An alternative high output tissue microarray technique

Somatostatin receptor subtype 2A expression and genetics in 184 paragangliomas: a single center retrospective observational study

PURPOSE

Adrenal and extra-adrenal paragangliomas (PGLs) are a group of neuroendocrine tumors (NETs) with strong heterogeneity, which often express somatostatin receptor subtype 2 A (SSTR2A). However, the association between SSTR2A expression and genetic status of PGLs remains unclear. The purpose of the study was to identify whether various pathogenic variants (PVs) had an impact on SSTR2A expression in PGLs.

METHODS

This retrospective study included 184 patients with pathologically confirmed PGLs. The immunohistochemical expression of SSTR2A were studied in 184 tumors and PVs were tested in 159 tumor samples. Clinical and genetic data were compared in SSTR2A positive and negative PGLs.

RESULTS

SSTR2A was positive in 63.6% (117/184) of all tumors. PGLs with negative SSTR2A were more likely to be extra-adrenal (37.0% vs 18.0%; P = 0.005) and exhibited a considerably greater proportion of PVs (75.4% vs. 49.0%; P = 0.001) than those with positive SSTR2A. Compared to those without PVs, a higher proportion of PGLs with PVs in cluster 1B (P = 0.004) and cluster 2 (P = 0.004) genes, especially VHL (P = 0.009), FGFR1 (P = 0.010) and HRAS (P = 0.007), were SSTR2A negative. SSTR2A was positive in all tumors (4/4) with SDHx PVs and in 87.5% (7/8) of metastatic PGLs.

CONCLUSIONS

SSTR2A negativity was correlated with extra-adrenal tumor location and PVs in cluster 1B and cluster 2 genes such as VHL, FGFR1 and HRAS. Immunohistochemistry of SSTR2A should be taken into consideration in the personalized management of PGLs.

Abnormal p16 expression and prognostic significance in esophageal squamous cell carcinoma

BACKGROUND

The purpose of this study was to analyze p16 expression status and evaluate whether abnormal p16 expression was associated with prognosis in a large-scale esophageal squamous cell carcinoma (ESCC) cohort of patients.

METHODS

We retrospectively evaluated p16 expression status of 525 ESCC samples using immunohistochemistry. Associations between abnormal p16 expression and survival were analyzed.

RESULTS

P16 negative, focal expression and overexpression were found in 87.6%, 6.9% and 5.5% of ESCC patients. No significant association was observed between abnormal p16 expression and age, sex, tumor site and location, differentiation, vessel and nerve invasion, T stage and lymph node metastasis. In all patients, the survival of p16 focal expression group tended to be better compared with negative group (disease free survival/DFS P=0.040 and overall survival/OS P=0.052) and overexpression group (DFS P=0.201 and OS P=0.258), and there was no survival difference between negative group and overexpression group. The multivariate analysis for OS and DFS found that only clinical stage was a significantly independent prognostic factor (P<0.001). When patients were divided into I-II stage (n=290) and III-IVa stage (n=235), the survival of focal expression group was better compared with negative group (DFS P=0.015 and OS P=0.019), and tended to be better compared with overexpression group (DFS P=0.405 and OS P=0.432) in I-II stage ESCC, which was not found in III-IVa stage ESCC.

CONCLUSION

P16 overexpression or negative expression tend to be associated with unfavorable outcomes, especially in I-II stage ESCC. Our study will help to identify a subgroup of ESCC patients with excellent prognosis after surgical therapy.

Prognostic significance of CCND1 amplification/overexpression in smoking patients with esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is the main subtype of esophageal cancer, with 5-year survival rate less than 30%. In order to offer an individual therapeutic approach, it is necessary to identify novel prognostic factors to recognize high-risk patients. Given the high frequency of CCND1 abnormalities and the important biological effects of smoking in ESCC, we explored the potential relationship between CCND1 abnormalities and smoking in ESCC patients. CCND1 status was examined by fluorescence in situ hybridization and immunohistochemical staining in ESCC tissue microarrays (n = 519). CCND1 amplification and cyclinD1 overexpression were found in 53.2 and 34.1% ESCC, respectively. CCND1 amplification (P = 0.142 for DFS and P = 0.191 for OS) and cyclinD1 overexpression (P = 0.035 for DFS and P = 0.092 for OS) tended to be poorer prognostic factors in all patients. Among smoking patients, those with CCND1 amplification had significantly poorer prognosis, with a median DFS and OS of 25.0 and 30.0 months compared to not reached and 52.0 months for those without CCND1 amplification (P = 0.020 and 0.018). A similar trend was found in the 68 patients with cyclinD1 overexpression (P = 0.043 and 0.048). Further univariate and multivariate analysis revealed CCND1 amplification was independently poorer prognostic factor in smoking patients, which was not found in non-smoking patients. Smokers with CCND1 amplification or cyclinD1 overexpression have poorer survival, which help us to identify distinct groups of patients with apparently poorer outcome and would enable appropriate follow-up and treatment strategies.

Optimization of tissue microarray technique for breast cancer patients: a short communication

Background

Tissue microarray (TMA) is a novel technique for studying different types of cancer tissues in one block. TMA is not yet established in Syria, so we aimed in this project to apply and set the most optimal conditions of TMA creation of breast cancer tissues at the Pathology Department of our institute.

