Magnetic Resonance Deep Learning Radiomic Model Based on Distinct Metastatic Vascular Patterns for Evaluating Recurrence-Free Survival in Hepatocellular Carcinoma

BACKGROUND

The metastatic vascular patterns of hepatocellular carcinoma (HCC) are mainly microvascular invasion (MVI) and vessels encapsulating tumor clusters (VETC). However, most existing VETC-related radiological studies still focus on the prediction of VETC status.

PURPOSE

This study aimed to build and compare VETC-MVI related models (clinical, radiomics, and deep learning) associated with recurrence-free survival of HCC patients.

STUDY TYPE

Retrospective.

POPULATION

398 HCC patients (349 male, 49 female; median age 51.7 years, and age range: 22-80 years) who underwent resection from five hospitals in China. The patients were randomly divided into training cohort (n = 358) and test cohort (n = 40).

FIELD STRENGTH/SEQUENCE

3-T, pre-contrast T1-weighted imaging spoiled gradient recalled echo (T1WI SPGR), T2-weighted imaging fast spin echo (T2WI FSE), and contrast enhanced arterial phase (AP), delay phase (DP).

ASSESSMENT

Two radiologists performed the segmentation of HCC on T1WI, T2WI, AP, and DP images, from which radiomic features were extracted. The RFS related clinical characteristics (VETC, MVI, Barcelona stage, tumor maximum diameter, and alpha fetoprotein) and radiomic features were used to build the clinical model, clinical-radiomic (CR) nomogram, deep learning model. The follow-up process was done 1 month after resection, and every 3 months subsequently. The RFS was defined as the date of resection to the date of recurrence confirmed by radiology or the last follow-up. Patients were followed up until December 31, 2022.

STATISTICAL TESTS

Univariate COX regression, least absolute shrinkage and selection operator (LASSO), Kaplan-Meier curves, log-rank test, C-index, and area under the curve (AUC). P < 0.05 was considered statistically significant.

RESULTS

The C-index of deep learning model achieved 0.830 in test cohort compared with CR nomogram (0.731), radiomic signature (0.707), and clinical model (0.702). The average RFS of the overall patients was 26.77 months (range 1-80 months).

DATA CONCLUSION

MR deep learning model based on VETC and MVI provides a potential tool for survival assessment.

EVIDENCE LEVEL

3 TECHNICAL EFFICACY: Stage 3.

BioSTD: A New Tensor Multi-View Framework via Combining Tensor Decomposition and Strong Complementarity Constraint for Analyzing Cancer Omics Data

Advances in omics technology have enriched the understanding of the biological mechanisms of diseases, which has provided a new approach for cancer research. Multi-omics data contain different levels of cancer information, and comprehensive analysis of them has attracted wide attention. However, limited by the dimensionality of matrix models, traditional methods cannot fully use the key high-dimensional global structure of multi-omics data. Moreover, besides global information, local features within each omics are also critical. It is necessary to consider the potential local information together with the high-dimensional global information, ensuring that the shared and complementary features of the omics data are comprehensively observed. In view of the above, this article proposes a new tensor integrative framework called the strong complementarity tensor decomposition model (BioSTD) for cancer multi-omics data. It is used to identify cancer subtype specific genes and cluster subtype samples. Different from the matrix framework, BioSTD utilizes multi-view tensors to coordinate each omics to maximize high-dimensional spatial relationships, which jointly considers the different characteristics of different omics data. Meanwhile, we propose the concept of strong complementarity constraint applicable to omics data and introduce it into BioSTD. Strong complementarity is used to explore the potential local information, which can enhance the separability of different subtypes, allowing consistency and complementarity in the omics data to be fully represented. Experimental results on real cancer datasets show that our model outperforms other advanced models, which confirms its validity.

NLRRC: A Novel Clustering Method of Jointing Non-Negative LRR and Random Walk Graph Regularized NMF for Single-Cell Type Identification

The development of single-cell RNA sequencing (scRNA-seq) technology has opened up a new perspective for us to study disease mechanisms at the single cell level. Cell clustering reveals the natural grouping of cells, which is a vital step in scRNA-seq data analysis. However, the high noise and dropout of single-cell data pose numerous challenges to cell clustering. In this study, we propose a novel matrix factorization method named NLRRC for single-cell type identification. NLRRC joins non-negative low-rank representation (LRR) and random walk graph regularized NMF (RWNMFC) to accurately reveal the natural grouping of cells. Specifically, we find the lowest rank representation of single-cell samples by non-negative LRR to reduce the difficulty of analyzing high-dimensional samples and capture the global information of the samples. Meanwhile, by using random walk graph regularization (RWGR) and NMF, RWNMFC captures manifold structure and cluster information before generating a cluster allocation matrix. The cluster assignment matrix contains cluster labels, which can be used directly to get the clustering results. The performance of NLRRC is validated on simulated and real single-cell datasets. The results of the experiments illustrate that NLRRC has a significant advantage in single-cell type identification.

[Comparison between laparoscopic-assisted natural orifice specimen extraction surgery and conventional laparoscopic surgery for left colorectal cancer: 5-year follow-up results of a randomized controlled study]

Objective: To evaluate the long-term efficacy of laparoscopic-assisted natural orifice specimen extraction surgery (NOSES) colectomy using Cai tube for treating left-sided colorectal cancer. Methods: This was a randomized controlled trial. Inclusion criteria were as follows: preoperative pathological diagnosis of left-sided colorectal adenocarcinoma (rectal, sigmoid colon, descending colon, or left transverse colon cancer with the caudad margin ≥8 cm from the anal margin); preoperative abdominal and pelvic computed tomography (or magnetic resonance imaging) showing maximum tumor diameter <4.5 cm; and BMI <30 kg/m2. Patients with synchronous multiple primary cancers or recurrent cancers, a history of neoadjuvant chemoradiotherapy, preoperative evidence of significant local infiltration, distant metastasis, or complications such as intestinal obstruction and intestinal perforation, or who were not otherwise considered suitable for laparoscopic surgery were excluded. A random number table was used to randomize sequential patients to NOSES surgery using Cai tube (non-assisted incision anal sleeve: patent number ZL201410168748.2) (NOSES group) or traditional laparoscopic-assisted surgery (CLS group). Relevant clinical data of the two groups of patients were analyzed, the main outcomes being disease-free survival, overall survival, overall recurrence rate, and local recurrence rate 5 years after surgery. Results: Patients in both study groups completed the surgery successfully with no requirement for additional surgery. After mean 70 (7-83) months postoperative follow-up, the 5-year overall postoperative survival in the NOSES and CLS groups was 90.0% and 83.3%, respectively (P=0.455); disease free survival was 90.0% and 83.3%, respectively (P=0.455); overall recurrence rate 6.6% and 10.0%, respectively (P=0.625); and local recurrence rate both were 3.3% (P=0.990), respectively. None of these differences was statistically significant. Conclusions: NOSES and CLS have similar long-term efficacy, and NOSES deserves to be used in clinical practice.

Multi-View Enhanced Tensor Nuclear Norm and Local Constraint Model for Cancer Clustering and Feature Gene Selection

The analysis of cancer data from multi-omics can effectively promote cancer research. The main focus of this article is to cluster cancer samples and identify feature genes to reveal the correlation between cancers and genes, with the primary approach being the analysis of multi-view cancer omics data. Our proposed solution, the Multi-View Enhanced Tensor Nuclear Norm and Local Constraint (MVET-LC) model, aims to utilize the consistency and complementarity of omics data to support biological research. The model is designed to maximize the utilization of multi-view data and incorporates a nuclear norm and local constraint to achieve this goal. The first step involves introducing the concept of enhanced partial sum of tensor nuclear norm, which significantly enhances the flexibility of the tensor nuclear norm. After that, we incorporate total variation regularization into the MVET-LC model to further augment its performance. It enables MVET-LC to make use of the relationship between tensor data structures and sparse data while paying attention to the feature details of the tensor data. To tackle the iterative optimization problem of MVET-LC, the alternating direction method of multipliers is utilized. Through experimental validation, it is demonstrated that our proposed model outperforms other comparison models.

