Applications of immunohistochemistry

Progress and challenge for computational quantification of tissue immune cells

Tissue immune cells have long been recognized as important regulators for the maintenance of balance in the body system. Quantification of the abundance of different immune cells will provide enhanced understanding of the correlation between immune cells and normal or abnormal situations. Currently, computational methods to predict tissue immune cell compositions from bulk transcriptomes have been largely developed. Therefore, summarizing the advantages and disadvantages is appropriate. In addition, an examination of the challenges and possible solutions for these computational models will assist the development of this field. The common hypothesis of these models is that the expression of signature genes for immune cell types might represent the proportion of immune cells that contribute to the tissue transcriptome. In general, we grouped all reported tools into three groups, including reference-free, reference-based scoring and reference-based deconvolution methods. In this review, a summary of all the currently reported computational immune cell quantification tools and their applications, limitations, and perspectives are presented. Furthermore, some critical problems are found that have limited the performance and application of these models, including inadequate immune cell type, the collinearity problem, the impact of the tissue environment on the immune cell expression level, and the deficiency of standard datasets for model validation. To address these issues, tissue specific training datasets that include all known immune cells, a hierarchical computational framework, and benchmark datasets including both tissue expression profiles and the abundances of all the immune cells are proposed to further promote the development of this field.

Expression Characteristics and Clinical Correlations of BRD1 in Colorectal Cancer Samples

The incidence of colorectal cancer (CRC), as well as subsequent patient mortality, has increased in the last decade; an unhealthy diet is considered to be the leading cause. Previous studies have shown the potential of the bromodomain containing 1 (BRD1) gene as a therapeutic target for CRC based on its specificity; however, the genetic mode of action and expression in CRC cells are yet to be investigated. In this study, target genes were screened from single-cell transcriptome sequencing data, and the collected clinical specimens were subjected to immunohistochemistry (IHC) to identify the protein expression of target genes; the results were verified in the GSE17536 array set. Receiver operating characteristic curves (ROC) and overall survival (OS) were used to test target genes as biomarkers and independent predictive markers for CRC. Based on these results, BRD1 was screened as a target gene, and IHC results showed that BRD1 protein expression in CRC was higher than that in normal tissues and was significantly upregulated in poorly differentiated (PD) CRC. ROC analysis showed that the area under the curve in the collected clinical specimens and GSE17536 were 0.6062 and 0.6094, respectively. OS analysis showed that higher BRD1 protein expression was associated with a significantly shorter survival time. In conclusion, BRD1 expression was positively correlated with PD CRC and negatively correlated with OS, indicating that BRD1 could predict the differentiation state of CRC and may be a novel predictive biomarker.

Classification of Cancer Pathology Reports: A Large-Scale Comparative Study

We report about the application of state-of-the-art deep learning techniques to the automatic and interpretable assignment of ICD-O3 topography and morphology codes to free-text cancer reports. We present results on a large dataset (more than 80 000 labeled and 1 500 000 unlabeled anonymized reports written in Italian and collected from hospitals in Tuscany over more than a decade) and with a large number of classes (134 morphological classes and 61 topographical classes). We compare alternative architectures in terms of prediction accuracy and interpretability and show that our best model achieves a multiclass accuracy of 90.3% on topography site assignment and 84.8% on morphology type assignment. We found that in this context hierarchical models are not better than flat models and that an element-wise maximum aggregator is slightly better than attentive models on site classification. Moreover, the maximum aggregator offers a way to interpret the classification process.

Conjugating immunoassays to mass spectrometry: Solutions to contemporary challenges in clinical diagnostics

Developments in immunoassays and mass spectrometry have independently influenced diagnostic technology. However, both techniques possess unique strengths and limitations, which define their ability to meet evolving requirements for faster, more affordable and more accurate clinical tests. In response, hybrid techniques, which combine the accessibility and ease-of-use of immunoassays with the sensitivity, high throughput and multiplexing capabilities of mass spectrometry are continually being explored. Developments in antibody conjugation methodology have expanded the role of these biomolecules to applications outside of conventional colorimetric assays and histology. Furthermore, the range of different mass spectrometry ionisation and analysis technologies has enabled its successful adaptation as a detection method for numerous clinically relevant immunological assays. Several recent examples of combined mass spectrometry-immunoassay techniques demonstrate the potential of these methods as improved diagnostic tests for several important human diseases. The present challenges are to continue technological advancements in mass spectrometry instrumentation and develop improved bioconjugation methods, which can overcome their existing limitations and demonstrate the clinical significance of these hybrid approaches.

