Why microscopy will remain a cornerstone of surgical pathology

Digital quantification of Ki67 and PRAME in challenging melanocytic lesions - A novel diagnostic tool

The interpretation of immunohistochemical markers in melanocytic lesions possesses difficulties due to expression in non-melanocytic cells and the time-consuming, non-reproducible nature of manual assessment. A digital tool that accurately quantifies Ki67 and PRAME may valuably aid pathologists in the diagnostic classification of melanocytic lesions. The aim of this study was to assess the diagnostic performance of digitally quantified Ki67 and PRAME in challenging melanocytic lesions utilizing double nuclear staining methods for accurate identification of melanocytic cells. We explored the difference in Ki67 and PRAME expression by WHO-lesion-groups and Melanocytic Pathology Assessment Tool and Hierarchy for Diagnosis version 2.0 (MPATH-Dx V2.0). Tissue slides from a cohort of 156 melanocytic lesions were stained with the Ki67/SOX10 double nuclear stain and the PRAME/SOX10 virtual double nuclear stain. Melanocytic cell specific Ki67/SOX10- and PRAME/SOX10-indexes were quantified by AI-driven digital image analysis (DIA) and compared to non-specific Ki67- and PRAME-indexes. The results showed that ROC AUC of the Ki67/SOX10-index was increased compared to the non-specific Ki67-index (p < 0.001), as opposed to the AUC of the PRAME/SOX10-index compared to non-specific PRAME-index (p = 0.090). The medians of digitally quantified Ki67- and PRAME-indexes differed significantly for the overall WHO-groups and MPATH-Dx V2.0 classes (p < 0.001). In conclusion, we found that double nuclear staining improved the diagnostic performance of Ki67, but not PRAME. The combination of digitally quantified Ki67- and PRAME-indexes may potentially serve as a tool for diagnostic classification of challenging melanocytic lesions. The proposed diagnostic tool presents the results visually, graphically, and quantitatively to optimally aid the pathologist.

Zoom in on learning with a virtual microscope: A convergent parallel mixed-method study

Knowledge of histology is essential for many disciplines in professional health education. Virtual Microscopes (VMs) are increasingly becoming popular as a cost-effective teaching tool for histology. However, a lack of hands-on experience with traditional light microscopes and glass slides concerns many educators. Although studies have reported improvement or no difference in students' knowledge and/or performance using either virtual or optical microscopes, reports on the impact of VMs on students' understanding of magnification and orientation are scarce. We conducted a convergent, parallel mixed-method study to assess dental students' understanding of magnification and orientation after using a virtual microscope to study oral histology. Six hours of mandatory lab sessions and critical thinking assignment questions were designed for the 1st year students in the Doctor of Dental Surgery (DDS) program. Quantitative data were collected from students' performance in orientation and magnification-related questions in the summative assessments. Students' written responses to reflective questions were the qualitative data, analyzed using manifest content analysis. All 32 students accurately answered 3 out of 5 questions, requiring them to apply the knowledge of magnification and orientation. 30 and 29 students correctly answered the remaining questions, respectively. 97% of the class agreed to improve their understanding of magnification and orientation after using the VM. All (100%) students (n = 32) completed the reflective assignment, generating 64 meaning units. 17 codes were generated and compiled into seven subcategories, which were further condensed into two categories: refinement of mental models and enhanced learning. Although our study is limited by a small sample size, it sheds light on the strategies adopted by dental students to improve their senses of magnification and orientation while using a VM.

A Proof-of-Concept Solution for Co-locating 2D Histology Images in 3D for Histology-to-CT and MR Image Registration: Closing the Loop for Bone Sarcoma Treatment Planning

This work presents a proof-of-concept solution designed to facilitate more accurate radiographic feature characterisation in pre-surgical CT/MR volumes. The solution involves 3D co-location of 2D digital histology slides within ex-vivo, tumour tissue CT volumes. Initially, laboratory dissection measurements seed the placement of histology slices in corresponding CT volumes, followed by in-plane point-based registration of bone in histology images to the bone in CT. Validation using six bisected canine humerus ex-vivo CT datasets indicated a plane misalignment of 0.19 ± 1.8 mm. User input sensitivity was assessed at 0.08 ± 0.2 mm for plane translation and 0-1.6° deviation. These results show a similar magnitude of error to related prostate histology co-location work. Although demonstrated with a femoral canine sarcoma tumour, this solution can be generalised to various orthopaedic geometries and sites. It supports high-fidelity histology image co-location to improve understanding of tissue characterisation accuracy in clinical radiology. This solution requires only minimal adjustment to routine workflows. By integrating histology insights earlier in the presentation-diagnosis-planning-surgery-recovery loop, this solution guides data co-location to support the continued evaluation of safe pre-surgical margins.

Trends and Challenges of the Modern Pathology Laboratory for Biopharmaceutical Research Excellence

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.

The tumour histopathology "glossary" for AI developers

The applications of artificial intelligence (AI) and deep learning (DL) are leading to significant advances in cancer research, particularly in analysing histopathology images for prognostic and treatment-predictive insights. However, effective translation of these computational methods requires computational researchers to have at least a basic understanding of histopathology. In this work, we aim to bridge that gap by introducing essential histopathology concepts to support AI developers in their research. We cover the defining features of key cell types, including epithelial, stromal, and immune cells. The concepts of malignancy, precursor lesions, and the tumour microenvironment (TME) are discussed and illustrated. To enhance understanding, we also introduce foundational histopathology techniques, such as conventional staining with hematoxylin and eosin (HE), antibody staining by immunohistochemistry, and including the new multiplexed antibody staining methods. By providing this essential knowledge to the computational community, we aim to accelerate the development of AI algorithms for cancer research.

