Rampant C-to-U deamination accounts for the intrinsically high mutation rate in SARS-CoV-2 spike gene.

The high mutation rate of SARS-CoV-2 largely complicates our control of the pandemic. In particular, it is currently unclear why the spike (S) gene has an extraordinarily high mutation rate among all SARS-CoV-2 genes. By analyzing the occurrence of fixed synonymous mutations between SARS-CoV-2 and RaTG13, and profiling the DAF (derived allele frequency) of polymorphic synonymous sites among millions of worldwide SARS-CoV-2 strains, we found that both fixed and polymorphic mutations show higher mutation rates in the S gene than other genes. The majority of mutations are C-to-T, representing the APOBEC-mediated C-to-U deamination instead of the previously proposed A-to-I deamination. Both in silico and in vivo evidence indicated that the S gene is more likely to be single-stranded compared to other SARS-CoV-2 genes, agreeing with the APOBEC preference of ssRNA. We conclude that the single-stranded property of the S gene makes it a favorable target for C-to-U deamination, leading to its excessively high mutation rate compared to other non-S genes. In conclusion, APOBEC, rather than ADAR, is the "editor-in-chief" of SARS-CoV-2 RNAs. This work helps us to understand the molecular mechanism underlying the mutation and evolution of SARS-CoV-2, and we believe it will contribute to the control of the pandemic.

Modeling Novel Aqueous Particle and Cloud Chemistry Processes of Biomass Burning Phenols and Their Potential to Form Secondary Organic Aerosols.

Phenols emitted from biomass burning contribute significantly to secondary organic aerosol (SOA) formation through the partitioning of semivolatile products formed from gas-phase chemistry and multiphase chemistry in aerosol liquid water and clouds. The aqueous-phase SOA (aqSOA) formed via hydroxyl radical (•OH), singlet molecular oxygen (1O2*), and triplet excited states of organic compounds (3C*), which oxidize dissolved phenols in the aqueous phase, might play a significant role in the evolution of organic aerosol (OA). However, a quantitative and predictive understanding of aqSOA has been challenging. Here, we develop a stand-alone box model to investigate the formation of SOA from gas-phase •OH chemistry and aqSOA formed by the dissolution of phenols followed by their aqueous-phase reactions with •OH, 1O2*, and 3C* in cloud droplets and aerosol liquid water. We investigate four phenolic compounds, i.e., phenol, guaiacol, syringol, and guaiacyl acetone (GA), which represent some of the key potential sources of aqSOA from biomass burning in clouds. For the same initial precursor organic gas that dissolves in aerosol/cloud liquid water and subsequently reacts with aqueous phase oxidants, we predict that the aqSOA formation potential (defined as aqSOA formed per unit dissolved organic gas concentration) of these phenols is higher than that of isoprene-epoxydiol (IEPOX), a well-known aqSOA precursor. Cloud droplets can dissolve a broader range of soluble phenols compared to aqueous aerosols, since the liquid water contents of aerosols are orders of magnitude smaller than cloud droplets. Our simulations suggest that highly soluble and reactive multifunctional phenols like GA would predominantly undergo cloud chemistry within cloud layers, while gas-phase chemistry is likely to be more important for less soluble phenols. But in the absence of clouds, the condensation of low-volatility products from gas-phase oxidation followed by their reversible partitioning to organic aerosols dominates SOA formation, while the SOA formed through aqueous aerosol chemistry increases with relative humidity (RH), approaching 40% of the sum of gas and aqueous aerosol chemistry at 95% RH for GA. Our model developments of biomass-burning phenols and their aqueous chemistry can be readily implemented in regional and global atmospheric chemistry models to investigate the aqueous aerosol and cloud chemistry of biomass-burning organic gases in the atmosphere.

Protective effect of apelin-13 on ventilator-induced acute lung injury.