Precise microdissection of gastric mixed adeno-neuroendocrine carcinoma dissects its genomic landscape and evolutionary clonal origins

Gastric mixed adenoneuroendocrine carcinoma (MANEC) is a clinically aggressive and heterogeneous tumor composed of adenocarcinoma (ACA) and neuroendocrine carcinoma (NEC). The genomic properties and evolutionary clonal origins of MANEC remain unclear. We conduct whole-exome and multiregional sequencing on 101 samples from 33 patients to elucidate their evolutionary paths. We identify four significantly mutated genes, TP53, RB1, APC, and CTNNB1. MANEC resembles chromosomal instability stomach adenocarcinoma in that whole-genome doubling in MANEC is predominant and occurs earlier than most copy-number losses. All tumors are of monoclonal origin, and NEC components show more aggressive genomic properties than their ACA counterparts. The phylogenetic trees show two tumor divergence patterns, including sequential and parallel divergence. Furthermore, ACA-to-NEC rather than NEC-to-ACA transition is confirmed by immunohistochemistry on 6 biomarkers in ACA- and NEC-dominant regions. These results provide insights into the clonal origin and tumor differentiation of MANEC.

[Comparison between laparoscopic-assisted natural orifice specimen extraction surgery and conventional laparoscopic surgery for left colorectal cancer: a randomized controlled study with 3-year follow-up results]

Objective: To evaluate the mid-term efficacy of laparoscopic-assisted natural orifice specimen extraction surgery (NOSES) colectomy using the Cai tube in the treatment of left colorectal cancer. Methods: A prospective randomized control trial (China Clinical Trials Registration Number: ChiCTR-OOR-15007060) was performed. Sixty patients with left colorectal cancer at Department of Gastrointestinal Surgery of Zhongshan Hospital from September 2015 to August 2017 were prospectively enrolled. Case inclusion criteria: (1) left colorectal adenocarcinoma (rectal cancer with distance ≥ 8 cm from tumor low margin to anal edge, sigmoid colon cancer, descending colon cancer and left transverse colon cancer) confirmed by preoperative pathology; (2) satisfactory conditions of conventional laparoscopic surgery; (3) maximum diameter of the tumor < 4.5 cm confirmed by preoperative abdominal and pelvic CT or MRI; (4) BMI < 30 kg/m². Case exclusion criteria: (1) benign lesions, mucinous adenocarcinoma, signet-ring cell carcinoma and other special pathological types of tumors confirmed by preoperative pathological examination; (2) multiple or recurrent cancers; (3) with a history of neoadjuvant chemoradiotherapy; (4) obvious regional infiltration or distant metastasis indicated by preoperative imaging examination; (5) intestinal obstruction, intestinal perforation, etc. Participants were randomly assigned to NOSES group (using the Cai tube) and conventional laparoscopy (CL) group by random number table method. Clinical data between two groups were compared and analyzed, including perioperative conditions, tumor exfoliation cell detection and bacterial culture results of intraperitoneal lavage fluid, postoperative complications (Clavien-Dindo grading), postoperative pain [visual simulation scoring (VAS) assessment], anal function (Kirwan anal function grading assessment), and postoperative 3-year disease-free survival (DFS), overall survival (OS), overall recurrence rate, and local recurrence rate. Results: A total of 60 patients were enrolled, with 30 in the NOSES group and 30 in the CL group. All the patients in the NOSES group successfully completed operation with Cai tube. Baseline data between the two groups were not significantly different (all P>0.05). There were no statistically significant differences between two groups in conversion rate to open surgery, number of lymph node harivested, proximal and distal resection margin of tumor, negative rate of circumferential margin, operation time, blood loss, inflammatory indexes, postoperative anal function, postoperative hospital stay, hospitalization cost, morbidity of postoperative complications (Clavien-Dindo grade II or above) (all P>0.05). Compared to the CL group, the NOSES group had lower maximum postoperative VAS score (2.5±0.3 vs. 5.1±0.4, t=3.187, P<0.01), and fewer use of additional postoperative analgesia [6.7% (2/30) vs. 33.3% (10/30),χ²=6.670, P=0.02]. The postoperative time to gas passage was shorter in the NOSES group [(2.2±1.4) days vs. (3.1±1.2) days,P=0.026]. No tumor cells and bacterial contamination were found in abdominal lavage fluid before and after operation in either group. The anal function at postoperative 3-month of all the patients in the NOSES group was Kirwan grade I to II, while in the CL group, anal function of 2 cases (6.7%) was Kirwan grade III, and of 28 cases was also Kirwan grade I to II, whose difference was not statistically significant (P>0.05). In the NOSES group and the CL group, 3-year DFS was 96.7% and 83.3% (P=0.090), OS was 100% and 90% (P=0.096), overall recurrence rate was 3.3% and 10.0% (P=0.166), and local recurrence rate was 3.3% and 3.3% (P=0.999), respectively, whose differences were not statistically significant (all P>0.05). Conclusions: In the treatment of left colorectal cancer, compared with conventional laparoscopic colectomy, NOSES colectomy using Cai tube exhibits less scar, less postoperative pain, shorter recovery of gastrointestinal function, and similar mid-term outcomes. Given proper surgical indications, the surgical procedure is safe and feasible.

Cisapride induced hypoglycemia via the KCNH6 potassium channel

Mutations in KCNH6 has been proved to cause hypoinsulinemia and diabetes in human and mice. Cisapride is a stomach-intestinal motility drug used to treat gastrointestinal dysfunction. Cisapride has been reported to be a potential inhibitor of the KCNH family, but it remained unclear whether cisapride inhibited KCNH6. Here, we discovered the role of cisapride on glucose metabolism, focusing on the KCNH6 potassium channel protein. Cisapride reduced blood glucose level and increased serum insulin secretion in wild-type (WT) mice fed standard normal chow/a high-fat diet or in db/db mice, especially when combined with tolbutamide. This effect was much stronger after 4 weeks of intraperitoneal injection. Whole-cell patch-clamp showed that cisapride inhibited KCNH6 currents in transfected HEK293 cells in a concentration-dependent manner. Cisapride induced an increased insulin secretion through the disruption of intracellular calcium homeostasis in a rat pancreatic β-cell line, INS-1E. Further experiments revealed that cisapride did not decrease blood glucose or increase serum insulin in KCNH6 β-cell knockout (Kcnh6-β-KO) mice when compared with WT mice. Cisapride also ameliorated glucose-stimulated insulin secretion (GSIS) in response to high glucose in WT but not Kcnh6-β-KO mice. Thus, our data reveal a novel way for the effect of KCNH6 in cisapride-induced hypoglycemia.

[Systematic review on the reform of disease prevention and control system in China]

Objective: To systematically understand the reform progress of disease prevention and control system in China. Methods: The literature regarding the reform of China's disease prevention and control system was searched by using the keywords including disease prevention and control, center for disease prevention and control (CDC), disease control, reform, and system from 2003 to 2020 in China CNKI, Wanfang Data knowledge service platform, VIP information and China biomedical literature database. The language is limited to Chinese. A total of 25 studies were included to analyze the information about the organizational structure, functional orientation, financing mechanism and personnel system of China's disease prevention and control system. Results: The 25 studies described the specific changes and reform suggestions of China's disease prevention and control system, including key policies (7 studies), organizational structure transformation (4 studies), institutional function transformation (7 studies), financing mechanism transformation (5 studies), personnel system reform (2 studies), and performance-based salary system reform (4 studies). Meanwhile, the reform suggestions were concluded at the top-level design system reform (two aspects), organization structure (three aspects), functioning (four aspects), and personnel guarantee mechanism (three aspects). Conclusions: This study indicates that there is a lack of empirical evidence regarding specific reform effects and content analysis at the micro level of disease prevention and control system in China. Future study should strengthen the rigorousness of study design and focus on the quantitative impacts of reform implementation in China.

