Molecular Characteristics of Basaloid Squamous Cell Carcinoma of the Esophagus: Analysis of KRAS, BRAF, and PIK3CA Mutations and LINE-1 Methylation

A comparative analysis of clinicopathological factors and survival between esophageal basaloid squamous cell carcinoma and conventional esophageal squamous cell carcinoma

INTRODUCTION

Recently, the number of diagnosed esophageal basaloid squamous cell carcinoma (EBSCC) has gradually increased. However, available data on EBSCC are limited to date.

METHODS

A total of 165 EBSCC (Cohort 1) and 515 conventional esophageal squamous cell carcinoma (ESCC) (Cohort 2) were retrospectively analyzed.

RESULTS

In Cohort 1, 70 cases only had invasive EBSCC component (42.4%, defined as Group 1), 73 cases had concomitant invasive ESCC component (44.2%, Group 2), and 22 had concomitant invasive poor-differentiated component (13.3%, Group 3). Lymph node metastasis rates of Group 3, Group 2 and Group 1 were ranked from high to low (P = 0.044). There were higher patient age (P = 0.047), smaller tumor size (P = 0.009), more nerve invasion (P < 0.001), and lower pTNM stage (P < 0.001) in EBSCC (Cohort 1), compared with ESCC (Cohort 2). In Cohort 1 and Cohort 2, pTNM stage was an independent prognostic factor for both DFS and OS. No significant survival difference was found between EBSCC (Cohort 1) and ESCC (Cohort 2) in pIA-B stage, pIIA-B stage, pIIIA-B stage and pIVA-B stage (P > 0.05).

CONCLUSION

Our analysis of the largest EBSCC series from a single institution to date with conventional ESCC demonstrated that EBSCC carried a similar prognosis with ESCC in pIA-B stage, pIIA-B stage, pIIIA-B stage and pIVA-B stage. And pure EBSCC, didn't have poorer survival than mixed EBSCC with concomitant ESCC or other components. Our findings may be valuable in the better understanding of EBSCC's biological behaviors, and the related molecular mechanism is needed to be explored in the future.

Clinicopathological and mutational analysis of esophageal basaloid squamous cell carcinoma

Esophageal basaloid squamous cell carcinoma (EBSCC) is a poorly differentiated variant of esophageal squamous cell carcinoma (ESCC). We aimed to investigate the clinicopathological and molecular biological characteristics of EBSCC and enrolled 58 patients with EBSCCs. Clinicopathological factors including age, sex, tumor size and location, gross tumor type (superficial, protrusive, ulcerative, and unclassifiable), lymphovascular invasion, infiltrative growth, intramural invasion, TNM stage, and dominant histological type were examined. EBSCCs were classified into four types (solid, cribri, microcystic, and tubular) according to the dominant histology. Next-generation sequencing (NGS) of a cancer hotspot panel was performed in 19 cases. NGS identified TP53 as the most frequently mutated gene, and copy number variation analysis revealed the most frequent loss of heterozygosity (LOH) at the ataxia telangiectasia mutated (ATM) and retinoblastoma 1 (RB1) loci. Target sequencing for TP53 was performed for the remaining 39 cases. We also performed LOH analysis for TP53, ATM, and RB1 and immunohistochemical staining for p53, ATM, and Rb in all cases. The rates of TP53 mutations and LOH and p53 aberrant expression were high (79.3%, 63.2%, and 72.4%, respectively); however, the frequencies were similar to those reported for ESCC. LOH rates of the RB1 and ATM loci were also high (55.3% and 67.2%, respectively). Overall survival rate was 66.5%, and recurrence-free survival rate was 55.0%. Only conventional clinicopathological factors had a prognostic impact in EBSCC; the microcystic type had the poorest prognosis. Our findings could be useful in developing novel treatment strategies for EBSCC.

