GEO series

Novel Immunotherapy-Induced Tertiary Lymphoid Aggregates Accumulate as Intratumoral Nodal Structures of Immune Regulation in Pancreatic Cancer

GSE52171 Homo sapiens (human) Expression microarray 20 samples Submitted 2014/08/05 Platform GPL570

At a glance

Expression microarray · human · 20 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Pancreatic cancerThis series is part of our curated briefing on it.
Samples: 20 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Immunotherapy provides an alternative approach for cancer treatment. However, in-depth analyses of the effects of immunotherapy on the tumor microenvironment (TME) have not been conducted in non-melanoma tumors. Here we describe changes in the pancreatic ductal adenocarcinoma (PDAC) TME following immunotherapy treatment, and show for the first time that vaccine-based immunotherapy directly alters the TME, inducing neogenesis of tertiary lymphoid structures that convert immunologically quiescent tumors into immunologically active tumors.

Read the full summary ↓

Alterations in five pathways important for immune modulation and lymphoid structure development (TH17/Treg, NFkB, Ubiquitin-proteasome, Chemokines/chemokine receptors, and Integrins/adhesion molecules) in vaccine-induced intratumoral lymphoid aggregates were associated with improved post-vaccination responses. Additional studies in other cancers and patients treated with other forms of immunotherapy are warranted to further develop signatures defined in intratumoral lymphoid structures into biomarkers that predict effective anti-tumor immune responses. These signatures may also expose therapeutic targets for promoting more robust antitumor immune responses in the TME.

This dataset

Open GSE52171 in finder → Find more human microarray datasets → Pancreatic cancer landscape →

Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE52171_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA227088. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 24942756) ↗

Samples in this study

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+ 20 more — browse all 20 samples with per-sample file links →

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GSE102238 Gene expression signatures associated with Perineural Invasion in pancreatic ductal adenocarcinoma 100 samples same disease briefing · shares pancreatic
GSE107610 Gene expression data of organoids derived from human pancreatic tumor and normal pancrea samples. 57 samples same disease briefing · shares pancreatic
GSE14245 Multiple Salivary Biomarkers for Early Detection of Pancreatic Cancer 24 samples same disease briefing · shares pancreatic
GSE132956 Gene Expression Data of Pancreatic Ductal Adenocarcinoma and Normal Tissue 15 samples same disease briefing · shares pancreatic
GSE107818 A serum-induced transcriptome and serum cytokine signature obtained at diagnosis correlates with the development of early pancreatic ductal adenocarcinoma metastasis 11 samples same disease briefing · shares pancreatic
GSE132946 Tumor Infiltrating Lymphocytes and Immune-Related Genes as Predictors of Outcome in Pancreatic Adenocarcinoma 6 samples same disease briefing · shares pancreatic

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