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Arteriolar hyalinosis in kidneys is an independent predictor of cardiovascular disease, the main cause of mortality in chronic kidney disease (CKD). The underlying molecular mechanisms of protein accumulation in the subendothelial space are not well understood. Using single cell transcriptomic data and whole slide images from kidney biopsies of patients with CKD and acute kidney injury in the Kidney Precision Medicine Project, the molecular signals associated with arteriolar hyalinosis were evaluated. Co-expression network analysis of the endothelial genes yielded three gene set modules as significantly associated with arteriolar hyalinosis. Pathway analysis of these modules showed enrichment of transforming growth factor beta / Bone morphogenetic protein (TGFβ / BMP) and vascular endothelial growth factor (VEGF) signaling pathways in the endothelial cell signatures. Ligand-receptor analysis identified multiple integrins and cell adhesion receptors as over-expressed in arteriolar hyalinosis, suggesting a potential role of integrin-mediated TGFβ signaling in arteriolar hyalinosis. Further analysis of arteriolar hyalinosis associated endothelial module genes identified focal segmental glomerular sclerosis as an enriched term. On validation in gene expression profiles from the Nephrotic Syndrome Study Network cohort, one of the three modules was significantly associated with the composite endpoint (> 40% reduction in estimated glomerular filtration rate (eGFR) or kidney failure) independent of age, sex, race, and baseline eGFR, suggesting poor prognosis with elevated expression of genes in this module. Thus, integration of structural and single cell molecular features yielded biologically relevant gene sets, signaling pathways and ligand-receptor interactions, underlying arteriolar hyalinosis and putative targets for therapeutic intervention.

Background Image-based machine learning tools hold great promise for clinical applications in pathology research. However, the ideal end-users of these computational tools (e.g., pathologists and biological scientists) often lack the programming experience required for the setup and use of these tools which often rely on the use of command line interfaces. Methods We have developed Histo-Cloud, a tool for segmentation of whole slide images (WSIs) that has an easy-to-use graphical user interface. This tool runs a state-of-the-art convolutional neural network (CNN) for segmentation of WSIs in the cloud and allows the extraction of features from segmented regions for further analysis. Results By segmenting glomeruli, interstitial fibrosis and tubular atrophy, and vascular structures from renal and non-renal WSIs, we demonstrate the scalability, best practices for transfer learning, and effects of dataset variability. Finally, we demonstrate an application for animal model research, analyzing glomerular features in three murine models. Conclusions Histo-Cloud is open source, accessible over the internet, and adaptable for segmentation of any histological structure regardless of stain.

Additional file 1: Table S1. Definition and calculations of gray-level co-occurrence matrix texture features [30, 40–42].

OBJECTIVE: Reported associations between kidney risk variants (G1 and G2) in APOL1, encoding apolipoprotein L1 (APOL1), and cardiovascular disease have been conflicting. We sought to explore associations of APOL1 risk variants with cause of sudden death using the CVPath Sudden Death Autopsy Registry. APPROACH AND RESULTS: APOL1 haplotypes and causes of sudden death, as determined through autopsy and histopathology, were obtained for 764 African Americans. Genotyping revealed APOL1 risk alleles in 452 of 764 (59%) subjects with 347 (77%) subjects carrying one risk allele and 105 (23%) subjects harboring two risk alleles. APOL1 risk allele carrier status was associated with a significantly increased risk of coronary thrombosis due to plaque rupture, versus non-carriers (OR for rupture 1.655, 95% CI 1.079 – 2.539; p = 0.021). Histological examinations showed coronary plaques in carriers of two APOL1 risk alleles had larger necrotic cores compared to non-carriers (necrotic core area/total plaque area: 46.79% ± 6.47% vs. 20.57% ± 5.11%; p = 0.0343 in ruptured plaques, and 41.48% ± 7.49% vs. 18.93% ± 3.97%; p = 0.0342 in non-ruptured plaques), and immunohistochemical and immunofluorescent staining revealed APOL1-positive areas localized primarily to the necrotic core. CONCLUSIONS: APOL1 risk alleles were independently associated with an increased risk of thrombotic coronary death due to plaque rupture. Our results suggest that carriers of both one and two APOL1 risk alleles have greater accumulation of APOL1 protein within culprit plaques and greater necrotic core sizes than non-carriers. These findings suggest that APOL1 plays a role in determining plaque stability.