Digital analysis of the prostate tumor microenvironment with high-order chromogenic multiplexing

As our understanding of the tumor microenvironment grows, the pathology field is increasingly utilizing multianalyte diagnostic assays to understand important characteristics of tumor growth. In clinical settings, brightfield chromogenic assays represent the gold-standard and have developed significant trust as the first-line diagnostic method. However, conventional brightfield tests have been limited to low-order assays that are visually interrogated. We have developed a hybrid method of brightfield chromogenic multiplexing that overcomes these limitations and enables high-order multiplex assays. However, how compatible high-order brightfield multiplexed images are with advanced analytical algorithms has not been extensively evaluated. In the present study, we address this gap by developing a novel 6-marker prostate cancer assay that targets diverse aspects of the tumor microenvironment such as prostate-specific biomarkers (PSMA and p504s), immune biomarkers (CD8 and PD-L1), a prognostic biomarker (Ki-67), as well as an adjunctive diagnostic biomarker (basal cell cocktail) and apply the assay to 143 differentially graded adenocarcinoma prostate tissues. The tissues were then imaged on our spectroscopic multiplexing imaging platform and mined for proteomic and spatial features that were correlated with cancer presence and disease grade. Extracted features were used to train a UMAP model that differentiated healthy from cancerous tissue with an accuracy of 89% and identified clusters of cells based on cancer grade. For spatial analysis, cell-to-cell distances were calculated for all biomarkers and differences between healthy and adenocarcinoma tissues were studied. We report that p504s positive cells were at least 2× closer to cells expressing PD-L1, CD8, Ki-67, and basal cell in adenocarcinoma tissues relative to the healthy control tissues. These findings offer a powerful insight to understand the fingerprint of the prostate tumor microenvironment and indicate that high-order chromogenic multiplexing is compatible with digital analysis. Thus, the presented chromogenic multiplexing system combines the clinical applicability of brightfield assays with the emerging diagnostic power of high-order multiplexing in a digital pathology friendly format that is well-suited for translational studies to better understand mechanisms of tumor development and growth.

Head-to-head: Should Ki67 proliferation index be included in the formal classification of pulmonary neuroendocrine neoplasms?

The reporting of lung neuroendocrine neoplasms (NENs) according to the 2021 World Health Organisation (WHO) is based on mitotic count per 2 mm2, necrosis assessment and a constellation of cytological and immunohistochemical details. Accordingly, typical carcinoid and atypical carcinoid are low- to intermediate-grade neuroendocrine tumours (NETs), while large-cell neuroendocrine carcinoma (NEC) and small-cell lung carcinoma are high-grade NECs. In small-sized diagnostic material (cytology and biopsy), the noncommittal term of carcinoid tumour/NET not otherwise specified (NOS) and metastatic carcinoid NOS have been introduced with regard to primary and metastatic diagnostic settings, respectively. Ki-67 antigen, a well-known marker of cell proliferation, has been included in the WHO classification as a non-essential but desirable criterion, especially to distinguish NETs from high-grade NECs and to delineate the provisional category of carcinoid tumours/NETs with elevated mitotic counts (> 10 mitoses per mm2) and/or Ki-67 proliferation index (≥ 30%). However, a wider use of this marker in the spectrum of lung NENs continues to be highly reported and debated, thus witnessing a never-subsided attention. Therefore, the arguments for and against incorporating Ki-67 in the classification and clinical practice of these neoplasms are discussed herein in detail.

ResSAT: Enhancing Spatial Transcriptomics Prediction from H&E- Stained Histology Images with Interactive Spot Transformer

Spatial transcriptomics (ST) revolutionizes RNA quantification with high spatial resolution. Hematoxylin and eosin (H&E) images, the gold standard in medical diagnosis, offer insights into tissue structure, correlating with gene expression patterns. Current methods for predicting spatial gene expression from H&E images often overlook spatial relationships. We introduce ResSAT (Residual networks - Self-Attention Transformer), a framework generating spatially resolved gene expression profiles from H&E images by capturing tissue structures and using a self-attention transformer to enhance prediction.Benchmarking on 10× Visium datasets, ResSAT significantly outperformed existing methods, promising reduced ST profiling costs and rapid acquisition of numerous profiles.

Anti-fibrotic Effect of Oral Versus Intraperitoneal Administration of Gold Nanoparticles in Hepatic Schistosoma mansoni-Infected Mice

BACKGROUND

Schistosomiasis significantly impacts public health, as it causes severe morbidity. Infections caused by Schistosoma mansoni (S. mansoni) can be treated with gold nanoparticles (AuNPs). This study aims to determine the most effective route of AuNPs administration and the magnitude of its anti-fibrotic effect.

METHODS

In the five groups' in vivo assay design, AuNPs were administered intraperitoneally (1 mg/kg) and orally (1 mg/100 g) to S. mansoni-infected mice. Biochemical parameters (serum levels of albumin and liver enzymes alanine aminotransferase (ALT), and aspartate aminotransferase (AST) were measured. The histological changes of the liver in distinct groups were evaluated using Hematoxylin and Eosin, Masson's trichrome, and immunohistochemical stains.

RESULTS

Infection with S. mansoni was associated with substantial changes in the histological architecture of liver tissue and abnormal levels of hepatic function tests (albumin, AST, and ALT). Schistosoma infected hepatocytes exhibited an abnormal microscopic morphology, granuloma formation and aggressive fibrosis. AuNPs restored the liver histological architecture with a highly significant anti-fibrotic effect and significantly corrected hepatic function test levels. Intraperitoneal administration of AuNPs resulted in the most significant anti-fibrotic effect against hepatic S. mansoni infection as observed in all histological sections with Masson's trichrome being the best stain to represent this fact.

CONCLUSION

For treating S. mansoni-induced chronic liver fibrosis, intraperitoneal administration of AuNPs is a successful and effective route of administration that can be recommended.

Built to Last? Reproducibility and Reusability of Deep Learning Algorithms in Computational Pathology

Recent progress in computational pathology has been driven by deep learning. While code and data availability are essential to reproduce findings from preceding publications, ensuring a deep learning model's reusability is more challenging. For that, the codebase should be well-documented and easy to integrate into existing workflows and models should be robust toward noise and generalizable toward data from different sources. Strikingly, only a few computational pathology algorithms have been reused by other researchers so far, let alone employed in a clinical setting. To assess the current state of reproducibility and reusability of computational pathology algorithms, we evaluated peer-reviewed articles available in PubMed, published between January 2019 and March 2021, in 5 use cases: stain normalization; tissue type segmentation; evaluation of cell-level features; genetic alteration prediction; and inference of grading, staging, and prognostic information. We compiled criteria for data and code availability and statistical result analysis and assessed them in 160 publications. We found that only one-quarter (41 of 160 publications) made code publicly available. Among these 41 studies, three-quarters (30 of 41) analyzed their results statistically, half of them (20 of 41) released their trained model weights, and approximately a third (16 of 41) used an independent cohort for evaluation. Our review is intended for both pathologists interested in deep learning and researchers applying algorithms to computational pathology challenges. We provide a detailed overview of publications with published code in the field, list reusable data handling tools, and provide criteria for reproducibility and reusability.