Materials and Methods

Eighty-eight blocks of breast cancer tissues were selected, considering the inclusion criteria. The tissue specimens of breast cancer patients were manually placed in the block by punching a core from a paraffin block, which was then released into a recipient block using a small trocar. Three different conditions were tested on the constructed TMA block.

Results

We determined the most effective parameters that proved high quality: incubating the newly constructed block at a temperature of 43°C for 24 h in the oven and then cutting it the next day after cooling it to room temperature; also, cutting with a 5 μm thickness created the preferable stained slides later. CD3 staining showed high expression of tumor-infiltrating lymphocytes among triple-negative breast cancer patients and high expression of CD3 in triple-negative cancer patients.

Conclusion

The optimization of parameters presented in our study resulted in perfect TMA generation and successful immunohistochemistry staining for cancer research at our institution.

A Simplified Method of Manually Constructing Small Format Tissue Microarray for Use in Resource-Constrained Settings

Background & Objective

Tissue microarray (TMA) is a method of harvesting small tissue cores from a number of donor paraffin tissue blocks and arraying them in a recipient paraffin block. It has numerous advantages and applications but is expensive. This study aimed to develop a simple yet efficient method of manual, small-format TMA block construction.

Methods

Disposable skin punch biopsy needles were used to manually core out 4-mm cylinders from the archival donor blocks comprising tissue from 60 thyroidectomy specimens. These cores were oriented in the embedding cassette in accordance with the grid design. The molten wax was slowly dispensed and allowed to be set. Sectioning, mounting, and hematoxylin and eosin (H&E) staining were performed by a conventional method. Immunohistochemical studies, using HBME-1, CK19, and S100 antibodies, were also performed on these tissue array sections.

Results

There was no core loss during processing. Technical issues like core tilt and floatation were easily tackled. Morphological identification, histological typing, and immunohistochemical analysis could be satisfactorily performed in these TMA sections. Donor blocks did not break after punching.

Conclusion

This TMA construction method is simple, feasible, easily reproducible, and time-saving. It can serve as an excellent cost-effective alternative for resource-poor laboratories for carrying out immunohistochemical studies.

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.

Constructing high-density tissue microarrays with a novel method and a self-made tissue-arraying instrument

Tissue microarrays (TMAs), also called tissue chips, contain hundreds to thousands of tissue cores obtained from different tissue donor blocks. By using TMA technology, a molecular marker, such as protein, RNA or DNA, can be simultaneously examined in hundreds of different specimens under the same experimental conditions. A growing number of previous studies have introduced different methods for constructing TMAs. Many authors tried to use various methods to implant more tissue cores in a single recipient block, and most of these methods involved reducing the diameter of the tissue cores and/or the spacing between adjacent tissue cores. However, when creating TMAs, it is difficult to reduce the distance between tissue cores to zero except with extremely expensive automatic TMA arrayers. Here, we introduce a novel method to construct a high-density TMA that does not have spacing between the tissue cores. We also introduce a method for preparing a self-made tissue-arraying instrument. With this method and the tissue-arraying instrument, we successfully created a TMA containing 126 tissue cores that were 2 mm in diameter. H&E staining and immunohistochemical staining were performed on the sections cut from the TMA without any tissue spot loss. This method is easy to operate, and the materials for creating the tissue-arraying instrument are inexpensive and can be purchased anywhere. Therefore, this method can be applied in all laboratories.

Prognostic Significance of CDK6 Amplification in Esophageal Squamous Cell Carcinoma

Dysregulation of CDK6 plays crucial roles in the carcinogenesis of many kinds of human malignancies. However, the role of CDK6 in esophageal squamous cell carcinoma (ESCC) is not well known. We investigated the frequency and prognostic value of CDK6 amplification to improve the risk stratification in patients with ESCC. Pan-cancer analysis of CDK6 was conducted on The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx) and Gene Expression Omnibus (GEO) databases. CDK6 amplification was detected in 502 ESCC samples by Fluorescence in situ hybridization (FISH) through tissue microarrays (TMA). Pan-cancer analysis revealed that CDK6 mRNA level was much higher in multiple kinds of cancers and higher CDK6 mRNA level indicated a better prognosis in ESCC. In this study, CDK6 amplification was detected in 27.5% (138/502) of patients with ESCC. CDK6 amplification was significantly correlated with tumor size (p = 0.044). Patients with CDK6 amplification tended to have a longer disease-free survival (DFS) (p = 0.228) and overall survival (OS) (p = 0.200) compared with patients without CDK6 amplification but of no significance. When further divided into I-II and III-IV stage, CDK6 amplification was significantly associated with longer DFS and OS in III-IV stage group (DFS, p = 0.036; OS, p = 0.022) rather than in I-II stage group (DFS, p = 0.776; OS, p = 0.611). On univariate and multivariate analysis of Cox hazard model, differentiation, vessel invasion, nerve invasion, invasive depth, lymph node metastasis and clinical stage were significantly associated with DFS and OS. Moreover, invasion depth was an independent factor for ESCC prognosis. Taken together, for ESCC patients in III-IV stage, CDK6 amplification indicated a better prognosis.

