Biology subjects

Fritzsche, S.

Publications and source records attributed to Fritzsche, S..

7 recordsLinked to original sources

bioRxiv2025

OpenDVP: An experimental and computational framework for community-empowered deep visual proteomics

Deep visual proteomics (DVP) is an emerging approach for cell type-specific and spatially resolved proteomics. However, its broad adoption has been constrained by the lack of an open-source end-to-end workflow in a community-driven ecosystem. Here, we introduce openDVP, an experimental and computational framework for simplifying and democratizing DVP. OpenDVP integrates open-source software for image analysis, including MCMICRO, QuPath, and Napari, and uses the scverse data formats AnnData and SpatialData for multi-omics integration. It offers two workflows: a fast-track pipeline requiring no image analysis expertise and an artificial intelligence (AI)-powered pipeline with recent algorithms for image pre-processing, segmentation, and spatial analysis. We demonstrate openDVPs versatility in three archival tissue studies, profiling human placenta, early-stage lung cancer, and locally relapsed breast cancer. In each study, our framework provided insights into health and disease states by integrating spatial single-cell phenotypes with exploratory proteomic data. Finally, we introduce deep proteomic profiling of cellular neighborhoods as a scalable approach to accelerate spatial discovery proteomics across biological systems.

systems biology↗

bioRxiv2025

An ultrasensitive spatial tissue proteomics workflow exceeding 100 proteomes per day

Achieving high-resolution spatial tissue proteomes requires careful balancing and integration of optimized sample processing, chromatography, and MS acquisition. Here, we present an advanced cellenONE protocol for loss-reduced tissue processing and compare all Evosep ONE Whisper Zoom gradients (20, 40, 80, and 120 samples per day), along with three common DIA acquisition schemes on a timsUltra AIP mass spectrometer. We found that tissue type was as important as gradient length and sample amount in determining proteome coverage. Moreover, the benefit of increased tissue sampling was gradient- and dynamic range-dependent. Analyzing mouse liver, a high dynamic range tissue, over tenfold more tissue sampling led to only ~30% gain in protein identification for short gradients (120 SPD and 80 SPD). However, even the lowest tested tissue amount (0.04 nL, 40,000 {micro}m3) yielded 3,200 reproducibly quantified proteins for the 120 SPD method. Longer gradients (40 SPD and 20 SPD) instead significantly benefited from more tissue sampling, quantifying over 7,500 proteins from 0.5 nL of tonsil T-cell niches. Finally, we applied our workflow to a rare squamous cell carcinoma of the oral cavity, uncovering disease-associated pathways and region-specific protein level changes. Our study demonstrates that more than 100 high-quality spatial tissue proteomes can be prepared and acquired daily, laying a strong foundation for cohort-size spatial tissue proteomics in translational research.

systems biology↗

bioRxiv2025

Deep spatial proteomics of ovarian cancer precursor lesions delineates early disease changes and cell-of-origin signatures

High-grade serous ovarian cancer (HGSOC) is a devastating disease that is frequently detected at an incurable stage. Advances in ultrasensitive mass spectrometry-based spatial proteomics have provided a unique opportunity to uncover early molecular events in tumorigenesis and common dysregulated pathways with high therapeutic potential. Here, we present a comprehensive proteomic analysis of serous tubal intraepithelial carcinoma (STIC), the HGSOC precursor lesion, covering more than 10,000 proteins. We found that STICs and concurrent invasive carcinomas were indistinguishable at the global proteomic level, revealing a similar level of molecular heterogeneity. Using cell-type resolved tissue proteomics, we revealed strong cell-of-origin signatures preserved in STICs and invasive tumors and identified early dysregulated pathways of therapeutic relevance, such as an onco-metabolic increase in cholesterol biosynthesis. Finally, we uncovered substantial remodeling of the co-evolving tumor microenvironment, affecting approximately one-third of the stromal proteome, and derived a common signature associated with progressive immunosuppression and extracellular matrix restructuring. In summary, our study highlights the power of spatially resolved quantitative proteomics to dissect the molecular underpinnings of early carcinogenesis and provides a rich proteomic resource for future biomarker and drug target research in ovarian cancer.

systems biology↗

bioRxiv2024

Differences in size and number of embryonic type-II neuroblast lineages are associated with divergent timing of central complex development between beetle and fly

Despite its conserved basic structure, the morphology of the insect brain and the timing of its development underwent evolutionary adaptations. However, little is known about the developmental processes that create this diversity. The central complex is a brain centre required for multimodal information processing and an excellent model to understand neural development and divergence. It is produced in large parts by type-II neuroblasts, which produce intermediate progenitors, another type of cycling precursor, to increase their neural progeny. These neural stem cells are believed to be conserved among insects, but little is known on their molecular characteristics in insects other than flies. Tribolium castaneum has emerged as a valuable new insect model for brain development and evolution. However, type-II neuroblast lineages and their role in central complex development have so far not been studied in this beetle. Using CRISPR-Cas9 we created a fluorescent enhancer trap marking expression of Tribolium fez/earmuff, a key marker for type-II neuroblast derived intermediate progenitors. Using combinatorial labelling of further markers including Tc-pointed, Tc-deadpan, Tc-asense and Tc-prospero we characterized the type-II neuroblast lineages present in the Tribolium embryo and their sub-cell-types. Intriguingly, we found 9 type-II neuroblast lineages per hemisphere in the Tribolium embryo while Drosophila produces only 8 per brain hemisphere. In addition, these lineages are significantly larger at the embryonic stage of Tribolium than they are in Drosophila and contain more intermediate progenitors. Finally, we mapped these lineages to the domains of early expressed head patterning genes. Notably, Tc-otd is absent from all type-II neuroblasts and intermediate progenitors, whereas Tc-six3 marks an anterior subset of the type-II-lineages. The placodal marker Tc-six4 specifically marks the territory where anterior medial type-II neuroblasts differentiate. In conclusion, we identified a conserved pattern of gene expression in holometabolan central complex forming type-II neuroblast lineages, and conserved head patterning genes emerged as new candidates for conferring spatial identity to individual lineages. The higher number and greater lineage size of the embryonic type-II neuroblasts in the beetle correlate with a previously described embryonic phase of central complex formation which is not found in the fly. These findings stipulate further research on the causal link between timing of stem cell activity and temporal and structural differences in central complex development.

