Requirement for NF-κB in maintenance of molecular and behavioral circadian rhythms in mice.

The mammalian circadian clock is encoded by an autoregulatory transcription feedback loop that drives rhythmic behavior and gene expression in the brain and peripheral tissues. Transcriptomic analyses indicate cell type-specific effects of circadian cycles on rhythmic physiology, although how clock cycles respond to environmental stimuli remains incompletely understood. Here, we show that activation of the inducible transcription factor NF-κB in response to inflammatory stimuli leads to marked inhibition of clock repressors, including the Period, Cryptochrome, and Rev-erb genes, within the negative limb. Furthermore, activation of NF-κB relocalizes the clock components CLOCK/BMAL1 genome-wide to sites convergent with those bound by NF-κB, marked by acetylated H3K27, and enriched in RNA polymerase II. Abrogation of NF-κB during adulthood alters the expression of clock repressors, disrupts clock-controlled gene cycles, and impairs rhythmic activity behavior, revealing a role for NF-κB in both unstimulated and activated conditions. Together, these data highlight NF-κB-mediated transcriptional repression of the clock feedback limb as a cause of circadian disruption in response to inflammation.

miR-328 functions as an RNA decoy to modulate hnRNP E2 regulation of mRNA translation in leukemic blasts.

MicroRNAs and heterogeneous ribonucleoproteins (hnRNPs) are posttranscriptional gene regulators that bind mRNA in a sequence-specific manner. Here, we report that loss of miR-328 occurs in blast crisis chronic myelogenous leukemia (CML-BC) in a BCR/ABL dose- and kinase-dependent manner through the MAPK-hnRNP E2 pathway. Restoration of miR-328 expression rescues differentiation and impairs survival of leukemic blasts by simultaneously interacting with the translational regulator poly(rC)-binding protein hnRNP E2 and with the mRNA encoding the survival factor PIM1, respectively. The interaction with hnRNP E2 is independent of the microRNA's seed sequence and it leads to release of CEBPA mRNA from hnRNP E2-mediated translational inhibition. Altogether, these data reveal the dual ability of a microRNA to control cell fate both through base pairing with mRNA targets and through a decoy activity that interferes with the function of regulatory proteins.

Optimization of a mouse model of pancreatic cancer to simulate the human phenotypes of metastasis and cachexia.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) presents with a high mortality rate. Two important features of PDAC contribute to this poor outcome. The first is metastasis which occurs in ~ 80% of PDAC patients. The second is cachexia, which compromises treatment tolerance for patients and reduces their quality of life. Although various mouse models of PDAC exist, recapitulating both metastatic and cachectic features have been challenging. METHODS: Here, we optimize an orthotopic mouse model of PDAC by altering several conditions, including the subcloning of parental murine PDAC cells, implantation site, number of transplanted cells, and age of recipient mice. We perform spatial profiling to compare primary and metastatic immune microenvironments and RNA sequencing to gain insight into the mechanisms of muscle wasting in PDAC-induced cachexia, comparing non-metastatic to metastatic conditions. RESULTS: These modifications extend the time course of the disease and concurrently increase the rate of metastasis to approximately 70%. Furthermore, reliable cachexia endpoints are achieved in both PDAC mice with and without metastases, which is reminiscent of patients. We also find that cachectic muscles from PDAC mice with metastasis exhibit a similar transcriptional profile to muscles derived from mice and patients without metastasis. CONCLUSION: Together, this model is likely to be advantageous in both advancing our understanding of the mechanism of PDAC cachexia, as well as in the evaluation of novel therapeutics.

Molecular and Developmental Signatures of Genital Size Macro-Evolution in Bugs.

