Nanoscale detection of carbon dots-induced changes in actin skeleton of neural cells.

Understanding the cytotoxicity of fluorescent carbon dots (CDs) is crucial for their applications, and various biochemical assays have been used to study the effects of CDs on cells. Knowledge on the effects of CDs from a biophysical perspective is integral to the recognition of their cytotoxicity, however the related information is very limited. Here, we report that atomic force microscopy (AFM) can be used as an effective tool for studying the effects of CDs on cells from the biophysical perspective. We achieve this by integrating AFM-based nanomechanics with AFM-based imaging. We demonstrate the performance of this method by measuring the influence of CDs on living human neuroblastoma (SH-SY5Y) cells at the single-cell level. We find that high-dose CDs can mechanically induce elevated normalized hysteresis (energy dissipation during the cell deformation) and structurally impair actin skeleton. The nanomechanical change highly correlates with the alteration of actin filaments, indicating that CDs-induced changes in SH-SY5Y cells are revealed in-depth from the AFM-based biophysical aspect. We validate the reliability of the biophysical observations using conventional biological methods including cell viability test, fluorescent microscopy, and western blot assay. Our work contributes new and significant information on the cytotoxicity of CDs from the biophysical perspective.

Near-Field Terahertz Morphological Reconstruction Nanoscopy for Subsurface Imaging of Protein Layers.

Protein layers formed on solid surfaces have important applications in various fields. High-resolution characterization of the morphological structures of protein forms in the process of developing protein layers has significant implications for the control of the layer's quality as well as for the evaluation of the layer's performance. However, it remains challenging to precisely characterize all possible morphological structures of protein in various forms, including individuals, networks, and layers involved in the formation of protein layers with currently available methods. Here, we report a terahertz (THz) morphological reconstruction nanoscopy (THz-MRN), which can reveal the nanoscale three-dimensional structural information on a protein sample from its THz near-field image by exploiting an extended finite dipole model for a thin sample. THz-MRN allows for both surface imaging and subsurface imaging with a vertical resolution of ∼0.5 nm, enabling the characterization of various forms of proteins at the single-molecule level. We demonstrate the imaging and morphological reconstruction of single immunoglobulin G (IgG) molecules, their networks, a monolayer, and a heterogeneous double layer comprising an IgG monolayer and a horseradish peroxidase-conjugated anti-IgG layer. The established THz-MRN presents a useful approach for the label-free and nondestructive study of the formation of protein layers.

Terahertz label-free detection of nicotine-induced neural cell changes and the underlying mechanisms.

Nicotine exposure can lead to neurological impairments and brain tumors, and a label-free and nondestructive detection technique is urgently required by the scientific community to assess the effects of nicotine on neural cells. Herein, a terahertz (THz) time-domain attenuated total reflection (TD-ATR) spectroscopy approach is reported, by which the effects of nicotine on normal and cancerous neural cells, i.e., HEB and U87 cells, are successfully investigated in a label/stain-free and nondestructive manner. The obtained THz absorption coefficients of HEB cells exposed to low-dose nicotine and high-dose nicotine are smaller and larger, respectively, than the untreated cells. In contrast, the THz absorption coefficients of U87 cells treated by nicotine are always smaller than the untreated cells. The THz absorption coefficients can be well related to the proliferation properties (cell number and compositional changes) and morphological changes of neural cells, by which different types of neural cells are differentiated and the viabilities of neural cells treated by nicotine are reliably assessed. Collectively, this work sheds new insights on the effects of nicotine on neural cells, and provides a useful tool (THz TD-ATR spectroscopy) for the study of chemical-cell interactions.

Rapid on-site evaluation in percutaneous core needle biopsies of renal masses: Cytologic-histologic concordance and diagnostic challenges.

