Mitotic Block and Epigenetic Repression Underlie Neurodevelopmental Defects and Neurobehavioral Deficits in Congenital Heart Disease

Poor neurodevelopment is often observed with congenital heart disease (CHD), especially with mutations in chromatin modifiers. Here analysis of mice with hypoplastic left heart syndrome (HLHS) arising from mutations in Sin3A associated chromatin modifier Sap130 , and adhesion protein Pcdha9, revealed neurodevelopmental and neurobehavioral deficits reminiscent of those in HLHS patients. Microcephaly was associated with impaired cortical neurogenesis, mitotic block, and increased apoptosis. Transcriptional profiling indicated dysregulated neurogenesis by REST, altered CREB signaling regulating memory and synaptic plasticity, and impaired neurovascular coupling modulating cerebral blood flow. Many neurodevelopmental/neurobehavioral disease pathways were recovered, including autism and cognitive impairment. These same pathways emerged from genome-wide DNA methylation and Sap130 chromatin immunoprecipitation sequencing analyses, suggesting epigenetic perturbation. Mice with Pcdha9 mutation or forebrain-specific Sap130 deletion without CHD showed learning/memory deficits and autism-like behavior. These novel findings provide mechanistic insights indicating the adverse neurodevelopment in HLHS may involve cell autonomous/nonautonomous defects and epigenetic dysregulation and suggest new avenues for therapy.

Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease

Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease with 30% mortality from heart failure (HF) in the first year of life, but the cause of early HF remains unknown. Induced pluripotent stem-cell-derived cardiomyocytes (iPSC-CM) from patients with HLHS showed that early HF is associated with increased apoptosis, mitochondrial respiration defects, and redox stress from abnormal mitochondrial permeability transition pore (mPTP) opening and failed antioxidant response. In contrast, iPSC-CM from patients without early HF showed normal respiration with elevated antioxidant response. Single-cell transcriptomics confirmed that early HF is associated with mitochondrial dysfunction accompanied with endoplasmic reticulum (ER) stress. These findings indicate that uncompensated oxidative stress underlies early HF in HLHS. Importantly, mitochondrial respiration defects, oxidative stress, and apoptosis were rescued by treatment with sildenafil to inhibit mPTP opening or TUDCA to suppress ER stress. Together these findings point to the potential use of patient iPSC-CM for modeling clinical heart failure and the development of therapeutics.

Genetic resiliency associated with dominant lethal TPM1 mutation causing atrial septal defect with high heritability

Analysis of large-scale human genomic data has yielded unexplained mutations known to cause severe disease in healthy individuals. Here, we report the unexpected recovery of a rare dominant lethal mutation in TPM1, a sarcomeric actin-binding protein, in eight individuals with large atrial septal defect (ASD) in a five-generation pedigree. Mice with Tpm1 mutation exhibit early embryonic lethality with disrupted myofibril assembly and no heartbeat. However, patient-induced pluripotent-stem-cell-derived cardiomyocytes show normal beating with mild myofilament defect, indicating disease suppression. A variant in TLN2, another myofilament actin-binding protein, is identified as a candidate suppressor. Mouse CRISPR knock-in (KI) of both the TLN2 and TPM1 variants rescues heart beating, with near-term fetuses exhibiting large ASD. Thus, the role of TPM1 in ASD pathogenesis unfolds with suppression of its embryonic lethality by protective TLN2 variant. These findings provide evidence that genetic resiliency can arise with genetic suppression of a deleterious mutation.

Mitochondrial Respiration Defects in Single-Ventricle Congenital Heart Disease

Background: Congenital heart disease (CHD) with single-ventricle (SV) physiology is now survivable with a three-stage surgical course ending with Fontan palliation. However, 10-year transplant-free survival remains at 39–50%, with ventricular dysfunction progressing to heart failure (HF) being a common sequela. For SV-CHD patients who develop HF, undergoing the surgical course would not be helpful and could even be detrimental. As HF risk cannot be predicted and metabolic defects have been observed in Ohia SV-CHD mice, we hypothesized that respiratory defects in peripheral blood mononuclear cells (PBMCs) may allow HF risk stratification in SV-CHD.

Methods: SV-CHD (n = 20), biventricular CHD (BV-CHD; n = 16), or healthy control subjects (n = 22) were recruited, and PBMC oxygen consumption rate (OCR) was measured using the Seahorse Analyzer. Respiration was similarly measured in Ohia mouse heart tissue.