Comparative Analysis of Clinicopathological Characteristics, Survival Features, and Protein Expression Between Basaloid and Squamous Cell Carcinoma of the Esophagus

Background

Basaloid squamous cell carcinoma (BSCC) is a rare variant of squamous cell carcinoma (SCC) of the esophagus. This study aimed to assess the discrepancy in clinicopathological characteristics and protein expression between esophageal BSCC and typical esophageal SCC.

Study Design

We reviewed 40 cases of esophageal BSCC. As controls, 63 well-differentiated SCC (WSCC) patients, 70 moderately differentiated SCC (MSCC) patients, and 51 poorly differentiated SCC (PSCC) patients were selected. The clinicopathologic characteristics and immunoreactivity of Ki-67, p53, p63, and epidermal growth factor receptor (EGFR) were then evaluated in the BSCC and typical SCC patients.

Results

The 5-year survival rates for the BSCC patients were 27.5%. The prognostic outcomes of the BSCC group were similar to those of the PSCC and MSCC groups but worse than that of the WSCC group, with a significant difference (P=0.045). Ki-67 expression was significantly higher in the BSCC group than that in the WSCC group (P < 0.05). Meanwhile, there were no significant differences in the expression of the other molecular markers (p53, p63, and EGFR) between the typical SCC and BSCC groups (P > 0.05). The median survival time of esophageal the BSCC patients with low p53 expression was significantly longer than that of the patients with high p53 expression (P=0.026). Further, the median survival time of the esophageal BSCC patients with high p63 expression was significantly longer than that of the patients with low p63 expression (P=0.041). Meanwhile, Ki-67 and EGFR expressions were not correlated with OS in the BSCC group.

Conclusion

Esophageal BSCC has a more clinically virulent course. Notably, p53 and p63 expression are associated with prognosis in BSCC. These findings conject that evaluation of multiple cancer biomarkers might be a promising auxiliary diagnostic indicator in BSCC.

V-Raf murine sarcoma viral oncogene homolog B1 (BRAF) as a prognostic biomarker of poor outcomes in esophageal cancer patients

BACKGROUND

Esophageal cancer is one of the most aggressive malignancies, and is associated with multiple genetic mutations. At present, the v-Raf murine sarcoma viral oncogene homolog B1 (BRAF) gene mutation has been observed in esophageal cancer and is associated with poor prognosis. This study aimed to investigate the protein expression of BRAF in esophageal cancer and determine its effect on patient outcomes.

METHODS

We used immunohistochemistry to detect the expression of BRAF via tissue microarrays in esophageal cancer samples, the Kaplan-Meier method to perform survival analysis, and the Cox proportional hazards regression model to explore the risk factors of esophageal cancer. The role of BRAF in the proliferation, invasion, and metastasis of esophageal cancer was studied by clone formation, scratch test, Transwell invasion and migration test. The tumor-bearing model of BRAF inhibitor was established using TE-1 cells, and corresponding negative control was set up to observe the growth rate of the two models.

RESULTS

The results revealed that BRAF overexpression was significantly correlated with Ki67 (P < 0.05). Survival analysis showed that BRAF overexpression contributed to a shorter overall survival (P = 0.014) in patients with esophageal cancer. Univariate and multivariate regression analyses demonstrated that BRAF was a prognostic factor for poor esophageal cancer outcomes (P < 0.05). Small interfering RNA knockdown of BRAF significantly reduced the cell clone formation rate compared to the control group. Transwell assay analysis showed that the migration and invasion of cells in the experimental group were significantly inhibited relative to the control group, and the inhibition rates of the small interfering RNA group were 67% and 60%, respectively. In the scratch test, the wound healing ability of the BRAF knockdown group was significantly weaker than that of the control group. There were significant differences in tumor growth volume and weight between the two groups in nude mice.

CONCLUSION

BRAF overexpression may serve as an effective predictive factor for poor prognosis.

