A Method to Reuse Archived H&E Stained Histology Slides for a Multiplex Protein Biomarker Analysis

An end-to-end workflow for nondestructive 3D pathology

Recent advances in 3D pathology offer the ability to image orders of magnitude more tissue than conventional pathology methods while also providing a volumetric context that is not achievable with 2D tissue sections, and all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis, however, is not trivial and requires careful attention to a series of details during tissue preparation, imaging and initial data processing, as well as iterative optimization of the entire process. Here, we provide an end-to-end procedure covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. Although 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol focuses on the use of a fluorescent analog of hematoxylin and eosin, which remains the most common stain used for gold-standard pathological reports. We present our guidelines for a broad range of end users (e.g., biologists, clinical researchers and engineers) in a simple format. The end-to-end workflow requires 3-6 d to complete, bearing in mind that data analysis may take longer.

An end-to-end workflow for non-destructive 3D pathology

Recent advances in 3D pathology offer the ability to image orders-of-magnitude more tissue than conventional pathology while providing a volumetric context that is lacking with 2D tissue sections, all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis is non-trivial, requiring careful attention to many details regarding tissue preparation, imaging, and data/image processing in an iterative process. Here we provide an end-to-end protocol covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. While 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol will focus on a fluorescent analog of hematoxylin and eosin (H&E), which remains the most common stain for gold-standard diagnostic determinations. We present our guidelines for a broad range of end-users (e.g., biologists, clinical researchers, and engineers) in a simple tutorial format.

Restaining-based annotation for cancer histology segmentation to overcome annotation-related limitations among pathologists

Numerous cancer histopathology specimens have been collected and digitized over the past few decades. A comprehensive evaluation of the distribution of various cells in tumor tissue sections can provide valuable information for understanding cancer. Deep learning is suitable for achieving these goals; however, the collection of extensive, unbiased training data is hindered, thus limiting the production of accurate segmentation models. This study presents SegPath-the largest annotation dataset (>10 times larger than publicly available annotations)-for the segmentation of hematoxylin and eosin (H&E)-stained sections for eight major cell types in cancer tissue. The SegPath generating pipeline used H&E-stained sections that were destained and subsequently immunofluorescence-stained with carefully selected antibodies. We found that SegPath is comparable with, or outperforms, pathologist annotations. Moreover, annotations by pathologists are biased toward typical morphologies. However, the model trained on SegPath can overcome this limitation. Our results provide foundational datasets for machine-learning research in histopathology.

Improving mitotic cell counting accuracy and efficiency using phosphohistone-H3 (PHH3) antibody counterstained with haematoxylin and eosin as part of breast cancer grading

BACKGROUND

Mitotic count in breast cancer is an important prognostic marker. Unfortunately, substantial inter- and intraobserver variation exists when pathologists manually count mitotic figures. To alleviate this problem, we developed a new technique incorporating both haematoxylin and eosin (H&E) and phosphorylated histone H3 (PHH3), a marker highly specific to mitotic figures, and compared it to visual scoring of mitotic figures using H&E only.

METHODS

Two full-face sections from 97 cases were cut, one stained with H&E only, and the other was stained with PHH3 and counterstained with H&E (PHH3-H&E). Counting mitoses using PHH3-H&E was compared to traditional mitoses scoring using H&E in terms of reproducibility, scoring time, and the ability to detect mitosis hotspots. We assessed the agreement between manual and image analysis-assisted scoring of mitotic figures using H&E and PHH3-H&E-stained cells. The diagnostic performance of PHH3 in detecting mitotic figures in terms of sensitivity and specificity was measured. Finally, PHH3 replaced the mitosis score in a multivariate analysis to assess its significance.

RESULTS

Pathologists detected significantly higher mitotic figures using the PHH3-H&E (median ± SD, 20 ± 33) compared with H&E alone (median ± SD, 16 ± 25), P < 0.001. The concordance between pathologists in identifying mitotic figures was highest when using the dual PHH3-H&E technique; in addition, it highlighted mitotic figures at low power, allowing better agreement on choosing the hotspot area (k = 0.842) in comparison with standard H&E (k = 0.625). A better agreement between image analysis-assisted software and the human eye was observed for PHH3-stained mitotic figures. When the mitosis score was replaced with PHH3 in a Cox regression model with other grade components, PHH3 was an independent predictor of survival (hazard ratio [HR] 5.66, 95% confidence interval [CI] 1.92-16.69; P = 0.002), and even showed a more significant association with breast cancer-specific survival (BCSS) than mitosis (HR 3.63, 95% CI 1.49-8.86; P = 0.005) and Ki67 (P = 0.27).