BACKGROUND: Image-guided fine needle aspirations (FNAs) and core needle biopsies (CNBs) play the critical role in diagnosis of renal lesions. Rapid on-site evaluation (ROSE) can potentially increase the adequacy rate and improve diagnostic yield, while providing additional information for rapid clinical decisions. The aim of this study is to evaluate the diagnostic utility of ROSE in obtaining adequate tissue for diagnosis of renal lesions in our institution. METHODS: We retrospectively reviewed all percutaneous renal CNB cases with available ROSE interpretations for a 11-year period. The ROSE interpretations and CNB diagnoses was compared and the concordance rate was calculated accordingly. The discrepant cases were re-reviewed and the possible causes for discrepancy were analyzed. RESULTS: A total of 189 cases were identified. Definitive diagnoses were rendered in 164 (87%) cases on the final CNBs, including primary renal lesions in 151 cases and metastatic malignancies in 13 cases. At the time of ROSE, samples were deemed to be adequate in the majority of cases (83%). The calculated concordance rate between ROSE interpretations and CNB final diagnoses was 84.6%. Sampling issue and scant tumor cells were the main causes for the discordance between ROSE interpretations and CNB diagnoses. CONCLUSION: Our study showed a relatively high-concordance rate of 84.6% between ROSE interpretations and CNB final diagnoses, suggesting that ROSE is a valuable tool for procurement of adequate renal CNB samples for diagnosis.

Terahertz time-domain attenuated total reflection spectroscopy integrated with a microfluidic chip.

The integration of a microfluidic chip into terahertz time-domain attenuated total reflection (THz TD-ATR) spectroscopy is highly demanded for the accurate measurement of aqueous samples. Hitherto, however little work has been reported on this regard. Here, we demonstrate a strategy of fabricating a polydimethylsiloxane microfluidic chip (M-chip) suitable for the measurement of aqueous samples, and investigate the effects of its configuration, particularly the cavity depth of the M-chip on THz spectra. By measuring pure water, we find that the Fresnel formulae of two-interface model should be applied to analyze the THz spectral data when the depth is smaller than 210 µm, but the Fresnel formula of one-interface model can be applied when the depth is no less than 210 µm. We further validate this by measuring physiological solution and protein solution. This work can help promote the application of THz TD-ATR spectroscopy in the study of aqueous biological samples.

Molecular testing in cytology.

In the era of personalized medicine, molecular testing plays a critical role in patient care. The rapid advance of molecular techniques, especially next-generation sequencing, makes molecular diagnosis feasible in daily practice. Molecular testing can be used as a valuable ancillary test to increase diagnostic sensitivity and specificity, especially in small biopsy or cytology samples. In addition, molecular testing plays an important role in selecting patients for appropriate treatment by detecting therapeutic and predictive biomarkers in tissue or cytology samples. Molecular studies can be applied in all cytology samples, sometimes with better results than histology. As molecular testing has become essential for patient care and is often requested to be performed in cytology samples, it is critical for cytopathologists to understand the basics of molecular diagnostic methods, indications for molecular testing, and how to best utilize different cytologic samples for this purpose. In this special issue, experts in various areas of cytopathology and molecular pathology review the literature and discuss the basics of molecular techniques and the application of molecular testing in various types of cytology samples. It is our hope that after reading the articles in this special issue, the readers can know better about the possibilities of molecular cytology, a very exciting field of pathology.

NLRP3 inflammasome inhibitor MCC950 reduces cerebral ischemia/reperfusion induced neuronal ferroptosis.

The role of nucleotide-binding oligomerization domainlike receptor pyrin domain containing 3 (NLRP3) inflammasome in cerebral ischemia-reperfusion (I/R) induced neuroinflammation and neuronal pyroptosis has been widely recognized. Latest studies revealed that NLRP3 inflammasome engage in not only pyroptosis but also other types of cell death. Ferroptosis has been proved to be closely associated with cerebral I/R injury. In this study, our objectives were to verify the inhibitory effect of the NLRP3-specific inhibitor MCC950 on cerebral I/R-mediated neuronal pyroptosis, and to explore the regulation and possible mechanism of MCC950 on cerebral I/R-mediated neuronal ferroptosis. Our data showed that the NLRP3-specific inhibitor, MCC950, effectively reversed the I/R-mediated NLRP3 inflammasome activation and neuronal pyroptosis. Furthermore, we found that I/R increased iron concentrations and levels of malondialdehyde (MDA), downregulated glutathione peroxidase 4 (GPX4) expression, and upregulated long chain fatty acid-CoA ligase 4 (FACL4) and prostaglandin endoperoxide synthase 2 (PTGS2) expression. Interestingly, these changes were also reversed by the MCC950. Finally, in vitro, we found that MCC950 significantly reduced ROS levels in OGD/R treated HT22 cells. In conclusion, pharmaceutical inhibition of NLRP3 by MCC950 attenuates I/R-induced neuronal ferroptosis, possibly by reducing ROS accumulation.

