Journal: Science Advances

Article Title: Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib

doi: 10.1126/sciadv.aea2475

Figure Lengend Snippet: ( A ) Change in SPI values from short-read sequencing of mRNA in IM 1h (top) or 18 h (bottom) relative to CTRL. Introns ( n = ~35,300) detected by at least 500 reads and with significant changes in SPI (adjusted P value < 0.05) are marked in blue (20 in IM 1h and 193 in IM 18h). Adjusted P values were determined using chi-square tests for pairs of replicates and the Benjamini-Hochberg procedure. ( B ) Significant changes in alternative splicing in cells treated with JTE or IM 18h. A3SS or A5SS, alternative 3′ or 5′ splice site; MXE, mutually exclusive events. Number of significant events [false discovery rate (FDR) < 0.05] detected by at least 20 reads and with absolute inclusion level difference to CTRL > 0.1. ( C ) Comparison of genes with RTI ≥ 0.2 (RTI) and genes with significant changes in RI and CE at the level of nuclear RNA in IM 18h. Only single intersections with RTI are presented. ( D ) Comparison of genes with significant changes in RI (left) or CE (right) in IM or JTE 18h. ( E ) Sashimi plot for EIF4H (left) and quantification of isoform usage (right) in CTRL versus JTE or IM 18h. Isoforms 1 and 2 represent the skipping and inclusion, respectively, of exon 5 (beige highlight). Percentage of transcripts belonging to each isoform in three replicates (means ± SEM). Significance based on two-tailed Student’s t test (* P < 0.05; *** P < 0.001).

Article Snippet: Long- and short-read sequencing raw data are available through the National Center for Biotechnology Information (NCBI) under GEO accession numbers: GSE283849 , GSE283813 , and GSE310243 .

Techniques: Sequencing, Alternative Splicing, Comparison, Two Tailed Test

Journal: Science Advances

Article Title: Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib

doi: 10.1126/sciadv.aea2475

Figure Lengend Snippet: ( A ) Examples of reads aligned to RBM14 and RBM4 from long- and short-read sequencing of IM-treated cells. Chimeric reads marked in blue. ( B ) Sashimi plot for RBM14 and RBM4 (chromosome 11: 66616624 to 66644972) based on a single representative CTRL replicate. Only splicing events detected more than five times are shown. Black represents read coverage density in RPKM, gray lines represent splicing events within gene bodies, and the red line represents chimeric splicing. ( C ) Scheme of primer design for real-time PCR semiquantification (qPCR) of chimera expression. ( D ) Expression of selected chimeras [red primers in (C)] in CD34 + -enriched cells from three healthy donors (HD) and two patients with CML (CML), normalized to spike-in controls and presented relative to the expression level of the last exon in the upstream gene [beige primers in (C)]. ( E ) Comparison of readthrough chimeras identified by SOAPfuse analysis of mRNA-seq for CTRL or IM-treated K562 cells. ( F ) Changes in chimera transcript expression normalized to spike-in control referenced to the last exon in the upstream gene and expressed as fold change upon IM treatment. Level in CTRL as 1.0, marked with the dashed line. Significance based on two-way ANOVA test (* P < 0.05; ** P < 0.005; *** P < 0.001).

Article Snippet: Long- and short-read sequencing raw data are available through the National Center for Biotechnology Information (NCBI) under GEO accession numbers: GSE283849 , GSE283813 , and GSE310243 .

Techniques: Sequencing, Real-time Polymerase Chain Reaction, Expressing, Comparison, Control

Journal: JID Innovations

Article Title: Assessing T-Cell Profile Shifts through IL-23 Inhibition by Guselkumab on Psoriasis

doi: 10.1016/j.xjidi.2025.100433

Figure Lengend Snippet: Gene expression analysis at baseline predicting the effects of guselkumab. ( a) Clustering of transcriptomic profile–based moderate responder (blue) and transcriptomic profile–based high responder (red) groups using UMAP analysis of RNA-seq data of pretreatment CD4 + cells in peripheral blood. Box plots show the comparison of clinical response to guselkumab. ( b) Comparison of total Treg and each Treg subset in lesional skin blood and peripheral blood at 4W after guselkumab administration between the moderate and high responder groups. Box plots display the distribution of values, with the bars indicating the median, the box showing the interquartile range, and the whiskers covering the whole range of the data. ( c) Heatmap of serum levels of various cytokines and chemokines in peripheral blood at 0W from the moderate and high responder groups. The scale represents z-score, with red indicating higher expression. The moderate responder group showed significantly higher levels of the 6 cytokines/chemokines highlighted by the yellow box than the high responder group. ( d) Levels of cytokines associated with Th17 cells (eg, TGF-β1, IL-23, IL-6) and chemokines associated with immune cells in psoriasis (eg, GRO-α/CXCL1, ENA-78/CXCL5, I-TAC/CXCL11) in peripheral blood samples from moderate and high responder groups at different time points (0W, 4W, and 12W). All data were treated as nonparametric, and comparisons were conducted using the Mann–Whitney test for unpaired data. Statistical significance is indicated with asterisks (∗ P < .05, ∗∗ P < .01, and ∗∗∗ P < .001). 0W, 0 week; 12W, 12 week; 4W, 4 week; RNA-seq, RNA-sequencing; Th, T helper; Treg, regulatory T cell; UMAP, Uniform Manifold Approximation and Projection.

Article Snippet: Raw sequencing data (fastq files) were received from Macrogen Japan.

Techniques: Gene Expression, RNA Sequencing, Comparison, Expressing, MANN-WHITNEY

Journal: JID Innovations

Article Title: Assessing T-Cell Profile Shifts through IL-23 Inhibition by Guselkumab on Psoriasis

doi: 10.1016/j.xjidi.2025.100433

Figure Lengend Snippet: Differential gene expression and analysis of genes associated with Th17 and Tregs in different responder groups. (a) Volcano plot of differential gene expression between the transcriptomic profile–based high responder and transcriptomic profile–based moderate responder groups using RNA-seq data of pretreatment CD4+ cells in peripheral blood. Red highlights genes upregulated in high responders, and blue highlights genes upregulated in moderate responders. ( b) Log 2 expression of SGK1, GZMB , and meteorin-like protein (METRNL , Th17-associated genes) at different time points (0W, 4W, and 12W) in the high and moderate responder groups. ( c) Mean log 2 expression of NR4a2 and AREG (Treg-associated genes) at different time points (0W, 4W, and 12W) in the high and moderate responder groups. All data were treated as nonparametric, and comparisons were conducted using the Mann–Whitney test for unpaired data. Mean values with SD are indicated by the blue and red lines. Significant differences are marked by asterisks (∗ P < .05, ∗∗ P < .01, and ∗∗∗ P < .001). 0W, 0 week; 12W, 12 week; 4W, 4 week; GZMB, granzyme B; RNA-seq, RNA-sequencing; Th, T helper; Treg, regulatory T cell.

Article Snippet: Raw sequencing data (fastq files) were received from Macrogen Japan.

Techniques: Gene Expression, RNA Sequencing, Expressing, MANN-WHITNEY