Our understanding of the genetic architecture of phenotypic traits has experienced drastic growth over the last years. Nevertheless, the majority of studies associating genotypes and phenotypes have been conducted at the ontogenetic level. Thus, we still have an elusive knowledge of how these genetic-developmental architectures evolve themselves and how their evolution is mirrored in the phenotypic change across evolutionary time. We tackle this gap by reconstructing the evolution of male genital size, one of the most complex traits in insects, together with its underlying genetic architecture. Using the order Hemiptera as a model, spanning over 350 million years of evolution, we estimate the correlation between genitalia and three features: development rate, body size, and rates of DNA substitution in 68 genes associated with genital development. We demonstrate that genital size macro-evolution has been largely dependent on body size and weakly influenced by development rate and phylogenetic history. We further revealed significant correlations between mutation rates and genital size for 19 genes. Interestingly, these genes have diverse functions and participate in distinct signaling pathways, suggesting that genital size is a complex trait whose fast evolution has been enabled by molecular changes associated with diverse morphogenetic processes. Our data further demonstrate that the majority of DNA evolution correlated with the genitalia has been shaped by negative selection or neutral evolution. Thus, in terms of sequence evolution, changes in genital size are predominantly facilitated by relaxation of constraints rather than positive selection, possibly due to the high pleiotropic nature of the morphogenetic genes.

Domain-specific introduction to machine learning terminology, pitfalls and opportunities in CRISPR-based gene editing.

The use of machine learning (ML) has become prevalent in the genome engineering space, with applications ranging from predicting target site efficiency to forecasting the outcome of repair events. However, jargon and ML-specific accuracy measures have made it hard to assess the validity of individual approaches, potentially leading to misinterpretation of ML results. This review aims to close the gap by discussing ML approaches and pitfalls in the context of CRISPR gene-editing applications. Specifically, we address common considerations, such as algorithm choice, as well as problems, such as overestimating accuracy and data interoperability, by providing tangible examples from the genome-engineering domain. Equipping researchers with the knowledge to effectively use ML to better design gene-editing experiments and predict experimental outcomes will help advance the field more rapidly.

The inequity of targeted cystic fibrosis reproductive carrier screening tests in Australia.

OBJECTIVE: European and Australian guidelines for cystic fibrosis (CF) reproductive carrier screening recommend testing a small number of high frequency CF causing variants, rather than comprehensive CFTR sequencing. The study objective was to determine variant detection rates of commercially available targeted reproductive carrier screening tests in Australia. METHODS: Next-generation DNA sequencing of the CFTR gene was performed on 2552 individuals from a whole population sample to identify CF causing variants. The variant detection rates of two commercially available Australian reproductive carrier screening tests, which target 50 or 175 CF causing variants, in this population were calculated. The ethnicity of individuals was determined using principal component analysis. RESULTS: Variant detection rates of the tests for 50 and 175 CF causing variants were 88.2% and 90.8%, respectively. No CF causing variants in individuals of East Asian ethnicity (n = 3) were detected by either test, while >86.6% (n = 69) of CF causing variants in Europeans would be identified by either test. CONCLUSIONS: Reproductive carrier screening tests for a targeted set of high frequency CF variants are unable to detect approximately 10% of CF variants in a multiethnic Australian population, and individuals of East Asian ethnicity are disproportionally affected by this test limitation.

Optimized nickase- and nuclease-based prime editing in human and mouse cells.

Precise genomic modification using prime editing (PE) holds enormous potential for research and clinical applications. In this study, we generated all-in-one prime editing (PEA1) constructs that carry all the components required for PE, along with a selection marker. We tested these constructs (with selection) in HEK293T, K562, HeLa and mouse embryonic stem (ES) cells. We discovered that PE efficiency in HEK293T cells was much higher than previously observed, reaching up to 95% (mean 67%). The efficiency in K562 and HeLa cells, however, remained low. To improve PE efficiency in K562 and HeLa, we generated a nuclease prime editor and tested this system in these cell lines as well as mouse ES cells. PE-nuclease greatly increased prime editing initiation, however, installation of the intended edits was often accompanied by extra insertions derived from the repair template. Finally, we show that zygotic injection of the nuclease prime editor can generate correct modifications in mouse fetuses with up to 100% efficiency.

Relationship between Protein Digestibility and the Proteolysis of Legume Proteins during Seed Germination.

