PMID- 37323566
OWN - NLM
STAT- MEDLINE
DCOM- 20230619
LR  - 20231207
IS  - 2667-2375 (Electronic)
IS  - 2667-2375 (Linking)
VI  - 3
IP  - 5
DP  - 2023 May 22
TI  - Subcellular spatially resolved gene neighborhood networks in single cells.
PG  - 100476
LID - 10.1016/j.crmeth.2023.100476 [doi]
LID - 100476
AB  - Image-based spatial omics methods such as fluorescence in situ hybridization 
      (FISH) generate molecular profiles of single cells at single-molecule resolution. 
      Current spatial transcriptomics methods focus on the distribution of single 
      genes. However, the spatial proximity of RNA transcripts can play an important 
      role in cellular function. We demonstrate a spatially resolved gene neighborhood 
      network (spaGNN) pipeline for the analysis of subcellular gene proximity 
      relationships. In spaGNN, machine-learning-based clustering of subcellular 
      spatial transcriptomics data yields subcellular density classes of multiplexed 
      transcript features. The nearest-neighbor analysis produces heterogeneous gene 
      proximity maps in distinct subcellular regions. We illustrate the 
      cell-type-distinguishing capability of spaGNN using multiplexed error-robust FISH 
      data of fibroblast and U2-OS cells and sequential FISH data of mesenchymal stem 
      cells (MSCs), revealing tissue-source-specific MSC transcriptomics and spatial 
      distribution characteristics. Overall, the spaGNN approach expands the spatial 
      features that can be used for cell-type classification tasks.
CI  - (c) 2023 The Authors.
FAU - Fang, Zhou
AU  - Fang Z
AD  - Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of 
      Technology and Emory University, Atlanta, GA, USA.
AD  - Machine Learning Graduate Program, Georgia Institute of Technology, Atlanta, GA, 
      USA.
FAU - Ford, Adam J
AU  - Ford AJ
AD  - Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of 
      Technology and Emory University, Atlanta, GA, USA.
FAU - Hu, Thomas
AU  - Hu T
AD  - Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of 
      Technology and Emory University, Atlanta, GA, USA.
AD  - School of Electrical and Computer Engineering, Georgia Institute of Technology, 
      Atlanta, GA, USA.
FAU - Zhang, Nicholas
AU  - Zhang N
AD  - Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of 
      Technology and Emory University, Atlanta, GA, USA.
AD  - Interdisciplinary Bioengineering Graduate Program, Georgia Institute of 
      Technology, Atlanta, GA, USA.
FAU - Mantalaris, Athanasios
AU  - Mantalaris A
AD  - Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of 
      Technology and Emory University, Atlanta, GA, USA.
FAU - Coskun, Ahmet F
AU  - Coskun AF
AD  - Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of 
      Technology and Emory University, Atlanta, GA, USA.
AD  - Interdisciplinary Bioengineering Graduate Program, Georgia Institute of 
      Technology, Atlanta, GA, USA.
AD  - Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of 
      Technology, Atlanta, GA 30332, USA.
LA  - eng
GR  - K25 AI140783/AI/NIAID NIH HHS/United States
GR  - T32 GM142616/GM/NIGMS NIH HHS/United States
PT  - Journal Article
DEP - 20230512
PL  - United States
TA  - Cell Rep Methods
JT  - Cell reports methods
JID - 9918227360606676
SB  - IM
MH  - In Situ Hybridization, Fluorescence/methods
MH  - *Single-Cell Analysis/methods
MH  - *Gene Expression Profiling/methods
MH  - Gene Regulatory Networks
MH  - Fibroblasts
PMC - PMC10261906
OTO - NOTNLM
OT  - RNA proximity
OT  - RNA-RNA interactions
OT  - cell-type classification
OT  - gene neighborhood networks
OT  - spatial omics
OT  - subcellular transcriptomics
COIS- The authors declare no competing interests.
EDAT- 2023/06/16 06:42
MHDA- 2023/06/19 13:08
PMCR- 2023/05/12
CRDT- 2023/06/16 04:00
PHST- 2022/07/30 00:00 [received]
PHST- 2023/02/18 00:00 [revised]
PHST- 2023/04/18 00:00 [accepted]
PHST- 2023/06/19 13:08 [medline]
PHST- 2023/06/16 06:42 [pubmed]
PHST- 2023/06/16 04:00 [entrez]
PHST- 2023/05/12 00:00 [pmc-release]
AID - S2667-2375(23)00099-1 [pii]
AID - 100476 [pii]
AID - 10.1016/j.crmeth.2023.100476 [doi]
PST - epublish
SO  - Cell Rep Methods. 2023 May 12;3(5):100476. doi: 10.1016/j.crmeth.2023.100476. 
      eCollection 2023 May 22.