tRigon: an R package and Shiny App for integrative (path-)omics data analysis.

BACKGROUND: Pathomics facilitates automated, reproducible and precise histopathology analysis and morphological phenotyping. Similar to molecular omics, pathomics datasets are high-dimensional, but also face large outlier variability and inherent data missingness, making quick and comprehensible data analysis challenging. To facilitate pathomics data analysis and interpretation as well as support a broad implementation we developed tRigon (Toolbox foR InteGrative (path-)Omics data aNalysis), a Shiny application for fast, comprehensive and reproducible pathomics analysis. RESULTS: tRigon is available via the CRAN repository ( https://cran.r-project.org/web/packages/tRigon ) with its source code available on GitLab ( https://git-ce.rwth-aachen.de/labooratory-ai/trigon ). The tRigon package can be installed locally and its application can be executed from the R console via the command 'tRigon::run_tRigon()'. Alternatively, the application is hosted online and can be accessed at https://labooratory.shinyapps.io/tRigon . We show fast computation of small, medium and large datasets in a low- and high-performance hardware setting, indicating broad applicability of tRigon. CONCLUSIONS: tRigon allows researchers without coding abilities to perform exploratory feature analyses of pathomics and non-pathomics datasets on their own using a variety of hardware.

[Advances in computational quantitative nephropathology]. / Fortschritte in der computergestützten quantitativen Nephropathologie.

BACKGROUND: Semiquantitative histological scoring systems are frequently used in nephropathology. In computational nephropathology, the focus is on generating quantitative data from histology (so-called pathomics). Several recent studies have collected such data using next-generation morphometry (NGM) based on segmentations by artificial neural networks and investigated their usability for various clinical or diagnostic purposes. AIM: To present an overview of the current state of studies regarding renal pathomics and to identify current challenges and potential solutions. MATERIALS AND METHODS: Due to the literature restriction (maximum of 30 references), studies were selected based on a database search that processed as much data as possible, used innovative methodologies, and/or were ideally multicentric in design. RESULTS AND DISCUSSION: Pathomics studies in the kidney have impressively demonstrated that morphometric data are useful clinically (for example, for prognosis assessment) and translationally. Further development of NGM requires overcoming some challenges, including better standardization and generation of prospective evidence.

Mapping cardiac remodeling in chronic kidney disease.

Patients with advanced chronic kidney disease (CKD) mostly die from sudden cardiac death and recurrent heart failure. The mechanisms of cardiac remodeling are largely unclear. To dissect molecular and cellular mechanisms of cardiac remodeling in CKD in an unbiased fashion, we performed left ventricular single-nuclear RNA sequencing in two mouse models of CKD. Our data showed a hypertrophic response trajectory of cardiomyocytes with stress signaling and metabolic changes driven by soluble uremia-related factors. We mapped fibroblast to myofibroblast differentiation in this process and identified notable changes in the cardiac vasculature, suggesting inflammation and dysfunction. An integrated analysis of cardiac cellular responses to uremic toxins pointed toward endothelin-1 and methylglyoxal being involved in capillary dysfunction and TNFα driving cardiomyocyte hypertrophy in CKD, which was validated in vitro and in vivo. TNFα inhibition in vivo ameliorated the cardiac phenotype in CKD. Thus, interventional approaches directed against uremic toxins, such as TNFα, hold promise to ameliorate cardiac remodeling in CKD.

Semiautomated pipeline for quantitative analysis of heart histopathology.

