VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts

Mechanistic disease progression studies using animal models require objective and quantifiable assessment of tissue pathology. Currently quantification relies heavily on staining methods which can be expensive, labor/time-intensive, inconsistent across laboratories and batch, and produce uneven staining that is prone to misinterpretation and investigator bias. We developed an automated semantic segmentation tool utilizing deep learning for rapid and objective quantification of histologic features relying solely on hematoxylin and eosin stained pancreatic tissue sections. The tool segments normal acinar structures, the ductal phenotype of acinar-to-ductal metaplasia (ADM), and dysplasia with Dice coefficients of 0.79, 0.70, and 0.79, respectively. To deal with inaccurate pixelwise manual annotations, prediction accuracy was also evaluated against biological truth using immunostaining mean structural similarity indexes (SSIM) of 0.925 and 0.920 for amylase and pan-keratin respectively. Our tool’s disease area quantifications were correlated to the quantifications of immunostaining markers (DAPI, amylase, and cytokeratins; Spearman correlation score = 0.86, 0.97, and 0.92) in unseen dataset (n = 25). Moreover, our tool distinguishes ADM from dysplasia, which are not reliably distinguished with immunostaining, and demonstrates generalizability across murine cohorts with pancreatic disease. We quantified the changes in histologic feature abundance for murine cohorts with oncogenic Kras-driven disease, and the predictions fit biological expectations, showing stromal expansion, a reduction of normal acinar tissue, and an increase in both ADM and dysplasia as disease progresses. Our tool promises to accelerate and improve the quantification of pancreatic disease in animal studies and become a unifying quantification tool across laboratories.

Nootropic Effect of Fenugreek Seed Extract against Scopolamine Induced Cognitive Decline in Experimental Mice

Background: Alzheimer’s disease affecting about 24 million people world-wide. The socio-economic burden on world-economies costing more than 172 billion US $ annually for the US alone. Objectives: To prepare aqueous extract of T. foenum graecum seeds (FSE) to explore the possible treatment for cognitive deficit in experimental animals. Materials and methods: FSE was subjected to preliminary phytochemical evaluation and antioxidant effect using free radical scavenging method (DPPH). All the animal behavior was video recorded with no human intervention during observation and animal groupings were blinded to avoid investigator bias. Different doses of FSE (5%, 10% and 20%), control, standard (Piracetam, 200 mg/kg, IP.) were given for male albino mice a period of 15 days followed by cognitive assessment in elevated plus maze and novel objection recognition tests. Ttransfer latencies and time exploring novel and familiar objects were recorded in respective tests. Retention of this learned-task was examined again 24 h later and inflexion ratio (IR) and discriminative index (DI) were calculated respectively. Next in the second set of experiment same groups and treatments were continued but scopolamine was administered to all the groups except normal control one hour after the last dose and examined similarly. Results: FSE showed potential antioxidant effect and a dose dependent increase in transfer latency and improved DI indicating a nootropic effect. FSE at 20% showed significant reversal of scopolamine induced dementia in the second set of experiment. Conclusion: FSE improved memory as well as reversed the chemically induced memory deficits in experimental mice.

Quantitative Imaging Assessment for Clinical Trials in Oncology

Background: Objective radiographic assessment is crucial for accurately evaluating therapeutic efficacy and patient outcomes in oncology clinical trials. Imaging assessment workflow can be complex; can vary with institution; may burden medical oncologists, who are often inadequately trained in radiology and response criteria; and can lead to high interobserver variability and investigator bias. This article reviews the development of a tumor response assessment core (TRAC) at a comprehensive cancer center with the goal of providing standardized, objective, unbiased tumor imaging assessments, and highlights the web-based platform and overall workflow. In addition, quantitative response assessments by the medical oncologists, radiologist, and TRAC are compared in a retrospective cohort of patients to determine concordance. Patients and Methods: The TRAC workflow includes an image analyst who pre-reviews scans before review with a board-certified radiologist and then manually uploads annotated data on the proprietary TRAC web portal. Patients previously enrolled in 10 lung cancer clinical trials between January 2005 and December 2015 were identified, and the prospectively collected quantitative response assessments by the medical oncologists were compared with retrospective analysis of the same dataset by a radiologist and TRAC. Results: This study enlisted 49 consecutive patients (53% female) with a median age of 60 years (range, 29–78 years); 2 patients did not meet study criteria and were excluded. A linearly weighted kappa test for concordance for TRAC versus radiologist was substantial at 0.65 (95% CI, 0.46–0.85; standard error [SE], 0.10). The kappa value was moderate at 0.42 (95% CI, 0.20–0.64; SE, 0.11) for TRAC versus oncologists and only fair at 0.34 (95% CI, 0.12–0.55; SE, 0.11) for oncologists versus radiologist. Conclusions: Medical oncologists burdened with the task of tumor measurements in patients on clinical trials may introduce significant variability and investigator bias, with the potential to affect therapeutic response and clinical trial outcomes. Institutional imaging cores may help bridge the gap by providing unbiased and reproducible measurements and enable a leaner workflow.

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy

SummaryThe success of immunotherapy has led to a myriad of new clinical trials. Connected to these trials are efforts to discover biomarkers providing mechanistic insight and predictive signatures for personalization. Still, the plethora of immune monitoring technologies can face investigator bias, missing unanticipated cellular responses in limited clinical material. We here present a mass cytometry workflow for standardized, systems-level biomarker discovery in immunotherapy trials. To broadly enumerate human immune cell identity and activity, we established and extensively assessed a reference panel of 33 antibodies to cover major cell subsets, simultaneously quantifying activation and immune checkpoint molecules in a single assay. The resulting assay enumerated ≥ 98% of peripheral immune cells with ≥ 4 positively identifying antigens. Robustness and reproducibility were demonstrated on multiple samples types, across research centers and by orthogonal measurements. Using automated analysis, we monitored complex immune dynamics, identifying signatures in bone-marrow transplantation associated graft-versus-host disease. This validated and available workflow ensures comprehensive immunophenotypic analysis, data comparability and will accelerate biomarker discovery in immunomodulatory therapeutics.

Validating Whole Slide Digital Morphometric Analysis as a Microscopy Tool

Whole slide imaging (WSI) can be used to quantify multiple responses within tissue sections during histological analysis. Feature Analysis on Consecutive Tissue Sections (FACTS®) allows the investigator to perform digital morphometric analysis (DMA) within specified regions of interest (ROI) across multiple serial sections at faster rates when compared with manual morphometry methods. Using FACTS® in conjunction with WSI is a powerful analysis tool, which allows DMA to target specific ROI across multiple tissue sections stained for different biomarkers. DMA may serve as an appropriate alternative to classic, manual, histologic morphometric measures, which have historically relied on the selection of high-powered fields of views and manual scoring (e.g., a gold standard). In the current study, existing preserved samples were used to determine if DMA would provide similar results to manual counting methods. Rodent hearts (n=14, left ventricles) were stained with Masson’s trichrome, and reacted for cluster of differentiation 68 (CD-68). This study found no statistical significant difference between a classic, manual method and the use of digital algorithms to perform the similar counts (p=0.38). DMA offers researchers the ability to accurately evaluate morphological characteristics in a reproducible fashion without investigator bias and with higher throughput.