Single-cell transcriptome profiling reveals intratumoural heterogeneity and malignant progression in retinoblastoma

Abstract

Retinoblastoma is a childhood retinal tumour that is the most common primary malignant intraocular tumour. However, it has been challenging to identify the cell types associated with genetic complexity. Here, we performed single-cell RNA sequencing on 14,739 cells from two retinoblastoma samples to delineate the heterogeneity and the underlying mechanism of retinoblastoma progression. Using a multiresolution network-based analysis, we identified two major cell types in human retinoblastoma. Cell trajectory analysis yielded a total of 5 cell states organized into two main branches, and the cell cycle-associated cone precursors were the cells of origin of retinoblastoma that were required for initiating the differentiation and malignancy process of retinoblastoma. Tumour cells differentiation reprogramming trajectory analysis revealed that cell-type components of multiple tumour-related pathways and predominantly expressed UBE2C were associated with an activation state in the malignant progression of the tumour, providing a potential novel “switch gene” marker during early critical stages in human retinoblastoma development. Thus, our findings improve our current understanding of the mechanism of retinoblastoma progression and are potentially valuable in providing novel prognostic markers for retinoblastoma.

Spatial transcriptomic profiling of human retinoblastoma

“…Consistent with previous scRNA-seq studies in RB 5,11,12 , our results highlighted high intratumoral heterogeneity in RB. We identified 10 subpopulations representing different stages of RB with varying malignancy.…”

“…Early mouse studies suggest that RB can arise from amacrine cells 84 , horizontal cells 85 or Müller glia cells 86 . In contrast, recent studies point to cone precursors as the origin of RB in humans 5,11,12,20 . Consistent with this, we showed a dominant presence of cone precursors in RB tumor, as well as presence of highly proliferated cone precursors, CAFs and glial cells to form a complex TME.…”

“…Recent studies using human pluripotent stem cells and retinal organoids provided a valuable in vitro model to study the cellular abnormalities caused by biallelic mutations of the RB1 9,10 . In addition, to study the cellular heterogeneity of RB, a number of recent studies have profiled primary RB tumors using single cell RNAseq (scRNA-seq) 5,11,12 , advancing our understanding of the cellular origin of RB and the pathological mechanisms driving RB. However, these single cell transcriptomic datasets do not retain structural information which would be important to study the collective tissue architecture of RB.…”

Single-cell characterization of malignant phenotypes and microenvironment alteration in retinoblastoma

“…Therefore, it is important to understand how the intratumoral heterogeneity and microenvironment are related to the occurrence and malignant degrees of RB, which will facilitate development of new treatment strategy of RB. Recently, two RB single-cell studies [ 22 , 23 ] discussed the heterogeneity of RB tumors. Because these two studies included only two samples, with a relatively small number of cells (8086/14,739), they did not identify many rare cell types, such as CAF, TAM, and astrocyte-like, which had been confirmed to exist in RB [ 11 ].…”

“…Collin et al [ 22 ] revealed G2/M cone precursors as the cell of origin in RB. Yang et al [ 23 ] revealed that the RB cells originated from the cell cycle-assoicated cone precursors. However, due to the limited number of cells (8086/14,739) and samples (two samples) in these two studies, how the malignant progression in RB is determined by the heterogeneity of tumor cells and TME remains uncharacterized.…”