crossing96/oncoscreening huggingface dataset:
Expression and prognostic significance of the polymeric immunoglobulin receptor in esophageal and gastric adenocarcinoma.	INTRODUCTION: The polymeric immunoglobulin receptor (PIGR) has been proposed to be a candidate prognostic biomarker in a few cancer forms, and one previous study reported that reduced PIGR expression signifies more aggressive tumours of the distal esophagus and gastroesophageal junction (GEJ). In the present study, we examined the expression, clinicopathological correlates and prognostic significance of PIGR expression in an extended cohort of adenocarcinoma of the upper gastrointestinal tract. MATERIALS AND METHODS: Immunohistochemical PIGR expression was examined in a consecutive cohort of patients with surgically resected, radio-chemonaive adenocarcinoma of the esophagus, GE-junction and stomach (n = 173), including paired samples of benign-appearing squamous epithelium (n = 51), gastric mucosa (n = 114), Barrett's esophagus (BE) or intestinal metaplasia (IM) (n = 57) and lymph node metastases (n = 75). Non-parametric tests were applied to explore associations between PIGR expression in primary tumours and clinicopathological characteristics. Classification and regression tree analysis was applied for selection of prognostic cut-off. The impact of PIGR expression on overall survival (OS) and recurrence-free survival (RFS) was assessed by Kaplan-Meier analysis and hazard ratios (HR) calculated by adjusted and unadjusted Cox proportional hazards modelling. RESULTS: PIGR expression was significantly higher in intestinal metaplasia (BE or gastric IM) compared to normal tissues and cancer (p < 0.001). Reduced PIGR expression in primary tumours was significantly associated with more advanced tumour stage (p = 0.002) and inversely associated with involved margins (p = 0.034). PIGR expression did not differ between primary tumours and lymph node metastases. There was no significant difference in PIGR expression between tumours with and without a background of intestinal metaplasia. High PIGR expression was an independent predictor of a prolonged OS (HR = 0.60, 95% CI 0.36-0.99) and RFS (HR = 0.49, 95% CI 0.27-0.90) in patients with radically resected (R0) primary tumours and of an improved RFS (HR = 0.32, 95% CI 0.15-0.69) in curatively treated patients with R0 resection/distant metastasis-free disease. CONCLUSION: High PIGR expression independently predicts a decreased risk of recurrence and an improved survival in patients with adenocarcinoma of the upper gastrointestinal tract. These findings are of potential clinical relevance and merit further validation.	esophagus
Multimodal approach for cervical esophageal carcinoma: role of neoadjuvant chemotherapy.	AIM: To examine the outcome of patients with cervical esophageal cancer treated by a multimodal protocol. PATIENTS AND METHODS: We retrospectively analyzed the outcome and prognostic factors for 20 patients with cervical esophageal cancer who received multimodal treatment at the Kurume University Hospital between 2003 and 2009. One case of stage I, seven of stage II and 12 of stage III disease (2 T1, 3 T2, 4 T3, 11 T4 and 14 N1) were included. Radiotherapy was administered at a median dose of 60 Gy (range=30-70 Gy). The median follow-up time was 32 months for surviving patients (14-94 months). Platinum-based neoadjuvant chemotherapy (NAC) was performed in 14 cases and all received chemoradiotherapy. RESULTS: median survival was 20 months and overall survival rates at 1, 2, and 5-years were 70%, 60% and 30%, respectively. T-Category, length of the primary lesion, N-category, stage, hemoglobin levels and response to induction chemotherapy were statistically significant predisposing factors for overall survival rate. According to NAC response, 10 good responders (complete response or partial response) showed 2-year survival rates of 80% (5 survivors), whereas that for poor responder (stable disease and progressive disease) was 0% (p=0.006), respectively. Response to NAC was the only statistically significant predisposing factor for increased progression-free survival (p=0.03). Severe acute toxicities of grade 3 or more appeared in 5 patients; two grade 5 (esophageal perforations and lung fistula), one grade 4 (bilateral recurrent nerve palsy), and two grade three (pneumonitis and mucositis). CONCLUSION: Although severe prognosis was identified for cervical esophageal cancer, good response to NAC indicates a good prognosis with organ preservation even for those with T4 tumor.	esophagus
