The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain.

Mutations in the tyrosine phosphatase SHP2 are associated with a variety of human diseases. Most mutations in SHP2 increase its basal catalytic activity by disrupting auto-inhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, some disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, and molecular dynamics simulations. We show that, while some of these mutations alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also substantially alters ligand-binding specificity, despite being 8-10 Å from the specificity-determining region of the SH2 domain. This mutation exerts its effect on sequence specificity by remodeling the phosphotyrosine binding pocket, altering the mode of engagement of both the phosphotyrosine and surrounding residues on the ligand. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands and enhances downstream signaling. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.

Objective quantification of posterior capsule opacification after cataract surgery with swept-source optical coherence tomography.

PURPOSE: To evaluate the application of swept-source optical coherence tomography (SS-OCT) and pentacam scheimpflug tomography in posterior capsule opacification (PCO) severity assessment. METHODS: The posterior capsule image region segmentation and adaptive threshold algorithm are used to process the SS-OCT scanned image to obtain the posterior capsule thickness (PCT). Scheimpflug tomography reconstructed and analysized by image J software can obtain the average gray value and evaluate the effectiveness with the two methods. RESULT: One hundred sixty-two IOL eyes of 101 patients were divided into two groups, laser group (65 eyes) with the mean PCT was 8.0 ± 2.7 pixel unit and the mean gray value of the eyes was 66 ± 33 pixel unit. However, these figures in the control group (97 eyes) were 5.0 ± 0.9 and 11 ± 17. The sensitivity, specificity and area under curve(AUC) of SS-OCT PCT were 85%, 74% and 0.942,the sensitivity, specificity and AUC of Pentacam gray value were 91%, 76% and 0.947, respectively. After using the multivariable model of generalized estimation equation to corrected the dependence of subjects' eyes, it was found that SS-OCT PCT, Pentacam gray value, low vision quality of life questionnaire (LVQ questionnaire) for distance vision, and mobility and lighting dimension were significantly correlated with the PCO score (P = 0.012, P = 0.001, P = 0.005, respectively). CONCLUSION: The region segmentation and adaptive threshold algorithm of posterior capsule image will accurately quantify the posterior capsule. Computer aided quantifications of posterior capsule are of great significance in the early surgical decision-making of PCO. The average occurrence time of most PCO was around 34 months, and the severity of PCO worsened with increasing postoperative time.

A pairwise immune gene model for predicting overall survival and stratifying subtypes of colon adenocarcinoma.

OBJECTIVES: There is increasing evidence for a close correlation between risk stratification, prognosis and the immune environment in colon adenocarcinoma (COAD). However, the efficacy of immunotherapy is different among different patients with COAD. Therefore, the current work tends to use immune-related gene to develop a gene-pair model to evaluate the COAD prognosis, and to develop a new method for risk stratification of COAD, which is conducive to better predict the immunotherapy effect of patients. METHODS: Specifically, from the TCGA and GEO (GSE14333 and GSE39582) databases, we first collected gene expression profiles, associated survival follow-up information of COAD patients. Through systematic bioinformatics analysis, we established a prognosis-related model of colon cancer with three pairs of "immune gene pairs", with uni- and multivariate and lasso cox regression analyses verifying the model stability. Most immune cells showed markedly different levels of infiltration between the two risk subgroups calculated by the model. More, single-cell RNA-seq analyses were also performed to validate the selected genes in the immune gene-pair model. RESULTS: A prognosis-related model of colon cancer with three pairs of "immune gene pairs" were built and validated by several datasets. The analysis of immune landscape of COAD revealed that low-risk subgroup obtained by the prognosis-related model for COAD can be further divided into three subclusters with different prognosis. Then, we applied the Tumor online Prognostic analyses Platform (ToPP) to construct a prognostic model using these five genes. Results show that APOD, ISG20 and STC2 are risk factors, while CXCL9 and IL7R are protection factors. We also found that only the five-gene model could also predict the prognosis of COAD patients, indicating the robustness of the gene-pair model. Among the five genes, including CXCL9, APOD, STC2, ISG20, and IL7R, in the gene-pair model, single-cell RNA sequencing reveals the high expression of CXCL9 and IL7R in inflammatory macrophages. Using cell-cell interaction and trajectory analysis, data indicate that CXCL9+/IL7R+ pro-inflammatory macrophages were capable of secreting and activating more anti-tumor pathways than CXCL9-/IL7R- pro-inflammatory macrophages. CONCLUSIONS: In short, we have successfully developed an "immune gene pair" related model that can judge the prognostic status of patients with COAD and may contribute to risk stratification and evaluate potential beneficiaries of immunotherapy, providing new ideas for the anti-COAD management and therapy.

