Biology subjects

Pfirrmann, T.

Publications and source records attributed to Pfirrmann, T..

4 recordsLinked to original sources

bioRxiv2026

CiliAI: Automated segmentation and compartment specific fluorescence quantification of primary cilia in confocal microscopy images

Primary cilia regulate essential signaling pathways controlling cell proliferation, differentiation, and tissue homeostasis. Quantitative analysis of ciliary morphology and compartment-specific protein localization by confocal microscopy is labor-intensive, user-dependent, and difficult to scale, particularly for multiplexed 3D image datasets. Here, we present CiliAI, a web-based deep-learning workflow for automated detection, substructure segmentation, and quantitative analysis of primary cilia in confocal microscopy images. CiliAI identifies ciliary substructures including the basal body, transition zone, and axoneme from multiplexed 3D image stacks and performs automated measurements of cilium length and compartment-specific fluorescence intensity. In NIH-3T3 cells, automated cilium length measurements showed close agreement with manual quantification and no statistically significant difference between methods (mean difference -0.214 {micro}m, p = 0.213). Automated fluorescence analysis reproduced previously reported reductions in transition zone-associated Cep290 signal intensity in Rpgrip1l-deficient cells and identified the absence of significant Rpgrip1l accumulation changes in Rmnd5a-deficient cells. Automated processing reduced analysis time from days of manual quantification to minutes. Together, these findings establish CiliAI as an automated framework for quantitative analysis of ciliary morphology and compartment-specific protein abundance in confocal microscopy datasets.

bioinformatics↗

bioRxiv2026

The primary cilium controls programmed cell death via its proteasome-regulating function

Primary cilia are tiny cellular protrusions of nearly every vertebrate cell controlling multiple cellular processes, such as proliferation, differentiation, migration etc. Their dysfunction results in severe human diseases collectively referred to as ciliopathies. Remarkably, many ciliopathies are associated with increased programmed cell death (PCD). However, it is largely unknown how primary cilia regulate PCD. In in vitro (murine and human cells) and in vivo (Xenopus laevis and mouse) models, we observed elevated PCD in the absence of the ciliopathy protein RPGRIP1L. Mechanistically, our data elucidated that RPGRIP1L controls PCD by governing the activity of the ciliary proteasome. By using super-resolution microscopy, we first showed that the apoptosis inducer MOAP1 localises to primary cilia. Furthermore, our investigations revealed that RPGRIP1L controls PCD via the degradation of MOAP1 by the ciliary proteasome. Based on our finding that two more ciliopathy proteins, TCTN1 and CEP290, modulate PCD via regulating the activity of the ciliary proteasome, we suggest that the proteasomal degradation of MOAP1 represents a general mechanism by which primary cilia control PCD.

cell biology↗

bioRxiv2025

Oxidative stress causes a reversible decrease of deubiquitylases activity in old vertebrate brains

The ubiquitin-proteasome system is essential for neuronal proteostasis, and its activity declines with age. How deubiquitylating enzymes (DUBs) are affected by aging in the vertebrate brain remains unclear. Here, we profiled cysteine protease DUBs using activity-based proteomics in aging mouse and killifish brains. Despite stable protein levels, we identified a subset of DUBs that progressively lose catalytic activity with age. We demonstrated that oxidative stress impairs DUB function through thiol oxidation and that antioxidant treatment restores their activity in vitro and in vivo. Further, inhibition of DUBs in human iPSC-derived neurons significantly recapitulated ubiquitylation changes observed in aged brains, and temporal analysis in mice revealed that DUB inhibition precedes proteasome decline in the brain during aging. Together, these findings indicate a redox-sensitive subset of DUBs that undergo an age-associated decline in activity and suggest that impaired deubiquitylation is an early, yet potentially reversible, driver of proteostasis decline in the aging brain.

biochemistry↗

bioRxiv2023

Seed Longevity is Controlled by Metacaspases

To survive extreme desiccation, seeds enter dormancy that can last millennia. This dormancy involves the accumulation of protective but structurally disordered storage proteins through unknown adjustments of proteolytic surveillance mechanisms. Mutation of all six types II metacaspases (MCAs)-II in the model plant Arabidopsis revealed their essential role in modulating these proteolytic mechanisms. MCA-II mutant seeds fail to properly target at the endoplasmic reticulum (ER) the AAA ATPase Cell Division Cycle 48 (CDC48) to dispose of misfolded proteins. MCA-IIs cleave a CDC48 adaptor, the ubiquitination regulatory X domain-containing (PUX) responsible for localizing CDC48 to the lipid droplets. When cleaved, CDC48-PUX is inactivated and allows a lipid droplet-to-ER shuttling of CDC48, an important step in the regulation of seeds lifespan. In sum, we uncover antagonism between proteolytic pathways bestowing longevity. One-Sentence SummaryMetacaspase proteases confer seed longevity by antagonizing CDC48 activity.

plant biology↗