crossing96/oncoscreening huggingface dataset:
Bioinformatics analysis of gene expression profiles of esophageal squamous cell carcinoma.	The objective of this study is to explore the potential target genes in the pathogenesis of esophageal squamous cell carcinoma (ESCC). The mRNA expression profile data of GSE17351 were downloaded from the Gene Expression Omnibus database, including five paired ESCC and normal tissue samples from five ESCC patients. The differentially expressed genes (DEGs) between ESCC and normal samples were identified using the limma package. The identified DEGs were then performed clustering analysis and functional enrichment analysis. Additionally, gene-miRNA network, gene-transcription factor network, and protein-protein interaction (PPI) network for the DEGs were constructed, and then significant modules were selected from the constructed PPI network. Furthermore, esophageal carcinoma RNAseq data including 185 esophageal carcinoma and 13 normal samples were downloaded from The Cancer Genome Atlas database to confirm our results. A total of 409 up- and 341 downregulated DEGs were identified. The DEGs were separated into two clusters and were mainly enriched in cell cycle function. CHEK1, CCNA2, COL11A1, and MME were hub nodes in the PPI network. Besides, total seven modules were selected in the PPI network. Genes in the most significant module were upregulated and were enriched in cell cycle. The Cancer Genome Atlas data validation identified 370 DEGs, all of which were differentially expressed in the GSE17351 dataset. Besides, the expression change direction was consistent with the DEGs in GSE17351. Cell cycle may play a role in ESCC development. The genes such as CHEK1, CCNA2, COL11A1, and MME may be served as target genes in ESCC treatment.	esophagus
Stability of cervical esophagogastrostomy via hand-sewn anastomosis after esophagectomy for esophageal cancer.	The aim of the present study is to evaluate the outcome of hand-sewn esophagogastric anastomosis during radical esophagectomy for esophageal cancer. The outcomes of 467 consecutive esophageal cancer patients who underwent cervical esophagogastric anastomosis using interrupted and double-layered sutures after radical esophagectomy via right thoracotomy or thoracoscopic surgery were retrospectively reviewed. Anastomotic leakage, including conduit necrosis, occurred in 11 of 467 patients (2.4%); 7 of 11 (63.6%) cases experienced only minor leakage, whereas the other four (36.4%) patients had major leakage that required surgical or radiologic intervention, including two patients of conduit necrosis. Anastomotic leakages were more frequently observed after retrosternal reconstruction compared with the posterior mediastinal route (P < 0.0001). The median time to healing of leakage was 40 days (range: 14-97 days). Two patients (2/467, 0.4%) died in the hospital due to sepsis caused by the leakage and conduit necrosis. Twelve patients (2.6%) developed anastomotic stenosis, which was improved by dilatation in all patients. Hand-sewn cervical esophagogastric anastomosis is a stable and highly safe method of radical esophagectomy for esophageal cancer.	esophagus
Disease Progression in Barrett's Low-Grade Dysplasia With Radiofrequency Ablation Compared With Surveillance: Systematic Review and Meta-Analysis.	OBJECTIVES: Barrett's esophagus (BE) is the only identifiable premalignant condition for esophageal adenocarcinoma (EAC). Management of BE with low-grade dysplasia continues to be controversial. We aimed to conduct a systematic review and meta-analysis comparing the risk of progression to high-grade dysplasia or EAC among patients with BE with low-grade dysplasia treated with radiofrequency ablation (RFA) compared with surveillance endoscopy. METHODS: Our search included Medline, Embase, and Cochrane Central, was limited to English language articles, and was last searched on 31 December 2015. Studies were reviewed by title and abstract, and then full text by two independent reviewers. Two independent reviewers extracted data. Differences were resolved by consensus. The primary outcome of interest was the relative risk of disease progression among patients with BE with low-grade dysplasia treated with RFAcompared with surveillance. RESULTS: Our search resulted in 2,029 citations, 19 studies were included in the final analysis, totaling 2,746 patients. Relative risk of disease progression in RFA compared with surveillance was 0.14% (95% confidence interval: 0.04-0.45), P=0.001. This measure was stable when only all studies were included. Absolute risk reduction was 10.9% and the number needed to treat was 9.2. Results were stable over several quality measures, overtime, and when excluding randomized trials. The cumulative rate of progression to high-grade dysplasia/EAC was lower in RFA compared with surveillance (1.7% vs. 12.6%, P<0.001). CONCLUSIONS: Similarly, the incidence rate of progression among patients with surveillance was significantly higher from those treated with RFA (0.022 vs. 0.005, P<0.001). RFA results in a significant reduction risk of disease progression to high-grade dysplasia/EAC among patients with BE with low-grade dysplasia.	esophagus
