NAD deficiency contributes to progressive kidney disease in HIV nephropathy mice.

HIV disease remains prevalent in the USA and is particularly prevalent in sub-Saharan Africa. Recent investigations revealed that mitochondrial dysfunction in kidney contributes to HIV-associated nephropathy (HIVAN) in Tg26 transgenic mice. We hypothesized that nicotinamide adenine dinucleotide (NAD) deficiency contributes to energetic dysfunction and progressive tubular injury. We investigated metabolomic mechanisms of HIVAN tubulopathy. Tg26 and wild-type (WT) mice were treated with the farnesoid-X receptor (FXR) agonist INT-747 or nicotinamide riboside (NR) from 6 to 12 weeks of age. Multi-omic approaches were used to characterize kidney tissue transcriptomes and metabolomes. Treatment with INT-747 or NR ameliorated kidney tubular injury, as shown by serum creatinine, the tubular injury marker urinary neutrophil-associated lipocalin and tubular morphometry. Integrated analysis of metabolomic and transcriptomic measurements showed that NAD levels and production were globally downregulated in Tg26 mouse kidney, especially nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in the NAD salvage pathway. Further, NAD-dependent deacetylase sirtuin3 activity and mitochondrial oxidative phosphorylation activity were lower in ex vivo proximal tubules from Tg26 mouse kidneys compared to those of WT mice. Restoration of NAD levels in kidney improved these abnormalities. These data suggest that NAD deficiency might be a treatable target for HIVAN.

Hybrid Clot Histomic-Transcriptomic Models Predict Functional Outcome After Mechanical Thrombectomy in Acute Ischemic Stroke.

BACKGROUND AND OBJECTIVES: Histologic and transcriptomic analyses of retrieved stroke clots have identified features associated with patient outcomes. Previous studies have demonstrated the predictive capacity of histology or expression features in isolation. Few studies, however, have investigated how paired histologic image features and expression patterns from the retrieved clots can improve understanding of clot pathobiology and our ability to predict long-term prognosis. We hypothesized that computational models trained using clot histomics and mRNA expression can predict early neurological improvement (ENI) and 90-day functional outcome (modified Rankin Scale Score, mRS) better than models developed using histological composition or expression data alone. METHODS: We performed paired histological and transcriptomic analysis of 32 stroke clots. ENI was defined as a delta-National Institutes of Health Stroke Score/Scale > 4, and a good long-term outcome was defined as mRS ≤2 at 90 days after procedure. Clots were H&E-stained and whole-slide imaged at 40×. An established digital pathology pipeline was used to extract 237 histomic features and to compute clot percent composition (%Comp). When dichotomized by either the ENI or mRS thresholds, differentially expressed genes were identified as those with absolute fold-change >1.5 and q < 0.05. Machine learning with recursive feature elimination (RFE) was used to select clot features and evaluate computational models for outcome prognostication. RESULTS: For ENI, RFE identified 9 optimal histologic and transcriptomic features for the hybrid model, which achieved an accuracy of 90.8% (area under the curve [AUC] = 0.98 ± 0.08) in testing and outperformed models based on histomics (AUC = 0.94 ± 0.09), transcriptomics (AUC = 0.86 ± 0.16), or %Comp (AUC = 0.70 ± 0.15) alone. For mRS, RFE identified 7 optimal histomic and transcriptomic features for the hybrid model. This model achieved an accuracy of 93.7% (AUC = 0.94 ± 0.09) in testing, also outperforming models based on histomics (AUC = 0.90 ± 0.11), transcriptomics (AUC = 0.55 ± 0.27), or %Comp (AUC = 0.58 ± 0.16) alone. CONCLUSION: Hybrid models offer improved outcome prognostication for patients with stroke. Identified digital histology and mRNA signatures warrant further investigation as biomarkers of patient functional outcome after thrombectomy.

Decoding Molecular Mechanisms Underlying Outcomes After Ischemic Stroke Thrombectomy by RNA Sequencing of Retrieved Clots.

