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Association of post-COVID phenotypic manifestations with new-onset psychiatric disease.
Get PDFAcute COVID-19 infection can be followed by diverse clinical manifestations referred to as Post Acute Sequelae of SARS-CoV2 Infection (PASC). Studies have shown an increased risk of being diagnosed with new-onset psychiatric disease following a diagnosis of acute COVID-19. However, it was unclear whether non-psychiatric PASC-associated manifestations (PASC-AMs) are associated with an increased risk of new-onset psychiatric disease following COVID-19. A retrospective electronic health record (EHR) cohort study of 2,391,006 individuals with acute COVID-19 was performed to evaluate whether non-psychiatric PASC-AMs are associated with new-onset psychiatric disease. Data were obtained from the National COVID Cohort Collaborative (N3C), which has EHR data from 76 clinical organizations. EHR codes were mapped to 151 non-psychiatric PASC-AMs recorded 28-120 days following SARS-CoV-2 diagnosis and before diagnosis of new-onset psychiatric disease. Association of newly diagnosed psychiatric disease with age, sex, race, pre-existing comorbidities, and PASC-AMs in seven categories was assessed by logistic regression. There were significant associations between a diagnosis of any psychiatric disease and five categories of PASC-AMs with odds ratios highest for neurological, cardiovascular, and constitutional PASC-AMs with odds ratios of 1.31, 1.29, and 1.23 respectively. Secondary analysis revealed that the proportions of 50 individual clinical features significantly differed between patients diagnosed with different psychiatric diseases. Our study provides evidence for association between non-psychiatric PASC-AMs and the incidence of newly diagnosed psychiatric disease. Significant associations were found for features related to multiple organ systems. This information could prove useful in understanding risk stratification for new-onset psychiatric disease following COVID-19. Prospective studies are needed to corroborate these findings
Monoallelic TTN Truncation Variants Identified in Individuals With DCM May Cause a Mild Skeletal Myopathy.
No full textImpact of environment on pediatric and adult brain tumors: The 2023 Brain Tumor Epidemiology Consortium meeting report.
No full textThe Brain Tumor Epidemiology Consortium (BTEC) is an international organization with membership of individuals from the scientific community with interests related to brain tumor epidemiology including surveillance, classification, methodology, etiology, and factors associated with morbidity and mortality. The 2023 annual BTEC meeting entitled Impact of Environment on Pediatric and Adult Brain Tumors was held in Lexington, KY, USA on May 22 - 24, 2023. The meeting gathered scientists from the United States, Canada, Australia, and Europe and included four keynote sessions covering genomic, epigenomic, and metabolomic considerations in brain tumor epidemiology, cancer clusters, environmental risk factors, and new approaches to cancer investigation. The meeting also included three abstract sessions and a brainstorming session. A summary of the meeting content is included in this report
Syntactic Grooming Classification in Mice with Computer Vision
No full textBehavior analysis is a challenging yet elucidating part of disease research. Specifically behaviors such as grooming, which models many stereotyped, repetitive, or comforting behaviors in humans, can provide much insight when studying models of psychiatric disease in mice – Autism Spectrum Disorder or Obsessive Compulsive Behavior for example. However, grooming is only a broad behavior label for a set of more intricate grooming types, or syntaxes. It has been observed that these grooming syntaxes are typically linked together in certain orders to form syntactic chains. A mouse’s inclination to follow said syntactic chains or lack thereof can be especially elucidating, as it can tell us alot about the physical and psychiatric state of the animal, as well as if it may be affected by environmental conditions such as stress. The challenge with using this behavior remains that these syntaxes are difficult and inefficient to manually annotate. This limits the duration and setting in which these metrics can be analyzed. Here, we provide an automated solution using computer vision to classify grooming syntaxes and identify syntactic chains across a wide variety of mice strains. Our multiclass classifier provides an efficient way of processing high-throughput data, enabling more comprehensive interventional studies concerning diseases with related behavioral phenotypes. We compare syntax distributions across a strain-survey containing 62 distinct mouse strains. Further, we apply the field’s standard protocol to investigate mice’s inclination towards a pre-defined syntactic chain, and discover that the established chain definitions fail to account for the vast majority of grooming bouts
Identifying Genetic Modifiers of Epilepsy Resilience and Susceptibility
