Thyroid tissue is sensitive to the effects of endocrine disrupting substances, and this represents a significant health concern. Histopathological analysis of tissue sections of the rat thyroid gland remains the gold standard for the evaluation for agrochemical effects on the thyroid. However, there is a high degree of variability in the appearance of the rat thyroid gland, and toxicologic pathologists often struggle to decide on and consistently apply a threshold for recording low-grade thyroid follicular hypertrophy. This research project developed a deep learning image analysis solution that provides a quantitative score based on the morphological measurements of individual follicles that can be integrated into the standard pathology workflow. To achieve this, a U-Net convolutional deep learning neural network was used that not just identifies the various tissue components but also delineates individual follicles. Further steps to process the raw individual follicle data were developed using empirical models optimized to produce thyroid activity scores that were shown to be superior to the mean epithelial area approach when compared with pathologists' scores. These scores can be used for pathologist decision support using appropriate statistical methods to assess the presence or absence of low-grade thyroid hypertrophy at the group level.

Off-target evaluation is essential in preclinical safety assessments of novel biotherapeutics, supporting lead molecule selection, endpoint selection in toxicology studies, and regulatory requirements for first-in-human trials. Off-target interaction of a therapeutic antibody and antibody derivatives has been historically assessed via the Tissue Cross-Reactivity (TCR) study, in which the candidate molecule is used as a reagent in immunohistochemistry (IHC) to assess binding of the candidate molecule to a panel of human tissue sections. The TCR approach is limited by the performance of the therapeutic as an IHC reagent, which is often suboptimal to outright infeasible. Furthermore, binding of the therapeutic in IHC conditions typically has poor in vitro to in vivo translation and lacks qualitative data of the identity of putative off-targets limiting the decisional value of the data. More recently, cell-based protein arrays (CBPA) that allow for screening against a large portion of the human membrane proteome and secretome have emerged as a complement, and likely a higher value alternative, to IHC-based off-target assessment. These arrays identify specific protein interactions and may be useful for testing nontraditional antibody-based therapeutic formats that are unsuitable for TCR studies. This article presents an overview of CBPA technologies in the context of TCR and off-target assessment studies. Selected case examples and strategic considerations covering a range of different modalities are presented.

Hematoxylin and eosin (H&E) staining is a suitable approach for detecting substantial structural changes in neural tissues but is less sensitive for identifying subtle alterations to subcellular structures and various chemical constituents, including myelin. Neurohistological methods to better evaluate myelin integrity by light microscopy include acidophilic dyes (eg, eriochrome cyanine R, toluidine blue [used with hard plastic sections]); lipoprotein-binding dyes (eg, Luxol fast blue [LFB], Weil's iron hematoxylin); lipid impregnation with metals (eg, Marchi's, which uses osmium tetroxide for en bloc staining before embedding); and immunohistochemical (IHC) methods to highlight various antigens (eg, myelin basic protein [MBP] and peripheral myelin protein 22 [PMP22]). Some IHC methods reveal enhanced marker expression in damaged myelin (eg, matrix metalloproteinase-9 [MMP9], S100). In neuropathology investigations, H&E is the first-tier screening method, whereas myelin stains (often LFB alone or in combination with dyes that highlight other structural elements) are second-tier procedures performed in combination with other neurohistological procedures to examine neuroaxonal injury and/or glial responses. The choice of myelin method depends on such considerations as cost, institutional preference, the procedure (fixation and embedding medium), and the study objective.

Recent trends in toxicological pathology include implementation of digital platforms that have gained rapid momentum in the field. Are we ready to fully implement this new modality? This opinion piece provides some practical perspectives on digital pathology such as its cost limitations, relative time requirements, and a few technical issues, some of which are encountered for specific lesions, that warrant caution. Although the potential for digital pathology assessment with whole slide images has made great strides, we are of the opinion that it is not yet ready for complete replacement of glass slides in toxicologic pathology safety assessments.

