crossing96/oncoscreening huggingface dataset:
Malignancies in Giant Cell Arteritis: A Population-based Cohort Study.	OBJECTIVE: To investigate the risk of cancer in patients with biopsy-proven giant cell arteritis (GCA) from a defined population in southern Sweden. METHODS: The study cohort consisted of 830 patients (mean age at GCA diagnosis was 75.3 yrs, 74% women) diagnosed with biopsy-proven GCA between 1997 and 2010. Temporal artery biopsy results were retrieved from a regional database and reviewed to ascertain GCA diagnosis. The cohort was linked to the Swedish Cancer Registry. The patients were followed from GCA diagnosis until death or December 31, 2013. Incident malignancies registered after GCA diagnosis were studied. Based on data on the first malignancy in each organ system, age- and sex-standardized incidence ratios (SIR) with 95% CI were calculated compared to the background population. RESULTS: One hundred seven patients (13%) were diagnosed with a total of 118 new malignancies after the onset of GCA. The overall risk for cancer after the GCA diagnosis was not increased (SIR 0.98, 95% CI 0.81-1.17). However, there was an increased risk for myeloid leukemia (2.31, 95% CI 1.06-4.39) and a reduced risk for breast cancer (0.33, 95% CI 0.12-0.72) and upper gastrointestinal tract cancer (0.16, 95% 0.004-0.91). Rates of other site-specific cancers were not different from expected. CONCLUSION: In this Swedish population-based cohort of GCA, the overall risk for cancer was not increased compared to the background population. However, there was an increased risk for leukemia and a decreased risk for breast and upper gastrointestinal tract cancer.	esophagus
Endoscopic features and associated histology of an basaloid squamous cell carcinoma of the esophagus at the very early stage.	BACKGROUND: Basaloid squamous cell carcinoma of the esophagus (BSCCE) is generally detected at advanced stage and the prognosis is poorer than advanced conventional esophageal squamous cell carcinoma. Therefore, early detection is a critical to improve patients' survival. However, only a few cases of early BSCCE have been reported and the endoscopic features of early BSCCE are not well described. We herein report the endoscopic features and associated histology of an early BSCCE limited within the mucosal lamina propria (m2). To our knowledge, this is the earliest BSCCE reported to date. CASE PRESENTATION: A 62-year-old male patient was admitted to our hospital because of epigastric pain for 3 months. White light endoscopy revealed a flat lesion with mild sloping at the periphery. The lesion was covered with leukoplakia, and normal vascular network could not be seen in the lesion. Magnifying endoscopy with narrow-band imaging showed abnormal intra-papillary capillary loop categorized as type B1 according to the classification of the Japan Esophageal Society. Iodine staining revealed a less-stained lesion. The lesion was completely resected through endoscopic submucosal dissection. Histopathologically, tumor cells, which were limited within the mucosal lamina propria, formed solid nests and lobule structures, with ribbon-like arrangement of sparse cytoplasm and round to ovoid hyperchromatic nuclei. A final diagnosis of early BSCCE was established. CONCLUSIONS: This is the earliest BSCCE reported to date. The prominent lesion with a gentle rising slope and less-staining or abnormal stain might be initial feature of early BSCCE.	esophagus
Circulating Tumor Cell cluster phenotype allows monitoring response to treatment and predicts survival.	Circulating tumor cells (CTCs) are putative markers of tumor prognosis and may serve to evaluate patient's response to chemotherapy. CTCs are often detected as single cells but infrequently as clusters and are indicative of worse prognosis. In this study, we developed a short-term culture of nucleated blood cells which was applied to blood samples from breast, lung, esophageal and bladder cancer patients. Clusters of different degrees of compactness, classified as very tight, tight and loose were observed across various cancer types. These clusters show variable expression of cytokeratins. Cluster formation from blood samples obtained during the course of chemotherapy was found to be associated with disease progression and shorter overall survival. The short-term cultures offer a robust and highly reliable method for early prediction of treatment response in different cancer types.	esophagus
