FAM81A is a postsynaptic protein that regulates the condensation of postsynaptic proteins via liquid-liquid phase separation.

Proteome analyses of the postsynaptic density (PSD), a proteinaceous specialization beneath the postsynaptic membrane of excitatory synapses, have identified several thousands of proteins. While proteins with predictable functions have been well studied, functionally uncharacterized proteins are mostly overlooked. In this study, we conducted a comprehensive meta-analysis of 35 PSD proteome datasets, encompassing a total of 5,869 proteins. Employing a ranking methodology, we identified 97 proteins that remain inadequately characterized. From this selection, we focused our detailed analysis on the highest-ranked protein, FAM81A. FAM81A interacts with PSD proteins, including PSD-95, SynGAP, and NMDA receptors, and promotes liquid-liquid phase separation of those proteins in cultured cells or in vitro. Down-regulation of FAM81A in cultured neurons causes a decrease in the size of PSD-95 puncta and the frequency of neuronal firing. Our findings suggest that FAM81A plays a crucial role in facilitating the interaction and assembly of proteins within the PSD, and its presence is important for maintaining normal synaptic function. Additionally, our methodology underscores the necessity for further characterization of numerous synaptic proteins that still lack comprehensive understanding.

The extracellular matrix supports breast cancer cell growth under amino acid starvation by promoting tyrosine catabolism.

Breast tumours are embedded in a collagen I-rich extracellular matrix (ECM) network, where nutrients are scarce due to limited blood flow and elevated tumour growth. Metabolic adaptation is required for cancer cells to endure these conditions. Here, we demonstrated that the presence of ECM supported the growth of invasive breast cancer cells, but not non-transformed mammary epithelial cells, under amino acid starvation, through a mechanism that required macropinocytosis-dependent ECM uptake. Importantly, we showed that this behaviour was acquired during carcinoma progression. ECM internalisation, followed by lysosomal degradation, contributed to the up-regulation of the intracellular levels of several amino acids, most notably tyrosine and phenylalanine. This resulted in elevated tyrosine catabolism on ECM under starvation, leading to increased fumarate levels, potentially feeding into the tricarboxylic acid (TCA) cycle. Interestingly, this pathway was required for ECM-dependent cell growth and invasive cell migration under amino acid starvation, as the knockdown of p-hydroxyphenylpyruvate hydroxylase-like protein (HPDL), the third enzyme of the pathway, opposed cell growth and motility on ECM in both 2D and 3D systems, without affecting cell proliferation on plastic. Finally, high HPDL expression correlated with poor prognosis in breast cancer patients. Collectively, our results highlight that the ECM in the tumour microenvironment (TME) represents an alternative source of nutrients to support cancer cell growth by regulating phenylalanine and tyrosine metabolism.

Retrospective evaluation of MRI findings in arthroscopically confirmed cases of hypermobile lateral meniscus.

OBJECTIVE: To identify preoperative MRI findings in patients with arthroscopically confirmed hypermobile lateral meniscus utilizing a standard MRI knee protocol, with comparison to normal control and lateral meniscal tear groups. SUBJECTS AND METHODS: All patients with arthroscopically confirmed hypermobile lateral meniscus diagnosed at our institution were retrospectively identified. The following structures were evaluated on preoperative knee MRIs: superior and inferior popliteomeniscal fascicles, lateral meniscus and meniscocapsular junction, popliteal hiatus, and soft tissue edema around the popliteal hiatus. The same MRI features were evaluated in the normal control and lateral meniscal tear groups. RESULTS: Study, normal control, and lateral meniscal tear patients (18 each) were included. In the study group, 94.4% had superior popliteomeniscal fascicle abnormality, 89.0% had inferior popliteomeniscal fascicle abnormality, and 72.2% had lateral meniscal abnormality. Incidence of these abnormalities was significantly higher than in the normal control group. Meniscal abnormalities in the study group all involved the posterior horn meniscocapsular junction, 12/13 of which had vertical signal abnormality at the junction and 1/13 with anterior subluxation of the entire posterior horn. Popliteus hiatus measurements were largest in the lateral meniscal tear group. CONCLUSION: In patients with hypermobile lateral meniscus, the combination of popliteomeniscal fascicle abnormality and vertical signal abnormality at the meniscocapsular junction was seen in the majority of patients. Popliteomeniscal fascicle signal abnormality without identifiable lateral meniscal injury was the next most common imaging appearance. Radiologists may provide valuable information by suggesting the diagnosis of hypermobile lateral meniscus in such cases.