Proteomic analysis reveals key differences between squamous cell carcinomas and adenocarcinomas across multiple tissues

Squamous cell carcinoma (SCC) and adenocarcinoma (AC) are two main histological subtypes of solid cancer; however, SCCs are derived from different organs with similar morphologies, and it is challenging to distinguish the origin of metastatic SCCs. Here we report a deep proteomic analysis of 333 SCCs of 17 organs and 69 ACs of 7 organs. Proteomic comparison between SCCs and ACs identifies distinguishable pivotal pathways and molecules in those pathways play consistent adverse or opposite prognostic roles in ACs and SCCs. A comparison between common and rare SCCs highlights lipid metabolism may reinforce the malignancy of rare SCCs. Proteomic clusters reveal anatomical features, and kinase-transcription factor networks indicate differential SCC characteristics, while immune subtyping reveals diverse tumor microenvironments across and within diagnoses and identified potential druggable targets. Furthermore, tumor-specific proteins provide candidates with differentially diagnostic values. This proteomics architecture represents a public resource for researchers seeking a better understanding of SCCs and ACs.

PMS2 Expression With Combination of PD-L1 and TILs for Predicting Survival of Esophageal Squamous Cell Carcinoma

Background

DNA mismatch repair (MMR) deficiency (dMMR) has been recognized as an important biomarker for immunotherapy in esophageal squamous cell carcinoma (ESCC), along with programmed death ligand 1 (PD-L1) expression and/or tumor-infiltrated lymphocytes (TILs). However, in ESCC, MMR protein assessment has not been well studied at present.

Methods

A total of 484 ESCC tissues treated between 2007 and 2010, in our hospital, were enrolled. Immunohistochemical expression of MLH1, MSH2, MSH6, PMS2, and PD-L1 on tissue microarray specimens and clinicopathological features, including TILs, were analyzed retrospectively.

Results

Out of the 484 studied cases, loss of MLH1, MSH2, MSH6, and PMS2 expression were found in 6.8%, 2.1%, 8.7%, and 4.8% patients, respectively. dMMR was found in 65 patients, 37 cases involved in one MMR protein, 17 cases involved in two proteins, 7 cases involved in three proteins, and 4 cases involved in four proteins. There was no significant survival difference between pMMR (MMR-proficient) and dMMR patients (P>0.05). However, 224 patients with low PMS2 expression had better DFS and OS than 260 patients with high PMS2 expression (P=0.006 for DFS and 0.008 for OS), which was identified as an independent prognostic factor in multivariate analyses. Positive PD-L1 expression was detected in 341 (70.5%) samples. In stage I-II disease, patients with PD-L1 expression had better DFS and OS than those without PD-L1 expression(P<0.05), which was not found in stage III-IV disease. With the ITWG system, 40.1% of cases were classified as high TILs. Patients in the high-TILs group tended to have better DFS (P=0.055) and OS (P=0.070) than those in the low-TILs group and the differences were statistically significant in pMMR, high MSH6, or PMS2 expression cases (P<0.05). Also, high PMS2 expression patients with both PD-L1 expression and high TILs, had similar DFS and OS compared with low PMS2 expression patients (P>0.05), which were much better than other high PMS2 expression patients.

Conclusion

The expression level of MMR proteins could also be used as a prognostic factor in ESCC and PMS2 expression outperformed other MMR proteins for predicting survival. The combination of PD-L1 expression and TILs may lead to more efficient risk stratification of ESCC.

HER2 Positivity Is Affected by the Papillary Structure and Has a Bidirectional Prognostic Value for Gallbladder Carcinoma

Gallbladder carcinoma (GBC) is responsible for 80%–95% of biliary tract malignancies and has a dismal prognosis. Human epidermal growth factor receptor 2 (HER2) is a promising therapeutic target of GBC. Through immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) methods, HER2 expression and gene amplification were identified on high-output tissue microarrays (TMAs) developed in 306 GBC cases to investigate its relationship with GBC and clinicopathological characteristics. Adenocarcinomas accounted for 223 (72.9%) of the cases, with 62 (27.8%) being papillary adenocarcinoma or having partial papillary structure. HER2 positivity was studied in 16.1% (36/223) of patients with adenocarcinoma and 41.9% (26/62) in adenocarcinoma with papillary structures. For 143 radically resected primary GBC cases with 24 HER2-positive tumors, survival data were valid; the median survival time was not reached, and the 5-year survival rate was 52.9%. All patients in stages 0–I survived, and the results of the HER2-positive group and the stage II HER2-negative group were similar (p = 0.354). However, in stage III, the mortality rate in the HER2-positive group was reduced (p = 0.005) and that in stage IV was higher (p = 0.005). In conclusion, HER2 positivity was significantly higher in patients with papillary GBC. The predictive value of HER2 varies by clinical stage, with no prediction in the early stages, better in stage III, and worse in stage IV.

HER2 promotes epithelial-mesenchymal transition through regulating osteopontin in gastric cancer

AIMS

HER2 and osteopontin (OPN) are both important biomarkers in gastric cancer (GC). The relationships between them remain to be revealed. The purpose of this study is to explore the role of OPN in epithelial-mesenchymal transition (EMT) in HER2 positive GCs.

METHODS

Nanostring analysis was used to compare the mRNA levels of 730 cancer related genes between paired HER2 3+ and non-3+ areas in GC patients. Immunohistochemistry (IHC) staining was performed to analyze the expression levels of OPN, as well as EMT markers including E-cad, N-cad, twist and vimentin in both areas. To further verify the role of OPN in EMT, the expression levels of OPN and EMT markers, tumor invasion/migration were analyzed after down-regulating HER2 and OPN in GC cell lines MKN-45 and N-87.

