PhIN: A Protein Pharmacology Interaction Network Database

Network pharmacology is a new and hot concept in drug discovery for its ability to investigate the complexity of polypharmacology, and becomes more and more important in drug development. Here we report a protein pharmacology interaction network database (PhIN), aiming to assist multitarget drug discovery by providing comprehensive and flexible network pharmacology analysis. Overall, PhIN contains 1,126,060 target–target interaction pairs in terms of shared compounds and 3,428,020 pairs in terms of shared scaffolds, which involve 12,419,700 activity data, 9,414 targets, 314 viral targets, 652 pathways, 1,359,400 compounds, and 309,556 scaffolds. Using PhIN, users can obtain interacting target networks within or across human pathways, between human and virus, by defining the number of shared compounds or scaffolds under an activity cutoff. We expect PhIN to be a useful tool for multitarget drug development. PhIN is freely available at http://cadd.pharmacy.nankai.edu.cn/phin/.

An evaluation comparing Californium252 neutron brachytherapy with neoadjuvant intra-arterial embolism chemotherapy assisted surgery effect for treating advanced cervical carcinoma patients

PURPOSE OF INVESTIGATION

To compare the therapeutic and side effects of using Californium252 (252Cf) neutron brachytherapy with neoadjuvant intra-arterial embolism chemotherapy in combination with surgery for treating Stage Ib2-IIb cervical cancers (CCs).

MATERIALS AND METHODS

Thirty-two Stage Ib2-IIb CC patients were enrolled and randomly divided into two groups from January 2007 to April 2010 in the present Hospital. Prior to surgery within four weeks, a total of 17 cases were treated with 252Cf neutron brachytherapy (700-800 cGy doses at point A) once a week (Group A), and 15 cases were treated by neoadjuvant intra-arterial embolism chemotherapy using a combination of bleomycin, carboplatin, and cyclophosphamide twice (Group B). The clinical symptoms and signs, side effects, and relapse condition follow up until July 2013 were compared between the two groups for the perioperation.

RESULTS

Reductions in tumor mass and CR+PR were not significantly different between the groups before the surgery (p > 0.05). Abdominal pain and pelvic adhesions were significantly more severe in Group B (p < 0.05). There were no significant differences in surgical time, blood loss or the other side effects between Groups A and B (p > 0.05). The percentage of pelvic tumor recurrences in Group A was lower than that of the patients in Group B (11.8% vs 20.0%) although with no significant difference at present. No distant metastasis has been found in both two groups.

CONCLUSION

Except for less abdominal pain and pelvic adhesions, 252Cf neutron brachytherapy has perioperative effects similar to those of neoadjuvant intra-arterial embolism chemotherapy.

Do genetic risk scores for body mass index predict risk of phobic anxiety? Evidence for a shared genetic risk factor

BACKGROUND

Obesity and anxiety are often linked but the direction of effects is not clear.

METHOD

Using genetic instrumental variable (IV) analyses in 5911 female participants from the Nurses' Health Study (NHS, initiated 1976) and 3697 male participants from the Health Professional Follow-up Study (HPFS, initiated 1986), we aimed to determine whether obesity increases symptoms of phobic anxiety. As instrumental variables we used the fat mass and obesity-associated (FTO) gene, the melanocortin 4 receptor (MC4R) gene and a genetic risk score (GRS) based on 32 single nucleotide polymorphisms (SNPs) that significantly predict body mass index (BMI). 'Functional' GRSs corresponding with specific biological pathways that shape BMI (adipogenesis, appetite and cardiopulmonary) were considered. The main outcome was phobic anxiety measured by the Crown Crisp Index (CCI) in 2004 in the NHS and in 2000 in the HPFS.

RESULTS

In observational analysis, a 1-unit higher BMI was associated with higher phobic anxiety symptoms [women: β = 0.05, 95% confidence interval (CI) 0.030-0.068; men: β = 0.04, 95% CI 0.016-0.071). IV analyses showed that BMI was associated with higher phobic anxiety symptoms in the FTO-instrumented analysis (p = 0.005) but not in the GRS-instrumented analysis (p = 0.256). Functional GRSs showed heterogeneous, non-significant effects of BMI on phobic anxiety symptoms.

CONCLUSIONS

Our findings do not provide conclusive evidence in favor of the hypothesis that higher BMI leads to higher levels of phobic anxiety, but rather suggest that genes that influence obesity, in particular FTO, may have direct effects on phobic anxiety, and hence that obesity and phobic anxiety may share common genetic determinants.

