Beyond the marks: reader-effectors as drivers of epigenetics and chromatin engineering.

Chromatin is a system of proteins and DNA that regulates chromosome organization and gene expression in eukaryotes. Essential features that support these processes include biochemical marks on histones and DNA, 'writer' enzymes that generate or remove these marks and proteins that translate the marks into transcriptional regulation: reader-effectors. Here, we review recent studies that reveal how reader-effectors drive chromatin-mediated processes. Advances in proteomics and epigenomics have accelerated the discovery of chromatin marks and their correlation with gene states, outpacing our understanding of the corresponding reader-effectors. Therefore, we summarize the current state of knowledge and open questions about how reader-effectors impact cellular function and human disease and discuss how synthetic biology can deepen our knowledge of reader-effector activity.

First Genotype-Phenotype Study in TBX4 Syndrome: Gain-of-Function Mutations Causative for Lung Disease.

Rationale: Despite the increased recognition of TBX4 (T-BOX transcription factor 4)-associated pulmonary arterial hypertension (PAH), genotype-phenotype associations are lacking and may provide important insights. Objectives: To compile and functionally characterize all TBX4 variants reported to date and undertake a comprehensive genotype-phenotype analysis. Methods: We assembled a multicenter cohort of 137 patients harboring monoallelic TBX4 variants and assessed the pathogenicity of missense variation (n = 42) using a novel luciferase reporter assay containing T-BOX binding motifs. We sought genotype-phenotype correlations and undertook a comparative analysis with patients with PAH with BMPR2 (Bone Morphogenetic Protein Receptor type 2) causal variants (n = 162) or no identified variants in PAH-associated genes (n = 741) genotyped via the National Institute for Health Research BioResource-Rare Diseases. Measurements and Main Results: Functional assessment of TBX4 missense variants led to the novel finding of gain-of-function effects associated with older age at diagnosis of lung disease compared with loss-of-function effects (P = 0.038). Variants located in the T-BOX and nuclear localization domains were associated with earlier presentation (P = 0.005) and increased incidence of interstitial lung disease (P = 0.003). Event-free survival (death or transplantation) was shorter in the T-BOX group (P = 0.022), although age had a significant effect in the hazard model (P = 0.0461). Carriers of TBX4 variants were diagnosed at a younger age (P < 0.001) and had worse baseline lung function (FEV1, FVC) (P = 0.009) than the BMPR2 and no identified causal variant groups. Conclusions: We demonstrated that TBX4 syndrome is not strictly the result of haploinsufficiency but can also be caused by gain of function. The pleiotropic effects of TBX4 in lung disease may be in part explained by the differential effect of pathogenic mutations located in critical protein domains.

Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data.

Trio-based whole-exome sequence (WES) data have established confident genetic diagnoses in ∼40% of previously undiagnosed individuals recruited to the Deciphering Developmental Disorders (DDD) study. Here we aim to use the breadth of phenotypic information recorded in DDD to augment diagnosis and disease variant discovery in probands. Median Euclidean distances (mEuD) were employed as a simple measure of similarity of quantitative phenotypic data within sets of ≥10 individuals with plausibly causative de novo mutations (DNM) in 28 different developmental disorder genes. 13/28 (46.4%) showed significant similarity for growth or developmental milestone metrics, 10/28 (35.7%) showed similarity in HPO term usage, and 12/28 (43%) showed no phenotypic similarity. Pairwise comparisons of individuals with high-impact inherited variants to the 32 individuals with causative DNM in ANKRD11 using only growth z-scores highlighted 5 likely causative inherited variants and two unrecognized DNM resulting in an 18% diagnostic uplift for this gene. Using an independent approach, naive Bayes classification of growth and developmental data produced reasonably discriminative models for the 24 DNM genes with sufficiently complete data. An unsupervised naive Bayes classification of 6,993 probands with WES data and sufficient phenotypic information defined 23 in silico syndromes (ISSs) and was used to test a "phenotype first" approach to the discovery of causative genotypes using WES variants strictly filtered on allele frequency, mutation consequence, and evidence of constraint in humans. This highlighted heterozygous de novo nonsynonymous variants in SPTBN2 as causative in three DDD probands.

A Paternal Fish Oil Diet Preconception Modulates the Gut Microbiome and Attenuates Necrotizing Enterocolitis in Neonatal Mice.

