Carsten Hopf

Hochschule Mannheim · Center for Mass Spectrometry and Optical Spectroscopy (CeMOS)

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) has emerged as a key technology for label-free bioanalysis of the spatial distribution of biomolecules, pharmaceuticals and other xenobiotics in tissue sections. Recent advances in instrumentation, sample preparation, multimodal workflows, quantification, analytical s...

Cell-based assays for compound screening and profiling are fundamentally important in life sciences, chemical biology and pharmaceutical research. Most cell assays measure the amount of a single reporter molecule or cellular endpoint, and require the use of fluorescence or other labeled materials. Consequently, there is high demand for label-free t...

Insufficient vacuum-stability of matrix chemicals is a major limitation in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) of large tissue sample cohorts. Here, we designed and synthesized the photo-cleavable caged molecule 4,5-dimethoxy-2-nitrobenzyl-2,5-dihydroxyacetophenone (DMNB-2,5-DHAP) and employed it for...

Mass spectrometry imaging vows to enable simultaneous spatially resolved investigation of hundreds of metabolites in tissues, but it primarily relies on traditional ion images for non-data-driven metabolite visualization and analysis. The rendering and interpretation of ion images neither considers non-linearities in the resolving power of mass spe...

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a fast-growing technique for visualization of the spatial distribution of the small molecular and macromolecular biomolecules in tissue sections. Challenges in MALDI-MSI, such as poor sensitivity for some classes of molecules or limited specificity, for instance re...

Sequential proteolysis of the amyloid precursor protein (APP) by gamma-secretases (GSECs) generates amyloid-beta (A beta) and defines the proportion of short-to-long A beta peptides, which is tightly connected to Alzheimer's disease (AD) pathogenesis. Here, we study the mechanism controlling substrate processing by GSECs and defining product length...

Amyloid beta (Abeta) peptides accumulating in the brain are proposed to trigger Alzheimer's disease (AD). However, molecular cascades underlying their toxicity are poorly defined. Here, we explored a novel hypothesis for Abeta42 toxicity that arises from its proven affinity for gamma-secretases. We hypothesized that the reported increases in Abeta4...

Simple Summary Routine clinical approaches for cancer diagnosis demand fast, cost-efficient, and reliable methods, and the implementation of these methods within clinical settings. Currently, histopathology is the gold standard for tissue-based clinical diagnosis. Recently, spatially resolved molecular profiling techniques such as mass spectrometry...

Regulated intramembrane proteolysis (RIP) describes the protease-dependent cleavage of transmembrane proteins within the hydrophobic core of cellular membranes. Intramembrane-cleaving proteases (I-CliPs) that catalyze these reactions are found in all kingdoms of life and are involved in a wide range of cellular processes, including signaling and pr...

Complex molecular alterations underlying cancer pathophysiology are intensely studied with omics methods using bulk tissue extracts. For spatially resolved tissue diagnostics using needle biopsy cores, however, histopathological analysis using stained FFPE tissue and immuno-histochemistry (IHC) of few marker proteins is currently the main clinical...

Insufficient vacuum‐stability of matrix chemicals is a major limitation in matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) of large tissue sample cohorts. Here, we designed and synthesized the photo‐cleavable caged molecule 4,5‐dimethoxy‐2‐nitrobenzyl‐2,5‐dihydroxyacetophenone (DMNB‐2,5‐DHAP) and employed it for...

Limited supply and catabolism restrict the essential amino acid tryptophan (Trp) in tumors. How tumors sustain translation under Trp stress remains unclear. Unlike other amino acids, Trp stress activates the EGFR, which enhances macropinocytosis and RAS signaling to the MTORC1 and p38/MAPK kinases, sustaining translation. The AHR forms part of the...

Metabolomic and proteomic analyses of human plasma and serum samples harbor the power to advance our understanding of disease biology. Pre-analytical factors may contribute to variability and bias in the detection of analytes, especially when multiple labs are involved, caused by sample handling, processing time, and differing operating procedures....

