Cell and tissue microarray technologies for protein and nucleic acid expression profiling

TMA-Mate: An open-source modular toolkit for constructing tissue microarrays of arbitrary layouts

Biomedical research and quality control procedures often demand a variety of microscopic analysis of numerous formalin-fixed and paraffin-embedded (FFPE) tissue samples from different individuals of both healthy and diseased regions of interest. Depending on the number of samples to be analyzed, conventional processing of each FFPE block separately can be laborious or impracticable. This effort can be drastically reduced by using tissue microarrays (TMAs). TMAs have a wide range of applications and can be considered as a high-throughput method to process up to hundreds of miniaturized tissue samples simultaneously on a single microscopy slide, in order to reduce labor, costs and sample consumption, and to increase results comparability. Several commercial and self-made solutions to fabricate TMAs with varying degrees of automation are available. However, these solutions may not be suitable for every situation, either due to high costs, high complexity, lack of precision or lack of flexibility, especially when diagnostically oriented pathology institutes or laboratories with constrained resources are considered. This article introduces the TMA-Mate, an open-source 3D printable modular toolkit for constructing high-density TMAs of arbitrary layouts, providing an affordable, lightweight, and accessible procedure to implement TMAs into existing histology processing pipelines. Step-by-step demonstrations for replicating the hardware and constructing TMAs are included.

PD-1, PD-L1 and cAMP immunohistochemical expressions are associated with worse oncological outcome in patients with bladder cancer

PURPOSE

In this study, we aimed to identify prognostic factors of cancer mortality in patients who received radical cystectomy and to identify genomic alterations in a sub-cohort of patients with locally advanced (pT3-4) and/or positive lymph nodes bladder cancer (BC).

METHODS

We collected 101 BC samples from 2010 to 2018 who previously received radical cystectomy. Immunohistochemical slides were evaluated for PPAR, cAMP, IMP3, Ki67, CDK4, POU5F1, Cyclin E and MDM2, p65, CD3, CD4, CD8, CD20, CD68, CD163, FOXP3, PD-1 and PD-L1 expression. We calculated a prognostic score (PS) based on the positivity to PD-1, PD-L1 and of cAMP (final score ranging from 0 to 3). DNA of each sample have been used for sequencing by NGS in a sub-cohort of 6 patients with locally advanced (pT3-4) and/or positive lymph nodes BC.

RESULTS

PD-1 ⁺ (HR [hazard ratio] 2.59; p = 0.04), PD-L1⁺ (HR = 6.46; p < 0.01) and cAMP⁺ (HR 3.04; p = 0.02) were independent predictors of cancer-specific mortality (CSM). Increase of PS (score = 0 as reference) was associated with CSM, 0.81 (p = 0.80), 4.72 (p = 0.01) and 10.51 (p < 0.0) for PS 1, 2 and 3, respectively. ERBB2 was the gene most frequently mutated.

CONCLUSION

BC exhibited heterogenous protein expression and variable genomic features. Identification of expression of PD-1, PD-L1 and cAMP could help in predicting oncological outcomes.

Insulin signaling, androgen receptor and PSMA immunohistochemical analysis by semi-automated tissue microarray in prostate cancer with diabetes (DIAMOND study)

In the last years, many studies have highlighted the hypothesis that diabetes and hyperglycemia could be relevant for prostate cancer (PC) development and progression. We aimed to identify the prognostic value of tissue expression of androgen receptor (AR), Prostate-Specific Membrane Antigen (PSMA), Ki-67, insulin receptors (IR)  α and β, insulin growth factor-1 (IGF-1) receptor, in patients with PC and to evaluate their association with diabetes. We retrospectively collected data from 360 patients who underwent radical prostatectomy for PC or surgery for benign prostatic hyperplasia (BPH), between 2010 and 2020. We constructed tissue microarray for immunohistochemistry (IHC) analysis. In the final cohort (76 BPH and 284 PC), 57 (15.8%) patients had diabetes, 17 (22.37%) in BPH and 40 (14.08%) in PC (P = 0.08). IR-α was more expressed in patients with PC compared to the BPH Group (95.96% vs 4.04%; P <0.01). We found that AR was associated with increased risk of International Society of Urological Pathology (ISUP) score ≥4 (OR: 2.2; P <0.05), higher association with Ki-67 (OR: 2.2; P <0.05) and IR-α (OR: 5.7; P <0.05); IGF-1 receptor was associated with PSMA (OR: 2.8; P <0.05), Ki-67 (OR: 3.5; P <0.05) and IR-β (OR: 5.1; P <0.05). Finally, IGF-1 receptor was predictive of ISUP ≥ 4 (OR: 16.5; P =0.017) in patients with PC and diabetes. In the present study we highlighted how prostate cancer patients have a different protein expression in the tissue. This expression, and in particular that relating to IGF-1R, is associated with greater tumor aggressiveness in those patients with diabetes. We suppose that these results are attributable to an alteration of the insulin signal which therefore determines a greater mitogenic activity that can influence tumor progression.

