Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced somatic mutation rates in survival outliers of glioblastoma

The study of survival outliers of glioblastoma can provide important clues on gliomagenesis as well as on the ways to alter clinical course of this almost uniformly lethal cancer type. However, there has been little consensus on genetic and epigenetic signatures of the long-term survival outliers of glioblastoma. Although the two classical molecular markers of glioblastoma including isocitrate dehydrogenase 1 or 2 (IDH1/2) mutation and O6-methylguanine DNA methyltransferase (MGMT) promoter methylation are associated with overall survival rate of glioblastoma patients, they are not specific to the survival outliers. In this study, we compared the two groups of survival outliers of glioblastoma with IDH wild-type, consisting of the glioblastoma patients who lived longer than 3 years (n = 17) and the patients who lived less than 1 year (n = 12) in terms of genome-wide DNA methylation profile. Statistical analyses were performed to identify differentially methylated sites between the two groups. Functional implication of DNA methylation patterns specific to long-term survivors of glioblastoma were investigated by comprehensive enrichment analyses with genomic and epigenomic features. We found that the genome of long-term survivors of glioblastoma is differentially methylated relative to short-term survivor patients depending on CpG density: hypermethylation near CpG islands (CGIs) and hypomethylation far from CGIs. Interestingly, these two patterns are associated with distinct oncogenic aspects in gliomagenesis. In the long-term survival glioblastoma-specific sites distant from CGI, somatic mutations of glioblastoma are enriched with higher DNA methylation, suggesting that the hypomethylation in long-term survival glioblastoma can contribute to reduce the rate of somatic mutation. On the other hand, the hypermethylation near CGIs associates with transcriptional downregulation of genes involved in cancer progression pathways. Using independent cohorts of IDH1/2- wild type glioblastoma, we also showed that these two patterns of DNA methylation can be used as molecular markers of long-term survival glioblastoma. Our results provide extended understanding of DNA methylation, especially of DNA hypomethylation, in cancer genome and reveal clinical importance of DNA methylation pattern as prognostic markers of glioblastoma.This research was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Ministry of Science & ICT (NRF-2018M3A9H3021707). in Korea, and the Seoul National University Hospital Research Fund (3020180010)

Gene-Chip Diagnostics for Personalized Global Medicine

Single nucleotide polymorphisms (SNP) in a gene sequence are markers for variety of human diseases. Their detection with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme based methods or fluorophore-labeled assays that are time consuming, need lab-scale settings, and are expensive. Electrical detection of DNA has been advancing rapidly, with to achieve high specificity, sensitivity and portability. However, existing electrical charge-based SNP detectors have insufficient specificity and accuracy limiting their effectiveness. Its actual implementation is still in infancy because of the low specificity, especially for analytically optimal and practically useful length of target DNA strands. Most of the research so far has focused on the enhancement of the sensitivity of DNA biosensors while the specificity problem has remained unresolved. The low specificity is primarily due to the non-specific binding during hybridization of probe and the target DNA. Here, we have addressed these limitations by designing a functional prototype of electrical biosensors for SNP detection. We demonstrate the use of DNA strand displacement-based probes on a graphene field effect transistor (FET) for high specificity single nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double helix DNA strands (e.g., 47 nucleotides) minimize false positive. We describe the first integrated dynamic DNA nanotechnology and 2-D material electronics, to overcome current limitations for the detection of DNA single nucleotide polymorphism (SNP). Existing SNP detection systems have poor sensitivity and specificity and lack portability and real-time wireless transmission of detected molecular signals. We have integrated two different kinds of dynamic DNA nano-devices as nucleic acid-sensing probes with electrical biosensors using graphene FET and analytical wireless communication platform. The signal was transmitted remotely using a microcontroller board and Bluetooth standard to personal electronics, including smart phones, tablets and computers. Our electrical sensor-based SNP detection technology without labeling and without apparent cross-hybridization artifacts would allow fast, sensitive and portable SNP detection with single-nucleotide resolution. Practical implementation of this enabling technology will provide cheaper, faster and portable point-of-care molecular diagnostic devices for personalized global health management. It will have wide applications in digital and implantable biosensors and high-throughput DNA genotyping with transformative implications for personalized medicine