BACKGROUND: Mechanical Ventilation (MV) is an essential mechanism of life support in the clinic. It may also lead to ventilator-induced acute lung injury (VILI) due to local alveolar overstretching and/or repeated alveolar collapse. However, the pathogenesis of VILI is not completely understood, and its occurrence and development may be related to physiological processes such as the inflammatory response, oxidative stress, and apoptosis. Some studies have found that the the apelin/APJ axis is an endogenous antagonistic mechanism activated during acute respiratory distress syndrome(ARDS), that can counteract the injury response and prevent uncontrolled lung injury. To indicate that apelin-13 plays a protective role in VILI, an animal model of VILI was established in this study to explore whether apelin-13 can alleviate VILI in rats by inhibiting inflammation, apoptosis and oxidative stress. METHODS: SD rats were divided into four groups: control, high tidal volume, high tidal volume + normal saline and high tidal volume + apelin-13. After tracheotomy, the rats in control maintained spontaneous breathing, and the other rats were connected to the small animal ventilator for 4 h to establish the rat VILI model. The mRNA expression of apelin was measured by real-time quantitative polymerase chain reaction(qRT-PCR), immunofluorescence and Western blotting(WB) were used to detect the expression level of APJ, and WB was used to detect the expression of the apoptotic proteins Bax and bcl-2. The degree of lung injury was evaluated by pathological staining of lung tissue,W/D ratio, and BALF total protein concentration. The expression of inflammatory factors(IL-1ß, IL-6, TNF-α) in alveolar lavage fluid was measured using ELISA. The activities of MPO and cat and the content of MDA, an oxidative product, in lung tissue were measured to evaluate the degree of oxidative stress in the lung. RESULTS: After treatment with apelin-13, the apelin/APJ axis in the lung tissue of VILI model rats was activated, and the effect was further enhanced. The pathological damage of lung tissue was alleviated, the expression of the antiapoptotic protein Bcl-2 and the proapoptotic protein Bax was reversed, and the levels of the inflammatory cytokines IL-1ß, IL-6, TNF-α levels were all decreased. MPO activity and MDA content decreased, while CAT activity increased. CONCLUSION: The apelin/apj axis is activated in VILI. Overexpression of apelin-13 further plays a protective role in VILI, mainly by including reducing pathological damage, the inflammatory response, apoptosis and antioxidant stress in lung tissue, thus delaying the occurrence and development of VILI.

Age-dependent changes in brain iron deposition and volume in deep gray matter nuclei using quantitative susceptibility mapping.

BACKGROUND: Microstructural changes in deep gray matter (DGM) nuclei are related to physiological behavior, cognition, and memory. Therefore, it is critical to study age-dependent trajectories of biomarkers in DGM nuclei for understanding brain development and aging, as well as predicting cognitive or neurodegenerative diseases. OBJECTIVES: We aimed to (1) characterize age-dependent trajectories of mean susceptibility, adjusted volume, and total iron content simultaneously in DGM nuclei using quantitative susceptibility mapping (QSM); (2) examine potential contributions of sex related effects to the different age-dependence trajectories of volume and iron deposition; and (3) evaluate the ability of brain age prediction by combining mean magnetic susceptibility and volume of DGM nuclei. METHODS: Magnetic susceptibilities and volumetric values of DGM nuclei were obtained from 220 healthy participants (aged 10-70 years) scanned on a 3T MRI system. Regions of interest (ROIs) were drawn manually on the QSM images. Univariate regression analysis between age and each of the MRI measurements in a single ROI was performed. Pearson correlation coefficients were calculated between magnetic susceptibility and adjusted volume in a single ROI. The statistical significance of sex differences in age-dependent trajectories of magnetic susceptibilities and adjusted volumes were determined using one-way ANCOVA. Multiple regression analysis was used to evaluate the ability to estimate brain age using a combination of the mean susceptibilities and adjusted volumes in multiple DGM nuclei. RESULTS: Mean susceptibility and total iron content increased linearly, quadratically, or exponentially with age in all six DGM nuclei. Negative linear correlation was observed between adjusted volume and age in the head of the caudate nucleus (CN; R2 = 0.196, p < 0.001). Quadratic relationships were found between adjusted volume and age in the putamen (PUT; R2 = 0.335, p < 0.001), globus pallidus (GP; R2 = 0.062, p = 0.001), and dentate nucleus (DN; R2 = 0.077, p < 0.001). Males had higher mean magnetic susceptibility than females in the PUT (p = 0.001), red nucleus (RN; p = 0.002), and substantia nigra (SN; p < 0.001). Adjusted volumes of the CN (p < 0.001), PUT (p = 0.030), GP (p = 0.007), SN (p = 0.021), and DN (p < 0.001) were higher in females than those in males throughout the entire age range (10-70 years old). The total iron content of females was higher than that of males in the CN (p < 0.001), but lower than that of males in the PUT (p = 0.014) and RN (p = 0.043) throughout the entire age range (10-70 years old). Multiple regression analyses revealed that the combination of the mean susceptibility value of the PUT, and the volumes of the CN and PUT had the strongest associations with brain age (R2 = 0.586). CONCLUSIONS: QSM can be used to simultaneously investigate age- and sex- dependent changes in magnetic susceptibility and volume of DGM nuclei, thus enabling a comprehensive understanding of the developmental trajectories of iron accumulation and volume in DGM nuclei during brain development and aging.

