MRI-based deep learning and radiomics for prediction of occult cervical lymph node metastasis and prognosis in early-stage oral and oropharyngeal squamous cell carcinoma: a diagnostic study.

INTRODUCTION: The incidence of occult cervical lymph node metastases (OCLNM) is reported to be 20%-30% in early-stage oral cancer and oropharyngeal cancer. There is a lack of an accurate diagnostic method to predict occult lymph node metastasis and to help surgeons make precise treatment decisions. AIM: To construct and evaluate a preoperative diagnostic method to predict occult lymph node metastasis (OCLNM) in early-stage oral and oropharyngeal squamous cell carcinoma (OC and OP SCC) based on deep learning features (DLFs) and radiomics features. METHODS: A total of 319 patients diagnosed with early-stage OC or OP SCC were retrospectively enrolled and divided into training, test and external validation sets. Traditional radiomics features and DLFs were extracted from their MRI images. The least absolute shrinkage and selection operator (LASSO) analysis was employed to identify the most valuable features. Prediction models for OCLNM were developed using radiomics features and DLFs. The effectiveness of the models and their clinical applicability were evaluated using the area under the curve (AUC), decision curve analysis (DCA) and survival analysis. RESULTS: Seventeen prediction models were constructed. The Resnet50 deep learning (DL) model based on the combination of radiomics and DL features achieves the optimal performance, with AUC values of 0.928 (95% CI: 0.881-0.975), 0.878 (95% CI: 0.766-0.990), 0.796 (95% CI: 0.666-0.927) and 0.834 (95% CI: 0.721-0.947) in the training, test, external validation set1 and external validation set2, respectively. Moreover, the Resnet50 model has great prediction value of prognosis in patients with early-stage OC and OP SCC. CONCLUSION: The proposed MRI-based Resnet50 deep learning model demonstrated high capability in diagnosis of OCLNM and prognosis prediction in the early-stage OC and OP SCC. The Resnet50 model could help refine the clinical diagnosis and treatment of the early-stage OC and OP SCC.

A comprehensive AI model development framework for consistent Gleason grading.

BACKGROUND: Artificial Intelligence(AI)-based solutions for Gleason grading hold promise for pathologists, while image quality inconsistency, continuous data integration needs, and limited generalizability hinder their adoption and scalability. METHODS: We present a comprehensive digital pathology workflow for AI-assisted Gleason grading. It incorporates A!MagQC (image quality control), A!HistoClouds (cloud-based annotation), Pathologist-AI Interaction (PAI) for continuous model improvement, Trained on Akoya-scanned images only, the model utilizes color augmentation and image appearance migration to address scanner variations. We evaluate it on Whole Slide Images (WSI) from another five scanners and conduct validations with pathologists to assess AI efficacy and PAI. RESULTS: Our model achieves an average F1 score of 0.80 on annotations and 0.71 Quadratic Weighted Kappa on WSIs for Akoya-scanned images. Applying our generalization solution increases the average F1 score for Gleason pattern detection from 0.73 to 0.88 on images from other scanners. The model accelerates Gleason scoring time by 43% while maintaining accuracy. Additionally, PAI improve annotation efficiency by 2.5 times and led to further improvements in model performance. CONCLUSIONS: This pipeline represents a notable advancement in AI-assisted Gleason grading for improved consistency, accuracy, and efficiency. Unlike previous methods limited by scanner specificity, our model achieves outstanding performance across diverse scanners. This improvement paves the way for its seamless integration into clinical workflows.

Gleason grading is a well-accepted diagnostic standard to assess the severity of prostate cancer in patients' tissue samples, based on how abnormal the cells in their prostate tumor look under a microscope. This process can be complex and time-consuming. We explore how artificial intelligence (AI) can help pathologists perform Gleason grading more efficiently and consistently. We build an AI-based system which automatically checks image quality, standardizes the appearance of images from different equipment, learns from pathologists' feedback, and constantly improves model performance. Testing shows that our approach achieves consistent results across different equipment and improves efficiency of the grading process. With further testing and implementation in the clinic, our approach could potentially improve prostate cancer diagnosis and management.

Regulating Lipid Metabolism via Mitochondrial Dynamics in Tongue Squamous Cell Carcinoma Cancer Stem Cells.