Feasibility and safety of synchrotron-based X-ray phase contrast imaging as a technique complementary to histopathology analysis

X-ray phase contrast imaging (X-PCI) is a powerful technique for high-resolution, three-dimensional imaging of soft tissue samples in a non-destructive manner. In this technical report, we assess the quality of standard histopathological techniques performed on formalin-fixed, paraffin-embedded (FFPE) human tissue samples that have been irradiated with different doses of X-rays in the context of an X-PCI experiment. The data from this study demonstrate that routine histochemical and immunohistochemical staining quality as well as DNA and RNA analyses are not affected by previous X-PCI on human FFPE samples. From these data we conclude it is feasible and acceptable to perform X-PCI on FFPE human biopsies.

Histology as a paradigm for a science-based learning experience: Visits by histology education spirits of past, present, and future

The term "histology" was coined a little over 200 years ago and the subject has always relied on microscopy as its defining technology. Microscopy was and still is an essential approach for the description of cellular components and their arrangements in living organisms. For more than a century and a half, histology or microanatomy has also been part of the basic science education for biomedical students. Traditionally, it has been taught in two major components, a didactic transfer of information, either in a lecture or self-learning format, and in active-learning laboratory sessions. These two modes of histology instruction conform with the dual-processing theory of learning, one being more automatic and depending mainly on rote memorization, whereas the other is analytical, requiring more advanced reasoning skills. However, these two components of histology education are not separate and independent, but rather complementary and part of a multi-step learning process that encourages a scientific analysis of visual information and involves higher-level learning skills. Conventional, as well as modern electronic instruction methods (e-learning) have been used in complementary ways to support the integrated succession of individual learning steps as outlined in this manuscript. However, as recent curricular reforms have curtailed instructional time, this traditional format of teaching histology is no longer sustainable and a reflective reassessment of the role of histology in modern biomedical education is a timely necessity.

Virtual Microscopy Goes Global: The Images Are Virtual and the Problems Are Real

For the last two centuries, the scholarly education of histology and pathology has been based on technology, initially on the availability of low-cost, high-quality light microscopes, and more recently on the introduction of computers and e-learning approaches to biomedical education. Consequently, virtual microscopy (VM) is replacing glass slides and the traditional light microscope as the main instruments of instruction in histology and pathology laboratories. However, as with most educational changes, there are advantages and disadvantages associated with a new technology. The use of VM for the teaching of histology and pathology requires an extensive infrastructure and the availability of computing devices to all learners, both posing a considerable financial strain on schools and students. Furthermore, there may be valid reasons for practicing healthcare professionals to maintain competency in using light microscopes. In addition, some educators may be reluctant to embrace new technologies. These are some of the reasons why the introduction of VM as an integral part of histology and pathology instruction has been globally uneven. This paper compares the teaching of histology and pathology using traditional or VM in five different countries and their adjacent regions, representing developed, as well as developing areas of the globe. We identify general and local roadblocks to the introduction of this still-emerging didactic technology and outline solutions for overcoming these barriers.

The evolving landscape of anatomic pathology

Anatomic pathology has changed dramatically in recent years. Although the microscopic assessment of tissues and cells is and will remain the mainstay of cancer diagnosis molecular profiling has become equally relevant. Thus, to stay abreast of the evolving landscape of today's anatomic pathology, modern pathologists must be able to master the intricate world of predictive molecular pathology. To this aim, pathologists have had to acquire additional knowledge to bridge the gap between clinicians and molecular biologists. This new role is particularly important, as cases are now collegially discussed in molecular tumor boards (MTBs). Moreover, as opposed to traditional pathologists, modern pathologists have also adamantly embraced innovation while keeping a constant eye on tradition. In this article, we depict the highlights and shadows of the upcoming "Anatomic Pathology 2.0" by placing particular emphasis on the pathologist's growing role in the management of cancer patients.

Machine learning-enabled cancer diagnostics with widefield polarimetric second-harmonic generation microscopy

The extracellular matrix (ECM) collagen undergoes major remodeling during tumorigenesis. However, alterations to the ECM are not widely considered in cancer diagnostics, due to mostly uniform appearance of collagen fibers in white light images of hematoxylin and eosin-stained (H&E) tissue sections. Polarimetric second-harmonic generation (P-SHG) microscopy enables label-free visualization and ultrastructural investigation of non-centrosymmetric molecules, which, when combined with texture analysis, provides multiparameter characterization of tissue collagen. This paper demonstrates whole slide imaging of breast tissue microarrays using high-throughput widefield P-SHG microscopy. The resulting P-SHG parameters are used in classification to differentiate tumor from normal tissue, resulting in 94.2% for both accuracy and F1-score, and 6.3% false discovery rate. Subsequently, the trained classifier is employed to predict tumor tissue with 91.3% accuracy, 90.7% F1-score, and 13.8% false omission rate. As such, we show that widefield P-SHG microscopy reveals collagen ultrastructure over large tissue regions and can be utilized as a sensitive biomarker for cancer diagnostics and prognostics studies.

A deep learning model for molecular label transfer that enables cancer cell identification from histopathology images

Deep-learning classification systems have the potential to improve cancer diagnosis. However, development of these computational approaches so far depends on prior pathological annotations and large training datasets. The manual annotation is low-resolution, time-consuming, highly variable and subject to observer variance. To address this issue, we developed a method, H&E Molecular neural network (HEMnet). HEMnet utilizes immunohistochemistry as an initial molecular label for cancer cells on a H&E image and trains a cancer classifier on the overlapping clinical histopathological images. Using this molecular transfer method, HEMnet successfully generated and labeled 21,939 tumor and 8782 normal tiles from ten whole-slide images for model training. After building the model, HEMnet accurately identified colorectal cancer regions, which achieved 0.84 and 0.73 of ROC AUC values compared to p53 staining and pathological annotations, respectively. Our validation study using histopathology images from TCGA samples accurately estimated tumor purity, which showed a significant correlation (regression coefficient of 0.8) with the estimation based on genomic sequencing data. Thus, HEMnet contributes to addressing two main challenges in cancer deep-learning analysis, namely the need to have a large number of images for training and the dependence on manual labeling by a pathologist. HEMnet also predicts cancer cells at a much higher resolution compared to manual histopathologic evaluation. Overall, our method provides a path towards a fully automated delineation of any type of tumor so long as there is a cancer-oriented molecular stain available for subsequent learning. Software, tutorials and interactive tools are available at: https://github.com/BiomedicalMachineLearning/HEMnet.