RESULTS

Nanostring analysis identified 8 differential expression genes between HER2 3+ and non-3+ areas. Among them, the expression level of OPN was positively correlated with that of HER2. In GC specimens, OPN showed higher expression level in HER2 3+ areas where higher E-cad expression levels and lower N-cad and twist levels were also found. After knocking down OPN and HER2 by siRNA, both cell lines show decreased invasion/migration abilities, along with the down-regulation of the EMT phenotype, supporting by the decrease of E-cad, and the increase of N-cad and twist at both mRNA and protein levels. In addition, HER2 knock-down lead to a dramatic decrease of OPN expression.

CONCLUSIONS

These findings indicate that HER2 may promote EMT via the regulation of OPN in GCs.

Simple method for constructing and repairing tissue microarrays using simple equipment

OBJECTIVE

Many methods for tissue microarray (TMA) construction were described in previous reports. Because TMA-based methods are expensive and complicated, their widespread application may be restricted. This study aimed to develop a simple method for TMA construction.

METHODS

High-density TMAs were constructed using simple equipment, and hematoxylin and eosin and immunohistochemical staining were performed to analyze the effect on the TMA block.

RESULTS

A recipient block with 162 holes of 0.9 mm in diameter was prepared using a mini-drill and plastic mold. Tissue cores of 1.0 mm in diameter were obtained from multiple donor blocks with stainless-steel capillary tubes driven by the mini-drill. Under the fixation and guidance of the plastic mold, tissue cores could be easily injected into the holes in the recipient block by inserting a stainless-steel wire into the stainless-steel tube with the tissue core and then pressing using the stainless-steel wire.

CONCLUSION

A high-density TMA block with 162 1.0-mm cores was created. This new modified technique could be a good alternative in many laboratories.

CDK4 Amplification in Esophageal Squamous Cell Carcinoma Associated With Better Patient Outcome

In the present study, we aimed to investigate the clinical and prognostic values of CDK4 amplification and improve the risk stratification in patients with esophageal squamous cell carcinoma. CDK4 amplification was analyzed by fluorescence in situ hybridization using tissue microarray consisting of representative tissues of 520 patients with esophageal squamous cell carcinoma, and its correlation with clinicopathological features and clinical outcomes were evaluated. CDK4 amplification was found in 8.5% (44/520) of patients with esophageal squamous cell carcinoma. CDK4 amplification was negatively correlated with disease progression (P = 0.003) and death (P = 0.006). Patients with CDK4 amplification showed a significantly better disease-free survival (P = 0.016) and overall survival (P = 0.023) compared with those patients without CDK4 amplification. When patients were further stratified into I–II stage groups and III–IV stage groups, CDK4 amplification was significantly associated with both better disease-free survival (P = 0.023) and overall survival (P = 0.025) in the I–II stage group rather than the III–IV stage group. On univariate and multivariate analysis, invasive depth and CDK4 amplification were associated with disease-free survival and overall survival. Taken together, CDK4 amplification was identified as an independent prognostic factor for survival, which could be incorporated into the tumor–node–metastasis staging system to refine risk stratification of patients with esophageal squamous cell carcinoma.

SOX2 amplification and chromosome 3 gain significantly impact prognosis in esophageal squamous cell carcinoma

Background

We aimed to investigate the prevalence and prognostic role of Sex determining region Y-box 2 (SOX2) amplification and expression in surgically resected esophageal squamous cell carcinoma (ESCC).

Methods

We evaluated 450 ESCC samples using fluorescence in-situ hybridization and immunohistochemistry for SOX2 gene amplification and protein expression, respectively. The relationships of gene status with various clinicopathological characteristics and patient survival were statistically analyzed.

Results

SOX2 amplifications and chromosome 3 gain were observed in 4.4% and 12.9% of patients with ESCC. SOX2 amplification was associated with later clinical stage, and chromosome 3 gain was associated with earlier clinical stage (P=0.025). Low and high SOX2 expression were found in 28.9% and 24.7% of cases, respectively. SOX2 expression was significantly associated with gene copy number variation (P=0.007). SOX2 amplification was associated with a significantly shorter disease-free survival (DFS) or overall survival (OS). However, chromosome 3 gain was associated with a significantly longer DFS or OS (P<0.001). Multivariate analysis using the Cox proportional hazard model indicated that SOX2 amplification was an independently poorer prognostic factor (DFS, P<0.001, HR 2.638, 95% CI, 1.581–4.403; OS, P<0.001, HR 2.608, 95% CI, 1.562–4.355), along with pathology tumor-node-metastasis (pTNM) stage, whereas chromosome 3 gain was an independently better prognostic factor (DFS, P=0.003, HR 0.486, 95% CI, 0.300–0.789; OS, P=0.003, HR 0.474, 95% CI, 0.289–0.779) for ESCC.

Conclusions

This is the first study wherein SOX2 amplification and chromosome 3 gain in a large cohort of ESCC were evaluated. SOX2 amplification is an independently poorer prognostic factor, whereas chromosome 3 gain is an independently favorable prognostic factor. Our results suggest that SOX2 amplification and chromosome 3 gain are potential biomarkers related to tumor progression and risk stratification in ESCC.

The prognostic role of c-MYC amplification in schistosomiasis-associated colorectal cancer

OBJECTIVE

The purpose of this study was to explore the prognostic role of c-MYC amplification in colorectal cancer, particularly in schistosomiasis-associated colorectal cancer.

