Journal: BMC Cancer

Article Title: Overcoming acquired resistance to HSP90 inhibition by targeting JAK-STAT signalling in triple-negative breast cancer

doi: 10.1186/s12885-019-5295-z

Figure Lengend Snippet: Differential RNA expression in HSP90i-resistant clones compared to parental Hs578T cells. RNA samples from DMSO-treated and ganetespib-treated Hs578T, CR2 and CR3 cells were analysed for whole transcriptome profiling with RNA-sequencing. Differential gene expression analyses were performed between DMSO-treated parental Hs578T cells with either DMSO-treated CR2 or CR3 and the significantly upregulated genes observed in these clones were mostly overlapping. Pathway enrichment analysis using Metacore™ was performed on the significantly upregulated overlapping genes. The graph represents the top 20 most significantly upregulated pathways in the HSP90i-resistant clones, with FDR (false discovery rate) value < 0.05. Pathways highlighted in blue are linked to JAK-STAT signalling

Article Snippet: Duplicate samples (1 μg RNA in 30 μl) were subjected to RNA Sequencing (RNA-seq) analysis (Oxford Gene Technology) and gene expression was quantified using their analysis pipeline [ ].

Techniques: RNA Expression, Clone Assay, RNA Sequencing, Gene Expression

Journal: Cancers

Article Title: Common and Unique Transcription Signatures of YAP and TAZ in Gastric Cancer Cells

doi: 10.3390/cancers12123667

Figure Lengend Snippet: RNA-sequencing (RNA-seq) of the samples generated with gastric cancer MKN28 cells and activated mutants of YAP or TAZ genes. ( A ) Western blot analysis of YAP knockout (KO) and TAZ KO clones generated via the CRISPR/Cas9 system using two independent guide RNA sequences (labelled as 1 and 2) against human YAP and human TAZ. The wild type (WT) sample is shown in the first and last lane. β-actin is used as a loading control. The protein molecular weight size marker (unit: kDa) is depicted along the left of the Western blot images. The uncropped western blot figures in . ( B ) Representative immunofluorescence images of YAP and TAZ in WT, two clones of YAP KO and TAZ KO. ( C ) Western blot analysis of YAP KO cells transduced with empty vector (EV, control) or TAZ S89A (overexpression, OE). GAPDH is used as a loading control. ( D ) Western blot analysis of TAZ KO cells transduced with empty vector (EV) or YAP S127A (OE). β-actin is used as a loading control. The uncropped western blot figures in . ( E ) A schematic diagram of the samples prepared for RNA-seq.

Article Snippet: Quality check on the RNA samples, RNA-seq library preparation, sequencing, pre-processing and quantification of sequencing reads were done by AITbiotech (AITbiotech, Singapore, Singapore).

Techniques: RNA Sequencing, Generated, Western Blot, Knock-Out, Clone Assay, CRISPR, Control, Molecular Weight, Marker, Immunofluorescence, Transduction, Plasmid Preparation, Over Expression

Journal: The Journal of Infectious Diseases

Article Title: Measles Virus Infects and Programs MAIT Cells for Apoptosis

doi: 10.1093/infdis/jiaa407

Figure Lengend Snippet: MAIT cells express the highest levels of SLAMF1/CD150 among PBMC subsets. A, Publicly available scRNA-Seq data from 11 769 PBMCs were analyzed. The 9432 cells that passed quality control filters are visualized on a t-SNE projection (left panel) demonstrating clusters corresponding to CD14+ monocytes (n = 2992), CD16+ monocytes (n = 328), cDCs (n = 74), pDCs (n = 68), NK cells (n = 544), B cells (n = 1419), CD4+ T cells (n = 2643), CD8+ T cells (n = 720), MAIT cells (n = 592), and platelets (n = 52). Each dot represents a single cell. The expression of SLAMF1 across indicated clusters, quantified as normalized and scaled count data, is shown in a violin plot (right panel), in which dots represent single cells and widths denote cell densities. B and C, MAIT cells and other peripheral blood T cell subsets were examined for CD150 expression. MAIT and iNKT cells were identified by MR1 tetramer staining (PubMed IDs 24101382 and 24695216) and CD1d tetramer staining (PubMed IDs 10839805 and 10974039), respectively. Open and filled histograms correspond to the staining of PBMCs with anti-CD150 and isotype control, respectively, after gating on CD3+MR1 tetramer+ MAIT cells (B). The frequencies of CD150+ cells and the gMFI of CD150 staining (C) in indicated T cell subsets are summarized using Box-and-Whisker plots, with each symbol representing an individual donor. *, *** and **** denote differences with P < .05, P < .001, and P < .0001, respectively, using matched one-way ANOVA with Dunnett post-hoc analysis. D, PBMCs (n = 4) were left untreated or stimulated with rhIL-12 plus rhIL-18. The frequencies of MAIT cells expressing CD150, CD69, or CD46 were determined 24 hours later by flow cytometry. ** denotes a difference with P < .05 by paired Student t test. Abbreviations: 5-OP-RU, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil; APC, allophycocyanin; cDC, classic dendritic cell; FITC, fluorescein isothiocyanate; gMFI, geometric mean fluorescence intensity; iNKT, invariant natural killer T cell; MAIT, mucosa-associated invariant T cell; MR1, MHC-related protein 1; NK cell, natural killer cell; NS, not significant; PBMC, peripheral blood mononuclear cell; pDC, plasmacytoid pre-dendritic cell; PE, phycoerythrin; rhIL, recombinant human interleukin; scRNA-Seq, single-cell RNA sequencing; TCM, central memory T cell; TEM, effector memory T cell; TN, naive T cell; t-SNE, t-distributed stochastic neighbor embedding.

