crossing96/oncoscreening huggingface dataset:
Heterozygote of TAP1 Codon637 decreases susceptibility to HPV infection but increases susceptibility to esophageal cancer among the Kazakh populations.	BACKGROUND: The role of human papillomavirus (HPV) may be involved in the development of esophageal cancer (EC) and the polymorphic immune response gene transporter associated with antigen processing (TAP) may be involved in HPV persistence and subsequent cancer carcinogenesis. The current study aims to provide association evidence for HPV with EC, to investigate TAP1 polymorphisms in EC and assess its association with HPV statuses and EC in Kazakhs. METHODS: The HPV genotypes in 361 patients with EC and 66 controls selected from Kazakh population were evaluated using PCR. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to detect two SNPs of TAP1 in 150 cases comprised of 75 HPV(+) and 75 HPV(-) patients and 283 pure ethnic population of Kazakh and evaluate their associations with susceptibility to EC. A case-to-case comparison based on the genotyping results was conducted to address the function of TAP1 variants in the involvement of HPV. RESULTS: The presence of four HPV genotypes in EC tissues - including HPV 16, 18, 31, 45 - was significantly higher at 64.6 % than those in controls at 18.2 % (P < 0.001). Such presence was strongly associated with increased risk of EC (OR 8.196; 95 % CI 4.280-15.964). The infection of HPV16, and multi-infection of 16 and 18 significantly increase the risk for developing EC (OR 4.616, 95 % CI 2.099-10.151; and OR 6.029, 95 % CI 1.395-26.057 respectively). Heterozygote of TAP1 D637G had a significantly higher risk for developing EC (OR 1.626; 95 % CI 1.080-2.449). The odds ratio for HPV infection was significantly lower among carriers of TAP1 D637G polymorphism (OR 0.281; 95 % CI 0.144-0.551). CONCLUSIONS: HPV infection exhibits a strong positive association with the risk of EC in Kazakhs. Heterozygote of TAP1 D637G decreases susceptibility to HPV infection in patients with EC but increases susceptibility to EC among the Kazakh populations.	esophagus
Patient-reported outcomes during and after definitive chemoradiotherapy for oesophageal cancer.	BACKGROUND: Limited data describe patient-reported outcomes (PROs) of localised oesophageal cancer treated with definitive chemoradiotherapy(CRT). The phase 2/3 SCOPE-1 trial assessed the effectiveness of CRT±cetuximab. The trial for the first time provided an opportunity to describe PROs from a multi-centre group of patients treated with CRT that are presented here. METHODS: Patients undergoing CRT±cetuximab within the SCOPE-1 trial (258 patients from 36 UK centres) completed generic-, disease- and treatment-specific health-related quality of life (HRQL) questionnaires (EORTC QLQ-C30, QLQ-OES18, Dermatology Life-Quality Index (DLQI)) at baseline and at 7, 13, 24, 52 and 104 weeks. Mean EORTC functional scale scores (>15 point change significant), DLQI scores (>4 point change significant) and proportions of patients (>15% significant) with 'minimal' or 'severe' symptoms are presented. RESULTS: Questionnaire response rates were good. At baseline, EORTC functional scores were high (>75%) and few symptoms were reported except for severe problems with fatigue, insomnia and eating-related symptoms (e.g., appetite loss, dysphagia, dry mouth) in both groups(>15%). Functional aspects of health deteriorated and symptoms increased with treatment and by week 13 global quality of life, physical, role and social function significantly deteriorated and more problems with fatigue, dyspnoea, appetite loss and trouble with taste were reported. Recovery occurred by 6 months (except severe fatigue and insomnia in >15% of patients) and maintained at follow-up with no differences between groups. CONCLUSIONS: CRT for localised oesophageal cancer has a significant detrimental impact on many aspects of HRQL; however, recovery is achieved by 6 months and maintained with the exception of persisting problems with severe fatigue and insomnia. The data suggest that the HRQL recovery after definitive CRT is quicker, and there is little lasting deficit compared with treatment including surgery. These data need to be compared with HRQL data from studies evaluating treatments including surgery for oesophageal cancer.	esophagus