Results: Post-Fontan SV-CHD patients with HF showed higher maximal respiratory capacity (p = 0.004) and respiratory reserve (p < 0.0001), parameters important for cell stress adaptation, while the opposite was found for those without HF (reserve p = 0.037; maximal p = 0.05). This was observed in comparison to BV-CHD or healthy controls. However, respiration did not differ between SV patients pre- and post-Fontan or between pre- or post-Fontan SV-CHD patients and BV-CHD. Reminiscent of these findings, heart tissue from Ohia mice with SV-CHD also showed higher OCR, while those without CHD showed lower OCR.

Conclusion: Elevated mitochondrial respiration in PBMCs is correlated with HF in post-Fontan SV-CHD, suggesting that PBMC respiration may have utility for prognosticating HF risk in SV-CHD. Whether elevated respiration may reflect maladaptation to altered hemodynamics in SV-CHD warrants further investigation.

Common deletion variants causing protocadherin-α deficiency contribute to the complex genetics of BAV and left-sided congenital heart disease

Bicuspid aortic valve (BAV) with ~1%-2% prevalence is the most common congenital heart defect (CHD). It frequently results in valve disease and aorta dilation and is a major cause of adult cardiac surgery. BAV is genetically linked to rare left-heart obstructions (left ventricular outflow tract obstructions [LVOTOs]), including hypoplastic left heart syndrome (HLHS) and coarctation of the aorta (CoA). Mouse and human studies indicate LVOTO is genetically heterogeneous with a complex genetic etiology. Homozygous mutation in the Pcdha protocadherin gene cluster in mice can cause BAV, and also HLHS and other LVOTO phenotypes when accompanied by a second mutation. Here we show two common deletion copy number variants (delCNVs) within the PCDHA gene cluster are associated with LVOTO. Analysis of 1,218 white individuals with LVOTO versus 463 disease-free local control individuals yielded odds ratios (ORs) at 1.47 (95% confidence interval [CI], 1.13-1.92; p = 4.2 × 10-3) for LVOTO, 1.47 (95% CI, 1.10-1.97; p = 0.01) for BAV, 6.13 (95% CI, 2.75-13.7; p = 9.7 × 10-6) for CoA, and 1.49 (95% CI, 1.07-2.08; p = 0.019) for HLHS. Increased OR was observed for all LVOTO phenotypes in homozygous or compound heterozygous PCDHA delCNV genotype comparison versus wild type. Analysis of an independent white cohort (381 affected individuals, 1,352 control individuals) replicated the PCDHA delCNV association with LVOTO. Generalizability of these findings is suggested by similar observations in Black and Chinese individuals with LVOTO. Analysis of Pcdha mutant mice showed reduced PCDHA expression at regions of cell-cell contact in aortic smooth muscle and cushion mesenchyme, suggesting potential mechanisms for BAV pathogenesis and aortopathy. Together, these findings indicate common variants causing PCDHA deficiency play a significant role in the genetic etiology of common and rare LVOTO-CHD.

scds: computational annotation of doublets in single-cell RNA sequencing data

MOTIVATION

Single-cell RNA sequencing (scRNA-seq) technologies enable the study of transcriptional heterogeneity at the resolution of individual cells and have an increasing impact on biomedical research. However, it is known that these methods sometimes wrongly consider two or more cells as single cells, and that a number of so-called doublets is present in the output of such experiments. Treating doublets as single cells in downstream analyses can severely bias a study's conclusions, and therefore computational strategies for the identification of doublets are needed.

RESULTS

With scds, we propose two new approaches for in silico doublet identification: Co-expression based doublet scoring (cxds) and binary classification based doublet scoring (bcds). The co-expression based approach, cxds, utilizes binarized (absence/presence) gene expression data and, employing a binomial model for the co-expression of pairs of genes, yields interpretable doublet annotations. bcds, on the other hand, uses a binary classification approach to discriminate artificial doublets from original data. We apply our methods and existing computational doublet identification approaches to four datasets with experimental doublet annotations and find that our methods perform at least as well as the state of the art, at comparably little computational cost. We observe appreciable differences between methods and across datasets and that no approach dominates all others. In summary, scds presents a scalable, competitive approach that allows for doublet annotation of datasets with thousands of cells in a matter of seconds.

