Project description:In order to study how chemoresistance in breast cancer cells influences immune cells, MDA-MB-468 cells resistant to paclitaxel were generated. Bulk RNAseq were used to assess resistant associated changes.
Project description:This study elucidates the effect of the E2F1-regulated melanoma-secreted factors on the phenotype and transcriptional program of immune cells (CD4+ T and CD8+ T cells) in the melanoma immune microenvironment. In order to determine the immune modulatory effect of the secretome on immune cells, we established a co-culture system where different melanoma cell lines (high-E2F1/invasive and low E2F1/non-invasive) were co-cultured with CD4+ or CD8+ T cells without direct interaction. These data describe the transcriptomes of immune cells and for the two melanoma cell lines Mel147 and C8161, both in co- and monoculture condition, with stable E2F1 knockdowns and corresponding controls.
Project description:We found the bone marrow stromal-derived neural progenitor cells secretome have the neural protection effect. Proteomic analysis was performed nn order to analyze the protection factor in the secretome. Keywords: Neural protection, secretome
Project description:Cancer secretome is a reservoir for aberrant glycosylation. How therapies alter this post59 translational cancer hallmark and the consequences thereof remain elusive. Here we show that an elevated secretome fucosylation is a pan-cancer signature of both response and resistance to multiple targeted therapies. Large-scale pharmacogenomics revealed that fucosylation genes display widespread association with resistance to these therapies. In both cancer cell cultures and patients, targeted kinase inhibitors distinctively induced core fucosylation of secreted proteins less than 60 kDa. Label-free proteomics of N-glycomes revealed that fucosylation of the antioxidant PON1 is a critical component of the therapy66 induced secretome. Core fucosylation in the Golgi impacts PON1 stability and folding prior to secretion, promoting a more degradation-resistant PON1. Non-specific and PON1-specific secretome deglycosylation both limited the expansion of resistant clones in a tumor regression model. Our findings demonstrate that core fucosylation is a common modification indirectly induced by targeted therapies that paradoxically promotes resistance.
Project description:The Skeletal muscle is a metabolic active tissue that secretes various proteins. These so called myokines act auto-, para- and endocrine affecting muscle physiology and exert systemic effects on other tissues and organs. Myokines are also described to play a crucial role in the pathophysiology of metabolic diseases. Combining three different mass spectrometry based non-targeted and one antibody based targeted approach we investigated the secretome of differentiated primary human skeletal muscle cells derived from adult donors. A total of 548 non-redundant proteins were detected by combined proteomic profiling. Expression was confirmed on mRNA level for 501. Stringent consecutive filtering recruiting several database, i.e. SignalP, SecretomeP and ER_retention signals, the computational analysis assigned 306 as secretory proteins including 33 potentially novel myokines. This comprehensive profiling study of the human skeletal muscle secretome expands our knowledge of the composition of the human myokinome and further highlights the pivotal role of myokines in the regulation of multiple biological processes. We performed gene expression microarray analysis of primary human myotubes derived from twelve healthy individuals
Project description:Protein secretion can mediate communication of distant cells in a multicellular organism and can control a broad range of physiological functions. Regulation of this process is crucial, especially for cells of the immune system that sense pathogens through specific receptors and release proteins that initiate and orchestrate the immune response. This secretome is today analyzed using antibody-based assays, but mass spectrometry could provide an unbiased and comprehensive alternative. Here we developed a quantitative, high resolution mass spectrometric workflow to detect and quantify proteins that are released from macrophages upon Toll-like receptor 4 (TLR4) activation by the microbial component lipopolysaccharide (LPS)5. We quantified the time-resolved release of 775 proteins, including 52 annotated cytokines, from only 150.000 primary cells per condition. The dynamic range of the secretory induction was at least 10,000 fold and we achieved sensitivity in the low picogram range. Comparison to the transcriptome revealed high correlation for some protein classes but also anti-correlation resulting from the transcriptionally decoupled release of lysosomal proteins. Using gene knockout (KO) mouse strains as genetic models with intracellular signaling adaptor deficiencies, we defined distinct secretory profiles depending on which arms of the signaling pathways are missing. We show that MyD88 dominates over TRIF in the number and fold-induction of secreted proteins6,7. Interestingly, the sum of the two signaling arms does not equal the wild-type response; instead, protein secretion is tuned by synergistic and predominantly redundant mechanisms. The kinetic data reveals that the release of anti-inflammatory proteins dampens the initial pro-inflammatory response. Our study provides a paradigm for the sensitive and time-resolved identification of receptor activation induced cellular secretomes, including proteins with unexpected extracellular presence, and allows the characterization of the underlying signal transduction pathways.
Project description:Background: Advanced Renal cell carcinoma (RCC) is therapeutically challenging. RCC progression is facilitated by mesenchymal stem/stromal cells (MSCs) that exert remarkable tumor tropism. The specific mechanisms mediating MSCs’ migration to RCC remain unknown. Here, we comprehensively analyzed RCC secretome to identify MSCs attractants. Methods: Conditioned media (CM) were collected from five RCC-derived cell lines (Caki-1, 786-O, A498, KIJ265T, KIJ308T) and non-tumorous control cell line (RPTEC/TERT1) and analyzed using cytokine arrays targeting 274 cytokines in addition to global CM proteomics. MSCs were isolated from bone marrow of patients undergoing standard orthopedic surgeries. RCC CM and the selected recombinant cytokines were used to analyze their influence on MSCs migration and microarray-targeted gene expression. The expression of genes encoding cytokines was evaluated in 100 matched-paired control-RCC tumor samples. Results: When compared with normal cells, CM from advanced RCC cell lines (Caki-1, KIJ265T) were the strongest stimulators of MSCs migration. Targeted analysis of 274 cytokines and global proteomics of RCC CM revealed decreased DPP4 and EGF, as well as increased AREG, FN1, and MMP1, with consistently altered gene expression in RCC cell lines and tumors. AREG and FN1 stimulated, while DPP4 attenuated MSCs migration. RCC CM induced MSCs’ transcriptional reprogramming, stimulating the expression of CD44, PTX3, and RAB27B. RCC cells secreted hyaluronic acid (HA), a CD44 ligand mediating MSCs’ homing to the kidney. AREG emerged as an upregulator of MSCs’ transcription. Conclusions: advanced RCC cells secrete AREG, FN1 and HA to induce MSCs migration, while DPP4 loss prevents its inhibitory effect on MSCs homing. RCC secretome induces MSCs’ transcriptional reprograming to facilitate their migration. The identified components of RCC secretome represent potential therapeutic targets. We used microarrays to determine the effect of the conditioned media (CM) collected from two RCC-derived cell lines (Caki-1, KIJ265T) and non-tumorous control cell line (RPTEC/TERT1) on the transcriptome change in mesenchymal stem/stromal cells (MSCs).