Ultrasound-based radiomics for early predicting response to neoadjuvant chemotherapy in patients with breast cancer: a systematic review with meta-analysis.

OBJECTIVE: This study aims to evaluate the diagnostic accuracy of ultrasound imaging (US)-based radiomics for the early prediction of response to neoadjuvant chemotherapy (NAC) in breast cancer patients. METHODS: We comprehensively searched PubMed, Cochrane Library, Embase, and Web of Science databases up to 1 January 2023 for eligible studies. We assessed the methodological quality of the enrolled studies with Radiomics Quality Score (RQS) and the Quality Assessment of Diagnostic Accuracy Studies-2 tools. We performed meta-analyses to summarize the diagnostic efficacy of US-based radiomics in response to NAC in breast cancer patients. RESULTS: Eight studies proved eligible. Eligible studies exhibited an average RQS score of 12.88 (35.8% of the total score), with the RQS score ranging from 8 to 19. In the meta-analyses, the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were 0.87 (95% CI 0.81-0.92), 0.78 (95% CI 0.72-0.83), 4.02 (95% CI 3.18-5.08), 0.16 (95% CI 0.10-0.25), and 25.17 (95% CI 15.10-41.95), respectively. Results from subgroup analyses indicated that prospective studies apparently exhibited more optimal sensitivity than retrospective studies. Sensitivity analyses exhibited similar results to the primary analyses. CONCLUSION: US-based radiomics may be a potentially crucial adjuvant method for evaluating the response of breast cancer to NAC. Due to limited data available and low quality of eligible studies, more multicenter prospective studies with rigorous methods are required to confirm our findings.

Investigation of synthetic MRI with quantitative parameters for discriminating axillary lymph nodes status in invasive breast cancer.

OBJECTIVE: To investigate the potential value of quantitative parameters derived from synthetic magnetic resonance imaging (syMRI) for discriminating axillary lymph nodes metastasis (ALNM) in breast cancer patients. MATERIALS AND METHODS: A total of 56 females with histopathologically proven invasive breast cancer who underwent both conventional breast MRI and additional syMRI examinations were enrolled in this study, including 30 patients with ALNM and 26 with non-ALNM. SyMRI has enabled quantification of T1 relaxation time (T1), T2 relaxation time (T2) and proton density (PD). The syMRI quantitative parameters of breast primary tumors before (T1tumor, T2tumor, PDtumor) and after (T1+tumor, T2+tumor, PD+tumor) contrast agent injection were obtained. Similarly, measurements were taken for axillary lymph nodes before (T1LN, T2LN, PDLN) and after (T1+LN, T2+LN, PD+LN) the injection, then theΔT1 (T1-T1+), ΔT2 (T2-T2+), ΔPD (PD-PD+), T1/T2 and T1+/T2+ were calculated. All parameters were compared between ANLM and non-ALNM group. Intraclass correlation coefficient for assessing interobserver agreement. The independent Student's t test or Mann-Whitney U test to determine the relationship between the mean quantitative values and the ALNM. Multivariate logistic regression analyses followed by receiver operating characteristics (ROC) analysis for discriminating ALN status. A P value < 0.05 was considered statistically significant. RESULTS: The short-diameter of lymph nodes (DLN) in ALNM group was significantly longer than that in the non-ALNM group (10.22 ± 3.58 mm vs. 5.28 ± 1.39 mm, P < 0.001). The optimal cutoff value was determined to be 5.78 mm, with an AUC of 0.894 (95 % CI: 0.838-0.939), a sensitivity of 86.7 %, and a specificity of 90.2 %. In syMRI quantitative parameters of breast tumors, T2tumor, ΔT2tumor and ΔPDtumor values showed statistically significant differences between the two groups (P < 0.05). T2tumor value had the best performance in discriminating ALN status (AUC = 0.712), and the optimal cutoff was 90.12 ms, the sensitivity and specificity were 65.0 % and 83.6 % respectively. In terms of syMRI quantitative parameters of lymph nodes, T1LN, T2LN, T1LN/T2LN, T2+LN and ΔT1LN values were significantly different between the two groups (P < 0.05), and their AUCs were 0.785, 0.840, 0.886, 0.702 and 0.754, respectively. Multivariate analyses indicated that the T1LN value was the only independent predictor of ALNM (OR=1.426, 95 % CI: 1.130-1.798, P = 0.039). The diagnostic sensitivity and specificity of T1LN was 86.7 % and 69.4 % respectively at the best cutoff point of 1371.00 ms. The combination of T1LN, T2LN, T1LN/T2LN, ΔT1LN and DLN had better performance for differentiating ALNM and non-ALNM, with AUCs of 0.905, 0.957, 0.964 and 0.897, respectively. CONCLUSION: The quantitative parameters derived from syMRI have certain value for discriminating ALN status in invasive breast cancer, with T2tumor showing the highest diagnostic efficiency among breast lesions parameters. Moreover, T1LN acted as an independent predictor of ALNM.