Epidemiology and animal studies suggest that a paternal history of toxicant exposure contributes to the developmental origins of health and disease. Using a mouse model, our laboratory previously reported that a paternal history of in utero exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) increased his offspring's risk of developing necrotizing enterocolitis (NEC). Additionally, our group and others have found that formula supplementation also increases the risk of NEC in both humans and mice. Our murine studies revealed that intervening with a paternal fish oil diet preconception eliminated the TCDD-associated outcomes that are risk factors for NEC (e.g., intrauterine growth restriction, delayed postnatal growth, and preterm birth). However, the efficacy of a paternal fish oil diet in eliminating the risk of disease development in his offspring was not investigated. Herein, reproductive-age male mice exposed to TCDD in utero were weaned to a standard or fish oil diet for one full cycle of spermatogenesis, then mated to age-matched unexposed females. Their offspring were randomized to a strict maternal milk diet or a supplemental formula diet from postnatal days 7-10. Offspring colon contents and intestines were collected to determine the onset of gut dysbiosis and NEC. We found that a paternal fish oil diet preconception reduced his offspring's risk of toxicant-driven NEC, which was associated with a decrease in the relative abundance of the Firmicutes phylum, but an increase in the relative abundance of the Negativicutes class.

A survey on knowledge and attitudes towards molar-incisor hypomineralization among undergraduate and postgraduate students at the School of Stomatology, Wuhan University.

BACKGROUND: Molar incisor hypomineralization (MIH) is a developmental dental disease, and its clinical management challenges dentists. This study aimed to investigate the knowledge about MIH and the attitudes towards learning more about MIH among undergraduate and postgraduate students attending the School of Stomatology, Wuhan University. METHODS: This survey was based on a questionnaire modified based on previous studies. The questionnaire was sent to 540 undergraduate and postgraduate students from the School of Stomatology, Wuhan University. The questions covered their clinical experience, perceptions, clinical management, and preferences for further training. Data were analysed with the Chi-square test. RESULTS: We collected 368 questionnaires (response rate: 68%). Among them, 89% (328/368) were eligible for analysis. Most respondents (80%) had heard of MIH, primarily from classroom teaching. However, only 40% of the students had observed the disease clinically, and a relatively low proportion of students were familiar with the aetiology, prevalence, differential diagnosis, and treatment of MIH. Most respondents were highly enthusiastic and had great expectations about further systematic teaching about MIH. CONCLUSION: Most students in this study had heard of MIH, but few were familiar with the principles of its differential diagnosis. Systematic teaching about MIH is warranted.

Very early-onset of RBD with ADHD: a case report study.

We experienced a case of very early-onset REM sleep behavior disorder (RBD) with ADHD. This case showed typical RBD symptoms with REM sleep without atonia on polysomnography. Methylphenidate, which enhances the dopamine system, attenuated his ADHD symptoms but not RBD symptoms. We speculate that the dysfunction of the laterodorsal tegmental nucleus in the pontine was responsible for the symptoms of RBD and ADHD in this case. Very early-onset RBD is rare, and its profile is not well known. ADHD with dysfunction in the laterodorsal tegmental nucleus may form asubtype of ADHD that is commonly comorbid with very early-onset RBD.

Multifocal bone and bone marrow lesions in children - MRI findings.

Polyostotic bone and bone marrow lesions in children may be due to various disorders. Radiographically, lytic lesions may become apparent after loss of more than 50% of the bone mineral content. Scintigraphy requires osteoblastic activity and is not specific. MRI may significantly contribute to the correct diagnosis and management. Accurate interpretation of MRI examinations requires understanding of the normal conversion pattern of bone marrow in childhood and of the appearances of red marrow rests and hyperplasia. Differential diagnosis is wide: Malignancies include metastases, multifocal primary sarcomas and hematological diseases. Benign entities include benign tumors and tumor-like lesions, histiocytosis, infectious and inflammatory diseases, multiple stress fractures/reactions and bone infarcts/ischemia.

Regulation of PtdIns(3,4,5)P3/Akt signalling by inositol polyphosphate 5-phosphatases.

The phosphoinositide 3-kinase (PI3K) generated lipid signals, PtdIns(3,4,5)P3 and PtdIns(3,4)P2, are both required for the maximal activation of the serine/threonine kinase proto-oncogene Akt. The inositol polyphosphate 5-phosphatases (5-phosphatases) hydrolyse the 5-position phosphate from the inositol head group of PtdIns(3,4,5)P3 to yield PtdIns(3,4)P2. Extensive work has revealed several 5-phosphatases inhibit PI3K-driven Akt signalling, by decreasing PtdIns(3,4,5)P3 despite increasing cellular levels of PtdIns(3,4)P2. The roles that 5-phosphatases play in suppressing cell proliferation and transformation are slow to emerge; however, the 5-phosphatase PIPP [proline-rich inositol polyphosphate 5-phosphatase; inositol polyphosphate 5-phosphatase (INPP5J)] has recently been identified as a putative tumour suppressor in melanoma and breast cancer and SHIP1 [SH2 (Src homology 2)-containing inositol phosphatase 1] inhibits haematopoietic cell proliferation. INPP5E regulates cilia stability and INPP5E mutations have been implicated ciliopathy syndromes. This review will examine 5-phosphatase regulation of PI3K/Akt signalling, focussing on the role PtdIns(3,4,5)P3 5-phosphatases play in developmental diseases and cancer.

