Alignment of single-cell trajectories by tuMap enables high-resolution quantitative comparison of cancer samples.
cancer metric
quantitative comparison of cancer samples
single-cell trajectories
tailored alignment
trajectory alignment
Journal
Cell systems
ISSN: 2405-4720
Titre abrégé: Cell Syst
Pays: United States
ID NLM: 101656080
Informations de publication
Date de publication:
19 01 2022
19 01 2022
Historique:
received:
17
01
2020
revised:
20
06
2021
accepted:
09
09
2021
pubmed:
9
10
2021
medline:
20
4
2022
entrez:
8
10
2021
Statut:
ppublish
Résumé
Single-cell technologies allow characterization of cancer samples as continuous developmental trajectories. Yet, the obtained temporal resolution cannot be leveraged for a comparative analysis due to the large phenotypic heterogeneity existing between patients. Here, we present the tuMap algorithm that exploits high-dimensional single-cell data of cancer samples exhibiting an underlying developmental structure to align them with the healthy development, yielding the tuMap pseudotime axis that allows their systematic, meaningful comparison. We applied tuMap on single-cell mass cytometry data of acute lymphoblastic and myeloid leukemia to reveal associations between the tuMap pseudotime axis and clinics that outperform cellular assignment into developmental populations. Application of the tuMap algorithm on single-cell RNA sequencing data further identified gene signatures of stem cells residing at the very-early parts of the cancer trajectories. The quantitative framework provided by tuMap allows generation of metrics for cancer patients evaluation.
Identifiants
pubmed: 34624253
pii: S2405-4712(21)00340-9
doi: 10.1016/j.cels.2021.09.003
pmc: PMC8776581
mid: NIHMS1747399
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
71-82.e8Subventions
Organisme : NIAID NIH HHS
ID : P01 AI153559
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA231325
Pays : United States
Informations de copyright
Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests S.S.S.-O. and E.S. hold equity in and consult for CytoReason. The remaining authors declare no competing interests.
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