Virtual reality-empowered deep-learning analysis of brain cells.

Automated detection of specific cells in three-dimensional datasets such as whole-brain light-sheet image stacks is challenging. Here, we present DELiVR, a virtual reality-trained deep-learning pipeline for detecting c-Fos+ cells as markers for neuronal activity in cleared mouse brains. Virtual reality annotation substantially accelerated training data generation, enabling DELiVR to outperform state-of-the-art cell-segmenting approaches. Our pipeline is available in a user-friendly Docker container that runs with a standalone Fiji plugin. DELiVR features a comprehensive toolkit for data visualization and can be customized to other cell types of interest, as we did here for microglia somata, using Fiji for dataset-specific training. We applied DELiVR to investigate cancer-related brain activity, unveiling an activation pattern that distinguishes weight-stable cancer from cancers associated with weight loss. Overall, DELiVR is a robust deep-learning tool that does not require advanced coding skills to analyze whole-brain imaging data in health and disease.

Whole-body cellular mapping in mouse using standard IgG antibodies.

Whole-body imaging techniques play a vital role in exploring the interplay of physiological systems in maintaining health and driving disease. We introduce wildDISCO, a new approach for whole-body immunolabeling, optical clearing and imaging in mice, circumventing the need for transgenic reporter animals or nanobody labeling and so overcoming existing technical limitations. We identified heptakis(2,6-di-O-methyl)-ß-cyclodextrin as a potent enhancer of cholesterol extraction and membrane permeabilization, enabling deep, homogeneous penetration of standard antibodies without aggregation. WildDISCO facilitates imaging of peripheral nervous systems, lymphatic vessels and immune cells in whole mice at cellular resolution by labeling diverse endogenous proteins. Additionally, we examined rare proliferating cells and the effects of biological perturbations, as demonstrated in germ-free mice. We applied wildDISCO to map tertiary lymphoid structures in the context of breast cancer, considering both primary tumor and metastases throughout the mouse body. An atlas of high-resolution images showcasing mouse nervous, lymphatic and vascular systems is accessible at http://discotechnologies.org/wildDISCO/atlas/index.php .

Deciphering sources of PET signals in the tumor microenvironment of glioblastoma at cellular resolution.

Various cellular sources hamper interpretation of positron emission tomography (PET) biomarkers in the tumor microenvironment (TME). We developed an approach of immunomagnetic cell sorting after in vivo radiotracer injection (scRadiotracing) with three-dimensional (3D) histology to dissect the cellular allocation of PET signals in the TME. In mice with implanted glioblastoma, translocator protein (TSPO) radiotracer uptake per tumor cell was higher compared to tumor-associated microglia/macrophages (TAMs), validated by protein levels. Translation of in vitro scRadiotracing to patients with glioma immediately after tumor resection confirmed higher single-cell TSPO tracer uptake of tumor cells compared to immune cells. Across species, cellular radiotracer uptake explained the heterogeneity of individual TSPO-PET signals. In consideration of cellular tracer uptake and cell type abundance, tumor cells were the main contributor to TSPO enrichment in glioblastoma; however, proteomics identified potential PET targets highly specific for TAMs. Combining cellular tracer uptake measures with 3D histology facilitates precise allocation of PET signals and serves to validate emerging novel TAM-specific radioligands.

Immune-mediated denervation of the pineal gland underlies sleep disturbance in cardiac disease.

Disruption of the physiologic sleep-wake cycle and low melatonin levels frequently accompany cardiac disease, yet the underlying mechanism has remained enigmatic. Immunostaining of sympathetic axons in optically cleared pineal glands from humans and mice with cardiac disease revealed their substantial denervation compared with controls. Spatial, single-cell, nuclear, and bulk RNA sequencing traced this defect back to the superior cervical ganglia (SCG), which responded to cardiac disease with accumulation of inflammatory macrophages, fibrosis, and the selective loss of pineal gland-innervating neurons. Depletion of macrophages in the SCG prevented disease-associated denervation of the pineal gland and restored physiological melatonin secretion. Our data identify the mechanism by which diurnal rhythmicity in cardiac disease is disturbed and suggest a target for therapeutic intervention.

