Enhancing Specific Fluorescence In Situ Hybridization with Quantum Dots for Single-Molecule RNA Imaging in Formalin-Fixed Paraffin-Embedded Tumor Tissues

Single-molecule fluorescence in situ hybridization (smFISH) represents a promising approach for the quantitative analysis of nucleic acid biomarkers in clinical tissue samples. However, low signal intensity and high background noise are complications that arise from diagnostic pathology when performed with smFISH-based RNA imaging in formalin-fixed paraffin-embedded (FFPE) tissue specimens. Moreover, the associated complex procedures can produce uncertain results and poor image quality. Herein, by combining the high specificity of split DNA probes with the high signal readout of ZnCdSe/ZnS quantum dot (QD) labeling, we introduce QD split-FISH, a high-brightness smFISH technology, to quantify the expression of mRNA in both cell lines and clinical FFPE tissue samples of breast cancer and lung squamous carcinoma. Owing to its high signal-to-noise ratio, QD split-FISH is a fast, inexpensive, and sensitive method for quantifying mRNA expression in FFPE tumor tissues, making it suitable for biomarker imaging and diagnostic pathology.

A novel case of cutaneous, nasal and systemic fusariosis in a goat

The clinical findings associated with nasal, cutaneous and systemic fusariosis in a 3-year-old billy Boer goat are summarised. The clinical features, treatment, postmortem findings and laboratory diagnostics are reported and discussed in the context of existing knowledge on mycoses of small ruminants. The goat presented primarily for respiratory signs (inspiratory dyspnoea) with unilateral left-sided mucopurulent nasal discharge, and multifocal variably ulcerative and necrotic cutaneous nodules. Histopathology of nasal and cutaneous biopsies revealed necrotising pyogranulomatous inflammation with intralesional septate hyphal elements that correlated with culture of Fusarium oxysporum. The patient continued to deteriorate clinically during treatment with oxytetracycline and meloxicam, with the addition of sodium iodide and potassium iodide, and was humanely euthanased. Postmortem examination revealed multifocal nodular lesions throughout the kidneys, abdominal lymph nodes and lungs. These lesions were consistent with those identified antemortem from which F. oxysporum was cultured. Although treatment was unsuccessful, to the author's knowledge, no instance of rhinofacial or systemic caprine infection with Fusarium spp. has been documented in the veterinary literature, making this the first recognised instance of this form of infection in small ruminant species.

Carcinoma Cuniculatum of the Maxilla Arising From Oroantral Fistula: A Report of an Extremely Rare Case

Carcinoma cuniculatum (CC) is extremely rare in the maxilla. Here, we report a case of CC arising from an oroantral fistula (OAF). The patient was a 70-year-old Japanese man who was followed up for a non-closing OAF. Although there were no findings based on an intraoral examination, follow-up contrast-enhanced computed tomography and magnetic resonance imaging showed a 22-mm mass in the maxilla close to the OAF. Histologically, cystic and endophytic papillary proliferation of squamous epithelium with abundant keratinization mimicking rabbit burrows occupied the alveolar bone. This tumor was directly connected to the atypical proliferation of the covering epithelium of the OAF. The tumor cells showed mild cytological atypia and a few mitoses. Finally, the patient was diagnosed with CC arising from an OAF. CC is often misdiagnosed; nonetheless, the unique endophytic, branching, and tunnel-like structure is a hallmark of this tumor. We present the first well-documented case of CC arising from an OAF, discuss its diagnostic features, and highlight its differences from other common benign and malignant pathological entities.

Common and Not-So-Common Pathologic Findings of the Gastrointestinal Tract of Rhesus and Cynomolgus Macaques

Rhesus and cynomolgus macaques are the most frequently used nonhuman primate (NHP) species for biomedical research and toxicology studies of novel therapeutics. In recent years, there has been a shortage of laboratory macaques due to a variety of competing factors. This was most recently exacerbated by the surge in NHP research required to address the severe acute respiratory syndrome (SARS)-coronavirus 2 pandemic. Continued support of these important studies has required the use of more varied cohorts of macaques, including animals with different origins, increased exposure to naturally occurring pathogens, and a wider age range. Diarrhea and diseases of the gastrointestinal tract are the most frequently occurring spontaneous findings in macaques of all origins and ages. The purpose of this review is to alert pathologists and scientists involved in NHP research to these findings and their impact on animal health and study endpoints, which may otherwise confound the interpretation of data generated using macaques.

