CRISIS AFAR: an international collaborative study of the impact of the COVID-19 pandemic on mental health and service access in youth with autism and neurodevelopmental conditions.

BACKGROUND: Heterogeneous mental health outcomes during the COVID-19 pandemic are documented in the general population. Such heterogeneity has not been systematically assessed in youth with autism spectrum disorder (ASD) and related neurodevelopmental disorders (NDD). To identify distinct patterns of the pandemic impact and their predictors in ASD/NDD youth, we focused on pandemic-related changes in symptoms and access to services. METHODS: Using a naturalistic observational design, we assessed parent responses on the Coronavirus Health and Impact Survey Initiative (CRISIS) Adapted For Autism and Related neurodevelopmental conditions (AFAR). Cross-sectional AFAR data were aggregated across 14 European and North American sites yielding a clinically well-characterized sample of N = 1275 individuals with ASD/NDD (age = 11.0 ± 3.6 years; n females = 277). To identify subgroups with differential outcomes, we applied hierarchical clustering across eleven variables measuring changes in symptoms and access to services. Then, random forest classification assessed the importance of socio-demographics, pre-pandemic service rates, clinical severity of ASD-associated symptoms, and COVID-19 pandemic experiences/environments in predicting the outcome subgroups. RESULTS: Clustering revealed four subgroups. One subgroup-broad symptom worsening only (20%)-included youth with worsening across a range of symptoms but with service disruptions similar to the average of the aggregate sample. The other three subgroups were, relatively, clinically stable but differed in service access: primarily modified services (23%), primarily lost services (6%), and average services/symptom changes (53%). Distinct combinations of a set of pre-pandemic services, pandemic environment (e.g., COVID-19 new cases, restrictions), experiences (e.g., COVID-19 Worries), and age predicted each outcome subgroup. LIMITATIONS: Notable limitations of the study are its cross-sectional nature and focus on the first six months of the pandemic. CONCLUSIONS: Concomitantly assessing variation in changes of symptoms and service access during the first phase of the pandemic revealed differential outcome profiles in ASD/NDD youth. Subgroups were characterized by distinct prediction patterns across a set of pre- and pandemic-related experiences/contexts. Results may inform recovery efforts and preparedness in future crises; they also underscore the critical value of international data-sharing and collaborations to address the needs of those most vulnerable in times of crisis.

Autistic children and adolescents with frequent restricted interest and repetitive behavior showed more difficulty in social cognition during mask-wearing during the COVID-19 pandemic: a multisite survey.

BACKGROUND: The public health measures enacted in order to control the coronavirus disease (COVID-19) pandemic have caused considerable changes to daily life. For autistic children and adolescents, adapting to the "new normal," including mask-wearing, may be difficult because of their restricted interest and repetitive behavior (RRB) characteristics. We aimed to examine the relationships between RRB characteristics and the impact of mask-wearing on their social communications during the pandemic. METHODS: We recruited participants with a clinical diagnosis of autism spectrum disorder based on DSM-5 diagnostic criteria from two outpatient clinics in Tokyo, Japan, between November 2020 and April 2021 using a convenience sampling methodology. As a result, the participants consisted of 102 children and adolescents (mean (SD) age = 11.6 (5.3)). We collected data on RRB characteristics frequency before and during the pandemic using the CoRonavIruS Health Impact Survey (CRISIS) - Adapted for Autism and Related Neurodevelopmental conditions (AFAR). We then conducted factor analyses to compute the RRB severity composite scores, which are divided into lower- (e.g., sensory seeking), and higher-order (e.g., restricted interest). We also investigated mask-wearing culture using a bespoke questionnaire, and using Spearman's rank correlation analyses, we examined the relationships between before pandemic RRB characteristics, and the impact of mask-wearing on social communications during the pandemic. RESULTS: We found that children and adolescents who exhibited lower-order RRB before the pandemic had difficulties in going-out with mask-wearing (rho = -0.25, q = .031), more challenges with mask-wearing (rho = - 0.34, q = .0018), and difficulty in referring to others' emotions while wearing masks (rho = - 0.36, q = .0016). We also found an association between higher-order RRB before the pandemic and an uncomfortable sensation (rho = - 0.42, q = .0002) and difficulties in referring to other's emotions while wearing masks (rho = - 0.25, q = .031). CONCLUSIONS: We revealed that various behaviors, such as sensory seeking, repetitive motor mannerisms and movements, and rituals and routines, undertaken before the pandemic could be important predictors of difficulties with mask-wearing and social communication for autistic children and adolescents during the pandemic. Caregivers and teachers wearing masks may need to provide extra support for social communication to autistic children and adolescents showing RRB characteristics frequently.

Arabidopsis tiling array analysis to identify the stress-responsive genes.

Plants respond and adapt to drought, cold, and high-salinity stresses. Stress-inducible gene products function in the stress response and tolerance in plants. Using cDNA microarrays and oligonucleotide microarrays, stress-inducible genes have been identified in various plant species so far. Recently, tiling array technology has become a powerful tool for the whole-genome transcriptome analysis. We applied the Arabidopsis Affymetrix tiling arrays to study the whole-genome transcriptome under drought, cold, and high-salinity stresses and identified a large number of drought, cold, and high-salinity stress-inducible genes and transcriptional units (TUs).

Transcriptome analyses revealed diverse expression changes in ago1 and hyl1 Arabidopsis mutants.