All-trans retinoic acid suppresses the angiopoietin-Tie2 pathway and inhibits angiogenesis and metastasis in esophageal squamous cell carcinoma.	Esophageal squamous cell carcinoma (ESCC) is the second common cancer in Henan province and is well-known for aggressiveness and dismal prognosis. Adjuvant therapies, chemotherapy, radiotherapy and endoscopic treatment have not improved survival rates in patients with late stage esophageal carcinoma. All-trans retinoic acid (ATRA) is the active ingredient of Vitamin A and affects a wide spectrum of biological processes including development, growth, neural function, immune function, reproduction, and vision. It is one of the most potent therapeutic agents used for treating cancers, especially lung adenocarcinomas. ATRA inhibits metastatic potential and angiogenesis in several tumor models. We investigated the effects of ATRA on the expression of angiopoietin 1 (Ang-1), angiopoietin 2 (Ang-2) and receptor Tie-2 in EC1 cells in vitro. We also assessed the growth and migration of EC1 cells in vitro. ATRA treatment caused 29.5% and 40.3% reduction of the growth of EC1 cells after 24 hours and 48 hours, relative to the control. ATRA plus fluorouracil treatment reduced the viability more strongly than either drug alone, indicating an additive effect. Moreover, ATRA decreased EC1 migration by 87%. Furthermore, ATRA treatment led to a marked decrease of the transcript levels of Ang-1, Ang-2, Tie-2, VEGF, and VEGF receptors, as assessed by real-time RT-PCR. Importantly, the protein levels of Ang-1, Ang-2 and Tie-2 were reduced by ATRA treatment. In vivo, we found ATRA treatment suppressed the tumor growth and improved the cachexia of mice. Importantly, ATRA treatment decreased the expression of CD31, Ang-1, Ang-2 and Tie-2 in subcutaneous tumors of EC1 cells. Collectively, our findings demonstrate that ATRA exhibits a dose- and temporal-dependent effect on the metastatic behavior, suppresses the angiopoietin-Tie2 pathway and inhibits angiogenesis and the progression of xenograft tumors of EC1 cells.	esophagus
Association of Genetic Variants of CYP2C19 and CYP2D6 with Esophageal Squamous Cell Carcinoma Risk in Northern India, Kashmir.	Genetic polymorphism in xenobiotic metabolizing enzymes (XMEs) is associated with various malignancies. However, the association of esophageal cancer with XMEs is mixed. The current study was aimed to explore the association of genetic polymorphisms of cytochrome (CYP) 2C19 and CYP2D6 genotypes with esophageal squamous cell carcinoma (ESCC) risk in Kashmir, India. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and sequencing methods were used for genotyping of 492 ESCC cases and equal number of individually matched controls. Conditional logistic regression models were used to assess odds ratios (ORs) and 95% confidence intervals. Increased ESCC risk was observed in subjects with variant genotypes of CYP2C19 (OR = 3.3) or CYP2D6 (OR = 2.1) and risk was higher (OR = 4.6) in subjects who harbored both the genotypes. Almost same but higher risk turned when subjects were smokers and carried a variant genotype of CYP2C19 (OR = 4.4) or CYP2D6 (OR = 4.7). Risk was appreciably increased in subjects who had family history of any cancer and also harbored a variant genotype of either CYP2C19 (OR = 15.5) or CYP2D6 (OR = 9.7). Subjects harboring a variant genotype of CYP2D6 showed an added risk when they used biomass as fuel (OR = 4.6). In conclusion, variant genotypes of CYP2C19 and CYP2D6 are associated with an increased risk of ESCC.	esophagus
Genetic Alterations in Esophageal Tissues From Squamous Dysplasia to Carcinoma.	