[Experimental study on the effect of three-dimensional porous structures on the vascularization rate of artificial dermis]

Objective: To explore the effects of orienting three-dimensional porous network (type A) and honeycomb briquette-shaped vertically penetrating three-dimensional porous network (type B) on the vascularization rate of artificial dermis. Methods: The experimental research method was used. The artificial dermis was composed of a double layer of silicone layer and scaffold layer. Based on the difference of scaffold layer, they were divided into type A and type B artificial dermis (type A dermis and type B dermis, for short) containing type A and type B structure, respectively. The type A and type B structures were prepared by gradient freeze-drying technique and physical pore-making technique, respectively. The micro-morphology of two kinds of dermis scaffold was observed by scanning electron microscopy. The porosity of two kinds of dermis scaffold was measured by the Pyrex method. According to the method of national medical industry standard, the hydroxyproline content in degradation liquids and their residues in two kind of dermis were determined after degradation at 4, 8, 13, and 24 h, reflecting the degradation rates of two kinds of dermis. According to the random number table, L929 cells were divided into type A dermis group, type B dermis group, negative control group, and positive control group. The positive control group was added with minimum essential medium (MEM) containing 5% dimethyl sulfoxide, The negative control group was added with high-density polyethylene extract, and the other two groups were added with the corresponding extract. At 24 hours after culture, the growth rate of L929 cells was detected by methyl thiazolyl tetrazolium, and the cytotoxicity was graded. L929 cells and human umbilical vein endothelial cells (HUVECs) were inoculated into pore plates with two kinds of dermis preinstalled. On 1, 4, 7, and 14 d after inoculating, the adhesion and growth of L929 cells on the surfaces of the two kinds of scaffolds were detected by immunofluorescence method. On 7 d after inoculating, the migration of the above two kinds of cells into the two kinds of dermal scaffolds was detected by immunofluorescence and hematoxylin-eosin (HE) staining. Three full-thickness skin defect wounds of 5.0 cm×5.0 cm were created on both sides of the back of three 6-month-old healthy male Ba-Ma mini pigs. According to the random number table, six columns of wounds were divided into type A dermis two-step method group, type B dermis two-step method group, and type B dermis one-step method group. The wounds in type A dermis two-step method group and type B dermis two-step method group were transplanted with type A or type B dermis respectively before, and with autologous split-thickness skin grafting later. The wounds in type B dermis one-step method group were transplanted in a synchronous procedure including type B dermis (without silicone layer) and autologous skin grafting simultaneously. The bleeding, exudation, and infection of the wounds on the back in type A dermis two-step method group and type B dermis two-step method group on the 7th day after the second transplantation and in type B dermis one-step method group on the 14th day after the first transplantation were generally observed. The area of autologous skin graft was measured by the transparent film grid method, and the survival rate of autologous skin was calculated. On 4, 7, and 14 d after the first transplantation, the inflammatory cells, fibroblasts (Fbs), and capillary infiltration into the scaffolds of the three groups were detected by HE staining. On 7, 14 d after the first transplantation, the vascularization of the scaffolds was further observed by immunohistochemistry. On 28, 90 d after the first operation, the degradation of the scaffolds of type A dermis and type B dermis was observed by HE staining. Data were statistically analyzed with one-way analysis of variance, independent sample t test, and Bonferroni correction. Results: A large number of round and oval micropores were evenly distributed on the surface of type A scaffold, and the cylindrical hole walls could be observed arranging in a parallel direction in the longitudinal section. The honeycomb briquette-shaped penetrating macropores on the surface of type B scaffold were arranged in an orderly matrix. The pore walls of the honeycomb briquette-shaped penetrating macropores were connected by micropores to form a network structure. The porosity of type A dermis was (93.21±0.72)%, which was similar to (95.88±1.00)% of type B dermis (t=4.653, P>0.05). The degradation rates of type A dermis at 4, 8, 13, and 24 h were similar to those of type B dermis at the corresponding time point (t=0.232, 0.856, 0.258, 7.716, P>0.05). At 24 h after culture, the proliferation rates of L929 cells in the type A dermis group, type B dermis group, and negative control group were significantly higher than those of the positive control group (t=2 393.46, 2 538.27, 1 077.77, P<0.01). The cytotoxicity rating of cells in positive control group was grade 4, while that of the other three groups was grade zero. On 1, 4, 7, and 14 d after inoculation, both L929 cells and HUVECs proliferated in a time-dependent manner in two kinds of dermal scaffolds. The adhesion growth and proliferation rate of the two kinds of cells on the surface of type B dermis was higher than that of type A dermis. On 7 d after inoculation, both L929 cells and HUVECs covered the surface of type B dermis and migrated into one side of the silicone layer. However, the above two kinds of cells migrated slowly into type A dermis, and only a few cells were found on one side of the silicone layer. There was no bleeding, exudation, or infection in the wounds repaired by type A and type B dermis. The survival rate of autologous skin grafting of 6 wounds in each group was 100%. On 4, 7, and 14 d after the first operation, inflammatory cells, Fbs, and capillaries gradually infiltrated into the scaffold layer, and the cell infiltration rate from high to low was type B dermis one-step method group, type B dermis two-step method group, and type A dermis two-step method group. The scaffold in wound in the type B dermis one-step method group gradually collapsed on 28 d after the first operation, and completely degraded in 3 months after the first operation. The scaffold degradation rate of type A dermis two-step method group was similar to that mentioned above. Conclusions: The honeycomb briquette-shaped vertically penetrating three-dimensional porous network structure of type B scaffold can accelerate its vascularization process, which is beneficial to autogenous split-thickness skin in one-step procedure to repair full-thickness skin defects wound in Ba-Ma mini pigs. Compared with the "two-step method" of staged transplantation of type A scaffold and autologous split-thickness skin, and one-step transplantation has equal efficacy and can provide a better choice for wound treatment.

[Research progress on building of disease control and prevention system of the international experience]

Through literature search in regular database and official websites of relevant countries, this paper combs and summarizes the main characteristics of disease prevention and control systems in five countries, the United States, Germany, South Korea, Australia and Japan, and the European Union at key levels including legal construction, organizational structure, financing, personnel construction and international cooperation, in order to provide decision support for the construction of disease prevention and control system in China in the future.

[Policy analysis of disease control and prevention system in China from the perspective of policy instruments from 2000 to 2020]

Objective: To analyze the related polities about disease control and prevention system in China from 2000 to 2020, and to provide implication for the policy formulation of disease control and prevention system in the future. Methods: Policy documents were searched in the official websites of relevant government departments including the State Council, National Health Commission, National Development and Reform Commission, Ministry of Human Resources and Social Security, and Ministry of Finance by using the keywords related to disease control and prevention from 2000 to 2020. Thematic framework and content analysis were performed to analyze the eligible policy documents based on the theory of policy instruments. Results: A total of 37 policy documents were included in this study. The application of single policy instrument was common (81.1%), of which the capacity building instrument was the most frequently used (32.4%), followed by mandate instrument (21.6%) and inducement instrument (13.5%), while system-changing instrument (8.1%) and symbolic and hortatory instrument were less used (5.4%). The main policy themes were personnel system (15.2%) and system construction (15.2%), followed by personnel development (13.0%) and information construction (2.2%). Conclusion: In the policy formulation process, the government should strengthen the comprehensive application of multiple policy instruments. Particularly about the inducement instrument and symbolic and hortatory instrument to further stimulate the internal motivation of disease control and prevention system and institutions in China.

