Scanning Ion Conductance Microscopy Study Reveals the Disruption of the Integrity of the Human Cell Membrane Structure by Oxidative DNA Damage

Imaging Structural and Electrical Changes of Aging Cells Using Scanning Ion Conductance Microscopy

The local charge density and distribution of extracellular membranes play a crucial role in the various cellular processes, such as regulation and localization of membrane proteins, electrophysiological signal transduction, transcriptional control, cell growth, and cell death. In this study, a novel scanning ion conductance microscopy-based method is employed to extracellular membrane mapping. This method allows to not only visualize the dynamic topography and surface charge distribution around individual cells, but also distinguish the charge difference. To validate the accuracy and effectiveness of this method, the charge density on model sample surfaces are initially manipulated and the charge sensing mechanism using finite element modeling (FEM) is explored subsequently. By applying this method, both the extracellular charge distributions and topography structures of normal and senescent human dental pulp stem cells (hDPSCs) are able to monitor. Interestingly, it is observed that the surface charge became significantly more negative after cellular senescence. This innovative approach enables us to gain valuable insights into surface charge changes during cellular senescence, which can contribute to a better understanding of the underlying mechanisms and potential therapeutic strategies for age-related diseases.

Obesity increases genomic instability at DNA repeat-mediated endogenous mutation hotspots

Obesity is associated with increased cancer risk, yet the underlying mechanisms remain elusive. Obesity-associated cancers involve disruptions in metabolic and cellular pathways, which can lead to genomic instability. Repetitive DNA sequences capable of adopting alternative DNA structures (e.g., H-DNA) stimulate mutations and are enriched at mutation hotspots in human cancer genomes. However, it is not known if obesity impacts DNA repeat-mediated endogenous mutation hotspots. We address this gap by measuring mutation frequencies in obese and normal-weight transgenic reporter mice carrying either a control human B-DNA- or an H-DNA-forming sequence (from a translocation hotspot in c-MYC in Burkitt lymphoma). Here, we discover that H-DNA-induced DNA damage and mutations are elevated in a tissue-specific manner, and DNA repair efficiency is reduced in obese mice compared to those on the control diet. These findings elucidate the impact of obesity on cancer-associated endogenous mutation hotspots, providing mechanistic insight into the link between obesity and cancer.

DNA Base Damage Repair Crosstalks with Chromatin Structures to Contract Expanded GAA Repeats in Friedreich's Ataxia

Trinucleotide repeat (TNR) expansion is the cause of over 40 neurodegenerative diseases, including Huntington's disease and Friedreich's ataxia (FRDA). There are no effective treatments for these diseases due to the poor understanding of molecular mechanisms underlying somatic TNR expansion and contraction in neural systems. We and others have found that DNA base excision repair (BER) actively modulates TNR instability, shedding light on the development of effective treatments for the diseases by contracting expanded repeats through DNA repair. In this study, temozolomide (TMZ) was employed as a model DNA base damaging agent to reveal the mechanisms of the BER pathway in modulating GAA repeat instability at the frataxin (FXN) gene in FRDA neural cells and transgenic mouse mice. We found that TMZ induced large GAA repeat contraction in FRDA mouse brain tissue, neurons, and FRDA iPSC-differentiated neural cells, increasing frataxin protein levels in FRDA mouse brain and neural cells. Surprisingly, we found that TMZ could also inhibit H3K9 methyltransferases, leading to open chromatin and increasing ssDNA breaks and recruitment of the key BER enzyme, pol β, on the repeats in FRDA neural cells. We further demonstrated that the H3K9 methyltransferase inhibitor BIX01294 also induced the contraction of the expanded repeats and increased frataxin protein in FRDA neural cells by opening the chromatin and increasing the endogenous ssDNA breaks and recruitment of pol β on the repeats. Our study provides new mechanistic insight illustrating that inhibition of H3K9 methylation can crosstalk with BER to induce GAA repeat contraction in FRDA. Our results will open a new avenue for developing novel gene therapy by targeting histone methylation and the BER pathway for repeat expansion diseases.

