Fatih Demir

Fatih Demir
Aarhus University | AU · Department of Biomedicine

Dr. rer. nat.
Investigating proteolysis in human plasma and the link to disease severity for inflammatory diseases

About

48
Publications
8,091
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
679
Citations
Citations since 2016
42 Research Items
626 Citations
2016201720182019202020212022050100150
2016201720182019202020212022050100150
2016201720182019202020212022050100150
2016201720182019202020212022050100150
Additional affiliations
September 2020 - August 2021
Aarhus University
Position
  • PostDoc Position
Description
  • Investigations of proteolysis in chronic kidney disease
August 2015 - August 2020
Forschungszentrum Jülich
Position
  • PostDoc Position
Description
  • Proteomics / Degradomics
February 2014 - January 2015
Heinrich-Heine-Universität Düsseldorf
Position
  • Fellow
Education
February 2007 - December 2010
University of Wuerzburg
Field of study
  • Plant physiology
September 2001 - December 2006
Heidelberg University
Field of study
  • Biology

Publications

Publications (48)
Article
The lipid kinase VPS34 orchestrates autophagy, endocytosis, and metabolism and is implicated in cancer and metabolic disease. The proximal tubule in the kidney is a key metabolic organ that controls reabsorption of nutrients such as fatty acids, amino acids, sugars, and proteins. Here, by combining metabolomics, proteomics, and phosphoproteomics an...
Preprint
Full-text available
Increasing drought phenomena pose a serious threat to agricultural productivity. Although plants have multiple ways to respond to the complexity of drought stress, the underlying mechanisms of stress sensing and signalling remain unclear. The role of the vasculature, in particular the phloem, in facilitating inter-organ communication is critical. H...
Preprint
Full-text available
Kidney organoids are a promising model to study kidney disease, but use is constrained by limited knowledge of their functional protein expression profile. We aimed to define the organoid proteome and transcriptome trajectories over culture duration and upon exposure to TNFα, a cytokine stressor. Older organoids increased deposition of extracellula...
Article
Full-text available
Hypertension and kidney disease have been repeatedly associated with genomic variants and alterations of lysine metabolism. Here, we combined stable isotope labeling with untargeted metabolomics to investigate lysine’s metabolic fate in vivo. Dietary 13C6 labeled lysine was tracked to lysine metabolites across various organs. Globally, lysine react...
Article
The podocyte is a key cell in maintaining renal filtration barrier integrity. Several recent studies have analyzed the entity of genome-coded molecules in the podocyte at deep resolution. This avenue of "podocyte-ome" research was enabled by a variety of techniques, including single-cell transcriptomics, FACS-sorting with and without genetically en...
Article
BACKGROUND AND AIMS Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. It is unclear how their proteome changes during differentiation, and if more complex disease processes such as inflammatory tissue responses co...
Chapter
Protein N-termini provide unique and distinguishing information on proteolytically processed or N-terminally modified proteoforms. Also splicing, use of alternative translation initiation sites, and a variety of co- and post-translational N-terminal modifications generate distinct proteoforms that are unambiguously identified by their N-termini. Ho...
Chapter
Substrate sequence specificity is a fundamental characteristic of proteolytic enzymes. Hundreds of proteases are encoded in plant genomes, but the vast majority of them have not been characterized and their distinct specificity remains largely unknown. Here we present our current protocol for profiling sequence specificity of plant proteases using...
Chapter
A large variety of enrichment procedures for protein N-termini have been developed to trace protease activity and determine precise cleavage sites, as well as other N-terminal protein modifications. Typically, enriched N-terminal peptides are identified by tandem mass spectrometry using standard database search engines, in many cases the popular Ma...
Article
Full-text available
Protein modification by enzymatic breaking and forming of peptide bonds significantly expands the repertoire of genetically encoded protein sequences. The dual protease-ligase legumain exerts the two opposing activities within a single protein scaffold. Primarily localized to the endolysosomal system, legumain represents a key enzyme in the generat...
Article
Full-text available
Proteases play a central role in regulating renal pathophysiology and are increasingly evaluated as actionable drug targets. Here, we review the role of proteolytic systems in inflammatory kidney disease. Inflammatory kidney diseases are associated with broad dysregulations of extracellular and intracellular proteolysis. As an example of a proteoly...
Article
Full-text available
Background: The glomerulus comprises podocytes, mesangial, and endothelial cells, which jointly determine glomerular filtration. Understanding this intricate functional unit beyond the transcriptome requires bulk isolation of these cell-types for biochemical investigations. We developed a globally applicable t ripartite i solation method for m urin...
