Plasma Cell-Free Adenomatous Polyposis Coli Gene Promoter Methylation as a Prognostic Biomarker for Hepatocellular Carcinoma.

INTRODUCTION: Hepatocellular carcinoma (HCC) is a leading cause of cancer death worldwide. Lack of biomarkers for follow-up after treatment is a clinical challenge. DNA methylation has been proposed to be a potential biomarker in HCC. However, there is still lacking of evidence of its clinical use. This study aims to evaluate the value of using plasma Adenomatous Polyposis Coli promoter methylation level (APC-MET) as a potential biomarker in HCC treatment. METHOD: A total of 96 patients with HCC at BCLC stage B underwent local tumor ablation treatment were prospectively included in this study. APC-MET was examined from the plasma of each patient before and 1 months after treatment. The prediction value of APC-MET for survival outcome and disease status after treatment were analyzed, and adjusted with alpha-fetoprotein and protein induced by vitamin K absence-II using cox regression analysis. RESULTS: Univariate cox regression analysis showed preoperative APC-MET >0 (HR, 2.9, 95% CI 1.05－8.05, p=0.041) and postoperative APC-MET >0 (HR, 3.47, 95% CI 1.16－10.4, p=0.026) were both predictors of death, and preoperative APC-MET >0 was a predictor of disease progression after treatment (HR, 2.04, 95% CI 1.21－3.44, p=0.007). In multivariate models, pre-op APC-MET >0 was a significant predictor of disease progression after adjusting with other two traditional biomarkers (HR, 1.82, 95% CI 1.05－3.17, p=0.034). CONCLUSIONS: Hypermethylation of APC promoter appears to be a potential biomarker that could predict patient survival and disease progression outcome in patients with intermediate stage HCC after local ablation treatment.

DNA Methylation Biomarkers as Prediction Tools for Therapeutic Response and Prognosis in Intermediate-Stage Hepatocellular Carcinoma.

INTRODUCTION: Alfa-fetoprotein (AFP), as the main serum tumor marker of hepatocellular carcinoma (HCC), is limited in terms of specificity and ability to predict outcomes. This study investigated the clinical utility of DNA methylation biomarkers to predict therapeutic responses and prognosis in intermediate-stage HCC. METHODS: This study enrolled 72 patients with intermediate-stage HCC who underwent locoregional therapy (LRT) between 2020 and 2021. The immediate therapeutic response and disease status during a two-year follow-up were recorded. Analysis was performed on 10 selected DNA methylation biomarkers via pyrosequencing analysis of plasma collected before and after LRT. RESULTS: Analysis was performed on 53 patients with complete responses and 19 patients with disease progression after LRT. The mean follow-up duration was 2.4 ± 0.6 years. A methylation prediction model for tumor response (MMTR) and a methylation prediction model for early progression (MMEP) were constructed. The area under the curve (AUC) for sensitivity and specificity of MMTR was 0.79 for complete response and 0.759 for overall survival. The corresponding AUCs for sensitivity and specificity of AFP and protein induced by vitamin K absence-II (PIVKA-II) were 0.717 and 0.708, respectively. Note that the MMTR index was the only significant predictor in multivariate analysis. The AUC for sensitivity and specificity of the MMEP in predicting early progression was 0.79. The corresponding AUCs for sensitivity and specificity of AFP and PIVKA-II were 0.758 and 0.714, respectively. Multivariate analysis revealed that platelet count, beyond up-to-7 criteria, and the MMEP index were strongly correlated with early tumor progression. Combining the indexes and serum markers further improved the predictive accuracy (AUC = 0.922). Multivariate analysis revealed the MMEP index was the only independent risk factor for overall survival. DISCUSSION/CONCLUSIONS: This study indicates that these methylation markers could potentially outperform current serum markers in terms of accuracy and reliability in assessing treatment response and predicting outcomes. Combining methylation markers and serum markers further improved predictive accuracy, indicating that a multi-marker approach may be more effective in clinical practice. These findings suggest that DNA methylation biomarkers may be a useful tool for managing intermediate-stage HCC patients and guiding personalized treatment, particularly for those who are at high risk for close surveillance or adjuvant treatment after LRT.

Defective antiviral responses of induced pluripotent stem cells to baculoviral vector transduction.

Genetic engineering of induced pluripotent stem cells (iPSCs) is important for their clinical applications, and baculovirus (BV) holds promise as a gene delivery vector. To explore the feasibility of using BV for iPSCs transduction, in this study we first examined how iPSCs responded to BV. We determined that BV transduced iPSCs efficiently, without inducing appreciable negative effects on cell proliferation, apoptosis, pluripotency, and differentiation. BV transduction slightly perturbed the transcription of 12 genes involved in the Toll-like receptor (TLR) signaling pathway, but at the protein level BV elicited no well-known cytokines (e.g., interleukin-6 [IL-6], tumor necrosis factor alpha [TNF-α], and beta interferon [IFN-ß]) except for IP-10. Molecular analyses revealed that iPSCs expressed no TLR1, -6, -8, or -9 and expressed merely low levels of TLR2, -3, and -4. In spite of evident expression of such RNA/DNA sensors as RIG-I and AIM2, iPSCs barely expressed MDA5 and DAI (DNA-dependent activator of IFN regulatory factor [IRF]). Importantly, BV transduction of iPSCs stimulated none of the aforementioned sensors or their downstream signaling mediators (IRF3 and NF-κB). These data together confirmed that iPSCs responded poorly to BV due to the impaired sensing and signaling system, thereby justifying the transduction of iPSCs with the baculoviral vector.

