GEO series

Molecular differentiation between complete and incomplete responders to neoadjuvant therapy in rectal cancer

GSE242786 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2024/08/09 Platform GPL11154

At a glance

RNA-seq (gene expression) · human · 15 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Topic: Colorectal cancerThis series is part of our curated briefing on it.
Samples: 15 samples: 5 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Molecular differentiation between complete and incomplete responders to neoadjuvant therapy in rectal cancerResearch square · 2024

Summary (written by the submitters)

Neoadjuvant chemoradiotherapy (nCRT) is the standard treatment for locally advanced rectal cancer, but less than half of patients have a clinical complete response to this treatment. To define the molecular features that are associated with response to neoadjuvant therapy, we generated and collected genomic and transcriptomic data from 712 cancers prior to treatment from our own data and from publicly available data.

Read the full summary ↓

We found that patients with a complete response have decreased risk of local recurrence and future metastasis. We identified multiple differences in DNA mutations and transcripts between complete and incomplete responders. Complete responder tumors have a higher tumor mutation burden and many more significant co-occurring mutations than the incomplete responder tumors. In addition, mutations in DNA repair genes (across multiple mechanisms of repair) were enriched in complete responders and they also had lower expression of these genes indicating that defective DNA repair is associated with complete response to nCRT. Using logistic regression, we identified three significant predictors of complete response: tumor size, mutations within specific network genes, and the existence of three or more concurrent mutations. In tumors that do not completely respond to nCRT, abnormal cell-cell interaction and increased cancer associated fibroblasts were associated with recurrence. Additionally,gene expression analysis identified a subset of immune hot tumors with worse outcomes and upregulation of immune checkpoint proteins. Overall, our study provides a comprehensive understanding of the molecular features associated with response to nCRT and the molecular differences in non-responder tumors that later reoccur. This knowledge may provide critical insight into the development of precision therapy for rectal cancer.

Published in

Molecular differentiation between complete and incomplete responders to neoadjuvant therapy in rectal cancer

Chong Z, Huang F, McLeod M et al. · Research square 2024 · PMID 39011117 · doi:10.21203/rs.3.rs-4456000/v1

This dataset

Open GSE242786 in finder → Find more human RNA-seq datasets → Colorectal cancer landscape →

Download · which file do I need?

Direct links to NCBI and ENA, 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, or the whole study as GSE242786_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1014721 and SRA study SRP459457. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39011117) ↗

Study design

5 conditions, mostly in triplicate

CR, tumor, NP10 ×4 CR, tumor, NP05 ×3 ICR, tumor, NP17 ×3 CR, tumor, NP ×2 ICR, tumor, NP19 ×2 ICR, tumor, NP ×1

Supports a between-group comparison across 14 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 14 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM7770474 CR, tumor, NP02 CR, tumor, NP
GSM7770475 CR, tumor, NP05_1 CR, tumor, NP05
GSM7770476 CR, tumor, NP05_2 CR, tumor, NP05
GSM7770477 CR, tumor, NP05_3 CR, tumor, NP05
GSM7770478 CR, tumor, NP20 CR, tumor, NP
GSM7770479 CR, tumor, NP10_1 CR, tumor, NP10
GSM7770480 CR, tumor, NP10_2 CR, tumor, NP10
GSM7770481 CR, tumor, NP10_3 CR, tumor, NP10
GSM7770482 CR, tumor, NP10_4 CR, tumor, NP10
GSM7770483 ICR, tumor, NP14
GSM7770484 ICR, tumor, NP17_1 ICR, tumor, NP17
GSM7770485 ICR, tumor, NP17_2 ICR, tumor, NP17
GSM7770486 ICR, tumor, NP17_3 ICR, tumor, NP17
GSM7770487 ICR, tumor, NP19_1 ICR, tumor, NP19
GSM7770488 ICR, tumor, NP19_2 ICR, tumor, NP19

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GSE254249 Remodeling of T and endothelial cells during total neoadjuvant therapy in rectal cancer 92 samples shares neoadjuvant, therapy, rectal
GSE318268 CMS subtypes correlate with complete response in trial of neoadjuvant Galunisertib plus chemoradiation in rectal cancer 73 samples shares neoadjuvant, complete, rectal
GSE213331 Identification of four immune subtypes in locally advanced rectal cancer treated with neoadjuvant chemotherapy for predicting the efficacy of subsequent immune checkpoint blockade 27 samples shares neoadjuvant, therapy, rectal
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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.