BACKGROUND: Heart diseases are among the leading causes of death worldwide, many of which lead to pathological cardiomyocyte hypertrophy and capillary rarefaction in both patients and animal models, the quantification of which is both technically challenging and highly time-consuming. Here we developed a semiautomated pipeline for quantification of the size of cardiomyocytes and capillary density in cardiac histology, termed HeartJ, by generating macros in ImageJ, a broadly used, open-source, Java-based software. METHODS: We have used modified Gomori silver staining, which is easy to perform and digitize in high throughput, or Fluorescein-labeled lectin staining. The latter can be easily combined with other stainings, allowing additional quantitative analysis on the same section, e.g., the size of cardiomyocyte nuclei, capillary density, or single-cardiomyocyte protein expression. We validated the pipeline in a mouse model of cardiac hypertrophy induced by transverse aortic constriction, and in autopsy samples of patients with and without aortic stenosis. RESULTS: In both animals and humans, HeartJ-based histology quantification revealed significant hypertrophy of cardiomyocytes reflecting other parameters of hypertrophy and rarefaction of microvasculature and enabling the analysis of protein expression in individual cardiomyocytes. The analysis also revealed that murine and human cardiomyocytes had similar diameters in health and extent of hypertrophy in disease confirming the translatability of our murine cardiac hypertrophy model. HeartJ enables a rapid analysis that would not be feasible by manual methods. The pipeline has little hardware requirements and is freely available. CONCLUSIONS: In summary, our analysis pipeline can facilitate effective and objective quantitative histological analyses in preclinical and clinical heart samples.

Deep Learning-Based Segmentation and Quantification in Experimental Kidney Histopathology.

BACKGROUND: Nephropathologic analyses provide important outcomes-related data in experiments with the animal models that are essential for understanding kidney disease pathophysiology. Precision medicine increases the demand for quantitative, unbiased, reproducible, and efficient histopathologic analyses, which will require novel high-throughput tools. A deep learning technique, the convolutional neural network, is increasingly applied in pathology because of its high performance in tasks like histology segmentation. METHODS: We investigated use of a convolutional neural network architecture for accurate segmentation of periodic acid-Schiff-stained kidney tissue from healthy mice and five murine disease models and from other species used in preclinical research. We trained the convolutional neural network to segment six major renal structures: glomerular tuft, glomerulus including Bowman's capsule, tubules, arteries, arterial lumina, and veins. To achieve high accuracy, we performed a large number of expert-based annotations, 72,722 in total. RESULTS: Multiclass segmentation performance was very high in all disease models. The convolutional neural network allowed high-throughput and large-scale, quantitative and comparative analyses of various models. In disease models, computational feature extraction revealed interstitial expansion, tubular dilation and atrophy, and glomerular size variability. Validation showed a high correlation of findings with current standard morphometric analysis. The convolutional neural network also showed high performance in other species used in research-including rats, pigs, bears, and marmosets-as well as in humans, providing a translational bridge between preclinical and clinical studies. CONCLUSIONS: We developed a deep learning algorithm for accurate multiclass segmentation of digital whole-slide images of periodic acid-Schiff-stained kidneys from various species and renal disease models. This enables reproducible quantitative histopathologic analyses in preclinical models that also might be applicable to clinical studies.

Empagliflozin improves left ventricular diastolic function of db/db mice.

OBJECTIVES: Investigation of the effect of SGLT2 inhibition by empagliflozin on left ventricular function in a model of diabetic cardiomyopathy. BACKGROUND: SGLT2 inhibition is a new strategy to treat diabetes. In the EMPA-REG Outcome trial empagliflozin treatment reduced cardiovascular and overall mortality in patients with diabetes presumably due to beneficial cardiac effects, leading to reduced heart failure hospitalization. The relevant mechanisms remain currently elusive but might be mediated by a shift in cardiac substrate utilization leading to improved energetic supply to the heart. METHODS: We used db/db mice on high-fat western diet with or without empagliflozin treatment as a model of severe diabetes. Left ventricular function was assessed by pressure catheter with or without dobutamine stress. RESULTS: Treatment with empagliflozin significantly increased glycosuria, improved glucose metabolism, ameliorated left ventricular diastolic function and reduced mortality of mice. This was associated with reduced cardiac glucose concentrations and decreased calcium/calmodulin-dependent protein kinase (CaMKII) activation with subsequent less phosphorylation of the ryanodine receptor (RyR). No change of cardiac ketone bodies or branched-chain amino acid (BCAA) metabolites in serum was detected nor was cardiac expression of relevant catabolic enzymes for these substrates affected. CONCLUSIONS: In a murine model of severe diabetes empagliflozin-dependent SGLT2 inhibition improved diastolic function and reduced mortality. Improvement of diastolic function was likely mediated by reduced spontaneous diastolic sarcoplasmic reticulum (SR) calcium release but independent of changes in cardiac ketone and BCAA metabolism.