Molecular diagnostics of infectious disease: Detection and characterization of microbial agents in cytology samples.

BACKGROUND: Cytology samples are widely used to diagnose various infectious diseases by detection and identification of causative infectious agents, including bacteria, fungi, and viruses. The role of cytopathology in infectious disease has expanded tremendously in the past decades with the advances in molecular techniques. Molecular diagnostic methods, compared to conventional methods, have shown improved patient outcome, reduction in cost, and shortened hospital stay times. The aim of this article is to review molecular testing in cytology samples for diagnosis of infectious diseases. METHODS: The literature search for molecular testing in common cytology samples for diagnosis of infectious diseases was performed. The findings of the studies were summarized. The common cytology samples included in this article were gynecologic specimens, cerebrospinal fluid, bronchoalveolar lavage, and urine samples. CONCLUSIONS: There are a number of molecular diagnostic tests that are available to be used in common cytology samples to detect infectious agents. Each test has its own advantages and limitations. It is our hope that upon reading this review article, the readers will have better understanding of molecular diagnostic testing of infectious diseases utilizing commonly sampled cytology specimens in daily practice.

The basics of commonly used molecular techniques for diagnosis, and application of molecular testing in cytology.

Molecular diagnostics has expanded to become the standard of care for a variety of solid tumor types. With limited diagnostic material, it is often desirable to use cytological preparations to provide rapid and accurate molecular results. This review covers important pre-analytic considerations and limitations, and a description of common techniques that the modern cytopathologist should understand when ordering and interpreting molecular tests in practice.

Utility of rapid on-site evaluation in procurement of adrenal gland tissue biopsies.

BACKGROUND: While the number of adrenal biopsies has increased due to more "incidentalomas" were detected by widespread use of imaging studies, there have been very limited studies to evaluate the utility of rapid on-site evaluation (ROSE) in obtaining adequate core needle biopsy (CNB) tissue for diagnosis of adrenal lesions. METHODS: We retrospectively reviewed all percutaneous adrenal CNB cases with available ROSE for a 12-year period in our institute in order to assess the usefulness of ROSE in adrenal CNB sampling. RESULTS: A total of 83 cases were identified in our database. The majority of cases (52/83, 63%) were diagnosed as metastatic malignancies with the lung being the most common primary site. Adrenal hyperplasia/adenoma was the most common primary adrenal lesion. The concordance between the ROSE interpretations and CNB final diagnoses is 80%. The interpretation errors accounted for majority (11/17, 65%) of the discordant cases. CONCLUSION: ROSE assessment during adrenal CNB procedures is a helpful tool for obtaining adequate diagnostic tissue. Pathologists should be familiar with adrenal cytology in order to reduce interpretation errors at ROSE.

Evaluation of classification in single cell atac-seq data with machine learning methods.

BACKGROUND: The technologies advances of single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) allowed to generate thousands of single cells in a relatively easy and economic manner and it is rapidly advancing the understanding of the cellular composition of complex organisms and tissues. The data structure and feature in scRNA-seq is similar to that in scATAC-seq, therefore, it's encouraged to identify and classify the cell types in scATAC-seq through traditional supervised machine learning methods, which are proved reliable in scRNA-seq datasets. RESULTS: In this study, we evaluated the classification performance of 6 well-known machine learning methods on scATAC-seq. A total of 4 public scATAC-seq datasets vary in tissues, sizes and technologies were applied to the evaluation of the performance of the methods. We assessed these methods using a 5-folds cross validation experiment, called intra-dataset experiment, based on recall, precision and the percentage of correctly predicted cells. The results show that these methods performed well in some specific types of the cell in a specific scATAC-seq dataset, while the overall performance is not as well as that in scRNA-seq analysis. In addition, we evaluated the classification performance of these methods by training and predicting in different datasets generated from same sample, called inter-datasets experiments, which may help us to assess the performance of these methods in more realistic scenarios. CONCLUSIONS: Both in intra-dataset and in inter-dataset experiment, SVM and NMC are overall outperformed others across all 4 datasets. Thus, we recommend researchers to use SVM and NMC as the underlying classifier when developing an automatic cell-type classification method for scATAC-seq.