[Changes of the number of disease control and prevention staffs at provincial level in China from 2002 to 2018: an interrupted time series analysis]

Objective: To analyze the change of the number of staff at the provincial center for disease control and prevention (CDC) in China before and after the new health care reform. Methods: The data was from publicly reported health statistics yearbooks from 2002 to 2018. Descriptive analysis and interrupted time series analysis (ITS) were conducted in Stata/SE 15. Results: The decreasing trend of total number and average number of CDC staff per ten thousand people further exacerbated in the eastern and central areas after the new health care reform, while the total number of CDC staff in the western area changed from a decreasing trend to an increasing tend and the decreasing trend of average number of CDC staff per ten thousand people slowed down. After controlling the provincial and time fixed effects, the ITS analysis showed that before the reform, the number of CDC staff in central area showed a decreasing trend (P=0.012). After the reform, no statistically significant changes were observed in the number of CDC staff in the eastern, central and western areas increased instantaneously (P>0.05), and the decreasing trend (slope) of the number of CDC staff in the eastern and central areas further increased. The number of CDC staff in the western area changed to an increasing trend (P>0.05). Conclusion: After the new health care reform, the total number and average number of CDC staff at the provincial level have not improved, therefore targeted reform strategies are needed to reverse the continuous reduction of CDC staff and reflect regional differences in the future.

Similarity and Dissimilarity Regularized Nonnegative Matrix Factorization for Single-Cell RNA-seq Analysis

In traditional sequencing techniques, the different functions of cells and the different roles they play in differentiation are often ignored. With the advancement of single-cell RNA sequencing (scRNA-seq) techniques, scientists can measure the gene expression value at the single-cell level, and it is helping to understand the heterogeneity hidden in cells. One of the most powerful ways to find heterogeneity is using the unsupervised clustering method to get separate subpopulations. In this paper, we propose a novel clustering method Similarity and Dissimilarity Regularized Nonnegative Matrix Factorization (SDCNMF) that simultaneously impose similarity and dissimilarity constraints on low-dimensional representations. SDCNMF both considers the similarity of closer cells and the dissimilarity of cells that are farther away. It can not only keep the similar cells getting closer in low-dimensional space, but also can push the dissimilar cells away from each other. We test the validity of our proposed method on five scRNA-seq datasets. Clustering results show that SDCNMF is better than other comparative methods, and the gene markers we find are also consistent with previous studies. Therefore, we can conclude that SDCNMF is effective in scRNA-seq data analysis. This paper proposes a novel clustering method Similarity and Dissimilarity Regularized Nonnegative Matrix Factorization (SDCNMF) that simultaneously impose similarity and dissimilarity constraints on low-dimensional representations. SDCNMF both considers the similarity of closer cells and the dissimilarity of cells that are farther away. It can not only keep the similar cells getting closer in low-dimensional space, but also can push the dissimilar cells away from each other. Clustering results show that SDCNMF is better than other comparative methods, and the gene markers we find are also consistent with previous studies.

The clinicopathological significance and predictive value for immunotherapy of programmed death ligand-1 expression in Epstein-Barr virus-associated gastric cancer

The effect of anti-programmed cell death 1 (PD-1) antibody in Epstein-Barr virus-associated gastric cancer (EBVaGC) was debatable, and no predictive biomarkers for efficacy have been reported. Public reports on anti-PD-1 antibody monotherapy-treated EBVaGC with available programmed death ligand-1 (PD-L1) expression status were summarized and analyzed. Relevance with clinicopathologic characteristics of PD-L1 expression by immunohistochemistry was analyzed in 159 patients diagnosed with EBVaGC. Relevance with genomic transcriptome and mutation profile of PD-L1 status in EBVaGC was assessed with three datasets, the cancer genome atlas (TCGA), Gene Expression Omnibus (GEO) GSE51575, and GSE62254. Based on the data from 8 reports, patients with positive PD-L1 expression (n = 30) had significantly superior objective response rate (ORR) than patients with negative PD-L1 expression (n = 9) (63.3% vs. 0%, P = .001) in EBVaGC receiving anti-PD-1 antibody monotherapy. PD-L1 positivity was associated with less aggressive clinicopathological characteristics and was an independent predictor for a longer disease-free survival (hazard ratio [HR] and 95% CI: 0.45 [0.22–0.92], P = .03) and overall survival (HR and 95% CI: 0.17 [0.06–0.43], P < .001). Analysis of public EBVaGC transcriptome and mutation datasets revealed enhanced immune-related signal pathways in PD-L1^high EBVaGC and distinct mutation patterns in PD-L1^low EBVaGC. PD-L1 positivity indicates a subtype of EBVaGC with ‘hot’ immune microenvironment, lower aggressiveness, better prognosis, and higher sensitivity to anti-PD-1 immunotherapy.

Joint Lp-Norm and L2,1-Norm Constrained Graph Laplacian PCA for Robust Tumor Sample Clustering and Gene Network Module Discovery

The dimensionality reduction method accompanied by different norm constraints plays an important role in mining useful information from large-scale gene expression data. In this article, a novel method named Lp-norm and L2,1-norm constrained graph Laplacian principal component analysis (PL21GPCA) based on traditional principal component analysis (PCA) is proposed for robust tumor sample clustering and gene network module discovery. Three aspects are highlighted in the PL21GPCA method. First, to degrade the high sensitivity to outliers and noise, the non-convex proximal Lp-norm (0 < p < 1)constraint is applied on the loss function. Second, to enhance the sparsity of gene expression in cancer samples, the L2,1-norm constraint is used on one of the regularization terms. Third, to retain the geometric structure of the data, we introduce the graph Laplacian regularization item to the PL21GPCA optimization model. Extensive experiments on five gene expression datasets, including one benchmark dataset, two single-cancer datasets from The Cancer Genome Atlas (TCGA), and two integrated datasets of multiple cancers from TCGA, are performed to validate the effectiveness of our method. The experimental results demonstrate that the PL21GPCA method performs better than many other methods in terms of tumor sample clustering. Additionally, this method is used to discover the gene network modules for the purpose of finding key genes that may be associated with some cancers.

Efficacy and Mechanism of a Chinese Classic Prescription of Yueju in Treating Nonalcoholic Steatohepatitis and Protecting Hepatocytes from Apoptosis

Yueju, a famous classic Chinese prescription, has been extensively used in treating depression syndromes for hundreds of years. Recent studies have reported that Yueju showed good effects in treating metabolic diseases, such as obesity and hyperlipidemia. Nonalcoholic steatohepatitis (NASH), which leads to cirrhosis and severe cardiovascular diseases, is closely linked to obesity and abnormal lipid metabolism. In this study, Yueju could decrease the levels of alanine aminotransferase, aspartate transaminase, triglyceride, cholesterol, and low-density lipoprotein-C but increase the high-density lipoprotein-C in the serum of the NASH rat model induced by high-fat and high-cholesterol diet. Yueju could alleviate hepatosteatosis by increasing the phosphorylation of acetyl-CoA carboxylase and inhibiting the expression of fatty acid synthase and stearoyl-CoA desaturase 1. Yueju downregulated the expression of α-smooth muscle actin and collagen type 1A1, ameliorating the liver fibrilization. Yueju could also protect the hepatocytes from apoptosis by upregulating antiapoptosis protein Bcl-2 and X-linked inhibitor of apoptosis protein and downregulating apoptotic proteins Bax and cleaved poly ADP-ribose polymerase. Thus, Yueju could improve liver function, regulate lipid metabolism, alleviate hepatosteatosis and fibrosis, and protect hepatocytes from apoptosis against NASH. Yueju may be used as an alternative effective medicine for NASH treatment.

Atonal bHLH transcription factor 1 is an important factor for maintaining the balance of cell proliferation and differentiation in tumorigenesis

Establishing the link between cellular processes and oncogenesis may aid the elucidation of targeted and effective therapies against tumor cell proliferation and metastasis. Previous studies have investigated the mechanisms involved in maintaining the balance between cell proliferation, differentiation and migration. There is increased interest in determining the conditions that allow cancer stem cells to differentiate as well as the identification of molecules that may serve as novel drug targets. Furthermore, the study of various genes, including transcription factors, which serve a crucial role in cellular processes, may present a promising direction for future therapy. The present review described the role of the transcription factor atonal bHLH transcription factor 1 (ATOH1) in signaling pathways in tumorigenesis, particularly in cerebellar tumor medulloblastoma and colorectal cancer, where ATOH1 serves as an oncogene or tumor suppressor, respectively. Additionally, the present review summarized the associated therapeutic interventions for these two types of tumors and discussed novel clinical targets and approaches.