Gene-Chip Diagnostics for Personalized Global Medicine

Single nucleotide polymorphisms (SNP) in a gene sequence are markers for variety of human diseases. Their detection with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme based methods or fluorophore-labeled assays that are time consuming, need lab-scale settings, and are expensive. Electrical detection of DNA has been advancing rapidly, with to achieve high specificity, sensitivity and portability. However, existing electrical charge-based SNP detectors have insufficient specificity and accuracy limiting their effectiveness. Its actual implementation is still in infancy because of the low specificity, especially for analytically optimal and practically useful length of target DNA strands. Most of the research so far has focused on the enhancement of the sensitivity of DNA biosensors while the specificity problem has remained unresolved. The low specificity is primarily due to the non-specific binding during hybridization of probe and the target DNA. Here, we have addressed these limitations by designing a functional prototype of electrical biosensors for SNP detection. We demonstrate the use of DNA strand displacement-based probes on a graphene field effect transistor (FET) for high specificity single nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double helix DNA strands (e.g., 47 nucleotides) minimize false positive. We describe the first integrated dynamic DNA nanotechnology and 2-D material electronics, to overcome current limitations for the detection of DNA single nucleotide polymorphism (SNP). Existing SNP detection systems have poor sensitivity and specificity and lack portability and real-time wireless transmission of detected molecular signals. We have integrated two different kinds of dynamic DNA nano-devices as nucleic acid-sensing probes with electrical biosensors using graphene FET and analytical wireless communication platform. The signal was transmitted remotely using a microcontroller board and Bluetooth standard to personal electronics, including smart phones, tablets and computers. Our electrical sensor-based SNP detection technology without labeling and without apparent cross-hybridization artifacts would allow fast, sensitive and portable SNP detection with single-nucleotide resolution. Practical implementation of this enabling technology will provide cheaper, faster and portable point-of-care molecular diagnostic devices for personalized global health management. It will have wide applications in digital and implantable biosensors and high-throughput DNA genotyping with transformative implications for personalized medicine

Plasmonic Biosensors Based on Deformed Graphene

Rapid, accurate, and label-free detection of biomolecules and chemical substances remains a challenge in healthcare. Optical biosensors have been considered as biomedical diagnostic tools required in numerous areas including the detection of viruses, food monitoring, diagnosing pollutants in the environment, global personalized medicine, and molecular diagnostics. In particular, the broadly emerging and promising technique of surface plasmon resonance has established to provide real-time and label-free detection when used in biosensing applications in a highly sensitive, specific, and cost-effective manner with small footprint platform. In this study we propose a novel plasmonic biosensor based on biaxially crumpled graphene structures, wherein plasmon resonances in graphene are utilized to detect variations in the refractive index of the sample medium. Shifts in the resonance wavelength of the plasmon modes for a given change in the RI of the surrounding analyte are calculated by investigating the optical response of crumpled graphene structures on different substrates using theoretical computations based on the finite element method combined with the semiclassical Drude model. The results reveal a high sensitivity of 4990 nm/RIU, corresponding to a large figure-of-merit of 20 for biaxially crumpled graphene structures on polystyrene substrates. We demonstrate that biaxially crumpled graphene exhibits superior sensing performance compared with a uniaxial structure. According to the results, crumpled graphene structures on a titanium oxide substrate can improve the sensor sensitivity by avoiding the damping effects of polydimethylsiloxane substrates. The enhanced sensitivity and broadband mechanical tunability of the biaxially crumpled graphene render it a promising platform for biosensing applications

Zinc molybdate/functionalized carbon nanofiber composites modified electrodes for high-performance amperometric detection of hazardous drug Sulfadiazine

Pharmaceuticals are generally designed to be nondegradable or slowly degradable to prevent chemical degradation as it is employed as therapeutics for human or animal. This results in a widespread risk when they enter, accumulate or persist in the environment. Pharmaceutical pollution is emerging as wide-reaching concern due to its ostensible consequences, by dissemination in the environment. This demands for inventing novel analytical routes to monitor and mitigate pharmaceutical pollutants. Therefore, this paper presents synthesis of Zinc molybdate nano particles embedded on functionalized carbon nanofibers to fabricate glassy carbon electrode towards sensitive detection of Sulfadiazine (SDZ). The synergistic effect produced in the composite had enabled it with improved charge transfer kinetics and benefited with more active surface area. The proposed ZnMoO4/f-CNF sensor shows significant static characteristics such as wide linear response ranges (0.125 to1575.2 μM), low detection limit (0.0006 μM) and selectivity, and increased stability. Also, its practicability was analyzed by SDZ detection in real samples

Energetically biased DNA motor containing a thermodynamically stable partial strand displacement state.

Current work in tuning DNA kinetics has focused on changing toehold lengths and DNA concentrations. However, kinetics can also be improved by enhancing the completion probability of the strand displacement process. Here, we execute this strategy by creating a toehold DNA motor device with the inclusion of a synthetic nucleotide, inosine, at selected sites. Furthermore, we found that the energetic bias can be tuned such that the device can stay in a stable partially displaced state. This work demonstrates the utility of energetic biases to change DNA strand displacement kinetics and introduces a complementary strategy to the existing designs

Energetically Biased DNA Motor Containing a Thermodynamically Stable Partial Strand Displacement State

Current work in tuning DNA kinetics has focused on changing toehold lengths and DNA concentrations. However, kinetics can also be improved by enhancing the completion probability of the strand displacement process. Here, we execute this strategy by creating a toehold DNA motor device with the inclusion of a synthetic nucleotide, inosine, at selected sites. Furthermore, we found that the energetic bias can be tuned such that the device can stay in a stable partially displaced state. This work demonstrates the utility of energetic biases to change DNA strand displacement kinetics and introduces a complementary strategy to the existing designs