crossing96/oncoscreening huggingface dataset:
Cell type-specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics.	Single-cell transcriptomics have revolutionized our understanding of the cell composition of tumors and allowed us to identify new subtypes of cells. Despite rapid technological advancements, single-cell analysis remains resource-intense hampering the scalability that is required to profile a sufficient number of samples for clinical associations. Therefore, more scalable approaches are needed to understand the contribution of individual cell types to the development and treatment response of solid tumors such as esophageal adenocarcinoma where comprehensive genomic studies have only led to a small number of targeted therapies. Due to the limited treatment options and late diagnosis, esophageal adenocarcinoma has a poor prognosis. Understanding the interaction between and dysfunction of individual cell populations provides an opportunity for the development of new interventions. In an attempt to address the technological and clinical needs, we developed a protocol for the separation of esophageal carcinoma tissue into leukocytes (CD45+), epithelial cells (EpCAM+), and fibroblasts (two out of PDGFRα, CD90, anti-fibroblast) by fluorescence-activated cell sorting and subsequent RNA sequencing. We confirm successful separation of the three cell populations by mapping their transcriptomic profiles to reference cell lineage expression data. Gene-level analysis further supports the isolation of individual cell populations with high expression of CD3, CD4, CD8, CD19, and CD20 for leukocytes, CDH1 and MUC1 for epithelial cells, and FAP, SMA, COL1A1, and COL3A1 for fibroblasts. As a proof of concept, we profiled tumor samples of nine patients and explored expression differences in the three cell populations between tumor and normal tissue. Interestingly, we found that angiogenesis-related genes were upregulated in fibroblasts isolated from tumors compared with normal tissue. Overall, we suggest our protocol as a complementary and more scalable approach compared with single-cell RNA sequencing to investigate associations between clinical parameters and transcriptomic alterations of specific cell populations in esophageal adenocarcinoma.	esophagus
Dietary factors and risk of mortality among patients with esophageal cancer: a systematic review.	BACKGROUND: The effects of dietary factors on prognosis of esophageal cancer remain unclear. This systematic review and meta-analysis aimed to assess the association between dietary intake and the risk of mortality among patients with esophageal cancer. METHODS: Six electronic databases (PubMed, Web of Science, OVID, ProQuest, CNKI and Wanfang) were searched for studies published up to Oct. 2019 that examined the association between dietary intake and all-cause mortality, esophageal cancer-specific mortality and esophageal cancer recurrence. The pooled hazard ratio (HR) with 95% confidence interval (CI) were derived by comparing the highest with the lowest categories of each dietary item and by using random effect models. RESULTS: A total of 15 cohort studies were included in this study and all reported pre-diagnosis dietary exposure; two focused on dietary folate, 12 on alcohol consumption and three on other dietary components (sugary beverages, phytochemicals and preserved vegetables). When comparing the highest with the lowest categories, dietary folate intake was associated with a reduced risk of esophageal cancer-specific mortality in patients with esophageal squamous cell carcinoma (HR: 0.41, 95% CI: 0.25-0.69), with low heterogeneity (I(2) = 0%, P = 0.788). When comparing the highest with the lowest categories of alcohol consumption, alcohol consumption was associated with an increased risk of all-cause mortality in patients with esophageal squamous cell carcinoma (HR: 1.29, 95% CI: 1.07-1.55; heterogeneity: I(2) = 53%, P = 0.030), but this increased risk was not significant in patients with esophageal adenocarcinoma (HR = 1.05, 95% CI: 0.84-1.32). CONCLUSIONS: This review with pre-diagnostic dietary exposure showed that dietary folate intake was associated with a reduced risk of mortality of esophageal squamous cell carcinoma, whereas alcohol consumption was associated with an increased risk. More studies are needed to investigate effect of dietary factors, especially post-diagnosis dietary consumption, on esophageal cancer prognosis.	esophagus
Case Control Study on Radioactive Stents Versus Conventional Stents for Inoperable Esophageal Squamous Cell Carcinoma.	PURPOSE: The purpose of this study was to compare the relative clinical efficacy of radioactive and normal stent insertion for the treatment of inoperable obstructive esophageal squamous cell carcinoma (OESCC). MATERIALS AND METHODS: Between January 2014 and December 2018, consecutive OESCC patients were treated via either radioactive or normal stent insertion. RESULTS: A total of 42 and 39 OESCC patients were treated via radioactive and normal stent insertion, respectively. These procedures were both technically and clinically successful in all patients. Massive hemorrhage was observed in 7 (16.7%) and 1 (2.6%) patients in radioactive and normal stent groups, respectively (P=0.080). Median stent patency durations were 175 and 136 days in radioactive and normal stent groups, respectively (P=0.004). Median overall survival were 187 and 145 days in the radioactive and normal stent groups, respectively (P=0.011). CONCLUSION: Relative to normal stent, radioactive stents showed a higher patency and overall survival in OESCC patients.	esophagus
Family History of Colorectal or Esophageal Cancer in Barrett's Esophagus and Potentially Explanatory Genetic Variants.	INTRODUCTION: We aimed to estimate the effects of a family history of colorectal cancer (CRC) or esophageal cancer on the risk of Barrett's esophagus (BE) and identify variants in cancer genes that may explain the association. METHODS: Men scheduled for screening colonoscopy were recruited to undergo upper endoscopy. Cases and noncases were screenees with and without BE, respectively. The effects of family histories on BE were estimated with logistic regression, adjusting for the potential confounders. We additionally recruited men recently diagnosed with BE by clinically indicated endoscopies. Banked germline DNA from cases of BE with ≥2 first-degree relatives (FDRs) with CRC and/or an FDR with esophageal cancer underwent next-generation sequencing using a panel of 275 cancer genes. RESULTS: Of the 822 men screened for CRC who underwent upper endoscopy, 70 were newly diagnosed with BE (8.5%). BE was associated with family histories of esophageal cancer (odds ratio = 2.63; 95% confidence interval = 1.07-6.47) and CRC in ≥2 vs 0 FDRs (odds ratio = 3.73; 95% confidence interval = 0.898-15.4). DNA analysis of subjects with both BE and a family history of cancer identified one or more germline variants of interest in genes associated with cancer predisposition in 10 of 14 subjects, including the same novel variant in EPHA5 in 2 unrelated individuals. DISCUSSION: We found an increased risk for BE associated with a family history of esophageal cancer or CRC. Although analysis of germline DNA yielded no clinically actionable findings, discovery of the same EPHA5 variant of uncertain significance in 2 of 14 cases merits additional investigation.	esophagus
Time to diagnosis of symptomatic gastric and oesophageal cancer in the Netherlands: Where is the room for improvement?	BACKGROUND: An efficient diagnostic pathway and early stage diagnosis for cancer patients is widely pursued. This study aims to chart the duration of the diagnostic pathway for patients with symptomatic oesophageal and gastric cancer, to identify factors associated with long duration and to assess the association of duration with tumour stage at diagnosis. METHODS: This was a retrospective cohort study, using electronic health records of six routine primary care databases covering about 640,000 patients, partly linked to the Netherlands Cancer Registry. Symptomatic patients with oesophageal and gastric cancer (2010-2015) that presented in primary care were included. Duration of four diagnostic intervals was determined: patient interval; first symptoms to primary care consultation, primary care interval; consultation to referral, secondary care interval; referral to diagnosis, and the diagnostic interval; consultation to diagnosis. Characteristics associated with 'long duration' (≥P75 duration) were assessed using log-binomial regression. Median durations were stratified for tumour stages. RESULTS: Among 312 symptomatic patients with upper gastrointestinal cancer, median durations were: patient interval: 29 days (interquartile interval 15-73), primary care interval: 12 days (interquartile interval 1-43), secondary care interval: 13 days (interquartile interval 6-29) and diagnostic interval: 31 days (11-74). Patient interval duration was comparable for patients with and without alarm symptoms. Absence of cancer-specific alarm symptoms was associated with 'long duration' of primary care interval and secondary care interval: relative risk 5.0 (95% confidence interval 2.7-9.1) and 2.1 (95% confidence interval 1.3-3.7), respectively. Median diagnostic interval duration for local stage disease was 51 days (interquartile interval 13-135) versus 27 days (interquartile interval 11-71) for advanced stage (p = 0.07). CONCLUSION: In the diagnostic pathway of upper gastrointestinal cancers, the longest interval is the patient interval. Reducing time to diagnosis may be achieved by improving patients' awareness of alarm symptoms and by diagnostic strategies which better identify cancer patients despite low suspicion.	esophagus
Definitive chemoradiotherapy for squamous cell carcinoma of the esophagus: outcomes for borderline-resectable disease.	Definitive chemoradiotherapy (dCRT) is the standard treatment for unresectable esophageal cancer. Induction chemotherapy has been actively investigated for borderline-resectable and unresectable disease, but the superiority over dCRT has yet to be confirmed. The purpose of this study was to evaluate the outcome of dCRT with special interest in borderline-resectable disease. Patients with esophageal cancer treated with dCRT between January 2004 and November 2016 were included in this retrospective analysis. Chemotherapy consisted of two cycles of cisplatin (70-75 mg/m2) on day 1 and 5-fluorouracil (700-1000 mg/m2 per day) on days 1-4 or low-dose cisplatin (10 mg/m2 per day) and 5-fluorouracil (175 mg/m2 per day) for 20 days. Radiotherapy was given with a daily fraction of 1.8-2 Gy to a total dose of 50-70 Gy. A total of 104 patients were included: 34 were resectable, 35 were borderline-resectable and 35 were unresectable. Complete response was achieved in 44 patients (42%). Eighteen patients (17%) suffered Grade 2 or greater cardiopulmonary toxicity and seven patients (7%) suffered Grade 3 cardiopulmonary toxicity. At the time of this analysis, 59 patients were dead and 45 were censored. The 3-year overall survival proportions for resectable, borderline-resectable and unresectable patients were 64%, 46% and 21%, respectively. The overall survival for borderline-resectable patients with complete response and noncomplete response was significantly different (P < 0.001), with 3-year survival of 70% and 8%, respectively. The overall survival for complete response patients with borderline-resectable disease was encouraging. Further investigation to find a subgroup fit for esophagus-preserving treatment is warranted.	esophagus
The Design of and Rationale for the Effect of Perioperative Inhaled Tiotropium for Patients with Chronic Obstructive Pulmonary Disease in Esophageal Cancer Surgery (EPITOPE): an Open-Label, Randomized, Parallel-Group Study.	INTRODUCTION: Pneumonia is one of the most frequently occurring complications after esophagectomy and is associated with increased operative mortality. Chronic obstructive pulmonary disease (COPD) is known to be a risk factor for pulmonary complications and operative mortality. However, in COPD patients preparing for esophagectomy, preventive measures against postoperative pneumonia have not yet been discovered. In this study, we evaluate the effect of perioperative inhaled tiotropium, a long-acting, antimuscarinic bronchodilator used in the management of COPD, on patients with COPD who undergo esophageal cancer surgery. METHODS/DESIGN: This study investigates the effect of perioperative inhaled tiotropium on patients with COPD who undergo esophagectomy. It is an open-label, randomized controlled trial conducted in a single center (EPITOPE study). A total of 32 enrolled patients are randomly assigned in a 1:1 ratio to either conventional management or inhalation of tiotropium in addition to the conventional management. Patients included in the intervention group receive tiotropium Respimat 5 μg (two inhalations of 2.5 μg) for at least 2 weeks before the esophagectomy. Following the esophagectomy, tiotropium is re-delivered, starting as early as possible and continuing until the postoperative evaluation (between 30 and 44 days after the operation). The primary outcome is the incidence of pneumonia within 30 days after esophagectomy. Secondary outcomes are the incidence of cardiovascular complications within 30 days after esophagectomy, the incidence of any postoperative complications within 30 days after esophagectomy, pulmonary function (preintervention, preoperative, and postoperative), walking distance in the incremental shuttle walking test (preintervention, preoperative, and postoperative), the incidence of adverse events, and mortality within 30 days after esophagectomy. DISCUSSION: The EPITOPE study is the first pilot study on the effects of perioperative inhaled tiotropium on patients with COPD undergoing esophagectomy. After completing this study, we will plan a multicenter RCT with the appropriate outcomes in the future.	esophagus