Skeletal muscle provides a pro-browning microenvironment for transplanted brown adipose tissue to maintain its effect to ameliorate obesity in ob/ob mice.

Brown adipose tissue (BAT) transplantation is a promising means of increasing whole-body energy metabolism to ameliorate obesity. However, the changes in BAT following transplantation and the effects of the microenvironment of the recipient site on graft function have yet to be fully characterized. Therefore, we aimed to determine the effects of transplanting BAT from C57BL/6 mice into the dorsal subcutaneous region or deep to the quadriceps femoris muscle of leptin-deficient ob/ob mice. Subcutaneously transplanted BAT lost features of BAT and demonstrated greater inflammatory cell infiltration and more oil cysts 16 weeks following transplantation. By contrast, the sub-muscularly transplanted BAT maintained features of BAT and was more highly vascularized. Interestingly, sub-muscular BAT transplantation led to a significant increase in oxygen consumption and less inflammation in subcutaneous fat, which was associated with long-term reductions in insulin resistance and body mass gain, whereas the subcutaneous transplants failed after 16 weeks. These results demonstrate that the beneficial effects of BAT transplantation depend upon the microenvironment of the recipient site. Skeletal muscle may provide a microenvironment that maintains the inherent features of BAT grafts over a long period of time, which facilitates a reduction in obesity and improvements in glucose homeostasis.

Assisted clustering of gene expression data using regulatory data from partially overlapping sets of individuals.

BACKGROUND: As omics measurements profiled on different molecular layers are interconnected, integrative approaches that incorporate the regulatory effect from multi-level omics data are needed. When the multi-level omics data are from the same individuals, gene expression (GE) clusters can be identified using information from regulators like genetic variants and DNA methylation. When the multi-level omics data are from different individuals, the choice of integration approaches is limited. METHODS: We developed an approach to improve GE clustering from microarray data by integrating regulatory data from different but partially overlapping sets of individuals. We achieve this through (1) decomposing gene expression into the regulated component and the other component that is not regulated by measured factors, (2) optimizing the clustering goodness-of-fit objective function. We do not require the availability of different omics measurements on all individuals. A certain amount of individual overlap between GE data and the regulatory data is adequate for modeling the regulation, thus improving GE clustering. RESULTS: A simulation study shows that the performance of the proposed approach depends on the strength of the GE-regulator relationship, degree of missingness, data dimensionality, sample size, and the number of clusters. Across the various simulation settings, the proposed method shows competitive performance in terms of accuracy compared to the alternative K-means clustering method, especially when the clustering structure is due mostly to the regulated component, rather than the unregulated component. We further validate the approach with an application to 8,902 Framingham Heart Study participants with data on up to 17,873 genes and regulation information of DNA methylation and genotype from different but partially overlapping sets of participants. We identify clustering structures of genes associated with pulmonary function while incorporating the predicted regulation effect from the measured regulators. We further investigate the over-representation of these GE clusters in pathways of other diseases that may be related to lung function and respiratory health. CONCLUSION: We propose a novel approach for clustering GE with the assistance of regulatory data that allowed for different but partially overlapping sets of individuals to be included in different omics data.

Low-complexity Volterra-inspired neural network equalizer in 100-G band-limited IMDD PON system.