MicroRNAs (miRNAs) are 20-24 nucleotide endogenous regulatory molecules conserved in higher eukaryotes. In Arabidopsis, miRNAs are produced through step-wise cleavages of primary miRNA precursors (pri-miRNAs) by DICER-LIKE1 (DCL1). This cleavage step is also supported by a double-stranded RNA-binding protein, HYPONASTIC LEAVES1 (HYL1). In many cases, mature miRNA is predominantly incorporated into an endonuclease, ARGONAUTE1 (AGO1), which degrades miRNA-targeted mRNAs. Here, we examined and revealed whole genome transcriptomes in ago1-25 and hyl1-2 mutants using tiling arrays. The data in this paper are valuable for understanding the relationship between the miRNA pathway and its effect on transcriptomes.

Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis.

The nonsense-mediated mRNA decay (NMD) pathway is a well-known eukaryotic surveillance mechanism that eliminates aberrant mRNAs that contain a premature termination codon (PTC). The UP-Frameshift (UPF) proteins, UPF1, UPF2, and UPF3, are essential for normal NMD function. Several NMD substrates have been identified, but detailed information on NMD substrates is lacking. Here, we noticed that, in Arabidopsis, most of the mRNA-like nonprotein-coding RNAs (ncRNAs) have the features of an NMD substrate. We examined the expression profiles of 2 Arabidopsis mutants, upf1-1 and upf3-1, using a whole-genome tiling array. The results showed that expression of not only protein-coding transcripts but also many mRNA-like ncRNAs (mlncRNAs), including natural antisense transcript RNAs (nat-RNAs) transcribed from the opposite strands of the coding strands, were up-regulated in both mutants. The percentage of the up-regulated mlncRNAs to all expressed mlncRNAs was much higher than that of the up-regulated protein-coding transcripts to all expressed protein- coding transcripts. This finding demonstrates that one of the most important roles of NMD is the genome-wide suppression of the aberrant mlncRNAs including nat-RNAs.

Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana.

Post-translational modification of histone N-tails affects eukaryotic gene activity. In Arabidopsis, the histone modification level correlates with gene activation and repression in vernalization and flowering processes, but there is little information on changes in histone modification status and nucleosome structure under abiotic stresses. We determined the temporal and spatial changes in nucleosome occupancy and levels of H3K4me3, H3K9ac, H3K14ac, H3K23ac and H3K27ac in the histone H3 N-tail on the regions of four Arabidopsis drought stress-inducible genes, RD29A, RD29B, RD20 and At2g20880 [corrected], under drought stress conditions by chromatin immunoprecipitation analysis. We found two types of regulatory mechanisms of nucleosome occupancy function in the drought stress response. For RD29A and RD29B genes, nucleosome occupancy of promoter regions is low compared with that of coding regions, and no notable nucleosome loss occurs under drought stress. In contrast, nucleosome density is gradually decreased in response to drought stress on RD20 and At2g20880 [corrected] genes. Enrichments of H3K4me3 and H3K9ac correlate with gene activation in response to drought stress in all four genes. Interestingly, establishment of H3K4me3 occurs after accumulation of RNAPII on the coding regions of RD29A and At2g20880 [corrected]. Enrichment of H3K23ac and H3K27ac occurs in response to drought stress on the coding regions of RD29B, RD20 and At2g20880 [corrected], but not on the coding region of At2g20880 [corrected]. Our results indicate that histone modifications on the H3 N-tail are altered with gene activation on the coding regions of drought stress-responsive genes under drought stress conditions and that several patterns of nucleosome changes function in the drought stress response.

Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis.

RNA-directed DNA methylation (RdDM) is a process in which 24 nucleotide (nt) small interfering RNAs (siRNAs) guide de novo cytosine methylation in the homologous genomic DNA region. Of several factors involving 24 nt siRNA accumulation, RNA-dependent RNA polymerase 2 (RDR2) is a key component, because accumulation of 24 nt siRNA disappears in the Arabidopsis rdr2 mutant. Here, we compared expression profiles among wild-type, rdr2-1 and ddc (drm1drm2cmt3), DNA methyltransferase triple mutant, using a whole genome tiling array to identify the candidate genes directly downregulated by RdDM-related 24 nt siRNAs. Of the transcripts upregulated in the mutants, we searched for those whose coding regions or flanking regions have siRNA-generating loci. We found upregulated expression of 18 transcripts with AGI codes and 19 predicted transcriptional units (TUs) with siRNA loci in both rdr2-1 and ddc. Our study provided important information for understanding the relationship between RdDM and the identified candidate genes.

Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array.

Plants respond and adapt to drought, cold and high-salinity stresses in order to survive. In this study, we applied Arabidopsis Affymetrix tiling arrays to study the whole genome transcriptome under drought, cold, high-salinity and ABA treatment conditions. The bioinformatic analysis using the tiling array data showed that 7,719 non-AGI transcriptional units (TUs) exist in the unannotated "intergenic" regions of Arabidopsis genome. These include 1,275 and 181 TUs that are induced and downregulated, respectively, by the stress or ABA treatments. Most of the non-AGI TUs are hypothetical non-protein-coding RNAs. About 80% of the non-AGI TUs belong to pairs of the fully overlapping sense-antisense transcripts (fSATs). Significant linear correlation between the expression ratios (treated/untreated) of the sense TUs and the ratios of the antisense TUs was observed in the SATs of AGI code/non-AGI TU. We studied the biogenesis mechanisms of the stress- or ABA-inducible antisense RNAs and found that the expression of sense TUs is necessary for the stress- or ABA-inducible expression of the antisense TUs in the fSATs (AGI code/non-AGI TU).