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?
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?
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DOI：
10.1167/iovs.62.6.18
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发表时间：
2021-05-03
影响因子：
4.4
通讯作者：
Lako M
中科院分区：
文献类型：
--
作者：
Collin J;Queen R;Zerti D;Steel DH;Bowen C;Parulekar M;Lako M
视网膜母细胞瘤 (Rb) 是一种在视网膜发育过程中由于 RB1 基因突变而产生的恶性肿瘤。 RB1 两个拷贝的丢失或失活会导致视网膜母细胞瘤的发生；然而，肿瘤的持续生长和扩散需要额外的基因改变。离体研究表明，在人类中，视网膜母细胞瘤可能始于 RB1 耗尽的视锥细胞前体细胞。尽管如此，尚不可能在体内评估肿瘤本身内的全谱克隆类型以及起源细胞发生的分子变化，从而使其恶性转化。为了克服这些挑战，我们对原发性肿瘤组织进行了首次单细胞 (sc) RNA 和 ATAC-Seq 分析，使我们能够剖析人类 Rb 肿瘤中增殖锥体前体的转录和染色质可及性异质性。将两个分别具有两个致病性 RB1 突变的 Rb 肿瘤解离为单细胞，并使用 10× Genomics 平台进行 scRNA-Seq 和 scATAC-Seq。此外，9 个人类胚胎和胎儿视网膜样本被分离成单细胞并进行 scRNA 和 ATAC-Seq 分析。 scRNA 和 ATAC-Seq 数据使用统一流形近似和投影进行嵌入，并使用基于 Seurat 图的聚类进行聚类。对 Rb 肿瘤和人胚胎/胎儿视网膜样本进行集成 scATAC-Seq 分析，以鉴定 Rb 锥体富集的亚簇。使用 Monocle 对 Rb 样品中的增殖锥体进行伪时间分析。 Ingenuity Pathway Analysis 用于识别 Rb 锥体富集亚簇中的信号通路和上游调节因子。我们的单细胞分析揭示了 Rb 肿瘤中细胞周期不同阶段的锥体前体的主要存在，以及将 G2/M 子集确定为起源细胞类型的肿瘤中。 scATAC-Seq 分析鉴定出两个富含 Rb 的视锥亚簇，每个亚簇的特征是激活不同的上游调节因子和信号通路，使增殖的视锥前体能够逃避细胞周期停滞和/或凋亡。我们的研究提供了 Rb 肿瘤异质性的证据，并定义了可用于确定新治疗策略的分子途径。
Retinoblastoma (Rb) is a malignant neoplasm arising during retinal development from mutations in the RB1 gene. Loss or inactivation of both copies of RB1 results in initiation of retinoblastoma tumors; however, additional genetic changes are needed for the continued growth and spread of the tumor. Ex vivo research has shown that in humans, retinoblastoma may initiate from RB1-depleted cone precursors. Notwithstanding, it has not been possible to assess the full spectrum of clonal types within the tumor itself in vivo and the molecular changes occurring at the cells of origin, enabling their malignant conversion. To overcome these challenges, we have performed the first single cell (sc) RNA- and ATAC-Seq analyses of primary tumor tissues, enabling us to dissect the transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human Rb tumors. Two Rb tumors each characterized by two pathogenic RB1 mutations were dissociated to single cells and subjected to scRNA-Seq and scATAC-Seq using the 10× Genomics platform. In addition, nine human embryonic and fetal retina samples were dissociated to single cells and subjected to scRNA- and ATAC-Seq analyses. The scRNA- and ATAC-Seq data were embedded using Uniform Manifold Approximation and Projection and clustered with Seurat graph–based clustering. Integrated scATAC-Seq analysis of Rb tumors and human embryonic/fetal retina samples was performed to identify Rb cone enriched subclusters. Pseudo time analysis of proliferating cones in the Rb samples was performed with Monocle. Ingenuity Pathway Analysis was used to identify the signaling pathway and upstream regulators in the Rb cone–enriched subclusters. Our single cell analyses revealed the predominant presence of cone precursors at different stages of the cell cycle in the Rb tumors and among those identified the G2/M subset as the cell type of origin. scATAC-Seq analysis identified two Rb enriched cone subclusters, each characterized by activation of different upstream regulators and signaling pathways, enabling proliferating cone precursors to escape cell cycle arrest and/or apoptosis. Our study provides evidence of Rb tumor heterogeneity and defines molecular pathways that can be targeted to define new treatment strategies.
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影响因子：
11.2
作者：
Brennan RC;Federico S;Bradley C;Zhang J;Flores-Otero J;Wilson M;Stewart C;Zhu F;Guy K;Dyer MA
通讯作者：
Dyer MA
在发育，重编程和肿瘤发生过程中，视网膜的动态表观遗传景观。
影响因子：
16.2
作者：
Aldiri I;Xu B;Wang L;Chen X;Hiler D;Griffiths L;Valentine M;Shirinifard A;Thiagarajan S;Sablauer A;Barabas ME;Zhang J;Johnson D;Frase S;Zhou X;Easton J;Zhang J;Mardis ER;Wilson RK;Downing JR;Dyer MA;St. Jude Children’s Research Hospital—Washington University Pediatric Cancer Genome Project
通讯作者：
St. Jude Children’s Research Hospital—Washington University Pediatric Cancer Genome Project
DOI：
10.1007/s00249-016-1144-z
发表时间：
2016-10
影响因子：
2
作者：
Buchanan, Paul J.;McCloskey, Karen D.
通讯作者：
McCloskey, Karen D.
影响因子：
8.8
作者：
Diacou, Raven;Zhao, Yilin;Liu, Wei
通讯作者：
Liu, Wei
影响因子：
30.8
作者：
Cao, Qin;Anyansi, Christine;Yip, Kevin Y.
通讯作者：
Yip, Kevin Y.