Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cancer Cell Discrimination Using Host-Guest "Doubled" Arrays.

ABSTRACT: We report a nanosensor that uses cell lysates to rapidly profile the tumorigenicity of cancer cells. This sensing platform uses host-guest interactions between cucurbit[7]uril and the cationic headgroup of a gold nanoparticle to non-covalently modify the binding of three fluorescent proteins of a multi-channel sensor in situ. This approach doubles the number of output channels to six, providing single-well identification of cell lysates with 100% accuracy. Significantly, this classification could be extended beyond the training set, determining the invasiveness of novel cell lines. The unique fingerprint of these cell lysates required minimal sample quantity (200 ng, ?1000 cells), making the methodology compatible with microbiopsy technology.

SUBMITTER: Le NDB

PROVIDER: S-EPMC5848078 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Cancer Cell Discrimination Using Host-Guest "Doubled" Arrays.

Le Ngoc D B NDB Yesilbag Tonga Gulen G Mout Rubul R Kim Sung-Tae ST Wille Marcos E ME Rana Subinoy S Dunphy Karen A KA Jerry D Joseph DJ Yazdani Mahdieh M Ramanathan Rajesh R Rotello Caren M CM Rotello Vincent M VM

Journal of the American Chemical Society 20170601 23

We report a nanosensor that uses cell lysates to rapidly profile the tumorigenicity of cancer cells. This sensing platform uses host-guest interactions between cucurbit[7]uril and the cationic headgroup of a gold nanoparticle to non-covalently modify the binding of three fluorescent proteins of a multi-channel sensor in situ. This approach doubles the number of output channels to six, providing single-well identification of cell lysates with 100% accuracy. Significantly, this classification coul ...[more]

PMID: 28535040

Similar Datasets

Synthetic lectin arrays for the detection and discrimination of cancer associated glycans and cell lines.

Project description:Aberrant glycosylation is a hallmark of various disease states, including cancer, and effective detection and discrimination between healthy and diseased cells is an important challenge for the diagnosis and treatment of many diseases. Here, we describe the use of boronic acid functionalized synthetic lectins (SLs) in an array format for the differentiation of structurally similar cancer associated glycans and cancer cell lines; discrimination is based on subtle variations in glycosylation patterns. We further demonstrate the utility of our SLs in recognizing glycoproteins with up to 50-fold selectivity, even in 95% human serum. Given their robust and selective nature, these SLs were able to effectively distinguish (a) five structurally similar glycans with 94% accuracy; (b) seven normal, cancerous and metastatic colon cancer cell lines, including three isogenic cell lines, with 92% accuracy; and (c) these same seven cell lines using a guided statistical analysis to improve our analysis to 97% accuracy. In total, these data suggest that an SL-based array will be useful for the diagnosis of cancer.

| S-EPMC5645074 | biostudies-literature

Supramolecular Host-Guest Chemistry-Based Folate/Riboflavin Functionalization and Cancer Cell Labeling of Nanoparticles.

Project description:Nanoparticle-based cellular probes are commonly designed via covalent conjugation with affinity biomolecules. Those nanobioconjugates selectively interact with cell surface receptors and induce endocytosis followed by intracellular trafficking. However, this approach requires functional modification of biomolecules that may alter their biochemical activity. Here, we show that supramolecular host-guest chemistry can be utilized as an alternative approach in nanoparticle functionalization and selective cell labeling. We have used cyclodextrin-conjugated quantum dots (QDs) for supramolecular host-guest interaction-based functionalization with folate (QD-folate) and riboflavin (QD-riboflavin), where cyclodextrin acts as a host for the folate/riboflavin guest. We demonstrate that QD-folate and QD-riboflavin selectively label cells that have over-expressed folate/riboflavin receptors and induce the endocytosis pathway similar to covalently conjugated folate-/riboflavin-based nanoprobes. However, labeling is highly sensitive to the molar ratio of folate/riboflavin to cyclodextrin and incubation time. The presented functionalization/labeling approach is unique as it does not require covalent conjugation and may be extended for in vivo targeting application via simultaneous delivery of host and guest molecules.

| S-EPMC6045387 | biostudies-literature

Stepwise control of host-guest interaction using a coordination polymer gel.

