Simultaneous Visualization of Multiple mRNAs and Matrix Metalloproteinases in Living Cells Using a Fluorescence Nanoprobe

Molecular imaging of tumour-associated pathological biomarkers with smart nanoprobe: From "Seeing" to "Measuring"

Although the extraordinary progress has been made in molecular biology, the prevention of cancer remains arduous. Most solid tumours exhibit both spatial and temporal heterogeneity, which is difficult to be mimicked in vitro. Additionally, the complex biochemical and immune features of tumour microenvironment significantly affect the tumour development. Molecular imaging aims at the exploitation of tumour-associated molecules as specific targets of customized molecular probe, thereby generating image contrast of tumour markers, and offering opportunities to non-invasively evaluate the pathological characteristics of tumours in vivo. Particularly, there are no "standard markers" as control in clinical imaging diagnosis of individuals, so the tumour pathological characteristics-responsive nanoprobe-based quantitative molecular imaging, which is able to visualize and determine the accurate content values of heterogeneous distribution of pathological molecules in solid tumours, can provide criteria for cancer diagnosis. In this context, a variety of "smart" quantitative molecular imaging nanoprobes have been designed, in order to provide feasible approaches to quantitatively visualize the tumour-associated pathological molecules in vivo. This review summarizes the recent achievements in the designs of these nanoprobes, and highlights the state-of-the-art technologies in quantitative imaging of tumour-associated pathological molecules.

A dual-functional magnetic microsphere for ICP-MS quantification and fluorescence imaging of matrix metalloproteinase 2 in cell secretion

Matrix metalloproteinase 2 (MMP2) plays an important role in tumor growth, invasion and metastasis. In this work, a dual-functional magnetic microsphere probe was designed for ICP-MS quantification and fluorescence imaging of MMP2 in cell secretion. In the designed probe, a NH₂-peptide (-FAM)-biotin was used as a bridge for the combination of carboxylated magnetic beads (MBs-COOH) and streptavidin functionalized gold nanoparticle (Au NP-SA). Initially, the fluorescence of FAM was quenched by Au NP. Since the NH₂-peptide (-FAM)-biotin had a MMP2-specifically recognized sequence, the peptide was specifically cleaved in the presence of MMP2, thus releasing Au NP for the ICP-MS quantification of MMP2 and turning on the fluorescence of FAM for the fluorescence imaging of MMP2. Under the optimal experimental conditions, a linear range of 0.05-50 ng mL^-1 and a limit of detection of 0.02 ng mL^-1 were obtained for MMP2. The relative standard deviation (n = 7, c = 0.1 ng mL^-1) of the proposed method was 5.4%. With good sensitivity and good accuracy, the proposed method realized the quantification and imaging of MMP2 in A549 cell secretion. The proposed method was applied to monitor the expression of MMP2 in the A549 cell secretion under the stimulation of Cd²⁺, providing a new detection strategy in the study of MMP2-related life process.

Nanoneedle-Based Materials for Intracellular Studies

Nanoneedles, defined as high aspect ratio structures with tip diameters of 5 to approximately 500 nm, are uniquely able to interface with the interior of living cells. Their nanoscale dimensions mean that they are able to penetrate the plasma membrane with minimal disruption of normal cellular functions, allowing researchers to probe the intracellular space and deliver or extract material from individual cells. In the last decade, a variety of strategies have been developed using nanoneedles, either singly or as arrays, to investigate the biology of cancer cells in vitro and in vivo. These include hollow nanoneedles for soluble probe delivery, nanocapillaries for single-cell biopsy, nano-AFM for direct physical measurements of cytosolic proteins, and a wide range of fluorescent and electrochemical nanosensors for analyte detection. Nanofabrication has improved to the point that nanobiosensors can detect individual vesicles inside the cytoplasm, delineate tumor margins based on intracellular enzyme activity, and measure changes in cell metabolism almost in real time. While most of these applications are currently in the proof-of-concept stage, nanoneedle technology is poised to offer cancer biologists a powerful new set of tools for probing cells with unprecedented spatial and temporal resolution.