The Immunomodulatory Effects of A2 ß-Casein on Immunosuppressed Mice by Regulating Immune Responses and the Gut Microbiota.

The aim of this study was to investigate the immunomodulatory effects of A2 ß-casein (ß-CN) in cyclophosphamide-induced immunosuppressed BALB/c mice. Experiments conducted in vitro revealed that A2 ß-CN digestive products have potent immunostimulatory activities. Animal studies demonstrated that A2 ß-CN improved the immunological organ index reduction trend caused by cyclophosphamide, reduced the pathological damage to the spleen tissue in immunosuppressed mice, increased the release of IL-17A, IgG, and IgA, and reduced the production of IL-4. By regulating the relative abundance of advantageous bacteria like Oscillospira, Lactobacillus, and Bifidobacteria and harmful bacteria like Coprococcus and Desulfovibrionaceae, A2 ß-CN improved gut microbiota disorders in immunosuppressed mice. Moreover, A2 ß-CN promoted the production of short-chain fatty acids and increased the diversity of the gut microbiota. Therefore, ingestion of A2 ß-CN is beneficial to the host's immune system and gut health. These findings provide insights for the future application of A2 ß-CN-related dairy products.

Essential oil from Artemisia argyi alleviated liver disease in zebrafish (Danio rerio) via the gut-liver axis.

The popularity of intensive fish farming has led to the emergence of fish diseases characterized by hepatobiliary syndrome. Artemisia argyi (A. argyi) essential oils have anti-inflammatory and anti-oxidant effects. However, their alleviating effects and mechanism on liver disease in fish are still unclear. Thus, adult zebrafish were used to construct an animal model to observe histopathological damages, determine biochemical parameters and expression of inflammatory cytokines and mRNAs in the PPAR-γ/NF-κB pathway, and conduct 16 S sequencing of intestinal microbiota. The results found that after treatment with A. argyi essential oil, the histopathological damage caused by ethanol was relieved; the CAT, SOD, and GSH levels were remarkably elevated, while the MDA level was obviously lowered (P < 0.05); the expression levels of IL-10 and IFN-γ mRNAs were enhanced, but the levels of IL-1ß, IL-6, PPAR-γ, NF-κB, and TNF-α mRNAs were reduced (P < 0.05) relative to the EtOH group. A. argyi essential oil remarkably attenuated the damage to intestinal tissue structure, and elevated the levels of Muc2, ZO-1, Claudin-1, and Occludin mRNA (P < 0.05). Sequencing of the gut flora showed that A. argyi essential oil significantly altered the composition of gut microbes compared with the EtOH group. In addition, KEGG and COG analyses also showed significant (P < 0.05) changes in acetate cycling metabolism in the EtOH group, catechol 2, 3-dioxygenase and nitroreductase were significantly increased (P < 0.001), and lipid metabolism and terpenoid synthesis were significantly elevated (P < 0.001) in A. argyi essential oil group. The results indicate that A. argyi essential oil could effectively relieve ethanol-caused histopathological damage of livers by modulating the composition of gut microbiota, thus inhibiting the level of IL-1ß and mRNAs in the PPAR-γ/NF-κB pathway, increasing the IL-10 level, reducing the oxidative stress. This may offer a rationale for further research on the rationality of A. argyi as a substitute for feed antibiotics in aquaculture.

