Biology subjects

Goedecke, N.

Publications and source records attributed to Goedecke, N..

4 recordsLinked to original sources

bioRxiv2022

PDGFRα+ fibroblasts are a major site of cytomegalovirus replication in vivo and genome maintenance during latency

To date, no herpesvirus has been shown to latently persist in fibroblastic cells. Here, we demonstrate that mouse CMV (MCMV), a {beta}-herpesvirus, persists for the long term and across organs in PDGFR+ fibroblastic cells, with similar or higher genome loads than in the previously known sites of MCMV latency. Whereas MCMV gene transcription in PDGFR+ fibroblastic cells was almost completely silenced at 5 months post-infection, these cells gave rise to reactivated virus ex vivo, arguing that they supported latent MCMV infection. Notably, PDGFR+ fibroblastic cells also supported productive virus replication during primary MCMV infection. Mechanistically, Stat1-deficiency resulted in increased lytic but abolished latent infection of fibroblastic cells in vivo. In sum, fibroblastic cells have a dual role as a site of lytic MCMV replication and a reservoir of latent MCMV in vivo and Stat1 is critically involved in the regulation of MCMV latency.

microbiology↗

bioRxiv2021

The stiffness-sensitive transcriptome of human tendon stromal cells

Matrix stiffness and its effects on tensional homeostasis act as major regulators of cellular states in health and disease. Stiffness-sensing studies are typically performed using cells that have acquired "mechanical memory" through prolonged propagation in rigid mechanical environments, e.g. tissue culture plastic (TCP). This may potentially mask the full extent of the stiffness-driven mechanosensing programs. To address this, we developed a biomaterial system composed of two-dimensional mechano-variant silicone substrates that is permissive to large-scale cell culture expansion processes. We broadly mapped the stiffness-mediated mechano-responses by performing RNA sequencing on human tendon-derived stromal cells. We find that matrix rigidities approximating tendon microscale stiffness range (E. ~35 kPa) distinctly favor programs related to chromatin remodeling and Hippo signaling; whereas more compliant stiffnesses (E. 2 kPa) were enriched in responses related to pluripotency, synapse assembly and angiogenesis. We also find that tendon stromal cells undergo dramatic phenotypic drift on conventional TCP, with near-complete suppression of tendon-related genes and emergence of expression signatures skewed towards fibro-inflammatory and metabolic activation. Strikingly, mechano-variant substrates abrogate fibroblasts activation, with tenogenic stiffnesses inducing a transcriptional program that strongly correlate with established tendon tissue-specific signatures. Computational inference predicted that AKT1 and ERK1/2 are major signaling hubs mediating stiffness-sensing in tendon cells. Together, our findings highlight how the underlying biophysical cues may dictate the transcriptional identity of resident cells, and how matrix mechano-reciprocity regulates diverse sets of previously underappreciated mechanosensitive processes in tendon stromal fibroblasts.

bioengineering↗

bioRxiv2018

Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer

In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, while mass spectra are acquired in about 100 microseconds with time-of-fight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive due to its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation - serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al., PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 800,000 fragmentation spectra in standard 120 min LC runs are easily achievable, which can be used for near exhaustive precursor selection in complex mixtures or re-sequencing weak precursors. MaxQuant identified more than 6,400 proteins in single run HeLa analyses without matching to a library, and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,900 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.

systems biology↗

bioRxiv2018

Neuroligins mediate presynaptic maturation through brain-derived neurotrophic factor signaling

Maturation is a process that allows synapses to acquire full functionality; failures in synaptic maturation may contribute to neurodevelopmental disorders. Neuroligins are postsynaptic cell-adhesion molecules essential for synapse maturation, but the underlying pathways are incompletely understood. Here, we show that maturational increases in active zone stability and synaptic vesicle recycling rely on the joint action of Neuroligins and brain-derived neurotrophic factor (BDNF). Applying BDNF to neuronal cultures mimicked the maturation-promoting effects of overexpressing the Neuroligin isoforms NL1 or NL2. Inhibiting BDNF signaling reduced the effects of NL1 and NL2 on presynaptic maturation and of NL2 on synapse formation. Applying BDNF to NL1-knockout mouse cultures rescued defective presynaptic maturation, indicating that BDNF acts downstream of NL1 and can restore presynaptic maturation at late stages of network development. Our data introduce BDNF as a novel and essential component in a transsynaptic pathway linking Neuroligin-mediated cell adhesion, neurotrophin action and presynaptic maturation.

neuroscience↗