Project description:Oncogenic cell-surface membrane proteins contribute to the phenotypic and functional characteristics of cancer stem cells (CSCs). We quantitatively analyzed cell-surface membrane proteins that are in close proximity to CD147 in CSCs using proximity-labeling proteomic approach. Moreover, we compared CSCs to non-CSCs to identify CSC-specific cell-surface membrane proteins that are the nearest neighbors of CD147 and revealed that lateral interaction between CD147 and CD276 (B7H3) concealed within the lipid raft microdomain in CSCs confers resistance to docetaxel, known to treat many types of cancer patients including metastatic breast cancer. Furthermore, we found that co-expression of CD147 and CD276 in patients with HER2+ breast cancer who received chemotherapy had poor disease-free survival (DFS) and Overall survival (OS) rates (p = 0.04 and 0.08, respectively). Subsequent immunohistochemical analysis indicated that co-expression of CD147 and CD276 may be associated with poor response to chemotherapy in an independent HER2+ BC cohort. Altogether, our study suggests that the lateral interaction between CD147 and its proximal partners, such as CD276, may be related to a poor prognostic factor in BC and a predictive marker for the critical phenotypic determinant of breast cancer stemness.
Project description:Siglec-1 is a macrophage lectin-like receptor that mediates sialic acid-dependent cellular interactions. It was shown previously to promote inflammation in autoimmune disease through suppressing the expansion of regulatory T cells (Tregs). We have investigated the molecular basis for Siglec-1 binding to these cells using in vitro-induced Tregs. A proximity labelling and proteomics strategy were used to identify glycoproteins expressed by activated Tregs that may function as Siglec-1 counter-receptors.
Project description:Siglec-1 is a macrophage lectin-like receptor that mediates sialic acid-dependent cellular interactions. It was shown previously to promote inflammation in autoimmune disease through suppressing the expansion of regulatory T cells (Tregs). We have investigated the molecular basis for Siglec-1 binding to these cells using in vitro-induced Tregs. A proximity labelling and proteomics strategy were used to identify glycoproteins expressed by activated Tregs that may function as Siglec-1 counter-receptors.
Project description:This new method highlights the use of membrane-tethered exogenous biotinylators for small-scale membrane proteome characterization of extracellular vesicles and cells.
Project description:The project aimed to profile the cell surface proteins of Nomo-1 (AML cell line) using structural surfaceomics for identification of protein conformation-based cancer antigens thereby expanding the toolkit for cancer target discovery for immunotherapeutic targeting. To achieve the goal, cell surface capture (CSC) was integrated with cross-linking mass spectrometry (XL-MS). PhoX was used as a cross-linker to freeze the structural conformations of protein in three-dimensional space, followed by biotinylation of cell surface proteins to enable enrichment of cell surface proteins to allow focused XL-MS analysis of those enriched proteins. PhoX having in-built phosphonate-based IMAC handle which allowed additional enrichment of cross-linked peptides.
Project description:CD38 is a surface ectoenzyme expressed at high levels on myeloma plasma cells and is the target for the monoclonal antibodies (mAbs) daratumumab and isatuximab. CD38 density on tumor cells is an important determinant of mAb efficacy while CD38 is lost after mAb treatment. Several small molecules have been found to increase tumor surface CD38, with the goal of boosting mAb efficacy in a co-treatment strategy. Here we sought to extend our currently limited insight into CD38 surface expression by using a multi-omics approach. Genome-wide CRISPR-interference screens integrated with patient-centered epigenetic analysis confirmed known regulators of CD38, such as RARA, while revealing XBP1 and SPI1 as other key transcription factors governing surface CD38 levels. CD38 knockdown followed by cell surface proteomics demonstrated no significant remodeling of the myeloma “surfaceome” after genetically-induced loss of this antigen. Integrated transcriptome and surface proteome data confirmed high specificity of all-trans retinoic acid in upregulating CD38 in contrast to broader effects of azacytidine and panobinostat. Finally, unbiased phosphoproteomics identified inhibition of MAP kinase pathway signaling in tumor cells after daratumumab treatment. Our work provides a resource to design strategies to enhance efficacy of CD38-targeting immunotherapies in myeloma.
Project description:Odorant-Binding Proteins (OBP) are players of perireceptor events in olfaction. A molecular mechanism explaining their specificity for odors and pheromones has still to be proposed. A new track comes from the analysis of pig olfactory secretome, which is mainly composed of OBP isoforms, generated from 3 gene products by PTM, phosphorylation and O‐β‐N‐acetylglucosaminylation (O-GlcNAcylation), which are unusual for secreted proteins. These diverse isoforms could display different binding properties towards ligands. Before testing such a function, both post-translational modifications, although assessed by specific antibodies, have to be identified by mass spectrometry. We report here for the first time, the identification of phosphorylation and O-GlcNAcylation on peptides coming from trypsin digestion of OBP by ESI-HCD-MS/MS. PEAKS software analysis of raw MS data allowed selecting spectra that were analyzed manually to identify PTM. Four peptides corresponding to two different portions of OBP sequence were modified either by a phosphate group or by a hexNAc moiety. Due to the high energy used in HCD, the data did not allow precise localization of the modified sites. We suggest that these two PTM, by generating multiple isoforms, should extend the binding repertoire of secreted OBPs
Project description:We and others have previously shown that glomerular endothelial cells and podocytes express hypoxia-inducible transcription factors (HIFs). HIFs bind to hypoxia response elements in target genes, such as vascular endothelial growth factor, which is continually produced by podocytes throughout life. To further assess function of HIFs in podocyte biology, podocin-Cre mice were mated with floxed von Hippel-Lindau (VHL) mice to selectively delete VHL, a component of an E3 ligase complex responsible for degradation of HIFs in normoxia. We reasoned that cells lacking VHL would overexpress stable HIFs and upregulate hypoxia-responsive genes. Progeny from these crosses displayed two phenotypes, non-proteinuric with glomerular basement membrane (GBM) defects and proteinuric with GBM defects and end-stage renal failure at ~6 months of age. Gene changes associated with the mild, non-proteinuric phenotype were studied using isolated glomeruli from wildtype and Pod-Cre fVHL mice. At 4 weeks of age, urine was collected and urinary albumin was quantified by Albuwell elisa from Pod-Cre fVHL litters. At 6 weeks of age, glomeruli from 3 wildtype littermate controls and 3 non-proteinuric Pod-Cre fVHL mice were collected using the magnetic bead method. RNA was extracted and hybridized to Affymetrix microarrays.
Project description:B cell receptor (BCR) signaling and oncogenic tyrosine kinases that mimic BCR-signaling in B-lineage leukemia and lymphoma depend on assembly of membrane proximal signaling complexes. Signalosomes in normal BCR- and oncogene (e.g. BCR-ABL1, RAS-pathway lesions) signal transduction are recruited to phospholipid anchors in lipid rafts. The robustness of these complexes depends on cholesterol accumulation in lipid rafts. Here we identified the interferon-induced transmembrane protein IFITM3 as a central regulator of cholesterol in lipid rafts.