Biology subjects

Ludwig, K. U.

Publications and source records attributed to Ludwig, K. U..

5 recordsLinked to original sources

bioRxiv2026

Time-resolved inference of gene regulatory networks underlying human cranial neural crest development suggests novel risk genes for orofacial clefting.

Cranial neural crest cells (CNCCs) play a central role in shaping the human head and face. Aberrant CNCC differentiation contributes to craniofacial birth defects, particularly non-syndromic cleft lip with or without cleft palate (nsCL/P), one of the most common congenital disorders. Although the number of genetic variants associated with this condition is steadily increasing, it remains challenging to determine if and how these variants may contribute to disease development. The majority of these variants lie within non-coding regulatory elements that govern cell-type and stage-specific gene expression, which is orchestrated by dynamic gene regulatory networks (GRNs). Despite extensive work in model organisms, a time-resolved, multi-omics perspective of GRNs controlling CNCC differentiation in a human system is still lacking. To fill this gap, we generated paired transcriptomic and chromatin accessibility data at four timepoints during in vitro differentiation of CNCCs derived from human induced pluripotent stem cells. Integrating these two modalities enabled time-resolved inference of GRNs and identification of dynamic regulatory relationships, including stage-specific roles of core transcription factors. Leveraging these time-resolved GRNs, we mapped 29 nsCL/P associated variants linked to 70 putative target genes, with 40 located outside the associated genomic loci, suggesting novel distal regulatory relationships. Integration of these data with complementary time-course scRNA-seq data revealed an ectomesenchymal-biased subpopulation of CNCCs as particularly sensitive to genetic variants associated with nsCL/P. We provide a time-resolved inference of GRN in human CNCC differentiation, allowing us to determine the dynamics of stage-specific core regulatory programs that are otherwise missed in analyses based on a single time snapshot. To our knowledge, the data represent the first multi-omics map of human CNCC with temporal resolution, which expands the understanding of early human craniofacial development, refines variant-to-gene assignment, prioritizes candidate risk genes and cell states relevant to nsCL/P. Our findings demonstrate the relevance of studying the dynamics upon differentiation rather than just one fixed timepoint and offer a valuable basis for further investigation of non-coding variation in CNCC-related disorders.

bioinformatics↗

bioRxiv2022

Epigenetic plasticity via adaptive DNA hypermethylation and clonal expansion underlie resistance to oncogenic pathway inhibition in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor prognosis. Drug resistance is the major cause for therapeutic failure in PDAC patients with progressive disease. The mechanisms underlying resistance formation are complex and remain poorly understood. To gain insights into molecular changes during the formation of resistance to oncogenic MAPK pathway inhibition we utilized short-term passaged primary tumor cells from ten PDACs of genetically engineered mice. We followed gain and loss of resistance upon MEKi exposure and withdrawal by longitudinal integrative analysis of whole genome sequencing, whole genome bisulfite sequencing, RNA-sequencing and mass spectrometry data. We found that resistant cell populations under increasing MEKi treatment evolved by the expansion of a single clone but were not a direct consequence of known resistance-conferring mutations. Rather, resistant cells showed adaptive DNA hypermethylation of 209 and hypomethylation of 8 genomic sites, most of which overlap with regulatory elements known to be active in murine PDAC cells. Both DNA methylation changes and MEKi resistance were transient and reversible upon drug withdrawal. The effector caspase CASP3 is one of the 114 genes for which transcriptional downregulation inversely correlated with the methylation status of the associated DNA region. CASP3 inactivation in resistant cells led to attenuation of drug-induced apoptosis which could be reversed by DNA methyltransferase inhibition with remarkable sensitivity exclusively in the resistant cells. Overall, our data provide a context for characterization and targeting of epigenetically mediated resistance mechanisms in PDAC.

cancer biology↗

bioRxiv2022

Predicting the pathogenicity of missense variants using features derived from AlphaFold2

Each individual genome harbors multiple missense variants, which can be systematically identified via genome or exome sequencing. This class of genetic variation can alter the functional properties of the respective protein, and thereby lead to clinically relevant phenotypes, such as cancer or Mendelian diseases. Despite advances in computational prediction scores, the classification of missense variants as clinically significant or benign remains a major challenge. Recently, the structure of the human proteome was derived with unprecedented accuracy using the artificial intelligence system AlphaFold2. However, the question of whether AlphaFold2 structures can improve the accuracy of computational pathogenicity prediction for missense variants remains unclear. To address this, we first engineered a set of features for each amino acid from these structures. We then trained a random forest to distinguish between proxy-benign and proxy-pathogenic missense variants derived from gnomAD. This yielded a novel AlphaFold2-based pathogenicity prediction score, termed AlphScore. Important feature classes used by AlphScore are solvent accessibility, amino acid network related features, features describing the physicochemical environment, and AlphaFold2s quality parameter (pLDDT). AlphScore alone showed lower performance than existing scores, such as CADD or REVEL. However, when AlphScore was added to those scores, the performance always increased, as measured by the approximation of deep mutational scan data, as well as the prediction of expert-curated missense variants from the ClinVar database. Overall, our data indicate that the integration of AlphaFold2 predicted structures can improve pathogenicity prediction of missense variants.

genetics↗

bioRxiv2018

Genome Wide Association Scan identifies new variants associated with a cognitive predictor of dyslexia.

Developmental dyslexia (DD) is one of the most prevalent learning disorders among children and is characterized by deficits in different cognitive skills, including reading, spelling, short term memory and others. To help unravel the genetic basis of these skills, we conducted a Genome Wide Association Study (GWAS), including nine cohorts of reading-impaired and typically developing children of European ancestry, recruited across different countries (N=2,562-3,468).\n\nWe observed a genome-wide significant effect (p<1x10-8) on rapid automatized naming of letters (RANlet) for variants on 18q12.2 within MIR924HG (micro-RNA 924 host gene; p = 4.73x10-9), and a suggestive association on 8q12.3 within NKAIN3 (encoding a cation transporter; p = 2.25 x10-8). RAN represents one of the best universal predictors of reading fluency across orthographies and linkage to RAN has been previously reported within CELF4 (18q12.2), a gene highly expressed in the fetal brain which is co-expressed with NKAIN3 and predicted to be a target of MIR924. These findings suggest new candidate DD susceptibility genes and provide insights into the genetics and neurobiology of dyslexia.

genomics↗

bioRxiv2018

DNA methylation mediates genetic liability to non-syndromic cleft lip/palate

BackgroundNon-syndromic cleft lip/palate (nsCL/P) is a complex trait with genetic and environmental risk factors. Around 40 distinct genetic risk loci have been identified for nsCL/P, but many reside in non-protein-coding regions with an unclear function. We hypothesised that one possibility is that the genetic risk variants influence susceptibility to nsCL/P through gene regulation pathways, such as those involving DNA methylation.\n\nMethodsUsing nsCL/P Genome-wide association study summary data and methylation data from four studies, we used Mendelian randomization and joint likelihood mapping to identify putative loci where genetic liability to nsCL/P may be mediated by variation in DNA methylation in blood.\n\nResultsThere was evidence at three independent loci, VAX1 (10q25.3), LOC146880 (17q23.3) and NTN1 (17p13.1), that liability to nsCL/P and variation in DNA methylation might be driven by the same genetic variant. Follow up analyses using DNA methylation data, derived from lip and palate tissue, and gene expression catalogues provided further insight into possible biological mechanisms.\n\nConclusionsGenetic variation may increase liability to nsCL/P by influencing DNA methylation and gene expression at VAX1, LOC146880 and NTN1.

genetics↗