An Autopsy Case of Idiopathic Rhabdomyolysis in 1979: Immunoperoxidase Detection of Myoglobin Casts in Formalin-Fixed, Paraffin-Embedded Sections of the Kidney

In 1979, the author in his younger days experienced an autobiographical case of idiopathic rhabdomyolysis. The heme casts in formalin-fixed, paraffin-embedded sections of the kidney were immunoreactive for myoglobin. In these days, the immunoperoxidase technique had been utilized as a research seed by using paraformaldehyde-fixed frozen sections. The precious experience prompted the young author of his younger days to apply the immunoperoxidase method to diagnostic pathology using formalin-fixed paraffin-embedded sections. A brief history of early development of chromogenic immunostaining in diagnostic pathology in Japan is summarized.

Morphological Characteristics of Alveolar and Cystic Echinococcosis Lesions in Human Liver and Bone

Among echinococcoses diseases of human interest, two have a global public health impact: cystic and alveolar echinococcosis caused by Echinococcus granulosus sensu lato and Echinococcus multilocularis, respectively. Cystic and alveolar echinococcosis are neglected infectious diseases epidemiologically and are clinically vastly different with distinct microscopic features. Because of the rareness of these zoonotic diseases, pathologists have limited diagnostic experience in the analysis of the lesions caused by Echinococcus tapeworms. Here, we describe the main microscopic features to be considered to characterize these lesions: laminated layer, central necrosis, growth pattern, and delineation from adjacent tissue. Moreover, immunohistology using monoclonal antibodies is of great diagnostic help in reaching a definitive diagnosis by identifying the laminated body and small particles of E. multilocularis (spems) and small particles of E. granulosus (spegs).

Artificial Intelligence in Digital Pathology: What Is the Future? Part 2: An Investigation on the Insiders

Motivation: This study deals with the introduction of artificial intelligence (AI) in digital pathology (DP). The study starts from the highlights of a companion paper. Objective: The aim was to investigate the consensus and acceptance of the insiders on this issue. Procedure: An electronic survey based on the standardized package Microsoft Forms (Microsoft, Redmond, WA, USA) was proposed to a sample of biomedical laboratory technicians (149 admitted in the study, 76 males, 73 females, mean age 44.2 years). Results: The survey showed no criticality. It highlighted (a) the good perception of the basic training on both groups, and (b) a uniformly low perceived knowledge of AI (as arisen from the graded questions). Expectations, perceived general impact, perceived changes in the work-flow, and worries clearly emerged in the study. Conclusions: The of AI in DP is an unstoppable process, as well as the increase of the digitalization in the health domain. Stakeholders must not look with suspicion towards AI, which can represent an important resource, but should invest in monitoring and consensus training initiatives based also on electronic surveys.

Improving Generalization of Deep Learning Models for Diagnostic Pathology by Increasing Variability in Training Data: Experiments on Osteosarcoma Subtypes

BACKGROUND

Artificial intelligence has an emerging progress in diagnostic pathology. A large number of studies of applying deep learning models to histopathological images have been published in recent years. While many studies claim high accuracies, they may fall into the pitfalls of overfitting and lack of generalization due to the high variability of the histopathological images.

AIMS AND OBJECTS

Use the model training of osteosarcoma as an example to illustrate the pitfalls of overfitting and how the addition of model input variability can help improve model performance.

MATERIALS AND METHODS

We use the publicly available osteosarcoma dataset to retrain a previously published classification model for osteosarcoma. We partition the same set of images into the training and testing datasets differently than the original study: the test dataset consists of images from one patient while the training dataset consists images of all other patients. We also show the influence of training data variability on model performance by collecting a minimal dataset of 10 osteosarcoma subtypes as well as benign tissues and benign bone tumors of differentiation.

RESULTS

The performance of the re-trained model on the test set using the new partition schema declines dramatically, indicating a lack of model generalization and overfitting. We show the additions of more and moresubtypes into the training data step by step under the same model schema yield a series of coherent models with increasing performances.

CONCLUSIONS

In conclusion, we bring forward data preprocessing and collection tactics for histopathological images of high variability to avoid the pitfalls of overfitting and build deep learning models of higher generalization abilities.