Off-label use of common predictive biomarkers in gastrointestinal malignancies: a critical appraisal

The use of immunohistochemistry (IHC) as a companion diagnostic is an increasingly important part of the case workup by pathologists and is often central to clinical decision making. New predictive molecular markers are constantly sought for to improve treatment stratification parallel to drug development. Unfortunately, official biomarker guidelines lag behind, and pathologists are often left hesitating when medical oncologists request off-labelled biomarker testing. We performed a literature review of five commonly requested off-label IHC predictive biomarkers in gastrointestinal tract (GIT) malignancies: HER2, mismatch repair (MMR), PD-L1, BRAF V600E and ROS1. We found that HER2 amplification is rare and poorly associated to IHC overexpression in extracolonic and extragastric GIT cancers; however in KRAS wild type colorectal cancers, which fail conventional treatment, HER2 IHC may be useful and should be considered. For MMR testing, more evidence is needed to recommend reflex testing in GIT cancers for treatment purposes. MMR testing should not be discouraged in patients considered for second line checkpoint inhibitor therapy. With the exception of gastric tumors, PD-L1 IHC is a weak predictor of checkpoint inhibitor response in the GIT and should be replaced by MMR in this context. BRAF inhibitors showed activity in BRAF V600E mutated cholangiocarcinomas and pancreatic carcinomas in non-first line settings. ROS1 translocation is extremely rare and poorly correlated to ROS1 IHC expression in the GIT; currently there is no role for ROS1 IHC testing in GIT cancers. Overall, the predictive biomarker literature has grown exponentially, and official guidelines need to be updated more regularly to support pathologists’ testing decisions.

A Rare Case of Stage IV Basaloid Squamous Cell Cancer with Intrapulmonary and Brain Metastases

BACKGROUND Metastatic basaloid squamous cell carcinoma is a fatal, high-grade variant of squamous cell carcinoma that is extremely rare in the oral cavity. We present a rare case of metastatic basaloid squamous cell carcinoma arising from the hypopharynx with pulmonary and brain metastases. Recognizing this diagnostic subtype is of critical importance due to the aggressive nature and high incidence of recurrence, lymph node metastases, and mortality. CASE REPORT A 42-year-old male arrived at the Emergency Department reporting a 1-week headache. Six months prior, he reported throat pain and neck swelling. Triple endoscopy revealed a large ulcerative tumor. A carbon dioxide laser procedure debulked and removed the mass. Incisional biopsy with histopathology was consistent with invasive basaloid squamous cell carcinoma. Computed tomography (CT) of the neck with contrast demonstrated bilateral cervical level II/III necrotic adenopathy, and CT chest with contrast demonstrated bilateral pulmonary nodules. The patient completed chemoradiation therapy with cisplatin; however, repeat CT chest revealed enlarging intrapulmonary metastases. CT brain without contrast demonstrated a central brainstem lesion. The patient started treatment with pembrolizumab. On day 14 of treatment, he presented to the Emergency Department again for headache. MRI of brain with contrast demonstrated a new lesion with vasogenic edema. Intravenous dexamethasone was started and the decision to pursue stereotactic radiosurgery was made. CONCLUSIONS The diagnosis of basaloid squamous cell carcinoma in the setting of intrapulmonary and brain metastases is an extremely rare, high-grade bimorphic aggressive variant of squamous cell carcinoma that needs to be histopathologically differentiated from other tumors. Given its high mortality rate and poor prognosis the decision to pursue further treatment versus aggressive palliative care should be discussed.

PIK3CA mutations are frequent in esophageal squamous cell carcinoma associated with chagasic megaesophagus and are associated with a worse patient outcome

Background

Chronic diseases such as chagasic megaesophagus (secondary to Chagas’ disease) have been suggested as etiological factors for esophageal squamous cell carcinoma; however, the molecular mechanisms involved are poorly understood.

Objective

We analyzed hotspot PIK3CA gene mutations in a series of esophageal squamous cell carcinomas associated or not with chagasic megaesophagus, as well as, in chagasic megaesophagus biopsies. We also checked for correlations between the presence of PIK3CA mutations with patients’ clinical and pathological features.

