Isolation, expansion, differentiation, and histological processing of human nasal epithelial cells.

This protocol is intended as a guide for implementing or refining the usage of the air-liquid interface (ALI) model system to generate airway mucociliary tissue in vitro. We present a streamlined protocol for isolating the stem cells from inferior nasal turbinates of donors, allowing for a simple and low-cost supply of primary cells for research. We also provide our detailed protocols for ALI tissue processing and immunofluorescence to aid in the standardization of these techniques between research groups. For complete details on the use and execution of this protocol, please refer to Hussain et al., (2014)Yang et al., (2016)Im et al., (2019).

An optimized method for adult zebrafish brain-tissue dissociation that allows access mitochondrial function under healthy and epileptic conditions.

Mitochondria play key roles in brain metabolism. Not surprisingly, mitochondria dysfunction is a ubiquitous cause of neurodegenerative diseases. In turn, acquired forms of epilepsy etiology is specifically intriguing since mitochondria function and dysfunction remain not completely enlightened. Investigation in the field includes models of epileptic disorder using mainly rodents followed by mitochondrial function evaluation, which in general evidenced controversial data. So, we considered the efforts and limitations in this research field and we took into account that sample preparation and quality are critical for bioenergetics investigation. For these reasons the aim of the present study was to develop a thorough protocol for adult zebrafish brain-tissue dissociation to evaluate oxygen consumption flux and reach the bioenergetics profile in health and models of epileptic disorder in both, in vitro using pentylenetetrazole (PTZ) and N-methyl-D-Aspartic acid (NMDA), and in vivo after kainic acid (KA)-induced status epilepticus. In conclusion, we verify that fire-polished glass Pasteur pipette is eligible to brain-tissue dissociation and to study mitochondrial function and dysfunction in adult zebrafish. The results give evidence for large effect size in increase of coupling efficiency respiration (p/O2) correlated to treatment with PTZ and spare respiratory capacity (SRC) in KA-induced model indicating oxidative phosphorylation (OXPHOS) variable alterations. Further investigation is needed in order to clarify the bioenergetics role as well as other mitochondrial functions in epilepsy.

Navigating across multi-dimensional space of tissue clearing parameters.

Optical tissue clearing refers to physico-chemical treatments which make thick biological samples transparent by removal of refractive index gradients and light absorbing substances. Although tissue clearing was first reported in 1914, it was not widely used in light microscopy until 21th century, because instrumentation of that time did not permit to acquire and handle images of thick (mm to cm) samples as whole. Rapid progress in optical instrumentation, computers and software over the last decades made micrograph acquisition of centimeter-thick samples feasible. This boosted tissue clearing use and development. Numerous diverse protocols have been developed. They use organic solvents or water-miscible substances, such as detergents and chaotropic agents; some protocols require application of electric field or perfusion with special devices. There is no 'best-for-all' tissue clearing method. Depending on the case, one or another protocol is more suitable. Most of protocols require days or even weeks to complete, thus choosing an unsuitable protocol may cause an important waste of time. Several inter-dependent parameters should be taken into account to choose a tissue clearing protocol, such as: (1) required image quality (resolution, contrast, signal to noise ratio etc), (2) nature and size of the sample, (3) type of labels, (4) characteristics of the available instrumentation, (5) budget, (6) time budget, and (7) feasibility. Present review focusses on the practical aspects of various tissue clearing techniques. It is aimed to help non-experts to choose tissue clearing techniques which are optimal for their particular cases.

Practical Approaches for Cryo-FIB Milling and Applications for Cellular Cryo-Electron Tomography.

Cryo-electron tomography (cryo-ET) is a powerful technique to examine cellular structures as they exist in situ. However, direct imaging by TEM for cryo-ET is limited to specimens up to ∼400 nm in thickness, narrowing its applicability to areas such as cellular projections or small bacteria and viruses. Cryo-focused ion beam (cryo-FIB) milling has emerged in recent years as a method to generate thin specimens from cellular samples in preparation for cryo-ET. In this technique, specimens are thinned with a beam of gallium ions to gradually ablate cellular material in order to leave a thin, electron-transparent section (a lamella) through the bulk material. The lamella can be used for high-resolution cryo-ET to visualize cells in 3D in a near-native state. This approach has proved to be robust and relatively simple for new users and exhibits minimal sectioning artifacts. In this chapter, we describe a general approach to cryo-FIB milling for users with prior cryo-EM experience, with extensive notes on operation and troubleshooting.

