Biology subjects

Wuchty, S.

Publications and source records attributed to Wuchty, S..

10 recordsLinked to original sources

bioRxiv2025

Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity

Short tandem repeat (STR) instability is a major cause of disease association, yet their full length-distributions and sequence content have been difficult to resolve with short-read sequencing. By analyzing long-read sequencing genomes from 2,645 participants of the All of Us Research Program, we establish a comprehensive STR resource of 23 billion alleles covering a catalog of 4.4 million loci. We find that known disease-associated STR loci exhibit markedly elevated allelic variability relative to genome-wide distributions, which is most pronounced when based on the length of uninterrupted, pure repeat motifs (Odds Ratio: 244, p=1.62e-29). We establish the Pure Length Variability Index (PLVI) as a measure of this instability, which is robust across ancestries and replicated in 500 samples from the 1000 Genomes Project (Odds Ratio: 84, p=2.72e-28). To illustrate, we identify 55 unstable coding CAG and 5-UTR CGG STR loci with this metric, 60% of which have not been associated with disease. From this set, we document potential pathogenic repeat expansions for FAM193B and EP400 by integrating PLVI with single-genome length outlier analysis. These data establish a population-scale framework for STR discovery in rare and common diseases using long-read sequencing cohorts.

genomics↗

bioRxiv2023

Epidermal Eg5 promotes X-ROS dependent paclitaxel neurotoxicity

Taxanes are chemotherapeutic agents that induce microtubule modifications in cancer cells, resulting in cell cycle modifications and tumor remission. Here we show that paclitaxel, a widely used taxane, also induces microtubule modifications in healthy epidermal keratinocytes leading to chemotherapy-induced peripheral neuropathy (CIPN). Paclitaxel activates the cell cycle regulator, Kinesin-5 (Eg5), which promotes microtubule detyrosination and fasciculation (dfMT). Eg5 loss protects neurons from paclitaxel neurotoxicity, whereas keratinocyte-specific overexpression promotes axon degeneration. In vivo imaging and 3D reconstructions of dfMTs and nuclei, combined with mechanotransduction studies further show that dfMTs constrict keratinocyte nuclei, leading to nuclear Nox-dependent reactive oxygen species (X-ROS) formation upstream of MMP-13 and cutaneous sensory axon degeneration. This new insight facilitates our understanding of chemotherapy side effects and highlights the need for targeted therapies.

cell biology↗

bioRxiv2023

MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing is a global mechanism for the regulation of alternative splicing

While RNA secondary structures are critical to regulate alternative splicing of long-range pre-mRNA, the factors that modulate RNA structure and interfere with the recognition of the splice sites are largely unknown. Previously, we identified a small, non-coding microRNA that sufficiently affects stable stem structure formation of Nmnat pre-mRNA to regulate the outcomes of alternative splicing. However, the fundamental question remains whether such microRNA-mediated interference with RNA secondary structures is a global molecular mechanism for regulating mRNA splicing. We designed and refined a bioinformatic pipeline to predict candidate microRNAs that potentially interfere with pre-mRNA stem-loop structures, and experimentally verified splicing predictions of three different long-range pre-mRNAs in the Drosophila model system. Specifically, we observed that microRNAs can either disrupt or stabilize stem-loop structures to influence splicing outcomes. Our study suggests that MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS) is a novel regulatory mechanism for the transcriptome-wide regulation of alternative splicing, increases the repertoire of microRNA function and further indicates cellular complexity of post-transcriptional regulation. One-Sentence SummaryMicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS) is a novel regulatory mechanism for the transcriptome-wide regulation of alternative splicing.

