crossing96/oncoscreening huggingface dataset:
Prediction models for venous thromboembolism in ambulatory adults with pancreatic and gastro-oesophageal cancer: protocol for systematic review and meta-analysis.	INTRODUCTION: Venous thromboembolism (VTE) is a common complication of cancer. Pancreatic and gastro-oesophageal cancers are among malignancies that have the highest rates of VTE occurrence. VTE can increase cancer-related morbidity and mortality and disrupt cancer treatment. The risk of VTE can be managed with measures such as using anticoagulant drugs, although the risk of bleeding may be an impeding factor. Therefore, a VTE risk assessment should be performed before the start of anticoagulation in individual patients. Several prediction models have been published, but most of them have low sensitivity and unknown clinical applicability in pancreatic or gastro-oesphageal cancers. We intend to do this systematic review to identify all applicable published predictive models and compare their performance in those types of cancer. METHODS AND ANALYSIS: All studies in which a prediction model for VTE have been developed, validated or compared using adult ambulatory patients with pancreatic or gastro-oesphageal cancers will be identified and the reported predictive performance indicators will be extracted. Full text peer-reviewed journal articles of observational or experimental studies published in English will be included. Five databases (Medline, EMBASE, Web of Science, CINAHL and Cochrane) will be searched. Two reviewers will independently undertake each of the phases of screening, data extraction and risk of bias assessment. The quality of the selected studies will be assessed using Prediction model Risk Of Bias Assessment Tool. The results from the review will be used for a narrative information synthesis, and if the same models have been validated in multiple studies, meta-analyses will be done to pool the predictive performance measures. ETHICS AND DISSEMINATION: There is no need for ethics approval because the review will use previously peer-reviewed articles. The results will be published. PROSPERO REGISTRATION NUMBER: CRD42021253887.	esophagus
The Relationship between MACC1/c-Met/Cyclin D1 Axis Expression and Prognosis in ESCC.	BACKGROUND: Esophageal cancer is one of the most common malignant tumors of the digestive system, with high incidence and mortality. METHODS: Immunohistochemical method was used to detect the expression of MACC1, c-Met, and cyclin D1 in ESCC and its adjacent tissues. Statistical analysis was done by SPSS 23.0. RESULTS: The high expression of MACC1 and cyclin D1 was significantly correlated with tumor size. High c-Met expression was associated with patient ethnicity. MACC1 expression was positively correlated with both c-Met and cyclin D1. c-Met expression was also positively correlated with cyclin D1. Patients with high expression of MACC1 and c-Met had worse OS; patients with high c-Met expression also had worse PFS. CONCLUSION: MACC1, c-Met, and cyclin D1 proteins are closely related to the occurrence and development of esophageal squamous cell carcinoma. MACC1 may affect the prognosis of ESCC by regulating the expression of the c-Met/cyclin D1 axis.	esophagus
Prognostic significance of platelet-to-albumin ratio in patients with esophageal squamous cell carcinoma receiving definitive radiotherapy.	Accumulating evidence indicates that inflammation and nutrition status are associated with clinical outcomes in patients with various malignancies. This study aimed to evaluate the prognostic significance of the pretreatment platelet to albumin ratio (PAR) in esophageal squamous cell carcinoma (ESCC) patients undergoing definitive radiotherapy. A total of 470 patients who underwent definitive radiotherapy with or without chemotherapy were enrolled. The optimal cut-off values of PAR and other indicators were determined by the X-tile. The Kaplan-Meier method, multivariate analyses Cox regression were conducted to identify the association between those indicators and the survival outcomes. The median follow-up time was 23.5 months. The optimal cut-off value of PAR was 5.7 × 10(9) and patients were stratified as the low PAR group and the high PAR group. In the univariate analysis, a low overall survival rate was significantly associated with T stage (P = 0.005), TNM stage (P < 0.001), Adjuvant chemotherapy (P = 0.007), neutrophil to lymphocyte ratio (NLR) (P = 0.006), platelet to lymphocyte ratio (P < 0.001), systemic immune-inflammation index (P < 0.001), prognostic nutritional index (P < 0.001) and platelet to albumin ratio (PAR) (P < 0.001). Patients with high PAR were associated with poorer OS and PFS than patients with low PAR. On multivariate analysis, TNM stage (P = 0.001), adjuvant chemotherapy (P < 0.001), and PAR (P = 0.033) were independent prognostic factors in ESCC treated with definitive radiotherapy. PAR is a novel, convenient, and inexpensive prognostic indicator for patients with ESCC undergoing definitive radiotherapy. Future validation from prospective larger-scale studies is warranted.	esophagus