Influence of lymphatic endothelial cells on proliferation and invasiveness of esophageal carcinoma cells in vitro and lymphangiogenesis in vivo.	The aim of the study was to investigate the interaction between esophageal carcinoma cells with different differentiation degree and esophageal carcinoma-related lymphatic endothelial cells. Different lymphatic endothelial cell conditioned mediums were used to cultivate well-differentiated esophageal carcinoma EC9706 cells and poorly differentiated esophageal carcinoma KYSE150 cells, and immunocytochemistry and Western blot analyses were applied to detect the expression of MMP-9 protein and TIMP-2 protein in each group; in situ hybridization and RT-PCR methods were used to detect the expression of MMP-9 and TIMP-2 mRNA in each group; CCK-8 method was used to detect cell proliferation in each group; and transwell method was utilized to detect cell invasiveness in each group. Through constructing the transplanted tumor model of esophageal carcinoma of nude mice, the D2-40 and LYVE-1 immunohistochemical staining was performed on transplanted tumors and surrounding tissues, lymphatic microvessels were marked, and lymphatic microvessel density (LMVD) was measured. The expression of MMP-9 protein and mRNA in experimental group was significantly higher than that in control groups (P < 0.05); TIMP-2 protein and mRNA expression in experimental group was significantly lower than that in control groups (P < 0.05); cell proliferation ability and invasiveness ability in experimental group were significantly higher than those in control groups (P < 0.05); LMVD-marked D2-40 and LMVD-marked LYVE-1 of transplanted tumor tissue in the experimental group were significantly higher than those in control groups (P < 0.05). The esophageal squamous carcinoma-related lymphatic microvessel could promote the proliferation and invasive ability of esophageal squamous carcinoma cells in vitro. It had different effects on esophageal carcinoma cells with different differentiation degree and had more obvious influence on poorly differentiated esophageal carcinoma cells, which may be related to the up-regulated MMP-2 expression and down-regulated TIMP-2 expression of esophageal carcinoma cells. The esophageal squamous carcinoma-related lymphatic microvessel endothelial cells could promote the growth of esophageal carcinoma-transplanted tumor of nude mice and lymphangiogenesis.	esophagus
Overexpression of CD55 from Barrett's esophagus is associated with esophageal adenocarcinoma risk.	BACKGROUND AND AIM: Although several molecular biomarkers for esophageal adenocarcinoma (EAC) have been shown to be useful disease indicators, none has been established as a reliable indicator for risk of EAC or have progressed to routine use. The aim was to identify biomarkers of high risk for EAC in patients with Barrett's esophagus (BE). METHODS: Following endoscopic observation by magnified endoscopy with narrow band imaging (ME-NBI), brushing was followed by obtaining biopsy samples from columnar-lined esophagus (CLE) and from EAC lesions of EAC patients, and from age- and sex-matched non-EAC controls with BE. Total RNA was extracted for microarray analysis using Affymetrix GeneChip Human Genome U133 plus 2.0 Array. Real-time-PCR analysis of identified candidate genes was used to confirm the results. RESULTS: Overall, 9 EAC patients and 50 patients with BE were studied. Seventy-nine candidate genes were identified by microarray analysis based on a proportional hazards model (P < 0.005). Six genes exhibited significantly differential expressions in both BE and cancer lesions of the EAC group compared to BE of the controls. In the brushing samples, median CD55 relative expression levels in cancer lesions were highest and decreased in BE of EAC group and BE of the controls, in that order (P < 0.001). CONCLUSION: Over expression of CD55 in brushing samples taken from BE may be associated with the risk of EAC.	esophagus
The efficacy of uracil DNA glycosylase pretreatment in amplicon-based massively parallel sequencing with DNA extracted from archived formalin-fixed paraffin-embedded esophageal cancer tissues.	Advances in mutation testing for molecular-targeted cancer therapies have led to the increased use of archived formalin-fixed paraffin-embedded (FFPE) tumors. However, DNA extracted from FFPE tumors (FFPE DNA) is problematic for mutation testing, especially for amplicon-based massively parallel sequencing (MPS), owing to DNA fragmentation and artificial C:G > T:A single nucleotide variants (SNVs) caused by deamination of cytosine to uracil. Therefore, to reduce artificial C:G > T:A SNVs in amplicon-based MPS using FFPE DNA, we evaluated the efficacy of uracil DNA glycosylase (UDG) pretreatment, which can eliminate uracil-containing DNA molecules, with 126 archived FFPE esophageal cancer specimens. We also examined the association between the frequency of C:G > T:A SNVs and DNA quality, as assessed by a quantitative PCR (qPCR)-based assay. UDG pretreatment significantly lowered the frequency of C:G > T:A SNVs in highly fragmented DNA (by approximately 60%). This effect was not observed for good- to moderate-quality DNA, suggesting that a predictive assay (i.e., DNA quality assessment) needs to be performed prior to UDG pretreatment. These results suggest that UDG pretreatment is efficacious for mutation testing by amplicon-based MPS with fragmented DNA from FFPE samples.	esophagus
