Chromodomain helicase binding protein 8 (Chd8) is a novel A-kinase anchoring protein expressed during rat cardiac development

Full-length Chd1 of Coprinopsis cinerea is expressed after the dark period required for fruiting body maturation and impacts meiotic progression

The maturation of the fruiting body primordia in the Agaricomycete Coprinopsis cinerea is triggered by light exposure, followed by a required dark period to complete maturation. During this maturation phase, meiosis occurs within basidia arranged on the surface of the gills (lamellae) on the underside of the cap. However, the molecular events required during the dark period for fruiting body maturation remain elusive. We identified a developmental mutant that fails to mature fruiting bodies under light/dark conditions. The mutant fruiting bodies resembled those arrested by the wild-type strains cultured under continuous light. The gene responsible for this mutant phenotype encodes a chromodomain helicase DNA-binding protein 1 (Chd1) homolog, Cc.Chd1. RNA-seq revealed a low transcriptional region (LTcR) within the Cc.chd1 gene. This suggests that a short version of Cc.Chd1 (predicted 1125 aa, Cc.Chd1S) is translated from the vegetative mycelium stage until before karyogamy. In contrast, the full-length Cc.Chd1 (predicted 1441 aa, Cc.Chd1L) is translated during or after the dark period when karyogamy occurs in the basidia. Western blot analysis confirmed these types of Cc.Chd1 at the expected stages. Microscopic observations further revealed that meiotic chromosomes in basidia become arrested at prophase I in the Cc.chd1-1 mutant and wild-type strains cultured under continuous light. These findings suggest that Cc.Chd1L is required for progression from meiotic prophase I to metaphase I. Additionally, the Cc.chd1 mutant exhibits defects in light-induced secondary knot formation, suggesting a role for Cc.Chd1S in this process.

Expansion of phenotypic and genotypic data in autism spectrum disorders due to variants in the CHD8 gene

Autism spectrum disorders are a group of the most common disorders of neuropsychiatric development, characterized by difficulties in social interaction and adherence to stereotypic behavioral patterns. This group of conditions frequently co-occurs with intellectual disability, epilepsy, attention-deficit hyperactivity disorder, connective tissue disorders and others. Among the most common molecular-genetic causes of autism spectrum disorders are pathogenic variants in the CHD8 gene. CHD8 codes for chromodomain-helicase-DNA-binding protein 8 - a chromatin remodeler that regulates cellular proliferation and brain development in embryogenesis. 6 children and 1 adult (mother of 1 of the children) and were found to have clinically significant variants in CHD8 on whole genome sequencing (3 children and 1 adult had likely pathogenic variants, 3 children- variants of unknown significance). Their phenotype consisted of autism spectrum disorders, developmental delay, ataxia, overgrowth and other signs typically observed in patients with pathogenic variants in CHD8, as well as common comorbidities of autism spectrum disorders, such as attention-deficit hyperactivity disorder and connective tissue disorders. Additionally, 4 patients had hepatomegaly and 2- hyperbilirubinemia (1 had both) - clinical features have not been previously associated with pathogenic variants in CHD8. 2 patients also presented with cardiovascular abnormalities, primarily arrythmias and, in 1 case, cardiomyopathy- also uncharacteristic of patients with pathogenic variants in CHD8. Further research is required to determine the mechanisms underlying the abovementioned clinical features, which are likely carried out through complex interactions between CHD8 and other regulatory proteins.

In-Hospital Outcomes in Patients With Non-ST Segment Elevation Myocardial Infarction and Concomitant Neurodevelopmental Disorders in the United States: Insights From the National Inpatient Sample 2011-2020

Patients with neurodevelopmental disorders (NDDs) encounter significant barriers to receiving quality health care, particularly for acute conditions such as non-ST segment elevation myocardial infarction (NSTEMI). This study addresses the critical gap in knowledge regarding in-hospital outcomes and the use of invasive therapies in this demographic. By analyzing data from the National Inpatient Sample database from 2011 to 2020 using the International Classification of Diseases, Ninth Edition (ICD-9) and Tenth Edition (ICD-10) codes, we identified patients with NSTEMI, both with and without NDDs, and compared baseline characteristics, in-hospital outcomes, and the application of invasive treatments. The analysis involved a weighted sample of 7,482,216 NSTEMI hospitalizations, of which 30,168 (0.40%) patients had NDDs. There were significantly higher comorbidity-adjusted odds of in-hospital mortality, cardiac arrest, endotracheal intubation, infectious complications, ventricular arrhythmias, and restraint use among the NDD cohort. Conversely, this group exhibited lower adjusted odds of undergoing left heart catheterization, percutaneous coronary intervention, or coronary artery bypass graft surgery. These findings underscore the disparities faced by patients with NDDs in accessing invasive cardiac interventions, highlighting the need for further research to address these barriers and improve care quality for this vulnerable population.

