High Throughput Single Cell Long-Read Sequencing Analyses of Same-Cell Genotypes and Phenotypes in Human Tumors

Authors

Cheng-Kai Shiau
Lina Lu
Rachel Kieser
Kazutaka Fukumura
Timothy Pan
Hsiao-Yun Lin
Jie Yang
Eric L Tong
GaHyun Lee
Yuanqing Yan
Jason T Huse
Ruli Gao

Publication Date

7-11-2023

Journal

Nature Communications

Abstract

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.

Keywords

Humans, Genotype, High-Throughput Nucleotide Sequencing, Phenotype, Carcinoma, Intraductal, Noninfiltrating, Kidney Neoplasms, Phosphoric Diester Hydrolases

Comments

Supplementary Material

PMID: 37433798

DOI

10.1038/s41467-023-39813-7

PMID

37433798

PMCID

PMC10336110

PubMedCentral® Posted Date

July 2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes