Radiogenomic analysis for predicting lymph node metastasis and molecular annotation of radiomic features in pancreatic cancer.

BACKGROUND: To provide a preoperative prediction model for lymph node metastasis in pancreatic cancer patients and provide molecular information of key radiomic features. METHODS: Two cohorts comprising 151 and 54 pancreatic cancer patients were included in the analysis. Radiomic features from the tumor region of interests were extracted by using PyRadiomics software. We used a framework that incorporated 10 machine learning algorithms and generated 77 combinations to construct radiomics-based models for lymph node metastasis prediction. Weighted gene coexpression network analysis (WGCNA) was subsequently performed to determine the relationships between gene expression levels and radiomic features. Molecular pathways enrichment analysis was performed to uncover the underlying molecular features. RESULTS: Patients in the in-house cohort (mean age, 61.3 years ± 9.6 [SD]; 91 men [60%]) were separated into training (n = 105, 70%) and validation (n = 46, 30%) cohorts. A total of 1,239 features were extracted and subjected to machine learning algorithms. The 77 radiomic models showed moderate performance for predicting lymph node metastasis, and the combination of the StepGBM and Enet algorithms had the best performance in the training (AUC = 0.84, 95% CI = 0.77-0.91) and validation (AUC = 0.85, 95% CI = 0.73-0.98) cohorts. We determined that 15 features were core variables for lymph node metastasis. Proliferation-related processes may respond to the main molecular alterations underlying these features. CONCLUSIONS: Machine learning-based radiomics could predict the status of lymph node metastasis in pancreatic cancer, which is associated with proliferation-related alterations.

Application of ultrasonography in predicting the biological risk of gastrointestinal stromal tumors.

OBJECTIVES: To explore and establish a reliable and noninvasive ultrasound model for predicting the biological risk of gastrointestinal stromal tumors (GISTs). MATERIALS AND METHODS: We retrospectively reviewed 266 patients with pathologically-confirmed GISTs and 191 patients were included. Data on patient sex, age, tumor location, biological risk classification, internal echo, echo homogeneity, boundary, shape, blood flow signals, presence of necrotic cystic degeneration, long diameter, and short/long (S/L) diameter ratio were collected. All patients were divided into low-, moderate-, and high-risk groups according to the modified NIH classification criteria. All indicators were analyzed by univariate analysis. The indicators with inter-group differences were used to establish regression and decision tree models to predict the biological risk of GISTs. RESULTS: There were statistically significant differences in long diameter, S/L ratio, internal echo level, echo homogeneity, boundary, shape, necrotic cystic degeneration, and blood flow signals among the low-, moderate-, and high-risk groups (all p < .05). The logistic regression model based on the echo homogeneity, shape, necrotic cystic degeneration and blood flow signals had an accuracy rate of 76.96% for predicting the biological risk, which was higher than the 72.77% of the decision tree model (based on the long diameter, the location of tumor origin, echo homogeneity, shape, and internal echo) (p = .008). In the low-risk and high-risk groups, the predicting accuracy rates of the regression model reached 87.34 and 81.82%, respectively. CONCLUSIONS: Transabdominal ultrasound is highly valuable in predicting the biological risk of GISTs. The logistic regression model has greater predictive value than the decision tree model.

A six-gene-based signature for breast cancer radiotherapy sensitivity estimation.

Breast cancer (BRCA) represents the most common malignancy among women worldwide with high mortality. Radiotherapy is a prevalent therapeutic for BRCA that with heterogeneous effectiveness among patients. Here, we proposed to develop a gene expression-based signature for BRCA radiotherapy sensitivity estimation. Gene expression profiles of BRCA samples from the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) were obtained and used as training and independent testing dataset, respectively. Differential expression genes (DEGs) in BRCA samples compared with their paracancerous samples in the training set were identified by using the edgeR Bioconductor package. Univariate Cox regression analysis and LASSO Cox regression method were applied to screen optimal genes for constructing a radiotherapy sensitivity estimation signature. Nomogram combining independent prognostic factors was used to predict 1-, 3-, and 5-year OS of radiation-treated BRCA patients. Relative proportions of tumor infiltrating immune cells (TIICs) calculated by CIBERSORT and mRNA levels of key immune checkpoint receptors was adopted to explore the relation between the signature and tumor immune response. As a result, 603 DEGs were obtained in BRCA tumor samples, six of which were retained and used to construct the radiotherapy sensitivity prediction model. The signature was proved to be robust in both training and testing sets. In addition, the signature was closely related to the immune microenvironment of BRCA in the context of TIICs and immune checkpoint receptors' mRNA levels. In conclusion, the present study obtained a radiotherapy sensitivity estimation signature for BRCA, which should shed new light in clinical and experimental research.