Establishment of prognostic models for adenocarcinoma of oesophagogastric junction patients with neoadjuvant chemoradiotherapy: a real-world study.	BACKGROUND: Multimodal therapies based on surgical resection have been recommended for the treatment of adenocarcinoma of the oesophagogastric junction (AEG). We aimed to evaluate prognostic factors in AEG patients receiving neoadjuvant chemoradiotherapy and to build predictive models. METHODS: T3 - T4N + M0 AEG patients with resectable Siewert type II/III tumours were enrolled in this study. All patients underwent neoadjuvant chemoradiation, followed by radical surgery or systemic therapy according to clinical response. Survival analysis was performed using the Kaplan-Meier method; multivariate analysis using the Cox proportional hazards method was also conducted. The Harrell concordance index (C-index) was used to test the prognostic value of models involving prognostic factors, and consistency between actual and predicted survival rates was evaluated by calibration curves. RESULTS: From February 2009 to February 2018, 79 patients were treated with neoadjuvant chemoradiotherapy; 60 patients of them underwent radical surgery. The R0 resection rate was 98.3%, and 46.7% of patients achieved a major pathologic response (MPR), namely, a residual tumour issue less than 10%. The 5-year overall survival (OS) rate was 63%, and the 5-year progression-free survival (PFS) rate was 48%. The incidence of grade 3 complications was 21.5%, and no grade 4 complications were reported. According to the results of univariate and multivariate analyses, we included the neutrophil-lymphocyte ratio (NLR), prognostic nutrition index (PNI), eosinophilic granulocyte (EOS) and postoperative pathologic stage in nomogram analysis to establish prediction models for OS and PFS; the C-index of each model was 0.814 and 0.722, respectively. Both the C-index and calibration curves generated to validate consistency between the actual and predicted survival indicated that the models were well calibrated and of good predictive value. CONCLUSIONS: AEG patients achieved favourable downstaging and pathologic response after neoadjuvant chemoradiation, with acceptable adverse effects. Inflammation-based and nutrition-related factors and postoperative pathologic stage had a significant influence on OS and PFS, and the predictive value was verified through prognostic models.	esophagus
Circular RNA hsa_circ_0000277 promotes tumor progression and DDP resistance in esophageal squamous cell carcinoma.	BACKGROUND: Circular RNAs (circRNAs) are well-known regulators of cancer progression and chemoresistance in various types of cancers. This study was performed to investigate the function of hsa_circ_0000277 in esophageal squamous cell carcinoma (ESCC). METHODS: RNA levels were analyzed via the reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Cell Counting Kit-8 (CCK-8) assay was applied to determine cell proliferation and half maximal inhibitory concentration (IC50) of cisplatin (DDP). Colony formation ability was evaluated by colony formation assay. Cell cycle and apoptosis were measured using flow cytometry. RNA immunoprecipitation (RIP), pull-down assay and dual-luciferase reporter assays were performed for target interaction analysis. The protein levels were determined through western blot. Xenograft models were established for researching hsa_circ_0000277 function in vivo. RESULTS: Hsa_circ_0000277 expression was increased in ESCC cells and tissues, and it had important clinical significance. Downregulation of hsa_circ_0000277 repressed ESCC cell proliferation, colony formation, cell cycle, and DDP resistance. Hsa_circ_0000277 acted as a microRNA-873-5p (miR-873-5p) sponge and Sry-related high-mobility group box 4 (SOX4) was validated as a target of miR-873-5p. Moreover, hsa_circ_0000277/miR-873-5p axis and miR-873-5p/SOX4 axis regulated ESCC cell progression and DDP resistance. Hsa_circ_0000277/miR-873-5p axis activated SOX4/Wnt/β-catenin signaling pathway. Hsa_circ_0000277 facilitated tumorigenesis and DDP resistance by miR-873-5p/SOX4 axis in vivo. CONCLUSION: These findings unraveled that hsa_circ_0000277 promoted ESCC progression and DDP resistance via miR-873-5p/SOX4/Wnt/β-catenin axis, showing a specific molecular mechanism of carcinogenesis and chemoresistance in ESCC.	esophagus
