Biology subjects

Hentges, K. E.

Publications and source records attributed to Hentges, K. E..

6 recordsLinked to original sources

bioRxiv2026

Prpf8N1531S homozygous mutant mouse embryos have multiple defects in cardiac development and show aberrant splicing of the cardiac transcription factor Tead1

Mutations in the spliceosomal gene PRPF8 are associated with a range of human diseases. Studies in mouse and zebrafish suggest that Prpf8 also has a developmental function. Here, using a Prpf8 mutant mouse line isolated from a chemical induced mutagenesis screen, we uncover a previously unrecognised and essential role for Prpf8 in heart development, consistent with the embryonic lethality observed in Prpf8N1531S homozygous mutants. Prpf8N1531S mutant embryos display severe defects in ventricular trabeculation and compact zone formation, accompanied by increased cardiomyocyte proliferation specifically in the compact zone. Mutant embryonic hearts also exhibit disrupted cellular organisation, altered cytoskeletal architecture and changes in extracellular matrix protein expression. Notably, these cardiac abnormalities were exacerbated in embryos exhibiting cardiac looping defects. Transcriptomic analysis identified multiple aberrantly spliced transcripts in Prpf8N1531S mutant embryos, among which the cardiac transcription factor Tead1 was selected as a key functional candidate due to it known role in cardiac ventricle wall developemnt. Tead1 mis-splicing generated an in-frame, lower molecular weight protein isoform, associated with reduced overall TEAD1 expression. The Tead1 mis-spliced isoform showed altered nuclear localisation and dysregulation of TEAD1-dependent gene network important for heart development, including known cardiac sarcomeric genes. In addition, we observed reduced levels of the intracellular domain of the NOTCH1 receptor (NICD1), indicating impaired Notch signalling.. These findings suggest that impaired TEAD1-dependent transcription and Notch signalling contribute to abnormal cardiac trabeculation and compact zone development, highlighting a critical role for Prpf8 in maintaining proper heart development through the regulation of cardiac transcription factor expression and associated signalling networks. This study offers new mechanistic insights into congenital heart diseases linked to spliceosomal gene mutations.

developmental biology↗

bioRxiv2025

CAKUT variants in PRPF8, DYRK2, and CEP78: implications for splicing and ciliogenesis

IntroductionCongenital anomalies of the kidney and urinary tract (CAKUT) are the leading cause of chronic kidney disease in children and young adults. Although over 50 monogenic causes have been identified, many remain unresolved. PRPF8 is a core spliceosome component, essential for pre-mRNA splicing, and further localizes to the distal mother centriole to promote ciliogenesis. MethodsWe performed trio exome sequencing in 208 CAKUT families and identified strong variants in PRPF8 and the EDD-DYRK2-DDB1VprBP complex. Functional validation included splicing assays in yeast (Saccharomyces cerevisiae), Sonic hedgehog (Shh) signaling in RPE-1 cells, co-immunoprecipitation for protein complex assembly, and in situ hybridization in mouse embryos. Protein interactions were modeled using AlphaFold. ResultsWe identified heterozygous de novo or inherited variants in PRPF8, DYRK2, DDB1, EDD and CEP78. Yeast assays revealed that while most PRPF8 variants preserved growth and splicing at consensus splice sites, the de novo PRPF8R1681W variant impaired splicing of non-consensus splice sites and was inviable at elevated temperature. CAKUT variants failed to rescue prp28-1 and U4-cs1 alleles but showed variant-specific synthetic interactions with brr2-1, including weak suppression or synthetic sickness at elevated temperatures. Shh signaling was reduced in [~]50% of PRPF8 variants expressed in RPE-1 cells. CEP78 truncating variants abrogated binding to CEP350 and VPRBP. Two DYRK2 variants disrupted EDD-DYRK2-DDB1VprBP complex formation without affecting kinase activity. In situ hybridization revealed strong Prpf8 expression in the developing collecting duct and urothelium. ConclusionVariants in PRPF8 and components of the EDD-DYRK2-DDB1VprBP complex may contribute to CAKUT through impaired pre-mRNA splicing and defective ciliogenesis. These findings uncover an entirely new functional network of candidate genes for CAKUT and ciliopathies, significantly broadening our understanding of disease mechanisms and offering novel entry points for mechanistic studies. Translational StatementOur study identifies a previously unrecognized molecular network involving PRPF8 and the EDD-DYRK2-DDB1VprBP complex, revealing a novel pathogenic mechanism in CAKUT. These results introduce a new class of candidate genes and pathways essential for kidney development. As the genetic etiology of CAKUT remains unknown in most patients, our findings underscore the need for targeted genetic testing and functional studies to enhance diagnosis, advance mechanistic insight, and enable more personalized clinical management.

genetics↗

bioRxiv2025

The RNA splicing factor PRPF8 is required for left-right organiser cilia function and determination of cardiac left-right asymmetry via regulation of Arl13b splicing

Cilia function in the left-right organizer (LRO) is critical for determining internal organ asymmetry in vertebrates. To further understand the genetics of left-right asymmetry, we isolated a mouse mutant with laterality defects, l11Jus27, from a random mutagenesis screen. l11Jus27 mutants carry a missense mutation in the pre-mRNA processing factor, Prpf8. cephaloph[o]nus (cph) mutant zebrafish, carrying a protein truncating mutation in prpf8, phenocopy the laterality defects of l11Jus27 mutants. Prpf8 mutant mouse and fish embryos have increased expression of an alternative transcript encoding the cilium-associated protein, ARL13B, that lacks exon 9. In zebrafish, over-expression of the arl13b transcript lacking exon 9 perturbed cilium formation and caused laterality defects. The shorter ARL13B protein isoform lacked interactions with intraflagellar transport proteins. Our data suggest that PRPF8 plays a prominent role in LRO cilia by through the regulation of alternative splicing of ARL13B, thus uncovering a new mechanism for cilia-linked developmental defects.