Whole-mouse clearing and imaging at the cellular level with vDISCO.

Homeostatic and pathological phenomena often affect multiple organs across the whole organism. Tissue clearing methods, together with recent advances in microscopy, have made holistic examinations of biological samples feasible. Here, we report the detailed protocol for nanobody(VHH)-boosted 3D imaging of solvent-cleared organs (vDISCO), a pressure-driven, nanobody-based whole-body immunolabeling and clearing method that renders whole mice transparent in 3 weeks, consistently enhancing the signal of fluorescent proteins, stabilizing them for years. This allows the reliable detection and quantification of fluorescent signal in intact rodents enabling the analysis of an entire body at cellular resolution. Here, we show the high versatility of vDISCO applied to boost the fluorescence signal of genetically expressed reporters and clear multiple dissected organs and tissues, as well as how to image processed samples using multiple fluorescence microscopy systems. The entire protocol is accessible to laboratories with limited expertise in tissue clearing. In addition to its applications in obtaining a whole-mouse neuronal projection map, detecting single-cell metastases in whole mice and identifying previously undescribed anatomical structures, we further show the visualization of the entire mouse lymphatic system, the application for virus tracing and the visualization of all pericytes in the brain. Taken together, our vDISCO pipeline allows systematic and comprehensive studies of cellular phenomena and connectivity in whole bodies.

Deep learning-enabled multi-organ segmentation in whole-body mouse scans.

Whole-body imaging of mice is a key source of information for research. Organ segmentation is a prerequisite for quantitative analysis but is a tedious and error-prone task if done manually. Here, we present a deep learning solution called AIMOS that automatically segments major organs (brain, lungs, heart, liver, kidneys, spleen, bladder, stomach, intestine) and the skeleton in less than a second, orders of magnitude faster than prior algorithms. AIMOS matches or exceeds the segmentation quality of state-of-the-art approaches and of human experts. We exemplify direct applicability for biomedical research for localizing cancer metastases. Furthermore, we show that expert annotations are subject to human error and bias. As a consequence, we show that at least two independently created annotations are needed to assess model performance. Importantly, AIMOS addresses the issue of human bias by identifying the regions where humans are most likely to disagree, and thereby localizes and quantifies this uncertainty for improved downstream analysis. In summary, AIMOS is a powerful open-source tool to increase scalability, reduce bias, and foster reproducibility in many areas of biomedical research.

A novel fluorescent probe based on isocoumarin for Hg2+ and Fe3+ ions and its application in live-cell imaging.

Synthesis of the 2-amino-4-phenyl-6- (isocoumarin-3-yl) -3-cyanopyridine (APICP) containing both isocoumarin and pyridine ring in its structure was carried out, and this compound was characterized by ATR-FTIR, 1H NMR, and 13C NMR spectral techniques. A fluorescence sensor determining Hg2+ and Fe3+ ions in DMSO/HEPES buffer solution (9/1 v/v, 5 µM, pH 7.0) was developed using the synthesized compound, and the detection limits of the sensor with exquisite selectivity were calculated as 8.12 nM and 5.51 nM for Hg2+ and Fe3+ ions, respectively. Jobs plot method was used to determine the stoichiometry of APICP-Hg2+/Fe3+ complexes as 2:1 and FT-IR and ESI-MS methods confirmed the results. Besides, cell growth inhibitory potentials of the sensor over HepG2 cells and in vivo fluorescent cell imaging experiments were conducted. Findings revealed the relatively low cytotoxic effects of the synthesized sensor (IC50: 0.541 ±â€¯0.039 mM), and it could be utilized as an intracellular imaging agent for the determination of Fe3+ and Hg2+ ions in biological systems.

Deep Learning Reveals Cancer Metastasis and Therapeutic Antibody Targeting in the Entire Body.

