A Systems Biology Approach for Defining the Molecular Framework of the Hematopoietic Stem Cell Niche
Pierre Charbord,Claire Pouget,Hans Binder,Florent Dumont,Gregoire Stik,Gregoire Stik,Pacifique Levy,Pacifique Levy,Fabrice Allain,Fabrice Allain,Céline Marchal,Céline Marchal,Jenna Richter,Benjamin Uzan,Françoise Pflumio,Franck Letourneur,Henry Wirth,Elaine Dzierzak,David Traver,Thierry Jaffredo,Thierry Jaffredo,Charles Durand,Charles Durand +22 more
69
TL;DR: The gene set contains most known HSPC regulators as well as a number of unexpected ones, such as Pax9 and Ccdc80, as validated by functional studies in zebrafish embryos and will inform ongoing efforts to instruct HSPP ex vivo amplification and formation from pluripotent precursors.
read more
About: This article is published in Cell Stem Cell. The article was published on 04 Sep 2014. and is currently open access. The article focuses on the topics: Hematopoietic stem cell niche.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Identifying niche-mediated regulatory factors of stem cell phenotypic state: a systems biology approach.
TL;DR: A systems biology view is proposed that considers stem cell–niche interactions as a many‐body problem amenable to simplification by the concept of mean field approximation, which enables approximation of the niche effect on stem cells as a constant field that induces sustained activation/inhibition of specific stem cell signaling pathways.
8
BAP1 shapes the bone marrow niche for lymphopoiesis by fine-tuning epigenetic profiles in endosteal mesenchymal stromal cells
J. Jeong,In Mok Jung,Ji Hoon Kim,Shin Jeon,Do Young Hyeon,Hyungyu Min,Byeonggeun Kang,Jin-Ju Nah,Daehee Hwang,Soo-Jong Um,Myunggon Ko,Rho Hyun Seong +11 more
TL;DR: In this paper , a key role for BAP1 expressed in endosteal mesenchymal stromal cells (MSCs) in controlling normal hematopoiesis in mice was uncovered.
7
A multistep computational approach reveals a neuro-mesenchymal cell population in the embryonic hematopoietic stem cell niche.
Olivera Miladinovic,P. Canto,C. Pouget,Olivier Piau,Nevenka Radic,Priscilla Freschu,Alexandre Megherbi,Carla Brujas Prats,Sebastien Jacques,Estelle Hirsinger,Audrey Geeverding,Sylvie Dufour,Laurence Petit,Michèle Souyri,Trista North,Hervé Isambert,David Traver,Thierry Jaffredo,Pierre Charbord,Charles Durand +19 more
TL;DR: A multistep computational approach identifies a novel neuro-mesenchymal cell population in the embryonic hematopoietic stem cell niche.
5
Systems-Based Technologies in Profiling the Stem Cell Molecular Framework for Cardioregenerative Medicine
TL;DR: A brief summarization of OMICS-based strategies including transcriptomics, proteomics, and metabolomics used to understand stem cell fate and to outline molecular processes involved in heart development are provided.
Altered mesenchymal niche cells impede generation of normal hematopoietic progenitor cells in leukemic bone marrow
M. Lim,Y. Pang,S. Ma,Sha Hao,H. Shi,Y. Zheng,C. Hua,X. Gu,Fengchun Yang,Weiping Yuan,Tao Cheng +10 more
- Leukemia
TL;DR: Leukemic MSCs may serve as a cellular target for improving normal hematopoietic regeneration therapeutically and osteoprotegerin was identified as a cytokine to improve the function of T-ALL M SCs and to enhance normal HPC output via the p38/ERK pathway.
2
References
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder,Steve Horvath +1 more
TL;DR: The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software.
Landscape of transcription in human cells
Sarah Djebali,Carrie A. Davis,Angelika Merkel,Alexander Dobin,Timo Lassmann,Ali Mortazavi,Ali Mortazavi,Andrea Tanzer,Julien Lagarde,Wei Lin,Felix Schlesinger,Chenghai Xue,Georgi K. Marinov,Jainab Khatun,Brian A. Williams,Chris Zaleski,Joel Rozowsky,Marion S. Röder,Felix Kokocinski,Rehab F. Abdelhamid,Tyler Alioto,Igor Antoshechkin,Michael T. Baer,Nadav Bar,Philippe Batut,Kimberly Bell,Ian Bell,Sudipto K. Chakrabortty,Xian Chen,Jacqueline Chrast,Joao Curado,Thomas Derrien,Jorg Drenkow,Erica Dumais,Jacqueline Dumais,Radha Duttagupta,Emilie Falconnet,Meagan Fastuca,Kata Fejes-Toth,Pedro G. Ferreira,Sylvain Foissac,Melissa J. Fullwood,Hui Gao,David Gonzalez,Assaf Gordon,Harsha P. Gunawardena,Cédric Howald,Sonali Jha,Rory Johnson,Philipp Kapranov,Brandon King,Colin Kingswood,Oscar Junhong Luo,Eddie Park,Kimberly Persaud,Jonathan B. Preall,Paolo Ribeca,Brian A. Risk,Daniel Robyr,Michael Sammeth,Lorian Schaffer,Lei-Hoon See,Atif Shahab,Jørgen Skancke,Ana Maria Suzuki,Hazuki Takahashi,Hagen Tilgner,Diane Trout,Nathalie Walters,Huaien Wang,John A. Wrobel,Yanbao Yu,Xiaoan Ruan,Yoshihide Hayashizaki,Jennifer Harrow,Mark Gerstein,Tim Hubbard,Alexandre Reymond,Stylianos E. Antonarakis,Gregory J. Hannon,Morgan C. Giddings,Morgan C. Giddings,Yijun Ruan,Barbara J. Wold,Piero Carninci,Roderic Guigó,Thomas R. Gingeras,Thomas R. Gingeras +87 more
TL;DR: Evidence that three-quarters of the human genome is capable of being transcribed is reported, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs that prompt a redefinition of the concept of a gene.
Osteoblastic cells regulate the haematopoietic stem cell niche
Laura M. Calvi,Gregor B. Adams,Kathryn W. Weibrecht,Jonathan M. Weber,David P. Olson,M. C. Knight,Roderick P. Martin,Ernestina Schipani,P. Divieti,F. R. Bringhurst,Laurie A. Milner,Henry M. Kronenberg,David T. Scadden +12 more
TL;DR: Osteoblastic cells are a regulatory component of the haematopoietic stem cell niche in vivo that influences stem cell function through Notch activation.
SLAM Family Receptors Distinguish Hematopoietic Stem and Progenitor Cells and Reveal Endothelial Niches for Stem Cells
Mark J. Kiel,Ömer H. Yilmaz,Toshihide Iwashita,Osman H. Yilmaz,Cox Terhorst,Sean J. Morrison +5 more
TL;DR: This work compared the gene expression profiles of highly purified HSCs and non-self-renewing multipotent hematopoietic progenitors and found that both groups occupied multiple niches, including sinusoidal endothelium in diverse tissues.
3.4K