crossing96/oncoscreening huggingface dataset:
A Patient-Derived Orthotopic Xenograft Model of Gastroesophageal-Junction Adenocarcinoma Translated to the Clinic by Tumor-Targeting Fluorescent Antibodies to Carcinoembryonic-Antigen-Related Cell-Adhesion Molecules.	BACKGROUND/AIM: During surgical resection of gastroesophageal-junction (GEJ) adenocarcinoma, the margin status is often difficult to visualize resulting in high recurrence rates. The aim of the present study was to develop a labelling technique that would allow improved visualization of GEJ tumor margins for surgeons to reduce recurrence rates in a patient-like model. MATERIALS AND METHODS: A patient GEJ tumor was obtained from an endoscopic biopsy and implanted subcutaneously in a nude mouse. A patient-derived orthotopic xenograft (PDOX) model was established by implanting tumor fragments grown from a subcutaneous model to the cardia of the stomach of nude mice. CC1/3/5-SAB, an antibody to carcinoembryonic-antigen-related cell-adhesion molecules, was conjugated with infrared dye IRDye800 to create SAB-IR800. Forty-eight hours after i.v. injection of SAB-IR800, GEJ-PDOX mice were imaged. RESULTS: Fluorescence imaging with SAB-IR800 brightly visualized the GEJ adenocarcinoma demonstrating specific targeting. In the PDOX model, injection of SAB-IR800 (50 μg) resulted in a tumor to background ratio of 1.78 at 48 hours and 1.86 at 72 hours. CONCLUSION: PDOX models of GEJ tumors can be established from patients by endoscopic biopsy without undergoing surgical resection. GEJ PDOX models should be useful for developing novel diagnostics and therapeutics for this recalcitrant disease.	esophagus
SNORA42 promotes oesophageal squamous cell carcinoma development through triggering the DHX9/p65 axis.	Small nucleolar RNAs (snoRNAs) are an important group of non-coding RNAs that have been reported to play a key role in the occurrence and development of various cancers. Here we demonstrate that Small nucleolar RNA 42 (SNORA42) enhanced the proliferation and migration of Oesophageal squamous carcinoma cells (ESCC) via the DHX9/p65 axis. Our results found that SNORA42 was significantly upregulated in ESCC cell lines, tissues and serum of ESCC patients. The high expression level of SNORA42 was positively correlated with malignant characteristics and over survival probability of patients with ESCC. Through in vitro and in vivo approaches, we demonstrated that knockdown of SNORA42 significantly impeded ESCC growth and metastasis whereas overexpression of SNORA42 got opposite effects. Mechanically, SNORA42 promoted DHX9 expression by attenuating DHX9 transports into the cytoplasm, to protect DHX9 from being ubiquitinated and degraded. From the KEGG analysis of Next-Generation Sequencing, the NF-κB pathway was one of the most regulated pathways by SNORA42. SNORA42 enhanced phosphorylation of p65 and this effect could be reversed by NF-κB inhibitor, BAY11-7082. Moreover, SNORA42 activated NF-κB signaling through promoting the transcriptional co-activator DHX9 interacted with p-p65, inducing NF-κB downstream gene expression. In summary, our study highlights the potential of SNORA42 is up-regulated in ESCC and promotes ESCC development partly via interacting with DHX9 and triggering the DHX9/p65 axis.	esophagus
Endoscopic Submucosal Dissection in Europe: Results of 1000 Neoplastic Lesions From the German Endoscopic Submucosal Dissection Registry.	BACKGROUND AND AIMS: Endoscopic submucosal dissection (ESD) enables the curative resection of early malignant lesions and is associated with reduced recurrence risk. Due to the lack of comprehensive ESD data in the West, the German ESD registry was set up to evaluate relevant outcomes of ESD. METHODS: The German ESD registry is a prospective uncontrolled multicenter study. During a 35-month period, 20 centers included 1000 ESDs of neoplastic lesions. The results were evaluated in terms of en bloc, R0, curative resection rates, and recurrence rate after a 3-month and 12-month follow-up. Additionally, participating centers were grouped into low-volume (≤20 ESDs/y), middle-volume (20-50/y), and high-volume centers (>50/y). A multivariate analysis investigating risk factors for noncurative resection was performed. RESULTS: Overall, en bloc, R0, and curative resection rates of 92.4% (95% confidence interval [CI], 0.90-0.94), 78.8% (95% CI, 0.76-0.81), and 72.3% (95% CI, 0.69-0.75) were achieved, respectively. The overall complication rate was 8.3% (95% CI, 0.067-0.102), whereas the recurrence rate after 12 months was 2.1%. High-volume centers had significantly higher en bloc, R0, curative resection rates, and recurrence rates and lower complication rates than middle- or low-volume centers. The lesion size, hybrid ESD, age, stage T1b carcinoma, and treatment outside high-volume centers were identified as risk factors for noncurative ESD. CONCLUSION: In Germany, ESD achieves excellent en bloc resection rates but only modest curative resection rates. ESD requires a high level of expertise, and results vary significantly depending on the center's yearly case volume.	esophagus