Tricolor imaging of MMPs to investigate the promoting roles of inflammation on invasion and migration of tumor cells

The expression levels of matrix metalloproteinases (MMPs) are closely related to the degree of inflammation which facilitates tumor cells' invasion and migration. A tricolor fluorescence nanoprobe based on high-fidelity gold-selenium (Au-Se) nanoplatform was designed and constructed for simultaneously imaging matrix metalloproteinase-2 (MMP-2), matrix metalloproteinase-7 (MMP-7) and matrix metalloproteinase-9 (MMP-9) to thoroughly investigate the tumor cells' invasion and migration behaviors under inflammation environment. The nanoprobe was assembled by attaching Au NPs with three different peptide substrates respectively labeled with fluorescein isothiocyanate (FITC), 5-carboxytetramethylrhodamine (5-TAMRA) and cyanine 5 (Cy5) via the Au-Se bond. The nanoprobe can specifically respond to MMP-2/7/9, thereby triggering the fluorophores' fluorescence that quenched previously by fluorescence resonance energy transfer (FRET) to realize the MMP-2/7/9's visualization in biological systems. Moreover, as the inflammation stimulated by different concentrations lipopolysaccharide (LPS), the expression of MMP-2/7/9 in SMMC-7721 cells was observed to be significantly enhanced by confocal laser scanning microscope (CLSM) imaging, and inflammation was further proved to intensify SMMC-7721 cells' invasion and migration by transwell invasion and migration experiments. Therefore, the nanoprobe can be used to monitor biomarkers to provide a visual system for the degree of invasion and migration of tumor cells in an inflammatory environment, and also offer a new strategy for the study of the correlation between various active biomacromolecules and specific intracellular pathways in cells.

Integrating the Polydopamine Nanosphere/Aptamers Nanoplatform with a DNase-I-Assisted Recycling Amplification Strategy for Simultaneous Detection of MMP-9 and MMP-2 during Renal Interstitial Fibrosis

Matrix metalloproteinase-9 (MMP-9) and matrix metalloproteinase-2 (MMP-2) play important roles in the progression of renal interstitial fibrosis (RIF). There is an increasing demand to construct a novel method for the simultaneous detection of MMP-9 and MMP-2 to monitor the progression of RIF. Herein, a strategy based on the nanoplatform composed of the polydopamine nanosphere and fluorescence-labeled aptamers is developed to simultaneously detect MMP-9 and MMP-2 with DNase-I-assisted recycling signal amplification. In the light of tracing the recovered fluorescence intensity at 520 and 610 nm upon adding MMP-9 and MMP-2, the increased fluorescence intensity is linear to the different concentrations of MMP-9 and MMP-2 with the detection limits of 9.6 and 25.6 pg/mL for MMP-9 and MMP-2, respectively. More intriguingly, the results of unilateral ureteral obstruction mice show that the concentration of MMP-9 in urine is increased with the extension of ligation time while the concentration of MMP-2 is reversed, indicating that the ratio of MMP-9 to MMP-2 could be considered as the potential urinary biomarker to evaluate the progress of RIF and the therapeutic effect of Huangkui capsule on RIF. Therefore, this study provides a paradigmatic strategy for the simultaneous detection of the dual markers of RIF, which is promising for the auxiliary clinical diagnosis and assessment of the prognosis of chronic kidney disease.

Nucleic-Acid Structures as Intracellular Probes for Live Cells

The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.