Reliable detection of disseminated tumor cells and of the biodistribution of tumor-targeting therapeutic antibodies within the entire body has long been needed to better understand and treat cancer metastasis. Here, we developed an integrated pipeline for automated quantification of cancer metastases and therapeutic antibody targeting, named DeepMACT. First, we enhanced the fluorescent signal of cancer cells more than 100-fold by applying the vDISCO method to image metastasis in transparent mice. Second, we developed deep learning algorithms for automated quantification of metastases with an accuracy matching human expert manual annotation. Deep learning-based quantification in 5 different metastatic cancer models including breast, lung, and pancreatic cancer with distinct organotropisms allowed us to systematically analyze features such as size, shape, spatial distribution, and the degree to which metastases are targeted by a therapeutic monoclonal antibody in entire mice. DeepMACT can thus considerably improve the discovery of effective antibody-based therapeutics at the pre-clinical stage. VIDEO ABSTRACT.

An inhibitory antibody targeting carbonic anhydrase XII abrogates chemoresistance and significantly reduces lung metastases in an orthotopic breast cancer model in vivo.

Carbonic anhydrase XII (CAXII) is a membrane-tethered ectoenzyme involved in intracellular pH regulation and overexpressed across various types of human cancer. Because CAXII inhibition shows antitumor activity in vitro, it is thought that the enzyme is mandatory for maximum tumor growth, above all under hypoxic conditions. Recently, it has been shown that CAXII is co-expressed along with the P-glycoprotein (P-GP) on many tumor cells and that both proteins physically interact. Of interest, blocking CAXII activity also decreases P-GP activity in cancer cells both in vitro and in vivo. Previously, we have reported on the development of a monoclonal antibody, termed 6A10, which specifically and efficiently blocks human CAXII activity. Here, we demonstrate that 6A10 also indirectly reduces P-GP activity in CAXII/P-GP double-positive chemoresistant cancer cells, resulting in enhanced chemosensitivity as revealed by enhanced accumulation of anthracyclines and increased cell death in vitro. Even more important, we show that mice carrying human triple-negative breast cancer xenografts co-treated with doxorubicin (DOX) and 6A10 show a significantly reduced number of metastases. Collectively, our data provide evidence that the inhibition of CAXII with 6A10 is an attractive way to reduce chemoresistance of cancer cells and to interfere with the metastatic process in a clinical setting.

Posterior laminoforaminotomy in the treatment of lateralcervical herniated disc and foraminal stenosis.

BACKGROUND/AIM: Posterior cervical laminoforaminotomy is an effective surgical treatment in selected cases of cervical radiculopathy caused by posterolateral herniated discs or foraminal stenosis. The aim of the present study was to evaluate the surgical techniques, rates of complications, long-term outcomes, advantages, and disadvantages of keyhole foraminotomy retrospectively. MATERIALS AND METHODS: Keyhole foraminotomy was performed in 83 patients. In 51 patients (61.5%) soft disc herniation was removed, and in 32 of them (38.5%) osteophytes were evident. The clinical data were evaluated according to Odom's criteria, and the mean follow-up time was 6 months. RESULTS: Postoperative results were classed as excellent in 66 patients (79.5%), good in 13 patients (15.7%), fair in 3 patients (3.6%), and poor in only 1 patient (1.2%). Radiculopathy symptoms regressed in 79 patients (95%). Among the 83 patients, surgical complications (dural injury and level error) were noted in 2 patients (2.4%). CONCLUSION: Posterior laminoforaminotomy is applied to selected patients with a low complication rate. The advantages of this surgery are suitable visualization of the nerve root, preserved motion of the operated segment, avoidance of cervical instability, and a decrease in the length of hospital stay.

Surgical management of Juxtafacet cysts in the lumbar spine.