Accurate diagnosis of atopic dermatitis by combining transcriptome and microbiota data with supervised machine learning.

Atopic dermatitis (AD) is a common skin disease in childhood whose diagnosis requires expertise in dermatology. Recent studies have indicated that host genes-microbial interactions in the gut contribute to human diseases including AD. We sought to develop an accurate and automated pipeline for AD diagnosis based on transcriptome and microbiota data. Using these data of 161 subjects including AD patients and healthy controls, we trained a machine learning classifier to predict the risk of AD. We found that the classifier could accurately differentiate subjects with AD and healthy individuals based on the omics data with an average F1-score of 0.84. With this classifier, we also identified a set of 35 genes and 50 microbiota features that are predictive for AD. Among the selected features, we discovered at least three genes and three microorganisms directly or indirectly associated with AD. Although further replications in other cohorts are needed, our findings suggest that these genes and microbiota features may provide novel biological insights and may be developed into useful biomarkers of AD prediction.

Association Between Types of Posterior Staphyloma and Refractive Error After Cataract Surgery for High Myopia.

Purpose: To investigate the association between different types of posterior staphyloma (PS) and refractive error (RE) after cataract surgery in patients with high myopia. Methods: This retrospective study included 113 eyes of 113 highly myopic patients with PS. PS was detected using a wide-field fundus imaging system. PS was classified into wide macular, narrow macular, and other types. RE equaled the actual spherical equivalent (SE) minus the targeted SE values 3 months after cataract surgery. Results: The rates of wide macular, narrow macular, and other types of PS were 46.02, 39.82, and 14.16%, respectively. There were no significant differences in best corrected distance visual acuity (BCDVA) or SE among the three classifications of PS before cataract surgery (P > 0.05). However, postoperative BCDVA and SE were significantly different among the three types of PS patients (P < 0.05). The average RE values were 0.98 ± 1.00 D, 0.19 ± 0.87 D, 0.13 ± 0.59 D, respectively; the statistical differences of RE were <0.01, <0.01, and 0.81 (wide macular vs. narrow macular, wide macular vs. other types, narrow macular vs. other types), respectively. Multivariate linear regression analysis revealed that higher hyperopia RE after surgery was associated with wide macular staphyloma (P < 0.001), more myopic SE (P = 0.003), and increased BCDVA (P = 0.002) before surgery. Conclusions: Wide macular PS may be associated with more hyperopic RE; it may serve as a critical biomarker of hyperopic RE after cataract surgery in highly myopic patients.

An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19.

The global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires an urgent need to find effective therapeutics for the treatment of coronavirus disease 2019 (COVID-19). In this study, we developed an integrative drug repositioning framework, which fully takes advantage of machine learning and statistical analysis approaches to systematically integrate and mine large-scale knowledge graph, literature and transcriptome data to discover the potential drug candidates against SARS-CoV-2. Our in silico screening followed by wet-lab validation indicated that a poly-ADP-ribose polymerase 1 (PARP1) inhibitor, CVL218, currently in Phase I clinical trial, may be repurposed to treat COVID-19. Our in vitro assays revealed that CVL218 can exhibit effective inhibitory activity against SARS-CoV-2 replication without obvious cytopathic effect. In addition, we showed that CVL218 can interact with the nucleocapsid (N) protein of SARS-CoV-2 and is able to suppress the LPS-induced production of several inflammatory cytokines that are highly relevant to the prevention of immunopathology induced by SARS-CoV-2 infection.

