PXD039480

PXD039480 is an original dataset announced via ProteomeXchange.

Title	Rhabdomyosarcoma surfaceome profiling with six fusion-positive (FP) RMS cell lines, five fusion-negative (FN) RMS cell lines, and three ARMS patient-derived xenografts (PDXs)
Description	Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. Prognosis for patients with high grade and metastatic disease is still very poor, and survivors are burdened with long-lasting side effects. Therefore, more effective and less toxic therapies are needed. Surface proteins are ideal targets for antibody-based therapies, like bispecific antibodies, antibody drug conjugates, or chimeric antigen receptor (CAR) T cell. Specific surface targets for RMS are scarce. Here, we performed a surfaceome profiling based on differential centrifugation enrichment of surface/membrane proteins and detection by LC-MS on six fusion-positive (FP) RMS cell lines, five fusion-negative (FN) RMS cell lines, and three RMS patient-derived xenografts (PDXs). 699 proteins were detected in the three RMS groups. Ranking based on expression levels and comparison to expression in normal MRC-5 fibroblasts and myoblasts, followed by statistical analysis, highlighted known RMS targets such as FGFR4, NCAM1, and CD276/B7-H3, and revealed AGRL2, JAM3, MEGF10, GPC4, CADM2, as potential targets for immunotherapies of RMS. L1CAM expression was investigated in RMS tissues and strong L1CAM expression was observed in more than 80% of alveolar RMS tumors, making it a practicable target for antibody-based therapies of alveolar RMS.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:43:41.452.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michele Bernasconi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-16 13:35:17	ID requested
1	2023-03-11 10:57:37	announced
⏵ 2	2023-11-14 08:43:47	announced	2023-11-14: Updated project metadata.

Timpanaro A, Piccand C, Uldry AC, Bode PK, Dzhumashev D, Sala R, Heller M, R, ö, ssler J, Bernasconi M, Surfaceome Profiling of Cell Lines and Patient-Derived Xenografts Confirm FGFR4, NCAM1, CD276, and Highlight AGRL2, JAM3, and L1CAM as Surface Targets for Rhabdomyosarcoma. Int J Mol Sci, 24(3):(2023) [pubmed]

submitter keyword: rhabdomyosarcoma,Surfaceome

Michele Bernasconi
contact affiliation	Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Switzerland
contact email	michele.bernasconi@unibe.ch
lab head
Michele Bernasconi
contact affiliation	Insel University Hospital Bern
contact email	michele.bernasconi@unibe.ch
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/03/PXD039480

PRIDE project URI

• PRIDE
  1. PXD039480
     1. Label: PRIDE project
     2. Name: Rhabdomyosarcoma surfaceome profiling with six fusion-positive (FP) RMS cell lines, five fusion-negative (FN) RMS cell lines, and three ARMS patient-derived xenografts (PDXs)