Mel285 and Mel290: the odd two out

Abstract

Purpose : In uveal melanoma (UM) research, several established primary and metastatic cell lines are available worldwide and are frequently used in preclinical studies. These previous studies showed that UM cell lines differ substantially from each other, both in genotype and phenotype. Cell lines Mel285 and Mel290 lack expression of melanoma markers and do not harbour a typical GNAQ or GNA11 mutation, even if the primary tumour of Mel285 has a GNA11 mutation Q209L. We aimed at better classifying Mel285 and Mel290 and understanding if the genetic differences could be the cause of the different protein and mRNA expression profiles.

Methods : We studied a cohort of 14 UM cell lines with proteomics and RNA sequencing (RNAseq), determined the presence of Single Nucleotide Variants (SNV) and small Insertions and Deletions (InDel) with next generation sequencing (NGS) and chromosomal abnormalities with single nucleotide polymorphism (SNP) array.

Results : Mel285 has several chromosome copy number alterations, among which 1p loss, loss of 3p, partial loss of 3q and loss of 8q, while Mel290 shows loss of 1p and of the entire chromosome 6. NGS shows that Mel285 and Mel290 lack typical UM mutations, including those in CYSLTR2 or PLCB4. The results of proteomics and RNASeq analyses are very similar to each other. In PCA plots, Mel285 and Mel290 cluster separately from both BAP1-positive and BAP1-negative cell lines (Figure 1). New differential expression analysis shows that melanocyte-related markers and pathways are downregulated in Mel285 and Mel290 compared to the GNA-mutated cell lines (Figure 2).

Conclusions : While Mel285 and Mel290 share similar RNAseq and proteomic patterns, and their chromosome aberrations resemble those in UM, the data from proteomics, RNASeq and NGS show that Mel285 and Mel290 belong to a separate group than other analysed UM cell lines. Therefore, they may not be representative models to test potential therapeutic targets for UM.

This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.

 

Figure 1: PCA plots showing distances between cell lines. 1a: Normalised protein abundance data, each cell line plotted in triplicate. Blue = BAP1 negative, Orange = BAP1 positive. (Proteome Discoverer) 1b: Vst-transformed RNAseq data. (ggplot2).

 

Figure 2: Heatmaps showing expression of pigment-related genes, euclidean distances, scaled after clustering, 1a: Grouped protein abundance, one value per cell line. (Proteome Discoverer) 2b: Vst-transformed RNAseq data. (heatmap.2)