Associations of maternal hyperglycemia in the second and third trimesters of pregnancy with prematurity

Hyperglycemia in pregnancy (HIP) is related to adverse pregnancy outcomes. However, women with hyperglycemia in the second and third trimester of pregnancy (HISTTP) were not been observed. We aim to reveal associations between HISTTP and prematurity. To confirm which risk factor is better in predicting preterm delivery.This retrospective study included 660 patients, of which 132 have HISTTP and 528 have euglycemia. Univariate analysis was used to extract risk factors and multivariates logistic regression analysis to obtain odds ratio (OR) for prematurity. Mean decrease gini (MDG) in random forest algorithm was used to rank the risk factors.HISTTP women have higher prepregnancy BMI and a higher percentage of family history of hypertension, maternal adiposity, maternal anemia, gestational diabetes mellitus (GDM), prematurity, neonatal asphyxia in 1-minute (P < .05). Univariate analysis of prematurity showed that preterm women had higher rate of HISTTP (P < .01), second births, elderly pregnancy, hypertention, family history of hypertention and multiple perinatal infant (P < .05). Multivariate logistic regression analysis indicates that HISTTP (OR = 2.984, P = .0017), maternal hypertension (OR = 5.208, P = .001) and multiple perinatal infants (OR = 59.815, P < .0001) are independent risk factors for prematurity. After ranked the MDG, the top 3 risk factors were multiple perinatal infants, maternal hypertension, HISTTP. MDG of HISTTP is higher than that of GDM.Women with HISTTP deserve to be concerned, whose prematurity rate are increased. HISTTP is an independent risk factor and a better predictor of prematurity.

A new method for mining information of co-expression network based on multi-cancers integrated data

Background

Gene co-expression network is a favorable method to reveal the nature of disease. With the development of cancer, the way to build gene co-expression networks based on cancer data has been become a hot spot. However, there are still a limited number of current node measurement methods and node mining strategies for multi-cancers network construction.

Methods

In this paper, we introduce a new method for mining information of co-expression network based on multi-cancers integrated data, named PMN. We construct the network by combining the different types of relevant measures (linear and nonlinear rules) for different nodes based on integrated gene expression data of multi-cancers from The Cancer Genome Atlas (TCGA). For mining genes, we combine different properties (local and global characteristics) of the nodes.

Results

We uncover more suspicious abnormally expressed genes and shared pathways of different cancers. And we have also found some proven genes and pathways; of course, there are some suspicious factors and molecules that need clinical validation.

Conclusions

The results demonstrate that our method is very effective in excavating gene co-expression genes of multi-cancers.

A New Model of Identifying Differentially Expressed Genes via Weighted Network Analysis Based on Dimensionality Reduction Method

Background:

As a method to identify Differentially Expressed Genes (DEGs), Non- Negative Matrix Factorization (NMF) has been widely praised in bioinformatics. Although NMF can make DEGs to be easily identified, it cannot provide more associated information for these DEGs.

Objective:

The methods of network analysis can be used to analyze the correlation of genes, but they caused more data redundancy and great complexity in gene association analysis of high dimensions. Dimensionality reduction is worth considering in this condition.

Methods:

In this paper, we provide a new framework by combining the merits of two: NMF is applied to select DEGs for dimensionality reduction, and then Weighted Gene Co-Expression Network Analysis (WGCNA) is introduced to cluster on DEGs into similar function modules. The combination of NMF and WGCNA as a novel model accomplishes the analysis of DEGs for cholangiocarcinoma (CHOL).

Results:

Some hub genes from DEGs are highlighted in the co-expression network. Candidate pathways and genes are also discovered in the most relevant module of CHOL.

Conclusion:

The experiments indicate that our framework is effective and the works also provide some useful clues to the reaches of CHOL.

LncRNA-Disease Associations Prediction Using Bipartite Local Model With Nearest Profile-Based Association Inferring

There is much evidence that long non-coding RNA (lncRNA) is associated with many diseases. However, it is time-consuming and expensive to identify meaningful lncRNA-disease associations (LDAs) through medical or biological experiments. Therefore, investigating how to identify more meaningful LDAs is necessary, and at the same time it is conducive to the prevention, diagnosis and treatment of complex diseases. Considering the limitations of some current prediction models, a novel model based on bipartite local model with nearest profile-based association inferring, BLM-NPAI, is developed for predicting LDAs. This model predicts novel LDAs from the lncRNA side and the disease side, respectively. More importantly, for some lncRNAs and diseases without any association, the model can also be predicted by their nearest neighbors. Leave-one-out cross validation (LOOCV) and 5-fold cross validation are implemented for BLM-NPAI to evaluate the performance of this model. Our model is superior to current advanced methods in most cases. In addition, to verify the validity and reliability of BLM-NPAI, three disease cases and three lncRNA cases are analyzed to further evaluate BLM-NPAI. Finally, these predicted novel LDAs are confirmed by using the LncRNA-disease database.

L2,1-GRMF: an improved graph regularized matrix factorization method to predict drug-target interactions

Background

Predicting drug-target interactions is time-consuming and expensive. It is important to present the accuracy of the calculation method. There are many algorithms to predict global interactions, some of which use drug-target networks for prediction (ie, a bipartite graph of bound drug pairs and targets known to interact). Although these algorithms can predict some drug-target interactions to some extent, there is little effect for some new drugs or targets that have no known interaction.

Results

Since the datasets are usually located at or near low-dimensional nonlinear manifolds, we propose an improved GRMF (graph regularized matrix factorization) method to learn these flow patterns in combination with the previous matrix-decomposition method. In addition, we use one of the pre-processing steps previously proposed to improve the accuracy of the prediction.

Conclusions

Cross-validation is used to evaluate our method, and simulation experiments are used to predict new interactions. In most cases, our method is superior to other methods. Finally, some examples of new drugs and new targets are predicted by performing simulation experiments. And the improved GRMF method can better predict the remaining drug-target interactions.

The association of calcium channel blockers with β-cell function in type 2 diabetic patients: A cross-sectional study

Type 2 diabetes mellitus (T2DM) patients are often accompanied with hypertension. However, the association of antihypertensive drugs with β-cell function has not been well studied. To investigate this question, the authors performed a cross-sectional study involving 882 hypertensive T2DM patients. To assess β-cell function, patients were given 75g glucose orally and C-peptide levels before and 1, 2, and 3 hours after glucose intake were measured. Homa-β was computed by Homeostasis Model Assessment model to evaluate β-cell function using fasting C-peptide and glucose levels in the plasma. Multivariable-adjusted analysis was performed to evaluate the association of antihypertensive drugs with C-peptide levels, HbA1c, and Homa-β. Among 882 hypertensive patients, 547 (62.0%) received antihypertensive treatment. Multivariate-adjusted analysis demonstrated that use of calcium channel blockers (CCBs) was negatively associated with HbA1c levels (CCBs: 0.95 [95% CI: 0.92-0.98], P = 0.002). Our data further illustrated that the C-peptide levels before and 1, 2, and 3 hours of OGTT were 1.10-, 1.18-, 1.19-, and 1.15-fold increase in T2DM patients taking CCBs (P = 0.084 for fasting C-peptide levels; P ≤ 0.024 for C-peptide levels at 1, 2, and 3 hours after OGTT) in comparison with non-CCB users. Nevertheless, usage of any other antihypertensive drugs did neither associated with HbA1c nor associated with C-peptide levels (P ≥ 0.11). In conclusion, CCB treatment was negatively associated with HbA1c levels but positively associated with β-cell function in hypertensive T2DM patients, implying that CCBs could be considered to treat hypertensive T2DM patients with reduced β-cell function.