Optimised tissue clearing minimises distortion and destruction during tissue delipidation.

AIMS: A variety of tissue clearing techniques have been developed to render intact tissue transparent. For thicker samples, additional partial tissue delipidation is required before immersion into the final refractive index (RI)-matching solution, which alone is often inadequate to achieve full tissue transparency. However, it is difficult to determine a sufficient degree of tissue delipidation, excess of which can result in tissue distortion and protein loss. Here, we aim to develop a clearing strategy that allows better monitoring and more precise determination of delipidation progress. METHODS: We combined the detergent sodium dodecyl sulphate (SDS) with OPTIClear, a RI-matching solution, to form a strategy termed Accurate delipidation with Optimal Clearing (Accu-OptiClearing). Accu-OptiClearing allows for a better preview of the final tissue transparency achieved when immersed in OPTIClear alone just before imaging. We assessed for the changes in clearing rate, protein loss, degree of tissue distortion, and preservation of antigens. RESULTS: Partial delipidation using Accu-OptiClearing accelerated tissue clearing and better preserved tissue structure and antigens than delipidation with SDS alone. Despite achieving similar transparency in the final OPTIClear solution, more lipids were retained in samples cleared with Accu-OptiClearing compared to SDS. CONCLUSIONS: Combining the RI-matching solution OPTIClear with detergents, Accu-OptiClearing, can avoid excessive delipidation, leading to accelerated tissue clearing, less tissue damage and better preserved antigens.

Ex vivo MR microscopy of a human brain with multiple sclerosis: Visualizing individual cells in tissue using intrinsic iron.

PURPOSE: To perform magnetic resonance microscopy (MRM) on human cortex and a cortical lesion as well as the adjacent normal appearing white matter. To shed light on the origins of MRI contrast by comparison with histochemical and immunostaining. METHODS: 3D MRM at a nominal isotropic resolution of 15 and 18 µm was performed on 2 blocks of tissue from the brain of a 77-year-old man who had MS for 47 years. One block contained normal appearing cortical gray matter (CN block) and adjacent normal appearing white matter (NAWM), and the other also included a cortical lesion (CL block). Postmortem ex-vivo MRI was performed at 11.7T using a custom solenoid coil and T2*-weighted 3D GRE sequence. Histochemical and immunostaining were done after paraffin embedding for iron, myelin, oligodendrocytes, neurons, blood vessels, macrophages and microglia, and astrocytes. RESULTS: MRM could identify individual iron-laden oligodendrocytes with high sensitivity (70% decrease in signal compared to surrounding) in CN and CL blocks, as well as some iron-laden activated macrophages and microglia. Iron-deficient oligodendrocytes seemed to cause relative increase in MRI signal within the cortical lesion. High concentration of myelin in the white matter was primarily responsible for its hypointense appearance relative to the cortex, however, signal variations within NAWM could be attributed to changes in density of iron-laden oligodendrocytes. CONCLUSION: Changes in iron accumulation within cells gave rise to imaging contrast seen between cortical lesions and normal cortex, as well as the patchy signal in NAWM. Densely packed myelin and collagen deposition also contributed to MRM signal changes. Even though we studied only one block each from normal appearing and cortical lesions, such studies can help better understand the origins of histopathological and microstructural correlates of MRI signal changes in multiple sclerosis and contextualize the interpretation of lower-resolution in vivo MRI scans.

Quantitative assessment of optical clearing methods on formalin-fixed human lymphoid tissue.

