A novel 3q29 deletion associated with autism, intellectual disability, psychiatric disorders, and obesity

Mitochondrial dynamics and psychiatric disorders: The missing link

Elucidating the molecular mechanisms of psychopathology is crucial for optimized diagnosis and treatment. Accumulating literature has underlined how mitochondrial bioenergetics affect major psychiatric disorders. However, how mitochondrial dynamics, a term addressing mitochondria quality control, including mitochondrial fission, fusion, biogenesis and mitophagy, is implicated in psychopathologies remains elusive. In this review we summarize the existing literature on mitochondrial dynamics perturbations in psychiatric disorders/neuropsychiatric phenotypes. We include preclinical/clinical literature on mitochondrial dynamics recalibrations in anxiety, depression, post-traumatic stress disorder (PTSD), bipolar disorder and schizophrenia. We discuss alterations in mitochondrial network, morphology and shape; molecular markers of the mitochondrial dynamics machinery and mitochondrial DNA copy number (mtDNAcn) in animal models and human cohorts in brain and peripheral material. By looking for common altered mitochondrial dynamics patterns across diagnoses/phenotypes, we highlight mitophagy and biogenesis as regulators of anxiety and depression pathophysiology, respectively, as well as the fusion mediator dynamin-like 120kDa protein (Opa1) as a molecular hub contributing to psychopathology. Finally, we comment on limitations and future directions in this novel neuropsychiatry field.

Genetic underpinnings explored: OPA1 deletion and complex phenotypes on chromosome 3q29

BACKGROUND

Copy number variations (CNVs) have emerged as significant contributors to the elusive genetic causality of inherited eye diseases. In this study, we describe a case with optic atrophy and a brain aneurysm, in which a de novo CNV 3q29 deletion was identified.

CASE PRESENTATION

A 40-year-old female patient was referred to our department after undergoing aneurysm transcatheter arterial embolization for a brain aneurysm. She had no history of systemic diseases, except for unsatisfactory best-corrected visual acuity (BCVA) since elementary school. Electrophysiological tests confirmed the findings in retinal images, indicating optic nerve atrophy. Chromosomal microarray analysis revealed a de novo deletion spanning 960 kb on chromosome 3q29, encompassing OPA1 and six neighboring genes. Unlike previously reported deletions in this region associated with optic atrophy, neuropsychiatric disorders, and obesity, this patient displayed a unique combination of optic atrophy and a brain aneurysm. However, there is no causal relationship between the brain aneurysm and the CNV.

CONCLUSION

In conclusion, the optic atrophy is conclusively attributed to the OPA1 deletion, and the aneurysm could be a coincidental association. The report emphasizes the likelihood of underestimating OPA1 deletions due to sequencing technology limitations. Recognizing these constraints, healthcare professionals must acknowledge these limitations and consistently search for OPA1 variants/deletions in Autosomal Dominant Optic Atrophy (ADOA) patients with negative sequencing results. This strategic approach ensures a more comprehensive exploration of copy-number variations, ultimately enhancing diagnostic precision in the field of genetic disorders.

Behavioral Phenotypes and Comorbidity in 3q29 Deletion Syndrome: Results from the 3q29 Registry

3q29 deletion syndrome (3q29del) is associated with a significantly increased risk for neurodevelopmental and neuropsychiatric disorders. However, the full spectrum of behavioral phenotypes associated with 3q29del is still evolving. Individuals with 3q29del (n = 96, 60.42% male) or their guardian completed the Achenbach Child or Adult Behavior Checklist (CBCL/ABCL) via the online 3q29 registry (3q29deletion.org). Typically developing controls (n = 57, 49.12% male) were ascertained as a comparison group. We analyzed mean performance on the CBCL/ABCL for individuals with 3q29del and controls across composite, DSM-keyed, and developmental scales; and the relationship between CBCL/ABCL performance and clinical and developmental phenotypes for individuals with 3q29del. Individuals with 3q29del showed significantly elevated behavioral and developmental impairment relative to controls across CBCL/ABCL domains. A substantial proportion of study participants with 3q29del scored in the Borderline or Clinical range for composite and DSM-keyed scales, indicating significant behavioral problems that may require clinical evaluation. We found that the preschool CBCL DSM-keyed autism spectrum problems scale is a potential screening tool for autism spectrum disorder (ASD) for individuals with 3q29del; CBCL/ABCL DSM-keyed scales were not accurate screeners for anxiety disorders or attention-deficit/hyperactivity disorder (ADHD) in our study sample. We identified a high degree of psychiatric comorbidity in individuals with 3q29del, with 60.42% (n = 58) of individuals with 3q29del scoring in the Borderline or Clinical range on two or more DSM-keyed CBCL/ABCL scales. Finally, we found that the degree of developmental delay in participants with 3q29del does not explain the increased behavioral problems observed on the CBCL/ABCL. The CBCL/ABCL can be used as screening tools in populations such as 3q29del, even in the presence of substantial psychiatric comorbidity. These results expand our understanding of the phenotypic spectrum of 3q29del and demonstrate an effective method for recruiting and phenotyping a large sample of individuals with a rare genetic disorder.