Characterizing the expression of novel targets in normal and diseased tissues is a fundamental component of a target validation data package. Often these targets are presented to the pathology team for assessment with bulk or single-cell RNAseq data and limited to no spatial tissue expression data. hybridization to detect mRNA (RNAscope) is a valuable tool to (1) identify cells that may express the target protein and to corroborate protein expression during immunohistochemical (IHC) assay development or (2) to use as surrogate for single-cell expression IHC when antibodies are not available. Chromogenic RNAscope hybridization (CISH) can be performed on frozen or formalin-fixed, paraffin-embedded (FFPE) tissues. This CISH workflow starts with RNA qualification of the tissue (to assess RNA integrity) by measuring the expression of housekeeping genes. RNA-qualified tissues then undergo CISH for the target in question, and positive CISH signals are quantified in VisioPharm by a combination of color deconvolution, size gating, and dot density thresholding. This RNA workflow can complement IHC or standalone in target validation for spatial characterization of novel targets.

Small interfering RNAs (siRNAs) have been successfully used as therapeutics to silence disease-causing genes when conjugated to ligands or formulated in lipid nanoparticles to target relevant cell types for efficacy while sparing other cells for safety. To support the development of new methods for delivery of siRNA therapeutics, we developed and characterized a panel of antibodies generated against chemically modified nucleotides used in therapeutic siRNA molecules, identifying a monoclonal antibody that detects a broad range of siRNA representing distinct sequences and modification patterns. By integrating this anti-siRNA antibody with additional reagents, we created a multiplex siRNA immunoassay that simultaneously quantifies siRNA uptake, trafficking, and silencing activity. Using immunohistochemistry (IHC), we applied our method on tissues from mice treated with unconjugated, GalNAc-conjugated, or cholesterol-conjugated siRNAs and quantitatively assessed the biodistribution and activity of siRNAs in various organs. In addition, we used high-content imaging (HCI) and applied our multiplex siRNA immunoassay in tissue culture to enable simultaneous quantification of siRNA uptake, activity, and intracellular colocalization with endosome markers. These methods provide a robust platform for testing nucleic acid delivery methods and , allowing precise analysis and visualization of the pharmacokinetics and pharmacodynamics of siRNA therapeutics with cellular and subcellular resolution.

A retrospective study was performed to determine the incidences of spontaneous findings in control laboratory New Zealand White (NZW) and Dutch Belted (DB) rabbits. Terminal body and organ weights data were also collected. A total of 2170 NZW (526 males/1644 females), 100 DB rabbits (50 animals per sex), aged 4- to 7-month-old were obtained from 158 non-clinical studies evaluated between 2013 and 2022. The NZW rabbits had greater mean terminal body weights than DB strain. Mixed cell infiltration in the lung was the most recorded finding in both strains, followed by pulmonary inflammation/mononuclear cell infiltration. Differentiation between pulmonary "infiltration"/"inflammation" remained challenging as interpretation of guidelines for diagnostic terminology may vary amongst pathologists. Other common findings included mineralization and basophilia of the renal tubules; hepatic/renal mononuclear cell infiltration, all more common in females. Cysts were commonly recorded, with high prevalence in the oviduct, thyroid gland, ovary in NZW strain, while uterine, pituitary gland, and thyroid gland cysts were the most identified in DB rabbits. Neoplasms and infectious etiologies were absent. Most of the animals were sexually mature. To our knowledge, this is the most recent comprehensive study of spontaneous lesions and organ weights in both rabbit strains and should facilitate the differentiation of spontaneous and induced lesions in safety studies.

The so-called undruggable space is an exciting area of potential growth for drug development. Undruggable proteins are defined as those unable to be targeted via conventional small molecule drugs. New modalities are being developed to potentially target these proteins. Targeted protein degradation (TPD) is one such new modality, which over the last two decades has moved from academia to industry. TPD makes use of the endogenous degradation machinery present in all cells, in which E3 ubiquitin ligases mark proteins for degradation via ubiquitin attachment. This session explored the challenges and perspectives of using protein degraders as novel therapeutic agents. The session began with a general introduction to the modality, followed by considerations in evaluating their on- and off-target toxicities including data from an IQ Consortium working group survey. Unique absorption, distribution, metabolism, and excretion (ADME) properties of degrader molecules were presented in relation to their effect on drug development and nonclinical safety assessment. The role of transgenic models in evaluating hemotoxicity associated with cereblon-based therapies was then discussed. A case study to derisk dose-limiting thrombocytopenia was also presented. Finally, a regulatory perspective on the challenges of having toxicity associated with protein degraders was presented.

