Objective:To construct and evaluate a radiomics model for predicting perineural invasion in patients with intrahepatic cholangiocarcinoma (ICC).Methods:Clinical data of 144 patients with ICC undergoing surgery in the People’s Hospital of Zhengzhou University ( n=113) and the Affiliated Cancer Hospital of Zhengzhou University ( n=31) from January 2018 to June 2023 were retrospectively analyzed, including 80 males and 64 females, aged (58.8±10.1) years. The patients were randomly divided into a training set ( n=100) and a test set ( n=44) at a ratio of 7: 3. The former set was used to build the model for predicting perineural invasion, and the latter was used to evaluate the model. Enhanced CT images and clinical data of the patients were collected, and features related to perineural invasion were screened. A light gradient boosting machine was used to construct an imaging genomics model. The model was evaluated using the receiver operating characteristic (ROC) curve, calibration curve, and decision curve analysis (DCA). Results:Univariate and multivariate logistic regression analysis showed that none of the clinical features were associated with neural invasion in ICC patients (all P>0.05). Six, 25, 32, and 37 radiomics features were obtained by screening the intratumoral, 2 mm peritumoral, 5 mm peritumoral, and 8 mm peritumoral regions, respectively. The area under the ROC curve for predicting perineural invasion in ICC patients was 0.849 (95% CI: 0.774-0.923) in the training set and 0.745 (95% CI: 0.597-0.894) in the test set for the intratumoral model, 0.966 (95% CI: 0.938-0.995) and 0.750 (95% CI: 0.604-0.896) for the 5mm peritumoral model, 0.936 (95% CI: 0.892-0.980) and 0.792 (95% CI: 0.644-0.939) for the 2mm peritumoral model, and 0.961 (95% CI: 0.929-0.992) and 0.689 (95% CI: 0.526-0.853) for the 8mm peritumoral model. The area under the ROC curve, accuracy, sensitivity, and specificity of the combined intratumoral and 5mm peritumoral model for predicting perineural invasion were 0.927 (95% CI: 0.878-0.976), 88.0%, 84.5%, and 89.8% in the training set, and 0.849 (95% CI: 0.737-0.960), 77.3%, 85.2%, and 72.0% in the test set, respectively. The calibration curve showed a deviation between the calibration curve of the combined intratumoral and 5mm peritumoral model and the ideal line, but it could achieve basic consistency. DCA showed that when the threshold was between 0.18 and 0.70, the combined intratumoral and 5mm peritumoral model could bring clinical net benefit to patients when predicting neural invasion. Conclusion:The intratumoral and 5mm peritumoral imaging genomics model based on enhanced CT features can effectively predict neural invasion and offer clinical benefits in patients with ICC.

AIM:To optimize the clinical dosage and administration regimen of a novel long-acting injectable aripiprazole microsphere(LZMT05)using plasma concentration data from two clinical trials.METHODS:Plasma concentrations were collected from 196 schizophrenia patients administered LZMT05,and a population pharmacokinetic(Pop-PK)model was developed.The therapeutic window was defined as the steady-state trough-to-peak concentration range(94.0-534 ng/mL)of oral ar-ipiprazole.Multiple clinical scenarios were simulat-ed to identify the optimal regimen.RESULTS:A one-compartment model with dual first-order ab-sorption and first-order elimination characterized LZMT05 pharmacokinetics.Covariates like sex and CYP2D6 genotype were integrated into the final model.Simulations demonstrated that switching from 10 mg oral aripiprazole to 350 mg LZMT05 ev-ery 4 weeks sustained concentrations within the therapeutic window with minimal peak-to-trough fluctuations.CONCLUSION:The PopPK-guided opti-mized LZMT05 regimen maintained drug exposure within the therapeutic window,suggesting favor-able efficacy and safety.

AIM:To optimize the clinical dosage and administration regimen of a novel long-acting injectable aripiprazole microsphere(LZMT05)using plasma concentration data from two clinical trials.METHODS:Plasma concentrations were collected from 196 schizophrenia patients administered LZMT05,and a population pharmacokinetic(Pop-PK)model was developed.The therapeutic window was defined as the steady-state trough-to-peak concentration range(94.0-534 ng/mL)of oral ar-ipiprazole.Multiple clinical scenarios were simulat-ed to identify the optimal regimen.RESULTS:A one-compartment model with dual first-order ab-sorption and first-order elimination characterized LZMT05 pharmacokinetics.Covariates like sex and CYP2D6 genotype were integrated into the final model.Simulations demonstrated that switching from 10 mg oral aripiprazole to 350 mg LZMT05 ev-ery 4 weeks sustained concentrations within the therapeutic window with minimal peak-to-trough fluctuations.CONCLUSION:The PopPK-guided opti-mized LZMT05 regimen maintained drug exposure within the therapeutic window,suggesting favor-able efficacy and safety.