A gold-selenium-bonded nanoprobe for real-time in situ imaging of the upstream and downstream relationship between uPA and MMP-9 in cancer cells

A novel Au-Se nanoprobe with remarkable anti-interference ability for glutathione was developed for real-time in situ monitoring of the upstream and downstream regulatory relationship between uPA and MMP-9 proteins in the pathway.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

A peptide-based four-color fluorescent polydopamine nanoprobe for multiplexed sensing and imaging of proteases in living cells

A novel peptide-based four-color fluorescent polydopamine nanoprobe has been developed for multiplexed sensing and imaging of tumor-related proteases in living cells. This nanoprobe responds rapidly and selectively, enabling accurate differentiation between cancer cells and normal cells.

Multiplex microRNA imaging in living cells using DNA-capped-Au assembled hydrogels

Non-invasively imaging multiplex microRNAs (miRNAs) in living cells is pivotal to understanding their physiological functions and pathological development due to the key regulatory roles of miRNAs in gene expression. However, developing smart delivery systems with large gene loading capacity, biocompatibility and responsiveness remains a significant challenge. Herein, we successfully incorporated DNA-capped Au nanoparticles (NPs) and their complementary fluorescent DNA sequences into a porous 3D hydrogel network (AuDH), in which hairpin-locked DNAzyme strands and active metal ions were loaded (AuDH/M n+/H) for simultaneously imaging multiplex miRNAs in living cells. After transfection into cells, the specific miRNAs trigger the strand-displacement reaction and sequentially activate the DNAzyme-assisted target recycling, leading to a strong increase in the corresponding fluorescence intensity for imaging. This enables simultaneous assessment of the abundance of multiplex cancer-related miRNAs, even if at a very low expression level, in different cells through the different fluorescence intensities due to the dual signal amplification, and the change in abundance of miRNAs induced by siRNA or miRNA mimics in living cells can also be efficiently monitored. The versatile and responsive DNA hydrogel system holds great potential for miRNA biomedical applications.

Simultaneous Fluorescence Visualization of Epithelial-Mesenchymal Transition and Apoptosis Processes in Tumor Cells for Evaluating the Impact of Epithelial-Mesenchymal Transition on Drug Efficacy

The epithelial-mesenchymal transition (EMT) process plays a pivotal role in acquiring invasive and metastatic properties and has been recognized as a crucial driver of epithelial-derived tumor malignancies. It is necessary to determine the role of EMT in promoting or suppressing carcinoma progression through investigating the relationship between EMT and apoptosis. We designed a multicolor fluorescent nanoprobe for simultaneously imaging the epithelial biomarker E-cadherin mRNA, the mesenchymal marker vimentin mRNA, and the apoptotic marker caspase-3. EMT and apoptosis progresses could be visually detected, which were used to study the effect of EMT on apoptosis and further assess the influence of EMT on drug efficacy in different cancer cells. We believe the designed nanoprobe can offer a new strategy for visualizing EMT and apoptosis in tumor cells and will be a promising tool to investigate the efficiency of drugs targeting EMT-related therapies in living cells.

A graphene-based fluorescent nanoprobe for simultaneous monitoring of miRNA and mRNA in living cells

Since microRNA-21 (miR-21) and protein programmed cell death 4 (PDCD4) are implicated in tumor progression, simultaneous monitoring of the dynamic variation of miR-21 and PDCD4 mRNA in living cells is of great interest for understanding their relationship in the pathology of the disease. Herein, a versatile nanoprobe based on graphene oxide (GO) and DNA was prepared which can simultaneously monitor and visualize miR-21 and PDCD4 mRNA in living cells. In vitro experiments demonstrate that the nanoprobe exhibits outstanding selectivity and high sensitivity towards miR-21 and PDCD4 mRNA. Moreover, by exploiting the DNA/GO sensing platform, simultaneous imaging of miR-21 and PDCD4 mRNA in MCF-7 human breast cancer cells has been realized. More significantly, an inverse correlation between miR-21 and PDCD4 mRNA was verified by fluorescence confocal imaging and RT-PCR results, indicating the distinguishing ability of the nanoprobe at various expression levels of RNAs. The current strategy provides a promising tool to implement the detection of miR-21 and PDCD4 mRNA in cancer cells and can be expected to be applied for other biomolecular sensing.

