GEO series

NF1 modulates microtubular repair and dictates sensitivity to maytansinoid antibody-drug conjugates in HER2-positive breast cancer

GSE267855 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2024/12/01 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 18 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: Breast cancerThis series is part of our curated briefing on it.
Samples: 18 samples: 6 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.

Summary (written by the submitters)

NF1 is a tumor suppressor widely mutated across several cancers. Its best characterized function is the inhibition of RAS signaling through its GTPase-Activating Protein (GAP) domain. Additional functions have been proposed but not deeply investigated, due to its large size and complex domain structure. Here, combining patient data, in vitro/in vivo models and protein biochemistry, we show that NF1 is a novel Microtubule-Associated Protein (MAP) that modulates microtubular dynamics and intra-tubular repair.

Read the full summary ↓

NF1 loss results in mitotic defects such as prolonged mitosis, supranumerary centrosomes and chromosome missegregation, leading to low-grade aneuploidy in cell lines and patients. Loss of NF1-mediated intratubular repair creates a liability specifically targetable by maytansinoids, a class of microtubule-depolymerizing agents widely used as payloads in Antibody-Drug Conjugates such as Trastuzumab-Emtansine (T-DM1). Our results directly imply loss of intratubular repair as a driver of tumorigenesis, and NF1 as the first ADC payload-associated biomarker.

This dataset

Open GSE267855 in finder → Find more human RNA-seq datasets → Breast 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 GSE267855_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 PRJNA1113536 and SRA study SRP508641. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

mock_ctrl ×3 mock_TDM1 ×3 NF1KO3_ctrl ×3 NF1KO3_TDM1 ×3 NF1KOAE6_ctrl ×3 NF1KOAE6_TDM1 ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM8279890 mock_ctrl_1 mock_ctrl
GSM8279891 mock_ctrl_2 mock_ctrl
GSM8279892 mock_ctrl_3 mock_ctrl
GSM8279893 mock_TDM1_1 mock_TDM1
GSM8279894 mock_TDM1_2 mock_TDM1
GSM8279895 mock_TDM1_3 mock_TDM1
GSM8279896 NF1KO3_ctrl_1 NF1KO3_ctrl
GSM8279897 NF1KO3_ctrl_2 NF1KO3_ctrl
GSM8279898 NF1KO3_ctrl_3 NF1KO3_ctrl
GSM8279899 NF1KO3_TDM1_1 NF1KO3_TDM1
GSM8279900 NF1KO3_TDM1_2 NF1KO3_TDM1
GSM8279901 NF1KO3_TDM1_3 NF1KO3_TDM1
GSM8279902 NF1KOAE6_ctrl_1 NF1KOAE6_ctrl
GSM8279903 NF1KOAE6_ctrl_2 NF1KOAE6_ctrl
GSM8279904 NF1KOAE6_ctrl_3 NF1KOAE6_ctrl
GSM8279905 NF1KOAE6_TDM1_1 NF1KOAE6_TDM1
GSM8279906 NF1KOAE6_TDM1_2 NF1KOAE6_TDM1
GSM8279907 NF1KOAE6_TDM1_3 NF1KOAE6_TDM1

More Breast cancer datasets

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GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing
GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing
GSE277806 NF1 Loss Promotes EGFR Activation and Confers Sensitivity to EGFR Inhibition in NF1 Mutant Melanoma 32 samples shares nf1, sensitivity
GSE307748 ZNF180 modulates tumor intrinsic immunotherapy resistance in melanoma through driving plasticity [RNA-Seq] 12 samples shares nf1, modulates
GSE277807 NF1 Loss Promotes EGFR Activation and Confers Sensitivity to EGFR Inhibition in NF1 Mutant Melanoma 6 samples shares nf1, sensitivity

Search all human RNA-seq datasets in GEO →

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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.