Biology subjects

Lukas, C.

Publications and source records attributed to Lukas, C..

3 recordsLinked to original sources

bioRxiv2021

AI-driven Deep Visual Proteomics defines cell identity and heterogeneity

The systems-wide analysis of biomolecules in time and space is key to our understanding of cellular function and heterogeneity in health and disease1. Remarkable technological progress in microscopy and multi-omics technologies enable increasingly data-rich descriptions of tissue heterogeneity2,3,4,5. Single cell sequencing, in particular, now routinely allows the mapping of cell types and states uncovering tremendous complexity6. Yet, an unaddressed challenge is the development of a method that would directly connect the visual dimension with the molecular phenotype and in particular with the unbiased characterization of proteomes, a close proxy for cellular function. Here we introduce Deep Visual Proteomics (DVP), which combines advances in artificial intelligence (AI)-driven image analysis of cellular phenotypes with automated single cell laser microdissection and ultra-high sensitivity mass spectrometry7. DVP links protein abundance to complex cellular or subcellular phenotypes while preserving spatial context. Individually excising nuclei from cell culture, we classified distinct cell states with proteomic profiles defined by known and novel proteins. AI also discovered rare cells with distinct morphology, whose potential function was revealed by proteomics. Applied to archival tissue of salivary gland carcinoma, our generic workflow characterized proteomic differences between normal-appearing and adjacent cancer cells, without admixture of background from unrelated cells or extracellular matrix. In melanoma, DVP revealed immune system and DNA replication related prognostic markers that appeared only in specific tumor regions. Thus, DVP provides unprecedented molecular insights into cell and disease biology while retaining spatial information.

systems biology↗

bioRxiv2020

Adaptive mitochondrial regulation of the proteasome

The proteasome is the main proteolytic system for targeted protein degradation in the cell. Its function is fine-tuned according to cellular needs. Regulation of proteasome function by mitochondrial metabolism, however, is unknown. Here, we demonstrate that mitochondrial dysfunction reduces the assembly and activity of the 26S proteasome in the absence of oxidative stress. Impaired respiratory complex I function leads to metabolic reprogramming of the Krebs cycle and deficiency in aspartate. Aspartate supplementation activates assembly and activity of 26S proteasomes via transcriptional activation of the proteasome assembly factors p28 and Rpn6. This metabolic adaptation of 26S proteasome function involves sensing of aspartate via the mTORC1 pathway. Metformin treatment of primary human cells similarly reduced assembly and activity of 26S proteasome complexes, which was fully reversible and rescued by supplementation of aspartate or pyruvate. Of note, respiratory dysfunction conferred resistance towards the proteasome inhibitor Bortezomib. Our study uncovers a fundamental novel mechanism of how mitochondrial metabolism adaptively adjusts protein degradation by the proteasome. It thus unravels unexpected consequences of defective mitochondrial metabolism in disease or drug-targeted mitochondrial reprogramming for proteasomal protein degradation in the cell. As metabolic inhibition of proteasome function can be alleviated by treatment with aspartate or pyruvate, our results also have therapeutic implications.

cell biology↗

bioRxiv2017

Mutational signatures reveal the role of RAD52 in p53-independent p21 driven genomic instability

BackgroundGenomic instability promotes evolution and heterogeneity of tumors. Unraveling its mechanistic basis is essential to design appropriate therapeutic strategies. In a recent study we reported an unexpected oncogenic property of p21WAF1/Cip1 showing that its chronic expression, in a p53-deficient environment, causes genomic instability by deregulating the replication licensing machinery.\n\nResultsExtending on this work we now demonstrate that p21WAF1/Cip1 can further fuel genomic instability by suppressing the repair capacity of low and high fidelity pathways that deal with nucleotide abnormalities. Consequently, fewer single nucleotide substitutions (SNSs) occur, while formation of highly deleterious DNA double-strand breaks (DSBs) is enhanced, crafting a characteristic mutational signature landscape. Guided by the mutational signatures formed, we found at the mechanistic level that the DSBs were repaired by Rad52-dependent Break-Induced Replication (BIR) and Single-Strand Annealing (SSA). Conversely, the error-free synthesis-dependent strand annealing (SDSA) repair route was deficient. Surprisingly, Rad52 was activated transcriptionally in an E2F1-dependent manner, rather than post-translationally as is common for DNA repair factor activation.\n\nConclusionsOur results signify the importance of mutational signatures as guides to disclose the \"repair history\" leading to genomic instability. In this vein, following this approach we unveiled how chronic p21WAF1/Cip1 expression rewires the repair process, identifying Rad52 as a source of genomic instability and a candidate therapeutic target.

cancer biology↗