Deep learning enables ultraviolet photoacoustic microscopy based histological imaging with near real-time virtual staining

Histological images can reveal rich cellular information of tissue sections, which are widely used by pathologists in disease diagnosis. However, the gold standard for histopathological examination is based on thin sections on slides, which involves inevitable time-consuming and labor-intensive tissue processing steps, hindering the possibility of intraoperative pathological assessment of the precious patient specimens. Here, by incorporating ultraviolet photoacoustic microscopy (UV-PAM) with deep learning, we show a rapid and label-free histological imaging method that can generate virtually stained histological images (termed Deep-PAM) for both thin sections and thick fresh tissue specimens. With the tissue non-destructive nature of UV-PAM, the imaged intact specimens can be reused for other ancillary tests. We demonstrated Deep-PAM on various tissue preparation protocols, including formalin-fixation and paraffin-embedding sections (7-µm thick) and frozen sections (7-µm thick) in traditional histology, and rapid assessment of intact fresh tissue (~ 2-mm thick, within 15 min for a tissue with a surface area of 5 mm × 5 mm). Deep-PAM potentially serves as a comprehensive histological imaging method that can be simultaneously applied in preoperative, intraoperative, and postoperative disease diagnosis.

A commemoration of the "digital" side of Juan Rosai: a junior's perspective of the legacy of an all-round pathologist

Juan Rosai, the “Maradona” of surgical pathology, played a role not only as a diagnostician but also as a researcher, a consultant and a teacher, distinguishing himself as a real icon at all levels of modern pathology. He was an innovative promoter of emerging technologies including digital pathology.

These few lines commemorate the digital side of the “Maestro” Juan Rosai from a junior’s perspective highlighting how Rosai supported digital pathology and remembering that, according to his own words, digital pathology “will revolutionize the field of pathology, if it is not doing that already”.

Transcriptomic and Immunophenotypic Characterization of Tumor Immune Microenvironment in Squamous Cell Carcinoma of the Oral Tongue

The tumor immune microenvironment of oral tongue squamous cell carcinoma may be accountable for differences in clinical behavior, particularly between different age groups. We performed RNA expression profiling and evaluated tumor infiltrating lymphocytes (TILs) and their T-cell subsets in order to assess the functional status of oral tongue squamous cell carcinoma tumor microenvironment and detect potentially clinically useful associations. Archival surgical pathology material from sixteen oral tongue squamous cell carcinoma patients was microscopically evaluated for TIL densities. RNA was extracted from macrodissected whole tumor sections and normal controls and RNA expression profiling was performed by the NanoString PanCancer IO 360 Gene Expression Panel. Immunostains for CD4, CD8 and FOXP3 were evaluated manually and by digital image analysis. Oral tongue squamous cell carcinomas had increased TIL densities, numerically dominated by CD4 + T cells, followed by CD8 + and FOXP3 + T cells. RNA expression profiling of tumors versus normal controls showed tumor signature upregulation in inhibitory immune signaling (CTLA4, TIGIT and PD-L2), followed by inhibitory tumor mechanisms (IDO1, TGF-β, B7-H3 and PD-L1). Patients older than 44 years showed a tumor microenvironment with increased Tregs and CTLA4 expression. Immunohistochemically assessed CD8% correlated well with molecular signatures related to CD8 + cytotoxic T-cell functions. FOXP3% correlated significantly with CTLA4 upregulation. CTLA4 molecular signature could be predicted by FOXP3% assessed by immunohistochemistry (R2 = 0.619, p = 0.026). Oral tongue squamous cell carcinoma hosts a complex inhibitory immune microenvironment, partially reflected in immunohistochemically quantified CD8 + and FOXP3 + T-cell subsets. Immunohistochemistry can be a useful screening tool for detecting tumors with upregulated expression of the targetable molecule CTLA4.

Towards safer non-volatile tissue fixatives: Evaluation of choline-based ionic liquids for fixing ocular tissues

Volatile organic chemicals (VOCs) are routinely used for processing biological tissue samples in clinical laboratories. Recognizing their serious health and environmental impacts, a few non-volatile green solvents (choline based ionic liquids, ILs) were evaluated as tissue fixatives here. Microscopic evaluation of histo-morphology, fixation and staining quality, and macromolecular integrity (DNA and proteins) were assessed in human eye tissues (sclera, choroid, retinal layers and retinal pigmented epithelium, eyelid and orbit) after IL-fixation. Formalin-fixed tissues were used as standard reference. Microscopic examination revealed favorable histomorphology, tissue fixation and staining characteristics in most tissues immersed in ILs. Time taken to fix, and stability over a period of time (24 h, 48 h, 1 week, 1 month) was also recorded. Electrophoretic analysis revealed stability of cellular proteins and nucleic acids in IL-fixed scleral tissues. Heterogeneity in tissue fixation property relative to the type of ocular tissue, duration of fixation and storage, warrant further design and optimization of ILs to fix biological tissues. The simple cholinium salts based ILs tested here show favorable potential for tissue fixation application, and as an alternative approach to the use of VOCs, towards sustainable biomedical practice.

