crossing96/oncoscreening huggingface dataset:
Prognostic Biomarkers Identification in Esophageal Cancer Based on WGCNA and Single-Cell Analysis.	BACKGROUND: Esophageal cancer is one of the most common cancers worldwide. Dysregulation of genes plays an important role in cancer. In this study, we aimed to investigate the prognostic biomarkers in esophageal cancer based on comprehensive bioinformatics analysis including WGCNA and single cell analysis. METHODS: RNA sequencing data of esophageal cancer was downloaded from GSE75241 dataset in the GEO database. We also selected esophageal cancer patients from public databases (Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA)). WGCNA was used to construct a scale-free coexpression network of genes. Multifactor Cox analysis model was constructed as the prognostic model in esophageal cancer. Furthermore, single-cell gene analysis was used to discover the mechanism of hub genes in esophageal cancer. RESULTS: WGCNA discovered 182 genes for further analysis. Among 182 genes, four genes including ANGPT2, VCAN, MS4A4A, and FOS had significant prognostic value in esophageal cancer. In single cell analysis, seven types of cells subsets were distinguished including T cells, B cells, NK cells, monocytes, macrophages, DCs, neutrophils. The expression of four hub genes (ANGPT2, VCAN, MS4A4A, and FOS) in inflammatory cell subsets was evaluated, respectively. Hub genes were correlated with inflammatory cells in esophageal cancer. In addition, the subgroups of specific inflammatory cells such as macrophages, monocytes, and DCs were analyzed to identify the function of hub genes, either. Hub genes were correlated with differentiation of inflammatory cells including monocytes, macrophages, and DCs in tumor environment. CONCLUSIONS: We identified specific hub genes correlated with prognosis of esophageal cancer. These hub genes play critical roles by regulating inflammatory cells status in esophageal cancer.	esophagus
Liver Injury in Patients With Distal Esophageal Carcinoma After Precision Radiation Therapy: Systematic Review of FDG-PET/CT Patterns.	OBJECTIVE: To determine the incidence and various patterns of radiation-induced liver injury (RILI) and its temporal evolution on fluorodeoxiglucose-positron emission tomography/computed tomography (FDG-PET/CT) after neoadjuvant chemoradiation using precision radiation in patients with esophageal carcinoma. MATERIAL AND METHODS: We evaluated 639 patients with locally advanced esophageal carcinoma who had serial FDG-PET/CTs after neoadjuvant chemoradiation. Two readers reviewed the imaging studies in consensus and recorded the cases where new foci of increased FDG uptake were identified within the radiated liver parenchyma. RILI was confirmed by follow-up imaging or percutaneous biopsy. RESULTS: FDG-avid RILI developed in 39/639 (6%) of patients. The caudate and left hepatic lobe were involved in all cases. There were various patterns of increased FDG uptake: 38% of patients had a single focus of increased FDG uptake and 62% had 2 regions of increased FDG uptake, which were focal nodular or diffuse or a combination of focal nodular and diffuse FDG uptake. On CT, 72% of patients had a poorly-marginated region of low attenuation and 28% had a well-defined region of low attenuation with sharp, well-defined linear borders in the location of the radiation, as confirmed by the treatment plan. CONCLUSION: The caudate and left hepatic lobes were involved in all cases of RILI. The various imaging patterns of RILI on FDG-PET/CT include 1 or 2 regions of increased FDG uptake with a nodular, diffuse, or combined appearance. Awareness of this potential complication of radiation therapy and knowledge of the imaging manifestations of RILI is important to avoid misinterpretation as a metastasis.	esophagus
TWIST1 Plays Role in Expression of Stemness State Markers in ESCC.	BACKGROUND: Stemness markers play critical roles in the maintenance of key properties of embryonic stem cells (ESCs), including the pluripotency, stemness state, and self-renewal capacities, as well as cell fate decision. Some of these features are present in cancer stem cells (CSCs). TWIST1, as a bHLH transcription factor oncogene, is involved in the epithelial-mesenchymal transition (EMT) process in both embryonic and cancer development. Our aim in this study was to investigate the functional correlation between TWIST1 and the involved genes in the process of CSCs self-renewal in human esophageal squamous cell carcinoma (ESCC) line KYSE-30. METHODS: TWIST1 overexpression was enforced in the ESCC KYSE-30 cells using retroviral vector containing the specific pruf-IRES-GFP-hTWIST1 sequence. Following RNA extraction and cDNA synthesis, the