crossing96/oncoscreening huggingface dataset:
Identification of Molecular Biomarkers and Key Pathways for Esophageal Carcinoma (EsC): A Bioinformatics Approach.	Esophageal carcinoma (EsC) is a member of the cancer group that occurs in the esophagus; globally, it is known as one of the fatal malignancies. In this study, we used gene expression analysis to identify molecular biomarkers to propose therapeutic targets for the development of novel drugs. We consider EsC associated four different microarray datasets from the gene expression omnibus database. Statistical analysis is performed using R language and identified a total of 1083 differentially expressed genes (DEGs) in which 380 are overexpressed and 703 are underexpressed. The functional study is performed with the identified DEGs to screen significant Gene Ontology (GO) terms and associated pathways using the Database for Annotation, Visualization, and Integrated Discovery repository (DAVID). The analysis revealed that the overexpressed DEGs are principally connected with the protein export, axon guidance pathway, and the downexpressed DEGs are principally connected with the L13a-mediated translational silencing of ceruloplasmin expression, formation of a pool of free 40S subunits pathway. The STRING database used to collect protein-protein interaction (PPI) network information and visualize it with the Cytoscape software. We found 10 hub genes from the PPI network considering three methods in which the interleukin 6 (IL6) gene is the top in all methods. From the PPI, we found that identified clusters are associated with the complex I biogenesis, ubiquitination and proteasome degradation, signaling by interleukins, and Notch-HLH transcription pathway. The identified biomarkers and pathways may play an important role in the future for developing drugs for the EsC.	esophagus
Factors associated with access and approach to esophagectomy for cancer: a National Cancer Database study.	BACKGROUND: Minimally invasive esophagectomy (MIE) for esophageal cancer has been associated with decreased pain, less blood loss, and shorter hospital stay with comparable survival to open surgery. To date, there is minimal information regarding what factors are associated with access to MIE. METHODS: The National Cancer Database (NCDB) was used to compare rates of MIE (either robotic or laparoscopic) and open esophagectomy (OE) by demographic and clinical factors. Continuous variables were compared using a linear trend test, and categorical variables were compared using Mantel-Haenszel tests. Binomial regression was performed to examine significant factors after adjusting for confounding variables. RESULTS: There were 18,366 patients included in the analysis. Of all esophagectomies performed in the US, 49% were performed by OE and 51% were performed by MIE. Patients who had undergone MIE were more likely to live in the Eastern US as compared with the Midwest [odds ratio (OR) 1.72; 95% confidence interval (CI) 1.58, 1.88] or the South (OR 1.31; 95% CI 1.19, 1.44). They were also more likely to be treated at an academic center (OR 1.64; 95% CI 1.53, 1.75) rather than a community hospital, and to be of White race as compared with Asian race (OR 1.46; 95% CI 1.10, 1.92). There was not a significant difference in the rates of MIE between White and Black patients (OR 1.12; 95% CI 0.96, 1.32). MIE was more likely with each passing year, and higher TNM stages of cancer were less likely to be treated with MIE (P < 0.001 for all). CONCLUSION: While MIE is evolving, OE is still considered standard of care with robotic approaches representing a minority of MIE. While there are several factors associated with access to MIE, including race, facility type and geographic location, these factors should be further explored to help increase access to MIE.	esophagus
Percutaneous endoscopic gastrostomy prior to esophagectomy for esophageal cancer - a systematic review and meta-analysis.	BACKGROUND: For resectable esophageal cancer (EC), it remains controversial whether to place percutaneous endoscopic gastrostomy (PEG) before the curative surgery to provide nutritional support during the neoadjuvant therapy. OBJECTIVE: To compare surgical outcomes for patients who received preoperative PEG and those without PEG placement (No-PEG) insertion prior to surgery in a potentially operable EC. METHODS: A comprehensive literature search was conducted to identify randomized and non-randomized studies comparing PEG and No-PEG groups. RESULTS: Four retrospective studies with a total number of 1,027 patients were identified and included in this meta-analysis. The differences in anastomotic leakage, anastomotic stricture, morbidity, pulmonary complications, wound infection, and hospital stay were not statistically significant between the two groups. Operation time was significantly shorter in the PEG group. There was no PEG-related gastric conduit failure and no leak from the PEG site in the PEG group. CONCLUSION: We conclude preoperative PEG for resectable EC is a safe procedure with no adverse effect on the gastric tube construction and anastomosis, it can be selectively inserted for EC patients with marked weight loss and malnutrition or those at risk of developing malnutrition during neoadjuvant therapy.	esophagus