Distinct Histopathological Features at Diagnosis of Very Early Onset Inflammatory Bowel Disease

BACKGROUND AND AIMS

Children with very early onset inflammatory bowel disease [VEO-IBD] represent a unique cohort, often with a severe phenotype that is refractory to conventional medications, and some cases have underlying primary immunodeficiencies. Previous work has identified distinct histopathological patterns in the gastrointestinal tract in patients with primary immunodeficiencies. The aim of this study is to characterise the diagnostic histological findings in patients with VEO-IBD as compared with older onset paediatric IBD, and determine if there are unique pathological changes that can shed light on the driving forces of the disease, particularly immunodeficiencies.

METHODS

Clinical retrospective chart review, including disease characteristics and endoscopic findings, was performed on all included subjects. Two paediatric pathologists reviewed biopsies from diagnostic upper endoscopies and colonoscopies of subjects with very early onset inflammatory bowel disease and older onset inflammatory bowel disease, to evaluate for the presence of 11 histological features previously associated with inflammatory bowel disease and primary immunodeficiencies.

RESULTS

The diagnostic gastrointestinal biopsies of subjects with very early onset inflammatory bowel disease differed from those in older onset paediatric IBD, demonstrated by increased frequency of apoptosis, severe chronic architectural changes, small intestine villous blunting, and eosinophils in the crypts, lamina propria, and surface epithelium.

CONCLUSIONS

The diagnostic biopsies of children with very early onset inflammatory bowel disease can identify characteristic features that may be important in guiding the diagnostic work-up in this population.

Pathologic, histochemical, and immunohistochemical findings in pulmonary and encephalitic cryptococcosis in a goat

We describe the pathologic, histochemical, and immunohistochemical findings associated with pulmonary and encephalitic cryptococcosis in a 3-y-old, mixed-breed, nanny goat from central-west Brazil. The goat had progressive neurologic signs over 30 d; cryptococcosis was diagnosed antemortem by cytologic evaluation of cerebrospinal fluid. Treatment was initiated, but the animal died spontaneously shortly thereafter. Grossly, there was a large space-occupying gelatinous mass (cryptococcoma) in the left lung and smaller masses in the cerebral temporal and frontal cortex, thalamus, hippocampus, basal nuclei, and mesencephalon with consequent internal hydrocephalus. Histologic evaluation revealed marked granulomatous cryptococcal pneumonia and meningoencephalitis. Intralesional narrow-necked budding cryptococcal yeasts were identified on special stains (Mayer mucicarmine and Grocott methenamine silver) in sections of lung and brain. Immunohistochemistry utilizing a panel of monoclonal antibodies that selectively label capsules of Cryptococcus spp. was consistent with C. neoformans var. grubii.

Nonproliferative and Proliferative Lesions of the Rat and Mouse Endocrine System

The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions in Rats and Mice) Project (www.toxpath.org/inhand.asp) is a joint initiative among the Societies of Toxicological 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 microscopic lesions observed in the endocrine organs (pituitary gland, pineal gland, thyroid gland, parathyroid glands, adrenal glands and pancreatic islets) of laboratory rats and mice, with color photomicrographs illustrating examples of the lesions. 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 spontaneous and aging lesions as well as lesions induced by exposure to test materials. A widely accepted and utilized international harmonization of nomenclature for endocrine lesions in laboratory animals will decrease confusion among regulatory and scientific research organizations in different countries and provide a common language to increase and enrich international exchanges of information among toxicologists and pathologists.

Systemic Histomoniasis in a Leucistic Indian Peafowl (Pavo cristatus) from Southern Brazil

The pathological and molecular findings associated with Histomonas meleagridis are described in a leucistic Indian peafowl (Pavo cristatus) from Southern Brazil. The most significant gross findings were multifocal necrotizing hepatitis and diphtheric typhlitis. Histopathologic evaluation of the liver, ceca, kidney, spleen, and small intestine revealed systemic histomoniasis (SH) associated with intralesional and intravascular accumulations of histomonad organisms consistent with H. meleagridis. PCR was used to amplify the DNA of H. meleagridis from the liver, ceca, small intestine, spleen, lungs, and kidneys. Direct sequencing and phylogenetic analyses confirmed that the isolate of the flagellated trichomonad identified from this investigation is more phylogenetically related to H. meleagridis than Tetratrichomonas gallinarum, Tritrichomonas foetus, and Dientamoeba fragilis. These results confirmed the occurrence of SH in this peafowl and add to the diagnosis of this disease in birds from Brazil. This report might represent the first complete identification of spontaneous histomoniasis in a peafowl due to pathological and molecular characteristics and one of the few documented cases of SH in non-commercial birds.

