Biology subjects

Seemann, J.

Publications and source records attributed to Seemann, J..

7 recordsLinked to original sources

bioRxiv2023

RNA scaffolds the Golgi ribbon by forming condensates with GM130

The mammalian Golgi apparatus is composed of stacks of cisternae that are laterally linked to form a continuous ribbon like structure, but the molecular mechanisms that maintain the Golgi ribbon remain unclear. Here, we show that ribbon formation is mediated by biomolecular condensates of RNA and the Golgi resident protein GM130. We identified GM130 as a membrane-bound RNA binding protein at the Golgi. Acute degradation of either RNA or GM130 in cells disrupted the Golgi ribbon. Under stress conditions, RNA was displaced from GM130 and the ribbon was disjoint, which was restored after cells recovered from stress. When overexpressed in cells, GM130 formed RNA-dependent liquid-like condensates. GM130 contains an intrinsically disordered domain at its N-terminus, which was sufficient to recruit RNA to drive condensate assembly in vitro. Condensates of the N-terminal domain of GM130 and RNA were sufficient to link purified rat liver Golgi membranes which is a reconstruction of aspects of lateral linking of stacks into a ribbon-like structure. Together, these studies reveal that biomolecular condensates of GM130-RNA scaffold the Golgi ribbon.

cell biology↗

bioRxiv2022

ERK-dependent DICER1 phosphorylation promotes open chromatin state and lineage plasticity to mediate tumor progression

DICER1 controls micro(mi)RNA-mediated epithelial-to-mesenchymal transition (EMT) to regulate tumorigenesis of lung adenocarcinomas (LUADs). We discovered that DICER1 is phosphorylated by ERK and nuclear translocated and phospho-DICER1 contributes to tumorigenesis. Mechanisms through which phospho-DICER1 regulates tumor progression remain undefined. We show that phospho-nuclear DICER1 associates with invasive human LUADs with oncogenic KRAS mutations and promotes late-stage tumor progression in mice with oncogenic Kras mutations. Surprisingly, phosphomimetic DICER1 regulates LUAD progression independent of miRNAs and EMT. Integrating single-cell RNA sequencing, fluorescent in situ RNA hybridization, immunofluorescence, and ATAC-sequencing, in mice, we discovered that phosphomimetic DICER1 generates an open chromatin state in the lung tumor alveolar cells leading to expression of gastrointestinal genes and altered AT2 cell identity. Strikingly, we also observe the gastric gene signature in human LUADs with phospho-DICER1 and KRAS mutations. We propose that phosphorylated nuclear DICER1 regulates chromatin remodeling leading to tumor cell reprogramming which drives lung cancer progression.

cancer biology↗

bioRxiv2021

Turning movements in real life capture subtle longitudinal and preataxic changes in cerebellar ataxia

OBJECTIVESClinical and regulatory acceptance of upcoming molecular treatments in degenerative ataxias might greatly benefit from ecologically valid endpoints which capture change in ataxia severity in patients real life. This longitudinal study aimed to unravel quantitative motor biomarkers in degenerative ataxias in real life turning movements which are sensitive for changes both longitudinally and at the preataxic stage. METHODSCombined cross-sectional (n=30) and longitudinal (n=14, 1-year interval) observational study in degenerative cerebellar disease (including 8 pre-ataxic mutation carriers) compared to 23 healthy controls. Turning movements were assessed by three body-worn inertial sensors in three conditions: (1) instructed laboratory assessment, (2) supervised free walking, and (3) unsupervised real-life movements. RESULTSMeasures which quantified dynamic balance during turning - lateral velocity change (LVC) and outward acceleration -, but not general turning measures such as speed, allowed differentiating ataxic against healthy subjects in real life with high effect size ({delta}=0.68), with LVC also differentiating preataxic against healthy subjects ({delta}=0.53). LVC was highly correlated with clinical ataxia severity (SARA score, effect size {rho}=0.79) and subjective balance confidence (ABC score, {rho}=0.66). Moreover, LVC in real life - but not general turning measures, gait measures, or the SARA score - allowed detecting significant longitudinal change in one-year follow-up with high effect size (rprb=0.66). CONCLUSIONSMeasures of turning allow to capture specific changes of dynamic balance in degenerative ataxia in real life, with high sensitivity to longitudinal differences in ataxia severity and to the preataxic stage. They thus present promising ecologically valid motor biomarkers for capturing change in real life, even in the highly treatment-relevant early stages of degenerative cerebellar disease.

