Tumor microenvironment characterization in colorectal cancer to identify prognostic and immunotherapy genes signature.

BACKGROUND: The tumor microenvironment (TME) plays a crucial role in tumorigenesis, progression, and therapeutic response in many cancers. This study aimed to comprehensively investigate the role of TME in colorectal cancer (CRC) by generating a TMEscore based on gene expression. METHODS: The TME patterns of CRC datasets were investigated, and the TMEscores were calculated. An unsupervised clustering method was used to divide samples into clusters. The associations between TMEscores and clinical features, prognosis, immune score, gene mutations, and immune checkpoint inhibitors were analyzed. A TME signature was constructed using the TMEscore-related genes. The results were validated using external and clinical cohorts. RESULTS: The TME pattern landscape was for CRC was examined using 960 samples, and then the TMEscore pattern of CRC datasets was evaluated. Two TMEscore clusters were identified, and the high TMEscore cluster was associated with early-stage CRC and better prognosis in patients with CRC when compared with the low TMEscore clusters. The high TMEscore cluster indicated elevated tumor cell scores and tumor gene mutation burden, and decreased tumor purity, when compared with the low TMEscore cluster. Patients with high TMEscore were more likely to respond to immune checkpoint therapy than those with low TMEscore. A TME signature was constructed using the TMEscore-related genes superimposing the results of two machine learning methods (LASSO and XGBoost algorithms), and a TMEscore-related four-gene signature was established, which had a high predictive value for discriminating patients from different TMEscore clusters. The prognostic value of the TMEscore was validated in two independent cohorts, and the expression of TME signature genes was verified in four external cohorts and clinical samples. CONCLUSION: Our study provides a comprehensive description of TME characteristics in CRC and demonstrates that the TMEscore is a reliable prognostic biomarker and predictive indicator for patients with CRC undergoing immunotherapy.

Oxaliplatin related lncRNAs prognostic models predict the prognosis of patients given oxaliplatin-based chemotherapy.

BACKGROUND: Oxaliplatin-based chemotherapy is the first-line treatment for colorectal cancer (CRC). Long noncoding RNAs (lncRNAs) have been implicated in chemotherapy sensitivity. This study aimed to identify lncRNAs related to oxaliplatin sensitivity and predict the prognosis of CRC patients underwent oxaliplatin-based chemotherapy. METHODS: Data from the Genomics of Drug Sensitivity in Cancer (GDSC) was used to screen for lncRNAs related to oxaliplatin sensitivity. Four machine learning algorithms (LASSO, Decision tree, Random-forest, and support vector machine) were applied to identify the key lncRNAs. A predictive model for oxaliplatin sensitivity and a prognostic model based on key lncRNAs were established. The published datasets, and cell experiments were used to verify the predictive value. RESULTS: A total of 805 tumor cell lines from GDSC were divided into oxaliplatin sensitive (top 1/3) and resistant (bottom 1/3) groups based on their IC50 values, and 113 lncRNAs, which were differentially expressed between the two groups, were selected and incorporated into four machine learning algorithms, and seven key lncRNAs were identified. The predictive model exhibited good predictions for oxaliplatin sensitivity. The prognostic model exhibited high performance in patients with CRC who underwent oxaliplatin-based chemotherapies. Four lncRNAs, including C20orf197, UCA1, MIR17HG, and MIR22HG, displayed consistent responses to oxaliplatin treatment in the validation analysis. CONCLUSION: Certain lncRNAs were associated with oxaliplatin sensitivity and predicted the response to oxaliplatin treatment. The prognostic models established based on the key lncRNAs could predict the prognosis of patients given oxaliplatin-based chemotherapy.

Application of artificial intelligence to digital-rapid on-site cytopathology evaluation during endoscopic ultrasound-guided fine needle aspiration: A proof-of-concept study.

BACKGROUND: During endoscopic ultrasound-guided fine needle aspiration (EUS-FNA), cytopathology with rapid on-site evaluation (ROSE) can improve diagnostic yield and accuracy. However, ROSE is unavailable in most Asian and European institutions because of the shortage of cytopathologists. Therefore, developing computer-assisted diagnostic tools to replace manual ROSE is crucial. Herein, we reported the validation of an artificial intelligence (AI)-based model (ROSE-AI model) to substitute manual ROSE during EUS-FNA. METHODS: A total of 467 digitized images from Diff-Quik (D&F)-stained EUS-FNA slides were divided into training (3642 tiles from 367 images) and internal validation (916 tiles from 100 images) datasets. The ROSE-AI model was trained and validated using training and internal validation datasets, respectively. The specificity was emphasized while developing the model. Then, we evaluated the AI model on a 693-image external dataset. We assessed the performance of the AI model to detect cancer cells (CCs) regarding the accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). RESULTS: The ROSE-AI model achieved an accuracy of 83.4% in the internal validation dataset and 88.7% in the external test dataset. The sensitivity and PPV were 79.1% and 71.7% in internal validation dataset and 78.0% and 60.7% in external test dataset, respectively. CONCLUSION: We provided a proof of concept that AI can be used to replace manual ROSE during EUS-FNA. The ROSE-AI model can address the shortage of cytopathologists and make ROSE available in more institutes.