Article
Full-text available
Site-specific proteolytic processing is an important, irreversible post-translational protein modification with implications in many diseases. Enrichment of protein N-terminal peptides followed by mass spectrometry-based identification and quantification enables proteome-wide characterization of proteolytic processes and protease substrates but is...
Article
Plants secrete various defence-related proteins into the apoplast, including proteases. Papain-like cysteine proteases (PLCPs) are central components of the plant immune system. To overcome plant immunity and successfully colonise their hosts, several plant pathogens secrete effector proteins inhibiting plant PLCPs. We hypothesized that not only pa...
Article
Full-text available
The ATP-dependent metalloprotease FtsH12 (filamentation temperature sensitive protein H 12) has been suggested to participate in a heteromeric motor complex, driving protein translocation into the chloroplast. FtsH12 was immuno-detected in proplastids, seedlings, leaves, and roots. Expression of Myc-tagged FtsH12 under its native promotor allowed i...
Preprint
Full-text available
Plants secrete various defence-related proteins into the apoplast, including proteases. Papain-like cysteine proteases (PLCPs) are central components of the plant immune system. To overcome plant immunity and successfully colonise their hosts, several plant pathogens secrete effector proteins inhibiting plant PLCPs. We hypothesized that not only pa...
Article
Full-text available
The vacuolar cysteine protease legumain plays important functions in seed maturation and plant programmed cell death. Because of their dual protease and ligase activity, plant legumains have become of particular biotechnological interest e.g. for the synthesis of cyclic peptides for drug design or for protein engineering. However, the molecular mec...
Article
Full-text available
The mammalian mitochondrial proteome consists of more than 1100 annotated proteins and their proteostasis is regulated by only a few ATP-dependent protease complexes. Technical advances in protein mass spectrometry allowed for detailed description of the mitoproteome from different species and tissues and their changes under specific conditions. Ho...
Article
Full-text available
Bottom-up mass spectrometry-based proteomics utilizes proteolytic enzymes with well character-ized specificities to generate peptides amenable for identification by high throughput tandem mass spectrometry. Trypsin, which cuts specifically after the basic residues lysine and arginine, is the predominant enzyme used for proteome digestion, although...
Article
Full-text available
Protein N termini unambiguously identify truncated, alternatively translated or modified proteoforms with distinct functions and reveal perturbations in disease. Selective enrichment of N-terminal peptides is necessary to achieve proteome-wide coverage for unbiased identification of site-specific regulatory proteolytic processing and protease subst...
Article
Full-text available
Ustilago maydis is a biotrophic fungus causing corn smut disease in maize. The secreted effector protein Pit2 is an inhibitor of papain-like cysteine proteases (PLCPs) essential for virulence. Pit2 inhibitory function relies on a conserved 14 amino acids motif (PID14). Here we show that synthetic PID14 peptides act more efficiently as PLCP inhibito...
Preprint
Full-text available
Protein N-termini reveal fundamental regulatory mechanisms and their perturbation in disease. Current terminome identification approaches are limited to whole organs or expandable cultured cells. We present a robust, sensitive, scalable and automatable method for system-wide identification of thousands of N-termini from minute samples. Identificati...
Article
Full-text available
Site-specific proteolytic processing is an irreversible post-translational protein modification with essential regulatory functions. Dedicated methods enable proteome-wide characterization of differentially processed proteoforms based on their distinct protease-generated N termini. Exemplary profiling of murine glomeruli revealed processed forms of...
Article
Full-text available
Background Vitamin K (VK)‐dependent proteases are major players in blood coagulation including the initiation as well as the regulation of the cascade. Five different members of this protease family have been described comprising the coagulation factors VII (FVII), IX (FIX), X (FX), protein C (PC) and prothrombin (FII). FVII, FIX, FX and PC share a...
Article
Acute kidney injury (AKI) leads to significant morbidity and mortality; unfortunately, strategies to prevent or treat AKI are lacking. In recent years, several preconditioning protocols have been shown to be effective in inducing organ protection in rodent models. Here, we characterized two of these interventions—caloric restriction and hypoxic pre...
Article
Mass developments of toxin-producing cyanobacteria are frequently observed in freshwater ecosystems due to eutrophication and global warming. These mass developments can partly be attributed to cyanobacterial toxins, such as protease inhibitors (PIs), which inhibit digestive serine proteases of Daphnia, the major herbivore of phytoplankton and cyan...