BACKGROUND & AIMS: Esophageal squamous cell carcinoma (ESCC) is the most common subtype of esophageal cancer. Little is known about the genetic changes that occur in esophageal cells during the development of ESCC. We performed next-generation sequence analyses of esophageal nontumor, intraepithelial neoplasia (IEN), and ESCC tissues from the same patients to track genetic changes during tumor development. METHODS: We performed whole-genome, whole-exome, or targeted sequence analyses of 227 esophageal tissue samples from 70 patients with ESCC undergoing resection at Shantou University Medical College in China from 2012 through 2015 (no patients had received chemotherapy or radiation therapy); we analyzed normal tissues, tissues with simple hyperplasia, dysplastic tissues (IEN), and ESCC tissues collected from different regions of the esophagus at the same time. We also obtained 1191 nontumor esophageal biopsy specimens from the Chaoshan region (a high-risk region for ESCC) of China (a high-risk region for ESCC) and performed immunohistochemical and histologic analyses to detect inflammation. RESULTS: IEN and ESCC tissues had similar mutations and copy number alterations, at similar frequencies; these differed from mutations detected in tissues with simple hyperplasia. IEN tissues had mutations associated with apolipoprotein B messenger RNA editing enzyme, catalytic polypeptide-like-mediated mutagenesis (a DNA damage mutational signature). Genetic analyses indicated that most ESCCs were formed from early stage IEN clones. Trunk mutations (mutations shared by >10% of paired IEN and ESCC tissues) were in genes that regulate DNA repair and cell apoptosis, proliferation and adhesion. Mutations in TP53 and CDKN2A and copy number alterations in 11q (contains CCND1), 3q (contains SOX2), 2q (contains NFE2L2), and 9p (contains CDKN2A) were considered to be trunk variants; these were dominant mutations detected at high frequencies in clones of paired IEN and ESCC samples. In the esophageal biopsy samples from high-risk individuals (residing in the Chaoshan region), 68.9% had an evidence of chronic inflammation; the level of inflammation was correlated with atypical cell structures and markers of DNA damage. CONCLUSIONS: We analyzed mutations and gene copy number changes in nontumor, IEN, and ESCC samples, collected from 70 patients. IEN and ESCCs each had similar mutations and markers of genomic instability, including apolipoprotein B messenger RNA editing enzyme, catalytic polypeptide-like. Genomic changes observed in precancerous lesions might be used to identify patients at risk for ESCC.	esophagus
Protein coding gene CRNKL1 as a potential prognostic biomarker in esophageal adenocarcinoma.	BACKGROUND: Esophageal adenocarcinoma (EAC) is one of the most aggressive gastroesophageal cancers. PTGS2, EGFR, ERBB2 and TP53 are the traditional EAC prognostic biomarkers, but they are still limited in their ability to effectively predict the overall survival. OBJECTIVES: To identify an improved biomarker for predicting the prognosis of EAC by using the expression profile. MATERIALS AND METHODS: Differential co-expression analysis and differential expression analysis were performed to identify the related genes of EAC. The 5-fold cross-validation was used to select a prognostic biomarker from the 532 EAC related genes. RESULTS: CRNKL1 was identified as a prognostic biomarker to predict the survival of EAC patients. It could significantly stratify EAC patients into high-risk and low-risk groups and was much better than the traditional biomarkers. Furthermore, ROC curve also verified that CRNKL1 with the highest area under the curve (AUC), reaching a sensitivity of 83.33% and a specificity of 78.57%. CONCLUSIONS: Our research proposed that CRNKL1 might be a novel prognostic biomarker with better predictive ability by comparing with the traditional biomarkers, which provided a preferable opportunity in the clinical applications of EAC.	esophagus
Multidisciplinary Approach to the Management of Esophageal Malignancies.	INTRODUCTION: A multidisciplinary approach in the management of complex malignancies is becoming more common, and likewise, adopting such an approach to the care of patients with locally advanced esophageal is recommended in order to optimize clinical outcomes. METHODS: In this review, we discuss both the surgical and medical oncology perspectives in the management of patients with locally advanced esophageal cancer. We review the data supporting the current standard-of-care approach, namely trimodality therapy with neoadjuvant chemo-radiotherapy followed by surgery. Other aspects of managing these patients including the control of dysphagia and pain as well as nutritional support are discussed. Finally, we review data that support the importance of incorporating a multidisciplinary streamlined approach in the management of these patients. RESULTS: Rather than having patients see each provider separately, a multidisciplinary approach to esophageal cancer allows for the seamless flow of communication and proactive management of the patient's symptoms. These benefits include increasing the likelihood of evidence-based decision making, shorter time to treatment, and increased patient quality of life, all of which can result in improved patient outcomes. CONCLUSION: The use of a multidisciplinary team can lead to a more accurate staging paradigm and thereby, better management decisions that translate to improved clinical outcomes. Therefore, optimizing the multidisciplinary approach for the care of patients with locally advanced esophageal cancer is essential for successful and individualized patient care.	esophagus