mRNA expression profile of TWIST1 and the stem cell markers, including BMI1, CRIPTO1, DPPA2, KLF4, SOX2, NANOG, and MSI1, were assessed using relative comparative real-time PCR. RESULTS: Ectopic expression of TWIST1 in KYSE-30 cells resulted in an increased expression of TWIST1 compared to control GFP cells by nearly 9-fold. Transduction of TWIST1-retroviral particles caused a significant enhancement in BMI1, CRIPTO1, DPPA2, KLF4, and SOX2 mRNA expression, approximately 4.5-, 3.2-, 5.5-, 3.5-, and 3.7-folds, respectively, whereas this increased TWIST1 expression caused no change in the mRNA expression of NANOG and MSI1 genes. CONCLUSIONS: TWIST1 gene ectopic expression in KYSE-30 cells enhanced the level of cancer stem cell markers' mRNA expression. These results may emphasize the role of TWIST1 in the self-renewal process and may corroborate the involvement of TWIST1 in the stemness state capacity of ESCC cell line KYSE-30, as well as its potential as a therapeutic target.	esophagus
Development and Validation of a Prognostic Model for Esophageal Adenocarcinoma Based on Necroptosis-Related Genes.	Necroptosis is a newly developed cell death pathway that differs from necrosis and apoptosis; however, the potential mechanism of necroptosis-related genes in EAC and whether they are associated with the prognosis of EAC patients remain unclear. We obtained 159 NRGs from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and performed differential expression analysis of the NRGs in 9 normal samples and 78 EAC tumor samples derived from The Cancer Genome Atlas (TCGA). Finally, we screened 38 differentially expressed NRGs (DE-NRGs). The results of the GO and KEGG analyses indicated that the DE-NRGs were mainly enriched in the functions and pathways associated with necroptosis. Protein interaction network (PPI) analysis revealed that TNF, CASP1, and IL-1B were the core genes of the network. A risk score model based on four DE-NRGs was constructed by Least Absolute Shrinkage and Selection Operator (LASSO) regression, and the results showed that the higher the risk score, the worse the survival. The model achieved more efficient diagnosis compared with the clinicopathological variables, with an area under the receiver operating characteristic (ROC) curve of 0.885. The prognostic value of this model was further validated using Gene Expression Omnibus (GEO) datasets. Gene set enrichment analyses (GSEA) demonstrated that several metabolism-related pathways were activated in the high-risk population. Single-sample GSEA (ssGSEA) provided further confirmation that this prognostic model was remarkably associated with the immune status of EAC patients. Finally, the nomogram map exhibited a certain prognostic prediction efficiency, with a C-index of 0.792 and good consistency. Thus, the prognostic model based on four NRGs could better predict the prognosis of EAC and help to elucidate the mechanism of necroptosis-related genes in EAC, which can provide guidance for the target prediction and clinical treatment of EAC patients.	esophagus
Recent advances in esophageal squamous cell precancerous conditions: A review.	Esophageal squamous cell carcinoma (ESCC) is a common cancer in many developing countries in Asia and Africa, with a 5-year survival rate of approximately 20%. Most cases are diagnosed at an advanced age when there is no effective treatment strategy. Esophageal precancerous conditions have a much better prognosis, with a 5-year survival rate of over 90% by endoscopic diagnosis and treatment. Nevertheless, limitations, contraindications, and lymph node metastasis incompetency of endoscopy. Thus, the diagnosis and treatment of esophageal precancerous lesions remain a significant challenge. Biomarker investigations provide opportunities for target detection and therapy. Additionally, drug development is ongoing. Changes in lifestyle habits, such as diet balance, smoking and alcohol cessation, are beneficial for the prognosis of esophageal precancerous lesions. Collectively, multiple and sequential diagnoses and treatments are essential for curing esophageal precancerous lesions and reducing the incidence and mortality of ESCC.	esophagus
