PXD050416 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Proteomics-derived biomarker panel facilitates distinguishing primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) from lung metastatic colorectal cancer (lmCRC) |
Description | The diagnosis of primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) remains challenging due to the overlapping histomorphological, immunohistochemical and genetic characteristics with lung metastatic colorectal cancer (lmCRC). This study aimed to explore the protein biomarkers that could distinguish between PAIM and lmCRC. To uncover differences between the two diseases, we used tandem mass tagging (TMT)-based shotgun proteomics to characterize proteomes of formalin-fixed paraffin-embedded (FFPE) tumor samples of PAIM (n = 22) and lmCRC (n = 17). Then three machine learning algorithms, namely support vector machine (SVM), random forest and the Least Absolute Shrinkage and Selection Operator (LASSO), were utilized to select protein features with diagnostic significance. These candidate proteins were further validated in an independent cohort (PAIM, n = 11; lmCRC, n = 19) by immunochemistry (IHC) to confirm their diagnostic performance. In total, 105 proteins out of 7871 proteins were significantly dysregulated between PAIM and lmCRC samples and well-separated two groups by Uniform Manifold Approximation and Projection (UMAP). The upregulated proteins in PAIM were involved in actin cytoskeleton organization, platelet degranulation, and regulation of leukocyte chemotaxis, while downregulated ones were involved in mitochondrial transmembrane transport, vasculature development, and stem cell proliferation. A set of 10 candidate proteins (high-level expression in lmCRC: CDH17, ATP1B3, GLB1, OXNAD1, LYST, FABP1; high-level expression in PAIM: NARR, MLPH, S100A14, CK7) was ultimately selected to distinguish PAIM from lmCRC by machine learning algorithms. We further confirmed using IHC that the five protein biomarkers including CDH17, CK7, MLPH, FABP1 and NARR were effective biomarkers for distinguishing PAIM from lmCRC. Our study depicts PAIM-specific proteomic characteristics and demonstrates the potential utility of new protein biomarkers for the differential diagnosis of PAIM and lmCRC. These findings may contribute to improving the diagnostic accuracy and guide appropriate treatments for these patients. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_06:47:04.111.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Tiannan Guo |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-03-06 13:13:37 | ID requested | |
1 | 2024-06-23 01:58:44 | announced | |
⏵ 2 | 2024-10-22 06:47:04 | announced | 2024-10-22: Updated project metadata. |
Publication List
Keyword List
submitter keyword: primary lung adenocarcinomas |
intestinal or mucinous differentiation |
lung metastatic colorectal cancer |
proteomics |
Contact List
Tiannan Guo |
contact affiliation | School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China |
contact email | guotiannan@westlake.edu.cn |
lab head | |
Tiannan Guo |
contact affiliation | Westlake University |
contact email | guotiannan@westlake.edu.cn |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD050416
- Label: PRIDE project
- Name: Proteomics-derived biomarker panel facilitates distinguishing primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) from lung metastatic colorectal cancer (lmCRC)