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bioRxiv · 10.1101/2025.09.16.676212

dCas9 targeted proteome profiling reveals p300-mediated reciprocal regulation of SMAD and SP1 as a driver of GM2 synthase transcription in renal cell carcinoma

Banerjee, S.·Banerjee, A.·Ray, A.·Paul, D.·Dastidar, S. G.·Willard, B.·Biswas, K.
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Abstract

Glycolipids constitute an important component of the plasma membrane based on both abundance as well as function. Gangliosides, being a class of structurally diverse and functionally varied glycolipids, can act both as a receptor as well as a ligand and therefore is established as a crucial player in several normal cellular processes. In certain diseases, and in particular cancer, select gangliosides are over-expressed often leading to disease manifestation. GM2-synthase, the enzyme responsible for the formation of a pro-tumorigenic ganglioside, GM2 is well reported to be over-expressed across various cancer tissues and cell lines. This over-expression of GM2-synthase has been linked with increased migration, invasion and epithelial to mesenchymal transition (1) as well as induction of a local and systemic host immune suppression in cancer. Despite only a handful of studies demonstrating an epigenetic regulation underlying the transcriptional regulation of GM2-synthase (B4GalNT1) gene, the detailed mechanism still remains unclear. Here we identified the total proteome associated with the GM2-synthase promoter through a two-step CRISPR-dCas9 based proteome profiling approach by categorizing all the identified proteins leading to a detailed elucidation of the molecular drivers behind GM2-synthase transcription. While the previous study identified an acetylation-dependent de-repression of the transcription factor SP1 causing GM2-synthase activation, the underlying molecular mechanism driving its activation wasnt clear. This study demonstrated that the histone acetyl transferase (2), p300 acts as a pivotal factor which on one hand cause acetylation-mediated degradation of SP1, and on the other hand activates SMAD2/4 to have a direct positive impact on GM2-synthase gene transcription. We identified p300 to have an activator role in GM2-synthase gene transcription through knock out, knock down and over-expression experiments. Furthermore, SP1 degradation, SMAD activation and their DNA binding patterns show the reciprocal role of p300 on SP1 and SMAD complexes. Altogether we have identified SMAD 2/4 as an activator complex, p300 as a positive regulator and uncovered a critical p300-SMAD-SP1 regulatory axis in GM2-synthase transcriptional regulation.

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Banerjee, S., Banerjee, A., Ray, A., Paul, D., Dastidar, S. G., Willard, B., Biswas, K.. 2025-09-18. dCas9 targeted proteome profiling reveals p300-mediated reciprocal regulation of SMAD and SP1 as a driver of GM2 synthase transcription in renal cell carcinoma. https://doi.org/10.1101/2025.09.16.676212

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