bioengineering↗

bioRxiv2020

Rapid degradation of GRASP55 and GRASP65 reveals their immediate impact on the Golgi structure

GRASP65 and GRASP55 have been implicated in stacking of Golgi cisternae and lateral linking of stacks within the Golgi ribbon. However, loss of gene function approaches by RNAi or gene knockout to dissect their respective roles often resulted in conflicting conclusions. Here, we gene-edited GRASP55 and/or GRASP65 with a degron tag in human fibroblasts, allowing for the induced rapid degradation by the proteasome. We show that acute depletion of either GRASP55 or GRASP65 does not affect the Golgi ribbon, while chronic degradation of GRASP55 disrupts lateral connectivity of the Golgi ribbon. Acute double depletion of both GRASPs coincides with the loss of the vesicle tethering proteins GM130, p115 and Golgin-45 from the Golgi and compromises ribbon linking. Furthermore, neither GRASP55 and/or GRASP65 are required for maintaining stacks or de novo assembly of stacked cisternae at the end of mitosis. These results demonstrate that both GRASPs are dispensable for Golgi stacking, but are involved in maintaining the integrity of Golgi ribbon together with GM130 and Golgin-45.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗

bioRxiv2020

TPX2 activation by GM130 controls astral microtubule formation and spindle orientation

Spindle orientation is important in multiple developmental processes as it determines cell fate and function. The correct orientation of the mitotic spindle depends on the assembly of a proper astral microtubule network. Here, we report that the spindle assembly factor TPX2 regulates the astral microtubule network. TPX2 in the spindle pole area is activated by GM130 on mitotic Golgi membranes to promote astral microtubule growth. GM130 relieves TPX2 inhibition by competing for importin binding. During mitosis, phosphorylation of importin at Serine 62 by Cdk1 switches its substrate preference from TPX2 to GM130, thereby enabling competition-based activation. Importin S62A impedes local TPX2 activation and compromises astral microtubule formation, ultimately resulting in misoriented spindles. Blocking the GM130-importin -TPX2 pathway impairs astral microtubule growth. Our results reveal a novel role for TPX2 in the organization of astral microtubules. Furthermore, we show that the substrate preference of the important mitotic modulator importin is regulated by Cdk1 phosphorylation.

cell biology↗

bioRxiv2019

Towards ecologically valid biomarkers: real-life gait assessment in cerebellar ataxia

BACKGROUNDWith disease-modifying drugs on the horizon for degenerative ataxias, motor biomarkers are highly warranted. While ataxic gait and its treatment-induced improvements can be captured in laboratory-based assessments, quantitative markers of ataxic gait in real life will help to determine ecologically meaningful improvements.\n\nOBJECTIVESTo unravel and validate markers of ataxic gait in real life by using wearable sensors.\n\nMETHODSWe assessed gait characteristics of 43 patients with degenerative cerebellar disease (SARA:9.4{+/-}3.9) compared to 35 controls by 3 body-worn inertial sensors in three conditions: (1) laboratory-based walking; (2) supervised free walking; (3) real-life walking during everyday living (subgroup n=21). Movement analysis focussed on measures of movement smoothness and spatio-temporal step variability.\n\nRESULTSA set of gait variability measures was identified which allowed to consistently identify ataxic gait changes in all three conditions. Lateral step deviation and a compound measure of step length categorized patients against controls in real life with a discrimination accuracy of 0.86. Both were highly correlated with clinical ataxia severity (effect size {rho}=0.76). These measures allowed detecting group differences even for patients who differed only 1 point in the SARAp&g subscore, with highest effect sizes for real-life walking (d=0.67).\n\nCONCLUSIONSWe identified measures of ataxic gait that allowed not only to capture the gait variability inherent in ataxic gait in real life, but also demonstrate high sensitivity to small differences in disease severity - with highest effect sizes in real-life walking. They thus represent promising candidates for quantitative motor markers for natural history and treatment trials in ecologically valid contexts.

bioengineering↗

bioRxiv2019

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition, but most studies to date have evaluated its effectiveness in single habitats and for conspicuous taxonomic groups in temperate ecosystems. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean.

ecology↗