Rising interest in three-dimensional volume imaging of biological tissues for diagnostic and research purposes, calls for appropriate optical clearing methods as an indispensable requirement for high-resolution imaging on a cellular level. In recent years, many clearing protocols have emerged, though most of them focus on murine central nervous tissue. Peripheral organs or tissues of human origin have only been investigated sparsely. Therefore, we tested eight established clearing methods (BABB, Ce3D, CUBIC, ECi, ChemScale, ChemScaleQQ5, SeeDB2 and PACT) on formaldehyde-fixed human tonsils. This application-oriented taxonomy can help researchers restrict the space of their survey on clearing techniques for lymphatic tissue as it provides information on each method in regard to its efficacy, clearing speed, preservation of fluorescence labelling, toxicity, expenditure and monetary costs. We found that all of the applied clearing protocols could render the sample tissues transparent. Ce3D and PACT achieved the highest degrees of tissue transparency. Since it requires less preparing and processing time and is lower in toxicity, we recommend Ce3D for the clearing of human lymphoid tissue.

Description of a new biosafe procedure for cytological specimens from patients with COVID-19 processed by liquid-based preparations.

BACKGROUND: Coronavirus disease 2019 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and represents the causative agent of a potentially fatal disease. The spread of the infection and the severe clinical disease have led to the widespread adoption of social distancing measures. Special attention and efforts to protect or reduce transmission have been applied at all social levels, including health care operators. Hence, this reports focuses on the description of a new protocol for the safe management of cytological samples processed by liquid-based cytology (LBC) with an evaluation of the changes in terms of morphology and immunoreactivity. METHODS: From March 11 to April 25, 2020, 414 cytological cases suspicious for SARS-CoV-2 were processed with a new virus-inactivating method suggested by Hologic, Inc, for all LBC specimens. RESULTS: The samples showed an increased amount of fibrin in the background. A slight decrease in cellular size was also observed in comparison with the standard method of preparation. Nonetheless, the nuclear details of the neoplastic cells were well identified, and the immunoreactivity of the majority of those cells was maintained. The cell blocks did not show significant differences in morphology, immunoreactivity, or nucleic acid stability. CONCLUSIONS: Despite some minor changes in the morphology of the cells, the results of this study highlight that the adoption of the new protocol for the biosafety of LBC-processed samples in pathology laboratories is important for minimizing the risk for personnel, trainees, and cytopathologists without impairing the diagnostic efficacy of the technique.

Analyzing contrast in cryo-transmission electron microscopy: Comparison of electrostatic Zach phase plates and hole-free phase plates.

Phase plates (PPs) are beneficial devices to improve the phase contrast of life-science objects in cryo-transmission electron microscopy (TEM). The development of the hole-free (HF) PP, which consists of a thin carbon film, has led to impressive results due to its ease in fabrication, implementation and application. However, the phase shift of the HFPP can be controlled only indirectly. The electrostatic Zach PP uses a strongly localized and adjustable electrostatic potential to generate well-defined and variable phase shifts between scattered and unscattered electrons. However, artifacts in phase-contrast TEM images are induced by the presence of the PP rod in the diffraction plane. We present a detailed analysis and comparison of the contrast-enhancing capabilities of both PP types and their emerging artifacts. For this purpose, cryo-TEM images of a standard T4-bacteriophage test sample were acquired with both PP types. Simulated images reproduce the experimental images well and substantially contribute to the understanding of contrast formation. An electrostatic Zach PP was used in this work to acquire cryo-electron tomograms with enhanced contrast, which are of similar quality as tomograms obtained by HFPP TEM.

Hair cross-sectioning in uncombable hair syndrome: An epoxy embedding technique.

Uncombable hair syndrome is a rare disorder of the hair shaft that leads to silvery and unruly hair. The hair shaft anomaly is characterized by a longitudinal groove that is detected by scanning electronic microscopy-considered to be the gold standard for diagnosis. Recently, hair cross-sectioning has been reported as a viable alternative, but currently available methods still have some flaws, especially because of hair samples' processing specificities. Here, we present two cases of uncombable hair syndrome and a new embedding technique using epoxy to perform the diagnosis.

Is cell block technique useful to predict histological type in patients with ovarian mass and/or body cavity fluids?

