Journal: Human Genomics

Article Title: Global transcriptome modulation by xenobiotics: the role of alternative splicing in adaptive responses to chemical exposures

doi: 10.1186/s40246-024-00694-6

Figure Lengend Snippet: Xenobiotics used to Probe Structure-Activity Relationships and Global Splicing Modulation in Primary Rat Hepatocytes. The figure illustrates the three xenobiotics investigated for their effects on alternative splicing across the primary rat hepatocyte (PRH) transcriptome. Two methylene-dioxybenzene (MDB) compounds, C1-MDB (4-n-methyl-methylene-dioxybenzene) with a short aliphatic chain and C6-MDB (4-n-hexyl-methylene-dioxybenzene) with an extended chain, were included to explore structure-activity relationships influencing alternative gene splicing and expression. These MDBs are known to induce differential splicing of Cyp2b genes, providing a basis to examine their broader splicing effects across other gene families. Additionally, carbamazepine (CBZ), an FDA-approved drug with mixed CYP induction properties, acts as a comparative standard by modulating the expression of several CYP isoforms overlapping with those influenced by the MDB compounds. This selection allows us to probe whether structural variations drive unique splicing patterns, despite similar changes in gene expression

Article Snippet: Cryopreserved primary rat hepatocytes were purchased from Sekisui Xenotech (#R1000.H15+, Lot No. 1710122; Kansas City, Kansas).

Techniques: Activity Assay, Alternative Splicing, Expressing, Selection

Journal: Human Genomics

Article Title: Global transcriptome modulation by xenobiotics: the role of alternative splicing in adaptive responses to chemical exposures

doi: 10.1186/s40246-024-00694-6

Figure Lengend Snippet: Global RNAseq Analysis of Differential Gene Expression in C1-MDB, C6-MDB, and CBZ-treated PRHs. (a) Principal Component Analysis (PCA) of RNA-seq data from untreated, control (VEH_05 and VEH_1), and treated (C1-MDB, C6-MDB, and CBZ) primary rat hepatocyte groups, showing strong clustering across groups. Notable outliers include C6-MDB replicate 2 along PC1 and variance in C1-MDB along PC2. To maintain a comprehensive dataset, all replicates were included in downstream analyses to capture the full scope of gene expression and splicing changes in the PRH model. (b) Venn diagram depicting the overlap of differentially expressed genes (DEGs), relative to control (VEH_05), across treatments (C1-MDB, C6-MDB, and CBZ) based on DESeq2 analysis. The central overlap represents over 10,000 commonly expressed genes, though not all are differentially regulated. Each xenobiotic modulated approximately 50 to 150 unique genes, indicating treatment-specific regulation, while the central set reflects genes expressed under all conditions. (c) Venn diagram from DEG analysis using rSeqDiff, identifying 58 genes commonly altered across all treatments (C1-MDB, C6-MDB, CBZ) compared to control. Unlike the DESeq2 analysis, the control (VEH_05) is not shown, focusing instead on shared gene changes between treatments. C6-MDB and C1-MDB showed more substantial gene expression changes (488 and 368 genes, respectively) compared to CBZ (182). CBZ and C1-MDB shared the highest number of commonly modulated genes (136), compared to CBZ and C6-MDB (88) or C1-MDB and C6-MDB (92). Detailed control comparisons are provided in Supplemental Tables – (Additional Materials)

Article Snippet: Cryopreserved primary rat hepatocytes were purchased from Sekisui Xenotech (#R1000.H15+, Lot No. 1710122; Kansas City, Kansas).

Techniques: Expressing, RNA Sequencing Assay, Control