Alternative splicing of ceramide synthase 2 alters levels of specific ceramides and modulates cancer cell proliferation and migration in Luminal B breast cancer subtype

Trishna Pani,Harsh Sharma,Nihal Medatwal,Aneeshkumar G Arimbasseri,Dipankar Malakar,Tushar Kanti Maiti,Arnab Mukhopadhyay,Sharwan Kumar,Animesh Kar,Kajal Rajput,Gagan Dev,Rituparna Basak,Ujjaini Dasgupta,Ravi Datta Sharma,Sandhini Saha,Avinash Bajaj,S V S Deo,Siddhi Gupta

doi:10.1038/s41419-021-03436-x

Abstract

Global dysregulation of RNA splicing and imbalanced sphingolipid metabolism has emerged as promoters of cancer cell transformation. Here, we present specific signature of alternative splicing (AS) events of sphingolipid genes for each breast cancer subtype from the TCGA-BRCA dataset. We show that ceramide synthase 2 (CERS2) undergoes a unique cassette exon event specifically in Luminal B subtype tumors. We validated this exon 8 skipping event in Luminal B cancer cells compared to normal epithelial cells, and in patient-derived tumor tissues compared to matched normal tissues. Differential AS-based survival analysis shows that this AS event of CERS2 is a poor prognostic factor for Luminal B patients. As Exon 8 corresponds to catalytic Lag1p domain, overexpression of AS transcript of CERS2 in Luminal B cancer cells leads to a reduction in the level of very-long-chain ceramides compared to overexpression of protein-coding (PC) transcript of CERS2. We further demonstrate that this AS event-mediated decrease of very-long-chain ceramides leads to enhanced cancer cell proliferation and migration. Therefore, our results show subtype-specific AS of sphingolipid genes as a regulatory mechanism that deregulates sphingolipids like ceramides in breast tumors, and can be explored further as a suitable therapeutic target.

Highlights

Sphingolipids help in maintaining the structural integrity of cell membranes, and aid in numerous signaling processes in response to different stimuli[1,2,3]
We used ‘Normal-like’ as the reference based on the understanding that the “Normal-like” tumors probably had only a few tumor cells and a large number of normal breast epithelium[33], and they have a profile measuring nearest to the normal breast epithelium
This is evident from the large repertoire of subtype-specific cassette exon (CE) and intron retention (IR) events scored from our study on TCGA-BRCA RNA sequencing (RNA-Seq) data

Summary

Introduction

Sphingolipids help in maintaining the structural integrity of cell membranes, and aid in numerous signaling processes in response to different stimuli[1,2,3]. Dysregulation of the sphingolipid pathway is one of the important contributing factors for breast cancer pathogenesis as it is implicated in various aspects of cancer initiation, progression, invasion, metastasis, and drug resistance[4,5]. Any. Ceramides are key precursors of complex sphingolipids that are synthesized via de novo as well as through salvage pathway. De novo pathway involves conjugation of specific fatty acyl chains to sphinganine using ceramide synthases, whereas salvage pathway involves degradation of sphingomyelins and complex sphingolipids to ceramides[9]. Human breast cancer tissues usually have high expression of ceramide species as compared to normal tissue samples[10]. There is an increased expression of Official journal of the Cell Death Differentiation Association

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Conclusion