PMID- 34123352
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20220204
IS  - 2042-8898 (Print)
IS  - 2042-8901 (Electronic)
IS  - 2042-8898 (Linking)
VI  - 11
IP  - 4
DP  - 2021 Jun
TI  - Logical modelling of in vitro differentiation of human monocytes into dendritic 
      cells unravels novel transcriptional regulatory interactions.
PG  - 20200061
LID - 10.1098/rsfs.2020.0061 [doi]
LID - 20200061
AB  - Dendritic cells (DCs) are the major specialized antigen-presenting cells, thereby 
      connecting innate and adaptive immunity. Because of their role in establishing 
      adaptive immunity, they constitute promising targets for immunotherapy. Monocytes 
      can differentiate into DCs in vitro in the presence of colony-stimulating factor 
      2 (CSF2) and interleukin 4 (IL4), activating four signalling pathways (MAPK, 
      JAK/STAT, NFKB and PI3K). However, the downstream transcriptional programme 
      responsible for DC differentiation from monocytes (moDCs) remains unknown. By 
      analysing the scientific literature on moDC differentiation, we established a 
      preliminary logical model that helped us identify missing information regarding 
      the activation of genes responsible for this differentiation, including missing 
      targets for key transcription factors (TFs). Using ChIP-seq and RNA-seq data from 
      the Blueprint consortium, we defined active and inactive promoters, together with 
      differentially expressed genes in monocytes, moDCs and macrophages, which 
      correspond to an alternative cell fate. We then used this functional genomic 
      information to predict novel targets for previously identified TFs. By 
      integrating this information, we refined our model and recapitulated the main 
      established facts regarding moDC differentiation. Prospectively, the resulting 
      model should be useful to develop novel immunotherapies targeting moDCs.
CI  - (c) 2021 The Authors.
FAU - Nunez-Reza, Karen J
AU  - Nunez-Reza KJ
AUID- ORCID: 0000-0002-5459-8461
AD  - Laboratorio Internacional de Investigacion sobre el Genoma Humano, Universidad 
      Nacional Autonoma de Mexico, Juriquilla, Mexico.
FAU - Naldi, Aurelien
AU  - Naldi A
AD  - Computational Systems Biology team, Institut de Biologie de l'Ecole Normale 
      Superieure, Inserm, CNRS, Universite PSL, Paris, France.
FAU - Sanchez-Jimenez, Arantza
AU  - Sanchez-Jimenez A
AUID- ORCID: 0000-0001-9572-2951
AD  - Laboratorio Internacional de Investigacion sobre el Genoma Humano, Universidad 
      Nacional Autonoma de Mexico, Juriquilla, Mexico.
FAU - Leon-Apodaca, Ana V
AU  - Leon-Apodaca AV
AD  - Laboratorio Internacional de Investigacion sobre el Genoma Humano, Universidad 
      Nacional Autonoma de Mexico, Juriquilla, Mexico.
FAU - Santana, M Angelica
AU  - Santana MA
AD  - Centro de Investigacion en Dinamica Celular (IICBA), Universidad Autonoma del 
      Estado de Morelos, Cuernavaca, Mexico.
FAU - Thomas-Chollier, Morgane
AU  - Thomas-Chollier M
AD  - Computational Systems Biology team, Institut de Biologie de l'Ecole Normale 
      Superieure, Inserm, CNRS, Universite PSL, Paris, France.
FAU - Thieffry, Denis
AU  - Thieffry D
AD  - Computational Systems Biology team, Institut de Biologie de l'Ecole Normale 
      Superieure, Inserm, CNRS, Universite PSL, Paris, France.
FAU - Medina-Rivera, Alejandra
AU  - Medina-Rivera A
AD  - Laboratorio Internacional de Investigacion sobre el Genoma Humano, Universidad 
      Nacional Autonoma de Mexico, Juriquilla, Mexico.
LA  - eng
SI  - figshare/10.6084/m9.figshare.c.5428716
PT  - Journal Article
DEP - 20210611
PL  - England
TA  - Interface Focus
JT  - Interface focus
JID - 101531990
PMC - PMC8193469
OTO - NOTNLM
OT  - dendritic cells
OT  - differentiation
OT  - logical modelling
OT  - regulatory networks
EDAT- 2021/06/15 06:00
MHDA- 2021/06/15 06:01
PMCR- 2021/06/11
CRDT- 2021/06/14 09:43
PHST- 2021/04/15 00:00 [accepted]
PHST- 2021/06/14 09:43 [entrez]
PHST- 2021/06/15 06:00 [pubmed]
PHST- 2021/06/15 06:01 [medline]
PHST- 2021/06/11 00:00 [pmc-release]
AID - rsfs20200061 [pii]
AID - 10.1098/rsfs.2020.0061 [doi]
PST - epublish
SO  - Interface Focus. 2021 Jun 11;11(4):20200061. doi: 10.1098/rsfs.2020.0061. 
      eCollection 2021 Jun.