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PXD050416

PXD050416 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProteomics-derived biomarker panel facilitates distinguishing primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) from lung metastatic colorectal cancer (lmCRC)
DescriptionThe 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:47:04.111.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTiannan Guo
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-03-06 13:13:37ID requested
12024-06-23 01:58:44announced
22024-10-22 06:47:04announced2024-10-22: Updated project metadata.
Publication List
10.1016/j.mcpro.2024.100766;
Liu J, Chang X, Qian L, Chen S, Xue Z, Wu J, Luo D, Huang B, Fan J, Guo T, Nie X, Proteomics-Derived Biomarker Panel Facilitates Distinguishing Primary Lung Adenocarcinomas With Intestinal or Mucinous Differentiation From Lung Metastatic Colorectal Cancer. Mol Cell Proteomics, 23(5):100766(2024) [pubmed]
Keyword List
submitter keyword: primary lung adenocarcinomas
intestinal or mucinous differentiation
lung metastatic colorectal cancer
proteomics
Contact List
Tiannan Guo
contact affiliationSchool of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
contact emailguotiannan@westlake.edu.cn
lab head
Tiannan Guo
contact affiliationWestlake University
contact emailguotiannan@westlake.edu.cn
dataset submitter
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