CBD2: A functional biomarker database for colorectal cancer.

The rapidly evolving landscape of biomarkers for colorectal cancer (CRC) necessitates an integrative, updated repository. In response, we constructed the Colorectal Cancer Biomarker Database (CBD), which collected and displayed the curated biomedicine information for 870 CRC biomarkers in the previous study. Building on CBD, we have now developed CBD2, which includes information on 1569 newly reported biomarkers derived from different biological sources (DNA, RNA, protein, and others) and clinical applications (diagnosis, treatment, and prognosis). CBD2 also incorporates information on nonbiomarkers that have been identified as unsuitable for use as biomarkers in CRC. A key new feature of CBD2 is its network analysis function, by which users can investigate the visible and topological network between biomarkers and identify their relevant pathways. CBD2 also allows users to query a series of chemicals, drug combinations, or multiple targets, to enable multidrug, multitarget, multipathway analyses, toward facilitating the design of polypharmacological treatments for CRC. CBD2 is freely available at http://www.eyeseeworld.com/cbd.

EBD: an eye biomarker database.

MOTIVATION: Many ophthalmic disease biomarkers have been identified through comprehensive multiomics profiling, and hold significant potential in advancing the diagnosis, prognosis, and management of diseases. Meanwhile, the eye itself serves as a natural biomarker for several systemic diseases including neurological, renal, and cardiovascular systems. We aimed to collect and standardize this eye biomarkers information and construct the eye biomarker database (EBD) to provide ophthalmologists with a platform to search, analyze, and download these eye biomarker data. RESULTS: In this study, we present the EBD , a world-first online compilation comprising 889 biomarkers for 26 ocular diseases and 939 eye biomarkers for 181 systemic diseases. The EBD also includes the information of 78 "nonbiomarkers"-the objects that have been proven cannot be biomarkers. Biological function and network analysis were conducted for these ocular disease biomarkers, and several hub pathways and common network topology characteristics were newly identified, which may promote future ocular disease biomarker discovery and characterizes the landscape of biomarkers for eye diseases at the pathway and network level. The EBD is expected to yield broader utility among developmental biologists and clinical scientists in and outside of the eye field by assisting in the identification of biomarkers linked to eye disorders and related systemic diseases. AVAILABILITY AND IMPLEMENTATION: EBD is available at http://www.eyeseeworld.com/ebd/index.html.

Identification of prostate cancer specific methylation biomarkers from a multi-cancer analysis.

BACKGROUND: Detecting prostate cancer at a non-aggressive stage is the main goal of prostate cancer screening. DNA methylation has been widely used as biomarkers for cancer diagnosis and prognosis, however, with low clinical translation rate. By taking advantage of multi-cancer data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we aimed to identify prostate cancer specific biomarkers which can separate between non-aggressive and aggressive prostate cancer based on DNA methylation patterns. RESULTS: We performed a comparison analysis of DNA methylation status between normal prostate tissues and prostate adenocarcinoma (PRAD) samples at different Gleason stages. The candidate biomarkers were selected by excluding the biomarkers existing in multiple cancers (pan-cancer) and requiring significant difference between PRAD and other urinary samples. By least absolute shrinkage and selection operator (LASSO) selection, 8 biomarkers (cg04633600, cg05219445, cg05796128, cg10834205, cg16736826, cg23523811, cg23881697, cg24755931) were identified and in-silico validated by model constructions. First, all 8 biomarkers could separate PRAD at different stages (Gleason 6 vs. Gleason 3 + 4: AUC = 0.63; Gleason 6 vs. Gleason 4 + 3 and 8-10: AUC = 0.87). Second, 5 biomarkers (cg04633600, cg05796128, cg23523811, cg23881697, cg24755931) effectively detected PRAD from normal prostate tissues (AUC ranged from 0.88 to 0.92). Last, 6 biomarkers (cg04633600, cg05219445, cg05796128, cg23523811, cg23881697, cg24755931) completely distinguished PRAD with other urinary samples (AUC = 1). CONCLUSIONS: Our study identified and in-silico validated a panel of prostate cancer specific DNA methylation biomarkers with diagnosis value.

Skp2 regulates DNA damage repair and apoptosis via interaction with Ku70.