Cortistatin attenuates titanium particle-induced osteolysis through regulation of TNFR1-ROS-caspase-3 signaling in osteoblasts.

Aseptic loosening is a major complication of prosthetic joint surgery and is associated with impaired osteoblast homeostasis. Cortistatin (CST) is a neuropeptide that protects against inflammatory conditions. In this study, we found that expression of CST was diminished in patients with prosthetic joint loosening and in titanium (Ti) particle-induced animal models. A Ti particle-induced calvarial osteolysis model was established in wild-type and CST gene knockout mice; CST deficiency enhanced, while exogenously added CST attenuated, the severity of Ti particle-mediated osteolysis. CST protected against inflammation as well as apoptosis and maintained the osteogenic function of MC3T3-E1 osteoblasts upon stimulation with Ti particles. Furthermore, CST antagonized reactive oxygen species production and suppressed caspase-3-associated apoptosis mediated by Ti particles in osteoblasts. Additionally, CST protects against Ti particle-induced osteolysis through tumor necrosis factor receptor 1. Taken together, CST might provide a therapeutic strategy for wear debris-induced inflammatory osteolysis.

Inhibition of PRMT5 attenuates cerebral ischemia/reperfusion-Induced inflammation and pyroptosis through suppression of NF-κB/NLRP3 axis.

Protein methylation is a prevalent post-translational modification after cerebral ischemia. Protein arginine methyltransferase 5 (PRMT5) is a type of methyltransferase enzyme that can catalyse the formation of methylated residues on histones and non-histone proteins. Accumulating evidence suggested that PRMT5 might play a carcinogenic role in various cancers. However, the role of PRMT5 in cerebral ischaemia/reperfusion (I/R) injury remains unclear. In this project, middle cerebral artery occlusion/reperfusion (MCAO/R) model in mice and oxygen-glucose deprivation/reoxygenation (OGD/R) model in human neuroblastoma SH-SY5Y cells were utilized to mimic disease state of cerebral I/R. We found that expression of inflammatory-related factors [Interleukin (IL)-1ß and IL-6)] and pyroptotic-related factor [N-term cleaved Gasdermin-D (GSDMD-N)] were up-regulated in both MCAO/R mice and OGD/R SH-SY5Y cells. In addition, both in vivo and in vitro, PRMT5 was aberrantly upregulated during cerebral I/R. However, these alterations induced by I/R were blocked by PRMT5 inhibitor LLY-283, and enhanced by overexpression of PRMT5. Furthermore, rescue experiment proved that PRMT5 plays a pro-inflammatory and pro-pyroptotic role by activating nuclear factor kappa B (NF-κB)/nucleotide-binding oligomerization domainlike receptor pyrin domain containing 3 (NLRP3) axis. Finally, we observed that treatment of LLY-283 alleviated neurological deficits and reduced infarct volume in the MCAO/R mice. Taken together, PRMT5 may be a potential therapeutic target for cerebral I/R injury.

Performance of Afirma Gene Sequencing Classifier versus Gene Expression Classifier in thyroid nodules with indeterminate cytology.

INTRODUCTION: About 15% to 30% of thyroid fine-needle aspiration (FNA) nodules have indeterminate cytology. The Afirma (Veracyte Inc, South San Francisco, CA) Gene Expression Classifier (GEC)/Gene Sequencing Classifier (GSC) tests were designed to improve risk stratification of the indeterminate thyroid nodules. This study aimed to evaluate and compare the performance of the Afirma GEC and GSC tests in the indeterminate thyroid lesions. METHODS: Thyroid FNA cases with indeterminate cytology were searched in the pathology database and only those with available Afirma results were selected for this study. Each patient's demographic, sonographic, cytologic, molecular, and subsequent surgical follow-up results were collected and analyzed. RESULTS: There were 100 cases with indeterminate thyroid FNA results, including 49 cases tested by GEC and 51 cases by GSC. In the GEC group, benign call rate (BCR) was 53% (26 of 49) and the calculated negative predictive value (NPV) and positive predictive value (PPV) were 88% and 47% respectively. In the GSC group, the BCR was 63% (32 of 51) and the calculated NPV and PPV were 100% and 64%, respectively. Whereas only 17% (1 of 6) of benign oncocytic lesions were tested benign by the GEC, 60% (3 of 5) of benign oncocytic nodules were tested benign by the GSC. CONCLUSION: We demonstrated in this study that a little more than half of the indeterminate thyroid nodules had negative Afirma GEC/GSC results and the BCR using the Afirma GSC test was higher than GEC. The Afirma GSC showed higher NPV and PPV than GEC. In addition, the Afirma GSC appeared to be superior for differentiating benign and malignant oncocytic thyroid lesions.

