ATG4B and pS383/392-ATG4B serve as potential biomarkers and therapeutic targets of colorectal cancer.

BACKGROUND: Autophagy related protease 4B (ATG4B) is a protease required for autophagy processing, which is strongly implicated in cancer progression.  Phosphorylation of ATG4B is crucial for activation of its protease activity.  However, little is known about the relationship of ATG4B and its phosphorylated form at Ser 383 and 392 sites (pS383/392-ATG4B), with clinical outcomes, particularly in colorectal cancer (CRC). METHODS: The ATG4B gene expression in CRC patients was obtained from The Cancer Genome Atlas (TCGA) database to analyze its clinical relevance. Tissue microarrays composed of 118 CRC patient specimens were used to determine the associations of ATG4B and pS383/392-ATG4B protein levels with prognosis. The biological functions of ATG4B in CRC cells were inspected with cell proliferation, mobility and spheroid culture assays. RESULTS: ATG4B gene expression was elevated in tumor tissues of CRC patients compared to that in adjacent normal tissues and high level of ATG4B expression was associated with poor survival. Similarly, protein levels of ATG4B and pS383/392-ATG4B were highly correlated with worse overall survival and disease-free survival. Stratification analysis results showed that high level of ATG4B had significantly higher risk of mortality in males and elderly patients compared to those female patients and patients 60 years or younger. In contrast, multivariate Cox's regression analysis indicated that high level of pS383/392-ATG4B was significantly linked to unfavorable overall survival and disease-free survival of males and elderly patients, whereas, it had no correlation with female patients and patients 60 years or younger. Moreover, high level of ATG4B was positively associated with increased mortality risk in patients with advanced AJCC stages (III and IV) and lymph node invasion (N1 and N2) for both overall survival and disease-free survival. Nevertheless, high level of pS383/392-ATG4B was positively correlated with increased mortality risk in patients with early AJCC stages (I and II) and without lymph node invasion (N0). In addition, silencing ATG4B attenuated migration, invasion, and further enhanced the cytotoxic effects of chemotherapeutic drugs in two and three-dimensional cultures of CRC cells. CONCLUSIONS: Our results suggest that ATG4B and pS383/392-ATG4B might be suitable biomarkers and therapeutic targets for CRC.

Helical structure motifs made searchable for functional peptide design.

The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided. Here, we extract 1.7 million helices from the PDB and compile them into a database (Therapeutic Peptide Design database; TP-DB) that allows queries of compounded patterns to facilitate the identification of sequence motifs of helical structures. We show how TP-DB helps us identify a known purification-tag-specific antibody that can be repurposed into a diagnostic kit for Helicobacter pylori. We also show how the database can be used to design a new antimicrobial peptide that shows better Candida albicans clearance and lower hemolysis than its template homologs. Finally, we demonstrate how TP-DB can suggest point mutations in helical peptide blockers to prevent a targeted tumorigenic protein-protein interaction. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/ .

Enhancement of irradiation effects on cancer cells by cross-linked dextran-coated iron oxide (CLIO) nanoparticles.

We investigated iron oxide nanoparticles with two different surface modifications, dextran coating and cross-linked dextran coating, showing that their different internalization affects their capability to enhance radiation damage to cancer cells. The internalization was monitored with an ultrahigh resolution transmission x-ray microscope (TXM), indicating that the differences in the particle surface charge play an essential role and dominate the particle-cell interaction. We found that dextran-coated iron oxide nanoparticles cannot be internalized by HeLa and EMT-6 cells without being functionalized with amino groups (the cross-linked dextran coating) that modify the surface potential from -18 mV to 13.4 mV. The amount of cross-linked dextran-coated iron oxide nanoparticles uptaken by cancer cells reached its maximum, 1.33 x 10(9) per HeLa cell, when the co-culture concentration was 40 microg Fe mL(-1) or more. Standard tests indicated that these internalized nanoparticles increased the damaging effects of x-ray irradiation, whereas they are by themselves biocompatible. These results could lead to interesting therapy applications; furthermore, iron oxide also produces high contrast for magnetic resonance imaging (MRI) in the diagnosis and therapy stages.

Requirements for the upregulation of interleukin-6 by herpes simplex virus-infected gingival fibroblasts.

Interleukin (IL)-6 is an important proinflammatory and immunoregulatory cytokine expressed by various cells. This study examined the production of IL-6 by human gingival keratinocytes and gingival fibroblasts following herpes simplex virus (HSV) infection. Virus-cell interactions responsible for IL-6 induction by HSV-1 were determined. The amounts of IL-6 secreted by primary human gingival keratinocytes and gingival fibroblasts were determined using enzyme-linked immunosorbent assay. IL-6 expression in gingival fibroblasts was also determined using immunofluorescence staining. To further delineate the viral requirements for this induction, gingival fibroblasts were treated with antibody-neutralized viruses, UV- or heat-inactivated viruses or viral glycoprotein D of HSV-1 (gD-1). The results showed that infection of gingival fibroblasts, but not gingival keratinocytes, with HSV-1 induced production of IL-6. This modulation was blocked by neutralizing antibodies against HSV-1, suggesting that HSV-1 is required for this induction. Moreover, this induction was not abrogated when virus infectivity was destroyed by UV irradiation or heat, indicating that a complete viral life cycle is not required. Further studies showed that gD-1 alone was able to induce IL-6 secretion in gingival fibroblasts. Collectively, our data suggest that HSV-1 infection of gingival fibroblasts up-regulates production of IL-6 through a mechanism involving the interaction of gD-1 with cellular receptors.

Direct binding of herpes simplex virus type 1 virions to complement C3.

Glycoprotein C (gC) of type 1 herpes simplex virus (HSV-1) binds the human complement C3 as purified proteins, or when expressed on the surface of infected cells. However, it is not clear whether the purified HSV virion binds directly to C3. In this study, direct binding of purified virions, HSV-1(KOS) or HSV-1(hrR3), to C3-coated plate was demonstrated by an enzyme-linked immunosorbent assay (ELISA). Captured virions on C3-coated plates were still infectious as determined by adding Vero cells to allow for infection to occur. The binding of virions to C3 was abolished if C3 was heat-inactivated, confirming a requirement for complement. In addition, the interaction was inhibited by preincubation of purified virions with heparin. In conclusion, a direct interaction of C3 with the HSV-1 virions was demonstrated.