Biology subjects

Weiss, C. A. M.

Publications and source records attributed to Weiss, C. A. M..

3 recordsLinked to original sources

bioRxiv2025

Tree-based quantification infers proteoform regulation in bottom-up proteomics data

Quantitative readout is essential in proteomics, yet current bioinformatics methods lack a framework to handle the inherent multi-level nature of the data (fragments, MS1 isotopes, charge states, modifications, peptides and genes). We present AlphaQuant, which introduces tree-based quantification. This approach organizes quantitative data into a hierarchical tree across levels. It allows differential analyses at fragment and MS1 level, recovering up to 50-fold more regulated proteins compared to a state-of-the-art approach. Using gradient boosting on tree features, we address the largely unsolved challenge of scoring quantification accuracy, as opposed to precision. Our method clusters peptides with similar quantitative behavior, providing a new approach to the protein grouping problem and enabling identification of regulated proteoforms directly from bottom-up data. Combined with deep learning classification, we infer phosphopeptides from proteome data alone, validating our findings with EGFR stimulation data. We then describe proteoform diversity across mouse tissues, revealing distinct patterns of post translational modifications and alternative splicing.

bioinformatics↗

bioRxiv2024

The proteomic landscape of proteotoxic stress in a fibrogenic liver disease

Protein misfolding diseases, including alpha-1 antitrypsin deficiency (AATD), pose significant health challenges, with their cellular progression still poorly understood1-3. We utilize spatial proteomics by mass spectrometry and machine learning to map AATD in human liver tissue. Combining Deep Visual Proteomics (DVP) with single-cell analysis4,5, we probe intact patient biopsies to resolve molecular events during hepatocyte stress in pseudo-time across fibrosis stages. We achieve unprecedented proteome depth of up to 3,800 proteins from a third of a single cell in formalin-fixed, paraffin-embedded (FFPE) tissue. This dataset revealed a potentially clinically actionable peroxisomal upregulation that precedes the canonical unfolded protein response. Our single-cell proteomics data show alpha-1 antitrypsin accumulation is largely cell-intrinsic, with minimal stress propagation between hepatocytes. We integrated proteomic data with AI-guided image-based phenotyping across multiple disease stages, revealing a terminal hepatocyte state characterized by globular protein aggregates and distinct proteomic signatures, notably including elevated TNFSF10/TRAIL expression. This phenotype may represent a critical disease progression stage. Our study offers novel insights into AATD pathogenesis and introduces a powerful methodology for high-resolution, in situ proteomic analysis of complex tissues. This approach holds potential to unravel molecular mechanisms in various protein misfolding disorders, setting a new standard for understanding disease progression at the single-cell level in human tissue.

cell biology↗

bioRxiv2024

Transcription arrest induces formation of protective RNA granules in mitochondria

Mitochondrial gene expression regulation is required for the biogenesis of oxidative phosphorylation (OXPHOS) complexes, yet the spatial organization of mitochondrial RNAs (mt-RNAs) remains unknown. Here, we investigated the spatial distribution of mt-RNAs during various cellular stresses using single-molecule RNA-FISH. We discovered that transcription inhibition leads to the formation of distinct RNA granules within mitochondria, which we term inhibition granules. These structures differ from canonical mitochondrial RNA granules (MRGs) and form in response to multiple transcription arrest conditions, including ethidium bromide treatment, specific inhibition of the mitochondrial RNA polymerase, and depletion of the SUV3 helicase. Inhibition granules appear to serve a protective function, stabilizing certain mt-mRNAs during prolonged transcription inhibition. This phenomenon coincides with an imbalance in OXPHOS complex expression, where mitochondrial-encoded transcripts decrease while nuclear-encoded subunits remain stable. We found that cells recover from transcription inhibition via resolving the granules, restarting transcription and repopulating the mitochondrial network with mt-mRNAs within hours. We suggest that inhibition granules may act as a reservoir to help overcome OXPHOS imbalance during recovery from transcription arrest.

cell biology↗