ABSTRACT: The impact of NatC and UBR4 on the human proteome (protein abundance). Analysis of HAP1 WT siCtr, HAP1 WT siUBR4, HAP1 NAA30 KO siCtr, and HAP1 NAA30 KO siUBR4 cells.
Project description:The impact of NatC subunits NAA30, NAA35 and NAA38 on the human N-terminal acetylome. Analysis of HAP1 WT, NAA30 KO, NAA35 KO and NAA38 KO cells
Project description:The impact of NatC subunits NAA30, NAA35 and NAA38 on the human proteome (protein abundance). Analysis of HAP1 WT, NAA30 KO, NAA35 KO and NAA38 KO cells
Project description:We provide the first comprehensive analysis of nasal cell responses to SARS-COV-2 using single cell transcriptomics and proteomics. The immune response to SARS-CoV-2 is dominated by a delayed type I and III IFN response, which is too slow to contain viral replication. Cells transitioning from secretory to ciliated states are highly permissive to SARS-CoV-2, whereas goblet cells are relatively resistant. Cell-type differences in the production and response to IFN-I/III correlate with permissiveness. Pre-treatment with recombinant IFNs potently restricts SARS-CoV-2. Nasal delivery of recombinant IFNs is a promising prophylactic strategy for SARS-CoV-2
Project description:A differential label-fee proteomics approach was performed using 27 biopsies from patients with HCV-associated hepatic fibrosis. For statistical analysis the patients were grouped into a low and a high fibrosis group. The low fibrosis group contained 13 patients of fibrosis stages 0, 1 and 2, whereas the high fibrosis group contained 14 patients of fibrosis stages 3 and 4 (fibrosis stages according to Batts-Ludwig classification).
Project description:Gene knockdown of NAT12/NAA30 led to decreased proliferation, sphere forming ability and mitochondrial hypoxia tolerance in the GSC T65 culture. Intracranial transplantation of these cells into SCID mice showed that the decreased NAT12/NAA30 expression correlated with the prolonged animal survival and reduced tumor size
Project description:Magnaporthe oryzae snodprot1 homologous protein (MSP1) has been shown to act as a pathogen-associated molecular pattern (PAMPs) and trigger PAMP-triggered immunity (PTI) response involving programmed cell death and expression of various defense-related genes in rice. The involvement of several post-translational modifications (PTMs) in the regulation of plant immune response, especially PTI, during pathogen infection is well established, however, the information on the regulatory roles of these PTMs in response to MSP1-induced signaling in rice is currently elusive. Here, we report the phosphoproteome, ubiquitinome, and acetylproteome to investigate the MSP1-induced PTMs alterations in MSP1 overexpressed rice. Our analysis identified a total of 4,666 PTM modified sites in rice leaves including 4,292 phosphosites, 189 ubiquitin sites, and 185 acetylation sites. Among these, PTM status of 437 phosphorylated, 53 ubiquitinated, and 68 acetylated peptides were significantly changed by MSP1. Functional annotation of MSP1 modulated peptides by MapMan analysis revealed that these were majorly associated with cellular immune responses such as signaling, transcription factors, DNA and RNA regulation, and protein metabolism, among others. Taken together, this study uncovers the MSP1-induced PTMs changes in rice proteins and identified several novel components of rice-MSP1 interaction.
Project description:Patients with polycystic kidney disease (PKD) encounter a high risk of clear cell renal cell carcinoma (ccRCC), a malignant tumor with dysregulated lipid metabolism. SET domain–containing 2 (SETD2) has been identified as an important tumor suppressor gene in ccRCC. However, the role of SETD2 in tumorigenesis during the transition from PKD to ccRCC remains largely unexplored. Herein, we performed metabolomics, lipidomics, transcriptomics and proteomics with SETD2 loss induced PKD-ccRCC transition mouse model. To characterize biological responses triggered by SETD2 deletion during PKD-ccRCC transition at the protein level, we conducted global proteomics studies.
Project description:Gene knockdown of NAT12/NAA30 led to decreased proliferation, sphere forming ability and mitochondrial hypoxia tolerance in the GSC T65 culture. Intracranial transplantation of these cells into SCID mice showed that the decreased NAT12/NAA30 expression correlated with the prolonged animal survival and reduced tumor size Total RNA isolated from GSC cultures featuring NAT12/NAA30 gene knock-down (shRNA) was compared to total RNA from non-silencing control GSC cultures (NS-shRNA).
Project description:Amino acids (AA) are essential molecules for life because they are precursors for the synthesis of proteins and other organic compounds. Their metabolism in plants involves more than one cellular compartment, among which the chloroplast plays a key role. From the 20 essential AA, ten (Arg, Lys, Thr, Leu, Ile, Val, Trp, Phe, Tyr and His) are only synthesized in the plastids and seven (Asp, Cys, Gln, Glu, Gly, Ser and Met) can be synthesized in both chloroplast and other parts of the cell. Despite knowing the roles of AA in plant physiology, little has been assessed in plants with albino phenotypes, lacking chloroplasts. To assess the effect of chloroplast biogenesis disturbances on AA metabolism in albino and variegated somaclonal variations of Agave angustifolia Haw., a comparative proteomic based TMT- synchronous precursor selection (SPS)-MS3 strategy was used to determine the status of AA biosynthetic pathways. Besides the 20 essential AA was quantified to underpin proteomics finding. A total of 2,442 different proteins were identified in the proteome of the somaclonal variants, from which 82 correspond to enzymes participating in AA biosynthesis. From these 82, 32 proteins were differentially accumulated. On the other hand, the concentration of 16 and 12 of the AA synthesized by the chloroplast were over-accumulated in the variegated and albino somaclonal variant, respectively. In plantlets devoid of functional chloroplasts, there is a surprising increase of AA and key enzymes of the AA biosyntethic pathways, compared to green plantlets. This could suggest que la activation of AA biosynthesis is key to sustaining albino and variegated plantlets survival that lack chloroplasts.
Project description:Schwann cells (SCs) are not only decisive to produce the axon-wrapping myelin sheath thus ensuring a proper nerve conduction but also exhibit with trophic function and can direct repair mechanisms of the peripheral nervous system. Consequently, suitable and well-characterized SC in vitro models are needed to perform appropriate pre-clinical studies including the investigation of the complex biochemical adaptations occurring in the peripheral nervous system (PNS) under different (patho)physiological conditions. MSC80 cells represent a SC line derived from mouse used in laboratories as a suitable in vitro system for neuropathological studies. As a comprehensive MSC80 protein catalogue remained elusive, here we introduce the most abundant 9532 proteins identified via mass spectrometry based protein analytics and thus provide the most comprehensive SC protein catalogue published thus far. Hereby, not only proteins causative for inherited neuropathies were covered but it has also been demonstrated that apart from cytoplasmic and nuclear proteins, mitochondrial proteins and such belonging to the protein processing machinery are very well covered. Moreover, we addressed the suitability of MSC80 to examine molecular effect of a drug-treatment by analyzing the proteomic signature of Vitamin C-treated MSC80 cells. Proteomic findings along with further immunological and functional experiments support the concept of a beneficial role influence of Vitamin C on oxidative stress and identified TMX1 as an oxidative stress protective factor in SC which might represent a promising target for therapeutic intervention of PNS disorders with marked oxidative stress burden such as diabetic neuropathy.