Current Concepts in Treatment of Barrett's Esophagus With and Without Dysplasia.	BACKGROUND: Around 10-15% of patients with gastroesophageal reflux disease will develop Barrett's esophagus (BE). The development of novel endoscopic modalities has changed the management of BE in the last decade. AIM: The aim of this study was to review the current evidence for the treatment of BE with and without dysplasia. RESULTS: In patients with BE without dysplasia, antireflux surgery should not be suggested as a modality to prevent the malignant transformation of BE, but its indications should be the same as for other patients with gastroesophageal reflux. Endoscopic surveillance at intervals of 3-5 years is recommended for these patients. For patients with BE with low-grade dysplasia, radiofrequency ablation (RFA) is the preferred treatment modality, while endoscopic surveillance every 12 months is an acceptable alternative in patients with life-limiting comorbidities. For most patients with BE and high-grade dysplasia, RFA is the preferred treatment strategy. Patients with intramucosal adenocarcinoma (T1a), should be treated with EMR followed by ablative therapy, in order to eradicate the remaining intestinal metaplasia. Endoscopic resection may be suitable for low-risk T1b tumors (well-differentiated, without lymphovascular invasion, and with superficial submucosal invasion); however, further data are necessary to better risk stratify this group. CONCLUSIONS: Patients with BE without dysplasia should undergo endoscopic surveillance every 3-5 years. Endoscopic ablative therapy (RFA) is the preferred treatment modality for dysplastic BE. Patients with T1a adenocarcinoma should be treated with EMR followed by ablative therapy. Low-risk T1b tumors may be suitable for endoscopic resection.	esophagus
A Prognostic Scoring Model for the Utility of Induction Chemotherapy Prior to Neoadjuvant Chemoradiotherapy in Esophageal Cancer.	OBJECTIVES: The aim of this study was to identify patients with esophageal cancer who may benefit from induction chemotherapy (IC) before neoadjuvant chemoradiotherapy (nCRT) on the basis of a prognostic scoring model. METHODS: Between 1998 and 2015, 535 patients with esophageal cancer who underwent nCRT were included for analysis, including 218 patients who received IC before nCRT (IC group) and 317 patients who did not receive IC (non-IC group). A prognostic scoring model was developed to predict disease-free survival (DFS) on the basis of a Cox proportional hazards model. RESULTS: The median follow-up time was 63.5 months (range 8.0-178.5) for survivors. The 5-year DFS rates were similar between the IC and non-IC groups (53.7% vs. 45.1%, p = 0.196). Multivariate analysis determined that histologic grade, tumor location, baseline positron emission tomography maximum standard uptake value, and lymph node size were independent prognostic factors for DFS. A prognostic scoring system was constructed by using these four factors, with the total score ranging from 0 to 6.2. When the median value was used as a cutoff, low-risk (≤3.5) and high-risk (>3.5) groups were identified. In the high-risk group, patients who received IC had a nonsignificantly higher pathologic complete response rate (p = 0.272) and a significantly better DFS (p = 0.03) than patients who did not receive IC. After propensity score matching, the high-risk group demonstrated a significantly improved DFS with IC, a benefit that was not observed in the low-risk group. CONCLUSIONS: On the basis of the prognostic scoring model, the addition of IC to nCRT may provide a DFS benefit in high-risk patients with a risk score higher than 3.5. Prospective validation is warranted.	esophagus
Obesity-associated digestive cancers: A review of mechanisms and interventions.	The prevalence of obesity has steadily increased over the past few decades. Previous studies suggest that obesity is an oncogenic factor and that over 20% of all cancers are obesity-related. Among such cancers, digestive system malignancies (including esophageal adenocarcinomas, colorectal cancers, and cancers of the gastric cardia, liver, and pancreas) are reported most frequently. While the 5-year survival rates of cancers of the breast and prostate are 90%, that rate is only 45% for digestive cancers. In this review, the mechanisms of obesity-associated digestive cancers are discussed, with an emphasis on obesity-related gene mutations, insulin and insulin-like growth factor signaling pathways, chronic inflammation, and altered adipokine levels. Evidence that these factors often function interdependently rather than independently in carcinogenesis is presented. Recommended interventions that may reduce the burden of obesity-associated digestive cancers, such as participation in physical activity, diet modulation, and calorie restriction, are also described.	esophagus