Legume seed protein is an important source of nutrition, but generally it is less digestible than animal protein. Poor protein digestibility in legume seeds and seedlings may partly reflect defenses against herbivores. Protein changes during germination typically increase proteolysis and digestibility, by lowering the levels of anti-nutrient protease inhibitors, activating proteases, and breaking down storage proteins (including allergens). Germinating legume sprouts also show striking increases in free amino acids (especially asparagine), but their roles in host defense or other processes are not known. While the net effect of germination is generally to increase the digestibility of legume seed proteins, the extent of improvement in digestibility is species- and strain-dependent. Further research is needed to highlight which changes contribute most to improved digestibility of sprouted seeds. Such knowledge could guide the selection of varieties that are more digestible and also guide the development of food preparations that are more digestible, potentially combining germination with other factors altering digestibility, such as heating and fermentation. Techniques to characterize the shifts in protein make-up, activity and degradation during germination need to draw on traditional analytical approaches, complemented by proteomic and peptidomic analysis of mass spectrometry-identified peptide breakdown products.

Cell-Penetrating Milk-Derived Peptides with a Non-Inflammatory Profile.

Milk-derived peptides are known to confer anti-inflammatory effects. We hypothesised that milk-derived cell-penetrating peptides might modulate inflammation in useful ways. Using computational techniques, we identified and synthesised peptides from the milk protein Alpha-S1-casein that were predicted to be cell-penetrating using a machine learning predictor. We modified the interpretation of the prediction results to consider the effects of histidine. Peptides were then selected for testing to determine their cell penetrability and anti-inflammatory effects using HeLa cells and J774.2 mouse macrophage cell lines. The selected peptides all showed cell penetrating behaviour, as judged using confocal microscopy of fluorescently labelled peptides. None of the peptides had an effect on either the NF-κB transcription factor or TNFα and IL-1ß secretion. Thus, the identified milk-derived sequences have the ability to be internalised into the cell without affecting cell homeostatic mechanisms such as NF-κB activation. These peptides are worthy of further investigation for other potential bioactivities or as a naturally derived carrier to promote the cellular internalisation of other active peptides.

The multifaceted aspects of sleep and sleep-wake disorders following stroke.

Sleep-wake disorders (SWD) are acknowledged risk factors for both ischemic stroke and poor cardiovascular and functional outcome after stroke. SWD are frequent following stroke, with sleep apnea (SA) being the most frequent SWD affecting more than half of stroke survivors. While sleep disturbances and SWD are frequently reported in the acute phase, they may persist in the chronic phase after an ischemic stroke. Despite the frequency and risk associated with SWD following stroke, screening for SWD remains rare in the clinical setting, due to challenges in the assessment of post-stroke SWD, uncertainty regarding the optimal timing for their diagnosis, and a lack of clear treatment guidelines (i.e., when to treat and the optimal treatment strategy). However, little evidence support the feasibility of SWD treatment even in the acute phase of stroke and its favorable effect on long-term cardiovascular and functional outcomes. Thus, sleep health recommendations and SWD treatment should be systematically embedded in secondary stroke prevention strategy. We therefore propose that the management of SWD associated with stroke should rely on a multidisciplinary approach, with an integrated diagnostic, treatment, and follow-up strategy. The challenges in the field are to improve post-stroke SWD diagnosis, prognosis and treatment, through a better appraisal of their pathophysiology and temporal evolution.

Different time course recovery of muscle edema within the quadriceps femoris and functional performance after single- vs multi-joint exercises.

This study aimed to verify the time course recovery of muscle edema within the quadriceps femoris and functional performance after lower-body single- and multi-joint exercises. For this within-participant unilateral and contralateral experimental design, fourteen untrained young males performed a unilateral knee extension exercise (KE), and a unilateral leg press (LP) exercise in a counterbalanced order. At pre-, post-, 24 h, 48 h, 72 h, and 96 h after exercise, the peak torque (PT), unilateral countermovement jump (uCMJ) performance, and rectus femoris (RF) and vastus lateralis (VL) muscle thicknesses were recorded in both legs. The PT decreased immediately after (p = 0.01) both exercises (KE and LP) and was fully recovered 24 h after KE (p = 0.38) and 48 h after LP (p = 0.68). Jump height and power, in the uCMJ, followed the same PT recovery pattern after both exercises. However, vertical stiffness (Kvert) was not affected at any time point after both protocols. The RF thickness increased after both exercises (p = 0.01) and was fully restored 48 h after KE (p = 0.86) and 96 h after LP (p = 1.00). The VL thickness increased after both exercises (p = 0.01) and was fully restored 24 h after LP (p = 1.00) and 48 h after KE (p = 1.00). The LP exercise, compared to KE, induced more prolonged impairment of functional performance and delayed recovery of RF muscle edema. However, the VL edema-induced muscle swelling recovery was delayed after the KE exercise. The different recovery kinetics between functional performance and muscle damage should be taken into consideration depending on the objectives of the next training sessions.