BACKGROUND: Cancer stem cells (CSCs) are a sub-population of cancer cells present in many kinds of malignant tumors that have the potential for self-proliferation and differentiation. These cells have been demonstrated as the main cause of tumor recurrence and metastasis. Strong evidence indicates that CSCs prefer reprogrammed fatty acid ß-oxidation over oxidative phosphorylation for sustaining energy supply. Although mitochondrial dynamics participate in the regulation of cancer stemness, the correlation between the inhibition of mitochondrial fission and the regulation of lipid metabolism in CSCs remains poorly understood. METHODS: The human tongue squamous cell carcinoma (TSCC) cell lines CAL27 and SAS were used to obtain the CSCs by 3D Spheroid Culture. Then,western blot methods, RT-PCR and flow cytometry analysis were used to identify the TSCC CSCs. Next, Immunofluorescence method, transmission electron microscopy detection and western blot methods were used to evaluate the mitochondrial morphology and the quantity of lipid droplets (LDs). Lastly, lipidomic analysis was applied to explored the lipidomic alterations of TSCC CSCs with different mitochondrial morphology. RESULTS: Here, we show that the quantity of lipid droplets containing intracellular triglyceride (TG) can be decreased by regulating mitochondrial morphology. Lipidomic analysis using ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) also compared alterations in lipid metabolites in tongue squamous cell carcinoma (TSCC) CSCs, TSCC cells (non-CSCs), and CSCs with different mitochondrial morphology. Discriminant lipids of statistical significance were successfully annotated, including phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), sphingomyelins (SMs), triacylglycerols (TGs), phosphatidylglycerols (PGs), phosphatidylserines (PSs), lysophosphatidylcholines (LPCs), and lysophosphatidylethanolamines (LPEs). CONCLUSION: This study provides a deeper insight into the alterations of lipid metabolism associated with TSCC CSCs, non-CSCs and CSCs regulated by mitochondrial dynamics and thus serves as a guide toward novel targeted therapies.

Integrated Single-cell and Bulk RNA Sequencing Analysis Cross Talk between Ferroptosis-related Genes and Prognosis in Oral Cavity Squamous Cell Carcinoma.

BACKGROUND: Ferroptosis is a new type of programmed apoptosis and plays an important role in tumour inhibition and immunotherapy. OBJECTIVE: In this study, we aimed to explore the potential role of ferroptosis-related genes (FRGs) and the potential therapeutic targets in oral cavity squamous cell carcinoma (OCSCC). METHODS: The transcription data of OCSCC samples were obtained from the Cancer Genome Atlas (TCGA) database as a training dataset. The prognostic FRGs were extracted by univariate Cox regression analysis. Then, we constructed a prognostic model using the least absolute shrinkage and selection operator (LASSO) and Cox analysis to determine the independent prognosis FRGs. Based on this model, risk scores were calculated for the OCSCC samples. The model's capability was further evaluated by the receiver operating characteristic curve (ROC). Then, we used the GSE41613 dataset as an external validation cohort to confirm the model's predictive capability. Next, the immune infiltration and somatic mutation analysis were applied. Lastly, single-cell transcriptomic analysis was used to identify the key cells. RESULTS: A total of 12 prognostic FRGs were identified. Eventually, 6 FRGs were screened as independent predictors and a prognostic model was constructed in the training dataset, which significantly stratified OCSCC samples into high-risk and low-risk groups based on overall survival. The external validation of the model using the GSE41613 dataset demonstrated a satisfactory predictive capability for the prognosis of OCSCC. Further analysis revealed that patients in the highrisk group had distinct immune infiltration and somatic mutation patterns from low-risk patients. Mast cell infiltrations were identified as prognostic immune cells and played a role in OCSCC partly through ferroptosis. CONCLUSION: We successfully constructed a novel 6 FRGs model and identified a prognostic immune cell, which can serve to predict clinical prognoses for OCSCC. Ferroptosis may be a new direction for immunotherapy of OCSCC.

Predicting survival in patients with buccal cancer: A study based on SEER database and external validation in China.