Exploring the recent trend in esophageal adenocarcinoma incidence and mortality using comparative simulation modeling.	BACKGROUND: The incidence of esophageal adenocarcinoma (EAC) has increased five-fold in the United States since 1975. The aim of our study was to estimate future U.S. EAC incidence and mortality and to shed light on the potential drivers in the disease process that are conduits for the dramatic increase in EAC incidence. METHODS: A consortium of three research groups calibrated independent mathematical models to clinical and epidemiologic data including EAC incidence from the Surveillance, Epidemiology, and End Results (SEER 9) registry from 1975 to 2010. We then used a comparative modeling approach to project EAC incidence and mortality to year 2030. RESULTS: Importantly, all three models identified birth cohort trends affecting cancer progression as a major driver of the observed increases in EAC incidence and mortality. All models predict that incidence and mortality rates will continue to increase until 2030 but with a plateauing trend for recent male cohorts. The predicted ranges of incidence and mortality rates (cases per 100,000 person years) in 2030 are 8.4 to 10.1 and 5.4 to 7.4, respectively, for males, and 1.3 to 1.8 and 0.9 to 1.2 for females. Estimates of cumulative cause-specific EAC deaths between both sexes for years 2011 to 2030 range between 142,300 and 186,298, almost double the number of deaths in the past 20 years. CONCLUSIONS: Through comparative modeling, the projected increases in EAC cases and deaths represent a critical public health concern that warrants attention from cancer control planners to prepare potential interventions. IMPACT: Quantifying this burden of disease will aid health policy makers to plan appropriate cancer control measures. Cancer Epidemiol Biomarkers Prev; 23(6); 997-1006. ©2014 AACR.	esophagus
Genomic and molecular characterization of esophageal squamous cell carcinoma.	Esophageal squamous cell carcinoma (ESCC) is prevalent worldwide and particularly common in certain regions of Asia. Here we report the whole-exome or targeted deep sequencing of 139 paired ESCC cases, and analysis of somatic copy number variations (SCNV) of over 180 ESCCs. We identified previously uncharacterized mutated genes such as FAT1, FAT2, ZNF750 and KMT2D, in addition to those already known (TP53, PIK3CA and NOTCH1). Further SCNV evaluation, immunohistochemistry and biological analysis suggested their functional relevance in ESCC. Notably, RTK-MAPK-PI3K pathways, cell cycle and epigenetic regulation are frequently dysregulated by multiple molecular mechanisms in this cancer. Our approaches also uncovered many druggable candidates, and XPO1 was further explored as a therapeutic target because it showed both gene mutation and protein overexpression. Our integrated study unmasks a number of novel genetic lesions in ESCC and provides an important molecular foundation for understanding esophageal tumors and developing therapeutic targets.	esophagus
Clinically staged cT2 adenocarcinomas of the gastroesophageal junction: accuracy of staging and therapeutic consequences.	BACKGROUND: Multimodality treatment options in locally advanced adenocarcinomas of the esophagogastric junction (AEGs) have been established in the last years. However, the therapeutic approach in patients with clinically staged cT2 tumors remains controversial. The most important determinant is the accuracy of clinical staging. We aimed to evaluate the association of clinical and histopathological staging in patients with cT2 tumors in respect of possible therapeutic consequences. PATIENTS AND METHODS: Between 2001 and 2011, 71 patients with AEG tumors were clinically staged as cT2 (cN0 = 48 (68%); cN+ = 23 (32%)) and underwent surgical resection. RESULTS: A primary tumor resection was performed in 59 (83%) patients while 12 (17%) patients received neoadjuvant therapy. Primarily resected patients showed the following pT/pN categories: pT1: 13 (22%), pT2: 35 (59%), pT3: 11 (19%), pN0: 23 (39%), whereas the clinical/histopathological pN category included 55% of the patients. Neoadjuvantly treated patients showed the following pT/pN categories: ypT0: 3 (25%), ypT1: 3 (25%), ypT2: 6 (50%), ypN0: 6 (50%). The overall survival of primarily resected patients compared with patients undergoing neoadjuvant therapy was not significantly different. CONCLUSIONS: The accuracy of clinical staging in patients with cT2 tumors of the gastroesophageal junction is poor. As in primarily resected patients, over- and understaging balance each other; correct pretherapeutic staging occurs in just about 60% of the patients. Moreover, our study suggests that a radical surgical resection with adequate lymphadenectomy seems to be appropriate for cT2N0 and even in cT2N+ tumors, since down-categorizing and prognosis are not improved for neoadjuvantly treated patients. However, the data have to be interpreted with caution because of the small patient numbers.	esophagus
