| 1. |
- Arora, Abishek, et al.
(author)
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Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics
- 2023
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In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13
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Journal article (peer-reviewed)abstract
- Research continues to identify genetic variation, environmental exposures, and their mixtures underlying different diseases and conditions. There is a need for screening methods to understand the molecular outcomes of such factors. Here, we investigate a highly efficient and multiplexable, fractional factorial experimental design (FFED) to study six environmental factors (lead, valproic acid, bisphenol A, ethanol, fluoxetine hydrochloride and zinc deficiency) and four human induced pluripotent stem cell line derived differentiating human neural progenitors. We showcase the FFED coupled with RNA-sequencing to identify the effects of low-grade exposures to these environmental factors and analyse the results in the context of autism spectrum disorder (ASD). We performed this after 5-day exposures on differentiating human neural progenitors accompanied by a layered analytical approach and detected several convergent and divergent, gene and pathway level responses. We revealed significant upregulation of pathways related to synaptic function and lipid metabolism following lead and fluoxetine exposure, respectively. Moreover, fluoxetine exposure elevated several fatty acids when validated using mass spectrometry-based metabolomics. Our study demonstrates that the FFED can be used for multiplexed transcriptomic analyses to detect relevant pathway-level changes in human neural development caused by low-grade environmental risk factors. Future studies will require multiple cell lines with different genetic backgrounds for characterising the effects of environmental exposures in ASD.
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| 2. |
- Arora, Abishek
(author)
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Genetic vulnerability, environmental exposures and neurodevelopmental disorders : clinical insights and in-vitro consequences
- 2023
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Doctoral thesis (other academic/artistic)abstract
- An understanding of how different genetic backgrounds and environmental exposures interact and contribute to diverse medical conditions like neurodevelopmental disorders (NDDs), is key to better health outcomes. A considerable overlap exists in the underlying genetics and physiology, often leading to their co-diagnoses. There is a lack of robust biomarkers for ASD and ADHD. Furthermore, no efficient resource exists to evaluate potential gene-environment interactions during early human neurodevelopment. This thesis addressed these knowledge gaps through five clinical and in-vitro studies. Study I explored the utility of genetic information from exome sequencing in predicting intervention outcomes of a social skills group training (SSGT) clinical trial for ASD. A genetic score was developed for common and rare variants in relevant genetic pathways, followed by generating a predictive machine learning (ML) model for individual responses. Variant carriers demonstrated significantly less improvement after standard care at postintervention. A higher rare variant genetic score for synaptic transmission was linked to less efficacy after SSGT at follow-up, while an opposite effect was observed for regulation of transcription from RNA polymerase II. The ML model emphasised the importance of rare variants in predicting intervention outcomes. Study II deployed urine-based untargeted metabolomics to investigate ASD-related biomarkers in a twin cohort with ultra-high performance liquid chromatography and mass spectrometry (UHPLC-MS). For the first time, any associations with autistic traits were also evaluated. No metabolite was found to be significantly associated with ASD. Based on nominal significance, an elevation in phenylpyruvate and taurine, and a decline in carnitine were detected, amongst others. These were found to be enriched in the arginine and proline metabolism pathway. More nominally significant metabolites were associated with autistic traits, and indole-3-acetate was positively associated with autistic traits within twin pairs. Study III also utilised a twin cohort to detect urinary and faecal metabolites associated with ADHD using nuclear magnetic resonance (NMR) and UHPLC-MS, respectively. Males with ADHD had increased levels of urinary hippurate, a metabolite produced by microbial-host co-metabolism. Hippurate was also negatively associated with intelligence quotient (IQ) levels in males and differentially associated with faecal metabolites from the gut microbiome. ADHD faecal profiles were characterised by higher levels of 1-stearoyl-2-linoleoyl-snglycerol (SLG), flavine adenine dinucleotide (FAD) and 3,7-dimethylurate. Reduced levels of aspartate, xanthine, orotate and other metabolites were also detected. Study IV dissected the impact