OBJECTIVE: Buccal mucosa cancer (BMC) is one of the most common oral cancers and has poor prognosis. The study aimed to develop and validate nomograms for predicting the 1-, 3-, and 5-year overall survival (OS) and cancer-specific survival (CSS) of BMC patients. METHODS: We collected and reviewed information on BMC patients diagnosed between 2004 and 2019 from the Surveillance Epidemiology and End Results database. Two nomograms were developed and validated to predict the OS and CSS based on predictors identified by univariate and multivariate Cox regression. An extra external validation was further performed using data from Sun Yat-sen Memorial Hospital (SYSMH). RESULTS: A total of 3154 BMC patients included in this study were randomly assigned to training and validation groups in a 2:1 ratio. Independent prognostic predictors were identified, confirmed, and fitted into nomograms for OS and CSS, respectively. The C-indices are 0.767 (Training group OS), 0.801 (Training group CSS), 0.763 (Validation group OS), and 0.781 (Validation group OS), respectively. Moreover, the nomograms exhibited remarkable precision in forecasting and significant clinical significance, as evidenced by receiver operating characteristic (ROC) curves, calibration curves, and decision curve analyses (DCA). The final validation using our data from SYSMH also showed high accuracy and substantial clinical benefits within the nomograms. The C-indices are 0.849 (SYSMH group OS) and 0.916 (SYSMH group CSS). These indexes are better than tumor, node, and metastasis stage based on prediction results. CONCLUSIONS: The nomograms developed with great performance predicted 1-, 3-, and 5-year OS and CSS of BMC patients. Use of the nomograms in clinical practices shall bring significant benefits to BMC patients.

How Can the Trust-Change Direction be Measured and Identified During Takeover Transitions in Conditionally Automated Driving? Using Physiological Responses and Takeover-Related Factors.

OBJECTIVE: This paper proposes an objective method to measure and identify trust-change directions during takeover transitions (TTs) in conditionally automated vehicles (AVs). BACKGROUND: Takeover requests (TORs) will be recurring events in conditionally automated driving that could undermine trust, and then lead to inappropriate reliance on conditionally AVs, such as misuse and disuse. METHOD: 34 drivers engaged in the non-driving-related task were involved in a sequence of takeover events in a driving simulator. The relationships and effects between drivers' physiological responses, takeover-related factors, and trust-change directions during TTs were explored by the combination of an unsupervised learning algorithm and statistical analyses. Furthermore, different typical machine learning methods were applied to establish recognition models of trust-change directions during TTs based on takeover-related factors and physiological parameters. RESULT: Combining the change values in the subjective trust rating and monitoring behavior before and after takeover can reliably measure trust-change directions during TTs. The statistical analysis results showed that physiological parameters (i.e., skin conductance and heart rate) during TTs are negatively linked with the trust-change directions. And drivers were more likely to increase trust during TTs when they were in longer TOR lead time, with more takeover frequencies, and dealing with the stationary vehicle scenario. More importantly, the F1-score of the random forest (RF) model is nearly 77.3%. CONCLUSION: The features investigated and the RF model developed can identify trust-change directions during TTs accurately. APPLICATION: Those findings can provide additional support for developing trust monitoring systems to mitigate both drivers' overtrust and undertrust in conditionally AVs.

Multiple Langerhans cell histiocytosis with spinal involvement.

Aims: The aim of this study was to report the long-term prognosis of patients with multiple Langerhans cell histiocytosis (LCH) involving the spine, and to analyze the risk factors for progression-free survival (PFS). Methods: We included 28 patients with multiple LCH involving the spine treated between January 2009 and August 2021. Kaplan-Meier methods were applied to estimate overall survival (OS) and PFS. Univariate Cox regression analysis was used to identify variables associated with PFS. Results: Patients with multiple LCH involving the spine accounted for 15.4% (28/182 cases) of all cases of spinal LCH: their lesions primarily involved the thoracic and lumbar spines. The most common symptom was pain, followed by neurological dysfunction. All patients presented with osteolytic bone destruction, and 23 cases were accompanied by a paravertebral soft-tissue mass. The incidence of vertebra plana was low, whereas the oversleeve-like sign was a more common finding. The alkaline phosphatase was significantly higher in patients with single-system multifocal bone LCH than in patients with multisystem LCH. At final follow-up, one patient had been lost to follow-up, two patients had died, three patients had local recurrence, six patients had distant involvement, and 17 patients were alive with disease. The median PFS and OS were 50.5 months (interquartile range (IQR) 23.5 to 63.1) and 60.5 months (IQR 38.0 to 73.3), respectively. Stage (hazard ratio (HR) 4.324; p < 0.001) and chemotherapy (HR 0.203; p < 0.001) were prognostic factors for PFS. Conclusion: Pain is primarily due to segmental instability of the spine from its destruction by LCH. Chemotherapy can significantly improve PFS, and radiotherapy has achieved good results in local control. The LCH lesions in some patients will continue to progress. It may initially appear as an isolated or single-system LCH, but will gradually involve multiple sites or systems. Therefore, long-term follow-up and timely intervention are important for patients with spinal LCH.

