crossing96/oncoscreening huggingface dataset:
Dietary proportions of carbohydrates, fat, and protein and risk of oesophageal cancer by histological type.	BACKGROUND: Dietary habits influence the risk of cancer of the oesophagus and oesophago-gastric junction, but the role of proportions of the main dietary macronutrients carbohydrates, fats and proteins is uncertain. METHODS: Data was derived from a nationwide Swedish population-based case-control study conducted in 1995-1997, in which case ascertainment was rapid, and all cases were uniformly classified. Information on the subjects' history of dietary intake was collected in personal interviews. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using logistic regression, with adjustment for potentially confounding factors. RESULTS: Included were 189 oesophageal adenocarcinomas, 262 oesophago-gastric adenocarcinomas, 167 oesophageal squamous cell carcinomas, and 820 control subjects. Regarding oesophageal or oesophago-gastric junctional adenocarcinoma, a high dietary proportion of carbohydrates decreased the risk (OR 0.50, CI 0.34-0.73), and a high portion of fat increased the risk (OR 1.96, CI 1.34-2.87), while a high proportion of protein did not influence the risk (OR 1. 08, 95% CI 0.75-1.56). Regarding oesophageal squamous cell carcinoma, the single macronutrients did not influence the risk statistically significantly. CONCLUSIONS: A diet with a low proportion of carbohydrates and a high proportion of fat might increase the risk of oesophageal adenocarcinoma.	esophagus
No evidence for BRAF-V600E mutations in gastroeosophageal tumors: results from a high-throughput analysis of 534 cases using a mutation-specific antibody.	BACKGROUND: BRAF-V600E mutations are found in a broad spectrum of cancer types and can be successfully targeted by specific therapeutic compounds. Little data on the prevalence of BRAF-V600E mutations in tumors of the upper gastrointestinal tract are available. MATERIALS AND METHODS: We constructed tissue microarrays of formalin-fixed and paraffin-embedded specimens of 534 gastroesophageal tumors (119 squamous cell cancers and 72 adenocarcinomas of the esophagus, 63 cancers of the gastroesophageal junction/cardia, 199 gastric cancers of the corpus or antrum, 81 gastric gastrointestinal stromal tumors) and performed anti-BRAF-V600E immunostaining using the mutation-specific antibody VE1. As control tissue we used 3 melanoma cases with confirmed BRAF-V600E mutation and distinct VE1 immunostaining. RESULTS: None of the gastroesophageal tumor cases showed a positive immunostaining signal. CONCLUSIONS: BRAF-V600E mutation is not a relevant oncogenic driver in gastroesophageal tumors. Immunohistochemical analysis using mutation-specific antibodies on tissue microarrays is a feasible, time-efficient and cost-efficient approach to high-throughput screening for specific mutations in large tumor series.	esophagus
The telomere/telomerase binding factor PinX1 is a new target to improve the radiotherapy effect of oesophageal squamous cell carcinomas.	Chemoradiotherapy (CRT) is a standard treatment for oesophageal squamous cell carcinoma (ESCC) in its advanced stages. The telomerase/telomere interacting protein PinX1 contributes to telomere maintenance, tumourigenicity, and influences the DNA damage agent-induced apoptotic response in telomerase-positive cancer cells. However, the clinical and biological significance of PinX1 in human ESCCs remains unclear. We examined the expression dynamics of PinX1 by immunohistochemistry in a learning cohort (n = 98) and a validation cohort (n = 59) of ESCC patients treated with definite chemoradiotherapy (CRT). A series of in vivo and in vitro assays were performed to elucidate the effect of PinX1 on ESCC cells' CRT response and underlying mechanisms. Knockdown of PinX1 did not affect ESCC cells' chemosensitivities to 5-fluorouracil and cisplatin, but substantially increased ESCC cells' therapeutic efficacy of radiation both in vitro and in vivo. Ectopic overexpression of PinX1 dramatically enhanced ESCC cells' resistance to radiotherapy. Furthermore, we demonstrated that PinX1 resistance to radiotherapy (RT) was attributed to PinX1 maintaining telomere stability, reducing ESCC cell death by RT-induced mitosis catastrophe (MC). High expression of Pinx1 correlated positively with ESCC's resistance to CRT, and was a strong and independent predictor for short disease-specific survival (DSS) of ESCC patients. Our data suggest that PinX1 could serve as a novel predictor for a CRT response to ESCC patients, and the pathway of PinX1-mediated telomere stability might represent a new target to improve the RT effect of ESCC.	esophagus
