Biology subjects

von Kuegelgen, N.

Publications and source records attributed to von Kuegelgen, N..

4 recordsLinked to original sources

bioRxiv2025

StemCNV-check: a pipeline for human pluripotent stem cell (hPSC) genomic integrity control using SNP array data and copy number variant scoring

Human pluripotent stem cells (hPSCs) and other continuously cultured cell lines are prone to acquiring mutations and genomic aberrations over time, even when derived from well-characterized cell banks. To ensure experimental reproducibility and maintain cell line integrity, routine monitoring for genomic abnormalities is essential. Single nucleotide polymorphism (SNP) arrays represent a cost-effective and widely accessible method for detecting copy number variations (CNVs) with genome-wide resolution, making them particularly suitable for quality control (QC) in cell culture systems. Despite the established utility of SNP arrays for CNV detection, there remains a lack of comprehensive, user-friendly software solutions that support end-to-end analysis tailored to hPSC line quality assessment. Existing tools are either limited to discrete analysis steps requiring specialized bioinformatics expertise or are proprietary solutions that do not adequately address the specific needs of cell line monitoring. To bridge this gap, we developed an accessible and integrated analysis pipeline for SNP array-based QC of hPSC lines. The pipeline facilitates all stages of analysis--from raw data processing to the generation of interpretable reports--and includes specialized features such as sample-to-reference comparison, a CNV scoring system according to CNV biological impact, single nucleotide variation (SNV) evaluation and identity verification via SNP genotyping profiles, all tailored to hPSC. We benchmarked the pipeline against established methodologies and implemented strategies to enhance CNV detection reliability through expert-guided improvement process.

cell biology↗

bioRxiv2024

Neuromuscular dysfunction in patient-derived FUSR244RR-ALS iPSC model via axonal downregulation of neuromuscular junction proteins

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative condition characterized by the progressive degeneration of motor neurons, ultimately resulting in death due to respiratory failure. A common feature among ALS cases is the early loss of axons, pointing to defects in axonal transport and translation as initial disease indicators. Here, we established a FUSR244RR-ALS hiPSC-derived model that recapitulates the motor neuron survival and muscle contractility defects characteristic of ALS patients. Analysis of the protein and mRNA expression profiles in axonal and somatodendritic compartments of ALS-afflicted and isogenic control motor neurons revealed a selective downregulation of proteins essential for the neuromuscular junction function in FUS-ALS axons. Furthermore, analysis of FUS CLIP and RIP data showed that FUS binds mRNAs encoding these proteins. This work shed light on the pathogenic mechanisms of ALS and emphasized the importance of axonal gene expression analysis in elucidating the mechanisms of neurodegenerative disorders.

cell biology↗

bioRxiv2021

Massively parallel identification of zipcodes in primary cortical neurons

Cells adopt highly polarized shapes and form distinct subcellular compartments largely due to the localization of many mRNAs to specific areas, where they are translated into proteins with local functions. This mRNA localization is mediated by specific cis-regulatory elements in mRNAs, commonly called "zipcodes." Their recognition by RNA-binding proteins (RBPs) leads to the integration of the mRNAs into macromolecular complexes and their localization. While there are hundreds of localized mRNAs, only a few zipcodes have been characterized. Here, we describe a novel neuronal zipcode identification protocol (N-zip) that can identify zipcodes across hundreds of 3UTRs. This approach combines a method of separating the principal subcellular compartments of neurons - cell bodies and neurites - with a massively parallel reporter assay. Our analysis identifies the let-7 binding site and (AU)n motif as de novo zipcodes in mouse primary cortical neurons and suggests a strategy for detecting many more.

molecular biology↗

bioRxiv2021

The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression

SARS-CoV-2, responsible for the ongoing global pandemic, must overcome a conundrum faced by all viruses. To achieve its own replication and spread, it simultaneously depends on and subverts cellular mechanisms. At the early stage of infection, SARS-CoV-2 expresses the viral nonstructural protein 1 (NSP1), which inhibits host translation by blocking the mRNA entry tunnel on the ribosome; this interferes with the binding of cellular mRNAs to the ribosome. Viral mRNAs, on the other hand, overcome this blockade. We show that NSP1 enhances expression of mRNAs containing the SARS-CoV-2 leader. The first stem-loop (SL1) in viral leader is both necessary and sufficient for this enhancement mechanism. Our analysis pinpoints specific residues within SL1 (three cytosine residues at the positions 15, 19 and 20) and another within NSP1 (R124) which are required for viral evasion, and thus might present promising drug targets. Additionally, we carried out analysis of a functional interactome of NSP1 using BioID and identified components of anti-viral defense pathways. Our analysis therefore suggests a mechanism by which NSP1 inhibits the expression of host genes while enhancing that of viral RNA. This analysis helps reconcile conflicting reports in the literature regarding the mechanisms by which the virus avoids NSP1 silencing.

molecular biology↗