Identification and validation of immunohistochemical marker panels to predict the prognosis of muscle invasive bladder cancer.

Background: Currently, the treatment regimen of bladder cancer depends on the stage and grade. Yet, patients with similar histopathological characteristics may have distinct prognosis. Luminal/basal subtyping had proved to be a satisfactory subtyping method. Here we intended to evaluate immunohistochemistry, a more clinically-practical method, in luminal/basal classification and further risk-stratification. Methods: Patients diagnosed with urothelial carcinoma of the bladder in Changhai Hospital were retrospectively recruited and corresponding formalin-fixed paraffin embedded blocks were acquired. Tissue microarrays (TMAs) of these patients were established followed by immunohistochemical (IHC) staining of 14 markers. Patients were classified into luminal or basal subtype according to CK5/6, CK14, CK20 and GATA3 expression. Further subtyping of luminal and basal tumors was performed according to the expression of other markers. Results: A total of 236 patients were included: 163 and 73 patients were assigned to training and validation cohorts, respectively. Patients with basal tumor were related with poorer prognosis compared to those with luminal tumor (P=0.025 and 0.008 in training and validation cohorts, respectively). We further revealed luminal muscle invasive bladder cancer (MIBC) patients could be further categorized into subgroups with different risks. Cytoplasmic YAP1 and CCNB1 were selected as classifier, patients with low expression of cytoplasmic YAP1 or CCNB1 were independent risk factor for poorer prognosis (hazard ratio =2.19, P=0.04). Conclusions: Molecular subtyping into luminal/basal subtype and risk stratification method using a 2-marker method by immunohistochemistry can be an economical, clinically practical method to predict patient prognosis and could help to develop treatment strategy and follow-up schedule in clinical practice.

The Tai Chi Flap: A Novel Design for the Radial Forearm Flap.

OBJECTIVE: Tai Chi is an ancient philosophy used to explain the universe. The Tai Chi symbol is represented by Yin/Yang fishes. The authors describe a novel radial forearm flap (RFF) design for the reconstruction of circular defects based on the Tai Chi symbol. METHODS: Eleven consecutive patients with craniofacial skin or mucus defects underwent reconstruction with a Tai Chi RFF. Patient perioperative and follow-up information was collected. RESULTS: The diameter of the Tai Chi RFF was 5 to 6 cm. All flaps healed uneventfully without ischemic problems, and all donor site defects were closed primarily without skin grafts. Remarkably, 2 patients received a tattoo to mark the Tai Chi symbol and greatly appreciate the shape of the flap. CONCLUSIONS: The Tai Chi flap is an economically friendly flap design that can be used to prevent skin grafts while providing psychological comfort to patients.

Tooth Loss after Jaw Curettage Surgery: Associated Factors and Potential Benefit of Splint Application.

