Proteomic Changes Following SMARCA4 Knockdown in Medulloblastoma

A 2026 proteomics study by Medha Gayathri J. Pai used quantitative DIA mass spectrometry to analyze protein expression changes after SMARCA4 knockdown in HD-MB03 Group 3 medulloblastoma cells. The dataset, shared via figshare, includes validated findings on dysregulated pathways like lipid metabolism and SWI/SNF complex subunits.

Use Cases

• Identify protein biomarkers like SMARCA2, CRABP2, and FABP5 upregulated after SMARCA4 loss for target validation.
• Analyze enrichment of pathways such as steroid biosynthesis and fatty acid biosynthesis from proteomic data.
• Validate dysregulation of SWI/SNF complex subunits and histone proteins using the separate validatory set.
• Correlate suppressed pathways like DNA replication and amino acid catabolism with SMARCA4 knockdown status.

Strengths

• Data generated using DIA-MS, noted for superior proteome depth over DDA methods.
• Includes a separate validatory set for confirming key candidate proteins.
• Shared under a clear CC-BY-NC-4.0 license.

Limitations

• Dataset size is only 817.2 KB, indicating limited scope and likely a focused subset of results.
• No row or column counts are provided, obscuring the dataset's full dimensions.
• Data is from a single cell line model (HD-MB03), limiting generalizability.

Provenance

Source

Medha Gayathri J. Pai via figshare.

Collection Method

Quantitative DIA mass spectrometry on HD-MB03 cells with doxycycline-inducible SMARCA4 shRNA knockdown.

Time Range

Experimental study, specific dates not provided.

Freshness

Last updated March 2026.