Three-dimensional (3D) human cell culture models have emerged as a key technology for personalized medicine and for phenotypic compound screening in more disease-like in-vitro systems. Mass spectrometry imaging (MSI) is one of the most versatile label-free techniques that enables simultaneous generation of spatial maps for multiple relevant molecul...

In the current drug discovery process, the synthesis of compound libraries is separated from biological screenings both conceptually and technologically. One of the reasons is that parallel on‐chip high‐throughput purification of synthesized compounds is still a major challenge. Here, on‐chip miniaturized high‐throughput liquid–liquid extraction in...

On-tissue enzymatic digestion is a prerequisite for MALDI mass spectrometry imaging (MSI) and spatialomic analysis of tissue proteins and their N-glycan conjugates. Despite the more widely accepted importance of N-glycans as diagnostic and prognostic biomarkers of many diseases and their potential as pharmacodynamic markers, the crucial sample prep...

Alzheimer's disease (AD) pathogenesis has been linked to the accumulation of longer, aggregation-prone amyloid β (Aβ) peptides in the brain. Γ-secretases generate Aβ peptides from the amyloid precursor protein (APP). Γ-secretase modulators (GSMs) promote the generation of shorter, less-amyloidogenic Aβs and have therapeutic potential. However, poor...

Metabolomic and proteomic analyses of human plasma and serum samples harbour the power to advance our understanding of disease biology. Pre-analytical factors may contribute to variability and bias in the detection of analytes, especially when multiple labs are involved, caused by sample handling, processing time, and differing operating procedures...

Pathological microglia activation can promote neuroinflammation in many neurodegenerative diseases, and it has therefore emerged as a potential therapeutic target. Increasing evidence suggests alterations in lipid metabolism as modulators and indicators in microglia activation and its effector functions. Yet, how lipid dynamics in activated microgl...

Matrix-assisted laser desorption and ionization (MALDI) mass spectrometry (MS) is an indispensable tool in modern lipid research since it is fast, sensitive, tolerates sample impurities and provides spectra without major analyte fragmentation. We will discuss some methodological aspects, the related ion-forming processes and the MALDI MS characteri...

Understanding of Alzheimer's disease (AD) pathophysiology requires molecular assessment of how key pathological factors, specifically amyloid β (Aβ) plaques, influence the surrounding microenvironment. Here, neuronal lipids have been implicated in Aβ plaque pathology, though the lipid microenvironment in direct proximity to Aβ plaques is still not...

Mass spectrometry imaging (MSI) vows to enable simultaneous spatially-resolved investigation of hundreds of metabolites in tissue sections, but it still relies on poorly defined ion images for data interpretation. Here, we outline moleculaR , a computational framework in R, that introduces systematic probabilistic mapping and point-for-point statis...

Mass spectrometry imaging (MSI) vows to enable simultaneous spatially-resolved investigation of hundreds of metabolites in tissue sections, but it still relies on poorly defined ion images for data interpretation. Here, we outline moleculaR, a computational framework (https://github.com/CeMOS-Mannheim/moleculaR) that introduces probabilistic mappin...

Understanding of Alzheimer’s disease (AD) pathophysiology, requires molecular assessment of how key pathological factors, specifically amyloid β (Aβ) plaques, influence the surrounding microenvironment. Here, neuronal lipids are particularly of interest as these are implicated in pathological- and neurodegenerative processes in AD. The exact molecu...

Understanding of Alzheimer’s disease (AD) pathophysiology, requires molecular assessment of how key pathological factors, specifically amyloid β (Aβ) plaques, influence the surrounding microenvironment. Here, neuronal lipids are particularly of interest as these are implicated in pathological- and neurodegenerative processes in AD. The exact molecu...