Objective:To construct and evaluate a radiomics model for predicting perineural invasion in patients with intrahepatic cholangiocarcinoma (ICC).Methods:Clinical data of 144 patients with ICC undergoing surgery in the People’s Hospital of Zhengzhou University ( n=113) and the Affiliated Cancer Hospital of Zhengzhou University ( n=31) from January 2018 to June 2023 were retrospectively analyzed, including 80 males and 64 females, aged (58.8±10.1) years. The patients were randomly divided into a training set ( n=100) and a test set ( n=44) at a ratio of 7: 3. The former set was used to build the model for predicting perineural invasion, and the latter was used to evaluate the model. Enhanced CT images and clinical data of the patients were collected, and features related to perineural invasion were screened. A light gradient boosting machine was used to construct an imaging genomics model. The model was evaluated using the receiver operating characteristic (ROC) curve, calibration curve, and decision curve analysis (DCA). Results:Univariate and multivariate logistic regression analysis showed that none of the clinical features were associated with neural invasion in ICC patients (all P>0.05). Six, 25, 32, and 37 radiomics features were obtained by screening the intratumoral, 2 mm peritumoral, 5 mm peritumoral, and 8 mm peritumoral regions, respectively. The area under the ROC curve for predicting perineural invasion in ICC patients was 0.849 (95% CI: 0.774-0.923) in the training set and 0.745 (95% CI: 0.597-0.894) in the test set for the intratumoral model, 0.966 (95% CI: 0.938-0.995) and 0.750 (95% CI: 0.604-0.896) for the 5mm peritumoral model, 0.936 (95% CI: 0.892-0.980) and 0.792 (95% CI: 0.644-0.939) for the 2mm peritumoral model, and 0.961 (95% CI: 0.929-0.992) and 0.689 (95% CI: 0.526-0.853) for the 8mm peritumoral model. The area under the ROC curve, accuracy, sensitivity, and specificity of the combined intratumoral and 5mm peritumoral model for predicting perineural invasion were 0.927 (95% CI: 0.878-0.976), 88.0%, 84.5%, and 89.8% in the training set, and 0.849 (95% CI: 0.737-0.960), 77.3%, 85.2%, and 72.0% in the test set, respectively. The calibration curve showed a deviation between the calibration curve of the combined intratumoral and 5mm peritumoral model and the ideal line, but it could achieve basic consistency. DCA showed that when the threshold was between 0.18 and 0.70, the combined intratumoral and 5mm peritumoral model could bring clinical net benefit to patients when predicting neural invasion. Conclusion:The intratumoral and 5mm peritumoral imaging genomics model based on enhanced CT features can effectively predict neural invasion and offer clinical benefits in patients with ICC.

Objective:To construct and validate a machine learning model for preoperative prediction of perineural invasion (PNI) status in intrahepatic cholangiocarcinoma (ICC).Methods:Clincial data of 329 patients, including 245 admitted to Zhengzhou University People's Hospital from January 2018 to June 2023 and 84 admitted to the Affiliated Cancer Hospital of Zhengzhou University from January 2013 to January 2020 were retrospectively analyzed. Patients were divided into a training set ( n=231) and a validation set ( n=98). Clinicopathological data including age, gender, hepatitis B virus (HBV) infection status were collected. Predictive variables were determined using least absolute shrinkage and selection operator (LASSO) regression analysis. Six machine learning algorithms including random forest (RF), logistic regression, and linear kernel-based support vector machine were selected to construct the preoperative prediction model for PNI in ICC. Performance metrics of the model were calculated using a confusion matrix, and the final model was selected. The model performance was evaluated in the validation set. Calibration curves were plotted to evaluate the final model, and a Pareto chart was used to visualize the importance of predictive variables. Results:LASSO regression identified nine predictive variables included in the prediction model, including carbohydrate antigen 19-9 (CA19-9), HBV infection status, alkaline phosphatase, alanine aminotransferase, prothrombin time, total bilirubin, albumin, neutrophil times gamma-glutamyl transferase to lymphocyte ratio, and tumor burden score. Among the trained six models, the area under the curve (AUC) of the RF model was 0.909, with a sensitivity of 0.842 and an accuracy of 0.870. Compared with the AUC of the RF model, the AUCs of the other 5 models were lower (all P<0.05). The AUC of the RF model for predicting PNI in ICC in validation set was 0.736. Calibration curves showed good fit of the RF model's prediction of PNI in ICC in both training and validation sets. The Pareto chart showed that CA19-9 was the most important predictive variable in the model, followed by HBV infection status. Conclusion:The machine learning model based on the RF algorithm has a high accuracy in preoperative prediction of PNI status in ICC.