Potential miRNA-disease association prediction based on kernelized Bayesian matrix factorization.	Many biological experimental studies have confirmed that microRNAs (miRNAs) play a significant role in human complex diseases. Exploring miRNA-disease associations could be conducive to understanding disease pathogenesis at the molecular level and developing disease diagnostic biomarkers. However, since conducting traditional experiments is a costly and time-consuming way, plenty of computational models have been proposed to predict miRNA-disease associations. In this study, we presented a neoteric Bayesian model (KBMFMDA) that combines kernel-based nonlinear dimensionality reduction, matrix factorization and binary classification. The main idea of KBMFMDA is to project miRNAs and diseases into a unified subspace and estimate the association network in that subspace. KBMFMDA obtained the AUCs of 0.9132, 0.8708, 0.9008±0.0044 in global and local leave-one-out and five-fold cross validation. Moreover, KBMFMDA was applied to three important human cancers in three different kinds of case studies and most of the top 50 potential disease-related miRNAs were confirmed by many experimental reports.	esophagus
Analysis of patients scheduled for neoadjuvant therapy followed by surgery for esophageal cancer, who never made it to esophagectomy.	BACKGROUND: Neoadjuvant treatment followed by esophagectomy is standard practice in locally advanced esophageal cancer. However, not all patients who started neoadjuvant treatment will undergo esophageal resection. The purpose of our study was to investigate the group of patients, scheduled for neoadjuvant treatment followed by esophagectomy, who never made it to esophageal resection. METHODS: We retrospectively analyzed patients treated between 2002 and 2015 for locally advanced esophageal cancer, who did not undergo esophagectomy after neoadjuvant treatment. Subanalysis was performed according to time period (2002-2010 versus 2011-2015) and histology (adenocarcinoma versus squamous cell carcinoma). RESULTS: In 114 of 679 patients (16.8%), surgery was not performed after neoadjuvant treatment. Reasons for cancelation were disease progression (50 patients, 43.9%), poor general condition (26 patients, 22.8%), irresectability (14 patients, 12.3%), patients' own decision (15 patients, 13.2%), and death during neoadjuvant treatment (9 patients, 7.9%). In the second time period, there were less irresectable tumors (17.7% versus 5.8%; p = 0.044). Median overall survival was not different over time (9.2 versus 12.5 months; p = 0.937). Irresectability (p = 0.032), patients' refusal (p = 0.012), and poor general condition (p = 0.002) were more frequent as reasons for cancelation in squamous cell carcinoma patients. Median overall survival was, respectively, 12.5 and 9.9 months for adenocarcinoma and squamous cell carcinoma patients (p = 0.441). The majority of patients refusing surgery had a clinical complete response (73.3%). They had a median overall survival of 33.2 months. CONCLUSIONS: One in six patients starting neoadjuvant treatment for locally advanced esophageal cancer never made it to esophagectomy, more than half of them for oncological reasons, but also 1.3% because of death during treatment. Over time, irresectability as reason decreased. As a result, the relative weight of medical inoperability increased, indicating the importance of upfront testing of medical operability. Cancelation of surgery was significantly more common in patients with a squamous cell carcinoma, and this histology seems to represent a more complex oncological and functional entity. Refusal of esophagectomy based on clinical complete response showed a significant survival benefit compared to those who did not undergo esophagectomy because of other reasons.	esophagus
FOLFOX alone or combined with rilotumumab or panitumumab as first-line treatment for patients with advanced gastroesophageal adenocarcinoma (PRODIGE 17-ACCORD 20-MEGA): a randomised, open-label, three-arm phase II trial.	BACKGROUND: Epidermal growth factor receptor (EGFR) and hepatocyte growth factor (HGF)/mesenchymal-epithelial transition (MET) pathways, which promote tumour growth and proliferation, are often deregulated in advanced gastroesophageal adenocarcinomas. We assessed whether adding panitumumab (an EGFR inhibitor) or rilotumumab (a HGF inhibitor) to first-line fluoropyrimidine-based and platinum-based chemotherapy (modified oxaliplatin, leucovorin and fluorouracil [mFOLFOX6]) benefits to patients with advanced gastroesophageal adenocarcinoma. PATIENTS AND METHODS: This phase II, open-label, randomised, three-arm study enrolled patients ≥18 years, with advanced gastroesophageal adenocarcinoma, Eastern Cooperative Oncology Group performance status 0-1 and no known HER2 overexpression. Patients were randomly assigned (1:1:1) mFOLFOX6 (oxaliplatin 85 mg/m(2), leucovorin 400 mg/m(2), 5-fluorouracil 400 mg/m(2) bolus then 2400 mg/m(2) over 46 h) alone or combined with panitumumab (6 mg/kg) or rilotumumab (10 mg/kg) every 2 weeks until limiting toxicity, patient's refusal or disease progression. The primary end-point was the 4-month progression-free survival (PFS) rate. Secondary end-points included overall survival (OS) and tolerance. RESULTS: The study enrolled 162 patients in 29 French centres. The median follow-up was 23.6 months (interquartile range = 16.4-29.0). The 4-month PFS rate was 71% (95% confidence interval [CI] = 57-82) with chemotherapy alone, 57% (95% CI = 42-71) combined with panitumumab and 61% (95% CI = 47-74) combined with rilotumumab. Median OS was 13.1 months (95% CI = 8.7-16.9) with chemotherapy alone, 8.3 months (95% CI = 6.2-13.2) combined with panitumumab and 11.5 months (95% CI = 7.9-17.1) combined with rilotumumab. Adverse events grade ≥III occurred less frequently with chemotherapy alone (62%) than with panitumumab (83%) and rilotumumab (89%). CONCLUSIONS: We found no benefit in adding panitumumab or rilotumumab to mFOLFOX6 first-line chemotherapy to treat advanced gastroesophageal adenocarcinoma patients. TRIAL REGISTRATION: European Clinical Trials Database, number 2009-012797-12.	esophagus
Highly expressed microRNA-124 inhibits migration and promotes apoptosis of esophageal cancer cells by degrading PDCD6.	PURPOSE: To investigate whether microRNA (miR)-124 could affect the proliferation, migration and apoptosis of esophageal cancer cells and participate in the occurrence of esophageal cancer through regulating PDCD6 expression. METHODS: The expression of miR-124 in cancer tissues and adjacent tissues of esophageal cancer patients were detected by quantitative real time-polymerase chain reaction (qRT-PCR). Esophageal cancer cells TE-1 and SKYE30 were cultured. The effects of miR-124 on tumor size and metastasis were analyzed. The functions of miR-124 in cell proliferation, migration and apoptosis were detected by cell counting kit-8 (CCK-8), transwell and flow cytometry, respectively. Rescue experiments were performed to assess whether miR-124 could regulate the proliferation, migration and apoptosis of esophageal cancer cells by inhibiting PDCD6 expression. RESULTS: The expression of miR-124 in cancer tissues of esophageal cancer patients were lower than that of the control group. In addition, its expression in patients with stage III-IV esophageal cancer was remarkably lower than that in patients with stage I-II. Based on the level of miR-124, we divided the patients into high and low expression group, and found significant differences in tumor size, tumor metastasis and lymph node metastasis between the two groups. Also, overexpression of miR-124 reduced the proliferation and migration of TE-1 and SKYSE30 cells and increased the apoptosis, and vice versa. Luciferase reporting assay results confirmed that PDCD6 was one of the target genes of miR-124. A further mechanism study demonstrated that overexpression of PDCD6 in TE-1 and SKYSE30 cells could partially reverse the effect of miR-124 on cell apoptosis. CONCLUSIONS: The low expression of miR-124 can promote the proliferation as well as migration of esophageal cancer cells and inhibit cell apoptosis. The mechanism may be that miR-124 can regulate the expression of PDCD6.	esophagus
Expression and prognostic significance of MAGE-A11 and transcription factors (SP1,TFCP2 and ZEB1) in ESCC tissues.	OBJECTIVE: To evaluate the clinical characteristics and prognostic significance of MAGE-A11 and transcription factors (SP1, TFCP2 and ZEB1) in patients with esophageal squamous cell carcinoma (ESCC). METHODS: To assess the expression of MAGE-A11 and transcription factors (SP1, TFCP2 and ZEB1) in 121 ESCC samples were respectively detected by immunohistochemical method. RESULTS: The results showed MAGE-A11 and transcription factors (SP1,TFCP2 and ZEB1) expression were associated with some clinical features in patients, such as pathological differentiation, tumor size, clinical stage, lymph node metastasis and distant metastasis. Kaplan-Meier analysis showed that patients with ESCC having high MAGE-A11 and transcription factors (SP1,TFCP2 and ZEB1) expression had a worse prognosis compared to the patients with low expression. Multivariate Cox proportional hazards regression model revealed that MAGE-A11 expression, TFCP2 expression, lymph node metastasis and distant metastasis were independently associated with ESCC patients' survival. CONCLUSIONS: High expression of MAGE-A11 and transcription factors (SP1,TFCP2 and ZEB1) in ESCC tissues suggests promoting ESCC progression and poor prognosis, co-expression of MAGE-A11 and transcription factors even worse.	esophagus