Chromatin gatekeeper and modifier CHD proteins in development, and in autism and other neurological disorders

Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and responds to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation. In this review, we first discuss the structural and functional domains of the CHD proteins, and their binding sites, and phosphorylation, acetylation, and methylation sites. The conservation of important amino acids in SWItch/sucrose non-fermenting (SWI/SNF) domains, and their protein and mRNA tissue expression profiles are discussed. Next, we convey the important binding partners of CHD proteins, their protein complexes and activities, and their involvements in epigenetic regulation. We also show the ChIP-seq binding dynamics for CHD1, CHD2, CHD4, and CHD7 proteins at promoter regions of histone genes, as well as several genes that are critical for neurodevelopment. The role of CHD proteins in development is also discussed. Finally, this review provides information about CHD protein mutations reported in autism and neurodevelopmental disorders, and their pathogenicity. Overall, this review provides information on the progress of research into CHD proteins, their structural and functional domains, epigenetics, and their role in stem cell, development, and neurological disorders.

Genetic data visualization using literature text-based neural networks: Examples associated with myocardial infarction

Data visualization is critical to unraveling hidden information from complex and high-dimensional data. Interpretable visualization methods are critical, especially in the biology and medical fields, however, there are limited effective visualization methods for large genetic data. Current visualization methods are limited to lower-dimensional data and their performance suffers if there is missing data. In this study, we propose a literature-based visualization method to reduce high-dimensional data without compromising the dynamics of the single nucleotide polymorphisms (SNP) and textual interpretability. Our method is innovative because it is shown to (1) preserves both global and local structures of SNP while reducing the dimension of the data using literature text representations, and (2) enables interpretable visualizations using textual information. For performance evaluations, we examined the proposed approach to classify various classification categories including race, myocardial infarction event age groups, and sex using several machine learning models on the literature-derived SNP data. We used visualization approaches to examine clustering of data as well as quantitative performance metrics for the classification of the risk factors examined above. Our method outperformed all popular dimensionality reduction and visualization methods for both classification and visualization, and it is robust against missing and higher-dimensional data. Moreover, we found it feasible to incorporate both genetic and other risk information obtained from literature with our method.

Genetic mouse models of autism spectrum disorder present subtle heterogenous cardiac abnormalities

Autism spectrum disorder (ASD) and congenital heart disease (CHD) are linked on a functional and genetic level. Most work has investigated CHD‐related neurodevelopmental abnormalities. Cardiac abnormalities in ASD have been less studied. We investigated the prevalence of cardiac comorbidities relative to ASD genetic contributors. Using high frequency ultrasound imaging, we screened 9 ASD‐related genetic mouse models (Arid1b^(+/−), Chd8^(+/−), 16p11.2 (deletion), Sgsh^(+/−), Sgsh^(−/−), Shank3 Δexon 4–9^(+/−), Shank3 Δexon 4–9^(−/−), Fmr1^(−/−), Vps13b^(+/−)), and pooled wild‐type littermates (WTs). We measured heart rate (HR), aorta diameter (AoD), thickness and thickening of the left‐ventricular (LV) anterior and posterior walls, LV chamber diameter, fractional shortening, stroke volume and cardiac output, mitral inflow Peak E and A velocity ratio, ascending aorta velocity time integral (VTI). Mutant groups presented small‐scale alterations in cardiac structure and function compared to WTs (LV anterior wall thickness and thickening, chamber diameter and fractional shortening, HR). A greater number of significant differences was observed among mutant groups than between mutant groups and WTs. Mutant groups differed primarily in structural measures (LV chamber diameter and anterior wall thickness, HR, AoD). The mutant groups with most differences to WTs were 16p11.2 (deletion), Fmr1^(−/−), Arid1b^(+/−). The mutant groups with most differences from other mutant groups were 16p11.2 (deletion), Sgsh^(+/−), Fmr1^(−/−). Our results recapitulate the associated clinical findings. The characteristic ASD heterogeneity was recapitulated in the cardiac phenotype. The type of abnormal measures (morphological, functional) can highlight common underlying mechanisms. Clinically, knowledge of cardiac abnormalities in ASD can be essential as even non‐lethal abnormalities impact normal development.