Typhoid toxin hijacks Wnt5a to establish host senescence and Salmonella infection.

Damage to our genome causes acute senescence in mammalian cells, which undergo growth arrest and release a senescence-associated secretory phenotype (SASP) that propagates the stress response to bystander cells. Thus, acute senescence is a powerful tumor suppressor. Salmonella enterica hijacks senescence through its typhoid toxin, which usurps unidentified factors in the stress secretome of senescent cells to mediate intracellular infections. Here, transcriptomics of toxin-induced senescent cells (TxSCs) and proteomics of their secretome identify the factors as Wnt5a, INHBA, and GDF15. Wnt5a establishes a positive feedback loop, driving INHBA and GDF15 expression. In fibroblasts, Wnt5a and INHBA mediate autocrine senescence in TxSCs and paracrine senescence in naive cells. Wnt5a synergizes with GDF15 to increase Salmonella invasion. Intestinal TxSCs undergo apoptosis without Wnt5a, which is required for establishing intestinal TxSCs. The study reveals how an innate defense against cancer is co-opted by a bacterial pathogen to cause widespread damage and mediate infections.

Decision-making processes in image guided radiotherapy: A think aloud study.

INTRODUCTION: 3D Image Guided Radiotherapy (IGRT) using Cone Beam Computer Tomography (CBCT) has been implemented for a range of treatment sites across the UK in the last decade. A paucity of evidence exists to understand how radiation therapists (RTTs) make clinical decisions during image interpretation as part of the IGRT process. The aim of this study was to investigate the decision-making processes used by RTTs during image interpretation of IGRT. METHOD: Case study methodology was adopted utilising a think aloud observational method with follow-up interviews. 12 RTTs were observed and interviewed across three UK radiotherapy centres. Participants were observed reviewing and making clinical decisions in a simulated environment using clinical scenarios developed in partnership with each centres' Clinical Imaging Lead. Protocol analysis was used to analyse the observational data and thematic analysis was used to analyse the interview data. RESULTS: A range of approaches to decision-making was observed which varied in length from nine phrases to 57 (mean 24) per case. Six themes emerged from the data: Set Sequence, Site Specific Clinical Priorities, Initial Gross Review, Decision to treat, Compromise and experience. In addition, three cognitive decision-making processes were identified: Simple linear, Linear repeating and Intuitive decision-making process. The findings of the study align with general principles of expert performance, whereby experience in a specific scope of practice is more beneficial in developing expertise than overall experience. CONCLUSION: This study has provided new and original insight in the decision-making processes of RTTs. The study has highlighted three process models to explain how RTTs make decisions during IGRT: Simple linear, Linear repeating and Intuitive decision-making process. Intuitive processes are widely accepted to be error prone and linked to bias. When using this process, some RTTs followed this with a confirmation phase. This second phase of the process should be encouraged when teaching IGRT. The results of the study support the concept of expert performance, where performance and expertise are only improved by exposing individuals to specific types of experiences. RTTs, managers and Higher Education Institutions are encouraged to review these models and implement them into IGRT training. It is clear from the evidence base that understanding how we make decisions, enables us to develop expertise and reduce errors during the decision-making process.

Outcomes in patients with clinically suspected pedal osteomyelitis based on bone marrow signal pattern on MRI.