Project description:Precise control of host-guest interaction as seen in biological processes is difficult to achieve with artificial systems. Herein we have exploited the thermodynamic benefits of a system in equilibrium to achieve controlled stepwise release and capture of cyclodextrin (guest) using a coordination polymer (Mg-CP) as the host and temperature as the stimulus. Since temperature is not a precision stimulus for artificial host-guest interaction, the present system is a distinct prototype that manifests temperature-controlled natural host-guest interaction. The described coordination polymeric host system, when incorporated into a hydrogel matrix, provides a microenvironment that facilitates the stepwise release of ?-CD in response to temperature variation within a quasi-solid state. The work demonstrated here may pave the way towards thermally controlled delivery and monitoring of otherwise spectroscopically silent molecules such as cyclodextrins.

| S-EPMC5959896 | biostudies-other

Controlling the alignment of 1D nanochannel arrays in oriented metal-organic framework films for host-guest materials design.

Project description:Controlling the direction of molecular-scale pores enables the accommodation of guest molecular-scale species with alignment in the desired direction, allowing for the development of high-performance mechanical, thermal, electronic, photonic and biomedical organic devices (host-guest approach). Regularly ordered 1D nanochannels of metal-organic frameworks (MOFs) have been demonstrated as superior hosts for aligning functional molecules and polymers. However, controlling the orientation of MOF films with 1D nanochannels at commercially relevant scales remains a significant challenge. Here, we report the fabrication of macroscopically oriented films of Cu-based pillar-layered MOFs having regularly ordered 1D nanochannels. The direction of 1D nanochannels is controllable by optimizing the crystal growth process; 1D nanochannels align either perpendicular or parallel to substrates, offering molecular-scale pore arrays for a macroscopic alignment of functional guest molecules in the desired direction. Due to the fundamental interest and widespread technological importance of controlling the alignment of functional molecules and polymers in a particular direction, orientation-controllable MOF films will open up the possibility of realising the potential of MOFs in advanced technologies.

| S-EPMC8163233 | biostudies-literature

Fluorescence detecting of paraquat using host-guest chemistry with cucurbit[8]uril.

Project description:Paraquat (PQ) is one of the most widely used herbicides in the world, which has a good occupational safety record when used properly. While, it presents high mortality index after intentional exposure. Accidental deaths and suicides from PQ ingestion are relatively common in developing countries with an estimated 300,000 deaths occurring in the Asia-Pacific region alone each year, and there are no specific antidotes. Good predictors of outcome and prognosis may be plasma and urine testing within the first 24 h of intoxication. A fluorescence enhancement of approximately 30 times was seen following addition of PQ to a solution of the supramolecular compound 2MB@CB[8], which comprised two methylene blue (MB) molecules within one cucurbit[8]uril (CB[8]) host molecule. The fluorescence intensity was linearly proportional to the amount of PQ added over the concentration range 2.4 × 10(-10) M-2.5 × 10(-4) M. The reaction also occurred in living cells and within live mice.

| S-EPMC3880963 | biostudies-literature

Defined Host-Guest Chemistry on Nanocarbon for Sustained Inhibition of Cancer.

Project description:Signal transducer and activator of transcription factor 3 (STAT-3) is known to be overexpressed in cancer stem cells. Poor solubility and variable drug absorption are linked to low bioavailability and decreased efficacy. Many of the drugs regulating STAT-3 expression lack aqueous solubility; hence hindering efficient bioavailability. A theranostics nanoplatform based on luminescent carbon particles decorated with cucurbit[6]uril is introduced for enhancing the solubility of niclosamide, a STAT-3 inhibitor. The host-guest chemistry between cucurbit[6]uril and niclosamide makes the delivery of the hydrophobic drug feasible while carbon nanoparticles enhance cellular internalization. Extensive physicochemical characterizations confirm successful synthesis. Subsequently, the host-guest chemistry of niclosamide and cucurbit[6]uril is studied experimentally and computationally. In vitro assessments in human breast cancer cells indicate approximately twofold enhancement in IC50 of drug. Fourier transform infrared and fluorescence imaging demonstrate efficient cellular internalization. Furthermore, the catalytic biodegradation of the nanoplatforms occur upon exposure to human myeloperoxidase in short time. In vivo studies on athymic mice with MCF-7 xenograft indicate the size of tumor in the treatment group is half of the controls after 40 d. Immunohistochemistry corroborates the downregulation of STAT-3 phosphorylation. Overall, the host-guest chemistry on nanocarbon acts as a novel arsenal for STAT-3 inhibition.

| S-EPMC5542878 | biostudies-literature

Energy-entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host-guest challenge.