Development of a diagnostic and risk prediction model for Alzheimer's disease through integration of single-cell and bulk transcriptomic analysis of glutamine metabolism

Background

In this study, we present a novel system for quantifying glutamine metabolism (GM) to enhance the effectiveness of Alzheimer's disease (AD) diagnosis and risk prediction.

Methods

Single-cell RNA sequencing (scRNA-seq) analysis was utilized to comprehensively assess the expression patterns of GM. The WGCNA algorithm was applied to investigate the most significant genes related to GM. Subsequently, three machine learning algorithms (Boruta, LASSO, and SVM-RFE) were employed to identify GM-associated characteristic genes and develop a risk model. Patients were divided into high- and low-risk groups based on this model. Moreover, we explored biological properties, distinct signaling pathways, and immunological characteristics of AD patients at different risk levels. Finally, in vitro and in vivo models of AD were constructed to validate the characteristics of the feature genes.

Results

Both scRNA-seq and bulk transcriptomic analyses revealed increased GM activity in AD patients, specifically in certain cell subsets (pDC, Tem/Effector helper T cells (LTB), and plasma cells). Cells with higher GM scores demonstrated more significant numbers and strengths of interactions with other cell types. The WGCNA algorithm identified 360 genes related to GM, and a risk score was constructed based on nine characteristic genes (ATP13A4, PIK3C2A, CD164, PHF1, CES2, PDGFB, LCOR, TMEM30A, and PLXNA1) identified through multiple machine learning algorithms displayed reliable diagnostic efficacy for AD onset. Nomograms, calibration curves, and decision curve analysis (DCA) based on these characteristic genes provided significant clinical benefits for AD patients. High-risk AD patients exhibited higher levels of immune-related functions and pathways, increased immune cell infiltration, and elevated expressions of immune modulators. RT-qPCR analysis revealed that the majority of the nine characteristic genes were differentially expressed in AD-induced rat neurons. Knocking down PHF1 could protect against neurite loss and alleviate cell injury in AD neurons. In vivo, down-regulation of PHF1 in AD models decreases GM metabolism levels and modulates the immunoinflammatory response in the brain.

Conclusion

This comprehensive identification of gene expression patterns contributes to a deeper understanding of the underlying pathological mechanisms driving AD pathogenesis. Furthermore, the risk model based on the nine-gene signature offers a promising theoretical foundation for developing individualized treatments for AD patients.

Autism spectrum disorder symptom expression in individuals with 3q29 deletion syndrome

BACKGROUND

The 1.6 Mb 3q29 deletion is associated with neurodevelopmental and neuropsychiatric phenotypes, including a 19-fold increased risk for autism spectrum disorder (ASD). Previous work by our team identified elevated social disability in this population via parent-report questionnaires. However, clinical features of ASD in this population have not been explored in detail.

METHODS

Thirty-one individuals with 3q29 deletion syndrome (3q29del, 61.3% male) were evaluated using two gold-standard clinical ASD evaluations: the Autism Diagnostic Observation Schedule, Second Edition (ADOS-2), and the Autism Diagnostic Interview, Revised (ADI-R). Four matched comparators for each subject were ascertained from the National Database for Autism Research. Item-level scores on the ADOS-2 and ADI-R were compared between subjects with 3q29del and matched comparators.

RESULTS

Subjects with 3q29del and no ASD (3q29del-ASD) had greater evidence of social disability compared to typically developing (TD) comparison subjects across the ADOS-2. Subjects with 3q29del and ASD (3q29del + ASD) were largely indistinguishable from non-syndromic ASD (nsASD) subjects on the ADOS-2. 3q29del + ASD performed significantly better on social communication on the ADI-R than nsASD (3q29 + ASD mean = 11.36; nsASD mean = 15.70; p = 0.01), and this was driven by reduced deficits in nonverbal communication (3q29 + ASD mean = 1.73; nsASD mean = 3.63; p = 0.03). 3q29del + ASD reported significantly later age at the first two-word phrase compared to nsASD (3q29del + ASD mean = 43.89 months; nsASD mean = 37.86 months; p = 0.01). However, speech delay was not related to improved nonverbal communication in 3q29del + ASD.

LIMITATIONS

There were not enough TD comparators with ADI-R data in NDAR to include in the present analysis. Additionally, our relatively small sample size made it difficult to assess race and ethnicity effects.

CONCLUSIONS

3q29del is associated with significant social disability, irrespective of ASD diagnosis. 3q29del + ASD have similar levels of social disability to nsASD, while 3q29del-ASD have significantly increased social disability compared to TD individuals. However, social communication is reasonably well preserved in 3q29del + ASD relative to nsASD. It is critical that verbal ability and social disability be examined separately in this population to ensure equal access to ASD and social skills evaluations and services.