SRSF-1 and microvessel density immunohistochemical analysis by semi-automated tissue microarray in prostate cancer patients with diabetes (DIAMOND study)

OBJECTIVE

To study the association between insulin receptors (isoforms α and β), insulin growth factor-1 (IGF1) and serine/arginine splicing factor 1 (SRSF-1) in patients with prostate cancer (PC) and diabetes.

MATERIALS AND METHODS

We retrospectively analyzed data from 368 patients who underwent surgery for PC or benign prostatic hyperplasia (BPH) between 2010 and 2020 at the Department of Urology, University of Catania. Tissue microarray slides were constructed and they were stained for androgen receptor (AR), insulin receptor-α and -β, IGF1 (IGF1-R), Ki-67, and prostate specific membrane antigen (PSMA) expression using validated score.

RESULTS

The final cohort was represented by 100 patients with BPH and 268 with PC, with a median age of 68 years. We found that SRSF-1 expression was associated with AR (odds ratio [OR]: 1.66), PSMA (OR: 2.13), Ki-67 (OR: 5.99), insulin receptor (IR)-α (OR: 2.38), IR-β (OR: 3.48), IGF1-R (OR: 1.53), and microvascular density (MVD) was associated with PSMA (OR: 3.44), Ki-67 (OR: 2.23), IR-α (OR: 2.91), IR-β (OR: 3.02), IGF1-R (OR: 2.95), and SRSF-1 (OR: 2.21). In the sub cohort of PC patients, we found that SRSF-1 expression was associated with AR (OR: 2.34), Ki-67 (OR: 6.77), IR-α (OR: 2.7), and MVD (OR: 1.98). At the Kaplan-Meier analysis, SRSF-1⁺ patients had worse 5- and 9-year biochemical recurrence (36% and 6%) respect to SRSF-1^- (67% and 7%; p < .01) and similarly MVD⁺ patients (44% and 7%) respect to MVD^- (64% and 8%; p < .01). Restricting the analysis only in patients with PC and diabetes, we found that SRSF-1⁺ was associated with Ki-67⁺ (OR: 8.75; p < .05) and MVD⁺ (OR: 7.5; p < .05).

CONCLUSIONS

PC exhibits widespread heterogeneity in protein expression. In particular, the expressions of the SRSF-1 protein and of the MVD are associated with a worse prognosis and in particular with a greater cell proliferation. These results, although preliminary, may offer new future scientific insights with the aim of highlighting possible genetic alterations linked to a greater expression of SRSF-1 and associated with a worse prognosis.

Data-Driven Discovery of Molecular Targets for Antibody-Drug Conjugates in Cancer Treatment

Antibody-drug conjugate therapy has attracted considerable attention in recent years. Since the selection of appropriate targets is a critical aspect of antibody-drug conjugate research and development, a big data research for discovery of candidate targets per tumor type is outstanding and of high interest. Thus, the purpose of this study was to identify and prioritize candidate antibody-drug conjugate targets with translational potential across common types of cancer by mining the Human Protein Atlas, as a unique big data resource. To perform a multifaceted screening process, XML and TSV files including immunohistochemistry expression data for 45 normal tissues and 20 tumor types were downloaded from the Human Protein Atlas website. For genes without high protein expression across critical normal tissues, a quasi H-score (range, 0-300) was computed per tumor type. All genes with a quasi H - score ≥ 150 were extracted. Of these, genes with cell surface localization were selected and included in a multilevel validation process. Among 19670 genes that encode proteins, 5520 membrane protein-coding genes were included in this study. During a multistep data mining procedure, 332 potential targets were identified based on the level of the protein expression across critical normal tissues and 20 tumor types. After validation, 23 cell surface proteins were identified and prioritized as candidate antibody-drug conjugate targets of which two have interestingly been approved by the FDA for use in solid tumors, one has been approved for lymphoma, and four have currently been entered in clinical trials. In conclusion, we identified and prioritized several candidate targets with translational potential, which may yield new clinically effective and safe antibody-drug conjugates. This large-scale antibody-based proteomic study allows us to go beyond the RNA-seq studies, facilitates bench-to-clinic research of targeted anticancer therapeutics, and offers valuable insights into the development of new antibody-drug conjugates.

Association of immunohistochemical markers of tumor subtype with response to neoadjuvant chemotherapy and survival in patients with muscle-invasive bladder cancer

Purpose

A readily accessible biomarker to identify which patients with bladder cancer are more likely to respond to neoadjuvant chemotherapy (NAC) could help clinicians avoid unnecessary chemotherapy and prevent its subsequent complications in some patients. The primary objective of this study was to investigate the association of immunohistochemical markers of tumor subtype with response to NAC and survival of patients with muscle-invasive bladder cancer (MIBC).