Structural differences of amyloid-ß fibrils revealed by antibodies from phage display.

BACKGROUND: Beside neurofibrillary tangles, amyloid plaques are the major histological hallmarks of Alzheimer's disease (AD) being composed of aggregated fibrils of ß-amyloid (Aß). During the underlying fibrillogenic pathway, starting from a surplus of soluble Aß and leading to mature fibrils, multiple conformations of this peptide appear, including oligomers of various shapes and sizes. To further investigate the fibrillization of ß-amyloid and to have tools at hand to monitor the distribution of aggregates in the brain or even act as disease modulators, it is essential to develop highly sensitive antibodies that can discriminate between diverse aggregates of Aß. RESULTS: Here we report the generation and characterization of a variety of amyloid-ß specific human and human-like antibodies. Distinct fractions of monomers and oligomers of various sizes were separated by size exclusion chromatography (SEC) from Aß42 peptides. These antigens were used for the generation of two Aß42 specific immune scFv phage display libraries from macaque (Macaca fascicularis). Screening of these libraries as well as two naïve human phage display libraries resulted in multiple unique binders specific for amyloid-ß. Three of the obtained antibodies target the N-terminal part of Aß42 although with varying epitopes, while another scFv binds to the α-helical central region of the peptide. The affinities of the antibodies to various Aß42 aggregates as well as their ability to interfere with fibril formation and disaggregation of preformed fibrils were determined. Most significantly, one of the scFv is fibril-specific and can discriminate between two different fibril forms resulting from variations in the acidity of the milieu during fibrillogenesis. CONCLUSION: We demonstrated that the approach of animal immunization and subsequent phage display based antibody selection is applicable to generate highly specific anti ß-amyloid scFvs that are capable of accurately discriminating between minute conformational differences.

Retinopathy of prematurity and brain damage in the very preterm newborn.

PURPOSE: To explain why very preterm newborns who develop retinopathy of prematurity (ROP) appear to be at increased risk of abnormalities of both brain structure and function. METHODS: A total of 1,085 children born at <28 weeks' gestation had clinically indicated retinal examinations and had a developmental assessment at 2 years corrected age. Relationships between ROP categories and brain abnormalities were explored using logistic regression models with adjustment for potential confounders. RESULTS: The 173 children who had severe ROP, defined as prethreshold ROP (n = 146) or worse (n = 27) were somewhat more likely than their peers without ROP to have brain ultrasound lesions or cerebral palsy. They were approximately twice as likely to have very low Bayley Scales scores. After adjusting for risk factors common to both ROP and brain disorders, infants who developed severe ROP were at increased risk of low Bayley Scales only. Among children with prethreshold ROP, exposure to anesthesia was not associated with low Bayley Scales. CONCLUSIONS: Some but not all of the association of ROP with brain disorders can be explained by common risk factors. Most of the increased risks of very low Bayley Scales associated with ROP are probably not a consequence of exposure to anesthetic agents.

Impaired visual fixation at the age of 2 years in children born before the twenty-eighth week of gestation. Antecedents and correlates in the multicenter ELGAN study.

BACKGROUND: Very little is known about the prevalence, antecedents, and correlates of impaired visual fixation in former very preterm newborns. METHODS: In the multicenter ELGAN study sample of 1057 infants born before the twenty-eighth week of gestation who had a developmental assessment at 2 years corrected age, we identified 73 who were unable to follow an object across the midline. We compared them to the 984 infants who could follow an object across the midline. RESULTS: In this sample of very preterm newborns, those who had impaired visual fixation were much more likely than those without impaired visual fixation to have been born after the shortest of gestations (odds ratio, 3.2; 99% confidence interval, 1.4-7.5) and exposed to maternal aspirin (odds ratio, 5.2; 99% confidence interval, 2.2-12). They were also more likely than their peers to have had prethreshold retinopathy of prematurity (odds ratio, 4.1; 99% confidence interval, 1.8-9.0). At age 2 years, the children with impaired fixation were more likely than others to be unable to walk (even with assistance) (odds ratio, 7.5; 99% confidence interval, 2.2-26) and have a Mental Development Index more than three standard deviations below the mean of a normative sample (odds ratio, 3.6; 99% confidence interval, 1.4-8.2). CONCLUSION: Risk factors for brain and retinal damages, such as very low gestational age, appear to be risk factors for impaired visual fixation. This inference is further supported by the co-occurrence at age 2 years of impaired visual fixation, inability to walk, and a very low Mental Development Index.