CONCLUSION

Using PHH3-H&E-stained slides can reliably be used in routine scoring of mitotic figures and integrating both techniques will compensate for each other's limitations and improve diagnostic accuracy, quality, and precision.

Flow chamber staining modality for real-time inspection of dynamic phenotypes in multiple histological stains

Traditional histological stains, such as hematoxylin-eosin (HE), special stains, and immunofluorescence (IF), have defined myriads of cellular phenotypes and tissue structures in a separate stained section. However, the precise connection of information conveyed by the various stains in the same section, which may be important for diagnosis, is absent. Here, we present a new staining modality-Flow chamber stain, which complies with the current staining workflow but possesses newly additional features non-seen in conventional stains, allowing for (1) quickly switching staining modes between destain and restain for multiplex staining in one single section from routinely histological preparation, (2) real-time inspecting and digitally capturing each specific stained phenotype, and (3) efficiently synthesizing graphs containing the tissue multiple-stained components at site-specific regions. Comparisons of its stains with those by the conventional staining fashions using the microscopic images of mouse tissues (lung, heart, liver, kidney, esophagus, and brain), involving stains of HE, Periodic acid-Schiff, Sirius red, and IF for Human IgG, and mouse CD45, hemoglobin, and CD31, showed no major discordance. Repetitive experiments testing on targeted areas of stained sections confirmed the method is reliable with accuracy and high reproducibility. Using the technique, the targets of IF were easily localized and seen structurally in HE- or special-stained sections, and the unknown or suspected components or structures in HE-stained sections were further determined in histological special stains or IF. By the technique, staining processing was videoed and made a backup for off-site pathologists, which facilitates tele-consultation or -education in current digital pathology. Mistakes, which might occur during the staining process, can be immediately found and amended accordingly. With the technique, a single section can provide much more information than the traditional stained counterpart. The staining mode bears great potential to become a common supplementary tool for traditional histopathology.

Repeat Brn3a immunolabeling rescues faded staining and improves detection of retinal ganglion cells

Immunofluorescence is used in numerous research areas including eye research to detect specific antigens in cells and tissues. One limitation is that fluorescent signal can fade, causing detection problems if data recording was not completed in a timely manner or if additional data acquisition is required. The ability to repeat immunostaining for the same antigen after initial fluorescence has faded may require time-consuming and potentially damaging steps to remove primary antibodies. Our studies assessed whether immunofluorescence could be reapplied to previously labeled retinal ganglion cells (RGCs). To examine whether immunostaining of Brn3a, a commonly used RGC marker, could be repeated in retinas with previously faded immunostaining, retinal whole mounts were labeled with anti-Brn3a primary antibodies and green fluorescent secondary antibodies, then allowed to fade over time. Faded retinas were restained with anti-Brn3a antibody followed by secondary antibody, or with secondary antibody alone. Results show restaining with anti-Brn3a primary antibody followed by Alexa-fluor green secondary antibody is effective for RGC detection. Repeat RGC labeling improved the clarity of staining compared with original staining prior to fading, with significant reduction in the percentage of blurry/out of focus fluorescent cells (6 vs 26%); whereas, repeat application of secondary antibody alone was not effective. Preflattening retinas under a coverslip prior to initial Brn3a staining also increased the clarity of staining, and facilitated significantly more accurate automated counting of RGCs. Findings suggest Brn3a antigen remains accessible for repeat immunofluorescence labeling after original staining fades. Staining retinas after flattening tissue may enhance the clarity of staining and accuracy of automated RGC counting. Repeat immunofluorescence staining, without the need to strip off prior bound antibodies, may be useful in other tissues as well and warrants future examination.