of six environmental factors (lead, valproic acid, bisphenol A, ethanol, fluoxetine and zinc deficiency) in human induced pluripotent stem cell (iPSC) derived neuronal progenitors after differentiation for 5 days using the fractional factorial experimental design (FFED) coupled with RNA-sequencing. This was followed by a stratified analytical approach. Several gene and pathway level changes, that were both convergent and divergent for the environmental factor exposures, were identified. Pathways related to synaptic function and lipid metabolism were significantly elevated by lead and fluoxetine, respectively. Furthermore, fluoxetine increased the levels of several fatty acids when validated with direct infusion electrospray ionisation mass spectrometry (ESI-MS). Study V evaluated the differential in-vitro effects of four commonly prescribed selectively serotonin reuptake inhibitors (SSRIs: fluoxetine, citalopram, sertraline and paroxetine) in iPSC-derived neuronal progenitors. Total reactive oxygen species (ROS) and adenosine triphosphate (ATP) levels were determined at day 5 and 28 of differentiation. Concurrently, untargeted metabolomics was performed using ESI-MS. Sertraline and paroxetine significantly decreased ROS and ATP levels. Sertraline mediated early metabolite changes at day 5, while both sertraline and paroxetine drove such effects at day 28. Combined effects were driven by LPC 18:0 and LPC 16:0. Overall, metabolites were enriched in phospholipid biosynthesis and amino acid metabolism pathways. In conclusion, this thesis highlighted that genetic information can be used as an indicator for ASD interventions, encouraging further exploration. Urine and faecal metabolites are potential biomarkers for ASD and ADHD, pending validation. A multiplexable resource for studying gene-environment interactions was developed, along with a rich dataset outlining molecular changes in ASD. Lastly, the thesis demonstrated that different SSRIs elicit both shared and unique in-vitro responses, with a need to evaluate probable in-utero effects. The findings can guide future clinical studies to generate greater insights into ASD, ADHD and other conditions with aberrant neurodevelopmental trajectories.
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| 3. |
- Li, Danyang, et al.
(author)
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Rare variants in the outcome of social skills group training for autism
- 2022
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In: Autism Research. - : Wiley. - 1939-3792 .- 1939-3806. ; 15:3, s. 434-446
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Journal article (peer-reviewed)abstract
- Exome sequencing has been proposed as the first-tier genetic testing in autism spectrum disorder (ASD). Here, we performed exome sequencing in autistic individuals with average to high intellectual abilities (N = 207) to identify molecular diagnoses and genetic modifiers of intervention outcomes of social skills group training (SSGT) or standard care. We prioritized variants of clinical significance (VCS), variants of uncertain significance (VUS) and generated a pilot scheme to calculate genetic scores of rare and common variants in ASD-related gene pathways. Mixed linear models were used to test the association between the carrier status of VCS/VUS or the genetic scores with intervention outcomes measured by the social responsiveness scale. Additionally, we combined behavioral and genetic features using a machine learning (ML) model to predict the individual response. We showed a rate of 4.4% and 11.3% of VCS and VUS in the cohort, respectively. Individuals with VCS or VUS had improved significantly less after standard care than non-carriers at post-intervention (β = 9.35; p = 0.036), while no such association was observed for SSGT (β = −2.50; p = 0.65). Higher rare variant genetic scores for synaptic transmission and regulation of transcription from RNA polymerase II were separately associated with less beneficial (β = 8.30, p = 0.0044) or more beneficial (β = −6.79, p = 0.014) effects after SSGT compared with standard care at follow-up, respectively. Our ML model showed the importance of rare variants for outcome prediction. Further studies are needed to understand genetic predisposition to intervention outcomes in ASD.
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| 4. |
- Mastropasqua, Francesca, et al.
(author)
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Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.
- 2023
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In: Biology open. - : The Company of Biologists. - 2046-6390. ; 12:10
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Journal article (peer-reviewed)abstract
- Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level HNRNPU downregulation leads to an increased fraction of neural progenitors in the maturing neuronal population. We conclude that the HNRNPU locus is involved in delayed commitment of neural progenitors to differentiate in cell types with hindbrain profile.
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