Data_Sheet_1_Analyzing alternative splicing in Alzheimer’s disease postmortem brain: a cell-level perspective.ZIP

Alzheimer’s disease (AD) is a neurodegenerative disease with no effective cure that attacks the brain’s cells resulting in memory loss and changes in behavior and language skills. Alternative splicing is a highly regulated process influenced by specific cell types and has been implicated in age-related disorders such as neurodegenerative diseases. A comprehensive detection of alternative splicing events (ASEs) at the cellular level in postmortem brain tissue can provide valuable insights into AD pathology. Here, we provided cell-level ASEs in postmortem brain tissue by employing bioinformatics pipelines on a bulk RNA sequencing study sorted by cell types and two single-cell RNA sequencing studies from the prefrontal cortex. This comprehensive analysis revealed previously overlooked splicing and expression changes in AD patient brains. Among the observed alterations were changed in the splicing and expression of transcripts associated with chaperones, including CLU in astrocytes and excitatory neurons, PTGDS in astrocytes and endothelial cells, and HSP90AA1 in microglia and tauopathy-afflicted neurons, which were associated with differential expression of the splicing factor DDX5. In addition, novel, unknown transcripts were altered, and structural changes were observed in lncRNAs such as MEG3 in neurons. This work provides a novel strategy to identify the notable ASEs at the cell level in neurodegeneration, which revealed cell type-specific splicing changes in AD. This finding may contribute to interpreting associations between splicing and neurodegenerative disease outcomes.</p

Data_Sheet_2_Analyzing alternative splicing in Alzheimer’s disease postmortem brain: a cell-level perspective.DOCX

Alzheimer’s disease (AD) is a neurodegenerative disease with no effective cure that attacks the brain’s cells resulting in memory loss and changes in behavior and language skills. Alternative splicing is a highly regulated process influenced by specific cell types and has been implicated in age-related disorders such as neurodegenerative diseases. A comprehensive detection of alternative splicing events (ASEs) at the cellular level in postmortem brain tissue can provide valuable insights into AD pathology. Here, we provided cell-level ASEs in postmortem brain tissue by employing bioinformatics pipelines on a bulk RNA sequencing study sorted by cell types and two single-cell RNA sequencing studies from the prefrontal cortex. This comprehensive analysis revealed previously overlooked splicing and expression changes in AD patient brains. Among the observed alterations were changed in the splicing and expression of transcripts associated with chaperones, including CLU in astrocytes and excitatory neurons, PTGDS in astrocytes and endothelial cells, and HSP90AA1 in microglia and tauopathy-afflicted neurons, which were associated with differential expression of the splicing factor DDX5. In addition, novel, unknown transcripts were altered, and structural changes were observed in lncRNAs such as MEG3 in neurons. This work provides a novel strategy to identify the notable ASEs at the cell level in neurodegeneration, which revealed cell type-specific splicing changes in AD. This finding may contribute to interpreting associations between splicing and neurodegenerative disease outcomes.</p

Top statistically related signaling pathways to miR-141 and miR-200a targetome obtained from different databases by means of DAVID tool.

<p>Top statistically related signaling pathways to miR-141 and miR-200a targetome obtained from different databases by means of DAVID tool.</p

Target genes of miR-141 and miR-200a specified <i>in-silico</i> were tested for further analysis and the expression level of target genes of miR-141 and miR-200a in CD4⁺ T cells of relapsing group (n = 20), remitting group (n = 20) and healthy controls (n = 10) were assessed.

<p>Results are normalized relative to expression level of reference gene, <i>18srRNA</i> (*p < 0.05 and **p < 0.01, non-parametric Mann-Whitney <i>t</i>-test) (RP: Relapsing patient, MP: Remitting patient, HV: Healthy volunteer).</p

Up-regulation of miR-141 and miR-200a in relapsing phase of MS patients.

<p>RT-qPCR analysis of miR-141 expression level in CD4^<b>+</b> T cells of MS patients in relapsing phase (n = 20), remitting phase (n = 20) and healthy controls (n = 10) (<i>A</i>). RT-qPCR analysis of miR-200a expression level in CD4^<b>+</b> T cells of MS patients in the same groups (<i>B</i>). Results are normalized relative to expression level of reference gene, <i>RNU48</i> (*p < 0.05, **p < 0.01 and ***p < 0.005, non-parametric Mann-Whitney <i>t</i>-test) (RP: Relapsing patient, MP: Remitting patient, HV: Healthy volunteer).</p

Flow cytometry of FoxP3⁺ CD4⁺ T cells and RORɣt+ CD4+ T cells.

<p>CD4^<b>+</b> T cells were isolated by CD4+ Tcell isolation kit II human of Miltenyi Biotec and stained with respective antibodies and evaluated in relapsing phase (n = 20) and remitting phase (n = 20) of MS patients and healthy controls (n = 10). A forward and side scatter gate was used to select lymphocyte population and fluorescence compensation was set according to labeled lymphocytes with only green and only red fluorescent separately versus isotype control (<i>A</i>). Percentage of RORγt+ CD4+ T cells measured by Flow cytometry, shows meaningful increase in relapsing group (<i>B</i>) while percentage of FoxP3^<b>+</b> CD4^<b>+</b> T cells elevates in remitting group (<i>C</i>) (*p < 0.05, **p < 0.01 and ***p < 0.005, non-parametric Mann-Whitney <i>t</i>-test) (RP: Relapsing patient, MP: Remitting patient, HV: Healthy volunteer).</p

The expression level of master markers of Th17& Treg cells and <i>IL-17A</i> in CD4⁺ T cells of relapsing group (n = 20), remitting group (n = 20) and healthy controls (n = 10) in MS patients.

<p>Results are normalized relative to expression level of reference gene, <i>18srRNA</i> (*p < 0.05, **p < 0.01 and ***p < 0.005, non-parametric Mann-Whitney <i>t</i>-test) (RP: Relapsing patient, MP: Remitting patient, HV: Healthy volunteer).</p

Heatmap view of pathways in which validated targets of miR-141 and miR-200a are involved.

<p>The heatmap was drawn in consequent of enrichment analysis on miR-141 and miR-200a targetome (for valid targets) in which a merged p-value is calculated for each pathway by applying Fisher’s meta-analysis manner. The resulting p-value represents the examined pathways that are significantly enriched with gene targets of miR-141 and miR-200a. Color gradient displays the importance of mentioned pathways. Heatmap was drawn based on validated targets of miR-141 and miR-200a, according to DIANA miRPath. Notably, mTOR signaling pathway was specified as one of the major pathways based on its involvement in differentiation of Th17 cells. Analysis shows that miR-141 affects mTOR pathway more effective than miR-200a does.</p