Hsa_circ_0007380 silencing restrains the growth and enhances radiosensitivity in esophagus cancer by miR-644a/Spindlin 1 axis.	Circular RNAs are frequently dysregulated and show important regulatory function of tumorigenesis in cancers. Hsa_circ_0007380 was found to be elevated in human radioresistant esophageal cancer cells. Here, this study aimed to investigate the action and mechanism of hsa_circ_0007380 in esophageal cancer carcinogenesis and radiosensitivity. Quantitative real-time PCR and western blotting were performed to detect levels of genes and proteins. Functional experiments were conducted using MTT assay, EdU assay, clonogenic survival assay, flow cytometry and murine xenograft model assay, respectively. The binding between miR-644a and hsa_circ_0007380 or spindlin1 (SPIN1) was validated using dual-luciferase activity assay. Hsa_circ_0007380 was highly expressed in esophagus cancer tissues and cells, knockdown of hsa_circ_0007380 suppressed esophagus cancer cell proliferation, induced apoptosis and enhanced radiosensitivity in vitro, and the same effects were also confirmed in nude mice. Mechanistically, hsa_circ_0007380 sequestered miR-644a to release SPIN1 expression, implying the hsa_circ_0007380/miR-644a/SPIN1 competing endogenous RNA network esophagus cancer cells. miR-644a was decreased in esophagus cancer, re-expression of miR-644a restrained cell growth and conferred radiosensitivity in esophagus cancer, which were reversed by SPIN1 overexpression. Besides that, inhibition of miR-644a abolished the promoting action of hsa_circ_0007380 knockdown on esophagus cancer apoptosis and radiosensitivity. Hsa_circ_0007380 silencing impedes cell growth and reinforces radiosensitivity in esophagus cancer by miR-644a/SPIN1 axis, suggesting a promising therapeutic target for esophagus cancer combined treatment.	esophagus
Safety and efficacy of letetresgene autoleucel alone or with pembrolizumab for relapsed/refractory multiple myeloma.	This pilot study assessed the safety and efficacy of letetresgene autoleucel (lete-cel; GSK3377794), a genetically modified autologous T-cell therapy targeting New York esophageal squamous cell carcinoma-1 (NY-ESO-1)/L antigen family member 1 isoform A (LAGE-1a)-positive myeloma cells, alone or in combination with pembrolizumab in patients with relapsed/refractory multiple myeloma. Eligible patients expressed NY-ESO-1 and/or LAGE-1a and either HLA-A∗02:01, ∗02:05, or ∗02:06. Patients received lete-cel single infusion alone (arm 1) or with pembrolizumab (arm 2). 127 patients were screened, and 6 patients (3 per arm) were enrolled; patients in arm 1 and 2 received lete-cel alone, or with pembrolizumab, respectively. All patients exhibited grade 3/4 cytopenias, which resolved or improved to grade 1. One patient (arm 1) had grade 3/4 lete-cel-related adverse events (AEs); 2 patients (arm 2) had grade 3/4 AEs related to lete-cel and lymphodepletion. Three patients with grade 1/2 cytokine release syndrome (CRS) exhibited elevated post-lete-cel interleukin-6 levels versus those without CRS. Pooled overall response rate was 50% including 1 patient each with confirmed clinical response, very good clinical response, and partial response, and progression-free survival ranged from 1.3 to 5.2 months. Responders (arm 1: n = 1; arm 2: n = 2) had a time-to-response of 3 weeks, duration of response of 2.1 months. Two responders, but no nonresponders, exhibited elevated cytokine levels after lete-cel infusion. Lete-cel had a manageable safety profile and demonstrated clear but transient antitumor activity in patients with relapsed/refractory multiple myeloma. This trial was registered at www.clinicaltrials.gov as #NCT03168438.	esophagus
Anti-cancer effect of entacaponeon esophageal cancer cells via apoptosis induction and cell cycle modulation.	BACKGROUND: Esophageal cancer (EC) is the sixth leading cause of cancer-related death, despite many advances in treatment, the survival of patients still remains poor. In recent years, the N6-methyladenosine (m6A) has been introduced as one of the most important modifications at the epitranscriptome level, with an important role in the mRNA regulation in various diseases, such as cancers. The m6A is regulated by different factors, including FTO as a demethylase. The m6A modification, especially through FTO overexpression has an oncogenic role in different cancer types such as EC. Recent studies showed that entacapone, a catechol-o-methyl transferase (COMT) inhibitor currently applied for Parkinson's disease, can inhibit FTO enzyme. AIMS: In this study, we aimed to investigate the effect of entacapone as an FTO inhibitor on the m6A level and also apoptosis and cell cycle response in KYSE-30 and YM-1 of esophageal squamous cancer cell (ESCC) lines. METHODS: Cell toxicity and IC50 of entacapone were evaluated using The MTT assay in YM-1 and KYSE-30 cells. Cells were treated into two groups: DMSO (control) and entacapone (mean IC(50) ). Total RNA was extracted, and m6A levels were measured via the ELISA method. Subsequently, the apoptosis and cell cycle dys-regulation were detected by annexin-V-FITC/PI staining and PI staining via flow cytometry. RESULTS: Entacapone has the cytotoxicity effect on both esophageal cancer cell lines compared to normal PBMC cells. As well, entacapone treatment (140 μM) can induce apoptosis (KYSE-30: 50%. YM-1:22.6%) and has a modulatory effect on cell cycle progression in both YM-1 and KYSE-30 cells (p-value<.05). However, no significant difference in the m6A concentration was observed. CONCLUSION: Our findings suggested that entacapone has the inhibitory effect on ESCC cell lines through induction of the apoptosis and modulation of the cell cycle without toxicity on the normal PBMC.	esophagus
