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Series GSE199102 Query DataSets for GSE199102
Status Public on May 12, 2022
Title Spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here we construct a high-resolution molecular landscape of the multicellular subtypes and spatial communities that compose PAC using single-nucleus RNA-seq and whole-transcriptome digital spatial profiling (SP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment-naïve. We uncovered expression programs across malignant cells and fibroblasts, including a newly-identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities: classical, squamoid-basaloid, and treatment-enriched. Our refined molecular and cellular taxonomy can advance precision oncology in PAC through stratification in clinical trials and as roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.
 
Overall design 14 specimens received no treatment prior to resection; 7 specimens received neoadjuvant chemotherapy, radiotherapy, losartan, and/or nivolumab prior to resection
 
Contributor(s) Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Su J, Shiau C, Jacks T, Regev A
Citation(s) 35902743
Submission date Mar 21, 2022
Last update date Sep 11, 2023
Contact name Karthik Jagadeesh
E-mail(s) kjag@broadinstitute.org
Phone 4088919573
Organization name Broad Institute
Department Human Cell Atlas
Lab Regev Lab
Street address 415 Main St
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (608)
GSM5965787 DSP-1001660003683-G-A04
GSM5965788 DSP-1001660003683-G-A12
GSM5965789 DSP-1001660003683-G-A01
Relations
BioProject PRJNA818705

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
GSE199102_Broad_PDAC_WTA_AllSamples_SegmentProperties.txt.gz 68.6 Kb (ftp)(http) TXT
GSE199102_RAW.tar 32.7 Mb (http)(custom) TAR (of DCC)
GSE199102_dfs_Q321-6.RDS.gz 22.9 Mb (ftp)(http) RDS
GSE199102_dfs_detrendApproach21-6-2.RDS.gz 34.6 Mb (ftp)(http) RDS
GSE199102_geomx_ngs_data_second_acquisition_WTA_Hs_R_NGS_WTA_v1.0.pkc.gz 1.9 Mb (ftp)(http) PKC
GSE199102_hPDAC_WTA_20210222T2101_BioProbeCountMatrix.txt.gz 9.3 Mb (ftp)(http) TXT
GSE199102_hPDAC_WTA_20210222T2101_LabWorksheet.txt.gz 7.9 Kb (ftp)(http) TXT
GSE199102_hPDAC_WTA_20210222T2101_NegNorm_TargetCountMatrix.txt.gz 61.6 Mb (ftp)(http) TXT
GSE199102_hPDAC_WTA_20210222T2101_Q3Norm_TargetCountMatrix.txt.gz 22.3 Mb (ftp)(http) TXT
GSE199102_hPDAC_WTA_20210222T2101_TargetCountMatrix.txt.gz 8.9 Mb (ftp)(http) TXT
GSE199102_ssGSEA_detrendApproach21-6-2.RDS.gz 228.4 Kb (ftp)(http) RDS
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Raw data are available in SRA
Processed data provided as supplementary file

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