Biology subjects

Klingenstein, S.

Publications and source records attributed to Klingenstein, S..

3 recordsLinked to original sources

bioRxiv2026

ViTAMIn-O: Democratizing computer vision-based machine learning for stem cell research

Deep Learning (DL) holds exciting potential in automating the prediction of organoid differentiation results. Nevertheless, current models lack adaptability, openness, and robustness in performance. Additionally, broad employments of predictive models in wet-lab settings necessitate machine learning expertise, often not readily available in biologically oriented laboratories. To offer an intuitive solution, we present ColabViTAMIn-O, a code-free platform together with ViTAMIn-O. ViTAMIn-O is a fully open organoid-specific DL model trained and tested on a total of 34 organoid categories, incorporating annotated images across transmitted light microscopy (TLM) modalities at single-organoid resolution. It is adaptable to downstream prediction tasks of varying dataset sizes and outperforms established models even with linear-probing. It performs reliably within a few-shot framework and is even extensible to human embryo TLM imaging data at single specimen level. By releasing our platform, centralized model hub, and datasets, we hope to encourage broader deployments of specialized DL models in stem-cell laboratories.

bioinformatics↗

bioRxiv2024

Electrophysiological signatures of a developmental delay in a stem cell model of KCNQ2 developmental and epileptic encephalopathy

BackgroundKCNQ2, encoding KV7.2 ion channels, has emerged as one of the prominent genes causing early onset seizures with developmental delay (KCNQ2 developmental and epileptic encephalopathy; KCNQ2-DEE). KCNQ2 de novo loss-of-function (LOF) and associated neuronal hyperexcitability have been accepted as mechanisms contributing to seizures. To investigate the developmental impact of KCNQ2 LOF, we generated patient iPSC-derived models for two previously reported de novo variants, p.(Arg325Gly) and p.(Gly315Arg), linked to severe congenital DEE. MethodsFunctional investigation of the two variants was initially performed in Xenopus laevis oocyte system. Patient-derived iPSC lines were differentiated using NGN2- and embryoid body-based protocols yielding neurons roughly corresponding to mid- and mid-late gestational stages, respectively. KV7- mediated M-current, passive neuronal properties, action potential generation and spontaneous oscillatory network activities were analysed with whole-cell patch clamping. FindingsStudied KCNQ2 variants showed LOF with a dominant-negative effect in the heterologous system. Reduced M-currents in patient iPSC-derived neurons corroborated a LOF as the main pathomechanism. Interestingly, this led to the reduced neuronal firing of the early neurons and to a disruption of complex oscillatory activity, with significantly reduced duration and amplitude of these events in patient iPSC-derived neurons. InterpretationWe provide experimental evidence for changing roles of the M-current throughout development and place disease variant-mediated M-current reduction in the context of the neuronal maturation in the prenatal brain. Based on the reduced neuronal firing and disrupted oscillatory activity seen in patient iPSC-derived neurons, we propose that a delayed/impaired maturation of neuronal and network properties underlies KCNQ-DEE caused by LOF variants.

neuroscience↗

bioRxiv2020

Evidence of SARS-CoV2 entry protein ACE2 in the human nose and olfactory bulb

Usually, pandemic COVID-19 disease, caused by SARS-CoV2, presents with mild respiratory symptoms such as fever, cough but frequently also with anosmia and neurological symptom. Virus-cell fusion is mediated by Angiotensin-Converting Enzyme 2 (ACE2) and Transmembrane Serine Protease 2 (TMPRSS2) with their organ expression pattern determining viral tropism. Clinical presentation suggests rapid viral dissemination to central nervous system leading frequently to severe symptoms including viral meningitis. Here, we provide a comprehensive expression landscape of ACE2 and TMPRSS2 proteins across human, post-mortem nasal and olfactory tissue. Sagittal sections through the human nose complemented with immunolabelling of respective cell types represent different anatomically defined regions including olfactory epithelium, respiratory epithelium of the nasal conchae and the paranasal sinuses along with the hardly accessible human olfactory bulb. ACE2 can be detected in the olfactory epithelium, as well as in the respiratory epithelium of the nasal septum, the nasal conchae and the paranasal sinuses. ACE2 is located in the sustentacular cells and in the glandular cells in the olfactory epithelium, as well as in the basal cells, glandular cells and epithelial cells of the respiratory epithelium. Intriguingly, ACE2 is not expressed in mature or immature olfactory receptor neurons and basal cells in the olfactory epithelium. Similarly ACE2 is not localized in the olfactory receptor neurons albeit the olfactory bulb is positive. Vice versa, TMPRSS2 can also be detected in the sustentacular cells and the glandular cells of the olfactory epithelium. Our findings provide the basic anatomical evidence for the expression of ACE2 and TMPRSS2 in the human nose, olfactory epithelium and olfactory bulb. Thus, they are substantial for future studies that aim to elucidate the symptom of SARS-CoV2 induced anosmia of via the olfactory pathway.

cell biology↗