Is Thoracic Duct Resection Necessary for Esophageal Squamous Cell Carcinoma Patients Treated with Neoadjuvant Chemoradiotherapy? A Propensity-Matched Analysis Based on the Comprehensive Registry of Esophageal Cancer in Japan.	BACKGROUND: The thoracic duct (TD) plays an important role in nutrition and immunity but is often resected with the esophagus when dissecting surrounding lymph nodes in patients with esophageal squamous cell carcinoma (ESCC). We examined whether indiscriminate TD resection improved the prognosis of patients with ESCC treated with neoadjuvant chemoradiotherapy (NACRT) followed by esophagectomy. METHODS: A total of 440 patients treated with NACRT followed by esophagectomy between 2007 and 2012 were analyzed using data from the Comprehensive Registry of Esophageal Cancer in Japan. The propensity score-matched TD resection and TD preservation groups were compared in terms of short- and long-term outcomes. RESULTS: After matching, there were 85 patients in both groups. No significant differences were found between groups in either overall survival or cause-specific survival rates at 5 years: 44.2% and 49.0% in the TD resection group, and 39.8% and 47.2% in the TD preservation group, respectively. Furthermore, the number of retrieved mediastinal lymph nodes was significantly greater in the TD resection group than in the TD preservation group (26 vs. 15, p < 0.0001). In contrast, TD resection was associated with metastasis to a significantly greater number of distant organs than TD preservation (49 vs. 32, p = 0.049). CONCLUSIONS: TD resection did not contribute to improved survival in patients with ESCC but did lead to metastases in more organs than TD preservation. Consequently, indiscriminate TD resection might be avoided in patients with ESCC treated with NACRT followed by esophagectomy.	esophagus
Chemoradiotherapy with concurrent durvalumab for the palliative treatment of oligometastatic oesophageal and gastrooesophageal carcinoma with dysphagia: a single arm phase II clinical trial (PALEO, sponsored by the Australasian Gastro-Intestinal Trials Group).	BACKGROUND: Oesophageal and gastrooesophageal junction (GOJ) carcinoma frequently present with dysphagia and de novo metastatic disease. There is scope to improve treatment paradigms to both address symptoms and improve survival. One method is integrating immune checkpoint inhibition with novel treatment combinations. METHODS: PALEO is a single arm, phase II clinical trial in patients with previously untreated, oligometastatic or locoregionally advanced oesophageal or GOJ carcinoma and dysphagia. PALEO is sponsored by the Australasian Gastro-Intestinal Trials Group (AGITG). Participants receive 2 weeks of therapy with concurrent hypofractionated radiotherapy of 30Gy in 10 fractions to the primary tumour, weekly carboplatin AUC2, weekly paclitaxel 50 mg/m(2) and durvalumab 1500 mg q4 weekly, followed by durvalumab monotherapy continuing at 1500 mg q4weekly until disease progression, unacceptable toxicity or 24 months of therapy. A single metastasis is treated with stereotactic radiotherapy of 24Gy in 3 fractions in week 7. The trial primary endpoint is the progression free survival rate at 6 months. Secondary endpoints include duration of dysphagia relief, nutritional status change, quality of life, response rate, toxicity, progression free survival and overall survival. The tertiary endpoint is prediction of outcome based on biomarkers identified from patient serial blood samples collected pre- and post-radiotherapy. DISCUSSION: This unique investigator-initiated clinical trial is designed to simultaneously address the clinically relevant problems of dysphagia and distant disease control. The overarching aims are to improve patient nutrition, quality of life and survival with low toxicity therapy. AGITG PALEO is a multidisciplinary collaboration and will add to the understanding of the relationship between radiotherapy and the anti-tumour immune response. TRIAL REGISTRATION: Australian and New Zealand Clinical Trials Registry: ACTRN12619001371189 , registered 8 October 2019.	esophagus