Is there a correlation between molecular markers and response to neoadjuvant chemoradiotherapy in locally advanced squamous cell esophageal cancer?	PURPOSE: To evaluate the expression of epidermal growth factor receptor (EGFR), p53, p21 and thymidylate synthase (TS) in a pretherapy biopsy specimen of locally advanced squamous cell esophageal cancer and correlate these markers with response to neoadjuvant chemoradiotherapy. METHODS: Sixty-two patients with histopathologically proven locally advanced (T3 or greater) squamous cell esophageal cancer were enrolled. The expression of EGRF, p53, p21 and TS markers was assessed with immunohistochemistry. Semiquantitative assessment of expression of these markers was performed based on the percent of the stained cells. Radiotherapy (45-50.4 Gy) was delivered concomitantly with 5-fluorouracil (5-FU)/leucovorin (LV)/cisplatin (CIS) chemotherapy. Five to 6 weeks after chemoradiation, response to treatment was assessed. Medically fit and operable patients were operated. The resected material underwent histopathological evaluation of tumor expansion, histological classification after initial multimodality treatment (yp TNM), residual status and tumor regression grade (TRG). RESULTS: Out of 62 patients enrolled, 41 (66%) were evaluated for molecular markers. Clinical response rate was 43.9%. Out of 41 patients, 12 (29%) underwent surgery. TRG 1 was noted in 58% of the patients. In a pretherapy tumor specimen, positive expression was noted in 80, 90, 80 and 71% for EGFR, p53, p21 and TS, respectively. We noted no statistically significant difference neither between tumor marker expression and clinical response to chemoradiation, nor between tumor marker expression and TRG. CONCLUSION: We registered no difference in response to treatment between EGFR, TS, p21 and p53 positive and negative staining.	esophagus
Hypomethylation of noncoding DNA regions and overexpression of the long noncoding RNA, AFAP1-AS1, in Barrett's esophagus and esophageal adenocarcinoma.	BACKGROUND & AIMS: Alterations in methylation of protein-coding genes are associated with Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). Dysregulation of noncoding RNAs occurs during carcinogenesis but has never been studied in BE or EAC. We applied high-resolution methylome analysis to identify changes at genomic regions that encode noncoding RNAs in BE and EAC. METHODS: We analyzed methylation of 1.8 million CpG sites using massively parallel sequencing-based HELP tagging in matched EAC, BE, and normal esophageal tissues. We also analyzed human EAC (OE33, SKGT4, and FLO-1) and normal (HEEpic) esophageal cells. RESULTS: BE and EAC exhibited genome-wide hypomethylation, significantly affecting intragenic and repetitive genomic elements as well as noncoding regions. These methylation changes targeted small and long noncoding regions, discriminating normal from matched BE or EAC tissues. One long noncoding RNA, AFAP1-AS1, was extremely hypomethylated and overexpressed in BE and EAC tissues and EAC cells. Its silencing by small interfering RNA inhibited proliferation and colony-forming ability, induced apoptosis, and reduced EAC cell migration and invasion without altering the expression of its protein-coding counterpart, AFAP1. CONCLUSIONS: BE and EAC exhibit reduced methylation that includes noncoding regions. Methylation of the long noncoding RNA AFAP1-AS1 is reduced in BE and EAC, and its expression inhibits cancer-related biologic functions of EAC cells.	esophagus
[Judging the postoperative lymph node metastasis of esophagus cancer patients with pN0 stage by detecting MTA1 protein expression].	