Cancer heterogeneity and imaging

Optical-resolution photoacoustic microelastography system for elasticity mapping: Phantom study and practical application

Elastography is a noninvasive technique for characterizing the mechanical properties of biological tissues. Conventional methods have limitations in resolution and sensitivity, hindering disease detection in clinical diagnostics. To address these issues, this study developed an optical-resolution photoacoustic microelastography (OR-PAME) system. Using an agar tissue phantom with varying agar concentrations and contrast agents, PAME evaluated elasticity distribution under compression in both lateral and axial dimensions. It indirectly measured elastic properties by correlating photoacoustic responses, temporal lags, and induced displacement. We also applied the system to the study of the distribution of elastic characteristics of the liver tissue after ablation, which confirmed the potential of OR-PAME in the study of elastic characteristics. Quantitative analysis showed greater lateral displacement in regions with reduced agar concentrations, indicating decreased stiffness. PAME also detected vertical displacement along the axial plane, validating its efficacy in elastographic imaging. By improving resolution and penetration, PAME provides superior visualization of elasticity distribution. Its methodology correlates microstructural alterations with tissue biomechanics, holding potential implications in medical diagnostics.

Development of clinical and magnetic resonance imaging-based radiomics nomograms for the differentiation of nodular fasciitis from soft tissue sarcoma

BACKGROUND

Accurate differentiation of nodular fasciitis (NF) from soft tissue sarcoma (STS) before surgery is essential for the subsequent diagnosis and treatment of patients.

PURPOSE

To develop and evaluate radiomics nomograms based on clinical factors and magnetic resonance imaging (MRI) for the preoperative differentiation of NF from STS.

MATERIAL AND METHODS

This retrospective study analyzed the MRI data of 27 patients with pathologically diagnosed NF and 58 patients with STS who were randomly divided into training (n = 62) and validation (n = 23) groups. Univariate and multivariate analyses were performed to identify the clinical factors and semantic features of MRI. Radiomics analysis was applied to fat-suppressed T1-weighted (T1W-FS) images, fat-suppressed T2-weighted (T2W-FS) images, and contrast-enhanced T1-weighted (CE-T1W) images. The radiomics nomograms incorporating the radiomics signatures, clinical factors, and semantic features of MRI were developed. ROC curves and AUCs were carried out to compare the performance of the clinical factors, radiomics signatures, and clinical radiomics nomograms.

RESULTS

Tumor location, size, heterogeneous signal intensity on T2W-FS imaging, heterogeneous signal intensity on CE-T1W imaging, margin definitions on CE-T1W imaging, and septa were independent predictors for differentiating NF from STS (P < 0.05). The performance of the radiomics signatures based on T2W-FS imaging (AUC = 0.961) and CE-T1W imaging (AUC = 0.938) was better than that based on T1W-FS imaging (AUC = 0.833). The radiomics nomograms had AUCs of 0.949, which demonstrated good clinical utility and calibration.

CONCLUSION

The non-invasive clinical radiomics nomograms exhibited good performance in the differentiation of NF from STS, and they have clinical application in the preoperative diagnosis of diseases.

The use of radiomics and machine learning for the differentiation of chondrosarcoma from enchondroma

PURPOSE

To construct and compare machine learning models for differentiating chondrosarcoma from enchondroma using radiomic features from T1 and fat suppressed Proton density (PD) magnetic resonance imaging (MRI).

METHODS

Eighty-eight patients (57 with enchondroma, 31 with chondrosarcoma) were retrospectively included. Histogram matching and N4ITK MRI bias correction filters were applied. An experienced musculoskeletal radiologist and a senior resident in radiology performed manual segmentation. Voxel sizes were resampled. Laplacian of Gaussian filter and wavelet-based features were used. One thousand eight hundred eighty-eight features were obtained for each patient, with 944 from T1 and 944 from PD images. Sixty-four unstable features were removed. Seven machine learning models were used for classification.