Central Macular Thickness Monitoring after a Taxane-Based Therapy in Visually Asymptomatic Patients.	BACKGROUND: Taxanes are drugs used in various chemotherapeutical protocols to treat solid tumors. They have multiple systemic adverse effects, such as bone marrow suppression, alopecia, nausea, and vomiting, and may rarely cause ocular symptoms. In the past decade, a few reported cases have shown the occurrence of a cystoid macular edema with significant visual loss after the use of a taxane-based chemotherapy. The aim of this study was to compare the central macular thickness (CMT) before and after the initiation of a taxane-based therapy in visually asymptomatic patients and to elucidate the possible impact of these drugs on the vision of cancer patients. METHODS: Patients with a confirmed diagnosis of a solid tumor were screened for any ophthalmic disease before inclusion and had a baseline macular spectral domain optical coherence tomography (OCT; RTVue-100; Optovue Inc., Fremont, CA, USA) before the initiation of a taxane-based chemotherapy according to different protocols, such as 4EC-4T, 3FEC/3T, or 4TC. OCT was repeated after 4 cycles (or 3 months) of treatment, and CMT was compared to baseline. Patients presenting diabetic retinopathy, age-related macular degeneration or any condition that causes macular edema confirmed by ophthalmic examination were excluded. RESULTS: Fifty eyes of 25 patients were included; 92% of the subjects were female with a mean age of 48.52 years, 88% were diagnosed with breast cancer, 8% with esophageal cancer, and 4% with ovarian cancer. Docetaxel was the taxane administered to 92% of the patients. The received dose of docetaxel ranged between 110 and 160 mg. The other patients had paclitaxel in their protocols. No significant macular edema or drop in visual acuity were noted in any patient. Nevertheless, the mean CMT was found to be increased, particularly in the parafoveal and perifoveal areas (mean difference of +2.22 μm; p = 0.001). CONCLUSION: Taxane-based chemotherapy regimens seem to increase macular thickness, with a relative sparing of the fovea, in patients without significant macular edema. Further research is required to better explain the pathophysiology and possible impact of this phenomenon.	esophagus
Impact of Surgical Approach on Long-term Survival in Esophageal Adenocarcinoma Patients With or Without Neoadjuvant Chemoradiotherapy.	OBJECTIVE: To compare overall survival in patients with esophageal adenocarcinoma who underwent transhiatal esophagectomy (THE) with limited lymphadenectomy or transthoracic esophagectomy (TTE) with extended lymphadenectomy with or without neoadjuvant chemoradiotherapy (nCRT). BACKGROUND: The application of neoadjuvant therapy might change the association between the extent of lymphadenectomy and survival in patients with esophageal adenocarcinoma. This may influence the choice of surgical approach in patients treated with nCRT. METHODS: Patients with potentially curable subcarinal esophageal adenocarcinoma treated with surgery alone or nCRT followed by surgery in 7 centers were included. The effect of surgical approach on overall survival, differentiated by the addition or omission of nCRT, was analyzed using a multivariable Cox regression model that included well-known prognostic factors and factors that might have influenced the choice of surgical approach. RESULTS: In total, 701 patients were included, of whom 318 had TTE with extended lymphadenectomy and 383 had THE with limited lymphadenectomy. TTE had differential effects on survival (P for interaction = 0.02), with a more favorable prognostic effect in patients who were treated with surgery alone [hazard ratio (HR) = 0.77, 95% confidence interval (CI) 0.58-1.03]. This association was statistically significant in a subgroup of patients with 1 to 8 positive lymph nodes in the resection specimen (HR = 0.62, 95% CI 0.43-0.90). The favorable prognostic effect of TTE over THE was absent in the nCRT and surgery group (HR = 1.16, 95% CI 0.80-1.66) and in the subgroup of nCRT patients with 1 to 8 positive lymph nodes in the resection specimen (HR = 1.00, 95% CI 0.61-1.68). CONCLUSIONS: Compared to surgery alone, the addition of nCRT may reduce the need for TTE with extended lymphadenectomy to improve long-term survival in patients with esophageal adenocarcinoma.	esophagus