P5B-ATPases in the mammalian polyamine transport system and their role in disease

Polyamines (PAs) are physiologically relevant molecules that are ubiquitous in all organisms. The vitality of PAs to the healthy functioning of a cell is due to their polycationic nature causing them to interact with a vast plethora of cellular players and partake in numerous cellular pathways. Naturally, the homeostasis of such essential molecules is tightly regulated in a strictly controlled interplay between intracellular synthesis and degradation, uptake from and secretion to the extracellular compartment, as well as intracellular trafficking. Not surprisingly, dysregulated PA homeostasis and signaling are implicated in multiple disorders, ranging from cancer to neurodegeneration; leading many to propose rectifying the PA balance as a potential therapeutic strategy. Despite being well characterized in bacteria, fungi and plants, the molecular identity and properties of the PA transporters in animals are poorly understood. This review brings together the current knowledge of the cellular function of the mammalian PA transport system (PTS). We will focus on the role of P5B-ATPases ATP13A2-5 which are PA transporters in the endosomal system that have emerged as key players in cellular PA uptake and organelle homeostasis. We will discuss recent breakthroughs on their biochemical and structural properties as well as their implications for disease and therapy.

Autism spectrum disorder and personality disorders: Comorbidity and differential diagnosis

BACKGROUND

Differential diagnosis, comorbidities and overlaps with other psychiatric disorders are common among adults with autism spectrum disorder (ASD), but clinical assessments often omit screening for personality disorders (PD), which are especially common in individuals with high-functioning ASD where there is less need for support.

AIM

To summarize the research findings on PD in adults with ASD and without intellectual disability, focusing on comorbidity and differential diagnosis.

METHODS

PubMed searches were performed using the key words "Asperger's Syndrome", "Autism", "Personality", "Personality disorder" and "comorbidity" in order to identify relevant articles published in English. Grey literature was identified through searching Google Scholar. The literature reviews and reference sections of selected papers were also examined for additional potential studies. The search was restricted to studies published up to April 2020. This review is based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses method.

RESULTS

The search found 22 studies carried out on ASD adults without intellectual disability that met the inclusion criteria: 16 evaluated personality profiles or PD in ASD (comorbidity), five compared ASD and PD (differential diagnosis) and one performed both tasks. There were significant differences in the methodological approaches, including the ASD diagnostic instruments and personality measures. Cluster A and cluster C PD are the most frequent co-occurring PD, but overlapping features should be considered. Data on differential diagnosis were only found with cluster A and cluster B PD.

CONCLUSION

ASD in high-functioning adults is associated with a distinct personality profile even if variability exists. Further studies are needed to explore the complex relationship between ASD and PD.

Stereotypies in the Autism Spectrum Disorder: Can We Rely on an Ethological Model?

BACKGROUND

Stereotypic behaviour can be defined as a clear behavioural pattern where a specific function or target cannot be identified, although it delays on time. Nonetheless, repetitive and stereotypical behaviours play a key role in both animal and human behaviour. Similar behaviours are observed across species, in typical human developmental phases, and in some neuropsychiatric conditions, such as Autism Spectrum Disorder (ASD) and Intellectual Disability. This evidence led to the spread of animal models of repetitive behaviours to better understand the neurobiological mechanisms underlying these dysfunctional behaviours and to gain better insight into their role and origin within ASD and other disorders. This, in turn, could lead to new treatments of those disorders in humans.

METHOD

This paper maps the literature on repetitive behaviours in animal models of ASD, in order to improve understanding of stereotypies in persons with ASD in terms of characterization, pathophysiology, genomic and anatomical factors.

RESULTS

Literature mapping confirmed that phylogenic approach and animal models may help to improve understanding and differentiation of stereotypies in ASD. Some repetitive behaviours appear to be interconnected and mediated by common genomic and anatomical factors across species, mainly by alterations of basal ganglia circuitry. A new distinction between stereotypies and autotypies should be considered.

CONCLUSIONS

Phylogenic approach and studies on animal models may support clinical issues related to stereotypies in persons with ASD and provide new insights in classification, pathogenesis, and management.

Distinct Associations of BMI and Fatty Acids With DNA Methylation in Fasting and Postprandial States in Men

We have previously shown that blood global DNA methylation (DNAm) differs between postprandial state (PS) and fasting state (FS) and is associated with BMI and polyunsaturated fatty acid (PUFA) (negatively and positively, respectively) in 12 metabolically healthy adult Mexican men (AMM cohort) equally distributed among conventional BMI classes. Here, we detailed those associations at CpG dinucleotide level by exploiting the Infinium methylation EPIC array (Illumina). We sought differentially methylated CpG (dmCpG) that were (1) associated with BMI (BMI-dmCpG) and/or fatty acids (FA) (FA-dmCpG) in FS or PS and (2) different across FS and PS within a BMI class. BMI-dmCpG and FA-dmCpG were more numerous in FS compared to PS and largely prandial state-specific. For saturated and monounsaturated FA, dmCpG overlap was higher across than within the respective saturation group. Several BMI- and FA-dmCpG mapped to genes involved in metabolic disease and in some cases matched published experimental data sets. Notably, SETDB1 and MTHFS promoter dmCpG could explain the previously observed associations between global DNAm, PUFA content, and BMI in FS. Surprisingly, overlap between BMI-dmCpG and FA-dmCpG was limited and the respective dmCpG were differentially distributed across functional genomic elements. BMI-dmCpG showed the highest overlap with dmCpG of the saturated FA palmitate, monounsaturated C20:1 and PUFA C20:2. Of these, selected promoter BMI-dmCpG showed opposite associations with palmitate compared to C20:1 and C20:2. As for the comparison between FS and PS within BMI classes, dmCpG were strikingly more abundant and variably methylated in overweight relative to normoweight or obese subjects (∼70–139-fold, respectively). Overweight-associated dmCpG-hosting genes were significantly enriched in targets for E47, SREBP1, and RREB1 transcription factors, which are known players in obesity and lipid homeostasis, but none overlapped with BMI-dmCpG. We show for the first time that the association of BMI and FA with methylation of disease-related genes is distinct in FS and PS and that limited overlap exists between BMI- and FA-dmCpG within and across prandial states. Our study also identifies a transcriptional regulation circuitry in overweight that might contribute to adaptation to that condition or to transition to obesity. Further work is necessary to define the pathophysiological implications of these findings.