Materials and Methods

MIBC patients treated with NAC were retrospectively included. The tissue microarrays were assembled from transurethral resection of bladder tumor (TURBT) specimens and immunohistochemistry (IHC) was performed. The association of independent variables, including IHC markers, and clinical covariates with clinical complete response to NAC and with overall survival was assessed by using logistic regression and Cox proportional hazard regression analysis, respectively. Kaplan-Meier curves were plotted for different IHC-based tumor subtypes.

Results

Data from 140 MIBC patients treated with NAC were retrospectively reviewed. A total of 63 patients with available TURBT specimens were eligible to be included in the analysis. Our results showed that the IHC signature of KRT5/6(+)/KRT20(−), as a combined marker of basal subtype, was the only covariate significantly associated with complete response to NAC (p=0.037). Moreover, we found no statistically significant differences in overall survival between different IHC-based subtypes (p=0.721).

Conclusions

The IHC expression of KRT5/6 and KRT20, as a readily accessible combined marker, may help us to identify the patients most likely to benefit from chemotherapy. The clinical utility of this marker needs to be established in larger prospective studies.

Association Between Toll-Like Receptor 4 (TLR4) and Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) Genetic Variants and Clinical Progression of Huntington's Disease

BACKGROUND

Although Huntington's disease (HD) is caused by a single dominant gene, it is clear that there are genetic modifiers that may influence the age of onset and disease progression.

OBJECTIVES

We sought to investigate whether new inflammation-related genetic variants may contribute to the onset and progression of HD.

METHODS

We first used postmortem brain material from patients at different stages of HD to look at the protein expression of toll-like receptor 4 (TLR4) and triggering receptor expressed on myeloid cells 2 (TREM2). We then genotyped the TREM2 R47H gene variant and 3 TLR4 single nucleotide polymorphisms in a large cohort of HD patients from the European Huntington's Disease Network REGISTRY.

RESULTS

We found an increase in the number of cells expressing TREM2 and TLR4 in postmortem brain samples from patients dying with HD. We also found that the TREM2 R47H gene variant was associated with changes in cognitive decline in the large cohort of HD patients, whereas 2 of 3 TLR4 single nucleotide polymorphisms assessed were associated with changes in motor progression in this same group.

CONCLUSIONS

These findings identify TREM2 and TLR4 as potential genetic modifiers for HD and suggest that inflammation influences disease progression in this condition. © 2019 International Parkinson and Movement Disorder Society.

Cell adhesion molecule profiles, proliferation activity and p53 expression in advanced epithelial ovarian cancer induced malignant ascites-Correlation of tissue microarray and cytology microarray

INTRODUCTION

Peritoneal dissemination accompanied by ascites formation is common in epithelial ovarian cancer (EOC). Adhesion molecules are crucial in metastatic spread and the latter involves epithelial-mesenchymal transition (EMT). This study aimed at: (1) clarifying whether E-cadherin and β-catenin expression and proliferative activity in metastatic ovarian cancer are inter-related; (2) Identifying possible correlations between cell adhesion molecular expression profiles, the proliferative activity and p53 expression of tumor cells and tumor grade and stage; (3) testing the cytology microarray (CMA) technique in analyzing metastasis formation.

MATERIAL AND METHODS

Both tumorous and ascitic samples from 27 EOC patients were examined by using tissue microarray (TMA) and cytology microarray (CMA), respectively. CMA blocks were constructed using cores from each cell block of the ascitic specimens. Expression of E-cadherin, β-catenin, Ki-67 and p53 was immunohistochemically detected both in TMA and CMA blocks.

RESULTS

E-cadherin expression was higher in ascitic cells than in primary tumor cells (p = .294). β-catenin expression was significantly lower in ascitic cells than in primary tumor cells (p = .006). Expression of Ki-67 was lower and expression of p53 was higher in primary tumors than in ascitic cells, for p53 the difference was significant (p = .001). Both Ki-67 and p53 expression elevated significantly in high-grade primary tumor cells and in ascites cells (p = .039, and p = .004, respectively).

CONCLUSION

Epithelial-mesenchymal transition- mesenchymal-epithelial transition is suggested as the best descriptive term for our IHC observations which accompany increased proliferative activity of ascitic cells. The CMA method is an adequate and reliable method for the analysis of ascitic tumor cells disseminating from ovarian malignancies.