A robust computational quest: Discovering potential hits to improve the treatment of pyrazinamide-resistant Mycobacterium tuberculosis

The rise of pyrazinamide (PZA)-resistant strains of Mycobacterium tuberculosis (MTB) poses a major challenge to conventional tuberculosis (TB) treatments. PZA, a cornerstone of TB therapy, must be activated by the mycobacterial enzyme pyrazinamidase (PZase) to convert its active form, pyrazinoic acid, which targets the ribosomal protein S1. Resistance, often associated with mutations in the RpsA protein, complicates treatment and highlights a critical gap in the understanding of structural dynamics and mechanisms of resistance, particularly in the context of the G97D mutation. This study utilizes a novel integration of computational techniques, including multiscale biomolecular and molecular dynamics simulations, physicochemical and medicinal chemistry predictions, quantum computations and virtual screening from the ZINC and Chembridge databases, to elucidate the resistance mechanism and identify lead compounds that have the potential to improve treatment outcomes for PZA-resistant MTB, namely ZINC15913786, ZINC20735155, Chem10269711, Chem10279789 and Chem10295790. These computational methods offer a cost-effective, rapid alternative to traditional drug trials by bypassing the need for organic subjects while providing highly accurate insight into the binding sites and efficacy of new drug candidates. The need for rapid and appropriate drug development emphasizes the need for robust computational analysis to justify further validation through in vitro and in vivo experiments.

Rapid scanning method for SICM based on autoencoder network

Scanning Ion Conductance Microscopy (SICM) enables non-destructive imaging of living cells, which makes it highly valuable in life sciences, medicine, pharmacology, and many other fields. However, because of the uncertainty retrace height of SICM hopping mode, the time resolution of SICM is relatively low, which makes the device fail to meet the demands of dynamic scanning. To address above issues, we propose a fast-scanning method for SICM based on an autoencoder network. Firstly, we cut under-sampled images into small image lists. Secondly, we feed them into a self-constructed primitive-autoencoder super-resolution network to compute high-resolution images. Finally, the inferred scanning path is determined using the computed images to reconstruct the real high-resolution scanning path. The results demonstrate that the proposed network can reconstruct higher-resolution images in various super-resolution tasks of low-resolution scanned images. Compared to existing traditional interpolation methods, the average peak signal-to-noise ratio improvement is greater than 7.5823 dB, and the average structural similarity index improvement is greater than 0.2372. At the same time, using the proposed method for high-resolution image scanning leads to a 156.25% speed improvement compared to traditional methods. It opens up possibilities for achieving high-time resolution imaging of dynamic samples in SICM and further promotes the widespread application of SICM in the future.

Scanning ion conductance microscopy reveals differential effect of PM2.5 exposure on A549 lung epithelial and SH-SY5Y neuroblastoma cell membranes

Numerous studies have linked a wide range of diseases including respiratory illnesses to harmful particulate matter (PM) emissions indoors and outdoors, such as incense PM and industrial PM. Because of their ability to penetrate the lower respiratory tract and the circulatory system, fine particles with diameters of 2.5 µm or less (PM2.5) are believed to be more hazardous than larger PMs. Despite the enormous number of studies focusing on the intracellular processes associated with PM2.5 exposure, there have been limited reports studying the biophysical properties of cell membranes, such as nanoscale morphological changes induced by PM2.5. Our study assesses the membrane topographical and structural effects of PM2.5 from incense PM2.5 exposure in real time on A549 lung carcinoma epithelial cells and SH-SY5Y neuroblastoma cells that had been fixed to preclude adaptive cell responses. The size distribution and mechanical properties of the PM2.5 sample were characterized with atomic force microscopy (AFM). Nanoscale morphological monitoring of the cell membranes utilizing scanning ion conductance microscopy (SICM) indicated statistically significant increasing membrane roughness at A549 cells at half an hour of exposure and visible damage at 4 h of exposure. In contrast, no significant increase in roughness was observed on SH-SY5Y cells after half an hour of PM2.5 exposure, although continued exposure to PM2.5 for up to 4 h affected an expansion of lesions already present before exposure commenced. These findings suggest that A549 cell membranes are more susceptible to structural damage by PM2.5 compared to SH-SY5Y cell membranes, corroborating more enhanced susceptibility of airway epithelial cells to exposure to PM2.5 than neuronal cells.

Observation of α-Synuclein Preformed Fibrils Interacting with SH-SY5Y Neuroblastoma Cell Membranes Using Scanning Ion Conductance Microscopy

Parkinson's disease (PD) is the second-most prevalent neurodegenerative disorder in the U.S. α-Synuclein (α-Syn) preformed fibrils (PFFs) have been shown to propagate PD pathology in neuronal populations. However, little work has directly characterized the morphological changes on membranes associated with α-Syn PFFs at a cellular level. Scanning ion conductance microscopy (SICM) is a noninvasive in situ cell imaging technique and therefore uniquely advantageous to investigate PFF-induced membrane changes in neuroblastoma cells. The present work used SICM to monitor cytoplasmic membrane changes of SH-SY5Y neuroblastoma cells after incubation with varying concentrations of α-Syn PFFs. Cell membrane roughness significantly increased as the concentration of α-Syn PFFs increased. Noticeable protrusions that assumed a more crystalline appearance at higher α-Syn PFF concentrations were also observed. Cell viability was only slightly reduced, though statistically significantly, to about 80% but independent of the dose. These observations indicate that within the 48 h treatment period, PFFs continue to accumulate on the cell membranes, leading to membrane roughness increase without causing prominent cell death. Since PFFs did not induce major cell death, these data suggest that early interventions targeting fibrils before further aggregation may prevent the progression of neuron loss in Parkinson's disease.