We created a custom pipeline (histo-fetch) to efficiently extract random patches and labels from pathology whole slide images (WSIs) for input to a neural network on-the-fly. We prefetch these patches as needed during network training, avoiding the need for WSI preparation such as chopping/tiling. We demonstrate the utility of this pipeline to perform artificial stain transfer and image generation using the popular networks CycleGAN and ProGAN, respectively., 5 pages, 2 figures

Additional file 4 Supplementary Figure 1. Myofiber nuclei analysis. a A UMAP of all myofiber nuclei with fiber type noted. b Myosin heavy chain expression used to assign the myofiber types. c Myosin heavy chain expression and number of nuclei by fiber type demonstrating overlapping expression of Myh genes in some fiber types. Supplementary Figure 2. Comparison of the Fast 2Xc1 and Fast 2Xc2 subsets. a Twenty-two neuronal or NMJ-related genes are detected in most cells, but enriched in Fast 2Xc2 (middle left) cells. b Three neural genes (Cdh4, Kirrel3, Ntn1), an endothelial specific gene (Pecam1) and a smooth muscle cell gene (Smtn) are all increased in Fast 2Xc2 subsets suggesting overall increase of ambient RNA in these cells. c Total gene counts are elevated in Fast2Xc2 subsets despite no increase in total reads or % mitochondria. d Typically abundant genes, Ttn, mt-Rnr1, and mt-Rnr2 are all of lower expression in Fast 2Xc2 cells.

Combined Phylogenetics and Proteomics for Diagnostic Identification of Clinically Important Bacterial Pathogens

Supplemental material, 2020-00025R1_Production_Supplemental_Table_online_supp for BK Virus RNA in Renal Allograft Biopsies by Francesca Costigliolo, Kara Lombardo, Lois J. Arend, Avi Z. Rosenberg, Andres Matoso, Naima Carter-Monroe and Serena M. Bagnasco in Journal of Histochemistry & Cytochemistry

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

A gradual decline in renal function occurs even in healthy aging individuals. In addition to aging per se, concurrent metabolic syndrome and hypertension, which are common in the aging population, can induce mitochondrial dysfunction, endoplasmic reticulum stress, oxidative stress, inflammation, altered lipid metabolism, and profibrotic growth factors in the kidney, which collectively contribute to age-related kidney disease. With increasing population of older individuals and the increasing incidence of acute kidney injury and chronic kidney disease, identifying preventable or treatable aspects of age-related nephropathy becomes of critical importance. In this regard we studied the role of the nuclear hormone receptors, the estrogen related receptors (ERRs), whose expression levels are decreased in aging human and mouse kidneys. Our studies have identified the estrogen related receptors ERRα, ERRβ, and ERRγ as important modulators of age-related mitochondrial dysfunction, cellular senescence, and inflammation. Significantly these pathways are also regulated by lifelong caloric restriction (CR), which is known to prevent several age-related complications including kidney disease. ERRα, ERRβ, and ERRγ expression levels are decreased in the aging kidney, and CR and pharmacological treatment with a pan ERR agonist results in increases in expression of ERRα, ERRβ, and ERRγ in the kidney. Remarkably, only a 4-week treatment of 21-month-old mice with the pan ERR agonist reversed the age-related mitochondrial dysfunction, the cellular senescence marker p21, and inflammatory cytokines, including the STAT3 and STING signaling pathways.

ObjectivePatients with systemic lupus erythematosus (SLE) have an increased risk of cardiovascular disease (CVD) and impaired endothelial repair. Although vitamin D deficiency is associated with increased CVD risk in the general population, a causal relationship has not been demonstrated. We aimed to determine whether vitamin D deficiency directly modulates endothelial dysfunction and immune responses in a murine model of SLE.MethodsVitamin D deficiency was induced in lupus-prone MRL/lpr mice by dietary restriction for 6 weeks. Endothelium-dependent vasorelaxation was quantified using aortic ring myography, and endothelial repair mechanisms were assessed by evaluating the phenotype and function of bone marrow endothelial progenitor cells (EPCs) and with the use of an in vivo Matrigel plug model. Lupus disease activity was determined by evaluating expression of interferon-stimulated genes (ISGs) in splenic tissue, positivity for serum autoantibodies, and renal histology. To validate the findings, expression of ISGs was also measured in whole blood from vitamin D–deficient and vitamin D–sufficient patients with SLE.ResultsVitamin D deficiency resulted in impaired endothelium-dependent vasorelaxation and decreases in neoangiogenesis without a change in the total number of EPCs. There were no differences in anti–double-stranded DNA titers, proteinuria, or glomerulonephritis (activity or chronicity) between vitamin D–deficient or sufficient mice. Vitamin D deficiency was associated with a trend toward increased ISG expression both in mice and in patients with SLE.ConclusionThese findings indicate that vitamin D deficiency is associated with hampered vascular repair and reduced endothelial function, and may modulate type I interferon responses.

NY-ESO-1 (CTAG 1B) is highly expressed in the majority of synovial sarcomas and myxoid/round cell liposarcomas as well as in a subset of melanomas, but only rarely in other mesenchymal tumors. This points to a potential for using NY-ESO-1 in the differential diagnosis of these lesions. Furthermore, promising results have been obtained in clinical trials testing NY-ESO-1-targeted immunotherapy in subsets of melanoma and synovial sarcoma patients.

In renal biopsy reporting, quantitative measurements, such as glomerular number and percentage of globally sclerotic glomeruli, is central to diagnostic accuracy and prognosis. The aim of this study is to determine the number of glomeruli and percent globally sclerotic in renal biopsies by means of registration of serial tissue sections and manual enumeration, compared to the numbers in pathology reports from routine light microscopic assessment.