One of the most promising solutions for 100 Gb/s line-rate passive optical networks (PONs) is intensity modulation and direct detection (IMDD) technology together with a digital signal processing- (DSP-) based equalizer for its advantages of system simplicity, cost-effectiveness, and energy-efficiency. However, due to restricted hardware resources, the effective neural network (NN) equalizer and Volterra nonlinear equalizer (VNLE) have the drawback of high implementation complexity. In this paper, we incorporate an NN with the physical principles of a VNLE to construct a white-box low-complexity Volterra-inspired neural network (VINN) equalizer. This equalizer has better performance than a VNLE at the same complexity and attains similar performance with much lower complexity than a VNLE with optimized structural hyperparameter. The effectiveness of the proposed equalizer is verified in 1310 nm band-limited IMDD PON systems. A 30.5-dB power budget is achieved with the 10-G-class transmitter.

Predictive nomogram for soft robotic hand rehabilitation of patients with intracerebral hemorrhage.

BACKGROUND: Few studies focused on the risk factors for hand rehabilitation of intracerebral hemorrhage (ICH) using of soft robotic hand therapy (SRHT). The aim of this study was to establish a predictive nomogram for soft robotic hand rehabilitation in patients with ICH. METHODS: According to the Brunnstrom motor recovery (BMR) stage, the patients were grouped into poor and good motor function groups. The data of patient demographic information and serum level of C-terminal Agrin Fragment (CAF), S100B and neurofilament light (NfL) were collected. The logistic regression was used to analyze the risk factors for poor hand function. RESULTS: Finally, we enrolled 102 and 103 patients in the control and SRHT groups. For the SRHT group, there were 17 and 86 cases with poor and good motor function at 6-months follow-up respectively. In the good motor function group, the Fugl-Meyer Assessment-Wrist and Hand (FMA-WH score) and BMR score at admission were all better than that in the poor motor function group respectively (p < 0.001). The mean serum level of CAF, S100B and NfL in the good motor function group were 2.5 ± 0.82 ng/mL, 286.6 ± 236.4 ng/L and 12.1 ± 10.4 pg/mL respectively, which were lower than that in the poor motor function group (p < 0.001, Table 3). The multivariate logistic regression showed that hematoma volume (OR = 1.47, p = 0.007), FMA-WH score admission (OR = 0.78, p = 0.02), S100B (OR = 1.32, p = 0.04), and NfL (OR = 1.24, p = 0.003) were all significant predictors of poor motor function. CONCLUSIONS: We found that Soft robotic hands therapy benefited in hand function in patients with ICH and hematoma volume, FMA-WH score admission, S100B, and NfL were all significant predictors for poor motor function of patients with ICH.

Brain controllability and morphometry similarity of internet gaming addiction.

Internet gaming addiction (IGD) is a common disease in teenagers which usually reflects the abnormalities in brain function or structure. Several computational models have been applied to investigate the characteristic of IGD brain networks, for instance, the conception of brain controllability. The primary objective of this study was to explore the relationship between brain controllability and IGD related clinical behaviour. A sample of 101 subjects, including 49 IGD patients and 52 normal controls, were recruited to undergo MR T1 and DTI scanning. Specifically, the MR images were used to generate the white matter connectivity matrix and the morphometry similarity network. The morphometry similarity network was then divided into several communities using modular decomposition. After, average controllability, modal controllability and synchronizability were calculated through measuring the adjacency matrix. The results indicated that the IGD group had greater synchronizability and modal controllability compared to that of the control group, and different morphological-based brain communities had different controllability properties. Furthermore, the addiction demonstrated the mediating effects between nodal or modular brain controllability as well as anxiety. In conclusion, brain controllability could be a potential biomarker of IGD.

c-Fos is a mechanosensor that regulates inflammatory responses and lung barrier dysfunction during ventilator-induced acute lung injury.