Breast cancer classification application based on QGA-SVM

Early diagnosis of breast cancer plays an important role in improving survival rate. Physiological changes of breast tissue can be observed and measured through medical electrical impedance, and the results can be used as a preliminary diagnosis by doctors before treatment. In this paper, quantum genetic algorithm (QGA) and support vector machine (SVM) were combined to classify breast tissues to help clinicians in diagnosis. The algorithm uses QGA to optimize the parameters of SVM and improve the classification performance of SVM. In this experiment, the electrical impedance data measured from breast tissue provided by UCI [58] was used as the data set. Objectively speaking, the data volume of the data set is small and the representativeness is not strong enough. However, the experimental results show that QGA-SVM shows better classification performance, and it is better than SVM.

Paraquat induced oxidative stress, DNA damage, and cytotoxicity in lymphocytes

Paraquat (PQ) is a herbicide belonging to the group of bipyridylium salts. The objective of this study was to evaluate oxidative stress, DNA damage, and cytotoxicity induced by paraquat in peripheral lymphocyte cells in vivo as well as pathological changes in various tissues. For this purpose, 28 male Wistar rats in 6 different groups were poisoned by paraquat gavage and blood samples were taken from the hearts of rats after during the poisoning period. Oxidative stress, DNA damage, cell membrane integrity, serum lactate dehydrogenase, and cytotoxicity, were investigated by Ferric Reducing Antioxidant Potential (FRAP) test, alkaline comet assay, measuring serum lactate dehydrogenase (LDH), Hoechst staining and flow cytometry with propidium iodide (PI) respectively. The lung, kidney, and liver tissues were also examined pathologically. Paraquat caused dose-dependent DNA damage in peripheral lymphocyte cells and significant oxidative cell membrane damage. The most damage was caused by a single dose of 200 mg/kg b.w of paraquat by gavage. The gradual exposure to a dose of 300 mg/kg b.w of paraquat showed less damage, which could be due to the activation of the antioxidant defense mechanism.

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Paraquat induced oxidative stress.

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Paraquat increases serum lactate dehydrogenase.

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Oxidative stress Inducted by exposure to paraquat Inducted DNA damage.

Development of multifunctional nanopipettes for controlled intracellular delivery and single-entity detection

The intracellular delivery of biomolecules and nanoscale materials to individual cells has gained remarkable attention in recent years owing to its wide applications in drug delivery, clinical diagnostics, bio-imaging and single-cell analysis. It remains a challenge to control and measure the delivered amount in one cell. In this work, we developed a multifunctional nanopipette - containing both a nanopore and nanoelectrode (pyrolytic carbon) at the apex - as a facile, minimally invasive and effective platform for both controllable single-cell intracellular delivery and single-entity counting. While controlled by a micromanipulator, the baseline changes of the nanopore ionic current (I) and nanoelectrode open circuit potential (V) help to guide the nanopipette tip insertion and positioning processes. The delivery from the nanopore barrel can be facilely controlled by the applied nanopore bias. To optimize the intracellular single-entity detection during delivery, we studied the effects of the nanopipette tip geometry and solution salt concentration in controlled experiments. We have successfully delivered gold nanoparticles and biomolecules into the cell, as confirmed by the increased scattering and fluorescence signals, respectively. The delivered entities have also been detected at the single-entity level using either one or both transient I and V signals. We found that the sensitivity of the single-entity electrochemical measurement was greatly affected by the local environment of the cell and varied between cell lines.

Highly sensitive detection of DNA damage in living cells by SERS and electrochemical measurements using a flexible gold nanoelectrode

Guanine (G) oxidation products, such as 8-hydroxy-2'-deoxyguanosine (8-OHdG) and 8-oxo-guanine (8-OXOG), have been widely studied as promising biomarkers for DNA oxidative damage. In this work, we develop a new method to detect G oxidative products released from live cells after chromium (vi) ion or hydrogen peroxide treatments by using a glass nanopipette-based flexible gold nanoelectrode (fGNE). Specific response to G oxidative products with high sensitivity can be detected from the fGNE tip through integrated electrochemical measurements and surface-enhanced Raman spectroscopy. The fGNE apex can be positioned very close to the cell membrane noninvasively because of its high flexibility and nanoscale tip size. With the assistance of the electrophoretic force, the fGNEs can effectively collect and detect the G-derived DNA damage products released from individual cells in the cell culture medium with high sensitivity.