Idiopathic pulmonary fibrosis (IPF): Diagnostic routes using novel biomarkers.

Idiopathic pulmonary fibrosis (IPF) diagnosis is still the diagnosis of exclusion. Differentiating from other forms of interstitial lung diseases (ILDs) is essential, given the various therapeutic approaches. The IPF course is now unpredictable for individual patients, although some genetic factors and several biomarkers have already been associated with various IPF prognoses. Since its early stages, IPF may be asymptomatic, leading to a delayed diagnosis. The present review critically examines the recent literature on molecular biomarkers potentially useful in IPF diagnostics. The examined biomarkers are grouped into breath and sputum biomarkers, serologically assessed extracellular matrix neoepitope markers, and oxidative stress biomarkers in lung tissue. Fibroblasts and complete blood count have also gained recent interest in that respect. Although several biomarker candidates have been profiled, there has yet to be a single biomarker that proved specific to the IPF disease. Nevertheless, various IPF biomarkers have been used in preclinical and clinical trials to verify their predictive and monitoring potential.

Recent advances using MXenes in biomedical applications.

An MXene is a novel two-dimensional transition metal carbide or nitride, with a typical formula of Mn+1XnTx (M = transition metals, X = carbon or nitrogen, and T = functional groups). MXenes have found wide application in biomedicine and biosensing, owing to their high biocompatibility, abundant reactive surface groups, good conductivity, and photothermal properties. Applications include photo- and electrochemical sensors, energy storage, and electronics. This review will highlight recent applications of MXene and MXene-derived materials in drug delivery, tissue engineering, antimicrobial activity, and biosensors (optical and electrochemical). We further elaborate on recent developments in utilizing MXenes for photothermal cancer therapy, and we explore multimodal treatments, including the integration of chemotherapeutic agents or magnetic nanoparticles for enhanced therapeutic efficacy. The high surface area and reactivity of MXenes provide an interface to respond to the changes in the environment, allowing MXene-based drug carriers to respond to changes in pH, reactive oxygen species (ROS), and electrical signals for controlled release applications. Furthermore, the conductivity of MXene enables it to provide electrical stimulation for cultured cells and endows it with photocatalytic capabilities that can be used in antibiotic applications. Wearable and in situ sensors incorporating MXenes are also included. Major challenges and future development directions of MXenes in biomedical applications are also discussed. The remarkable properties of MXenes will undoubtedly lead to their increasing use in the applications discussed here, as well as many others.

Upconversion nanoparticle-based fluorescence resonance energy transfer sensing of programmed death ligand 1 using sandwich epitope-imprinted polymers.

Programmed death ligand 1 (PD-L1) has been shown to suppress the anti-tumor immune response of some lung cancer patients, and thus PD-L1 expression may be a valuable predictor of the efficacy of anti-PD-1/PD-L1 monoclonal therapy in such patients. In this work, a sandwich approach to fluorescence resonance energy transfer (FRET) was used with green-emitting Yb3+/Ho3+-doped upconversion nanoparticles (UCNPs) and a rhodamine-conjugated conductive polymer as donor and acceptor, respectively. Yb3+/Ho3+-doped UCNPs were synthesized and then coated with poly(ethylene-co-vinyl alcohol), pEVAL, imprinted with PD-L1 peptide. Epitope-imprinted composite nanoparticles were characterized by dynamic light scattering, superconducting quantum interference magnetometry, and atomic force microscopy. Poly(triphenylamine rhodamine-3-acetic acid-co-3,4-ethoxylenedioxythiophene)s copolymers (p(TPAR-co-EDOT)) were imprinted with various epitopes of PD-L1 by in situ electrochemical polymerization. The epitope-imprinted polymer-coated electrodes were then characterized by scanning electron microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. Finally, the sandwich sensing of various PD-L1 concentrations with peptide-imprinted p(TPAR-co-EDOT)-coated substrate and UCNP-containing magnetic peptide-imprinted pEVAL nanoparticles by FRET was conducted to measure the concentration of PD-L1 in A549 lung cancer cell lysate.