Methods

The study included three different groups of patients: i) 23 patients with chagasic megaesophagus associated with esophageal squamous cell carcinoma (CM/ESCC); ii) 38 patients with esophageal squamous cell carcinoma not associated with chagasic megaesophagus (ESCC); and iii) 28 patients with chagasic megaesophagus without esophageal squamous cell carcinoma (CM). PIK3CA hotspot mutations in exons 9 and 20 were evaluated by PCR followed by direct sequencing technique.

Results

PIK3CA mutations were identified in 21.7% (5 out of 23) of CM/ESCC cases, in 10.5% (4 out of 38) of ESCC and in only 3.6% (1 case out of 28) of CM cases. In the CM/ESCC group, PIK3CA mutations were significantly associated with lower survival (mean 5 months), when compared to wild-type patients (mean 2.0 years). No other significant associations were observed between PIK3CA mutations and patients’ clinical features or TP53 mutation profile.

Conclusion

This is the first report on the presence of PIK3CA mutations in esophageal cancer associated with chagasic megaesophagus. The detection of PIK3CA mutations in benign chagasic megaesophagus lesions suggests their putative role in esophageal squamous cell carcinoma development and opens new opportunities for targeted-therapies for these diseases.

Value of the preoperative neutrophil-to-lymphocyte ratio as a prognostic factor for long-term survival in postoperative esophageal squamous cell carcinoma patients

BACKGROUND

This study investigated the relationship between the neutrophil-to-lymphocyte ratio (NLR) and clinicopathological features and prognosis in patients with postoperative esophageal squamous cell carcinoma (ESCC).

METHODS

The preoperative NLR was evaluated in 419 patients who underwent esophagectomy for ESCC. A receiver operating characteristic (ROC) curve was plotted to verify the accuracy of the NLR for predicting survival. Correlation between the NLR and clinicopathological characteristics was analyzed using the χ2 test. Prognostic influence was calculated by using the Kaplan-Meier method and the difference was assessed by log-rank test. Multivariate Cox regression models were applied to evaluate the independent prognostic value.

RESULTS

The cutoff value of the NLR was 2.998, the area under the curve was 0.735, and the sensitivity and specificity were 69.3% and 69.3%, respectively. Tumor length (P = 0.0317), lymph node metastasis (P = 0.0352), pathological tumor node metastasis (pTNM) stage (P = 0.0271), and postoperative radiotherapy (P = 0.0385) were significantly different between the groups. Multivariate analysis showed that pTNM stage (P = 0.0098), lymph node metastasis (P = 0.001), and NLR (P = 0.0022) were independent prognostic factors for survival. Moreover, when patients were stratified by TNM stage, the adverse effects of preoperative NLR on cancer-specific survival were greater in patients with stage II and III ESCC and in patients with lymph node metastasis.

CONCLUSIONS

The preoperative NLR is significantly correlated with long-term prognosis in postoperative patients with ESCC, particularly in patients with lymph node metastasis and stage II and III ESCC.

Comparative Analysis of Clinical, Treatment, and Survival Characteristics of Basaloid and Squamous Cell Carcinoma of the Esophagus

BACKGROUND

Basaloid squamous cell carcinoma (BSC) is a rare variant of squamous cell carcinoma (SqCC) of the esophagus. Even though pathologically thought to be more aggressive than SqCC, there is discrepancy in the literature regarding the outcomes of BSC compared with those of SqCC.

STUDY DESIGN

We conducted a retrospective cohort study using the Surveillance Epidemiology and End Results (SEER) database. All patients with a histologic diagnosis of BSC and SqCC between 2004 and 2013 were included. We compared treatment and survival characteristics of patients with BSC and SqCC.