BACKGROUND: Transcriptomic profiling has emerged as a powerful tool for exploring the molecular landscape of ischemic stroke clots and providing insights into the pathophysiological mechanisms underlying stroke progression and recovery. In this study, we aimed to investigate the relationship between stroke clot transcriptomes and stroke thrombectomy outcome, as measured by early neurological improvement (ENI) 30 (i.e., a 30% reduction in NIHSS at 24 h post-thrombectomy). HYPOTHESIS: We hypothesized that there exist distinct clot gene expression patterns between good and poor neurological outcomes. METHODS: Transcriptomic analysis of 32 stroke clots retrieved by mechanical thrombectomy was conducted. Transcriptome data of these clots were analyzed to identify differentially expressed genes (DEGs), defined as those with a log(fold-change) ≥ 1.5 and q < 0.05 between samples with good and poor early neurological outcomes. Gene ontology and bioinformatics analyses were performed on genes with p < 0.01 to identify enriched biological processes and Ingenuity Pathway Analysis canonical pathways. Moreover, AUC analysis assessed the predictive power of DEGs for 90-day function outcome (mRS ≤ 2) and cellular composition of clot was predicted using CIBERSORT. We also assessed whether differential enrichment of immune cell types could indicate patient survival. RESULTS: A total of 41 DEGs were identified. Bioinformatics showed that enriched biological processes and pathways emphasized the chronic immune response and matrix metalloproteinase inhibition. Moreover, 25 of the DEGs were found to be significant predictors of 90-day mRS. These genes were indicative of monocytes enrichment and neutrophil depletion in patients with poorer outcomes. CONCLUSION: Our study revealed a distinct gene expression pattern and dysregulated biological pathways associated with ENI. This expression pattern was also predictive of long-term outcome, suggesting a biological link between those ENIs and 90-day mRS.

ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology.

Artificial intelligence (AI) has extensive applications in a wide range of disciplines including healthcare and clinical practice. Advances in high-resolution whole-slide brightfield microscopy allow for the digitization of histologically stained tissue sections, producing gigapixel-scale whole-slide images (WSI). The significant improvement in computing and revolution of deep neural network (DNN)-based AI technologies over the last decade allow us to integrate massively parallelized computational power, cutting-edge AI algorithms, and big data storage, management, and processing. Applied to WSIs, AI has created opportunities for improved disease diagnostics and prognostics with the ultimate goal of enhancing precision medicine and resulting patient care. The National Institutes of Health (NIH) has recognized the importance of developing standardized principles for data management and discovery for the advancement of science and proposed the Findable, Accessible, Interoperable, Reusable, (FAIR) Data Principles1 with the goal of building a modernized biomedical data resource ecosystem to establish collaborative research communities. In line with this mission and to democratize AI-based image analysis in digital pathology, we propose ComPRePS: an end-to-end automated Computational Renal Pathology Suite which combines massive scalability, on-demand cloud computing, and an easy-to-use web-based user interface for data upload, storage, management, slide-level visualization, and domain expert interaction. Moreover, our platform is equipped with both in-house and collaborator developed sophisticated AI algorithms in the back-end server for image analysis to identify clinically relevant micro-anatomic functional tissue units (FTU) and to extract image features.

MicroCT and Histological Analysis of Clot Composition in Acute Ischemic Stroke : A Comparative Study of MT-Retrieved Clots and Clot Analogs.