Nanoparticle-mediated CRISPR/dCas9a activation of multiple transcription factors to engineer insulin-producing cells.

Insulin may help to control blood glucose levels in diabetes; however, the long-term release of insulin is important for therapy. In this work, four guide RNAs (gRNA) for factors that promote specification and maturation of insulin-producing cells were synthesized: pancreatic and duodenal homeobox 1 (PDX1), protoendocrine factor (neurogenin 3, NGN3), NK6 homeobox 1 (NKX6.1), and musculoaponeurotic fibrosarcoma oncogene family A (MAFA). These gRNAs were used to form ribonucleoproteins (RNPs) with tracRNA and dCas9-VPR, and were then immobilized on magnetic peptide-imprinted chitosan nanoparticles, which enhanced transfection. The production and release of insulin from transfected cells were then measured using ELISA and staining with anti-insulin antibodies. The expression of the genes was evaluated using qRT-PCR; this was also used to investigate the cascade of additional transcriptional regulators. The magnitude and duration of insulin production were evaluated for single and repeated transfections (using different transfection schedules) to identify the most promising protocol.

Biocompatibility of a Ti-Rich Medium-Entropy Alloy with Glioblastoma Astrocytoma Cells.

Titanium and titanium alloys are widely used in medical devices and implants; thus, the biocompatibility of these metals is of great importance. In this study, glioblastoma astrocytoma cellular responses to Ti65-Zr18-Nb16-Mo1 (Ti65M, metastable medium-entropy alloy), Ti-13Nb-7Sn-4Mo (TNSM, titanium alloy), and commercially pure titanium (CP-Ti) were studied. Several physical parameters (crystal phase structure, surface roughness and hardness) of the titanium alloys were measured, and the correlation with the cellular viability was investigated. Finally, the relative protein expression in cellular proliferation pathways was measured and compared with mRNA expression assessed with quantitative real-time reverse transcription polymerase chain reaction assay (qRT-PCR).

Peptide Selection of MMP-1 for Electrochemical Sensing with Epitope-Imprinted Poly(TPARA-co-EDOT)s.

Instead of molecularly imprinting a whole protein molecule, imprinting protein epitopes is gaining popularity due to cost and solubility issues. Belonging to the matrix metalloproteinase protein family, MMP-1 is an interstitial collagenase that degrades collagen and may be involved in cell migration, cell proliferation, the pro-inflammatory effect, and cancer progression. Hence, it can serve as a disease protein biomarker and thus be useful in early diagnosis. Herein, epitopes of MMP-1 were identified by screening its crystal structure. To identify possible epitopes for imprinting, MMP-1 was cleaved in silico with trypsin, pepsin at pH = 1.3, and pepsin at pH > 2.0 using Peptide Cutter, generating peptide fragments containing 8 to 12 amino acids. Five criteria were applied to select the peptides most suitable as potential epitopes for MMP-1. The triphenylamine rhodanine-3-acetic acid (TPARA) functional monomer was synthesized to form a stable pre-polymerization complex with a selected template epitope. The complexed functional monomer was then copolymerized with 3,4-ethoxylenedioxythiophene (EDOT) using potentiodynamic electropolymerization onto indium−tin−oxide (ITO) electrodes. The composition of the molecularly imprinted poly(TPARA-co-EDOT) (MIP) was optimized by maximizing the film's electrical conductivity. Cyclic voltammetry was used to determine MMP-1 concentration in the presence of the Fe(CN)63−/Fe(CN)64− redox probe actuating the "gate effect." A calibration curve was constructed and used to determine the usable concentration range and the limit of detection as ca. 0.001 to 10.0 pg/mL and 0.2 fg/mL MMP-1, respectively. Finally, the MMP-1 concentration in the A549 human lung (carcinoma) culture medium was measured, and this determination accuracy was confirmed using an ELISA assay.

NIR-Triggered Generation of Reactive Oxygen Species and Photodynamic Therapy Based on Mesoporous Silica-Coated LiYF4 Upconverting Nanoparticles.

