Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing
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Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for resolving transcriptional heterogeneity. However, its application to studying cancerous tissues is currently hampered by the lack of coverage across key mutation hotspots in the vast majority of cells; this lack of coverage prevents the correlation of genetic and transcriptional readouts from the same single cell. To overcome this, we developed TARGET-seq, a method for the high-sensitivity detection of multiple mutations within single cells from both genomic and coding DNA, in parallel with unbiased whole-transcriptome analysis. Applying TARGET-seq to 4,559 single cells, we demonstrate how this technique uniquely resolves transcriptional and genetic tumor heterogeneity in myeloproliferative neoplasms (MPN) stem and progenitor cells, providing insights into deregulated pathways of mutant and non-mutant cells. TARGET-seq is a powerful tool for resolving the molecular signatures of genetically distinct subclones of cancer cells.
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The IGP-specific gene signature was highly specific to neutrophils in an available dataset of immune cells under inflammatory conditions (COVID-19), providing evidence against a general inflammatory signature and further supporting the predicted lineage fate.
“We identified that the IGP-specific gene signature was highly specific to neutrophils, providing evidence against a general inflammatory signature and further supporting the predicted lineage fate ( Fig. 1i ).”
From Type 1 interferon perturbates clonal competition by reshaping human blood development (2026) · cites this paper as [38]
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STAR: ultrafast universal RNA-seq aligner
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- Authors
- Rodriguez-Meira, A., Buck, G., Clark, S.-A., Povinelli, B. J., Alcolea, V., Louka, E., McGowan, S., Hamblin, A., Sousos, N., Barkas, N., Giustacchini, A., Psaila, B., Jacobsen, S. E. W., Thongjuea, S., & Mead, A. J.
- Affiliations
- University of Oxford (GB)
- National Institute for Health and Care Research (GB)
- Karolinska University Hospital (SE)
- Corresponding author
- Mead, Adam J.
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2019-03
- Volume
- 73
- Issue
- 6
- Pages
- 1292-1305.e8
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC6436961
- OpenAlex
- W2901656544
- Cited by
- 305
- References
- 9
- Citations by year
- 2026: 24 · 2025: 34 · 2024: 42 · 2023: 51 · 2022: 47 · 2021: 46 · 2020: 44 · 2019: 16
- FWCI
- 12.65
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Molecular Cell (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- Medical Research Council (MRC) Senior Clinical FellowshipMedical Research Council (MRC) Senior Clinical Fellowship (MR/L006340/1)
- Cancer Research UK (CRUK) DPhil Prize StudentshipCancer Research UK (CRUK) DPhil Prize Studentship (C5255/A20936)
- MRC Molecular Haematology Unit (MC_UU_12009/5)
- MRC Weatherall Institute of Molecular Medicine
- Oxford Consortium for Single-Cell Biology (MR/M00919X/1)
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre
- WIMM Flow Cytometry Facility
- MRC Human Immunology Unit (MC_UU_12009)
- John Fell Fund (131/030, 101/517, CF182, CF170)
- WIMM Strategic Alliance (G0902418, MC_UU_12025))
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- intratumoral heterogeneity, single-cell RNA sequencing, myeloproliferative neoplasms, cancer stem cells, progenitor cells, tumor subclones, mutational hotspots, transcriptional heterogeneity
- MeSH terms
- DNA Mutational Analysis, Humans, Leukemia, Mutation, Schizosaccharomyces, Biomarkers, Tumor, Reproducibility of Results, Sequence Analysis, RNA, Genetic Heterogeneity, Jurkat Cells, K562 Cells, Single-Cell Analysis, High-Throughput Nucleotide Sequencing
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