SinCMat: A single-cell-based method for predicting functional maturation transcription factors

cell engineering; cellular therapy; functional cell maturation; scRNA-seq; transcription factors; Cell Biology; Developmental Biology; Genetics; Biochemistry

Abstract :

[en] A major goal of regenerative medicine is to generate tissue-specific mature and functional cells. However, current cell engineering protocols are still unable to systematically produce fully mature functional cells. While existing computational approaches aim at predicting transcription factors (TFs) for cell differentiation/reprogramming, no method currently exists that specifically considers functional cell maturation processes. To address this challenge, here, we develop SinCMat, a single-cell RNA sequencing (RNA-seq)-based computational method for predicting cell maturation TFs. Based on a model of cell maturation, SinCMat identifies pairs of identity TFs and signal-dependent TFs that co-target genes driving functional maturation. A large-scale application of SinCMat to the Mouse Cell Atlas and Tabula Sapiens accurately recapitulates known maturation TFs and predicts novel candidates. We expect SinCMat to be an important resource, complementary to preexisting computational methods, for studies aiming at producing functionally mature cells.

Disciplines :

Life sciences: Multidisciplinary, general & others

Author, co-author :

BARVAUX, Sybille ^✱; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Computational Biology

OKAWA, Satoshi ; University of Luxembourg

DEL SOL MESA, Antonio ^✱; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Computational Biology

^✱ These authors have contributed equally to this work.

External co-authors :

yes

Language :

English

Title :

SinCMat: A single-cell-based method for predicting functional maturation transcription factors

Original title :

[en] SinCMat: A single-cell-based method for predicting functional maturation transcription factors.

Publication date :

11 January 2024

Journal title :

Stem Cell Reports

eISSN :

2213-6711

Publisher :

Elsevier BV, United States

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

https://api.elsevier.com/content/article/PII:S221367112300499X?httpAccept=text/xml

Funders :

Fonds National de la Recherche Luxembourg

Available on ORBilu :

since 19 January 2024

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