To date, the increase in reactive oxygen species (ROS) production for effectual photodynamic therapy (PDT) treatment still remains challenging. In this study, a facile and effective approach is utilized to coat mesoporous silica (mSiO2) shell on the ligand-free upconversion nanoparticles (UCNPs) based on the LiYF4 host material. Two kinds of mesoporous silica-coated UCNPs (UCNP@mSiO2) that display green emission (doped with Ho3+) and red emission (doped with Er3+), respectively, were successfully synthesized and well characterized. Three photosensitizers (PSs), merocyanine 540 (MC 540), rose bengal (RB), and chlorin e6 (Ce6), with the function of absorption of green or red emission, were selected and loaded into the mSiO2 shell of both UCNP@mSiO2 nanomaterials. A comprehensive study for the three UCNP@mSiO2/PS donor/acceptor pairs was performed to investigate the efficacy of fluorescence resonance energy transfer (FRET), ROS generation, and in vitro PDT using a MCF-7 cell line. ROS generation detection showed that as compared to the oleate-capped and ligand-free UCNP/PS pairs, the UCNP@mSiO2/PS nanocarrier system demonstrated more pronounced ROS generation due to the UCNP@mSiO2 nanoparticles in close vicinity to PS molecules and a higher loading capacity of the photosensitizer. As a result, the three LiYF4 UCNP@mSiO2/PS nanoplatforms displayed more prominent therapeutic efficacies in PDT by using in vitro cytotoxicity tests.

Doping of MXenes enhances the electrochemical response of peptide-imprinted conductive polymers for the recognition of C-Reactive protein.

The level of C-reactive protein (CRP) in serum is frequently used to evaluate risk of coronary heart disease, and its concentration is related to cardiovascular disease, fibrosis and inflammation, cancer, and viral infections. In this work, three novel peptides, never previously used as imprinted templates, were selected, synthesized, and employed for epitope imprinting. Various imprinting concentrations of the template and various ratios of aniline (AN) to m-aminobenzenesulfonic acid (MSAN) were used in electropolymerization to form molecularly imprinted polymers (MIPs). The imprinting template and functional monomer concentrations were optimized to maximize the electrochemical response to target peptides. The surface morphologies of peptide- and non-imprinting poly(AN-co-MSAN) were observed using a scanning electron microscope (SEM) and an atomic force microscope (AFM). Moreover, the effect of doping of MIPs with a very small percentage of an MXene (e.g. Ti2C at 0.1 wt% in the preparation solution) on the electrochemical response was also studied. Ti2C doping dramatically increased sensing range from 0.1 to 100 fg/mL to 10000 fg/mL, and electrochemical responses were amplified by a factor of approximately 1.3 within the sensing range. Finally, commercially available serum was diluted and then measured using the MXene-doped PIP-coated electrodes to estimate the accuracy compared with ELISA results.

Sensing of C-Reactive Protein Using an Extended-Gate Field-Effect Transistor with a Tungsten Disulfide-Doped Peptide-Imprinted Conductive Polymer Coating.

C-reactive protein (CRP) is a non-specific biomarker of inflammation and may be associated with cardiovascular disease. In recent studies, systemic inflammatory responses have also been observed in cases of coronavirus disease 2019 (COVID-19). Molecularly imprinted polymers (MIPs) have been developed to replace natural antibodies with polymeric materials that have low cost and high stability and could thus be suitable for use in a home-care system. In this work, a MIP-based electrochemical sensing system for measuring CRP was developed. Such a system can be integrated with microfluidics and electronics for lab-on-a-chip technology. MIP composition was optimized using various imprinting template (CRP peptide) concentrations. Tungsten disulfide (WS2) was doped into the MIPs. Doping not only enhances the electrochemical response accompanying the recognition of the template molecules but also raises the top of the sensing range from 1.0 pg/mL to 1.0 ng/mL of the imprinted peptide. The calibration curve of the WS2-doped peptide-imprinted polymer-coated electrodes in the extended-gate field-effect transistor platform was obtained and used for the measurement of CRP concentration in real human serum.