Article
AMPA receptors are essential for fast excitatory transmission in the CNS. Autoantibodies to AMPA receptors have been identified in humans with autoimmune encephalitis and severe defects of hippocampal function. Here, combining electrophysiology and high-resolution imaging with neuronal culture preparations and passive-transfer models in wild-type a...
Data
Table S1. Clinical, magnetic resonance imaging, and electroencephalography findings in patients with anti‐NMDAR encephalitis. Table S2. Routine CSF and PB analysis and antibody titers of patients with anti‐NMDAR encephalitis. Table S3. Neuropsychological domains with respective tests applied during neuropsychological testing of patients with anti...
Article
Full-text available
Objective Autoimmune encephalitis is most frequently associated with anti‐NMDAR autoantibodies. Their pathogenic relevance has been suggested by passive transfer of patients' cerebrospinal fluid (CSF) in mice in vivo. We aimed to analyze the intrathecal plasma cell repertoire, identify autoantibody‐producing clones, and characterize their antibody...
Article
Full-text available
Regulated intracellular proteostasis, controlled in part by proteolysis, is essential in maintaining the integrity of podocytes and the glomerular filtration barrier of the kidney. We applied a novel proteomics technology that enables proteome-wide identification, mapping, and quantification of protein N-termini to comprehensively characterize clea...
Conference Paper
Autoimmune encephalitis (AIE) syndromes comprise a recently identified group of inflammatory CNS disorders characterized by symptoms of limbic and extra-limbic dysfunction. Typically, AIE syndromes are associated with distinct autoantibody signatures specific for neuronal cell surface or synaptic protein antigens. One of the more frequent AIE syndr...
Article
I. II. III. IV. V. VI. VII. References SUMMARY: Proteolysis is a central regulatory mechanism of protein homeostasis and protein function that affects all aspects of plant life. Higher plants encode for hundreds of proteases, but their physiological substrates and hence their molecular functions remain mostly unknown. Current quantitative mass spec...
Chapter
Protein N termini are a unique window to the functional state of the proteome, revealing translation initiation sites, co-translation truncation and modification, posttranslational maturation, and further proteolytic processing into different proteoforms with distinct functions. As a direct readout of proteolytic activity, protein N termini further...
Article
Full-text available
Aims In the central nervous system, NMDA receptors play a pivotal role, however, their role in pancreatic islets has been largely unexplored or is controversial. We hypothesized that NMDA receptors are involved in glucose stimulated insulin secretion from beta cells and might serve as novel drug targets for diabetes treatment. Methods We generated...
Article
Full-text available
The phytohormone abscisic acid (ABA) plays a key role in the plant response to drought stress. Hence, ABA-dependent gene transcription and ion transport is regulated by a variety of protein kinases and phosphatases. However, the nature of the membrane-delimited ABA signal transduction steps remains largely unknown. To gain insight into plasma membr...
Article
Full-text available
Background Sterols and Sphingolipids form lipid clusters in the plasma membranes of cell types throughout the animal and plant kingdoms. These lipid domains provide a medium for protein signaling complexes at the plasma membrane and are also observed to be principal regions of membrane contact at the inception of infection. We visualized different...
Data
Figure S1. FM4-64/BD-SM staining of protoplasts. FM4-64/BD-SM staining on protoplasts, 20 h post cell wall removal. Polarization was even more enhanced after this time period (A-H). (A; E) FM4-64 fluorescence. (B; F) BD-SM fluorescence. In the merged images clear-cut polarizations were detected (C; G, arrows). Tranmission images (D; H).
Data
Figure S2. Example for correlation analyses. For statistically relevant correlation analyses two ROI’s within the plasma membranes of protoplasts were chosen and the Pearson and Spearman correlation coefficients calculated from confocal images (see methods section). The images selected are of (A) an unpolarized protoplast from Figure 5, C and two 1...
Article
Full-text available
Arabidopsis thaliana (A.th.) mesophyll cells play a pivotal role in the regulation of the drought stress response. The signaling & transport components involved in drought stress regulation within lipid rafts of the plasma membrane were investigated by DRM isolation from highly purified plasma membranes. Detergent treatment with Brij-98 and Triton...

Questions

Question (1)
Question
It is (1+) and strongly present with high ACN content at the end of our LC gradients (Setup: Ultimate 3000RSLCnano HPLC coupled to an impactII MS running plant proteomics samples). Didn't find any information about such a mass - it is also present in blanks and we have already exchanged solvents to highest purity (Merck hypergrade ACN) which improves situation but the signal seems to return.

Network

Cited By

Projects

Projects (2)
Project
Investigating specific proteolysis in plants. All kind of flavors.