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Series GSE168013 Query DataSets for GSE168013
Status Public on Mar 03, 2021
Title High-plex spatial RNA profiling reveals cell type-specific biomarker expression during melanoma development
Organism Homo sapiens
Experiment type Other
Summary Early diagnosis of melanoma is critical for improved survival. However, biomarkers of early melanoma evolution and their origin within the tumor and its microenvironment, including the keratinocytes, are poorly defined. To address this, we used spatial transcript profiling that maintains the morphological tumor context to measure expression of >1,000 RNAs in situ in patient-derived formalin-fixed, paraffin-embedded tissue sections in primary melanoma and melanocytic nevi. We profiled 134 200µm-diameter regions of interest enriched in melanocytes, neighboring keratinocytes or immune cells. This approach captured distinct expression patterns across cell types and tumor types during melanoma development. Unexpectedly, we discovered that S100A8 is expressed by keratinocytes within the tumor microenvironment during melanoma growth. Immunohistochemistry of 252 tumors showed prominent keratinocyte-derived S100A8 expression in melanoma but not in benign tumors and confirmed the same pattern for S100A8’s binding partner S100A9, suggesting that injury to the epidermis may be an early and easily detectable indicator of melanoma development Together, our results establish a framework for high-plex, spatial and cell type-specific resolution of gene expression in archival tissue applicable to the development of biomarkers and characterization of tumor-microenvironment interactions in tumor evolution.
In this dataset, we capture the GeoMx DSP RNA profiling data associated with this study. The files here represent patients with melanocytic tumors (n = 16) which were profiled with the NanoString GeoMx pilot panel (n=4 patients, n=108 gene targets) or CTA developmental panel v1.0 (n=12 patients, n=1,412 gene targets). These panels were read out using Illumina sequencing according to manufacturer protocols. For access to high resolution (single channel, composite, or ROI) images please contact mkriner@nanostring.com.
 
Overall design This dataset contains expression data from patient FFPE samples collected during skin biopsy. Up to 16 ROIs were collected from each patient sample. H&E-stained serial sections were used to guide ROI selection by an experienced dermatopathologist.
 
Contributor(s) Kriner MA, Kiuru M, McPherson JD, Zhu G, Terrell JR, Wong S, Li Q, Hoang M, Beechem J
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Mar 02, 2021
Last update date Mar 06, 2021
Contact name Michelle Kriner
E-mail(s) makriner@gmail.com
Organization name NanoString Technologies
Street address 500 Fairview Ave North
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (325)
GSM5123428 Phase I benign nevus ROI1 rep1.1 [NS1-A-1-1]
GSM5123429 Phase I benign nevus ROI1 rep1.2 [NS1-A-1-2]
GSM5123430 Phase I benign nevus ROI2 rep1.1 [NS1-A-2-1]
Relations
BioProject PRJNA705876
SRA SRP308815

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
GSE168013_200825_CTA_Dev_platform_file.xlsx 320.2 Kb (ftp)(http) XLSX
GSE168013_MK006_dedup.txt.gz 349.9 Kb (ftp)(http) TXT
GSE168013_MK006_rep1_summarized_counts.txt.gz 98.9 Kb (ftp)(http) TXT
GSE168013_MK006_rep2_summarized_counts.txt.gz 99.0 Kb (ftp)(http) TXT
GSE168013_MK008_20190821_summarized_counts.txt.gz 1.4 Mb (ftp)(http) TXT
GSE168013_MK008_dedup.txt.gz 919.7 Kb (ftp)(http) TXT
GSE168013_MK008_finalData.txt.gz 1.0 Mb (ftp)(http) TXT
GSE168013_RAW.tar 9.4 Mb (http)(custom) TAR (of DCC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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