PURPOSE: Skp2, an oncoprotein, regulates tumor proliferation, invasion and metastasis. Ku70 is a critical component of the non-homologous end-joining (NHEJ) process. Both Skp2 and Ku70 are positively associated in multiple cancers. However, there is no report about the relationship between Skp2 and Ku70 proteins. METHODS: In this study, we carried out Bioinformatics and molecular biological methods to investigate the relationship between Skp2 and Ku70 proteins. RESULTS: We first observed Skp2 and Ku70 mRNAs were significantly increased in cervical cancer tissues. And we identified Ku70 as a Skp2-binding protein and the binding site located in the C-terminal of Ku70 protein. We further found that Skp2 knockdown decreased the Ku70 protein level in cells, and increase the cellular apoptosis and DNA damage, suggesting Skp2 mediates the Ku70 protein stability and function via post-translational modification. CONCLUSION: The direct interaction between Skp2 and Ku70 proteins mediates the DNA damage repair and cellular apoptosis by regulating Ku70 stability and function via post-translational modification. The molecular mechanisms how Skp2 stabilize Ku70 would be clarified in our following research work.

Atractyloside mimics BORIS knockdown to induce DNA damage in colorectal cancer cells.

The Brother of Regulator of Imprinted Sites (BORIS) is expressed abnormally in colorectal cancer and is predicted to be a potential diagnostic and prognostic target. However, little is known about BORIS-related signaling pathways and no bioactive drugs have been found to target BORIS. We screened the gene regulation panels of BORIS-silenced colorectal cancer cells by microarray assay and applied the regulated gene list in a connectivity map (CMap) database to screen for bioactive drugs which regulate gene panels similar to BORIS knockdown. Gene set enrichment analysis (GSEA) suggests a correlation between BORIS knockdown and apoptosis. Screening revealed atractyloside treatment as a drug similar to BORIS siRNA in regulating genes in colorectal cancer cells. Atractyloside treatment or BORIS knockdown induced the expression of XRCC4, which suggested DNA damage was induced by knockdown of the BORIS signaling pathway. H2A.X immunofluorescence stain indicated BORIS knockdown indeed created DNA damage. As atractyloside synergized with 5-Fluoruracil (5-FU) to suppress colorectal cancer cell proliferation, we concluded that the inhibition of BORIS downstream by atractyloside amplifies the effect of 5-FU by promoting DNA damage.

WBSCR22 confers oxaliplatin resistance in human colorectal cancer.

Human WBSCR22 gene is involved in tumor metastasis, cell growth and invasion, however, its role in chemosensitivity to antitumor agents remains unknown. In this study, we analyzed the TCGA cohort and found the expression of WBSCR22 was significantly elevated in human colorectal cancer (CRC) tissue. WBSCR22 could be served as an independent risk predictor for overall survival (OS), and up-regulated WBSCR22 could predict unfavorable OS for CRC patients. Knockdown of WBSCR22 significantly sensitized CRC cells to oxaliplatin in vitro and in vivo, while overexpression of WBSCR22 led to cellular resistance to oxaliplatin treatment. Although WBSCR22 knockdown did not change cell cycle, it increased the oxaliplatin-induced cellular apoptosis. WBSCR22 knockdown augmented the oxaliplatin-induced intracellular reactive oxygen species (ROS) production and ROS-induced 8-oxoguanine (8-oxoG) oxidative lesion accumulation, likely sensitizing oxaliplatin treatment. These results demonstrate that WBSCR22 is involved in CRC resistance to oxaliplatin, suggesting WBSCR22 may represent a novel oxaliplatin resistance biomarker as well as a potentail target for CRC therapeutics.

E-26 Transformation-specific Related Gene Expression and Outcomes in Cytogenetically Normal Acute Myeloid Leukemia: A Meta-analysis.