Objective: confluent T1 hypointense marrow signal is widely accepted to represent osteomyelitis on MRI. Some authors have suggested that non-confluent bone marrow signal abnormality should be considered early osteomyelitis. The purpose of this study was to address this issue by comparing the rate of osteomyelitis and amputation based on T1 marrow signal characteristics. Materials and methods: a total of 112 patients who underwent MRI of the foot for the evaluation of possible osteomyelitis were included. Patients were assigned to confluent T1 hypointense, reticulated T1 hypointense, and normal bone marrow signal groups. Results: patients with confluent T1 hypointense signal on MRI had significantly higher rates of osteomyelitis and amputation at 2 and 14 months post-MRI than the reticulated T1 hypointense group ( p < 0.001 ). Six patients had normal T1 signal, 16.7 % of whom had osteomyelitis and underwent amputation by 2 months post-MRI. Of 61 patients with reticulated T1 hypointense signal, 19.7 % had a diagnosis of osteomyelitis at 2 months post-MRI and 30.8 % had a diagnosis of osteomyelitis at 14 months post-MRI; moreover, 14.8 % and 31.5 % underwent amputation by 2 and 14 months post-MRI, respectively. Of 45 patients with confluent T1 hypointense signal, 73.3 % of patients had osteomyelitis at 2 months post-MRI and 82.5 % had osteomyelitis at 14 months post-MRI. In this group, 66.7 % underwent amputation by 2 months post-MRI and 77.8 % underwent amputation by 14 months post-MRI. Conclusions: over half of the patients with suspected pedal osteomyelitis who had reticulated or normal T1 bone marrow signal on MRI healed with conservative measures. Therefore, we recommend terminology such as "osteitis", "reactive osteitis", or "nonspecific reactive change" to describe bone marrow edema-like signal and reticulated hazy T1 hypointense signal without associated confluent T1 hypointensity. Moreover, we recommend that the MRI diagnosis of osteomyelitis is reserved for confluent T1 hypointense bone signal in the area of concern.

A Randomized Controlled Trial to Compare Immunogenicity to Cell-Based Versus Live-Attenuated Influenza Vaccines in Children.

BACKGROUND: Few studies have focused on the immune response to more recent influenza vaccine formulations such as cell-cultured inactivated influenza vaccine (ccIIV4) or live-attenuated influenza vaccine (LAIV4) in older children and young adults, or differences in immunoglobulin response using newer antibody landscape technology. METHODS: Participants ages 4-21 were randomized to receive ccIIV4 (n = 112) or LAIV4 (n = 118). A novel high-throughput multiplex influenza antibody detection assay was used to provide detailed IgG, IgA, and IgM antibody isotypes, along with hemagglutination inhibition levels (HAI), measured pre- and 28 days post-vaccination. RESULTS: The HAI and immunoglobulin isotype response to ccIIV4 was greater than LAIV4, with significant increases in IgG but not IgA or IgM. The youngest participants had the highest LAIV4 response. Prior LAIV4 vaccination was associated with a higher response to current season ccIIV4. Cross-reactive A/Delaware/55/2019(H1N1)pdm09 antibodies were present pre-vaccination and increased in response to ccIIV4, but not LAIV4. Immunoglobulin assays strongly correlated with and confirmed the findings of HAI titers to measure immune response. CONCLUSIONS: Age and prior season vaccination may play a role in the immune response in children and young adults to ccIIV4 and LAIV4. While immunoglobulin isotypes provide high-level antigen-specific information, HAI titers alone can provide a meaningful representation of day 28 post-vaccination response. CLINICAL TRIALS NO: NCT03982069.

Utility of preoperative MRI for assessing proximal fragment vascularity in scaphoid nonunion.