Routine contrast esophagram has minimal impact on the postoperative management of patients undergoing esophagectomy for esophageal cancer.	BACKGROUND: Routine contrast esophagram is frequently performed after esophagectomy in order to detect occult anastomotic leak (AL). This modality has a low sensitivity, and its routine use has been called into question. Accordingly, we sought to demonstrate the clinical impact of routine contrast esophagography in the management of patients undergoing esophagectomy for malignant disease. METHODS: All patients undergoing esophagectomy from 2005 to 2011 for malignancy at a North American University hospital were identified from a prospectively collected database. Barium esophagram (BE) was performed within the first week postoperatively. Patients were dichotomized according to whether they had an AL, and the sensitivity and specificity of BE was determined. The clinical impact of the BE result, defined as cessation of enteral feeding, additional interventions, or delay in discharge, was determined. RESULTS: Overall, 221 patients underwent esophagectomy. Thirty (13.6 %) developed an AL, of which 10 (30 %) had a positive BE, 12 (40 %) had a negative BE, and 8 (26.7 %) had no BE and were diagnosed clinically (1/8), by computed tomography (CT) (3/8), endoscopically (3/8), or at reoperation (1/7). AL in patients with a negative BE was confirmed clinically (4/12), by CT (6/12), endoscopically (1/12), or at reoperation (1/12). The sensitivity and specificity of BE was 45.5 and 97.8 %, respectively. BE altered postoperative management in 8/221 (3.6 %) patients, with 5/221 (2.3 %) undergoing therapeutic intervention. Conversely, 3/221 (1.4 %) patients demonstrated clinically insignificant AL, delaying discharge and feeding without intervention. CONCLUSION: Contrast esophagram is not an effective screening modality for AL when employed routinely following esophagectomy.	esophagus
Hormone replacement therapy and oral contraceptives and risk of oesophageal adenocarcinoma: a systematic review and meta-analysis.	There is an unexplained strong male predominance in the aetiology of oesophageal adenocarcinoma (OAC). The hypothesis that oestrogens are protective, deserves attention. A potential protective influence of exogenous oestrogen exposure, that is, hormone replacement therapy (HRT) and oral contraceptives (OC) has been addressed only in studies of limited statistical power, and the individual studies have not provided conclusive results. We conducted a systematic literature search and meta-analysis on HRT and OC and the risk of OAC. We used the databases PubMed and the Web of Science. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by the Mantel-Haenszel random-effect method. A total of five studies were included. Compared to never users, ever users of HRT had a statistically significantly decreased risk of OAC (pooled OR = 0.75; 95% CI: 0.58-0.98), and ever users of OC had a borderline significantly decreased risk of this cancer (pooled OR = 0.76; 95% CI: 0.57-1.00). In conclusion, HRT and OC use seems to be associated with a decreased risk of OAC. However, further research is warranted.	esophagus
Dairy consumption and risk of esophageal squamous cell carcinoma: A meta-analysis of observational studies.	