PURPOSE: Assessing clot composition on prethrombectomy computed tomography (CT) imaging may help in stroke treatment planning. In this study we seek to use microCT imaging of fabricated blood clots to understand the relationship between CT radiographic signals and the biological makeup. METHODS: Clots (n = 10) retrieved by mechanical thrombectomy (MT) were collected, and 6 clot analogs of varying RBC composition were made. We performed paired microCT and histological image analysis of all 16 clots using a ScanCo microCT 100 (4.9 µm resolution) and standard H&E staining (imaged at 40×). From these data types, first order statistic (FOS) radiomics were computed from microCT, and percent composition of RBCs (%RBC) was computed from histology. Polynomial and linear regression (LR) were used to build statistical models based on retrieved thrombus microCT and %RBC that were evaluated for their ability to predict the %RBC of clot analogs from mean HU. Correlation analyses of microCT FOS with composition were completed for both retrieved clots and analogs. RESULTS: The LR model fits relating MT-retrieved clot %RBC with mean (R2 = 0.625, p = 0.006) and standard deviation (R2 = 0.564, p < 0.05) in HUs on microCT were significant. Similarly, LR models relating analog histological %RBC to analog protocol %RBC (R2 = 0.915, p = 0.003) and mean HUs on microCT (R2 = 0.872, p = 0.007) were also significant. When the LR model built using MT-retrieved clots was used to predict analog %RBC from mean HUs, significant correlation was observed between predictions and actual histological %RBC (R2 = 0.852, p = 0.009). For retrieved clots, significant correlations were observed for energy and total energy with %RBC and %FP (|R| > 0.7, q < 0.01). Analogs further demonstrated significant correlation between FOS energy, total energy, variance and %WBC (|R| > 0.9, q < 0.01). CONCLUSION: MicroCT can be used to build models that predict AIS clot composition from routine CT parameters and help us to better understand radiomic signatures associated with clot composition and first pass outcomes. In future work, such observations can be used to better infer clot composition and inform thrombectomy prognostics from pretreatment CTs.

APOL1 kidney risk variants in glomerular diseases modeled in transgenic mice.

APOL1 high-risk variants partially explain the high kidney disease prevalence among African ancestry individuals. Many mechanisms have been reported in cell culture models, but few have been demonstrated in mouse models. Here we characterize two models: (1) HIV-associated nephropathy (HIVAN) Tg26 mice crossed with bacterial artificial chromosome (BAC)/APOL1 transgenic mice and (2) interferon-γ administered to BAC/APOL1 mice. Both models showed exacerbated glomerular disease in APOL1-G1 compared to APOL1-G0 mice. HIVAN model glomerular bulk RNA-seq identified synergistic podocyte-damaging pathways activated by the APOL1-G1 allele and by HIV transgenes. Single-nuclear RNA-seq revealed podocyte-specific patterns of differentially-expressed genes as a function of APOL1 alleles. Eukaryotic Initiation factor-2 pathway was the most activated pathway in the interferon-γ model and the most deactivated pathway in the HIVAN model. HIVAN mouse model podocyte single-nuclear RNA-seq data showed similarity to human focal segmental glomerulosclerosis (FSGS) glomerular bulk RNA-seq data. Furthermore, single-nuclear RNA-seq data from interferon-γ mouse model podocytes (in vivo) showed similarity to human FSGS single-cell RNA-seq data from urine podocytes (ex vivo) and from human podocyte cell lines (in vitro) using bulk RNA-seq. These data highlight differences in the transcriptional effects of the APOL1-G1 risk variant in a model specific manner. Shared differentially expressed genes in podocytes in both mouse models suggest possible novel glomerular damage markers in APOL1 variant-induced diseases. Transcription factor Zbtb16 was downregulated in podocytes and endothelial cells in both models, possibly contributing to glucocorticoid-resistance. In summary, these findings in two mouse models suggest both shared and distinct therapeutic opportunities for APOL1 glomerulopathies.

Tectonic infarct analysis: A computational tool for automated whole-brain infarct analysis from TTC-stained tissue.