Development of a model to predict the prognosis of esophageal carcinoma based on autophagy-related genes.	Aim: To identify a potential prognostic signature of esophageal carcinoma based on autophagy-related genes (ARGs). Methods: RNA sequencing and clinical data were downloaded from the Cancer Genome Atlas. Significantly different ARGs were identified by Wilcoxon signed-rank test. A prognostic model was established employing Cox regression analysis. The model was evaluated by receiver operating characteristic and Kaplan-Meier curve. Results: A total of 28 significantly different ARGs were identified. Seven ARGs were screened to construct the prognostic model. The efficacy of the model was verified. A nomogram also validated the role of risk score in predicting prognosis. Enrichment analyses showed the possible underlying mechanisms. Conclusion: The seven-ARGs prognostic model was validated to be promising for predicting the prognosis of patients with esophageal carcinoma.	esophagus
[Effect of Biweekly-DCF Neoadjuvant Chemotherapy on Skeletal Muscle Mass of Esophageal Cancer Patients].	INTRODUCTION: Several studies reported that skeletal muscle mass affects the clinical response and quality of life of cancer patients during chemotherapy. Here we examined the adverse events and effects of anticancer drugs on the skeletal muscle mass of patients with esophageal cancer who received biweekly docetaxel, cisplatin, and 5-fluorouracil(DCF)neoadjuvant chemotherapy in our department. SUBJECTS AND METHODS: We retrospectively analyzed 105 patients with esophageal cancer who received biweekly-DCF neoadjuvant chemotherapy in 2009-2019. The cross-sectional area of the psoas muscle at the level of the third lumbar vertebra on computed tomography was assessed to calculate the psoas muscle index(PMI). Patients were divided into the high PMI group(high-group)and low PMI group(low-group)by cut-off value(male: 6.36 cm2/m2; female: 3.92 cm2/m2). Hematological toxicity, non-hematological toxicity, and therapeutic effect were retrospectively examined. RESULTS: Male in the high-group had significantly less ≥Grade 3 hematological toxicity than those in the low-group. Univariate and multivariate analyses showed that PMI(odds ratio: 1, p<0.05)was significantly related to decreased hematological toxicity. CONCLUSION: In preoperative chemotherapy for esophageal cancer, the incidence of hematological toxicity was significantly higher in patients with low skeletal muscle mass. Thus, skeletal muscle mass may be a marker for determining optimal anticancer drug dosage.	esophagus
[Preoperative Esophageal Decompression and Enteral Nutrition Using a W-ED Tube in Patients with Esophagogastric Junction Cancer-A Case Report].	The patient was a 67-year-old male diagnosed with adenocarcinoma of the esophagogastric junction. The esophagus was markedly dilated due to severe stenosis, and aspiration pneumonia was observed. Therefore, he was treated with a W- ED tube for simultaneous esophageal decompression and enteral nutrition. Two weeks of W-ED tube placement improved esophageal dilatation and pneumonia while maintaining nutritional status; thus, he underwent proximal gastrectomy, lower esophagectomy and combined resection of distal pancreas, spleen and left crus of diaphragm with jejunal interposition reconstruction. His postoperative course was uneventful, and he was discharged 16 days after surgery without any postoperative infectious complications such as pneumonia, anastomotic leakage, pancreatic fistula and enterocolitis. In the preoperative management for patients with esophagogastric junction cancer with severe stenosis, simultaneous esophageal decompression and enteral nutrition using a W-ED tube is very useful because it can improve aspiration pneumonia, reduce the risk of anastomotic leakage by improving esophageal edema, and prevent disuse atrophy of small intestinal villi.	esophagus