SHIFT: speedy histological-to-immunofluorescent translation of a tumor signature enabled by deep learning

Spatially-resolved molecular profiling by immunostaining tissue sections is a key feature in cancer diagnosis, subtyping, and treatment, where it complements routine histopathological evaluation by clarifying tumor phenotypes. In this work, we present a deep learning-based method called speedy histological-to-immunofluorescent translation (SHIFT) which takes histologic images of hematoxylin and eosin (H&E)-stained tissue as input, then in near-real time returns inferred virtual immunofluorescence (IF) images that estimate the underlying distribution of the tumor cell marker pan-cytokeratin (panCK). To build a dataset suitable for learning this task, we developed a serial staining protocol which allows IF and H&E images from the same tissue to be spatially registered. We show that deep learning-extracted morphological feature representations of histological images can guide representative sample selection, which improved SHIFT generalizability in a small but heterogenous set of human pancreatic cancer samples. With validation in larger cohorts, SHIFT could serve as an efficient preliminary, auxiliary, or substitute for panCK IF by delivering virtual panCK IF images for a fraction of the cost and in a fraction of the time required by traditional IF.

Immune contexture analysis in immuno-oncology: applications and challenges of multiplex fluorescent immunohistochemistry

The tumor microenvironment is an integral player in cancer initiation, tumor progression, response and resistance to anti-cancer therapy. Understanding the complex interactions of tumor immune architecture (referred to as 'immune contexture') has therefore become increasingly desirable to guide our approach to patient selection, clinical trial design, combination therapies, and patient management. Quantitative image analysis based on multiplexed fluorescence immunohistochemistry and deep learning technologies are rapidly developing to enable researchers to interrogate complex information from the tumor microenvironment and find predictive insights into treatment response. Herein, we discuss current developments in multiplexed fluorescence immunohistochemistry for immune contexture analysis, and their application in immuno-oncology, and discuss challenges to effectively use this technology in clinical settings. We also present a multiplexed image analysis workflow to analyse fluorescence multiplexed stained tumor sections using the Vectra Automated Digital Pathology System together with FCS express flow cytometry software. The benefit of this strategy is that the spectral unmixing accurately generates and analyses complex arrays of multiple biomarkers, which can be helpful for diagnosis, risk stratification, and guiding clinical management of oncology patients.

A machine learning algorithm for simulating immunohistochemistry: development of SOX10 virtual IHC and evaluation on primarily melanocytic neoplasms

Immunohistochemistry (IHC) is a diagnostic technique used throughout pathology. A machine learning algorithm that could predict individual cell immunophenotype based on hematoxylin and eosin (H&E) staining would save money, time, and reduce tissue consumed. Prior approaches have lacked the spatial accuracy needed for cell-specific analytical tasks. Here IHC performed on destained H&E slides is used to create a neural network that is potentially capable of predicting individual cell immunophenotype. Twelve slides were stained with H&E and scanned to create digital whole slide images. The H&E slides were then destained, and stained with SOX10 IHC. The SOX10 IHC slides were scanned, and corresponding H&E and IHC digital images were registered. Color-thresholding and machine learning techniques were applied to the registered H&E and IHC images to segment 3,396,668 SOX10-negative cells and 306,166 SOX10-positive cells. The resulting segmentation was used to annotate the original H&E images, and a convolutional neural network was trained to predict SOX10 nuclear staining. Sixteen thousand three hundred and nine image patches were used to train the virtual IHC (vIHC) neural network, and 1,813 image patches were used to quantitatively evaluate it. The resulting vIHC neural network achieved an area under the curve of 0.9422 in a receiver operator characteristics analysis when sorting individual nuclei. The vIHC network was applied to additional images from clinical practice, and was evaluated qualitatively by a board-certified dermatopathologist. Further work is needed to make the process more efficient and accurate for clinical use. This proof-of-concept demonstrates the feasibility of creating neural network-driven vIHC assays.

Histological-Based Stainings using Free-Floating Tissue Sections

Immunohistochemistry is a widely used technique to visualize specific tissue structures as well as protein expression and localization. Two alternative approaches are widely used to handle the tissue sections during the staining procedure, one approach consists of mounting the sections directly on glass slides, while a second approach, the free-floating, allows for fixed sections to be maintained and stained while suspended in solution. Although slide-mounted and free-floating approaches may yield similar results, the free-floating technique allows for better antibody penetration and thus should be the method of choice when thicker sections are to be used for 3D reconstruction of the tissues, for example when the focus of the experiment is to gain information on dendritic and axonal projections in brain regions. In addition, since the sections are kept in solution, a single aliquot can easily accommodate 30 to 40 sections, handling of which is less laborious, particularly in large-scale biomedical studies. Here, we illustrate how to apply the free-floating method to fluorescent immunohistochemistry staining, with a major focus on brain sections. We will also discuss how the free-floating technique can easily be modified to fit the individual needs of researchers and adapted to other tissues as well as other histochemical-based stainings, such as hematoxylin and eosin and cresyl violet, as long as tissue samples are properly fixed, typically with paraformaldehyde or formalin.

