[Identification of characteristic methylation sites in gastric cancer using genomics-based machine learning].

Objective: To construct a prediction model of gastric cancer related methylation using machine learning algorithms based on genomic data. Methods: The gene mutation data, gene expression data and methylation chip data of gastric cancer were downloaded from The Caner Genome Atlas database, feature selection was conducted, and support vector machine (radial basis function), random forest and error back propagation (BP) neural network models were constructed; the model was verified in the new data set. Results: Among the three machine learning models, BP neural network had the highest test efficiency (F1 score=0.89,Kappa=0.66, area under curve=0.93). Conclusion: Machine learning algorithms, particularly BP neural network, can be used to take advantages of the genomic data for discovering molecular markers, and to help identify characteristic methylation sites of gastric cancer.

Chinese Medicine in Cancer Treatment - How is it Practised in the East and the West?

Chinese medicine therapies in cancer treatment are very common in the East. Although it is usually classified as a form of complementary and alternative therapy in the West, Chinese medicine is an independent medical profession in Hong Kong and mainland China. It has a different perspective in understanding health and diseases compared with Western medicine. In oncology practice, whereas Western medicine focuses on direct tumour eradication by surgery, radiation therapy and systemic therapies, Chinese medicine focuses on restoring body balance and enhancing the body's defences (immunity), in addition to some cytotoxic herbal therapies. Most often patients, especially those in the East, receive both treatments. Chinese medicine is also commonly used to reduce side-effects from chemotherapy or radiation therapy, to aid recovery after an operation, to palliate symptoms and to address survivorship issues. However, this raises concerns of drug-herb interactions and toxicity in combination therapies. Commonly used Chinese medicine treatment modalities include acupuncture, moxibustion, diet therapy, prescribed Chinese medicine herbal decoction, single Chinese medicine herbs or supplements and tai chi. Although there is an increasing trend of Chinese medicine use in cancer patients in both the East and the West, the scientific evidence of safety and efficacy is often questioned by oncologists. This article reviews the current evidence in different Chinese medicine therapies in cancer management in both the East and the West.

Expression and prognostic roles of magnesium-dependent phosphatase-1 in gastric cancer.

OBJECTIVE: Gastric cancer is a leading cause of cancer deaths and has a poor prognosis after diagnosis. Previous studies showed that Magnesium-Dependent Phosphatase-1 (MDP-1) might be a key component for glycosylation in human protein repair, and an alteration of its function has been involved in some aspects of cellular metabolic networks linked to either normal or pathological processe. In this study, we investigate the MDP-1 status in patients with gastric carcinoma, and determine the potential relationship between MDP-1 and clinical outcome. PATIENTS AND METHODS: One hundred and seventy-one consecutive patients with stage I-III gastric carcinoma who had received a D2 gastrectomy were recruited. The MDP-1 expression was determined by immunohistochemistry (IHC). Disease-free survival (DFS) and overall survival (OS) were evaluated. RESULTS: We generate an IHC score on a continuous scale of 0-7. The IHC cutoff point generated by ROC analysis and the threshold IHC score was 2. Low MDP-1 expression was scored for 61 (35.7%) and high MDP-1 expression for 110 (64.3%) patients. We saw a significant down-regulation of MDP-1 expression in G3-4 and stage III tumor tissue compared with G1-2 and stage I-II tumors, p=0.023 and p=0.047. In univariate survival analysis, high expression of MDP-1 predicted a significantly better DFS (56.0 months vs. 25.0 months, p=0.029) and OS (59.0 months vs. 41.0 months, p=0.043) compared with low expression. In a multivariate analysis, the tumor stage was a significant predictor for DFS and OS even after adjustment for all other covariates. The MDP-1 status was a joint predictor for DFS and OS with a multivariate HR 0.728, 95% CI 0.530-0.999, p=0.049 and a multivariate HR 0.745, 95% CI 0.543-1.022, p=0.068, respectively. CONCLUSIONS: We showed that down-regulation of MDP-1 expression was correlated with poorly differentiated carcinoma and later tumor stage, and it predicted a significantly poorer DFS and OS. Down-regulation of MDP-1 expression was a predictor of a poor prognosis for gastric cancer patients, and it may refer to tumor cells that have lost a protective enzymatic system.

[Expression of long non-coding RNA SNHG8 in Epstein-Barr virus-related gastric cancer and clinical outcome].