The mutational landscape of upper gastrointestinal adenocarcinomas- A study of similarities and differences.	PURPOSE: The gastrointestinal tract is home to a wide variety of neoplasms. Gastrointestinal adenocarcinomas display distinct prognostic patterns. With the advent of next generation sequencing, attempts are being made to delineate distinct molecular characteristics of these adenocarcinomas from adjoining anatomical sites. METHODS: Thirty-seven cases of upper gastrointestinal adenocarcinomas including those of the esophagus, gastroesophageal junction, stomach, small intestine and gallbladder were retrieved. Next generation sequencing data consisting of base substitutions, copy number variations, indels and rearrangements, in 324 genes, were analyzed for recurrent genetic abnormalities. Statistical analysis was performed using IBM SPSS25 and SAS software. RESULTS: Genetic alterations were found in 181 genes. APC mutations were found in 50% of the esophageal adenocarcinomas, 5% of the gastric adenocarcinomas and 33.3% of the small intestinal adenocarcinomas (p = 0.04). PIK3 gene family mutations were found in 10% of the gastric adenocarcinomas, 66% of the gall bladder adenocarcinomas and 66% of the small intestinal adenocarcinomas (p = 0.002). The mutations were found exclusively in the PIK3 class 1 family. TP53 mutations were more common in tumors with intact DNA mismatch repair protein expression as assessed by immunohistochemistry (p = 0.042). CONCLUSION: In this study, APC gene mutations were found to be more frequent in esophageal and small intestinal adenocarcinomas than previously reported. PIK3 class 1 gene family mutations were found to be more frequent in gallbladder and small intestinal adenocarcinomas. An inverse relationship was found between TP53 mutations and loss of DNA mismatch repair protein expression.	esophagus
Clinicopathological features and prognosis of gastric tube cancer after esophagectomy for esophageal cancer: a nationwide study in Japan.	BACKGROUND: Survivors of esophageal cancer post-esophagectomy may sometimes develop gastric tube cancer (GTC). However, its clinical characteristics have not been elucidated. We conducted a retrospective nationwide survey of GTCs to clarify them. METHODS: A questionnaire on GTCs was sent by e-mail and mail to 116 institutions certified by the Japan Esophageal Society. A total of 608 GTC cases diagnosed and treated between 2001 and 2015 were registered from 62 institutions. RESULTS: The median age at diagnosis was 71 years, with 88.9% being diagnosed with stage I. Sixty percent of GTC cases were in the anal third of the gastric tube and 79.7% were differentiated adenocarcinomas. The median interval between esophagectomy and GTC diagnosis was 6 years, with approximately 25% of patients being diagnosed more than 10 years later. The 5-year overall survivals (5-OSs) after endoscopic and surgical treatments for GTC were 75.9% and 52.7%, respectively. Patients whose GTC was diagnosed without symptoms or by regular follow-up examination showed better 5-OSs compared to others (69.7% vs. 41.2%, p < 0.0001; and 71.4% vs. 41.8%, p < 0.0001, respectively). The prognosis of GTC cases diagnosed within 2 years of the preceding upper gastrointestinal endoscopy (UGI) was better than that in cases diagnosed longer than 2 years (5-OS: 73.4% vs. 48.8%, p < 0.05). CONCLUSION: This nationwide survey revealed the clinicopathological features of GTCs for the first time. Early detection is important in improving the prognosis of GTC, and it is recommended that UGI endoscopy be continued every 2 years for 10 or more years after esophagectomy.	esophagus
