Journal: bioRxiv

Article Title: A simple circuit to sustain intact tumor microenvironments for complex drug interrogations

doi: 10.1101/2025.10.26.684624

Figure Lengend Snippet: A: Boxplots showing changes in mRNA expression of MAPK, EGFR, and PI3K after 48 hr of perfusion with control or cetuximab for tumors from Patient 30 and Patient 31. Arrows denote an increase (up) or decrease (down) in expression after treatment with cetuximab or control. B: Heatmap of mRNA expression signatures from Patient 30 and 31 tumors treated with cetuximab based on bulk RNA-seq and Xenium single cell spatial transcriptomics. C: Pan-anti-HLA mAb W6/32 competes for binding sites of LILRB1 & LILRB2 but not for TCR. For comparison of crystallographically defined binding footprints, the coordinates of the HLA H of W6/32/HLA-B*27:05 complex (7T0L) were superposed on the HLA H chain of the indicated structures using Chimera X ( https://www.rbvi.ucsf.edu/chimerax/ ). Left: LILRB1/HLA-G (6AEE), LILRB2/HLA-G (2DYP). Right: TCR/HLA-A*02 (6VMA), TCR9a/HLA-C*08:02 (6ULN). For HLA molecules, only HLA-B*27:05 (teal), peptide (red) and is β 2 m (salmon) are shown. W6/32 Fab is violet; GP100 HLA-A*02 TCR is blue and KRAS HLA-C*08:02 TCR9a is yellow; LILRB1 is blue and LILRB2 is green. D: Flow cytometric analysis of the expression of NKp46 on NK cells, IL-15Ra and CD86 expression on CD14 + monocytes from TILs isolated from metastatic colorectal cancer (TOP) and metastatic pancreatic cancer (BOTTOM) perfused for 48 hr in presence of control hIgG1LALAPG or W6/32LALAPG monoclonal antibodies. E: Bar graph of cell percentages derived from cell deconvolution of RNA-seq performed on tumors from Patient 10 and Patient 11 treated with bintrafusp alpha or control. F: Representative tissue mask images based on low-plex protein analysis showing the presence of CD8 + cells inside and outside of the tumor zones of tumors from Patient 10 and Patient 11 treated bintrafusp alpha or control. G: Bar graph showing differences in cytokine levels between control-treated and bintrafusp alpha -treated tumors from Patient 10 and 11 tumors at 48 hr. H: Bar graph showing differences in RNA-based signature activity between control-treated and bintrafusp alpha -treated tumors from Patient 10 and 11 tumors. I: Scatter plot of changes in expression of TGF-β pathway-associated genes based on GeoMx analysis of bintrafusp alpha-treated versus control-treated tumors from Patient 10 and 11. J: Boxplots depicting PD-L1 expression and TGF-β signature activity in tumors from Patient 10 and Patient 11 tumors treated with bintrafusp alpha or control. Each dot represents detection at a unique RO I in the tissue based on GeoMx analysis. In the boxplots, the bottom whisker indicates the maximum value or 75th percentile + 1.5 interquartile range (IQ R); the top whisker indicates the minimum value or 25th percentile - 1.5 IQ R. Significance was calculated with non-adjusted Mann- W hitney- W ilcoxon non-parametric U test. K: Volcano plot of responder/non-responder signature based on expression changes derived from GeoMx DSP data after bintrafusp alpha treatment of tumors from Patients 10 and Patient 11. L: Boxplots showing expression of bintrafusp alpha Responsive (R) and non-responsive (NR) signatures applied to the combined bulk RNA-seq of tumors at baseline and after bintrafusp alpha treatment. In the boxplots, the bottom whisker indicates the maximum value or 75th percentile + 1.5 interquartile range (IQR); the top whisker indicates the minimum value or 25th percentile − 1.5 IQR. Significance was calculated with non-adjusted Mann-Whitney-Wilcoxon non-parametric U test.