Genotype-phenotype associations in colorectal adenocarcinomas and their matched metastases

Although primary colorectal carcinomas (CRCs) frequently share genetic alterations with their metastases, morphologic surrogates reflecting the genotype contexture of metastases remain largely unknown. We investigated phenotype/genotype associations in paired primary and metastatic colorectal adenocarcinomas from 75 patients. Thirty-three (44%) metastatic lesions were synchronous and 42 (56%) were metachronous. Tumor budding, micronecrosis, and tumor-infiltrating lymphocyte (TIL) density were compared with matched next-generation sequencing genotypes. Micronecrosis in the primary were significantly associated with nodal status (P = 0.0054) and with micronecrosis in metastatic sites (P = 0.0216), particularly in metachronous metastases (P = 0.0033). With a 57-gene panel, one or more mutations were identified in 64 (85.3%) cases. In metastases, high (brisk) TILs were associated with overall mutational burden (P = 0.0058) and with mutations in EGF (P = 0.0325), RAS genes (P = 0.0043), and MMR genes (P = 0.0069), whereas high-level micronecrosis correlated with mutations in APC (P = 0.0004) and MSH6 (P = 0.0385) genes. Genomic alterations were shared in 90.1% of primary/metastatic pairs, but clonality of the same mutation was shared in only 57.1% of paired lesions. Compared with synchronous, metachronous metastases had more private clonal alterations (P = 0.0291); in this group, clonal alterations coincided with brisk TILs (P = 0.0334) and high micronecrosis (P = 0.0133). High TILs in metastatic lesions were predictive of favorable overall survival (log-rank P = 0.044). The observed phenotype/genotype associations favor the clonal evolution model in CRC metastases that seems accompanied by intense host immune response. If the role of micronecrosis and brisk TILs in metachronous metastases is validated in larger studies, these histologic parameters will be worth adding in the armamentarium for the evaluation of metastatic CRC.

Cellular resolution in clinical MALDI mass spectrometry imaging: the latest advancements and current challenges

Mass spectrometry (MS) is the workhorse of metabolomics, proteomics and lipidomics. Mass spectrometry imaging (MSI), its extension to spatially resolved analysis of tissues, is a powerful tool for visualizing molecular information within the histological context of tissue. This review summarizes recent developments in MSI and highlights current challenges that remain to achieve molecular imaging at the cellular level of clinical specimens. We focus on matrix-assisted laser desorption/ionization (MALDI)-MSI. We discuss the current status of each of the analysis steps and remaining challenges to reach the desired level of cellular imaging. Currently, analyte delocalization and degradation, matrix crystal size, laser focus restrictions and detector sensitivity are factors that are limiting spatial resolution. New sample preparation devices and laser optic systems are being developed to push the boundaries of these limitations. Furthermore, we review the processing of cellular MSI data and images, and the systematic integration of these data in the light of available algorithms and databases. We discuss roadblocks in the data analysis pipeline and show how technology from other fields can be used to overcome these. Finally, we conclude with curative and community efforts that are needed to enable contextualization of the information obtained.

Beyond the H&E: Advanced Technologies for in situ Tissue Biomarker Imaging

For decades, histopathology with routine hematoxylin and eosin staining has been and remains the gold standard for reaching a morphologic diagnosis in tissue samples from humans and veterinary species. However, within the past decade, there has been exponential growth in advanced techniques for in situ tissue biomarker imaging that bridge the divide between anatomic and molecular pathology. It is now possible to simultaneously observe localization and expression magnitude of multiple protein, nucleic acid, and molecular targets in tissue sections and apply machine learning to synthesize vast, image-derived datasets. As these technologies become more sophisticated and widely available, a team-science approach involving subspecialists with medical, engineering, and physics backgrounds is critical to upholding quality and validity in studies generating these data. The purpose of this manuscript is to detail the scientific premise, tools and training, quality control, and data collection and analysis considerations needed for the most prominent advanced imaging technologies currently applied in tissue sections: immunofluorescence, in situ hybridization, laser capture microdissection, matrix-assisted laser desorption ionization imaging mass spectrometry, and spectroscopic/optical methods. We conclude with a brief overview of future directions for ex vivo and in vivo imaging techniques.

Hematoxylin: Mesoamerica’s Gift to Histopathology. Palo de Campeche (Logwood Tree), Pirates’ Most Desired Treasure, and Irreplaceable Tissue Stain

Hematoxylin is a basic dye derived from the heartwood of Palo de Campeche ( Haematoxylum campechianum), the logwood tree native to Mexico and Central America. Haematoxylum means “bloodwood” in reference to its dark-red heartwood and campechianum refers to its site of origin, the coastal city of Campeche on the Yucatan Peninsula, Mexico. Hematoxylin is colorless but it turns into the color dye hematein after oxidation (ripening). The dyeing property of logwood was well-known to the natives of the Yucatan Peninsula before the arrival of the Spaniards who brought it to Europe shortly after the discovery of the Americas. An important trade soon developed related to growing and preparing hematoxylin for dyeing fabrics. Pirates discovered that one shipload of logwood was equivalent to a year’s value from any other cargo, and by 1563, more than 400 pirate vessels wandered the Atlantic Ocean and attacked Spanish galleons transporting gold, silver, and logwood from the Americas to Europe. Hematoxylin and eosin is a staining method that dates back to the late 19th century. In 1865 and 1891, Böhmer and Meyer, respectively, first used hematoxylin in combination with a mordant (alum). Later, with the use of anilines by Ehrlich, the repertoire of stains expanded rapidly resulting in the microscopic descriptions of multiple diseases that were defined by their stainable features. Today hematoxylin, along with eosin, remains the most popular stain in histology.

Comparitive efficacies of a natural fixative with a conventional fixative

Introduction:

The quest for formalin substitutes has long been going on due to its health hazards. Honey has been recognized as a safe substitute for formalin. However, we explored jaggery as a natural substitute for formalin. The aim of this study was to compare the tissue fixation abilities of jaggery syrup (30%) with that of 10% neutral-buffered formalin (NBF) and to determine the best fixative among both.

Materials and Methods:

A study was conducted with 65 pathological tissues. Each specimen was divided into two equal parts. One part was fixed in 30% jaggery solution (Group A), while the other half was fixed in 10% NBF solution (Group B). 24 h tissue fixation was attained at room temperature followed by evaluation of pre- and post-fixation, tissue shrinkage, weight difference and ease of sectioning, followed by evaluation of conventional processing and staining. The histomorphological assessment for each slide was made based on evaluation of cellular outline, cytoplasmic details, nuclear details, staining quality and overall morphology under light microscopy. Each criterion was rated on a scale of 1–4. Nominal categorical data between the groups were compared using Chi-squared test.

Results:

The preservation of tissue specimen by jaggery syrup was comparable to that of formalin and surprisingly overall nuclear detail of the tissue was better than conventional formalin fixative.

Conclusion:

Jaggery can be successfully adopted in routine histopathology laboratories in place of formalin.