Circulating Hematopoietic Stem/Progenitor Cells are Associated with Coronary Stenoses in Patients with Coronary Heart Disease

Inflammatory cells in atherosclerotic plaque exclusively originate from hematopoietic stem/progenitor cells (HSPCs). In this study, we investigated whether circulating HSPCs frequency related to coronary stenosis in patients with coronary heart disease (CHD). Coronary angiography was performed in 468 participants who were recruited at Cardiology Centre in LuHe Hospital from March 2016 to May 2017. Among these subjects, 344 underwent echocardiography. Mononuclear cells isolated from peripheral blood were stained with an antibody cocktail containing anti-human CD34, anti-human lineage, anti-human CD38, and anti-human CD45RA. Lineage^-CD38^-CD45RA^dimCD34⁺HSPCs were quantified by flow cytometry. CHD was defined as coronary stenosis ≥50% and the extent of CHD was further categorised by coronary stenosis ≥70%. A p < 0.0031 was regarded statistically significant by the Bonferroni correction. Circulating HSPCs frequency was 1.8-fold higher in CHD patients than non-CHD participants (p = 0.047). Multivariate-adjusted logistic analysis demonstrated that HSPCs was the only marker that was associated with the odds ratio of having mild vs. severe coronary stenosis (2.08 (95% CI, 1.35-3.21), p = 0.0009). Left ventricular ejection fraction was inversely correlated with HSPCs frequency and CRP in CHD patients (p < 0.05 for both). In conclusion, HSPCs frequency in circulation is intimately related to coronary stenoses in CHD patients.

[Analysis of sonographic characteristics of thyroid nodules diagnosed as false positive or negative results in shear wave elastography]

Objective:In order to improve diagnostic accuracy, we study the characteristics of two dimensional ultrasound and shear wave elastography in the diagnosis of false negative or false positive thyroid nodules by shear wave elastography.Method:One hundred and eighty-nine nodules in 189 consecutive patients who had been determined by surgical operation and pathology. Conventional ultrasound features and SWE elasticity imaging characteristics and properties of the final postoperative pathology were recorded. A comparative study between true and false results of quantitative SWE elasticity imaging, and the corresponding conventional ultrasound nodule characteristics were compared.Result:Postoperative pathology showed 189 nodules, 74(39.2%) were benign and 115(60.8%) were malignant. The sensitivity, specificity of conventional ultrasound in the diagnosis of thyroid nodules were 56.5% and 81.1% respectively, and those of SWE were 60.9% and 85.1%. The false positive rate of shear wave elastography in diagnosing benign nodules and the false negative rate of malignant nodules were 14.9% and 39.1%, respectively. The false negative rate was higher than the false positive rate. A vertical growth (P< 0.01) and smaller diameter of the masses were significantly associated with false SWE findings (P< 0.01).Conclusion:The SWE imaging has important significance for differentiating benign and malignant thyroid nodules, but false results are inevitable, which requires clinicians conjunction with other test results to prevent errors judgment when reviewing the SWE imaging.

Angiopoietin-Like Protein 4 Is a High-Density Lipoprotein (HDL) Component for HDL Metabolism and Function in Nondiabetic Participants and Type-2 Diabetic Patients

Background

ANGPTL4 (angiopoietin‐like protein 4) is a LPL (lipoprotein lipase) inhibitor and is present in high‐density lipoprotein (HDL). However, it is not defined whether ANGPTL4 in HDLs could affect HDL metabolism and function in type 2 diabetes mellitus (T2DM).

Methods and Results

ANGPTL4 levels in the circulation and HDLs were quantified in nondiabetic participants (n=201, 68.7% females) and T2DM patients (n=185, 66.5% females). HDLs were isolated from nondiabetic controls and T2DM patients to assess cholesterol efflux or subjected to endothelial lipase (EL)‐overexpressed HEK293 cells for EL hydrolysis in vitro. The association between ANGPTL4 in HDLs and HDL components and function was analyzed in nondiabetic participants or diabetic patients, respectively. Plasma or HDLs of ANGPTL4+/+ and ANGPTL4−/− mice was subjected for cholesterol efflux or EL hydrolysis, respectively. ANGPTL4 levels in the plasma and HDLs were 1.7‐ and 2.0‐fold higher in T2DM patients than nondiabetic controls, respectively (P<0.0001). Multivariable analysis demonstrated that per 1 doubling increase of ANGPTL4 levels in HDLs, the changes amounted to +0.27% cholesterol efflux (P=0.03), +0.06 μg/mL apolipoprotein A‐I (P=0.09) and −9.41 μg/L serum amyloid A (P=0.02) in nondiabetic controls. In T2DM patients, the corresponding estimates were −0.06% cholesterol efflux (P=0.10), −0.06 μg/mL apolipoprotein A‐I (P=0.38), and +3.64 μg/L serum amyloid A (P=0.72). HDLs isolated from ANGPTL4−/− mice showed accelerated hydrolysis by EL and reduced cholesterol efflux compared with ANGPTL4+/+ littermates.

Conclusions

Physically, ANGPTL4 in HDLs protected HDLs from hydrolysis. Resulting from increased circulating ANGPTL4 levels in T2DM, ANGPTL4 levels in HDLs were elevated but with compromised inhibitory effect on EL, leading to increased HDL hydrolysis and dysfunction.

[Role and clinical significance of Th17/Treg balance in patients with severe exacerbation of hepatitis B]

OBJECTIVE

To investigate the role of Th17/Treg balance in immune mechanism in severe exacerbation of hepatitis B.

METHODS

The clinical data of 41 patients with chronic hepatitis B were collected, and according to the conditions during hospitalization, these patients were divided into exacerbation group (19 patients) and improvement group (22 patients). On admission, at weeks 1 and 2 of treatment, and at the end of treatment, flow cytometry was used to measure the frequencies of Th17 and Treg cells in peripheral blood, and enzyme-linked immunosorbent assay was used to determine the serum levels of interleukin-17 (IL-17), interleukin-10 (IL-10), and transforming growth factor-β (TGF-β). The dynamic changes in the frequencies of Th17 and Treg cells were compared between the two groups, and the correlation between clinical indices for hepatitis and cytokines was analyzed. The t-test was used for comparison between groups, a one-way analysis of variance was used for comparison within one group across different time points, and Pearson correlation analysis was performed.

RESULTS

With disease progression, the exacerbation group showed an increase in the frequency of Th17 cells and a relatively low frequency of Treg cells; compared with the improvement group, the exacerbation group had a higher frequency of Th17 cells and a lower frequency of Treg cells. Th17/Treg ratio gradually increased with exacerbation and decreased with improvement in conditions; in the exacerbation group and the improvement group, Th17/Treg ratio was positively correlated with total bilirubin and negatively correlated with prothrombin activity. In the exacerbation group and the improvement group, Th17 cells were positively correlated with IL-17, and Treg cells were positively correlated with IL-10 and TGF-β.

CONCLUSION

Th17 and Treg cells play important roles in severe exacerbation of hepatitis B, and Th17/Treg ratio may be used as an immunobiological marker for the judgment of severity during severe exacerbation of hepatitis B.

Different relationship between ANGPTL3 and HDL components in female non-diabetic subjects and type-2 diabetic patients

Background

Angiopoietin-like protein 3 (ANGPTL3) is a major lipoprotein regulator and shows positive correlation with high-density lipoprotein-cholesterol (HDL-c) in population studies and ANGPTL3 mutated subjects. However, no study has looked its correlation with HDL components nor with HDL function in patients with type 2 diabetes mellitus (T2DM).