Cancer Attributable to Asbestos Exposure in Shipbreaking Workers: A Matched-Cohort Study.	PURPOSE: Long-term follow-up studies of asbestos-related cancer in shipbreaking workers are lacking. This study examines the relationship between cancer incidence and asbestos exposure among former Taiwan shipbreaking workers. METHODS: A total of 4,427 shipbreaking workers and 22,135 population-based matched controls were successfully followed in this study. The study cohort was linked to the Taiwan Cancer Registry for new cancer cases. The adjusted hazard ratio (aHR) for cancer was calculated for the shipbreaking workers with Total Exposure Potential Scores (TEP) for asbestos. RESULTS: Follow-up generated 109,932 person-years, with 940 deaths and 436 cancer cases, among 4,427 shipbreaking workers from 1985 to 2008. The high asbestos exposure group also had a statistically significant increase in the risk of overall cancer (aHR= 1.71; 95% CI: 1.42-2.05), esophagus cancer (aHR= 2.31; 95% CI: 1.00-5.41), liver and intrahepatic bile duct cancer (aHR= 1.60; 95% CI: 1.08-2.36), and trachea, bronchus, and lung cancer (aHR= 3.08; 95% CI: 1.80-5.25). Mesothelioma cases were found in the high asbestos exposure group. Moreover, overall cancer, esophagus cancer, and trachea, bronchus, and lung cancer were seen in a dose-dependent relationship with asbestos exposure. CONCLUSIONS: This study presented the elevated trend of asbestos exposure with cancer incidence for overall cancer, esophagus cancer, and trachea, bronchus, and lung cancer among shipbreaking workers. Those workers previously exposed to asbestos should receive persistent monitoring in order to early detect adverse health outcomes.	esophagus
Is tumor length a prognostic indicator for esophageal squamous cell carcinoma? A single larger study among Chinese patients.	OBJECTIVE: In esophageal cancer, depth of wall penetration, reflected by T classification, represents the most important prognostic variable. Our study aimed to investigate the impact of tumor length, measured as the longitudinal length, on the outcome of esophageal squamous cell carcinoma (ESCC) patients. METHODS: The survival data of 362 ESCC patients who underwent surgical resection as the primary treatment between 1999 and 2007 were collected retrospectively. Receiver-operator characteristic analysis was applied to identify the optimal cut-off values. RESULTS: 4.0 cm was identified as the optimal cut-off value within the whole group. Tumor length greater than 4.0 cm was associated with increasing T stage (P=0.001), N stage (P=0.046), and tumor differentiation (P=0.033). Univariate analysis and multivariate analysis both found that tumor length greater than 4.0 cm was associated with worse overall survival compared with shorter tumors (P<0.001). It appeared to have a greater impact on N0-N1 (P<0.001, P=0.026, respectively) than N2-N3 and appeared to have a higher impact on the lower-stage patients than the higher-stage patients. CONCLUSIONS: Tumor length proved to be an independent prognostic parameter for ESCC patients, especially for node-negative and lower-stage patients. More attention should be paid to its role in the management of ESCC.	esophagus
Closure of esophagotracheal fistula after esophagectomy for esophageal cancer.	Fistula between the trachea and esophagogastric anastomosis after esophagectomy is rare. We successfully treated a 75-year-old woman with such a lesion by single-stage repair. The patient had undergone radical esophagectomy 20 years ago, and repeatedly developed aspiration pneumonia for recent 5 years. Radiological and endoscopic examinations demonstrated the fistula between the trachea at the level of sternal notch and esophagogastric anastomosis. The fistula was separated and the defects on both sides were closed. A sternocleidomastoid muscle flap was inserted between the two structures. The postoperative course was uneventful.	esophagus