[Two Cases of Esophageal Neuroendocrine Carcinoma That Were Successfully Controlled by Multi-Modality Therapy].	Esophageal neuroendocrine carcinoma is extremely rare, and its treatment strategy has not been established. We report 2 cases esophageal neuroendocrine carcinoma. Case 1: A 74-year-old man was diagnosed as having esophageal neuroendocrine carcinoma(clinical T3N4M0, Stage Ⅳa). He received 60 Gy of radiation therapy with etoposide(100 mg/m2)plus cisplatin(80 mg/m2). No recurrence has been detected 1 year after treatment. Case 2: A 78-year-old man was diagnosed as esophageal neuroendocrine carcinoma(clinical T3N0M0, Stage Ⅱ). He underwent esophagectomy with 3 field lymph nodes dissection. Adjuvant chemotherapy was administered with irinotecan(60 mg/m2)plus cisplatin(60 mg/m2). After chemotherapy, he survived 1 year without recurrence.	esophagus
Robot-assisted versus video-assisted thoraco-laparoscopic McKeown's esophagectomy for esophageal cancer: a propensity score-matched analysis of minimally invasive approaches.	Minimally invasive esophagectomy for esophageal cancer decreases overall complication rate and leads to faster postoperative recovery. Robot-assisted minimally invasive esophagectomy is becoming more common. Its three-dimensional view and wristed instruments may provide advantages over traditional thoraco-laparoscopic techniques. There are limited studies comparing robotic and conventional thoraco-laparoscopic esophagectomy. This study aimed to evaluate short-term outcomes of robot-assisted McKeown esophagectomy (RAME) and video-assisted McKeown esophagectomy (VAME). All consecutive patients undergoing minimally invasive McKeown esophagectomy for middle and distal third esophageal cancer between January 2016 and December 2018 at our center were included in this study. Data on baseline characteristics, pathological data and short-term outcomes were collected in a dedicated database. Postoperative complications were defined as per recommendations of Esophagectomy Complications Consensus Group. Histopathologic assessment was performed as per College of American Pathologists guidelines. Propensity score matching was performed for comparison between RAME and VAME groups using age, gender, performance status, American Society of Anesthesiologists grade, body mass index, Charlson Index, tumor location, clinical tumor stage, and neoadjuvant treatment as covariates. A total of 74 patients were included, 25 of whom underwent RAME and 49 underwent VAME. Propensity score matching on 1:1 basis produced 25 pairs of patients, comparable in terms of baseline characteristics. Total operative time and estimated blood loss was similar between the two groups. Length of hospital stay was significantly lower in RAME group. Major postoperative complications (Clavien-Dindo grade ≥ 3A) were more common in VAME group, but not statistically significant. Median number of harvested lymph nodes and R0 resection rate did not differ in between the two groups. In our experience, robot-assisted McKeown esophagectomy was comparable to video-assisted McKeown esophagectomy in terms of safety, feasibility and oncologic adequacy. Use of the robot was associated with reduced hospital stay. Further randomized controlled studies with larger patient samples are needed to compare the two.	esophagus
A case of severe vasculitis after FLOT chemotherapy in a patient with metastatic gastric cancer who received multiple line chemotherapy.	INTRODUCTION: Leukocytoclastic vasculitis is a histopathological term describing vasculitis in which the inflammatory infiltrate in small vessels consists of neutrophils. Although FLOT is given perioperatively in locally advanced, resectable gastric or gastroesophageal junction adenocarcinoma, it has recently become a popular treatment option for metastatic cancers. In this case report, we present a case of FLOT-induced LCV. CASE REPORT: We present a 52-year-old patient with metastatic gastric adenocarcinoma treated with FLOT. The patient developed necrotizing vasculitis in the lower extremity after 5 cycles of FLOT. MANAGEMENT & OUTCOME: After discontinuation of the FLOT regimen, the necrotizing morbid LCV gradually regressed with steroid therapy. DISCUSSION: To the best of our knowledge, our case is the first case of LCV that developed after FLOT chemotherapy. The clinical appearance of the patient, occurrence after chemotherapy, erythematous rash developing on bilateral lower extremities, and palpable purpuric vasculitis made us suspect. We found a potential relationship between FLOT and vasculitis according to the Naranjo scale (score 4 + ).	esophagus