INTRODUCTION: Juxtafacet cysts of the lumbar spine are extradural degenerative lesions associated with symptoms of lower back pain and radiculopathy. The aim of this study is to evaluate the efficacy of surgery and address controversial issues in the treatment of symptomatic juxta facet cysts in the Neurosurgical Department of our hospital and review of the literature. METHODS: Data from seven patients (age range 58-68 years, mean age 63 years) with low back and radicular leg pain due to a lumbar facet joint cyst were retrospectively analyzed. Demographic data, cyst level, presence of concominant local pathology, treatment and results of treatment were recorded. After surgery there was no case of a recurrent cyst during the follow-up period. The mean follow-up period of patients at the time of this study was 4 years. RESULTS: All patients had back pain, while five also experienced unilateral radicular leg pain and two had bilateral leg pain. Four patients had neurogenic claudication. MRI identified the cyst and highlighted underlying pathology in all cases. All patients underwent surgical cyst excision. Post-operatively, all patients showed a total resolution of symptoms with sustained benefit at final evaluation. CONCLUSION: Surgery is a safe and effective treatment for lumbar juxtafacet cysts.

Local pruning of dendrites and spines by caspase-3-dependent and proteasome-limited mechanisms.

Synapse loss occurs normally during development and pathologically during neurodegenerative disease. Long-term depression, a proposed physiological correlate of synapse elimination, requires caspase-3 and the mitochondrial pathway of apoptosis. Here, we show that caspase-3 activity is essential--and can act locally within neurons--for regulation of spine density and dendrite morphology. By photostimulation of Mito-KillerRed, we induced caspase-3 activity in defined dendritic regions of cultured neurons. Within the photostimulated region, local elimination of dendritic spines and dendrite retraction occurred in a caspase-3-dependent manner without inducing cell death. However, pharmacological inhibition of inhibitor of apoptosis proteins or proteasome function led to neuronal death, suggesting that caspase activation is spatially restricted by these "molecular brakes" on apoptosis. Caspase-3 knock-out mice have increased spine density and altered miniature EPSCs, confirming a physiological involvement of caspase-3 in the regulation of spines in vivo.

High-resolution imaging of entire organs by 3-dimensional imaging of solvent cleared organs (3DISCO).

One goal in neuroscience is to dissect neuronal connections within the nervous system in health and disease. To accomplish this, neurons and their extensions need to be imaged and followed in the entire brain and spinal cord. While non-invasive imaging methods such as MRI do not have sufficient resolution to trace individual cells, standard histology - serial tissue sectioning and tracing in consecutive sections - is time consuming and prone to mistakes. Here, we review an alternative method called "3D imaging of solvent cleared organs" or "3DISCO" that can achieve high-resolution imaging of neuronal connections in several millimeters of depth without tissue sectioning. 3DISCO is fast: imaging of an entire organ at a cellular resolution can be completed within a few hours. 3DISCO is versatile: it is applicable to various tissues including the spinal cord, brain, lung, mammary glands, immune organs and tumors; it can be executed using various microscopy techniques, including light-sheet, widefield epifluorescence, confocal, 2-photon, light microscopy and optical coherent tomography. Here, we review the application of 3DISCO along with other popular clearing and imaging methods, their limitations and the obstacles that remain.

Three-dimensional imaging of solvent-cleared organs using 3DISCO.

The examination of tissue histology by light microscopy is a fundamental tool for investigating the structure and function of organs under normal and disease states. Many current techniques for tissue sectioning, imaging and analysis are time-consuming, and they present major limitations for 3D tissue reconstruction. The introduction of methods to achieve the optical clearing and subsequent light-sheet laser scanning of entire transparent organs without sectioning represents a major advance in the field. We recently developed a highly reproducible and versatile clearing procedure called 3D imaging of solvent-cleared organs, or 3DISCO, which is applicable to diverse tissues including brain, spinal cord, immune organs and tumors. Here we describe a detailed protocol for performing 3DISCO and present its application to various microscopy techniques, including example results from various mouse tissues. The tissue clearing takes as little as 3 h, and imaging can be completed in ∼45 min. 3DISCO is a powerful technique that offers 3D histological views of tissues in a fraction of the time and labor required to complete standard histology studies.

