title: Glycoproteins in Claudin-Low Breast Cancer Cell Lines Have a Unique Expression Profile.
abstract: Claudin proteins are components of epithelial tight junctions; a subtype of breast cancer has been defined by the reduced expression of mRNA for claudins and other genes. Here, we characterize the expression of glycoproteins in breast cell lines for the claudin-low subtype using liquid chromatography/tandem mass spectrometry. Unsupervised clustering techniques reveal a group of claudin-low cell lines that is distinct from nonmalignant, basal, and luminal lines. The claudin-low cell lines express F11R, EPCAM, and other proteins at very low levels, whereas CD44 is expressed at a high level. Comparison of mRNA expression to glycoprotein expression shows modest correlation; the best agreement occurs when the mRNA expression level is lowest and little or no protein is detected. These findings from cell lines are compared to those for tumor samples by the Clinical Proteomic Tumor Analysis Consortium (CPTAC). The CPTAC samples contain a group low in CLDN3. The samples low in CLDN3 proteins share many differentially expressed glycoproteins with the claudin-low cell lines. In contrast to the situation for cell lines or patient samples classified as claudin-low by RNA expression, however, most of the tumor samples low in CLDN3 protein express the estrogen receptor or HER2. These tumor samples express CD44 protein at low rather than high levels. There is no correlation between CLDN3 gene expression and protein expression in these CPTAC samples; hence, the claudin-low subtype defined by gene expression is not the same group of tumors as that defined by low expression of CLDN3 protein.
authors.affiliation: Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Biology, San Francisco State University , 1600 Holloway Ave., San Francisco, California 94132, United States.
authors.forename: Ten-Yang
authors.initials: TY
authors.lastname: Yen
authors.affiliation: Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Biology, San Francisco State University , 1600 Holloway Ave., San Francisco, California 94132, United States.
authors.forename: Spencer
authors.initials: S
authors.lastname: Bowen
authors.affiliation: Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Biology, San Francisco State University , 1600 Holloway Ave., San Francisco, California 94132, United States.
authors.forename: Roger
authors.initials: R
authors.lastname: Yen
authors.affiliation: Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Biology, San Francisco State University , 1600 Holloway Ave., San Francisco, California 94132, United States.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Piryatinska
authors.affiliation: Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Biology, San Francisco State University , 1600 Holloway Ave., San Francisco, California 94132, United States.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Macher
authors.affiliation: Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Biology, San Francisco State University , 1600 Holloway Ave., San Francisco, California 94132, United States.
authors.forename: Leslie C
authors.identifier: 0000-0002-2398-4765
authors.initials: LC
authors.lastname: Timpe
mesh_terms: D014408:Biomarkers, Tumor / Q000096:biosynthesis / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D062465:Claudin-3 / Q000096:biosynthesis / Q000235:genetics*; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006023:Glycoproteins / Q000096:biosynthesis / Q000235:genetics; D006801:Humans; D018960:Hyaluronan Receptors / Q000096:biosynthesis / Q000235:genetics*; D013058:Mass Spectrometry / Q000379:methods; D011379:Prognosis; D040901:Proteomics; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000096:biosynthesis / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; D062465:Claudin-3; D006023:Glycoproteins; D018960:Hyaluronan Receptors; D018719:Erb-b2 Receptor Tyrosine Kinases; C497483:CD44 protein, human; C568122:CLDN3 protein, human; C508053:ERBB2 protein, human
keywords: breast cancer; cell lines; claudin; glycoprotein; mass spectrometry; supervised classification