Holographic image-guided thoracoscopic surgery: possibility of usefulness for esophageal cancer patients with abnormal artery.	BACKGROUND: With the recent improvement of medical image analysis technology, three-dimensional (3D) holograms technology is beginning to be used as intraoperative image support. CASE PRESENTATION: We used a wearable holographic computer during thoracoscopic esophagectomy in a 70-year-old man with esophageal cancer. During lymph node dissection around the right recurrent laryngeal nerve, abnormal blood vessels were observed beside the right subclavian artery (RSA). As a result of confirming the anatomical variation of the right vertebral artery (RVA) using the 3D holograms, it was possible to understand that the RVA branched from a low position on the RSA. CONCLUSIONS: Holographic image-guided thoracoscopic esophagectomy using wearable holographic computer provided better spatial recognition of vascular variation and safe lymph node dissection.	esophagus
Using estimated probability of pre-diagnosis behavior as a predictor of cancer survival time: an example in esophageal cancer.	BACKGROUND: Information on the associations between pre-diagnosis health behavior and post-diagnosis survival time in esophageal cancer could assist in planning health services but can be difficult to obtain using established study designs. We postulated that, with a large data set, using estimated probability for a behavior as a predictor of survival times could provide useful insight as to the impact of actual behavior. METHODS: Data from a national health survey and logistic regression were used to calculate the probability of selected health behaviors from participant's demographic characteristics for each esophageal cancer case within a large cancer registry data base. The associations between survival time and the probability of the health behaviors were investigated using Cox regression. RESULTS: Observed associations include: a 0.1 increase in the probability of smoking 1 year prior to diagnosis was detrimental to survival (Hazard Ratio (HR) 1.21, 95% CI 1.19,1.23); a 0.1 increase in the probability of hazardous alcohol consumption 10 years prior to diagnosis was associated with decreased survival in squamous cell cancer (HR 1.29, 95% CI 1.07, 1.56) but not adenocarcinoma (HR 1.08, 95% CI 0.94,1.25); a 0.1 increase in the probability of physical activity outside the workplace is protective (HR 0.83, 95% CI 0.81,0.84). CONCLUSIONS: We conclude that probability for health behavior estimated from demographic characteristics can provide an initial assessment of the association between pre-diagnosis health behavior and post-diagnosis health outcomes, allowing some sharing of information across otherwise unrelated data collections.	esophagus
Risk factors for serious adverse events associated with multiband mucosectomy in Barrett's esophagus: an international multicenter analysis of 3827 endoscopic resection procedures.	BACKGROUND AND AIMS: Multiband mucosectomy (MBM) is a widely used technique for the treatment of Barrett's esophagus (BE). However, large multicenter studies enabling a generalizable estimation of the risk of serious adverse events, such as perforation and postprocedural bleeding, are lacking. The aim of this study was to estimate the rate of, and risk factors for, serious adverse events associated with MBM. METHODS: In this retrospective analysis, consecutive patients who underwent MBM for treatment of BE in 14 tertiary referral centers in Europe, the United States, Canada, and Australia were included. Primary outcomes were perforation and postprocedural bleeding rate. Potential risk factors were identified by logistic regression. RESULTS: Between 2001 and 2016, a total of 3827 MBM procedures were performed in 2447 patients (84% male, mean age 66 years, median BE length C2M4). Perforation occurred in 17 procedures (0.4%; 95% confidence interval [CI], 0.3-0.7), of which 15 could be treated endoscopically or conservatively. Female gender was an independent risk factor for perforation (odds ratio [OR], 2.77; 95% CI, 1.02-7.57; P = .05). Postprocedural bleeding occurred after 35 procedures (0.9%; 95% CI, 0.6-1.3). The number of resections (OR, 1.15; 95% CI, 1.06-1.25; P < .001) was significantly associated with postprocedural bleeding. CONCLUSION: The results of this study show that MBM for BE is safe with a low risk of serious adverse events. In addition, most of the adverse events could be managed endoscopically or conservatively. The number of resections was an independent risk factor for postprocedural bleeding.	esophagus