Article Snippet: Transcriptomic Analysis of Peripheral Blood Mononuclear Cells The pbmc_10k_v3 dataset, consisting of single-cell RNA sequencing (scRNA-Seq) data from 11 769 peripheral blood mononuclear cells (PBMCs), was created by 10x Genomics ( https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_10k_v3 ).

Techniques: Control, Expressing, Staining, Whisker Assay, Flow Cytometry, Fluorescence, Recombinant, RNA Sequencing

Journal: EMBO Reports

Article Title: TMPRSS11B promotes an acidified microenvironment and immune suppression in squamous lung cancer

doi: 10.1038/s44319-025-00631-1

Figure Lengend Snippet: ( A ) RNA sequencing analysis of tumors from various mouse models of lung cancer. The y-axis represents the normalized counts for Tmprss11b . One-way ANOVA with Dunnett’s multiple comparisons test was used for the statistical analysis (RPR2 mice n = 5; RPM mice n = 15; SNL mice n = 4; LP mice n = 6; SL mice n = 9; KP mice n = 8, biological replicates), **** P < 0.0001 (RPR2, RPM, KP), * P = 0.0133 (LP). Plot represents mean ± SD. ( B ) Schematic representation of Ad-Cre mediated tumor induction in SNL mice. Figure created in BioRender. ( C ) Representative MRI images of the mice in ( B ), 3- & 4-months post infection. Red outlines denote tumors (Biological replicates n > 3). ( D ) Representative H&E images of SNL mouse lung, 7 months post infection with Ad-Cre showing distinct regions of LUSC and mucinous LUAD (Biological replicates n > 3). Scale bar, 100 μm. ( E ) H&E image of SNL mouse lung (11 months post infection with Ad-Cre) and RNAscope of Tmprss11b on a serial section. Left, red outline denotes squamous tumors based on H&E staining. Right, yellow outline denotes regions with Tmprss11b expression (red) corresponding to the regions of squamous tumors. The staining was repeated three times with serial sections (technical replicates) and with lung sections from different mice ( n = 4, biological replicates). Scale bar, 2 mm. ( F ) Zoom-in of ( E ) showing Tmprss11b expression by RNAScope in squamous tumors (top panel) and normal lung (bottom panel). Scale bar, 200 μm. ( G ) Representative H&E image with annotations and RNAscope analysis of Tmprss11b (red) and Sox2 (green) in SNL lung sections. Scale bar, 400 μm. .

Article Snippet: We obtained reference single-cell RNA sequencing (scRNA-seq) data from The Tabla Muris Consortium ( Nature 2018) (Schaum et al, ) and spatial transcriptomics (ST) data from relevant datasets.

Techniques: RNA Sequencing, Infection, RNAscope, Staining, Expressing

Journal: EMBO Reports

Article Title: TMPRSS11B promotes an acidified microenvironment and immune suppression in squamous lung cancer

doi: 10.1038/s44319-025-00631-1

Figure Lengend Snippet: ( A ) Top downregulated Keratin genes from differential gene expression analysis of control shRNA versus Tmprss11b shRNA bulk RNA sequencing from the KLN205 syngeneic experiment in Fig. . The log2FC change depicts the reduction in expression of the indicated genes in the Tmprss11b knockdown tumors compared to the control. ( B ) Top Keratin genes from the differential gene expression (DEG) analysis of the Tmprss11b -high versus low in LUSC spatial data from SNL lung tumors. ( C ) Top keratin genes from the differential gene expression (DEG) analysis of the Tmprss11b -high LUSC versus LUAD spatial data from SNL lung tumors. ( D ) Top Keratin genes from the differential gene expression (DEG) analysis of TMPRSS11B -high versus low LUSC human tumors from TCGA. ( E ) Venn diagram depicting overlapping Keratin genes from the gene lists in ( A – D ).

Article Snippet: We obtained reference single-cell RNA sequencing (scRNA-seq) data from The Tabla Muris Consortium ( Nature 2018) (Schaum et al, ) and spatial transcriptomics (ST) data from relevant datasets.

Techniques: Gene Expression, Control, shRNA, RNA Sequencing, Expressing, Knockdown