Single-cell genome and transcriptome sequencing without upfront whole-genome amplification reveals cell state plasticity of melanoma subclones
Single-cell multi-omics methods enable the study of cell state diversity, which is largely determined by the interplay of the genome, epigenome, and transcriptome. Here, we describe Gtag&T-seq, a genome-and-transcriptome sequencing (G&T-seq) protocol of the same single cells that omits whole-genome amplification (WGA) by using direct genomic tagmentation (Gtag). Gtag drastically decreases the cost and improves coverage uniformity at single-cell and pseudo-bulk levels compared to WGA-based G&T-seq. We also show that transcriptome-based DNA copy number inference has limited resolution and accuracy, underlining the importance of affordable multi-omic approaches. Applying Gtag&T-seq to a melanoma xenograft model before treatment and at minimal residual disease revealed differential cell state plasticity and treatment response between cancer subclones. In summary, Gtag&T-seq is a low-cost and accurate single-cell multi-omics method that explores genetic alterations and their functional consequences in single cells at scale.
Authors
- Aljosja Rogiers (ORCID: https://orcid.org/0000-0002-3807-9696)
- Jean‐Christophe Marine (ORCID: https://orcid.org/0000-0003-2433-9837)
- Jonas Demeulemeester (ORCID: https://orcid.org/0000-0002-2660-2478)
- Daniel V. Brown (ORCID: https://orcid.org/0000-0002-3594-5851)
- Eleonora Leucci (ORCID: https://orcid.org/0000-0002-2898-748X)
- Thierry Voet (ORCID: https://orcid.org/0000-0003-1204-9963)
- Florian Rambow (ORCID: https://orcid.org/0000-0002-9727-8986)
- Nina Van Raemdonck (ORCID: https://orcid.org/0000-0002-8913-6275)
- Alejandro Sifrim (ORCID: https://orcid.org/0000-0001-8247-4020)
- I. Claes
- Oskar Marín-Béjar (ORCID: https://orcid.org/0000-0002-6889-6566)
- Koen Theunis (ORCID: https://orcid.org/0000-0002-0699-6676)
- Michiel Van der Haegen (ORCID: https://orcid.org/0000-0002-6564-8057)
- Sebastiaan Vanuytven (ORCID: https://orcid.org/0000-0001-6723-0132)
- Jarne Geurts (ORCID: https://orcid.org/0000-0002-1194-781X)
Institutions
- Walter and Eliza Hall Institute of Medical Research (AU)
- Cancer Institute (WIA) (IN)
- VIB-KU Leuven Center for Cancer Biology (BE)
- KU Leuven (BE)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-02-21
- DOI
- https://doi.org/10.1093/nar/gkaf173
- Citations
- 6
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 4.84
Funders
- Melanoma Research Alliance
- Marie Curie
- Fonds Wetenschappelijk Onderzoek
- KU Leuven
- Vlaams Instituut voor Biotechnologie
- Stichting Tegen Kanker
- Kom op tegen Kanker
- Fondation contre le Cancer
- European Social Fund