Analysis of the function of MAGE-A in esophageal carcinoma by bioinformatics.	BACKGROUND: Melanoma-associated antigen-A (MAGE-A) was recognized as high-expressed in many solid tumors including esophageal carcinoma (EC), nevertheless, was reported to be low/not-expressed in normal tissues. Thus, it was considered as an extraordinary appropriate target for treatment especially in immunotherapy. Therefore, it demanded more detail knowledge on the precise function of MAGE-A. METHODS: In this study, we used the data from the Cancer Genome Atlas dataset (TCGA-ESCA) to analyze the expression and survival for MAGE A3/4/11 (the subtype of MAGE-A) using the online tool of UALCAN. Furthermore, the high-throughput sequencing data of the patients with esophageal squamous-cell carcinoma (ESCC) from TCGA dataset were performed to analyze the correlation test, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of MAGE A3/4/9/11 using LinkeDomics (online tool) and ClueGO (inner software of Cytoscape). Finally, relative gene expressions of MAGE A3/4/9/11 were verified by quantitative real-time PCR (q-PCR) in the patients with EC. RESULTS: MAGE A3/4/11 was high-expressed in tissues of patients with ESCC, and there was no difference in survival time for patients between the high-expressed with the low/medium-expressed. The Go enrichment analysis showed that the 4 MAGE-A subtypes (MAGE-A3/4/9/11) were enriched in the regulation of the adaptive immune response, translational initiation, interleukin-4 production, response to type I interferon, and skin development, respectively. The KEGG results showed that they were enriched in T cell receptor signaling pathway (MAGE-A3), Th1 and Th2 differentiation, antigen processing and presentation (MAGE-A4), cytokine-cytokine receptor interaction (MAGE-A9), and chemokine signaling pathway (MAGE-A11). CONCLUSION: MAGE A3/4/9/11 was high-expressed in EC, and were enrolled in the regulation of immune response. They may consider as candidate immune target for EC treatment and provided the messages for further research in the function of MAGE-A.	esophagus
Lymph Node Metastasis and Recurrence in Primary Small Cell Carcinoma of the Esophagus: A Retrospective Study of 125 Cases.	Objective: The aim of this study was to investigate and analyze the prognostic factors affecting lymph node (LN) metastasis and postoperative recurrence in patients with primary small cell carcinoma of the esophagus (SCCE). Methods: A total of 125 primary SCCE patients who received surgical resection in the Fourth Hospital of Hebei Medical University between March 2005 and August 2009 were included in this retrospective study. All the potential prognostic variables, including the patients' characteristics, tumor features, and treatment modalities, were analyzed by a Cox regression model to explore LN metastasis and the factors associated with postoperative recurrence. Results: LN metastasis rate was significantly correlated with depth of tumor invasion (p < 0.001) and tumor length (p = 0.006). LN metastasis ratio was positively correlated with pathological type (p < 0.001), tumor location (p = 0.002), depth of tumor invasion (p < 0.001), and tumor length (p < 0.001). LN stage and chemotherapy were found to be the independent risk factors for progression-free survival (PFS). Conclusion: Depth of tumor invasion and tumor length were main factors associated with LN metastasis in primary SCCE. The stage of LN metastasis and chemotherapy was independent factors affecting the postoperative PFS.	esophagus
Skill-up study of systemic endoscopic examination technique using narrow band imaging of the head and neck region of patients with esophageal squamous cell carcinoma: Prospective multicenter study.	OBJECTIVE: To evaluate the usefulness of a training program on endoscopic head and neck surveillance for beginner endoscopists. METHODS: This prospective multicenter study included 13 beginner endoscopists from 10 institutions who received training in systematic observation techniques and diagnostic criteria, and the training involved hands-on learning. Between May 2016 and February 2017, enrolled patients with current or previously diagnosed esophageal squamous cell carcinomas underwent head and neck surveillance using narrow band imaging (NBI) endoscopy, and histologically confirmed head and neck squamous cell carcinoma (HNSCC) detection rates, endoscopic image quality, and examination times were compared before (group A) and after (group B) the training program. Maximum possible score for the endoscopic images was 30 points. RESULTS: A total of 330 patients, comprising 181 in group A and 149 in group B, were enrolled. Three patients with HNSCC were detected in group A (1.7%) and in group B (2.0%; P = 1.000). Mean ± standard deviation (SD) examination times were 157 ± 71 s and 174 ± 109 s in groups A and B, respectively, (P = 0.073). Mean ± SD scores of the endoscopic images were 25.04 ± 5.47 points and 27.01 ± 4.35 points in groups A and B, respectively, (P < 0.001). CONCLUSION: The HNSCC detection rate based on the use of NBI on patients with ESCC did not improve after the training program for beginner endoscopists; however, endoscopic image quality improved significantly after the training program.	esophagus