Methods

We studied 298 non-diabetic subjects and 300 T2DM patients who were randomly recruited in the tertiary referral centre. Plasma levels of ANGPTL3 were quantified by ELISA. Plasma samples were fractionated to obtain HDLs. HDL components including apolipoprotein A-I (apoA-I), triglyceride, serum amyloid A (SAA), phospholipid and Sphingosine-1-phosphate were measured. HDLs were isolated from female controls and T2DM patients by ultracentrifugation to assess cholesterol efflux against HDLs. A Pearson unadjusted correlation analysis and a linear regression analysis adjusting for age, body mass index and lipid lowering drugs were performed in male or female non-diabetic participants or diabetic patients, respectively.

Results

We demonstrated that plasma level of ANGPTL3 was lower in female T2DM patients than female controls although no difference of ANGPTL3 levels was detected between male controls and T2DM patients. After adjusting for confounding factors, one SD increase of ANGPTL3 (164.6 ng/ml) associated with increase of 2.57 mg/dL cholesterol and 1.14 μg/mL apoA-I but decrease of 47.07 μg/L of SAA in HDL particles of non-diabetic females (p < 0.05 for cholesterol and SAA; p < 0.0001 for apoA-I). By contrast, 1-SD increase of ANGPTL3 (159.9 ng/ml) associated with increase of 1.69 mg/dl cholesterol and 1.25 μg/mL apoA-I but decrease of 11.70 μg/L of SAA in HDL particles of female diabetic patients (p < 0.05 for cholesterol; p < 0.0001 for apoA-I; p = 0.676 for SAA). Moreover, one SD increase of ANGPTL3 associated with increase of 2.11 % cholesterol efflux against HDLs in non-diabetic females (p = 0.071) but decrease of 1.46 % in female T2DM patients (p = 0.13) after adjusting for confounding factors.

Conclusions

ANGPTL3 is specifically correlated with HDL-c, apoA-I, SAA and HDL function in female non-diabetic participants. The decrease of ANGPTL3 level in female T2DM patients might contribute to its weak association to HDL components and function. ANGPTL3 could be considered as a novel therapeutic target for HDL metabolism for treating diabetes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12933-016-0450-1) contains supplementary material, which is available to authorized users.

HERG Protein Plays a Role in Moxifloxacin-Induced Hypoglycemia

The purpose of this study was to investigate the effect of moxifloxacin on HERG channel protein and glucose metabolism. HERG expression was investigated using immunohistochemistry. The whole-cell patch clamp method was used to examine the effect of moxifloxacin on HERG channel currents. A glucose tolerance test was used to analyze the effects of moxifloxacin on blood glucose and insulin concentrations in mice. Results show that HERG protein was expressed in human pancreatic β-cells. Moxifloxacin inhibited HERG time-dependent and tail currents in HEK293 cells in a concentration-dependent manner. The IC50 of moxifloxacin inhibition was 36.65 μmol/L. Moxifloxacin (200 mg/kg) reduced blood glucose levels and increased insulin secretion in wild-type mice at 60 min after the start of the glucose tolerance test. In contrast, moxifloxacin did not significantly alter blood glucose and insulin levels in HERG knockout mice. Serum glucose levels increased and insulin concentrations decreased in HERG knockout mice when compared to wild-type mice. The moxifloxacin-induced decrease in blood glucose and increase in insulin secretion occurred via the HERG protein; thus, HERG protein plays a role in insulin secretion.

Altered p-JAK1 expression is associated with estrogen receptor status in breast infiltrating ductal carcinoma

The mammalian Janus kinase (JAK) family consists of four members, namely JAK1, JAK2, JAK3 and TYK2, which play a critical role in cytokine/growth factor signaling and is increasingly associated with human cancers. Aberrant activation of these non-receptor tyrosine kinases may contribute to carcinogenesis. Herein, we focused on exploring the potential role of p-JAK1 in breast cancer. The expression profiles of p-JAK1 were analyzed in 68 pairs of cancer and non-cancer breast tissues from the same infiltrating ductal carcinoma case by using immunoblotting technique. The results obtained were further correlated with clinicopathological characteristics. Intriguingly, p-JAK1 expression was decreased in 55.9% of breast cancer tissues as compared to the matched non-cancer tissues. Further immunohistochemistry study showed an intense p-JAK1 staining predominantly in adjacent normal breast tissues but not the matched cancer lesions. Decreased p-JAK1 expression in breast cancer tissues was significantly correlated with positive estrogen receptor (ER) status and increased tumor size (p=0.010 and 0.009). We also found that p-JAK1 expression was high in ERalpha-negative breast cancer cell lines but was low in ERalpha-positive breast cell lines. Transfection of ERalpha-positive MCF-7 cells with an ERalpha-specific siRNA upregulated the expression of p-JAK1. In summary, our results indicated that an altered p-JAK1 expression might be involved in the development of breast infiltrating ductal carcinoma in an ERalpha-related manner.

Arsenite-induced nitric oxide generation is cell cycle-dependent and aberrant in NBS cells

Exposure to arsenic has been reported to cause DNA damage and eventually the occurrence of bladder, lung and skin cancers. A previous report has demonstrated that arsenite-induced phosphorylation of Mre11, a protein involved in the repair of DNA double strand breaks (DSBs), is M phase-dependent and requires the Nijmegen breakage syndrome (NBS) protein, NBS1 [DNA Repair 1 (2002) 137]. Furthermore, arsenite treatment arrests cells at the M phase and the cells eventually go through apoptosis [Biochemical Pharmacology 60 (2000) 771]. Here we demonstrate that arsenite treatment enhances the generation of nitric oxide (NO), and that the enhanced NO generation is dominant at the G2/M phase. Arsenite-induced NO generation is impaired in DSB repair-defective NBS cells, but not in NBS1-reconstituted NBS cells, suggesting NBS1 is required for effective NO generation. In summary, our study showed, for the first time, that arsenite-induced NO generation is cell-cycle- and NBS1-dependent.

Functional link between ataxia-telangiectasia and Nijmegen breakage syndrome gene products

Ataxia-telangiectasia (A-T) and Nijmegen breakage syndrome (NBS) are recessive genetic disorders with susceptibility to cancer and similar cellular phenotypes. The protein product of the gene responsible for A-T, designated ATM, is a member of a family of kinases characterized by a carboxy-terminal phosphatidylinositol 3-kinase-like domain. The NBS1 protein is specifically mutated in patients with Nijmegen breakage syndrome and forms a complex with the DNA repair proteins Rad50 and Mrel1. Here we show that phosphorylation of NBS1, induced by ionizing radiation, requires catalytically active ATM. Complexes containing ATM and NBS1 exist in vivo in both untreated cells and cells treated with ionizing radiation. We have identified two residues of NBS1, Ser 278 and Ser 343 that are phosphorylated in vitro by ATM and whose modification in vivo is essential for the cellular response to DNA damage. This response includes S-phase checkpoint activation, formation of the NBS1/Mrel1/Rad50 nuclear foci and rescue of hypersensitivity to ionizing radiation. Together, these results demonstrate a biochemical link between cell-cycle checkpoints activated by DNA damage and DNA repair in two genetic diseases with overlapping phenotypes.

BRCA2 is required for ionizing radiation-induced assembly of Rad51 complex in vivo

Mutations in BRCA1 and BRCA2 account for the majority of familial breast cancers. Cells with mutated BRCA1 or BRCA2 are hypersensitive to ionizing radiation (IR) and exhibit defective DNA repair. Both BRCA1 and BRCA2 have been reported to bind Rad51, a protein essential for homologous recombination and the recombinational repair of DNA double-strand breaks. In normal cells, a redistribution of Rad51 protein, manifested as formation of Rad51 nuclear foci, is seen upon IR treatment. Here we demonstrate that IR-induced Rad51 foci formation is aberrant in BRCA2- but not BRCA1-deficient tumor cells. In Capan-1 cells, which do not express functional BRCA2, there was little Rad51 foci formation in response to a wide range of radiation dosages. Moreover, forced expression of a fusion protein containing green fluorescent protein and the first Rad51-binding BRC repeat of BRCA2 in cells with wild-type BRCA2 rendered them hypersensitive to IR and cisplatin and compromised IR-induced Rad51 foci formation. In HCC1937 cells, which harbor mutation of BRCA1, IR-induced Rad51 foci were readily detected. This study suggests a requirement of BRCA2 protein for the IR-induced assembly of Rad51 complex in vivo.