The international system for serous fluid cytopathology: Interobserver agreement.

BACKGROUND: A number of categorization systems had been developed for the reporting of cytology specimens with the aim of providing uniform definitions, criteria, and diagnostic terminology. The intention of these systems is to improve reproducibility of diagnostic categorization with standardized estimates of malignancy risk. Required for the success of these systems is a high level of interobserver reproducibility for category assignment. Recently, the international system for serous fluid cytopathology (TIS) was proposed using the categories nondiagnostic, negative for malignancy, atypia of undetermined significance (AUS), suspicious for malignancy, and malignant. Little data exists documenting the interobserver agreement for these categories. DESIGN: A search of the cytology records at the University of Missouri was performed for all pleural fluid specimens obtained between January 2014 and December 2019. A total of 200 specimens were reviewed independently by three board-certified cytopathologists. Specimens were characterized as nondiagnostic, negative, AUS, suspicious for malignancy, and malignant. Interobserver agreement was analyzed using Cohen's kappa. RESULTS: Overall observer agreement was 68% and chance-corrected weighted agreement (weighted kappa) was 0.63. Agreement was good for categories negative and malignant, but poor for categories atypia of uncertain significance, and suspicious for malignancy. CONCLUSIONS: The TIS has performance characteristics similar to other cytologic classification schemes. Interobserver agreement is best for the negative (76%) and malignant (81%) categories. Interobserver agreement is poor for the category's AUS, and suspicious for malignancy. This is similar to interobserver agreement associated with other published categorization systems.

Study on an artificial phenomenon observed in terahertz biological imaging.

Terahertz (THz) wave-based imaging of biological samples is an emerging but promising field. In the present work, we report an artificial phenomenon observed in imaging melanoma slices, which can lead to mistakenly interpretation of the experimental results. It was observed that a structure similar to but smaller than the sample contour appeared inside the melanoma slice image. The underlying mechanism of this phenomenon was then investigated both experimentally and theoretically. By imaging a regular standard sample (vinyl coverslip) with a THz time domain spectroscopy (THz-TDS) system and reconstructing its images at 0.8 and 1.2 THz, we can clearly observe the afore-mentioned artifacts. The experimental results are highly consistent with the simulations based on the Fresnel-Kirchhoff diffraction theory in which possible optical aberrations were incorporated. It can be concluded that this artifact was caused by the frequency-dependent diffraction of the sample edge. The work demonstrated here is essential for correct interpretation of the images obtained by the THz-TDS technique.

Terahertz, infrared and Raman absorption spectra of tyrosine enantiomers and racemic compound.

The application of terahertz (THz)-based techniques in biomolecule study is very promising but still in its infancy. In the present work, we employed THz time-domain spectroscopy (THz-TDS) and THz time-domain attenuated total reflection (THz-TD-ATR) spectroscopy to investigate the properties of tyrosine (Tyr) enantiomers (L- and D-Tyr) and racemate (DL-Tyr) in solid state and aqueous solutions, respectively. THz absorption spectra of solid L- and D-Tyr show similar absorption spectra with peaks at 0.95, 1.92, 2.06 and 2.60 THz, which are obviously different from the spectrum of DL-Tyr with peaks at 1.5, 2.15 and 2.40 THz. In contrast, although THz absorption spectra of L-Tyr solution and D-Tyr solution are similar and different from the spectrum of DL-Tyr solution, both of them have no observable peaks. Interestingly, it was found that the solution containing equal amounts of L- and D-Tyr has a similar spectrum as that of DL-Tyr solution, as far as the mass concentrations of the two types of solutions are kept the same. On other hand, solid L-, D- and DL-Tyr were also investigated with infrared spectroscopy and Raman spectroscopy, respectively. The results show that the spectra of L- and D-Tyr can be regarded the same but they are slightly different from the spectrum of DL-Tyr. With the aid of principal component analysis (PCA), the difference between L-/D-Tyr and DL-Tyr can be confirmed without any ambiguity. Overall, this work systematically interrogated and evaluated the performance of THz-based techniques in the detection of the chirality of tyrosine.

