The proteomic landscape of genotoxic stress-induced micronuclei

Micronuclei (MN) are induced by various genotoxic stressors and amass nuclear- and cytoplasmic-resident proteins, priming the cell for MN-driven signaling cascades. Here, we measured the proteome of micronuclear, cytoplasmic, and nuclear fractions from human cells exposed to a panel of six genotoxins, comprehensively profiling their MN protein landscape. We find that MN assemble a proteome distinct from both surrounding cytoplasm and parental nuclei, depleted of spliceosome and DNA damage repair components while enriched for a subset of the replisome. We show that the depletion of splicing machinery within transcriptionally active MN contributes to intra-MN DNA damage, a known precursor to chromothripsis. The presence of transcription machinery in MN is stress-dependent, causing a contextual induction of MN DNA damage through spliceosome deficiency. This dataset represents a unique resource detailing the global proteome of MN, guiding mechanistic studies of MN generation and MN-associated outcomes of genotoxic stress.

The Essential Role of Proteoglycans and Glycosaminoglycans in Odontogenesis

Tooth development and regeneration are regulated through a complex signaling network. Previous studies have focused on the exploration of intracellular signaling regulatory networks, but the regulatory roles of extracellular networks have only been revealed recently. Proteoglycans, which are essential components of the extracellular matrix (ECM) and pivotal signaling molecules, are extensively involved in the process of odontogenesis. Proteoglycans are composed of core proteins and covalently attached glycosaminoglycan chains (GAGs). The core proteins exhibit spatiotemporal expression patterns during odontogenesis and are pivotal for dental tissue formation and periodontium development. Knockout of core protein genes Biglycan, Decorin, Perlecan, and Fibromodulin has been shown to result in structural defects in enamel and dentin mineralization. They are also closely involved in the development and homeostasis of periodontium by regulating signaling transduction. As the functional component of proteoglycans, GAGs are negatively charged unbranched polysaccharides that consist of repeating disaccharides with various sulfation groups; they provide binding sites for cytokines and growth factors in regulating various cellular processes. In mice, GAG deficiency in dental epithelium leads to the reinitiation of tooth germ development and the formation of supernumerary incisors. Furthermore, GAGs are critical for the differentiation of dental stem cells. Inhibition of GAGs assembly hinders the differentiation of ameloblasts and odontoblasts. In summary, core proteins and GAGs are expressed distinctly and exert different functions at various stages of odontogenesis. Given their unique contributions in odontogenesis, this review summarizes the roles of proteoglycans and GAGs throughout the process of odontogenesis to provide a comprehensive understanding of tooth development.

Investigating adverse genomic and regulatory changes caused by replacement of the full-length CFTR cDNA using Cas9 and AAV

A "universal strategy" replacing the full-length CFTR cDNA may treat >99% of people with cystic fibrosis (pwCF), regardless of their specific mutations. Cas9-based gene editing was used to insert the CFTR cDNA and a truncated CD19 (tCD19) enrichment tag at the CFTR locus in airway basal stem cells. This strategy restores CFTR function to non-CF levels. Here, we investigate the safety of this approach by assessing genomic and regulatory changes after CFTR cDNA insertion. Safety was first assessed by quantifying genetic rearrangements using CAST-seq. After validating restored CFTR function in edited and enriched airway cells, the CFTR locus open chromatin profile was characterized using ATAC-seq. The regenerative potential and differential gene expression in edited cells was assessed using scRNA-seq. CAST-seq revealed a translocation in ∼0.01% of alleles primarily occurring at a nononcogenic off-target site and large indels in 1% of alleles. The open chromatin profile of differentiated airway epithelial cells showed no appreciable changes, except in the region corresponding to the CFTR cDNA and tCD19 cassette, indicating no detectable changes in gene regulation. Edited stem cells produced the same types of airway cells as controls with minimal alternations in gene expression. Overall, the universal strategy showed minor undesirable genomic changes.

The characteristics of pre-existing humoral imprint determine efficacy of S. aureus vaccines and support alternative vaccine approaches

The failure of the Staphylococcus aureus (SA) IsdB vaccine trial can be explained by the recall of non-protective immune imprints from prior SA exposure. Here, we investigate natural human SA humoral imprints to understand their broader impact on SA immunizations. We show that antibody responses against SA cell-wall-associated antigens (CWAs) are non-opsonic, while antibodies against SA toxins are neutralizing. Importantly, the protective characteristics of the antibody imprints accurately predict the failure of corresponding vaccines against CWAs and support vaccination against toxins. In passive immunization platforms, natural anti-SA human antibodies reduce the efficacy of the human monoclonal antibodies suvratoxumab and tefibazumab, consistent with the results of their respective clinical trials. Strikingly, in the absence of specific humoral memory responses, active immunizations are efficacious in both naive and SA-experienced mice. Overall, our study points to a practical and predictive approach to evaluate and develop SA vaccines based on pre-existing humoral imprint characteristics.