AIM: Inconsistent results regarding the relations between consumption of dairy products and the risk of esophageal squamous cell carcinoma (ESCC) have been reported. In this report, we summarized the evidence by a meta-analysis of observational studies. METHODS: Eligible studies published up to January 31, 2013 were retrieved via both computer searches and a manual review of references. Random-effects models were used to calculate the summary relative risk (SRR) based on high versus low and dose-response analysis. RESULTS: A total of 19 studies with 4315 ESCC cases were included in this meta-analysis. Overall, there were no significant associations between intakes of total dairy products, milk, cheese and butter and ESCC for the highest versus lowest intake categories (total dairy products: SRR 1.03, 95% confidence interval [CI]: 0.60-1.77; milk: SRR 0.93, 95% CI: 0.74-1.16; cheese: SRR 0.84, 95% CI: 0.61-1.15; butter: SRR 1.77, 95% CI 0.85-3.75). A significant inverse association was found for yogurt consumption (SRR 0.73, 95% CI: 0.54-0.98). There was high heterogeneity among studies on total dairy products, milk and butter; however, little or no heterogeneity was observed among studies on cheese and yogurt. CONCLUSION: No associations between consumption of milk, dairy products, butter or cheese and risk of ESCC were found, while yogurt consumption may have a protective effect. However, these associations may be subject to high levels of heterogeneity or confounding, and further efforts should be made to confirm these findings.	esophagus
Identification of genomic alterations in oesophageal squamous cell cancer.	Oesophageal cancer is one of the most aggressive cancers and is the sixth leading cause of cancer death worldwide. Approximately 70% of global oesophageal cancer cases occur in China, with oesophageal squamous cell carcinoma (ESCC) being the histopathological form in the vast majority of cases (>90%). Currently, there are limited clinical approaches for the early diagnosis and treatment of ESCC, resulting in a 10% five-year survival rate for patients. However, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we describe a comprehensive genomic analysis of 158 ESCC cases, as part of the International Cancer Genome Consortium research project. We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases, plus an additional 70 ESCC cases not used in the whole-genome and whole-exome sequencing, were subjected to array comparative genomic hybridization analysis. We identified eight significantly mutated genes, of which six are well known tumour-associated genes (TP53, RB1, CDKN2A, PIK3CA, NOTCH1, NFE2L2), and two have not previously been described in ESCC (ADAM29 and FAM135B). Notably, FAM135B is identified as a novel cancer-implicated gene as assayed for its ability to promote malignancy of ESCC cells. Additionally, MIR548K, a microRNA encoded in the amplified 11q13.3-13.4 region, is characterized as a novel oncogene, and functional assays demonstrate that MIR548K enhances malignant phenotypes of ESCC cells. Moreover, we have found that several important histone regulator genes (MLL2 (also called KMT2D), ASH1L, MLL3 (KMT2C), SETD1B, CREBBP and EP300) are frequently altered in ESCC. Pathway assessment reveals that somatic aberrations are mainly involved in the Wnt, cell cycle and Notch pathways. Genomic analyses suggest that ESCC and head and neck squamous cell carcinoma share some common pathogenic mechanisms, and ESCC development is associated with alcohol drinking. This study has explored novel biological markers and tumorigenic pathways that would greatly improve therapeutic strategies for ESCC.	esophagus
Chemoprevention of esophageal cancer with black raspberries, their component anthocyanins, and a major anthocyanin metabolite, protocatechuic acid.	Diets containing either freeze-dried black raspberries (BRBs) or their polyphenolic anthocyanins (ACs) have been shown to inhibit the development of N-nitrosomethylbenzylamine (NMBA)-induced esophageal cancer in rats. The present study was conducted to determine whether PCA, a major microbial metabolite of black raspberry (BRB) ACs, also prevents NMBA-induced esophageal cancer in rats. F344 rats were injected with NMBA three times a week for 5 weeks and then fed control or experimental diets containing 6.1% BRBs, an anthocyanin (AC)-enriched fraction derived from BRBs, or protocatechuic acid (PCA). Animals were exsanguinated at weeks 15, 25, and 35 to quantify the development of preneoplastic lesions and tumors in the esophagus, and to relate this to the expression of inflammatory biomarkers. At weeks 15 and 25, all experimental diets were equally effective in reducing NMBA-induced esophageal tumorigenesis, as well as in reducing the expression of pentraxin-3 (PTX3), a cytokine produced by peripheral blood mononuclear cells in response to interleukin (IL)-1β and TNF-α. All experimental diets were also active at reducing tumorigenesis at week 35; however, the BRB diet was significantly more effective than the AC and PCA diets. Furthermore, all experimental diets inhibited inflammation in the esophagus via reducing biomarker (COX-2, iNOS, p-NF-κB, and sEH) and cytokine (PTX3) expression. Overall, our data suggest that BRBs, their component ACs, and PCA inhibit NMBA-induced esophageal tumorigenesis, at least in part, by their inhibitory effects on genes associated with inflammation.	esophagus