More than meets the eye: the changing face of histopathology

This personal reflection on trends in histopathology over the past 50 years draws upon experience of professional training and practice in the specialty in the UK. Developments during this period often resulted from new therapies (and their adverse effects) necessitating greater precision in the histopathological classification of disease, for which morphology alone can be insufficient. Conversely, histopathology has contributed to advances in our understanding of disease, leading directly to novel and more effective treatments. New infections, some involving histopathology in their discovery, have also led to fresh diagnostic challenges. Increasingly, patients have benefited from fundamental changes in professionalism in pathology. Through audit, external quality assurance, continuing professional development, standardized reporting, and increasing specialization, the consistency and reliability of histopathological diagnoses have steadily improved. Regarding the specialty's future, some now see rivalry between the morphological and molecular approaches to diagnosis and classification, particularly for neoplastic disease. An integrated strategy led by the specialty is more likely to strengthen histopathology and ultimately to have the greatest benefit for patients.

The Vital Role of Pathology in Improving Reproducibility and Translational Relevance of Aging Studies in Rodents

Pathology is a discipline of medicine that adds great benefit to aging studies of rodents by integrating in vivo, biochemical, and molecular data. It is not possible to diagnose systemic illness, comorbidities, and proximate causes of death in aging studies without the morphologic context provided by histopathology. To date, many rodent aging studies do not utilize end points supported by systematic necropsy and histopathology, which leaves studies incomplete, contradictory, and difficult to interpret. As in traditional toxicity studies, if the effect of a drug, dietary treatment, or altered gene expression on aging is to be studied, systematic pathology analysis must be included to determine the causes of age-related illness, moribundity, and death. In this Commentary, the authors discuss the factors that should be considered in the design of aging studies in mice, with the inclusion of robust pathology practices modified after those developed by toxicologic and discovery research pathologists. Investigators in the field of aging must consider the use of histopathology in their rodent aging studies in this era of integrative and preclinical geriatric science (geroscience).

Diagnosis and Molecular Classification of Lung Cancer

Lung cancer is a complex disease composed of diverse histological and molecular types with clinical relevance. The advent of large-scale molecular profiling has been helpful to identify novel molecular targets that can be applied to the treatment of particular lung cancer patients and has helped to reshape the pathological classification of lung cancer. Novel directions include the immunotherapy revolution, which has opened the door for new opportunities for cancer therapy and is also redefining the classification of multiple tumors, including lung cancer. In the present chapter, we will review the main current basis of the pathological diagnosis and classification of lung cancer incorporating the histopathological and molecular dimensions of the disease.

Coccidioidomycosis in Biopsies with Presumptive Diagnosis of Malignancy in Dogs: Report of Three Cases and Comparative Discussion of Published Reports

Coccidioidomycosis is a respiratory fungal infection with occasional systemic dissemination. The disseminated coccidioidomycosis is considered a multifaceted disease. In medicine, disseminated coccidioidomycosis is included within a group of infectious diseases that have been referred as the great imitators. In many cases, malignancies are included in the presumptive diagnosis. In veterinary medicine, disseminated coccidioidomycosis is common in dogs. Nonetheless, despite of being a diagnostic dilemma, disseminated coccidioidomycosis is underestimated and frequently not included into differentials, even in endemic zones. Herein, we describe three cases of granulomatous inflammation caused by Coccidioides spp. which were masquerading malignancies in dogs (0.39 %). The presumptive diagnoses in these cases were osteosarcoma, lymphoma and neurofibroma, respectively. A PCR assay employing tissues in paraffin blocks resulted positive for C. posadasii in one of these cases. A comparative discussion on the ambiguous clinic-pathological presentation of disseminated coccidioidomycosis in dogs and humans is included.

Does everything a surgeon takes out have to be seen by a pathologist? A review of the current pathology practice

Histopathologic examination of surgically removed tissues and organs is an important aspect of modern hospital quality health care. Most surgical specimens deserve to be submitted for pathologic examination, which may yield valuable new information relevant for the future treatment of the patient. A small number of specimens, recognized as providing limited or no valuable clinical data during pathologic examination, may be placed on the list of specimens "exempt from submission" or those that are labeled as "for gross examination only." Guidelines written by the committees of the national regulatory organizations provide general orientation on how to deal with various specimens, but the final decision on which type of specimen to eliminate and which ones to include for pathologic examination rests on local governing and advisory bodies of each institution. Particular lists of specimens exempt from pathologic examination are best generated through a consensus agreement of clinical and laboratory physicians. Even though there is general nationwide and even international consensus on which types of specimens deserve pathologic examination and which do not, there are still discussions about the necessity of some pathologic examinations.

Transit fixatives: an innovative study

BACKGROUND

Universally accepted fixative is 10% formalin which has been used for preserving the tissues and their architecture. In certain conditions, formalin might not be readily available for immediate fixation. We here by explore more economical, eco-friendly and easily available solutions that can be used as transit media/ transporting media for tissue specimens.

MATERIALS AND METHODS

The study included commonly available solutions like Spirit, Saline, Betadine solution, Hydrogen peroxide (H2O2), Local anesthesia (L.A), Rose water, Coconut oil, Coconut water, Ice cold water, Honey and Milk while keeping formalin as control. The fresh tissue sample was cut into multiple bits and placed in different containers for a period of 8 hours before transferring to formalin solution.

CONCLUSION

Transit fixatives are very important in certain situations where formalin is not readily available. These fixatives can be used to fix the tissues for a period of at least 8 hours without causing any damage or distortion before they are fixed in formalin solution.

A nuclear circularity-based classifier for diagnostic distinction of desmoplastic from spindle cell melanoma in digitized histological images

Context:

Distinction of spindle cell melanoma (SM) and desmoplastic melanoma (DM) is clinically important due to differences in metastatic rate and prognosis; however, histological distinction is not always straightforward. During a routine review of cases, we noted differences in nuclear circularity between SM and DM.

Aim:

The primary aim in our study was to determine whether these differences in nuclear circularity, when assessed using a basic ImageJ-based threshold extraction, can serve as a diagnostic classifier to distinguish DM from SM.

Settings and Design:

Our retrospective analysis of an established patient cohort (SM n = 9, DM n = 9) was employed to determine discriminatory power.

Subjects and Methods:

Regions of interest (total n = 108; 6 images per case) were selected from scanned H and E-stained histological sections, and nuclear circularity was extracted and quantified by computational image analysis using open source tools (plugins for ImageJ).