RESULTS

There were 16,158 patients included in this study; 173 patients (1.1%) had BSC. There were no significant differences between the 2 groups based on age, sex, marital status, insurance, or geographic region of diagnosis, but patients with BSC were more likely to be Caucasian (73.4% vs 64.7%; p = 0.017). Among staged patients, baseline tumor stage was similar in both groups. However, BSC tumors were more likely to be of high pathologic grade (56.8% vs 38.2%; p < 0.001). Patients with SqCC were more likely to receive radiation therapy (36.9% vs 53.9%; p < 0.001), while patients with BSC were more likely to undergo resection (32.4% vs 17.0%; p < 0.001). Median overall survival was similar in both groups (14 vs 9 months; log rank = 0.144), and this relationship persisted after stratification by treatment.

CONCLUSIONS

Even though more likely to be poorly differentiated at presentation, BSC of the esophagus seems to have similar clinical features and survival outcomes when compared with SqCC. Patients with BSC and SqCC should undergo stage-specific treatment to achieve optimal outcomes.

A novel gene expression scoring system for accurate diagnosis of basaloid squamous cell carcinoma of the esophagus

Basaloid squamous cell carcinoma of the esophagus (BSCE) is a rare variant of squamous cell carcinoma that is difficult to distinguish from other carcinomas by preoperative endoscopic biopsy because of its histological varieties. Accurate diagnosis is essential for adequate treatment, and the methods proposed so far (e.g., immunohistochemical staining) have limitations. In this study, we tried to identify the characteristic bundles of gene expression in BSCE using comprehensive gene expression analysis (CGEA). Subsequently, we constructed a gene expression scoring system for the proper diagnosis of BSCE. Fifty-seven surgical specimens, including seven BSCEs, obtained from 30 patients who underwent esophagectomy were used for constructing the scoring system. Three hundred and twelve biopsy specimens, including eight BSCEs, obtained from 80 patients and 20 commercially available formalin-fixed paraffin-embedded (FFPE) specimens diagnosed as esophageal cancer, including 13 BSCEs, were used for validation. After our original mathematical extraction algorithm, 75 genes were extracted to distinguish BSCE from non-BSCE. The cumulative converted values (gene expression score) of the respective 75 genes from each specimen were obtained and lined up in ascending order to assess the optimal gene expression cut-off score for a definitive diagnosis of BSCE. The validation of this scoring system showed high prediction of the biopsy specimens [area under the curve (AUC)=0.981; 95% confidence interval (CI): 0.952‑1.000] and the commercially available FFPE specimens (AUC=0.901; 95% CI: 0.750-1.000). In conclusion, using CGEA in a gene expression scoring system helps in differentiating BSCE from non-BSCE with high accuracy and may contribute in improving BSCE treatment.

The Preoperative Neutrophil-To-Lymphocyte Ratio Is a Novel Immune Parameter for the Prognosis of Esophageal Basaloid Squamous Cell Carcinoma

Background

The pretreatment neutrophil-to-lymphocyte ratio (NLR) is an independent predictor of prognosis in various malignancies, but its predictive capacity in basaloid squamous cell carcinoma of the esophagus (BSCCE) remains unclear. We aim to determine the value of the inflammation-related factors, including the NLR, neutrophil-to-monocyte ratio (NMR), and albumin levels, in predicting BSCCE prognosis.

Methods

We retrospectively analyzed the records of 121 patients with pathologically diagnosed BSCCE that underwent a curative esophagectomy from January 2007 to December 2014. Univariate and multivariate analyses were used to identify prognostic factors for overall survival (OS) and recurrence-free survival (RFS).

Results

The preoperative NLR was correlated with the tumor length and NMR. In OS univariate analyses, a high NLR (>1.77), high NMR (>12.31), and low albumin (≤40.0 g/L) level were significantly associated with a poorer survival in BSCCE. The median OS was significantly greater in low NLR (≤1.77) than in the high NLR (>1.77) patients (51.0 vs. 31.0 months; P = 0.008). In multivariate analyses, only the NLR was an independent prognostic factor for OS (hazard ratio (HR), 2.030; 95% confidence interval (CI), 1.262–3.264; P = 0.003). A high NLR was also an independent predictor of a poorer RFS in BSCCE (HR, 2.222; 95% CI, 1.407–3.508; P = 0.001); the median RFS for low (≤1.77) and high (> 1.77) NLR patients was 44.0 months and 14.0 months, respectively. NLR remained a strong prognostic indicator for OS in stage I/II patients and a preoperative NLR>1.77 was predictive of a poor RFS in both stage I/II and stage III patients.