Baseball bat-like gastric tube for end-to-side oesophageal-gastric anastomosis decreased risks of anastomotic leakage after oesophagectomy for oesophageal cancer: A retrospective propensity score matched comparative study with 613 patients.	PURPOSE: To investigate the relationship between baseball bat-like gastric tubes for end-to-side oesophageal-gastric anastomosis and occurrence of anastomotic leakage after oesophagectomy for oesophageal cancer. METHODS: From July 2019 to June 2021, 613 patients with bat-like or narrow gastric tubes for end-to-side oesophageal-gastric anastomosis in oesophagectomy were retrospectively enrolled, in which 120 patients had narrow gastric tubes and 493 had bat-like gastric tubes. Clinical data including baseline characteristics, in-hospital variables and follow-up outcomes were collected. RESULTS: Higher occurrence of anastomotic leak was observed in the narrow group in the unmatched cohort (14.2%, 17/120 vs. 7.3%, 36/493; P = 0.016) or the matched cohort after Propensity Score Matching (PSM) analysis (14.2%, 17/120 vs. 7.5%, 27/360, P = 0.028) when compared to the bat-like group; Multivariable analysis for risk factors of postoperative anastomotic leak in the unmatched cohort showed that the use of bat-like gastric tube was an independent protective factor (OR: 0.502, 95% CI: 0.270-0.935, P = 0.030). CONCLUSIONS: Bat-like gastric tube can be used for end-to-side oesophageal-gastric anastomosis in oesophagectomy. This technique by improving blood supply to the area distal to the anastomosis decreased the incidence of anastomotic leak.	esophagus
CAF-derived exosomes deliver LINC01410 to promote epithelial-mesenchymal transition of esophageal squamous cell carcinoma.	Exosomes mediate cellular communications in cancer by transmitting active molecules. However, the CAFs-derived molecular determinants that regulate esophageal squamous cell carcinoma (ESCC) metastasis have not been fully characterized. The purpose of this study was to investigate the potential roles of exosomal LINC01410 of ESCC cells. The characteristics of exosomes were identified using transmission electron microscope (TEM), Nanoparticle Tracking Analysis (NTA). The expression of LINC01410 and miR-122-5p was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) assay. The biological roles of LINC01410 in ESCC cells were investigated using transwell assay. Western blot assay was employed to detect protein levels. The potential downstream molecular mechanism of LINC01410 was demonstrated with dual-luciferase reporter assay, RNA immunoprecipitation (RIP) assay and RNA pull down. CAFs promote the metastasis and epithelial-mesenchymal transition (EMT) of ESCC cells. CAFs exert their roles by transferring exosomes to ESCC cells, leading to a significant increase of LINC01410 level in ESCC cells. Mechanically, LINC01410 secreted by CAFs-Exo could contribute to metastasis and EMT by sponging miR-122-5p and increasing PKM2 level in TE-1 and Eca-109 cells. Additionally, LINC01410/miR-122-5p/PKM2 axis affecting ESCC metastasis and EMT in vitro and in vivo.	esophagus
Diagnostic value of circulating microRNAs for esophageal cancer: a meta-analysis based on Asian data.	BACKGROUND AND OBJECTIVE: esophageal cancer (EC) is one of the most common gastrointestinal malignant diseases. We conducted a comprehensive meta-analysis to explore the clinical applicability of circulating microRNA for the diagnosis of EC. METHODS: as of September 10, 2021, a comprehensive literature search was conducted on PubMed, Embase, Web of Science, Cochrane Library, Wanfang Database, and China National Knowledge Infrastructure (CNKI) to identify eligible studies. The sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve (AUC) were pooled to evaluate the test performance. The potential sources of heterogeneity were analyzed by subgroup analysis. Deeks' funnel plot was used to assess publication bias. RESULTS: 85 studies from 50 articles were included in the current meta-analysis. The overall pooled sensitivity was 0.82 (95 % CI, 0.79-0.84), specificity was 0.84 (95 % CI, 0.81-0.86), PLR was 4.9 (95 % CI, 4.2-5.9), NLR was 0.22 (95 % CI, 0.19-0.25), DOR was 22 (95 % CI, 17-29) and AUC was 0.89 (95 % CI, 0.86-0.92), respectively. Subgroup analysis suggested that miRNA clusters with a large sample size showed better diagnostic accuracy. Publication bias was not found. CONCLUSIONS: circulating miRNAs can be used as a potential non-invasive biomarker for the diagnosis of EC in Asian populations.	esophagus