Influence of cataract surgery on macular vascular density in patients with myopia using optical coherence tomography angiography.

The aim of the present study was to evaluate macular vascular density (MVD) variation after uneventful cataract surgery using optical coherence tomography angiography (OCTA) in patients with high myopia. Patients with cataracts scheduled for cataract surgery were divided into a high-myopia group [spherical equivalent (SE)≤-6.0 diopter (D) and axial length (AL)≥25 mm] and a low-myopia group (SE>-6.0 D and AL<25 mm). All patients were examined for MVD and retinal thickness (RT) with OCTA pre-operatively and post-operatively (1 day, 1 week, and 1 and 3 months after surgery). A total of 55 eyes from 44 patients were included. MVD and RT both changed after cataract surgery. The mean change in superficial vascular density (SVD) in patients with high myopia was significantly lower than that in the low-myopia group at the four post-operative time-points (all P<0.05). In addition, the RT of eyes with high myopia exhibited a different variation compared with that of the low-myopia group. Significant correlations were identified between AL, RT, intraocular pressure and SVD after surgery. In conclusion, superficial retinal perfusion in patients with high myopia was significantly lower than that in low myopia patients, which may lead to complications caused by poor perfusion.

Curative Effects of Valsartan Alone or Combined with Alpha-lipoic Acid on Inflammatory Cytokines and Renal Function in Early-stage Diabetic Kidney Disease.

The aim of this study was to compare curative effects of valsartan alone or combined with alpha-lipoic acid (ALA) on inflammatory cytokine indices including hypersensitive C-reactive protein (hs-CRP), tumor necrosis factor-alpha (TNF-α) and renal function indices including urinary albumin excretion rate (UAER), ß2-microglobulin (ß2-MG) and cystatin C (Cys C) of patients with early-stage diabetic kidney disease (DKD). One hundred and two patients with early-stage DKD were randomly divided into group A and group B, with 51 patients in each group. Group A was administered with valsartan alone, while group B was administered with valsartan combined with ALA. Research showed that 14 days after treatment, group B had significantly lowered hs-CRP, TNF-α, UAER, ß2-MG and Cys C when compared with group A (all p<0.001). Compared to valsartan alone, valsartan combined with ALA can reduce level of inflammatory cytokines in serum and improve renal function.

Diagnostic accuracy of Golgi protein 73 in primary hepatic carcinoma using ELISA: a systematic review and meta-analysis.

BACKGROUND: Primary hepatic carcinoma (PHC) is currently one of the most common worldwide causes of cancer death. Golgi protein 73 (GP73) has been proposed as potential diagnostic marker. However, it is controversial because of inconsistent diagnostic accuracy in different studies. The aim of this study was to assess the diagnostic accuracy of GP73 for PHC. METHODS: All the studies relating to the diagnostic accuracy of GP73 for patients with PHC from 1978 to January 2013 were collected. Methodological quality was assessed by Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2). The overall diagnostic sensitivity, specificity, and area under the receiver operating characteristic curve were used to evaluate the diagnostic accuracy of GP73 using Meta-DiSc statistical software. RESULTS: Altogether 5,637 subjects were included in the 25 selected studies. The sensitivity and specificity (95% confidence interval) of GP73 was 0.75 (0.73-0.76) and 0.84 (0.83 - 0.86), respectively. The area under the summary receiver operating characteristic curve (AUC) and Q* index of GP73 was 0.8616 and 0.8021. CONCLUSIONS: Serum GP73 has a relatively high diagnostic accuracy in primary hepatic carcinoma with better sensitivity and high specificity than AFP.