Real-world emetic risk of chemotherapy and the corresponding antiemetic therapy in Japan: A study based on a nationwide database.	BACKGROUND: Chemotherapy-induced nausea and vomiting (CINV) is a major concern of patients with cancer, leading to suboptimal treatment. AIM: This study assessed the emetic risk associated with intravenous and oral chemotherapy and the prophylactic antiemetic drugs by cancer type in a real-world setting. METHODS AND RESULTS: We used the health services utilisation data for patients with cancer diagnosed in 2016. Patients aged at least 20 years at the time of diagnosis and who started their first course of chemotherapy were included. The emetic risk of chemotherapy was determined according to the cancer type and was classified based on clinical practice guidelines. The prescription of antiemetic drugs was assessed. Overall, 172 133 patients were evaluated, of whom 121 103 (70.4%) received intravenous chemotherapy. High-emetic-risk chemotherapy (HEC) was prescribed in 46 458 (27.0%) patients. HEC was prescribed most for patients with oesophageal cancer (80.3%), followed by malignant lymphoma (60.2%) and breast cancer (53.8%). Moderate-emetic-risk chemotherapy (MEC) was prescribed in 60 528 (35.2%) patients and was mostly prescribed for small cell lung cancer (59.9%). Meanwhile, more than 50% of the chemotherapy prescribed for patients with gastric, colorectal, and pancreatic cancer was low-emetic-risk chemotherapy. HEC was accompanied by three-drug antiemetic prophylaxis in more than 90% of patients with small cell lung, non-small cell lung, breast, and oesophageal cancer, whereas only 13.5% of patients with malignant lymphoma were administered CHOP (cyclophosphamide, doxorubicin, vincristine sulphate, and prednisolone) with prophylaxis. CONCLUSION: The risk of CINV differs with cancer type. HEC was less prescribed compared with MEC. Most patients received the recommended anti-emetic prophylaxis.	esophagus
Creation and provision of a question and answer resource for esophageal cancer based on medical professionals' reports of patients' and families' views and preferences.	"BACKGROUND: In the rapidly-progressing healthcare environment, it is essential to improve treatment quality through continuous clarification of the needs and concerns of esophageal cancer patients and their families. Effective collaboration between information providers and academic associations could help make such clarified information available. METHODS: We analyzed esophageal cancer patients' views and preferences (PVPs) using data that were previously obtained from medical staff in Japan. Based on these PVPs, we created a question and answer (Q&A) resource through collaboration with the Cancer Information Service in Japan (CISJ) and the Japan Esophageal Society (JES). RESULTS: Regarding esophageal cancer, ""diet and eating behavior"" was the most frequent PVP mentioned by patients and their families, followed by ""treatment-related symptoms and adverse effects"" and ""daily life, recuperation, and survivorship."" These PVPs were noted by a wide variety of medical specialties. By analyzing the PVPs, the CISJ developed 11 proposed questions and sent them to the JES, which then created answers based on evidence and clinical-practice-associated consensus. The resultant Q&A resource was uploaded to the CISJ website with mutual linkage to the JES website. CONCLUSIONS: This study showed the usefulness of collecting esophageal-cancer-related PVPs from medical staff and fostering successful collaboration between a cancer-information provider and an academic association. This arrangement may represent a model case for developing a sustainable system that can satisfactorily respond to PVPs regarding other cancers and/or issues."	esophagus