Single Cell Transcriptomes, Lineage, and Differentiation of Functional Airway Microfold Cells

The airway epithelium is frequently exposed to pathogens and allergens, but the cells that are responsible for sampling these inhaled environmental agents have not been fully defined. Thus, there is a critical void in our understanding of how luminal antigens are delivered to the immune cells that drive the appropriate immune defenses against environmental assaults. In this study, we report the first single cell transcriptomes of airway Microfold (M) cells, whose gut counterparts have long been known for their antigen sampling abilities. Given their very recent discovery in the lower respiratory airways, the mechanisms governing the differentiation and functions of airway M cells are largely unknown. Here, we shed light on the pathways of airway M cell differentiation, establish their lineage, and identify a functional M cell-specific endocytic receptor, the complement receptor 2 (CR2). Lastly, we demonstrate that airway M cells can endocytose Aspergillus fumigatus conidia in a CR2-dependent manner. Collectively, this work lays a foundation for deepening our understanding of lung mucosal immunology and the mechanisms that drive lung immunity and tolerance.

Molecular Evidence for Olfactory Neuroblastoma as a Tumor of Malignant Globose Basal Cells

Olfactory neuroblastoma (ONB, esthesioneuroblastoma) is a sinonasal cancer with an underdeveloped diagnostic toolkit, and is the subject of many incidents of tumor misclassification throughout the literature. Despite its name, connections between the cancer and normal cells of the olfactory epithelium have not been systematically explored and markers of olfactory epithelial cell types are not deployed in clinical practice. Here, we utilize an integrated human-mouse single-cell atlas of the nasal mucosa, including the olfactory epithelium, to identify transcriptomic programs that link ONB to a specific population of stem/progenitor cells known as olfactory epithelial globose basal cells (GBCs). Expression of a GBC transcription factor NEUROD1 distinguishes both low- and high-grade ONB from sinonasal undifferentiated carcinoma, a potential histologic mimic with a distinctly unfavorable prognosis. Furthermore, we identify a reproducible subpopulation of highly proliferative ONB cells expressing the GBC stemness marker EZH2, suggesting that EZH2 inhibition may play a role in the targeted treatment of ONB. Finally, we study the cellular states comprising ONB parenchyma using single-cell transcriptomics and identify evidence of a conserved GBC transcriptional regulatory circuit that governs divergent neuronal-versus-sustentacular differentiation. These results link ONB to a specific cell type for the first time and identify conserved developmental pathways within ONB that inform diagnostic, prognostic, and mechanistic investigation.

Longitudinal associations between alcohol use, smoking, genetic risk scoring and symptoms of depression in the general population: a prospective 6-year cohort study

BACKGROUND

Alcohol consumption, smoking and mood disorders are leading contributors to the global burden of disease and are highly comorbid. Yet, their interrelationships have remained elusive. The aim of this study was to examine the multi-cross-sectional and longitudinal associations between (change in) smoking and alcohol use and (change in) number of depressive symptoms.

METHODS

In this prospective, longitudinal study, 6646 adults from the general population were included with follow-up measurements after 3 and 6 years. Linear mixed-effects models were used to test multi-cross-sectional and longitudinal associations, with smoking behaviour, alcohol use and genetic risk scores for smoking and alcohol use as independent variables and depressive symptoms as dependent variables.

RESULTS

In the multi-cross-sectional analysis, smoking status and number of cigarettes per day were positively associated with depressive symptoms (p < 0.001). Moderate drinking was associated with less symptoms of depression compared to non-use (p = 0.011). Longitudinally, decreases in the numbers of cigarettes per day and alcoholic drinks per week as well as alcohol cessation were associated with a reduction of depressive symptoms (p = 0.001-0.028). Results of genetic risk score analyses aligned with these findings.

CONCLUSIONS

While cross-sectionally smoking and moderate alcohol use show opposing associations with depressive symptoms, decreases in smoking behaviour as well as alcohol consumption are associated with improvements in depressive symptoms over time. Although we cannot infer causality, these results open avenues to further investigate interventions targeting smoking and alcohol behaviours in people suffering from depressive symptoms.

Comparative transcriptomic analysis reveals candidate genes for seasonal breeding in the male Lion-Head goose

1. Due to seasonal breeding, geese breeds from Southern China have low egg yield. The genetic makeup underlying performance of local breeds is largely unknown, and few studies have investigated this problem. This study integrated 21 newly generated and 50 publicly existing RNA-seq libraries, representing the hypothalamus, pituitary and testis, to identify candidate genes and importantly related pathways associated with seasonal breeding in male Lion-Head geese.2. In total, 19, 119 and 302 differentially expressed genes (DEGs) were detected in the hypothalamus, pituitary and testis, respectively, of male Lion-Head geese between non-breeding and breeding periods. These genes were significantly involved in the neuropeptide signalling pathway, gland development, neuroactive ligand-receptor interaction, JAK-STAT signalling pathway, cAMP signalling pathway, PI3K-Akt signalling pathway and Foxo signalling pathway.3. By integrating another 50 RNA-seq samples 4, 18 and 40 promising DEGs were confirmed in hypothalamus, pituitary and testis, respectively.4. HOX genes were identified as having important roles in the development of testis between non-breeding and breeding periods of male Lion-Head geese.

Correlation study between apparent diffusion coefficients and the prognostic factors in breast cancer

AIM

To analyse the correlation between apparent diffusion coefficients (ADC) derived from intratumoural and peritumoural regions with prognostic factors and immune-inflammatory markers in breast cancer (BC).

