Exome sequencing in multiplex families with left-sided cardiac defects has high yield for disease gene discovery.

Congenital heart disease (CHD) is a common group of birth defects with a strong genetic contribution to their etiology, but historically the diagnostic yield from exome studies of isolated CHD has been low. Pleiotropy, variable expressivity, and the difficulty of accurately phenotyping newborns contribute to this problem. We hypothesized that performing exome sequencing on selected individuals in families with multiple members affected by left-sided CHD, then filtering variants by population frequency, in silico predictive algorithms, and phenotypic annotations from publicly available databases would increase this yield and generate a list of candidate disease-causing variants that would show a high validation rate. In eight of the nineteen families in our study (42%), we established a well-known gene/phenotype link for a candidate variant or performed confirmation of a candidate variant's effect on protein function, including variants in genes not previously described or firmly established as disease genes in the body of CHD literature: BMP10, CASZ1, ROCK1 and SMYD1. Two plausible variants in different genes were found to segregate in the same family in two instances suggesting oligogenic inheritance. These results highlight the need for functional validation and demonstrate that in the era of next-generation sequencing, multiplex families with isolated CHD can still bring high yield to the discovery of novel disease genes.

Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity.

BACKGROUND: Cancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased tissues. Transcriptomic profiling using short-read sequencing has utility in providing a cost-effective approach for evaluating isoform expression, although short-read assembly displays limitations in the accurate inference of full-length transcripts. Long-read RNA sequencing (Iso-Seq), using the Pacific Biosciences (PacBio) platform, can overcome such limitations by providing full-length isoform sequence resolution which requires no read assembly and represents native expressed transcripts. A constraint of the Iso-Seq protocol is due to fewer reads output per instrument run, which, as an example, can consequently affect the detection of lowly expressed transcripts. To address these deficiencies, we developed a concatenation workflow, PacBio Full-Length Isoform Concatemer Sequencing (PB_FLIC-Seq), designed to increase the number of unique, sequenced PacBio long-reads thereby improving overall detection of unique isoforms. In addition, we anticipate that the increase in read depth will help improve the detection of moderate to low-level expressed isoforms. RESULTS: In sequencing a commercial reference (Spike-In RNA Variants; SIRV) with known isoform complexity we demonstrated a 3.4-fold increase in read output per run and improved SIRV recall when using the PB_FLIC-Seq method compared to the same samples processed with the Iso-Seq protocol. We applied this protocol to a translational cancer case, also demonstrating the utility of the PB_FLIC-Seq method for identifying differential full-length isoform expression in a pediatric diffuse midline glioma compared to its adjacent non-malignant tissue. Our data analysis revealed increased expression of extracellular matrix (ECM) genes within the tumor sample, including an isoform of the Secreted Protein Acidic and Cysteine Rich (SPARC) gene that was expressed 11,676-fold higher than in the adjacent non-malignant tissue. Finally, by using the PB_FLIC-Seq method, we detected several cancer-specific novel isoforms. CONCLUSION: This work describes a concatenation-based methodology for increasing the number of sequenced full-length isoform reads on the PacBio platform, yielding improved discovery of expressed isoforms. We applied this workflow to profile the transcriptome of a pediatric diffuse midline glioma and adjacent non-malignant tissue. Our findings of cancer-specific novel isoform expression further highlight the importance of long-read sequencing for characterization of complex tumor transcriptomes.

Quality of Life in the Danish Fontan Population is Unchanged Over the Past Decade-A Nationwide Longitudinal Study.

Knowledge about health-related quality of life (HRQoL) over time in Fontan patients is sparse. We aimed to describe HRQoL over a ten-year period in a population-based Fontan cohort. Further, we compared HRQoL in Fontan patients with the general population. In 2011, Danish Fontan patients were invited to participate in a nationwide study assessing HRQoL. Depending on age, 152 participants filled out either the Pediatric Quality of Life Inventory or the 36-Item Short Form Health Survey. After a decade, patients from the initial study were invited to participate in a follow-up study. All were given the same questionnaire as in the first study, plus the 12-Item Short Form Health Survey (SF-12) as part of the Danish National Health Survey. HRQoL over time was described, and SF-12 scores were compared with the general population. A total of 109 Fontan patients completed the questionnaires in both studies. The mean patient age was 14.9 ± 6.6 years and 25.6 ± 6.5 years respectively. Despite an increase in complications, HRQoL did not decrease during the study period. Physical HRQoL scores were lower than mental HRQoL scores at both time points. The SF-12 physical component score was significantly lower in Fontan patients than in the general population (median score 52 vs. 56, p < 0.001), while the SF-12 mental component score was comparable (median score 51 vs. 50, p = 0.019). HRQoL remained stable over a ten-year period in a contemporary Danish Fontan cohort. Still, the physical HRQoL remained significantly lower than that of the general population.

