RNA Sequencing-Based Identification of Ganglioside GD2-Positive Cancer Phenotype

Abstract

The tumor-associated ganglioside GD2 represents an attractive target for cancer immunotherapy. GD2-positive tumors are more responsive to such targeted therapy, and new methods are needed for the screening of GD2 molecular tumor phenotypes. In this work, we built a gene expression-based binary classifier predicting the GD2-positive tumor phenotypes. To this end, we compared RNA sequencing data from human tumor biopsy material from experimental samples and public databases as well as from GD2-positive and GD2-negative cancer cell lines, for expression levels of genes encoding enzymes involved in ganglioside biosynthesis. We identified a 2-gene expression signature combining ganglioside synthase genes ST8SIA1 and B4GALNT1 that serves as a more efficient predictor of GD2-positive phenotype (Matthews Correlation Coefficient (MCC) 0.32, 0.88, and 0.98 in three independent comparisons) compared to the individual ganglioside biosynthesis genes (MCC 0.02–0.32, 0.1–0.75, and 0.04–1 for the same independent comparisons). No individual gene showed a higher MCC score than the expression signature MCC score in two or more comparisons. Our diagnostic approach can hopefully be applied for pan-cancer prediction of GD2 phenotypes using gene expression data.

Exploiting Gangliosides for the Therapy of Ewing’s Sarcoma and H3K27M-Mutant Diffuse Midline Glioma

“…This hypothesis, however, needs to be further validated. Recently, a two-gene signature composed of ST8SIA1 + B4GALNT1 has been suggested as efficient predictor of GD2-positive phenotype [ 56 ]. It is possible that GD2-negative clones formed the metastasis in the first instance, and that GD2 was subsequently re-expressed due to an uneven distribution of large molecules such as antibodies in huge tumors.…”

RNA Sequencing Data for FFPE Tumor Blocks Can Be Used for Robust Estimation of Tumor Mutation Burden in Individual Biosamples

“…It was recently published that RNAseq data can serve as the alternative to immunohistochemical tests for several major cancer markers like HER2, ESR1, PGR, and PD-L1 ( 22 ). It can reliably estimate concentrations of cancer drug targets ( 53 ), which is also true for the emerging non-protein molecular target ganglioside GD2 ( 27 ). In addition, RNAseq data obtained for FFPE biosamples may be used to identify clinically actionable or new fusion oncogenes ( 26 ) and to generate gene signatures that can establish statuses of important tumor biomarkers like microsatellite instability ( 25 , 54 , 55 ) and oncogenic mutations ( 56 ) or that can predict individual sensitivity of a tumor to targeted ( 28 , 57 , 58 ) and non-targeted ( 59 ) therapies.…”

“…RNA sequencing was performed according to the previous protocol used to generate ANTE collection of healthy tissue RNAseq profiles (23) and several cancer expression collections (22,(24)(25)(26)(27)(28). To isolate RNA preps, 10-mM-thick paraffin slices were trimmed from each FFPE tissue block with a microtome.…”

Evaluation and Optimization of Poly-d-Lysine as a Non-Natural Cationic Polypeptide for Gene Transfer in Neuroblastoma Cells

“…This would open new possibilities to target using siRNAs certain genes related to neuroblastomas such as MYCN, which is overexpressed in more than 25% of high-risk diagnosed patients [ 55 , 56 ]. Other candidates for targeting include the ST8SIA1 and B4GALNT1 genes, which are directly involved in the synthesis of GD2 [ 57 , 58 ], a glycosylated lipid molecule belonging to the class of glycosphingolipids, which are involved in the adhesion of cancerous cells to the extracellular matrix.…”