The virtual control group (VCG) concept was originally developed in the IMI2 project eTRANSAFE, using data of control animals which pharmaceutical companies have accrued over decades from animal toxicity studies. This control data could be repurposed to create virtual control animals to reduce or replace concurrent controls in animal studies. Initial work demonstrated the general feasibility of the VCG concept, but implementation requires significant further collaborative efforts. The new Innovative Health Initiative (IHI) project VICT3R aims to address these challenges and to obtain regulatory acceptance for the VCG concept. To achieve these goals, VICT3R will build a database comprising high-quality, standardized, and duly annotated control animal data from past and forthcoming toxicity studies. The VICT3R project will create workflows and computational tools to generate adequate VCGs based on statistical and artificial intelligence (AI) approaches. The validity, reproducibility, and robustness of the resulting VCGs will be assessed by comparing the performance of their use with that of real control groups.

Mass spectrometry imaging (MSI) was used to investigate and provide insights into observed biliary pathology found in dogs and rats after administration of two different compounds. Both compounds were associated with peribiliary inflammatory infiltrates and proliferation of the bile duct epithelium. However, MSI revealed very different spatial distribution profiles for the two compounds: Compound A showed significant accumulation within the bile duct epithelium with a much higher concentration than in the parenchymal hepatocytes, while Compound T exhibited only a slight increase in the bile duct epithelium compared to parenchymal hepatocytes. These findings implicate cholangiocyte uptake and accumulation as a key step in the mechanism of biliary toxicity. In both cases, compounds are shown at the site of toxicity in support of a direct mechanism of toxicity on the biliary epithelium. MSI is a powerful tool for localizing small molecules within tissue sections and improvements in sensitivity have enabled localization down to the cellular level in some cases. MSI was also able to identify biomarker candidates of toxicity by differential analysis of ion profiles comparing treated and control cholangiocytes from tissue sections.

Before the COVID-19 pandemic, digital pathology was increasingly used in veterinary education, diagnostics, and research. The pandemic accelerated this adoption as institutions needed to maintain operations amidst lockdowns. It also enabled pharmaceutical companies to conduct peer reviews digitally, circumventing travel restrictions. At the 2023 Society of Toxicologic Pathology Annual Symposium, a Town Hall Meeting highlighted the current use of digital pathology. A majority of the respondents viewed whole slide images (WSI) favorably. Many institutions use digital pathology primarily for non-GLP and GLP conforming primary reads and peer reviews. Takeda has long utilized digital pathology, incorporating scanners and an image management repository, and recently adopted a cloud-based platform tailored for toxicologic pathology, enhancing efficiency and collaboration. Digital pathology not only saves time but also reduces travel needs and environmental impact. Technological advancements and wider adoption are expected to further enhance the field, promising significant benefits for the overall digital pathology infrastructure.

Adeno-associated virus (AAV) gene therapy vectors are an accepted platform for treating severe neurological diseases. Test article (TA)-related and procedure-related neuropathological effects following administration of AAV-based vectors are observed in the central nervous system (CNS) and peripheral nervous system (PNS). Leukocyte accumulation (mononuclear cell infiltration > inflammation) may occur in brain, spinal cord, spinal nerve roots (SNRs), sensory and autonomic ganglia, and rarely nerves. Leukocyte accumulation may be associated with neuron necrosis (sensory ganglia > CNS) and/or glial changes (microgliosis and/or astrocytosis in the CNS, increased satellite glial cellularity in ganglia and/or Schwann cellularity in nerves). Axonal degeneration secondary to neuronal injury may occur in the SNR (dorsal > ventral), spinal cord (dorsal and occasionally lateral funiculi), and brainstem centrally and in nerves peripherally. Patterns of AAV-associated microscopic findings in the CNS and PNS differ for TAs administered into brain parenchyma (where tissue at the injection site is affected most) versus TAs delivered into cerebrospinal fluid (CSF) or systemically (which primarily impacts sensory ganglion neurons and their processes in SNR and spinal cord). Changes related to the TA and procedure may overlap. While often interpreted as adverse, AAV-associated neuronal necrosis and axonal degeneration of limited severity generally do not preclude clinical testing.