Embedded Upconversion Nanoparticles in Magnetic Molecularly Imprinted Polymers for Photodynamic Therapy of Hepatocellular Carcinoma.

In this work, high-temperature pyrolysis was used to prepare both the core and shell of lantha-nide-doped UCNPs with lithium yttrium tetrafluoride (LiYF4) to enhance the green luminescence. Merocyanine 540 (MC540)-grafted magnetic nanoparticles were incorporated in the PD-L1 pep-tide-imprinted poly(ethylene-co-vinyl alcohol) particles, which were formed by precipitation in a non-solvent. UCNPs in the non-solvent bath were thus entrapped in the imprinted particles to generate composite nanoparticles for the targeting and photodynamic therapy of PD-L1 in tumor cells. Finally, the in vitro cytotoxicity of the nanoparticles in HepG2 human liver cancer cells was evaluated with the continuous administration of MC540/MNPs@MIPs/UCNPs under irradiation by an NIR laser. To understand the delivery of the UCNP-embedded molecularly imprinted pol-ymers, the intrinsic and extrinsic pathways were also investigated.

Synthesis of Multifunctional Nanoparticles for the Combination of Photodynamic Therapy and Immunotherapy.

Programmed death-ligand 1 protein (PD-L1) has been posited to have a major role in suppressing the immune system during pregnancy, tissue allografts, autoimmune disease and other diseases, such as hepatitis. Photodynamic therapy uses light and a photosensitizer to generate singlet oxygen, which causes cell death (phototoxicity). In this work, photosensitizers (such as merocyanine) were immobilized on the surface of magnetic nanoparticles. One peptide sequence from PD-L1 was used as the template and imprinted onto poly(ethylene-co-vinyl alcohol) to generate magnetic composite nanoparticles for the targeting of PD-L1 on tumor cells. These nanoparticles were characterized using dynamic light scattering, high-performance liquid chromatography, Brunauer-Emmett-Teller analysis and superconducting quantum interference magnetometry. Natural killer-92 cells were added to these composite nanoparticles, which were then incubated with human hepatoma (HepG2) cells and illuminated with visible light for various periods. The viability and apoptosis pathway of HepG2 were examined using a cell counting kit-8 and quantitative real-time polymerase chain reaction. Finally, treatment with composite nanoparticles and irradiation of light was performed using an animal xenograft model.

Cellular reprogramming with multigene activation by the delivery of CRISPR/dCas9 ribonucleoproteins via magnetic peptide-imprinted chitosan nanoparticles.

Induced pluripotent stem cells are usually derived by reprogramming transcription factors (OSKM), such as octamer-binding transcription factor 4 (OCT4), (sex determining region Y)-box 2 (SOX2), Krüppel-like factor 4 (KLF4), and cellular proto-oncogene (c-Myc). However, the genomic integration of transcription factors risks the insertion of mutations into the genome of the target cells. Recently, the clustered regularly interspaced short palindromic repeat-associated protein 9 (CRISPR/Cas9) system has been used to edit genomes. In this work, dCas9-VPR (dCas9 with a gene activator, VP64-p65-Rta (VPR), fused to its c-terminus) and guide RNA (gRNA) combined to form ribonucleoproteins, which were immobilized on magnetic peptide-imprinted chitosan nanoparticles. These were then used to activate OSKM genes in human embryonic kidney (HEK) 293T cells. Four pairs of gRNAs were used for the binding site recognition to activate the OSKM genes. Transfected HEK293T cells were then prescreened for the high expression of OSKM proteins by immunohistochemistry images. The optimal gRNAs for OSKM expression were identified using quantitative real-time polymerase chain reaction and the staining of OSKM proteins. Finally, we found that the activated expression of one of the OSKM genes is up to three-fold higher than that of the other genes, enabling precise control of the cell differentiation.

Epitope recognition of magnetic peptide-imprinted chitosan composite nanoparticles for the extraction of CRISPR/dCas9a proteins from transfected cells.