LncRNA Erbb4-IR promotes esophageal squamous cell carcinoma (ESCC) by downregulating miR-145.	Erbb4-IR is a recently identified lncRNA with pivotal functions in renal injury. The present study investigated the roles of Erbb4-IR in esophageal squamous cell carcinoma (ESCC). It was observed that Erbb4-IR was upregulated in tumor tissues of patients with ESCC. Plasma levels of Erbb4-IR in patients with ESCC were positively correlated with expression levels of Erbb4-IR in tumor tissues. MicroRNA-145 (miR-145) was downregulated in tumor tissues and inversely correlated with Erbb4-IR only in tumor tissues. Erbb4-IR overexpression led to downregulated miR-145, and increased rates of ECSS cell proliferation and decreased rates of ECSS cell apoptosis. Overexpression of miR-145 showed no significant effects on Erbb4-IR expression, but played an opposite role on cancer cell proliferation and apoptosis. In addition, miR-145 overexpression attenuated the effects of Erbb4-IR overexpression. Therefore, lncRNA Erbb4-IR may promote ESCC by downregulating miR-145.	esophagus
High expression of DNA methyltransferase 1 in Kazakh esophageal epithelial cells may promote malignant transformation induced by N-methyl-N'-nitro-N-nitrosoguanidine.	We examined the role of DNA methyltransferase 1 (DNMT1) in N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced malignant transformation of Kazakh esophageal epithelial (EE) cells to better understand the pathogenesis of esophageal cancer (EC). The 3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-di- phenytetrazoliumromide method and colony formation assays were performed to determine the MNNG dose for malignant transformation. Colony formation assays showed the effects of different frequencies of MNNG exposure and different cell passages on malignant transformation. A nude mouse tumor experiment indicated the malignancy of Kazakh EE cells expressing high DNMT1 levels and of transformed cells. The result shows that when the dose, frequency, and time of MNNG exposure increased, cell morphology became irregular, cell-contact suppression disappeared, and cell tolerance and growth rate increased. Colony formation occurred in the Kazakh-DNMT1 group after 14 transfections and 27 passages. Significant differences in DNMT1 mRNA and protein levels were observed in different types of cells and tumor tissues (F = 140.644, p < 0.001; F = 105.545, p < 0.001). Our study demonstrated that DNMT1 could promote MNNG to induce malignant transformation of EE cells, and this study will help understand EC better in order to develop appropriate treatment strategies.	esophagus
miRNA‑30a‑3p inhibits metastasis and enhances radiosensitivity in esophageal carcinoma by targeting insulin‑like growth factor 1 receptor.	It has been demonstrated that microRNAs (miRNAs) serve important roles in various biological processes, such as tumorigenesis. In the present study, the role of miR‑30a‑3p in the pathogenesis of esophageal carcinoma (EC) was investigated. Reverse transcription‑quantitative polymerase chain reaction was performed to determine the levels of miR‑30a‑3p expression in EC tissues and cell lines. Then, the effects of miR‑30a‑3p on the migration, invasion and radiosensitivity of EC cells were investigated using scratch‑wound, Transwell and radiosensitivity assays, respectively. A dual‑luciferase reporter assay was performed to determine potential interactions between miR‑30a‑3p and the 3'‑untranslated region (3'‑UTR) of insulin‑like growth factor 1 receptor (IGF‑1R). The results demonstrated that the levels of miR‑30a‑3p expression in EC tissues and cell lines were significantly decreased compared with those in paired healthy tissues and a human esophageal epithelial cell line. Upregulation of miR‑30a‑3p expression significantly suppressed migration, invasion and epithelial‑mesenchymal transition (EMT), and enhanced radiosensitivity in EC cells. Analysis of luciferase activity demonstrated that miR‑30a‑3p interacted with the 3'‑UTR of IGF‑1R, and knockdown of IGF‑1R induced similar effects on the migration, invasion, EMT and radiosensitivity of EC cells. The results indicated that miR‑30a‑3p suppressed metastasis and enhanced the radiosensitivity of EC cells via downregulation IGF‑1R, suggesting that miR‑30a‑3p may be a potential therapeutic target in the treatment of EC.	esophagus