Diagnostic value of PET with different radiotracers and MRI for recurrent glioma: a Bayesian network meta-analysis.

OBJECTIVE: The purpose of this study was to evaluate the diagnostic accuracy of 6 different imaging modalities for differentiating glioma recurrence from postradiotherapy changes by performing a network meta-analysis (NMA) using direct comparison studies with 2 or more imaging techniques. DATA SOURCES: PubMed, Scopus, EMBASE, the Web of Science and the Cochrane Library were searched from inception to August 2021. The Confidence In Network Meta-Analysis (CINeMA) tool was used to evaluate the quality of the included studies with the criterion for study inclusion being direct comparison using 2 or more imaging modalities. DATA EXTRACTION AND SYNTHESIS: The consistency was evaluated by examining the agreement between direct and indirect effects. NMA was performed and the surface under the the cumulative ranking curve (SUCRA) values was obtained to calculate the probability of each imaging modality being the most effective diagnostic method. The CINeMA tool was used to evaluate the quality of the included studies. MAIN OUTCOMES AND MEASURES: Direct comparison, inconsistency test, NMA and SUCRA values. RESULTS: A total of 8853 potentially relevant articles were retrieved and 15 articles met the inclusion criteria. 18F-FET showed the highest SUCRA values for sensitivity, specificity, positive predictive value and accuracy, followed by 18F-FDOPA. The quality of the included evidence is classified as moderate. CONCLUSION AND RELEVANCE: This review indicates that 18F-FET and 18F-FDOPA may have greater diagnostic value for glioma recurrence relative to other imaging modalities (Grading of Recommendations, Assessment, Development and Evaluations B). PROSPERO REGISTRATION NUMBER: CRD42021293075.

Diagnostic and predictive value of liquid biopsy-derived exosome miR-21 for breast cancer: a systematic review and meta-analysis.

BACKGROUND AND PURPOSE: Studies have revealed that miR-21 is abnormally expressed in breast cancer patients, suggesting that miR-21 could be exploited as a possible diagnostic biomarker for clinical applications. In order to provide clinical evidence that is supported by research, we investigate the diagnostic utility of miR-21 in breast cancer in this study. METHODS: From their inception to 23 January 2022, the PubMed, EMBASE, Web of Science, Cochrane Library, and Scopus databases were searched for all pertinent English literature. QUADAS-2 for literature quality assessment, GRADE for evidence grading. Statistical analyses were performed using the R 4.0.1 and Revman 5.3. The results were validated using Stata 15.1 software. Subgroup analysis was also performed according to the source of miR-21 and miR-21 combinations. RESULTS: Nine publications with 2048 patients were reviewed for inclusion. All of the included studies are of moderate-high quality. Meta-analysis was performed using a mixed-effects model. The pooled sensitivity, specificity, diagnostic odds ratio (DOR), negative likelihood ratio (NLR) and positive likelihood ratio (PLR) were 0.91 [95% CI (0.86, 0.95)], 0.85 [95% CI (0.77, 0.91)], 56.62 [95% CI (21.00, 184.83)], 0.11 [95% CI (0.05, 0.18)] and 6.35 [95% CI (3.66, 11.16)], respectively. The GRADE classification for miR-21 was A, indicating a strong recommendation for breast cancer screening. CONCLUSIONS: The available evidence suggests that miR-21 has sufficient diagnostic value as a biomarker for breast cancer. Its diagnostic precision can be further improved by combining it with other miRNAs. Based on the GRADE review, miR-21 is strongly recommended for breast cancer screening.

Different Imaging Modalities for the Diagnosis of Axillary Lymph Node Metastases in Breast Cancer: A Systematic Review and Network Meta-Analysis of Diagnostic Test Accuracy.