Qualitative Differences in Attribution of Mental States to Other People in Autism and Schizophrenia: What are the Tools for Differential Diagnosis?

The differential diagnosis between schizophrenia spectrum disorders (SSD) and autism spectrum disorders (ASD) remains an important clinical question, because they have overlap in clinical diagnosis. This study explored the differences between ASD (n = 44) and SSD patients (n = 59), compared to typically developing peers (n = 63), in completing an advanced Theory of Mind (ToM) task. The outcome found several differences between groups. The SSD patients showed greater difficulty in understanding social scenarios, while ASD individuals understood the stories, but did not correctly identify the protagonist’s intention. The interesting aspect of the results is that some ToM stories are more informative about the mentalistic reasoning of the two clinical groups, namely, the stories that investigate pretend, persuasion, double bluff and ironic joke constructs.

Tissue-specific enhancer functional networks for associating distal regulatory regions to disease

Systematic study of tissue-specific function of enhancers and their disease associations is a major challenge. We present an integrative machine-learning framework, FENRIR, that integrates thousands of disparate epigenetic and functional genomics datasets to infer tissue-specific functional relationships between enhancers for 140 diverse human tissues and cell types, providing a regulatory-region-centric approach to systematically identify disease-associated enhancers. We demonstrated its power to accurately prioritize enhancers associated with 25 complex diseases. In a case study on autism, FENRIR-prioritized enhancers showed a significant proband-specific de novo mutation enrichment in a large, sibling-controlled cohort, indicating pathogenic signal. We experimentally validated transcriptional regulatory activities of eight enhancers, including enhancers not previously reported with autism, and demonstrated their differential regulatory potential between proband and sibling alleles. Thus, FENRIR is an accurate and effective framework for the study of tissue-specific enhancers and their role in disease. FENRIR can be accessed at fenrir.flatironinstitute.org/.

Autism Spectrum Disorder from the Womb to Adulthood: Suggestions for a Paradigm Shift

The wide spectrum of unique needs and strengths of Autism Spectrum Disorders (ASD) is a challenge for the worldwide healthcare system. With the plethora of information from research, a common thread is required to conceptualize an exhaustive pathogenetic paradigm. The epidemiological and clinical findings in ASD cannot be explained by the traditional linear genetic model, hence the need to move towards a more fluid conception, integrating genetics, environment, and epigenetics as a whole. The embryo-fetal period and the first two years of life (the so-called 'First 1000 Days') are the crucial time window for neurodevelopment. In particular, the interplay and the vicious loop between immune activation, gut dysbiosis, and mitochondrial impairment/oxidative stress significantly affects neurodevelopment during pregnancy and undermines the health of ASD people throughout life. Consequently, the most effective intervention in ASD is expected by primary prevention aimed at pregnancy and at early control of the main effector molecular pathways. We will reason here on a comprehensive and exhaustive pathogenetic paradigm in ASD, viewed not just as a theoretical issue, but as a tool to provide suggestions for effective preventive strategies and personalized, dynamic (from womb to adulthood), systemic, and interdisciplinary healthcare approach.

Prenatal detection of a 3q29 microdeletion in a fetus with ventricular septum defect: A case report and literature review

RATIONALE

Chromosomal 3q deletion is a recurrent genomic alternation, which is rarely reported in clinic.

PATIENT CONCERNS

A 27-year-old woman underwent amniocentesis for cytogenetic analysis and single nucleotide polymorphism (SNP) array analysis at 27 weeks of gestation, due to ventricular septum defect in prenatal ultrasound findings.

DIAGNOSES

G-banding analysis showed the karyotype of the fetus was normal and the couple also had normal karyotypes. However, SNP array detected a 1.71 Mb microdelection in 3q29, which was described as arr[hg19]3q29(194184392-195887205) × 1. There are 12 genes located in this locus.

INTERVENTIONS

The couple refused SNP array to testify the 3q29 microdeletion was inherited or de novo and they chose termination of pregnancy.