The impact of PD-L1 N-linked glycosylation on cancer therapy and clinical diagnosis

N-linked glycosylation is one of the most abundant posttranslational modifications of membrane-bound proteins in eukaryotes and affects a number of biological activities, including protein biosynthesis, protein stability, intracellular trafficking, subcellular localization, and ligand-receptor interaction. Accumulating evidence indicates that cell membrane immune checkpoint proteins, such as programmed death-ligand 1 (PD-L1), are glycosylated with heavy N-linked glycan moieties in human cancers. N-linked glycosylation of PD-L1 maintains its protein stability and interaction with its cognate receptor, programmed cell death protein 1 (PD-1), and this in turn promotes evasion of T-cell immunity. Studies have suggested targeting PD-L1 glycosylation as a therapeutic option by rational combination of cancer immunotherapies. Interestingly, structural hindrance by N-glycan on PD-L1 in fixed samples impedes its recognition by PD-L1 diagnostic antibodies. Notably, the removal of N-linked glycosylation enhances PD-L1 detection in a variety of bioassays and more accurately predicts the therapeutic efficacy of PD-1/PD-L1 inhibitors, suggesting an important clinical implication of PD-L1 N-linked glycosylation. A detailed understanding of the regulatory mechanisms, cellular functions, and diagnostic limits underlying PD-L1 N-linked glycosylation could shed new light on the clinical development of immune checkpoint inhibitors for cancer treatment and deepen our knowledge of biomarkers to identify patients who would benefit the most from immunotherapy. In this review, we highlight the effects of protein glycosylation on cancer immunotherapy using N-linked glycosylation of PD-L1 as an example. In addition, we consider the potential impacts of PD-L1 N-linked glycosylation on clinical diagnosis. The notion of utilizing the deglycosylated form of PD-L1 as a predictive biomarker to guide anti-PD-1/PD-L1 immunotherapy is also discussed.

Multiplex protein-specific microscopy with ultraviolet surface excitation

Immunohistochemical techniques, such as immunofluorescence (IF) staining, enable microscopic imaging of local protein expression within tissue samples. Molecular profiling enabled by IF is critical to understanding pathogenesis and is often involved in complex diagnoses. A recent innovation, known as microscopy with ultraviolet surface excitation (MUSE), uses deep ultraviolet (≈280 nm) illumination to excite labels at the tissue surface, providing equivalent images without fixation, embedding, and sectioning. However, MUSE has not yet been integrated into traditional IF pipelines. This limits its application in more complex diagnoses that rely on protein-specific markers. This paper aims to broaden the applicability of MUSE to multiplex immunohistochemistry using quantum dot nanoparticles. We demonstrate the advantages of quantum dot labels for protein-specific MUSE imaging on both paraffin-embedded and intact tissue, significantly expanding MUSE applicability to protein-specific applications. Furthermore, with recent innovations in three-dimensional ultraviolet fluorescence microscopy, this opens the door to three-dimensional IF imaging with quantum dots using ultraviolet excitation.

Preserving Single Cells in Space and Time for Analytical Assays

Analytical assays performed within clinical laboratories influence roughly 70% of all medical decisions by facilitating disease detection, diagnosis, and management. Both in clinical and academic research laboratories, single-cell assays permit measurement of cell diversity and identification of rare cells, both of which are important in the understanding of disease pathogenesis. For clinically utility, the single-cell assays must be compatible with the clinical workflow steps of sample collection, sample transportation, pre-analysis processing, and single-cell assay; therefore, it is paramount to preserve cells in a state that resembles that in vivo rather than measuring signaling behaviors initiated in response to stressors such as sample collection and processing. To address these challenges, novel cell fixation (and more broadly, cell preservation) techniques incorporate programmable fixation times, reversible bond formation and cleavage, chemoselective reactions, and improved analyte recovery. These technologies will further the development of individualized, precision therapies for patients to yield improved clinical outcomes.

