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Series GSE263733 Query DataSets for GSE263733
Status Public on Apr 25, 2024
Title Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Intratumoral heterogeneity (ITH) and tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) play important roles in tumor evolution and patient outcomes. However, the precise characterization of diverse cell populations and their crosstalk associated with PDAC progression and metastasis is still challenging. We performed single-cell RNA sequencing (scRNA-seq) of treatment-naive primary PDAC samples with and without paired liver metastasis samples to understand the interplay between ITH and TME in the PDAC evolution and its clinical associations. scRNA-seq analysis revealed that even a small proportion (~30%) of basal-like malignant ductal cells could lead to poor chemotherapy response and patient survival and that epithelial-mesenchymal transition programs were largely subtype-specific. The clonal homogeneity significantly increased with more prevalent and pronounced copy number gains of oncogenes, such as KRAS and ETV1, and losses of tumor suppressor genes, such as SMAD2 and MAP2K4, along PDAC progression and metastasis. Moreover, diverse immune cell populations, including naive SELLhi regulatory T cells (Tregs) and activated TIGIThi Tregs, contributed to shaping immunosuppressive TMEs of PDAC through cellular interactions with malignant ductal cells in PDAC evolution. Importantly, the proportion of basal-like ductal cells negatively correlated with that of immunoreactive cell populations, such as cytotoxic T cells, but positively correlated with that of immunosuppressive cell populations, such as Tregs. We uncover that the proportion of basal-like subtype is a determinant for chemotherapy response and patient outcome, and that PDAC clonally evolves with subtype-specific dosage changes of cancer-associated genes by forming immunosuppressive microenvironments in its progression and metastasis.
 
Overall design All remaining tissues are collected in MACS Tissue Storage Solution (Miltenyi Biotec., Auburn, CA, USA) on ice, and processed to the single cell dissociation immediately. Specimens can be maintained in MACS Tissue Storage Solution (Miltenyi Biotec.) for 48 hours at 4C without showing background effects like cell activation or apoptosis induction. Biopsy tissues are placed on a petri dish with a small volume of enzyme mixture solution (Tumor Dissociation Kit, Miltenyi Biotec.), and minced into small pieces under 1-2 mm with surgical blades. Minced pieces are transferred to gentleMACSTM C-tube containing enzyme mixture solution. By choosing an appropriate program of gentleMACSTM Dissociator, Tissue pieces are further dissociated three times with two interval incubations for 30 minutes at 37C under continuous rotation using the MACSmix Tube Rotator. Resuspended samples are applied to a cell strainer (70 m) placed on a 15 ml cornical tube, and washed with 10 ml of RPMI1640 media. After a centrifugation at 400xg for 5 minutes, cells were resuspended in an appropriate volume of RPMI1640 media, and counted after trypan blue staining or acridine orange/ propidium iodide staining. Optionally, erythrocytes are removed by red blood cell lysis solution for 10 min before counting.
 
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BioProject PRJNA948891
Submission date Apr 11, 2024
Last update date Apr 25, 2024
Contact name Semin Lee
E-mail(s) seminlee@unist.ac.kr
Organization name Ulsan National Institute of Science and Technology
Department Biomedical Engineering
Street address 50, UNIST-gil
City Ulsan
ZIP/Postal code 44919
Country South Korea
 
Platforms (1)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (218)
GSM8197348 adult pancreas; PB2032-PAAD-T_S1_L001
GSM8197349 adult pancreas; PB2032-PAAD-T_S1_L002
GSM8197350 adult pancreas; PB2032-PAAD-T_S1_L003

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
GSE263733_Cell_annotation.txt.gz 420.7 Kb (ftp)(http) TXT
GSE263733_Raw_counts.txt.gz 200.8 Mb (ftp)(http) TXT
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