OUTCOMES

The deleted region in the fetus overlapped with part 3q29 microdeletion syndrome, which was characterized by learning disability, speech delay, mental deficiency, ocular abnormalities and craniofacial features. In addition, no similar/overlapping 3q29 microdeletion cases were reported according to the published literature and database.

LESSONS

For the chromosomal microscopic imbalances partially overlapping with the defined pathogenic syndrome, deleted/duplicated size, genetic materials and phenotypic diversity should be taken into consideration when genetic counseling is offered by the clinicians.

The Gut-Brain-Immune Axis in Autism Spectrum Disorders: A State-of-Art Report

The interest elicited by the large microbial population colonizing the human gut has ancient origins and has gone through a long evolution during history. However, it is only in the last decades that the introduction of high-throughput technologies has allowed to broaden this research field and to disentangle the numerous implications that gut microbiota has in health and disease. This comprehensive ecosystem, constituted mainly by bacteria but also by fungi, parasites, and viruses, is proven to be involved in several physiological and pathological processes that transcend the intestinal homeostasis and are deeply intertwined with apparently unrelated body systems, such as the immune and the nervous ones. In this regard, a novel speculation is the relationship between the intestinal microbial flora and the pathogenesis of some neurological and neurodevelopmental disorders, including the clinical entities defined under the umbrella term of autism spectrum disorders. The bidirectional interplay has led researchers to coin the term gut-brain-immune system axis, subverting the theory of the brain as an immune-privileged site and underscoring the importance of this reciprocal influence already from fetal life and especially during the pre- and post-natal neurodevelopmental process. This revolutionary theory has also unveiled the possibility to modify the gut microbiota as a way to treat and even to prevent different kinds of pathologies. In this sense, some attempts have been made, ranging from probiotic administration to fecal microbiota transplantation, with promising results that need further elaboration. This state-of-art report will describe the main aspects regarding the human gut microbiome and its specific role in the pathogenesis of autism and its related disorders, with a final discussion on the therapeutic and preventive strategies aiming at creating a healthy intestinal microbial environment, as well as their safety and ethical implications.

RKDOSCNV: A Local Kernel Density-Based Approach to the Detection of Copy Number Variations by Using Next-Generation Sequencing Data

Copy number variations (CNVs) are significant causes of many human cancers and genetic diseases. The detection of CNVs has become a common method by which to analyze human diseases using next-generation sequencing (NGS) data. However, effective detection of insignificant CNVs is still a challenging task. In this study, we propose a new detection method, RKDOSCNV, to meet the need. RKDOSCNV uses kernel density estimation method to evaluate the local kernel density distribution of each read depth segment (RDS) based on an expanded nearest neighbor (k-nearest neighbors, reverse nearest neighbors, and shared nearest neighbors of each RDS) data set, and assigns a relative kernel density outlier score (RKDOS) for each RDS. According to the RKDOS profile, RKDOSCNV predicts the candidate CNVs by choosing a reasonable threshold, which it uses split read approach to correct the boundaries of candidate CNVs. The performance of RKDOSCNV is assessed by comparing it with several current popular methods via experiments with simulated and real data at different tumor purity levels. The experimental results verify that the performance of RKDOSCNV is superior to that of several other methods. In summary, RKDOSCNV is a simple and effective method for the detection of CNVs from whole genome sequencing (WGS) data, especially for samples with low tumor purity.

Autism in Adulthood: Clinical and Demographic Characteristics of a Cohort of Five Hundred Persons with Autism Analyzed by a Novel Multistep Network Model

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in communication and relational skills, associated with repetitive verbal and motor behaviors, restricted patterns of interest, need for a predictable and stable environment, and hypo- or hypersensitivity to sensory inputs. Due to the challenging diagnosis and the paucity of specific interventions, persons with autism (PWA) reaching the adult age often display a severe functional regression. In this scenario, the Regional Center for Autism in Adulthood in Turin seeks to develop a personalized rehabilitation and enablement program for PWA who received a diagnosis of autism in childhood/adolescence or for individuals with suspected adulthood ASD. This program is based on a Multistep Network Model involving PWA, family members, social workers, teachers, and clinicians. Our initial analysis of 500 PWA shows that delayed autism diagnosis and a lack of specific interventions at a young age are largely responsible for the creation of a “lost generation” of adults with ASD, now in dire need of effective psychosocial interventions. As PWA often present with psychopathological co-occurrences or challenging behaviors associated with lack of adequate communication and relational skills, interventions for such individuals should be mainly aimed to improve their self-reliance and social attitude. In particular, preparing PWA for employment, whenever possible, should be regarded as an essential part of the intervention program given the social value of work. Overall, our findings indicate that the development of public centers specialized in assisting and treating PWA can improve the accuracy of ASD diagnosis in adulthood and foster specific habilitative interventions aimed to improve the quality of life of both PWA and their families.

mRNA expression of the P5 ATPase ATP13A4 is increased in Broca's area from subjects with schizophrenia