Application of Radiomics for Personalized Treatment of Cancer Patients

Radiomics is a novel concept that relies on obtaining image data from examinations such as computed tomography (CT), magnetic resonance imaging (MRI), or positron emission tomography (PET). With the appropriate algorithm, the extracted results have broad applicability and potential for a massive positive impact in radiology. For example, clinicians can verify treatment efficiency, predict the location of tumor metastasis, correlate results with a histopathological examination, or more accurately define the type of cancer. Combining radiomics with other testing techniques allows every patient to have a personalized treatment plan that is essential for advanced examination and treatment. This article explains the process of radiomics, including data collection mechanisms, combined use with genomics, and artificial intelligence and immunology techniques, which may solve many of the challenges faced by doctors in diagnosing and treating their patients.

Detection of MERS-CoV antigen on formalin-fixed paraffin-embedded nasal tissue of alpacas by immunohistochemistry using human monoclonal antibodies directed against different epitopes of the spike protein

Middle East respiratory syndrome (MERS) represents an important respiratory disease accompanied by lethal outcome in one third of human patients. In recent years, several investigators developed protective antibodies which could be used as prophylaxis in prospective human epidemics. In the current study, eight human monoclonal antibodies (mAbs) with neutralizing and non-neutralizing capabilities, directed against different epitopes of the MERS-coronavirus (MERS-CoV) spike (MERS-S) protein, were investigated with regard to their ability to immunohistochemically detect respective epitopes on formalin-fixed paraffin-embedded (FFPE) nasal tissue sections of MERS-CoV experimentally infected alpacas. The most intense immunoreaction was detected using a neutralizing antibody directed against the receptor binding domain S1B of the MERS-S protein, which produced an immunosignal in the cytoplasm of ciliated respiratory epithelium and along the apical membranous region. A similar staining was obtained by two other mAbs which recognize the sialic acid-binding domain and the ectodomain of the membrane fusion subunit S2, respectively. Five mAbs lacked immunoreactivity for MERS-CoV antigen on FFPE tissue, even though they belong, at least in part, to the same epitope group. In summary, three tested human mAbs demonstrated capacity for detection of MERS-CoV antigen on FFPE samples and may be implemented in double or triple immunohistochemical methods.

Neuroendocrine Adenoma of Middle Ear Causing Acute Onset Facial Palsy- A Rare Case Report

INTRODUCTION

Acute facial nerve palsy secondary to neuroendocrine adenoma of the middle ear (NAME) is a rare disorder. There is only one case report in the literature describing similar findings.

CASE REPORT

A 50-year-old man initially presented to ENT clinic with a right-sided middle ear mass and normal facial nerve function. Over the next six days, he developed House-Brackmann grade II facial paralysis. He underwent urgent surgical exploration of the tympanic cavity and excision of the middle ear mass via a post-auricular approach. Histopathological and immunohistochemical analysis revealed NAME. Three weeks after the surgery, facial nerve function returned to normal. No recurrence was found at a 3-year follow-up.

CONCLUSION

Acute onset facial palsy induced by NAME is an extremely rare disorder. For a patient already affected by hearing impairment resulted from middle ear mass, facial weakness can have a significant additional detrimental impact on their wellbeing. The early complete excision of tumor is recommended not only as a curative treatment but also restoration of facial function.

Analysis of Stem Cells and Their Activity in Human Skeletal Muscles by Immunohistochemistry

Immunohistochemistry (IHC) is a frequently used technique in life science and in clinic diagnostic. IHC is a high precision method to localize different cell types or their expression in tissue. Over the years, different approaches of IHC have emerged, and the technique has become more and more sophisticated. However, the principles still remains: the inherent and spontaneous non-covalent interaction between an antibody and (hypothetical) any target of interest. That means, using this technique allows you to analyze a wide range of histological tissues (muscles, organs, neurons, etc.) from humans or animals under the microscope. Literally, IHC makes the invisible to the human eye clearly visible. In this chapter, we present an approach how to analyze human skeletal muscle tissue for content and activity of muscle stem cells, termed satellite cells.

Deep dermal and subcutaneous canine hemangiosarcoma in the perianal area: diagnosis of perianal mass in a dog

BACKGROUND

Tumors of the perianal area occur frequently in dogs, and the two most common tumors are perianal gland adenoma and anal sac adenocarcinoma; others such as mast cell tumor, lymphoma and melanoma can also occur at this site. Diagnostic cytology is a useful technique and is usually used to establish a definitive diagnosis of some tumors in veterinary medicine. This report describes an extremely rare case of a deep dermal and subcutaneous canine hemangiosarcoma in the perianal area.

