ABSTRACT: LD3 knock out cells were generated in HEK293T and HMC3 cells. Proteomics was done to test if they have any significant changes in the abundance of proteins that metabolize sugar lipids like gangliosides.
Project description:This part of the data submission of PXD046505. LD3 knock out cells were generated in HEK293T and HMC3 cells. Proteomics was done to test if they have any significant changes in the abundance of proteins that metabolize sugar lipids like gangliosides.
Project description:Proteomic analysis of peptides in close association to PacL1 under replete metal conditions (Sauton’s media), in Mycobacterium Tuberculosis (Erdman strain).
Project description:A microfluidics technology was implemented to the immunoaffinity purification process of MHC peptides in Ligandomics/Immunopeptidomics. The thus purified HLA peptides were analysed by LCMS with the nanoElute LC and TimsTOF Pro Mass Spectrometer from Bruker. The aim of the microfluidics implementation was to improve the sensitivity and robustness while also reducing antibody and other material requirements in the immunoaffinity purification protocol.
Project description:Whole brain tissue proteomics from rat models of cerebral small vessel disease and Alzheimer's disease, including the rTg-DI model of Cerebral Amyloid Angiopathy (CAA) Type-1, the rTg-D model of CAA Type-2 with both hemizygous and homozygous animals, and the TgSD-AD model of Alzheimer's Disease.
Project description:Marine brown algae produce the highly recalcitrant polysaccharide fucoidan, contributing to long-term oceanic carbon storage and climate regulation. Fucoidan is degraded by specialized heterotrophic bacteria, which promote ecosystem function and global carbon turnover using largely uncharacterized mechanisms. Here, we isolate and study two Planctomycetota strains from the microbiome associated with the alga Fucus spiralis, which grow efficiently on chemically diverse fucoidans. One of the strains appears to internalize the polymer, while the other strain degrades it extracellularly. Multi-omic approaches show that fucoidan breakdown is mediated by the expression of divergent polysaccharide utilization loci, and endo-fucanases of family GH168 are strongly upregulated during fucoidan digestion. Enzymatic assays and structural biology studies reveal how GH168 endo-fucanases degrade various fucoidan cores from brown algae, assisted by auxiliary hydrolytic enzymes. Overall, our results provide insights into fucoidan processing mechanisms in macroalgal-associated bacteria.
Project description:We employed PeptiCHIP Immunopeptidomics to profile tumor associated antigens (TAA) actively targeted by tumor specific T cells by exploiting the trogocytosis effect, whereby antigen presenting cells (APCs) nibble portions of the cognate T cell containing the TCR. The antigen presenting cells were then processed by Immunoaffinity purification by peptiCHIP to identify the relevant HLA-I peptides by LCMS on the Bruker Tims TOF Pro instrument.
Project description:Myeloproliferative Neoplasms (MPNs) are a heterogenous group of hematologic cancers characterized by excessive JAK/STAT signaling. Mutations of JAK2 signaling components are among the most common drivers of MPN, but alterations in Suppressors of Cytokine Signaling (SOCS) proteins have been implicated in MPN pathogenesis and progression. Cullin 5 (Cul5) is an E3 ubiquitin ligase known to work with suppressors of cytokine signaling (SOCS) proteins which regulate the JAK/STAT pathway. Here we report that mice lacking Cul5 in hematopoietic stem and progenitor cells (HSPCs) develop an MPN-like disease with characteristic features including splenomegaly, extramedullary hematopoiesis, thrombocytosis, and anemia. Cul5-deficient HSPCs have higher phospho-STAT5 (pSTAT5) levels following stimulation with IL-3 and outcompete WT HSPCs in bone marrow transplants. Immunoprecipitation of Cul5 in cultured HSPCs showed interactions with STAT5 as well as several well-studied substrate receptors including SOCS2, SOCS6, ASB2, ASB3, ASB6 and CIS, as well as lesser-known WSB1 and LRRC41. Proteome analysis of Lin- Sca-1+ c-kit+ (LSK) cells from Cul5Vav-Cre bone marrow shared many upregulated genes and signatures with MPN patient cells. Finally, treatment with ruxolitinib, a JAK1/2 inhibitor, ameliorated MPN symptoms in Cul5-deficient mice. These studies demonstrate a novel function of Cul5 in hematopoiesis, delineating a contributing role in MPN.
Project description:Protein ubiquitination controls diverse processes within eukaryotic cells, including protein degradation, and is often dysregulated in diseases1. Moreover, protein degraders that redirect ubiquitination activities toward disease targets are an emerging and promising therapeutic class2. Over 600 E3 ubiquitin ligases are expressed in humans3,4, but their substrates remain largely elusive due to a lack of robust methods to identify E3 ligase substrates. Here we report the development of E-STUB (E3 substrate tagging by ubiquitin biotinylation), a ubiquitin-specific proximity labeling method that biotinylates ubiquitinated substrates in proximity to an E3 ligase of interest. E-STUB accurately identifies the direct ubiquitinated targets of protein degraders, including collateral targets and ubiquitylation events that do not exhibit a degradative outcome. It also detects known substrates of E3 ligase cereblon (CRBN) and von Hippel-Lindau (VHL) with high precision. With the ability to elucidate proximal ubiquitination events, E-STUB may facilitate the development of proximity-inducing drugs and act as a generalizable method for E3 substrate mapping.