Causes of cardiovascular and noncardiovascular death in the ISCHEMIA trial.

BACKGROUND: The International Study of Comparative Health Effectiveness with Medical and Invasive Approaches trial demonstrated no overall difference in the composite primary endpoint and the secondary endpoints of cardiovascular (CV) death/myocardial infarction or all-cause mortality between an initial invasive or conservative strategy among participants with chronic coronary disease and moderate or severe myocardial ischemia. Detailed cause-specific death analyses have not been reported. METHODS: We compared overall and cause-specific death rates by treatment group using Cox models with adjustment for pre-specified baseline covariates. Cause of death was adjudicated by an independent Clinical Events Committee as CV, non-CV, and undetermined. We evaluated the association of risk factors and treatment strategy with cause of death. RESULTS: Four-year cumulative incidence rates for CV death were similar between invasive and conservative strategies (2.6% vs 3.0%; hazard ratio [HR] 0.98; 95% CI [0.70-1.38]), but non-CV death rates were higher in the invasive strategy (3.3% vs 2.1%; HR 1.45 [1.00-2.09]). Overall, 13% of deaths were attributed to undetermined causes (38/289). Fewer undetermined deaths (0.6% vs 1.3%; HR 0.48 [0.24-0.95]) and more malignancy deaths (2.0% vs 0.8%; HR 2.11 [1.23-3.60]) occurred in the invasive strategy than in the conservative strategy. CONCLUSIONS: In International Study of Comparative Health Effectiveness with Medical and Invasive Approaches, all-cause and CV death rates were similar between treatment strategies. The observation of fewer undetermined deaths and more malignancy deaths in the invasive strategy remains unexplained. These findings should be interpreted with caution in the context of prior studies and the overall trial results.

A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping.

Oncogenesis and cancer can arise as a consequence of a wide range of genomic aberrations including mutations, copy number alterations, expression changes and epigenetic modifications encompassing multiple omics layers. Integrating genomic, transcriptomic, proteomic and epigenomic datasets via multi-omics analysis provides the opportunity to derive a deeper and holistic understanding of the development and progression of cancer. There are two primary approaches to integrating multi-omics data: multi-staged (focused on identifying genes driving cancer) and meta-dimensional (focused on establishing clinically relevant tumour or sample classifications). A number of ready-to-use bioinformatics tools are available to perform both multi-staged and meta-dimensional integration of multi-omics data. In this study, we compared nine different integration tools using real and simulated cancer datasets. The performance of the multi-staged integration tools were assessed at the gene, function and pathway levels, while meta-dimensional integration tools were assessed based on the sample classification performance. Additionally, we discuss the influence of factors such as data representation, sample size, signal and noise on multi-omics data integration. Our results provide current and much needed guidance regarding selection and use of the most appropriate and best performing multi-omics integration tools.

The RNA demethylase FTO is required for maintenance of bone mass and functions to protect osteoblasts from genotoxic damage.

