Evaluation of a Liquid Biopsy Protocol using Ultra-Deep Massive Parallel Sequencing for Detecting and Quantifying Circulation Tumor DNA in Colorectal Cancer Patients.

The identification and quantification of actionable mutations are critical for guiding targeted therapy and monitoring drug response in colorectal cancer. Liquid biopsy (LB) based on plasma cell-free DNA analysis has emerged as a noninvasive approach with many clinical advantages over conventional tissue sampling. Here, we developed a LB protocol using ultra-deep massive parallel sequencing and validated its clinical performance for detection and quantification of actionable mutations in three major driver genes (KRAS, NRAS and BRAF). The assay showed a 92% concordance for mutation detection between plasma and paired tissues and great reliability in quantification of variant allele frequency.

Retardation of arsenic transport through a Pleistocene aquifer.

Groundwater drawn daily from shallow alluvial sands by millions of wells over large areas of south and southeast Asia exposes an estimated population of over a hundred million people to toxic levels of arsenic. Holocene aquifers are the source of widespread arsenic poisoning across the region. In contrast, Pleistocene sands deposited in this region more than 12,000 years ago mostly do not host groundwater with high levels of arsenic. Pleistocene aquifers are increasingly used as a safe source of drinking water and it is therefore important to understand under what conditions low levels of arsenic can be maintained. Here we reconstruct the initial phase of contamination of a Pleistocene aquifer near Hanoi, Vietnam. We demonstrate that changes in groundwater flow conditions and the redox state of the aquifer sands induced by groundwater pumping caused the lateral intrusion of arsenic contamination more than 120 metres from a Holocene aquifer into a previously uncontaminated Pleistocene aquifer. We also find that arsenic adsorbs onto the aquifer sands and that there is a 16-20-fold retardation in the extent of the contamination relative to the reconstructed lateral movement of groundwater over the same period. Our findings suggest that arsenic contamination of Pleistocene aquifers in south and southeast Asia as a consequence of increasing levels of groundwater pumping may have been delayed by the retardation of arsenic transport.

Performance Evaluation of Non-GPS Based Localization Techniques under Shadowing Effects.

Non-GPS localization has gained much interest from researchers and industries recently because GPS might fail to meet the accuracy requirements in shadowing environments. The two most common range-based non-GPS localization methods, namely Received Signal Strength Indicator (RSSI) and Angle-of-Arrival (AOA), have been intensively mentioned in the literature over the last decade. However, an in-depth analysis of the weighted combination methods of AOA and RSSI in shadowing environments is still missing in the state-of-the-art. This paper proposes several weighted combinations of the two RSSI and AOA components in the form of pAOA + qRSSI, devises the mathematical model for analyzing shadowing effects, and evaluates these weighted combination localization methods from both accuracy and precision perspectives. Our simulations show that increasing the number of anchors does not necessarily improve the precision and accuracy, that the AOA component is less susceptible to shadowing than the RSSI one, and that increasing the weight of the AOA component and reducing that of the RSSI component help improve the accuracy and precision at high Signal-to-Noise Ratios (SNRs). This observation suggests that some power control algorithm could be used to increase automatically the transmitted power when the channel experiences large shadowing to maintain a high SNR, thus guaranteeing both accuracy and precision of the weighted combination localization techniques.

Evaluation of Physicochemical Properties of a Hydroxyapatite Polymer Nanocomposite for Use in Fused Filament Fabrication.