RESULTS

Classification with all features showed neural network was the best model for both readers' datasets with area under the curve (AUC), classification accuracy (CA), and F1 score of 0.979, 0.984; 0.920, 0.932; and 0.889, 0.903, respectively. Four features, including one common to both readers, were selected using fast correlation based filter. The best performing models with selected features were gradient boosting for Fatih Erdem's dataset and neural network for Gülen Demirpolat's dataset with AUC, CA, and F1 score of 0.990, 0.979; 0.943, 0.955; 0.921, 0.933, respectively. Neural Network was the second-best model for FE's dataset based on AUC (0.984).

CONCLUSION

Using pathology as a gold standard, this study defined and compared seven well-performing models to distinguish enchondromas from chondrosarcomas and provided radiomic feature stability and reproducibility among the readers.

Mathematical modelling of the dynamics of image-informed tumor habitats in a murine model of glioma

Tumors exhibit high molecular, phenotypic, and physiological heterogeneity. In this effort, we employ quantitative magnetic resonance imaging (MRI) data to capture this heterogeneity through imaging-based subregions or "habitats" in a murine model of glioma. We then demonstrate the ability to model and predict the growth of the habitats using coupled ordinary differential equations (ODEs) in the presence and absence of radiotherapy. Female Wistar rats (N = 21) were inoculated intracranially with 10⁶ C6 glioma cells, a subset of which received 20 Gy (N = 5) or 40 Gy (N = 8) of radiation. All rats underwent diffusion-weighted and dynamic contrast-enhanced MRI at up to seven time points. All MRI data at each visit were subsequently clustered using k-means to identify physiological tumor habitats. A family of four models consisting of three coupled ODEs were developed and calibrated to the habitat time series of control and treated rats and evaluated for predictive capability. The Akaike Information Criterion was used for model selection, and the normalized sum-of-square-error (SSE) was used to evaluate goodness-of-fit in model calibration and prediction. Three tumor habitats with significantly different imaging data characteristics (p < 0.05) were identified: high-vascularity high-cellularity, low-vascularity high-cellularity, and low-vascularity low-cellularity. Model selection resulted in a five-parameter model whose predictions of habitat dynamics yielded SSEs that were similar to the SSEs from the calibrated model. It is thus feasible to mathematically describe habitat dynamics in a preclinical model of glioma using biology-based ODEs, showing promise for forecasting heterogeneous tumor behavior.

Directionally Sensitive Fractal Radiomics Compatible With Irregularly Shaped Magnetic Resonance Tumor Regions of Interest: Association With Osteosarcoma Chemoresistance

BACKGROUND

Computational analysis of routinely acquired MRI has potential to improve the tumor chemoresistance prediction and to provide decision support in precision medicine, which may extend patient survival. Most radiomic analytical methods are compatible only with rectangular regions of interest (ROIs) and irregular tumor shape is therefore an important limitation. Furthermore, the currently used analytical methods are not directionally sensitive.

PURPOSE

To implement a tumor analysis that is directionally sensitive and compatible with irregularly shaped ROIs.

STUDY TYPE

Retrospective.

SUBJECTS

A total of 54 patients with histopathologic diagnosis of primary osteosarcoma on tubular long bones and with prechemotherapy MRI.

FIELD STRENGTH/SEQUENCE

A 1.5 T, T2-weighted-short-tau-inversion-recovery-fast-spin-echo.

ASSESSMENT

A model to explore associations with osteosarcoma chemo-responsiveness included MRI data obtained before OsteoSa MAP neoadjuvant cytotoxic chemotherapy. Osteosarcoma morphology was analyzed in the MRI data by calculation of the nondirectional two-dimensional (2D) and directional and nondirectional one-dimensional (1D) Higuchi dimensions (Dh). MAP chemotherapy response was assessed by histopathological necrosis.

STATISTICAL TESTS

The area under the receiver operating characteristic (ROC) curve (AUC) evaluated the association of the calculated features with the actual chemoresponsiveness, using tumor histopathological necrosis (95%) as the endpoint. Least absolute shrinkage and selection operator (LASSO) machine learning and multivariable regression were used for feature selection. Significance was set at <0.05.