BACKGROUND: This retrospective study is aimed at (I) assessment of tooth loss and related parameters after jaw curettage of benign lesions and (II) assessment of the outcome of jaw curettage supported by splint insertion after at least six months of follow-up. Material and Methods. For (I), patients who had jaw curettage surgery in the Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University (Guangzhou, China) from July 2015 to June 2019 were included. For part (II), consecutive patients who came to the department from July to December 2019 that were additionally treated with dental splinting were involved in this study. Based on the patient records, age, gender, initial tooth mobility, follow-up outcome, and potential tooth loss (intra- or postoperatively) were recorded. Based on available radiographs, alveolar crest bone loss and root surface area supported by bone (RSA) were determined. RESULTS: (I) 128 patients with 305 teeth were included, of which 40 teeth were lost (success rate 86.9%), without statistical difference in gender, age, or tooth type (P > 0.05). Tooth mobility, RSA, and the presence of alveolar crest bone defects were associated to tooth loss (P < 0.001). (II) 17 patients with a medium follow-up period of 11 months (range 9 to 13 months) were enrolled. All lesion-involving teeth supported by splint treatment at risks of loss were preserved, showing an effective tooth retention rate in 17/17 cases (74/74 teeth, success rate: 100%). CONCLUSIONS: Tooth mobility and bone loss (lesion-related and/or periodontal) are potential risk predictors for tooth loss in the first year after jaw curettage surgery. Dental splints could be recommendable for teeth involved by jaw benign lesions with little bone support.

A Pan-Cancer Analysis of the Oncogenic Role of Nuclear Transport Factor 2 in Human Cancers.

Nuclear transport factor 2 (NUTF2) is a GDP-binding protein that participates in the nucleocytoplasmic transport process. The role of NUTF2 in cancer development is largely unknown and lacks systemic assessment across human cancers. In this study, we performed a pan-cancer analysis of NUTF2 in human cancers. Out of 33 types of cancers, 19 types had significantly different expression of NUTF2 between tumor and normal tissues. Meanwhile, survival analysis showed that NUTF2 could be an independent prognostic factor in several tumor types. Further analysis suggested that the expression of NUTF2 expression was correlated with the infiltration of immune cells, such as CD8+ T cells, effector memory CD4+ T cells, and cancer-associated fibroblasts in kidney renal clear cell carcinoma. Moreover, co-expression analysis showed the positive association between NUTF2 and cell proliferation biomarkers (MKI67and PCNA) and epithelial-mesenchymal transition markers (VIM, TWIST1, SNAI1, SNAI2, FN1, and CDH2), suggesting that NUTF2 plays important roles in regulating cancer proliferation and metastasis. This pan-cancer analysis of NUTF2 provides a systemic understanding of its oncogenic role across different types of cancers.

RNA-binding protein MEX3A controls G1/S transition via regulating the RB/E2F pathway in clear cell renal cell carcinoma.

MEX3A is an RNA-binding protein that mediates mRNA decay through binding to 3' untranslated regions. However, its role and mechanism in clear cell renal cell carcinoma remain unknown. In this study, we found that MEX3A expression was transcriptionally activated by ETS1 and upregulated in clear cell renal cell carcinoma. Silencing MEX3A markedly reduced clear cell renal cell carcinoma cell proliferation in vitro and in vivo. Inhibiting MEX3A induced G1/S cell-cycle arrest. Gene set enrichment analysis revealed that E2F targets are the central downstream pathways of MEX3A. To identify MEX3A targets, systematic screening using enhanced cross-linking and immunoprecipitation sequencing, and RNA-immunoprecipitation sequencing assays were performed. A network of 4,000 genes was identified as potential targets of MEX3A. Gene ontology analysis of upregulated genes bound by MEX3A indicated that negative regulation of the cell proliferation pathway was highly enriched. Further assays indicated that MEX3A bound to the CDKN2B 3' untranslated region, promoting its mRNA degradation. This leads to decreased levels of CDKN2B and an uncontrolled cell cycle in clear cell renal cell carcinoma, which was confirmed by rescue experiments. Our findings revealed that MEX3A acts as a post-transcriptional regulator of abnormal cell-cycle progression in clear cell renal cell carcinoma.

How Deviation of Nasal Septum Affects Nasal Appearance in Unilateral Cleft Patients: A Study Using Cone-Beam Computed Tomography.

