Inferring Copy Number from Triple-Negative Breast Cancer Patient Derived Xenograft scRNAseq Data Using scCNA.
Cancer heterogeneity
Copy number aberration
Genomics
Inferred copy number
Single-cell RNA sequencing
Triple-negative breast cancer
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
30
9
2021
pubmed:
1
10
2021
medline:
6
1
2022
Statut:
ppublish
Résumé
Cancer can develop from an accumulation of alterations, some of which cause a nonmalignant cell to transform to a malignant state exhibiting increased rate of cell growth and evasion of growth suppressive mechanisms, eventually leading to tissue invasion and metastatic disease. Triple-negative breast cancers (TNBC) are heterogeneous and are clinically characterized by the lack of expression of hormone receptors and human epidermal growth factor receptor 2 (HER2), which limits its treatment options. Since tumor evolution is driven by diverse cancer cell populations and their microenvironment, it is imperative to map TNBC at single-cell resolution. Here, we describe an experimental procedure for isolating a single-cell suspension from a TNBC patient-derived xenograft, subjecting it to single-cell RNA sequencing using droplet-based technology from 10× Genomics and analyzing the transcriptomic data at single-cell resolution to obtain inferred copy number aberration profiles, using scCNA. Data obtained using this single-cell RNA sequencing experimental and analytical methodology should enhance our understanding of intratumor heterogeneity which is key for identifying genetic vulnerabilities and developing effective therapies.
Identifiants
pubmed: 34590283
doi: 10.1007/978-1-0716-1740-3_16
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
285-303Informations de copyright
© 2021. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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