Proanthocyanidins suppress NLRP3 inflammasome and M1 macrophage polarization to alleviate severe acute pancreatitis in mice.

The role of reactive oxygen species (ROS) is crucial for the pathogenesis of acute pancreatitis (AP). Proanthocyanidins (PAs) have been confirmed to exert antioxidant activity. Our study aimed to determine whether PAs alleviated SAP via reducing ROS, suppressing NLRP3 inflammasome, and inhibiting M1 macrophage polarization. Our study investigated the protective effects of PAs on pancreatic histopathological injury using SAP mice. The effects of PAs on macrophages were investigated in inflammatory RAW 264.7 cells or mouse bone marrow-derived macrophages (BMDMs) induced by lipopolysaccharide (LPS). Immunofluorescence staining and/or western blot assay were employed to evaluate NLRP3 inflammasome in macrophages and pancreatic tissue. Cell counting kit-8 (CCK-8) was used to access effects of PAs on cell viability and cytometry flow was used to determine the effects of the PAs on the ROS levels of the RAW 264.7 cells. Then, we evaluated M1 macrophage polarization using flow cytometry or real-time quantitative polymerase chain reaction (RT-qPCR). PAs administration alleviated pancreatic inflammation in SAP mice. The PAs depressed NLRP3 inflammasome and inhibited M1 macrophage polarization in pancreatic tissue. We also found that the PAs showed no cellular toxicity but decreased ROS levels in RAW 264.7 cells, downregulated the NLRP3 inflammasome in the macrophages, and inhibited cell M1 macrophage polarization. Our study indicates the anti-inflammatory properties of the PAs on SAP mice by decreasing ROS levels, suppressing NLRP3 inflammasome, and M1 macrophage polarization.

Tumor-infiltrating immune cells based TMEscore and related gene signature is associated with the survival of CRC patients and response to fluoropyrimidine-based chemotherapy.

Background: Tumor-infiltrating immune cells (TIICs) are associated with chemotherapy response. This study aimed to explore the prognostic value of a TIIC-related tumor microenvironment score (TMEscore) in patients with colorectal cancer (CRC) who underwent chemotherapy and construct a TMEscore-related gene signature to determine its predictive value. Methods: Gene profiles of patients who underwent fluoropyrimidine-based chemotherapy were collected, and their TIIC fractions were calculated and clustered. Differentially expressed genes (DEGs) between clusters were used to calculate the TMEscore. The association between the TMEscore, chemotherapy response, and survival rate was analyzed. Machine learning methods were used to identify key TMEscore-related genes, and a gene signature was constructed to verify the predictive value. Results: Two clusters based on the TIIC fraction were identified, and the TMEscore was calculated based on the DEGs of the two clusters. The TMEscore was higher in patients who responded to chemotherapy than in those who did not, and was associated with the survival rate of patients who underwent chemotherapy. Three machine learning methods, support vector machine (SVM), decision tree (DT), and Extreme Gradient Boosting (XGBoost), identified three TMEscore-related genes (ADH1C, SLC26A2, and NANS) associated with the response to chemotherapy. A TMEscore-related gene signature was constructed, and three external cohorts validated that the gene signature could predict the response to chemotherapy. Five datasets and clinical samples showed that the expression of the three TMEscore-related genes was increased in tumor tissues compared to those in control tissues. Conclusions: The TIIC-based TMEscore was associated with the survival of CRC patients who underwent fluoropyrimidine-based chemotherapy, and predicted the response to chemotherapy. The TMEscore-related gene signature had a better predictive value for response to chemotherapy than for survival.

Snare-assisted flexible endoscope in trans-gastric endoscopic gallbladder-preserving surgery: A pilot animal study.

BACKGROUND: Natural orifice transluminal endoscopic surgery (NOTES) gallbladder-preserving surgery by flexible endoscopy is an emerging technology. However, the gallbladder fails to obtain traction and positioning functions during the operation. AIM: To evaluate the feasibility and safety of a new surgical method, "snare-assisted pure NOTES gallbladder-preserving surgery". METHODS: Eight miniature pigs were randomly divided into the experimental group [NOTES gallbladder-preserving surgery using the snare device, snare assisted (SA)] and the control group (NOTES gallbladder-preserving surgery without using the snare device, NC), with four cases in each group. The differences between the two groups of animals in operating time, operating workload, complications, adverse events, white blood cells, and liver function were determined. RESULTS: No differences were found in the surgical success rate, gallbladder incision closure, white blood cell count, or liver function between the two groups. The total operating time, gallbladder incision blood loss, gallbladder disorientation time, gallbladder incision closure time, and workload scores on the National Aeronautics and Space Administration-Task Load Index were significantly reduced in the SA group (P < 0.05). CONCLUSION: These results indicated that snare-assisted pure NOTES gallbladder-preservation surgery using standard endoscopic instruments reduced the difficulty of operation, shortened operation time, and did not increase complications in pigs. A new method for pure NOTES gallbladder-preservation surgery was provided.