Background: Infarct volume measured from 2,3,5-triphenyltetrazolium chloride (TTC)-stained brain slices is critical to in vivo stroke models. In this study, we developed an interactive, tunable, software that automatically computes whole-brain infarct metrics from serial TTC-stained brain sections. Methods: Three rat ischemic stroke cohorts were used in this study (Total n = 91 rats; Cohort 1 n = 21, Cohort 2 n = 40, Cohort 3 n = 30). For each, brains were serially-sliced, stained with TTC and scanned on both anterior and posterior sides. Ground truth annotation and infarct morphometric analysis (e.g., brain-Vbrain, infarct-Vinfarct, and non-infarct-Vnon-infarct volumes) were completed by domain experts. We used Cohort 1 for brain and infarct segmentation model development (n = 3 training cases with 36 slices [18 anterior and posterior faces], n = 18 testing cases with 218 slices [109 anterior and posterior faces]), as well as infarct morphometrics automation. The infarct quantification pipeline and pre-trained model were packaged as a standalone software and applied to Cohort 2, an internal validation dataset. Finally, software and model trainability were tested as a use-case with Cohort 3, a dataset from a separate institute. Results: Both high segmentation and statistically significant quantification performance (correlation between manual and software) were observed across all datasets. Segmentation performance: Cohort 1 brain accuracy = 0.95/f1-score = 0.90, infarct accuracy = 0.96/f1-score = 0.89; Cohort 2 brain accuracy = 0.97/f1-score = 0.90, infarct accuracy = 0.97/f1-score = 0.80; Cohort 3 brain accuracy = 0.96/f1-score = 0.92, infarct accuracy = 0.95/f1-score = 0.82. Infarct quantification (cohort average): Vbrain (ρ = 0.87, p < 0.001), Vinfarct (0.92, p < 0.001), Vnon-infarct (0.80, p < 0.001), %infarct (0.87, p = 0.001), and infarct:non-infact ratio (ρ = 0.92, p < 0.001). Conclusion: Tectonic Infarct Analysis software offers a robust and adaptable approach for rapid TTC-based stroke assessment.

Multimodal CT imaging of ischemic stroke thrombi identifies scale-invariant radiomic features that reflect clot biology.

BACKGROUND: Biological interpretability of ischemic stroke clot imaging remains challenging. OBJECTIVE: To carry out paired CT/micro-CT imaging of ischemic stroke clots retrieved by thrombectomy with the aim of identifying interpretable image features that are correlated among pretreatment image modalities and post-treatment histopathology. METHODS: We performed multimodal CT imaging and histology for 10 stroke clots retrieved by mechanical thrombectomy. Clots were manually segmented from co-registered, pretreatment CT angiography (CTA) and non-contrast CT (NCCT). For the same cases, retrieved clots were iodine-stained, and imaged with a ScanCo micro-CT 100 (4.9 µm resolution). Afterwards, clots were subjected to histological processing (hematoxylin and eosin staining) and whole slide scanned (40X). Clot radiomic features (RFs) (n=93 per modality, 279 total) were extracted using PyRadiomics and histological composition was computed using Orbit Image Analysis. Correlation analysis was used to test associations between micro-CT and CTA (or NCCT) RFs as well as between RFs and histological composition. Statistical significance was considered at R≥0.65 and q<0.05. RESULTS: From paired RF correlation analysis, we identified 23 scale-invariant RFs with significant correlation between micro-CT and CTA (18), and micro-CT and NCCT (5). Correlation of unpaired RFs identified 377 positively and 36 negatively correlated RFs between micro-CT and CTA, and 168 positively and 41 negatively correlated RFs between micro-CT and NCCT. Scale-invariant RFs computed from CTA and NCCT demonstrated significant correlation with red blood cell and fibrin-platelet components, while micro-CT RFs were found to be correlated with white blood cell percent composition. CONCLUSION: Multimodal CT, radiomic, and histological analysis of stroke clots can help to bridge the gap between pretreatment imaging and clot pathobiology.

RNA Expression Signatures of Intracranial Aneurysm Growth Trajectory Identified in Circulating Whole Blood.