Statistical Analysis:

Using analysis of variance, t-tests, and Fisher's exact tests, we compared extracted quantitative shape measures; statistical significance was defined as P < 0.05.

Results:

Classifying circularity values into four shape categories (spindled, elongated, oval, round) demonstrated significant differences in the spindled and round categories. Paradoxically, DM contained more spindled nuclei than SM (P = 0.011) and SM contained more round nuclei than DM (P = 0.026). Performance assessment using a combined shape-classification of the round and spindled fractions showed 88.9% accuracy and a Youden index of 0.77.

Conclusions:

Spindle cell melanoma and DM differ significantly in their nuclear morphology with respect to fractions of round and spindled nuclei. Our study demonstrates that quantifying nuclear circularity can be used as an adjunct diagnostic tool for distinction of DM and SM.

Diminutive and Small Colorectal Polyps: The Pathologist's Perspective

Recent progress in advanced endoscopic imaging and electronic chromoendoscopy allows the real-time endoscopic estimation of the histologic type of polyps, mainly for the differentiation of adenomas from hyperplastic polyps. Accordingly, a "resect-and-discard" strategy applied to diminutive colorectal polyps is now one of the emerging issues among gastroenterologists. The strategy has a practical advantage in terms of the potential cost savings. However, it has a number of limitations in the medical, academic, and legal aspects. The major pitfalls include the endoscopic investigation of colorectal polyps with a wide variety of histogenetic origins, including serrated polyps, and the lack of a standardized method for polyp size measurement. Another issue is the importance of the pathologic diagnosis for legal purposes and medical research. Moreover, it is not certain whether the implementation of the strategy has economic benefit in countries with an undervalued reimbursement system for pathologic examination. There is no doubt that a highly confident optical diagnosis of polyp type is a novel valuable tool. It can provide a more steady symbiosis between gastroenterologists and pathologists to allow a more evident diagnosis and management of patients with colorectal polyps.

ΔNp63 (p40) and thyroid transcription factor-1 immunoreactivity on small biopsies or cellblocks for typing non-small cell lung cancer: a novel two-hit, sparing-material approach

INTRODUCTION

Diagnosing non-small cell lung cancer on biopsy/cellblock samples by morphology may be demanding. As sparing material for molecular testing is mandatory, a minimalist immunohistochemistry (IHC)-based diagnostic approach is warranted by means of novel, reliable, and easy-to-assess biomarkers.

METHODS

Forty-six consecutive biopsy/cellblock samples and the corresponding resection specimens (as the gold standard for morphology and IHC) from 30 adenocarcinomas (AD), 10 squamous carcinomas (SQC), 5 adenosquamous carcinomas (ADSQC), and 1 sarcomatoid carcinoma (SC) were IHC-evaluated for p40 [corresponding to nontransactivating ΔNp63 isoforms] and thyroid transcription factor-1 (TTF1) by semiquantitative assessment. For p40, also immunodecoration intensity was taken into account and dichotomized as strong or low.

RESULTS

Nonrandom and overlapping distributions of the relevant markers were found in biopsy/cellblock and surgical specimens, which closely correlated with each other and the diverse tumor categories, with no differences in area under curve-receiver-operating-characteristic curves for each marker between any two samples, including p40 and p63. Diagnostic combinations were p40-/TTF1+ or TTF1- for AD (where p40 was negative, apart from 5/30 AD showing at the best 1-2% tumor cells with low intensity); p40+/TTF1- (p40 strong and by far higher than 50%) for SQC; and p40+/TTF1+ or p40+/TTF1- (p40 strong and less than 50%) for ADSQC. The single SC case was p40-/TTF1-, suggesting glandular lineage. Practically, 41/46 (89%) tumors were correctly classified by IHC on small samples, including 30 AD, 10 SQC, 1/5 ADSQC, and no SC. Underdiagnosis of ADSQC was actually because of sampling error of biopsies/cellblocks rather than insufficient biomarker robustness, whereas underdiagnosis of SC was really because of the failure of either marker to highlight epithelial-mesenchymal transition.

CONCLUSIONS

This minimalist IHC-based model of p40 and TTF1 on biopsy/cellblock samples was effective to correctly subtype most cases of lung cancer.

Evaluation of a breast cancer nomogram for predicting risk of ipsilateral breast tumor recurrences in patients with ductal carcinoma in situ after local excision

PURPOSE

Prediction of patients at highest risk for ipsilateral breast tumor recurrence (IBTR) after local excision of ductal carcinoma in situ (DCIS) remains a clinical concern. The aim of our study was to evaluate a published nomogram from Memorial Sloan-Kettering Cancer Center to predict for risk of IBTR in patients with DCIS from our institution.

PATIENTS AND METHODS

We retrospectively identified 794 patients with a diagnosis of DCIS who had undergone local excision from 1990 through 2007 at the MD Anderson Cancer Center (MDACC). Clinicopathologic factors and the performance of the Memorial Sloan-Kettering Cancer Center nomogram for prediction of IBTR were assessed for 734 patients who had complete data.

RESULTS

There was a marked difference with respect to tumor grade, prevalence of necrosis, initial presentation, final margins, and receipt of endocrine therapy between the two cohorts. The biggest difference was that more patients received radiation in the MDACC cohort (75% at MDACC v 49% at MSKCC; P < .001). Follow-up time in the MDACC cohort was longer than in the MSKCC cohort (median 7.1 years v 5.6 years), and the recurrence rate was lower in the MDACC cohort (7.9% v 11%). The median 5-year probability of recurrence was 5%, and the median 10-year probability of recurrence was 7%. The nomogram for prediction of 5- and 10-year IBTR probabilities demonstrated imperfect calibration and discrimination, with a concordance index of 0.63.

CONCLUSION

Predictive models for IBTR in patients with DCIS who were treated with local excision are imperfect. Our current ability to accurately predict recurrence on the basis of clinical parameters alone is limited.

Systems pathology: a critical review

The technological advances of the last twenty years together with the dramatic increase in computational power have injected new life into systems-level thinking in Medicine. This review emphasizes the close relationship of Systems Pathology to Systems Biology and delineates the differences between Systems Pathology and Clinical Systems Pathology. It also suggests an algorithm to support the application of systems-level thinking to clinical research, proposes applying systems-level thinking to the health care systems and forecasts an acceleration of preventive medicine as a result of the coupling of personal genomics with systems pathology.