Fluorescent analysis of bioactive molecules in single cells based on microfluidic chips

Single-cell analysis of bioactive molecules is an essential strategy for a better understanding of cell biology, exploring cell heterogeneity, and improvement of the ability to detect early diseases. In single-cell analysis, highly efficient single-cell manipulation techniques and high-sensitive detection schemes are in urgent need. The rapid development of fluorescent analysis techniques combined with microfluidic chips have offered a widely applicable solution. Thus, in this review, we mainly focus on the application of fluorescence methods in components analysis on microchips at a single-cell level. By targeting different types of biological molecules in cells such as nucleic acids, proteins, and active small molecules, we specially introduce and comment on their corresponding fluorescent probes, fluorescence labelling and sensing strategies, and different fluorescence detection instruments used in single-cell analysis on a microfluidic chip. We hope that through this review, readers will have a better understanding of single-cell fluorescence analysis, especially for single-cell component fluorescence analysis based on microfluidic chips.

Au-Se-Bond-Based Nanoprobe for Imaging MMP-2 in Tumor Cells under a High-Thiol Environment

The gold nanosensors based on the Au-S bond have been widely applied to biochemical detections. However, signal distortion caused by biothiols has been seldom mentioned and urgently needs to be solved. Herein, we designed a novel but easily assembled gold nanoprobe by coupling a selenol-modified peptide with FITC onto the gold nanoparticle's surface via an Au-Se bond for fluorescence imaging of a tumor marker matrix, metalloproteinases 2 (MMP-2). Compared to the Au-S probes, the Au-Se probes display high thermal stability and a very good anti-interference ability toward glutathione under simulated physiological conditions. More importantly, the Au-Se nanoprobe exhibits a high-fidelity fluorescent signal toward MMP-2, effectively avoiding interference caused by high levels of thiol compounds in vivo. In addition, in vivo experiments further proved that no significant signal intensity change for the tumor cells treated by the Au-Se probes was observed before and after eliminating glutathione. Hence, we believe such Au-Se probes with in vivo glutathione interfering resistance offer new routes and perspectives in biology and medicine in the future.

Recent progress in live cell mRNA/microRNA imaging probes based on smart and versatile nanomaterials

We summarize the recent progress in live cell mRNA/miRNA imaging probes based on various versatile nanomaterials, describing their structures and their working principles of bio-imaging applications.

Nanocarriers with multi-locked DNA valves targeting intracellular tumor-related mRNAs for controlled drug release

The fabrication of well-behaved drug delivery systems that can transport drugs to specifically treat cancer cells rather than normal cells is still a tremendous challenge. A novel drug delivery system with two types of tumor-related mRNAs as "keys" to open the multiple valves of the nanocarrier to control drug release was developed. Hollow mesoporous silica nanoparticles were employed as the nanocarrier and dual DNAs targeting two intracellular mRNAs were employed as "multi-locks" to lock up the nanocarrier. When the nanocarrier enters the cancer cells, the overexpressed endogenous mRNA keys hybridize with the DNA multi-locks to open the valves and release the drug. Each single mRNA could not trigger the opening of the locks to release the cargo. Therefore, the nanocarrier can be applied for specific chemotherapy against cancer cells with minor side effects to normal cells. The current strategy could provide an important avenue towards advancing the practical applications of drug delivery systems used for cancer therapy.

Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes

RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.

