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ProteomicsCrosslinking of Ly6a metabolically reprogram CD8 T cells for cancer immunotherapy.
To evaluate the downstream effects of anti-Ly6a crosslinking, we examined the effect of anti-Ly6a antibodies on CD8+ T cell activity in the presence and absence of target tumor cells by high-resolution mass spectrometry proteomic analyses. Spleen cells were isolated from gp10025–33 TCR transgenic mi...
ORGANISM(S): Mus musculus (Mouse) 
2024-08-04 | PXD050734 | Pride
Uvb Cd8 t cells Cancer immunotherapy T cells metabolism 
ProteomicsClinical proteomics of invasive breast carcinoma reveals a major role for proline metabolism in imparting drug resistance
Aggressive breast tumors are routinely treated with pre-operative chemotherapy. However, a subset of patients have recurrence despite adjuvant treatment. To identify metabolic processes involved in drug resistance, we took a mass spectrometry-based proteomic approach, and analyzed a breast cancer co...
ORGANISM(S): Homo sapiens (Human) 
2020-08-24 | PXD012000 | Pride
Metabolism Neoadjuvant chemotherapy Clinical proteomics Proline biosynthesis 
ProteomicsNovel proteomic approach (PUNCH-P) reveals cell cycle-specific fluctuations in mRNA translation
Monitoring protein synthesis is essential to our understanding of gene expression regulation, as protein abundance is thought to be predominantly controlled at the level of translation. Mass-spectrometric and RNA sequencing methods have been recently developed for investigating mRNA translation at a...
ORGANISM(S): Homo sapiens (Human) 
2019-02-18 | PXD012727 | Pride
Translatome Ribosome Punch-p 
ProteomicsProteomics of melanoma response to immunotherapy reveals dependence on mitochondrial function
Immunotherapy has revolutionized cancer treatment, yet most patients do not respond. Here, we investigated mechanisms of response by deeply profiling the proteome of clinical samples from advanced stage melanoma patients undergoing either tumor infiltrating lymphocytes (TIL)-based or anti-PD1 immuno...
ORGANISM(S): Homo sapiens (Human) 
2019-07-29 | PXD006003 | Pride
Human Melanoma Lc-ms/ms 
ProteomicshnRNP C is a key regulator of protein synthesis in mitosis
Stringent post-transcriptional regulation of mRNA fate is critical for proper cell division. To detect proteins involved in such regulation, we analyzed the composition of intact polysomal complexes from mitotic and interphase cells by quantitative mass-spectrometry. Using this approach, we detected...
ORGANISM(S): Homo sapiens (Human) 
2017-07-11 | PXD004244 | Pride
Ribosomes Proteomics Cell cycle Mitosis Silac Translation 
ProteomicsUBQLN4, a regulator of protein dynamics at sites of DNA damage, is lost in a new genome instability syndrome and elevated in aggressive tumors
The ubiquitin-proteasome system (UPS) plays a crucial role in cellular homeostasis, but the mechanistic aspects of its involvement in the DNA damage response (DDR) remain largely elusive. Here, we identify a homozygous truncation mutation in the UBQLN4 gene in families with highly pleiotropic autoso...
ORGANISM(S): Homo sapiens (Human) 
2020-06-02 | PXD008299 | Pride
Dna damage Lc-ms Proteomics Ubqln4 
ProteomicsPDZD8 interacts with Protrudin and Rab7 to form an ER-late endosome membrane contact site that recruits mitochondria
Endosomes regulate a plethora of cellular processes including signaling, nutrient status and organelle quality control by controlling the fate of material entering the cells. Endosomes undergo a process of maturation which specifies whether material will be shuttled back to the cell surface or degra...
ORGANISM(S): Homo sapiens (Human) 
2020-06-02 | PXD015523 | Pride
Human Ls-ms/ms Q exactive plus 
ProteomicsSpecific inhibition of splicing factor activity by decoy RNA oligonucleotides
Alternative splicing, a fundamental step in gene expression, is deregulated in many diseases. Splicing factors (SFs), which regulate this process, are up- or down regulated or mutated in several diseases including cancer. To date, there are no inhibitors that directly inhibit the activity of SFs. We...
ORGANISM(S): Homo sapiens (Human) 
2019-01-31 | PXD012564 | Pride
Splicing factors Alternative splicing Rbfox2 Ptbp1 Cancer Lc-ms Srsf1 Decoy oligonucleotides 
ProteomicsClinical Proteomics of Breast Cancer Unravels a Novel Layer of Breast Cancer Classification
Breast cancer classification has been in the focus of numerous large worldwide efforts, analyzing the molecular basis of breast cancer subtypes, aiming to associate them with clinical outcome and improve the current diagnostic routine. Genomic and transcriptomic profiles of breast cancer have been w...
ORGANISM(S): Homo sapiens (Human) 
2019-07-29 | PXD009766 | Pride
Lc-ms Proteomics Breast cancer classification Breast cancer subtypes 
ProteomicsProteogenomic analysis of glioblstoma reveals survival related patterns
In the current work, we present the first proteogenomic dataset of GBM clinical samples to date. We have assembled a cohort of 87 GBM patients of varying survival rates and performed MS-based proteomics analysis as well as RNA-seq in order to identify the molecular differences associated with surviv...
ORGANISM(S): Homo sapiens (Human) 
2021-04-16 | PXD018024 | Pride
Proteogenomics Proteomics Mass spectrometry Glioblstoma Rna-seq 
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