crossing96/oncoscreening huggingface dataset:
Delayed esophagectomy for adenocarcinoma is associated with a negative impact on long-term survival and an increased risk of perioperative morbidity.	OBJECTIVE: Delayed esophagectomy (DE) following chemoradiation therapy (CXRT) for esophageal carcinoma is undertaken in selected patients. This study aimed to assess both short-term outcomes and long-term survival for patients with adenocarcinoma undergoing DE. METHODS: The National Cancer Database was queried for patients with American Joint Committee on Cancer clinical stage II-III esophageal adenocarcinoma undergoing esophagectomy after CXRT. Patients were categorized as (1) DE, ≥90 days between completion of CXRT and surgery or (2) nondelayed esophagectomy (NDE), <90 days. Cox regression was performed to identify factors associated with mortality. RESULTS: A total of 8157 patients met criteria. Age >69, nonwhite race, Medicare/Medicaid insured patients preferentially underwent DE. Five-year overall survival (OS) favored NDE (36% vs. 31%, p = 0.008). Cox regression identified DE, clinical stage >T2, or >N0 as factors associated with mortality. Within the DE group, OS favored early cT-status. DE fared worse than NDE in 30- and 90-day mortality (4.5%/11.1% vs. 2.9%/6.5%, p < 0.01/p < 0.001) and margin positive resection (7.1% vs. 4.2%, p < 0.001). CONCLUSIONS: For esophageal adenocarcinoma, DE is associated with decreased OS compared to NDE. For DE, cT-status is prognostic for OS, while cN-status was not. Increased 30-/90-day mortality and margin positive resection rates for DE question whether patients with locally advanced (cT3/T4) primary esophageal adenocarcinoma should undergo intentional DE.	esophagus
IGH repertoire analysis at scale: deciphering the complexity of B cell infiltration and migration in esophageal squamous cell carcinoma.	Tumor-infiltrating B-lineage cells have become predictors of prognosis and immunotherapy responses in various cancers. However, limited knowledge about their infiltration and migration patterns has hindered the understanding of their anti-tumor functions. Here, we examined the immunoglobulin heavy chain (IGH) repertoires in 496 multi-regional tumor, 107 normal tissue, and 48 metastatic lymph node samples obtained from 107 patients with esophageal squamous cell carcinoma (ESCC). Our study revealed higher IgG-type B-lineage cells infiltration in tumors than in healthy tissue, which was associated with improved patient outcomes. Genes such as ACTN1, COL6A5, and pathways like focal adhesion, which shapes the physical structure of tumors, could affect B-lineage cell infiltration. Notably, the IGH sequence was used as an identity-tag to monitor B cell migration, and their infiltration schema within the tumor were depicted based on our multi-regional tumor specimens. This analysis revealed an escalation in B cell clones overlapped between metastatic lymph nodes and tumors. Therefore, the Lymph Node Activation Index was defined, which could predict the outcomes of patients with lymph node metastasis. This research introduces a novel framework for probing B cell infiltration and migration within the tumor microenvironment using large-scale transcriptome data, while simultaneously providing fresh perspectives on B cell immunology within ESCC.	esophagus
Opportunities and challenges in combining immunotherapy and radiotherapy in esophageal cancer.	BACKGROUND: Immunotherapy has shown promise in the treatment of esophageal cancer, but using it alone only benefits a small number of patients. Most patients either do not have a significant response or develop secondary drug resistance. The combination of radiotherapy and immunotherapy appears to be a promising approach to treating esophageal cancer. PURPOSE: We reviewed milestone clinical trials of radiotherapy combined with immunotherapy for esophageal cancer. We then discussed potential biomarkers for radiotherapy combined with immunotherapy, including programmed cell death-ligand 1 (PD-L1) status, tumor mutation burden (TMB), tumor-infiltrating lymphocytes, ct-DNA, imaging biomarkers, and clinical factors. Furthermore, we emphasize the key mechanisms of radiation therapy-induced immune stimulation and immune suppression in order to propose strategies for overcoming immune resistance in radiation therapy (RT). Lastly, we discussed the emerging role of low-dose radiotherapy (LDRT) , which has become a promising approach to overcome the limitations of high-dose radiotherapy. CONCLUSION: Radiotherapy can be considered a triggering factor for systemic anti-tumor immune response and, with the assistance of immunotherapy, can serve as a systemic treatment option and potentially become the standard treatment for cancer patients.	esophagus