CASE PRESENTATION

A 13-year-old intact male spaniel was presented for evaluation of a 4 × 4 cm, ulcerated, and hemorrhagic mass presented in the right perianal region. In cytologic evaluation, malignant mesenchymal tumor with inflammation was diagnosed, and incidental heart worm microfilaremia was identified. Based on the cytologic evaluation, a punch biopsy (3 mm, three sites) was conducted under anesthesia and deep dermal and subcutaneous hemangiosarcoma (3 mitotic figures/10 high power field (400×)) was diagnosed by histopathological evaluation. It was also confirmed by immunohistochemistry results for cluster of differentiation 31 (CD31) and factor VIII-related antigen marker.

CONCLUSIONS

Deep dermal and subcutaneous hemangiosarcoma in the perianal region is a rare condition, and its prognosis is usually poor. Perianal gland adenoma and anal sac adenocarcinoma are the two most common tumors in the perianal region, but other different types of tumors may also occur as in this case; therefore, accurate diagnosis is required using cytology and/or histopathological examination.

Tristetraprolin attenuates brain edema in a rat model of cerebral hemorrhage

OBJECTIVES

We evaluated the protective effects of protein phosphatase 2A (PP2A)/tristetraprolin (TTP) against brain edema in a rat model of cerebral hemorrhage, bleeding in the brain that occurs in tissues and ventricles. TTP is a well-known mRNA-binding protein and essential regulatory molecule for gene expression.

METHODS

Cerebral hemorrhage was induced in male albino rats divided into four homogeneous groups: normal control (I), control (II), PP2A siRNA (III), and scrambled siRNA (IV). Neurological scores, caspase-3 mRNA and protein expression, PP2A and TTP protein expression, apoptosis, and water content in the brain were determined.

RESULTS

The neurological score decreased substantially to 8.2 in rats in which cerebral hemorrhage was induced and was further reduced to 7.4 and 7.7 in groups III and IV, respectively. Caspase-3 expression increased significantly by 90% in group II and by 26.9% in group III. Apoptosis increased by 26.1% in rats in which cerebral hemorrhage was induced and increased considerably by 35.3% and 33.4% in groups III and IV, respectively. PP2A and TTP protein expression increased significantly by 87% and 59%, as compared to their respective sham controls. However, PP2A and TTP siRNA treatment reduced the protein expression of PP2A and TTP in groups III and IV. The water content in the brain increased significantly by 77.4% in rats in which cerebral hemorrhage was induced (group II), as compared to the sham group. The water content in the brain increased by 84.1% and 78.7% in groups III and IV, respectively.

CONCLUSION

Taken together, these data indicate that TTP has a protective role against brain edema by reducing inflammation, apoptosis, and water content in the brain at 48 hr after cerebral hemorrhage. Our findings may be useful for developing important approaches to treating brain injury.

Immunofluorescence Analysis by Confocal Microscopy for Detecting Endogenous FOXO

Cancer cells are known to inactivate tumor suppressor proteins by triggering their anomalous subcellular location. It has been well established that the aberrant location of FOXO proteins is linked to tumor formation, progression of the same, or resistance to anti-neoplastic treatment. Furthermore, the abnormal location of FOXO has also been considered a potential biomarker for diabetic complications or longevity in different organisms. Here, we describe the immunodetection of endogenous FOXO by confocal microscopy, which can be used as a chemical tool to quantify FOXO expression levels, its cellular location, and even its active/inactive forms with relevant antibodies.

A method for manual and automated multiplex RNAscope in situ hybridization and immunocytochemistry on cytospin samples

In situ analysis of biomarkers is essential for clinical diagnosis and research purposes. The increasing need to understand the molecular signature of pathologies has led to the blooming of ultrasensitive and multiplexable techniques that combine in situ hybridization (ISH) and immunohistochemistry or immunocytochemistry (IHC or ICC). Most protocols are tailored to formalin-fixed paraffin embedded (FFPE) tissue sections. However, methods to perform such assays on non-adherent cell samples, such as patient blood-derived PBMCs, rare tumor samples, effusions or other body fluids, dissociated or sorted cells, are limited. Typically, a laboratory would need to invest a significant amount of time and resources to establish one such assay. Here, we describe a method that combines ultrasensitive RNAscope-ISH with ICC on cytospin cell preparations. This method allows automated, sensitive, multiplex ISH-ICC on small numbers of non-adherent cells. We provide guidelines for both chromogenic and fluorescent ISH/ICC combinations that can be performed either in fully automated or in manual settings. By using a CD8+ T cells in vitro stimulation paradigm, we demonstrate that this protocol is sensitive enough to detect subtle differences in gene expression and compares well to commonly used methods such as RT-qPCR and flow cytometry with the added benefit of visualization at the cellular level.

