Proteotranscriptomic Characterization of Human Retinoblastoma

Background: Retinoblastoma is a rare pediatric eye cancer caused by mutations in the RB1 gene, which regulates retinal cell growth. Early detection and treatment are critical for pre-venting vision loss and improving survival outcomes. This study aimed to perform an inte-grated proteotranscriptomic characterization of human retinoblastoma to provide a deeper understanding of disease biology and to identify novel therapeutic targets. Methods: Paired tumor and adjacent retinal tissue samples were dissected from seven eyes affected by retinoblastoma. The global transcriptome and proteome were determined using RNA sequencing and liquid chromatography-mass spectrometry from the same samples. The spatially resolved cellular landscape was assessed using Imaging Mass Cytometry (IMC). Results: The correlation between RNA and protein level was moderate (Pearson’s R = 0.339, p < 10-16) with variations across different pathways. While biological processes like visual perception were similarly regulated on the RNA and protein level, others, such as cell cycle processes and glycolysis were predominantly active at the protein level. IMC identified more than 67,000 single cells in distinct clusters, including antigen presenting cells, T cells, stroma cells, vascular cells and two clusters of proliferating and CD44/c-Myc positive tumor cells. In retinoblastoma, we observed increased apoptotic signals in T cells and higher ex-pression of CD68 in antigen presenting cells compared to control tissue. Conclusions: Retinoblastoma's key biological processes are predominantly regulated at either the RNA or protein level, underscoring the value of an integrated proteotranscriptomic approach. Elevated caspase 3 activity in tumor-associated T cells may indicate potential im-mune escape mechanisms and CD44+ and high-c-Myc-expressing tumor cells may repre-sent cancer stem cells with possible involvement in metastasis, warranting further validation. Our multilayered approach could pave the way for enhanced molecular assessments and novel targeted therapies for human retinoblastoma.