Conclusions

We show that the preoperative NLR, a convenient and cost-effective biomarker, may serve as a prognostic indicator for BSCCE patients following curative surgery.

Early-Stage Induction of SWI/SNF Mutations during Esophageal Squamous Cell Carcinogenesis

The SWI/SNF chromatin remodeling complex is frequently inactivated by somatic mutations of its various components in various types of cancers, and also by aberrant DNA methylation. However, its somatic mutations and aberrant methylation in esophageal squamous cell carcinomas (ESCCs) have not been fully analyzed. In this study, we aimed to clarify in ESCC, what components of the SWI/SNF complex have somatic mutations and aberrant methylation, and when somatic mutations of the SWI/SNF complex occur. Deep sequencing of components of the SWI/SNF complex using a bench-top next generation sequencer revealed that eight of 92 ESCCs (8.7%) had 11 somatic mutations of 7 genes, ARID1A, ARID2, ATRX, PBRM1, SMARCA4, SMARCAL1, and SMARCC1. The SMARCA4 mutations were located in the Forkhead (85Ser>Leu) and SNF2 family N-terminal (882Glu>Lys) domains. The PBRM1 mutations were located in a bromodomain (80Asn>Ser) and an HMG-box domain (1,377Glu>Lys). For most mutations, their mutant allele frequency was 31–77% (mean 61%) of the fraction of cancer cells in the same samples, indicating that most of the cancer cells in individual ESCC samples had the SWI/SNF mutations on one allele, when present. In addition, a BeadChip array analysis revealed that a component of the SWI/SNF complex, ACTL6B, had aberrant methylation at its promoter CpG island in 18 of 52 ESCCs (34.6%). These results showed that genetic and epigenetic alterations of the SWI/SNF complex are present in ESCCs, and suggested that genetic alterations are induced at an early stage of esophageal squamous cell carcinogenesis.

Expression of TP53, BCL-2, and VEGFA Genes in Esophagus Carcinoma and its Biological Significance

BACKGROUND

The pathogenesis of esophagus carcinoma involves a cascade process consisting of multiple factors and accumulation of gene mutations. It is known that vascular endothelial growth factor (VEGF) mainly regulates de novo vascular formation while B-cell lymphoma-2 (BCL-2) gene exerts a tumor-suppressing effect. The prominent expression of VEGFA and BCL-2 genes, along with the most famous tumor-suppressor gene, TP53, raise the possibly of gene interaction. This study therefore investigated the effect and correlation of TP53, BCL-2, and VEGFA genes on cell proliferation and apoptosis of esophagus carcinoma.

MATERIAL AND METHODS

A total of 30 male rats were prepared by subcutaneous injection of methyl-benzyl-nitrosamine (MBNA) to induce esophagus cancer, along with 30 controlled rats which received saline instead. After 4, 10, 20, or 30 weeks, rats were sacrificed to observe the morphological changes of esophageal mucosa. Cell apoptosis was quantified by terminal deoxynucleotidyl transferase-mediated dUTP nick-end-labeling (TUNEL) assay. Immunohistochemical (IHC) staining was employed to examine the expression of TP53, BCL-2 and VEGFA genes.

RESULTS

With the progression of cancer, pathological damages of esophageal tissue aggravated while the cancer cell apoptosis gradually decreased compared to controlled animals. Protein levels of p53, Bcl-2, and VEGF in the model group were significantly elevated at each time point. Positive correlations existed between p53 and Bcl-2 or VEGF.

CONCLUSIONS

Abnormally elevated expression of TP53, BCL-2, and VEGFA genes may participate in the proliferation of esophagus cancer cells in a synergistic manner.