BACKGROUND: As one of the basic treatments performed in the intensive care unit, mechanical ventilation can cause ventilator-induced acute lung injury (VILI). The typical features of VILI are an uncontrolled inflammatory response and impaired lung barrier function; however, its pathogenesis is not fully understood, and c-Fos protein is activated under mechanical stress. c-Fos/activating protein-1 (AP-1) plays a role by binding to AP-1 within the promoter region, which promotes inflammation and apoptosis. T-5224 is a specific inhibitor of c-Fos/AP-1, that controls the gene expression of many proinflammatory cytokines. This study investigated whether T-5224 attenuates VILI in rats by inhibiting inflammation and apoptosis. METHODS: The SD rats were divided into six groups: a control group, low tidal volume group, high tidal volume group, DMSO group, T-5224 group (low concentration), and T-5224 group (high concentration). After 3 h, the pathological damage, c-Fos protein expression, inflammatory reaction and apoptosis degree of lung tissue in each group were detected. RESULTS: c-Fos protein expression was increased within the lung tissue of VILI rats, and the pathological damage degree, inflammatory reaction and apoptosis in the lung tissue of VILI rats were significantly increased; T-5224 inhibited c-Fos protein expression in lung tissues, and T-5224 inhibit the inflammatory reaction and apoptosis of lung tissue by regulating the Fas/Fasl pathway. CONCLUSIONS: c-Fos is a regulatory factor during ventilator-induced acute lung injury, and the inhibition of its expression has a protective effect. Which is associated with the antiinflammatory and antiapoptotic effects of T-5224.

Biphasic positive airway pressure spontaneous breathing attenuates lung injury in an animal model of severe acute respiratory distress syndrome.

OBJECTIVE: To compare the effects of unassisted spontaneous breathing (SB) and complete muscle paralysis (PC) on early severe acute respiratory distress syndrome (ARDS) in an animal model, and to explore the possibility of biphasic positive airway pressure (BIPAP) as lung protective ventilation support for patients in the early stage of severe ARDS. METHODS: Twelve healthy beagle dogs between the ages of 10 and 15 months were randomly divided into two groups: the SB group (BIPAPSB) and the PC group (BIPAPPC). Arterial blood samples were drawn before modelling. Arterial blood gas analysis and mechanical tests were conducted. The animal model of severe ARDS was established using a deep intravenous injection of oleic acid, and BIPAP ventilation was performed for 8 hours. Lung tissue and blood were taken to detect lung function, inflammatory reactions and degree of pathological damage. RESULTS: At the beginning of the experiment, there was no significant difference in the arterial blood gas analysis between the two groups (p > 0.05). After successful modelling, the oxygenation index and the end-expiratory lung volume in the SB group were significantly higher than those in the PC group 8 hours after MV. Pathologically, the wet-dry ratio and pathological score of the PC group were higher than those of the SB group; the lung injury in the gravity-dependent area in the SB group was less than that in the PC group (p< 0.05). CONCLUSIONS: In the early stage of severe ARDS induced by oleic acid, compared with PC, retention of the BIPAP mode of SB can reduce the risk of lung injury and improve respiratory function.

Bronchoscopic intratumoral injections of cisplatin and endostar as concomitants of standard chemotherapy to treat malignant central airway obstruction.

STUDY PURPOSE: Malignant central airway obstruction (CAO) in non-small cell lung cancer (NSCLC) is associated with high morbidity and requires endobronchial palliative treatment to re-establish a free air passage. We investigate intratumoral therapy combining anti-angiogenic and cytotoxic as a feasible therapeutic modality to treat malignant CAO. STUDY DESIGN: Ten NSCLC subjects with symptomatic malignant CAO underwent endobronchial intratumoral cisplatin and Endostar co-injection after tumour debulking next to systemic cisplatin-based chemotherapy. Injection was performed immediately after debulking surgery and was then carried out on day 2, day 6 and day 10 past systemic chemotherapy. Nine subjects of control group constantly received traditional cisplatin-based chemotherapy. Bronchoscopy, CT scanning, histology, FEV1/FVC ratio, Karnofsky performance (KPS) and shortness of breath scores were analysed to assess therapeutic efficacy. RESULTS: All 10 subjects benefited from the intratumoral cisplatin and endostar co-injection and systemic chemotherapy combination therapy. Bronchoscopy and CT scanning analyses showed a massive airway widening after treatment. Increased KPS and reduced shortness of breath score were also observed. A substantial improvement of lung function was further confirmed by increased FEV1/FVC ratio. For subjects of control group, the improvement was moderate and obviously not as optimal as the 10 subjects with intratumoral injection. CONCLUSIONS: We have shown that the intratumoral injection of cytotoxic cisplatin plus anti-angiogenic Endostar is an effective and safe adjuvant therapeutic option to treat malignant CAO in clinical practice. This time-staggered local and systemic treatment combination improves quality of life and clinical parameters, thus may provide a feasible therapeutic option for symptomatic CAO.

