PMID- 25664616
OWN - NLM
STAT- MEDLINE
DCOM- 20150427
LR  - 20230603
IS  - 1476-4679 (Electronic)
IS  - 1465-7392 (Print)
IS  - 1465-7392 (Linking)
VI  - 17
IP  - 3
DP  - 2015 Mar
TI  - A high-throughput platform for stem cell niche co-cultures and downstream gene 
      expression analysis.
PG  - 340-9
LID - 10.1038/ncb3104 [doi]
AB  - Stem cells reside in 'niches', where support cells provide critical signalling 
      for tissue renewal. Culture methods mimic niche conditions and support the growth 
      of stem cells in vitro. However, current functional assays preclude statistically 
      meaningful studies of clonal stem cells, stem cell-niche interactions, and 
      genetic analysis of single cells and their organoid progeny. Here, we describe a 
      'microraft array' (MRA) that facilitates high-throughput clonogenic culture and 
      computational identification of single intestinal stem cells (ISCs) and niche 
      cells. We use MRAs to demonstrate that Paneth cells, a known ISC niche component, 
      enhance organoid formation in a contact-dependent manner. MRAs facilitate 
      retrieval of early enteroids for quantitative PCR to correlate functional 
      properties, such as enteroid morphology, with differences in gene expression. 
      MRAs have broad applicability to assaying stem cell-niche interactions and 
      organoid development, and serve as a high-throughput culture platform to 
      interrogate gene expression at early stages of stem cell fate choices.
FAU - Gracz, Adam D
AU  - Gracz AD
AD  - 1] Department of Cell Biology &Physiology, University of North Carolina at Chapel 
      Hill, Chapel Hill, North Carolina 27599, USA [2] Department of Medicine, 
      University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, 
      USA.
FAU - Williamson, Ian A
AU  - Williamson IA
AD  - Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, 
      North Carolina 27599, USA.
FAU - Roche, Kyle C
AU  - Roche KC
AD  - Department of Cell Biology &Physiology, University of North Carolina at Chapel 
      Hill, Chapel Hill, North Carolina 27599, USA.
FAU - Johnston, Michael J
AU  - Johnston MJ
AD  - Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, 
      North Carolina 27599, USA.
FAU - Wang, Fengchao
AU  - Wang F
AD  - Department of Pathology and Laboratory Medicine, University of Kansas, Kansas 
      City, Kansas 66160, USA.
FAU - Wang, Yuli
AU  - Wang Y
AD  - Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill 
      North Carolina 27599, USA.
FAU - Attayek, Peter J
AU  - Attayek PJ
AD  - UNC/NC State Biomedical Engineering, Chapel Hill North Carolina 27599, USA.
FAU - Balowski, Joseph
AU  - Balowski J
AD  - Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill 
      North Carolina 27599, USA.
FAU - Liu, Xiao Fu
AU  - Liu XF
AD  - Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, 
      North Carolina 27599, USA.
FAU - Laurenza, Ryan J
AU  - Laurenza RJ
AD  - Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, 
      North Carolina 27599, USA.
FAU - Gaynor, Liam T
AU  - Gaynor LT
AD  - Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, 
      North Carolina 27599, USA.
FAU - Sims, Christopher E
AU  - Sims CE
AD  - Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill 
      North Carolina 27599, USA.
FAU - Galanko, Joseph A
AU  - Galanko JA
AD  - Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, 
      North Carolina 27599, USA.
FAU - Li, Linheng
AU  - Li L
AD  - 1] Department of Pathology and Laboratory Medicine, University of Kansas, Kansas 
      City, Kansas 66160, USA [2] Stowers Institute for Medical Research, Kansas City, 
      Missouri 64110, USA.
FAU - Allbritton, Nancy L
AU  - Allbritton NL
AD  - 1] Department of Chemistry, University of North Carolina at Chapel Hill, Chapel 
      Hill North Carolina 27599, USA [2] UNC/NC State Biomedical Engineering, Chapel 
      Hill North Carolina 27599, USA.
FAU - Magness, Scott T
AU  - Magness ST
AD  - 1] Department of Cell Biology &Physiology, University of North Carolina at Chapel 
      Hill, Chapel Hill, North Carolina 27599, USA [2] Department of Medicine, 
      University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, 
      USA [3] UNC/NC State Biomedical Engineering, Chapel Hill North Carolina 27599, 
      USA.
LA  - eng
GR  - U01 DK085507-01/DK/NIDDK NIH HHS/United States
GR  - R01 DK091427/DK/NIDDK NIH HHS/United States
GR  - P30 DK034987/DK/NIDDK NIH HHS/United States
GR  - U01 DK085507/DK/NIDDK NIH HHS/United States
GR  - U24 DK085532/DK/NIDDK NIH HHS/United States
GR  - GM106421/GM/NIGMS NIH HHS/United States
GR  - P30CA06086/CA/NCI NIH HHS/United States
GR  - U01 DK085547/DK/NIDDK NIH HHS/United States
GR  - U01 DK085532/DK/NIDDK NIH HHS/United States
GR  - R03 EB013803/EB/NIBIB NIH HHS/United States
GR  - T32 DK007737/DK/NIDDK NIH HHS/United States
GR  - R01 EB012549/EB/NIBIB NIH HHS/United States
GR  - R43 GM106421/GM/NIGMS NIH HHS/United States
GR  - U01 DK085541/DK/NIDDK NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20150209
PL  - England
TA  - Nat Cell Biol
JT  - Nature cell biology
JID - 100890575
RN  - 0 (SOX9 Transcription Factor)
RN  - 0 (Sox9 protein, mouse)
RN  - 0 (enhanced green fluorescent protein)
RN  - 147336-22-9 (Green Fluorescent Proteins)
SB  - IM
MH  - Animals
MH  - Cell Differentiation
MH  - Coculture Techniques
MH  - Female
MH  - Gene Expression Profiling
MH  - *Gene Expression Regulation, Developmental
MH  - Genes, Reporter
MH  - Green Fluorescent Proteins/genetics/metabolism
MH  - *High-Throughput Screening Assays
MH  - Male
MH  - Mice
MH  - Mice, Transgenic
MH  - Paneth Cells/cytology/*metabolism
MH  - SOX9 Transcription Factor/genetics/metabolism
MH  - Signal Transduction
MH  - Single-Cell Analysis
MH  - Stem Cell Niche/genetics
MH  - Stem Cells/cytology/*metabolism
MH  - Tissue Array Analysis/instrumentation/*methods
PMC - PMC4405128
MID - NIHMS653259
EDAT- 2015/02/11 06:00
MHDA- 2015/04/29 06:00
PMCR- 2015/09/01
CRDT- 2015/02/10 06:00
PHST- 2014/01/29 00:00 [received]
PHST- 2015/01/05 00:00 [accepted]
PHST- 2015/02/10 06:00 [entrez]
PHST- 2015/02/11 06:00 [pubmed]
PHST- 2015/04/29 06:00 [medline]
PHST- 2015/09/01 00:00 [pmc-release]
AID - ncb3104 [pii]
AID - 10.1038/ncb3104 [doi]
PST - ppublish
SO  - Nat Cell Biol. 2015 Mar;17(3):340-9. doi: 10.1038/ncb3104. Epub 2015 Feb 9.