Objective:To explore the prognostic value of systemic immune-inflammatory index(SII)combined with tumor burden score (TBS) (hereinafter referred to as STS) in patients with intrahepatic cholangiocarcinoma (ICC) after radical resection, and to construct a nomogram model.Methods:The clinical data (including the degree of tumor differentiation, vascular cancer thrombus, and lymph node metastasis, etc.) of 258 ICC patients who received radical resection at People′s Hospital of Zhengzhou University (170 cases, training set) and Cancer Hospital of Zhengzhou University (88 cases, validation set) from January 1, 2016 to January 31, 2020 were retrospectively analyzed and graded by SII, TBS and STS. Multivariate Cox regression analysis were used to identify independent factors affecting the prognosis of patients with ICC. Kaplan-Meier survival curve and receiver operating characteristic curve (ROC) were drawn to evaluate the predictive efficiency of SII, TBS and STS in the overall survival of patients with ICC after radical resection. The nomogram prediction model was constructed and evaluate the performance of nomogram model using consistency index (C-index) and calibration curve.Results:Among 170 ICC patients in the training set, there were 106 cases of SII grade 1 and 64 cases of SII grade 2; 137 cases of TBS grade 1 and 33 cases of TBS grade 2; and 98 cases of STS grade 1, 47 cases of STS grade 2, and 25 cases of STS grade 3. Among 88 ICC patients in the validation set, there were 33 cases of SII grade 1 and 55 cases of SII grade 2; 66 cases of TBS grade 1 and 22 cases of TBS grade 2; and 30 case of STS grade 1, 39 cases of TBS grade 2, and 19 cases of TBS grade 3.The multivariate Cox regression analysis showed that tumor differentiation degree (highly differentiated vs. moderately differentiated HR=0.157, 95% confidence interval(95% CI) 0.045 to 0.546, highly differentiated vs. poorly differentiated HR=0.452, 95% CI 0.273 to 0.750), STS (grade 3 vs. grade 2 HR=1.966, 95% CI 1.148 to 3.469; grade 3 vs. grade 1 HR=1.405, 95% CI 0.890 to 2.216), vascular cancer thrombus ( HR=2.006, 95% CI 1.313 to 3.066), nerve invasion ( HR=1.865, 95% CI 1.221 to 2.850), and lymph node metastasis ( HR=1.802, 95% CI 1.121 to 2.896) were independent influencing factors of overall survival in ICC patients after radical resection (all P<0.05). The Kaplan-Meier survival curve showed that SII, TBS, and STS were independent influencing factors of overall survival in ICC patients (all P<0.05). The results of ROC analysis showed that the areas under the curve of SII, TBS and STS in predicting overall survival of ICC patients after radical resection were 0.566 (95% CI 0.479 to 0.652), 0.585 (95% CI 0.499 to 0.672), and 0.657 (95% CI 0.522 to 0.692), respectively. Tumor differentiation, vascular tumor thrombus, nerve invassion, lymph node metastasis, and STS were included to constract the nomogram model. The C-indexes of the training set and validation set based on the nomogram model were 0.792 (95% CI 0.699 to 0.825) and 0.776 (95% CI 0.716 to 0.833), respectively. The calibration curves of the survival rate of the training set and the validation set were close to the reference lines, and the nomogram model had better predictive ability in both the training set and the validation set. Conclusions:Preoperative STS grading is an effective and practical predictor of overall survival in ICC patients after radical section. Compared with SII and TBS alone, it has better predictive value for the prognosis of patients with ICC.