MicroRNA485-3p negatively regulates the transcriptional co-repressor CtBP1 to control the oncogenic process in osteosarcoma cells

Carboxyl-terminal binding protein 1 (CtBP1), a well-known transcriptional co-repressor, is highly expressed in a number of cancer types. However, it is still absent in osteosarcoma cells. Here, we found that CtBP1, but not CtBP2, is overexpressed in invasive osteosarcoma tissues and cells. The overexpressed CtBP1 in turn represses its downstream targets, such as the pro-apoptotic regulators Bax, Bim and p53 upregulated modulator of apoptosis (PUMA), cell adhesion molecule E-cadherin, and the cell cycle regulators p16, p21 and phosphatase and tensin homolog (PTEN). To explore the molecular mechanism of CtBP1 overexpression, we subjected three independent clinical samples to miRNA microarray analysis and found that miR-485-3p could specifically bind to the 3'-untranslated region (3'-UTR) of CtBP1, thereby negatively controlling CtBP1 expression. The overexpression of miR-485-3p in osteosarcoma cells significantly repressed CtBP1 levels and inhibited cell proliferation, colony formation, cell migration and sphere formation. Further analysis indicated that DNA hypermethylation in the promoter region of miR-485-3p caused the downregulation of miR-485-3p. Treatment with the DNA methylation inhibitor 5-aza-2'-deoxycytidine (AZA) resulted in the upregulation of miR-485-3p and the downregulation of CtBP1 as well as inhibited osteosarcoma cell growth. This study provides evidence that CtBP1 is also overexpressed in osteosarcoma cells and demonstrates the underlying mechanism regarding its overexpression. Thus, therapeutically targeting CtBP1 may represent an effective strategy for osteosarcoma therapy.

Impact of Phosphoproteomics in the Era of Precision Medicine for Prostate Cancer

Prostate cancer is the most common malignancy in men in the United States. While androgen deprivation therapy results in tumor responses initially, there is relapse and progression to metastatic castration-resistant prostate cancer. Currently, all prostate cancer patients receive essentially the same treatment, and there is a need for clinically applicable technologies to provide predictive biomarkers toward personalized therapies. Genomic analyses of tumors are used for clinical applications, but with a paucity of obvious driver mutations in metastatic castration-resistant prostate cancer, other applications, such as phosphoproteomics, may complement this approach. Immunohistochemistry and reverse phase protein arrays are limited by the availability of reliable antibodies and evaluates a preselected number of targets. Mass spectrometry-based phosphoproteomics has been used to profile tumors consisting of thousands of phosphopeptides from individual patients after surgical resection or at autopsy. However, this approach is time consuming, and while a large number of candidate phosphopeptides are obtained for evaluation, limitations are reduced reproducibility, sensitivity, and precision. Targeted mass spectrometry can help eliminate these limitations and is more cost effective and less time consuming making it a practical platform for future clinical testing. In this review, we discuss the use of phosphoproteomics in prostate cancer and other clinical cancer tissues for target identification, hypothesis testing, and possible patient stratification. We highlight the majority of studies that have used phosphoproteomics in prostate cancer tissues and cell lines and propose ways forward to apply this approach in basic and clinical research. Overall, the implementation of phosphoproteomics via targeted mass spectrometry has tremendous potential to aid in the development of more rational, personalized therapies that will result in increased survival and quality of life enhancement in patients suffering from metastatic castration-resistant prostate cancer.

Loss of P16 in Esophageal Adenocarcinoma Detected by Fluorescence in situ Hybridization and Immunohistochemistry

Molecular biology of esophageal adenocarcinoma (EAC) is not fully elucidated. The aim of this study was to assess the expression of cycle regulator and tumor suppressor p16 in esophageal adenocarcinoma. The expression of p16 at protein and gene level was investigated using immunohistochemistry and fluorescence in situ hybridization in thirteen EAC specimens obtained by endoscopic biopsies and surgical resections. The mean age of enrolled patients was 62 years and a male predominance was observed. Loss of p16 protein expression was detected in 77% of the cases and loss of p16 gene was found in 69% of cases as hemizygous deletion was the most common. Significant correlation was found between the absence of p16 protein expression and p16 allelic loss. Cell cycle disturbances seem to play role in the EAC carcinogenesis and probably p16 gene deletions are connected with the loss of p16 protein expression.