Ensembled CNN with artificial bee colony optimization method for esophageal cancer stage classification using SVM classifier.	BACKGROUND: Esophageal cancer (EC) is aggressive cancer with a high fatality rate and a rapid rise of the incidence globally. However, early diagnosis of EC remains a challenging task for clinicians. OBJECTIVE: To help address and overcome this challenge, this study aims to develop and test a new computer-aided diagnosis (CAD) network that combines several machine learning models and optimization methods to detect EC and classify cancer stages. METHODS: The study develops a new deep learning network for the classification of the various stages of EC and the premalignant stage, Barrett's Esophagus from endoscopic images. The proposed model uses a multi-convolution neural network (CNN) model combined with Xception, Mobilenetv2, GoogLeNet, and Darknet53 for feature extraction. The extracted features are blended and are then applied on to wrapper based Artificial Bee Colony (ABC) optimization technique to grade the most accurate and relevant attributes. A multi-class support vector machine (SVM) classifies the selected feature set into the various stages. A study dataset involving 523 Barrett's Esophagus images, 217 ESCC images and 288 EAC images is used to train the proposed network and test its classification performance. RESULTS: The proposed network combining Xception, mobilenetv2, GoogLeNet, and Darknet53 outperforms all the existing methods with an overall classification accuracy of 97.76% using a 3-fold cross-validation method. CONCLUSION: This study demonstrates that a new deep learning network that combines a multi-CNN model with ABC and a multi-SVM is more efficient than those with individual pre-trained networks for the EC analysis and stage classification.	esophagus
UPPER GASTROINTESTINAL TRACT ENDOSCOPY: A RETROSPECTIVE ANALYSIS OF INDICATIONS AND FINDINGS AT ATBUTH BAUCHI.	INTRODUCTION: Upper gastrointestinal (UGI) endoscopy is considered a safe procedure performed for diagnosis, monitoring the course of disease, early detection of complications, treatment, and responses to therapeutic intervention. The indications have increased over the years. This study aimed to analyse the indications, findings, and safety of UGI endoscopy in our environment. METHODOLOGY: A retrospective study of consecutive patients who had UGI endoscopy at ATBUTH over the period of two years (2014 -2016). Data extracted from the records of the patients including biodata, clinical presentation, indications, findings, and complications of the procedure was analyzed using SSPS version 26. The procedure was explained to each patient. After a spray of 10% xylocaine spray to the patient's pharynx, the procedure was carried out with an Olympus CV-170 machine using standard protocols and monitoring of vital signs throughout. RESULTS: Two hundred and fifty-two patients were included, 148 (58.7%) males, 104 (41.3%) females, age range of 17-85 years (mean age ± SD = 44.1 ± 15.2). The commonest indications were dyspepsia 160 (63.5%). Hematemesis 32 (12.7%), suspicion for gastric 9(3.6%), and oesophageal tumours 6(2.4%) were also indications. The most common finding was gastritis 67 (26.6%). There was increased detection of gastric 11(4.4%) and oesophageal tumours 8(3.2%) more than clinical acumen and in elderly patients with troublesome symptoms. None of the patients developed complications from the procedure. CONCLUSIONS: UGI endoscopy is a safe procedure, and detects gastric and oesophageal tumours more accurately than clinical acumen and is recommended in all patients with troublesome upper GI symptoms.	esophagus
The oesophageal adenocarcinoma tumour immune microenvironment dictates outcomes with different modalities of neoadjuvant therapy - results from the AGITG DOCTOR trial and the cancer evolution biobank.	A plateau in treatment effect can be seen for the current 'one-size-fits-all' approach to oesophageal adenocarcinoma (OAC) management using neoadjuvant chemoradiotherapy (nCRT) or chemotherapy (nCT). In OAC, the tumour microenvironment (TME) is largely immunosuppressed, however a subgroup of patients with an immune-inflamed TME exist and show improved outcomes. We aimed to understand the overall immune-based mechanisms underlying treatment responses and patient outcomes in OAC, and in relation to neoadjuvant therapy modality. This study included 107 patients; 68 patients were enrolled in the Australian Gastro-Intestinal Trials Group sponsored DOCTOR Trial, and 38 patients were included from the Cancer Evolution Biobank. Matched pre-treatment and post-treatment tumour biopsies were used to perform multi-modality analysis of the OAC TME including NanoString mRNA expression analysis, multiplex and single colour immunohistochemistry (IHC), and peripheral blood mononuclear cell analysis