Objectives: ATPase Type 13A4 (ATP13A4) is a cation-transporting, P₅-type ATPase that has been implicated in neurodevelopmental disorders. Our recent microarray study reported a significant increase in ATP13A4 mRNA levels in Brodmann's area (BA) nine in subjects with schizophrenia compared to controls. Following this discovery we have sought to determine whether ATP13A4 expression was altered in other regions of the CNS that are affected in schizophrenia.Methods: Quantitative PCR was used to measure the levels of ATP13A4 in BA 44 and BA 8, collected post-mortem, from 30 subjects with schizophrenia and 30 non-psychiatric control subjects. To address the potential confound of antipsychotic medication on our data, qPCR was used to measure Atp13a4 levels in rats treated with haloperidol.Results: There was a 2.6-fold increase in ATP13A4 expression (P < 0.001) in BB 44 from subjects with schizophrenia. Results from BA 8 were less clear. ATP13A4 levels were not affected by antipsychotic treatment.Conclusions: Our findings suggest ATP13A4 is involved in the pathophysiology of schizophrenia. The increase in ATP13A4 contrasts genetic studies that report ATP13A4 gene deletions in patients with schizophrenia. A greater understanding of the function of ATP13A4 in the CNS may lead to improved treatment strategies for the symptoms of schizophrenia.

Exploring genetic variants in obsessive compulsive disorder severity: A GWAS approach

BACKGROUND

The severity of Obsessive-Compulsive Disorder (OCD) varies significantly among probands. No study has specifically investigated the genetic base of OCD severity. A previous study from our group found an OCD polygenic risk score to predict pre- and post-treatment severity. This study explores the genomic bases of OCD severity.

METHODS

We administered the Yale-Brown Obsessive Compulsive Scale (Y-BOCS) to 401 patients at their first visit to our clinic to measure their OCD severity. Genotyping data was collected by using the Infinium PsychArray-24 BeadChip kit (Illumina). We analyzed genetic association with OCD severity in a linear regression analysis at single-nucleotide polymorphism (SNP)- and gene-levels, this last also considering rare variants. Enrichment analyses were performed from gene-based analyses' results.

RESULTS

No SNP reached significant association (p < 10^-8) with the YBOCS. Six markers showed suggestive association (p < 10^-5). The top SNP was an intergenic variant in chromosome 2: rs7578149 (p < 1.89 × 10^-6), located in a region suggestively associated with MDD. Linkage disequilibrium was found for two clusters of SNPs located between SLC16A14 and SP110 in chromosome 2, all of them forming one peak of association. Enrichment analyses revealed OCD genes to be associated with porin activity (FDR = 0.01) and transmembrane structure (FDR = 0.04).

LIMITATIONS

The size of the sample and the transversal nature of the severity measure are limitations of this study.

CONCLUSION

This study contributes to better characterize OCD at an individual level, helping to know more about the prognosis of the disorder and develop more individualized treatments.

Design of a multiplex ligation-dependent probe amplification assay for SLC20A2: identification of two novel deletions in primary familial brain calcification

Primary familial brain calcification (PFBC) is a rare disease characterized by brain calcifications that mainly affect the basal ganglia, thalamus, and cerebellum. Among the four autosomal-dominant genes known to be associated with the disease, SLC20A2 pathogenic variants are the most common, accounting for up to 40% of PFBC dominant cases; variants include both point mutations, small insertions/deletions and intragenic deletions. Over the last 7 years, we have collected a group of 50 clinically diagnosed PFBC patients, who were screened for single nucleotide changes and small insertions/deletions in SLC20A2 by Sanger sequencing. We found seven pathogenic/likely pathogenic variants: four were previously described by our group, and three are reported here (c.303delG, c.21delG, and c.1795-1G>A). We developed and validated a synthetic Multiplex Ligation-dependent Probe Amplification (MLPA) assay for SLC20A2 deletions, covering all ten coding exons and the 5' UTR (SLC20A2-MLPA). Using this method, we screened a group of 43 PFBC-patients negative for point mutations and small insertions/deletions, and identified two novel intragenic deletions encompassing exon 6 NC_000008.10:g.(42297172_42302163)_(423022281_42317413)del, and exons 7-11 including the 3'UTR NC_000008.10:g.(?_42275320)_(42297172_42302163)del. Overall, SLC20A2 deletions may be highly underestimated PFBC cases, and we suggest MLPA should be included in the routine molecular test for PFBC diagnosis.

Neuropsychiatric phenotypes and a distinct constellation of ASD features in 3q29 deletion syndrome: results from the 3q29 registry

Background

The 1.6 Mb 3q29 deletion is associated with neurodevelopmental and psychiatric phenotypes, including increased risk for autism spectrum disorder (ASD) and a 20 to 40-fold increased risk for schizophrenia. However, the phenotypic spectrum of the deletion, particularly with respect to ASD, remains poorly described.

Methods

We ascertained individuals with 3q29 deletion syndrome (3q29Del, “cases,” n = 93, 58.1% male) and typically developing controls (n = 64, 51.6% male) through the 3q29 registry (https://3q29deletion.patientcrossroads.org). Self-report of neuropsychiatric illness was evaluated for 93 cases. Subsets of participants were evaluated with the Social Responsiveness Scale (SRS, n = 48 cases, 56 controls), Social Communication Questionnaire (n = 33 cases, 46 controls), Autism Spectrum Screening Questionnaire (n = 24 cases, 35 controls), and Achenbach Behavior Checklists (n = 48 cases, 57 controls).