BACKGROUND: The E-26 transformation-specific related gene (ERG) is frequently expressed in cytogenetically normal acute myeloid leukemia (CN-AML). Herein, we performed a meta-analysis to investigate the relationship between the prognostic significance of ERG expression and CN-AML. METHODS: A systematic review of PubMed database and other search engines were used to identify the studies between January 2005 and November 2016. A total of 667 CN-AML patients were collected from seven published studies. Of the 667 patients underwent intensive chemotherapy, 429 had low expression of ERG and 238 had high expression of ERG. Summary odds ratio (OR) and the 95% confidence interval (CI) for the ERG expression and CN-AML were calculated using fixed- or random-effects models. Heterogeneity was assessed using Chi-squared-based Q- statistic test and I2 statistics. All statistical analyses were performed using R.3.3.1 software packages (R Foundation for Statistical Computing, Vienna, Austria) and RevMan5.3 (Cochrane Collaboration, Copenhagen, Denmark). RESULTS: Overall, patients with high ERG expression had a worse relapse (OR = 2.5127, 95% CI: 1.5177-4.1601, P = 0.0003) and lower complete remission (OR = 0. 3495, 95% CI: 0.2418-0.5051, P< 0.0001). With regard to the known molecular markers, both internal tandem duplications of the fms-related tyrosine kinase 3 gene (OR = 3.8634, 95% CI: 1.8285-8.1626, P = 0.004) and brain and acute leukemia, cytoplasmic (OR = 3.1538, 95% CI: 2.0537-4.8432, P< 0.0001) were associated with the ERG expression. In addition, the results showed a statistical significance between French-American-British (FAB) classification subtype (minimally differentiated AML and AML without maturation, OR = 4.7902, 95% CI: 2.7772-8.2624, P< 0.0001; acute monocytic leukemia, OR = 0.2324, 95% CI: 0.0899-0.6006, P = 0.0026) and ERG expression. CONCLUSION: High ERG expression might be used as a strong adverse prognostic factor in CN-AML.

Peony-Glycyrrhiza Decoction for Antipsychotic-Related Hyperprolactinemia in Women With Schizophrenia: A Randomized Controlled Trial.

OBJECTIVES: An herbal preparation called peony-glycyrrhiza decoction (PGD) may have the potential in reducing antipsychotic-related hyperprolactinemia (hyperPRL). This double-blind, randomized placebo-controlled study aimed to reevaluate the efficacy of PGD against antipsychotic-related hyperPRL. METHODS: Ninety-nine schizophrenic women who were under antipsychotic therapy and had symptomatic hyperPRL were randomly assigned to additional treatment with placebo (n = 50) or PGD (n = 49, 45 g/d) for 16 weeks. The severity of hyperPRL, psychosis, and abnormal involuntary movements was assessed at baseline and weeks 8 and 16 using standard instruments including the Prolactin Related Adverse Event Questionnaire. Blood levels of prolactin (PRL) and related pituitary and sex hormones were measured at the same time points. RESULTS: Peony-glycyrrhiza decoction treatment produced a significantly greater reduction of the Prolactin Related Adverse Event Questionnaire score at weeks 8 and 16 and a greater improvement on abnormal involuntary movements at end point compared with placebo, without altering the severity of psychosis. The group treated with PGD showed significantly higher proportion of having overall improvement on hyperPRL symptoms (χ = 4.010, P = 0.045) and menstrual resumption (χ = 4.549, P = 0.033) at week 8 than placebo. Serum PRL levels were similar in the 2 groups. CONCLUSIONS: Peony-glycyrrhiza decoction is effective in reducing antipsychotic-related hyperPRL and abnormal involuntary movement symptoms, but no reduction in blood PRL concentrations was observed. The underlying mechanisms of PGD's effects need further investigation (trial registration of NCT01852331 at www.clinicaltrials.gov).

Identification of miRNAs as non-invasive biomarkers for early diagnosis of lung cancers.

Current clinical diagnostic methods lack the specificity in detecting lung cancer patients. The issue is particularly critical for stage I and II patients. Considerable evidence showed microRNA plays a very important role in lung carcinogenesis. Here, we identified a panel of 41 miRNAs significantly elevated in patients with lung cancer, of which eight miRNAs were further validated in an independent sample cohort. Classification analysis using the panel of eight miRNAs generated a discriminatory power of 93.3 % sensitivity and 93.8 % specificity in separating non-small-cell lung cancer (NSCLC) patients from normal controls, indicating the miRNAs have a potential clinical utility in discriminating NSCLC. Interestingly, miR-1244 was found significantly elevated in the serum samples of lung cancer patients, and the test characteristics of the single miRNA were area under the curve (AUC) of 0.832 in NSCLC vs healthy controls, and 0.861 in NSCLC vs patients with unidentified pulmonary nodules. This is the first study showing serum miR-1244 could be a biomarker to screen lung cancer patients from the high-risk population.

Multiplexed Serum Biomarkers for the Detection of Lung Cancer.