Adeno-associated virus (AAV)-based vectors are the most frequently used platform for retinal gene therapy. Initially explored for the treatment of loss-of-function mutations underpinning many inherited retinal diseases, AAV-based ocular gene therapies are increasingly used to transduce endogenous cells to produce therapeutic proteins, thus producing site-specific biofactories. Relatively invasive ocular routes of administration (ROA) mean prominent procedure-related in-life, and histopathological findings may be observed with some regularity. Test article-related findings may vary with the ROA and cell populations transduced, with retinal pigmented epithelium (RPE) changes prominent (ranging from pigment alteration through degeneration, with or without associated degeneration of the overlying retina) with subretinal ROA, and more anterior changes (iris, ciliary body) generally observed with the intravitreal ROA. Ocular inflammation is the most frequent finding that occurs nonclinically and in patients, and is particularly pronounced with intravitreal administration. Extraocular findings may be observed in extraocular muscles, regional ganglia, or central visual pathways with multiple ocular ROA. Work is still needed to understand the mechanisms underpinning many of these ocular and extraocular findings. Emerging patient data is helping to clarify both the potential for translating nonclinical findings to predict possible human responses and the applicability of nonclinical biomonitoring methods to the clinical setting.

Enhanced histopathology of the immune system uses a precise, compartment-specific, and semi-quantitative evaluation of lymphoid organs in toxicology studies. The assessment of lymphocyte populations in tissues is subject to sampling variability and limited distinctive cytologic features of lymphocyte subpopulations as seen with hematoxylin and eosin (H&E) staining. Although immunohistochemistry is necessary for definitive characterization of T- and B-cell compartments, routine toxicologic assessments are based solely on H&E slides. Here, a deep learning (DL) model was developed using normal rats to quantify relevant compartments of the spleen, including periarteriolar lymphoid sheaths, follicles, germinal centers, and marginal zones from H&E slides. Slides were scanned, destained, dual labeled with CD3 and CD79a chromogenic immunohistochemistry, and rescanned to generate exact co-registered images that served as the ground truth for training and validation. The DL model identified individual splenic compartments with high accuracy (97.8% Dice similarity coefficient) directly from H&E-stained tissue. The DL model was utilized to study the normal range of lymphoid compartment area and cellularity. Future implementation of our DL model and expanding this approach to other lymphoid tissues have the potential to improve accuracy and precision in enhanced histopathology evaluation of the immune system with concurrent gains in time efficiency for the pathologist.

The 2024 annual Division of Translational Toxicology (DTT) Satellite Symposium, entitled "Pathology Potpourri," was held in Baltimore, Maryland, at the Society of Toxicologic Pathology's 42nd annual meeting. The goal of this symposium was to present and discuss challenging diagnostic pathology and/or nomenclature issues. This article presents summaries of the speakers' talks along with select images that were used by the audience for voting and discussion. Various lesions and topics covered during the symposium included induced nonneoplastic lesions in the mouse kidney, induced and spontaneous neoplastic lesions in the mouse lung, infectious and proliferative lesions in nonhuman primates, an interesting inflammatory lesion in a transgenic mouse strain, and a lesson on artifact recognition.

Test article (TA)-induced seizures represent a major safety concern in drug development. Seizures (altered brain wave [electrophysiological] patterns) present clinically as abnormal consciousness with or without tonic/clonic convulsions (where "tonic" = stiffening and "clonic" = involuntary rhythmical movements). Neuropathological findings following seizures may be detected using many methods. Neuro-imaging may show a structural abnormality underlying seizures, such as focal cortical dysplasia or hippocampal sclerosis in patients with chronic epilepsy. Neural cell type-specific biomarkers in blood or cerebrospinal fluid may highlight neuronal damage and/or glial reactions but are not specific indicators of seizures while serum electrolyte and glucose imbalances may induce seizures. Gross observations and brain weights generally are unaffected by TAs with seizurogenic potential, but microscopic evaluation may reveal seizure-related neuron death in some brain regions (especially neocortex, hippocampus, and/or cerebellum). Current globally accepted best practices for neural sampling in nonclinical general toxicity studies provide a suitable screen for brain regions that are known sites of electrical disruption and/or display seizure-induced neural damage. Conventional nonclinical studies can afford an indication that a TA has a potential seizure liability (via in-life signs and/or microscopic evidence of neuron necrosis), but confirmation requires measuring brain electrical (electroencephalographic) activity in a nonclinical study.

