Journal: Nature Communications

Article Title: A tissue-bioengineering strategy for modeling rare human kidney diseases in vivo

doi: 10.1038/s41467-021-26596-y

Figure Lengend Snippet: a Volcano plots showing the distribution of all differentially expressed genes (DEGs) in TSC2 −/− renal organoids compared to TSC2 +/+ (left) and TSC2 +/− (right) renal organoids (FDR < 0.05). Each dot represents a unique gene; red denotes log 2 (fold change) >2, upregulated genes in TSC2 −/− ; blue denotes log 2 (fold change) <-2, downregulated in TSC2 −/− . Selected statistically significant upregulated and downregulated genes (NCBI/Entrez names) are indicated, as determined by a two-sided Chi-Square test. b Principal Component Analysis (PCA) of RNA-Seq data from renal organoids of the three genotypes, n = 3 samples for each genotype, five organoids per sample. c Heatmap showing hierarchical clustering of three different genotypes of kidney organoids using the top 3000 most variable genes. Color scale representative of gene expression level: red denotes log 2 ≤ 3, blue denotes log 2 ≥ -3. d Representative enrichment plots corresponding to gene set enrichment analysis (GSEA) for pairwise comparison of TSC2 −/− vs . TSC2 +/− . e Venn diagrams indicating 187 common differentially expressed genes, including signature AML markers, in TSC2 −/− vs . TSC2 +/+ renal organoids and kidney AML vs . normal kidney. f Comparative mRNA expression levels for AML hallmark genes in TSC2 −/− , TSC2 +/+ , and TSC2 +/− renal organoids ( n = 3 each) compared to human kidney AML ( n = 28) and human kidney ( n = 8). P values for individual comparisons done using a two-sided Mann–Whitney U test are indicated. Gene expression is shown in FPKM values. g Comparative ENO2 mRNA expression levels in TSC2 +/+ and TSC2 +/− , TSC2 −/− renal organoids ( n = 3 each). P values for the indicated individual comparisons done using two-tailed Student’s t test are shown. Gene expression is shown in FPKM values. h , i Box-and-whisker plot showing minimum value, first quartile, median, third quartile and maximum value for ENO2 content ( g ) and for enolase activity ( h ) in whole extracts of TSC2 +/+ and TSC2 −/− renal organoids. P value for the 2-tailed Student’s t test comparing TSC2 −/− versus TSC2 +/+ is shown. n = 4 independent experiments, containing three organoids each.

Article Snippet: Enolase 2 activity was measured in whole organoid extracts using the human ENO2 ELISA kit (Proteintech, #KE00050), following the manufacturer’s instructions.

Techniques: RNA Sequencing, Gene Expression, Comparison, Expressing, MANN-WHITNEY, Two Tailed Test, Whisker Assay, Activity Assay