Dataset Information

Unsupervised Analysis Based on DCE-MRI Radiomics Features Revealed Three Novel Breast Cancer Subtypes with Distinct Clinical Outcomes and Biological Characteristics.

ABSTRACT: Background: This study aimed to reveal the heterogeneity of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) of breast cancer (BC) and identify its prognosis values and molecular characteristics. Methods: Two radiogenomics cohorts (n = 246) were collected and tumor regions were segmented semi-automatically. A total of 174 radiomics features were extracted, and the imaging subtypes were identified and validated by unsupervised analysis. A gene-profile-based classifier was developed to predict the imaging subtypes. The prognostic differences and the biological and microenvironment characteristics of subtypes were uncovered by bioinformatics analysis. Results: Three imaging subtypes were identified and showed high reproducibility. The subtypes differed remarkably in tumor sizes and enhancement patterns, exhibiting significantly different disease-free survival (DFS) or overall survival (OS) in the discovery cohort (p = 0.024) and prognosis datasets (p ranged from <0.0001 to 0.0071). Large sizes and rapidly enhanced tumors usually had the worst outcomes. Associations were found between imaging subtypes and the established subtypes or clinical stages (p ranged from <0.001 to 0.011). Imaging subtypes were distinct in cell cycle and extracellular matrix (ECM)-receptor interaction pathways (false discovery rate, FDR < 0.25) and different in cellular fractions, such as cancer-associated fibroblasts (p < 0.05). Conclusions: The imaging subtypes had different clinical outcomes and biological characteristics, which may serve as potential biomarkers.

SUBMITTER: Ming W

PROVIDER: S-EPMC9688868 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Unsupervised Analysis Based on DCE-MRI Radiomics Features Revealed Three Novel Breast Cancer Subtypes with Distinct Clinical Outcomes and Biological Characteristics.

Ming Wenlong W Li Fuyu F Zhu Yanhui Y Bai Yunfei Y Gu Wanjun W Liu Yun Y Liu Xiaoan X Sun Xiao X Liu Hongde H

Cancers 20221109 22

Background: This study aimed to reveal the heterogeneity of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) of breast cancer (BC) and identify its prognosis values and molecular characteristics. Methods: Two radiogenomics cohorts (n = 246) were collected and tumor regions were segmented semi-automatically. A total of 174 radiomics features were extracted, and the imaging subtypes were identified and validated by unsupervised analysis. A gene-profile-based classifier was developed ...[more]

PMID: 36428600

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Project description:Background: Breast cancer (BC) is a highly heterogeneous cancer. The interaction between immune system and BC is complex, widespread yet unclear. In this study, we aimed to reveal the heterogeneity of host systemic immune response to BC and understand the possible mechanisms that may drive the heterogeneity using transcriptomic data from peripheral blood mononuclear cells (PBMCs). Methods: Transcriptome-wide gene expressions of PBMCs in 33 BC patients were generated by RNA sequencing. An unsupervised clustering algorithm was employed to discover PBMC transcriptome subtypes among BC patients. Association analysis between PBMC subtypes and age, clinical stage, abundance of immune cells, and other clinical factors was performed to understand the underlying biological processes that may drive this heterogeneity. Immune gene signature identification and in silico survival analysis were performed to investigate the potential clinical implications of these PBMC subtypes. The findings were validated using the whole blood transcriptomes of an independent cohort. Results: We observed that established BC subtypes were not associated with PBMC gene expression profiles. Instead, we discovered and validated two new BC subtypes using PBMC transcriptome, which have distinct immune cell proportions, especially for lymphocytes (P = 5.22 × 10-12) and neutrophils (P = 1.13 × 10-14). Enrichment analysis of differentially expressed genes revealed that these two subtypes had distinct patterns of immune responses, including osteoclast differentiation and interleukin-10 signaling pathway. We developed two immune gene signatures that can differentiate these two BC PBMC subtypes. Further analysis suggested they had the ability to predict the clinical outcome of BC patients. Conclusions: PBMC transcriptome profiles can classify BC patients into two distinct subtypes. These two subtypes are mainly shaped by different immune cell abundance, which may have implications on clinical outcomes.

Project description:ObjectiveCurrent clinical evaluation may tend to lack precision in detecting depression in Parkinson's disease (DPD). Radiomics features have gradually shown potential as auxiliary diagnostic tools in identifying and distinguishing different subtypes of Parkinson's disease (PD), and a radiomic approach that combines unsupervised machine learning has the potential to identify DPD.MethodsAnalyze the clinical and imaging data of 272 Parkinson's disease (PD) patients from the PPMI dataset, along with 45 PD patients from the NACC dataset. Extract radiomic features from T1-weighted MRI images and employ principal component analysis (PCA) for dimensionality reduction. Subsequently, apply four unsupervised clustering methods including Gaussian mixture model (GMM), hierarchical clustering, K-means, and partitioning around medoids (PAM) to classify cases in the PPMI dataset into distinct subtypes. Identify high-risk subtypes of DPD on the basis of the time and number of depression progression, and validate these findings using the NACC dataset. The data from the high-risk subtype were divided into a training subtype and a testing subtype in a 7:3 ratio. Multiple logistic regression analysis was conducted on the training subtype data to develop a traditional logistic regression model for the high-risk subtype, which was subsequently compared with a supervised logistic regression model constructed for the entire PPMI cohort. Finally, the performance of both models was evaluated using receiver operating characteristic (ROC) curves. In addition, a decision tree (DT) model was constructed based on independent risk factors of high-risk subtypes and validated using low-risk subtype data. ROC curves were employed to validate this model across training subtype, testing subtype, and low-risk subtype datasets.ResultsThe PAM clustering method demonstrates superior performance compared to the other three clustering methods when the number of clusters is 2. High-risk subtypes of DPD can be effectively distinguished in both the PPMI and NACC datasets. A traditional logistic regression model was developed based on rapid-eye-movement behavior disorder, UPDRS I score, UPDRS II score, and ptau in high-risk subgroups. This model exhibits a diagnostic efficacy (AUC = 0.731) that surpasses that of the traditional regression model constructed using the entire PPMI cohort (AUC = 0.674). The prediction model based on high-risk subtypes had AUC values of 0.853 and 0.81 in the training and testing subtypes, sensitivities of 0.765 and 0.786, and specificities of 0.771 and 0.815, respectively. The AUC, sensitivity, and specificity in the nonhigh-risk subtype were 0.859, 0.654, and 0.852, respectively.ConclusionBy identifying MRI structural radiomics and clinical features as potential biomarkers, the radiomic approach and UCA provide new insights into the pathophysiology of DPD to support the clinical diagnosis with high prediction accuracy.

