Potential Therapeutic Effects of Long-Term Stem Cell Administration: Impact on the Gene Profile and Kidney Function of PKD/Mhm (Cy/+) Rats.

Cystic kidney disease (CKD) is a heterogeneous group of genetic disorders and one of the most common causes of end-stage renal disease. Here, we investigate the potential effects of long-term human stem cell treatment on kidney function and the gene expression profile of PKD/Mhm (Cy/+) rats. Human adipose-derived stromal cells (ASC) and human skin-derived ABCB5+ stromal cells (2 × 106) were infused intravenously or intraperitoneally monthly, over 6 months. Additionally, ASC and ABCB5+-derived conditioned media were administrated intraperitoneally. The gene expression profile results showed a significant reprogramming of metabolism-related pathways along with downregulation of the cAMP, NF-kB and apoptosis pathways. During the experimental period, we measured the principal renal parameters as well as renal function using an innovative non-invasive transcutaneous device. All together, these analyses show a moderate amelioration of renal function in the ABCB5+ and ASC-treated groups. Additionally, ABCB5+ and ASC-derived conditioned media treatments lead to milder but still promising improvements. Even though further analyses have to be performed, the preliminary results obtained in this study can lay the foundations for a novel therapeutic approach with the application of cell-based therapy in CKD.

A simple optical tissue clearing pipeline for 3D vasculature imaging of the mediastinal organs in mice.

Optical tissue clearing (OTC) methods render tissue transparent by matching the refractive index within a sample to enable three-dimensional (3D) imaging with advanced microscopes. The application of OTC method in mediastinal organs in mice remains poorly understand. Our aim was to establish a simple protocol pipeline for 3D imaging of the mediastinal organs in mice. Trachea, oesophagus, thymus and heart were harvested from mice after retrograde perfusion via the abdominal aorta. We combined and optimized antibody labelling of thick tissue samples, OTC with cheap and non-toxic solvent ethyl cinnamate (ECi), and light-sheet fluorescence microscopy (LSFM) or laser confocal fluorescence microscopy (LCFM) to visualize the vasculature of those tissues. A high degree of optical transparency of trachea, oesophagus, thymus and heart was achieved after ECi-based OTC. With anti-CD31 antibody immunofluorescence labelling before ECi-based OTC, the vasculature of these tissues with their natural morphology, location and organizational network was imaged using LSFM or LCFM. This simple protocol pipeline provides an easy-to-setup and comprehensive way to study the vasculature of mediastinal organs in 3D without any special equipment. We anticipate that it will facilitate diverse applications in biomedical research of thoracic diseases and even other organs.

Application of ethyl cinnamate based optical tissue clearing and expansion microscopy combined with retrograde perfusion for 3D lung imaging.

PURPOSE: 3 D imaging of the lung is not a trivial undertaking as during preparation the lung may collapse. Also serial sections and scans followed by 3 D reconstruction may lead to artifacts. The present study aims to figure out the best way to perform 3 D imaging in lung research. MATERIALS AND METHODS: We applied an optical tissue clearing (OTC) method, which uses ethyl cinnamate (ECi) as a fast, nontoxic and cheap clearing solvent, for 3 D imaging of retrograde perfused lungs by laser confocal fluorescence microscopy and light sheet fluorescence microscopy. We also introduced expansion microscopy (ExM), a cutting-edge technique, in 3 D imaging of lungs. We examined and compared the usefulness of these techniques for 3 D lung imaging. The ExM protocol was further extended to paraffin-embedded lung metastases blocks. RESULTS: The MHI148-PEI labeled lung vasculature was visualized by retrograde perfusion combined with trachea ligation and ECi based OTC. As compared with trans-cardiac perfusion, the retrograde perfusion results in a better maintenance of lung morphology. 3 D structure of alveoli, vascular branches and cilia in lung were revealed by immunofluorescence staining after ExM. 3 D distribution of microvasculature and neutrophil cells in 10 years old paraffin-embedded lung metastases were analyzed by ExM. CONCLUSIONS: The retrograde perfusion combined with trachea ligation technique could be applied in the lung research in mice. 3 D structure of lung vasculature can be visualized by MHI148-PEI perfusion and ECi based OTC in an efficient way. ExM and immunofluorescence staining protocol is highly recommended to perform 3 D imaging of fresh fixed lung as well as paraffin-embedded lung blocks.