Article Snippet: Bulk RNA sequencing TruSeq Stranded Total RNA (Illumina) was used for RNA library construction.

Techniques: Expressing, Control, RNA Sequencing, Binding Assay, Comparison, Isolation, Bioprocessing, Derivative Assay, Activity Assay, Whisker Assay, MANN-WHITNEY

Journal: The Journal of allergy and clinical immunology

Article Title: Reduced ALDH2 in the respiratory tract associates with dysregulated alcohol metabolism and respiratory reactions in AERD

doi: 10.1016/j.jaci.2025.08.011

Figure Lengend Snippet: A. ALDH2 transcript in cultured healthy nasal mucosa-derived ALIs with or without IL-4/13 (left) and in healthy lung-derived bronchial ALIs with or without IL-13 (right). B. ALDH2 protein levels in healthy nasal mucosa-derived submerged EpCs with or without IL-4/13. Data are shown as individual values. C. Bulk RNA-seq data of nasal scraping cells from paired patient samples (n=15) show the dupilumab-induced in vivo change in ALDH2 from baseline to after 1–3 months of dupilumab. Data are shown as individual values and means; analysis with paired t-tests.

Article Snippet: Mature ALIs were stimulated with 10 ng/mL IL-4 and IL-13 for 7 days, then lysed with TCL buffer, and Smart-Seq2 paired-end bulk RNA-seq was performed by the Harvard-MIT Broad Institute.

Techniques: Cell Culture, Derivative Assay, RNA Sequencing, In Vivo

Journal: Nature Communications

Article Title: Single-cell expression profiling of bat wing development

doi: 10.1038/s41467-025-61944-2

Figure Lengend Snippet: a Autopods from R. sinicus forelimbs and hindlimbs at developmental stages CS16, CS18, and CS20 are analyzed by single-cell RNA sequencing. UMAP visualization of color-coded cell populations in developing bat forelimbs and hindlimbs. b Absolute cell numbers and proportions for each cell population. c Dot plot showing marker gene expression for each cell population. d Genes with specific high expression for each cell population. e Top two terms from the tissue and functional enrichment analyses for the highly expressed genes of different cell populations. The P values are from two-sided Fisher’s exact tests and adjusted with the Benjamini–Hochberg method.

Article Snippet: The forelimbs and hindlimbs of RSI embryos at CS18 and CS20 were collected for bulk RNA sequencing on the Illumina platform, with each sample having two biological replicates.

Techniques: RNA Sequencing, Marker, Gene Expression, Expressing, Functional Assay

Journal: Cell Communication and Signaling : CCS

Article Title: Knockout of thyroid hormone receptor alpha a ( thraa ) enhances cardiac regeneration in zebrafish through metabolic and hypoxic regulation

doi: 10.1186/s12964-025-02350-5

Figure Lengend Snippet: Temporal transcriptomic profiles uncover cardiac injury response in zebrafish. ( A ) Schematic diagram shows the experimental design of the time-course experiment studying heart regeneration by bulk RNA-Seq. Uninj: uninjured state; hpi: hours post injury; dpi: days post injury. Figure was created using BioRender. ( B ) 3D PCA plot of the time-course transcriptome profiles in WT and thraa +/− mutants. Arrow illustrates the trajectory of samples from uninjured state to 15 dpi. ( C ) The hierarchical clustering of identified DEGs. DEGs were identified through time-course analysis in both WT and thraa +/− mutants. Nine clusters were identified by the expression patterns of genes. Highlighted genes in each cluster are labelled. n = number of genes in cluster. ( D ) Results of GSEA on HALLMARK gene set for both WT and thraa +/− through time-course analysis. NES: normalized enrichment score. +NES: upregulation; -NES: downregulation. HALLMARK gene sets are categorized according to their function and enriched genes

Article Snippet: Extracted RNA was sent to Novogene Ltd. (Beijing, China) for library construction and bulk RNA sequencing.

Techniques: RNA Sequencing, Expressing