Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microfluidics-enabled rational design of immunomagnetic nanomaterials and their shape effect on liquid biopsy.

ABSTRACT: Microfluidics brings unique opportunities for the synthesis of nanomaterials toward efficient liquid biopsy. Herein, we developed the microreactor-enabled flow synthesis of immunomagnetic nanomaterials with controllable shapes (sphere, cube, rod, and belt) by simply tuning the flow rates. The particle shape-dependent screening efficiency of circulating tumor cells was first investigated and compared with commercial ferrofluids, providing new insights into the rational design of a particulate system toward the screening and analysis of circulating tumor biomarkers.

SUBMITTER: Hao N

PROVIDER: S-EPMC6071334 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Microfluidics-enabled rational design of immunomagnetic nanomaterials and their shape effect on liquid biopsy.

Hao Nanjing N Nie Yuan Y Shen Ting T Zhang John X J JXJ

Lab on a chip 20180701 14

Microfluidics brings unique opportunities for the synthesis of nanomaterials toward efficient liquid biopsy. Herein, we developed the microreactor-enabled flow synthesis of immunomagnetic nanomaterials with controllable shapes (sphere, cube, rod, and belt) by simply tuning the flow rates. The particle shape-dependent screening efficiency of circulating tumor cells was first investigated and compared with commercial ferrofluids, providing new insights into the rational design of a particulate sys ...[more]

PMID: 29923569

Similar Datasets

Focused Ultrasound-enabled Brain Tumor Liquid Biopsy.

Project description:Although blood-based liquid biopsies have emerged as a promising non-invasive method to detect biomarkers in various cancers, limited progress has been made for brain tumors. One major obstacle is the blood-brain barrier (BBB), which hinders efficient passage of tumor biomarkers into the peripheral circulation. The objective of this study was to determine whether FUS in combination with microbubbles can enhance the release of biomarkers from the brain tumor to the blood circulation. Two glioblastoma tumor models (U87 and GL261), developed by intracranial injection of respective enhanced green fluorescent protein (eGFP)-transduced glioblastoma cells, were treated by FUS in the presence of systemically injected microbubbles. Effect of FUS on plasma eGFP mRNA levels was determined using quantitative polymerase chain reaction. eGFP mRNA were only detectable in the FUS-treated U87 mice and undetectable in the untreated U87 mice (maximum cycle number set to 40). This finding was replicated in GL261 mice across three different acoustic pressures. The circulating levels of eGFP mRNA were 1,500-4,800 fold higher in the FUS-treated GL261 mice than that of the untreated mice for the three acoustic pressures. This study demonstrated the feasibility of FUS-enabled brain tumor liquid biopsies in two different murine glioma models across different acoustic pressures.

| S-EPMC5919906 | biostudies-literature

Precision cell-free DNA extraction for liquid biopsy by integrated microfluidics.

Project description:Cell-free DNA (cfDNA) has been implicated as an important biomarker in cancer management. Thus, efficient techniques for cfDNA extraction are necessary for precision medicine. We developed a centrifugation-free cfDNA extraction microfluidic chip capable of extracting cfDNA from plasma samples through microfluidic circuits within 15 min under vacuum pressure using an immiscible solvent. The microfluidic chip had excellent performance that was comparable to the most widely used commercial product (QIAamp kit) in terms of extraction efficiency, purity, and quality of DNA samples. The microfluidic chip was validated for the continuous monitoring of HER-2 type breast cancer and was able to successfully detect a point mutation in phosphatidylinositol-4,5-bisphosphate 3-kinase (PIK3CA) during severe liver metastasis. The chip effectively eliminates the repetitive centrifugation processes and dramatically shortened the sample preparation time. The proposed platform could facilitate the development of a sample-to-answer system for use in liquid biopsy of cancers.

| S-EPMC7039987 | biostudies-literature

Rational Development of Liquid Biopsy Analysis in Renal Cell Carcinoma.

Project description:Renal cell carcinoma (RCC) is known for its variable clinical behavior and outcome, including heterogeneity in developing relapse or metastasis. Recent data highlighted the potential of somatic mutations as promising biomarkers for risk stratification in RCC. Likewise, the analysis of circulating tumor DNA (ctDNA) for such informative somatic mutations (liquid biopsy) is considered an important advance for precision oncology in RCC, allowing to monitor molecular disease evolution in real time. However, our knowledge about the utility of ctDNA analysis in RCC is limited, in part due to the lack of RCC-appropriate assays for ctDNA analysis. Here, by interrogating different blood compartments in xenograft models, we identified plasma cell-free (cf) DNA and extracellular vesicles (ev) DNA enriched for RCC-associated ctDNA. Additionally, we developed sensitive targeted sequencing and bioinformatics workflows capable of detecting somatic mutations in RCC-relevant genes with allele frequencies ≥ 0.5%. Applying this assay to patient-matched tumor and liquid biopsies, we captured tumor mutations in cf- and ev-DNA fractions isolated from the blood, highlighting the potentials of both fractions for ctDNA analysis. Overall, our study presents an RCC-appropriate sequencing assay and workflow for ctDNA analysis and provides a proof of principle as to the feasibility of detecting tumor-specific mutations in liquid biopsy in RCC patients.

| S-EPMC8616270 | biostudies-literature

Quantification of cyclic DNA polymerization with lanthanide coordination nanomaterials for liquid biopsy.