The cell block (CB) technique is a generalized method utilized for the diagnostic evaluation of body cavity fluids. Ascites cytology is one of the most important diagnostic processes for epithelial ovarian cancer. However, in clinical practice, the usefulness of the CB method to diagnose this tumor remains unelucidated. Between 2008 and 2017, 15 peritoneal or pleural fluid samples obtained from patients with ovarian or peritoneal carcinoma or other gastrointestinal malignancies were preoperatively subjected to a diagnostic evaluation to predict the histological type and original organ. The CBs were made from 10% formalin neutral buffer solution fixed sediments of fluid samples after cytological smears were made by conventional method. Four-µm thickness sections were prepared from the cell blocks and stained with immunohistochemical method, using 16 kinds of antibodies and hematoxylin eosin staining method. The cellularity, architectural patterns, and morphological details were also studied. The median (range) age of patients was 73 (35-87) years. The clinical features were identified as follows: pleural effusion in 4, ovarian mass in 7, peritoneal dissemination in 12, para-aortic nodal swelling in one, and liver tumor in one (some overlapping). Five patients had a history of prior malignancy. Finally, we could accurately diagnose the histological type in 9 patients based on subsequent biopsy, surgery, and autopsy. In all 9 women, the clinical diagnosis, CB diagnosis and final pathological diagnosis were consistent. The CB technique may be a helpful modality for evaluating fluid cytology to obtain a final histopathologic diagnosis.

Fast Localization and Sectioning of Mouse Locus Coeruleus.

The locus nucleus (LC) is a multifunctional nucleus which is also the source of norepinephrine in the brain. To date, there is no simple and easy method to locate the small LC in brain sectioning. Here we report a fast, accurate, and easy-to-follow protocol for the localization of mice LC in frozen sectioning. After fixation and dehydration, the intact brains of adult mice were placed on a horizontal surface and vertically cut along the posterior margin of the bilateral cerebral cortex. In the coronal cutting plane, the aqueduct of midbrain can be seen easily with the naked eyes. After embedding the cerebellum part with optimal cutting temperature (OCT) compound, coronal brain slices were cut from the cutting plane, within 1 mm, the aqueduct of midbrain disappeared and the fourth ventricle appeared, then the brain slices contained LC and were collected. From the first collection, at ~200 µm, the noradrenergic neurons' most enriched brain slices can be collected. The tyrosine hydroxylase immunofluorescence staining confirmed that the localization of LC with this method is accurate and the noradrenergic neuron most abundant slices can be determined with this method.

Using Pancreas Tissue Slices for the Study of Islet Physiology.

Studies on islet of Langerhans physiology are crucial to understand the role of the endocrine pancreas in diabetes pathogenesis and the development of new therapeutic approaches. However, so far most research addressing islet of Langerhans biology relies on islets obtained via enzymatic isolation from the pancreas, which is known to cause mechanical and chemical stress, thus having a major impact on islet cell physiology. To circumvent the limitations of islet isolation, we have pioneered a platform for the study of islet physiology using the pancreas tissue slice technique. This approach allows to explore the detailed three-dimensional morphology of intact pancreatic tissue at a cellular level and to investigate islet cell function under near-physiological conditions. The described procedure is less damaging and faster than alternative approaches and particularly advantageous for studying infiltrated and structurally damaged islets. Furthermore, pancreas tissue slices have proven valuable for acute studies of endocrine as well as exocrine cell physiology in their conserved natural environment. We here provide a detailed protocol for the preparation of mouse pancreas tissue slices, the assessment of slice viability, and the study of pancreas cell physiology by hormone secretion and immunofluorescence staining.

Determining Beta Cell Mass, Apoptosis, Proliferation, and Individual Beta Cell Size in Pancreatic Sections.

Pancreatic beta cells have a significant remodeling capacity which plays an essential role in the maintenance of glucose homeostasis. Beta cell apoptosis, replication, size, dedifferentiation, and (neo)generation contribute to the beta cell mass regulation. However, the extent of their respective contribution varies significantly depending on the specific condition, and it is the balance among them that determines the eventual change in beta cell mass. Thus, the study of the pancreatic beta cell mass regulation requires the determination of all these factors. In this chapter, we describe the quantification of beta cell replication based on the incorporation of thymidine analogs into replicated DNA strands and on the expression of Ki67 antigen and phosphorylation of histone H3. Beta cell apoptosis is analyzed by the TUNEL technique, and beta cell mass and cross-sectional area of individual beta cells are determined by computerized image processing methods.