RESULTS

The nondirectional 1D Dh reached an AUC of 0.88 in association with the 95% tumor necrosis, while the directional 1D analysis along 180 radial lines significantly improved this association according to the Hanley/McNeil test, reaching an AUC of 0.95. The model defined by variable selection using LASSO reached an AUC of 0.98. The directional analysis showed an optimal predictive range between 90° and 97° and revealed structural osteosarcoma anisotropy manifested by its directionally dependent textural properties.

DATA CONCLUSION

Directionally sensitive radiomics had superior predictive performance in comparison to the standard nondirectional image analysis algorithms with AUCs reaching 0.95 and full compatibility with irregularly shaped ROIs.

EVIDENCE LEVEL

3 TECHNICAL EFFICACY: Stage 1.

Evaluating the Accuracy of FUCCI Cell Cycle In Vivo Fluorescent Imaging to Assess Tumor Proliferation in Preclinical Oncology Models

PURPOSE

The primary goal of this study is to evaluate the accuracy of the fluorescence ubiquitination cell cycle indicator (FUCCI) system with fluorescence in vivo imaging compared to 3'-deoxy-3'-[18F]fluorothymidine ([18F]-FLT) positron emission tomography (PET)/computed tomography (CT) and biological validation through histology. Imaging with [18F]-FLT PET/CT can be used to noninvasively assess cancer cell proliferation and has been utilized in both preclinical and clinical studies. However, a cost-effective and straightforward method for in vivo, cell cycle targeted cancer drug screening is needed prior to moving towards translational imaging methods such as PET/CT.

PROCEDURES

In this study, fluorescent MDA-MB-231-FUCCI tumor growth was monitored weekly with caliper measurements and fluorescent imaging. Seven weeks post-injection, [18F]-FLT PET/CT was performed with a preclinical PET/CT, and tumors samples were harvested for histological analysis.

RESULTS

RFP fluorescent signal significantly correlated with tumor volume (r = 0.8153, p < 0.0001). Cell proliferation measured by GFP fluorescent imaging was correlated with tumor growth rate (r = 0.6497, p < 0.001). Also, GFP+ cells and [18F]-FLT regions of high uptake were both spatially located in the tumor borders, indicating that the FUCCI-IVIS method may provide an accurate assessment of tumor heterogeneity of cell proliferation. The quantification of total GFP signal was correlated with the sum of tumor [18F]-FLT standard uptake value (SUV) (r = 0.5361, p = 0.0724). Finally, histological analysis confirmed viable cells in the tumor and the correlation of GFP + and Ki67 + cells (r = 0.6368, p = 0.0477).

CONCLUSION

Fluorescent imaging of the cell cycle provides a noninvasive accurate depiction of tumor progression and response to therapy, which may benefit in vivo testing of novel cancer therapeutics that target the cell cycle.

Development of machine learning models integrating PET/CT radiomic and immunohistochemical pathomic features for treatment strategy choice of cervical cancer with negative pelvic lymph node by mediating COX-2 expression

Objectives: We aimed to establish machine learning models based on texture analysis predicting pelvic lymph node metastasis (PLNM) and expression of cyclooxygenase-2 (COX-2) in cervical cancer with PET/CT negative pelvic lymph node (PLN).

Methods: Eight hundred and thirty-seven texture features were extracted from PET/CT images of 148 early-stage cervical cancer patients with negative PLN. The machine learning models were established by logistic regression from selected features and evaluated by the area under the curve (AUC). The correlation of selected PET/CT texture features predicting PLNM or COX-2 expression and the corresponding immunohistochemical (IHC) texture features was analyzed by the Spearman test.

Results: Fourteen texture features were reserved to calculate the Rad-score for PLNM and COX-2. The PLNM model predicting PLNM showed good prediction accuracy in the training and testing dataset (AUC = 0.817, p < 0.001; AUC = 0.786, p < 0.001, respectively). The COX-2 model also behaved well for predicting COX-2 expression levels in the training and testing dataset (AUC = 0.814, p < 0.001; AUC = 0.748, p = 0.001). The wavelet-LHH-GLCM ClusterShade of the PET image selected to predict PLNM was slightly correlated with the corresponding feature of the IHC image (r = −0.165, p < 0.05). There was a weak correlation of wavelet-LLL-GLRLM LongRunEmphasis of the PET image selected to predict COX-2 correlated with the corresponding feature of the IHC image (r = 0.238, p < 0.05). The correlation between PET image selected to predict COX-2 and the corresponding feature of the IHC image based on wavelet-LLL-GLRLM LongRunEmphasis is considered weak positive (r = 0.238, p=<0.05).