BACKGROUND: Accurate diagnosis of axillary lymph node metastasis (ALNM) of breast cancer patients is important to guide local and systemic treatment. PURPOSE: To evaluate the diagnostic performance of different imaging modalities for ALNM in patients with breast cancer. STUDY TYPE: Systematic review and network meta-analysis (NMA). SUBJECTS: Sixty-one original articles with 8011 participants. FIELD STRENGTH: 1.5 T and 3.0 T. ASSESSMENT: We used the QUADAS-2 and QUADAS-C tools to assess the risk of bias in eligible studies. The identified articles assessed ultrasonography (US), MRI, mammography, ultrasound elastography (UE), PET, CT, PET/CT, scintimammography, and PET/MRI. STATISTICAL ANALYSIS: We used random-effects conventional meta-analyses and Bayesian network meta-analyses for data analyses. We used sensitivity and specificity, relative sensitivity and specificity, superiority index, and summary receiver operating characteristic curve (SROC) analysis to compare the diagnostic value of different imaging modalities. RESULTS: Sixty-one studies evaluated nine imaging modalities. At patient level, sensitivities of the nine imaging modalities ranged from 0.27 to 0.84 and specificities ranged from 0.84 to 0.95. Patient-based NMA showed that UE had the highest superiority index (5.95) with the highest relative sensitivity of 1.13 (95% confidence interval [CI]: 0.93-1.29) among all imaging methods when compared to US. At lymph node level, MRI had the highest superiority index (6.91) with highest relative sensitivity of 1.13 (95% CI: 1.01-1.23) and highest relative specificity of 1.11 (95% CI: 0.95-1.23) among all imaging methods when compared to US. SROCs also showed that UE and MRI had the largest area under the curve (AUC) at patient level and lymph node level of 0.92 and 0.94, respectively. DATA CONCLUSION: UE and MRI may be superior to other imaging modalities in the diagnosis of ALNM in breast cancer patients at the patient level and the lymph node level, respectively. Further studies are needed to provide high-quality evidence to validate our findings. EVIDENCE LEVEL: 3 TECHNICAL EFFICACY: Stage 2.

Lactobacillus reuteri J1 prevents obesity by altering the gut microbiota and regulating bile acid metabolism in obese mice.

Obesity is closely related to metabolic syndromes such as hyperlipidemia and diabetes and has become a global public health problem. Probiotics are now used as a treatment for obesity, but the mechanism by which probiotics treat obesity remains unclear. Herein, we investigated the effects of Lactobacillus reuteri J1 ( L. reuteri J1) on obese mice with the strain being administered at 1010, 109 and 108 CFU mL-1 and explored the possible underlying molecular mechanism. The results revealed that L. reuteri J1 prevented weight gain, lowered fat mass and relieved dyslipidemia, and improved glucose homeostasis and insulin sensitivity. Moreover, the effect of obesity reversal exhibited dose-dependence to some extent. More importantly, mice treated with L. reuteri J1 altered the gut microbiota and bile acid (BA) composition. Analysis of the gut microbiome showed that L. reuteri J1 increased the relative abundances of Lactobacillus, Akkermansia and Clostridium, which strongly correlated with ursodeoxycholic acid (UDCA) and lithocholic acid (LCA). UDCA and LCA are thought to inhibit farnesoid X receptor (FXR) and activate transmembrane G protein-coupled receptor 5 (TGR5) expression, respectively. Consistent with the increase in the BA pool, L. reuteri J1 treatment inhibited the ileum FXR/FGF15 signaling pathway but activated the hepatic FXR/SHP signaling pathway, resulting in reduced hepatic triglyceride accumulation. In addition, L. reuteri J1 treatment promoted adipose browning by upregulating the expression of uncoupling protein 1 (UCP1), which was mainly due to the BA receptor TGR5. These results demonstrated that L. reuteri J1 could treat obesity by inhibiting the FXR signaling pathways and remodeling white adipose tissue, linked with UDCA and LCA which are affected by intestinal microbiota.

Optimization of a Deep Learning Algorithm for Security Protection of Big Data from Video Images.