Predicting the risk of interval distant metastases in patients with esophageal squamous cell carcinoma undergoing chemoradiotherapy.	BACKGROUND: This study was conducted to identify risk factors for distant interval metastases (IM) in patients with esophageal squamous cell carcinoma (ESCC) who underwent chemoradiotherapy (CRT). METHODS: We retrospectively reviewed the clinical records of 358 patients with ESCC treated with CRT between 2006 and 2017. Distant IM were defined as systemic metastases developing during or shortly after CRT and identified during the restaging work-up period. A risk prediction nomogram for distant IM was developed based on independent pretreatment risk factors identified using multivariable logistic regression analysis. RESULTS: Distant IM occurred in 26 (7.3%) patients and had a significant adverse impact on survival (median survival: 8.7 months). The most common site of distant IM was the lung (n = 9), followed by non-regional lymph nodes (n = 8) and the bone (n = 8). Multivariable logistic regression analysis revealed that high baseline tumor SUVmax values were independently associated with an increased risk of distant IM (odds ratio [OR] = 1.059, p = 0.019), whereas older age was an independent protective factor (OR = 0.946, p = 0.032). A nomogram based on age, tumor SUVmax, tumor length, and the chemotherapy regimen showed a good predictive performance (c-statistic = 0.761), which was internally validated using 200 bias-corrected bootstrap replicates (c-statistic = 0.71). CONCLUSION: Distant IM were identified in 7.3% of patients with ESCC undergoing CRT. The nomogram described in our study may prove useful to predict the risk of distant IM in this patient group.	esophagus
Palliative Surgery Outcomes for Patients with Esophageal Cancer: An National Cancer Database Analysis.	INTRODUCTION: Many patients with esophageal cancer are not candidates for surgical resection with curative intent, given the advanced stage of disease at presentation. Palliative surgery is one treatment option, but relative survival of palliative surgery has not been described. This study aims to describe the outcomes of palliative surgery in patients with esophageal cancer. METHODS: We used the National Cancer Database to identify patients with esophageal cancer who received palliative surgery or non-surgical palliation-which consisted of palliative radiation and palliative chemotherapy without any surgery. The outcome of interest was overall survival. Characteristics of patients were compared between the palliative surgery group and the non-surgical group using rank sum test or chi square test. Survival differences between groups were compared using Kaplan Meier estimate and log rank test, and Cox proportional hazards model. RESULTS: A total of 14,589 patients were included in the analysis, including 2,812 (19.2%) receiving palliative surgery and 11,777 (80.7%) receiving non-surgical palliation (6,512 palliative radiation and 5,265 palliative chemotherapy). Median overall survival in palliative surgery patients was 5.5 mo, shorter than non-surgical palliation (6.4 mo, P = 0.004). However, when correcting for age, sex, nodal status, metastases, Charlson score, histology, academic center, and private insurance, there was no difference in survival between palliative surgery and non-surgical palliation in Cox proportional hazard modeling (HR 1.03 (0.975-1.090), P = 0.281). CONCLUSIONS: Palliative surgery in advanced esophageal cancer is associated with poor overall survival but is similar to other palliative modalities. Palliative Surgery for esophageal cancer patients should be used sparingly given these poor outcomes.	esophagus
Oxaliplatin/capecitabine or carboplatin/paclitaxel-based preoperative chemoradiation for resectable oesophageal adenocarcinoma (NeoSCOPE): Long-term results of a randomised controlled trial.	AIM: This is the first randomised study to evaluate toxicity and survival outcomes of two neoadjuvant chemoradiotherapy (CRT) regimens for patients with localised oesophageal adenocarcinoma (OAC) or gastro-oesophageal junction (GOJ) adenocarcinoma. The initial results showed comparable toxicity between regimens and pathological complete response (pCR) rate favouring CarPacRT. Herein, we report survival, progression patterns, and long-term toxicity after a median follow-up of 40.7 months. METHODS: NeoSCOPE was an open-label, UK multicentre, randomised, phase II trial. Eighty-five patients with resectable OAC or GOJ adenocarcinoma, ≥cT3 and/or ≥cN1 (TNM v7), suitable for neoadjuvant CRT, were recruited between October 2013 and February 2015. Patients were randomised to OxCapRT (oxaliplatin 85 mg/m(2) on Days 1, 15, and 29; capecitabine 625 mg/m(2) orally twice daily on days of radiotherapy [RT]) or CarPacRT (carboplatin AUC2; paclitaxel 50 mg/m(2) on Days 1, 8, 15, 22, and 29). RT dose was 45 Gy/25 fractions/5 weeks. Both arms received induction chemotherapy (two cycles oxaliplatin 130 mg/m(2) on Day 