AVAILABILITY AND IMPLEMENTATION

scds is implemented as a Bioconductor R package (doi: 10.18129/B9.bioc.scds).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Enhancing regeneration after acute kidney injury by promoting cellular dedifferentiation in zebrafish

Acute kidney injury (AKI) is a serious disorder for which there are limited treatment options. Following injury, native nephrons display limited regenerative capabilities, relying on the dedifferentiation and proliferation of renal tubular epithelial cells (RTECs) that survive the insult. Previously, we identified 4-(phenylthio)butanoic acid (PTBA), a histone deacetylase inhibitor (HDI), as an enhancer of renal recovery, and showed that PTBA treatment increased RTEC proliferation and reduced renal fibrosis. Here, we investigated the regenerative mechanisms of PTBA in zebrafish models of larval renal injury and adult cardiac injury. With respect to renal injury, we showed that delivery of PTBA using an esterified prodrug (UPHD25) increases the reactivation of the renal progenitor gene Pax2a, enhances dedifferentiation of RTECs, reduces Kidney injury molecule-1 (Kim-1) expression, and lowers the number of infiltrating macrophages. Further, we found that the effects of PTBA on RTEC proliferation depend upon retinoic acid signaling and demonstrate that the therapeutic properties of PTBA are not restricted to the kidney but also increase cardiomyocyte proliferation and decrease fibrosis following cardiac injury in adult zebrafish. These studies provide key mechanistic insights into how PTBA enhances tissue repair in models of acute injury and lay the groundwork for translating this novel HDI into the clinic.

This article has an associated First Person interview with the joint first authors of the paper.

Summary: Mortality associated with AKI is in part due to limited treatments available to ameliorate injury. The authors identify a compound that accelerates AKI recovery and promotes cellular dedifferentiation.

Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density

MicroRNAs (miRNAs) are post-transcriptional regulators that bind to their target mRNAs through base complementarity. Predicting miRNA targets is a challenging task and various studies showed that existing algorithms suffer from high number of false predictions and low to moderate overlap in their predictions. Until recently, very few algorithms considered the dynamic nature of the interactions, including the effect of less specific interactions, the miRNA expression level, and the effect of combinatorial miRNA binding. Addressing these issues can result in a more accurate miRNA:mRNA modeling with many applications, including efficient miRNA-related SNP evaluation. We present a novel thermodynamic model based on the Fermi-Dirac equation that incorporates miRNA expression in the prediction of target occupancy and we show that it improves the performance of two popular single miRNA target finders. Modeling combinatorial miRNA targeting is a natural extension of this model. Two other algorithms show improved prediction efficiency when combinatorial binding models were considered. ComiR (Combinatorial miRNA targeting), a novel algorithm we developed, incorporates the improved predictions of the four target finders into a single probabilistic score using ensemble learning. Combining target scores of multiple miRNAs using ComiR improves predictions over the naïve method for target combination. ComiR scoring scheme can be used for identification of SNPs affecting miRNA binding. As proof of principle, ComiR identified rs17737058 as disruptive to the miR-488-5p:NCOA1 interaction, which we confirmed in vitro. We also found rs17737058 to be significantly associated with decreased bone mineral density (BMD) in two independent cohorts indicating that the miR-488-5p/NCOA1 regulatory axis is likely critical in maintaining BMD in women. With increasing availability of comprehensive high-throughput datasets from patients ComiR is expected to become an essential tool for miRNA-related studies.

High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells

BACKGROUND

Transforming growth factor beta 1 (TGFβ1) plays a major role in many lung diseases including lung cancer, pulmonary hypertension, and pulmonary fibrosis. TGFβ1 activates a signal transduction cascade that results in the transcriptional regulation of genes in the nucleus, primarily through the DNA-binding transcription factor SMAD3. The objective of this study is to identify genome-wide scale map of SMAD3 binding targets and the molecular pathways and networks affected by the TGFβ1/SMAD3 signaling in lung epithelial cells.

METHODOLOGY

We combined chromatin immunoprecipitation with human promoter region microarrays (ChIP-on-chip) along with gene expression microarrays to study global transcriptional regulation of the TGFβ1/SMAD3 pathway in human A549 alveolar epithelial cells. The molecular pathways and networks associated with TGFβ1/SMAD3 signaling were identified using computational approaches. Validation of selected target gene expression and direct binding of SMAD3 to promoters were performed by quantitative real time RT-PCR and electrophoretic mobility shift assay on A549 and human primary lung epithelial cells.