OBJECTIVE: To investigate the feasibility for judging the postoperative lymph node metastasis of esophagus cancer patients with pN0 stage by detecting the protein expression of metastasis-associated protein 1 (MTA1). METHODS: Immunohistochemistry was used to detect the expression of MTA1 protein in lymph node of esophageal squamous cell carcinoma (ESCC) with pN0 stage. RESULTS: (1) There were no significant differences in age, gender and differentiation among the lymph node metastasis (P > 0.05), but not with pT stage (P < 0.05; χ(2) = 13.29). (2) There were no significant differences among the expression of MTA1 protein and age, gender and differentiation (P > 0.05), but not with differentiation and pT stage (P < 0.05; χ(2) = 18.61). Both stages pT1b and pT3 had higher expression of MTA1 protein than stage pT1a (P < 0.05; χ(2) = 25.54). (3) The curve of lymph node metastasis showed that the patients with no/lower MTA1 protein expression had a lower metastasis rate than those a higher MTA1 protein expression (P < 0.05; χ(2) = 16.63). (4) The results of multivariate analysis confirmed that T status and MTA1 protein over-expression were independent risk factors for pN0 stage ESCC. CONCLUSION: Detecting MTA1 protein expression is helpful for judging the lymph node metastasis of ESCC patients with pN0 stage. And its over-expression may used as a guide in the decision-making of postoperative adjuvant therapy.	esophagus
[Clinical analysis and surgical treatment of 14 cases of esophageal gastrointestinal stromal tumors].	OBJECTIVE: To explore the clinical features and surgical management of esophageal gastrointestinal stromal tumors (GIST). METHODS: The clinical data of patients with esophageal GISTs undergoing surgery at our hospital between January 1999 and April 2012 were retrospectively reviewed. RESULTS: Of 14 patients, the male: female ratio was 8:6; the median age of the patients was 42 years (range 33 - 63 years). Dysphagia was the most common symptom, and all cases were diagnosed postoperatively. The tumors were resected by enucleation or esophagectomy or endoscopic submucosal resection. The median follow-up was 43.5 months, ranging from 2 to 142 months, with all patients have no recurrence and metastasis. CONCLUSION: Esophageal GIST is rather rare. At present, surgical resection and postoperative diagnosis remain the mainstay for treatment of patients with esophageal GISTs in China.	esophagus
[The relationship between C20orf54 gene rs3746804 position single nucleotide polymorphism and susceptibility to esophageal squamous cell carcinoma].	OBJECTIVE: To explore the association of C20orf54 gene rs3746804 position single nucleotide polymorphism and susceptibility to esophageal squamous cell carcinoma (ESCC). METHODS: Purification of genomic DNA from whole blood was used the Maxwell(16) System. rs3746804 in C20orf54 was detected by direct sequencing in 434 ESCC patients from Changzhi (Shanxi province) and Linzhou (Henan province) and 554 healthy controls from Changzhi, Linzhou and including immigrators from Linzhou to Changzhi. RESULTS: For rs3746804, the genotypic frequencies of CT (37.5% vs 51.0%, 37.5% vs 52.0%), CC (44.2% vs 34.8%, 44.2% vs 33.0%) in Changzhi ESCC patients showed significant differences with healthy Changzhi controls and the healthy immigrator controls (all P < 0.05), and the frequencies of TT (18.3% vs 4.1%) and CC (44.2% vs 54.6%) in Changzhi ESCC patients showed significant differences with Linzhou ESCC patients (all P < 0.05). The genotypic frequencies of TT (4.1% vs 15.0%), CT (41.2% vs 52.0%) and CC(54.6% vs 33.0%) showed significant differences between Linzhou ESCC patients and the healthy immigrator controls (all P < 0.05), and the frequencies of TT (4.1% vs 14.1%) and CC(54.6% vs 34.8%) showed significant differences between Linzhou ESCC patients and Changzhi healthy controls (all P < 0.01). Meanwhile, there were significant differences between ESCC patients (including Changzhi and Linzhou ESCC patients) and healthy controls (including the healthy Changzhi, Linzhou and immigrator controls) in genotypic frequencies of CT (39.2% vs 48.7%) and CC (48.8% vs 38.2%) (all P < 0.01). CT and CT + TT genotype could decrease the risk of ESCC compared with the CC genotype (OR = 0.630, 95%CI 0.481 - 0.826; OR = 0.654, 95%CI 0.507 - 0.844). CONCLUSION: There is a closed relationship between SNP rs3746804 in C20orf54 and susceptibility to ESCC.	esophagus
BRCA1 mRNA expression as a predictive and prognostic marker in advanced esophageal squamous cell carcinoma treated with cisplatin- or docetaxel-based chemotherapy/chemoradiotherapy.	