MATERIALS AND METHODS

In this retrospective study, 89 patients (age range, 28-66 years; median, 45 years) with a diagnosis of invasive BC who underwent routine blood tests and multiparametric magnetic resonance imaging (MRI) were enrolled. The study cohort was stratified according to tumour maximum cross-section ≥20 mm, lymph node metastasis (LNM), time-signal intensity curve (TIC) type, and receptor status. Minimum, maximum, mean, and heterogeneity values of tumour ADC (ADC_tmin, ADC_tmax, ADC_tmean, and ADC_heter), maximum values of peritumoural ADC (ADC_pmax), and the ratio of peritumoural-tumour ADC (ADC_ratio) were obtained on the ADC maps. Linear regression analyses were performed to investigate the correlation between immune-inflammatory markers, prognostic factors and ADC values.

RESULTS

HER-2 was positively associated with ADC_tmax, ADC_tmean, and ADC_pmax values (β = 0.306, p=0.004; β = 0.283, p=0.007; β = 0.262, p=0.007, respectively), while platelet-to-lymphocyte ratio (PLR) was positively associated with ADC_pmax and ADC_ratio values (β = 0.227, p=0.020; β = 0.231, p=0.020, respectively). Among ADC parameters, ADC_pmax showed the highest predictive values for evaluating the presence of LNM (AUC, 0.751; sensitivity, 70.4%; specificity, 77.1%).

CONCLUSION

The ADC_pmax value could provide additional assistance in predicting prognostic factors of BC.

[Analysis of the usage of post-exposure prophylaxis and related factors among men who have sex with men]

A survey was conduct to analyze the usage situation of post-exposure prophylaxis(PEP) and related factors among men who have sex with men(MSM) in 6 cities of Shandong Province. Total of 2 620 subjects, the use ratio was 2.98% (78/2 620). Compared with age≤24 years,monthly income<5 000 yuan,non-commercial sex, non-DU,non-STD,role for being insert in the anal intercourse,MSM was more likely to use PEP with age≥45 years(OR=3.87, 95%CI:1.12-13.36),monthly income≥5 000 yuan(OR=1.87, 95%CI:1.07-3.28),commercial sex (OR=3.13, 95%CI:1.56-6.28), drug users (DUs) (OR=4.63, 95%CI:2.51-8.52),STD patient (OR=2.35,95%CI:1.05-5.27),the mixed sex role group(OR=2.25,95%CI:1.10-4.62).

Structural, functional, and immunogenicity implications of F9 gene recoding

Hemophilia B is a blood clotting disorder caused by deficient activity of coagulation factor IX (FIX). Multiple recombinant FIX proteins are currently approved to treat hemophilia B, and several gene therapy products are currently being developed. Codon optimization is a frequently used technique in the pharmaceutical industry to improve recombinant protein expression by recoding a coding sequence using multiple synonymous codon substitutions. The underlying assumption of this gene recoding is that synonymous substitutions do not alter protein characteristics because the primary sequence of the protein remains unchanged. However, a critical body of evidence shows that synonymous variants can affect cotranslational folding and protein function. Gene recoding could potentially alter the structure, function, and in vivo immunogenicity of recoded therapeutic proteins. Here, we evaluated multiple recoded variants of F9 designed to further explore the effects of codon usage bias on protein properties. The detailed evaluation of these constructs showed altered conformations, and assessment of translation kinetics by ribosome profiling revealed differences in local translation kinetics. Assessment of wild-type and recoded constructs using a major histocompatibility complex (MHC)-associated peptide proteomics assay showed distinct presentation of FIX-derived peptides bound to MHC class II molecules, suggesting that despite identical amino acid sequence, recoded proteins could exhibit different immunogenicity risks. Posttranslational modification analysis indicated that overexpression from gene recoding results in suboptimal posttranslational processing. Overall, our results highlight potential functional and immunogenicity concerns associated with gene-recoded F9 products. These findings have general applicability and implications for other gene-recoded recombinant proteins.

[Long-term observation of the effect of atlantoaxial fusion on the growth and development of children's cervical spine]

Objective: To explore the effect of atlantoaxial fusion on the growth and development of children's cervical spine. Methods: The clinical data of 12 children with atlantoaxial dislocation who underwent posterior atlantoaxial fusion at Department of Orthopaedics,the 909th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army from June 2002 to September 2013 were retrospective analyzed. There were 7 males and 5 females,with age of (8.1±3.1)years (range:3 to 13 years).Nine cases were traumatic and 3 cases were congenital malformations,1 of the children had Down syndrome. All children underwent posterior atlantoaxial fusion. Furthermore,the information of the height and anteroposterior width of the cervical vertebral bodies and vertical growth rate of the fusion mass were collected from all patients immediately postoperatively and during the follow-up.The range of motion in cervical spine were collected preoperatively and during follow-up period. Data were compared using independent sample t test, paired sample t test and repeated-measurement. Results: All 12 children had regular follow-up within (122.4±25.3)months(range:65 to 163 months). The height and anteroposterior width of the cervical vertebral bodies were similar to these results with those in published reports of growth in normal children of the same age(all P<0.01). At the last follow-up,atlantoaxial fusion of 11 cases had substantial growth (vertical growth rate of the fusion mass:11 cases ≥10%, 1 case <10%);the range of motion in cervical spine was close to the normal level (flexion(55.2±5.0)°,extension (65.3±4.9)°,left bending (41.7±4.5)°,right bending (42.4±4.4)°,left rotation (66.4±5.6)°,right rotation (68.5±5.8)°). Conclusions: Atlantoaxial fusion surgery is satisfactory in the treatment of pediatric atlantoaxial dislocation.During the follow-up,the growth and development of the cervical spine is close to that of normal children of the same age.In long-term observation,it has been found that the operation has no negative effect on the growth and development of the children's cervical spine.