Tryptophan (Trp)-catabolic enzymes (TCEs) produce metabolites that activate the aryl hydrocarbon receptor (AHR) and promote tumor progression and immunosuppression in glioblastoma. As therapies targeting TCEs or AHR become available, a better understanding of Trp metabolism is required. Methods: The combination of LC-MS/MS with chemical isobaric la...

Background: Mass spectrometry imaging (MSI) is a label-free analysis method for resolving bio-molecules or pharmaceuticals in the spatial domain. It offers unique perspectives for the examination of entire organs or other tissue specimens. Owing to increasing capabilities of modern MSI devices, the use of 3D and multi-modal MSI becomes feasible in...

The dynamics and phenotypes of intratumoral myeloid cells during tumor progression are poorly understood. Here we define myeloid cellular states in gliomas by longitudinal single-cell profiling and demonstrate their strict control by the tumor genotype: in isocitrate dehydrogenase (IDH)-mutant tumors, differentiation of infiltrating myeloid cells i...

β-Amyloid (Aβ) plaque formation is the major pathological hallmark of Alzheimer’s disease (AD) and constitutes a potentially critical, early inducer driving AD pathogenesis as it precedes other pathological events and cognitive symptoms by decades. It is therefore critical to understand how Aβ pathology is initiated and where and when distinct Aβ s...

Frozen section analysis is a frequently used method for examination of tissue samples, especially for tumour detection. In the majority of cases, the aim is to identify characteristic tissue morphologies or tumour margins. Depending on the type of tissue, a high number of misdiagnoses are associated with this process. In this work, a fast spectrosc...

In pharmaceutical research and development, cell‐based assays are primarily used with readout that rely on fluorescence‐based and other label‐dependent techniques for analysis of different cellular processes. Superhydrophobic–hydrophilic droplet microarrays (DMA) and matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS) have re...

Mass spectrometry imaging (MSI) has become an indispensible tool for spatially resolved molecular investigation of tissues. One of the key application areas is biomedical research, where matrix-assisted laser desorption/ionization (MALDI) MSI is predominantly used due to its high-throughput capability, flexibility in the molecular class to investig...

MALDI mass spectrometry imaging (MSI) enables label-free, spatially resolved analysis of a wide range of analytes in tissue sections. Quantitative analysis of MSI datasets is typically performed on single pixels or manually assigned regions of interest (ROIs). However, many sparse, small objects such as Alzheimer's disease (AD) brain deposits of am...

For our understanding of Alzheimer’s disease (AD) pathophysiology, it is of critical importance to determine how key pathological factors, specifically amyloid β (Aβ) plaque formation, are interconnected and implicated in neurodegeneration, disease progression and the development of clinical symptoms. Exactly how Aβ plaque formation is initiated an...

Over the last 10 years, considerable technical advances in mass spectrometry (MS)‐based bioanalysis have enabled the investigation of lipid signatures in neuropathological structures. In Alzheimer´s Disease (AD) research, it is now well accepted that lipid dysregulation plays a key role in AD pathogenesis and progression. This review summarizes cur...

Aryl hydrocarbon receptor (AHR) activation by tryptophan (Trp) catabolites enhances tumor malignancy and suppresses anti-tumor immunity. The context specificity of AHR target genes has so far impeded systematic investigation of AHR activity and its upstream enzymes across human cancers. A pan-tissue AHR signature, derived by natural language proces...

OATP2B1, a member of the solute carrier (SLC) transporter family, is an important mechanism of substrate drug uptake in the intestine and liver and therefore a determinant of clinical pharmacokinetics and site of drug-drug interactions. Other SLC transporters have emerged as pharmacology targets. Studies of SLC transporter uptake to-date relied on...

Mass spectrometry (MS) in hyphenated techniques is widely accepted as the gold standard quantitative tool in life sciences. However, MS possesses intrinsic analytical capabilities that allow it to be a stand-alone quantitative technique, particularly with current technological advancements. MS has a great potential for simplifying quantitative anal...

