Radiogenomics in Colorectal Cancer.
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ABSTRACT:
SUBMITTER: Badic B
PROVIDER: S-EPMC7956421 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Radiogenomics aims at investigating the relationship between imaging radiomic features and gene expression alterations. This study addressed the potential prognostic complementary value of contrast enhanced computed tomography (CE-CT) radiomic features and gene expression data in primary colorectal cancers (CRC). Sixty-four patients underwent CT scans and radiomic features were extracted from the delineated tumor volume. Gene expression analysis of a small set of genes, previously identified as relevant for CRC, was conducted on surgical samples from the same tumors. The relationships between radiomic and gene expression data was assessed using the Kruskal-Wallis test. Multiple testing was not performed, as this was a pilot study. Cox regression was used to identify variables related to overall survival (OS) and progression free survival (PFS). ABCC2 gene expression was correlated with N (p = 0.016) and M stages (p = 0.022). Expression changes of ABCC2, CD166, CDKNV1 and INHBB genes exhibited significant correlations with some radiomic features. OS was associated with Ratio 3D Surface/volume (p = 0.022) and ALDH1A1 expression (p = 0.042), whereas clinical stage (p = 0.004), ABCC2 expression (p = 0.035), and EntropyGLCM_E (p = 0.0031), were prognostic factors for PFS. Combining CE-CT radiomics with gene expression analysis and histopathological examination of primary CRC could provide higher prognostic stratification power, leading to improved patient management.
| S-EPMC6611779 | biostudies-literature
Project description:Objectives: To evaluate whether incorporating the radiomics, genomics, and clinical features allows prediction of metastasis in colorectal cancer (CRC) and to develop a preoperative nomogram for predicting metastasis. Methods: We retrospectively analyzed radiomics features of computed tomography (CT) images in 134 patients (62 in the primary cohort, 28 in the validation cohort, and 44 in the independent-test cohort) clinicopathologically diagnosed with CRC at Dazhou Central Hospital from February 2018 to October 2019. Tumor tissues were collected from all patients for RNA sequencing, and clinical data were obtained from medical records. A total of 854 radiomics features were extracted from enhanced venous-phase CT of CRC. Least absolute shrinkage and selection operator regression analysis was utilized for data dimension reduction, feature screen, and radiomics signature development. Multivariable logistic regression analysis was performed to build a multiscale predicting model incorporating the radiomics, genomics, and clinical features. The receiver operating characteristic curve, calibration curve, and decision curve were conducted to evaluate the performance of the nomogram. Results: The radiomics signature based on 16 selected radiomics features showed good performance in metastasis assessment in both primary [area under the curve (AUC) = 0.945, 95% confidence interval (CI) 0.892-0.998] and validation cohorts (AUC = 0.754, 95% CI 0.570-0.938). The multiscale nomogram model contained radiomics features signatures, four-gene expression related to cell cycle pathway, and CA 19-9 level. The multiscale model showed good discrimination performance in the primary cohort (AUC = 0.981, 95% CI 0.953-1.000), the validation cohort (AUC = 0.822, 95% CI 0.635-1.000), and the independent-test cohort (AUC = 0.752, 95% CI 0.608-0.896) and good calibration. Decision curve analysis confirmed the clinical application value of the multiscale model. Conclusion: This study presented a multiscale model that incorporated the radiological eigenvalues, genomics features, and CA 19-9, which could be conveniently utilized to facilitate the individualized preoperatively assessing metastasis in CRC patients.