molecular biology↗

bioRxiv2023

RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci

Tandem repeats (TRs) are polymorphic sequences of DNA that are composed of repeating units of motifs, whose lengths can vary depending on the type of TR. Expansions of TRs are responsible for approximately 50 monogenic diseases, compared to over 4,300 disease causing genes disrupted by single nucleotide variants and small indels. It appears thus reasonable to expect the discovery of additional pathogenic repeat expansions, which has the potential of significantly narrowing the current diagnostic gap in many diseases. Recently, short and long-read whole genome sequencing with the use of advanced bioinformatics tools, have identified a growing number of TR expansions in the human population. The majority of these loci are expanded in <1% of genomes. Categorizing and prioritizing such TR loci is a growing challenge to human genomic studies. We present a first-in-class machine learning tool, RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), which is designed to distinguish pathogenic from benign TR expansions. Leave-one-out cross validation results demonstrated that an ensemble approach comprised of support vector machines (SVM) and extreme gradient boosted decision tree (XGB) classify TRs with a precision of 92% and a recall of 90%. Further validation of RExPRT on unseen test data demonstrate a similar precision of 86%, and a recall of 60%. RExPRTs high precision in particular, will be of significant value to large-scale discovery studies, which require the prioritization of promising candidate loci for time-consuming and costly functional follow-up studies. Application of RExPRT to ~800,000 TRs in the reference genome identified ~30,000 TRs that would be likely pathogenic upon expansion. Thus, RExPRT establishes a foundation for the application of machine learning approaches to categorize the pathogenicity of tandem repeat loci.

bioinformatics↗

bioRxiv2022

Minor intron containing genes: Achilles' heel of viruses?

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed the worlds unpreparedness to deal with the emergence of novel pathogenic viruses, pointing to the urgent need to identify targets for broad-spectrum antiviral strategies. Here, we report that proteins encoded by Minor Intron-containing Genes (MIGs) are significantly enriched in datasets of cellular proteins that are leveraged by SARS-CoV-2 and other viruses. Pointing to a general gateway for viruses to tap cellular machinery, MIG-encoded proteins (MIG-Ps) that react to the disruption of the minor spliceosome are most important points of viral attack, suggesting that MIG-Ps may pan-viral drug targets. While contemporary anti-viral drugs shun MIG-Ps, we surprisingly found that anti-cancer drugs that have been repurposed to combat SARS-CoV-2, indeed target MIG-Ps, suggesting that such genes can potentially be tapped to efficiently fight viruses.

systems biology↗

bioRxiv2021

Minor intron splicing efficiency increases with the development of lethal prostate cancer

Here we explored the role of minor spliceosome (MiS) function and minor intron-containing gene (MIG) expression in prostate cancer (PCa). We show MIGs are enriched as direct interactors of cancer-causing genes and their expression discriminates PCa progression. Increased expression of MiS U6atac snRNA, including others, and 6x more efficient minor intron splicing was observed in castration-resistant PCa (CRPC) versus primary PCa. Notably, androgen receptor signalling influenced MiS activity. Inhibition of MiS through siU6atac in PCa caused minor intron mis-splicing and aberrant expression of MIG transcripts and encoded proteins, which enriched for MAPK activity, DNA repair and cell cycle. Single cell-RNAseq confirmed cell cycle defects and lineage dependency on the MiS from primary to CRPC and neuroendocrine PCa. siU6atac was [~]50% more efficient in lowering tumor burden of CRPC cells and organoids versus current state-of-the-art combination therapy. In all, MiS is a strong therapeutic target for lethal PCa and potentially other cancers. Graphical AbstractU6atac expression, MiS activity, and minor intron splicing correlate with PCa therapy resistance and PCa progression to CRPC-adeno and transdifferentiation to CRPC-NE. One major MiS regulator during that process is the AR-axis, which is re-activated during CRPC-adeno and blocked in CRPC-NE. Molecularly, an increase in MiS dependent splicing promotes changes of transcriptome and proteome. This results in cell cycle activation, increased MAPK signalling and increased DNA repair. U6atac mediated MiS inhibition renders MiS splicing error-prone through increased intron retention and alternative splicing events, which results in cell cycle block and decreased MAPK signalling and DNA repair. MiS inhibition blocks all stages of PCa. Figure created with BioRender.com. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/471104v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@1c1c296org.highwire.dtl.DTLVardef@1ce1416org.highwire.dtl.DTLVardef@88d842org.highwire.dtl.DTLVardef@2ddf96_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