With the rapid development of communication technology, digital technology has been widely used in all walks of life. Nevertheless, with the wide dissemination of digital information, there are many security problems. Aiming at preventing privacy disclosure and ensuring the safe storage and sharing of image and video data in the cloud platform, the present work proposes an encryption algorithm against neural cryptography based on deep learning. Primarily, the image saliency detection algorithm is used to identify the significant target of the video image. According to the significant target, the important region and nonimportant region are divided adaptively, and the encrypted two regions are reorganized to obtain the final encrypted image. Then, after demonstrating how attackers conduct attacks to the network under the ciphertext attack mode, an improved encryption algorithm based on selective ciphertext attack is proposed to improve the existing encryption algorithm of the neural network. Besides, a secure encryption algorithm is obtained through detailed analysis and comparison of the security ability of the algorithm. The experimental results show that Bob's decryption error rate will decrease over time. The average classification error rate of Eve increases over time, but when Bob and Alice learn a secure encryption network structure, Eve's classification accuracy is not superior to random prediction. Chosen ciphertext attack-advantageous neural cryptography (CCA-ANC) has an encryption time of 14s and an average speed of 69mb/s, which has obvious advantages over other encryption algorithms. The self-learning secure encryption algorithm proposed here significantly improves the security of the password and ensures data security in the video image.

Correlation between molecular prognostic factors and magnetic resonance imaging intravoxel incoherent motion histogram parameters in breast cancer.

OBJECTIVE: To explore the efficacy of the quantitative parameter histogram analysis of intravoxel incoherent motion (IVIM) for different molecular prognostic factors of breast cancer. MATERIALS AND METHODS: A total of 72 patients with breast cancer who were confirmed by surgical pathology and underwent preoperative magnetic resonance imaging (MRI) were analyzed retrospectively. A region of interest (ROI) was drawn in each slice of the IVIM images. Whole-tumor histogram parameters were obtained with Firevoxel's software by accumulating all ROIs. Next, Kolmogorov-Smirnov test, Student's t-test, Mann-Whitney U test, receiver operating characteristic curve analysis and spearman rank correlation analysis were used to assess the relationship between histogram parameters and molecular prognostic factors of breast cancer. RESULTS: Among estrogen receptor (ER)-negative ROCs, the apparent diffusion coefficient (ADC) 10th percentile had the highest ROC of 0.792, with a cut-off value of 0.788 × 10-3 mm2/s, and sensitivity and specificity of 0.714 and 0.867, respectively. The negative correlation between lymph node metastasis status and ADC standard deviation was significant (ρ = -0.44, the correlation coefficients was represented by ρ). Positive correlations were observed between hormonal expression of ER and progesterone receptor (PR) with heterogeneity metrics of ADC or perfusion fraction (f), such as ADC inhomogeneity (ρ = 0.37, ρ = 0.29) and f skewness (ρ = 0.32, ρ = 0.28). Negative correlations were observed with numerical metrics, such as the ADC median (ρ = -0.31, ρ = -0.34) and f 45th percentile (ρ = -0.35, ρ = -0.28). The positive correlations between human epidermal receptor factor-2 (HER2) and pseudo-diffusivity (Dp) numerical metrics, Ki-67 expression, and heterogeneity metrics of Dp were high. CONCLUSIONS: The ADC 10th percentile had the largest area under the curve in the ER-negative ROC analysis, and the ADC standard deviation was the most valuable in the correlation analysis of lymph node metastasis. Whole-lesion quantitative histogram parameters of IVIM could, therefore, provide a scientific basis for radiomics to further guide clinical practice in the prognosis of breast cancer.

The diagnostic performance of diffusion-weighted imaging and dynamic contrast-enhanced magnetic resonance imaging in evaluating the pathological response of breast cancer to neoadjuvant chemotherapy: A meta-analysis.