AIM: To quantitatively evaluate the relationship between nasal appearance and nasal septum deviation in unilateral complete cleft patients using cone-beam computed tomography.Method: Cone-beam computed tomography images of 180 patients with unilateral cleft lip/palate from June 2014 to June 2017 were used in the study. None of the subjects had undergone septoplasty. The data were compared between the 2 groups to elucidate the relationship between nasal appearance and deviated nasal septum in unilateral complete cleft patients. RESULTS: The mean age of a total of 180 patients (126 males and 54 females) was 14.58 years, with a standard deviation of 7.10 years, ranged from 6 years old to 49 years old. Columella nasi symmetry parameters show slight positive significant association with angle of nasal septal deviation on transerve plan (r = 0.250, P < 0.001), TRSD (r = 0.323, P < 0.001) and coronal range of nasal septal deviation (r = 0.294, P < 0.001), and moderate positive significant association with coronal angle about septal deviation (r = 0.404, P < 0.001). CONCLUSIONS: Columella nasi symmetry affected by septal deviation, whereas there is lack of evidence to say symmetry of nasal tip and base affected by septal deviation. The symmetry of nasal tip and alar base are not just determined by nasal septum deviation. The nasal septum deviation show difference in different cleft type.

Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma.

To reconstruct systematically hyperactive transcription factor (TF)-dependent transcription networks in squamous cell carcinomas (SCCs), a computational method (ELMER) was applied to 1293 pan-SCC patient samples, and 44 hyperactive SCC TFs were identified. As a top candidate, DLX5 exhibits a notable bifurcate re-configuration of its bivalent promoter in cancer. Specifically, DLX5 maintains a bivalent state in normal tissues; its promoter is hypermethylation, leading to DLX5 transcriptional silencing in esophageal adenocarcinoma (EAC). In stark contrast, DLX5 promoter gains active histone marks and becomes transcriptionally activated in ESCC, which is directly mediated by SOX2. Functionally, silencing of DLX5 substantially inhibits SCC viability both in vitro and in vivo. Mechanistically, DLX5 cooperates with TP63 in regulating ∼2000 enhancers and promoters, which converge on activating cancer-promoting pathways. Together, our data establish a novel and strong SCC-promoting factor and elucidate a new epigenomic mechanism - bifurcate chromatin re-configuration - during cancer development.

Calcifying pseudoneoplasms of the neuraxis (CAPNON). A case report.

Calcifying pseudoneoplasms of the neuraxis (CAPNON) are rare, slow-growing, benign lesions occurring throughout the neuroaxis that are frequently misdiagnosed and overlooked by clinicians. Here, we report a case of a 56-year-old woman who presented with a history of recurrent headache for the previous six years. Magnetic resonance imaging (MRI) revealed a 2.3-cm-sized solid mass in the right frontal lobe that was surrounded by marked edematous areas. The lesion demonstrated dense calcification and avid enhancement. The lesion was initially diagnosed as oligodendroglioma, and then found to be CAPNON based on histopathology of a surgically resected tissue. Genetic analysis revealed a nonsense mutation in the CUL4B gene. The patient's condition appeared to reflect a reactive, rather than neoplastic, process. Clinicians should be prepared to detect such pseudotumors histopathologically in order to avoid unnecessary differential tests of neoplastic or infectious diseases, as well as potentially harmful therapies.

The mediating effect of driver characteristics on risky driving behaviors moderated by gender, and the classification model of driver's driving risk.

High-risk drivers are more likely to be involved in traffic accidents, and the driving risk level of drivers could be affected by many potential factors, such as demographics and personality traits. Based on the Structural Equation Model (SEM), this study involves a sample of 3150 drivers from the Strategic Highway Research Program 2 (SHRP 2), to explore the relationships among drivers' demographic characteristics (gender, age, and cumulative driving years), sensation seeking, risk perception, and risky driving behaviors. More specifically, the mediation model of driver characteristics on risky driving behaviors moderated by gender is constructed by the SEM. The results show that the effects of driving experience on risky driving behaviors are partially mediated by sensation seeking and risk perception for male drivers, while those are completely mediated by sensation seeking and risk perception for female drivers. Moreover, the development trend of risky driving behavior engagements declines greater with the growing of driving experience for female drivers than male drivers. Finally, a classification model of the driver's driving risk is proposed by the Random Forest classifier, in which the driving risk level of the driver evaluated by the crash and near-crash rate could be classified through the driver's self-reported demographics, sensation seeking, risk perception, and risky driving behaviors. The classification accuracy achieves up to 90 percent, which offers an alternative approach to identifying potential high-risk drivers to reduce property losses, injuries, and death caused by traffic accidents.