The influence of antibody fragment format on phage display based affinity maturation of IgG.

Today, most approved therapeutic antibodies are provided as immunoglobulin G (IgG), whereas small recombinant antibody formats are required for in vitro antibody generation and engineering during drug development. Particularly,single chain (sc) antibody fragments like scFv or scFab are well suited for phage display and bacterial expression, but some have been found to lose affinity during conversion into IgG.In this study, we compared the influence of the antibody format on affinity maturation of the CD30-specific scFv antibody fragment SH313-F9, with the overall objective being improvement of the IgG. The variable genes of SH313-F9 were randomly mutated and then cloned into libraries encoding different recombinant antibody formats, including scFv, Fab, scFabΔC, and FabΔC. All tested antibody formats except Fab allowed functional phage display of the parental antibody SH313-F9, and the corresponding mutated antibody gene libraries allowed isolation of candidates with enhanced CD30 binding. Moreover, scFv and scFabΔC antibody variants retained improved antigen binding after subcloning into the single gene encoded IgG-like formats scFv-Fc or scIgG, but lost affinity after conversion into IgGs.Only affinity maturation using the Fab-like FabΔC format, which does not contain the carboxy terminal cysteines, allowed successful selection of molecules with improved binding that was retained after conversion to IgG. Thus, affinity maturation of IgGs is dependent on the antibody format employed for selection and screening. In this study, only FabΔC resulted in the efficient selection of IgG candidates with higher affinity by combination of Fab-like conformation and improved phage display compared with Fab.

Alphasphere as a successful ocular implant in primary enucleation and secondary orbital implant exchange.

PURPOSE: To describe the surgical technique for a novel poly-HEMA (2-hydroxyethyl methacralate)[PHEMA] implant (Alphasphere, Addition Technology, Des Plaines, IL) in primary enucleation and placement of secondary orbital implant. METHODS: Retrospective chart review of all patients receiving an Alphasphere implant for primary enucleation or secondary implant exchange from October 2009 to 2011. Interval follow-up was performed again on January 2013. Patient demographics, indications for surgery, and post-operative complications were reviewed. RESULTS: Twelve patients received an Alphasphere implant for primary enucleation (n = 10) or secondary exchange (n = 2), with follow-up that ranged from 2 weeks to 14 months. The study included 9 adult and 3 pediatric patients with a mean age of 40 years, range 8-82 years. The indication for enucleation included: painful blind eye (n = 9), enophthalmos with difficult prosthesis fit in cases of secondary implant exchange (n = 2), and prophylaxis for sympathetic ophthalmia (n = 1). Only one patient required removal of the implant, due to a sinus infection with subsequent extrusion of the implant. Otherwise, the only other complication experienced was slight implant migration (n = 1). CONCLUSION: This initial report indicates that Alphasphere can be successfully used in the management of an anophthalmic socket. The advantages of the Alphasphere implant include: it does not require tissue wrapping, extraocular muscles can be directly sutured to the implant, it maintains a smooth surface to limit risk of exposure due to conjunctival breakdown, and undergoes anterior orbital fibrovascular ingrowth which optimizes prosthesis location and socket motility.

Ophthalmic and systemic findings in interstitial deletions of chromosome 14q: a case report and literature review.

We report a patient with clinical anophthalmia, partial eyelid fusion and a hypoplastic socket on the right. The left eye has microphthalmia involving the anterior and posterior segments, microcornea, iris coloboma, chorioretinal dysgenesis, macular dysplasia, absence of retinal vessels, and optic nerve aplasia. Systemic abnormalities include microcephaly, bilateral hearing loss, and duodenal atresia. Electrophysiologic testing showed no response from either eye. Cytogenetic testing revealed a de novo interstitial deletion of chromosome 14q22.3q23.1. The literature of similar interstitial deletions and ongoing candidate gene studies are reviewed.