METHODS

Three hundred and fifty four cases of colorectal cancer, which were from Qingpu Branch of Zhongshan Hospital affiliated to Fudan University, were retrospectively analyzed in a tissue microarray (TMA) format, with fluorescence in situ hybridization (FISH) assay and immunohistochemistry (IHC).

RESULTS

c-MYC gene amplification was found in 14.1% (50 out of 354) of patients with colorectal cancer and was correlated with old age (P = 0.028), positive lymph node metastasis (P = 0.004) and advanced stage tumors (P = 0.002). The overexpression of c-MYC was closely associated with the amplification status (P = 0.023). Kaplan-Meier survival curves for overall survival (OS) showed a statistically significant difference for patients with c-MYC amplification in full cohort of colorectal cancer, stage III-IV set and patients with lymph node metastasis (P = 0.002, 0.034, 0.012, respectively). Further analysis found c-MYC amplification associated with poorer survival in the subgroup of colorectal cancer with schistosomiasis (CRC-S, P < 0.001), but not in colorectal cancer without schistosomiasis (CRC-NS, P = 0.155). By multivariate analysis, c-MYC amplification was an independent poor-prognostic factor in CRC-S set (P = 0.046).

CONCLUSIONS

Our study firstly found c-MYC amplification could predict poor prognosis in schistosomiasis-associated colorectal cancer, but not in colorectal cancer without schistosomiasis.

PALB2 as a potential prognostic biomarker for colorectal cancer

Partner and localizer of BRCA2 (PALB2) is regarded as a colorectal cancer (CRC) risk gene, but the prognostic implication of PALB2 in CRC remains unclear. In this study, we evaluate the prognostic value of the gene copy number alteration (CNA) and mRNA expression of PALB2 in The Cancer Genome Atlas (TCGA) database, and then validated with our database. We downloaded the copy number and mRNA data of PALB2 from TCGA database and examined the relationship among the genetic alterations, expression levels and survival outcomes. Gene ontology (GO) analysis was performed to study the function of PALB2. cBioPortal database was used to explore the potential co-expression genes of PALB2. There were 6.3% (37 of 582) CRC patients diagnosed as PALB2 gene deletion. The PALB2 deletion group expressed significantly lower of PALB2 mRNA than the non-deletion group (P < 0.001). Survival analysis showed that PALB2 deletion was significantly associated with shorter disease-free survival (DFS) (P = 0.026) and overall survival (OS) (P = 0.028). Low mRNA expression of PALB2 correlated with shorter OS (P < 0.001). Multivariate analysis also confirmed that PALB2 deletion and low mRNA expression of PALB2 were independent prognostic factors of poor OS in CRC (P = 0.019, 0.034, respectively). In validation cohort, negative expression of PALB2 was associated with shorter OS (P = 0.006) in stage I patients. Multivariate analysis confirmed that negative expression of PALB2 was a poor-prognostic factor (P = 0.002). GO analysis and co-expression analysis investigated that PALB2 is primarily involved in the DNA repair process. These results suggest that PALB2 gene copy number deletion and low mRNA expression could be novel prognostic biomarkers for CRC.

An introduction of an easy-operating and economical technique for tissue microarray preparation

AIM

Tissue microarray (TMA) is a powerful and effective tool for in situ tissue analysis. However, manual TMA construction methods showed varied qualities. This study aimed to raise a standardised TMA preparation technique that can be easily operated and is economical.

METHODS

A sampling needle was used to punch the tissue rods from the donor block and holes in the recipient block. To indicate the dots' positions and ensure vertical punching, a novel auxiliary device made using commercial three-dimensional printing technology was attached. The TMA block was made up of tissue rods and a recipient block.

RESULTS

A 77-rod (7×11) TMA block was constructed. The rows and columns were fixed in straight lines. There was no specimen loss during the process of embedding.

CONCLUSIONS

An alternative method for the construction of TMA blocks that met the basic requirement of many laboratories and can be effortlessly performed was presented.

Increased MET gene copy number negatively affects the survival of esophageal squamous cell carcinoma patients

BACKGROUNDS

Since Mesenchymal epithelial transition (MET) amplification has been regarded as a potential treatment target, the knowledge of its prevalence and prognostic importance is crucial. However, its clinical pathologic characteristics are not well known in esophageal squamous cell carcinoma (ESCC).

METHODS

We investigated MET gene status with fluorescence in situ hybridization (FISH) assay in 495 ESCC cases using tissue microarrays. Prognostic significance as well as correlations with various clinicopathological parameters was evaluated.

RESULTS

Among 495 patients, 28 (5.7%) cases were MET FISH positive, including 5 cases (1%) with true gene amplification. There were no statistically significant associations between MET FISH-positivity and clinicopathologic characteristics. A significantly poorer prognosis was observed in 28 patients with MET FISH-positivity (disease free survival/DFS, P < 0.001 and overall survival/OS, P = 0.001). Multivariate analysis revealed MET FISH-positivity was an independent prognostic factor for DFS (hazard ratio/HR, 1.953; 95% confidence interval/CI, 1.271-2.999; P = 0.002) and OS (HR, 1.926; 95% CI, 1.243-2.983; P = 0.003). MET FISH-positivity was associated with DFS (P = 0.022 and 0.020) and OS (P = 0.046 and 0.024) both in stage I-II ESCC and in stage III-IVa ESCC. No statistical significance (DFS, P = 0.492 and OS, P = 0.344) was detected between stage I-II ESCC with MET FISH-positivity and stage III-IVa ESCC with FISH-negativity.