The fat mass and obesity-associated gene (FTO) encodes an m6A RNA demethylase that controls mRNA processing and has been linked to both obesity and bone mineral density in humans by genome-wide association studies. To examine the role of FTO in bone, we characterized the phenotype of mice lacking Fto globally (FtoKO ) or selectively in osteoblasts (FtoOcKO ). Both mouse models developed age-related reductions in bone volume in both the trabecular and cortical compartments. RNA profiling in osteoblasts following acute disruption of Fto revealed changes in transcripts of Hspa1a and other genes in the DNA repair pathway containing consensus m6A motifs required for demethylation by FtoFto KO osteoblasts were more susceptible to genotoxic agents (UV and H2O2) and exhibited increased rates of apoptosis. Importantly, forced expression of Hspa1a or inhibition of NF-κB signaling normalized the DNA damage and apoptotic rates in Fto KO osteoblasts. Furthermore, increased metabolic stress induced in mice by feeding a high-fat diet induced greater DNA damage in osteoblast of FtoOc KO mice compared to controls. These data suggest that FTO functions intrinsically in osteoblasts through Hspa1a-NF-κB signaling to enhance the stability of mRNA of proteins that function to protect cells from genotoxic damage.

Modelling the Transitioning of SARS-CoV-2 nsp3 and nsp4 Lumenal Regions towards a More Stable State on Complex Formation.

During coronavirus infection, three non-structural proteins, nsp3, nsp4, and nsp6, are of great importance as they induce the formation of double-membrane vesicles where the replication and transcription of viral gRNA takes place, and the interaction of nsp3 and nsp4 lumenal regions triggers membrane pairing. However, their structural states are not well-understood. We investigated the interactions between nsp3 and nsp4 by predicting the structures of their lumenal regions individually and in complex using AlphaFold2 as implemented in ColabFold. The ColabFold prediction accuracy of the nsp3-nsp4 complex was increased compared to nsp3 alone and nsp4 alone. All cysteine residues in both lumenal regions were modelled to be involved in intramolecular disulphide bonds. A linker region in the nsp4 lumenal region emerged as crucial for the interaction, transitioning to a structured state when predicted in complex. The key interactions modelled between nsp3 and nsp4 appeared stable when the transmembrane regions of nsp3 and nsp4 were added to the modelling either alone or together. While molecular dynamics simulations (MD) demonstrated that the proposed model of the nsp3 lumenal region on its own is not stable, key interactions between nsp and nsp4 in the proposed complex model appeared stable after MD. Together, these observations suggest that the interaction is robust to different modelling conditions. Understanding the functional importance of the nsp4 linker region may have implications for the targeting of double membrane vesicle formation in controlling coronavirus infection.

[Apalutamide, Erleada®]. / Le Médicament du mois. Apalutamide, Erleada®.

Androgen-deprivation therapy (ADT), either bilateral orchiectomy or treatment with a gonadotropin-releasing hormone analogue agonist or antagonist, is the mainstay of treatment for advanced prostate cancer. In the metastatic setting, although ADT is initially effective, castration-resistant disease eventually develops in almost all men with prostate cancer. Since 2015, the addition of docetaxel, abiraterone, enzalutamide, apalutamide or darolutamide with docetaxel to ADT has been shown to improve overall survival (OS) of patients starting ADT for metastatic disease. Castration resistance occurs when disease progresses despite testosterone in the castrate range most commonly with or, more rarely, without detectable metastases. The addition of next-generation antiandrogens to ADT has been shown to improve OS in patients with high-risk nonmetastatic castration-resistant prostate cancer (nmCRPC) identified by a PSA doubling time (DT) ? 10 months. Apalutamide is a nonsteroidal antiandrogen agent that binds directly to the ligand-binding domain of the androgen receptor without agonist activity. When added to ADT apalutamide has been shown to improve OS by 35 % in patients starting ADT for metastatic prostate cancer both in patients with upfront metastatic disease or after previous treatment with curative intent. Similarly apalutamide has been shown to provide a 14-month OS improvement in patients with nmCRPC and short PSA DT. These OS benefits were obtained at no cost in terms of quality of life. Apalutamide is given orally once a day and is well tolerated. The most common side effects are fatigue, rash, hypertension and hot flushes. Potential interactions with concomitant medication should be taken into account.