| S-EPMC8113949 | biostudies-literature
Project description:Prostate cancer exhibits intra-tumoral heterogeneity that we hypothesize to be the leading confounding factor contributing to the underperformance of the current pre-treatment clinical-pathological and genomic assessment. These limitations impose an urgent need to develop better computational tools to identify men with low risk of prostate cancer versus others that may be at risk for developing metastatic cancer. The patient stratification will directly translate to patient treatments, wherein decisions regarding active surveillance or intensified therapy are made. Multiparametric MRI (mpMRI) provides the platform to investigate tumor heterogeneity by mapping the individual tumor habitats. We hypothesize that quantitative assessment (radiomics) of these habitats results in distinct combinations of descriptors that reveal regions with different physiologies and phenotypes. Radiogenomics, a discipline connecting tumor morphology described by radiomic and its genome described by the genomic data, has the potential to derive "radio phenotypes" that both correlate to and complement existing validated genomic risk stratification biomarkers. In this article we first describe the radiomic pipeline, tailored for analysis of prostate mpMRI, and in the process we introduce our particular implementations of radiomics modules. We also summarize the efforts in the radiomics field related to prostate cancer diagnosis and assessment of aggressiveness. Finally, we describe our results from radiogenomic analysis, based on mpMRI-Ultrasound (MRI-US) biopsies and discuss the potential of future applications of this technique. The mpMRI radiomics data indicate that the platform would significantly improve the biopsy targeting of prostate habitats through better recognition of indolent versus aggressive disease, thereby facilitating a more personalized approach to prostate cancer management. The expectation to non-invasively identify habitats with high probability of housing aggressive cancers would result in directed biopsies that are more informative and actionable. Conversely, providing evidence for lack of disease would reduce the incidence of non-informative biopsies. In radiotherapy of prostate cancer, dose escalation has been shown to reduce biochemical failure. Dose escalation only to determinate prostate habitats has the potential to improve tumor control with less toxicity than when the entire prostate is dose escalated.
| S-EPMC5703221 | biostudies-literature
Project description:Molecular analysis of the mutation status for EGFR and KRAS are now routine in the management of non-small cell lung cancer. Radiogenomics, the linking of medical images with the genomic properties of human tumors, provides exciting opportunities for non-invasive diagnostics and prognostics. We investigated whether EGFR and KRAS mutation status can be predicted using imaging data. To accomplish this, we studied 186 cases of NSCLC with preoperative thin-slice CT scans. A thoracic radiologist annotated 89 semantic image features of each patient's tumor. Next, we built a decision tree to predict the presence of EGFR and KRAS mutations. We found a statistically significant model for predicting EGFR but not for KRAS mutations. The test set area under the ROC curve for predicting EGFR mutation status was 0.89. The final decision tree used four variables: emphysema, airway abnormality, the percentage of ground glass component and the type of tumor margin. The presence of either of the first two features predicts a wild type status for EGFR while the presence of any ground glass component indicates EGFR mutations. These results show the potential of quantitative imaging to predict molecular properties in a non-invasive manner, as CT imaging is more readily available than biopsies.
| S-EPMC5282551 | biostudies-literature
Project description:In the last decade, the development of radiogenomics research has produced a significant amount of papers describing relations between imaging features and several molecular 'omic signatures arising from next-generation sequencing technology and their potential role in the integrated diagnostic field. The most vulnerable point of many of these studies lies in the poor number of involved patients. In this scenario, a leading role is played by The Cancer Genome Atlas (TCGA) and The Cancer Imaging Archive (TCIA), which make available, respectively, molecular 'omic data and linked imaging data. In this review, we systematically collected and analyzed radiogenomic studies based on TCGA-TCIA data. We organized literature per tumor type and molecular 'omic data in order to discuss salient imaging genomic associations and limitations of each study. Finally, we outlined the potential clinical impact of radiogenomics to improve the accuracy of diagnosis and the prediction of patient outcomes in oncology.
| S-EPMC6929079 | biostudies-literature
Project description:Advances in patient-specific information and biotechnology have contributed to a new era of computational medicine. Radiogenomics has emerged as a new field that investigates the role of genetics in treatment response to radiation therapy. Radiation oncology is currently attempting to embrace these recent advances and add to its rich history by maintaining its prominent role as a quantitative leader in oncologic response modeling. Here, we provide an overview of radiogenomics starting with genotyping, data aggregation, and application of different modeling approaches based on modifying traditional radiobiological methods or application of advanced machine learning techniques. We highlight the current status and potential for this new field to reshape the landscape of outcome modeling in radiotherapy and drive future advances in computational oncology.
