Biology subjects

Haas, D. T.

Publications and source records attributed to Haas, D. T..

3 recordsLinked to original sources

bioRxiv2024

C-COMPASS: A Neural Network Tool for Multi-Omic Classification of Cell Compartments

Functional compartmentalization in eukaryotic cells is essential for maintaining physiological processes. The development of systematic organelle proteomic techniques, such as Protein Correlation Profiling (PCP) and Localization of Organelle Proteins by Isotope Tagging (LOPIT), has enhanced our understanding of organelle dynamics and protein localization. However, the complexity of the data and the need for advanced computational skills limit their accessibility. To address this, we introduce C-COMPASS, an open-source software featuring a user-friendly interface that utilizes a neural network-based regression model to predict the spatial distribution of proteins across cellular compartments. C-COMPASS manages complex multilocalization patterns and integrates protein abundance information to model organelle composition changes under various biological conditions. Using C-COMPASS, we mapped the organelle proteomic landscapes of humanized liver mice in different metabolic states and modeled changes in organelle composition to provide insights into cellular adaptations. Additionally, we extended cellular maps to the lipid level by co-generating protein and lipid profiles. C-COMPASS trains neural networks with marker protein profiles to predict lipid localizations, enabling parallel mapping of lipid and protein localization. This approach overcomes the lack of knowledge of organelle-specific lipid markers and identifies previously unknown organelle-specific lipid species. C-COMPASS offers a comprehensive solution for studying organelle dynamics at the multi-omics level, designed to be accessible without requiring extensive computational expertise or specialized high-performance computing equipment.

cell biology↗

bioRxiv2023

Activating the NFE2L1-ubiquitin-proteasome system by DDI2 protects from ferroptosis

Ferroptosis is an iron-dependent, non-apoptotic form of cell death initiated by oxidative stress and lipid peroxidation. Recent evidence has linked ferroptosis to the action of the transcription factor Nuclear factor erythroid-2 derived,-like-1 (NFE2L1). NFE2L1 regulates proteasome abundance in an adaptive fashion, maintaining protein quality control to secure cellular homeostasis, but the regulation of NFE2L1 during ferroptosis and the role of the ubiquitin-proteasome system (UPS) herein are still unclear. In the present study, using an unbiased proteomic approach charting the specific ubiquitylation sites, we show that induction of ferroptosis leads to recalibration of the UPS. RSL3-induced ferroptosis inhibits proteasome activity and leads to global hyperubiquitylation, which is linked to NFE2L1 activation. As NFE2L1 resides in the endoplasmic reticulum tethered to the membrane, it undergoes complex posttranslational modification steps to become active and induce the expression of proteasome subunit genes. We show that proteolytic cleavage of NFE2L1 by the aspartyl protease DNA-damage inducible 1 homolog 2 (DDI2) is a critical step for the ferroptosis-induced feed-back loop of proteasome function. Cells lacking DDI2 cannot activate NFE2L1 in response to RSL3 and show global hyperubiquitylation. Genetic or chemical induction of ferroptosis in cells with a disrupted DDI2-NFE2L1 pathway diminishes proteasomal activity and promotes cell death. Also, treating cells with the clinical drug nelfinavir, which inhibits DDI2, sensitized cells to ferroptosis. In conclusion, our results provide new insight into the importance of the UPS in ferroptosis and highlight the role of the DDI2-NFE2L1 as a potential therapeutic target. Manipulating DDI2-NFE2L1 activity through chemical inhibition might help sensitizing cells to ferroptosis, thus enhancing existing cancer therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/547652v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@b3f899org.highwire.dtl.DTLVardef@18625feorg.highwire.dtl.DTLVardef@287bcborg.highwire.dtl.DTLVardef@1d758d1_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Nfe2l1-mediated proteasome function controls muscle energy metabolism in obesity

Muscle function is an important denominator of energy metabolism and metabolic health. Adapting the myocyte proteome to energetic challenges, in response to diet or fasting, is facilitated by programs of proteostasis, but the adaptive role of the ubiquitin-proteasome system (UPS) in muscle remains unclear. Here, we show that myocyte Nuclear factor erythroid derived 2,-like 1 (Nfe2l1, also known as Nrf1) is a key regulator of skeletal muscle proteostasis and function. In mice and humans, Nfe2l1 is highly expressed in skeletal myocytes, and its loss diminishes proteasomal activity and leads to hyperubiquitylation. Mice lacking myocyte Nfe2l1 display muscle fiber type switching and insulin resistance when fed a high-fed diet. Nfe2l1 protects myocytes from ferroptosis, which is enhanced in the presence of excess lipids. In conclusion, we define a new adaptive role for the Nfe2l1-ubiquitin proteasome system in the control of skeletal muscle function and energy metabolism.

physiology↗