Conclusion: This study underlined the significant application of the machine learning models based on PET/CT texture analysis for predicting PLNM and COX-2 expression, which could be a novel tool to assist the clinical management of cervical cancer with negative PLN on PET/CT images.

Automated multimodal fluorescence microscopy for hyperplex spatial-proteomics: Coupling microfluidic-based immunofluorescence to high resolution, high sensitivity, three-dimensional analysis of histological slides

In situ multiplexing analysis and in situ transcriptomics are now providing revolutionary tools to achieve the comprehension of the molecular basis of cancer and to progress towards personalized medicine to fight the disease. The complexity of these tasks requires a continuous interplay among different technologies during all the phases of the experimental procedures. New tools are thus needed and their characterization in terms of performances and limits is mandatory to reach the best resolution and sensitivity. We propose here a new experimental pipeline to obtain an optimized costs-to-benefits ratio thanks to the alternate employment of automated and manual procedures during all the phases of a multiplexing experiment from sample preparation to image collection and analysis. A comparison between ultra-fast and automated immunofluorescence staining and standard staining protocols has been carried out to compare the performances in terms of antigen saturation, background, signal-to-noise ratio and total duration. We then developed specific computational tools to collect data by automated analysis-driven fluorescence microscopy. Computer assisted selection of targeted areas with variable magnification and resolution allows employing confocal microscopy for a 3D high resolution analysis. Spatial resolution and sensitivity were thus maximized in a framework where the amount of stored data and the total requested time for the procedure were optimized and reduced with respect to a standard experimental approach.

Predicting chemotherapy response in non-small-cell lung cancer via computed tomography radiomic features: Peritumoral, intratumoral, or combined?

Purpose

This study aims to evaluate the ability of peritumoral, intratumoral, or combined computed tomography (CT) radiomic features to predict chemotherapy response in non-small cell lung cancer (NSCLC).

Methods

After excluding subjects with incomplete data or other types of treatments, 272 (Dataset 1) and 43 (Dataset 2, external validation) NSCLC patients who were only treated with chemotherapy as the first-line treatment were enrolled between 2015 and 2019. All patients were divided into response and nonresponse based on the response evaluation criteria in solid tumors, version 1.1. By using 3D slicer and morphological operations in python, the intra- and peritumoral regions of lung tumors were segmented from pre-treatment CT images (unenhanced) and confirmed by two experienced radiologists. Then radiomic features (the first order, texture, shape, et al.) were extracted from the above regions of interest. The models were trained and tested in Dataset 1 and further validated in Dataset 2. The performance of models was compared using the area under curve (AUC), confusion matrix, accuracy, precision, recall, and F1-score.

Results

The radiomic model using features from the peritumoral region of 0–3 mm outperformed that using features from 3–6, 6–9, 9–12 mm peritumoral region, and intratumoral region (AUC: 0.95 versus 0.87, 0.86, 0.85, and 0.88). By the fusion of features from 0–3 and 3–6 mm peritumoral regions, the logistic regression model achieved the best performance, with an AUC of 0.97. This model achieved an AUC of 0.85 in the external cohort. Moreover, among the 20 selected features, seven features differed significantly between the two groups (p < 0.05).

Conclusions

CT radiomic features from both the peri- and intratumoral regions can predict chemotherapy response in NSCLC using machine learning models. Combined features from two peritumoral regions yielded better predictions.