No full textEpilepsy is a family of diseases characterized by hyper-synchronized brain activity resulting in seizures. Most epilepsy is polygenic, meaning it is caused by several genetic and environmental factors. Due to the large amount of genetic variation between individuals with polygenic epilepsy, it is difficult to understand the underlying mechanisms of epilepsy risk and resilience. In contrast to human studies, mouse studies on epilepsy allow experimental induction of epilepsy to map genetic factors driving resilience. Meta- analysis of multiple genome-wide association studies (GWAS) further allows for the identification of single nucleotide polymorphisms (SNPs) that affect epilepsy prevalence and seizure severity across many such studies, and hence general mechanisms of risk and resilience. In this study, we conduct a GWAS meta-analysis on a collection of mouse studies, a network-based functional prediction of genes involved in epilepsy, and Genomic Evolutionary Rate Profiling (GERP) conservational analysis to identify the genes responsible for differential epilepsy phenotypes in our studied mouse populations. [Bl We discovered that 5 genes Tenm4, Dtna, /gsf21, Cadps2, and ltpk1 have mutations within highly conserved transcription factor binding motifs. These mutations are predicted to result in a significantly lower predicted transcription factor binding affinity, and thus a predicted decrease in gene expression. These genes are involved in neural development and decreased ability to adapt to adverse stimuli, providing insights into potential therapeutic targets
Activity-dependent transcriptional programs in memory regulate motor recovery after stroke.
Get PDFStroke causes death of brain tissue leading to long-term deficits. Behavioral evidence from neurorehabilitative therapies suggest learning-induced neuroplasticity can lead to beneficial outcomes. However, molecular and cellular mechanisms that link learning and stroke recovery are unknown. We show that in a mouse model of stroke, which exhibits enhanced recovery of function due to genetic perturbations of learning and memory genes, animals display activity-dependent transcriptional programs that are normally active during formation or storage of new memories. The expression of neuronal activity-dependent genes are predictive of recovery and occupy a molecular latent space unique to motor recovery. With motor recovery, networks of activity-dependent genes are co-expressed with their transcription factor targets forming gene regulatory networks that support activity-dependent transcription, that are normally diminished after stroke. Neuronal activity-dependent changes at the circuit level are influenced by interactions with microglia. At the molecular level, we show that enrichment of activity-dependent programs in neurons lead to transcriptional changes in microglia where they differentially interact to support intercellular signaling pathways for axon guidance, growth and synaptogenesis. Together, these studies identify activity-dependent transcriptional programs as a fundamental mechanism for neural repair post-stroke
Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants.
Get PDFThe diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement
B cells in perivascular and peribronchiolar granuloma-associated lymphoid tissue and B-cell signatures identify asymptomatic
Get PDFBecause most humans resist Mycobacterium tuberculosis infection, there is a paucity of lung samples to study. To address this gap, we infected Diversity Outbred mice with M. tuberculosis and studied the lungs of mice in different disease states. After a low-dose aerosol infection, progressors succumbed to acute, inflammatory lung disease within 60 days, while controllers maintained asymptomatic infection for at least 60 days, and then developed chronic pulmonary tuberculosis (TB) lasting months to more than 1 year. Here, we identified features of asymptomatic M. tuberculosis infection by applying computational and statistical approaches to multimodal data sets. Cytokines and anti-M. tuberculosis cell wall antibodies discriminated progressors vs controllers with chronic pulmonary TB but could not classify mice with asymptomatic infection. However, a novel deep-learning neural network trained on lung granuloma images was able to accurately classify asymptomatically infected lungs vs acute pulmonary TB in progressors vs chronic pulmonary TB in controllers, and discrimination was based on perivascular and peribronchiolar lymphocytes. Because the discriminatory lesion was rich in lymphocytes and CD4 T cell-mediated immunity is required for resistance, we expected CD4 T-cell genes would be elevated in asymptomatic infection. However, the significantly different, highly expressed genes were from B-cell pathways (e.g., Bank1, Cd19, Cd79, Fcmr, Ms4a1, Pax5, and H2-Ob), and CD20+ B cells were enriched in the perivascular and peribronchiolar regions of mice with asymptomatic M. tuberculosis infection. Together, these results indicate that genetically controlled B-cell responses are important for establishing asymptomatic M. tuberculosis lung infection
Transcription factor AP-2 gamma affects porcine early embryo development by regulating epigenetic modification.