Integrated age-related immunohistological changes occur in human olfactory epithelium and olfactory bulb

Olfactory epithelium (OE) is capable of lifelong regeneration due to presence of basal progenitor cells that respond to injury or neuronal loss with increased activity. However, this capability diminishes with advancing age and a decrease in odor perception in older individuals is well established. To characterize changes associated with age in the peripheral olfactory system, an in-depth analysis of the OE and its neuronal projections onto the olfactory bulb (OB) as a function of age was performed. Human olfactory tissue autopsy samples from 36 subjects with an average age of 74.1 years were analyzed. Established cell type-specific antibodies were used to identify OE component cells in whole mucosal sheets and epithelial sections as well as glomeruli and periglomerular structures in OB sections. With age, a reduction in OE area occurs across the mucosa progressing in a posterior-dorsal direction. Deterioration of the olfactory system is accompanied with diminution of neuron-containing OE, mature olfactory sensory neurons (OSNs) and OB innervation. On an individual level, the neuronal density within the epithelium appears to predict synapse density within the OB. The innervation of the OB is uneven with higher density at the ventral half that decreases with age as opposed to stable innervation at the dorsal half. Respiratory metaplasia, submucosal cysts, and neuromata, were commonly identified in aged OE. The finding of respiratory metaplasia and aneuronal epithelium with reduction in global basal cells suggests a progression of stem cell quiescence as an underlying pathophysiology of age-related smell loss in humans. KEY POINTS: A gradual loss of olfactory sensory neurons with age in human olfactory epithelium is also reflected in a reduction in glomeruli within the olfactory bulb. This gradual loss of neurons and synaptic connections with age occurs in a specific, spatially inhomogeneous manner. Decreasing mitotically active olfactory epithelium basal cells may contribute to age-related neuronal decline and smell loss in humans.

New management unit for conservation of the Endangered green turtle Chelonia mydas at the Xisha (Paracel) Islands, South China Sea

The Qilianyu cluster of the Xisha (Paracel) Islands has one of the few remaining green turtle Chelonia mydas rookeries in the China region. Genetic samples were obtained from dead green turtle embryos and hatchlings salvaged from post-hatched nests at Middle Island (n = 3), North Island (n = 9) and South Sand (n = 1) of the Qilianyu cluster in 2017-2019. The ~800 bp mitochondrial DNA control region was sequenced from the samples, and 5 haplotypes were identified belonging to 2 documented clades (clades III and VIII), including 2 new haplotypes (CmP243.1 and CmP244.1) and 3 previously reported haplotypes (CmP18.1, CmP19.1, CmP20.1). These results were combined with previously published mtDNA data for the Qilianyu cluster and nearby (~93 km) Yongle Islands indicating a lack of differentiation based on truncated 384 bp control region sequences (exact test, p = 0.0997; FST = 0.015, p = 0.2760), to represent a single Xisha Islands rookery. The rookery at the Xisha Islands was significantly differentiated (p < 0.01) from all 19 management units (MUs) documented in the Indo-Pacific and Japan regions, supporting recognition of the Xisha Islands rookery as a new independent MU. The results will help inform national and international conservation action plans by China and the countries around the South China Sea to protect green turtles in the West Pacific Ocean.

Cystic Fibrosis and the Cells of the Airway Epithelium: What Are Ionocytes and What Do They Do?

Cystic fibrosis (CF) is caused by defects in an anion channel, the cystic fibrosis transmembrane conductance regulator (CFTR). Recently, a new airway epithelial cell type has been discovered and dubbed the pulmonary ionocyte. Unexpectedly, these ionocytes express higher levels of CFTR than any other airway epithelial cell type. However, ionocytes are not the sole CFTR-expressing airway epithelial cells, and CF-associated disease genes are in fact expressed in multiple airway epithelial cell types. The experimental depletion of ionocytes perturbs epithelial physiology in the mouse trachea, but the role of these rare cells in the pathogenesis of human CF remains mysterious. Ionocytes have been described in diverse tissues(kidney and inner ear) and species (frog and fish). We draw on these prior studies to suggest potential roles of airway ionocytes in health and disease. A complete understanding of ionocytes in the mammalian airway will ultimately depend on cell type-specific genetic manipulation.

The association between diabetes and mortality in young adults presenting with myocardial infarction

Background

The incidence of diabetes mellitus and coronary artery disease continue to rise and collectively comprise two of the most prevalent and costly diseases worldwide. The goal of this study is to report the prognosis of young patients with diabetes presented with acute myocardial infarction (AMI).

Methods

This is a retrospective observational cohort study that included consecutive patients aged 18–45 years who underwent cardiac catheterization for AMI between 2006 and 2016 in an integrated healthcare system in Southern California. The prognosis of patients with diabetes were compared to those without diabetes.

Results

A total of 1,560 patients (average age 40.2±5.3 years, 25.6% female) presenting with AMI were included. Of these 272 (17.4%) had diabetes. Diabetics were older (41.1±4.4 vs 40.0±5.4 years), more likely to be female (32.4% vs 24.1%, p=0.006), Hispanic (51.5% vs 40.5%, p&lt;0.001), have a higher body mass index (BMI) (33.6±7.1 vs 31.2±6.8kg/m2, p&lt;0.001), have hypertension (HTN) (67.6% vs 23.8%, p&lt;0.001), hyperlipidemia (HLD) (78.3% vs 24.1%, p&lt;0.001), peripheral vascular disease (9.9% vs 1.9%, p&lt;0.001), chronic kidney disease (CKD) (23.2% vs 2.7%, p&lt;0.001), hypothyroidism (7% vs 4%, p=0.034), and prior strokes (4.4% vs 2.2%, p=0.034).