FOXC2 promotes colorectal cancer metastasis by directly targeting MET

Metastasis is the major cause of death in colorectal cancer (CRC). Although multiple genes have been identified to be responsible for the development of CRC, the molecular changes that enable CRC cells to undergo early local invasion and to form distant metastatic colonies still remain largely unknown. Herein, we investigated the role of Forkhead box protein C2 (FOXC2) and explored the underlying mechanisms in invasion and metastasis of CRC. We show that both high FOXC2 expression and nuclear localization of FOXC2 are significantly correlated with advanced TNM (T=primary tumor; N=regional lymph nodes; M=distant metastasis) stages. FOXC2 enhanced the invasive abilities of CRC cells in vitro and promoted local invasion and distant metastasis in an orthotopic mouse metastatic model of CRC. Microarray analysis revealed that overexpression of FOXC2 increased the proto-oncogene MET tyrosine kinase expression and activated the hepatocyte growth factor (HGF)-MET signaling pathway. Furthermore, luciferase reporter assays and chromatin immunoprecipitation assays revealed that FOXC2 directly associated with MET promoter to increase the transcriptional activity of MET. Inhibition of MET attenuates the invasive phenotype and metastatic potential of FOXC2-overexpressing CRC cells, indicating that MET is a major mediator of FOXC2-promoted metastasis. In addition, FOXC2 expression was positively correlated with MET expression in CRC tissue samples. Our findings suggest that FOXC2 has a crucial role in CRC metastasis by regulating HGF-MET signaling via inducing MET expression, highlighting FOXC2 as a potential therapeutic target for preventing or reducing metastasis in CRC.

Millennial-scale ocean acidification and late Quaternary decline of cryptic bacterial crusts in tropical reefs

Ocean acidification by atmospheric carbon dioxide has increased almost continuously since the last glacial maximum (LGM), 21,000 years ago. It is expected to impair tropical reef development, but effects on reefs at the present day and in the recent past have proved difficult to evaluate. We present evidence that acidification has already significantly reduced the formation of calcified bacterial crusts in tropical reefs. Unlike major reef builders such as coralline algae and corals that more closely control their calcification, bacterial calcification is very sensitive to ambient changes in carbonate chemistry. Bacterial crusts in reef cavities have declined in thickness over the past 14,000 years with largest reduction occurring 12,000-10,000 years ago. We interpret this as an early effect of deglacial ocean acidification on reef calcification and infer that similar crusts were likely to have been thicker when seawater carbonate saturation was increased during earlier glacial intervals, and thinner during interglacials. These changes in crust thickness could have substantially affected reef development over glacial cycles, as rigid crusts significantly strengthen framework and their reduction would have increased the susceptibility of reefs to biological and physical erosion. Bacterial crust decline reveals previously unrecognized millennial-scale acidification effects on tropical reefs. This directs attention to the role of crusts in reef formation and the ability of bioinduced calcification to reflect changes in seawater chemistry. It also provides a long-term context for assessing anticipated anthropogenic effects.

MicroRNA-922 promotes tau phosphorylation by downregulating ubiquitin carboxy-terminal hydrolase L1 (UCHL1) expression in the pathogenesis of Alzheimer's disease

Decreased levels of soluble ubiquitin carboxy-terminal hydrolase L1 (UCHL1) have been reported in the brains of sporadic Alzheimer's disease (AD) patients, and the introduction of UCHL1 rescued the synaptic and cognitive function of AD model mice. Obviously, a reduction in the levels of UCHL1 may play a role in the pathogenesis of AD. However, the mechanisms underlying the regulation of UCHL1 levels in AD have not been fully elucidated. MicroRNAs (miRs) have been shown to participate in the process of AD. In our study, we discovered that microRNA-922 decreased the levels of UCHL1. Neurofibrillary tangles (NFTs) mainly consisting of the hyperphosphorylated microtubule-associated protein tau are the defining pathological features of AD. In the present study, we found the levels of UCHL1 affected the levels of phosphorylated tau: the phosphorylated tau levels increased after knockdown of UCHL1 expression, and the phosphorylated tau levels decreased when UCHL1 was overexpressed. Furthermore, overexpression of microRNA-922 increased the phosphorylated tau levels. In conclusion, miR-922 increasing the levels of phosphorylated tau by regulating UCHL1 levels contributed to the pathogenesis of AD. Our study partly explained one of the mechanisms underlying the downregulation of UCHL1 levels in AD patients and could enrich the content of tau pathology in the pathogenesis of AD.