A multi-tiered map of EMT defines major transition points and identifies vulnerabilities

Epithelial to mesenchymal transition (EMT) is a complex cellular program proceeding through a hybrid E/M state linked to cancer-associated stemness, migration and chemoresistance. Deeper molecular understanding of this dynamic physiological landscape is needed to define events which regulate the transition and entry into and exit from the E/M state. Here, we quantified >60,000 molecules across ten time points and twelve omic layers in human mammary epithelial cells undergoing TGF{beta}-induced EMT. Deep proteomic profiles of whole cells, nuclei, extracellular vesicles, secretome, membrane and phosphoproteome defined state-specific signatures and major transition points. Parallel metabolomics showed metabolic reprogramming preceded changes in other layers, while single-cell RNA sequencing identified transcription factors controlling entry into E/M. Covariance analysis exposed unexpected discordance between the molecular layers. Integrative causal modeling revealed co-dependencies governing entry into E/M that were verified experimentally using combinatorial inhibition. Overall, this dataset provides an unprecedented resource on TGF{beta} signaling, EMT and cancer.

systems biology↗

bioRxiv2021

Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction

To predict interactions between human and viral proteins, we combine evolutionary sequence profile features with a Siamese convolutional neural network (CNN) architecture and a multi-layer perceptron (MLP). Our architecture outperforms various feature encodings-based machine learning and state-of-the-art prediction methods. As our main contribution, we introduce two types of transfer learning methods (i.e., frozen type and fine-tuning type) that reliably predict interactions in a target human-virus domain based on training in a source human-virus domain, by retraining CNN layers. Our transfer learning strategies can effectively apply prior knowledge transfer from large source dataset/task to small target dataset/task to improve prediction performance. Finally, we utilize the frozen type of transfer learning to predict human-SARS-CoV-2 PPIs, indicating that our predictions are topologically and functionally similar to experimentally known interactions. Source code and datasets are available at https://github.com/XiaodiYangCAU/TransPPI/.

bioinformatics↗

bioRxiv2019

MicroRNA miR-1002 enhances NMNAT-mediated stress response by modulating alternative splicing

Understanding endogenous regulation of stress resistance and homeostasis maintenance is critical to developing neuroprotective therapies. Nicotinamide mononucleotide adenylyltransferase (NMNAT) is a conserved essential enzyme that confers extraordinary protection and stress resistance in many neurodegenerative disease models. Drosophila Nmnat is alternatively spliced to two mRNA variants, RA and RB. RB translates to protein isoform PD with robust protective activity and is upregulated upon stress to confer enhanced neuroprotection. The mechanisms regulating alternative splicing and stress response of NMNAT remain unclear. We have discovered a Drosophila microRNA, dme-miR-1002, which promotes the splicing of NMNAT pre-mRNA to RB by disrupting a pre-mRNA stem-loop structure. While NMNAT pre-mRNA is preferentially spliced to RA in basal conditions, miR-1002 enhances NMNAT PD-mediated stress protection by binding via RISC component Argonaute1 to the pre-mRNA, facilitating the splicing switch to RB. These results outline a new process for microRNAs in regulating alternative splicing and modulating stress resistance.

neuroscience↗

bioRxiv2019

Controllability of molecular pathways

Inputs to molecular pathways that are the backbone of cellular activity drive the cell to certain outcomes and phenotypes. Here, we investigated proteins that topologically controlled different human pathways represented as independent molecular interaction networks, suggesting that a minority of proteins control a high number of pathways and vice versa. Transcending different topological levels, proteins that controlled a large number of pathways also controlled a network of interactions when all pathways were combined. Furthermore, control proteins that were robust when interactions were rewired or inverted also increasingly controlled an increasing number of pathways. As for functional characteristics, such control proteins were enriched with regulatory and signaling genes, disease genes and drug targets. Focusing on evolutionary characteristics, proteins that controlled different pathways had a penchant to be evolutionarily conserved as equal counterparts in other organisms, indicating the fundamental role that control analysis of pathways plays for our understanding of regulation, disease and evolution.

systems biology↗