Pneumonia due to Talaromyces marneffei in a Dog from Southern Brazil with Concomitant Canine Distemper Virus Infection

The pathological and molecular findings associated with Talaromyces marneffei-induced pneumonia with concomitant infection by canine distemper virus (CDV) are described in a dog. The principal pathological alteration occurred in the lungs. Histopathology confirmed multifocal granulomatous pneumonia associated with numerous intralesional and intracellular septate fission cells consistent with T. marneffei. A molecular assay designed to amplify a partial fragment of the 18S rRNA gene of T. marneffei provided positive results from two fungal cultures derived from the lung. Sequencing and phylogenetic analyses confirmed the results of polymerase chain reaction (PCR). Furthermore, antigens of the CDV N protein were identified within the bronchial epithelium by immunohistochemistry and a PCR assay amplified the CDV N gene from hepatic and pulmonary fragments. Collectively, the pathological and molecular techniques confirmed a diagnosis of T. marneffei-induced pneumonia with concomitant infection by CDV. These findings represent the first description of pulmonary penicilliosis in the dog and extend the geographical niche of this emerging infectious pathogen. In this case, infection by CDV may have induced immunosuppression, which facilitated the development of pulmonary penicilliosis.

Non-proliferative and Proliferative Lesions of the Cardiovascular System of the Rat and Mouse

The INHAND Project (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions in Rats and Mice) is a joint initiative of the Societies of Toxicologic Pathology from Japan (JSTP), Europe (ESTP), Great Britain (BSTP) and North America (STP) to develop an internationally-accepted nomenclature for proliferative and non-proliferative lesions in laboratory animals. The primary purpose of this publication is to provide a standardized nomenclature for characterizing lesions observed in the cardiovascular (CV) system of rats and mice commonly used in drug or chemical safety assessment. The standardized nomenclature presented in this document is also available electronically for society members on the internet (http://goreni.org). Accurate and precise morphologic descriptions of changes in the CV system are important for understanding the mechanisms and pathogenesis of those changes, differentiation of natural and induced injuries and their ultimate functional consequence. Challenges in nomenclature are associated with lesions or pathologic processes that may present as a temporal or pathogenic spectrum or when natural and induced injuries share indistinguishable features. Specific nomenclature recommendations are offered to provide a consistent approach.

Nonproliferative and Proliferative Lesions of the Rat and Mouse Skeletal Tissues (Bones, Joints, and Teeth)

The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions in Rats and Mice) Project (www.toxpath.org/inhand.asp) is an initiative of the Societies of Toxicological 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 microscopic lesions observed in the skeletal tissues and teeth of laboratory rats and mice, with color photomicrographs illustrating examples of many common lesions. The standardized nomenclature presented in this document is also available on the internet (http://www.goreni.org/). Sources of material were databases from government, academic and industrial laboratories throughout the world.

Nonproliferative and Proliferative Lesions of the Gastrointestinal Tract, Pancreas and Salivary Glands of the Rat and Mouse

The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions in Rats and Mice) project 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 and diagnostic criteria for nonproliferative and proliferative lesions in laboratory animals. The purpose of this publication is to provide a standardized nomenclature and diagnostic criteria for classifying lesions in the digestive system including the salivary glands and the exocrine pancreas of laboratory rats and mice. Most lesions are illustrated by color photomicrographs. The standardized nomenclature, the diagnostic criteria, and the photomicrographs are 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 spontaneous and age related lesions as well as lesions induced by exposure to test items. Relevant infectious and parasitic lesions are included as well. A widely accepted and utilized international harmonization of nomenclature and diagnostic criteria for the digestive system will decrease misunderstandings among regulatory and scientific research organizations in different countries and provide a common language to increase and enrich international exchanges of information among toxicologists and pathologists.

Detection of cancer/testis antigens as a diagnostic tool in routine pathology practice

Most of the studies on cancer/testis (CT) antigens performed to date have focused on their potential value as targets for immunotherapy. Several recent studies, however, revealed that CT antigens might represent useful tools for diagnostic pathology, in particular for the identification of squamous cell carcinoma and related pre-malignant lesions, as well as specific types of sarcoma.

