Towards reproducible and respectful autism research: Combining open and participatory autism research practices

Background Open research broadly refers to a set of practices that aim to increase transparency, rigor, reproducibility and inclusivity of research. Participatory research refers to incorporating the views and sharing power with the autism community to decide what research gets done, how it is done and how it is implemented. There is growing interest in both open and participatory practices in autism research. To date, however, these practices have tended to be considered separately. Method In this paper, we outline the value of both open and participatory approaches to the autism research field, highlighting key points of overlap. Results We propose three core principles underpinning open and participatory autism research: (1) the need for adequate expertise and infrastructure to facilitate high quality research, (2) the need for a greater degree of accessibility at all stages of the research process, and (3) the need to foster trusting relationships between the autistic and research communities. Conclusion There are various challenges and opportunities of adopting open and participatory principles in autism research. We hope our principles support researchers to embed these approaches more fully within their work.publishedVersio

Evaluating the Function of an Understudied Family of Antiviral Proteins

Human immune responses to viral infections are associated with the interferon system, which induces the expression of as many as 300 proteins. Many of these proteins are believed to have antiviral functions, yet many of the interferon stimulated genes (ISGs) remain poorly characterized. The goal of this research is to identify the functional role of ISGs that are members of the tripartite motif (TRIM) family of proteins. Here, we report the progress of TRIM gene cloning into plasmids used in the yeast two-hybrid assays. We hypothesize that protein-protein interactions identified in these assays will provide unbiased insights into the functional role of these putative antiviral proteins. The yeast-two hybrid assay is the cornerstone for a research pipeline designed to more fully characterize the TRIM proteins.https://digitalcommons.mtech.edu/urp_aug_2017/1002/thumbnail.jp

The impact of early stages of COVID-19 on the mental health of autistic adults in the United Kingdom:A longitudinal mixed-methods study

We used mixed methods to learn about the nature and drivers of mental health changes among autistic adults in the United Kingdom during the early stages of the COVID-19 pandemic. In quantitative analyses, we examined the nature and predictors of change in depression, anxiety and stress, prospectively measured in 70 autistic adults at Wave 1 (just before the United Kingdom’s first lockdown) and Wave 2 (10–15 weeks into the United Kingdom’s first lockdown). Retrospective Wave 2 reports of mental health change were also analysed for these 70 participants. For the qualitative analysis, 133 participants (including the 70 from the quantitative analyses) provided reports on their experiences of the pandemic at Wave 2. In quantitative analyses, retrospective reports indicated that participants’ mental health worsened, but prospective data showed a different picture, with overall anxiety and stress scores reducing between Waves 1 and 2. Nevertheless, the mental health impact of the pandemic on autistic adults was variable, with a sizable minority reporting a significant decline in mental health. Qualitative analysis yielded four themes that contributed to mental health changes: (a) adjusting to changes to the social world, (b) living with uncertainty, (c) disruptions to self-regulation, and (d) barriers to fulfilling basic needs. LAY ABSTRACT: During the COVID-19 pandemic, high levels of depression, anxiety and stress have been reported in the general population. However, much less has been reported about the impact of COVID-19 on the mental health of autistic people. What we did: In the present study, we investigated how the mental health of autistic adults in the United Kingdom changed during the early stages of the COVID-19 pandemic. In total, 133 participants completed an online survey at two different time points. Of the 133 participants, 70 completed the survey at the first time point just before the onset of the national lockdown. This allowed us to look at changes in their mental health, from before the lockdown to 10 to 15 weeks during lockdown. All participants (133) told us about their experiences of the pandemic. What we found: While many autistic adults told us that their mental health worsened, people’s experience varied. For some autistic adults, aspects of mental health (e.g. anxiety, stress) actually improved. Participants also described social changes that had occurred, at home and in the outside world. They described feelings of uncertainty during the pandemic, and discussed how the pandemic had affected some of their previous coping strategies. Participants also told us about their difficulties in accessing healthcare services and food during the early stages of the pandemic. In our article, we discuss these findings and focus on what needs to change to ensure that autistic people are better supported as the pandemic continues

Senataxin modulates resistance to cisplatin through an R-loop mediated mechanism in HPV-associated Head and Neck Squamous Cell Carcinoma