Comparison of genomic signatures of non-small cell lung cancer recurrence between two microarray platforms.

BACKGROUND: Cancer genomic signatures may vary using different platforms. We compared the differential gene expression in non-small cell lung cancer (NSCLC) between two platforms in order to find the most relevant genomic signatures of tumor recurrence. MATERIALS AND METHODS: We analyzed gene expression in frozen lung cancer tissue from 59 selected patients who had undergone surgical resection of NSCLC. These patients were divided into two groups: group R, patients who had a tumor recurrence within four years, n=37; group NR, patients who remained disease-free four years following initial surgery, n=22. Each RNA sample was assayed twice using both Affymetrix and Illumina GeneChip. Data were analyzed by principal component analysis and leave-one-out cross-validation. RESULTS: Using the same filtering criteria, 13 genes that were differentially expressed between R and NR were identified by Affymetrix, while 21 genes were identified by Illumina GeneChip. In common, a total of six genes were detected by both systems. Using univariate analysis, four (lipocalin 2, LCN2; parathyroid hormone-like hormone, PTHLH; ras-related protein Rab-38, RAB38; and four jointed box 1, FJX1) of these six genes were associated with survival. A risk score of survival was calculated according to the four-gene expression. There was a significant difference in overall survival between low- and high-risk groups. CONCLUSION: A four-gene signature is associated with survival among patients with early-stage NSCLC. Further validation of these findings is warranted.

Whole genome expression in peripheral-blood samples of workers professionally exposed to polycyclic aromatic hydrocarbons.

This study aims to examine global gene expression profiles before and after the work-shift among coke-oven workers (COWs). COWs work six consecutive days and then take two days off. Two blood and urine samples in each worker were collected before starting to work after two days off and end-of-shift in the sixth day of work in 2009. Altered gene expressions (ratio of gene expression levels between end-of-shift and preshift work) were performed by a Human OneArray expression system which probes ~30,000-transcription expression profiling of human genes. Sixteen workers, all men, were enrolled in this study. Median urinary 1-hydroxypyrene (1OHP) levels (µmol/mol creatinine) in end-of-shift work were significantly higher than those in preshift work (2.58 vs 0.29, p = 0.0002). Among the 20,341 genes which passed experimental quality control, 26 gene expression changes, 7 positive and 19 negative, were highly correlated with across-the-shift urinary 1OHP levels (end-of-shift-preshift 1OHP) (p-value <0.001). The high and low exposure groups of across-the-shift urinary 1OHP levels dichotomized in ~2.00 µmol/mol creatinine were able to be distinguished by these 26 genes. Some of them are known to be involved in apoptosis, chromosome stability/DNA repair, cell cycle control/tumor suppressor, cell adhesion, development/spermatogenesis, immune function, and neuronal cell function. These findings in COWs will be an ideal model to study the relationship of PAH exposure with acute changes of gene expressions.

Effect of co-axially hybridized gene targets on hybridization efficiency of microarrayed DNA probes.

The effect of relative size of two co-axially hybridized gene targets on the hybridization efficiency was studied for two DNA probe configurations and various probe concentrations. Each of two sets of microarrayed probes contained a pair of DNA probes and a pair of their complementary samples labeled with two distinct fluorescent dyes. The sequence of each probe is especially designed so that two targets are simultaneously complementary to two adjacent sections of the probe. The molecular steric effect on the hybridization efficiency is investigated by comparing the dye signals between configurations of one-target and two-target hybridization scenarios. The results show that a low probe concentration gives better hybridization efficiency and the first-hybridization conducted by a shorter-size DNA target improves the hybridization efficiency of the second target coupling onto the same probe.

Cigarette smoking and alcohol drinking and esophageal cancer risk in Taiwanese women.

AIM: To investigate the etiology of esophageal cancer among Taiwanese women. METHODS: This is a multi-center, hospital-based, case-control study. Case patients consisted of women who were newly diagnosed and pathology-proven to have esophageal squamous cell carcinoma (ESCC) from three large medical centers (one from Northern and two from Southern Taiwan, respectively) between August 2000 and December 2008. Each ESCC patient was matched with 4 healthy women based on age (within 3 years) and hospital of origin, from the Department of Preventive Medicine in each hospital. A total of 51 case patients and 204 controls, all women, were studied. RESULTS: Frequencies of smokers and drinkers among ESCC patients were 19.6% and 21.6%, respectively, which were significantly higher than smokers (4.4%) and drinkers (4.4%) among controls (OR = 4.07, 95% CI: 1.36-12.16, P = 0.01; OR = 3.55, 95% CI: 1.03-12.27, P = 0.04). Women who drank an amount of alcohol more than 158 g per week had a 20.58-fold greater risk (95% CI: 1.72-245.62, P = 0.02) of ESCC than those who never drank alcohol after adjusting for other covariates, although the sample size was small. CONCLUSION: Cigarette smoking and alcohol drinking, especially heavy drinking, are the major risks for developing ESCC in Taiwanese women.