Aims: The benefit of MRI in the preoperative assessment of scaphoid proximal fragment vascularity remains controversial. The purpose of this study is to compare preoperative MRI findings to intraoperative bleeding of the proximal scaphoid. Methods: A retrospective review of 102 patients who underwent surgery for scaphoid nonunion between January 2000 and December 2020 at a single institution were identified. Inclusion criteria were: isolated scaphoid nonunion; preoperative MRI assessing the proximal fragment vascularity; and operative details of the vascularity of the proximal fragment with the tourniquet deflated. MRI results and intraoperative findings were dichotomized as either 'yes' or 'no' for the presence of vascularity. A four-fold contingency table was used to analyze the utility of preoperative MRI with 95% confidence intervals. Relative risk was calculated for subgroups to analyze the association between variables and MRI accuracy. Results: Preoperative MRI identified 55 proximal scaphoid fragments with ischaemia and 47 with vascularized proximal fragments. After the proximal fragment was prepared, the tourniquet was deflated and assessed for bleeding; 63 proximal fragments had no bleeding and 39 demonstrated bleeding. MRI was not reliable or accurate in the assessment of proximal fragment vascularity when compared with intraoperative assessment of bleeding. No patient or MRI factors were identified to have a statistical impact on MRI accuracy. Conclusion: Current preoperative MRI protocols and diagnostic criteria do not provide a high degree of correlation with observed intraoperative assessment of proximal fragment bleeding. While preoperative MRI may assist in surgical planning, intraoperative assessment remains the best means for assessing proximal fragment vascularity in scaphoid nonunion. Future efforts should focus on the development of objective measures of osseous blood flow that may be performed intraoperatively.

A potential histone-chaperone activity for the MIER1 histone deacetylase complex.

Histone deacetylases 1 and 2 (HDAC1/2) serve as the catalytic subunit of six distinct families of nuclear complexes. These complexes repress gene transcription through removing acetyl groups from lysine residues in histone tails. In addition to the deacetylase subunit, these complexes typically contain transcription factor and/or chromatin binding activities. The MIER:HDAC complex has hitherto been poorly characterized. Here, we show that MIER1 unexpectedly co-purifies with an H2A:H2B histone dimer. We show that MIER1 is also able to bind a complete histone octamer. Intriguingly, we found that a larger MIER1:HDAC1:BAHD1:C1QBP complex additionally co-purifies with an intact nucleosome on which H3K27 is either di- or tri-methylated. Together this suggests that the MIER1 complex acts downstream of PRC2 to expand regions of repressed chromatin and could potentially deposit histone octamer onto nucleosome-depleted regions of DNA.

Sec22b is a critical and nonredundant regulator of plasma cell maintenance.

Despite the essential role of plasma cells in health and disease, the cellular mechanisms controlling their survival and secretory capacity are still poorly understood. Here, we identified the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) Sec22b as a unique and critical regulator of plasma cell maintenance and function. In the absence of Sec22b, plasma cells were hardly detectable and serum antibody titers were dramatically reduced. Accordingly, Sec22b-deficient mice fail to mount a protective immune response. At the mechanistic level, we demonstrated that Sec22b contributes to efficient antibody secretion and is a central regulator of plasma cell maintenance through the regulation of their transcriptional identity and of the morphology of the endoplasmic reticulum and mitochondria. Altogether, our results unveil an essential and nonredundant role for Sec22b as a regulator of plasma cell fitness and of the humoral immune response.

Multimodality evaluation of transfascial muscle and other soft tissue herniations of the extremities.

This review illustrates the multimodality assessment of transfascial muscle and other soft tissue herniations of the extremities. Transfascial herniations of the extremities can develop from congenital or acquired disruptions of the deep fascia, resulting in herniation of the underlying muscle, nerve, or soft tissue tumor into the subcutaneous tissues. While most patients present with a painless subcutaneous nodule that may change in size with muscle activation, some may experience focal or diffuse extremity symptoms such as pain and paresthesias. Although the diagnosis may be clinically suspected, radiologic evaluation is useful for definitive diagnosis and characterization. Ultrasound is the preferred modality for initial workup through a focused and dynamic examination. Magnetic resonance imaging can be utilized for equivocal, complicated, and preoperative cases. Computed tomography is less useful in the evaluation of transfascial herniations in the extremities due to similarities in the attenuation between muscle and fascia, which can decrease the conspicuity of small defects.

Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication.

New therapeutic targets are a valuable resource for treatment of SARS-CoV-2 viral infection. Genome-wide association studies have identified risk loci associated with COVID-19, but many loci are associated with comorbidities and are not specific to host-virus interactions. Here, we identify and experimentally validate a link between reduced expression of EXOSC2 and reduced SARS-CoV-2 replication. EXOSC2 was one of the 332 host proteins examined, all of which interact directly with SARS-CoV-2 proteins. Aggregating COVID-19 genome-wide association studies statistics for gene-specific eQTLs revealed an association between increased expression of EXOSC2 and higher risk of clinical COVID-19. EXOSC2 interacts with Nsp8 which forms part of the viral RNA polymerase. EXOSC2 is a component of the RNA exosome, and here, LC-MS/MS analysis of protein pulldowns demonstrated interaction between the SARS-CoV-2 RNA polymerase and most of the human RNA exosome components. CRISPR/Cas9 introduction of nonsense mutations within EXOSC2 in Calu-3 cells reduced EXOSC2 protein expression and impeded SARS-CoV-2 replication without impacting cellular viability. Targeted depletion of EXOSC2 may be a safe and effective strategy to protect against clinical COVID-19.

Radiation therapist perceptions on how artificial intelligence may affect their role and practice.

INTRODUCTION: The use of artificial intelligence (AI) has increased in medical radiation science, with advanced computing and modelling. Considering radiation therapists (RTs) perceptions of how this may affect their role is imperative, as this will contribute to increasing the efficiency of implementation and improve service delivery. METHODS: A peer-reviewed anonymous survey was developed and completed by 105 RTs between April and June 2021. The online survey was distributed via the Medical Radiation Practice Board of Australia and the Australian Society of Medical Imaging and Radiation Therapy newsletter as well as professional networks. The survey gained perceptions of the impact of AI on radiation therapy practice and RTs roles within Australia, and data were analysed using quantitative data analysis and thematic analysis. RESULTS: Automation is used throughout radiation therapy practice, with 68% of RTs being optimistic about this. The majority (63%) had little to no knowledge of working with AI and 96% would like to learn more including the underpinnings of AI and its safe and ethical use. Many (66%) perceived AI would affect their role, including increasing their skillset and reducing mundane tasks, whereas others (23%) perceived it would reduce job satisfaction by increasing repetition and limiting their problem-solving ability. AI was perceived to impact the patient positively (67%), increasing efficiency and accuracy of radiotherapy treatments; however, it could depersonalise patient care. CONCLUSION: RTs perceive embracing AI in radiotherapy has the potential to advance the profession and improve the service to patients. If AI is implemented with sufficient training for greater understanding, and management uses these benefits to improve patient care, rather than replace RTs roles, then overall any negatives will be outweighed by the benefits.

Advantages of CT Versus MRI for Preoperative Assessment of Osteochondritis Dissecans of the Capitellum.