Integrative Bioinformatics Analysis Demonstrates the Prognostic Value of Chromatin Accessibility Biomarkers in Clear Cell Renal Cell Carcinoma.

Clear cell renal cell carcinoma (ccRCC) accounts for 75%-85% of renal cell carcinoma (RCC) and has a poor 5-year survival rate. In recent years, medical advancement has promoted the understanding of the histopathological and molecular characterization of ccRCC; however, the carcinogenesis and molecular mechanisms of ccRCC remain unclear. Chromatin accessibility is an essential determinant of cellular phenotype. This study aimed to explore the potential role of chromatin accessibility in the development and progression of ccRCC. By the combination of open-access genome-wide chromatin accessibility profiles and gene expression profiles in ccRCC, we obtained a total of 13,474 crucial peaks, corresponding to 5,120 crucial genes and 9,185 differentially expressed genes. Moreover, two potential function modules (P2 and G4) that contained 129 upregulated genes were identified via the weighted gene co-expression network analysis (WGCNA). Furthermore, we obtained five independent predictors (FSCN1, SLC17A9, ANKRD13B, ADCY2, and MAPT), and a prognostic model was established based on these genes through the least absolute shrinkage and selection operator-proportional hazards model (LASSO-Cox) analysis. This model can stratify the ccRCC samples into a high-risk and a low-risk group, from which the patients have distinct prognosis. Further analysis demonstrated a completely different immune cell infiltration pattern between these two risk groups. This study also suggested that mast cell resting is associated with the prognosis of ccRCC and could be a target of immunotherapy. Overall, this study indicated that chromatin accessibility plays an essential role in ccRCC. The five prognostic chromatin accessibility biomarkers and the prognostic immune cells can provide a new direction for the treatment of ccRCC.

CEBPG promotes esophageal squamous cell carcinoma progression by enhancing PI3K-AKT signaling.

CCAAT/enhancer binding proteins (CEBPs, including CEBPA, CEBPB, CEBPD, CEBPE, CEBPG, and CEBPZ) play critical roles in a variety of physiological and pathological processes. However, the molecular characteristics and biological significance of CEBPs in esophageal squamous cell carcinoma (ESCC) have rarely been reported. Here, we show that most of the CEBPs are upregulated and accompanied with copy number amplifications in ESCC. Of note, high CEBPG expression is regulated by the ESCC specific transcription factor TP63 and serves as a prognostic factor for poor survival in ESCC patients. Functionally, CEBPG significantly promotes the proliferation and migration of ESCC cells both in vitro and in vivo. Mechanistically, CEBPG activates the PI3K-AKT signaling pathway through directly binding to distal enhancers and/or promoters of genes involved in this pathway, including genes of CCND1, MYC, CDK2, etc. These findings provide new insights into CEBPs dysregulation in ESCC and elucidate a crucial role for CEBPG in the progression of ESCC, highlighting its potential therapeutic value for ESCC treatment.

CATA: a comprehensive chromatin accessibility database for cancer.

Accessible chromatin refers to the active regions of a chromosome that are bound by many transcription factors (TFs). Changes in chromatin accessibility play a critical role in tumorigenesis. With the emergence of novel methods like Assay for Transposase-accessible Chromatin Sequencing, a sequencing method that maps chromatin-accessible regions (CARs) and enables the computational analysis of TF binding at chromatin-accessible sites, the regulatory landscape in cancer can be dissected. Herein, we developed a comprehensive cancer chromatin accessibility database named CATA, which aims to provide available resources of cancer CARs and to annotate their potential roles in the regulation of genes in a cancer type-specific manner. In this version, CATA stores 2 991 163 CARs from 23 cancer types, binding information of 1398 TFs within the CARs, and provides multiple annotations about these regions, including common single nucleotide polymorphisms (SNPs), risk SNPs, copy number variation, somatic mutations, motif changes, expression quantitative trait loci, methylation and CRISPR/Cas9 target loci. Moreover, CATA supports cancer survival analysis of the CAR-associated genes and provides detailed clinical information of the tumor samples. Database URL: CATA is available at http://www.xiejjlab.bio/cata/.