Project description:ObjectiveTo identify subgroups of patients with hepatocellular carcinoma (HCC) with different liver function reserves using an unsupervised machine-learning approach on the radiomics features from preoperative gadoxetic-acid-enhanced MRIs and to evaluate their association with the risk of post-hepatectomy liver failure (PHLF).MethodsClinical data from 276 consecutive HCC patients who underwent liver resections between January 2017 and March 2019 were retrospectively collected. Radiomics features were extracted from the non-tumorous liver tissue at the gadoxetic-acid-enhanced hepatobiliary phase MRI. The reproducible and non-redundant features were selected for consensus clustering analysis to detect distinct subgroups. After that, clinical variables were compared between the identified subgroups to evaluate the clustering efficacy. The liver function reserve of the subgroups was compared and the correlations between the subgroups and PHLF, postoperative complications, and length of hospital stay were evaluated.ResultsA total of 107 radiomics features were extracted and 37 were selected for unsupervised clustering analysis, which identified two distinct subgroups (138 patients in each subgroup). Compared with subgroup 1, subgroup 2 had significantly more patients with older age, albumin-bilirubin grades 2 and 3, a higher indocyanine green retention rate, and a lower indocyanine green plasma disappearance rate (all p < 0.05). Subgroup 2 was also associated with a higher risk of PHLF, postoperative complications, and longer hospital stays (>18 days) than that of subgroup 1, with an odds ratio of 2.83 (95% CI: 1.58-5.23), 2.41(95% CI: 1.15-5.35), and 2.14 (95% CI: 1.32-3.47), respectively. The odds ratio of our method was similar to the albumin-bilirubin grade for postoperative complications and length of hospital stay (2.41 vs. 2.29 and 2.14 vs. 2.16, respectively), but was inferior for PHLF (2.83 vs. 4.55).ConclusionsBased on the radiomics features of gadoxetic-acid-enhanced MRI, unsupervised clustering analysis identified two distinct subgroups with different liver function reserves and risks of PHLF in HCC patients. Future studies are required to validate our findings.

Project description:ObjectivesTo evaluate the feasibility and value of dynamic contrast-enhanced MRI (DCE-MRI) quantitative analysis and MRI-based radiomics in predicting the efficacy of microwave ablation (MWA) in lung cancers (LCs).MethodsForty-three patients with LCs who underwent DCE-MRI within 24 h of receiving MWA were enrolled in the study and divided into two groups according to the modified response evaluation criteria in solid tumors (m-RECIST) criteria: the effective treatment (complete response + partial response + stable disease, n = 28) and the ineffective treatment (progressive disease, n = 15). DCE-MRI datasets were processed by Omni. Kinetics software, using the extended tofts model (ETM) and exchange model (ECM) to yield pharmacokinetic parameters and their histogram features. Changes in quantitative perfusion parameters were compared between the two groups. Scientific research platform ( https://medresearch.shukun.net/ ) was used for radiomics analysis. A total of 1874 radiomic features were extracted for each tumor by manually segmentation of T1WI and Contrast-enhanced of T1WI (Ce-T1WI) fat inhibition sequence. The performances of radiomics models were evaluated by the receiver operating characteristic curve. Based on radiomics features, survival curves were generated by Kaplan-Meier survival analysis to evaluate patient outcomes. P < 0.05 was set for the significance threshold.ResultsThe Vp value of ECM was significantly higher in the ineffective group compared to the effective group (p = 0.027). Additionally, the skewness, and kurtosis of Vp (p = 0.020 and 0.013, respectively) derived from ETM and Fp (p = 0.027 and 0.030, respectively) from ECM as well as the quantiles were higher in the ineffective group than in the effective group. Significant statistical differences were observed in the energy and entropy of Ve (p = 0.044 and 0.025, respectively) and Vp (p = 0.025 and 0.026, respectively) between the two groups. In the process of model construction, seven features from T1WI, five features from Ce-T1WI, and ten features from combined sequences were ultimately selected. The area under the curve (AUC) values for the T1WI model, Ce-T1WI model, and combined model were 0.910, 0.890, 0.965 in the training group, and 0.850, 0.700, 0.850 in the test group, respectively.ConclusionsDCE-MRI quantitative analysis and MRI-based radiomics may be helpful in assessing the early response to MWA in patients with LCs.

Dataset Information

Unsupervised Analysis Based on DCE-MRI Radiomics Features Revealed Three Novel Breast Cancer Subtypes with Distinct Clinical Outcomes and Biological Characteristics.

Publications

Unsupervised Analysis Based on DCE-MRI Radiomics Features Revealed Three Novel Breast Cancer Subtypes with Distinct Clinical Outcomes and Biological Characteristics.

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