Two machine learning methods identify a metastasis-related prognostic model that predicts overall survival in medulloblastoma patients

Application of machine learning for high-throughput tumor marker screening

High-throughput sequencing and multiomics technologies have allowed increasing numbers of biomarkers to be mined and used for disease diagnosis, risk stratification, efficacy assessment, and prognosis prediction. However, the large number and complexity of tumor markers make screening them a substantial challenge. Machine learning (ML) offers new and effective ways to solve the screening problem. ML goes beyond mere data processing and is instrumental in recognizing intricate patterns within data. ML also has a crucial role in modeling dynamic changes associated with diseases. Used together, ML techniques have been included in automatic pipelines for tumor marker screening, thereby enhancing the efficiency and accuracy of the screening process. In this review, we discuss the general processes and common ML algorithms, and highlight recent applications of ML in tumor marker screening of genomic, transcriptomic, proteomic, and metabolomic data of patients with various types of cancers. Finally, the challenges and future prospects of the application of ML in tumor therapy are discussed.

Multiparametric MRI-Based Radiomics Signature with Machine Learning for Preoperative Prediction of Prognosis Stratification in Pediatric Medulloblastoma

RATIONALE AND OBJECTIVES

Despite advances in risk-stratified treatment strategies for children with medulloblastoma (MB), the prognosis for MB with short-term recurrence is extremely poor, and there is still a lack of evaluation of short-term recurrence risk or short-term survival. This study aimed to construct and validate a radiomics model for predicting the outcome of MB based on preoperative multiparametric magnetic resonance images (MRIs) and to provide an objective for clinical decision-making.

MATERIALS AND METHODS

The clinical and imaging data of 64 patients with MB admitted to Shenzhen Children's Hospital from December 2012 to December 2021 and confirmed by pathology were retrospectively collected. According to the 18-month progression-free survival, the cases were classified into a good prognosis group and a poor prognosis group, and all cases were divided into training group (70%) and validation group (30%) randomly. Radiomics features were extracted from MRI of each child. The consistency test, t-test, and the least absolute shrinkage and selection operator were used for feature selection. The support vector machine (SVM) and receiver operator characteristic were used to evaluate the distinguishing ability of the selected features to the prognostic groups. RAD score was calculated based on the selected features. The clinical characteristics and RAD score were included in the multivariate logistic regression, and prediction models were constructed by screening out independent influences. The radiomics nomogram was constructed, and its clinical significance was evaluated.

RESULTS

A total of 1930 radiomic features were extracted from the images of each patient, and 11 features were included in the construction of radiomics score after selected. The area under the curve (AUC) values of the SVM model in the training and validation groups were 0.946 and 0.797, respectively. The radiomics nomogram was constructed based on the training cohort, and the AUC values in the training group and the validation group were 0.926 and 0.835, respectively. The results of clinical decision curve analysis showed that a good net benefit could be obtained from the nomogram.

CONCLUSION

The radiomics nomogram established based on MRI can be used as a noninvasive predictive tool to evaluate the prognosis of children with MB, which is expected to help neurosurgeons better conduct preoperative planning and patient follow-up management.

Construction and experimental validation of a B cell senescence-related gene signature to evaluate prognosis and immunotherapeutic sensitivity in bladder cancer

Senescent B cells exhibit reduced antibody production and enhanced proinflammatory cytokine and chemokine secretion, exerting non-negligible functions in antitumor immunity. This study aims to clarify the prognosis value of B cell senescence-related genes in bladder cancer (BLCA). Twelve B cell senescence-related genes were identified based on previous studies and the single-cell RNA sequencing of a BLCA sample from Gene Expression Omnibus (GEO). The Cancer Genome Atlas BLCA cohort was used as the training dataset. Three cohorts from GEO, 35 clinical samples from the local hospital, and in vitro cell experiments were used for validation. The unsupervised clustering based on the 12 genes was associated with the prognosis and the tumor immunity. Through least absolute shrinkage and selection operator regression and random forest algorithm, G protein subunit gamma 11 (GNG11) and inhibitor of DNA binding 1 (ID1) of the 12 genes were determined as significant prognosis predictors and then included in the multivariate Cox regression model. The model was a reliable and robust prognosis biomarker across multiple large-scale cohorts (pooled HR = 1.76, 95% CI = 1.41-2.20). The tight association between the model and BLCA malignant degree was demonstrated in the local cohort (P < 0.01). The model could also predict the immunotherapeutic sensitivity, which was confirmed by the tumor immune dysfunction and exclusion algorithm (P < 0.0001) and IMvigor210 cohort (P < 0.0001). At last, in vitro cell experiments in IM-9 and GM12878 B cells indicated that GNG11 and ID1 were involved in the cellular aging process. Collectively, a B cell senescence-related gene signature was constructed to evaluate the prognosis and immunotherapeutic response in BLCA, providing novel insights into the biological mechanisms.

Ensemble learning based functional independence ability estimator for pediatric brain tumor survivors

A history of brain tumor strongly affects children’s cognitive abilities, performance of daily activities, quality of life, and functional outcomes. In light of the difficulties in cognition, communication, physical skills, and behavior that these patients may encounter, occupational therapists should perform a comprehensive needs-led assessment of their global functioning after recovery. Such an assessment would ensure that the patients receive adequate support and services at school, at home, and in the community. By predicting the functional activity performance of children with a history of brain tumor, clinical workers can determine the progress of their ability recovery and the optimal treatment plan. We selected several features for testing and employed common machine learning models to predict Functional Independence Measure (WeeFIM) scores. The ensemble learning models exhibited stronger predictive performance than did the individual machine learning models. The ensemble learning models effectively predicted WeeFIM scores. Machine learning models can help clinical workers predict the functional assessment scores of patients with childhood brain tumors. This study used machine learning models to predict the WeeFIM scores of patients with childhood brain tumors and to demonstrate that ensemble machine learning models are more suitable for this task than are individual machine learning models.