Journal: The Journal of Experimental Medicine

Article Title: Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis

doi: 10.1084/jem.20240109

Figure Lengend Snippet: FLNA editing impacts cell transcriptional profiles and inflammation in the healthy gut. (A) Scheme of scRNA-seq setup for FLNA R and FLNA Q mouse colons at basal conditions. (B) Cell clustering of colon mucosal cells. (C) Relative abundance of parenchymal (CD45 − ) and immune (CD45 + ) cells in FLNA R and FLNA Q intestines; left panel: EC progenitors (EC Prog.), ECs trans (I–III), proximal ECs (EC Prox. I–II), distal ECs (EC Dist. I–III), goblet cells, tuft cells, enteroendocrine cells (EEC), fibroblasts, and SMCs; right panel: B cells, proliferating T cells (T Prolif.), T helper CD4 + (Th CD4 + ), T helper 17 cells (Th17), regulatory T cells (Treg), classical cytotoxic CD8 + T cells (Tc CD8 + ), γδT cells (Tgd), invariant T cells (Tinv), NK/innate lymphoid cells (ILC), monocytes (Mono), macrophages (Mac), CD103 − and CD103 + DCs, neutrophils, and mast cells (MC). (D) Heatmaps of transcriptomic analysis of DEGs in intestinal structural cells of FLNA R and FLNA Q mice grouped by cellular processes. Heatmap color represents the log 2 -fold increase of expression in FLNA R (green) versus FLNA Q (purple). Rows represent specific cell types. Asterisks represent adjusted values of P < 0.05. (E) Heatmaps of transcriptomic analysis of DEGs in intestinal immune cells of FLNA R and FLNA Q mice grouped by cell type. Heatmap color represents log 2 -fold change of expression in FLNA R (green) and FLNA Q (purple). Rows represent specific cell types. Asterisks represent adjusted values of P < 0.05. (F) Bubble plot representing top 40 MSigDB HALLMARK pathways enriched in bulk RNA sequencing transcriptomes of FLNA R (green) and FLNA Q (purple) cells. Circle sizes indicate the number of DEGs associated with the respective pathway. Data in A–F are from single experiments (three mice pooled per group for single-cell sequencing, n = 4–5 per group for bulk sequencing). NES, normalized enrichment score.

Article Snippet: Chromium Fixed RNA Kit, Mouse Transcriptome, 4 rxns x 16 BC , 10X Genomics, Inc. , Cat#PN-1000497.

Techniques: Expressing, RNA Sequencing, Sequencing

Journal: The Journal of Experimental Medicine

Article Title: Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis

doi: 10.1084/jem.20240109

Figure Lengend Snippet: FLNA editing protects mice from DSS-induced colitis. (A) Scheme of DSS-induced colitis experiment. (B) Weight loss plotted in percent of body weight compared with treatment start (two-way ANOVA, F = 45.61, DF = 5). (C) Length measurements of colons at day 10 ( n = 6, Student’s t test). (D) Representative images of histologic colon sections; bar = 100 µm. (E–G) (E) Total, (F) distal colon, and (G) proximal colon colitis histology score. A higher score means more severe colitis. ( n = 6, Mann–Whitney U test). (H–K) Individual colitis histology scoring parameters for the whole colon length: Cellular (immune cell) infiltration, crypt damage, erosion and ulceration of epithelium, and thickening of colon wall ( n = 6; Student’s t test). (L) Volcano plot (DEGs, Padj ≤ 0.05) of FLNA R versus FLNA Q cells identified by DESeq2 analysis in whole distal colon bulk RNA sequencing. (M) Bubble plot representing the top 40 MSigDB HALLMARK pathways enriched in bulk transcriptomes of FLNA R (green) and FLNA Q (purple) mice at day 10 of DSS challenge. Circle sizes indicate the number of DEGs associated with the respective pathway. ****P < 0.0001; ***P < 0.001; **P < 0.01; *P < 0.05. Error bars show SEM. Data in A–K are representative of at least three individual experiments. Data in L and M: Bulk RNA sequencing were performed from one experiment ( n = 4–5 per group for bulk sequencing).

Article Snippet: Chromium Fixed RNA Kit, Mouse Transcriptome, 4 rxns x 16 BC , 10X Genomics, Inc. , Cat#PN-1000497.

Techniques: MANN-WHITNEY, RNA Sequencing, Sequencing

Journal: Journal for Immunotherapy of Cancer

Article Title: Combined PARP14 inhibition and PD-1 blockade promotes cytotoxic T cell quiescence and modulates macrophage polarization in relapsed melanoma

doi: 10.1136/jitc-2024-010683

Figure Lengend Snippet: Combined treatment of α-PD-1 with PARP14 inhibitor promotes dynamic adaptive resistance strategies in tumor cells which permit their persistence. ( A ) MNN corrected UMAP of tumor and cancer-associated fibroblasts (CAFs) cells (clusters 26–28, n=3,445). Subclustered using the Louvain method of community ordering and colored by subclusters. ( B ) Cell number changes in each subcluster by treatment: IgG2a; α-PD-1; PARP14i (RBN012759); combination treatment α-PD-1 + PARP14i (RBN012759). ( C ) Cell density projections of tumor and CAF cells by treatment. ( D ) Slingshot trajectory inference analysis of tumor cells with trajectory direction indicated by arrows (black). ( E ) Tumor subcluster identity, GSEA relevant terms of upregulated (red, FDR=0.05, logFC>1) and downregulated (blue, FDR=0.05, logFC≤1) genes in tumor subclusters 1–4 (Metascape analysis, values presented as −log 10 of p value). ( F ) PARP14i signature gene expression presented as high (red) to low (blue) average expression and ratio of cells expressing (circle size), across tumor and CAF subclusters in different treatments. ( G ) Cytokine and chemokine gene expression presented as high (red) to low (blue) average expression and ratio of cells expressing (circle size), across tumor and CAF subclusters. EMT, epithelial-mesenchymal transition; FDR, false discovery rate; GSEA, Gene Set Enrichment Analysis; IgG, immunoglobulin G; IL 17, interleukin 17; IRF1, interferon regulatory factor 1; MNN, mutual nearest neighbors; mRNA, messenger RNA; PARP14, Poly ADP ribosyl polymerase 14; PD-1, programmed cell death 1; STAT1, signal transducer and activator of transcription 1; UMAP, Uniform Manifold Approximation and Projection.

Article Snippet: Gene expression libraries were prepared from formaldehyde-fixed samples using the Chromium X and Chromium Fixed RNA kit, Mouse Transcriptome, 4 rxns × 16 BC (10x Genomics) according to the manufacturer’s protocol (CG000527 Rev C).

Techniques: Gene Expression, Expressing