CONCLUSIONS

Increased MET gene copy number is an independent prognostic factor in ESCC, and ESCC might have potentially been up-staged by increased MET gene copy number. The results indicate that increased MET gene copy number is a very promising parameter, in clinical therapy and follow-up plans.

Prognostic Significance of c-MYC Amplification in Esophageal Squamous Cell Carcinoma

BACKGROUND

We investigated the frequency of c-MYC amplification in esophageal squamous cell carcinoma (ESCC), including both stage I to II and III to IVa disease, and evaluated the correlation of c-MYC amplification with clinicopathologic variables and outcome.

METHODS

In 259 ESCCs resected at Zhongshan Hospital, Fudan University, from January 2007 to November 2010, c-MYC amplification was analyzed by using tissue microarray, with fluorescence in situ hybridization assay.

RESULTS

c-MYC gene amplification was found in 43.2% (112 of 259) of patients with ESCC. Significant differences were found between c-MYC amplification and patient age (p = 0.009) and lymph node metastasis (p = 0.046). The median follow-up period was 33 months (range: 4 to 102 months). A survival difference was found between patients with different c-MYC status. Among 112 patients with c-MYC amplification, a significantly poorer prognosis was observed, with a median disease-free survival (DFS) and overall survival (OS) of 24.0 and 31.0 months compared with 48.0 and 48.0 months, respectively, for patients without c-MYC amplification (p = 0.011 and 0.018). On univariate and multivariate analysis, site, clinical stage, lymph node metastasis, adjuvant therapy, and c-MYC amplification were associated with DFS and OS. When patients were divided into stage I to II and stage III to IV subgroups, c-MYC amplification tended to associate with poorer survival but without statistical difference (p > 0.05).

CONCLUSIONS

c-MYC amplification was associated with age and lymph node metastasis and was an independent poor-prognostic factor for DFS and OS in the full cohort of patients with ESCC.

Poor prognostic impact of FGF4 amplification in patients with esophageal squamous cell carcinoma

In the present study, we aimed to determine the prognostic impact and clinicopathological feature of FGF4 amplification in patients with esophageal squamous cell carcinoma (ESCC). Fluorescence in situ hybridization with FGF4 probe was analyzed using tissue microarray consisting of representative cores of 267 ESCC cases. FGF4 amplification was observed in 52.8% (141/267) of patients. Patients with FGF4 amplification showed a significantly shorter disease-free survival (DFS) or disease-specific overall survival (OS) compared with those without FGF4 amplification (both P < .05). Moreover, FGF4 amplification was an independent prognostic factor (DFS, P = .036; OS, P = .021) along with clinical stage and lymph node metastasis in multivariate analysis. Among stage I-II or III patients whose DFS was greater than or equal to 24 months (n = 125 or 32), patients with FGF4 amplification showed a significantly worse prognosis (OS, P = .027 or P = .010). Moreover, the survival curve of stage I-II patients with FGF4 amplification was identical to stage III patients without FGF4 amplification (DFS, P = .643; OS, P = .707). Taken together, FGF4 amplification was an independent prognostic factor in ESCC patients, and ESCC might have potentially been upstaged by FGF4 amplification. Therefore, FGF4 amplification in combination with clinical stage could be used as a relatively accurate predictor for the 5-year probability of death and recurrence for ESCC patients.

Gene Expression Detection Assay for Cancer Clinical Use

Cancer is a genetic disease where genetic variations cause abnormally functioning genes that appear to alter expression. Proteins, the final products of gene expression, determine the phenotypes and biological processes. Therefore, detecting gene expression levels can be used for cancer diagnosis, prognosis, and treatment prediction in a clinical setting. In this review, we investigated six gene expression assay systems (qRT-PCR, DNA microarray, nCounter, RNA-Seq, FISH, and tissue microarray) that are currently being used in clinical cancer studies. Some of these methods are also commonly used in a modified way; for example, detection of DNA content or protein expression. Herein, we discuss their principles, sample preparation, design, quantification and sensitivity, data analysis, time for sample preparation and processing, and cost. We also compared these methods according to their sample selection, particularly for the feasibility of using formalin-fixed paraffin-embedded (FFPE) samples, which are routinely archived for clinical cancer studies. We intend to provide a guideline for choosing an assay method with respect to its oncological applications in a clinical setting.

Independent prognostic role of PD-L1expression in patients with esophageal squamous cell carcinoma

Accumulating evidence has shown that PD-L1 expression is associated with clinicopathological features in various human malignancies. We searched for correlations between PD-L1 expression and clinicopathological data in esophageal squamous cell carcinoma (ESCC) patients. PD-L1 expression in primary tumors from 278 patients was evaluated using immunohistochemistry (IHC) in ESCC tissue microarray. Survival curves were constructed by using the Kaplan-Meier method. Univariate and multivariate Cox proportional hazard regression models were performed to identify associations with outcome variables. Overall, tumoral PD-L1 expression (≥10%, 20% or 30% as cut-off value) was associated with favorable DFS and OS upon multivariate analysis. When the patients stratified into stage I-II (168, 60.4%) and stage III-IV (110, 39.6%), or with lymph node metastasis (133, 47.8%), the prognostic role was not consistent. In patients with stage I-II disease, tumoral PD-L1 expression (≥5%, 10%, 20% or 30%) was associated with better DFS and OS upon multivariate analysis. In patients without lymph node metastasis, tumoral PD-L1 expression (≥1%, 5%, 10%, 20%, or 30%) was associated with improved DFS and OS in univariate or multivariate analysis. However, PD-L1 expression was not correlated with prognosis in patients with stage III-IV disease or with lymph node metastasis. Our results for the first time showed the prognostic role of tumoral PD-L1 expression was variable in different stages and lymph node status of ESCC. Tumoral PD-L1 expression was independent favorable predictor in ESCC patients with Stage I-II disease or without lymph node metastasis, not in stage III-IV or lymph node metastasis.

