GEO series

EMILIN1 suppresses cell proliferation by inactivating Aurora Kinase and cell cycle regulator in head and neck squamous cell carcinoma

GSE253677 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2025/01/15 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 36 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: Head and neck cancerThis series is part of our curated briefing on it.
Samples: 36 samples: 12 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: EMILIN-1 Suppresses Cell Proliferation through Altered Cell Cycle Regulation in Head and Neck Squamous Cell CarcinomaThe American journal of pathology · 2025

Summary (written by the submitters)

The extracellular matrix (ECM) proteins play an important role in the physiological and pathological processes of tumor development and progression. EMILIN1 (Elastic Microfibril Interface Located ProteIN-1), a homotrimeric ECM glycoprotein, has been reported to be associated with cell adhesion and migration. We previously identified downregulated-EMILIN1 as a prognostic biomarker for secondary primary malignancy in head and neck squamous cell carcinoma (HNSCC).

Read the full summary ↓

We hypothesized that EMILIN1 functions as a tumor suppressor in HNSCC. In this study, we overexpressed exogenous EMILIN1 expression in the FaDu and CAL27 cell lines and knockdown EMILIN1 expression in both HNSCC Cancer-Associated Fibroblast (CAF) and normal fibroblast cells. Our results showed that EMILIN1 overexpression decreased cell proliferation, cell migration, and cell invasion in FaDu and CAL27 cells. Knockdown EMILIN1 in CAFs also induced cell proliferation and migration. RNA-sequencing analysis revealed the cell cycle and Aurora kinase signaling as the most significant enrichment pathways, and we then confirmed this finding at the protein level. Furthermore, we studied the effect of EMILIN1 on tumor development in vivo using chick chorioallantoic membrane (CAM) assay. EMILIN1overexpression reduced tumor area, Ki67-positive cells, and increased cleaved caspase-3 apoptotic cells. These findings suggest the tumor suppressing role of EMILIN1 in HNSCC through the inactivation of cell cycle pathway and Aurora kinase signaling. To the best of our knowledge, this is the first study to show that Aurora kinases are the key players in EMILIN1 tumor suppressive functions in head and neck cancer cells.

Published in

EMILIN-1 Suppresses Cell Proliferation through Altered Cell Cycle Regulation in Head and Neck Squamous Cell Carcinoma

Chanpanitkitchote P, Nuanpirom J, Pongsapich W et al. · The American journal of pathology 2025 · PMID 39892781 · doi:10.1016/j.ajpath.2025.01.010

This dataset

Open GSE253677 in finder → Find more human RNA-seq datasets → Head and neck 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 GSE253677_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 PRJNA1066749. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39892781) ↗

Study design

12 conditions, mostly in triplicate

FADU, OverEMILIN1, ×3 FADU, Control, ×3 CAL27, OverEMILIN1, ×3 CAL27, Control, ×3 CAF2, shEMILIN1, ×3 CAF2, shControl, ×3 CAF3, shEMILIN1, ×3 CAF3, shControl, ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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

GSM8025574 FADU, OverEMILIN1, rep1 FADU, OverEMILIN1,
GSM8025575 FADU, OverEMILIN1, rep2 FADU, OverEMILIN1,
GSM8025576 FADU, OverEMILIN1, rep3 FADU, OverEMILIN1,
GSM8025577 FADU, Control, rep1 FADU, Control,
GSM8025578 FADU, Control, rep2 FADU, Control,
GSM8025579 FADU, Control, rep3 FADU, Control,
GSM8025580 CAL27, OverEMILIN1, rep1 CAL27, OverEMILIN1,
GSM8025581 CAL27, OverEMILIN1, rep2 CAL27, OverEMILIN1,
GSM8025582 CAL27, OverEMILIN1, rep3 CAL27, OverEMILIN1,
GSM8025583 CAL27, Control, rep1 CAL27, Control,
GSM8025584 CAL27, Control, rep2 CAL27, Control,
GSM8025585 CAL27, Control, rep3 CAL27, Control,
GSM8025586 CAF2, shEMILIN1, rep1 CAF2, shEMILIN1,
GSM8025587 CAF2, shEMILIN1, rep2 CAF2, shEMILIN1,
GSM8025588 CAF2, shEMILIN1, rep3 CAF2, shEMILIN1,
GSM8025589 CAF2, shControl, rep1 CAF2, shControl,
GSM8025590 CAF2, shControl, rep2 CAF2, shControl,
GSM8025591 CAF2, shControl, rep3 CAF2, shControl,
GSM8025592 CAF3, shEMILIN1, rep1 CAF3, shEMILIN1,
GSM8025593 CAF3, shEMILIN1, rep2 CAF3, shEMILIN1,
GSM8025594 CAF3, shEMILIN1, rep3 CAF3, shEMILIN1,
GSM8025595 CAF3, shControl, rep1 CAF3, shControl,
GSM8025596 CAF3, shControl, rep2 CAF3, shControl,
GSM8025597 CAF3, shControl, rep3 CAF3, shControl,
GSM8025598 NF2, shEMILIN1, rep1 NF2, shEMILIN1,
GSM8025599 NF2, shEMILIN1, rep2 NF2, shEMILIN1,
GSM8025600 NF2, shEMILIN1, rep3 NF2, shEMILIN1,
GSM8025601 NF2, shControl, rep1 NF2, shControl,
GSM8025602 NF2, shControl, rep2 NF2, shControl,
GSM8025603 NF2, shControl, rep3 NF2, shControl,
GSM8025604 NF3, shEMILIN1, rep1 NF3, shEMILIN1,
GSM8025605 NF3, shEMILIN1, rep2 NF3, shEMILIN1,
GSM8025606 NF3, shEMILIN1, rep3 NF3, shEMILIN1,
GSM8025607 NF3, shControl, rep1 NF3, shControl,
GSM8025608 NF3, shControl, rep2 NF3, shControl,
GSM8025609 NF3, shControl, rep3 NF3, shControl,

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