High-throughput Single-cell Method Research Articles

Abstract 6937: High throughput single cell simultaneous DNA and RNA sequencing identified cell-of-origin of breast cancer

Abstract Understanding the relationship between genotype and phenotype in breast cancer cells has been challenging at single cell resolution, mainly because existing high-throughput methods are limited to measuring a single modality and data must be integrated indirectly via computational methods. To address this challenge, we developed wellDR-seq, a high-throughput single cell method that can simultaneously measure the single cell whole genome and transcriptome directly from thousands of single cells in parallel. Using this method, we profiled 17,427 single cells in 6 different ER+ breast cancer patients with either premalignant disease (Ductal-carcinoma-in-situ) or invasive ductal carcinoma (IDC). From these data we identified the epithelial cell-of-origin in 3 cases, showing that ER+ breast cancer cells originated from Luminal Hormone Responsive (LumHR) in the normal breast tissues. We also found that autosomal somatic copy number aberrations were exclusively present in LumSec (< 2%) and LumHR epithelial cells, while chrX gain or loss also occurred in stromal cells (eg fibroblast and endothelial) but a low frequency (<2%) in our datasets. Additionally, our data show the impact of subclonal copy number profiles on gene expression programs, which reflects both gene dosage effects in CNA regions and more complex deregulation in copy-neutral regions. wellDR-seq offers a powerful tool for large-scale single cell genome and transcriptome simultaneous sequencing across different clinical samples, opens new avenue to investigate genotype and phenotypes interactions, identify tumor cells origins, reveal somatic copy number and mutation events, quantify the gene dosage effect and discerning differential genes expression between tumor subclones. Citation Format: Kaile Wang, Rui Ye, Shanshan Bai, Zhenna Xiao, Lei Yano, Jianzhuo Li, Yiyun Lin, Emi Sei, Steven Lin, Alastair Thompson, Savitri Krishnamurthy, Nicholas Navin. High throughput single cell simultaneous DNA and RNA sequencing identified cell-of-origin of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6937.

HSPCs display within-family homogeneity in differentiation and proliferation despite population heterogeneity.

High-throughput single-cell methods have uncovered substantial heterogeneity in the pool of hematopoietic stem and progenitor cells (HSPCs), but how much instruction is inherited by offspring from their heterogeneous ancestors remains unanswered. Using a method that enables simultaneous determination of common ancestor, division number, and differentiation status of a large collection of single cells, our data revealed that murine cells that derived from a common ancestor had significant similarities in their division progression and differentiation outcomes. Although each family diversifies, the overall collection of cell types observed is composed of homogeneous families. Heterogeneity between families could be explained, in part, by differences in ancestral expression of cell surface markers. Our analyses demonstrate that fate decisions of cells are largely inherited from ancestor cells, indicating the importance of common ancestor effects. These results may have ramifications for bone marrow transplantation and leukemia, where substantial heterogeneity in HSPC behavior is observed.

Bugs split to attack and gamble to survive.

Bugs split to attack and gamble to survive.