BACKGROUND: Magnetic resonance imaging (MRI) is considered to be the gold standard for imaging of osteochondritis dissecans (OCD). PURPOSE/HYPOTHESIS: The purpose was to determine the additional value of a preoperative computed tomography (CT) scan in adolescent patients with capitellar OCD of the elbow. Consistent with the fact that OCD is a lesion involving the subchondral bone, the hypothesis was that CT would be superior to MRI for imaging OCD of the capitellum. STUDY DESIGN: Cohort study (diagnosis); Level of evidence, 3. METHODS: All patients being treated surgically for an OCD of the capitellum between 2006 and 2016 at one institution were reviewed for preoperative imaging. A total of 28 patients met the inclusion criteria. Corresponding MRI and CT scans were compared retrospectively. Multiple parameters were recorded, with special emphasis on OCD lesion size, fragmentation, and tilt as well as joint surface integrity, loose bodies, and osteophytes. RESULTS: The OCD lesions were best seen on CT scans, whereas MRI T1-weighted images overestimated and T2-weighted images underestimated the size of defects. A subchondral fracture nonunion was found on CT scans in 18 patients, whereas this was seen on MRI T1-weighted images in only 2 patients (P < .001) and MRI T2-weighted images in 4 patients (P < .001). Fragmentation of the OCD fragment was found on CT scans in 17 patients but on MRI scans in only 9 patients (P = .05). Osteophytes as a sign of secondary degenerative changes were seen on CT scans in 24 patients and were seen on MRI scans in 15 patients (P = .02). Altogether, only 51 of 89 secondary changes including loose bodies, effects on the radial head and ulnohumeral joint, and osteophytes that were seen on CT scans were also seen on MRI scans (P = .002). CONCLUSION: OCD fragmentation and secondary changes were more often diagnosed on CT. These factors indicate OCD instability or advanced OCD stages, which are indications for surgery. In an adolescent who is considered at risk for OCD (baseball, gymnastics, weightlifting, tennis) and who has lateral elbow joint pain with axial or valgus load bearing, CT is our imaging modality of choice for diagnosing and staging OCD of the capitellum.

The EGFR/ErbB inhibitor neratinib modifies the neutrophil phosphoproteome and promotes apoptosis and clearance by airway macrophages.

Dysregulated neutrophilic inflammation can be highly destructive in chronic inflammatory diseases due to prolonged neutrophil lifespan and continual release of histotoxic mediators in inflamed tissues. Therapeutic induction of neutrophil apoptosis, an immunologically silent form of cell death, may be beneficial in these diseases, provided that the apoptotic neutrophils are efficiently cleared from the tissue. Previous research in our group identified ErbB inhibitors as able to induce neutrophil apoptosis and reduce neutrophilic inflammation both in vitro and in vivo. Here, we extend that work using a clinical ErbB inhibitor, neratinib, which has the potential to be repurposed in inflammatory diseases. We show that neratinib reduces neutrophilic migration o an inflammatory site in zebrafish larvae. Neratinib upregulates efferocytosis and reduces the number of persisting neutrophil corpses in mouse models of acute, but not chronic, lung injury, suggesting that the drug may have therapeutic benefits in acute inflammatory settings. Phosphoproteomic analysis of human neutrophils shows that neratinib modifies the phosphorylation of proteins regulating apoptosis, migration, and efferocytosis. This work identifies a potential mechanism for neratinib in treating acute lung inflammation by upregulating the clearance of dead neutrophils and, through examination of the neutrophil phosphoproteome, provides important insights into the mechanisms by which this may be occurring.

Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections.

B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise that increased ORF9b in B.1.1.7 is a direct consequence of a triple nucleotide mutation in nucleocapsid (28280:GAT > CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3' of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles to evaluate emerging potential variants of concern.

Traumatic rupture of the midportion of the interosseous membrane: a rare cause of acute lower leg pain in two soccer players kicked in the anterior shin.

The interosseous membrane (IOM) of the leg is a component of the tibiofibular syndesmosis that serves an important role in stabilization, as well as transferring forces to the fibula during weight-bearing. We present two separate cases of acute traumatic rupture of the midportion of the interosseous membrane in high school soccer players with blunt trauma to the anterior shin with MRI and ultrasound confirmation.

Developmental disruption to the cortical transcriptome and synaptosome in a model of SETD1A loss-of-function.

