Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

Although accumulating evidence has provided insight into the various functions of long-non-coding RNAs (lncRNAs), the exact functions of the majority of such transcripts are still unknown. Here, we report the first computational annotation of lncRNA functions based on public microarray expression profiles. A coding–non-coding gene co-expression (CNC) network was constructed from re-annotated Affymetrix Mouse Genome Array data. Probable functions for altogether 340 lncRNAs were predicted based on topological or other network characteristics, such as module sharing, association with network hubs and combinations of co-expression and genomic adjacency. The functions annotated to the lncRNAs mainly involve organ or tissue development (e.g. neuron, eye and muscle development), cellular transport (e.g. neuronal transport and sodium ion, acid or lipid transport) or metabolic processes (e.g. involving macromolecules, phosphocreatine and tyrosine)

Situs inversus totalis with carcinoma of gastric cardia: a case report

<p>Abstract</p> <p>Situs inversus is an uncommon anomaly with rare incidence. Some cases of situs inversus totalis have been described with different types of associations. Here we report a case of situs inversus with carcinoma of the gastric cardia.</p

Expression levels of HMGA2 and CD9 and its clinicopathological significances in the benign and malignant lesions of the gallbladder

<p>Abstract</p> <p>Background</p> <p>The objective of this study was to investigate CD9 and HMGA2 expression and its clinicopathological significance in benign and malignant lesion tissues of the gallbladder.</p> <p>Methods</p> <p>The resected specimens of 108 cases of gallbladder adenocarcinoma, 46 cases of adjacent tissue, 15 cases of polyps and 35 cases of chronic cholecystitis were made into conventional paraffin-embedded sections, using the method of EnVision immunohistochemistry to stain HMGA2 and CD9.</p> <p>Results</p> <p>HMGA2 expression of gallbladder adenocarcinoma was significantly higher than that of adenocarcinoma adjacent tissues (= 16.13, <it>P</it> <0.01), polyps (= 8.19, <it>P</it> <0.01) and chronic cholecystitis (= 21.41, <it>P</it> <0.01); but CD9 expression was the opposite (<it>P</it> <0.05 or <it>P</it> <0.01). The positive rate of HMGA2 expression from the cases that had well-differentiated adenocarcinoma, with the largest tumor diameter <2 cm, and without lymph node metastasis, and that did not invade the surrounding tissue was significantly lower than that of HMGA2 expression from the cases that had poorly differentiated adenocarcinoma, with the largest tumor diameter ≥2 cm, lymph node metastasis, and that invaded the surrounding tissues (<it>P</it> <0.05 or <it>P</it> <0.01). The positive rate of CD9 expression from the cases that had well-differentiated adenocarcinoma, with the largest tumor diameter <2 cm, and without lymph node metastasis, and that did not invade the surrounding tissue was significantly higher than that of CD9 expression from the cases that had poorly differentiated adenocarcinoma, with the largest tumor diameter ≥2 cm, lymph node metastasis, and which invaded the surrounding tissues (<it>P</it> <0.05 or <it>P</it> <0.01). The Kaplan-Meier survival analysis showed that after surgery, the survival period of HMGA2 expression-positive cases was significantly lower than that of HMGA2 expression- negative cases (<it>P</it> = 0.020), but the survival period of CD9 expression-positive cases was significantly higher than that of cases with CD9 expression-negative (<it>P</it> = 0.019). Cox multivariate regression analysis showed that the HMGA2 positive expression and/or CD9 negative expression was an important indicator reflecting the poor prognosis of gallbladder cancer.</p> <p>Conclusion</p> <p>The expression of HMGA2 and/or CD9 might be closely related to the carcinogenesis, clinical biological behaviors and prognosis of gallbladder adenocarcinoma.</p

Prognostic Value of Bismuth Typing and Modified T-stage in Hilar Cholangiocarcinoma

Aim: Hilar cholangiocarcinoma (HCC) has a very poor prognosis. Surgical resection is a radical treatment option for this disease. However, it is still difficult to cure, and prognostic traits are ambiguous. Evaluation of the tumor typing and staging may elucidate effective prognosis and provide helpful advice for clinical surgeon. This study aimed to analyze the prognostic value of tumor typing and staging in HCC. Methods: We conducted a retrospective review of 85 patients with HCC undergoing surgical resections procedures at the Second Xiangya Hospital in Hunan Province between 2002 and 2012. The Bismuth type, modified T-stage, postoperative complications, survival time, and other clinical manifestations associated with the surgical treatment were analyzed. Results: Patients were classified according to Bismuth typing: Subtype I (12 cases), Subtype II (4 cases), Subtype IIIa (3 cases), Subtype IIIb (16 cases), and Subtype IV (50 cases). Patients were classified according to the T staging: Stage T1 (19 cases), Stage T2 (5 cases), and Stage T3 (61 cases). Based on data collected from 67 patients who completed the follow-up survey, both the Bismuth type and modified T-stage were significantly correlated with survival time (each P = 0.01). Conclusion: The majority of our patients with HCC were characterized as Subtype IV in Bismuth typing and Stage T3 in modified T-stage. Both Bismuth typing and modified T-stage showed prognostic value in HCC. Compared with Bismuth typing, modified T-stage is a better indicator of the resectability of HCC

The Clinical and Pathological Significance of Nectin-2 and DDX3 Expression in Pancreatic Ductal Adenocarcinomas

Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant disease, but the genetic basis of PDAC is still unclear. In this study, Nectin-2 and DDX3 expression in 106 PDAC, 35 peritumoral tissues, 55 benign pancreatic lesions, and 13 normal pancreatic tissues were measured by immunohistochemical methods. Results showed that the percentage of positive Nectin-2 and DDX3 expression was significantly higher in PDAC tumors than in peritumoral tissues, benign pancreatic tissues, and normal pancreatic tissues (P<0.01). The percentage of cases with positive Nectin-2 and DDX3 expression was significantly lower in PDAC patients without lymph node metastasis and invasion and having TNM stage I/II disease than in patients with lymph node metastasis, invasion, and TNM stage III/IV disease (P<0.05 or P<0.01). Positive DDX3 expression is associated with poor differentiation of PDAC. Kaplan-Meier survival analysis showed that positive Nectin-2 and DDX3 expression were significantly associated with survival in PDAC patients (P<0.001). Cox multivariate analysis revealed that positive Nectin-2 and DDX3 expression were independent poor prognosis factors in PDAC patients. In conclusion, positive Nectin-2 and DDX3 expression are associated with the progression and poor prognosis in PDAC patients

Expression of UGP2 and CFL1 expression levels in benign and malignant pancreatic lesions and their clinicopathological significance

Abstract Background This study investigated UGP2 (uridine diphosphate-glucose pyrophosphorylase-2) and CFL1 (cofilin-1) expression in pancreatic ductal carcinoma (PDC), paracancerous tissue (PT), benign lesions (BL), and normal tissue (NT) and their clinicopathological significance. Methods Surgical specimens, which were collected from 106 cases of pancreatic ductal carcinoma, 35 cases of paracancerous tissues, 55 cases of benign lesions and 13 cases of normal pancreatic tissues, were fixed with 4% formaldehyde to prepare conventional paraffin-embedded sections. EnVision immunohistochemical was used to stain for UGP2 and CFL1. Kaplan-Meier survival analysis was performed to assess the correlation of expression pattern with survival. Results We found that positive UGP2 and CFL1 expression in PDC were significantly higher than those in PT, BL, and NT. In PT and BL with positive UGP2 and CFL1 expression, mild to severe atypical hyperplasia or intraepithelial neoplasia of grades II–III was observed in ductal epithelium. Positive UGP2 and CFL1 expression in cases with high differentiation, no lymph node metastasis, no surrounding invasion, and TNM (tumor-node-metastasis) staging I or/and II were significantly lower than those in cases with poor differentiation, lymph node metastasis, surrounding invasion, and TNM stage III and/or IV. Positive UGP2 expression in male patients was significantly lower than that in female patients. UGP2 and CFL1 expression in PDC were positively correlated. Kaplan-Meier survival analysis showed the degree of differentiation, tumor maximal diameter, TNM stage, lymph node metastasis, and surrounding invasion, and UGP2 and CFL1 expression were closely related to the average survival time of patients with PDC. The survival time of patients with positive UGP2 and CFL1 expression was significantly shorter than that of patients with negative expression. Cox multivariate analysis showed that poor differentiation, tumor maximal diameter ≥ 3 cm, TNM stage III or IV, lymph node metastasis, surrounding invasion, and positive UGP2 and CFL1 expression was negatively correlated with the postoperative survival rate and positively correlated with the mortality of patients with PDC. Conclusion Positive expression of UGP2 and CFL1 can serve a valuable prognostic factor in pancreatic cancer

Intratumoral CD8⁺ Cytotoxic Lymphocyte Is a Favorable Prognostic Marker in Node-Negative Breast Cancer

<div><p>Background</p><p>The prognostic effect of tumor infiltrating CD8⁺ cytotoxic lymphocytes (CTLs) in breast cancer is controversial. We analyzed the association between CD8⁺ CTLs and survival of untreated node-negative breast cancer patients.</p><p>Material and Methods</p><p>CD8⁺ CTLs infiltrate was evaluated by immunostaining in a cohort of 332 node-negative breast cancer patients with a median follow-up of 152 months. The prognostic significance of CD8⁺ CTLs for disease-free survival (DFS) and breast cancer-specific overall survival (OS) was evaluated with Kaplan-Meier survival analysis as well as univariate analysis and multivariate Cox analysis adjusted for age at diagnosis, pT stage, histological grade, estrogen receptor (ER) status, progesterone receptor (PR) status, Ki-67 expression and human epidermal growth factor receptor 2 (HER-2) status.</p><p>Results</p><p>285 (85.8%) patients showed strong CD8⁺ CTLs infiltrate positive status. Univariate analysis showed that CD8⁺ CTLs had statistically significant association with DFS (P = 0.004, hazard ratio [HR] = 0.454, 95% confidence interval [CI] = 0.265–0.777) and OS (P = 0.014, HR = 0.430, 95% CI = 0.220–0.840) in the entire cohort. The significance of CD8⁺ CTLs was especially strong in ER negative, HER-2 negative and ER, PR, HER-2 triple-negative breast cancers. In Kaplan-Meier analysis, CD8⁺ CTLs had significant effect on prognosis of patients (Log-rank test: P = 0.003 for DFS and P = 0.011 for OS), independent of established clinical factors for DFS (P = 0.002, HR = 0.418, 95% CI = 0.242–0.724) as well as for OS (P = 0.009, HR = 0.401, 95% CI = 0.202–0.797).</p></div

Correlations of CD8⁺ CTLs infiltrate status with clinicopathological variables (n = 332).

<p>*Correlation between variables was determined by Chi-Squared test.</p><p>CTLs cytotoxic T lymphocytes; HER-2 human epidermal growth factor receptor 2.</p>a<p>The total number of available cases for Ki-67 expression is 320.</p