Detection of brain somatic variation in epilepsy-associated developmental lesions.

OBJECTIVE: Epilepsy-associated developmental lesions, including malformations of cortical development and low-grade developmental tumors, represent a major cause of drug-resistant seizures requiring surgical intervention in children. Brain-restricted somatic mosaicism has been implicated in the genetic etiology of these lesions; however, many contributory genes remain unidentified. METHODS: We enrolled 50 children who were undergoing epilepsy surgery into a translational research study. Resected tissue was divided for clinical neuropathologic evaluation and genomic analysis. We performed exome and RNA sequencing to identify somatic variation and we confirmed our findings using high-depth targeted DNA sequencing. RESULTS: We uncovered candidate disease-causing somatic variation affecting 28 patients (56%), as well as candidate germline variants affecting 4 patients (8%). In agreement with previous studies, we identified somatic variation affecting solute carrier family 35 member A2 (SLC35A2) and mechanistic target of rapamycin kinase (MTOR) pathway genes in patients with focal cortical dysplasia. Somatic gains of chromosome 1q were detected in 30% (3 of 10) of patients with Type I focal cortical dysplasia (FCD)s. Somatic variation in mitogen-activated protein kinase (MAPK) pathway genes (i.e., fibroblast growth factor receptor 1 [FGFR1], FGFR2, B-raf proto-oncogene, serine/threonine kinase [BRAF], and KRAS proto-oncogene, GTPase [KRAS]) was associated with low-grade epilepsy-associated developmental tumors. RNA sequencing enabled the detection of somatic structural variation that would have otherwise been missed, and which accounted for more than one-half of epilepsy-associated tumor diagnoses. Sampling across multiple anatomic regions revealed that somatic variant allele fractions vary widely within epileptogenic tissue. Finally, we identified putative disease-causing variants in genes not yet associated with focal cortical dysplasia. SIGNIFICANCE: These results further elucidate the genetic basis of structural brain abnormalities leading to focal epilepsy in children and point to new candidate disease genes.

Self- and informant-reported executive function in young adults operated for atrial or ventricular septal defects in childhood.

BACKGROUND: Adults with simple congenital heart defects (CHD) have increased risk of neurodevelopmental challenges including executive dysfunction. It is unknown if the executive dysfunction is universal or if it is driven by dysfunction in specific clinical subscales and how it might affect psychosocial aspects of everyday life. METHODS: The self-reported and informant-reported executive function of adults with an average age of 26 ± 5 (range 18-41) who underwent childhood surgery for atrial septal defects (n = 34) or ventricular septal defects (n = 32) and matched controls (n = 40) were evaluated using the Behavior Rating Inventory of Executive Functions - Adult version (BRIEF-A). RESULTS: The CHD group reported having more executive dysfunction than controls in all BRIEF-A clinical subscales (p < 0.020) and more than their informants reported on their behalf (p < 0.006). The CHD group had received three times more special teaching (44% compared to 16%) and pedagogical psychological counselling (14% compared to none) and had a three times higher occurrence of psychiatric disorders than controls (33% compared to 11%). Lower educational levels and psychiatric disorders were associated with higher BRIEF-A scores (p < 0.03). CONCLUSIONS: Adults operated for septal defects in childhood report more challenges with all aspects of the executive functions than controls and more than relatives are aware of.

Gastroblastoma with a novel EWSR1-CTBP1 fusion presenting in adolescence.