Why is it crucial to reintegrate pathology into cancer research?

The integration of pathology with molecular biology is vital if we are to enhance the translational value of cancer research. Pathology represents a bridge between medicine and basic biology, it remains the gold standard for cancer diagnosis, and it plays an important role in discovery studies. In the past, pathology and cancer research were closely associated; however, the molecular biology revolution has shifted the focus of investigators toward the molecular alterations of tumors. The reductionist approach taken in molecular studies is producing great insight into the inner workings of neoplasia, but it can also minimize the importance of histopathology and of understanding the disease as a whole. In turn, pathologists can underestimate the role of molecular studies in developing new ancillary techniques for clinical diagnosis. A multidisciplinary approach that integrates pathology and molecular biology within a translational research system is needed. This process will require overcoming cultural barriers and can be achieved through education, a more effective incorporation of pathology into biological research, and conversely an integration of biological research into the pathology laboratory.

Immunohistochemical subtyping of nonsmall cell lung cancer not otherwise specified in fine-needle aspiration cytology: a retrospective study of 103 cases with surgical correlation

BACKGROUND

Histopathological subtyping of nonsmall cell lung cancer (NSCLC) is currently relevant in treatment decision because of a differential activity of specific therapeutic agents. Immunohistochemistry highlights cell differentiation lineages and, in this study, it was applied to maximize the proportion of accurately subtyped NSCLC not otherwise specified (NOS) on fine-needle aspiration cytology (FNAC) samples.

METHODS

Cell blocks from 103 FNAC samples with a morphological diagnosis of NSCLC-NOS were immunostained for cytokeratin (CK) 7, CK5, TTF1, and p63, whereas p40, napsin A (Naps-A), and desmocollin-3 (DSC-3) were only assessed in a subgroup of cases with discordant (CK7 and TTF1+ for nonsquamous, CK5 and p63+ for squamous) findings. Results were correlated with surgical specimens evaluated by morphology alone.

RESULTS

Thirty-seven (36%) tumors with CK7/TTF1+ and CK5/p63- corresponded to 35 cases of adenocarcinoma (ADC) and 2 cases of large cell carcinoma, whereas 9 (9%) cases with the reverse immunoprofile were squamous cell carcinoma (SQCC) at surgery (P < .001). Although the remaining 57 cases had different marker combinations, a correlation was found with ADC histology for TTF1+ samples (independent of other markers) and with SQCC for p63+/TTF1- immunophenotype (P < .001). p40 was never expressed in p63+ ADC, whereas Naps-A was restricted to ADC and DSC-3 to SQCC lineage. The percentage of unclassified NSCLC-NOS decreased from 36% to 14%. Combinations of 2 antibodies (TTF1/DSC-3 or p63/Naps-A) in the same section allowed diagnostic optimization in scant cytological samples.

CONCLUSIONS

[corrected] This 4-antibody panel approach may contribute to refine lung cancer classification in FNAC cell blocks, remarkably reducing the NSCLC-NOS diagnostic category.

The Classification of Lung Carcinoma: Time to Change the Morphology-Based Approach?

Morphology still remains the cornerstone in lung cancer classification and always has been accompanying pathologists in their daily activity, even though several ancillary techniques have been incorporated over time to improve diagnostic, prognostic, and predictive capabilities in lung cancer. Currently, we are also faced with a global rethinking of lung cancer care, especially once novel therapy strategies have been made available on the basis of the diverse characteristics of tumors. Although morphology still remains a not easily replaceable tool for lung cancer classification, we are now challenged by the need of offering clinicians more detailed subtyping of non-small-cell lung cancer especially in event of limited diagnostic material, poorly differentiated tumors, or unresectable lesions. Close integration of improved morphology, immunohistochemistry, and molecular tests will be able to not only sharpen our diagnostic algorithms and prognostic and predictive potentialities but also get insights into several lung cancer biology issues, such as histogenesis and new classification schemes.

Grading of nonrhabdomyosarcoma soft tissue sarcoma in children and adolescents: a comparison of parameters used for the Fédération Nationale des Centers de Lutte Contre le Cancer and Pediatric Oncology Group Systems

BACKGROUND

Two systems for grading soft tissue sarcoma are widely used currently: the National Cancer Institute (NCI) and the Fédération Nationale des Centers de Lutte Contre le Cancer (FNCLCC) systems. Both were developed using cohorts of predominantly adult patients. The Pediatric Oncology Group (POG) system, based on the NCI system, was adapted for grading pediatric nonrhabdomyosarcoma soft tissue sarcoma (NRSTS). The applicability and prognostic utility of the FNCLCC system in pediatric NRSTS has not been assessed or compared with the POG system.

METHODS

Tumors from 130 patients with malignant NRSTS enrolled on 3 completed multi-institutional clinical trials were assessed. Of 130 tumors, 102 (78%) were localized and 28 (22%) metastatic. Of the localized tumors, 55 of 102 (54%) were >5 cm. The estimated 5-year event-free survival (EFS) for the entire group was 47%.

RESULTS

As expected, stage and tumor sizes were predictive of EFS (P < .001). Both systems were predictive of 5-year EFS (POG, P = .0095 and FNCLCC, P = .0075). Patients whose tumors received discrepant grades (POG-G3 vs FNCLCC-G2/G1) (n = 44) had an intermediate outcome between those with concordant (G3 [n = 44] or G1/G2 [n = 42]) grades on both systems (P = .0018). By multivariate analysis, the mitotic index was predictive of EFS, using a cutoff of 10 mitotic figures per 10 high-power fields (P < .001).

CONCLUSIONS

In conclusion, both FNCLCC and POG systems provide an adequate prognostic measure of outcome for pediatric NRSTS; albeit, a sizeable subset of cases with apparently intermediate prognosis was graded differently by the 2 systems. The mitotic index appears to be a key parameter in grading pediatric NRSTS.

Would Virchow be a systems biologist? A discourse on the philosophy of science with implications for pathological research

Research in pathology spans from merely descriptive work to functional studies, "-omics" approaches and, more recently, systems biology. The work presented here aims at placing pathological research into an epistemological context. Aided by Rudolf Virchow, we give an overview on the philosophy of science including the Wiener Kreis, Popper, Kuhn, Fleck and Rheinberger and demonstrate their implications for routine diagnostics and science in pathology. A focus is on the fields of "-omics" and systems pathology.