Vision 20/20: Molecular-guided surgical oncology based upon tumor metabolism or immunologic phenotype: Technological pathways for point of care imaging and intervention

Surgical guidance with fluorescence has been demonstrated in individual clinical trials for decades, but the scientific and commercial conditions exist today for a dramatic increase in clinical value. In the past decade, increased use of indocyanine green based visualization of vascular flow, biliary function, and tissue perfusion has spawned a robust growth in commercial systems that have near-infrared emission imaging and video display capabilities. This recent history combined with major preclinical innovations in fluorescent-labeled molecular probes, has the potential for a shift in surgical practice toward resection guidance based upon molecular information in addition to conventional visual and palpable cues. Most surgical subspecialties already have treatment management decisions partially based upon the immunohistochemical phenotype of the cancer, as assessed from molecular pathology of the biopsy tissue. This phenotyping can inform the surgical resection process by spatial mapping of these features. Further integration of the diagnostic and therapeutic value of tumor metabolism sensing molecules or immune binding agents directly into the surgical process can help this field mature. Maximal value to the patient would come from identifying the spatial patterns of molecular expression in vivo that are well known to exist. However, as each molecular agent is advanced into trials, the performance of the imaging system can have a critical impact on the success. For example, use of pre-existing commercial imaging systems are not well suited to image receptor targeted fluorophores because of the lower concentrations expected, requiring orders of magnitude more sensitivity. Additionally the imaging system needs the appropriate dynamic range and image processing features to view molecular probes or therapeutics that may have nonspecific uptake or pharmacokinetic issues which lead to limitations in contrast. Imaging systems need to be chosen based upon objective performance criteria, and issues around calibration, validation, and interpretation need to be established before a clinical trial starts. Finally, as early phase trials become more established, the costs associated with failures can be crippling to the field, and so judicious use of phase 0 trials with microdose levels of agents is one viable paradigm to help the field advance, but this places high sensitivity requirements on the imaging systems used. Molecular-guided surgery has truly transformative potential, and several key challenges are outlined here with the goal of seeing efficient advancement with ideal choices. The focus of this vision 20/20 paper is on the technological aspects that are needed to be paired with these agents.

Simultaneous detection of multiple targets involved in the PI3K/AKT pathway for investigating cellular migration and invasion with a multicolor fluorescent nanoprobe

A fluorescent nanoprobe was developed for assessing cellular migration and invasion by imaging miRNA-221, PTEN mRNA and MMP-9 involved in the PI3K/AKT pathway regulating cellular mobility and invasiveness.

Dual-channel signals for intracellular mRNA detection via a PRET nanosensor

An intracellular nanosensor was designed and developed to accurately sense mRNA in living cells without false positive results.

In situ formation of pyronin dyes for fluorescence protease sensing

A cutting-edge strategy for fluorogenic sensing of proteases (leucine aminopeptidase for the proof of concept) and based on the “covalent-assembly” principle is reported. Non-fluorescent mixed bis-aryl ethers are readily converted into a fluorescent pyronin through a domino process triggered by the peptide bond cleavage event caused by the targeted enzyme.

Gold nanoparticles-based SPECT/CT imaging probe targeting for vulnerable atherosclerosis plaques

In order to realize accurate localization and precise evaluation of vulnerability of atherosclerotic plaques via dual-modal imaging, gold nanoparticles (GNPs) were firstly caped with a thin amino-PEGs cover and then conjugated with the targeting molecular Annexin V and radionuclide Tc-99m simultaneously to form SPECT/CT imaging probe targeting apoptotic macrophages. The as-synthesized (99m)Tc-GNPs-Annexin V was with uniform size (30.2 ± 2.9 nm) and high labeling rate (98.9 ± 0.5%) and stability. Targeting ability of Annexin V for apoptotic macrophages was kept and enhanced. For macrophages with 30% apoptosis, cellular uptakes of 3.52 ± 0.35% for (99m)Tc-GNPs-Annexin V, 2.41 ± 0.53% for (99m)Tc-GNPs and 1.68 ± 0.36% for (99m)Tc-Annexin V were achieved after 2 h incubation. ApoE knock out mice with high fat diet-induced atherosclerosis were scanned via (99m)Tc-GNPs-Annexin V SPECT/CT. With the introduction of targeting molecules, imaging probe was more efficient in accumulating in apoptotic macrophages. In practical evaluation, CT helps to restrict the lesions depiction more accurately, meanwhile, SPECT imaging intensity correlated with pathological changes tightly. In conclusion, Annexin V-modified hybrid gold nanoparticles were successfully synthesized, and this imaging system helped to better localize and diagnose those vulnerable AS plaques via specific targeting the apoptotic macrophages.