developmental biology↗

bioRxiv2023

A framework for ultra-low input spatial tissue proteomics

Spatial tissue proteomics combining microscopy-based cell phenotyping with ultra-sensitive mass spectrometry (MS)-based proteomics is an emerging and powerful concept for the study of cell function and heterogeneity in health and disease. However, optimized workflows that preserve morphological information for image-based phenotype discovery and maximize proteome coverage of few or even single cells from laser microdissected archival tissue, are currently lacking. Here, we report a robust and scalable workflow for the proteomic analysis of ultra-low input formalin-fixed, paraffin-embedded (FFPE) material. Benchmarking in the murine liver resulted in up to 2,000 quantified proteins from single hepatocyte contours and nearly 5,000 proteins from 50-cell regions with high quantitative reproducibility. Applied to human tonsil, we profiled 146 microregions including spatially defined T and B lymphocyte niches and quantified cell type specific markers, cytokines, immune cell regulators and transcription factors. These rich data also highlighted proteome dynamics in spatially defined zones of activated germinal centers, illuminating sites undergoing active B-cell proliferation and somatic hypermutation. Our results demonstrate the power of spatially-resolved proteomics for tissue phenotyping by integrating high-content imaging, laser microdissection, and ultra-sensitive mass spectrometry. This approach has broad implications for a wide range of biomedical applications, including early disease profiling, drug target discovery and biomarker research.

systems biology↗

bioRxiv2023

High-resolution molecular atlas of a lung tumor in 3D

Cells live and interact in three-dimensional (3D) cellular neighborhoods. However, histology and spatial omics methods mostly focus on 2D tissue sections. Here we present a 3D spatial atlas of a routine clinical sample, an aggressive human lung carcinoma, by combining in situ quantification of 960 cancer-related genes across [~]340,000 cells with measurements of tissue-mechanical components. 3D cellular neighborhoods subdivided the tumor microenvironment into tumor, stromal, and immune multicellular niches. Interestingly, pseudotime analysis suggested that pro-invasive epithelial-to-mesenchymal transition (EMT), detected in stroma-infiltrating tumor cells, already occurred in one region at the tumor surface. There, myofibroblasts and macrophages specifically co-localized with pre-invasive tumor cells and their multicellular molecular signature identified patients with shorter survival. Moreover, cytotoxic T-cells did not infiltrate this niche but colocalized with inhibitory dendritic and regulatory T cells. Importantly, systematic scoring of cell-cell interactions in 3D neighborhoods highlighted niche-specific signaling networks accompanying tumor invasion and immune escape. Compared to 2D, 3D neighborhoods improved the characterization of immune niches by identifying dendritic niches, capturing the 3D extension of T-cell niches and boosting the quantification of niche-specific cell-cell interactions, including druggable immune checkpoints. We believe that 3D communication analyses can improve the design of clinical studies investigating personalized, combination immuno-oncology therapies.

systems biology↗

bioRxiv2021

Inhibitory properties of microalgal extracts on the in vitro replication of cyprinid herpesvirus 3

Microalgae often stand out for their high biodiversity as well as their associated large number of potent bioactives. Therefore, they are interesting candidates as possible sources of antiviral substances, e.g. against cyprinid herpesvirus 3 (CyHV-3). Although this virus leads to high mortalities in aquacultures, there is no treatment available yet. Hence, ethanolic extracts produced with accelerated solvent extraction from six microalgal species (Arthrospira platensis, Chlamydomonas reinhardtii, Chlorella kessleri, Haematococcus pluvialis, Nostoc punctiforme and Scenedesmus obliquus) were examined in this study for inhibitory effects on viral replication. An inhibition of the in vitro replication of CyHV-3 in common carp brain cells could be confirmed for all six species, with the greatest effect for the C. reinhardtii and H. pluvialis extracts. At still non-cytotoxic concentrations viral DNA replication was reduced by over 3 orders of magnitude (> 99.9 %) each compared to the untreated replication controls, while the virus titers were at or even below the limit of detection. When pre-incubating cells and virus with C. reinhardtii and especially H. pluvialis extracts before inoculation, the reduction of viral DNA and virus titer was even stronger. Based on these results, an intervention in the initial replication steps like viral adsorption or membrane fusion is assumed. Moreover, a protection mechanism preventing the production of viral proteins and the assembly of mature virions is also possible. All in all, the results show that microalgae are a very promising source of natural antiviral substances against CyHV-3.

bioengineering↗