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Series GSE261348 Query DataSets for GSE261348
Status Public on Apr 09, 2024
Title Spatially preserved multi-region transcriptomic subtyping and biomarkers of outcome with chemoimmunotherapy in extensive-stage small cell lung cancer [IMfirst_DSP cohort]
Organism Homo sapiens
Experiment type Other
Summary Transcriptomic subtyping holds promise for personalized therapy in extensive stage small cell lung cancer (ES-SCLC). In this study, we aimed to assess intratumoral transcriptomic subtype diversity and to identify biomarkers associated with long-term chemoimmunotherapy benefit in human ES-SCLC. Our work highlights that high intratumoral heterogeneity, lack of consistent association with outcome, and unclear subtype-specific target expression are major challenges for SCLC subtype-based precision oncology. Pre-existing IFNϒ-driven immunity and mitochondrial metabolism seem key correlates of long-term efficacy for chemoimmunotherapy in ES-SCLC.
 
Overall design We used tumor samples from 32 ES-SCLC patients enrolled in the IMfirst clinical trial (EudraCT Number: 2019-002784-10) with adequate tumor material for spatially preserved transcriptomic analysis. The IMfirst study was a phase IIIb single arm multicenter trial evaluating the safety and effectiveness of PD-L1 blockade (atezolizumab) in combination with platinum-etoposide as first-line treatment in patients with ES-SCLC.
We retrieved pre-treatment, formalin-fixed and paraffin-embedded (FFPE), tumor specimens, which were centrally reviewed by an expert pathologist at the 12 de Octubre research facilities (Madrid, Spain).
Spatial mRNA profiling was done using the GeoMx Digital Spatial Profiling (DSP) system (NanoString). For this study, we used an mRNA assay that contained oligo-nucleotide-labeled, photocleavable, RNA-binding probes targeting the expression of ~1800 genes related to cancer pathways and anti-tumor immunity (Cancer Transcriptome Atlas, CTA, NanoString) plus additional custom-designed probes targeting the expression of three SCLC subtype-defining transcription factors not included in the CTA panel (NEUROD1, POU2F3, and YAP1).
 
Contributor(s) Zugazagoitia J
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Mar 11, 2024
Last update date Apr 10, 2024
Contact name Jon Zugazagoitia
E-mail(s) j.zugazagoitia.imas12@h12o.es
Organization name Hospital Universitario 12 de Octubre
Department Medical Oncology
Lab Tumor Microenvironment and Immunotherapy
Street address Avenida de Cordoba s/n
City Madrid
ZIP/Postal code 28041
Country Spain
 
Platforms (1)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (175)
GSM8140998 Patient IMF002 ROI 001
GSM8140999 Patient IMF003 ROI 005
GSM8141000 Patient IMF003 ROI 006
Relations
BioProject PRJNA1086533

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
GSE261348_GeoMx_Hs_CTA_v1.0.pkc.gz 558.0 Kb (ftp)(http) PKC
GSE261348_IMF002.png.gz 3.5 Mb (ftp)(http) PNG
GSE261348_IMF003.png.gz 16.3 Mb (ftp)(http) PNG
GSE261348_IMF004.png.gz 43.2 Mb (ftp)(http) PNG
GSE261348_IMF005.png.gz 96.9 Mb (ftp)(http) PNG
GSE261348_IMF006.png.gz 191.7 Mb (ftp)(http) PNG
GSE261348_IMF007.png.gz 165.8 Mb (ftp)(http) PNG
GSE261348_IMF008.png.gz 253.6 Mb (ftp)(http) PNG
GSE261348_IMF009.png.gz 127.6 Mb (ftp)(http) PNG
GSE261348_IMF010.png.gz 94.3 Mb (ftp)(http) PNG
GSE261348_IMF011.png.gz 74.8 Mb (ftp)(http) PNG
GSE261348_IMF012.png.gz 96.3 Mb (ftp)(http) PNG
GSE261348_IMF013.png.gz 52.0 Mb (ftp)(http) PNG
GSE261348_IMF016.png.gz 71.7 Mb (ftp)(http) PNG
GSE261348_IMF018.png.gz 48.1 Mb (ftp)(http) PNG
GSE261348_IMF019.png.gz 173.4 Mb (ftp)(http) PNG
GSE261348_IMF020.png.gz 5.1 Mb (ftp)(http) PNG
GSE261348_IMF021.png.gz 54.2 Mb (ftp)(http) PNG
GSE261348_IMF022.png.gz 8.0 Mb (ftp)(http) PNG
GSE261348_IMF024.png.gz 60.7 Mb (ftp)(http) PNG
GSE261348_IMF025.png.gz 81.3 Mb (ftp)(http) PNG
GSE261348_IMF026.png.gz 23.7 Mb (ftp)(http) PNG
GSE261348_IMF027.png.gz 23.9 Mb (ftp)(http) PNG
GSE261348_IMF028.png.gz 70.8 Mb (ftp)(http) PNG
GSE261348_IMF029.png.gz 512.0 Mb (ftp)(http) PNG
GSE261348_IMF030.png.gz 65.6 Mb (ftp)(http) PNG
GSE261348_IMF031.png.gz 38.9 Mb (ftp)(http) PNG
GSE261348_IMF033.png.gz 40.9 Mb (ftp)(http) PNG
GSE261348_IMF037.png.gz 90.4 Mb (ftp)(http) PNG
GSE261348_IMF039.png.gz 292.9 Mb (ftp)(http) PNG
GSE261348_IMF040.png.gz 145.8 Mb (ftp)(http) PNG
GSE261348_IMF042.png.gz 71.2 Mb (ftp)(http) PNG
GSE261348_IMF043.png.gz 126.6 Mb (ftp)(http) PNG
GSE261348_IMfirst_DSP_normalizedcounts.xlsx 5.1 Mb (ftp)(http) XLSX
GSE261348_IMfirst_DSP_rawcounts.xlsx 5.1 Mb (ftp)(http) XLSX
GSE261348_RAW.tar 6.1 Mb (http)(custom) TAR (of DCC)
GSE261348_Zugazagoitia_SQ-48831_v1.0.pkc.gz 3.0 Kb (ftp)(http) PKC
Raw data are available in SRA

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