Over the last decade, there has been an increasing interest in the use of bioceramics for biomedical purposes. Bioceramics, specifically those made of calcium phosphate, are commonly used in dental and orthopaedic applications. In this context, hydroxyapatite (HA) is considered a viable option for hard tissue engineering applications given its compositional similarity to bioapatite. However, owing to their poor mechanobiology and biodegradability, traditional HA-based composites have limited utilisation possibilities in bone, cartilage and dental applications. Therefore, the efficiency of nano HA (nHA) has been explored to address these limitations. nHA has shown excellent remineralising effects on initial enamel lesions and is widely used as an additive for improving existing dental materials. Furthermore, three-dimensional printing (3DP) or fused deposition modelling that can be used for creating dental and hard tissue scaffolds tailored to each patient's specific anatomy has attracted considerable interest. However, the materials used for producing hard tissue with 3DP are still limited. Therefore, the current study aimed to develop a hybrid polymer nanocomposite composed of nHA, nanoclay (NC) and polylactic acid (PLA) that was suitable for 3DP. The nHA polymer nanocomposites were extruded into filaments and their physiochemical properties were evaluated. The results showed that the addition of nHA and NC to the PLA matrix significantly increased the water absorption and contact angle. In addition, the hardness increased from 1.04 to 1.25 times with the incorporation of nHA. In sum, the nHA-NC-reinforced PLA could be used as 3DP filaments to generate bone and dental scaffolds, and further studies are needed on the biocompatibility of this material.

Dual-targeting exosomes for improved drug delivery in breast cancer.

Aims: The authors investigated whether displaying more than one homing peptide enhanced the tumor-targeting efficiency of exosomes. Materials & methods: Exosomes from human embryonic kidney cells (HEK293F) were engineered to display either mono- or dual-tumor-penetrating peptides, iRGD and tLyp1. Exosomes were purified via tangential flow filtration followed by ultracentrifugation. Results: When loaded with doxorubicin (Dox), the dual iRGD-tLyp1 exosomes strongly enhanced Dox uptake in both MCF-7 and MDA-MB-231 breast cancer cell lines, superior to single iRGD or tLyp1 exosomes. The dual iRGD-tLyp1 exosomal Dox was also the most potent, with IC50/GI50 values being 3.7-17.0-times lower than those of free Dox and other exosomal Dox. Conclusion: Selecting appropriate combinatorial homing peptides could be an approach for future precision nanomedicine.

Genetic landscape and personalized tracking of tumor mutations in Vietnamese women with breast cancer.

Breast cancer is the leading cause of cancer death in Vietnamese women, but its mutational landscape and actionable alterations for targeted therapies remain unknown. After treatment, a sensitive biomarker to complement conventional imaging to monitor patients is also lacking. In this prospective multi-center study, 134 early-stage breast cancer patients eligible for curative-intent surgery were recruited. Genomic DNA from tumor tissues and paired white blood cells were sequenced to profile all tumor-derived mutations in 95 cancer-associated genes. Our bioinformatic algorithm was then utilized to identify top mutations for individual patients. Serial plasma samples were collected before surgery and at scheduled visits after surgery. Personalized assay tracking the selected mutations were performed to detect circulating tumor DNA (ctDNA) in the plasma. We found that the mutational landscape of the Vietnamese was largely similar to other Asian cohorts, showing higher TP53 mutation frequency than in Caucasians. Alterations in PIK3CA and PI3K signaling were dominant, particularly in our triple-negative subgroup. Using top-ranked mutations, we detected ctDNA in pre-operative plasma in 24.6-43.5% of the hormone-receptor-positive groups and 76.9-80.8% of the hormone-receptor-negative groups. The detection rate was associated with breast cancer subtypes and clinicopathological features that increased the risk of relapse. Interim analysis after a 15-month follow-up revealed post-operative detection of ctDNA in all three patients that had recurrence, with a lead time of 7-13 months ahead of clinical diagnosis. Our personalized assay is streamlined and affordable with promising clinical utility in residual cancer surveillance. We also generated the first somatic variant dataset for Vietnamese breast cancer women that could lay the foundation for precision cancer medicine in Vietnam.

Autophagy in the intestinal epithelium reduces endotoxin-induced inflammatory responses by inhibiting NF-κB activation.