PKM2 and ACVR 1C are prognostic markers for poor prognosis of gallbladder cancer

PURPOSE

To identify biological markers related to the progression and prognosis of GBC.

METHODS

The expressions of pyruvate kinase isoenzyme type M2 (PKM2) and activin A receptor type IC (ACVR 1C) in 46 squamous cell/adenosquamous carcinomas (SC/ASC) and 80 adenocarcinomas (AC) were examined using immunohistochemistry.

RESULTS

Positive PKM2 and negative ACVR 1C expressions were significantly associated with lymph node metastasis, invasion and TNM stage of SC/ASCs and ACs. Univariate Kaplan-Meier analysis showed that either elevated PKM2 or loss of ACVR 1C expression significantly correlated with shorter average survival times in both SC/ASC and AC patients. Multivariate Cox regression analysis showed that positive PKM2 expression and loss of ACVR 1C expression were poor prognosis biomarkers in both SC/ASC and AC patients.

CONCLUSIONS

Our study suggested that PKM2 overexpression is a marker of metastasis, invasion and poor prognosis of GBC. ACVR 1C is a tumor suppressor, and lowered ACVR 1C expression is an important marker for the metastasis, invasion, and prognosis of GBC.

Abstract P4-01-20: Explore the differences and relationships between normal, ADH tissues and DCIS, IDC in breast by shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS)

Background: The mechanism that ADH changes to DCIS and even IDC is still not clear now. Raman spectroscopy is a powerful, non-invasive analytical tool which can provide detailed and meaningful information about biochemical composition of tissues at molecular level. Our aim was to find the differences and relationships between normal, ADH tissues and DCIS, IDC in breast based on their various biochemical characteristics by Raman spectroscopy.

Methods: The frozen sections were collected from 39 patients (all female; ages 27-74) who underwent surgical resection or mammotome biopsy at the Department of Breast Surgery, the First Hospital of Jilin University. After operation the samples were immediately frozen at -20∼-25°C and two contiguous sections (6 μm thickness) were cut from a sample by freezing microtome. One was stained with haematoxylin and eosin for routine histopathological analysis; the other was detected by Microscopic confocal Raman spectrometer (HORIBA JY Lab800, 633nm) with its mirror image (the H&E section). After the spectra we needed had been obtained, the Au@SiO2 shell-isolated nanoparticles (SHINs) were added to the surface of frozen sections immediately and then the spectra with SHINs were collected.

Results: A total of 475 Raman spectra and 470 SHINERS spectra were obtained from 9 normal breast tissues, 7 ADH, 8 DCIS, and 15 IDC breast tissues. The Raman signals were significantly enhanced by SHINs. The main spectral features of normal tissues at around 1301, 1442, 1654, and 1743 cm−1 are attributed to lipids. Meanwhile, no strong protein peaks emerged. The peaks of ADH, DCIS and IDC tissues located at 1004, 1033, 1610 and 1658 cm−1 from vibrational modes of proteins shows more stronger. 830, 880, 970, 1090 and 1157cm−1, representing DNA feature peaks, hold the same rules.

Table 1: Peak assignments of the Raman spectra of Breast tissues (wavenumbers in cm-1)NBADHDCISIDCMajor Assignments 880878880O-P-O stretch, DNA1003100410041003phenylalanine1092109210911090O-P-O stretch, DNA1301,14421302,14421303,14431303,1442CH2 twist and CH2 deformation, lipids  15261527C = C stretch of carotene 165816581658Amide I, α-helix1743174717451747C = O stretch, lipids

These show that diseased tissues contained more proteins and nucleic acids. The spectra of DCIS and IDC tissues contained 1527 cm−1, stemming from C = C stretching of carotene. The spectral features between ADH, DCIS and IDC tissues are described as followings: firstly, the concentrations of proteins, nucleic acids and carotene increased gradually but lipids content reduced from ADH to IDC. Secondly, ADH and DCIS tissues have extraordinary strong band of amide I, but in IDC tissues the peak almost cannot observed. Additionally, DCIS tissues have the red shifted and broad peak of CH2, which explains acyl backbone of lipids and proteins has fractured.