In the Era of the Leeds Protocol: A Systematic Review and A Meta-Analysis on the Effect of Resection Margins on Survival Among Pancreatic Ductal Adenocarcinoma Patients.

BACKGROUND AND AIMS: A positive resection margin is considered to be a factor associated with poor prognosis after pancreatic ductal adenocarcinoma resection. However, analysis of the resection margin is dependent on the pathological slicing technique. The aim of this systematic review and meta-analysis was to study the impact of resection margin on the survival of pancreatic ductal adenocarcinoma patients whose specimens were analyzed using the axial slicing technique. MATERIAL AND METHODS: A systematic search in the PubMed, Cochrane, and Embase datasets covering the time period from November 2006 to January 2019 was performed. Only studies with axial slicing technique (Leeds Pathology Protocol or Royal College of Pathology Protocol) were included in the final database. Meta-analysis between the marginal distance and survival was performed with the Inverse Variance Method in RevMan. RESULTS: The systematic search resulted in nine studies meeting the inclusion criteria. The median survival for a resection margin 0 mm ranged from 12.3 to 23.4 months, for resection margin <0.5 mm 16 months, for resection margin <1 mm ranged from 11 to 27.5 months, for resection margin <1.5 mm ranged from 16.9 to 21.2 months, and for resection margin >2 mm ranged from 53.9 to 63.1 months. Five studies were eligible for meta-analysis. The pooled multivariable hazard ratio favored resection margin ⩾1 mm (hazard ratio: 1.32 and 95% confidence interval: 1.03-1.68, p = 0.03). CONCLUSION: Resection margins ⩾1 mm seem to lead to better survival in pancreatic ductal adenocarcinoma patients than resection margin <1 mm. However, there is not enough data to evaluate the effect of oncologic therapy or to analyze the impact of other resection margin distances on survival.

Visualization and molecular characterization of whole-brain vascular networks with capillary resolution.

Structural elucidation and molecular scrutiny of cerebral vasculature is crucial for understanding the functions and diseases of the brain. Here, we introduce SeeNet, a method for near-complete three-dimensional visualization of cerebral vascular networks with high signal-to-noise ratios compatible with molecular phenotyping. SeeNet employs perfusion of a multifunctional crosslinker, vascular casting by temperature-controlled polymerization of hybrid hydrogels, and a bile salt-based tissue-clearing technique optimized for observation of vascular connectivity. SeeNet is capable of whole-brain visualization of molecularly characterized cerebral vasculatures at the single-microvessel level. Moreover, SeeNet reveals a hitherto unidentified vascular pathway bridging cerebral and hippocampal vessels, thus serving as a potential tool to evaluate the connectivity of cerebral vasculature.

Recutting Blocks of Prostate Needle Biopsies: How Much Diagnostic Yield Is Gained?

Objectives. The criteria for "active surveillance" depend in part on quantification of tumor extent and grade on prostate biopsies. It is known that false-negative biopsies may occur from incomplete sectioning of cores within the paraffin blocks. Methods. We retrospectively analyzed a prostate biopsy series, which were subjected to a second round of sections, in order to determine the rate of missed cancers. Results. Of 1324 sets of prostate biopsies, 4.5% (60) showed additional involved cores or higher grade tumor on recut sections. In 27 patients (2.0%), the changed diagnosis resulted in a potential mild increase in National Comprehensive Cancer Network (NCCN) risk, from negative to very low (12), very low to low (12), and low to favorable intermediate (3). In 3 patients (0.2%), the changed diagnosis resulted in a significant increase in NCCN risk. Comparison of the initial sets of slides to the recuts demonstrated areas of absent tissue in many of the cases in which tumor segments were missed. In 2/3 cases with the significant grade increase, gaps were present in one that should have alerted the pathologist to incomplete sections, and the tumor was fragmented at the edge of the core appearing incompletely sampled. Conclusions. A significant increase in risk was seen in this study in 0.2% of patients when blocks were recut for further sampling, with minor increases in 2%. While embedding issues only rarely resulted in clinically significant sampling error, the 3 significantly underdiagnosed cases underscore the need for pathologists to be alert to incomplete sections of prostate cores.