Artificial intelligence for multimodal data integration in oncology

In oncology, the patient state is characterized by a whole spectrum of modalities, ranging from radiology, histology, and genomics to electronic health records. Current artificial intelligence (AI) models operate mainly in the realm of a single modality, neglecting the broader clinical context, which inevitably diminishes their potential. Integration of different data modalities provides opportunities to increase robustness and accuracy of diagnostic and prognostic models, bringing AI closer to clinical practice. AI models are also capable of discovering novel patterns within and across modalities suitable for explaining differences in patient outcomes or treatment resistance. The insights gleaned from such models can guide exploration studies and contribute to the discovery of novel biomarkers and therapeutic targets. To support these advances, here we present a synopsis of AI methods and strategies for multimodal data fusion and association discovery. We outline approaches for AI interpretability and directions for AI-driven exploration through multimodal data interconnections. We examine challenges in clinical adoption and discuss emerging solutions.

Heparin Protects Severe Acute Pancreatitis by Inhibiting HMGB-1 Active Secretion from Macrophages

Heparin has shown benefits in severe acute pancreatitis (SAP) therapy, but the underlying mechanisms were unknown. Extracellular high-mobility group protein-1 (HMGB-1) has been regarded as a central mediator contributing to inflammation exacerbation and disease aggravation. We hypothesized heparin attenuated the disease by targeting HMGB-1-related pathways. In the present study, the possible therapeutic roles of heparin and its non-anticoagulant derivatives, 6-O-desulfulted heparin and N-acylated-heparin, were determined on mouse models induced by “Two-Hit” of L-arginine. The compounds exhibited potent efficiency by substantially decreasing the pancreatic necrosis, macrophage infiltration, and serum inflammatory cytokine (IL-6 and TNF-α) concentration. Moreover, they greatly reduced the rapidly increasing extracellular HMGB-1 levels in the L-arginine injured pancreases. As a result, multiple organ failure and mortality of the mice were inhibited. Furthermore, the drugs were incubated with the RAW264.7 cells activated with damaged pancreatic tissue of SAP mice in vitro. They were found to inhibit HMGB-1 transfer from the nucleus to the plasma, a critical step during HMGB-1 active secretion from macrophages. The results were carefully re-examined with a caerulein and LPS induced mouse model, and similar results were found. The paper demonstrated heparin alleviated SAP independent of the anti-coagulant functions. Therefore, non-anticoagulant heparin derivatives might become promising approaches to treat patients suffering from SAP.

Developmental changes in gene expression and gonad morphology during sex differentiation in Atlantic salmon (Salmo salar)

The Atlantic salmon (Salmo salar) is a globally important species for its value in fisheries and aquaculture, and as a research model. In order to characterise aspects of sex differentiation at the morphological and mRNA level in this species, the present study examined developmental changes in gonad morphology and gene expression in males and females between 0 and 79 days post hatch (dph). Morphological differentiation of the ovary (indicated by the formation of germ cell cysts) became apparent from 52 dph. By 79 dph, ovarian phenotype was evident in 100% of genotypic females. Testes remained in an undifferentiated-like state throughout the experiment, containing germ cells dispersed singularly within the gonadal region distal to the mesentery. There were no significant sex-related differences in gonad cross-section size, germ cell number or germ cell diameter during the experiment. The expression of genes involved in teleost sex differentiation (anti-müllerian hormone (amh), cytochrome P450, family 19, subfamily A, polypeptide 1a (cyp19a1a), forkhead box L2a (foxl2a), gonadal soma-derived factor (gsdf), r-spondin 1 (rspo1), sexually dimorphic on the Y chromosome (sdY)), retinoic acid-signalling (aldehyde dehydrogenase 1a2 (aldh1a2), cytochrome P450 family 26 a1 (cyp26a1), cytochrome P450 family 26 b1 (cyp26b1), t-box transcription factor 1 (tbx1a)) and neuroestrogen production (cytochrome P450, family 19, subfamily A, polypeptide 1b (cyp19a1b)) was investigated. Significant sex-related differences were observed only for the expression of amh, cyp19a1a, gsdf and sdY. In males, amh, gsdf and sdY were upregulated from 34, 59 and 44 dph respectively. In females, cyp19a1a was upregulated from 66 dph. Independent of sex, foxl2a expression was highest at 0 dph and had reduced ∼ 47-fold by the time of morphological sex differentiation at 52 dph. This study provides new insights into the timing and sequence of some physiological changes associated with sex differentiation in Atlantic salmon. These findings also reveal that some aspects of the mRNA sex differentiation pathways in Atlantic salmon are unique compared to other teleost fishes, including other salmonids.

Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm

Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.

