PXD068788 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Identification and functional validation of intracellular protein partners of phosphorothioate-splice switching oligonucleotides through AP-MS |
| Description | Despite growing interest in therapeutic antisense oligonucleotides (ASOs), the mechanisms governing their intracellular trafficking remain poorly understood. This study investigates the intracellular protein partners of splice-switching oligonucleotides (SSOs) modified with phosphorothioate (PS) backbones of three different chemistries: tricycloDNA (tcDNA), locked nucleic acid (LNA), and 2'-O-methoxyethyl (2′MOE). The SSO studied here targets the exon 51 of the dystrophin pre-mRNA (SSOEx51), as part of an exon skipping strategy for Duchenne muscular dystrophy (DMD). Pulldowns were performed using lysates from differentiated human muscle cells carrying a deletion in the exon 52 of the DMD gene (KM571). Biotinylated SSOs were immobilized on streptavidin-coated magnetic beads, and interacting proteins were captured and identified by nanoLC-MS/MS. In addition to analyzing the effect of different chemistries of ASOs on protein binding, we also evaluated the impact of sequence variation by comparing two additional tcDNA chemistry sequences (named TSB-T3 and TSB-C1). Finally, to enable enrichment analyses, we performed a characterization of the whole proteome of KM571 cells. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-01-20 |
| AnnouncementXML | Submission_2026-01-20_09:19:23.584.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Guilhem Clary |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | carbamoylated residue; acetylated residue; monohydroxylated residue |
| Instrument | timsTOF Pro |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-09-24 15:41:48 | ID requested | |
| ⏵ 1 | 2026-01-20 09:19:24 | announced | |
Publication List
Keyword List
| submitter keyword: Antisense oligonucleotides (ASOs) |
| phosphorothioate (PS) |
| splice switching oligonucleotides (SSOs) |
| Duchenne muscular dystrophy (DMD) |
| exon skipping |
| protein-oligonucleotide interaction |
| Affinity purification mass spectrometry (AP-MS) |
Contact List
| Aurélie GOYENVALLE |
|---|
| contact affiliation | Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France |
| contact email | aurelie.goyenvalle@uvsq.fr |
| lab head | |
| Guilhem Clary |
|---|
| contact affiliation | Istitut Cochin |
| contact email | guilhem.clary@inserm.fr |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
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| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD068788
- Label: PRIDE project
- Name: Identification and functional validation of intracellular protein partners of phosphorothioate-splice switching oligonucleotides through AP-MS