AbstractIntroductionOropharyngeal Squamous Cell Carcinoma (OPSCC) is a site defined subtype of head and neck cancer with two distinct clinical subtypes: HPV-associated (HPV+) and HPV-independent (HPV-); both of which are commonly treated with chemoradiotherapy involving cisplatin. Cisplatin creates DNA crosslinks, which lead to eventual cell death via apoptosis. Clinical outcomes in HPV-OPSCC are poor and although HPV+ has an improved response to therapy, a subset of patients suffer from distant metastases, with a poor prognosis. Therefore, there is a need to understand the molecular basis underlying treatment resistance. A common mechanism of chemotherapy resistance is upregulation of DNA repair, and a major source of endogenous DNA damage are DNA/RNA hybrids, known as R-loops. R-loops are three stranded DNA/RNA hybrids formed in the genome as a by- product of transcription and are normally transient; however, they can persist and become a source of genomic instability. The contribution of R-loops to the development of cisplatin resistance in OPSCC is unknown.MethodsHPV+ and HPV- cisplatin resistant cell lines were developed, and RNA-sequencing was used to investigate changes in gene expression. Changes in R-loop dynamics were explored using slot blots and DRIP-qPCR. The effect of depleting known R-loop regulators on cisplatin sensitivity was assessed using siRNA. R-loop burden in a cohort of HPV+ and HPV- OPSCC tumours was explored using S9.6 immunohistochemistry.ResultsDevelopment of cisplatin resistant clones led to changes in gene expression consistent with resistance, alongside alterations in the expression of known R-loop regulators. Both HPV+ and HPV- resistant cells had elevated global R-loop levels and in HPV+ resistant cells there was a corresponding upregulation of the R-loop resolving protein, senataxin, which was not observed in HPV- resistant cells. Depletion of senataxin led to increased sensitivity to cisplatin in both HPV+ and HPV- resistant cells, however, the effect was greater in HPV+ cells. Quantification of R-loop levels by S9.6 immunohistochemistry revealed that HPV+ tumours and tumours with bone metastases had a higher R-loop burden.ConclusionR-loops are involved in modulating sensitivity to cisplatin and may represent a potential therapeutic target.</jats:sec

The role of icIL-1RA in keratinocyte senescence and development of the senescence-associated secretory phenotype

There is compelling evidence that senescent cells, through the senescence-associated secretory phenotype (SASP), can promote malignant transformation and invasion. Interleukin-1 (IL-1) is a key mediator of this cytokine network, but the control of its activity in the senescence programme has not been elucidated. IL-1 signalling is regulated by IL-1RA, which has four variants. Here, we show that expression of intracellular IL-1RA type 1 (icIL-1RA1), which competitively inhibits binding of IL-1 to its receptor, is progressively lost during oral carcinogenesis ex vivo and that the pattern of expression is associated with keratinocyte replicative fate in vitro. We demonstrate that icIL-1RA1 is an important regulator of the SASP in mortal cells, as CRISPR/Cas9-mediated icIL-1RA1 knockdown in normal and mortal dysplastic oral keratinocytes is followed by increased IL-6 and IL-8 secretion, and rapid senescence following release from RhoA-activated kinase inhibition. Thus, we suggest that downregulation of icIL-1RA1 in early stages of the carcinogenesis process can enable the development of a premature and deregulated SASP, creating a pro-inflammatory state in which cancer is more likely to arise.A scholarship from Becas Chile, Comisión Nacional de Investigación Cientı́fica y Tecnológicahttps://journals.biologists.com/jcsam2022Oral Pathology and Oral Biolog

Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition

Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies

Feasibility, clinical efficacy, and well-being outcomes of an online singing intervention for postnatal depression in the UK: SHAPER-PNDO, a single-arm clinical trial

BACKGROUND: Postnatal depression (PND) affects over 12% of mothers, with numbers rising during COVID-19. Singing groups can support mothers with PND; however, online delivery has never been evaluated. SHAPER-PNDO, a single-arm clinical trial, evaluated the feasibility, clinical efficacy, and well-being outcomes of a 6-week online version of Breathe Melodies for Mums (M4M) singing intervention developed for mothers with PND during COVID-19 lockdowns. METHODS: The primary objective of this study was to assess the feasibility of a group online singing intervention for new mothers with postnatal depression. This was ascertained through recruitment rates, study retention rates, attendance rates to the singing sessions, and study completion rates. The secondary objective of the study was to assess the clinical efficacy and well-being outcomes of the singing intervention. Specifically, we measured change in Edinburgh Postnatal Depression Scale (EPDS), State-Trait Anxiety Inventory (STAI), Perceived Stress Scale (PSS), and Office for National Statistics Wellbeing Scale (ONS) scores from baseline to end-of-intervention (week 6); follow-up assessments were completed at weeks 3, 16, and 32. Mothers were eligible if they scored ≥10 on the baseline EPDS. RESULTS: Eighty-seven percent of the 37 recruited mothers completed the study, attending, on average, 5 of the 6 group singing sessions. With regard to secondary outcomes, at end-of-treatment, mothers experienced significant reductions in depression (EPDS, 16.6 ± 3.7 to 11.2 ± 5.3, 95% CI [0.79,1.65]), anxiety (STAI-S, 48.4 ± 27.1 to 41.7 ± 26.8, 95% CI [4.96, 17.65]) and stress (PSS, 29.0 ± 5.7 to 19.7 ± 5.3, 95% CI [1.33, 7.07]); and, furthermore, significant improvements in life satisfaction (ONS, 50.5 ± 23.0 to 72.8 ± 11.7, 95% CI [- 39.86, - 4.64]) and feelings of worthwhileness (ONS, 51.7 ± 30.4 to 78.6 ± 15.1, 95% CI [- 52.79, - 0.85]). Reduction on the EPDS correlated with a reduction on the BDI and the STAI-S and maternal childhood maltreatment was predictive of a smaller treatment response. CONCLUSIONS: M4M online was feasible to mothers who partook in the programme. Furthermore, M4M online supports the mental health and well-being of new mothers experiencing PND, especially when barriers to in-person treatment are present