RESULTS AND CONCLUSIONS

Known TGFβ1 target genes such as SERPINE1, SMAD6, SMAD7, TGFB1 and LTBP3, were found in both ChIP-on-chip and gene expression analyses as well as some previously unrecognized targets such as FOXA2. SMAD3 binding of FOXA2 promoter and changed expression were confirmed. Computational approaches combining ChIP-on-chip and gene expression microarray revealed multiple target molecular pathways affected by the TGFβ1/SMAD3 signaling. Identification of global targets and molecular pathways and networks associated with TGFβ1/SMAD3 signaling allow for a better understanding of the mechanisms that determine epithelial cell phenotypes in fibrogenesis and carcinogenesis as does the discovery of the direct effect of TGFβ1 on FOXA2.

In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach

BACKGROUND

The transcription factor OCT4 is highly expressed in pluripotent embryonic stem cells which are derived from the inner cell mass of mammalian blastocysts. Pluripotency and self renewal are controlled by a transcription regulatory network governed by the transcription factors OCT4, SOX2 and NANOG. Recent studies on reprogramming somatic cells to induced pluripotent stem cells highlight OCT4 as a key regulator of pluripotency.

RESULTS

We have carried out an integrated analysis of high-throughput data (ChIP-on-chip and RNAi experiments along with promoter sequence analysis of putative target genes) and identified a core OCT4 regulatory network in human embryonic stem cells consisting of 33 target genes. Enrichment analysis with these target genes revealed that this integrative analysis increases the functional information content by factors of 1.3 - 4.7 compared to the individual studies. In order to identify potential regulatory co-factors of OCT4, we performed a de novo motif analysis. In addition to known validated OCT4 motifs we obtained binding sites similar to motifs recognized by further regulators of pluripotency and development; e.g. the heterodimer of the transcription factors C-MYC and MAX, a prerequisite for C-MYC transcriptional activity that leads to cell growth and proliferation.

CONCLUSION

Our analysis shows how heterogeneous functional information can be integrated in order to reconstruct gene regulatory networks. As a test case we identified a core OCT4-regulated network that is important for the analysis of stem cell characteristics and cellular differentiation. Functional information is largely enriched using different experimental results. The de novo motif discovery identified well-known regulators closely connected to the OCT4 network as well as potential new regulators of pluripotency and differentiation. These results provide the basis for further targeted functional studies.

Incorporating evolution of transcription factor binding sites into annotated alignments

Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield "conserved TFBSs". Most current methods in this field adopt a multi-step approach that segregates the two aspects. Again, it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account. Although a plethora of approaches have been proposed for the prediction of conserved TFBSs, very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences. Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments. That is, alignments with parts annotated as gaplessly aligned TFBSs (pair-profile hits)are generated. Moreover,the pair- profile related parameters are derived in a sound statistical framework. In this article, we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework. We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models, previously used for modelling TFBS evolution. In a simulated setting, we provide a proof of concept that the approach works given the underlying assumptions,as compared to the original work. Finally, using a real dataset of experimentally verified binding sites in human-mouse sequence pairs,we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences, most comparative TFBS identification methods do not explicitly consider this.Additionally, prediction of conserved binding sites is carried out in a multi-step approach that segregates alignment from TFBS annotation. In this paper, we demonstrate how the simultaneous alignment and annotation approach of SimAnn can be further extended to incorporate TFBS evolutionary relationships. We study how alignments and binding site predictions interplay at varying evolutionary distances and for various profile qualities.

Osteopetrosis-variable otorhinolaryngological manifestations

Osteopetrosis is a rare hereditary metabolic disease associated with a myriad of otolaryngological presentations. Three cases with varying otolaryngological presentations are described here. A brief review of the radiological changes of interest to the otorhinolaryngologist is being made.

A neglected foreign body in the oesophagus

Foreign body ingestion is a clinical emergency requiring prompt action to ensure speedy recovery and minimise the complications. We report here a case of a neglected foreign body which remained within the oesophagus of a child for 6 years before the diagnosis was made and appropriate treatment given.

Role of polysomnography in tracheostomy decannulation in the paediatric patient

Tracheostomy in infants and children has been the subject of controversy in the medical literature, but decannulation in the paediatric patient is even more controversial. Various approaches and techniques have been used for decannulation, however in spite of all efforts it continues to be a problem. The objective of our study was to assess the role of polysomnography (PSG) in predicting readiness for decannulation. All subjects (n = 31) of the study were less than 12 years of age, and tracheostomized for periods of at least six months to ensure a minimum period of dependence on the tube. All had clinical, radiological and endoscopic clearance before PSG was performed. Twenty-one out of 22 patients with favourable PSG data were successfully decannulated. Attempts to decannulate all the nine patients with unfavourable PSG failed. The conclusion of the study was that PSG is a useful adjunct to the many methods of evaluating readiness for decannulation in children with long-term tracheostomy tubes.