of tumour-antigen specific T cell responses. Patients with the best clinicopathological outcomes and survival had an immune-inflamed TME enriched with anti-tumour immune cells and pathways. Those with the worst survival showed a myeloid T regulatory cell enriched TME, with decreased CD8(+) cell infiltration and increased pro-tumour immune cells. Multiplex IHC analysis identified that high intra-tumoural infiltration of CD8(+) cells, and low infiltration with CD163(+) cells was associated with improved survival. High tumour core CD8(+) T cell infiltration, and a low tumour margin infiltration of CD163(+) cells was also associated with improved survival. nCRT showed improved survival compared with nCT for patients with low CD8(+), or high CD163(+) cell infiltration. Poly-functional T cell responses were seen with tumour-antigen specific T cells. Overall, our study supports the development of personalised therapeutic approaches based on the immune microenvironment in OAC. Patients with an immune-inflamed TME show favourable outcomes regardless of treatment modality. However, in those with an immunosuppressed TME with CD163(+) cell infiltration, treatment with nCRT can improve outcomes. Our findings support previous studies into the TME of OAC and with more research, immune based biomarker selection of treatment modality may lead in improved outcomes in this deadly disease.	esophagus
Intractable chylous leak after radical esophagectomy treated with radiotherapy.	Postoperative chylous leak after esophagectomy is a rare but potentially life-threatening complication that results in hypovolemia, electrolyte imbalance, malnutrition, and immunologic deficiency. However, the management of postoperative chylous leak remains controversial. Following a diagnosis of esophageal cancer, a 64-year-old man was treated by video-assisted thoracoscopic esophagectomy, laparoscopic gastric tube formation, prophylactically thoracic duct ligation, and reconstruction with esophagogastrostomy at the neck level. Massive postoperative drainage from the thorax and abdomen did not initially meet the diagnostic criteria for chylothorax, which was ultimately diagnosed 3 weeks after the operation. Despite various treatments including total parenteral nutrition, octreotide and midodrine, reoperation (thoracic duct ligation and mechanical pleurodesis), and thoracic duct embolization, the chylous leak persisted. Finally, low-dose radiation therapy was administered with a daily dose of 2 Gy and completed at a total dose of 14 Gy. After this, the amount of pleural effusion gradually decreased over 2 weeks, and the last drainage tube was removed. The patient was alive and well at 60 months postoperatively. Herein, we describe a patient with intractable chylous leak after esophagectomy, which persisted despite conservative treatment, thoracic duct ligation, and embolization, but was finally successfully treated with radiotherapy.	esophagus
Dutch, UK and US professionals' perceptions of screening for Barrett's esophagus and esophageal adenocarcinoma: a concept mapping study.	BACKGROUND: Novel, less-invasive technologies to screen for Barrett's esophagus (BE) may enable a paradigm shift in early detection strategies for esophageal adenocarcinoma (EAC). Understanding professionals' perspectives on screening is important to determine how to proceed. We aimed to explore and compare professionals' perceptions of screening for BE and EAC screening in three countries. METHODS: In this study, 29 Dutch, 20 British and 18 American health care professionals (clinicians, researchers and policy makers) participated in concept mapping: a mixed-methods consensus building methodology. Statements on perceived barriers, facilitators, advantages, disadvantages, implications or worries associated with screening for BE and EAC were collected in asynchronous digital brainstorm sessions. Subsequently, participants sorted the statements into groups according to thematic similarity and assessed the relevance of each statement in evaluating the acceptability of BE and EAC screening. Multidimensional scaling and cluster analysis were used to map the associations between generated statements. RESULTS: Professionals across three countries identified eight consistent themes that relate to their perceptions of screening for BE and EAC: (1) Benefits, (2) Harms, (3) Clinical effectiveness concerns, (4) Screening population, (5) Screening modality, (6) Resources, (7) Ownership, and (8) Public communication. Dutch and American professionals prioritized the potential health benefits of screening but also questioned clinical impact. In contrast, British participants prioritized identification of the screening population and suitable test. CONCLUSIONS: Most professionals see potential in less-invasive screening tests for BE and EAC but underline the need to define the target screening population and determine benefits and harms before widely employing them. Successful implementation will require thoughtful consideration of the involvement of general practitioners, readiness of endoscopy and pathology services, balanced public communication, and country-specific regulations.	esophagus