A comparative study of two liquid-based preparation methods: membrane-based and sedimentation in fine needle aspiration cytology diagnosis in thyroid nodules.

BACKGROUND: As thyroid fine needle aspiration (FNA) shows a certain limitation in the diagnosis of conventional smears, novel approaches like liquid-based cytology (LBC) have been gradually applied recently. Studies have shown the difference between the conventional smears (CSs) and liquid-based smears on fine needle aspiration cytology (FNAC) diagnosis, but the impacts of different liquid-based preparation (LBP) methods, including membrane-based and sedimentation, on diagnosis are still not clear. In this study, the effects of liquid-based smears prepared by different methods on the cytological interpretation were studied. METHODS: A total of 221 thyroid liquid-based FNAC cases from January 2017 to October 2018 were collected. We retrospectively studied and compared the effects of the membrane-based and sedimentation LBP methods through The Bethesda System for Reporting Thyroid Cytopathology (TBS) diagnosis and risk of malignancy assessment. Besides, we made an evaluation on the diagnostic differences in the effects of different preparation methods on the cell morphology and tissue structure of papillary thyroid carcinoma (PTC) for more accurate FNAC diagnosis. RESULTS: Among the 221 cases reviewed, membrane-based method was applied in 153 cases and sedimentation in 68 cases. According to the diagnostic criteria of 2017 TBS, TBSVI and TBSV thyroid could be cytologically diagnosed by membrane-based (49.0% (75/153) and 25.5% (39/153)) and sedimentation (52.9(36/68) and 25(17/68)) methods, and both were confirmed as PTC through histopathological diagnosis after operation, with the malignancy degree as high as 100%. In addition, of the 30 cases that were diagnosed as TBSIII thyroid nodules with the membrane-based method, 15 cases were pathologically malignant after an operation, with the malignancy degree of 50% (15/30), while that in 11 cases using the sedimentation method was 45.4% (5/11). PTC could be detected in both the TBSIV and TBSII thyroid nodules diagnosed by membrane-based method, with the sensitivity of 87.0% (114/131) lower than that by sedimentation method (91.4% (53/58)), showing the lower consistency with the histopathological result (K = 0.635 vs K = 0.757). Among the membrane-based smears, 23.5% (36/153) had fewer follicular epithelial cells, 55.6% (20/36) of which were considered to be suspicious for PTC from cell karyotype and tissue arrangement. While among the sedimentation smears, 16.2% (11/68) had fewer follicular epithelial cells, and 63.6% (7/11) was suspicious for PTC. In 72.5% (95/131) membrane-based smears of PTC, the papillary and swirling structures were not obvious, showing as crowded syncytial cell masses, while in 55.2% (32/58) sedimentation smears, both structures were visible with obvious three-dimensional papillary structure, and the fibrovascular axis still remained. CONCLUSION: LBP technique is feasible for FNAC diagnosis, and the sedimentation shows more advantages, like higher PTC detection rate and good consistency with postoperative histopathological diagnosis. A clear understanding of the subtle differences in the effects of membrane-based and sedimentation methods on the cell morphology and tissue structure could be conducive to the definitive diagnosis of PTC before operation.

Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications.

Aberrations in histone post-translational modifications (PTMs) have been implicated with the development of numerous pathologies, including cancer. Therefore, profiling histone PTMs in patient samples could provide information useful for the identification of epigenetic biomarkers, as well as for the discovery of potential novel targets. While antibody-based methods have been traditionally employed to analyze histone PTM in clinical samples, mass spectrometry (MS) can provide a more comprehensive, unbiased and quantitative view on histones and their PTMs. To combine the power of MS-based methods and the potential offered by histone PTM profiling of clinical samples, we have recently developed a series of methods for the extraction and enrichment of histones from different types of patient samples, including formalin-fixed paraffin-embedded tissues, fresh- and optimal cutting temperature-frozen tissues, and primary cells. Here, we provide a detailed description of these protocols, together with indications on the expected results and the most suitable workflow to be used downstream of each procedure.