Diet-related inflammation and oesophageal cancer by histological type: a nationwide case-control study in Sweden.	PURPOSE: This project sought to test the role of diet-related inflammation in modulating the risk of oesophageal cancer. METHODS: A nationwide population-based case-control study was conducted from 1 December 1994 through 31 December 1997 in Sweden. All newly diagnosed patients with adenocarcinoma of the oesophagus or gastroesophageal junction and a randomly selected half of patients with oesophageal squamous cell carcinoma were eligible as cases. Using the Swedish Registry of the Total Population, the control group was randomly selected from the entire Swedish population and frequency-matched on age (within 10 years) and sex. The literature-derived dietary inflammatory index (DII) was developed to describe the inflammatory potential of diet. DII scores were computed based on a food frequency questionnaire. Higher DII scores indicate more pro-inflammatory diets. Odds ratios and 95 % confidence intervals (CI) were computed to assess risk associated between DII scores and oesophageal cancer using logistic regression adjusted by potential confounders. RESULTS: In total, 189 oesophageal adenocarcinomas, 262 gastroesophageal junctional adenocarcinomas, 167 oesophageal squamous cell carcinomas, and 820 control subjects were recruited into the study. Significant associations with DII were observed for oesophageal squamous cell carcinoma (ORQuartile4vs1 4.35, 95 % CI 2.24, 8.43), oesophageal adenocarcinoma (ORQuartile4vs1 3.59, 95 % CI 1.87, 6.89), and gastroesophageal junctional adenocarcinoma (ORQuartile4vs1 2.04, 95 % CI 1.24, 3.36). Significant trends across quartiles of DII were observed for all subtypes of oesophageal cancer. CONCLUSIONS: Diet-related inflammation appears to be associated with an increased risk of oesophageal cancer, regardless of histological type.	esophagus
Resource utilization in esophagectomy: When higher costs are associated with worse outcomes.	INTRODUCTION: Care of the esophagectomy patient requires significant resources. We sought to determine which patient and provider variables contribute to resource utilization and their association with clinical outcomes. METHODS: 6,737 patients undergoing esophagectomy were identified from the University Healthsystem Consortium (UHC). Linear and logistic regression models were used to determine whether characteristics, including age, severity of illness (SOI) and procedural volume were associated with mortality, length of stay (LOS), discharge disposition, readmission rates, and cost. RESULTS: Older patients were twice as likely to suffer post-operative death (OR 2.12; 95%CI 1.7-2.7), three times more likely to be discharged to extended care facilities (31.9% vs. 10.6%, P < 0.001), and cost 8.4% more ($27,628 vs. $25,481, P < 0.001). Similarly, patients with higher SOI were more likely to suffer post- operative death (OR 14.6; 4.7-45.9), be readmitted (OR 1.3; 1.1-1.6), and have longer hospital stays (RR 1.3; 1.8-2.1). Patients with the highest index hospital costs were five times more likely to be discharged to an extended care facility (P < 0.001). CONCLUSION: Older patients and those with a higher SOI have higher perioperative mortality, readmission rates, hospital costs, and require more post- operative care. With increasingly scrutinized health care costs, these data provide guidance for more careful patient selection.	esophagus
Constrictive pericarditis caused by a pericardial-occupying tumor due to esophageal cancer.	A 61-year-old female was admitted to our hospital for esophageal cancer treatment. Esophagectomy with 2-field lymphadenectomy was performed. Postoperative findings revealed the lesion was a poorly differentiated squamous cell carcinoma invading into the diaphragm and there were no carcinoma cells on the surgical margins. Eight months after surgery, a recurrence was suspected by the presence of tumors at the pericardia, right axillary lymph node and around the descending aorta. The patient was re-admitted for chemotherapy and administrated fluorouracil and cisplatin 4 days after admission. After 7 days, she complained of dysphagia. Esophagogastroduodenoscopy showed no abnormal lesion that could cause the symptom. Computed tomography revealed massive progression of the pericardial tumor, bilateral pleural effusion and congested liver. Echocardiography showed the diffuse pericardial tumor caused restriction of ventricular dilation and hemodynamics of constrictive pericarditis. The patient died 29 days after re-admission. Autopsy revealed squamous cell carcinoma involving the mediatinum and pericardium. The pericardium was completely full of cancer tissue but no fluid. We concluded that the direct cause of death was neoplastic constrictive pericarditis.	esophagus