Gastroblastomas are rare tumors with a biphasic epithelioid/spindle cell morphology that typically present in early adulthood and have recurrent MALAT1-GLI1 fusions. We describe an adolescent patient with Wiskott-Aldrich syndrome who presented with a large submucosal gastric tumor with biphasic morphology. Despite histologic features consistent with gastroblastoma, a MALAT1-GLI1 fusion was not found in this patient's tumor; instead, comprehensive molecular profiling identified a novel EWSR1-CTBP1 fusion and no other significant genetic alterations. The tumor also overexpressed NOTCH and FGFR by RNA profiling. The novel fusion and expression profile suggest a role for epithelial-mesenchymal transition in this tumor, with potential implications for the pathogenesis of biphasic gastric tumors such as gastroblastoma.

Discovery of clinically relevant fusions in pediatric cancer.

BACKGROUND: Pediatric cancers typically have a distinct genomic landscape when compared to adult cancers and frequently carry somatic gene fusion events that alter gene expression and drive tumorigenesis. Sensitive and specific detection of gene fusions through the analysis of next-generation-based RNA sequencing (RNA-Seq) data is computationally challenging and may be confounded by low tumor cellularity or underlying genomic complexity. Furthermore, numerous computational tools are available to identify fusions from supporting RNA-Seq reads, yet each algorithm demonstrates unique variability in sensitivity and precision, and no clearly superior approach currently exists. To overcome these challenges, we have developed an ensemble fusion calling approach to increase the accuracy of identifying fusions. RESULTS: Our Ensemble Fusion (EnFusion) approach utilizes seven fusion calling algorithms: Arriba, CICERO, FusionMap, FusionCatcher, JAFFA, MapSplice, and STAR-Fusion, which are packaged as a fully automated pipeline using Docker and Amazon Web Services (AWS) serverless technology. This method uses paired end RNA-Seq sequence reads as input, and the output from each algorithm is examined to identify fusions detected by a consensus of at least three algorithms. These consensus fusion results are filtered by comparison to an internal database to remove likely artifactual fusions occurring at high frequencies in our internal cohort, while a "known fusion list" prevents failure to report known pathogenic events. We have employed the EnFusion pipeline on RNA-Seq data from 229 patients with pediatric cancer or blood disorders studied under an IRB-approved protocol. The samples consist of 138 central nervous system tumors, 73 solid tumors, and 18 hematologic malignancies or disorders. The combination of an ensemble fusion-calling pipeline and a knowledge-based filtering strategy identified 67 clinically relevant fusions among our cohort (diagnostic yield of 29.3%), including RBPMS-MET, BCAN-NTRK1, and TRIM22-BRAF fusions. Following clinical confirmation and reporting in the patient's medical record, both known and novel fusions provided medically meaningful information. CONCLUSIONS: The EnFusion pipeline offers a streamlined approach to discover fusions in cancer, at higher levels of sensitivity and accuracy than single algorithm methods. Furthermore, this method accurately identifies driver fusions in pediatric cancer, providing clinical impact by contributing evidence to diagnosis and, when appropriate, indicating targeted therapies.

Sex Differences in Response to Deception Across Mate-Value Traits of Attractiveness, Job Status, and Altruism in Online Dating.

Sex differences in mate preferences are well established. It is also well understood that humans often seek to manipulate their standing on important mate-value traits. Yet, there is a paucity of work examining potential sex differences in response to deception along these important dimensions. In Study 1, a sample of 280 undergraduates (123 females) responded to a hypothetical online dating scenario asking participants to rank how upset they would be if deceived about a date's attractiveness, occupation, or volunteerism. Women ranked occupation deception as more upsetting than men did, and men ranked attractiveness deception as more upsetting than women did. Given potential measurement differences between forced-choice and continuous response options, Study 2 randomly assigned 364 undergraduates (188 females) to one of the deceptions conditions and asked them to report their level of upset and willingness to go on the date using a continuous response scale. Women were more likely than men to cancel the date if the deception involved volunteerism or occupation. There was no significant sex difference in the attractiveness condition. Neither mate value nor sociosexuality moderated the sex difference in the levels of upset due to the deception. Together, these findings demonstrate that women and men exhibit differences in the degree to which they become upset by opposite sex deceptions in online dating, regardless of self-perceived mate value and sociosexuality, in alignment with evolved sex differences in mate preferences.

Men's Mate Value Correlates with a Less Restricted Sociosexual Orientation: A Meta-Analysis.