On multivariate analysis accounting for other cardiovascular risk factors, the association remained significant (OR 1.82, 95% CI 1.04–3.19, p=0.036). At a median follow-up of 5.8 years (interquartile range 3.7–8.7 years), diabetes was independently associated with increased all-cause mortality (Hazard ratio [HR] 3.10, 95% CI 1.68–5.69, p&lt;0.001) when adjusting for age, sex, race, BMI, HTN, HLD, CKD, hypothyroidism, prior stroke, and ACS etiology. In a propensity score matched cohort, diabetes remained significantly associated with all-cause mortality (HR 5.29, 95% CI 2.34–12.02, p&lt;0.001).

Conclusion

Diabetes is an independent predictor of increased mortality in young adults &lt;45 years old presenting with AMI.

Funding Acknowledgement

Type of funding sources: Private hospital(s). Main funding source(s): KAISER PERMANENTE LOS ANGELES MEDICAL CENTER

The temporal analysis of elite breaststroke swimming during competition

Breaststroke is the only competitive stroke characterised by propulsive discontinuity. It is consequently paramount that swimmers optimally coordinate limb movements in order to maintain the highest average velocity possible. The present study aimed to investigate the temporal patterns of elite breaststroke swimmers. 50 m long-course competition footage of (1) 20 male 100 m races, (2) 24 female 100 m races, (3) 15 male 200 m races, and (4) 27 female 200 m races from 2018 to 2020 were digitised and analysed. Six points within each stroke cycle were identified and used to calculate 15 temporal parameters. Analyses revealed multiple temporal pattern differences between groups based on sex and race distance. It is recommended that coaches individualise swimmers' breaststroke temporal patterns based on individual needs, strengths, and morphological characteristics.

Atmospheric Carbon and Transport - America (ACT-America) Data Sets: Description, Management, and Delivery

The ACT-America project is a NASA Earth Venture Suborbital-2 mission designed to study the transport and fluxes of greenhouse gases. The open and freely available ACT-America data sets provide airborne in situ measurements of atmospheric carbon dioxide, methane, trace gases, aerosols, clouds, and meteorological properties, airborne remote sensing measurements of aerosol backscatter, atmospheric boundary layer height and columnar content of atmospheric carbon dioxide, tower-based measurements, and modeled atmospheric mole fractions and regional carbon fluxes of greenhouse gases over the Central and Eastern United States. We conducted 121 research flights during five campaigns in four seasons during 2016-2019 over three regions of the US (Mid-Atlantic, Midwest and South) using two NASA research aircraft (B-200 and C-130). We performed three flight patterns (fair weather, frontal crossings, and OCO-2 underflights) and collected more than 1,140 h of airborne measurements via level-leg flights in the atmospheric boundary layer, lower, and upper free troposphere and vertical profiles spanning these altitudes. We also merged various airborne in situ measurements onto a common standard sampling interval, which brings coherence to the data, creates geolocated data products, and makes it much easier for the users to perform holistic analysis of the ACT-America data products. Here, we report on detailed information of data sets collected, the workflow for data sets including storage and processing of the quality controlled and quality assured harmonized observations, and their archival and formatting for users. Finally, we provide some important information on the dissemination of data products including metadata and highlights of applications of ACT-America data sets.

Therapeutic drug monitoring in inflammatory bowel disease reduces unnecessary use of infliximab with substantial associated cost-savings

BACKGROUND

Therapeutic drug monitoring (TDM) of infliximab (IFX) levels in inflammatory bowel disease (IBD) patients can help to guide dose adjustments or changes to therapy for selected patients in remission or with secondary loss of response (LOR).

AIMS

To determine how IFX TDM is utilised in a real-life clinical setting and to quantify the potential for TDM to reduce the unnecessary use of IFX.

METHODS

Data from all public IBD IFX level testing performed across Australia were prospectively collected from June 2016 to July 2017 to assess physician-reported for testing indications (induction, in remission or LOR) and associated results. The hypothetical influence of IFX TDM was based on an optimal therapeutic range of 6-10 mg/L for mucosal healing.

RESULTS

Secondary LOR (reactive TDM) was the most common indication for TDM. These patients have consistently lower median IFX levels: 3.02 mg/L (IQR 1.14-6.67 mg/L) versus 5.22 mg/L (IQR 2.70-8.12 mg/L), P = 0.0001 compared with patients in remission (proactive TDM). TDM helped to identify unnecessary use of IFX in 30.6% of the TDM tests performed in luminal Crohn disease and ulcerative colitis patients, with an associated drug cost saving of $531.38 per IFX TDM test episode. Unnecessary IFX use was identified in 38.9% (96/247) of reactive IFX TDM tests performed and in 19.3% (35/181) of proactive testing.

CONCLUSION

Use of both reactive and proactive IFX TDM is cost-effective for IBD management as it informs the clinician where unnecessary use of IFX can be stopped.

Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions

Mechanisms underlying severe coronavirus disease 2019 (COVID-19) disease remain poorly understood. We analyze several thousand plasma proteins longitudinally in 306 COVID-19 patients and 78 symptomatic controls, uncovering immune and non-immune proteins linked to COVID-19. Deconvolution of our plasma proteome data using published scRNA-seq datasets reveals contributions from circulating immune and tissue cells. Sixteen percent of patients display reduced inflammation yet comparably poor outcomes. Comparison of patients who died to severely ill survivors identifies dynamic immune-cell-derived and tissue-associated proteins associated with survival, including exocrine pancreatic proteases. Using derived tissue-specific and cell-type-specific intracellular death signatures, cellular angiotensin-converting enzyme 2 (ACE2) expression, and our data, we infer whether organ damage resulted from direct or indirect effects of infection. We propose a model in which interactions among myeloid, epithelial, and T cells drive tissue damage. These datasets provide important insights and a rich resource for analysis of mechanisms of severe COVID-19 disease.

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.

Creating a content delivery network for general science on the internet backbone using XCaches

A general problem faced by opportunistic users computing on the grid is that delivering cycles is simpler than delivering data to those cycles. In this project XRootD caches are placed on the internet backbone to create a content delivery network. Scientific workflows in the domains of high energy physics, gravitational waves, and others profit from this delivery network to increases CPU efficiency while decreasing network bandwidth use.

Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients

COVID-19 has caused over 1 million deaths globally, yet the cellular mechanisms underlying severe disease remain poorly understood. By analyzing several thousand plasma proteins in 306 COVID-19 patients and 78 symptomatic controls over serial timepoints using two complementary approaches, we uncover COVID-19 host immune and non-immune proteins not previously linked to this disease. Integration of plasma proteomics with nine published scRNAseq datasets shows that SARS-CoV-2 infection upregulates monocyte/macrophage, plasmablast, and T cell effector proteins. By comparing patients who died to severely ill patients who survived, we identify dynamic immunomodulatory and tissue-associated proteins associated with survival, providing insights into which host responses are beneficial and which are detrimental to survival. We identify intracellular death signatures from specific tissues and cell types, and by associating these with angiotensin converting enzyme 2 (ACE2) expression, we map tissue damage associated with severe disease and propose which damage results from direct viral infection rather than from indirect effects of illness. We find that disease severity in lung tissue is driven by myeloid cell phenotypes and cell-cell interactions with lung epithelial cells and T cells. Based on these results, we propose a model of immune and epithelial cell interactions that drive cell-type specific and tissue-specific damage in severe COVID-19.

Collectively stabilizing and orienting posterior migratory forces disperses cell clusters in vivo

Individual cells detach from cohesive ensembles during development and can inappropriately separate in disease. Although much is known about how cells separate from epithelia, it remains unclear how cells disperse from clusters lacking apical-basal polarity, a hallmark of advanced epithelial cancers. Here, using live imaging of the developmental migration program of Drosophila primordial germ cells (PGCs), we show that cluster dispersal is accomplished by stabilizing and orienting migratory forces. PGCs utilize a G protein coupled receptor (GPCR), Tre1, to guide front-back migratory polarity radially from the cluster toward the endoderm. Posteriorly positioned myosin-dependent contractile forces pull on cell-cell contacts until cells release. Tre1 mutant cells migrate randomly with transient enrichment of the force machinery but fail to separate, indicating a temporal contractile force threshold for detachment. E-cadherin is retained on the cell surface during cell separation and augmenting cell-cell adhesion does not impede detachment. Notably, coordinated migration improves cluster dispersal efficiency by stabilizing cell-cell interfaces and facilitating symmetric pulling. We demonstrate that guidance of inherent migratory forces is sufficient to disperse cell clusters under physiological settings and present a paradigm for how such events could occur across development and disease.

RUVBL1 is an amplified epigenetic factor promoting proliferation and inhibiting differentiation program in head and neck squamous cancers

Mutations in histone modifying enzymes and histone variants were identified in multiple cancers in The Cancer Genome Atlas (TCGA) studies. However, very little progress and understanding has been made in identifying the contribution of epigenetic factors in head and neck squamous cell carcinoma (HNSCC). Here, we report the identification of RUVBL1 (TIP49a), a component of the TIP60 histone modifying complex as being amplified and overexpressed in HNSCC. RUVBL1 plays a key role in incorporating histone variant H2AZ in chromatin thereby regulating transcription of key genes involved in differentiation, cancer cell proliferation and invasion. H2AZ is also overexpressed in HNSCC tumors thereby regulating RUVBL1/H2AZ dependent transcriptional programs. Patient data analysis of multiple cohorts including TCGA and single cell HNSCC data indicated RUVBL1 overexpression as a poor prognostic marker and predicts poor survival. In vitro experiments indicate a pro-proliferative role for RUVBL1/H2AZ in HNSCC cells. RUVBL1 inversely correlates with differentiation program and positively correlates with oncogenic programs, making it a key contributor to tumorigenesis and a vulnerable therapeutic target in HNSCC patients.

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2), which causes the disease COVID-19. SARS-CoV-2 spike (S) protein binds angiotensin-converting enzyme 2 (ACE2), and in concert with host proteases, principally transmembrane serine protease 2 (TMPRSS2), promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues and the factors that regulate ACE2 expression remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 among tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells. Strikingly, we discovered that ACE2 is a human interferon-stimulated gene (ISG) in vitro using airway epithelial cells and extend our findings to in vivo viral infections. Our data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection.