Development and Validation of a Predictive Model of Therapeutic Effect in Patients with Esophageal Squamous Cell Carcinoma Who Received Neoadjuvant Treatment: A Nationwide Retrospective Study in Japan.	BACKGROUND: Neoadjuvant treatment has become the standard of care for patients with advanced esophageal cancer. However, few studies have elucidated the clinical factors that predict response to neoadjuvant therapy in a large multicenter cohort. We aimed to develop a predictive model of therapeutic effect in patients with esophageal squamous cell carcinoma (SCC) who received neoadjuvant treatment. METHODS: This nationwide study included 4078 patients from 85 institutions. Patients who received neoadjuvant treatment followed by surgery for esophageal SCC were eligible. We developed a logistic regression model to predict good pathological therapeutic effects, and a predictive nomogram was generated by applying the logistic regression formula. RESULTS: Among neoadjuvant regimens, cisplatin plus 5-fluorouracil (CF) was the most frequently used (60.2%), followed by docetaxel plus CF (DCF, 27.4%), CF with radiotherapy (CF-RT, 4.5%), adriamycin plus CF (3.6%), nedaplatin plus 5-fluorouracil (0.9%), and DCF-RT (0.5%). Multivariable analysis revealed that male sex, advanced cT category, and increased pretherapeutic SCC antigen level were independently associated with not achieving a good therapeutic effect. Moreover, intensified neoadjuvant regimens were independently associated with favorable therapeutic effects; DCF-RT elicited the best therapeutic effect, followed by CF-RT and DCF. A predictive model including nine commonly measured preoperative variables was generated, and the area under the curve was 0.679 (95% confidence interval: 0.658-0.700). This nomogram was also adequately validated internally. CONCLUSIONS: The model developed in this study was validated and predicts the therapeutic effect in patients with esophageal SCC who received neoadjuvant treatment. This model might contribute to individualized treatment strategies.	esophagus
Targeting USP10 induces degradation of oncogenic ANLN in esophageal squamous cell carcinoma.	Anillin (ANLN) is a mitosis-related protein that promotes contractile ring formation and cytokinesis, but its cell cycle-dependent degradation mechanisms in cancer cells remain unclear. Here, we show that high expression of ANLN promotes cytokinesis and proliferation in esophageal squamous cell carcinoma (ESCC) cells and is associated with poor prognosis in ESCC patients. Furthermore, the findings of the study showed that the deubiquitinating enzyme USP10 interacts with ANLN and positively regulates ANLN protein levels. USP10 removes the K11- and K63-linked ubiquitin chains of ANLN through its deubiquitinase activity and prevents ANLN ubiquitin-mediated degradation. Importantly, USP10 promotes contractile ring assembly at the cytokinetic furrow as well as cytokinesis by stabilizing ANLN. Interestingly, USP10 and the E3 ubiquitin ligase APC/C co-activator Cdh1 formed a functional complex with ANLN in a non-competitive manner to balance ANLN protein levels. In addition, the macrolide compound FW-04-806 (F806), a natural compound with potential for treating ESCC, inhibited the mitosis of ESCC cells by targeting USP10 and promoting ANLN degradation. F806 selectively targeted USP10 and inhibited its catalytic activity but did not affect the binding of Cdh1 to ANLN and alters the balance of the USP10-Cdh1-ANLN complex. Additionally, USP10 expression was positively correlated with ANLN level and poor prognosis of ESCC patients. Overall, targeting the USP10-ANLN axis can effectively inhibit ESCC cell-cycle progression.	esophagus
Update on therapeutic strategy for esophageal anastomotic leak: A systematic literature review.	Anastomotic leak is still a severe complication in esophageal surgery due to high mortality. This article reviews the updates on the treatment of anastomotic leak after esophagectomy in order to provide reference for clinical treatment and research. The relevant studies published in the Chinese Zhiwang, Wanfang, and MEDLINE databases to December 21, 2021 were retrieved, and esophageal carcinoma, esophagectomy, anastomotic leakage, and fistula selected as the keywords. A total of 78 studies were finally included. The treatments include traditional surgical drainage, new reverse drainage trans-fistula, stent plugging, endoscopic clamping, biological protein glue injection plugging, endoluminal vacuum therapy (EVT), and reoperation, etc. Early diagnosis, accurate classification and optimal treatment can promote the rapid healing of anastomotic leaks. EVT may be the most valuable approach, simultaneously with good commercial prospects. Reoperation should be considered in patients with complex fistula in which conservative treatment is insufficient or has failed.	esophagus