Men, relative to women, can benefit their total reproductive success by engaging in short-term pluralistic mating. Yet not all men enact such a mating strategy. It has previously been hypothesized that high mate value men should be most likely to adopt a short-term mating strategy, with this prediction being firmly grounded in some important mid-level evolutionary psychological theories. Yet evidence to support such a link has been mixed. This paper presents a comprehensive meta-analysis of 33 published and unpublished studies (N = 5928) in which we find that that self-reported mate value accounts for roughly 6% of variance in men's sociosexual orientation. The meta-analysis provides evidence that men's self-perceived mate value positively predicts their tendency to engage in short-term mating, but that the total effect size is small.

Pathogenic variants in E3 ubiquitin ligase RLIM/RNF12 lead to a syndromic X-linked intellectual disability and behavior disorder.

RLIM, also known as RNF12, is an X-linked E3 ubiquitin ligase acting as a negative regulator of LIM-domain containing transcription factors and participates in X-chromosome inactivation (XCI) in mice. We report the genetic and clinical findings of 84 individuals from nine unrelated families, eight of whom who have pathogenic variants in RLIM (RING finger LIM domain-interacting protein). A total of 40 affected males have X-linked intellectual disability (XLID) and variable behavioral anomalies with or without congenital malformations. In contrast, 44 heterozygous female carriers have normal cognition and behavior, but eight showed mild physical features. All RLIM variants identified are missense changes co-segregating with the phenotype and predicted to affect protein function. Eight of the nine altered amino acids are conserved and lie either within a domain essential for binding interacting proteins or in the C-terminal RING finger catalytic domain. In vitro experiments revealed that these amino acid changes in the RLIM RING finger impaired RLIM ubiquitin ligase activity. In vivo experiments in rlim mutant zebrafish showed that wild type RLIM rescued the zebrafish rlim phenotype, whereas the patient-specific missense RLIM variants failed to rescue the phenotype and thus represent likely severe loss-of-function mutations. In summary, we identified a spectrum of RLIM missense variants causing syndromic XLID and affecting the ubiquitin ligase activity of RLIM, suggesting that enzymatic activity of RLIM is required for normal development, cognition and behavior.

Diagnosis and Management of Lymphatic Disorders in Congenital Heart Disease.

PURPOSE OF REVIEW: Lymphatic disorders have received an increasing amount of attention over the last decade. Sparked primarily by improved imaging modalities and the dawn of lymphatic interventions, understanding, diagnostics, and treatment of lymphatic complications have undergone considerable improvements. Thus, the current review aims to summarize understanding, diagnostics, and treatment of lymphatic complications in individuals with congenital heart disease. RECENT FINDINGS: The altered hemodynamics of individuals with congenital heart disease has been found to profoundly affect morphology and function of the lymphatic system, rendering this population especially prone to the development of lymphatic complications such as chylous and serous effusions, protein-losing enteropathy and plastic bronchitis. Although improved, a full understanding of the pathophysiology and targeted treatment for lymphatic complications is still wanting. Future research into pharmacological improvement of lymphatic function and continued implementation of lymphatic imaging and interventions may improve knowledge, treatment options, and outcome for affected individuals.

Evaluating differences in the clinical impact of a free online weight loss programme, a resource-intensive commercial weight loss programme and an active control condition: a parallel randomised controlled trial.

BACKGROUND: Finding effective intervention strategies to combat rising obesity levels could significantly reduce the burden that obesity and associated non-communicable diseases places on both individuals and the National Health Service. METHODS: In this parallel randomised-controlled trial, 76 participants who are overweight or obese (50 female) were given free access to a fitness centre for the duration of the 12-week intervention and randomised to one of three interventions. The commercial intervention, the Healthy Weight Programme, (HWP, n = 25, 10/15 men/women) consisted of twelve 1-h nutrition coaching sessions with a nutritionist delivered as a mixture of group and 1 to 1 sessions. In addition, twice-weekly exercise sessions (24 in total) were delivered by personal trainers for 12 weeks. The NHS intervention (n = 25, 8/17 men/women) consisted of following an entirely self-managed 12-week online NHS resource. The GYM intervention (n = 26, 8/18 men/women) received no guidance or formal intervention. All participants were provided with a gym induction for safety and both the NHS and GYM participants were familiarised with ACSM physical activity guidelines by way of a hand-out. RESULTS: The overall follow-up rate was 83%. Body mass was significantly reduced at post-intervention in all groups (HWP: N = 18, - 5.17 ± 4.22 kg, NHS: N = 21-4.19 ± 5.49 kg; GYM: N = 24-1.17 ± 3.00 kg; p < 0.001) with greater reductions observed in HWP and NHS groups compared to GYM (p < 0.05). Out with body mass and BMI, there were no additional statistically significant time x intervention interaction effects. CONCLUSIONS: This is the first study to evaluate the efficacy of both a free online NHS self-help weight-loss tool and a commercial weight loss programme that provides face-to-face nutritional support and supervised exercise. The findings suggest that both interventions are superior to an active control condition with regard to eliciting short-term weight-loss. TRIAL REGISTRATION: ISRCTN Registry - ISRCTN31489026. Prospectively registered: 27/07/16.

ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for cyclic di-GMP synthesis and biofilm development by Pseudomonas aeruginosa.

The transcription factor AmrZ regulates genes important for P. aeruginosa virulence, including type IV pili, extracellular polysaccharides, and the flagellum; however, the global effect of AmrZ on gene expression remains unknown, and therefore, AmrZ may directly regulate many additional genes that are crucial for infection. Compared to the wild type strain, a ΔamrZ mutant exhibits a rugose colony phenotype, which is commonly observed in variants that accumulate the intracellular second messenger cyclic diguanylate (c-di-GMP). Cyclic di-GMP is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). We hypothesized that AmrZ limits the intracellular accumulation of c-di-GMP through transcriptional repression of gene(s) encoding a DGC. In support of this, we observed elevated c-di-GMP in the ΔamrZ mutant compared to the wild type strain. Consistent with other strains that accumulate c-di-GMP, when grown as a biofilm, the ΔamrZ mutant formed larger microcolonies than the wild-type strain. This enhanced biofilm formation was abrogated by expression of a PDE. To identify potential target DGCs, a ChIP-Seq was performed and identified regions of the genome that are bound by AmrZ. RNA-Seq experiments revealed the entire AmrZ regulon, and characterized AmrZ as an activator or repressor at each binding site. We identified an AmrZ-repressed DGC-encoding gene (PA4843) from this cohort, which we named AmrZ dependent cyclase A (adcA). PAO1 overexpressing adcA accumulates 29-fold more c-di-GMP than the wild type strain, confirming the cyclase activity of AdcA. In biofilm reactors, a ΔamrZ ΔadcA double mutant formed smaller microcolonies than the single ΔamrZ mutant, indicating adcA is responsible for the hyper biofilm phenotype of the ΔamrZ mutant. This study combined the techniques of ChIP-Seq and RNA-Seq to define the comprehensive regulon of a bifunctional transcriptional regulator. Moreover, we identified a c-di-GMP mediated mechanism for AmrZ regulation of biofilm formation and chronicity.

A cross-sectional investigation of parenting style and friendship as mediators of the relation between social class and mental health in a university community.

INTRODUCTION: This study tested a novel explanation for the positive relation between social class and mental health among university students. Students with a higher social class were expected to have experienced more authoritative and less authoritarian parenting styles; these parenting styles were expected to lead to greater friendship and social integration at university; and greater friendship and integration were expected to lead to better mental health. METHOD: To test this model, the researchers asked 397 Australian undergraduate students to complete an online survey. The research used a cross-sectional correlational design, and the data was analysed using bootstrapped multiple serial mediation tests. RESULTS: Consistent with predictions, parenting style, general friendship and support, and social integration at university mediated the relation between social class and mental health. CONCLUSIONS: The present results suggest that working-class parenting styles may inhibit the development of socially-supportive friendships that protect against mental health problems. The potential effectiveness of interventions based on (a) social integration and (b) parenting style is discussed. Future research in this area should employ a longitudinal research design in order to arrive at clearer causal conclusions about the relations between social class, parenting styles, friendship, social integration, and mental health.

Public discourse and wilful incommensurability: a case for attentive free speech.

