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Series GSE261345 Query DataSets for GSE261345
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 [CANTABRICO_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 26 ES-SCLC patients enrolled in the CANTABRICO clinical trial (EudraCT Number: 2020-002328-35) with adequate tumor material for spatially preserved transcriptomic analysis. The CANTABRICO study was a phase IIIb single arm multicenter trial evaluating the safety and effectiveness of PD-L1 blockade (durvalumab) 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).
Web link https://pubmed.ncbi.nlm.nih.gov/38630755/
 
Contributor(s) Zugazagoitia J
Citation(s) 38630755
Submission date Mar 11, 2024
Last update date Jul 17, 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 (121)
GSM8140828 Patient CAN001 ROI 001
GSM8140829 Patient CAN001 ROI 002
GSM8140830 Patient CAN001 ROI 003
Relations
BioProject PRJNA1086530

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
GSE261345_CAN001.png.gz 405.4 Mb (ftp)(http) PNG
GSE261345_CAN002.png.gz 138.3 Mb (ftp)(http) PNG
GSE261345_CAN003.png.gz 185.6 Mb (ftp)(http) PNG
GSE261345_CAN005.png.gz 107.7 Mb (ftp)(http) PNG
GSE261345_CAN007.png.gz 135.6 Mb (ftp)(http) PNG
GSE261345_CAN008.png.gz 176.2 Mb (ftp)(http) PNG
GSE261345_CAN009.png.gz 107.9 Mb (ftp)(http) PNG
GSE261345_CAN015.png.gz 93.7 Mb (ftp)(http) PNG
GSE261345_CAN017.png.gz 33.9 Mb (ftp)(http) PNG
GSE261345_CAN018.png.gz 6.0 Mb (ftp)(http) PNG
GSE261345_CAN019.png.gz 144.2 Mb (ftp)(http) PNG
GSE261345_CAN020.png.gz 149.2 Mb (ftp)(http) PNG
GSE261345_CAN021.png.gz 85.8 Mb (ftp)(http) PNG
GSE261345_CAN022.png.gz 33.0 Mb (ftp)(http) PNG
GSE261345_CAN023.png.gz 28.6 Mb (ftp)(http) PNG
GSE261345_CAN024.png.gz 14.4 Mb (ftp)(http) PNG
GSE261345_CAN028.png.gz 83.3 Mb (ftp)(http) PNG
GSE261345_CAN029.png.gz 69.9 Mb (ftp)(http) PNG
GSE261345_CAN037.png.gz 43.0 Mb (ftp)(http) PNG
GSE261345_CAN039.png.gz 26.2 Mb (ftp)(http) PNG
GSE261345_CAN040.png.gz 55.4 Mb (ftp)(http) PNG
GSE261345_CAN041.png.gz 57.7 Mb (ftp)(http) PNG
GSE261345_CAN042.png.gz 125.3 Mb (ftp)(http) PNG
GSE261345_CAN043.png.gz 17.5 Mb (ftp)(http) PNG
GSE261345_CAN044.png.gz 50.8 Mb (ftp)(http) PNG
GSE261345_CAN046.png.gz 35.6 Mb (ftp)(http) PNG
GSE261345_CANTABRICO_DSP_normalizedcounts.xlsx 3.9 Mb (ftp)(http) XLSX
GSE261345_CANTABRICO_DSP_rawcounts.xlsx 3.9 Mb (ftp)(http) XLSX
GSE261345_GeoMx_Hs_CTA_v1.0.pkc.gz 558.0 Kb (ftp)(http) PKC
GSE261345_RAW.tar 4.2 Mb (http)(custom) TAR (of DCC)
GSE261345_Zugazagoitia_SQ-48831_v1.0.pkc.gz 3.0 Kb (ftp)(http) PKC
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