Oncological outcomes of squamous cell carcinoma of the cervical esophagus treated with definitive (chemo-)radiotherapy: a systematic review and meta-analysis.	PURPOSE: To determine the oncological outcomes of cervical esophageal squamous cell carcinoma (CESCC) treated with definitive chemoradiotherapy (CRT). METHODS: A systematic review and meta-analysis was performed according to the PRISMA guidelines. RESULTS: A total of 1222 patients (median age: 63.0 years, 95% CI 61.0-65.0) were included from 22 studies. The median follow-up time was 34.0 months (n = 1181, 95% CI 26.4-36.0). Estimated pooled OS rates (95% CI) at 1, 3, and 5 years were 77.9% (73.9-82.2), 48.4% (43.2-54.3), and 35.3% (29.7-41.9), respectively. The median OS (95% CI) was 33.4 months (25.8-42.2). Estimated pooled PFS rates (n = 595; 95% CI) at 1, 3, and 5 years were 64.1% (57.9-71.0), 38.0% (33.3-45.5), and 29.8% (23.9-37.1), respectively. The median PFS (95% CI) was 19.8 months (14.9-26.6). CONCLUSIONS: Definitive CRT is a valuable first-line treatment for the management of CESCC. Further studies should focus on survival predictors able to define stage-based clinical guidelines.	esophagus
Association between body mass index and oesophageal cancer mortality: a pooled analysis of prospective cohort studies with >800 000 individuals in the Asia Cohort Consortium.	BACKGROUND: The association between body mass index (BMI) and oesophageal cancer (OC) has been consistently negative among Asians, whereas different associations based on histological OC subtypes have been observed in Europeans and North Americans. We examined the association between BMI and OC mortality in the Asia Cohort Consortium. METHODS: We performed a pooled analysis to evaluate the association between BMI and OC mortality among 842 630 Asians from 18 cohort studies. Cox regression models were used to estimate hazard ratios (HRs) and 95% CIs. RESULTS: A wide J-shaped association between BMI and overall OC mortality was observed. The OC mortality risk was increased for underweight (BMI <18.5 kg/m2: HR = 2.20, 95% CI 1.80-2.70) and extreme obesity (BMI ≥35 kg/m2: HR = 4.38, 95% CI 2.25-8.52) relative to the reference BMI (23-25 kg/m2). This association pattern was confirmed by several alternative analyses based on OC incidence and meta-analysis. A similar wide J-shaped association was observed in oesophageal squamous cell carcinoma (OSCC). Smoking and alcohol synergistically increased the OC mortality risk in underweight participants (HR = 6.96, 95% CI 4.54-10.67) relative to that in reference BMI participants not exposed to smoking and alcohol. CONCLUSION: Extreme obesity and being underweight were associated with an OC mortality risk among Asians. OC mortality and BMI formed a wide J-shaped association mirrored by OSCC mortality. Although the effect of BMI on OSCC and oesophageal adenocarcinoma mortality can be different in Asians, further research based on a large case-control study is recommended.	esophagus
A hybrid deep learning model for forecasting lymphocyte depletion during radiation therapy.	PURPOSE: Recent studies have shown that severe depletion of the absolute lymphocyte count (ALC) induced by radiation therapy (RT) has been associated with poor overall survival of patients with many solid tumors. In this paper, we aimed to predict radiation-induced lymphocyte depletion in esophageal cancer patients during the course of RT based on patient characteristics and dosimetric features. METHODS: We proposed a hybrid deep learning model in a stacked structure to predict a trend toward ALC depletion based on the clinical information before or at the early stages of RT treatment. The proposed model consisted of four channels, one channel based on long short-term memory (LSTM) network and three channels based on neural networks, to process four categories of features followed by a dense layer to integrate the outputs of four channels and predict the weekly ALC values. Moreover, a discriminative kernel was developed to extract temporal features and assign different weights to each part of the input sequence that enabled the model to focus on the most relevant parts. The proposed model was trained and tested on a dataset of 860 esophageal cancer patients who received concurrent chemoradiotherapy. RESULTS: The performance of the proposed model was evaluated based on several important prediction metrics and compared to other commonly used prediction models. The results showed that the proposed model outperformed off-the-shelf prediction methods with at least a 30% reduction in the mean squared error (MSE) of weekly ALC predictions based on pretreatment data. Moreover, using an extended model based on augmented first-week treatment, data reduced the MSE of predictions by 70% compared to the model based on the pretreatment data. CONCLUSIONS: In conclusion, our model performed well in predicting radiation-induced lymphocyte depletion for RT treatment planning. The ability to predict ALC will enable physicians to evaluate individual RT treatment plans for lymphopenia risk and to identify patients at high risk who would benefit from modified treatment approaches.	esophagus
