High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors

Single-cell nanopore sequencing of full-length mRNAs transforms single-cell multi-omics studies. However, challenges include high sequencing errors and dependence on short-reads and/or barcode whitelists. To address these, we develop scNanoGPS to calculate same-cell genotypes (mutations) and phenotypes (gene/isoform expressions) without short-read nor whitelist guidance. We apply scNanoGPS onto 23,587 long-read transcriptomes from 4 tumors and 2 cell-lines. Standalone, scNanoGPS deconvolutes error-prone long-reads into single-cells and single-molecules, and simultaneously accesses both phenotypes and genotypes of individual cells. Our analyses reveal that tumor and stroma/immune cells express distinct combination of isoforms (DCIs). In a kidney tumor, we identify 924 DCI genes involved in cell-type-specific functions such as PDE10A in tumor cells and CCL3 in lymphocytes. Transcriptome-wide mutation analyses identify many cell-type-specific mutations including VEGFA mutations in tumor cells and HLA-A mutations in immune cells, highlighting the critical roles of different mutant populations in tumors. Together, scNanoGPS facilitates applications of single-cell long-read sequencing technologies.

Anaplastic transformation in thyroid cancer revealed by single cell transcriptomics

The deadliest anaplastic thyroid cancer (ATC) often transforms from indolent differentiated thyroid cancer (DTC); however, the complex intra-tumor transformation process is poorly understood. We investigated an anaplastic transformation model by dissecting both cell lineage and cell fate transitions using single cell transcriptomes and genetic alteration data from patients with different subtypes of thyroid cancer. The resulting spectrum of ATC transformation included stress-responsive DTC cells, inflammatory ATC cells (iATCs), mitotic-defective ATC cells and extended all the way to mesenchymal ATC cells (mATCs). Further, our analysis identified two important milestones: 1) a diploid stage, where iATC cells were diploids with inflammatory phenotypes, and 2) an aneuploid stage, where mATCs gained aneuploid genomes and mesenchymal phenotypes producing excessive collagens and collagen-interacting receptors. In parallel, cancer-associated-fibroblasts showed strong interactions among mesenchymal cell-types, macrophages shifted from M1 to M2 states, and T cells reprogrammed from cytotoxic to exhausted states, highlighting new therapeutic opportunities for ATC.

Abstract 3131: Anaplastic transformation model in thyroid cancer revealed by single cell lineage and fate analysis

The deadliest anaplastic thyroid cancer (ATC) often transforms from indolent differentiated thyroid cancer (DTC), however the complex intra-tumor transformation process is poorly understood. We investigated an anaplastic transformation model by dissecting both cell lineage and cell fate transitions using single cell transcriptomes and genetic alterations data of patients with different subtypes of thyroid cancer. The resulting model started from stress-responsive DTC cells to inflammatory ATC cells, to mitotic defective ATC cells and extended all the way to mesenchymal ATC cells. In parallel with tumor cell evolution, macrophages shifted from anti-tumor to tumor-promoting states and T cells reprogrammed from cytotoxic to exhausted states. Further, our analysis identified two important milestones: 1) diploid stage, where ATC cells were commonly diploids with non-RAS mutations and inflammatory phenotypes. 2) aneuploid stage, where ATC cells gained aneuploidy with frequent RAS mutations and mesenchymal phenotypes leading to the extreme lethal stage of ATC progression.

Citation Format: Lina Lu, Jennifer Rui Wang, Ying C. Henderson, Shanshan Bai, Jie Yang, Min Hu, Yuanqing Yan, Tuan M Tran, Jianzhuo Li, Cheng-Kai Shiau, Rachel Kieser, Xiao Zhao, Jiping Wang, Roza Nurieva, Michelle D. Williams, Maria E. Cabanillas, Ramona Dadu, Naifa Lamki Busaidy, Mark Zafereo, Nicholas Navin, Stephen Y. Lai, Ruli Gao. Anaplastic transformation model in thyroid cancer revealed by single cell lineage and fate analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3131.

Delineating genotypes and phenotypes of individual cells from long-read single cell transcriptomes

Single-cell nanopore sequencing of full-length mRNAs (scNanoRNAseq) is transforming singlecell multi-omics studies. However, challenges include computational complexity and dependence on short-read curation. To address this, we developed a comprehensive toolkit, scNanoGPS to calculate same-cell genotypes-phenotypes without short-read guidance. We applied scNanoGPS onto 23,587 long-read transcriptomes from 4 tumors and 2 cell lines. Standalone, scNanoGPS accurately deconvoluted error-prone long-reads into single-cells and single-molecules. Further, scNanoGPS simultaneously accessed both phenotypes (expressions/isoforms) and genotypes (mutations) of individual cells. Our analyses revealed that tumor and stroma/immune cells often expressed significantly distinct combinations of isoforms (DCIs). In a kidney tumor, we identified 924 genes with DCIs involved in cell-type-specific functions such as PDE10A in tumor cells and CCL3 in lymphocytes. Moreover, transcriptome-wide mutation analyses identified many cell-type-specific mutations including VEGFA mutations in tumor cells and HLA-A mutations in immune cells, highlighting critical roles of different populations in tumors. Together, scNanoGPS facilitates applications of single-cell long-read sequencing.

Abstract 93: Single cell transcriptome analysis maps dynamic epithelial mesenchymal transition and immunological remodeling in thyroid cancer progression

Anaplastic thyroid cancer (ATC) is arguably the most lethal human malignancy, with a median survival of ~12 weeks. About half of ATC tumors arise from within differentiated forms of thyroid cancer types, most commonly papillary thyroid cancer (PTC), suggesting an evolutionary continuum from PTC to ATC. In contrast to the extreme lethality of ATC, PTC are typically indolent with long life-histories. The molecular mechanisms driving ATC progression from PTC have been challenging to resolve, mostly due to the heterogenous cellular populations that are undergoing dynamic changes during ATC progression. In this study, we applied high throughput 3'-scRNAseq in an unbiased analysis of cell populations in thyroid tumors. We analyzed 90,990 single cell transcriptomes from 8 ATC tumors, 8 PTC tumors and 5 normal thyroids. To make the precise inference of tumor cell lineages, we stratified the epithelial cells into 5 categories by calculating genotypes from scRNAseq data that include: (1) normal epithelial cells in normal thyroids, (2) PTC epithelial cells in PTC tumors, (3) PTC tumor cells in PTC tumors, (4) ATC epithelial cells in ATC tumors, (5) ATC tumor cells in ATC tumors. We then constructed the full epithelial cell development trajectories from normal epithelial to PTC and ATC tumor cells. Our results show that co-existing epithelial and mesenchymal phenotypes is a major characteristic of ATC tumor cells and epithelial-mesenchymal transition (EMT) drives ATC developmental trajectory. We further analyzed the transcriptional programs of immune cell types and their interactions with tumor cells. Our data suggested a unique sub-population of helper T cell and a distinct B cell subtype arise in the tumor microenvironment in response to ATC progression. Collectively, our results identify EMT as the major driving force of thyroid cancer aggressiveness and provide novel insights regarding the immunological remodeling in response to ATC progression.

Citation Format: Xi Chen, Jennifer Rui Wang, Ying Henderson, Yuanqing Yan, Shanshan Bai, Rachel Kieser, Min Hu, Jiping Wang, Nicholas Navin, Stephen Lai, Ruli Gao. Single cell transcriptome analysis maps dynamic epithelial mesenchymal transition and immunological remodeling in thyroid cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 93.