Adult tracheocele with large cervical presentation

A case is described in which a middle-aged male presented with a large tracheocele in the neck arising from the right postero-lateral aspect of trachea at the level of T2 vertebra. It was not associated with any predisposing factors and except for the swelling in the neck the patient was asymptomatic. It was excised completely through the cervical approach and there has been no recurrence in two years follow-up.

Tympanoplasty in children--a prospective study

Considerable controversy surrounds the subject of tympanoplasty in children. This prospective study looked at the results of type-I tympanoplasty in children. Forty-five children in the age group of five to 14 years were selected for the study. All these cases had a central perforation without any evidence of cholesteatoma. The ear to be operated had to be dry for at least six weeks before surgery. Type I tympanoplasty was performed on these patients with autograft temporalis fascia by either the underlay or overlay technique. The overall success rates in 45 operations evaluated one year post-operatively was 91.1 per cent. The age of the patient had no influence on the success rate. The two factors which adversely influenced the success rate were the presence of near total perforation and bilateral perforations. It was concluded that type-I tympanoplasty has a good chance of success in children regardless of age.

A clinical and videostroboscopic evaluation of laryngeal tuberculosis

A series of 31 cases of tuberculous laryngitis is reviewed to assess the diagnostic features of the disease. The condition generally presents in males of late middle age who have pulmonary tuberculosis. It presents in a manner similar to laryngeal carcinoma except that painful dysphagia is a prominent symptom. Histological examination of biopsy material is usually the diagnostic procedure. Stroboscopy was able to document a number of abnormalities which included abnormalities of laryngeal configuration, vibratory asymmetry, reduction of amplitude and mucosal wave. Symptoms responded well to antituberculous chemotherapy.

Auditory brainstem responses in high risk and normal newborns

We studied the auditory brainstem responses of 50 high risk neonates from NICU and compared with those of 25 normal neonates in order to determine the percentage of significant auditory impairment in NICU and correlated it to various risk factors. Infants with the risk factors of low birth weight, hyperbilirubinemia, asphyxia, septicemia and meningitis were included in the study group. All the 150 ears were tested at 4 intensities 30 dB, 46 dB, 60 dB and 75 dB. The study recorded prolongation of latency of wave V and I-V Interwave interval in the study group with a statistically significant difference denoting an impaired condition. Incidence of significant auditory impairment was 18%. On follow up at 6 months incidence of persistent auditory abnormality was 4%. On the basis of this study it is suggested that all high risk neonates should undergo screening for hearing impairment.

Tubercular retropharyngeal abscess in early childhood

We present two cases of Pott's lower cervical spine with retro-pharyngeal abscess presenting at an unusually young age. These children presented with a life threatening respiratory distress; one of them had neurological deficit in the form of paraparesis. External drainage of abscess without anterior cervical fusion was adequate as a surgical measure for their prompt recovery while these cases were on conventional anti-tubercular therapy.

Acute leukaemic cell infiltration of the nose

Leukaemic cell infiltration of the nose as a first manifestation of the disease is extremely rare. We report a case of a three-year-old child who had presented with a swelling at the root of the nose for one month and proptosis of the right eye for one week. CT scan revealed a mass infiltrating the nose and nasal cavity along with infiltration of the retro-orbital region. Biopsy showed it to be myeloid cell deposits. Patient was put on antileukaemic chemotherapy but died two months after the first appearance of the symptoms.

Congenital cysts of the larynx

Two cases of congenital cyst of larynx which is a rare condition, are reported.

Vascular hamartoma of the paranasal sinuses

A 12-year-old male child had spontaneous, recurrent bouts of profuse bleeding from the nose for 15 days. On examination of the nose a purplish polypoidal mass, which bled at touch filled the entire right nasal cavity. On lateral rhinotomy, a soft, greyish, cheesy mass was found, choking the maxillary, frontal, ethmoidal sinuses and the nasal cavity on the right side. It was completely excised. The histopathology report was vascular hamartoma (haemangioma).

Granulomatous osteomyelitis of the maxillary sinus

A case of granulomatous osteomyelitis of the maxilla, probably due to tuberculosis is reported, and the literature reviewed. Excision of the diseased tissue with antitubercular treatment forms the most effective line of treatment.