Currently, there is no available biomarker for lung cancer diagnosis. Here we recruited 844 lung cancer patients and 620 healthy participants from six hospitals. A total of four serum proteins was identified and subsequently assessed in the training and validation cohorts. The concentrations of four serum proteins were found to be significantly higher in lung cancer patients compared with healthy participants. The area under the curve (AUC) for the 4-biomarker were 0.86 in the training cohort, and 0.87 in the validation cohort. The classification improved to a corrected AUC of 0.90 and 0.89 respectively following addition of sex, age and smoking status. Similar results were observed for early-stage lung cancer. Remarkably, in a blinded test with a suspicious pulmonary nodule, the adjusted prediction model correctly discriminated the patients with 86.96% sensitivity and 98.25% specificity. These results demonstrated the 4-biomarker panel improved lung cancer prediction beyond that of known risk factors. Moreover, the biomarkers were valuable in differentiating benign nodules which will remain indolent from those that are likely to progress and therefore might serve as an adjuvant diagnosis tool for LDCT scanning.

Tumor necrosis factor-α as a diagnostic marker for neonatal sepsis: a meta-analysis.

Neonatal sepsis (NS) is an important cause of mortality in newborns and life-threatening disorder in infants. The meta-analysis was performed to investigate the diagnosis value of tumor necrosis factor-α (TNF-α ) test in NS. Our collectible studies were searched from PUBMED, EMBASE, and the Cochrane Library between March 1994 and August 2013. Accordingly, 347 studies were collected totally, in which 15 articles and 23 trials were selected to study the NS in our meta-analysis. The TNF-α test showed moderate accuracy of the diagnosis of NS both in early-onset neonatal sepsis (sensitivity = 0.66, specificity = 0.76, Q∗ = 0.74) and in late-onset neonatal sepsis (sensitivity = 0.68, specificity = 0.89, Q∗ = 0.87). We also found the northern hemisphere group in the test has higher sensitivity (0.84) and specificity (0.83). A diagnostic OR analysis found that the study population may be the major reason for the heterogeneity. Accordingly, we suggest that TNF-α is also a valuable marker in the diagnosis of NS.

Diagnosis value of the serum amyloid A test in neonatal sepsis: a meta-analysis.

Neonatal sepsis (NS), a common disorder for humans, is recognized as a leading global public health challenge. This meta-analysis was performed to assess the accuracy of the serum amyloid A (SAA) test for diagnosing NS. The studies that evaluated the SAA test as a diagnostic marker were searched in Pubmed, EMBASE, the Cochrane Library, and Google Network between January 1996 and June 2013. A total of nine studies including 823 neonates were included in our meta-analysis. Quality of each study was evaluated by the quality assessment of diagnostic accuracy studies tool (QUADAS). The SAA test showed moderate accuracy in the diagnosis of NS both at the first suspicion of sepsis and 8-96 h after the sepsis onset, both with Q* = 0.91, which is similar to the PCT and CRP tests for the diagnosis of NS in the same period. Heterogeneity between studies was also explained by cut-off point, SAA assay, and age of included neonates. On the basis of our meta-analysis, therefore, SAA could be promising and meaningful in the diagnosis of NS.

A randomized, crossover comparison of herbal medicine and bromocriptine against risperidone-induced hyperprolactinemia in patients with schizophrenia.

Hyperprolactinemia is a common adverse effect that occurs as a result of antipsychotic therapies, which often results in discontinuation. Empirical evidence has shown that some herbal medicines have suppressive effects on prolactin (PRL) hyperactivities. This study was designed to compare the herbal preparation called Peony-Glycyrrhiza Decoction (PGD) with bromocriptine (BMT), a dopamine agonist widely used for PRL-secreting disorders, in the treatment of risperidone-induced hyperprolactinemia. Twenty schizophrenic women who were under risperidone maintenance treatment, diagnosed with hyperprolactinemia (serum PRL levels >50 mug/L), and currently experiencing oligomenorrhea or amenorrhea were selected for the study. Subjects were randomized to additional treatment with PGD (45 g/d) followed by BMT (5 mg/d) or BMT followed by PGD at the same doses for 4 weeks each, with an interval of 4-week washout period between 2 treatment sessions. The severity of psychotic symptoms, adverse events, serum PRL, estradiol, testosterone, and progesterone levels were examined at baseline and end point. Peony-Glycyrrhiza Decoction treatment produced a significant baseline-end point decrease in serum PRL levels, without exacerbating psychosis and changing other hormones, and the decreased amplitudes were similar to those of BMT (24% vs 21%-38%). Moreover, there was a significantly greater proportion of patients during PGD treatment than BMT treatment showing improvements on adverse effects associated with hyperprolactinemia (56% vs 17%, P = 0.037). These results suggest that the herbal therapy can yield additional benefits while having comparable efficacy in treating antipsychotic-induced hyperprolactinemia in individuals with schizophrenia.