Accuracy of whole slide image based image analysis is adversely affected by preanalytical factors such as stained tissue slide and paraffin block age

Background

Personalized medicine and accurate quantification of tumor and biomarker expression have become the cornerstone of cancer diagnostics. This requires Quality Control (QC) of research tissue samples to confirm adequate targeted tumor tissue sampling. Digitalization of stained tissue slides offer a precious way to archive, preserve, and retrieve necessary information when needed. This study is aimed to assess the most significant pre-analytic and analytic factors that might contribute to the efficacy of obtaining accurate whole slide images (WSIs) interpretation. Various studies are needed to identifysuch factors to allow for appropriate AI application and adequate tumor area/percentage quantification.

Methods

Hematoxylene and Eosine (H&E) satined WSIs collected from tissue specimens provided by the Cooperative Human Tissue Network (CHTN) Midwestern Division (CHTNMWD) were analyzed. Tissue specimens were processed, fixed, stained, and scanned contemporaneously (within 1 month). Two cohorts of malignant, colorectal cancer, 20X WSI (ScanscopeXT, Leica Biosystems, Illinois), were assembled. The study identified a "recent cohort" that included 76 WSIs created on 2018 or later. "Aged cohort" included 73 WSIs from specimens procured in the period of (2012-2014). Twenty recent WSIs of adenocarcinoma cases were used to construct WSIs analysis algorithms (VIS, Visiopharm A/S, Denmark) using machine learning to produce morphometric maps and calculate tissue and tumor areas.

Results

Algorithmic analysis of 69 WSIs from rescanned aged slides vs. that of contemporaneous WSIs concluded 18 (28%) similar finding in tumor areas (within 10%), 56 (82%) had identicaltissue areas, and 54 (79%) had similar tumor percentages.

Conclusion

WSIs of aged H&E slides and stained paraffin block re-cuts produce different tumor quantification compared to those of original scanned sslides most likely due to pre-analytical factors. The difference in tumor area detected between original and rescanned WSIs trended upward in the period between 2012 and 2014. Less tumor area was detected as the slides age. Recut and H&E-stained tissues from stored paraffin blocks may detect more tumor due to excess eosinophilia. These results highlights the value of documenting archives of H&E WSIs collected at the procurement time. Such images provide a superior archive over glass slides and Formalin-Fixed Paraffin-Embedded (FFPE) blocks and contribute betterg to WSIs analysis application.

Deep Learning of Histopathology Images at the Single Cell Level

The tumor immune microenvironment (TIME) encompasses many heterogeneous cell types that engage in extensive crosstalk among the cancer, immune, and stromal components. The spatial organization of these different cell types in TIME could be used as biomarkers for predicting drug responses, prognosis and metastasis. Recently, deep learning approaches have been widely used for digital histopathology images for cancer diagnoses and prognoses. Furthermore, some recent approaches have attempted to integrate spatial and molecular omics data to better characterize the TIME. In this review we focus on machine learning-based digital histopathology image analysis methods for characterizing tumor ecosystem. In this review, we will consider three different scales of histopathological analyses that machine learning can operate within: whole slide image (WSI)-level, region of interest (ROI)-level, and cell-level. We will systematically review the various machine learning methods in these three scales with a focus on cell-level analysis. We will provide a perspective of workflow on generating cell-level training data sets using immunohistochemistry markers to "weakly-label" the cell types. We will describe some common steps in the workflow of preparing the data, as well as some limitations of this approach. Finally, we will discuss future opportunities of integrating molecular omics data with digital histopathology images for characterizing tumor ecosystem.

A Parallel Comparison Method of Early Gastric Cancer: The Light Transmission-Assisted Pathological Examination of Specimens of Endoscopic Submucosal Dissection

Objective

It is always challenging to diagnose and characterize early gastric cancer surrounded by non-cancerous mucosa, including the malignant diagnosis and extent and depth of the lesions. Therefore, we developed a light transmission-assisted pathological examination to diagnose and characterize early gastric cancer. Here, we performed a parallel comparison between the light transmission-assisted pathological examination under endoscopy and the histological examination for the diagnosis of early gastric cancer.