Influence of the PM2.5 Water-Soluble Compound on the Biophysical Properties of A549 Cells.

Understanding the influence of fine atmospheric particles (PM2.5) on cellular biophysical properties is an integral part for comprehending the mechanisms underlying PM2.5-induced diseases because they are closely related to the behaviors and functions of cells. However, hitherto little work has been done in this area. In the present work, we aimed to interrogate the influence of the PM2.5 water-soluble compound (PM2.5-WSC) on the biophysical performance of a human lung carcinoma epithelial cell line (A549) by exploring the cellular morphological and mechanical changes using atomic force microscopy (AFM)-based imaging and nanomechanics. AFM imaging showed that PM2.5-WSC treated cells exhibited evidently reduced lamellipodia and an increased height when compared to the control group. AFM nanomechanical measurements indicated that the treated cells had higher elastic energy and lower adhesion work than the control group. Our western blot assay and transmission electron microscopy (TEM) results revealed that after PM2.5-WSC treatment, the contents of cytoskeletal components (ß-actin and ß-tubulin) increased, but the abundance of cell surface microvilli decreased. The biophysical changes of PM2.5-WSC-treated cells measured by AFM can be well correlated to the alterations of the cytoskeleton and surface microvilli identified by the western blot assay and TEM imaging. The above findings confirm that the adverse risks of PM2.5 on cells can be reliably assessed biophysically by characterizing the cellular morphology and nanomechanics. The demonstrated technique can be used to diminish the gap of our understanding between PM2.5 and its harmful effects on cellular functions.

Detection of gene mutation responsible for Huntington's disease by terahertz attenuated total reflection microfluidic spectroscopy.

Terahertz absorption spectroscopy based on attenuated total reflection (ATR) from a microfluidic sample cell was designed and implemented to detect gene mutations leading to Huntington's disease (HD). The self-developed compact ATR microfluidic system was employed to detect two groups of base-repeated DNA molecules combined with a terahertz time-domain spectrometer in a marker-free manner. The first group featured different repetition patterns of oligonucleotide fragments, and the second group included the HD gene. For the oligonucleotides of different repetition patterns, there were significant differences among the three oligonucleotides with three repeats of the double bases, which could be unambiguously classified and identified; For the HD gene, it was found that the magnitude of the terahertz absorption coefficients of the four oligonucleotide solutions was, in ascending order, CAG-4 < CAG-16 < CAG-32 < CAG-40 (the numbers are the repeat times of the CAG base segment, with 40 repeats belonging to the HD gene), when the concentration of oligonucleotide was 1 mg/mL. Principal component analysis result indicated that the spectral differences of the four oligonucleotide solutions with different CAG repeat times were statistically significant and clearly distinguishable. These results demonstrate the potential of terahertz spectroscopy as a noninvasive, unmarked, fast and low-cost assay for gene diagnosis and clinical disease detection.

Near-Field Nanoscopic Terahertz Imaging of Single Proteins.

Terahertz (THz) biological imaging has attracted intense attention due to its capability of acquiring physicochemical information in a label-free, noninvasive, and nonionizing manner. However, extending THz imaging to the single-molecule level remains a challenge, partly due to the weak THz reflectivity of biomolecules with low dielectric constants. Here, the development of graphene-mediated THz scattering-type scanning near-field optical microscope for direct imaging of single proteins is reported. Importantly, it is found that a graphene substrate with high THz reflectivity and atomic flatness can provide high THz contrast against the protein molecules. In addition, a platinum probe with an optimized shaft length is found enabling the enhancement of the amplitude of the scattered THz near-field signals. By coupling these effects, the topographical and THz scattering images of individual immunoglobulin G (IgG) and ferritin molecules with the size of a few nanometers are obtained, simultaneously. The demonstrated strategy thus opens new routes to imaging single biomolecules with THz.