Project description:Quantification of circulating tumor DNA (ctDNA) is of great importance in liquid biopsy but difficult due to its low amount in bodily fluids. To meet this high demand, a novel method for ctDNA detection is established by quantifying cyclic DNA polymerization using lanthanide coordination polymers (Ln-CPs). Relying on the coordination between the pyrophosphate ion (PPi) and trivalent cerium ion (Ce3+), organic ligand-free PPi-Ce coordination polymer networks (PPi-Ce CPNs) with enhanced fluorescence are prepared for the first time. By surveying the optical properties of PPi-Ce CPNs, it is found that PPi regulates electric-dipole transition of Ce3+ to the lowest excited state, thus facilitating the emission of fluorescence. Therefore, fluorescence enhancement of PPi-Ce CPNs originates from the ligand field effect rather than the normal antenna effect. Moreover, a new strategy to quantify DNA polymerization is developed based on PPi-Ce CPNs. By introducing multifold cyclic DNA polymerization, a small amount of ctDNA triggers the exponential generation of PPi to form plenty of PPi-Ce CPNs. Accordingly, a biosensor is constructed for sensitive ctDNA detection by measuring the intense fluorescence of PPi-Ce CPNs. The biosensor is capable of sensing ctDNA at the sub-femtomolar level, which is far better than the analytical performances of commercial dyes. Besides, the analytical method is able to detect single nucleotide polymorphism and determine ctDNA in real samples. Considering that DNA polymerization is widely used in bio-recognition, bio-assembly and biomineralization, the work provides a versatile quantitative strategy of making relevant processes precise and controllable.

| S-EPMC8152624 | biostudies-literature

Rational Design of Sustainable Liquid Microcapsules for Spontaneous Fragrance Encapsulation.

Project description:The high volatility, water-immiscibility, and light/oxygen-sensitivity of most aroma compounds represent a challenge to their incorporation in liquid consumer products. Current encapsulation methods entail the use of petroleum-based materials, initiators, and crosslinkers as well as mixing, heating, and purification steps. Hence, more efficient and eco-friendly approaches to encapsulation must be sought. Herein, we propose a simple method by making use of a pre-formed amphiphilic polymer and employing the Hansen Solubility Parameters approach to determine which fragrances could be encapsulated by spontaneous coacervation in water. The coacervates do not precipitate as solids but they remain suspended as colloidally stable liquid microcapsules, as demonstrated by fluorescence correlation spectroscopy. The effective encapsulation of fragrance is proven through confocal Raman spectroscopy, while the structure of the capsules is investigated by means of cryo FIB/SEM, confocal laser scanning microscopy, and small-angle X-ray scattering.

| S-EPMC8596835 | biostudies-literature

Microfluidics-Enabled Multimaterial Maskless Stereolithographic Bioprinting.

Project description:A stereolithography-based bioprinting platform for multimaterial fabrication of heterogeneous hydrogel constructs is presented. Dynamic patterning by a digital micromirror device, synchronized by a moving stage and a microfluidic device containing four on/off pneumatic valves, is used to create 3D constructs. The novel microfluidic device is capable of fast switching between different (cell-loaded) hydrogel bioinks, to achieve layer-by-layer multimaterial bioprinting. Compared to conventional stereolithography-based bioprinters, the system provides the unique advantage of multimaterial fabrication capability at high spatial resolution. To demonstrate the multimaterial capacity of this system, a variety of hydrogel constructs are generated, including those based on poly(ethylene glycol) diacrylate (PEGDA) and gelatin methacryloyl (GelMA). The biocompatibility of this system is validated by introducing cell-laden GelMA into the microfluidic device and fabricating cellularized constructs. A pattern of a PEGDA frame and three different concentrations of GelMA, loaded with vascular endothelial growth factor, are further assessed for its neovascularization potential in a rat model. The proposed system provides a robust platform for bioprinting of high-fidelity multimaterial microstructures on demand for applications in tissue engineering, regenerative medicine, and biosensing, which are otherwise not readily achievable at high speed with conventional stereolithographic biofabrication platforms.

| S-EPMC6133710 | biostudies-literature

Profiling of mismatch discrimination in RNAi enabled rational design of allele-specific siRNAs.