CRP as an early indicator for anastomotic leakage after esophagectomy for cancer: a single tertiary gastro-esophageal center study.	PURPOSE: To determine the relationship between postoperative C-reactive protein (CRP) as an early indicator of anastomotic leakage (AL) after esophagectomy for esophageal cancer. METHODS: We reviewed patients diagnosed with esophageal or esophagogastric junctional cancer who underwent esophagectomy between 2006 and 2022 at the Karolinska University Hospital, Stockholm, Sweden. Multivariable logistic regression models estimated relative risk for AL by calculating the odds ratio (OR) with a 95% confidence interval (CI). The cut-off values for CRP were based on the maximum Youden's index using receiver operating characteristic curve analysis. RESULTS: In total, 612 patients were included, with 464 (75.8%) in the non-AL (N-AL) group and 148 (24.2%) in the AL group. Preoperative body mass index and the proportion of patients with the American Society of Anesthesiologists physical status classification 3 were significantly higher in the AL group than in the N-AL group. The median day of AL occurrence was the postoperative day (POD) 8. Trends in CRP levels from POD 2 to 3 and POD 3 to 4 were significantly higher in the AL than in the N-AL group. An increase in CRP of ≥ 4.65% on POD 2 to 3 was an independent risk factor for AL with the highest OR of 3.67 (95% CI 1.66-8.38, p = 0.001) in patients with CRP levels on POD 2 above 211 mg/L. CONCLUSION: Early changes in postoperative CRP levels may help to detect AL early following esophageal cancer surgery.	esophagus
Sex- and gender-specific differences in symptoms and health-related quality of life among patients with gastroesophageal reflux disease.	Gastroesophageal Reflux Disease (GERD) is a common chronic gastrointestinal disorder affecting both men and women. Nonerosive reflux disease generally affects more women, whereas GERD complications such as Barrett's esophagus (BE) or esophageal cancer affect more men. The aim of this study was to evaluate sex- and gender-specific symptoms and health-related quality of life (HRQoL) among men and women with GERD. Patients with clinical signs of reflux and completion of 24-hour pH-Impedance testing at the University Hospital Cologne were included into the study. Evaluation of symptoms and HRQoL included the following validated questionnaires: GERD-Health-Related Quality of Life (GERD HRQL), Gastrointestinal Quality of Life Index (GIQLI), and Hospital Anxiety and Depression Scale (HADS). In all, 509 women and 355 men with GERD were included. Men had a significantly higher DeMeester score (60.2 ± 62.6 vs. 43 ± 49.3, P < 0.001) and a higher incidence of BE (18.6 vs. 11.2%, P = 0.006). Women demonstrated significantly higher levels of anxiety (30.9 vs. 14.5%, P = 0.001), more severely impacting symptoms (45.3 ± 11.3 vs. 49.9 ± 12.3, P < 0.001), as well as physical (14.2 ± 5.7 vs. 16.7 ± 5.6, P < 0.001) and social dysfunction (13.3 ± 4.8 vs. 14.8 ± 4.3, P = 0.002). Women further reported a lower HRQoL (85.3 ± 22.7 vs. 92.9 ± 20.8, P < 0.001). Men and women differ on biological, psychological, and sociocultural levels.	esophagus
Global trends in esophageal cancer mortality with predictions to 2025, and in incidence by histotype.	BACKGROUND: Esophageal cancer (EC) is a malignancy with a poor prognosis. We provided a global overview of EC mortality, analyzing figures over the last three decades and estimating mortality rates for the year 2025. We also reported incidence trends and the distribution of squamous cell carcinoma (SCC) and adenocarcinoma (AC) in selected countries. METHODS: We considered EC trends in the age-standardised mortality rates (ASMR) from the World Health Organization database for selected countries. To estimate the number of deaths and ASMRs for 2025, we applied a Poisson linear regression model to the latest trend segment identified using a joinpoint model. We reported EC incidence trends according to histology using the Cancer Incidence in Five Continents database for the calendar period of 1990-2012. RESULTS: In 2015-19, the male ASMRs/100,000 were 4.01 in the EU-27, 4.28 in the USA, and 5.10 in Japan. The corresponding female rates ranged from 0.82 to 0.85/100,000. Male mortality showed a decreasing trend in most countries analyzed, with earlier and steeper declines in southern Europe. Conversely, ASMRs were increasing in Belarus, Finland, Greece, and