A novel school-based approach to screening for attention deficit hyperactivity disorder.

Current approaches to screening for ADHD result in high rates of false positives. A proof of concept study to investigate the added benefits in the school-based detection of ADHD of adding a standardised teacher to teacher interview to traditional parent and teacher report questionnaires. A school-based study of diagnostic accuracy of ADHD using a novel 2-stage screening process. Participants were all 1026 pupils enrolled in grades 1 to 6 (ages 6-12 years) of a school in Hunan Province, China. The primary outcome was a diagnosis of ADHD on the Kiddie Schedule for Affective Disorders and Schizophrenia Present Lifetime version. 230 (22.4%) of the 1026 students screened positive at Stage 1 (parent and teacher questionnaires) (Sensitivity 0.86 [95% CI, 0.75 to 0.96], specificity 0.80 [95% CI, 0.78-0.83], false positive rate 0.20 (95% CI, 0.18 to 0.23), false negative rate was 0.14 (95% CI, 0.12 to 0.16). 65 remained screen-positive at the Stage 2 screen (teacher to teacher SNAP-IV interview). 36/65 (55.4%) of these Stage 2 screen positive participants and 1/144 (0.7%) of the screen negative subjects met DSM-IV criteria for ADHD (sensitivity 0.83 [95% CI, 0.71-0.95]; specificity of 0.97 [95% CI, 0.96-0.98]; false positive rate 0.03 [95% CI, 0.01 to 0.04], false negative rate 0.16 [95% CI, 0.15 to 0.19]. Adding teacher to teacher interviews to traditional questionnaire-based screening has the potential to improve the clinical utility of school-based screening for ADHD reducing the proportion of false positives, without a negative impact on sensitivity.

HIV and Substance Use Stigma, Intersectional Stigma and Healthcare Among HIV-Positive PWID in Russia.

Little is known about the intersection of HIV stigma and substance use stigma. Using data from 188 HIV-positive people who inject drugs (PWID) in Russia, we examined the associations of these stigmas and their interaction with access and utilization of healthcare. While substance use stigma was significantly associated with poor access to care (AOR 2.31, 95%CI 1.50-3.57), HIV stigma was not. HIV stigma was associated with lower inpatient care utilization (AOR 0.32, 95%CI 0.14-0.65), while substance use stigma was not. We did not detect a significant interaction between the two forms of stigma for either of the primary outcomes. However, those with high levels of both substance use stigma and HIV stigma had higher odds of poor general access to healthcare (AOR 1.86, 95%CI 1.19-2.92), and lower odds of recent general outpatient (AOR 0.52, 95%CI 0.32-0.85) and any inpatient (AOR 0.48, 95%CI 0.22-0.99) care utilization compared to those with low levels of both types of stigma. Interventions addressing both substance use and HIV stigma in general healthcare settings might improve care in this HIV key population.

Photosensitized Reactions of a Phenolic Carbonyl from Wood Combustion in the Aqueous Phase-Chemical Evolution and Light Absorption Properties of AqSOA.

