Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.

Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of molecular crowding. In this work, we employed the coarse-grained model that was previously developed by us to predict 3D structures and stability of the mouse mammary tumor virus (MMTV) pseudoknot under different spatial confinements over a wide range of salt concentrations. The results show that spatial confinements can not only enhance the compactness and stability of MMTV pseudoknot structures but also weaken the dependence of the RNA structure compactness and stability on salt concentration. Based on our microscopic analyses, we found that the effect of spatial confinement on the salt-dependent RNA pseudoknot stability mainly comes through the spatial suppression of extended conformations, which are prevalent in the partially/fully unfolded states, especially at low ion concentrations. Furthermore, our comprehensive analyses revealed that the thermally unfolding pathway of the pseudoknot can be significantly modulated by spatial confinements, since the intermediate states with more extended conformations would loss favor when spatial confinements are introduced.

Disruption of pRb-p16INK4 pathway: a common event in ampullary carcinogenesis.

BACKGROUND/AIMS: Aberrations of the pRb (Retinoblastoma gene protein)-p16INK4 pathway play a critical role in carcinogenesis. Our objective is to evaluate its role in tumorigenesis and the development of ampullary cancer. METHODOLOGY: We examined expression status of p16INK4 protein and pRb immunohistochemically and assessed their possible prognostic relevance in 36 ampullary cancers. RESULTS: Thirty-four specimens (94.4%) exhibited alteration of p16INK4 and/or pRb expression, with 63.9% (23/36) of cancers showing p16INK4 negative expression and 94.4% (34/36) pRb abnormal expression. p16INK4 protein negative expression correlated significantly with tumor progression features such as advanced tumor stages (p=0.0291), lymph node metastasis (p=0.005), pancreas invasion (p=0.0002) and duodenum invasion (p=0.0101). Cases with both p16RNK4 protein negative expression and pRb overexpression showed poorer differentiation, more invasive growth (p=0.0425), higher level tumor stages (p=0.0079) and more frequent pancreas invasion (p=0.0024), compared with the others. p16INK4 protein expression showed no relationship with pRb expression (p=0.2199). No association was found in pRb expression status compared with any clinicopathological parameters analyzed. CONCLUSIONS: The disruption of the pRb-p16NK4 pathway plays an important role in ampullary carcinogenesis, the absence of p16INK4 protein expression might be involved in ampullary tumor progression.

Telomerase expression and p53 status in hepatocellular carcinoma.

OBJECTIVES: [corrected] Genomic instability is a driving force for tumorigenesis. Telomerase and p53 play central roles in maintaining genomic integrity. The purpose of this study was to assess the role of telomerase expression and p53 protein overexpression in hepatocellular carcinoma (HCC). METHODS: Telomerase activity and p53 overexpression were investigated in 63 patients undergoing hepatectomy for HCC by a telomeric repeat amplification protocol and immunohistochemistry, respectively. The associations among telomerase expression, p53 overexpression, and clinicopathological features were analyzed, and independent prognostic factors in the recurrence of HCC after hepatectomy were determined. RESULTS: Telomerase expression did not correlate with clinicopathological features except hepatitis virus status (p = 0.04) and was identified as a significant prognostic variable for HCC recurrence (p = 0.027) along with portal venous invasion (p = 0.001). In contrast, p53 overexpression strongly correlated with tumor differentiation (p < 0.0001) but did not reflect time to recurrence (p = 0.26). Telomerase expression did not correlate with p53 overexpression (p = 0.35). CONCLUSIONS: The reactivation of telomerase was of significant value in predicting the recurrence of HCC after hepatectomy. However, p53 overexpression did not correlate with telomerase expression in HCC, nor did it reflect the time to recurrence.

Deregulation of G1/S transition is a common event in carcinoma of the ampulla of vater.

BACKGROUND/AIMS: Aberrant expression of cell cycle regulators and subsequent deregulation of G1/S transition is one of the most important characteristics of human cancer. The aim of this study was to determine the overall pattern of deranged expression of the cell cycle regulators involved in the G1/S transition in ampullary carcinoma. METHODOLOGY: Using immunohistochemistry, we investigated the expression of p21WAF1/CIP1, p27Kip1, p16INK4, cyclin D1, cyclin E, pRb and p53 in 14 resected specimens of ampullary carcinoma and defined the proliferative activity of each tumor by quantifying Ki-67 antigen. RESULTS: Decreased expression of p21WAF1/CIP1, p27Kip1, and p16INK4 was detected in 6 (43%), 11 (79%), and 4 (29%) tumors, respectively. Four tumors (29%) overexpressed cyclin D1 and 8 (57%) overexpressed cyclin E. Eight tumors (57%) overexpressed pRb. Aberrant accumulation of p53 was observed in 10 (71%) of the tumors. Overall, the expression of two or more of these cell cycle regulators was altered in all of the 14 tumors. Decreased p21WAF1/CIP1 expression was related to higher TMN stage (P = 0.04) and lymphatic invasion (P = 0.04). The proliferative index was higher in tumors with decreased p27Kip expression (P = 0.005), and in tumors with cyclin E overexpression (P = 0.06). CONCLUSIONS: Our observations suggest that deregulation of G1/S transition is a very common event in ampullary carcinoma, and that altered expression of cell cycle regulators is associated with the aggressive behavior of this tumor. Correcting the G1/S transition regulatory machinery may provide a novel therapy for this malignancy.

Proliferative marker Ki-67 in gallbladder carcinomas: high expression level predicts early recurrence after surgical resection.

To evaluate the prognostic value of proliferative maker Ki-67, its expression was determined immunohistochemically in 37 gallbladder carcinomas (GBCs). A high Ki-67 index was significantly correlated with tumor lymphatic invasion (P=0.007) and vascular invasion (P=0.04). High Ki-67 index group and low Ki-67 index group showed different clinical courses. Five patients who experienced recurrences in high Ki-67 index group developed their recurrent diseases within one year after surgery and died soon after recurrence, while the recurrences (five cases) in low Ki-67 index group were distributed all stages after surgery. In conclusion, high Ki-67 index predicts early recurrence after surgery for GBCs.