After detection, identifying which intracranial aneurysms (IAs) will rupture is imperative. We hypothesized that RNA expression in circulating blood reflects IA growth rate as a surrogate of instability and rupture risk. To this end, we performed RNA sequencing on 66 blood samples from IA patients, for which we also calculated the predicted aneurysm trajectory (PAT), a metric quantifying an IA's future growth rate. We dichotomized dataset using the median PAT score into IAs that were either more stable and more likely to grow quickly. The dataset was then randomly divided into training (n = 46) and testing cohorts (n = 20). In training, differentially expressed protein-coding genes were identified as those with expression (TPM > 0.5) in at least 50% of the samples, a q-value < 0.05 (based on modified F-statistics with Benjamini-Hochberg correction), and an absolute fold-change ≥ 1.5. Ingenuity Pathway Analysis was used to construct networks of gene associations and to perform ontology term enrichment analysis. The MATLAB Classification Learner was then employed to assess modeling capability of the differentially expressed genes, using a 5-fold cross validation in training. Finally, the model was applied to the withheld, independent testing cohort (n = 20) to assess its predictive ability. In all, we examined transcriptomes of 66 IA patients, of which 33 IAs were "growing" (PAT ≥ 4.6) and 33 were more "stable". After dividing dataset into training and testing, we identified 39 genes in training as differentially expressed (11 with decreased expression in "growing" and 28 with increased expression). Model genes largely reflected organismal injury and abnormalities and cell to cell signaling and interaction. Preliminary modeling using a subspace discriminant ensemble model achieved a training AUC of 0.85 and a testing AUC of 0.86. In conclusion, transcriptomic expression in circulating blood indeed can distinguish "growing" and "stable" IA cases. The predictive model constructed from these differentially expressed genes could be used to assess IA stability and rupture potential.

Histologically interpretable clot radiomic features predict treatment outcomes of mechanical thrombectomy for ischemic stroke.

PURPOSE: Radiomics features (RFs) extracted from CT images may provide valuable information on the biological structure of ischemic stroke blood clots and mechanical thrombectomy outcome. Here, we aimed to identify RFs predictive of thrombectomy outcomes and use clot histomics to explore the biology and structure related to these RFs. METHODS: We extracted 293 RFs from co-registered non-contrast CT and CTA. RFs predictive of revascularization outcomes defined by first-pass effect (FPE, near to complete clot removal in one thrombectomy pass), were selected. We then trained and cross-validated a balanced logistic regression model fivefold, to assess the RFs in outcome prediction. On a subset of cases, we performed digital histopathology on the clots and computed 227 histomic features from their whole slide images as a means to interpret the biology behind significant RF. RESULTS: We identified 6 significantly-associated RFs. RFs reflective of continuity in lower intensities, scattered higher intensities, and intensities with abrupt changes in texture were associated with successful revascularization outcome. For FPE prediction, the multi-variate model had high performance, with AUC = 0.832 ± 0.031 and accuracy = 0.760 ± 0.059 in training, and AUC = 0.787 ± 0.115 and accuracy = 0.787 ± 0.127 in cross-validation testing. Each of the 6 RFs was related to clot component organization in terms of red blood cell and fibrin/platelet distribution. Clots with more diversity of components, with varying sizes of red blood cells and fibrin/platelet regions in the section, were associated with RFs predictive of FPE. CONCLUSION: Upon future validation in larger datasets, clot RFs on CT imaging are potential candidate markers for FPE prediction.

Profiling of Circulating Gene Expression Reveals Molecular Signatures Associated with Intracranial Aneurysm Rupture Risk.