PURPOSE: To evaluate and compare the diagnostic performance of diffusion-weighted imaging (DWI) and dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in predicting the pathological response of breast cancer to neoadjuvant chemotherapy (NAC). METHODS: We searched PubMed, EMBASE, Cochrane Library, and Web of Science systematically to identify relevant studies from inception to December 2020. The Quality Assessment of Diagnostic Accuracy Studies 2 tool was used to assess the methodological quality of the included studies. We extracted sufficient data to construct 2 × 2 tables and then used STATA 12.0 to perform data pooling, heterogeneity testing, meta-regression analysis and subgroup analysis. RESULTS: A total of 41 articles were enrolled in this study, including 27 studies (2107 patients) on DCE-MRI and 23 studies (1321 patients) on DWI. The pooled sensitivity and specificity of DCE-MRI were 0.75 and 0.79, and the pooled sensitivity and specificity of DWI were 0.77 and 0.75. There was no significant difference in sensitivity (P = 0.598) and specificity (P = 0.218) ​​between DCE-MRI and DWI. And meta-regression analysis showed that both magnetic field strength and the time of examination had significant effects on heterogeneity. CONCLUSIONS: DWI might be a potential substitute for DCE-MRI in predicting the pathological response of breast cancer to NAC as there was no significant difference in the diagnostic performance between the two. However, considering that not all included studies directly compared the diagnostic performance of DWI and DCE-MRI in the same patients and the heterogeneity of the included studies, caution should be exercised in applying our results.

Diagnostic role of 18F-FDG PET/MRI in the TNM staging of breast cancer: a systematic review and meta-analysis.

BACKGROUND: To investigate the value of 18F-fluorodeoxyglucose positron emission tomography/magnetic resonance imaging (18F-FDG PET/MRI) in diagnosing local tumor invasion (T stage), evaluating regional lymph node involvement (N stage), and detecting distant metastasis (M stage) in breast cancer patients. METHODS: A comprehensive computer search and manual search were performed to select any potentially eligible studies that evaluated the diagnostic efficacy of 18F-FDG PET/MRI in the tumor-node-metastasis (TNM) staging of breast cancer. Data from the included studies were extracted to calculate the pooled sensitivity, specificity, and area under the curve (AUC) to evaluate the value of 18F-FDG PET/MRI in TNM staging. Quality and publication bias were also assessed in this meta-analysis. RESULTS: Based on seven studies, the pooled sensitivity, specificity and AUC for the diagnosis of T stage were 91% (95% CI: 84-96%), 91% (95% CI: 81-96%), and 0.96 (95% CI: 0.94-0.98), respectively. For N stage evaluation, four studies were included, with values of 94% (95% CI: 83-98%), 90% (95% CI: 81-95%), and 0.96 (95% CI: 0.94-0.97). For M stage detection, five studies were evaluated, with values of 98% (95% CI: 96-99%), 96% (95% CI: 83-99%), and 0.99 (95% CI: 0.98-1.00). CONCLUSIONS: 18F-FDG PET/MRI demonstrates higher diagnostic value in the TNM staging of breast cancer and can serve as an effective and promising imaging biomarker for future evaluation of TNM stage in breast cancer patients.

Diagnostic Efficacy of Contrast-Enhanced MRI in Detecting Residual or Recurrent Hepatocellular Carcinoma After Transarterial Chemoembolization: A Systematic Review and Meta-analysis.

BACKGROUND: The diagnostic efficacy of contrast-enhanced magnetic resonance imaging (CEMRI) in diagnosing residual or recurrent hepatocellular carcinoma (HCC) after transarterial chemoembolization (TACE) is currently not completely clear. PURPOSE: To investigate the diagnostic efficacy of CEMRI in detecting residual or recurrent HCCs after TACE by meta-analysis. STUDY TYPE: Systematic review and meta-analysis. POPULATION: A systematic literature search was performed in PubMed, Embase, Web of Science, Ovid, and the Cochrane Library database up to June 2019 to find original studies on diagnosing patients suspected of residual or recurrent HCCs after TACE with CEMRI. Thirteen studies comprising 721 nodules were finally included. FIELD STRENGTH/SEQUENCE: 1.5T or 3.0T, CEMRI. ASSESSMENT: Quality assessment of the included studies was performed by applying the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool. STATISTICAL TESTS: Sensitivity and specificity were pooled with a bivariate random-effects model. Heterogeneity was assessed by the chi-square test. The potential sources of heterogeneity were explored by subgroup and publication bias analyses. RESULTS: The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the summary receiver operating characteristic (ROC) curve (AUC) of CEMRI in diagnosing residual or recurrent HCCs after TACE were 91% (95% confidence interval [CI]: 87%-96%), 93% (95% CI: 85%-97%), 12.22 (95% CI: 5.62-26.57), 0.09 (95% CI: 0.05-0.18), 126.99 (95% CI: 34.76-436.99) and 0.97 (95% CI: 0.95-0.98), respectively. Subgroup analysis revealed that CEMRI performed significantly better in prospective studies than in retrospective studies: 0.99 (95% CI: 0.96-1.00) vs. 0.95 (95% CI: 0.92-0.96) with P < 0.05. DATA CONCLUSION: Our meta-analysis suggested that CEMRI had high diagnostic efficacy in detecting residual or recurrent HCCs after TACE and may serve as an alternative method for further evaluation after TACE. LEVEL OF EVIDENCE: 5 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2020;52:1019-1028.