Cuba. Female mortality showed a slight increase in several European countries, while North America, Latin America, and Australasia showed favorable trends. Projections suggest that male EC mortality is expected to decline in all countries except the Russian Federation. Female favorable trends are also predicted in most countries, except for France, Germany, the Russian Federation, and Canada. SCC remained the most common histotype, but AC incidence showed an upward trend, particularly in high-income countries. CONCLUSION: The observed trends in EC mortality reflect variations in patterns of major risk factors. Effective control of risk factors would contribute to reducing the burden of EC, together with early diagnosis and potential improvements in treatments.	esophagus
m6A regulator-mediated methylation modification patterns and tumor microenvironment immune infiltration with prognostic analysis in esophageal cancer.	Esophageal cancer is a highly malignant disease with poor prognosis. Despite recent advances in the study of esophageal cancer, there has been only limited improvement in the treatment and prognosis. N6-methyladenosine (m6A), a type of RNA modification, has been extensively investigated and is involved in many biological behaviors, including tumorigenesis and progression. Thus, more research on m6A modification may increase our understanding of esophageal cancer pathogenesis and provide potential targets. In our study, we integrated the public data of esophageal cancer from The Cancer Genome Atlas (TCGA) and Gene-Expression Omnibus (GEO) databases. Unsupervised clustering analysis was used to classify patients into different groups. Gene set variation analysis (GSVA) was performed in a nonparametric and unsupervised mode. We evaluated immune cell infiltration by single sample gene set enrichment analysis (ssGSEA). Differentially expressed genes (DEGs) among m6A clusters were identified using Empirical Bayesian approach. Both multivariate and univariate Cox regression models were used for prognostic analysis. We provided an overview of gene variation and expression of 23 m6A regulators in esophageal cancer, as well as their effects on survival. Based on the overall expression level of m6A regulators, patients were classified into three m6A clusters (A-C) with different immune cell infiltration abundance, gene expression signatures and prognosis. Among m6A clusters, we identified 206 DEGs, according to which patients were classified into 4 gene clusters (A-D). Quantitative m6A score was calculated for each patient based on those DEGs with significant impact on survival. The infiltration of all types of immune cells except type 2 T helper (Th2) cells were negatively correlated with m6A score. M6Acluster C exhibited the lowest m6A score, the most abundant immune cell infiltration, and the worst prognosis, suggesting an immune excluded phenotype. Consistently, gene cluster D with the lowest m6A score showed the worst prognosis. In short, patients with esophageal cancer showed different m6A modification patterns. Quantitative scoring indicated that patients with the lowest m6A score exhibited the most abundant immune cell infiltration and the poorest prognosis. This m6A scoring system is promising to assess m6A modification pattern, characterize immune infiltration and guide personalized treatment and prognostic prediction.	esophagus
USP4 promotes the proliferation, migration, and invasion of esophageal squamous cell carcinoma by targeting TAK1.	Ubiquitin-specific protease 4 (USP4) represents a potential oncogene involved in various human cancers. Nevertheless, the biological roles and precise mechanism of USP4 in esophageal squamous cell carcinoma (ESCC) progression are not understood. Here, USP4 expression was found to be markedly upregulated in ESCC tumor tissues and cells. Loss- and gain-of-function assays suggested that USP4 silencing inhibited ESCC cell proliferation, migration, and invasion, while USP4 overexpression promoted these behaviors. Consistently, USP4 silencing repressed tumor growth and metastasis in an ESCC nude mouse model in vivo. As a target molecule of USP4, transforming growth factor-β-activated kinase 1 (TAK1) also showed high expression in ESCC. Moreover, we observed that USP4 specifically interacted with TAK1 and stabilized TAK1 protein levels via deubiquitination in ESCC cells. Importantly, USP4 promotes ESCC proliferation, migration, and invasion via the MEK/ERK signaling pathway and can be inhibited by U0126. Neutral red (NR), an inhibitor of USP4 can suppress ESCC progression in vitro and in vivo. Overall, this study revealed that USP4/TAK1 plays crucial roles in ESCC progression by modulating proliferation, migration, and invasion, and USP4 might be a potential therapeutic target in ESCC.	esophagus