1, capecitabine 625 mg/m(2) orally twice daily on Days 1-21) before CRT. Surgery was performed 6-8 weeks after CRT. The primary end-point was pCR. Secondary end-points were toxicity, progression-free survival (PFS), overall survival (OS), and patterns of progression. RESULTS: Eighty-five patients were recruited from 17 UK centres. The median OS was 41.7 months (95% confidence interval [CI] 19.6 to not reached) in the OxCapRT arm and was not reached in the CarPacRT arm (multivariable hazard ratio [HR] = 0.48, 95% CIs: 0.24-0.95, P = 0.035). The median PFS was 32.6 months (95% CIs: 17.1 to not reached) in the OxCapRT arm and was not reached in the CarPacRT arm (multivariable HR = 0.54, 95% CIs: 0.29-1.01, P = 0.053). In both arms, the distant progression was twice as common as locoregional progression. CONCLUSIONS: OS and PFS favoured neoadjuvant CarPacRT over OxCapRT. Distant was more common than locoregional progression; therefore, priority should be given to optimising the systemic treatment component. CLINICAL TRIAL INFORMATION: EudraCT Number: 2012-000640-10; ClinicalTrials.gov: NCT01843829.	esophagus
The efficacy of adjuvant chemotherapy with capecitabine and cisplatin after surgery in locally advanced esophageal squamous cell carcinoma: a multicenter randomized phase III trial.	There is limited evidence for the effectiveness of adjuvant chemotherapy in esophageal squamous cell carcinoma (ESCC). This study aimed to assess whether adjuvant capecitabine and cisplatin improve survival compared to surgery alone among patients with locally advanced ESCC. This is a multicenter randomized controlled trial. Patients were eligible if they underwent curative resection for ESCC staged T2-4 or N1 and M0 according to the TNM cancer staging system sixth edition. The intervention group received four cycles of adjuvant chemotherapy (capecitabine: 1,000 mg/m 2 b.i.d for 14 days, and intravenous cisplatin: 75 mg/m2 at day 1, every 3 weeks). A total of 136 patients were randomly assigned to either the adjuvant chemotherapy group (n = 68) or surgery-alone group (n = 68). Seven patients who rejected chemotherapy after randomization were excluded from the final analysis. The cumulative incidence of recurrence within 18 months after surgery was significantly lower in the adjuvant chemotherapy group than in the surgery-alone group (hazard ratio [HR]: 0.49; 95% confidence interval (CI): 0.25-0.95]. However, the 5- and 10-year disease-free survival did not differ between treatment groups (HR: 0.84; 95% CI: 0.53-1.34 and HR: 0.76; 95% CI: 0.50-1.18, respectively). Adjuvant chemotherapy after curative resection in patients with locally advanced ESCC reduced early recurrence but had no statistically significant increase in the long-term disease-free survival. Due to the limited sample size of this study, additional randomized controlled trials with larger sample sizes are necessary.	esophagus
Phase I dose-escalation study of endoscopic intratumoral injection of OBP-301 (Telomelysin) with radiotherapy in oesophageal cancer patients unfit for standard treatments.	PURPOSE: OBP-301 (Telomelysin) is an attenuated type-5 adenovirus that contains the human telomerase reverse transcriptase promoter to regulate viral replication. OBP-301 sensitises human cancer cells to ionising radiation by inhibiting DNA repair, and radiation enhances coxsackievirus and adenovirus receptor-mediated OBP-301 infection on the contrary. We assessed OBP-301 with radiotherapy in oesophageal cancer patients unfit for standard chemoradiation treatments. METHODS: A phase I dose-escalation study of OBP-301 with radiotherapy was conducted in 13 histologically confirmed oesophageal cancer patients deemed unfit to undergo surgery or chemotherapy. Study treatment consisted of OBP-301 administration by intratumoural needle injection using a flexible endoscope on days 1, 18 and 32. Radiotherapy was administered concurrently over 6 weeks, beginning on day 4, to a total of 60 Gy. RESULTS: Of the 13 patients, 7, 3 and 3 patients were treated with 10(10), 10(11) and 10(12) virus particles, respectively. Study group comprised 10 males and 3 females, with a median age of 82 years (range, 53-91 years). All patients developed a transient, self-limited lymphopenia. Distribution studies revealed transient virus shedding in the plasma. Eight patients had local complete response (CR); all of them exhibited no pathologically viable malignant cells in biopsy specimens, and 3 patients had a partial response. The objective response rate was 91.7%. The clinical CR rate was 83.3% in stage I and 60.0% in stage II/III. Histopathological examination revealed massive infiltration of CD8(+) cells and increased PD-L1 expression. CONCLUSION: Multiple courses of endoscopic intratumoural OBP-301 injection with radiotherapy are feasible and provide clinical benefits in patients with oesophageal cancer unfit for standard treatments.	esophagus