Large-scale genomic studies of schizophrenia implicate genes involved in the epigenetic regulation of transcription by histone methylation and genes encoding components of the synapse. However, the interactions between these pathways in conferring risk to psychiatric illness are unknown. Loss-of-function (LoF) mutations in the gene encoding histone methyltransferase, SETD1A, confer substantial risk to schizophrenia. Among several roles, SETD1A is thought to be involved in the development and function of neuronal circuits. Here, we employed a multi-omics approach to study the effects of heterozygous Setd1a LoF on gene expression and synaptic composition in mouse cortex across five developmental timepoints from embryonic day 14 to postnatal day 70. Using RNA sequencing, we observed that Setd1a LoF resulted in the consistent downregulation of genes enriched for mitochondrial pathways. This effect extended to the synaptosome, in which we found age-specific disruption to both mitochondrial and synaptic proteins. Using large-scale patient genomics data, we observed no enrichment for genetic association with schizophrenia within differentially expressed transcripts or proteins, suggesting they derive from a distinct mechanism of risk from that implicated by genomic studies. This study highlights biological pathways through which SETD1A LOF may confer risk to schizophrenia. Further work is required to determine whether the effects observed in this model reflect human pathology.

Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication.

New therapeutic targets are a valuable resource in the struggle to reduce the morbidity and mortality associated with the COVID-19 pandemic, caused by the SARS-CoV-2 virus. Genome-wide association studies (GWAS) have identified risk loci, but some loci are associated with co-morbidities and are not specific to host-virus interactions. Here, we identify and experimentally validate a link between reduced expression of EXOSC2 and reduced SARS-CoV-2 replication. EXOSC2 was one of 332 host proteins examined, all of which interact directly with SARS-CoV-2 proteins; EXOSC2 interacts with Nsp8 which forms part of the viral RNA polymerase. Lung-specific eQTLs were identified from GTEx (v7) for each of the 332 host proteins. Aggregating COVID-19 GWAS statistics for gene-specific eQTLs revealed an association between increased expression of EXOSC2 and higher risk of clinical COVID-19 which survived stringent multiple testing correction. EXOSC2 is a component of the RNA exosome and indeed, LC-MS/MS analysis of protein pulldowns demonstrated an interaction between the SARS-CoV-2 RNA polymerase and the majority of human RNA exosome components. CRISPR/Cas9 introduction of nonsense mutations within EXOSC2 in Calu-3 cells reduced EXOSC2 protein expression, impeded SARS-CoV-2 replication and upregulated oligoadenylate synthase ( OAS) genes, which have been linked to a successful immune response against SARS-CoV-2. Reduced EXOSC2 expression did not reduce cellular viability. OAS gene expression changes occurred independent of infection and in the absence of significant upregulation of other interferon-stimulated genes (ISGs). Targeted depletion or functional inhibition of EXOSC2 may be a safe and effective strategy to protect at-risk individuals against clinical COVID-19.

Transcriptional programs regulating neuronal differentiation are disrupted in DLG2 knockout human embryonic stem cells and enriched for schizophrenia and related disorders risk variants.

Coordinated programs of gene expression drive brain development. It is unclear which transcriptional programs, in which cell-types, are affected in neuropsychiatric disorders such as schizophrenia. Here we integrate human genetics with transcriptomic data from differentiation of human embryonic stem cells into cortical excitatory neurons. We identify transcriptional programs expressed during early neurogenesis in vitro and in human foetal cortex that are down-regulated in DLG2-/- lines. Down-regulation impacted neuronal differentiation and maturation, impairing migration, morphology and action potential generation. Genetic variation in these programs is associated with neuropsychiatric disorders and cognitive function, with associated variants predominantly concentrated in loss-of-function intolerant genes. Neurogenic programs also overlap schizophrenia GWAS enrichment previously identified in mature excitatory neurons, suggesting that pathways active during prenatal cortical development may also be associated with mature neuronal dysfunction. Our data from human embryonic stem cells, when combined with analysis of available foetal cortical gene expression data, de novo rare variants and GWAS statistics for neuropsychiatric disorders and cognition, reveal a convergence on transcriptional programs regulating excitatory cortical neurogenesis.