Autophagy is a lysosomal degradation pathway that is essential for survival, differentiation, development and homeostasis. There is growing evidence that impaired autophagy leads to the pathogenesis of diverse diseases. However, the role of autophagy in intestinal epithelium is not clearly understood, although previous studies have pointed out the possibility for the relationships of autophagy with bowel inflammation. In this study, we investigated the involvement of autophagy in intestinal epithelium with inflammatory responses. We generated the mice with a conditional deletion of Atg7, which is one of the autophagy regulated gene, in intestinal epithelium. In Atg7-deficient small intestinal epithelium, LPS-induced production of TNF-α and IL-1ß mRNA was enhanced in comparison to the control small intestinal tissues. In addition, the degree of LPS-induced activation of NF-κB was promoted in Atg7-deficient intestinal epithelium. These results demonstrate that autophagy can attenuate endotoxin-induced inflammatory responses in intestinal epithelium resulting in the maintenance of intestinal homeostasis.

Investigation of Mechanical, Chemical, and Antibacterial Properties of Electrospun Cellulose-Based Scaffolds Containing Orange Essential Oil and Silver Nanoparticles.

This study demonstrated a controllable release properties and synergistic antibacterial actions between orange essential oil (OEO) and silver nanoparticles (AgNPs) incorporated onto cellulose (CL) nanofibers. The preparation of AgNPs attached on CL nanofibers was conducted through multiple processes including the deacetylation process to transform cellulose acetate (CA) nanofibers to CL nanofibers, the in situ synthesis of AgNPs, and the coating of as-prepared silver composite CL nanofibers using OEO solutions with two different concentrations. The success of immobilization of AgNPs onto the surface of CL nanofibers and the incorporation of OEO into the polymer matrix was confirmed by SEM-EDS, TEM, XRD, and FT-IR characterizations. The tensile strength, elongation at break, and Young's modulus of the nanofibers after each step of treatment were recorded and compared to pristine CA nanofibers. The high antibacterial activities of AgNPs and OEO were assessed against Gram-positive B. subtilis and Gram-negative E. coli microorganisms. The combined effects of two antimicrobials, AgNPs and OEO, were distinctively recognized against E. coli.

Pathogenic Variant Profile of Hereditary Cancer Syndromes in a Vietnamese Cohort.

BACKGROUND: Hereditary cancer syndromes (HCS) are responsible for 5-10% of cancer cases. Genetic testing to identify pathogenic variants associated with cancer predisposition has not been routinely available in Vietnam. Consequently, the prevalence and genetic landscape of HCS remain unknown. METHODS: 1165 Vietnamese individuals enrolled in genetic testing at our laboratory in 2020. We performed analysis of germline mutations in 17 high- and moderate- penetrance genes associated with HCS by next generation sequencing. RESULTS: A total of 41 pathogenic variants in 11 genes were detected in 3.2% individuals. The carrier frequency was 4.2% in people with family or personal history of cancer and 2.6% in those without history. The percentage of mutation carriers for hereditary colorectal cancer syndromes was 1.3% and for hereditary breast and ovarian cancer syndrome was 1.6%. BRCA1 and BRCA2 mutations were the most prevalent with the positive rate of 1.3% in the general cohort and 5.1% in breast or ovarian cancer patients. Most of BRCA1 mutations located at the BRCA C-terminus domains and the top recurrent mutation was NM_007294.3:c.5251C>T (p.Arg1751Ter). One novel variant NM_000038.6(APC):c.6665C>A (p.Pro2222His) was found in a breast cancer patient with a strong family history of cancer. A case study of hereditary cancer syndrome was illustrated to highlight the importance of genetic testing. CONCLUSION: This is the first largest analysis of carrier frequency and mutation spectrum of HCS in Vietnam. The findings demonstrate the clinical significance of multigene panel testing to identify carriers and their at-risk relatives for better cancer surveillance and management strategies.

Genetic profiling of Vietnamese population from large-scale genomic analysis of non-invasive prenatal testing data.