Esophageal epithelium modeling based on globally coupled map: an approach toward precancerous lesion diagnosis.	Esophageal squamous cell carcinoma is the most predominant malignancy of the esophagus. Its histological precursors (dysplasia) emerge in the esophageal epithelium that their progression into the underlying layers leads to cancer. The epithelium is the origin of many solid cancers and, accordingly, the focus of numerous computational models. In this work, we proposed a framework to establish a two-dimensional, globally coupled map to model the epithelium dynamics. The model aims at diagnosing the early stage of dysplasia based on microscopic images of endoscopic biopsies. We used the logistic map as a black-box model for the epithelial cells. By relating between the structure and dynamic of the epithelium, we defined the coupling function and proposed a case-dependent model in which the parameters were adjusted based on fractal geometry of each pathological image. Thus, by assigning different attractors to the cells' behavior, the lattice dynamic was investigated by the Lyapunov exponent. The decreasing pattern of Lyapunov exponent variations across the epithelium thickness had reasonable performance in diagnosing the normal specimens from the low-grade dysplasia ones. The results showed that there could be a direct relationship between the structural complexity of this system and its uncertainty of dynamics. Graphical abstract The modeling process of the esophageal epithelium to classify the experimental data at normal and LGD stages.	esophagus
New insights into the functions of Cox-2 in skin and esophageal malignancies.	Understanding the cellular and molecular mechanisms of tumor initiation and progression for each cancer type is central to making improvements in both prevention and therapy. Identifying the cancer cells of origin and the necessary and sufficient mechanisms of transformation and progression provide opportunities for improved specific clinical interventions. In the last few decades, advanced genetic manipulation techniques have facilitated rapid progress in defining the etiologies of cancers and their cells of origin. Recent studies driven by various groups have provided experimental evidence indicating the cellular origins for each type of skin and esophageal cancer and have identified underlying mechanisms that stem/progenitor cells use to initiate tumor development. Specifically, cyclooxygenase-2 (Cox-2) is associated with tumor initiation and progression in many cancer types. Recent studies provide data demonstrating the roles of Cox-2 in skin and esophageal malignancies, especially in squamous cell carcinomas (SCCs) occurring in both sites. Here, we review experimental evidence aiming to define the origins of skin and esophageal cancers and discuss how Cox-2 contributes to tumorigenesis and differentiation.	esophagus
Effect of Muscle Mass Loss After Esophagectomy on Prognosis of Oesophageal Cancer.	BACKGROUND/AIM: To assess the prognostic effect of muscle loss after esophagectomy and before discharge. PATIENTS AND METHODS: This study retrospectively analysed 159 consecutive patients with oesophageal and gastroesophageal junction cancer who underwent esophagectomy between August 2011 and October 2015. Body composition was evaluated one week before surgery and at discharge using a bioelectrical impedance analyser. RESULTS: The median rate of muscle mass loss (RMML) was 4.38% (range=-3.3 to +18.8). Patients with increased RMML had significantly poorer outcomes of overall survival than those with decreased RMML (p=0.015). On multivariate analysis, RMML [≥4.38, hazard ratio (HR)=2.033, 95% confidence interval (CI)=1.018-5.924, p=0.044) and pathological tumour depth (≥2, HR=3.099, 95%CI=1.339-7.172, p=0.008) were selected as independent prognostic factors. CONCLUSION: RMML after esophagectomy is indicative of poor prognosis in patients with esophageal cancer.	esophagus
Role of FOXO3A in Trastuzumab Combination Chemotherapy in Esophageal Squamous Cell Carcinoma.	BACKGROUND/AIM: Targeting of the human epidermal growth factor receptor 2 (HER2) is suggested to be beneficial for esophageal squamous cell carcinoma (ESCC) patients with HER2 amplification. In this study, we evaluated the effects of combination chemotherapy with HER2-targeted drug trastuzumab in ESCC cells and examined the underlying mechanism contributing to these effects. MATERIALS AND METHODS: HER2 expression was verified, and the efficacy of chemotherapy with and without trastuzumab was investigated in vitro and in vivo. RESULTS: The combination of trastuzumab and a combined-modality therapy stimulated the PI3K/Akt pathway in ESCC cells overexpressing HER2. Trastuzumab treatment resulted in the intranuclear accumulation of FOXO3A in ESCC xenografts overexpressing HER2. The combination of trastuzumab and a combined-modality therapy enhanced antitumor effects in HER2-overexpressing ESCC xenografts. CONCLUSION: FOXO3A plays an important role in mediating the effects of trastuzumab, and combination chemotherapy may be a promising treatment for patients with HER2-overexpressing ESCC.	esophagus