Guaiacyl acetone (GA) is a phenolic carbonyl emitted in significant quantities by wood combustion that undergoes rapid aqueous-phase oxidation to produce aqueous secondary organic aerosol (aqSOA). We investigate the photosensitized oxidation of GA by an organic triplet excited state (3C*) and the formation and aging of the resulting aqSOA in wood smoke-influenced fog/cloud water. The chemical transformations of the aqSOA were characterized in situ using a high-resolution time-of-flight aerosol mass spectrometer. Additionally, aqSOA samples collected over different time periods were analyzed using high-performance liquid chromatography coupled with a photodiode array detector and a high-resolution Orbitrap mass spectrometer (HPLC-PDA-HRMS) to provide details on the molecular composition and optical properties of brown carbon (BrC) chromophores. Our results show efficient formation of aqSOA from GA, with an average mass yield around 80%. The composition and BrC properties of the aqSOA changed significantly over the course of reaction. Three generations of aqSOA products were identified via positive matrix factorization analysis of the aerosol mass spectrometry data. Oligomerization and functionalization dominated the production of the first-generation aqSOA, whereas fragmentation and ring-opening reactions controlled the formation of more oxidized second- and third-generation products. Significant formation of BrC was observed in the early stages of the photoreaction, while organic acids were produced throughout the experiment. High-molecular weight molecules (m/z > 180) with high aromaticity were identified via HPLC-PDA-HRMS and were found to account for a majority of the UV-vis absorption of the aqSOA.

miR-34a regulates phenotypic modulation of vascular smooth muscle cells in intracranial aneurysm by targeting CXCR3 and MMP-2.

MicroRNAs (miRNAs) dysregulation is tightly related to diseases including tumor, neuro disease and cardiovascular disease. In this study, we investigated the potential biological effects of miR-34a and its target CXCR3 in phenotypic modulation of vascular smooth muscle cells (VSMCs) of intracranial aneurysms (IAs). MiR-34a was found to be down-regulated in IAs patients tested by Real-time PCR and decreased in GEO data. Meanwhile, our study also showed miR-34a inhibited matrix metalloproteinases (MMPs) and migration of VSMCs. Besides, CXCR3 is a direct target of miR-34a identified via luciferase assay. CXCR3 showed inhibitory effect on SM-MHC, SM22 while promoted MMPs expression, cell proliferation and migration in VSMCs. MiR-34a reversed the effect of CXCR3 in VSMCs. In addition, MMP-2 is a competitive endogenous RNA (ceRNA) of CXCR3 sharing common miR-34a target. CXCR3 increased MMP-2 level through competitive endogenous RNA regulation by sponging endogenous miR-34a. In conclusion, miR-34a is down-regulated in IAs while CXCR3 is the direct target of miR-34a that regulates phenotypic modulation of VSMCs. CXCR3 increased MMP-2 level through competitive endogenous RNA regulation by sharing common miR-34a targets.

GC usage of SARS-CoV-2 genes might adapt to the environment of human lung expressed genes.

Understanding how SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) efficiently reproduces itself by taking resources from the human host could facilitate the development of drugs against the virus. SARS-CoV-2 translates its own proteins by using the host tRNAs, so that its GC or codon usage should fit that of the host cells. It is necessary to study both the virus and human genomes in the light of evolution and adaptation. The SARS-CoV-2 virus has significantly lower GC content and GC3 as compared to human. However, when we selected a set of human genes that have similar GC properties to SARS-CoV-2, we found that these genes were enriched in particular pathways. Moreover, these human genes have the codon composition perfectly correlated with the SARS-CoV-2, and were extraordinarily highly expressed in human lung tissues, demonstrating that the SARS-CoV-2 genes have similar GC usage as compared to the lung expressed human genes. RSCU (relative synonymous codon usage) and CAI (codon adaptation index) profiles further support the matching between SARS-CoV-2 and lungs. Our study indicates that SARS-CoV-2 might have adapted to the human lung environment by observing the high correlation between GC usage of SARS-CoV-2 and human lung genes, which suggests the GC content of SARS-CoV-2 is optimized to take advantage of human lung tissues.

Feasibility, patient compliance and acceptability of ovarian cancer surveillance using two serum biomarkers and Risk of Ovarian Cancer Algorithm compared to standard ultrasound and CA 125 among women with BRCA mutations.