La privation androgénique, chimique au moyen d'agonistes ou d'antagonistes de la LHRH, ou chirurgicale par orchidectomie, est un élément essentiel du traitement du cancer de la prostate avancé. Chez les patients métastatiques, son efficacité est cependant transitoire et une progression survient invariablement. Depuis 2015, une amélioration de la survie des patients métastatiques devant débuter une privation androgénique a été démontrée par l'instauration précoce soit d'une chimiothérapie par docétaxel, soit d'une hormonothérapie de nouvelle génération telle que l'abiratérone, l'enzalutamide, l'apalutamide, voire un traitement combinant docétaxel et darolutamide. Lorsque les patients progressent en dépit de la privation androgénique, on les dit résistants à la castration, le plus souvent en présence de métastases mais parfois en l'absence de lésion secondaire identifiable. Dans le cas des patients non métastatiques résistant à la castration à risque élevé d'évolution défavorable en raison d'un temps de doublement du PSA ? 10 mois, on a également démontré que l'ajout d'un anti-androgène de nouvelle génération améliorait la survie globale des patients. L'apalutamide, ou Erleada®, est un inhibiteur sélectif du récepteur aux androgènes, sans activité agoniste, administré par voie orale. Son instauration, en même temps que la privation androgénique, permet de réduire de 35 % la mortalité des patients métastatiques d'emblée ou secondairement après un traitement initial à visée curative. De même, l'apalutamide permet d'augmenter de 14 mois la survie des patients non métastatiques résistant à la castration à risque élevé d'évolution défavorable. Ces améliorations de la survie globale ont été obtenues sans détérioration de la qualité de vie. L'Erleada® est globalement bien toléré, et facile à administrer, s'agissant d'une prise orale unique quotidienne. La fatigue, la toxicité cutanée souvent modérée, l'hypertension artérielle et les bouffées de chaleur sont les effets secondaires les plus fréquents. Il convient également d'être attentif aux interactions médicamenteuses potentielles.

[CAR-T cells therapy in solid tumors : where are we now ?] / Les CAR-T cells dans le traitement des tumeurs solides : où en sommes-nous ?

Chimeric antigen receptor T cells (also known as CAR-T cells) have already made their way into the therapeutic arsenal of specific hematological cancers, significantly improving the prognosis of patients. The prospect of such an innovative and effective treatment in solid tumors is very attractive. For this reason, several clinical studies have been initiated. Unfortunately, the antigenic heterogeneity and microenvironmental hostility of these solid tumors currently limit the effectiveness of CAR-T cells. New strategies are being sought to counteract these therapeutic obstacles.

Les lymphocytes T porteurs d'un récepteur antigénique chimérique, appelés CAR-T cells, ont déjà fait leur chemin dans l'arsenal thérapeutique de certains cancers hématologiques, améliorant significativement le pronostic des patients. La perspective d'un tel traitement, aussi innovant qu'efficace, dans les tumeurs solides est très attrayante. C'est la raison pour laquelle plusieurs études cliniques ont vu le jour. Malheureusement, l'hétérogénéité antigénique et l'hostilité micro-environnementale de ces tumeurs solides limitent actuellement l'efficacité des CAR-T cells. De nouvelles stratégies sont recherchées pour contrer ces obstacles thérapeutiques.

Computational modelling of chromosomally clustering protein domains in bacteria.

BACKGROUND: In bacteria, genes with related functions-such as those involved in the metabolism of the same compound or in infection processes-are often physically close on the genome and form groups called clusters. The enrichment of such clusters over various distantly related bacteria can be used to predict the roles of genes of unknown function that cluster with characterised genes. There is no obvious rule to define a cluster, given their variability in size and intergenic distances, and the definition of what comprises a "gene", since genes can gain and lose domains over time. Protein domains can cluster within a gene, or in adjacent genes of related function, and in both cases these are chromosomally clustered. Here, we model the distances between pairs of protein domain coding regions across a wide range of bacteria and archaea via a probabilistic two component mixture model, without imposing arbitrary thresholds in terms of gene numbers or distances. RESULTS: We trained our model using matched gene ontology terms to label functionally related pairs and assess the stability of the parameters of the model across 14,178 archaeal and bacterial strains. We found that the parameters of our mixture model are remarkably stable across bacteria and archaea, except for endosymbionts and obligate intracellular pathogens. Obligate pathogens have smaller genomes, and although they vary, on average do not show noticeably different clustering distances; the main difference in the parameter estimates is that a far greater proportion of the genes sharing ontology terms are clustered. This may reflect that these genomes are enriched for complexes encoded by clustered core housekeeping genes, as a proportion of the total genes. Given the overall stability of the parameter estimates, we then used the mean parameter estimates across the entire dataset to investigate which gene ontology terms are most frequently associated with clustered genes. CONCLUSIONS: Given the stability of the mixture model across species, it may be used to predict bacterial gene clusters that are shared across multiple species, in addition to giving insights into the evolutionary pressures on the chromosomal locations of genes in different species.