The prognostic significance of MCL1 copy number gain in esophageal squamous cell carcinoma

Background

MCL1 copy number variations have been reported to be associated with cancer prognosis in several cancers. However, the role of MCL1 gain has not yet been determined in esophageal squamous cell carcinomas (ESCC).

Methods

Fluorescence in situ hybridization (FISH) for MCL1 was performed on 262 ESCC samples using tissue microarray (TMA).

Results

The median age of ESCC patients was 62 years (range 37-83), with frequencies between women (16.4%) and men (83.6%). Of the 262 tumors, 77 tumors (29.4%) had high MCL1 gain. In the multivariate analysis, lymph node metastasis (HR: 3.236, P<0.001 for DFS; HR: 3.501, P<0.001 for OS) and clinical stage (HR: 3.388, P<0.001 for DFS; HR: 3.616, P<0.001 for OS) were identified as independent worse prognostic factors. Interestingly, among patients without lymph node metastasis or stage I-II patients, high MCL1 gain was associated with better DFS (P=0.009 or 0.046) and OS (P=0.014 or 0.069) after disease free survival time was more than or equal to 12 months. Reversely, among patients with lymph node metastasis or stage III-IVa patients, high MCL1 gain was associated with poorer DFS (P=0.007 or 0.021) and OS (P=0.029 or 0.068) after disease free survival time was more than or equal to 29 months.

Conclusion

We observed that high MCL1 gain had bidirectional prognostic significance in ESCC patients with different lymph node status or clinical stage. These findings might provide the useful way of detailed risk stratification in patients with ESCC, and an insight into pathogenesis and mechanism of progression in ESCC.

High amplification of FGFR1 gene is a delayed poor prognostic factor in early stage ESCC patients

Amplification of the fibroblast growth factor receptor 1 (FGFR1) is believed to predict response to FGFR inhibitors. The aim of this study was to investigate the frequency and the prognostic impact of FGFR1 amplification in patients with resected esophageal squamous cell carcinoma (ESCC) by using fluorescent in situ hybridization. Microarrayed paraffin embedded blocks were constructed, and the cohort of tissues came from 506 patients with ESCC. FGFR1 high amplification (FGFR1^high) was defined by an FGFR1/centromere 8 ratio of ≥ 2.0, or average number of FGFR1 signals/tumor cell nucleus ≥ 6.0, or percentage of tumor cells containing ≥ 15 FGFR1 signals, or large cluster in ≥ 10% of cancer cells. FGFR1 low amplification was defined by ≥ 5 FGFR1 signals in ≥ 50% of cancer cells. Kaplan-Meier curves with log-rank tests and Cox proportional hazards model were used to analyze patients’ survival. Among 506 patients, high amplification, low amplification, and disomy were detected in 8.7%, 3.6% and 87.7%, respectively. In general, the FGFR1^high group trended towards worse disease-free survival (DFS) and overall survival (OS) compared to the FGFR1 low amplification/disomy (FGFR1^low/disomy) group (DFS, P=0.108; OS, P=0.112), but this trend was amplified for patients with DFS ≥ 30 months (DFS, P=0.009; OS, P=0.007). Furthermore, when patients were stratified into stage I-II and stage III-IV, the FGFR1^high group directly presented with adverse DFS and OS than the FGFR1^low/disomy group in stage I-II patients (DFS, P=0.019; OS, P=0.034), especially with DFS ≥ 30 months (DFS, P=0.002; OS, P=0.001). However, for patients in stage III-IV, FGFR1^high had no effect on prognosis regardless of DFS time. FGFR1^high occurs in a minority of ESCC, and it predicts delayed poor prognosis in stage I and II ESCC patients.

Tumour infiltrating lymphocytes correlate with improved survival in patients with esophageal squamous cell carcinoma

We undertook a study of tumour infiltrating lymphocytes (TILs) in a large and relatively homogeneous group of patients with completely resected esophageal squamous cell carcinoma (ESCC). Hematoxylin and eosin–stained sections of 235 ESCC tumours were evaluated for density of TILs in intratumoural (iTIL) and stromal compartments (sTIL). Foxp3+, CD4+, and CD8+ T cells in tumoural and stromal areas were evaluated by immunohistochemistry. Of the 235 tumours, high sTIL (>10%), and iTIL (>10%) were observed in 101 (43.0%) and 98 (41.7%), respectively. The median follow-up period was 36.0 months (95% CI 29.929–42.071). Univariate analysis revealed that sTIL (>10%), iTIL (>20%), vessels involvement, lymph node metastasis, and clinical stage were significantly associated with postoperative outcome. In multivariate analysis, high sTIL (HR: 0.664, P = 0.019 for Disease free survival; HR: 0.608, P = 0.005 for Overall survival) was identified as independent better prognostic factor. Further analysis, sTIL was identified as independently prognostic factor in Stage III-IVa disease, which was not found in Stage I-II disease. Our study demonstrated that sTIL was associated with better ESCC patients’ survival, especially in Stage III-IVa disease. Assessment of sTIL could be useful to discriminate biological behavior for ESCC patients.