New technical approaches for 3D morphological imaging and quantification of measurements.

3D imaging is becoming more and more popular, as it allows us to identify interactions between structures in organs. Furthermore, it gives the possibility to quantify and size these structures. To allow 3D imaging, the tissue sample has to be transparent. This is usually achieved by using optical tissue clearing protocols. Although using optical tissue clearing often results in perfect 3D images, these protocols have some pitfalls, like long duration of sample preparation (up to several weeks), use of toxic substances, damage to antibody staining, fluorescent proteins or dyes, high refractive indices, and high costs of sample processing.Recently we described [Huang et al., Scientific Reports 9(1): 521 (2019)] a fast, safe, and inexpensive ethyl cinnamate (ECi) based optical tissue clearing protocol. Here, we present extensions of our protocol with respect to the deparaffinization of old paraffin-embedded samples allowing 3D imaging of the blocks. In addition, we learned to remove ECi from the samples allowing the use of routine immunolabeling protocols. Furthermore, we demonstrate new pictures of lungs after expansion microscopy and adaptation of already existing protocols. The aim of our work is, in summary, to describe the advances in these methodologies, focusing on the morphological imaging of kidneys and lungs.

Bioreactor for mobilization of mesenchymal stem/stromal cells into scaffolds under mechanical stimulation: Preliminary results.

INTRODUCTION: Articular cartilage (AC) is a viscoelastic tissue with a limited regenerative capability because of the lack of vasculature. Mechanical stimulation contributes to the homeostasis of functional AC since it promotes the delivery of nutrients, cytokines and growth factors between the distant chondrocytes. We hypothesized that biomechanical stimulation might enhance mobilization of endogenous mesenchymal stem/stromal cells (MSCs) from neighboring niches as the bone marrow. AIM: This study aimed to introduce a bioreactor for inducing mobilization of MSCs from one compartment to another above by mechanical stimulation in vitro. METHODS: A novel mechanical system for evaluating mobilization of cells in a 3D context in vitro is presented. The system consists of a compression bioreactor able to induce loading on hydrogel-based scaffolds, custom-made software for settings management and data recording, and image based biological evaluation. Intermittent load was applied under a periodic regime with frequency of 0.3 Hz and unload phases of 10 seconds each 180 cycles over 24 hours. The mechanical stimulation acted on an alginate scaffold and a cell reservoir containing MSCs below it. The dynamic compression exerted amplitude of 200 µm as 10% strain regarding the original height of the scaffold. RESULTS: The bioreactor was able to stimulate the scaffolds and the cells for 24.4 (±1.7) hours, exerting compression with vertical displacements of 185.8 (±17.8) µm and a force-amplitude of 1.87 (±1.37; min 0.31, max 4.42) N. Our results suggest that continuous mechanical stimulation hampered the viability of the cells located at the cell reservoir when comparing to intermittent mechanical stimulation (34.4 ± 2.0% vs. 66.8 ± 5.9%, respectively). Functionalizing alginate scaffolds with laminin-521 (LN521) seemed to enhance the mobilization of cells from 48 (±21) to 194 (±39) cells/mm3 after applying intermittent mechanical loading. CONCLUSION: The bioreactor presented here was able to provide mechanical stimulation that seemed to induce the mobilization of MSCs into LN521-alginate scaffolds under an intermittent loading regime.

Transcutaneous Measurement of Glomerular Filtration Rate in Rodents.

Glomerular filtration rate (GFR) is considered the gold standard to test kidney function. However, the serial blood and/or urine sample collection required for the calculation of the GFR is stressful for the animal and time consuming for the experimenter. Here, we describe a transcutaneous assessment of renal function in conscious animals that does not require plasma or urine sampling and/or deep anesthesia. For the measurement, we use a near-infrared (NIR) device that records the excretion kinetic of the renal marker ABZWCY-HPßCD. ABZWCY-HPßCD is a new hydrophilic, stable, and nontoxic NIR fluorescent agent that can be used as a renal marker as it is filtrated and completely excreted through the kidneys into the urine without reabsorption or secretion and without accumulation in the skin. The data recorded in the device are then analyzed with "GFRmeasure," an open-source, freely downloadable, and user-friendly software.