Actual pressure generated by various suction technique and suctioning liquid weight through endoscopic ultrasound-guided aspiration needles.

OBJECTIVES: Suction pressure is one of the most important factors influencing the amount of tissue obtained during endoscopic ultrasound-guided fine-needle aspiration/biopsy (EUS-FNA/FNB). In this study we aimed to elucidate actual suction pressure generated by various suction methods and the weight of suctioning liquid. METHODS: Different types of fine needles and suction techniques were used, including the slow pull technique (SPT), dry suction technique (DST), wet suction technique (WST), neutralizing negative pressure technique (NNPT), and residual negative pressure technique (RNPT). Actual suction pressure was measured and the amount of suctioning liquid was weighed. RESULTS: Actual suction pressure and weight of the suctioning liquid were lower using SPT than using DST, while they were higher when using WST compared with those using DST. In general, the actual suction pressure increased and the weight of suctioning liquid decreased as the diameter of the FNA needles decreased. While weight of the suctioning liquid using FNB needles was significantly larger than that using FNA needles. In general, the actual suction pressure generated using RNPT was larger than that using NNPT. CONCLUSIONS: WST is superior to SPT and DST in terms of actual suction pressure and weight of suctioning liquid. Diameter of the FNA needle was an important factor that may affect the actual suction pressure and weight of suctioning liquid. FNB needles are superior to FNA needles when it comes to the weight of suctioning liquid. Actual suction pressure obtained by novel suction methods (NNPT and RNPT) may provide a basis for future research.

Diagnostic and Predictive Value of Immune-Related Genes in Crohn's Disease.

Abnormal immune cell infiltration is associated with the pathogenesis of Crohn's disease (CD). This study aimed to determine the diagnostic and predictive value of immune-related genes in CD. Seven Gene Expression Omnibus datasets that analyzed the gene expression in CD tissues were downloaded. Single-sample gene set enrichment analysis (ssGSEA) was used to estimate the infiltration of the immune cells in CD tissues. Immune-related genes were screened by overlapping the immune-related genes with differentially expressed genes (DEGs). The protein-protein interaction (PPI) network was used to identify key immune-related DEGs. Diagnostic value of CD and predictive value of anti-TNFα therapy were analyzed. Immunohistochemical (IHC) assay was used to verify gene expression in CD tissues. There were significant differences among CD tissues, paired CD tissues, and normal intestinal tissues regarding the infiltration of immune cells. AQP9, CD27, and HVCN1 were identified as the key genes of the three sub-clusters in the PPI network. AQP9, CD27, and HVCN1 had mild to moderate diagnostic value in CD, and the diagnostic value of AQP9 was better than that of CD27 and HVCN1. AQP9 expression was decreased in CD after patients underwent anti-TNFα therapy, but no obvious changes were observed in non-responders. AQP9 had a moderate predictive value in patients who had undergone treatment. IHC assay confirmed that the expression of AQP9, CD27, and HVCN1 in CD tissues was higher than that in normal intestinal tissues, and AQP9, CD27 was correlated with the activity of CD. Immune-related genes, AQP9, CD27, and HVCN1 may act as auxiliary diagnostic indicators for CD, and AQP9 could serve as a promising predictive indicator in patients who underwent anti-TNF therapy.

The Diagnostic and Prognostic Value of miR-200c in Gastric Cancer: A Meta-Analysis.

BACKGROUND: The role of miR-200c in gastric cancer remains controversial. This study is aimed at clarifying the diagnostic and prognostic value of miR-200c in gastric cancer through a meta-analysis. METHODS: A comprehensive literature search of PubMed, Embase, and Ovid library databases was conducted. The studies included were those conducted before December 2017. The sensitivity and specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under curve (AUC) were used to estimate the diagnostic value of miR-200c. Meanwhile, the pooled hazard ratio (HR) was used to estimate the prognostic value of miR-200c. RESULTS: For the diagnostic value of miR-200c, six studies that included 202 patients with gastric cancer and 250 normal controls were analyzed. The sensitivity, specificity, PLR, NLR, DOR, and AUC were 0.74, 0.66, 2.20, 0.40, 5.34, and 0.75, respectively. Subgroup analysis showed no significant difference in the type of the sample, method for testing miR-200c, and ethnicity among the patients. Meanwhile, for the prognostic value of miR-200c, seven studies comprising 935 patients with gastric cancer were analyzed. The pooled results showed that miR-200c expression was associated with overall survival (HR = 2.19) and disease-free survival (HR = 1.73), but not with progression-free survival (HR = 1.64) in patients with gastric cancer. There was no publication bias across the studies. CONCLUSIONS: Both serum and tissue miR-200c have moderate diagnostic accuracy in gastric cancer. miR-200c could also be used as a valuable indicator for predicting the prognosis of gastric cancer patients.