (D). * p < 0.05, ** p < 0.01, *** p < 0.001.

Article Snippet: GATA6 expression vector (Addgene, #120445) was packaged into a lentivirus transduction system and used to infect cancer cells.

Techniques: Gene Expression, Western Blot, Knock-Out, Quantitative RT-PCR, Double Knockout, Over Expression, Two Tailed Test

Journal: Advanced Science

Article Title: The TET3/GATA6 Axis Drives Lipid Metabolism and Therapeutic Vulnerabilities in Pancreatic Ductal Adenocarcinoma

doi: 10.1002/advs.202501774

Figure Lengend Snippet: TET3 promotes invasive PDAC through activation of TGF‐β signaling pathway. A) mRNA expression levels of TET3 in normal pancreatic tissues (n = 7), IPMA tissues (n = 6), and invasive PDAC tissues (n = 3) from GSE19650 (n = 16). B) Representative images and quantification of transwell invasion and migration assays in wild‐type (WT) and TET3 knockout (KO) PANC‐1 cells (n = 3). Scale bars = 200 µm. C) Western blot analysis of epithelial‐mesenchymal transition (EMT) markers E‐cadherin, N‐cadherin, and vimentin in WT and KO PANC‐1 cells. D) Western blot analysis of TGF‐β pathway proteins in WT, KO, and TET3 / GATA6 double knockout (KO‐sgGATA6) PANC‐1 cells. E) Western blot analysis of TGF‐β signaling proteins in wild‐type PANC‐1 cells constitutively overexpressing GATA6 (GATA6 OE ). F) Representative images and quantification of transwell invasion and migration assays in WT and KO in CFPAC‐1 cells (n = 3). G) Survival analysis of TCGA‐PAAD patients stratified by SMAD4 expression (high: top 50%, n = 89; low: bottom 50%, n = 89) and further subdivided by TET3 expression (high: top 25%, n = 22; low: bottom 25%, n = 22). Data are shown as mean ± SD. Statistical significance was assessed by one‐way ANOVA (A), two‐tailed unpaired t ‐test (B, F), or log‐rank Mantel‐Cox test (G). * p < 0.05, ** p < 0.01, *** p < 0.001.

Article Snippet: GATA6 expression vector (Addgene, #120445) was packaged into a lentivirus transduction system and used to infect cancer cells.

Techniques: Activation Assay, Expressing, Migration, Knock-Out, Western Blot, Double Knockout, Two Tailed Test

Journal: Advanced Science

Article Title: The TET3/GATA6 Axis Drives Lipid Metabolism and Therapeutic Vulnerabilities in Pancreatic Ductal Adenocarcinoma

doi: 10.1002/advs.202501774

Figure Lengend Snippet: Schematic representation of the TET3/GATA6 axis in regulating lipogenic metabolism and promoting tumor growth and invasion in pancreatic cancer.

Article Snippet: GATA6 expression vector (Addgene, #120445) was packaged into a lentivirus transduction system and used to infect cancer cells.

Techniques:

Journal: bioRxiv

Article Title: Cross-species single-cell atlases chart progression, therapy-driven remodelling and immune evasion in pancreatic cancer

doi: 10.64898/2026.03.19.712924

Figure Lengend Snippet: a) Schematic overview of the experimental design. Mouse PDAC cell lines were clonally barcoded using a lentiviral library (1), expanded and orthotopically transplanted into syngeneic immunocompetent mice (2–3), followed by scRNA-seq profiling of resultant tumours (4). Expressed barcode tracing enabled unambiguous separation of malignant (TAG⁺) from host-derived non-malignant cells (right panel, UMAPs depicting barcoded (TAG + ) (top) and malignant (bottom) cells). b-e) UMAPs of the integrated Mouse PDAC Atlas coloured by dataset (b), sex (c), treatment type (d), and model (orthotopic syngeneic immunocompetent allografts vs. autochthonous GEMMs (e). f) Sample-wise cell-type composition across treatment types, datasets, and models. Autochthonous tumours were dominated by classical epithelial-like malignant states, whereas orthotopic allografts displayed greater heterogeneity with an enrichment of EMT, hypoxic, and mesenchymal programs. g ) Level 3 hierarchical annotation of the Mouse Atlas using the same multi-tiered scheme as the Human Atlas, resolving lymphoid, myeloid, stromal, endocrine, exocrine, endothelial, and malignant compartments. h-j) Substate resolution of major immune and stromal lineages: CD4⁺ T cells (h), CD8⁺ T cells (i), and macrophages (j), showing distinct regulatory, effector, angiogenic, and lipid-processing programs. k) Validation of double-positive (DP) CD4⁺CD8⁺ T cells at the transcriptomics level (transcription density plots, left panel) and at the protein level by flow cytometry (right panel). l) UMAP showing DP T cells coloured by species (left) and Pearson correlation of mouse DP T cell gene expression against the human DP T cell archetype (right).

Article Snippet: For clonal and state-fate analysis by single-cell RNA-seq, primary mouse PDAC cells were clonally tagged with expressed DNA barcodes using the LARRY Barcode Library (Addgene #140024; RRID: Addgene 140024) .

Techniques: Derivative Assay, Biomarker Discovery, Transcriptomics, Flow Cytometry, Gene Expression