Radiation-induced assembly of Rad51 and Rad52 recombination complex requires ATM and c-Abl

Cells from individuals with the recessive cancer-prone disorder ataxia telangiectasia (A-T) are hypersensitive to ionizing radiation (I-R). ATM (mutated in A-T) is a protein kinase whose activity is stimulated by I-R. c-Abl, a nonreceptor tyrosine kinase, interacts with ATM and is activated by ATM following I-R. Rad51 is a homologue of bacterial RecA protein required for DNA recombination and repair. Here we demonstrate that there is an I-R-induced Rad51 tyrosine phosphorylation, and this induction is dependent on both ATM and c-Abl. ATM, c-Abl, and Rad51 can be co-immunoprecipitated from cell extracts. Consistent with the physical interaction, c-Abl phosphorylates Rad51 in vitro and in vivo. In assays using purified components, phosphorylation of Rad51 by c-Abl enhances complex formation between Rad51 and Rad52, which cooperates with Rad51 in recombination and repair. After I-R, an increase in association between Rad51 and Rad52 occurs in wild-type cells but not in cells with mutations that compromise ATM or c-Abl. Our data suggest signaling mediated through ATM, and c-Abl is required for the correct post-translational modification of Rad51, which is critical for the assembly of Rad51 repair protein complex following I-R.

Cloning and functional studies of a novel gene aberrantly expressed in RB-deficient embryos

The tumor suppressor RB regulates diverse cellular processes such as G1/S transition, cell differentiation, and cell survival. Indeed, Rb-knockout mice exhibit phenotypes including ectopic mitosis, defective differentiation, and extensive apoptosis in the neurons. Using differential display, a novel gene, Rig-1, was isolated based on its elevated expression in the hindbrain and spinal cord of Rb-knockout embryos. The longest open reading frame of Rig-1 encoded a polypeptide that consists of a putative extracellular segment with five immunoglobulin-like domains and three fibronectin III-like domains, a putative transmembrane domain, and a distinct intracellular segment. The Rig-1 sequence was 40% identical to the recently identified roundabout protein. Consistent with the predicted transmembrane nature of the protein, Rig-1 protein was present in the membranous fraction. Antisera raised against the putative extracellular and intracellular segments of Rig-1 reacted with an approximately 210-kDa protein in mouse embryonic CNS. Rig-1 mRNA was transiently expressed in the embryonic hindbrain and spinal cord. Elevated levels of Rig-1 mRNA and protein were found in Rb-/- embryos. Ectopic expression of a transmembrane form of Rig-1, but not the secreted form, promoted neuronal cell entrance to S phase and repressed the expression of a marker of differentiated neuron, Talpha1 tubulin. Thus Rig-1, a possible distant relative of roundabout, may mediate some of the pleiotropic roles of RB in the developing neurons.

Nuclease activities in a complex of human recombination and DNA repair factors Rad50, Mre11, and p95

Genetic studies in yeast have indicated a role of the RAD50 and MRE11 genes in homologous recombination, telomere length maintenance, and DNA repair processes. Here, we purify from nuclear extract of Raji cells a complex consisting of human Rad50, Mre11, and another protein factor with a size of about 95 kDa (p95), which is likely to be Nibrin, the protein encoded by the gene mutated in Nijmegen breakage syndrome. We show that the Rad50-Mre11-p95 complex possesses manganese-dependent single-stranded DNA endonuclease and 3' to 5' exonuclease activities. These nuclease activities are likely to be important for recombination, repair, and genomic stability.

Dual roles of the retinoblastoma protein in cell cycle regulation and neuron differentiation

To assess the functions of the retinoblastoma protein (RB) during normal development, we have analyzed mouse embryos that lack a functional copy of the retinoblastoma gene (genotype: Rb-1 delta 20/Rb-1 delta 20). Our findings demonstrate that RB plays an important role in the regulation of the neuronal cell cycle. In mutant embryos, dividing cells are found well outside of the normal neurogenic regions in both the central and peripheral nervous systems. In addition to abnormal cell cycle regulation, however, the mutant embryos show two less expected phenotypes. First, many of the ectopically dividing cells die by apoptosis shortly after their entrance into S phase. In sensory ganglia, most nerve cells die by this process, beginning at about the same time as normal target-related neuronal death. Second, although the expression of certain differentiation markers such as N-CAM and Brn-3.0 appears to be near normal, nerve cells, especially in sensory ganglia, do not mature properly. Their morphology is stunted and expression of neuronal beta II tubulin is greatly reduced. Preferential reduction in the expression of TrkA, TrkB, and the low-affinity neurotrophin receptor p75LNGFR may be relevant to neuronal cell death and lack of neuronal differentiation seen in the mutant embryos. Primary cultures of dorsal root and trigeminal ganglion cells from later stage mutant embryos reveal a decrease in neuronal cell survival and in neurite outgrowth even in the presence of the appropriate neurotrophins. Taken together, these results suggest that the p110RB protein not only regulates progression through the cell cycle but is also important for cell survival and differentiation.

Synthesis of 3,4-13C2-steroids

A-ring enollactones la, lb, or 9 derived from 4-cholesten-3-one, testosterone benzoate or 3-oxo-4-estren-17 beta-yl benzoate were condensed with [1,2-13C2]acetyl chloride to give intermediates 2a, 2b, or 10. 2a and 2b were cyclized by acid or base to give 3,4 13c-labeled 4-cholesten-3-one and testosterone, respectively. [3,4-13c2 14-Cholesten-3-one was converted via reduction of its trimethylsilyl enol ether to [3,4-13C2] cholesterol. Acetyl enollactone 10 was cyclized in acetic acid to [3,4-13c2] 3-oxo-4-estren-17beta-yl benzoate followed by aromatization and hydrolysis to produce ]3,4-13c2] estradiol-17 beta. Alternatively, cyclization of 10 with base afforded [3,4-13c2-oxo-4-estren-17 beta-ol directly, which was then oxidized and aromatized to yield ]3,4-13c2] estrone. Ozonolysis of progesterone, conversion to the diketal ester 16 and acylation followed by acid hydrolysis furnished [3,4-13c2] progesterone.

Synthesis and activity of (R)-(-)-m-trimethylacetoxy-alpha-[(methylamino)methyl]benzyl alcohol hydrochloride: a prodrug form of (R)-(-)-phenylephrine

Optically pure (R)-(-)-m-trimethylacetoxy-alpha-[(methylamino)methyl]benzyl alcohol hydrochloride was synthesized by the following sequence: (R)-(-)-phenylephrine was condensed with acetone in the presence of calcium carbide to give an oxazolidine derivative and then treated with thallous ethoxide in ether followed by trimethylacetyl chloride to yield the phenolic ester. Finally, the oxazolidine ring was cleaved by one equivalent of hydrogen chloride in ethanol. Condensation of phenylephrine with benzaldehyde, with or without solvents, gave either 1,1,2-trimethyl-4,6-dihydroxy-1,2,3,4-tetrahydroisoquinoline or a mixture of side-chain oxazolidine and the tetrahydroisoquinoline. Condensation of epinephrine with opianic acid in pyridine also gave a tetrahydroisoquinoline only. When applied on rabbit eyes, the prodrug (R)-(-)-m-trimethylacetoxy-alpha[(methylamino)methyl]benzyl alcohol hydrochloride exhibited an unexpected, three times higher mydriatic activity than the corresponding racemic prodrug and was 15 times more active than the parent, (R)-(-)-phenylephrine.