Project description:Silencing specificity is a critical issue in the therapeutic applications of siRNA, particularly in the treatment of single nucleotide polymorphism (SNP) diseases where discrimination against single nucleotide variation is demanded. However, no generally applicable guidelines are available for the design of such allele-specific siRNAs. In this paper, the issue was approached by using a reporter-based assay. With a panel of 20 siRNAs and 240 variously mismatched target reporters, we first demonstrated that the mismatches were discriminated in a position-dependent order, which was however independent of their sequence contexts using position 4th, 12th and 17th as examples. A general model was further built for mismatch discrimination at all positions using 230 additional reporter constructs specifically designed to contain mismatches distributed evenly along the target regions of different siRNAs. This model was successfully employed to design allele-specific siRNAs targeting disease-causing mutations of PIK3CA gene at two SNP sites. Furthermore, conformational distortion of siRNA-target duplex was observed to correlate with the compromise of gene silencing. In summary, these findings could dramatically simplify the design of allele-specific siRNAs and might also provide guide to increase the specificity of therapeutic siRNAs.

| S-EPMC2794185 | biostudies-literature

Machine learning enabled rational design for dynamic thermal emitters with phase change materials.

Project description:Dynamic thermal emitters have attracted considerable attention due to their potential in widespread applications such as radiative cooling, thermal switching, and adaptive camouflage. However, the state-of-art performances of dynamic emitters are still far below expectations. Here, customized to the special and stringent requirement of dynamic emitters, a neural network model is developed to effectively bridge the structural and spectral spaces and further realizes the inverse design with coupling to genetic algorithms, which considers the broadband spectral responses in different phase-states and utilizes comprehensive measures to ensure the modeling accuracy and computational speed. Besides achieving an outstanding emittance tunability of 0.8, the physics and empirical rules have also been mined qualitatively through decision trees and gradient analyses. The study demonstrates the feasibility of using machine learning to obtain the near-perfect performance of dynamic emitters, as well as guiding the design of other thermal and photonic nanostructures with multifunctions.

| S-EPMC10220477 | biostudies-literature

Rational Design of Rod-Like Liquid Crystals Exhibiting Two Nematic Phases.

Project description:Recently, a polar, rod-like liquid-crystalline material was reported to exhibit two distinct nematic mesophases (termed N and NX ) separated by a weakly first-order transition. Herein, we present our initial studies into the structure-property relationships that underpin the occurrence of the lower-temperature nematic phase, and report several new materials that exhibit this same transformation. We have prepared material with significantly enhanced temperature ranges, allowing us to perform a detailed study of both the upper- and lower-temperature nematic phases by using small-angle X-ray scattering. We observed a continuous change in d spacing rather than a sharp change at the phase transition, a result consistent with a transition between two nematic phases, structures of which are presumably degenerate.

| S-EPMC5656819 | biostudies-literature

Ultra-sensitive CTC-based liquid biopsy for pancreatic cancer enabled by large blood volume analysis.

Project description:The limited sensitivity of circulating tumor cell (CTC) detection in pancreatic adenocarcinoma (PDAC) stems from their extremely low concentration in the whole circulating blood, necessitating enhanced detection methodologies. This study sought to amplify assay-sensitivity by employing diagnostic leukapheresis (DLA) to screen large blood volumes. Sixty patients were subjected to DLA, with a median processed blood volume of ~ 2.8 L and approximately 5% of the resulting DLA-product analyzed using CellSearch (CS). Notably, DLA significantly increased CS-CTC detection to 44% in M0-patients and 74% in M1-patients, yielding a 60-fold increase in CS-CTC enumeration. DLA also provided sufficient CS-CTCs for genomic profiling, thereby delivering additional genomic information compared to tissue biopsy samples. DLA CS-CTCs exhibited a pronounced negative prognostic impact on overall survival (OS), evidenced by a reduction in OS from 28.6 to 8.5 months (univariate: p = 0.002; multivariable: p = 0.043). Additionally, a marked enhancement in sensitivity was achieved (by around 3-4-times) compared to peripheral blood (PB) samples, with positive predictive values for OS being preserved at around 90%. Prognostic relevance of CS-CTCs in PDAC was further validated in PB-samples from 228 PDAC patients, consolidating the established association between CTC-presence and reduced OS (8.5 vs. 19.0 months, p < 0.001). In conclusion, DLA-derived CS-CTCs may serve as a viable tool for identifying high-risk PDAC-patients and aiding the optimization of multimodal treatment strategies. Moreover, DLA enables comprehensive diagnostic profiling by providing ample CTC material, reinforcing its utility as a reliable liquid-biopsy approach. This high-volume liquid-biopsy strategy presents a potential pathway for enhancing clinical management in this malignancy.

| S-EPMC10641981 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data