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas9) technology is a powerful method for genetic modification (and regulation) that is of great current interest. The development of new, economical methods of detecting and extracting Cas9 (and/or dCas9) from transfected cells is thus an important advance. In this work, we employed molecular imprinting, using two peptides from the Cas9 protein, to make magnetic peptide-imprinted chitosan nanoparticles. dCas9 was encoded in a plasmid which was then transfected into human embryonic kidney (HEK293T) cells. The expression of dCas9 protein was measured by using total protein kits. Finally, the imprinted nanoparticles were used to extract dCas9 from transfected cell homogenates.

Doping of transition metal dichalcogenides in molecularly imprinted conductive polymers for the ultrasensitive determination of 17ß-estradiol in eel serum.

Molecularly imprinted polymers (MIPs) have been developed to replace antibodies for the recognition of target molecules (such as antigens), and have been integrated into electrochemical sensing approaches by polymerization onto an electrode. Electrochemical sensing is inexpensive and flexible, and has demonstrated utility in point-of-care devices. In this work, several 2D (conductive) materials were employed to improve the performance of MIP sensors. Screen-printed electrodes were coated by the electropolymerization of aniline and metanilic acid, commingled with target molecules and various 2D materials. Tungsten disulfide (WS2) with an average particle size of 2 µm was found to increase the sensitivity of detection of molecularly imprinted conductive polymer-coated electrodes to 17ß-estradiol. As estradiol concentrations are important to eel aquaculture, we screened eel serum samples to determine their 17ß-estradiol concentrations, which were found to be in the range 28.2 ± 3.6 to 73.0 ± 11.6 pg/mL after dilution. These results were in agreement with measurements using commercial immunoanalysis.

Immunotherapy of Hepatocellular Carcinoma with Magnetic PD-1 Peptide-Imprinted Polymer Nanocomposite and Natural Killer Cells.

Programmed cell death protein 1 (PD-1) is a biomarker on the surface of cells with a role in promoting self-tolerance by suppressing the inflammatory activity of T cells. In this work, one peptide of PD-1 was used as the template for molecular imprinting to form magnetic peptide-imprinted poly(ethylene-co-vinyl alcohol) composite nanoparticles (MPIP NPs). The nanoparticles were characterized by dynamic light scattering (DLS), high-performance liquid chromatography (HPLC), Brunauer-Emmett-Teller (BET) analysis, and superconducting quantum interference device (SQUID) analysis. Natural killer 92 (NK-92) cells were added to these composite nanoparticles and then incubated with human hepatoma (HepG2) cells. The viability and the apoptosis pathway of HepG2 were then studied using cell counting kit-8 (CCK8) and quantitative real-time polymerase chain reaction (qRT-PCR), respectively. These nanoparticles were found to significantly enhance the activity of natural killer cells toward HepG2 cells by increasing the expression of nuclear factor kappa B (NF-κB), caspase 8, and especially caspase 3.

A multichannel system integrating molecularly imprinted conductive polymers for ultrasensitive voltammetric determination of four steroid hormones in urine.

This work reports on a modularized electrochemical method for the determination of the hormones cortisol, progesterone, testosterone and 17ß-estradiol in urine. These hormones were employed as templates when generating molecular imprints from aniline and metanilic acid by electropolymerization on the surface of screen-printed electrodes. The electrically conductive imprint was characterized by SEM, AFM and cyclic voltammetry. A four-channel system was then established to enable simultaneous determination of the hormones by cyclic voltammetry. The detection limits for cortisol, progesterone, testosterone and 17ß-estradiol are as low as 2, 2.5, 10 and 9 ag·mL-1 (for S/N = 3). Graphical abstract A four-channel system was established to enable simultaneous determination of 4 steroid hormones by cyclic voltammetry and by using moleculalry imprinted polymers.

A DNA-based two-way thermometer to report high and low temperatures.