Factors influencing response enthusiasm to telephone follow-up in patients with oesophageal carcinoma after oesophagectomy.	Response enthusiasm to telephone follow-up is a precondition for obtaining exhaustive information; however, no study has yet examined this specific issue. This study aimed to investigate possible factors influencing response enthusiasm to telephone follow-up in patients with oesophageal carcinoma after oesophagectomy and to propose corresponding countermeasures. A telephone follow-up was conducted on patients who underwent oesophagectomy. The possible factors influencing response enthusiasm grades were investigated by univariate and logistic regression analyses. The study enrolled 346 eligible patients. Univariate analysis showed that the tumour, nodes, metastasis (TNM) staging (P = 0.004); survival status (P < 0.001); survival time (P < 0.001); complications/co-morbidities (P = 0.001); and the relationship between the patient and his/her contact person (P < 0.001) were significantly different among the three groups. The first group of patients had high response enthusiasm, the second group had moderate response enthusiasm, and the third group had low response enthusiasm. Logistic regression analysis demonstrated that only the complications/co-morbidities [confidence interval (CI) = -2.310 to -0.665, P < 0.001] and dysphagia status (CI = 0.039-1.509, P = 0.039) were independent factors affecting the response enthusiasm grades. The primary therapeutic results and the current complications and co-morbidities, especially the dysphagia status, were important factors influencing response enthusiasm grades. Planning a follow-up schedule with proper health instructions could be crucial to the quality of follow-up.	esophagus
Endoscopic submucosal dissection for malignant esophageal lesions.	The incidence of esophageal cancer has been increasing while the prognosis remains very poor. Endoscopic submucosal dissection (ESD) was developed in Japan for en bloc resection of early gastric cancer with excellent results. The use of ESD in early squamous cell cancer (SCC) of the esophagus in Japan has been increasing with long-term results comparable to those in early gastric cancer. The use of ESD in Barrett's neoplasia in western countries has been challenged by the low complete resection rates and the risk of metachronous lesions from surrounding non-dysplastic Barrett's epithelium. Efforts to combine ESD with other treatment modalities such as radiofrequency ablation in Barrett's neoplasia and chemoradiation in SCC appear to be promising. The use of steroid therapy (local or systemic) has been demonstrated to prevent post-ESD stenosis, which is the most common complication after esophageal ESD.	esophagus
Vocal cord assessment with transnasal endoscopy in intubated patients after esophagectomy.	BACKGROUND: Vocal cord paralysis (VCP) is one of the postoperative complications after radical esophagectomy. VCP may also lead to serious morbidities such as respiratory distress and aspiration pneumonia. Therefore, an early diagnosis of VCP is meaningful in the postoperative management of patients undergoing esophagectomy. We evaluated a new practical method for diagnosing postoperative VCP. METHODS: The laryngeal assessment of 30 patients was performed, and the presence of VCP was inferred while the following 15 patients by endoscopy before extubation after performing consecutive radical esophagectomy in 45 esophageal cancer patients. The vocal cord mobility, including adduction and abduction, were assessed by inserting the tip of a transnasal endoscope near the vocal cord in the awake patients with orotracheal intubation on the first postoperative day. The presence of VCP was reevaluated after extubation. RESULTS: Eleven of the 30 patients assessed after radical esophagectomy had unilateral VCP and one patient had bilateral VCP. The abduction findings were useful for assessing VCP and the sensitivity, specificity, positive and negative predictive values and accuracy were 97.9%, 100%, 100%, 92.9% and 98.3%, respectively. The results of the following 15 patients were closely similar. CONCLUSIONS: The VCP during orotracheal intubation is assessable by transnasal endoscopy.	esophagus