Nonproliferative and proliferative lesions of the rat and mouse female reproductive system

The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions in Rats and Mice) Project (www.toxpath.org/inhand.asp) is a joint initiative of the Societies of Toxicological 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 microscopic lesions observed in the female reproductive tract of laboratory rats and mice, with color photomicrographs illustrating examples of some lesions. 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 spontaneous and aging lesions as well as lesions induced by exposure to test materials. There is also a section on normal cyclical changes observed in the ovary, uterus, cervix and vagina to compare normal physiological changes with pathological lesions. A widely accepted and utilized international harmonization of nomenclature for female reproductive tract lesions in laboratory animals will decrease confusion among regulatory and scientific research organizations in different countries and provide a common language to increase and enrich international exchanges of information among toxicologists and pathologists.

Proliferative and non-proliferative lesions of the rat and mouse integument

The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions in Rats and Mice) project is a joint initiative of the societies of toxicological pathology from Europe (ESTP), Great Britain (BSTP), Japan (JSTP) and North America (STP). Its aim is to develop an internationally-accepted nomenclature for proliferative and non-proliferative lesions in laboratory rodents. A widely accepted international harmonization of nomenclature in laboratory animals will decrease confusion among regulatory and scientific research organizations in different countries and will provide a common language to increase and enrich international exchanges of information among toxicologists and pathologists. The purpose of this publication is to provide a standardized nomenclature for classifying microscopical lesions observed in the integument of laboratory rats and mice. Example colour images are provided for most lesions. The standardized nomenclature presented in this document and additional colour images are also available electronically at http://www.goreni.org. The nomenclature presented herein is based on histopathology databases from government, academia, and industrial laboratories throughout the world, and covers lesions that develop spontaneously as well as those induced by exposure to various test materials. (DOI: 10.1293/tox.26.27S; J Toxicol Pathol 2013; 26: 27S-57S).

Microarray techniques in pathology: tool or toy?

Microarray technology allows the simultaneous analysis of up to thousands of different genes in histological or cytological specimens. Although microarray technology has so far mainly been applied in the research setting, its clinical application in pathology is expected in the foreseeable future. This paper presents an overview of the technical "ins and outs" of microarray technology, and discusses several putative applications in diagnostic pathology, which include tumour classification, the prediction of responses to certain chemotherapeutical or hormonal agents, the biological staging of tumours, the risk assessment of premalignant lesions, and the detection of microorganisms.

New algorithms based on the Voronoi Diagram applied in a pilot study on normal mucosa and carcinomas

An adequate reproducibility in the description of tissue architecture is still a challenge to diagnostic pathology, sometimes with unfortunate prognostic implications. To assess a possible diagnostic and prognostic value of quantitiative tissue architecture analysis, structural features based on the Voronoi Diagram (VD) and its subgraphs were developed and tested. A series of 27 structural features were developed and tested in a pilot study of 30 cases of prostate cancer, 10 cases of cervical carcinomas, 8 cases of tongue cancer and 8 cases of normal oral mucosa. Grey level images were acquired from hematoxyline-eosine (HE) stained sections by a charge coupled device (CCD) camera mounted on a microscope connected to a personal computer (PC) with an image array processor. From the grey level images obtained, cell nuclei were automatically segmented and the geometrical centres of cell nuclei were computed. The resulting 2-dimensional (2D) swarm of pointlike seeds distributed in a flat plane was the basis for construction of the VD and its subgraphs. From the polygons, triangulations and arborizations thus obtained, 27 structural features were computed as numerical values. Comparison of groups (normal vs. cancerous oral mucosa, cervical and prostate carcinomas with good and poor prognosis) with regard to distribution in the values of the structural features was performed with Student's t-test. We demonstrate that some of the structural features developed are able to distinguish structurally between normal and cancerous oral mucosa (P = 0.001), and between good and poor outcome groups in prostatic (P = 0.001) and cervical carcinomas (P = 0.001). We present results confirming previous findings that graph theory based algorithms are useful tools for describing tissue architecture (e.g., normal versus malignant). The present study also indicates that these methods have a potential for prognostication in malignant epithelial lesions.