The prevalence, correlation, and co-occurrence of neuropathology in old age: harmonisation of 12 measures across six community-based autopsy studies of dementia

Background: Population-based autopsy studies provide valuable insights into the causes of dementia but are limited by sample size and restriction to specific populations. Harmonisation across studies increases statistical power and allows meaningful comparisons between studies. We aimed to harmonise neuropathology measures across studies and assess the prevalence, correlation, and co-occurrence of neuropathologies in the ageing population. Methods: We combined data from six community-based autopsy cohorts in the US and the UK in a coordinated cross-sectional analysis. Among all decedents aged 80 years or older, we assessed 12 neuropathologies known to be associated with dementia: arteriolosclerosis, atherosclerosis, macroinfarcts, microinfarcts, lacunes, cerebral amyloid angiopathy, Braak neurofibrillary tangle stage, Consortium to Establish a Registry for Alzheimer's disease (CERAD) diffuse plaque score, CERAD neuritic plaque score, hippocampal sclerosis, limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC), and Lewy body pathology. We divided measures into three groups describing level of confidence (low, moderate, and high) in harmonisation. We described the prevalence, correlations, and co-occurrence of neuropathologies. Findings: The cohorts included 4354 decedents aged 80 years or older with autopsy data. All cohorts included more women than men, with the exception of one study that only included men, and all cohorts included decedents at older ages (range of mean age at death across cohorts 88·0–91·6 years). Measures of Alzheimer's disease neuropathological change, Braak stage and CERAD scores, were in the high confidence category, whereas measures of vascular neuropathologies were in the low (arterioloscerosis, atherosclerosis, cerebral amyloid angiopathy, and lacunes) or moderate (macroinfarcts and microinfarcts) categories. Neuropathology prevalence and co-occurrence was high (2443 [91%] of 2695 participants had more than one of six key neuropathologies and 1106 [41%] of 2695 had three or more). Co-occurrence was strongly but not deterministically associated with dementia status. Vascular and Alzheimer's disease features clustered separately in correlation analyses, and LATE-NC had moderate associations with Alzheimer's disease measures (eg, Braak stage ρ=0·31 [95% CI 0·20–0·42]). Interpretation: Higher variability and more inconsistency in the measurement of vascular neuropathologies compared with the measurement of Alzheimer's disease neuropathological change suggests the development of new frameworks for the measurement of vascular neuropathologies might be helpful. Results highlight the complexity and multi-morbidity of the brain pathologies that underlie dementia in older adults and suggest that prevention efforts and treatments should be multifaceted. Funding: Gates Ventures

The risk of adverse pregnancy outcomes in women who are overweight or obese

Extent: 8p.Background: The prevalence of obesity amongst women bearing children in Australia is rising and has important implications for obstetric care. The aim of this study was to assess the prevalence and impact of mothers being overweight and obese in early to mid-pregnancy on maternal, peripartum and neonatal outcomes. Methods: A secondary analysis was performed on data collected from nulliparous women with a singleton pregnancy enrolled in the Australian Collaborative Trial of Supplements with antioxidants Vitamin C and Vitamin E to pregnant women for the prevention of pre-eclampsia (ACTS). Women were categorized into three groups according to their body mass index (BMI): normal (BMI 18.5-24.9 kg/m2); overweight (BMI 25-29.9 kg/m2) and; obese (BMI 30-34.9 kg/m2). Obstetric and perinatal outcomes were compared by univariate and multivariate analyses. Results: Of the 1661 women included, 43% were overweight or obese. Obese women were at increased risk of pre-eclampsia (relative risk (RR) 2.99 [95% confidence intervals (CI) 1.88, 4.73], p < 0.0001) and gestational diabetes (RR 2.10 [95%CI 1.17, 3.79], p = 0.01) compared with women with a normal BMI. Obese and overweight women were more likely to be induced and require a caesarean section compared with women of normal BMI (induction - RR 1.33 [95%CI 1.13, 1.57], p = 0.001 and 1.78 [95%CI 1.51, 2.09], p < 0.0001, caesarean section - RR 1.42 [95%CI 1.18, 1.70], p = 0.0002 and 1.63 [95%CI 1.34, 1.99], p < 0.0001). Babies of women who were obese were more likely to be large for gestational age (LFGA) (RR 2.08 [95%CI 1.47, 2.93], p < 0.0001) and macrosomic (RR 4.54 [95%CI 2.01, 10.24], p = 0.0003) compared with those of women with a normal BMI. Conclusion: The rate of overweight and obesity is increasing amongst the Australian obstetric population. Women who are overweight and obese have an increased risk of adverse pregnancy outcomes. In particular, obese women are at increased risk of gestational diabetes, pregnancy induced hypertension and pre-eclampsia. Effective preventative strategies are urgently needed.Chaturica Athukorala, Alice R Rumbold, Kristyn J Willson and Caroline A Crowthe