A structure-activity relationship of a thrombin-binding aptamer containing LNA in novel sites.

In this report, structural characterization, aptamer stability and thrombin of a new modified thrombin-ligand complex binding aptamer (TBA) containing anti-guanine bases and a loop position locked nucleic acid (LNA) are presented. NMR, circular dichroic spectroscopy and molecular modeling were used to characterize the three-dimensional structure of two G-quadruplexes. LNA-modification of the anti-guanosines yields G-quadruplexes that show affinity and inhibitory activity toward thrombin, whereas LNA-modification of a thymine nucleotide in the TGT loop increases the thermal stability of TBA. As assessed by denatured PAGE electrophoresis, all modified aptamers display an increase in environmental stability. The prothrombin time assay and fibrinogen assay showed that the aptamers still had good inhibitory activity, and 15 of them had the longest PT time. Therefore, the LNA modification is well suited to improve the physicochemical and biological properties of the native thrombin-binding aptamer.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal NHL domain of human TRIM2.

The tripartite motif-containing protein 2 (TRIM2) functions as an E3 ubiquitin ligase. Loss of function of TRIM2 has been shown to result in early-onset axonal neuropathy. As a member of the TRIM-NHL family of proteins, TRIM2 has a conserved modular architecture that includes N-terminal RING finger and B-box domains, a middle coiled-coil domain and a C-terminal NHL domain. To characterize the functional role of its NHL domain from the perspective of structural biology, a truncation of human TRIM2 (residues 465-744) was expressed, purified and crystallized. Rod-shaped crystals were obtained that diffracted X-rays to 1.7 Å resolution. The crystals belonged to space group P21, with unit-cell parameters a = 43.6, b = 76.4, c = 107.4 Å, α = 90.0, ß = 94.0, γ = 90.0°. A Matthews coefficient of 1.97 Å(3) Da(-1), corresponding to a solvent content of 37.6%, indicated the presence of three molecules per asymmetric unit, which was further confirmed by the phasing solution from molecular replacement.

Crystal structures and biochemical studies of human lysophosphatidic acid phosphatase type 6.

Lysophosphatidic acid (LPA) is an important bioactive phospholipid involved in cell signaling through Gprotein-coupled receptors pathways. It is also involved in balancing the lipid composition inside the cell, and modulates the function of lipid rafts as an intermediate in phospholipid metabolism. Because of its involvement in these important processes, LPA degradation needs to be regulated as precisely as its production. Lysophosphatidic acid phosphatase type 6 (ACP6) is an LPA-specific acid phosphatase that hydrolyzes LPA to monoacylglycerol (MAG) and phosphate. Here, we report three crystal structures of human ACP6 in complex with malonate, L-(+)-tartrate and tris, respectively. Our analyses revealed that ACP6 possesses a highly conserved Rossmann-foldlike body domain as well as a less conserved cap domain. The vast hydrophobic substrate-binding pocket, which is located between those two domains, is suitable for accommodating LPA, and its shape is different from that of other histidine acid phosphatases, a fact that is consistent with the observed difference in substrate preferences. Our analysis of the binding of three molecules in the active site reveals the involvement of six conserved and crucial residues in binding of the LPA phosphate group and its catalysis. The structure also indicates a water-supplying channel for substrate hydrolysis. Our structural data are consistent with the fact that the enzyme is active as a monomer. In combination with additional mutagenesis and enzyme activity studies, our structural data provide important insights into substrate recognition and the mechanism for catalytic activity of ACP6.