Primary Esophageal Extranasal NK/T Cell Lymphoma With Biphasic Morphology: A Case Report and Literature Review.	We report a case of esophageal extranasal NK/T cell lymphoma with biphasic morphologic features revealed by a deep large piecemeal biopsy. A 40-year-old man present with pharyngalgia, dysphagia, recurrent fever, and 5-kg weight loss for 8 months. Endoscopy demonstrated progressing longitudinal ulcers and mucosal bridges along the esophagus. The first and second biopsies obtained superficial mucosa with scattered bland-looking small lymphocytes. A subsequent large piecemeal snare abscission for biopsy showed atypical lymphoid cells infiltrating into the deep lamina propria and muscularis mucosae, whereas the superficial lamina propria was highly edematous with scant small lymphocytes. Immunohistochemical studies confirmed that both underlying atypical cells and superficial small lymphocytes were neoplastic, sharing an identical immunophenotype: positive for CD2, CD3, CD43, CD8, CD56, TIA-1 and granzyme B. Epstein-Barr virus-encoded small RNAs were found in both cells. The histologic findings were diagnostic of primary esophageal extranasal NK/T cell lymphoma. However, the patient developed bone marrow depression during chemotherapy and died of massive cerebral hemorrhage after the first cycle of chemotherapy. Primary esophageal extranodal NK/T cell lymphoma nasal type is extremely rare. We show the biphasic morphology of this disease, which highlights the importance of deep biopsy for accurate diagnosis.	esophagus
Metastatic lymph node ratio, 6th or 7th AJCC edition: witch is the best lymph node classification for esophageal cancer? Prognosis factor analysis in 487 patients.	BACKGROUND: The esophageal cancer is one of the most common and aggressive worldwide. Recently, the AJCC changed the staging system, considering, among others, the important role of the lymph node metastasis on the prognosis. AIM: To discuss the applicability of different forms of lymph node staging in a western surgical center. METHODS: Four hundred eighty seven patients with esophageal cancer were enrolled. Three staging systems were evaluated, the 6th and the 7th AJCC editions and the Lymph Node Metastatic Ratio. RESULTS: The majority of the cases were squamous cell carcinoma. The mean lymph node sample was eight. Considering the survival, there was no significant difference between the patients when they were classified by the 7th AJCC edition. Analysis of the Lymph Node Metastatic Ratio, just on the group of patients with 0 to 25%, has shown significant difference (p=0,01). The 6th AJCC edition shows the major significant difference between among the classifications evaluated. CONCLUSION: In this specific population, the 7th AJCC edition for esophageal cancer was not able to find differences in survival when just the lymph node analysis was considered.	esophagus
[Why oesophageal adenocarcinoma is occurring more frequently].	The incidence of oesophageal adenocarcinoma has increased rapidly over the past decades in the Western world. The prognosis is poor with a mean 5-year survival rate of 19% in the Netherlands. Important risk factors that might account for this rising incidence are reflux, obesity and the absence of Helicobacter pylori. Oesophageal adenocarcinoma is 9 times more likely in men than in women. The reason for this much higher incidence of adenocarcinoma in men is still unclear, but sex hormones may play a role.	esophagus
Patients' Preferences for Surgical Management of Esophageal Cancer: A Discrete Choice Experiment.	BACKGROUND: Obtaining insight into patients' preferences is important to optimize cancer care. We investigated patients' preferences for surgical management of esophageal cancer. METHODS: We conducted a discrete choice experiment among adult patients who had undergone esophagectomy for adenocarcinoma or squamous cell cancer of the esophagus. Patients' preferences were quantified with regression analysis using scenarios based on five aspects: risk of in-hospital mortality, risk of persistent symptoms, chance of 5-year survival, risk of surgical and non-surgical complications, and hospital volume of esophageal cancer surgery. RESULTS: The response rate was 68 % (104/142). All aspects proved to influence patients' preferences (p < 0.05). Persisting gastrointestinal symptoms and 5-year survival were the most important attributes, but preferences varied between patients. On average, patients were willing to trade-off 9.5 % (CI 2.4-16.6 %) 5-year survival chance to obtain a surgical treatment with 30 % lower risk of gastrointestinal symptoms, or 8.1 % (CI 4.0-12.2 %) 5-year survival chance for being treated in a high instead of a low-volume hospital. CONCLUSIONS: Patients are willing to trade-off some 5-year survival chance to achieve an improvement in early outcomes. Given the preference heterogeneity among participants, the present study underlines the importance of a patient-tailored approach when discussing prognosis and treatment.	esophagus