Precise description of temperature at the microscale level is essential in many biological applications. In this study, we prepared a DNA-based thermometer that reports low and high temperatures by providing two distinct optical signals. The system is a molecular beacon that carries a loop and a stem, whose conformation is subject to change from a hairpin to a random coil when the temperature changes from low to high. A fluorophore, Cy5, and a quencher, BHQ3, are terminally labeled at the stem ends. Moreover, perylene is included in the middle of the 3'-end stem. The signaling state of Cy5 relies on the relative distance to BHQ3. However, the perylene emission is regulated by its microenvironment (i.e., the oligonucleotide or duplex state). With a temperature variation, the designed thermometer undergoes a change in conformation that leads to two signal patterns with Cy5/off and perylene/on at low temperature and Cy5/on and perylene/off at high temperature. The reversibility and biocompatibility of the thermometer design were examined for potential applications in biological systems.

Electrochemical sensing of nuclear matrix protein 22 in urine with molecularly imprinted poly(ethylene-co-vinyl alcohol) coated zinc oxide nanorod arrays for clinical studies of bladder cancer diagnosis.

In 1996 and 2000, the US Food and Drug Administration (FDA) approved the use of Nuclear matrix protein 22 (NMP22) as a monitoring tool for predicting the recurrence/clearing of bladder cancer, and for screening undiagnosed individuals who have symptoms of, or are at risk for, that disease. The fabrication of electrodes for sensing NMP22 and their integration with a portable potentiostat in a homecare system may have great value. This work describes a sensing element comprised of molecularly imprinted polymers (MIPs) for the specific recognition of NMP22 target molecules. Zinc oxide (ZnO) nanorods (214 ± 45 nm in diameter and 1.08 ± 0.11 µm long) were hydrothermally grown on the sensing electrodes to increase the surface area to be coated with MIPs. A portable potentiostat was assembled and a data acquisition (DAQ) card and the Labview program were utilized to monitor electrochemical reaction to sense NMP22 in urine samples. Finally, in phase 0 clinical trials, measurements were made of samples from a few patients with bladder cancer using the NMP22 MIP-coated ZnO nanorods electrodes that were integrated into a portable potentiostat, revealing NMP 22 concentrations in the range 128 ± 19 to 588 ± 53 ng/mL.

Activation of tumor suppressor p53 gene expression by magnetic thymine-imprinted chitosan nanoparticles.

Chitosan is a natural biodegradable polysaccharide that has been used to enhance gene delivery, owing to the ease with which chitosan nanoparticles enter the nucleus of cells. To study the effects of nuclear delivery of telomeric gene sequences, which contain thymine, we formed magnetic thymine-imprinted chitosan nanoparticles (TIPs) by the precipitation of chitosan, mixed with thymine and magnetic nanoparticles (to aid in separations). The mean size of the TIPS was 116 ± 18 nm; the dissociation constant for thymine was 21.8 mg mL(-1). We then treated human hepatocellular carcinoma (HepG2) with TIPs nanoparticles bearing bound thymine or a bound telomeric DNA sequence. The expression of the tumor suppressor p53 gene increased when TIPs were applied and decreased when telomere-bound TIPs were applied.

Recognition of Rhodobacter sphaeroides by microcontact-imprinted poly(ethylene-co-vinyl alcohol).

The immobilization of cells or microorganisms is important for bioseparations, in bioreactors producing cellular metabolites, and as receptors for biosensing. Cell-imprinted polymers (CIPs) have been shown to have cavities with complementary shapes and also high affinities for the template cells or microorganisms. However, the effects of binding to CIPs on gene expression are only beginning to be studied. In this work, the purple bacteria Rhodobacter sphaeroides was employed as a model for the imprinting of microorganisms. R. sphaeroides was first adsorbed on a glass slide as the stamp and then microcontact-imprinted onto poly(ethylene-co-vinyl alcohol), EVAL. The surfaces of the R. sphaeroides-imprinted (RsIPs) and non-imprinted (NIPs) EVAL thin films were examined by Raman spectrometry and scanning electron microscopy. The expression of the nitrogenase (nitrogen fixation, nifH) gene of R. sphaeroides adsorbed on both the RsIPs and NIPs EVAL thin films was also measured by the quantitative reverse transcription polymerase chain reaction (qRT-PCR); cells grown on imprinted polymer showed dramatic differences in gene expression compared to controls.