The under-representation of several ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in many populations. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in many developing countries, including Vietnam. As one of the most rapidly adopted genetic tests, non-invasive prenatal testing (NIPT) data offers an alternative untapped resource for genetic studies. Here we performed a large-scale genomic analysis of 2683 pregnant Vietnamese women using their NIPT data and identified a comprehensive set of 8,054,515 single-nucleotide polymorphisms, among which 8.2% were new to the Vietnamese population. Our study also revealed 24,487 disease-associated genetic variants and their allele frequency distribution, especially 5 pathogenic variants for prevalent genetic disorders in Vietnam. We also observed major discrepancies in the allele frequency distribution of disease-associated genetic variants between the Vietnamese and other populations, thus highlighting a need for genome-wide association studies dedicated to the Vietnamese population. The resulted database of Vietnamese genetic variants, their allele frequency distribution, and their associated diseases presents a valuable resource for future genetic studies.

Pro-Inflammatory S100A9 Protein Aggregation Promoted by NCAM1 Peptide Constructs.

Amyloid cascade and neuroinflammation are hallmarks of neurodegenerative diseases, and pro-inflammatory S100A9 protein is central to both of them. Here, we have shown that NCAM1 peptide constructs carrying polycationic sequences derived from Aß peptide (KKLVFF) and PrP protein (KKRPKP) significantly promote the S100A9 amyloid self-assembly in a concentration-dependent manner by making transient interactions with individual S100A9 molecules, perturbing its native structure and acting as catalysts. Since the individual molecule misfolding is a rate-limiting step in S100A9 amyloid aggregation, the effects of the NCAM1 construct on the native S100A9 are so critical for its amyloid self-assembly. S100A9 rapid self-assembly into large aggregated clumps may prevent its amyloid tissue propagation, and by modulating S100A9 aggregation as a part of the amyloid cascade, the whole process may be effectively tuned.

Finke-Watzky Two-Step Nucleation-Autocatalysis Model of S100A9 Amyloid Formation: Protein Misfolding as "Nucleation" Event.

Quantitative kinetic analysis is critical for understanding amyloid mechanisms. Here we demonstrate the application of generic Finke-Watzky (F-W) two-step nucleation-autocatalytic growth model to the concentration-dependent amyloid kinetics of proinflammatory α-helical S100A9 protein at pH 7.4 and at 37 and 42 °C. The model is based on two pseudoelementary reaction steps applied without further analytical constraints, and its treatment of S100A9 amyloid self-assembly demonstrates that initial misfolding and ß-sheet formation, defined as "nucleation" step, spontaneously takes place within individual S100A9 molecules at higher rate than the subsequent fibrillar growth. The latter, described as an autocatalytic process, will proceed if misfolded amyloid-prone S100A9 is populated on a macroscopic time scale. Short lengths of S100A9 fibrils are consistent with the F-W model. The analysis of fibrillar length distribution by the Beker-Döring model demonstrates independently that such distribution is solely determined by slow fibril growth and there is no fragmentation or secondary pathways decreasing fibrillar length.

OMG U got flu? Analysis of shared health messages for bio-surveillance.

BACKGROUND: Micro-blogging services such as Twitter offer the potential to crowdsource epidemics in real-time. However, Twitter posts ('tweets') are often ambiguous and reactive to media trends. In order to ground user messages in epidemic response we focused on tracking reports of self-protective behaviour such as avoiding public gatherings or increased sanitation as the basis for further risk analysis. RESULTS: We created guidelines for tagging self protective behaviour based on Jones and Salathé (2009)'s behaviour response survey. Applying the guidelines to a corpus of 5283 Twitter messages related to influenza like illness showed a high level of inter-annotator agreement (kappa 0.86). We employed supervised learning using unigrams, bigrams and regular expressions as features with two supervised classifiers (SVM and Naive Bayes) to classify tweets into 4 self-reported protective behaviour categories plus a self-reported diagnosis. In addition to classification performance we report moderately strong Spearman's Rho correlation by comparing classifier output against WHO/NREVSS laboratory data for A(H1N1) in the USA during the 2009-2010 influenza season. CONCLUSIONS: The study adds to evidence supporting a high degree of correlation between pre-diagnostic social media signals and diagnostic influenza case data, pointing the way towards low cost sensor networks. We believe that the signals we have modelled may be applicable to a wide range of diseases.