Classification of cancer cell lines using matrix-assisted laser desorption/ionization time‑of‑flight mass spectrometry and statistical analysis

Over the past decade, matrix-assisted laser desorption/ionization time‑of‑flight mass spectrometry (MALDI‑TOF MS) has been established as a valuable platform for microbial identification, and it is also frequently applied in biology and clinical studies to identify new markers expressed in pathological conditions. The aim of the present study was to assess the potential of using this approach for the classification of cancer cell lines as a quantifiable method for the proteomic profiling of cellular organelles. Intact protein extracts isolated from different tumor cell lines (human and murine) were analyzed using MALDI‑TOF MS and the obtained mass lists were processed using principle component analysis (PCA) within Bruker Biotyper® software. Furthermore, reference spectra were created for each cell line and were used for classification. Based on the intact protein profiles, we were able to differentiate and classify six cancer cell lines: two murine melanoma (B16‑F0 and B164A5), one human melanoma (A375), two human breast carcinoma (MCF7 and MDA‑MB‑231) and one human liver carcinoma (HepG2). The cell lines were classified according to cancer type and the species they originated from, as well as by their metastatic potential, offering the possibility to differentiate non‑invasive from invasive cells. The obtained results pave the way for developing a broad‑based strategy for the identification and classification of cancer cells.

Role of inducible nitric oxide synthase and interleukin-6 expression in estimation of skin burn age and vitality

Estimation of age and vitality of burn injury both in the living and dead is essential in forensic practice. Nitric oxide and interleukin-6 (IL-6) play an important role in skin burn healing. In this study, the expression of inducible nitric oxide synthase (iNOS) and IL-6 proteins during skin burn healing in rats was studied for purposes of burn dating and to differentiate between ante-mortem and post-mortem burn. Ante-mortem skin burns were created on forty five rats. Normal and burnt skin samples were taken at 1, 3, 5, 7, 9, 11, 13, 15 and 21 days following burn induction (5 rats for each stage). Post-mortem burn was inflicted 6 h after scarification in another five rats. There was a statistically significant difference in both iNOS and IL-6 expression between the different time intervals of the ante-mortem burn. Expression of both iNOS and IL-6 decreased remarkably in the post-mortem burn with a statistically significant difference from ante-mortem intervals. A statistically significant positive association between the two markers was found. These results indicate that both iNOS and IL-6 expression in ante-mortem burnt skin was time dependent and significantly differed from post-mortem burn. Further research on humans is recommended.

HMGA1 expression levels are elevated in pancreatic intraepithelial neoplasia cells in the Ptf1a-Cre; LSL-KrasG12D transgenic mouse model of pancreatic cancer

BACKGROUND

Pancreatic cancer is currently the third leading cause of cancer deaths in the United States and it is predicted to become the second by the year 2030. High-mobility group A1 protein (HMGA1) is an oncogenic transcription factor, localised and active in cell nuclei, that is linked to tumour progression in many human cancers, including pancreatic cancer. Overexpression of HMGA1 renders cancer cells resistant to chemotherapy. Although the Ptf1a-Cre; LSL-KrasG12D transgenic mouse is perhaps the most widely utilised animal model for human pancreatic cancer, expression levels of HMGA1 in pancreata from this mouse model have not been characterised.

METHODS

Quantitative immunohistochemical analysis was used to determine nuclear HMGA1 levels in pancreatic tissue sections from Ptf1a-Cre; LSL-KrasG12D mice aged 5, 11, and 15 months. The H Score method was used for quantitative analysis.

RESULTS

The HMGA1 levels were significantly elevated in pancreatic intraepithelial neoplasia (PanIN) epithelia compared with untransformed acinar tissues or fibroinflammatory stroma.

CONCLUSIONS

The PanINs have long been regarded as precancerous precursors to pancreatic adenocarcinoma. Significantly elevated HMGA1 levels observed in the nuclei of PanINs in Ptf1a-Cre; LSL-KrasG12D mice validate this animal model for investigating the role that HMGA1 plays in cancer progression and testing therapeutic approaches targeting HMGA1 in human cancers.

Potential of RASSF1A promoter methylation as biomarker for endometrial cancer: A systematic review and meta-analysis

BACKGROUND

An epigenetic approach to explaining endometrial carcinogenesis necessitates good understanding of Ras association domain family 1 isoform A (RASSF1A) promoter methylation data from primary studies.

AIMS

Differential magnitude of reported associations between RASSF1A promoter methylation and endometrial cancer (EC) prompted a meta-analysis to obtain more precise estimates.

METHODS

Literature search yielded eight included articles. We calculated pooled odds ratios (OR) and 95% confidence intervals and subgrouped the data by race. Sources of heterogeneity were investigated with outlier analysis.