Get PDFRESEARCH QUESTION: What is the role and mechanism of action of transcription factor AP-2 gamma (TFAP2C) in porcine early embryo development?
DESIGN: TFAP2C siRNA were injected into porcine oocytes, which subsequently underwent IVF. Different stages of embryos were collected for RNA sequencing, quantitative polymerase chain reaction, immunofluorescence staining to explore the affects in gene expression and epigenetic modification. Porcine fetal fibroblasts were transfected with siRNA, and cells were collected for chromatin immunoprecipitation and dual luciferase reporter assays.
RESULTS: The deficiency of TFAP2C led to disorders in early embryonic development; 1208 genes were downregulated and 792 genes were upregulated in TFAP2C knockdown (TFAP2C-KD) embryos. The expression of epigenetic modification enzymes KDM5B, SETD2 were significantly elevated in the TFAP2C-KD group (P \u3c 0.001). Meanwhile, the modification levels of H3K4me3 and H3K4me2 were significantly decreased (P = 0.0021, P = 0.0029), and H3K36me3 and DNA methylation were significantly increased in TFAP2C-KD group (P = 0.0045, P = 0.0025). DNMT1 was mainly expressed in nuclei in the TFAP2C-KD group (P = 0.0103). In addition, TFAP2C could bind to the promoter region of SETD2, and the mutation of the TFAP2C binding site resulted in increased activity of SETD2 promoter (P \u3c 0.001).
CONCLUSIONS: The knockdown of TFAP2C affects early embryonic development by regulating histone modification and DNA methylation
Examining Intercage Transmission of
No full textChlamydia muridarum (Cm) has reemerged as a prevalent bacterial contaminant of academic research mouse colonies. A study was conducted to assess the effectiveness of husbandry and cage sanitization methods in preventing intercage transmission of Cm. To assess intercage transmission during cage change, a cage housing 2 Cm-free Swiss Webster (SW; Tac:SW) sentinel mice was placed randomly on each of 12 individually ventilated cage racks, housing cages with Cm-shedding mice, located in one of 2 animal holding rooms. Husbandry staff blinded to the study cages changed all cages in the animal holding rooms weekly using a microisolation cage technique. PCR testing performed at 180 d postplacement confirmed all mice remained negative for Cm. To assess the effectiveness of cage sanitization to eliminate Cm, we investigated transmission of Cm to a naive Cm-free SW and NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mouse cohoused for 7 d (repeated weekly for 4 wk) in cages assigned to one of 3 groups (n = 10 pairs of mice/group). Cages that previously housed 2 Cm-shedding BALB/c mice were either washed in a tunnel washer (82.2 °C [180 °F] final rinse for an average of 16 s per run; n = 10) with and without postwashing autoclaving (121 °C for 20 min; n = 10), or were untreated (bedding change only; n = 10). Pre- and postsanitization swabs of each cage were assayed for Cm by PCR. All pretreatment swabs tested positive, while posttreatment swabs from all cages (excluding bedding change) tested negative. All SW and NSG mice, irrespective of group, remained negative for Cm as determined by PCR. These findings suggest that infectious Cm does not persist in untreated cages or after mechanical washing with and without autoclaving. Collectively, these findings suggest that neither our husbandry protocols nor inadequate cage sanitization methods likely contributed to the observed prevalence of Cm in contemporary research mouse colonies