Objective:A predictive nomogram model for the prognosis of intrahepatic cholangiocarcinoma (ICC) patients after curative resection was constructed based on the albumin-bilirubin score and tumor burden score (ATS) grade, and the predictive performance of the nomogram model was evaluated.Methods:Retrospective analysis of clinical data was made, from ICC patients who underwent curative resection at Zhengzhou University People's Hospital and Zhengzhou University Cancer Hospital from January 2016 to January 2020. A total of 258 patients were included in the study, with 140 males and 118 females, with an average age of (56.5±9.5) years. The 258 ICC patients were randomly divided into a training set ( n=174) and a testing set ( n=84) in a 7∶3 ratio. Single-factor and multi-factor Cox regression analyses were performed to identify prognostic factors for ICC patients of the training set, and then a nomogram model was constructed. The performance of the nomogram model was evaluated by using the concordance index (C-index), calibration curve, and risky decision curve analysis. Results:In the training set, univariate Cox regression analysis indicated that albumin-bilirubin (ALBI), tumor burden score (TBS), carcinoembryonic antigen (CEA), tumor differentitation, lymphvascular invasion and ATS significantly influenced overall survival after radical resection for ICC (all P<0.05). Multifactorial Cox regression analysis revealed that ATS grade, CEA, tumor differentiation, lymphovascular invasion, and AJCC N stage are independent risk factors for the prognosis of ICC patients after curative resection (all P<0.05). Assessment of the postoperative survival prediction model based on multifactorial Cox regression yielded a C-index of 0.775(95% CI: 0.747-0.841) for the training set and 0.731(95% CI: 0.668-0.828) for the testing set. The calibration curves for both the training and testing sets indicated strong predictive capability of the model. Additionally, the risk decision curve also suggested high net benefit of the model. Conclusions:The preoperative ATS grade is an independent factor affecting the survival after ICC radical resection. The nomogram model constructed based on ATS grade demonstrates excellent predictive value for postoperative prognosis in ICC patients.

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatisNICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases.Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

Trichoderma reesei Rut-C30 is widely used in industrial cellulase production, and development of cellulase hyper-producer is of great importance for economic lignocellulosic biorefinery. In this study, T. reesei Rut-C30 was engineered with an artificial zinc finger proteins (AZFPs) library. Two mutants T. reesei M1 and M2 with improved cellulase production were obtained. Compared to the parent strain, the filter paper activity (FPase) of T. reesei M1 and M2 increased 100% and 53%, respectively. In addition, the total amount of extracellular protein from the M1 mutant increased 69%, whereas the endo-β-glucanase (CMCase) activity of the M2 mutant is 64% higher compared to the parental strain. Furthermore, RT-qPCR analysis showed that the major cellulase genes exhibited significantly increased expression in both mutants, but different patterns were observed in the two mutants. On the other hand, the cellulase transcriptional repressor ace1 was down-regulated in both mutants, but the transcription level of the activator xyr1 was only up-regulated in the strain M1. These results demonstrated that different AZFPs exert diverse regulatory mechanisms on cellulase production in T. reesei. Analysis of the target genes of AZFPs from T. reesei M1 and M2 will not only benefit further exploration of the regulatory mechanisms of cellulase biosynthesis in T. reesei, but also enable development of cellulase hyper-producing strains by metabolic engineering.
Cellulase ; Gene Library ; Transcription Factors ; Trichoderma ; Zinc Fingers

Objective:To explore the application of pyrophosphorolysis-activated polymerization(PAP)to monitor plasma cfDNA in ad-vanced non-small cell lung cancer(NSCLC).Methods:A total of 85 patients diagnosed with advanced NSCLC between March 2016 and June 2017 were enrolled in the present study. EGFR mutations in cfDNA extracted from the plasma were detected using PAP and ARMS-PCR technology.The concordance analysis of EGFR mutations involved plasma vs.tumor tissue and PAP vs.ARMS-PCR.Further-more,38 EGFR-positive patients were selected to monitor EGFR mutations with PAP.Results:No statistical differences in EGFR muta-tions were observed between plasma and tumor tissue(P=0.092),as well as PAP and ARMS-PCR(P=0.210).The detection rate of EGFR mutations in cfDNA was higher in the progressor than in the non-progressor(62.5% vs.21.3%,P<0.001).Conclusions:PAP can be used for detecting and monitoring EGFR mutations in cfDNA to predict disease progression.