Many thinkers lament the decline of liberal democracy. Some argue that, to rejuvenate it, we must think big. Thinking big involves generating new ideas about how to achieve an unprecedented level of social transformation aimed at cultivating solidarity, empowering citizen efficacy, and promoting the common good. We propose that fundamental to such a transformation must be a radical change in how people speak to one another. To this end, the primary objective of this paper is to offer a framework for understanding how speech currently erodes democratic engagement. The central idea is that much of speech today both reflects and perpetuates a culture of wilful incommensurability. The core features of this culture are totalizing safetyism, expressive safetyism, dismissive intransigence, and polarized alienation, all of which have been worsened by the current trajectory of social media. The result is that people are increasingly prone to engage in degraded free speech, which is characterized by a pervasive aversion to reach out, identify points of unity, benefit from diverse perspectives, and discover truth in all its potential complexity. In view of this diagnosis and the response of those who advocate for freedom of speech, a second objective of this paper is to introduce the concept of attentive free speech. Attentive free speech has similarities with civil discourse but is specifically characterized by discernment and thoughtfulness and is imbued with key dispositions such as courage, reverence, and love. We end by inviting future research into how such speech can promote the social and spiritual health of the public sphere and freedom itself at a practical level.

Salivary gland carcinosarcoma ex pleomorphic adenoma; a case report with molecular characterization.

True malignant mixed tumors, also known as salivary gland carcinosarcoma (SCS), are uncommon yet highly aggressive lesions associated with a poor prognosis. These tumors exhibit a distinctive biphasic structure characterized by both epithelial and mesenchymal components. Recent research has shown that the majority of SCS cases stem from pre-existing pleomorphic adenomas (PAs), suggesting a stepwise developmental pattern. In this report, we present a case of a 73-year-old female with SCS and describe the clinical, radiographic, and pathologic observations. Notably, the SCS was associated with a residual PA. The SCS displayed a CTNNB1::PLAG1 gene rearrangement, providing a molecular basis for its origin from the PA. Further DNA genomic analysis exposed mutations in BAP1, PER1, and LRPB1. Our findings provide support to the theory that SCS emerges from a pre-existing PA while highlighting the multiple genetic changes that could contribute to malignant transformation.

Sequential MRI Evaluation of Lymphatic Abnormalities over the Course of Fontan Completion.

Purpose To evaluate lymphatic abnormalities before and after Fontan completion using noncontrast lymphatic imaging and relate findings with postoperative outcomes. Materials and Methods This study is a retrospective review of noncontrast T2-weighted lymphatic imaging performed at The Children's Hospital of Philadelphia from June 2012 to February 2023 in patients with single ventricle physiology. All individuals with imaging at both pre-Fontan and Fontan stages were eligible. Lymphatic abnormalities were classified into four types based on severity and location of lymphatic vessels. Classifications were compared between images and related to clinical outcomes such as postoperative drainage and hospitalization, lymphatic complications, heart transplant, and death. Results Forty-three patients (median age, 10 years [IQR, 8-11]; 20 [47%] boys, 23 [53%] girls) were included in the study. Lymphatic abnormalities progressed in 19 individuals after Fontan completion (distribution of lymphatic classifications: type 1, 23; type 2, 11; type 3, 6; type 4, 3 vs type 1, 10; type 2, 18; type 3, 10; type 4, 5; P = .04). Compared with individuals showing no progression of lymphatic abnormalities, those progressing to a high-grade lymphatic classification had longer postoperative drainage (median time, 9 days [IQR, 6-14] vs 17 days [IQR, 10-23]; P = .04) and hospitalization (median time, 13 days [IQR, 9-25] vs 26 days [IQR, 18-30]; P = .03) after Fontan completion and were more likely to develop chylothorax (12% [three of 24] vs 75% [six of eight]; P < .01) and/or protein-losing enteropathy (0% [0 of 24] vs 38% [three of eight]; P < .01) during a median follow-up of 8 years (IQR, 5-9). Progression to any type was not associated with an increased risk of adverse events. Conclusion The study demonstrated that lymphatic structural abnormalities may progress in select individuals with single ventricle physiology after Fontan completion, and progression of abnormalities to a high-grade classification was associated with worse postoperative outcomes. Keywords: Congenital Heart Disease, Glenn, Fontan, Lymphatic Imaging, Cardiovascular MRI Supplemental material is available for this article. Published under a CC BY 4.0 license.