GEO series

Accessory fimbrial subunits and PPAD are necessary for TLR2 activation by Porphyromonas gingivalis

GSE332616 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2026/05/20 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 20 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)
Samples: 20 samples: 5 conditions, mostly with about 4 replicates eachGroups 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: Accessory fimbrial subunits and PPAD are necessary for TLR2 activation by Porphyromonas gingivalisMolecular oral microbiology · 2023

Summary (written by the submitters)

Porphyromonas gingivalis is an oral pathogen that promotes dysbiosis by quenching the bactericidal activity of the host immune system while maintaining chronic inflammation, leading to periodontitis. This involves the secretion of virulence factors such as P. gingivalis peptidyl arginine deiminase (PPAD), which converts the C-terminal Arg residues of bacterial and host-derived proteins and peptides into citrulline.

Read the full summary ↓

We have previously shown that PPAD activity and major fimbriae (containing FimA) are necessary for P. gingivalis to activate Toll-like receptor 2 (TLR2). TLR2 is an important component of the innate immune system and plays a predominant role in the recognition of P. gingivalis by host cells. Here, we extend those findings to show that P. gingivalis strains deficient for PPAD and fimbriae induced almost identical transcriptional profiles in infected primary human gingival fibroblasts (PHGFs), but these differed substantially from the transcriptome elicited by the wild-type ATCC 33277 strain. Apparently, PPAD-modified fimbriae trigger the host cell response to P. gingivalis, as confirmed by showing that the proinflammatory host cell response mediated by TLR2 is dependent on PPAD activity and the presence of fimbriae, with type I fimbriae as the most potent TLR2 activators. We also found that PPAD-modified accessory fimbrial subunits (FimC, FimD, and FimE) alone or in combination are TLR2 ligands in a reporter cell line. Although FimA polymerization to form the fimbrial shaft was not required for TLR2 activation, the secretion and proteolytic maturation of FimA were necessary for signaling by accessory Fim proteins. This was supported by showing that the proinflammatory activation of PHGFs is dependent on PPAD and accessory fimbrial subunits. We conclude that accessory fimbrial subunits are modified by PPAD and stimulate the response to P. gingivalis infection in a TLR2-dependent manner.

Published in

Accessory fimbrial subunits and PPAD are necessary for TLR2 activation by Porphyromonas gingivalis

Wielento A, Bereta GP, Szczęśniak K et al. · Molecular oral microbiology 2023 · PMID 37347653 · doi:10.1111/omi.12427

This dataset

Open GSE332616 in finder → Find more human RNA-seq datasets →

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 GSE332616_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 PRJNA1468674 and SRA study SRP702402. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37347653) ↗

Study design

5 conditions, mostly with about 4 replicates each

ATCC_WT ×4 control ×4 delFimA ×4 delPPAD ×4 W83 ×4

Supports a between-group comparison across 20 samples.

How we read this: 5 replicated groups read from 20 sample titles; they account for 20 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

GSM9751508 ATCC_WT_1 ATCC_WT
GSM9751509 ATCC_WT_2 ATCC_WT
GSM9751510 ATCC_WT_3 ATCC_WT
GSM9751511 ATCC_WT_4 ATCC_WT
GSM9751512 control_1 control
GSM9751513 control_2 control
GSM9751514 control_3 control
GSM9751515 control_4 control
GSM9751516 delFimA_1 delFimA
GSM9751517 delFimA_2 delFimA
GSM9751518 delFimA_3 delFimA
GSM9751519 delFimA_4 delFimA
GSM9751520 delPPAD_1 delPPAD
GSM9751521 delPPAD_2 delPPAD
GSM9751522 delPPAD_3 delPPAD
GSM9751523 delPPAD_4 delPPAD
GSM9751524 W83_1 W83
GSM9751525 W83_2 W83
GSM9751526 W83_3 W83
GSM9751527 W83_4 W83

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