Screening of CD96 and ASXL1 in 11 patients with Opitz C or Bohring-Opitz syndromes.

Opitz C trigonocephaly (or Opitz C syndrome, OTCS) and Bohring-Opitz syndrome (BOS or C-like syndrome) are two rare genetic disorders with phenotypic overlap. The genetic causes of these diseases are not understood. However, two genes have been associated with OTCS or BOS with dominantly inherited de novo mutations. Whereas CD96 has been related to OTCS (one case) and to BOS (one case), ASXL1 has been related to BOS only (several cases). In this study we analyze CD96 and ASXL1 in a group of 11 affected individuals, including 2 sibs, 10 of them were diagnosed with OTCS, and one had a BOS phenotype. Exome sequences were available on six patients with OTCS and three parent pairs. Thus, we could analyze the CD96 and ASXL1 sequences in these patients bioinformatically. Sanger sequencing of all exons of CD96 and ASXL1 was carried out in the remaining patients. Detailed scrutiny of the sequences and assessment of variants allowed us to exclude putative pathogenic and private mutations in all but one of the patients. In this patient (with BOS) we identified a de novo mutation in ASXL1 (c.2100dupT). By nature and location within the gene, this mutation resembles those previously described in other BOS patients and we conclude that it may be responsible for the condition. Our results indicate that in 10 of 11, the disease (OTCS or BOS) cannot be explained by small changes in CD96 or ASXL1. However, the cohort is too small to make generalizations about the genetic etiology of these diseases.

Piezo protein determines stem cell fate by transmitting mechanical signals.

Piezo ion channel is a mechanosensitive protein on the cell membrane, which contains Piezo1 and Piezo2. Piezo channels are activated by mechanical forces, including stretch, matrix stiffness, static pressure, and shear stress. Piezo channels transmit mechanical signals that cause different downstream responses in the differentiation process, including integrin signaling pathway, ERK1/2 MAPK signaling pathway, Notch signaling, and WNT signaling pathway. In the fate of stem cell differentiation, scientists found differences in Piezo channel expression and found that Piezo channel expression is related to developmental diseases. Here, we briefly review the structure and function of Piezo channels and the relationship between Piezo and mechanical signals, discussing the current understanding of the role of Piezo channels in stem cell fate and associated molecules and developmental diseases. Ultimately, we believe this review will help identify the association between Piezo channels and stem cell fate.

IMPROVE-DD: Integrating multiple phenotype resources optimizes variant evaluation in genetically determined developmental disorders.

Diagnosing rare developmental disorders using genome-wide sequencing data commonly necessitates review of multiple plausible candidate variants, often using ontologies of categorical clinical terms. We show that Integrating Multiple Phenotype Resources Optimizes Variant Evaluation in Developmental Disorders (IMPROVE-DD) by incorporating additional classes of data commonly available to clinicians and recorded in health records. In doing so, we quantify the distinct contributions of sex, growth, and development in addition to Human Phenotype Ontology (HPO) terms and demonstrate added value from these readily available information sources. We use likelihood ratios for nominal and quantitative data and propose a classifier for HPO terms in this framework. This Bayesian framework results in more robust diagnoses. Using data systematically collected in the Deciphering Developmental Disorders study, we considered 77 genes with pathogenic/likely pathogenic variants in ≥10 individuals. All genes showed at least a satisfactory prediction by receiver operating characteristic when testing on training data (AUC ≥ 0.6), and HPO terms were the best predictor for the majority of genes, though a minority (13/77) of genes were better predicted by other phenotypic data types. Overall, classifiers based upon multiple integrated phenotypic data sources performed better than those based upon any individual source, and importantly, integrated models produced notably fewer false positives. Finally, we show that IMPROVE-DD models with good predictive performance on cross-validation can be constructed from relatively few individuals. This suggests new strategies for candidate gene prioritization and highlights the value of systematic clinical data collection to support diagnostic programs.

