dba 2 strain  (Jackson Laboratory)

Journal: Nature Communications

Article Title: Type II innate lymphoid cell plasticity contributes to impaired reconstitution after allogeneic hematopoietic stem cell transplantation

doi: 10.1038/s41467-024-50263-7

Figure Lengend Snippet: a Schematic of murine bone marrow transplantation model. Lethally irradiated B6D2 mice received allogeneic (C57BL/6) T cell depleted bone marrow plus total splenic T cells with activated GFP-expressing ILC2s. After 20 days, eGFP + cells were isolated from the lamina propria (LP). b UMAP depicts embeddings of 5554 nuclei. Pre-transplant GFP + ILC2s (blue) and post-transplant LP-isolated GFP + cells (green) are shown. c Pre-transplant ILC2 and post-transplant cells are separately depicted. d Heatmap depicting differentially expressed genes (two-sided Wilcoxon rank sum test, p adj < 0.05, avglog2FC > 0) by comparing one pre-transplant cluster to the set of post-transplant clusters (Gene sets pre 1 – 3). Tick marks indicate genes shared across three pre-transplant gene sets (left) and post-transplant gene sets (right). e Gene ontology analysis was performed for each of the post-transplant associated gene sets (one-sided Fisher’s Exact test). The color indicates the proportion of differential genes found in each ontology. f The average expression of marker genes associated with each type of ILC (ILC1, ILC2, ILC3, and NK) . g Distribution of per cell average marker expression is shown. Pre signifies pre-transplant and post- indicates post-transplant (one-sided Mann Whitney U Test, ***p < 2.2 × 10 −16 ). h Regions of differential chromatin accessibility were identified between each pre- and post-transplant cluster from Fig. 2c. i – k Volcano plots showing the enrichment of DNA binding motifs at sites of increased chromatin accessibility in post-transplant clusters 1 ( i ), 2 ( j ), and 3 ( k ) relative to all the sites of open chromatin identified in the pre-transplant cell population. l , m Candidate regulators of pre- ( l ) and post- ( m ) transplant cells. n UMAP depicts a low-dimensional representation of the integrated RNA space, with each cell annotated with ILC cell type. o Scatter plot showing putative regulators of ILC1-like and ILC2s (Fig. 2n).

Article Snippet: C57BL/6 (strain 0000664) and C57BL/6 J × DBA/2 F1 (B6D2, strain 100006) mice were purchased from The Jackson Laboratory.

Techniques: Transplantation Assay, Irradiation, Expressing, Isolation, Marker, MANN-WHITNEY, Binding Assay

Journal: Nature Communications

Article Title: Type II innate lymphoid cell plasticity contributes to impaired reconstitution after allogeneic hematopoietic stem cell transplantation

doi: 10.1038/s41467-024-50263-7

Figure Lengend Snippet: a Schematic depicting ILC2s elicitation and isolation. b , c Representative flow cytometry plots of intracellular cytokine ( b ) and transcription factor expression ( c ) from cells expanded in vitro as described in 3 A. Error bars in ( c) represent SEM. d ILC gene expression profiles based on mRNA abundance. e Differential sites of CA (two-sided Wald Test DESeq2), p adj < 0.05) between ILC2 and pcILC2s. The heatmap displays a z-score normalized ATAC signal. R1 and R2 indicate replicate numbers. f Representative tracks of normalized ATAC signal. Tick marks indicate differential sites of CA (two-sided Wald Test (DESeq2), p adj < 0.05). kb = kilobase. g UMAP of integrated RNA abundance signal from 7918 nuclei. ILC2s cultured with IL-7 and IL-33 (blue), ILC2s grown with proinflammatory cytokines, pcILC2 (orange). h Average chromatin accessibility at murine ILC2 marker genes .The Red dot shows mean value, ILC2-pcILC2: p < 2.2 × 10 −16 , ILC2-ILC1-like: p = 7.46 x 10 −5 . i Average per cell expression of genes associated with ILC1, ILC2, shared between ILC1/2, and ILC1/3 . The analysis includes 4,758 ILC2 and 5641 pcILC2 nuclei. ***p < 2.2 × 10 −16 . j Candidate regulators of pcILC2 cells. k UMAP of integrated ILC2 and pcILC2s annotated with normalized gene expression. l UMAP of weighted nearest neighbor integration of single nucleus RNA and ATAC from in vitro ILC2s, pcILC2s, and post-transplant cells. The black arrow highlights ILC1-like cells. m , n Lethally irradiated B6D2 mice received T cell depleted bone marrow (BM, BM only), BM plus total splenic T cells (BM + T cells), BM plus T cells with activated ILC2s (BM, T cells + ILC2) or pcILC2s (BM, T cells + pcILC2). Mean ± SEM, n = 7–16. n Kaplan-Meier survival curve after allo-HSCT. Representative of 2 independent experiments with n = 6–10 mice. Log-rank (Mantel-Cox) test, *** P < 0.01. Boxplots ( h , i ), are centered at median. Box bounds represent the interquartile range (IQR), whiskers represent the min/max values, and outliers are not shown.

Article Snippet: C57BL/6 (strain 0000664) and C57BL/6 J × DBA/2 F1 (B6D2, strain 100006) mice were purchased from The Jackson Laboratory.

Techniques: Isolation, Flow Cytometry, Expressing, In Vitro, Cell Culture, Marker, Irradiation