Journal: bioRxiv

Article Title: Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam

doi: 10.1101/2025.06.03.657600

Figure Lengend Snippet: (A) Venn diagrams illustrating the overlap between significantly dysregulated transcripts in three tissues. Names of the shared genes between all combinations of two tissues are indicated. (B) Heatmap detailing the extent of the log 2 fold changes in shared genes in all three tissues with blue for down and red for upregulated genes. The grey color represents transcript not detected in those tissues. Significant p-values are reported on the plots. * p-val<0.05,** p-val<0.01, and *** p-val<0.001. Significance was calculated using Quasi-likelihood F-test. (C) Bar charts showing the top significantly enriched terms in KEGG analysis of shared differentially expressed transcripts. The bar lengths report the significance of the enrichments, and the number of genes associated with each category is reported inside each bar. The red colour represents the significant terms (-log10(p-val) = 1.3). (D) Protein-protein network is formed by dysregulated transcripts that overlap between the tissues, as shown in (A). The 4 clusters, which are formed by the contribution of DEGs for all three tissues, are: (i) Ribosome/translation formed by Dhttip2 (B & L), Mrpl36 (SC & L), Mrpl14 (SC & L), Mrps21 (B & L), Rps4x (SC & L), Rpl34 (SC & L), Rps27rt (B & L) and Mettl17 (B & SC); (ii) RNA Splicing/transport: Ing4 (SC & L), Arid4b (B & L), Snrpa1 (SC & L), Stoml2 (B & L), Smn1 (B & SC), Ppie (SC & L) and Thoc7 (SC & L); (iii) DNA Replication: Mcm5 (B & L), Smc4 (B & L), Smc2 (SC & L), Tacc3 (SC & L); (iv) Extracellular matrix: Col1a1 (B & L), Col1a2 (B & L), Cdkn1a (SC & L) and Spp1 (B & SC). B stands for brain, SC for spinal cord and L for liver.

Article Snippet: Western blotting was performed using primary antibodies against Col1A1 (Proteintech 67288-1-Ig, 1:2500) and SMN (mouse anti-SMN, BD Biosciences 610647, 1:1,000).

Techniques:

Journal: bioRxiv

Article Title: Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam

doi: 10.1101/2025.06.03.657600

Figure Lengend Snippet: (A) Quantification of qPCR analysis performed for the Col1a1 transcripts in cytoplasmic mRNAs from control and SMA brain, spinal cord and liver at the P5, P10, and P18 stages of SMA disease in Smn 2B/- mice. Data are mean ± s.e.m. among n = 3 biologically independent samples. Significant changes were assessed using unpaired two-sided t-tests. (B) Relative co-sedimentation profile of Col1a1 mRNAs in control (grey) and SMA (red) brain, spinal cord and liver at P10. Data are mean ± s.e.m. among n = 3 biologically independent samples. Significant changes were assessed using unpaired two-sided Student’s t-tests. * p-val<0.05. Brain (p-value fraction 3 p = 0.01101). (C-E) Protein levels of Col1a1 and SMN in the brain (C), spinal cord (D), and liver (E) at P10 and P18 in controls and SMA using western blot analysis. Quantification of immunoblots for Col1a1 is normalized to total protein stain. SMA expression values were normalized and compared with control values for each of the tissues. Data are mean ± s.e.m. among n = 3 biologically independent samples. Significant changes were assessed using unpaired two-sided Student’s t-tests. * p-val<0.05 and ** p-val<0.01. Brain (p-value P18 p = 0.00794), Spinal cord (p-value P18 p =0.00219). (F,G) Quantification of qPCR analysis for Col1a1 and Col1a2 (F) relative co-sedimentation profile of Col1a1 and Col1a2 mRNAs and protein levels of Col1a1 (G) in the spinal cord and cortex tissues of a mouse model of Amyotrophic Lateral Sclerosis (blue) and littermate controls (grey). ( H ). Data are mean ± s.e.m. among n = 3 biologically independent samples. Significant changes were assessed using unpaired two-sided Student’s t-tests.