Conclusion: The changes including content and molecular structure of lipids, carotene, proteins and nucleic acids accompany with deterioration, indicating the Raman spectroscopy can be used to explore the differences and relationships between normal, ADH tissues and DCIS, IDC in breast. Simultaneously, it might be used to discover the mechanism that ADH convert to DCIS.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-01-20.

Combination of endobronchial ultrasound-guided transbronchial needle aspiration with standard bronchoscopic techniques enhanced the diagnosis yields of pulmonary tuberculosis patients with lymphadenopathy

AIM

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) was reported to be useful for diagnosis of tuberculosis (TB) lymphadenitis, although its indication remains unclear for suspicious pulmonary TB patients. To clarify the role of EBUS-TBNA for the diagnosis of immunocompetent TB patients with intrathoracic lymphadenopathy, we compared two diagnostic modalities: traditional bronchoscopy alone and EBUS-TBNA combined with bronchoscopy.

METHODS

We retrospectively studied 175 patients of suspicious pulmonary TB with intrathoracic lymphadenopathy in a single institute (Tongji University, Shanghai, China) from January 2010 to May 2011.

RESULTS

Ninety-seven patients underwent traditional bronchoscopy alone while 78 received the combined diagnostic techniques. Sensitivity and specificity were 18.1% and 100%, respectively, in the bronchoscopy group alone, and 80% and 92.3%, respectively, in the EBUS-TBNA combination group (absolute increase in sensitivity, 61.9%; P<0.001; 95% CI, 48.7-75.1%). In the combination group, EBUS-TBNA alone was diagnostic of TB in 42 patients (64.6%, 95% CI, 53-76.2%). Bleeding without hemodynamic instability developed in two patients during the procedure of EBUS-TBNA and no hospitalization prolongation happened in the both arms.

CONCLUSION

Combination of EBUS-TBNA with standard bronchoscopic technique is safe and significantly increases the diagnostic yield in patients of suspicious pulmonary TB with lymphadenopathy.

Roles of pyrolysis on availability, species and distribution of Cu and Zn in the swine manure: chemical extractions and high-energy synchrotron analyses

Animal manures generally contain high levels of heavy metals that may pose a significant threat to soil and groundwater qualities. Pyrolysis as means of reducing metal availability in such feed stocks is recently encouraged, but systematic studies are currently lacking. The aim of this study was to assess the impact of pyrolysis temperature on the availability of Cu and Zn by chemical extraction, to determine the speciation of Cu and Zn by synchrotron-based X-ray spectroscopy, and finally to investigate the phase distribution of metal species in the carbonaceous materials by combining acid-base extractions and absorption spectroscopy data. The results showed that both Cu and Zn in the swine manure were mainly bound to organic functional groups. Cu (II) reduction and Cu (I)-S complexes were observed during the pyrolysis process. Zn species resembling ZnAc2 was still dominant, being 60.8-69.2%, and ZnS increased by 6.6-21.8% in the carbonaceous materials. The distribution of Cu and Zn in the mineral, carbonized and non-carbonized organic phases varied greatly with the pyrolysis temperature. The higher the temperature, the more the metals existed in the mineral phase and carbonized organic phase. The decrease of EDTA extractable Cu and Zn with pyrolysis temperature was due to the increase of metals in the carbonized organic phase and mineral phase. It is suggested that pyrolysis at the relatively higher temperature is a better choice for metal-containing manure according to the metal speciation, solubility and availability.

The results of surgery for colorectal hepatic metastases following expansion of the indications in 2005

AIM

Safety and survival were investigated in patients treated according to expanded surgical indications for colorectal hepatic metastases.

METHOD

A retrospective analysis of all consecutive patients who underwent resection of colorectal hepatic metastases at Zhongshan Hospital from 2000 to 2010 was conducted. The patients were divided into two groups based on a change in the surgical indications introduced in 2005. Patients in Group I underwent hepatic surgery between 2000 and 2004 and those in Group II between 2005 and 2010. The clinicopathological data and survival rates of both groups were analysed.

RESULTS

There were 530 patients who underwent hepatic surgery between 2000 and 2010. After the expansion of surgical indications, the rate of surgical resection rose from 25.1 to 35.1% (P < 0.05). There was no significant difference in perioperative mortality (2.2% vs 0.9%) or morbidity (20.9% vs 29.8%). Recurrence occurred in 27.5% and 36.7% in Groups I and II, respectively, and 5-year overall survival was 43% and 49%, respectively (not significant).

CONCLUSION

Expanding the indications for surgical resection of hepatic metastases increased the resection rate but had no significant effect on survival.