Paraffin-embedded Tissue Fragment Suspension (PETFS): A Novel Method for Quality Control Preparation in Immunohistochemistry

Immunohistochemistry (IHC) is one of the most important adjunctive techniques in surgical pathology. Quality controls are essential for staining interpretation. The most common controls are cut from the formalin-fixed, paraffin-embedded tissue blocks in advance. In contrast, we developed paraffin-embedded tissue fragment suspension (PETFS), a novel method in liquid form, for quality control preparation. The liquid form controls were cut from the donor formalin-fixed, paraffin-embedded paraffin blocks, stored in the 4°C fridge easily, and added to the top and bottom of the test slide directly by pipetting. The tissue fragments from the PETFS had a comparable IHC staining pattern to that of the control sections from the original donor blocks. Over a 180-day testing period, the IHC staining pattern and intensity remained strong and specific. The clinical value of PETFS method was further validated by their successful application as controls for the expression of estrogen receptor, progesterone receptor, and C-erbB-2 in 240 breast invasive ductal carcinomas. We concluded that PETFS is a fast, low-cost, and less donor tissue consumption robust technique as quality controls for routine IHC staining in surgical pathologic practice.

Prognostic impact and potential interaction of EGFR and c-Met in the progression of esophageal squamous cell carcinoma

This study is to examine EGFR and c-Met variation in precancerous lesion, early esophageal squamous cell carcinoma (ESCC), and advanced ESCC and to explore their prognostic significance. EGFR and c-Met were detected by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Of 158 endoscopy resection (ER) specimens, c-Met high expression and FISH positive were 44.9 and 12.6 %, respectively. EGFR high expression and FISH positive were 2.5 and 19.6 %, respectively. Of 84 surgical specimens, c-Met high expression and FISH positive were 50 and 8.3 %, respectively. EGFR high expression and FISH positive were 7.1 and 28.5 %, respectively. A significant correlation was observed between c-Met and EGFR FISH positive both in ER (P < 0.001) and surgical specimens (P = 0.029). Patients with EGFR high expression had poorer disease-free survival (DFS) and overall survival (OS) (P = 0.031 and P = 0.013) in c-Met high-expression group but not in c-Met low-expression group (P = 0.301 and P = 0.439). C-Met FISH positive did not represent a statistically significant adverse prognosis until 24 months later (P = 0.027 and 0.048). EGFR and c-Met might be involved in the tumorigenesis and development of ESCC. EGFR high expression has different prognostic significance in patients with differing c-Met expression status. C-Met FISH positive represent delayed prognostic factor.

The prognostic value of EGFR overexpression and amplification in Esophageal squamous cell Carcinoma

BACKGROUND

In view of the prominent role in cancer cell biology and alteration in substantial numbers of ESCC, defining EGFR molecular characteristics relevant to patient prognosis is of great importance. Therefore, we analyzed the protein expression and gene copy variation of the epithelial growth factor receptor (EGFR) in Chinese esophageal squamous cell carcinoma (ESCC) and explored the possible associations with various features of the tumors and survival of the patients.

METHODS

Sections were made from tissue microarray composed of 96 ESCC, and examined for EGFR expression by means of immunohistochemistry (IHC) and for EGFR gene amplification by means of fluorescence in situ hybridization (FISH). The results of IHC were evaluated with six different reported scoring systems. Correlation with clinical features and survival was evaluated using chi-square test and Kaplan-Meier analysis.

RESULTS

EGFR overexpression according to scoring system 1 significantly correlated with advanced lymph node involvement (P = 0.046), patient disease specific free survival (DFS) (P = 0.006) and overall survival (OS) (P = 0.007). No such association was observed using other 5 scoring systems (P > 0.05 ). EGFR amplification was associated with lymph node metastasis (P = 0.028), but not correlated with DFS and OS until 20 months.

CONCLUSIONS

EGFR IHC overexpression evaluated by scoring system 1 might be suitable to be used in predicting patients survival in ESCC. EGFR gene amplification showed delayed prognostic information after 20 months.

Overview on Techniques to Construct Tissue Arrays with Special Emphasis on Tissue Microarrays

With the advent of new histopathological staining techniques (histochemistry, immunohistochemistry, in situ hybridization) and the discovery of thousands of new genes, mRNA, and proteins by molecular biology, the need grew for a technique to compare many different cells or tissues on one slide in a cost effective manner and with the possibility to easily track the identity of each specimen: the tissue array (TA). Basically, a TA consists of at least two different specimens per slide. TAs differ in the kind of specimens, the number of specimens installed, the dimension of the specimens, the arrangement of the specimens, the embedding medium, the technique to prepare the specimens to be installed, and the technique to construct the TA itself. A TA can be constructed by arranging the tissue specimens in a mold and subsequently pouring the mold with the embedding medium of choice. In contrast, preformed so-called recipient blocks consisting of the embedding medium of choice have punched, drilled, or poured holes of different diameters and distances in which the cells or tissue biopsies will be deployed manually, semi-automatically, or automatically. The costs of constructing a TA differ from a few to thousands of Euros depending on the technique/equipment used. Remarkably high quality TAs can be also achieved by low cost techniques.

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.