A Reassessment of Copy Number Variations in Congenital Heart Defects: Picturing the Whole Genome

Copy number variations (CNVs) can modulate phenotypes by affecting protein-coding sequences directly or through interference of gene expression. Recent studies in cancer and limb defects pinpointed the relevance of non-coding gene regulatory elements such as long non-coding RNAs (lncRNAs) and topologically associated domain (TAD)-related gene-enhancer interactions. The contribution of such non-coding elements is largely unexplored in congenital heart defects (CHD). We performed a retrospective analysis of CNVs reported in a cohort of 270 CHD patients. We reviewed the diagnostic yield of pathogenic CNVs, and performed a comprehensive reassessment of 138 CNVs of unknown significance (CNV-US), evaluating protein-coding genes, lncRNA genes, and potential interferences with TAD-related gene-enhancer interactions. Fifty-two of the 138 CNV-US may relate to CHD, revealing three candidate CHD regions, 19 candidate CHD genes, 80 lncRNA genes of interest, and six potentially CHD-related TAD interferences. Our study thus indicates a potential relevance of non-coding gene regulatory elements in CNV-related CHD pathogenesis. Shortcomings in our current knowledge on genomic variation call for continuous reporting of CNV-US in international databases, careful patient counseling, and additional functional studies to confirm these preliminary findings.

Murine AKAP7 has a 2',5'-phosphodiesterase domain that can complement an inactive murine coronavirus ns2 gene

Viral 2′,5′-phosphodiesterases (2′,5′-PDEs) help disparate RNA viruses evade the antiviral activity of interferon (IFN) by degrading 2′,5′-oligoadenylate (2-5A) activators of RNase L. A kinase anchoring proteins (AKAPs) bind the regulatory subunits of protein kinase A (PKA) to localize and organize cyclic AMP (cAMP) signaling during diverse physiological processes. Among more than 43 AKAP isoforms, AKAP7 appears to be unique in its homology to viral 2′,5′-PDEs. Here we show that mouse AKAP7 rapidly degrades 2-5A with kinetics similar to that of murine coronavirus (mouse hepatitis virus [MHV]) strain A59 ns2 and human rotavirus strain WA VP3 proteins. To determine whether AKAP7 could substitute for a viral 2′,5′-PDE, we inserted AKAP7 cDNA into an MHV genome with an inactivated ns2 gene. The AKAP7 PDE domain or N-terminally truncated AKAP7 (both lacking a nuclear localization motif), but not full-length AKAP7 or a mutant, AKAP7^H185R, PDE domain restored the infectivity of ns2 mutant MHV in bone marrow macrophages and in livers of infected mice. Interestingly, the AKAP7 PDE domain and N-terminally deleted AKAP7 were present in the cytoplasm (the site of MHV replication), whereas full-length AKAP7 was observed only in nuclei. We suggest the possibility that viral acquisition of the host AKAP7 PDE domain might have occurred during evolution, allowing diverse RNA viruses to antagonize the RNase L pathway.

Early virus-host interactions determine whether an infection is established, highlighting the need to understand fundamental mechanisms regulating viral pathogenesis. Recently, our laboratories reported a novel mode of regulation of the IFN antiviral response. We showed that the coronavirus MHV accessory protein ns2 antagonizes the type I IFN response, promoting viral replication and hepatitis. ns2 confers virulence by cleaving 2′,5′-oligoadenylate (2-5A) activators of RNase L in macrophages. We also reported that the rotavirus VP3 C-terminal domain (VP3-CTD) cleaves 2-5A and that it may rescue ns2 mutant MHV. Here we report that a cellular protein, AKAP7, has an analogous 2′,5′-phosphodiesterase (2′,5′-PDE) domain that is able to restore the growth of chimeric MHV expressing inactive ns2. The proviral effect requires cytoplasmic localization of the AKAP7 PDE domain. We speculate that AKAP7 is the ancestral precursor of viral proteins, such as ns2 and VP3, that degrade 2-5A to evade the antiviral activity of RNase L.

AKAP signaling complexes: pointing towards the next generation of therapeutic targets?

A-kinase anchoring proteins (AKAPs) streamline signal transduction by localizing signaling enzymes with their substrates. Great strides have been made in elucidating the role of these macromolecular signaling complexes as new binding partners and novel AKAPs are continually being uncovered. The mechanics and dynamics of these multi-enzyme assemblies suggest that AKAP complexes are viable targets for therapeutic intervention. This review will highlight recent advances in AKAP research focusing on local signaling events that are perturbed in disease.