BACKGROUND: Following detection, rupture risk assessment for intracranial aneurysms (IAs) is critical. Towards molecular prognostics, we hypothesized that circulating blood RNA expression profiles are associated with IA risk. METHODS: We performed RNA sequencing on 68 blood samples from IA patients. Here, patients were categorized as either high or low risk by assessment of aneurysm size (≥ 5 mm = high risk) and Population, Hypertension, Age, Size, Earlier subarachnoid hemorrhage, Site (PHASES) score (≥ 1 = high risk). Modified F-statistics and Benjamini-Hochberg false discovery rate correction was performed on transcripts per million-normalized gene counts. Protein-coding genes expressed in ≥ 50% of samples with a q value < 0.05 and an absolute fold-change ≥ 2 were considered significantly differentially expressed. Bioinformatics in Ingenuity Pathway Analysis was performed to understand the biology of risk-associated expression profiles. Association was assessed between gene expression and risk via Pearson correlation analysis. Linear discriminant analysis models using significant genes were created and validated for classification of high-risk cases. RESULTS: We analyzed transcriptomes of 68 IA patients. In these cases, 31 IAs were large (≥ 5 mm), while 26 IAs had a high PHASES score. Based on size, 36 genes associated with high-risk IAs, and two were correlated with the size measurement. Alternatively, based on PHASES score, 76 genes associated with high-risk cases, and nine of them showed significant correlation to the score. Similar ontological terms were associated with both gene profiles, which reflected inflammatory signaling and vascular remodeling. Prediction models based on size and PHASES stratification were able to correctly predict IA risk status, with > 80% testing accuracy for both. CONCLUSIONS: Here, we identified genes associated with IA risk, as quantified by common clinical metrics. Preliminary classification models demonstrated feasibility of assessing IA risk using whole blood expression.

Variant APOL1 protein in plasma associates with larger particles in humans and mouse models of kidney injury.

BACKGROUND: Genetic variants in apolipoprotein L1 (APOL1), a protein that protects humans from infection with African trypanosomes, explain a substantial proportion of the excess risk of chronic kidney disease affecting individuals with sub-Saharan ancestry. The mechanisms by which risk variants damage kidney cells remain incompletely understood. In preclinical models, APOL1 expressed in podocytes can lead to significant kidney injury. In humans, studies in kidney transplant suggest that the effects of APOL1 variants are predominantly driven by donor genotype. Less attention has been paid to a possible role for circulating APOL1 in kidney injury. METHODS: Using liquid chromatography-tandem mass spectrometry, the concentrations of APOL1 were measured in plasma and urine from participants in the Seattle Kidney Study. Asymmetric flow field-flow fractionation was used to evaluate the size of APOL1-containing lipoprotein particles in plasma. Transgenic mice that express wild-type or risk variant APOL1 from an albumin promoter were treated to cause kidney injury and evaluated for renal disease and pathology. RESULTS: In human participants, urine concentrations of APOL1 were correlated with plasma concentrations and reduced kidney function. Risk variant APOL1 was enriched in larger particles. In mice, circulating risk variant APOL1-G1 promoted kidney damage and reduced podocyte density without renal expression of APOL1. CONCLUSIONS: These results suggest that plasma APOL1 is dynamic and contributes to the progression of kidney disease in humans, which may have implications for treatment of APOL1-associated kidney disease and for kidney transplantation.

PodoCount: A Robust, Fully Automated, Whole-Slide Podocyte Quantification Tool.

Introduction: Podocyte depletion is a histomorphologic indicator of glomerular injury and predicts clinical outcomes. Podocyte estimation methods or podometrics are semiquantitative, technically involved, and laborious. Implementation of high-throughput podometrics in experimental and clinical workflows necessitates an automated podometrics pipeline. Recognizing that computational image analysis offers a robust approach to study cell and tissue structure, we developed and validated PodoCount (a computational tool for automated podocyte quantification in immunohistochemically labeled tissues) using a diverse data set. Methods: Whole-slide images (WSIs) of tissues immunostained with a podocyte nuclear marker and periodic acid-Schiff counterstain were acquired. The data set consisted of murine whole kidney sections (n = 135) from 6 disease models and human kidney biopsy specimens from patients with diabetic nephropathy (DN) (n = 45). Within segmented glomeruli, podocytes were extracted and image analysis was applied to compute measures of podocyte depletion and nuclear morphometry. Computational performance evaluation and statistical testing were performed to validate podometric and associated image features. PodoCount was disbursed as an open-source, cloud-based computational tool. Results: PodoCount produced highly accurate podocyte quantification when benchmarked against existing methods. Podocyte nuclear profiles were identified with 0.98 accuracy and segmented with 0.85 sensitivity and 0.99 specificity. Errors in podocyte count were bounded by 1 podocyte per glomerulus. Podocyte-specific image features were found to be significant predictors of disease state, proteinuria, and clinical outcome. Conclusion: PodoCount offers high-performance podocyte quantitation in diverse murine disease models and in human kidney biopsy specimens. Resultant features offer significant correlation with associated metadata and outcome. Our cloud-based tool will provide end users with a standardized approach for automated podometrics from gigapixel-sized WSIs.