Results

3q29Del cases report a higher prevalence of autism diagnoses versus the general population (29.0% vs. 1.47%, p < 2.2E− 16). Notably, 3q29 deletion confers a greater influence on risk for ASD in females (OR = 41.8, p = 4.78E− 05) than in males (OR = 24.6, p = 6.06E− 09); this is aligned with the reduced male:female bias from 4:1 in the general population to 2:1 in our study sample. Although 71% of cases do not report a diagnosis of ASD, there is evidence of significant social disability (3q29Del SRS T-score = 71.8, control SRS T-score = 45.9, p = 2.16E− 13). Cases also report increased frequency of generalized anxiety disorder compared to controls (28.0% vs. 6.2%, p = 0.001), which is mirrored by elevated mean scores on the Achenbach diagnostic and statistical manual-oriented sub-scales (p < 0.001). Finally, cases show a distinct constellation of ASD features on the SRS as compared to idiopathic ASD, with substantially elevated Restricted Interests and Repetitive Behaviors, but only mild impairment in Social Motivation.

Conclusions

Our sample of 3q29Del is significantly enriched for ASD diagnosis, especially among females, and features of autism may be present even when an ASD diagnosis is not reported. Further, the constellation of ASD features in this population is distinct from idiopathic ASD, with substantially less impaired social motivation. Our study implies that ASD evaluation should be the standard of care for individuals with 3q29Del. From a research perspective, the distinct ASD subtype present in 3q29Del is an ideal entry point for expanding understanding of ASD.

Electronic supplementary material

The online version of this article (10.1186/s13229-019-0281-5) contains supplementary material, which is available to authorized users.

A Novel 3q29 Deletion in Association With Developmental Delay and Heart Malformation-Case Report With Literature Review

3q29 deletion syndrome is a rare disorder, causing a complex phenotype. Clinical features are variable and relatively non-specific. Our report aims to present an atypical, de novo deletion in chromosome band 3q29 in a preschool boy, first child of healthy non-consanguineous parents, presenting a particular phenotype (microcephaly, "full moon" face, flattened facial profile, large ears, auricular polyp, and dental dystrophies), motor and cognitive delay, characteristics of autism spectrum disorder and aggressive behavior. He also presented intrauterine growth restriction (birth weight 2,400 g) and a ventricular septal defect. SNP Array revealed a 962 kb copy number loss, on the chromosome 3q29 band (195519857-196482211), consistent with 3q29 microdeletion syndrome. FISH analysis using a RP11-252K11 probe confirmed the deletion in the proband, which was not present in the parents. Although the patient's deletion is relatively small, it partly overlaps the canonical 3q29 deletion (defined between TFRC and DLG1 gene) and extends upstream, associating a different facial phenotype compared to the classic 3q29 deletion, nonetheless showing a similar psychiatric disorder. This deletion is different from the canonical region, as it does not include the PAK2 and DLG1 genes, considered as candidates for causing intellectual disability. Thus, narrowing the genotype-phenotype correlation for the 3q29 band, FBX045 is suggested as a candidate gene for the neuropsychiatric phenotype.

The morphometric co-atrophy networking of schizophrenia, autistic and obsessive spectrum disorders

By means of a novel methodology that can statistically derive patterns of co-alterations distribution from voxel-based morphological data, this study analyzes the patterns of brain alterations of three important psychiatric spectra-that is, schizophrenia spectrum disorder (SCZD), autistic spectrum disorder (ASD), and obsessive-compulsive spectrum disorder (OCSD). Our analysis provides five important results. First, in SCZD, ASD, and OCSD brain alterations do not distribute randomly but, rather, follow network-like patterns of co-alteration. Second, the clusters of co-altered areas form a net of alterations that can be defined as morphometric co-alteration network or co-atrophy network (in the case of gray matter decreases). Third, within this network certain cerebral areas can be identified as pathoconnectivity hubs, the alteration of which is supposed to enhance the development of neuronal abnormalities. Fourth, within the morphometric co-atrophy network of SCZD, ASD, and OCSD, a subnetwork composed of eleven highly connected nodes can be distinguished. This subnetwork encompasses the anterior insulae, inferior frontal areas, left superior temporal areas, left parahippocampal regions, left thalamus and right precentral gyri. Fifth, the co-altered areas also exhibit a normal structural covariance pattern which overlaps, for some of these areas (like the insulae), the co-alteration pattern. These findings reveal that, similarly to neurodegenerative diseases, psychiatric disorders are characterized by anatomical alterations that distribute according to connectivity constraints so as to form identifiable morphometric co-atrophy patterns.