Urinary incontinence triggered by stretching exercises.

A 47-year-old female patient who experienced urinary urgency after having stretching exercises of her legs is presented. Stretching of the legs are thought to be responsible for conus medullaris tethering which in turn causes urinary complaints. What is interesting in this case is that her complaints about urinary urgency stopped as she quit stretching exercise movements of her legs. There are some examples of such cases in the literature. The urinary urgency after stretching exercises warned us to investigate this patient in regard to tethered conus medullaris. Tethering of the conus medullaris can be temporary and can cause reversible functional disorders of the bladder. Incontinence at any age should be evaluated cautiously as it could be a sign of an underlying important developmental failure.

Biomarkers of connective tissue disease in patients with intracranial aneurysms.

Connective tissue defects may play a significant role in the development of intracranial aneurysms (IAs). Multiorgan connective tissue disorders may, therefore, indicate a risk of IA development. We investigated biomarkers of connective tissue disease in patients with IAs. A series of 62 patients with IAs was studied by physical examination, echocardiography, ultrasound examination of the kidneys and abdomen, and microscopic examination of skin tissue (temporal area) and superficial temporal artery taken at operation. Patients with IAs had a higher incidence of biomarkers of systemic connective tissue disease than controls and identification of these markers may be important for screening for IAs. Microscopic investigation of biopsies of the skin and superficial temporal artery from patients and their relatives may become valuable for clinical diagnosis, identification of people at risk and basic studies of the pathogenesis of this vascular disease.

A chemical screen identifies novel compounds that overcome glial-mediated inhibition of neuronal regeneration.

A major barrier to regeneration of CNS axons is the presence of growth-inhibitory proteins associated with myelin and the glial scar. To identify chemical compounds with the ability to overcome the inhibition of regeneration, we screened a novel triazine library, based on the ability of compounds to increase neurite outgrowth from cerebellar neurons on inhibitory myelin substrates. The screen produced four "hit compounds," which act with nanomolar potency on several different neuronal types and on several distinct substrates relevant to glial inhibition. Moreover, the compounds selectively overcome inhibition rather than promote growth in general. The compounds do not affect neuronal cAMP levels, PKC activity, or EGFR (epidermal growth factor receptor) activation. Interestingly, one of the compounds alters microtubule dynamics and increases microtubule density in both fibroblasts and neurons. This same compound promotes regeneration of dorsal column axons after acute lesions and potentiates regeneration of optic nerve axons after nerve crush in vivo. These compounds should provide insight into the mechanisms through which glial-derived inhibitors of regeneration act, and could lead to the development of novel therapies for CNS injury.

Magnetic resonance spectroscopic imaging associated with analysis of fluid in cystic brain tumors.

OBJECTIVE: There is a growing interest in cystic lesions of the brain. Examining the cyst content of brain tumors may contribute in determining the malignancy of the given tumor accompanied by a cyst. METHODS: In this work, samples of cyst fluid from 18 patients with brain tumor were collected and studied biochemically regarding their protein, lactate contents and pH values; magnetic resonance spectroscopic images of these patients were also compared. We investigated the relation between the grade of malignancy and the lactate concentration and the discrepancy between the high levels of lactate in cysts and their alkaline environment. RESULTS: There appears to be a positive relation between the grade of malignancy and the concentration of lactate in the cysts' fluid. A significant two-fold increase in lactate concentration in malignant tumors cysts has been found as compared with the more benign tumor cysts (p<0.001). This increase in lactate level is probably because of aerobic glycolysis, which causes lactate production by the tumor. DISCUSSION: High lactate levels found through magnetic resonance spectroscopy are positively related to the grade of tumor malignancy. The pH values in the cyst fluids were above normal, resulting to a discrepancy in high levels of lactate in the cyst and the alkaline environment. This suggests efflux of H+ ions by a Na/H exchange mechanism to compensate for the change of pH.