OBJECTIVE: We assessed the feasibility, patient acceptability of and compliance of a new surveillance strategy for ovarian cancer surveillance in women with BRCA mutations, based on assessments of serum CA125 and HE4 every 4 months (Risk of Ovarian Cancer Algorithm (ROCA) arm), compared to Standard of Care (SOC) surveillance with CA125 blood tests and pelvic ultrasounds every 6 months. METHODS: Women were recruited 6/13/16-9/11/17 from an integrated health care system in California for this non-randomized prospective cohort study. Women were invited to participate in a novel serum biomarker surveillance strategy using ROCA or they could opt to be in the standard of care control arm with ultrasound and CA 125 every 6 months. Outcomes assessed included compliance, self-reported distress using the Impact of Event Scale (IES) and cancer anxiety using the Cancer Worry Scale. RESULTS: There were 159 women in the ROCA arm and 43 in the SOC arm. Overall, compliance was higher in the ROCA arm (83.2%) than in SOC (51.9%), p < 0.0001. Based on the IES, ROCA arm women reported less feelings about intrusion and avoidance at 12 months compared to baseline; the difference approached significance for intrusion (7.6% vs 4.1% severe, p = 0.057) and was statistically significant for avoidance (20.8% vs 9.9% severe, p = 0.034). CONCLUSIONS: This pilot demonstrated that compliance was high with blood tests performed every four months for ovarian cancer surveillance. Moreover, ROCA women had lower stress scores over time than SOC women. Given the lack of clinical utility and poor compliance shown with traditional ultrasound and CA125 tests, further investigation is warranted of longitudinal biomarker surveillance for early detection of ovarian cancer.

Development of a longitudinal two-biomarker algorithm for early detection of ovarian cancer in women with BRCA mutations.

OBJECTIVE: To develop a longitudinal algorithm combining two biomarkers, CA125 and HE4, for early detection of ovarian cancer in women with BRCA mutations. METHODS: Women with BRCA mutations and intact ovaries were invited to participate in a novel ovarian cancer early detection prospective study. The Risk of Ovarian Cancer Algorithm (ROCA) identifying significant increases above each woman's baseline in serum CA125 and HE4 was performed every four months; abnormal risks triggered a subsequent ultrasound. The study first used a risk algorithm for only CA125, a second algorithm was developed for HE4 and finally a risk algorithm combining the two biomarkers was implemented. The ROCA strategy was compared to Standard of Care (SOC) surveillance strategy. RESULTS: A total of 149 women enrolled in the ROCA arm while 43 women enrolled in the SOC arm. Abnormal scores were found in 24% of ROCA CA125 tests, 16% if ROCA CA125 or the novel ROCA HE4 were used independently and reduced to 8% using the new two-marker ROCA, significantly lower than the 15% of abnormal tests seen in the SOC arm (p = 0.042). The average false positive rate among women without ovarian cancer for two-marker ROCA for referral to ultrasound was 6.6% (specificity 93.4%), and for the two-marker ROCA plus ultrasound for referral to surgical consultation was 1.7% (specificity 98.3%). CONCLUSION: A newly developed two-marker ROCA administered every 4 months had lower call-back rates than SOC surveillance. Having established high specificity, the two-marker ROCA score deserves further evaluation for sensitivity in a larger trial.

Acetylation regulates gluconeogenesis by promoting PEPCK1 degradation via recruiting the UBR5 ubiquitin ligase.

Protein acetylation has emerged as a major mechanism in regulating cellular metabolism. Whereas most glycolytic steps are reversible, the reaction catalyzed by pyruvate kinase is irreversible, and the reverse reaction requires phosphoenolpyruvate carboxykinase (PEPCK1) to commit for gluconeogenesis. Here, we show that acetylation regulates the stability of the gluconeogenic rate-limiting enzyme PEPCK1, thereby modulating cellular response to glucose. High glucose destabilizes PEPCK1 by stimulating its acetylation. PEPCK1 is acetylated by the P300 acetyltransferase, and this acetylation stimulates the interaction between PEPCK1 and UBR5, a HECT domain containing E3 ubiquitin ligase, therefore promoting PEPCK1 ubiquitinylation and degradation. Conversely, SIRT2 deacetylates and stabilizes PEPCK1. These observations represent an example that acetylation targets a metabolic enzyme to a specific E3 ligase in response to metabolic condition changes. Given that increased levels of PEPCK are linked with type II diabetes, this study also identifies potential therapeutic targets for diabetes.