Article Snippet: Western blotting was performed using primary antibodies against Col1A1 (Proteintech 67288-1-Ig, 1:2500) and SMN (mouse anti-SMN, BD Biosciences 610647, 1:1,000).

Techniques: Control, Sedimentation, Western Blot, Staining, Expressing

Journal: bioRxiv

Article Title: Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam

doi: 10.1101/2025.06.03.657600

Figure Lengend Snippet: (A) COL1A1 mRNA levels in total RNA from healthy, carrier (H1-3 and C) and SMA patient-derived fibroblasts (P1-4, left). Data are mean ± s.e.m. among n = 3 independent technical replicates for each individual. Comparison between relative co-sedimentation profiles of COL1A1 mRNA from healthy (n=3) and SMA patient-derived fibroblasts SMA Type I (n = 2), SMA Type II (n = 2) (middle). Data are mean ± s.e.m. among n biological independent replicates. COL1A1 protein expression in healthy, carrier and SMA patient-derived fibroblasts (left), data are mean ± s.e.m. among n = 3 independent technical replicates. Expression values were normalized and compared with healthy control values. Significant changes between each healthy sample and the other samples were assessed using one-way ANOVA test, with Holm correction of p-values. Significant p-values are reported on the plots. (B, C) Comparison of COL1A1 protein expression in Coriell Institute cohort (Healthy n=3, SMA n=4) and UMCU cohort-paediatric (Healthy n=3, SMA n=6) and adult (Healthy n=5, SMA n=9). Data represent the mean ± s.e.m. of n individual, shown as a dot, for each group. Significant changes were assessed using unpaired two-sided Student’s t-tests. (D) Corelation between COL1A1/SMN protein expression and SMN2 copy number in SMA patients’ fibroblasts from the UMCU cohort. Data are plotted as mean of n=3 independent technical replicates. The regression line, its 99% confidence level interval, the Pearson correlation coefficient, and its p-value are displayed. Significant p-value<0.05 are highlighted in bold.

Article Snippet: Western blotting was performed using primary antibodies against Col1A1 (Proteintech 67288-1-Ig, 1:2500) and SMN (mouse anti-SMN, BD Biosciences 610647, 1:1,000).

Techniques: Derivative Assay, Comparison, Sedimentation, Expressing, Control

Journal: bioRxiv

Article Title: Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam

doi: 10.1101/2025.06.03.657600

Figure Lengend Snippet: (A) Schematic representation of the Risdiplam treatment. (B) Representative immunoblots for SMN in untreated (U) and Risdiplam-treated (R) patient-derived fibroblasts from 3 technical replicates of one paediatric patient and one healthy donor. The internal standard (Int. std.) is used to compare protein signal across different membranes. Each blot is accompanied by a corresponding total protein stain (lower panel). (C) Representative immunoblots for COL1A1 in untreated (U) and Risdiplam-treated (R) patient-derived fibroblasts from paediatric healthy donors, and paediatric and adult SMA patients. The internal standard (Int. std.) is used to compare protein signal across different membranes. Each blot is accompanied by a corresponding total protein stain (lower panel). (D) Quantification of SMN protein level of Risdiplam-treated (R) relative to the untreated (U) fibroblasts. Protein levels were normalized for total protein stain and internal standard. Data are mean ± s.e.m. among n = 3 technical independent replicates. Significant changes were assessed using unpaired two-sided Student’s t-test, with Holm correction of p-values. * p-val<0.05, ** p-val<0.01, *** p-val<0.001, and **** p-val<0.0001. (E) Quantification of COL1A1 protein level of Risdiplam-treated (R) relative to the untreated (U) fibroblasts. Protein levels were normalized for total protein stain and internal standard. Data are mean ± s.e.m. among n = 3 technical independent replicates. Significant changes were assessed using unpaired two-sided Student’s t-test, with Holm correction of p-values. * p-val<0.05, ** p-val<0.01, *** p-val<0.001, and **** p-val<0.0001.

Article Snippet: Western blotting was performed using primary antibodies against Col1A1 (Proteintech 67288-1-Ig, 1:2500) and SMN (mouse anti-SMN, BD Biosciences 610647, 1:1,000).

Techniques: Western Blot, Derivative Assay, Staining