Arthroscopic shoulder stabilization in the young athlete: return to sport and revision stabilization rates

BACKGROUND

Shoulder instability in young athletes is a complex problem with higher recurrence, higher reoperation, and lower return to sport (RTS) rates after arthroscopic shoulder stabilization compared with adults.

METHODS

This is a prospective case series of young athletes with anterior shoulder instability after arthroscopic stabilization surgery. Primary outcomes were RTS and revision surgery, minimum follow-up was 24 months. Exclusion criteria were more than 3 preoperative episodes of instability, significant bone loss, or primary posterior instability. Demographic data, recurrent instability, revision surgery, sports pre- and postsurgery, patient satisfaction, level of RTS, time to RTS, and Single Assessment Numeric Evaluation (SANE) scores were analyzed.

RESULTS

Sixty-seven athletes met inclusion criteria, 19 females and 48 males, with a mean age of 17.5 years (range, 13-21 years). Fifty-nine (88%) athletes returned to sport at an average of 7.1 months (standard deviation, ±1.8); 50 (75%) returned to the same level or higher. Football and lacrosse were the most common sports. Four of 67 athletes (6%), all male, underwent revision stabilization at 11-36 months for recurrent instability. The overall mean SANE score was 88.

CONCLUSION

This study demonstrates that when the high-risk athlete, 21 years old or younger, is appropriately selected for arthroscopic shoulder stabilization by excluding those with 3 or more preoperative shoulder instability episodes and those with off-track and engaging instability patterns, excellent outcomes can be achieved with low revision surgery rates, high RTS rates, and high patient satisfaction.

A Lightweight Door into Non-Grid Sites

The Open Science Grid (OSG) provides a common service for resource providers and scientific institutions, and supports sciences such as High Energy Physics, Structural Biology, and other community sciences. As scientific frontiers expand, so does the need for resources to analyze new data. For example, High Energy Physics experiments such as the LHC experiments foresee an exponential growth in the amount of data collected, which comes with corresponding growth in the need for computing resources. Allowing resource providers an easy way to share their resources is paramount to ensure the grow of resources available to scientists.

In this context, the OSG Hosted CE initiative provides site administrator a way to reduce the effort needed to install and maintain a Compute Element (CE), and represents a solution for sites who do not have the effort and expertise to run their own Grid middleware. An HTCondor Compute Element is installed on a remote VM at UChicago for each site that joins the Hosted CE initiative. The hardware/software stack is maintained by OSG Operations staff in a homogeneus and automated way, providing a reduction in the overall operational effort needed to maintain the CEs: one single organization does it in an uniform way, instead of each single resource provider doing it in their own way. Currently, more than 20 institutions joined the Hosted CE initiative. This contribution discusses the technical details behind a Hosted CE installation, highlighting key strengths and common pitfalls, and outlining future plans to further reduce operational experience.

Lou Gehrig's Disease (ALS): UBQLN2 Mutations Strike Out of Phase

In this issue of Structure, Dao et al. (2019) report that ALS-linked mutations in the Pxx domain of Ubiquilin 2 (UBQLN2) differentially influence the protein's phase separation abilities. The affect is by reducing the temperature and UBQLN2 concentration necessary for liquid-liquid phase separation droplet formation and by modulating UBQLN2 oligomerization.

A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity

Synonymous variants within coding regions may influence protein expression and function. We have previously reported increased protein expression levels ex vivo (~120% in comparison to wild-type) from a synonymous polymorphism variant, c.354G>A [p.P118P], of the ADAMTS13 gene, encoding a plasma protease responsible for von Willebrand Factor (VWF) degradation. In the current study, we investigated the potential mechanism(s) behind the increased protein expression levels from this variant and its effect on ADAMTS13 physico-chemical properties. Cell-free assays showed enhanced translation of the c.354G>A variant and the analysis of codon usage characteristics suggested that introduction of the frequently used codon/codon pair(s) may have been potentially responsible for this effect. Limited proteolysis, however, showed no substantial influence of altered translation on protein conformation. Analysis of post-translational modifications also showed no notable differences but identified three previously unreported glycosylation markers. Despite these similarities, p.P118P variant unexpectedly showed higher specific activity. Structural analysis using modeled interactions indicated that subtle conformational changes arising from altered translation kinetics could affect interactions between an exosite of ADAMTS13 and VWF resulting in altered specific activity. This report highlights how a single synonymous nucleotide variation can impact cellular expression and specific activity in the absence of measurable impact on protein structure.

Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies

Synonymous codons occur with different frequencies in different organisms, a phenomenon termed codon usage bias. Codon optimization, a common term for a variety of approaches used widely by the biopharmaceutical industry, involves synonymous substitutions to increase protein expression. It had long been presumed that synonymous variants, which, by definition, do not alter the primary amino acid sequence, have no effect on protein structure and function. However, a critical mass of reports suggests that synonymous codon variations may impact protein conformation. To investigate the impact of synonymous codons usage on protein expression and function, we designed an optimized coagulation factor IX (FIX) variant and used multiple methods to compare its properties to the wild-type FIX upon expression in HEK293T cells. We found that the two variants differ in their conformation, even when controlling for the difference in expression levels. Using ribosome profiling, we identified robust changes in the translational kinetics of the two variants and were able to identify a region in the gene that may have a role in altering the conformation of the protein. Our data have direct implications for codon optimization strategies, for production of recombinant proteins and gene therapies.