PD-1 blockade enhances chemotherapy toxicity in oesophageal adenocarcinoma.	Chemotherapy upregulates immune checkpoint (IC) expression on the surface of tumour cells and IC-intrinsic signalling confers a survival advantage against chemotherapy in several cancer-types including oesophageal adenocarcinoma (OAC). However, the signalling pathways mediating chemotherapy-induced IC upregulation and the mechanisms employed by ICs to protect OAC cells against chemotherapy remain unknown. Longitudinal profiling revealed that FLOT-induced IC upregulation on OE33 OAC cells was sustained for up to 3 weeks post-treatment, returning to baseline upon complete tumour cell recovery. Pro-survival MEK signalling mediated FLOT-induced upregulation of PD-L1, TIM-3, LAG-3 and A2aR on OAC cells promoting a more immune-resistant phenotype. Single agent PD-1, PD-L1 and A2aR blockade decreased OAC cell viability, proliferation and mediated apoptosis. Mechanistic insights demonstrated that blockade of the PD-1 axis decreased stem-like marker ALDH and expression of DNA repair genes. Importantly, combining single agent PD-1, PD-L1 and A2aR blockade with FLOT enhanced cytotoxicity in OAC cells. These findings reveal novel mechanistic insights into the immune-independent functions of IC-intrinsic signalling in OAC cells with important clinical implications for boosting the efficacy of the first-line FLOT chemotherapy regimen in OAC in combination with ICB, to not only boost anti-tumour immunity but also to suppress IC-mediated promotion of key hallmarks of cancer that drive tumour progression.	esophagus
The Hu antigen R/interferon-β axis modulates sensitivity of esophageal squamous cancer cells to cisplatin.	The incidence rate of esophageal squamous cell carcinoma (ESCC) has risen significantly in recent years. RNA binding protein (RBP) has been attracting increased attention in the treatment of ESCC. Therefore, the primary aim of this study was to explore the roles of the RBP Hu antigen R (HuR) in ESCC. The mRNA levels were detected via reverse transcription-quantitative PCR, while the expression levels of protein were evaluated using western blotting. Cell proliferation was estimated by cell counting kit-8 assay and colony formation assay. Flow cytometry was applied to measure cell apoptosis. Luciferase assay and RIP assay were applied to verify whether interferon-β (IFN-β) was targeted by HuR. The results unambiguously demonstrated that HuR was upregulated in ESCC. Overexpression of HuR alleviated chemosensitivity to cisplatin in ESCC cells, as evidenced by increased cell proliferation and decreased apoptosis. Moreover, IFN-β was found to be a target of HuR and downregulated in ESCC cells. And overexpression of IFN-β abrogated the effects of HuR on cisplatin-sensitivity of ESCC cells. Taken together, these findings suggested that HuR may alleviate the chemosensitivity of ESCC cells to cisplatin via binding to IFN-β. Therefore, the HuR/IFN-β axis may be a novel biomarker for improving the chemosensitivity of ESCC.	esophagus
Totally robotic enucleation of a mid-esophageal leiomyoma.	Enucleation of an esophageal leiomyoma is the treatment of choice in symptomatic patients. Several open or minimally invasive approaches have been shown to be safe and effective. Robotic approaches allow for delicate and precise dissection with improved three-dimensional visualization. The robotic operative technique for enucleation has not been well described. In this context, we present the case of a 53-year-old obese man struggling with dysphagia and odynophagia due to a mid-esophageal leiomyoma. In the case presentation, we review the preoperative workup with high-quality images, robotic port placement, equipment needed, intraoperative conduct, and postoperative course. We provide a step-by-step video tutorial encompassing the preoperative workup, operative steps, tips and tricks, and postoperative course using a totally robotic enucleation of a 7-cm mid-esophageal leiomyoma. This case presentation can serve as a comprehensive teaching case for trainees and a high-quality example of the conduct of the operation for practicing surgeons, including some tips and tricks for optimal results. We also highlight that an assistant port is not required.	esophagus