rna  (TaKaRa)

Journal: bioRxiv

Article Title: A Yeast Two-Hybrid Protein Domain Screening Approach for Ebola Virus-Human Protein Interactions Identifies PABPC1 as a Host Factor Required for Replication

doi: 10.64898/2026.03.05.709814

Figure Lengend Snippet: Inhibition of PABPC1 expression reduces EBOV replication. HeLa cells were mock-transfected (reagent only) or transfected with two distinct PABPC1 siRNAs or nontargeting AllStars negative control siRNAs. At 48 h post-transfection, cells were infected with EBOV at an MOI of 0.1. A.) At 16 hpi, samples were inactivated in 10% neutral-buffered formalin and RNAFISH was performed using probes detecting (+) sense NP and VP35 RNA (magenta). Nuclei were visualized by staining with Hoechst (blue). Scale bar = 250 μM. B.) Quantification of NP and VP35 RNA staining in panel A was performed in ImageJ by calculating the area occupied by mRNA signal and normalizing it to the area occupied by Hoechst (nuclei) signal. C.) In a parallel set of samples, total RNA was isolated by lysing the cells with Trizol reagent at 16 hours post infection. NP RNA levels were quantified by one-step RT-qPCR using a (+) sense NP probe to detect EBOV RNA and are normalized to the level of β-Actin RNA. D) Depletion of PABPC1 in siRNA-treated cells. A parallel set of samples were subjected to SDS-PAGE followed by western blotting with PABPC1 and actin antibodies. Molecular weight markers in kDa are shown at left.

Article Snippet: Human Reference Total RNA, a mixture of total RNA from five human tissues, was purchased from TaKaRa Clontech (#636690).

Techniques: Inhibition, Expressing, Transfection, Negative Control, Infection, Staining, Isolation, Quantitative RT-PCR, SDS Page, Western Blot, Molecular Weight

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