RESULTS

The pooled ORs indicated increased risk, mostly significant. The overall effect (OR 11.46) was reflected in the European outcome (OR 15.07). However, both findings were heterogeneous (I²=57-70%) which when subjected to outlier treatment, erased heterogeneity (I²=0%) and retained significance (OR 9.85-12.66). Significance of these pre- and post-outlier outcomes were pegged at P≤0.0001. Only the Asian pre-outlier (OR 6.85) and heterogeneous (I²=82%) outcome was not significant (P=0.12) but when subjected to outlier treatment, erased heterogeneity (I²=0%) and generated significance (OR 23.74, P≤0.0001).

CONCLUSIONS

Consistent increased risk associations underpinned by significance and robustness render RASSF1A with good biomarker potential for EC.

Evaluation of a panel of antibodies for the immunohistochemical identification of immune cells in paraffin-embedded lymphoid tissues of new- and old-world camelids

Different species of camelids play an important role in the epidemiology of various emerging infectious diseases such as Middle East respiratory syndrome. For precise investigations of the immunopathogenesis in these host species, appropriate immunohistochemical markers are highly needed in order to phenotype distinct immune cells populations in camelids. So far, specific immunohistochemical markers for camelid immune cells are rarely commercially available, and cross-reactivity studies are restricted to the use of frozen dromedary tissues. To bridge this gap, 14 commercially available primary antibodies were tested for their suitability to demonstrate immune cell populations on formalin fixed paraffin-embedded (FFPE) tissue sections of dromedaries, Bactrian camels, llamas, and alpacas in the present study. Out of these, 9 antibodies directed against CD3, CD20, CD79α, HLA-DR, Iba-1, myeloid/histiocyte antigen, CD204, CD208, and CD68 antigen exhibited distinct immunoreaction patterns to certain camelid immune cell subsets. The distribution of these antigens was comparatively evaluated in different anatomical compartments of thymus, spleen, mesenteric, and tracheobronchial lymph nodes. The presented results will provide a basis for further investigations in camelids, especially with respect to the role of the immune response in certain infectious diseases, which harbor a considerable risk to spill over to other species.

Multiplex Gene Expression Profiling of 16 Target Genes in Neoplastic and Non-Neoplastic Canine Mammary Tissues Using Branched-DNA Assay

Mammary gland tumors are one of the most common neoplasms in female dogs, and certain breeds are prone to develop the disease. The use of biomarkers in canines is still restricted to research purposes. Therefore, the necessity to analyze gene profiles in different mammary entities in large sample sets is evident in order to evaluate the strength of potential markers serving as future prognostic factors. The aim of the present study was to analyze the gene expression of 16 target genes (BRCA1, BRCA2, FOXO3, GATA4, HER2, HMGA1, HMGA2, HMGB1, MAPK1, MAPK3, MCL1, MYC, PFDN5, PIK3CA, PTEN, and TP53) known to be involved in human and canine mammary neoplasm development. Expression was analyzed in 111 fresh frozen (FF) and in 170 formalin-fixed, paraffin-embedded (FFPE) specimens of neoplastic and non-neoplastic canine mammary tissues using a multiplexed branched-DNA (b-DNA) assay. TP53, FOXO3, PTEN, and PFDN5 expression revealed consistent results with significant low expression in malignant tumors. The possibility of utilizing them as predictive factors as well as for assisting in the choice of an adequate gene therapy may help in the development of new and improved approaches in canine mammary tumors.

Porcine epidemic diarrhea virus: An overview of current virological and serological diagnostic methods

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Molecular assays such as rRT-PCR are the method of choice for PEDV diagnosis.

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Multiplex rRT-PCR allow simultaneous testing for PEDV, TGEV and PDCoV.

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Serological assays provide valuable information on previous exposure to PEDV and population immunity.

Porcine epidemic diarrhea virus (PEDV) is the causative agent of an acute, highly contagious, and severe enteric disease that leads to high mortality rates in suckling piglets. Therefore, accurate diagnosis of PEDV infection is critical for the implementation of control measures for the virus. Many diagnostic tests have been recently developed and are currently available for the detection of PEDV, its proteins or nucleic acid, including virus isolation, immunofluorescence (IF) or immunohistochemistry (IHC), polymerase chain reaction (PCR) and isothermal amplification assays. Additionally, several serological assays have been developed and are currently used for the detection of antibodies against PEDV. Molecular assays such as real-time reverse transcriptase-PCR (rRT-PCR) became the methods of choice for the diagnosis of PEDV infection, providing sensitive, specific and rapid detection of the virus RNA in clinical samples. Whereas serological assays have been widely used to monitor prior exposure to the virus and to evaluate the efficacy of novel vaccine candidates or vaccination strategies. Here we discuss the properties of current PEDV diagnostic assays and prospects for improving diagnostic strategies in the future.

Immunocapture strategies in translational proteomics

Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.