A cationic near infrared fluorescent agent and ethyl-cinnamate tissue clearing protocol for vascular staining and imaging.

Understanding vascular structures and dysfunction is a fundamental challenge. This task has been approached by using traditional methodologies such as microscopic computed tomography and magnetic resonance imaging. Both techniques are not only expensive but also time-consuming. Here, we present a new method for visualizing vascular structures in different organs in an efficient manner. A cationic near infrared (NIR) fluorescent dye was developed with attractive features to specifically stain blood vessels. Furthermore, we refined the process of organ staining and harvesting by retrograde perfusion and optimized the subsequent dehydration and clearing process by the use of an automatic tissue processor and a non-toxic substance, ethyl-cinnamate. Using this approach, the time interval between organ harvesting and microscopic analysis can be reduced from day(s) or weeks to 4 hours. Finally, we have demonstrated that the new NIR fluorescent agent in combination with confocal or light-sheet microscopy can be efficiently used for visualization of vascular structures, such as the blood vessels in different organs e.g. glomeruli in kidneys, with an extremely high resolution. Our approach facilitates the development of automatic image processing and the quantitative analysis to study vascular and kidney diseases.

AutoCellSeg: robust automatic colony forming unit (CFU)/cell analysis using adaptive image segmentation and easy-to-use post-editing techniques.

In biological assays, automated cell/colony segmentation and counting is imperative owing to huge image sets. Problems occurring due to drifting image acquisition conditions, background noise and high variation in colony features in experiments demand a user-friendly, adaptive and robust image processing/analysis method. We present AutoCellSeg (based on MATLAB) that implements a supervised automatic and robust image segmentation method. AutoCellSeg utilizes multi-thresholding aided by a feedback-based watershed algorithm taking segmentation plausibility criteria into account. It is usable in different operation modes and intuitively enables the user to select object features interactively for supervised image segmentation method. It allows the user to correct results with a graphical interface. This publicly available tool outperforms tools like OpenCFU and CellProfiler in terms of accuracy and provides many additional useful features for end-users.

A New Feedback-Based Method for Parameter Adaptation in Image Processing Routines.

The parametrization of automatic image processing routines is time-consuming if a lot of image processing parameters are involved. An expert can tune parameters sequentially to get desired results. This may not be productive for applications with difficult image analysis tasks, e.g. when high noise and shading levels in an image are present or images vary in their characteristics due to different acquisition conditions. Parameters are required to be tuned simultaneously. We propose a framework to improve standard image segmentation methods by using feedback-based automatic parameter adaptation. Moreover, we compare algorithms by implementing them in a feedforward fashion and then adapting their parameters. This comparison is proposed to be evaluated by a benchmark data set that contains challenging image distortions in an increasing fashion. This promptly enables us to compare different standard image segmentation algorithms in a feedback vs. feedforward implementation by evaluating their segmentation quality and robustness. We also propose an efficient way of performing automatic image analysis when only abstract ground truth is present. Such a framework evaluates robustness of different image processing pipelines using a graded data set. This is useful for both end-users and experts.

A Benchmark Data Set to Evaluate the Illumination Robustness of Image Processing Algorithms for Object Segmentation and Classification.

Developers of image processing routines rely on benchmark data sets to give qualitative comparisons of new image analysis algorithms and pipelines. Such data sets need to include artifacts in order to occlude and distort the required information to be extracted from an image. Robustness, the quality of an algorithm related to the amount of distortion is often important. However, using available benchmark data sets an evaluation of illumination robustness is difficult or even not possible due to missing ground truth data about object margins and classes and missing information about the distortion. We present a new framework for robustness evaluation. The key aspect is an image benchmark containing 9 object classes and the required ground truth for segmentation and classification. Varying levels of shading and background noise are integrated to distort the data set. To quantify the illumination robustness, we provide measures for image quality, segmentation and classification success and robustness. We set a high value on giving users easy access to the new benchmark, therefore, all routines are provided within a software package, but can as well easily be replaced to emphasize other aspects.