Several diseases are associated with disturbed redox signaling and altered metabolism of sulfur-containing metabolites and proteins. Importantly, oxidative degradation of fresh-frozen tissues begins within the normal timescale of MALDI MSI sample preparation. As a result, analytical methods that preserve the redox state of the tissue are urgently n...

OATP2B1 is an intestinal and hepatic drug uptake transporter. Intestinal OATP2B1 has been elucidated as the mechanism of unexpected clinical drug-drug interactions (DDIs), where drug exposure was unexpectedly decreased with unchanged half-life. Hepatic OATP2B1 may be an understudied clinical DDI mechanism. The aim of the present work was to underst...

The glycosphingolipid α-galactosylceramide (αGalCer), when presented by CD1d on antigen presenting cells, efficiently activates invariant natural killer T (iNKT) cells. Thereby, it modulates immune responses against tumors, microbial and viral infections and autoimmune diseases. Recently, the production of αGalCer by Bacteroidetes from the human gu...

Mass spectrometry imaging (MSI) is an enabling technology for label-free drug disposition studies at high spatial resolution in life science- and pharmaceutical research. We present the first extensive clinical matrix-assisted laser desorption/ionization (MALDI) quantitative mass spectrometry imaging (qMSI) study of drug uptake and distribution in...

Human cancers require fatty acid synthase (FASN)-dependent de novo long-chain fatty acid synthesis for proliferation. FASN is therefore an attractive drug target, but fast technologies for reliable label-free cellular compound profiling are lacking. Recently, MALDI-mass spectrometry (MALDI-MS) has emerged as an effective technology for discovery of...

Non-alcoholic steatohepatitis (NASH) is the leading cause of chronic liver injury and the third most common reason for liver transplantations in Western countries. It is unclear so far how different fat sources in Western diets (WD) influence the development of NASH. Our study investigates the impact of non-trans fat (NTF) and corn oil (Corn) as fa...

Mass spectrometry imaging (MSI) is an enabling technology for label-free drug disposition studies at high spatial resolution in life science- and pharmaceutical research. We present the first extensive clinical matrix-assisted laser desorption/ionization (MALDI) quantitative mass spectrometry imaging (qMSI) study of drug uptake and distribution in...

Current mass spectrometry (MS) technology provides an indispensable toolbox for epigenetic drug discovery. Two complementary MS methods exist to analyze proteins. In the top‐down proteomic strategy, the intact protein is directly analyzed by MS. In bottom‐up proteomics, peptides derived from digested proteins are analyzed with the mass spectrometer...

Purpose : To facilitate the transition of MALDI‐MS Imaging (MALDI‐MSI) from basic science to clinical application, it is necessary to analyze formalin‐fixed paraffin‐embedded (FFPE) tissues. Our aim was to improve in‐situ tryptic digestion for MALDI‐MSI of FFPE samples and determine if similar results would be reproducible if obtained from differen...

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a label-free technology for spatially resolved analysis of multiple compounds of interest in tissue sections. More specifically, MALDI-MSI enables visualization of spatial distributions of proteins, lipids, metabolites and drugs at cellular resolution. This innovat...

Aberrant protease activity has been implicated in the etiology of various prevalent diseases including neurodegeneration and cancer, in particular metastasis. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has recently been established as a key technology for bioanalysis of multiple biomolecular classes such as...

Recent advances in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry have enabled whole cell-MALDI mass spectrometry biotyping of drug-treated cultured cells for rapid monitoring of known abundant pharmacodynamic protein markers such as polyacetylated histones. In contrast, generic and automated analytical workflows for discover...

Alzheimer’s disease (AD) is characterized by progressive neurodegeneration and a concomitant loss of synapses and cognitive abilities. Recently, we have proposed that an alteration of neuronal membrane lipid microdomains increases neuronal resistance toward amyloid-β stress in cultured neurons and protects from neurodegeneration in a mouse model of...