Oriented assembly of invisible probes: towards single mRNA imaging in living cells

Due to the complexity of biological systems and the ultralow concentration of analytes, improving the signal-to-noise ratio and lowering the limit of detection to allow highly sensitive detection is key to biomolecule analysis, especially intracellular analysis. Here, we present a method for highly sensitive imaging of mRNA in living cells by using novel invisible oriented probes to construct a turn-on signal generation mechanism from zero background. Two DNA probes (S1 and S2) are asymmetrically modified on two small gold nanoparticles (AuNPs) with a diameter of 20 nm. The hybridization of the two DNA probes with a single target mRNA leads to the formation of an AuNP dimer which shows a prominent plasmonic coupling effect. It generates a strong scattering signal from zero-background under a dark-field spectral analysis system. The unique design of the oriented assembly dimer has the ability to easily discriminate the target signal from the inherent cellular background noise in intracellular detection, thus making this approach a valuable technique for imaging single survivin mRNA and monitoring the distribution of survivin mRNA in tumor cells.

Nanosensors for Continuous and Noninvasive Monitoring of Mesenchymal Stem Cell Osteogenic Differentiation

Assessing mesenchymal stem cell (MSC) differentiation status is crucial to verify therapeutic efficacy and optimize treatment procedures. Currently, this involves destructive methods including antibody-based protein detection and polymerase chain reaction gene analysis, or laborious and technically challenging genetic reporters. Development of noninvasive methods for real-time differentiation status assessment can greatly benefit MSC-based therapies. This report introduces a nanoparticle-based sensing platform that encapsulates two molecular beacon (MB) probes within the same biodegradable polymeric nanoparticles. One MB targets housekeeping gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as an internal reference, while another detects alkaline phosphatase (ALP), a functional biomarker. Following internalization, MBs are gradually released as the nanoparticle degrades. GAPDH MBs provide a stable reference signal throughout the monitoring period (18 days) regardless of differentiation induction. Meanwhile, ALP mRNA undergoes well-defined dynamics with peak expression observed during early stages of osteogenic differentiation. By normalizing ALP-MB signal with GAPDH-MB, changes in ALP expression can be monitored, to noninvasively validate osteogenic differentiation. As proof-of-concept, a dual-colored nanosensor is applied to validate MSC osteogenesis on 2D culture and polycaprolactone films containing osteo-inductive tricalcium phospate.

Molecular beacon-loaded polymeric nanoparticles for non-invasive imaging of mRNA expression

Assessment of intracellular mRNA expression is invaluable for understanding cellular signaling activities, identifying disease stages, and monitoring the gene expression pattern of therapeutic cells during their culture, expansion and/or differentiation process. Previous methods suffer from the need to disrupt the biological samples to perform polymerase chain reaction analysis which can be laborious, fragmented and destructive. Herein, we develop a mRNA nanosensor based on the sustained release of mRNA-specific molecular beacons (probes that fluoresce upon hybridization) from the biodegradable poly(d,l-lactide-co-glycolide) nanoparticles. Post cellular internalization, the particles gradually degrade and release the encapsulated probes which are initially weakly fluorescent. When the released probes meet and hybridize with target mRNA, they restore pre-quenched fluorescence. By virtue of quantifying the fluorescence intensity, we can estimate the cellular mRNA expression. As a case study, β-actin mRNA expression in mesenchymal stem cells cultured on a 3D matrix was monitored and compared with those cultured on a 2D plate for one week. Critically, the observed expression profile shows a great correlation with the established quantitative polymerase chain reaction analysis.