A novel three-dimensional aerogel biochip for molecular recognition of nucleotide acids.

Mesoporous aerogel was produced under regular atmospheric conditions using the sol-gel polymerization of tetraethyl orthosilicate with an ionic liquid as both solvent and active agent. This was then used to build a three-dimensional structure to recognize nucleotide acids. Fourier transformation infrared spectroscopy, scanning electron microscopy, (29)Si solid-state nuclear magnetic resonance, and Brunauer-Emmett-Teller instruments were used to characterize this 3D aerogel, demonstrating that it had high porosity and large internal networking surface area that could capture nucleotide acids. The functionality of molecular recognition on nucleotide acids was demonstrated by immobilizing an oligonucleotide to probe its DNA target and confirming the tagged fluorescent signals by confocal laser scanning microscopy. The results indicated that the as-prepared 3D bioaerogel was capable of providing a very large surface area to capture and recognize human gene ATP5O.

Baculovirus transduction of mesenchymal stem cells triggers the toll-like receptor 3 pathway.

Human mesenchymal stem cells (hMSCs) can be genetically modified with viral vectors and hold promise as a cell source for regenerative medicine, yet how hMSCs respond to viral vector transduction remains poorly understood, leaving the safety concerns unaddressed. Here, we explored the responses of hMSCs against an emerging DNA viral vector, baculovirus (BV), and discovered that BV transduction perturbed the transcription of 816 genes associated with five signaling pathways. Surprisingly, Toll-like receptor-3 (TLR3), a receptor that generally recognizes double-stranded RNA, was apparently upregulated by BV transduction, as confirmed by microarray, PCR array, flow cytometry, and confocal microscopy. Cytokine array data showed that BV transduction triggered robust secretion of interleukin-6 (IL-6) and IL-8 but not of other inflammatory cytokines and beta interferon (IFN-beta). BV transduction activated the signaling molecules (e.g., Toll/interleukin-1 receptor domain-containing adaptor-inducing IFN-beta, NF-kappaB, and IFN regulatory factor 3) downstream of TLR3, while silencing the TLR3 gene with small interfering RNA considerably abolished cytokine expression and promoted cell migration. These data demonstrate, for the first time, that a DNA viral vector can activate the TLR3 pathway in hMSCs and lead to a cytokine expression profile distinct from that in immune cells. These findings underscore the importance of evaluating whether the TLR3 signaling cascade plays roles in the immune response provoked by other DNA vectors (e.g., adenovirus). Nonetheless, BV transduction barely disturbed surface marker expression and induced only transient and mild cytokine responses, thereby easing the safety concerns of using BV for hMSCs engineering.

Dividable membrane with multi-reaction wells for microarray biochips.

This paper presents a multi-well membrane fabricated using polydimethylsiloxane (PDMS) as a part of a microarray biochip that allows dividable incubation chambers to be provided on a single chip. The conditions of the forming temperature, time, and mixing proportion of the materials were investigated to obtain optimal physical absorption with the surface of the chip substrate. To verify the properties of the multi-well chip, immunoassays were performed by the alpha-1-fetoprotein (AFP) antigen sandwich experiment. The results showed that the detection limit reached to the concentration of 10 ng/ml AFP antigen, and that the dynamic range was 30-3000 ng/ml. Attaining excellent physical absorption helps in avoiding cross-contamination or interference between different samples on the same biochip. The merits of dividable multi-well chips include promoting effective use of surface and multiple-sample experiments.

Kinetics of heterogeneous hybridization on indium tin oxide surfaces with and without an applied potential.

The rate of hybridization of oligonucleotide target sequences to chemically immobilized oligonucleotide probes has been studied both with and without an electrical field. The probe size was 20-24 nucleotides (nt) while the target size ranged from 157 to 864 nt. In agreement with previous studies, complete hybridization under normal conditions required 10-30 hours, depending on target size. The kinetics were characterized by a characteristic lag time followed by an asymptotic rise to the final value. In contrast, with an applied electrical field, all but the largest target hybridized in about 10 min while the longest hybridized within 1 h. Deleterious electrode reactions were avoided by close spacing of the anode and cathode and application of very small voltages. Our results suggest that probes and targets orient flat on the surface. A model is suggested to explain the kinetics observed that involves a series of surface states between initial target arrival and final hybridized state. Our results show that the electric field accelerated hybrid capture of solution-phase targets by surface-bound probes. This approach may have implications for enhancing array-based hybrid capture for mutation detection, copy number determination and/or gene expression profiling.