BACKGROUND: The molecular backgrounds that determine therapeutic effectiveness in esophageal cancer remain largely unknown. Breast cancer susceptibility gene 1 (BRCA1) expression has been found to switch the response to cisplatin- or paclitaxel-based chemotherapy. It remains unclear how variations in BRCA1 expression influence clinical outcomes in esophageal cancer. PATIENTS AND METHODS: Quantitative real-time polymerase chain reaction (qPCR) was performed to examine BRCA1 mRNA expressions in paraffin-embedded specimens from 144 patients with advanced or metastatic esophageal squamous cell carcinoma who received cisplatin- or docetaxel-based first-line treatments. RESULTS: Low BRCA1 mRNA expression correlated with increased response rate (RR; P = 0.025 and 0.017, respectively) and median overall survival (mOS; P = 0.002 and P<0.001, respectively) in cisplatin-based chemotherapy or chemoradiotherapy group and also correlated with decreased RR (P = 0.017 and 0.024, respectively) and mOS (both P<0.001) in docetaxel-based chemotherapy or chemoradiotherapy group. Multivariate analysis revealed that low BRCA1 expression was an independent prognostic factor in cisplatin-based chemotherapy (HR 0.29; 95%CI 0.12-0.71; P = 0.007) or chemoradiotherapy (HR 0.12; 95%CI 0.04-0.37; P<0.001) group and higher risk for mortality in docetaxel-based chemotherapy (HR 5.02; 95%CI 2.05-12.28; P<0.001) or chemoradiotherapy (HR 7.02; 95%CI 2.37-27.77; P<0.001) group. CONCLUSIONS: BRCA1 mRNA expression could be used as a predictive and prognostic marker in esophageal cancer who underwent first-line cisplatin- or docetaxel-based treatments.	esophagus
Exposure to bisphosphonates and risk of gastrointestinal cancers: series of nested case-control studies with QResearch and CPRD data.	OBJECTIVE: To investigate the association between use of bisphosphonates estimated from prescription information and risk of gastrointestinal cancers. DESIGN: Series of nested case-control studies. SETTING: General practices in the United Kingdom contributing to the QResearch primary care database (660) and the Clinical Practice Research Datalink (CPRD) (643). PARTICIPANTS: Patients aged ≥ 50 with a diagnosis of a primary gastrointestinal cancer in 1997-2011, each matched with up to five controls by age, sex, practice, and calendar year. MAIN OUTCOME MEASURES: Odds ratios for incident gastrointestinal cancers (colorectal, oesophageal, gastric) and use of bisphosphonates, adjusted for smoking status, ethnicity, comorbidities, and use of other drugs. RESULTS: 20,106 and 19,035 cases of colorectal cancer cases, 5364 and 5135 cases of oesophageal cancer cases, and 3155 and 3157 cases of gastric cancer were identified from QResearch and CPRD, respectively. Overall bisphosphonate use (at least one prescription) was not associated with risk of colorectal, oesophageal, or gastric cancers in either database. Adjusted odds ratios (95% confidence interval) for QResearch and CPRD were 0.97 (0.79 to 1.18) and 1.18 (0.97 to 1.43) for oesophageal cancer; 1.12 (0.87 to 1.44) and 0.79 (0.62 to 1.01) for gastric cancer; and 1.03 (0.94 to 1.14) and 1.10 (1.00 to 1.22) for colorectal cancer. Additional analyses showed no difference between types of bisphosphonate for risk of oesophageal and colorectal cancers. For gastric cancer, alendronate use was associated with an increased risk (1.47, 1.11 to 1.95; P=0.008), but only in data from the QResearch database and without any association with duration and with no definitive confirmation from sensitivity analysis. CONCLUSIONS: In this series of population based case-control studies in two large primary care databases, exposure to bisphosphonates was not associated with an increased risk of common gastrointestinal cancers.	esophagus
Endoscopic management of esophageal cancer after definitive chemoradiotherapy.	BACKGROUND: Concurrent chemoradiotherapy (CRT) is a potentially curative non-surgical option for locally advanced esophageal cancer, with pathological complete response (CR) ranging from 13 to 49 %. The rate of persistent and recurrent disease within the esophagus remains high at 40-60 %, and treatment of these tumors may improve disease-free survival. The aim of this review is to assess the efficacy of salvage endoscopic therapies for recurrent esophageal cancer. METHODS: Medline and Embase were searched for relevant studies published in the English-language literature that reported use of endoscopic modalities, including photodynamic therapy (PDT), endoscopic mucosal resection (EMR), and spray cryotherapy, as salvage therapies for esophageal cancer. RESULTS: A total of 12 studies were identified. In small case series of PDT, CR varied from 20 to 100 %, with 1-, 3-, and 5-year overall survival rates of 65-80, 34-47, and 36 %, respectively. Data from three studies of EMR in squamous cell cancer show CR in 50 % of cases, with 3- and 5-year overall survival of 56-81 and 49 %, respectively. Endoscopic spray cryotherapy has recently been used in this setting with an observed CR of 37.5 %. CONCLUSIONS: Endoscopic salvage therapies are options for those patients with disease limited to the superficial esophageal wall and those who are unfit to undergo salvage esophagectomy. Widespread application of endoscopic salvage therapies is limited by the lack of awareness and guidelines for endoscopic surveillance post-CRT and limited data on the effectiveness of endoscopic therapies.	esophagus
