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Series GSE147766 Query DataSets for GSE147766
Status Public on May 05, 2022
Title The immune cell atlas of human neuroblastoma
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Our current knowledge of the different immune cells in neuroblastoma is based on in vitro and in vivo studies mainly focusing on a single cell type. Importantly, different studies have conveyed conflicting results. Moreover, a comprehensive immune cell overview at the single-cell level is still missing and understanding the complete immune cell composition of neuroblastoma will be crucial for the development of novel immunotherapeutics against the disease. In this study, we performed single-cell RNA-sequencing on nineteen human neuroblastoma samples coupled with multiplex immunohistochemistry and survival analysis using additional datasets to provide a comprehensive cellular and molecular immune cell landscape of human neuroblastoma. Further, we contrasted our data with single-cell RNA-sequencing data from normal fetal adrenal gland to characterize cell-state changes from normal tissue to cancerous neuroblastoma. Our analysis revealed 27 immune cell subtypes including distinct subpopulations of myeloid, NK, B and T cells not identified in neuroblastoma before. Several immune cell subtypes demonstrated a survival benefit such as inflammatory monocytes, tumor associated macrophages, various T cell populations, and Active NK cells. Furthermore, in contrast to adult cancers and previous neuroblastoma studies, we demonstrated an increase in inflammatory monocyte cell-state when contrasting normal and tumor tissue, while we do not observe differences in cytotoxicity and exhaustion score for cytotoxic T cells, nor in Treg activity. Finally, we performed a systemic receptor-ligand interaction analysis between tumor, stroma and immune cells, where we showed the neuroblastoma tumor microenvironment is highly complex and strongly correlated to survival. In addition, we highlighted several interactions that we suggest to be tested in future studies as a therapeutic option in human neuroblastoma. Taken together, our study significantly adds to the in depth understanding of the immune cell landscape, the complexity of the tumor microenvironment and it provides a resource for the development of novel immunotherapeutics for neuroblastoma.
 
Overall design Neuroblastoma were disaggregated and profiled by 10X Genomics Single cell 3 gene expression V2.
*** RNA-Seq raw data to be made available through dbGaP (controlled access) due to patient privacy concerns: https://www.ncbi.nlm.nih.gov/gap/?term=phsxxxxx
 
Contributor(s) Baryawno N
Citation(s) 35688160
Submission date Mar 30, 2020
Last update date Jul 07, 2022
Contact name Shenglin Mei
E-mail(s) samleomei@gmail.com
Organization name Harvard medical school (DMBI)
Street address 10 Shattuck Street
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (19)
GSM4445608 NB01 (RNA-seq)
GSM4445609 NB02 (RNA-seq)
GSM4445610 NB09 (RNA-seq)
This SubSeries is part of SuperSeries:
GSE147777 Malignant Schwann cell precursors mediate intratumoral plasticity in human neuroblastoma
Relations
BioProject PRJNA616334

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE147766_RAW.tar 140.3 Mb (http)(custom) TAR (of CSV)
Processed data provided as supplementary file
Raw data not provided for this record

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