Quantitative magnetic resonance imaging and histological hoof wall assessment of 3-year-old Quarter Horses

BACKGROUND

Few noninvasive methods are available for equine hoof wall evaluation. The highly organised wall structures and composition of proteoglycans and collagens may make this region amenable to quantitative MRI (qMRI) techniques of T1ρ and T2 mapping to identify pathology related to proteoglycan content and collagen organisation respectively.

OBJECTIVE

To establish normative T1ρ and T2 values of the equine hoof wall of 3-year-old Quarter Horses with histological comparison.

STUDY DESIGN

Cadaveric anatomical study.

METHODS

Six cadaveric left thoracic feet from 3-year-old racing Quarter Horses with no reported lameness were evaluated using T1ρ and T2 mapping. Mapping was performed at six regions of interest at the toe of each hoof including proximal and distal regions of the inner epidermis, stratum lamellatum and corium. Histology was evaluated for standard hoof morphology and proteoglycan staining.

RESULTS

T2 values of the stratum lamellatum and corium were similar (42.9 [95% CI: 41.6-44.2] ms and 44 [95% CI: 42.7-45.3] ms respectively), but both were significantly different to the inner epidermis (35.8 [95% CI: 34.5-37.1] ms, P<0.001). T1ρ values for the inner epidermis, stratum lamellatum and corium were significantly different (25.1 [95% CI: 23.1-27.1] ms, 44.4 [95% CI: 42.4-46.4] ms and 50.1 [95% CI: 48.1-52.1] ms, respectively, P<0.001). Histology demonstrated normal organised morphology. Proteoglycan staining was only visible in the stratum lamellatum and corium.

MAIN LIMITATIONS

Cadaveric study with frozen samples used.

CONCLUSIONS

Variation of qMRI metrics through the depth of the equine hoof wall was found. Although the highly ordered environment of collagen may contribute to T2 values, there was lack of evidence to support proteoglycan content as a major contributor of T1ρ values. It is possible T1ρ values had a greater dependence on total water content as the lowest values were seen in the epidermis. Additional research using qMRI is needed to determine mapping values in different disease states.

Seven Novel and Three Known Mutations in FOXL2 in 10 Chinese Families with Blepharophimosis Syndrome

BACKGROUND

Blepharophimosis syndrome (BPES) is characterized by eyelid malformation with occasional premature ovarian failure. Mutations in FOXL2 underlie a fraction of BPES cases.

OBJECTIVE

We aimed to investigate the genetic basis of BPES in 26 Chinese families that included 78 patients.

METHODS

We performed ophthalmological examinations on each family member. We used Sanger sequencing to screen FOXL2 exons and their flanking sequences. We also performed bioinformatics studies, structural modeling and pathogenicity evaluations on all identified variations. Literature was reviewed and genotype-phenotype correlation analysis was performed.

RESULTS

The patients had typical manifestations of BPES. Ten mutations were identified in ten of the twenty-six families. Among these, seven were novel mutations. These included the six truncating mutations, p.Glu69*, p.Gly256Glyfs*14, p.Ala14Serfs*135, p.Pro333Profs*200, p.Pro290Leufs*70, and p.Pro157Profs*91, and one missense mutation, p.Tyr59Cys. The mutations were scattered within the gene, and no mutational hotspots were found. Genotype-phenotype correlation analysis showed that frameshift or nonsense mutations were correlated with type I BPES, while in-frame or missense mutations were associated with type II BPES.

CONCLUSION

We report the largest BPES cohort in China thus far as well as seven novel mutations in FOXL2. The identification of novel mutations has not only expanded the mutational spectrum of the gene (which is valuable for mutation detection-based screening) but also suggests that most mutations within the Chinese population may not have been characterized yet.

Decreased Expression of TIM-3 on Th17 Cells Associated with Ophthalmopathy in Patients with Graves' Disease

Purpose:

Thyroid-associated Ophthalmopathy (TAO) is one of the most common orbital immunological diseases in adults. CD4+ helper T (Th) cells play important roles in the pathogenesis of TAO. But the mechanisms regulating CD4+ T cell activity is unclear. This study examines T cell immunoglobulin domain and mucin domain 3 (TIM-3) expression in helper T cell type 1 (Th1), Th17, and regulatory T cells in sufferers of TAO.

Methods:

Participants were divided into 3 groups: patients with TAO, patients with Graves’ disease but without orbitopathy (GD), and healthy control patients (HC). Peripheral blood samples were collected for each patient in the designated group. Flow cytometry methods assessed the frequency of Th1 (CD4+IFN-γ+), Th17 (CD4+IL-17+), regulatory T cells (CD4+CD25hiCD127lo), and TIM-3 protein expression. Mean fluorescence intensity (MFI) measured the magnitude of TIM-3 expression and the percentage of TIM-3+ cells for each patient.

Results:

Compared to the GD group, TAO patients possessed higher frequencies of Th1 and Th17 cells in peripheral blood samples. The percentage of TIM-3+ Th1 and Th17 cells was significantly lower in the TAO patients than the GD group. Across all patients sampled, TIM-3+ cell percentage negatively correlated with Th1 cell frequency. Th1 and Th17 cells exhibited significantly decreased expression of TIM-3 in TAO patients compared to healthy controls. Regulatory T cells showed little TIM-3 expression and we observed no significant differences in frequency between groups.

Conclusion:

These results suggest a role for TIM-3 in the regulation of Th1 and Th17 cells and the pathogenesis of Graves’ ophthalmopathy.