Improving gastric cancer preclinical studies using diverse in vitro and in vivo model systems

BACKGROUND

"Biomarker-driven targeted therapy," the practice of tailoring patients' treatment to the expression/activity levels of disease-specific genes/proteins, remains challenging. For example, while the anti-ERBB2 monoclonal antibody, trastuzumab, was first developed using well-characterized, diverse in vitro breast cancer models (and is now a standard adjuvant therapy for ERBB2-positive breast cancer patients), trastuzumab approval for ERBB2-positive gastric cancer was largely based on preclinical studies of a single cell line, NCI-N87. Ensuing clinical trials revealed only modest patient efficacy, and many ERBB2-positive gastric cancer (GC) patients failed to respond at all (i.e., were inherently recalcitrant), or succumbed to acquired resistance.

METHOD

To assess mechanisms underlying GC insensitivity to ERBB2 therapies, we established a diverse panel of GC cells, differing in ERBB2 expression levels, for comprehensive in vitro and in vivo characterization. For higher throughput assays of ERBB2 DNA and protein levels, we compared the concordance of various laboratory quantification methods, including those of in vitro and in vivo genetic anomalies (FISH and SISH) and xenograft protein expression (Western blot vs. IHC), of both cell and xenograft (tissue-sectioned) microarrays.

RESULTS

The biomarker assessment methods strongly agreed, as did correlation between RNA and protein expression. However, although ERBB2 genomic anomalies showed good in vitro vs. in vivo correlation, we observed striking differences in protein expression between cultured cells and mouse xenografts (even within the same GC cell type). Via our unique pathway analysis, we delineated a signaling network, in addition to specific pathways/biological processes, emanating from the ERBB2 signaling cascade, as a potential useful target of clinical treatment. Integrated analysis of public data from gastric tumors revealed frequent (10 - 20 %) amplification of the genes NFKBIE, PTK2, and PIK3CA, each of which resides in an ERBB2-derived subpathway network.

CONCLUSION

Our comprehensive bioinformatics analyses of highly heterogeneous cancer cells, combined with tumor "omics" profiles, can optimally characterize the expression patterns and activity of specific tumor biomarkers. Subsequent in vitro and in vivo validation, of specific disease biomarkers (using multiple methodologies), can improve prediction of patient stratification according to drug response or nonresponse.

Evaluation of cross-sample contamination in tissue microarrays by polymerase chain reaction

In the past decade, the popularity and power of Tissue Microarray (TMA) technology has increased since it provides a method to detect diagnostic and prognostic markers in an array of clinical tissue specimens collected for translational research. TMAs allow for rapid and cost-effective analysis of hundreds of molecular markers at the nucleic acid and protein levels. This technology is particularly useful in the realization of the Human Protein Atlas Project, since it aims to create a reference database of non-redundant human proteins. In this context, it is important to assure the lack of cross-sample contamination due to the repeated use of the same needle in consecutive coring. Here we show that carry-over contamination from one tissue core to another does not occur, reinforcing the accuracy of the TMA technology in the simultaneous testing of multiple bio-samples.

Application of Tissue Microarray Technology to Stem Cell Research

There is virtually an unlimited number of possible Tissue Microarray (TMA) applications in basic and clinical research and ultimately in diagnostics. However, to assess the functional importance of novel markers, researchers very often turn to cell line model systems. The appropriate choice of a cell line is often a difficult task, but the use of cell microarray (CMA) technology enables a quick screening of several markers in cells of different origins, mimicking a genomic-scale analysis. In order to improve the morphological evaluations of the CMA slides we harvested the cells by conventional trypsinization, mechanical scraping and cells grown on coverslips. We show that mechanical scraping is a good evaluation method since keeps the real morphology very similar to those grown on coverslips. Immunofluorescence images are of higher quality, facilitating the reading of the biomarker cellular and subcellular localization. Here, we describe CMA technology in stem cell research.

An improved high-output cell microarray technology

AIMS

Cell microarray (CMA) is a high-throughput scientific research tool, which has greatly accelerated many analyses based at the cellular level. However, there are few described methods for constructing CMAs. Here, we introduce a new, simple, high-output CMA method that is applicable to a broad range of cellular samples.

METHODS

In this method, a recipient block (length, 3.6 cm; width, 2.7 cm; depth, 2 cm) with 40 dot markers was moulded using a transparent plastic box. Adenocarcinoma cells were collected from malignant pleural effusions, cell cylinders were moulded with plastic piping and the cylinders were manually arrayed one by one into the corresponding location of the 60 °C pre-softened recipient block using the guide holes drilled with a steel needle. We constructed a 40-cylinder CMA to prove this method. The expression of cytokeratin 7 (CK7) in the CMA was examined to confirm antigen preservation and epidermal growth factor receptor (EGFR) gene mutation was screened for in five samples.

RESULTS

The CMA prepared by this method had well-defined array configurations, good cellular morphology and well-preserved proteins and DNA. A total of 1000 sections could be easily gained from this CMA block.

CONCLUSIONS

This simple and low-cost method provides a novel way of preparing a high-output CMA.