Chromosomal microarray analysis in the genetic evaluation of 279 patients with syndromic obesity

BACKGROUND

Syndromic obesity is an umbrella term used to describe cases where obesity occurs with additional phenotypes. It often arises as part of a distinct genetic syndrome with Prader-Willi syndrome being a classical example. These rare forms of obesity provide a unique source for identifying obesity-related genetic changes. Chromosomal microarray analysis (CMA) has allowed the characterization of new genetic forms of syndromic obesity, which are due to copy number variants (CNVs); however, CMA in large cohorts requires more study. The aim of this study was to characterize the CNVs detected by CMA in 279 patients with a syndromic obesity phenotype.

RESULTS

Pathogenic CNVs were detected in 61 patients (22%) and, among them, 35 had overlapping/recurrent CNVs. Genomic imbalance disorders known to cause syndromic obesity were found in 8.2% of cases, most commonly deletions of 1p36, 2q37 and 17p11.2 (5.4%), and we also detected deletions at 1p21.3, 2p25.3, 6q16, 9q34, 16p11.2 distal and proximal, as well as an unbalanced translocation resulting in duplication of the GNB3 gene responsible for a syndromic for of childhood obesity. Deletions of 9p terminal and 22q11.2 proximal/distal were found in 1% and 3% of cases, respectively. They thus emerge as being new putative obesity-susceptibility loci. We found additional CNVs in our study that overlapped with CNVs previously reported in cases of syndromic obesity, including a new case of 13q34 deletion (CHAMP1), bringing to 7 the number of patients in whom such defects have been described in association with obesity. Our findings implicate many genes previously associated with obesity (e.g. PTBP2, TMEM18, MYT1L, POU3F2, SIM1, SH2B1), and also identified other potentially relevant candidates including TAS1R3, ALOX5AP, and GAS6.

CONCLUSION

Understanding the genetics of obesity has proven difficult, and considerable insight has been obtained from the study of genomic disorders with obesity associated as part of the phenotype. In our study, CNVs known to be causal for syndromic obesity were detected in 8.2% of patients, but we provide evidence for a genetic basis of obesity in as many as 14% of cases. Overall, our results underscore the genetic heterogeneity in syndromic forms of obesity, which imposes a substantial challenge for diagnosis.

A novel proximal 3q29 chromosome microdeletion in a Chinese patient with Chiari malformation type II and Sprengel's deformity

Background

Chiari malformation type II (CM-II) is mainly characterized by elongation and descent of the cerebellum through the foramen magnum into the spinal canal. Moreover, CM-II is uniquely associated with myelomeningocele. Sprengel’s deformity refers to the malposition of the scapula, i.e. scapular elevation which is sometimes accompanied with scapula dysplasia. Although few familial cases of CM-II and Sprengel’s deformity have been previously reported, both of these defects are considered to be sporadic, thus the exact etiology and causative genes have largely remained unknown.

Case presentation

The patient was diagnosed with CM-II accompanied with Sprengel’s deformity. Further genetic investigation revealed a novel 666 kb microdeletion located in 3q29 (chr3:194,532,035–195,198,585; Hg19). Subsequently, genes within the affected region were summarized, and XXYLT1 and ACAP2 were identified as the candidate genes.

Conclusion

We reported a case of a patient with CM-II and Sprengel’s deformity harboring a microdeletion in 3q29. This case highlights the importance of 3q29 in early neural and skeletal development, as well as expands the phenotype spectrum of this rare disorder.

Clinical significance of germline copy number variation in susceptibility of human diseases

Germline copy number variation (CNV) is considered to be an important form of human genetic polymorphisms. Previous studies have identified amounts of CNVs in human genome by advanced technologies, such as comparative genomic hybridization, single nucleotide genotyping, and high-throughput sequencing. CNV is speculated to be derived from multiple mechanisms, such as nonallelic homologous recombination (NAHR) and nonhomologous end-joining (NHEJ). CNVs cover a much larger genome scale than single nucleotide polymorphisms (SNPs), and may alter gene expression levels by means of gene dosage, gene fusion, gene disruption, and long-range regulation effects, thus affecting individual phenotypes and playing crucial roles in human pathogenesis. The number of studies linking CNVs with common complex diseases has increased dramatically in recent years. Here, we provide a comprehensive review of the current understanding of germline CNVs, and summarize the association of germline CNVs with the susceptibility to a wide variety of human diseases that were identified in recent years. We also propose potential issues that should be addressed in future studies.

Copy number variants analysis in a cohort of isolated and syndromic developmental delay/intellectual disability reveals novel genomic disorders, position effects and candidate disease genes

BACKGROUND

Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect copy number variants (CNVs) associated with developmental delay/intellectual disability (DD/ID).

AIMS

Identification of genomic disorders in DD/ID.

MATERIALS AND METHODS

We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs.

RESULTS

We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes. We further identified and discussed 51 cases with likely pathogenic CNVs spanning novel candidate genes, including genes encoding synaptic components and/or proteins involved in corticogenesis. Additionally, we identified two deletions spanning potential Topological Associated Domain (TAD) boundaries probably affecting the regulatory landscape.

DISCUSSION AND CONCLUSION

We show how phenotypic and genetic analyses of array-CGH data allow unraveling complex cases, identifying rare disease genes, and revealing unexpected position effects.