Objective: To investigate the expression of long non-coding RNA (lncRNA) SNHG8 in EB virus related gastric cancer and their correlation prognosis. Methods: The expression of SNHG8 in 93 gastric cancers and 93 cancer-free controls, matched by age and sex, were determined by real-time PCR. EB virus expression was detected by EBER in situ hybridization. Results: Forty-one gastric cancers were EB virus associated. For all gastric cancers, SNHG8 expression was 14 times higher (P=0.001) than that in non-cancer controls; in the EB virus related gastric cancers, SNHG8 expression was increased 25 times (P<0.05) over EB virus negative gastric cancers. SNHG8 expression level was also significantly associated with TNM staging (P<0.05). Conclusions: SNHG8 may act as a proto-oncogene, participating in gastric carcinogenesis.EB virus infection of gastric mucosa may promote SNHG8 expression.

Identification of a human chromosome-specific interstitial telomere-like sequence (ITS) at 22q11.2 using double-strand PRINS.

Interstitial telomeric sequences (ITSs), telomere-like repeats at intrachromosomal sites, are common in mammals and consist of tandem repeats of the canonical telomeric repeat, TTAGGG, or a repeat similar to this. We report that the ITS in human chromosome region 22q11.2 is, in the sequenced genome database, 101 tandem repeats of the sequence TTAGGGAGG. Using the primed in situ labeling (PRINS) technique and primers against the canonical telomeric repeat (TTAGGG), we illuminated telomeric sites for all chromosomes and an ITS locus at 22q11.2. Using the TTAGGGAGG sequence, we designed PRINS primers that efficiently and specifically illuminate the 22q11.2 ITS locus without illuminating telomeric and other ITS loci. The 22q11.2 locus has more repeat units than other ITSs loci enabling an unprecedented high detection frequency for this interstitial telomere locus. The 22q11.2 is associated with hot spots for disease-related chromosome breaks for multiple disorders, such as DiGeorge syndrome and chronic myeloid leukemia. We describe our findings that the ITS at 22q11.2 is in the same area of, and proximal to the common rearrangement region of multiple disorders. We suggest that the ITS might be involved in DNA repair processes in this area to protect the chromosome from more serious damage.

Crystallization and preliminary crystallographic studies of antibacterial polypeptide LCI expressed in Escherichia coli.

LCI is a type of novel antibacterial polypeptide secreted by a Bacillus subtilis strain. It consists of 47 residues with a molecular weight of 5468 Da. Using bioengineering, LCI was expressed in Escherichia coli DH5alpha with recombinant plasmid pBVAB16. It was crystallized using PEG 4000 as a precipitant. The crystal belongs to space group P6(2)22 or P6(4)22, with unit-cell parameters a = b = 29.30, c = 187.09 A, and diffracts to 2.44 A. A set of diffraction data to 2.8 A was collected.

[The dynamics of antigen and antibody in Schistosoma japonicum egg granuloma and its relationship with the granuloma response].

Synchronous Schistosoma japonicum egg granuloma in the lung of mouse model and PAP (peroxidas-anti-peroxidase) technique were employed to study the dynamics of antigen and antibody in the egg granuloma of S. japouicum and its relationship with the granuloma formation. The granulomatous response began on the 3.5 day after egg injection and increased to the maximal size at the 4th week. Lymphocyte populations and macrophage comprised an important part of lesions during the time of acute granulomatous response (7-28 day). Using PAP staining, the SEA within egg could be detected at high level on the first day after egg injection and then declined gradually. On the contrary, the SEA around egg was minimal at the first week and increased to the peak at the 4th week, then decreased gradually. No antibody could be detected throughout the experimental period (35 days). The results suggested that 1) the antigen of Schistosoma egg is the essential factor for the granuloma formation. 2) S. japonicum egg granuloma could be formed in unsensitized mouse. 3) The mechanism of egg granuloma formation of S. japonicum is similar to that of S. mansoni.

Allogeneic fetal liver transplantation in acute leukemia.

Three patients with acute leukemia in first complete remission were transplanted with fetal liver cells from May 1983 to June 1984. A conditioning regimen of cyclophosphamide (60-80 mg/kg) and TBI 600-700 rads (a dose rate of 5-7r per minute) was taken. The hemopoietic and immunological recovery was rapid and complete in every patient. There was proof of chimerism in case 1 as demonstrated by the existance of the XX karyotype of donor fetus in 68.7% and 75% of marrow metaphases, in 25% of peripheral blood metaphases, by the appearance of new HLA-antigens and RBC blood type antigens of donor origin. The serum alpha-fetoprotein level increased and maintained for 40 days in case 2, but definite evidence of engraftment was not observed. The allogeneic marker, the donor's HLA-antigens and RBC isoenzyme, were detected in case 3.