Methods

First, the endoscopic submucosal dissection (ESD) specimen was first placed on the surface of the light-emitting diode lamp to observe the mucosal surface structure and blood vessels. Second, the sliced and embedded tissue strips were cut into 3-µm sections for hematoxylin and eosin staining. Third, the histopathology of each section was projected onto a macroscopic image. Finally, the macroscopic and microscopic changes in the ESD specimens observed under endoscopy were compared. Seventy cases of early gastric adenocarcinoma were diagnosed and characterized using this new method.

Results

Using the conventional pathological method, the demarcation line of the lesions was seen in 40 of 70 (57.1%) cases. Furthermore, no surface structure or microvascular changes were observed in any of the cases. Based on the light transmission-assisted pathological examination, 58 of 70 (82.9%) cases presented clear edges of neoplastic and non-neoplastic epithelia, with a classifiable surface structure (88.6%) and microvascular type (78.8%).

Conclusions

This pilot method provided a practical bridge between endoscopic and pathological examinations. Compared to the histological examination, the light transmission-assisted pathological examination was an easier and more precise way to match the in vivo endoscopic observation and in vitro pathological examination.

Pitfalls and Caveats in Applying Chromogenic Immunostaining to Histopathological Diagnosis

Chromogenic immunohistochemistry (immunostaining using an enzyme-labeled probe) is an essential histochemical technique for analyzing pathogenesis and making a histopathological diagnosis in routine pathology services. In neoplastic lesions, immunohistochemistry allows the study of specific clinical and biological features such as histogenesis, behavioral characteristics, therapeutic targets, and prognostic biomarkers. The needs for appropriate and reproducible methods of immunostaining are prompted by technical development and refinement, commercial availability of a variety of antibodies, advanced applicability of immunohistochemical markers, accelerated analysis of clinicopathological correlations, progress in molecular targeted therapy, and the expectation of advanced histopathological diagnosis. However, immunostaining does have various pitfalls and caveats. Pathologists should learn from previous mistakes and failures and from results indicating false positivity and false negativity. The present review article describes various devices, technical hints, and trouble-shooting guides to keep in mind when performing immunostaining.

Emodin-Conjugated PEGylation of Fe3O4 Nanoparticles for FI/MRI Dual-Modal Imaging and Therapy in Pancreatic Cancer

BACKGROUND

Pancreatic cancer (PC) remains a difficult tumor to diagnose and treat. It is often diagnosed as advanced by reason of the anatomical structure of the deep retroperitoneal layer of the pancreas, lack of typical symptoms and effective screening methods to detect this malignancy, resulting in a low survival rate. Emodin (EMO) is an economical natural product with effective treatment and few side effects of cancer treatment. Magnetic nanoparticles (MNPs) can achieve multiplexed imaging and targeted therapy by loading a wide range of functional materials such as fluorescent dyes and therapeutic agents.

PURPOSE

The purpose of this study was to design and evaluate a multifunctional theranostic nanoplatform for PC diagnosis and treatment.

METHODS

In this study, we successfully developed EMO-loaded, Cy7-functionalized, PEG-coated Fe₃O₄ (Fe₃O₄-PEG-Cy7-EMO). Characteristics including morphology, hydrodynamic size, zeta potentials, stability, and magnetic properties of Fe₃O₄-PEG-Cy7-EMO were evaluated. Fluorescence imaging (FI)/magnetic resonance imaging (MRI) and therapeutic treatment were examined in vitro and in vivo.

RESULTS

Fe₃O₄-PEG-Cy7-EMO nanoparticles had a core size of 9.9 ± 1.2 nm, which showed long-time stability and FI/MRI properties. Bio-transmission electron microscopy (bio-TEM) results showed that Fe₃O₄-PEG-Cy7-EMO nanoparticles were endocytosed into BxPC-3 cells, while few were observed in hTERT-HPNE cells. Prussian blue staining also confirmed that BxPC-3 cells have a stronger phagocytic ability as compared to hTERT-HPNE cells. Additionally, Fe₃O₄-PEG-Cy7-EMO had a stronger inhibition effect on BxPC-3 cells than Fe₃O₄-PEG and EMO. The hemolysis experiment proved that Fe₃O₄-PEG-Cy7-EMO can be used in vivo experiments. In vivo analysis demonstrated that Fe₃O₄-PEG-Cy7-EMO enabled FI/MRI dual-modal imaging and targeted therapy in pancreatic tumor xenografted mice.

CONCLUSION

Fe₃O₄-PEG-Cy7-EMO may serve as a potential theranostic nanoplatform for PC.