Endothelial Cell-Specific Molecule-1 Inhibits Albuminuria in Diabetic Mice.

Background: Diabetic kidney disease (DKD) is the most common cause of kidney failure in the world, and novel predictive biomarkers and molecular mechanisms of disease are needed. Endothelial cell-specific molecule-1 (Esm-1) is a secreted proteoglycan that attenuates inflammation. We previously identified that a glomerular deficiency of Esm-1 associates with more pronounced albuminuria and glomerular inflammation in DKD-susceptible relative to DKD-resistant mice, but its contribution to DKD remains unexplored. Methods: Using hydrodynamic tail-vein injection, we overexpress Esm-1 in DKD-susceptible DBA/2 mice and delete Esm-1 in DKD-resistant C57BL/6 mice to study the contribution of Esm-1 to DKD. We analyze clinical indices of DKD, leukocyte infiltration, podocytopenia, and extracellular matrix production. We also study transcriptomic changes to assess potential mechanisms of Esm-1 in glomeruli. Results: In DKD-susceptible mice, Esm-1 inversely correlates with albuminuria and glomerular leukocyte infiltration. We show that overexpression of Esm-1 reduces albuminuria and diabetes-induced podocyte injury, independent of changes in leukocyte infiltration. Using a complementary approach, we find that constitutive deletion of Esm-1 in DKD-resistant mice modestly increases the degree of diabetes-induced albuminuria versus wild-type controls. By glomerular RNAseq, we identify that Esm-1 attenuates expression of kidney disease-promoting and interferon (IFN)-related genes, including Ackr2 and Cxcl11. Conclusions: We demonstrate that, in DKD-susceptible mice, Esm-1 protects against diabetes-induced albuminuria and podocytopathy, possibly through select IFN signaling. Companion studies in patients with diabetes suggest a role of Esm-1 in human DKD.

Realistic computer modelling of stent retriever thrombectomy: a hybrid finite-element analysis-smoothed particle hydrodynamics model.

Stent retriever thrombectomy is a pre-eminent treatment modality for large vessel ischaemic stroke. Simulation of thrombectomy could help understand stent and clot mechanics in failed cases and provide a digital testbed for the development of new, safer devices. Here, we present a novel, in silico thrombectomy method using a hybrid finite-element analysis (FEA) and smoothed particle hydrodynamics (SPH). Inspired by its biological structure and components, the blood clot was modelled with the hybrid FEA-SPH method. The Solitaire self-expanding stent was parametrically reconstructed from micro-CT imaging and was modelled as three-dimensional finite beam elements. Our simulation encompassed all steps of mechanical thrombectomy, including stent packaging, delivery and self-expansion into the clot, and clot extraction. To test the feasibility of our method, we simulated clot extraction in simple straight vessels. This was compared against in vitro thrombectomies using the same stent, vessel geometry, and clot size and composition. Comparisons with benchtop tests indicated that our model was able to accurately simulate clot deflection and penetration of stent wires into the clot, the relative movement of the clot and stent during extraction, and clot fragmentation/embolus formation. In this study, we demonstrated that coupling FEA and SPH techniques could realistically model stent retriever thrombectomy.