Pathology, a fundamental discipline that bridges basic scientific discovery to the clinic, is integral to successful drug development. Intrinsically multimodal and multidimensional, anatomic pathology continues to be empowered by advancements in molecular and digital technologies enabling the spatial tissue detection of biomolecules such as genes, transcripts, and proteins. Over the past two decades, breakthroughs in spatial molecular biology technologies and advancements in automation and digitization of laboratory processes have enabled the implementation of higher throughput assays and the generation of extensive molecular data sets from tissue sections in biopharmaceutical research and development research units. It is our goal to provide readers with some rationale, advice, and ideas to help establish a modern molecular pathology laboratory to meet the emerging needs of biopharmaceutical research. This manuscript provides (1) a high-level overview of the current state and future vision for excellence in research pathology practice and (2) shared perspectives on how to optimally leverage the expertise of discovery, toxicologic, and translational pathologists to provide effective spatial, molecular, and digital pathology data to support modern drug discovery. It captures insights from the experiences, challenges, and solutions from pathology laboratories of various biopharmaceutical organizations, including their approaches to troubleshooting and adopting new technologies.

Through two decades of research and development, adoptive cell therapies (ACTs) have revolutionized treatment for hematologic malignancies. Many of the seven US Food and Drug Administration (FDA)-approved products are proven to be a curative last line of defense against said malignancies. The ACTs, known more commonly as chimeric antigen receptor (CAR) T-cells, utilize engineered lymphocytes to target and destroy cancer cells in a patient-specific, major histocompatibility complex (MHC)-independent manner, acting as "living drugs" that adapt to and surveil the body post-treatment. Despite their efficacy, CAR T-cell therapies present unique challenges in preclinical safety assessment. The safety and pharmacokinetics of CAR T-cells are influenced by numerous factors including donor and recipient characteristics, product design, and manufacturing processes that are not well-predicted by existing in vitro and in vivo preclinical safety models. The CAR therapy-mediated toxicities in clinical settings primarily arise from unintended targeting of non-tumor cells, potential tumorigenicity, and severe immune activation syndromes like cytokine release syndrome and immune effector cell-associated neurotoxicity. Addressing these issues necessitates a deep understanding of CAR target expression in normal tissues, inclusive of the spatial microanatomical distribution, off-target screening, and a deep understanding CAR cell manufacturing practices and immunopathology.

The Golden Syrian hamster is a well-characterized rodent model for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2)-associated pneumonia. We sought to characterize the pulmonary disease course during SARS-CoV-2 infection (strain USA-WA1/2020) in the hamster model using micro-computed tomography (micro-CT) and compare radiologic observations with histopathologic findings. We observed a range of radiologic abnormalities, including ground glass opacities (GGOs), consolidations, air bronchograms, and pneumomediastinum. The appearance, distribution, and progression of these abnormalities in hamsters were similar to those observed in the lungs of coronavirus disease 2019 (COVID-19) patients by clinical CT and chest X-rays, and correlated with clinical signs and weight loss during the course of disease. Histopathological analysis of infected hamsters revealed lung pathology characteristic of COVID-19 pneumonia, and we observed a strong association between CT and histopathologic scorings. We also analyzed accumulation of air in the thoracic cavity by both manual and automated threshold-based segmentation and found that automated analysis significantly decreases the time needed for data analysis. Data presented here demonstrate that micro-CT imaging can be a major tool in preclinical investigative studies using animal models by providing early and detailed assessment of disease severity and outcomes.

The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions) Project (www.toxpath.org/ inhand.asp) is a joint initiative of the Societies of Toxicologic Pathology from Europe (ESTP), Great Britain (BSTP), Japan (JSTP), and North America (STP) to develop an internationally accepted nomenclature for proliferative and nonproliferative lesions in laboratory animals. The purpose of this publication is to provide a standardized nomenclature for classifying lesions observed in ocular tissues (eyes and glands and ocular adnexa) from laboratory nonrodent species (rabbits, dogs, minipigs, and nonhuman primates) used in nonclinical safety studies with an emphasis on ocular-targeted dosing. Some of the lesions are illustrated by color photomicrographs. The standardized nomenclature presented in this document is also available electronically on the Internet (http://www.goreni.org/). Sources of material included histopathology databases from government, academia, and industrial laboratories throughout the world. Content includes descriptions and visual depictions of spontaneous lesions and lesions induced by exposure to various test materials. A widely accepted and utilized internationally harmonized nomenclature for lesions in laboratory animals will provide a common language among regulatory and scientific research organizations in different countries and increase and enrich international exchanges of information among toxicologists and pathologists.