Project description:Free energy drives a wide range of molecular processes such as solvation, binding, chemical reactions and conformational change. Given the central importance of binding, a wide range of methods exist to calculate it, whether based on scoring functions, machine-learning, classical or electronic structure methods, alchemy, or explicit evaluation of energy and entropy. Here we present a new energy-entropy (EE) method to calculate the host-guest binding free energy directly from molecular dynamics (MD) simulation. Entropy is evaluated using Multiscale Cell Correlation (MCC) which uses force and torque covariance and contacts at two different length scales. The method is tested on a series of seven host-guest complexes in the SAMPL8 (Statistical Assessment of the Modeling of Proteins and Ligands) "Drugs of Abuse" Blind Challenge. The EE-MCC binding free energies are found to agree with experiment with an average error of 0.9 kcal mol-1. MCC makes clear the origin of the entropy changes, showing that the large loss of positional, orientational, and to a lesser extent conformational entropy of each binding guest is compensated for by a gain in orientational entropy of water released to bulk, combined with smaller decreases in vibrational entropy of the host, guest and contacting water.

| S-EPMC8367938 | biostudies-literature

Dual-action host-guest chemistry suppresses PAO1 virulence in A549 cell line model

Project description:Our study showed that selected pillararene was able to decrease the level of cell death and demage caused to human A549 epithelial cells by Pseudomonas aeruginosa PAO1 infection. To further understand the protective effects of pillararene during bacterial infections, we analyzed total mRNA isolated from the A549 epithelial cells. Our study showed that pillararene alone had minimal effect on A549 epithelial cells. The addition of PAO1 to A549 cells greatly altered expression levels. The addition of pillararene to infected A549 epithelial cells displayed a concentration-dependent reduction in the inflammatory response.

2023-02-27 | GSE182847 | GEO

Dual-action host-guest chemistry suppresses virulence in Pseudomonas aeruginosa

Project description:This study describes the influence of selected synthetic macrocycle on the gene expression in Pseudomonas aeruginosa PAO1. In this work, we propose two distinct functionalities responsible for a dual mechanism of action. We identified a water-soluble pillararene whose inner cavity tightly binds to specific homoserine lactones (HSLs) thereby interfering with interbacterial signalling, leading to effective synchronized suppression of exotoxins and biofilms in P. aeruginosa. An additional concerted mechanism of action is suggested that involves the cationic functional side groups on the pillararene that disrupt both the bacterial outer membrane and biofilms, to increase the penetration and efficacy of intracellular antibiotics.

2023-02-27 | GSE182853 | GEO

Host-pathogen interaction profiling using self-assembling human protein arrays.

Project description:Host-pathogen protein interactions are fundamental to every microbial infection, yet their identification has remained challenging due to the lack of simple detection tools that avoid abundance biases while providing an open format for experimental modifications. Here, we applied the Nucleic Acid-Programmable Protein Array and a HaloTag-Halo ligand detection system to determine the interaction network of Legionella pneumophila effectors (SidM and LidA) with 10?000 unique human proteins. We identified known targets of these L. pneumophila proteins and potentially novel interaction candidates. In addition, we applied our Click chemistry-based NAPPA platform to identify the substrates for SidM, an effector with an adenylyl transferase domain that catalyzes AMPylation (adenylylation), the covalent addition of adenosine monophosphate (AMP). We confirmed a subset of the novel SidM and LidA targets in independent in vitro pull-down and in vivo cell-based assays, and provided further insight into how these effectors may discriminate between different host Rab GTPases. Our method circumvents the purification of thousands of human and pathogen proteins, and does not require antibodies against or prelabeling of query proteins. This system is amenable to high-throughput analysis of effectors from a wide variety of human pathogens that may bind to and/or post-translationally modify targets within the human proteome.

| S-EPMC4467460 | 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