| S-EPMC5557376 | biostudies-literature
Project description:Radiogenomics or imaging genomics is a novel omics strategy of associating imaging data with genetic information, which has the potential to advance personalized medicine. Imaging features extracted from PET or PET/CT enable assessment of in vivo functional and physiological activity and provide comprehensive tumor information non-invasively. However, PET features are considered secondary to features on conventional imaging, and there has not yet been a review of the radiogenomic approach using PET features. This review article summarizes the current state of PET-based radiogenomic research for cancer, which discusses some of its limitations and directions for future study.
| S-EPMC7295928 | biostudies-literature
Project description:We aimed to develop a noninvasive radiomics approach to reveal the m6A methylation status and predict survival outcomes and therapeutic responses in patients. A total of 25 m6A regulators were selected for further analysis, we confirmed that expression level and genomic mutations rate of m6A regulators were significantly different between cancer and normal tissues. Besides, we constructed methylation modification models and explored the immune infiltration and biological pathway alteration among different models. The m6A subtypes identified in this study can effectively predict the clinical outcome of bladder cancer (including m6AClusters, geneClusters, and m6Ascore models). In addition, we observed that immune response markers such as PD1 and CTLA4 were significantly corelated with the m6Ascore. Subsequently, a total of 98 obtained digital images were processed to capture the image signature and construct image prediction models based on the m6Ascore classification using a radiomics algorithm. We constructed seven signature radiogenomics models to reveal the m6A methylation status, and the model achieved an area under curve (AUC) degree of 0.887 and 0.762 for the training and test datasets, respectively. The presented radiogenomics models, a noninvasive prediction approach that combined the radiomics signatures and genomics characteristics, displayed satisfactory effective performance for predicting survival outcomes and therapeutic responses of patients. In the future, more interdisciplinary fields concerning the combination of medicine and electronics remains to be explored.
| S-EPMC8559436 | biostudies-literature
Project description:ObjectiveThe aim of this study is to identify prognostic imaging biomarkers and create a radiogenomics nomogram to predict overall survival (OS) in gastric cancer (GC).MaterialRNA sequencing data from 407 patients with GC and contrast-enhanced computed tomography (CECT) imaging data from 46 patients obtained from The Cancer Genome Atlas (TCGA) and The Cancer Imaging Archive (TCIA) were utilized to identify radiogenomics biomarkers. A total of 392 patients with CECT images from the Nanfang Hospital database were obtained to create and validate a radiogenomics nomogram based on the biomarkers.MethodsThe prognostic imaging features that correlated with the prognostic gene modules (selected by weighted gene coexpression network analysis) were identified as imaging biomarkers. A nomogram that integrated the radiomics score and clinicopathological factors was created and validated in the Nanfang Hospital database. Nomogram discrimination, calibration, and clinical usefulness were evaluated.ResultsThree prognostic imaging biomarkers were identified and had a strong correlation with four prognostic gene modules (P < 0.05, FDR < 0.05). The radiogenomics nomogram (AUC = 0.838) resulted in better performance of the survival prediction than that of the TNM staging system (AUC = 0.765, P = 0.011; Delong et al.). In addition, the radiogenomics nomogram exhibited good discrimination, calibration, and clinical usefulness in both the training and validation cohorts.ConclusionsThe novel prognostic radiogenomics nomogram that was constructed achieved excellent correlation with prognosis in both the training and validation cohort of Nanfang Hospital patients with GC. It is anticipated that this work may assist in clinical preferential treatment decisions and promote the process of precision theranostics in the future.
| S-EPMC9257248 | biostudies-literature