Prognostic Significance of Preoperative Osteopenia in Patients Undergoing Esophagectomy for Esophageal Cancer.	BACKGROUND: Osteopenia, which exhibits low bone mineral density (BMD), has been linked to sarcopenia and recently reported as a prognostic factor in various cancers. However, the prognostic significance of osteopenia in esophageal cancer remains unclear. Hence, this study aimed to clarify the impact of osteopenia on the prognosis of patients undergoing esophagectomy for esophageal cancer. METHODS: We included 229 patients who underwent esophagectomy. BMD was calculated as the average pixel density (Hounsfield unit) within a circle in midvertebral core at the 11th thoracic vertebra on preoperative computed tomography. We then divided the patients into the Osteopenia group (n = 159) and the Non-Osteopenia group (n = 70) according to the optimal cutoff value obtained from the receiver operating characteristic curve. Their clinicopathological data, prognosis, and recurrence were analyzed. RESULTS: The mean age was significantly older in the Osteopenia group (p = 0.047). The Osteopenia group had significantly worse overall survival (OS) and relapse-free survival (RFS) than the Non-Osteopenia group (p = 0.001 and p = 0.012, respectively). Multivariate analysis revealed osteopenia was an independent prognostic factor for OS (p < 0.001; hazard ratio [HR], 2.243; 95% confidence interval [CI], 1.422-3.538) and RFS (p = 0.008; HR, 1.739; 95% CI, 1.154-2.620). In logistic regression model, advanced age and cStage III-IV were independent risk factors for preoperative osteopenia. CONCLUSIONS: Preoperative osteopenia is associated with poor survival and recurrence in patients undergoing esophagectomy for esophageal cancer.	esophagus
Arachidonic Acid Metabolism Controls Macrophage Alternative Activation Through Regulating Oxidative Phosphorylation in PPARγ Dependent Manner.	Macrophage polarization is mainly steered by metabolic reprogramming in the tissue microenvironment, thus leading to distinct outcomes of various diseases. However, the role of lipid metabolism in the regulation of macrophage alternative activation is incompletely understood. Using human THP-1 and mouse bone marrow derived macrophage polarization models, we revealed a pivotal role for arachidonic acid metabolism in determining the phenotype of M2 macrophages. We demonstrated that macrophage M2 polarization was inhibited by arachidonic acid, but inversely facilitated by its derived metabolite prostaglandin E2 (PGE2). Furthermore, PPARγ bridges these two seemingly unrelated processes via modulating oxidative phosphorylation (OXPHOS). Through inhibiting PPARγ, PGE2 enhanced OXPHOS, resulting in the alternative activation of macrophages, which was counterweighted by the activation of PPARγ. This connection between PGE2 biosynthesis and macrophage M2 polarization also existed in human and mouse esophageal squamous cell carcinoma. Our results highlight the critical role of arachidonic acid and metabolic PGE2 as immune regulators in modulating tissue homeostasis and pathological process.	esophagus
PD_BiBIM: Biclustering-based biomarker identification in ESCC microarray data.	To promote diligent analysis of the progression of a disease, it is important to identify interesting biomarkers for the disease. Biclustering has already been established as an effective technique to help identify such biomarkers of high biological significance. Although in the recent past, a good number of biclustering techniques have been introduced, most of them fail to perform consistently across multiple domains or datasets. To choose a single biclustering technique that can help the accomplishment of such a critical task for multiple diseases with high precision is extremely difficult. Hence, in this study, we considered several biclustering techniques and accepted those techniques and their results which are found significant from enrichment perspective for subsequent analysis. Based on biclustering results, we constructed biological networks and carried out a topological, pathway and causal analysis on the modules extracted from the networks. Our multiobjective study enabled us to identify several biomarkers for esophageal squamous cell carcinoma (ESCC) such as IFNGR1, CLIC1, CDK4, and COPS5, after applying a ranking scheme.	esophagus