Adjuvant Nivolumab in Esophageal or Gastroesophageal Junction Cancer: the Improvement in Progression-Free Survival Is Small.	Esophageal cancer is the seventh most common cancer globally, accounting more than a half million deaths per year. Despite several therapeutic options in neoadjuvant setting, including chemoradiotherapy and surgery, no adjuvant treatment has been established for patients at high risk of recurrence. Even so, findings from the recently published CheckMate 577 trial seem to suggest an important clinical impact, in terms of disease-free progression, for the use of adjuvant nivolumab, a PDL-1 inhibitor, in resected esophageal cancer or gastroesophageal junction cancer. The authors reported a benefit for the treatment arm of 22.4 months compared with 11.0 in the placebo group. Although median is commonly used as an endpoint in survival studies, it can be influenced by the timing of a few events in the descending portion of the Kaplan-Meier curve. Restricted mean survival time (RMST) considers the entire time-course of the curve and does not assume that event risks are constant over the follow-up. This may be helpful to a more realistic interpretation of survival outcomes. In this letter, we re-analyzed the study curves of the CheckMate 577 trial by application of RMST. While confirming the disease-free progression benefits for nivolumab compared with placebo (28.54 months for the treatment arms versus 22.70 for the controls), our analysis allows us to interpret the survival benefit in a more conservative manner.	esophagus
Time-spatial analysis of T cell receptor repertoire in esophageal squamous cell carcinoma patients treated with combined radiotherapy and PD-1 blockade.	T cell receptor (TCR) repertoire as a biomarker for predicting immunotherapy efficiency has been widely studied. However, its dynamics during radiotherapy combined with PD-1 blockade is little known. Using paired tumor and blood samples from the phase Ib clinical study (NCT03222440), we investigate the time-spatial TCR repertoire in esophageal squamous cell carcinoma (ESCC) patients treated with first-line definitive radiotherapy concurrently with anti-PD-1 antibody camrelizumab, and also evaluate the association between TCR repertoire and clinical outcomes. TCR sequencing was performed on tumor biopsies (n = 34, 15 pairs) and peripheral CD8(+) T cells (n = 36, 18 pairs) collected at baseline and during treatment (after 40 Gy radiation and 2 rounds of camrelizumab). Whole exome sequencing was applied to estimate genomic mutations and tumor mutation burden. We show that the intratumoral TCR repertoire at baseline was correlated with tumor microenvironment and presented heterogeneity inter-individually. T-cell clones inflowed mutually between tumors and peripheral blood under combination treatment, resulting in an elevation of intratumoral TCR diversity. The peripheral CD8(+) TCR diversity at baseline, increased tumor-peripheral Morisita-Horn overlap during treatment, and expansion of persistent intratumoral T-cell clones during treatment predicted improved survival. While it is unclear whether radiation contributed to the TCR changes versus PD-1 therapy alone, our results firstly reveal radiotherapy combined with PD-1 blockade greatly promoted time-spatial alteration of TCR repertoire between tumor and peripheral blood, which demonstrate the peripheral CD8(+) TCR diversity at baseline and dynamic alteration of intratumoral TCRs acted as potential effective biomarkers of radiotherapy combined with immunotherapy in ESCC.	esophagus
Fusobacterium nucleatum promotes esophageal squamous cell carcinoma progression via the NOD1/RIPK2/NF-κB pathway.	"Fusobacterium nucleatum, found in the oral cavity, influences the progression of gastrointestinal cancers. Additionally, our previous results suggested that F. nucleatum is associated with poor patient prognosis in esophageal squamous cell carcinoma (ESCC). However, the mechanism by which F. nucleatum affects aggressive tumor behavior has yet to be elucidated. We have conducted this clinical, in vitro, and in vivo study to clarify the mechanism of ESCC progression induced by F. nucleatum. Transmission electron microscopy revealed that F. nucleatum invaded and occupied ESCC cells and impacted gene and protein expression. Comprehensive mRNA expression and pathway enrichment analyses of F. nucleatum-treated ESCC cells identified the ""NF-κB"" and ""NOD-like receptor"" signaling pathways as enriched. We confirmed the relationship between the presence of F. nucleatum and NF-κB activation in resected ESCC tissues. Furthermore, F. nucleatum-treated ESCC cells demonstrated enhanced growth ability, and NF-κB activation, as well as overexpression of NOD1 and phosphorylated RIPK2. Furthermore, treated cells showed accelerated tumor growth, with NF-κB activation in xenograft models. F. nucleatum invaded ESCC cells and induced the NF-κB pathway through the NOD1/RIPK2 pathway, leading to tumor progression."	esophagus