Machine learning with neuroimaging data to identify autism spectrum disorder: a systematic review and meta-analysis.

PURPOSE: Autism Spectrum Disorder (ASD) is diagnosed through observation or interview assessments, which is time-consuming, subjective, and with questionable validity and reliability. Thus, we aimed to evaluate the role of machine learning (ML) with neuroimaging data to provide a reliable classification of ASD. METHODS: A systematic search of PubMed, Scopus, and Embase was conducted to identify relevant publications. Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) was used to assess the studies' quality. A bivariate random-effects model meta-analysis was employed to evaluate the pooled sensitivity, the pooled specificity, and the diagnostic performance through the hierarchical summary receiver operating characteristic (HSROC) curve of ML with neuroimaging data in classifying ASD. Meta-regression was also performed. RESULTS: Forty-four studies (5697 ASD and 6013 typically developing individuals [TD] in total) were included in the quantitative analysis. The pooled sensitivity for differentiating ASD from TD individuals was 86.25 95% confidence interval [CI] (81.24, 90.08), while the pooled specificity was 83.31 95% CI (78.12, 87.48) with a combined area under the HSROC (AUC) of 0.889. Higgins I2 (> 90%) and Cochran's Q (p < 0.0001) suggest a high degree of heterogeneity. In the bivariate model meta-regression, a higher pooled specificity was observed in studies not using a brain atlas (90.91 95% CI [80.67, 96.00], p = 0.032). In addition, a greater pooled sensitivity was seen in studies recruiting both males and females (89.04 95% CI [83.84, 92.72], p = 0.021), and combining imaging modalities (94.12 95% [85.43, 97.76], p = 0.036). CONCLUSION: ML with neuroimaging data is an exciting prospect in detecting individuals with ASD but further studies are required to improve its reliability for usage in clinical practice.

Evidence for polygenic and oligogenic basis of Australian sporadic amyotrophic lateral sclerosis.

BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with phenotypic and genetic heterogeneity. Approximately 10% of cases are familial, while remaining cases are classified as sporadic. To date, >30 genes and several hundred genetic variants have been implicated in ALS. METHODS: Seven hundred and fifty-seven sporadic ALS cases were recruited from Australian neurology clinics. Detailed clinical data and whole genome sequencing (WGS) data were available from 567 and 616 cases, respectively, of which 426 cases had both datasets available. As part of a comprehensive genetic analysis, 853 genetic variants previously reported as ALS-linked mutations or disease-associated alleles were interrogated in sporadic ALS WGS data. Statistical analyses were performed to identify correlation between clinical variables, and between phenotype and the number of ALS-implicated variants carried by an individual. Relatedness between individuals carrying identical variants was assessed using identity-by-descent analysis. RESULTS: Forty-three ALS-implicated variants from 18 genes, including C9orf72, ATXN2, TARDBP, SOD1, SQSTM1 and SETX, were identified in Australian sporadic ALS cases. One-third of cases carried at least one variant and 6.82% carried two or more variants, implicating a potential oligogenic or polygenic basis of ALS. Relatedness was detected between two sporadic ALS cases carrying a SOD1 p.I114T mutation, and among three cases carrying a SQSTM1 p.K238E mutation. Oligogenic/polygenic sporadic ALS cases showed earlier age of onset than those with no reported variant. CONCLUSION: We confirm phenotypic associations among ALS cases, and highlight the contribution of genetic variation to all forms of ALS.