Dissecting the Transcriptional and Chromatin Accessibility Heterogeneity of Proliferating Cone Precursors in Human Retinoblastoma Tumors by Single Cell Sequencing—Opening Pathways to New Therapeutic Strategies?

Collin, Joseph; Zerti, Darin; Steel, David; Bowen, Claire; Parulekar, Manoj; Lako, Majlinda

doi:10.1167/iovs.62.6.18

Cited by 20 publications

(19 citation statements)

References 55 publications

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“…Cone precursors and retinoblastoma cells, two major cell types with different transcriptomic profiles, were identified in retinoblastoma. Coincidentally, in 2021, Collin et al also used single-cell sequencing to verify that G2/M cone precursors subset was the cell of origin for retinoblastoma [ 30 ]. This was consistent with our conclusion.…”

Section: Discussionmentioning

confidence: 99%

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

Yang

Han

et al. 2021

Cell Death Dis

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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.

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Section: Discussionmentioning

confidence: 99%

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

Yang

Han

et al. 2021

Cell Death Dis

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“…More recently, attempts also have been made to understand cellular heterogeneity and origins of RB using scRNA-seq. 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.…”

Section: Introductionmentioning

confidence: 99%

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

Yang

Xiao

et al. 2022

Cell Death Dis

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Retinoblastoma (RB) is the most common primary intraocular malignancy of childhood. It is known that the tumor microenvironment (TME) regulates tumorigenesis and metastasis. However, how the malignant progression in RB is determined by the heterogeneity of tumor cells and TME remains uncharacterized. Here, we conducted integrative single-cell transcriptome and whole-exome sequencing analysis of RB patients with detailed pathological and clinical measurements. By single-cell transcriptomic sequencing, we profiled around 70,000 cells from tumor samples of seven RB patients. We identified that the major cell types in RB were cone precursor-like (CP-like) and MKI67+ cone precursor (MKI67+ CP) cells. By integrating copy number variation (CNV) analysis, we found that RB samples had large clonal heterogeneity, where the malignant MKI67+ CP cells had significantly larger copy number changes. Enrichment analysis revealed that the conversion of CP-like to MKI67+ CP resulted in the loss of photoreceptor function and increased cell proliferation ability. The TME in RB was composed of tumor-associated macrophages (TAMs), astrocyte-like, and cancer-associated fibroblasts (CAFs). Particularly, during the invasion process, TAMs created an immunosuppressive environment, in which the proportion of TAMs decreased, M1-type macrophage was lost, and the TAMs-related immune functions were depressed. Finally, we identified that TAMs regulated tumor cells through GRN and MIF signaling pathways, while TAMs self-regulated through inhibition of CCL and GALECTIN signaling pathways during the invasion process. Altogether, our study creates a detailed transcriptomic map of RB with single-cell characterization of malignant phenotypes and provides novel molecular insights into the occurrence and progression of RB.

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“…Among those, 4 clusters expressing cone and proliferation markers were selected for further analysis as follows: (1) proliferating cone precursors (cluster 1) composed of cells in S and G2/M phase of the cell cycle ( Fig. 4B ) and characterized by high expression of cone precursors ( DCT , PDE6H , AIPL1 , TULP1 , RXRγ ), proliferation markers ( HIST1H4C , TOP2A, MKi67 , PCNA , MCM3 , CDC25A , CDC25C , CHEK1 , E2F3 , PRC1 , SKP2 , UBE2C ), and DEK , KIF14 , MYCN , SYK (characteristic for Rb) which was defined as Rb-like cluster 21 , 22 , 42 , 49 , 50 ( Fig. S7A ); (2) cluster 8 , characterized by high expression of cone precursor markers ( PDE6H , GNB3 , RXRγ , ARR3 , GNGT2 ), retinoma marker ( CDCA7 , HELLS ), and PCNA proliferation marker, but greatly reduced expression of MKi67 , which was defined as retinoma-like cluster 9 , 42 ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…S8D ). Recently, our group has published single-cell RNA-Seq of human Rb tumors, 49 which were further assessed for marker co-expression indicated above. This analysis indicated co-expression of RXRγ with Ki67 and GAP43 or ONECUT1 in G2/M cone precursors clusters 8 and 12 ( Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Advances in next generation sequencing are enabling detailed expression and epigenetic studies of tumors, providing molecular insights at the single-cell level. Our group 49 and others 43 , 51 , 61 are utilizing these tools to understand the composition of Rb tumor tissues and to determine how pRB inactivation results in aberrant RNA processing events, genome instability and changes in metabolism and mitochondria biogenesis. These insights however focus on the end stage of tumor development, which precludes detailed insights into the transcriptional events of each state cell transition during Rb development.…”

Section: Discussionmentioning

confidence: 99%

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pRB-Depleted Pluripotent Stem Cell Retinal Organoids Recapitulate Cell State Transitions of Retinoblastoma Development and Suggest an Important Role for pRB in Retinal Cell Differentiation

Rozanska

Cerna-Chavez

Collin

et al. 2022

Stem Cells Translational Medicine

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Retinoblastoma (Rb) is a childhood cancer of the developing retina, accounting for up to 17% of all tumors in infancy. To gain insights into the transcriptional events of cell state transitions during Rb development, we established 2 disease models via retinal organoid differentiation of a pRB (retinoblastoma protein)-depleted human embryonic stem cell line (RB1-null hESCs) and a pRB patient-specific induced pluripotent (iPSC) line harboring a RB1 biallelic mutation (c.2082delC). Both models were characterized by pRB depletion and accumulation of retinal progenitor cells at the expense of amacrine, horizontal and retinal ganglion cells, which suggests an important role for pRB in differentiation of these cell lineages. Importantly, a significant increase in the fraction of proliferating cone precursors (RXRγ+Ki67+) was observed in both pRB-depleted organoid models, which were defined as Rb-like clusters by single-cell RNA-Seq analysis. The pRB-depleted retinal organoids displayed similar features to Rb tumors, including mitochondrial cristae aberrations and rosette-like structures, and were able to undergo cell growth in an anchorage-independent manner, indicative of cell transformation in vitro. In both models, the Rb cones expressed retinal ganglion and horizontal cell markers, a novel finding, which could help to better characterize these tumors with possible therapeutic implications. Application of Melphalan, Topotecan, and TW-37 led to a significant reduction in the fraction of Rb proliferating cone precursors, validating the suitability of these in vitro models for testing novel therapeutics for Rb.

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Dissecting the Transcriptional and Chromatin Accessibility Heterogeneity of Proliferating Cone Precursors in Human Retinoblastoma Tumors by Single Cell Sequencing—Opening Pathways to New Therapeutic Strategies?

Abstract: Dissecting the transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human retinoblastoma tumors by single cell sequencing-opening pathways to new therapeutic strategies?.

Cited by 20 publications

References 55 publications

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

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

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

pRB-Depleted Pluripotent Stem Cell Retinal Organoids Recapitulate Cell State Transitions of Retinoblastoma Development and Suggest an Important Role for pRB in Retinal Cell Differentiation

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