Automated detection and quantification of Wilms' Tumor 1-positive cells in murine diabetic kidney disease.

In diabetic kidney disease (DKD), podocyte depletion, and the subsequent migration of parietal epithelial cells (PECs) to the tuft, is a precursor to progressive glomerular damage, but the limitations of brightfield microscopy currently preclude direct pathological quantitation of these cells. Here we present an automated approach to podocyte and PEC detection developed using kidney sections from mouse model emulating DKD, stained first for Wilms' Tumor 1 (WT1) (podocyte and PEC marker) by immunofluorescence, then post-stained with periodic acid-Schiff (PAS). A generative adversarial network (GAN)-based pipeline was used to translate these PAS-stained sections into WT1-labeled IF images, enabling in silico label-free podocyte and PEC identification in brightfield images. Our method detected WT1-positive cells with high sensitivity/specificity (0.87/0.92). Additionally, our algorithm performed with a higher Cohen's kappa (0.85) than the average manual identification by three renal pathologists (0.78). We propose that this pipeline will enable accurate detection of WT1-positive cells in research applications.

The Presence and Location of Podocytes in Glomeruli as Affected by Diabetes Mellitus.

The primary purpose of the kidney, specifically the glomerulus, is filtration. Filtration is accomplished through the glomerular filtration barrier, which consists of the fenestrated endothelium, glomerular basement membrane, and specialized epithelial cells called podocytes. In pathologic states, such as Diabetes Mellitus (DM) and diabetic kidney disease (DKD), variable glomerular conditions result in podocyte injury and depletion, followed by progressive glomerular injury and DKD progression. In this work we quantified glomerulus and podocyte structural changes in histopathology image data derived from a murine model of DM. Using a variety of image processing techniques, we studied changes in podocyte morphology and intra-glomerular distribution across healthy, mild DM, and DM glomeruli. Our feature analysis provided feature trends which we believe are reflective of DKD pathology; while glomerular area peaked in mild DM, average podocyte number and distance from the urinary pole continued to decrease and increase, respectively, throughout DM. Ultimately, this study aims to augment the set of quantifiable image biomarkers used for evaluation of DKD progression in digital pathology, as well as underscore the importance of engineering biologically-inspired image features.

Neutrophil Extracellular Traps (NETs): An unexplored territory in renal pathobiology, a pilot computational study.

In the age of modern medicine and artificial intelligence, image analysis and machine learning have revolutionized diagnostic pathology, facilitating the development of computer aided diagnostics (CADs) which circumvent prevalent diagnostic challenges. Although CADs will expedite and improve the precision of clinical workflow, their prognostic potential, when paired with clinical outcome data, remains indeterminate. In high impact renal diseases, such as diabetic nephropathy and lupus nephritis (LN), progression often occurs rapidly and without immediate detection, due to the subtlety of structural changes in transient disease states. In such states, exploration of quantifiable image biomarkers, such as Neutrophil Extracellular Traps (NETs), may reveal alternative progression measures which correlate with clinical data. NETs have been implicated in LN as immunogenic cellular structures, whose occurrence and dysregulation results in excessive tissue damage and lesion manifestation. We propose that renal biopsy NET distribution will function as a discriminate, predictive biomarker in LN, and will supplement existing classification schemes. We have developed a computational pipeline for segmenting NET-like structures in LN biopsies. NET-like structures segmented from our biopsies warrant further study as they appear pathologically distinct, and resemble non-lytic, vital NETs. Examination of corresponding H&E regions predominantly placed NET-like structures in glomeruli, including globally and segmentally sclerosed glomeruli, and tubule lumina. Our work continues to explore NET-like structures in LN biopsies by: 1.) revising detection and analytical methods based on evolving NETs definitions, and 2.) cataloguing NET morphology in order to implement supervised classification of NET-like structures in histopathology images.