A review on microRNA detection and expression studies in dogs.

MicroRNAs (miRNAs) are small non-coding RNAs that function by post-transcriptional regulation of gene expression. Their stability and abundance in tissue and body fluids makes them promising potential tools for both the diagnosis and prognosis of diseases and attractive therapeutic targets in humans and dogs. Studies of miRNA expression in normal and disease processes in dogs are scarce compared to studies published on miRNA expression in human disease. In this literature review, we identified 461 peer-reviewed papers from database searches using the terms "canine," "dog," "miRNA," and "microRNA"; we screened 244 for inclusion criteria and then included a total of 148 original research peer-reviewed publications relating to specific miRNA expression in canine samples. We found an overlap of miRNA expression changes between the four groups evaluated (normal processes, non-infectious and non-inflammatory conditions, infectious and/or inflammatory conditions, and neoplasia) in 39 miRNAs, 83 miRNAs in three of the four groups, 110 miRNAs in two of the three groups, where 158 miRNAs have only been reported in one of the groups. Additionally, the mechanism of action of these overlapping miRNAs varies depending on the disease process, elucidating a need for characterization of the mechanism of action of each miRNA in each disease process being evaluated. Herein we also draw attention to the lack of standardization of miRNA evaluation, consistency within a single evaluation method, and the need for standardized methods for a direct comparison.

A Balancing Act: p53 Activity from Tumor Suppression to Pathology and Therapeutic Implications.

TP53, encoding the p53 transcription factor, is the most frequently mutated tumor suppressor gene across all human cancer types. While p53 has long been appreciated to induce antiproliferative cell cycle arrest, apoptosis, and senescence programs in response to diverse stress signals, various studies in recent years have revealed additional important functions for p53 that likely also contribute to tumor suppression, including roles in regulating tumor metabolism, ferroptosis, signaling in the tumor microenvironment, and stem cell self-renewal/differentiation. Not only does p53 loss or mutation cause cancer, but hyperactive p53 also drives various pathologies, including developmental phenotypes, premature aging, neurodegeneration, and side effects of cancer therapies. These findings underscore the importance of balanced p53 activity and influence our thinking of how to best develop cancer therapies based on modulating the p53 pathway.

Network and Evolutionary Analysis of Human Epigenetic Regulators to Unravel Disease Associations.

We carried out a system-level analysis of epigenetic regulators (ERs) and detailed the protein-protein interaction (PPI) network characteristics of disease-associated ERs. We found that most diseases associated with ERs can be clustered into two large groups, cancer diseases and developmental diseases. ER genes formed a highly interconnected PPI subnetwork, indicating a high tendency to interact and agglomerate with one another. We used the disease module detection (DIAMOnD) algorithm to expand the PPI subnetworks into a comprehensive cancer disease ER network (CDEN) and developmental disease ER network (DDEN). Using the transcriptome from early mouse developmental stages, we identified the gene co-expression modules significantly enriched for the CDEN and DDEN gene sets, which indicated the stage-dependent roles of ER-related disease genes during early embryonic development. The evolutionary rate and phylogenetic age distribution analysis indicated that the evolution of CDEN and DDEN genes was mostly constrained, and these genes exhibited older evolutionary age. Our analysis of human polymorphism data revealed that genes belonging to DDEN and Seed-DDEN were more likely to show signs of recent positive selection in human history. This finding suggests a potential association between positive selection of ERs and risk of developmental diseases through the mechanism of antagonistic pleiotropy.

Biology of RNA Surveillance in Development and Disease.

The 'RNA world', in which RNA molecules stored information and acquired enzymatic properties, has been proposed to have preceded organism life. RNA is now recognized for its central role in biology, with accumulating evidence implicating coding and noncoding (nc)RNAs in myriad mechanisms regulating cellular physiology and disequilibrium in transcriptomes resulting in pathological conditions. Nascently synthesized RNAs are subjected to stringent regulation by sophisticated RNA surveillance pathways. In this review, we integrate these pathways from a developmental viewpoint, proposing RNA surveillance as the convergence of mechanisms that ensure the exact titration of RNA molecules in a spatiotemporally controlled manner, leading to development without the onset of pathological conditions, including cancer.

Acute hindlimb lameness in a 6-month-old cat.

CLINICAL PRESENTATION: A 6-month-old female spayed domestic shorthair cat was presented for investigation of acute right hindlimb lameness and paresis. WHAT IS YOUR DIAGNOSIS?: Readers are encouraged to review the case history and consider what their diagnostic suspicion is. Also what is the preferred treatment for this injury? And what is the primary cause of this injury?