Hepatic and extrahepatic malignancies in cirrhosis caused by nonalcoholic steatohepatitis and alcoholic liver disease.	BACKGROUND: To clarify the carcinogenic factors associated with steatohepatitis, we investigated the characteristic features of hepatic and extrahepatic malignancies in patients with cirrhotic nonalcoholic steatohepatitis (NASH-LC) and cirrhotic alcoholic liver disease (ALD-LC). METHODS: A total of 72 patients with NASH-LC and 85 with ALD-LC (both biopsy-proven steatohepatitis without hepatocellular carcinoma [HCC]) were assessed with regard to the development of hepatic and extrahepatic malignancies. Risk factors for HCC were analyzed. RESULTS: During follow-up, 10 NASH-LC patients and 6 ALD-LC patients developed HCC. The 5-year HCC development rate was similar for these 2 groups, being 10.5% in the NASH-LC group and 12.3% in the ALD-LC group. After adjusting for age and gender, the HCC development rates were also similar. Risk factors for HCC in the NASH-LC group were older age, higher γ-GTP level, and higher Child-Pugh score as determined by Cox hazards analysis. Regarding risk factors in the ALD-LC group, no risk factor was found by Cox hazards analysis, although diabetes mellitus led to a significantly higher HCC rate by log-rank test (p = 0.013). Regarding extrahepatic cancer, only 1 NASH-LC patient (1.4%) developed endometrial cancer. In contrast, 7 ALD-LC patients (8.2%) had other cancers (p = 0.052). CONCLUSIONS: Comparison between NASH-LC and ALD-LC revealed similar HCC development curves. However, the risk factors for HCC and extrahepatic malignancies differed between the 2 diseases. In ALD-LC, the incidences of HCC and extrahepatic cancer are similar. When treating LC patients with NASH or ALD, the risk factors and extrahepatic malignancies associated with ALD-LC should be assessed.	esophagus
Dysphagia and an abnormal esophagram: a case report.	This case report details the history, diagnostic workup, and follow-up of an 82-year-old dysphagic African-American woman who presented for an esophagram/barium swallow study. Radiologic and endoscopic imaging results and findings are discussed. In addition, the patient's treatment regimen and follow-up care are presented to better educate the radiologic technology community.	esophagus
Evaluation of 18F-FDG PET/CT and CT/MRI with histopathologic correlation in patients undergoing central compartment neck dissection for squamous cell carcinoma of the larynx, hypopharynx, and esophagus.	OBJECTIVES: Central compartment lymph node metastasis (CLNM) in patients with laryngeal, hypopharyngeal, or cervical esophageal squamous cell carcinoma is associated with unfavorable clinical outcomes, but cannot be reliably detected using computed tomography (CT)/magnetic resonance imaging (MRI). Therefore, we assessed the clinical utility of using (18)F-fluorodeoxyglucose (FDG) positron emission tomography (PET)/CT to identify CLNM in these patients. PATIENTS AND METHODS: A total of 62 patients were preoperatively evaluated using (18)F-FDG PET/CT and CT/MRI. Histopathologic analysis of the dissected neck tissues was used as the gold standard for assessing these imaging techniques. The diagnostic value of (18)F-FDG PET/CT for detecting CLNM was calculated and compared with CT/MRI. Univariate and multivariate analyses were utilized to determine the factors predictive of CLNM. RESULTS: Of the 62 patients in the study cohort, 12 (19%) had CLNM. Compared with histology, both (18)F-FDG PET/CT and CT/MRI demonstrated low sensitivity for detecting CLNM (58% vs 42%, respectively, P = 0.625). The specificities of (18)F-FDG PET/CT and CT/MRI for the detection of CLNM were 88% and 90%, respectively (P = 1.000). Univariate and multivariate analyses showed that clinical metastasis to any cervical lymph node was significantly associated with CLNM (P = 0.018). CONCLUSIONS: Neither (18)F-FDG PET/CT nor CT/MRI is a sensitive diagnostic imaging modality for detecting CLNM. Routine elective central compartment dissection or radiotherapy should be advocated for the treatment of these patients.	esophagus