developmental biology↗

bioRxiv2024

A Machine Learning Classifier to Identify and Prioritise Genes Associated with Cardiac Development

Congenital heart disease (CHD) is a major cause of infant mortality and presents life-long challenges to individuals living with these conditions. Genetic causes are known for only a minority of types of CHD. Discovering further genetic causes is limited by challenges in prioritising candidate CHD genes. We examined a wide range of features of mouse genes, including sequence characteristics, protein localisation and interaction data, developmental expression data and gene ontology annotations. Many features differ between cardiac development and non-cardiac genes, suggesting that these two gene types can be distinguished by their attributes. Therefore, we developed a supervised machine learning (ML) method to identify Mus musculus genes with a high probability of being involved in cardiac development. These genes, when mutated, are candidates for causing human CHD. Our classifier showed a cross-validation accuracy of 81% in detecting cardiac and non-cardiac genes. From our classifier we generated predictions of the cardiac development association status for all protein-coding genes in the mouse genome. We also cross-referenced our predictions with datasets of known human CHD genes, determining which are orthologues of predicted mouse cardiac genes. Our predicted cardiac genes have a high overlap with human CHD genes. Thus, our predictions could inform the prioritisation of genes when evaluating CHD patient sequence data for genetic diagnosis. Knowledge of cardiac developmental genes may speed up reaching a genetic diagnosis for patients born with CHD. Author SummaryCongenital heart disease arises during pregnancy when the heart has formed incorrectly. These malformations affect [~]1% of newborns. Yet, despite their frequency, the underlying causes are still not known in many cases. It is clear that genetic factors contribute to these defects, and increasingly DNA sequencing is used to attempt to determine if an individual has a genetic change causative of their condition. However, analysis of patient sequence data often reveals changes that are difficult to interpret due to a lack of knowledge of the function of the gene harbouring a sequence change. We aimed to facilitate the process of sequence evaluation by predicting which genes of unknown function are likely involved in heart formation. Our predictions agree with novel experimental evidence about genes needed for heart development. We found that when mutated, a high proportion of the predicted cardiac genes do indeed cause heart defects. This result suggests that our predictions may be informative for expanding our understanding of the genetic basis of congenital heart disease.

genomics↗

bioRxiv2021

Glypican-6 deficiency causes dose-dependent conotruncal congenital heart malformations through abnormal remodelling of the endocardial cushions

Tetralogy of Fallot (TOF) is considered to be the commonest type of cyanotic congenital heart disease (CHD). A previous GWAS showed significant association between TOF and single nucleotide polymorphisms in chromosome 13q31. Here through integration of population genomic and chromosomal interaction data we identify the heparan sulfate proteoglycan glypican-6 (GPC6) as the potentially responsible gene at the associated locus. We showed that GPC6 is expressed in the endocardial cushions at the appropriate time in development to contribute to TOF risk. We generated mice homozygous for a Gpc6 KO allele, which exhibit 100% neonatal lethality with severe cardiac malformations, namely TOF-type double outlet right ventricle (DORV) with rightward mal-positioned aorta and perimembranous ventricular septal defect (VSD), together with right ventricular (RV) hypertrophy and narrowing of the pulmonary artery. We established a dose-response relationship between Gpc6 expression and the anatomical severity of cardiac malformations. We showed the mouse knockout phenotype arises from abnormal morphology of the endocardial cushions, and tissue-specific knockout of Gpc6 in endothelial and neural crest cell lineages produces a phenotype featuring VSD and aortic malposition analogous to human TOF. This successful identification of a CHD gene from GWAS data suggests that larger GWA studies may find additional causative genes.

genetics↗

bioRxiv2018

Re-Evaluating One-step Generation of Mice Carrying Conditional Alleles by CRISPR-Cas9-Mediated Genome Editing Technology

CRISPR-Cas9 gene editing technology has considerably facilitated the generation of mouse knockout alleles, relieving many of the cumbersome and time-consuming steps of traditional mouse embryonic stem cell technology. However, the generation of conditional knockout alleles remains an important challenge. An earlier study reported up to 16% efficiency in generating conditional knockout alleles in mice using 2 single guide RNAs (sgRNA) and 2 single-stranded oligonucleotides (ssODN) (2sgRNA-2ssODN). We re-evaluated this method from a large data set generated from a consortium consisting of 17 transgenic core facilities or laboratories or programs across the world. The dataset constituted 17,887 microinjected or electroporated zygotes and 1,718 live born mice, of which only 15 (0.87%) mice harbored 2 correct LoxP insertions in cis configuration indicating a very low efficiency of the method. To determine the factors required to successfully generate conditional alleles using the 2sgRNA-2ssODN approach, we performed a generalized linear regression model. We show that factors such as the concentration of the sgRNA, Cas9 protein or the distance between the placement of LoxP insertions were not predictive for the success of this technique. The major predictor affecting the methods success was the probability of simultaneously inserting intact proximal and distal LoxP sequences, without the loss of the DNA segment between the two sgRNA cleavage sites. Our analysis of a large data set indicates that the 2sgRNA-2ssODN method generates a large number of undesired alleles (>99%), and a very small number of desired alleles (<1%) requiring, on average 1,192 zygotes.

genetics↗