MRI Radiogenomics in Precision Oncology: New Diagnosis and Treatment Method

Precision medicine for cancer affords a new way for the most accurate and effective treatment to each individual cancer. Given the high time-evolving intertumor and intratumor heterogeneity features of personal medicine, there are still several obstacles hindering its diagnosis and treatment in clinical practice regardless of extensive exploration on it over the past years. This paper is to investigate radiogenomics methods in the literature for precision medicine for cancer focusing on the heterogeneity analysis of tumors. Based on integrative analysis of multimodal (parametric) imaging and molecular data in bulk tumors, a comprehensive analysis and discussion involving the characterization of tumor heterogeneity in imaging and molecular expression are conducted. These investigations are intended to (i) fully excavate the multidimensional spatial, temporal, and semantic related information regarding high-dimensional breast magnetic resonance imaging data, with integration of the highly specific structured data of genomics and combination of the diagnosis and cognitive process of doctors, and (ii) establish a radiogenomics data representation model based on multidimensional consistency analysis with multilevel spatial-temporal correlations.

MRI radiomics in the prediction of the volumetric response in meningiomas after gamma knife radiosurgery

PURPOSE

This report presents the first investigation of the radiomics value in predicting the meningioma volumetric response to gamma knife radiosurgery (GKRS).

METHODS

The retrospective study included 93 meningioma patients imaged by three Tesla MRI. Tumor morphology was quantified by calculating 337 shape, first- and second-order radiomic features from MRI obtained before GKRS. Analysis was performed on original 3D MR images and after their laplacian of gaussian (LoG), logarithm and exponential filtering. The prediction performance was evaluated by Pearson correlation, linear regression and ROC analysis, with meningioma volume change per month as the outcome.

RESULTS

Sixty calculated features significantly correlated with the outcome. The feature selection based on LASSO and multivariate regression started from all available 337 radiomic and 12 non-radiomic features. It selected LoG-sigma-1-0-mm-3D_firstorder_InterquartileRange and logarithm_ngtdm_Busyness as the predictively most robust and non-redundant features. The radiomic score based on these two features produced an AUC = 0.81. Adding the non-radiomic karnofsky performance status (KPS) to the score has increased the AUC to 0.88. Low values of the radiomic score defined a homogeneous subgroup of 50 patients with consistent absence (0%) of tumor progression.

CONCLUSION

This is the first report of a strong association between MRI radiomic features and volumetric meningioma response to radiosurgery. The clinical importance of the early and reliable prediction of meningioma responsiveness to radiosurgery is based on its potential to aid individualized therapy decision making.

Prediction of Response to Induction Chemotherapy Plus Concurrent Chemoradiotherapy for Nasopharyngeal Carcinoma Based on MRI Radiomics and Delta Radiomics: A Two-Center Retrospective Study

Objective

We aimed to establish an MRI radiomics model and a Delta radiomics model to predict tumor retraction after induction chemotherapy (IC) combined with concurrent chemoradiotherapy (CCRT) for primary nasopharyngeal carcinoma (NPC) in non-endemic areas and to validate its efficacy.

Methods

A total of 272 patients (155 in the training set, 66 in the internal validation set, and 51 in the external validation set) with biopsy pathologically confirmed primary NPC who were screened for pretreatment MRI were retrospectively collected. The NPC tumor was delineated as a region of interest in the two sequenced images of MRI before treatment and after IC, followed by radiomics feature extraction. With the use of maximum relevance minimum redundancy (mRMR) and least absolute shrinkage and selection operator (LASSO) algorithms, logistic regression was performed to establish pretreatment MRI radiomics and pre- and post-IC Delta radiomics models. The optimal Youden’s index was taken; the receiver operating characteristic (ROC) curve, calibration curve, and decision curve were drawn to evaluate the predictive efficacy of different models.

Results

Seven optimal feature subsets were selected from the pretreatment MRI radiomics model, and twelve optimal subsets were selected from the Delta radiomics model. The area under the ROC curve, accuracy, sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) of the MRI radiomics model were 0.865, 0.827, 0.837, 0.813, 0.776, and 0.865, respectively; the corresponding indicators of the Delta radiomics model were 0.941, 0.883, 0.793, 0.968, 0.833, and 0.958, respectively.

Conclusion

The pretreatment MRI radiomics model and pre- and post-IC Delta radiomics models could predict the IC-CCRT response of NPC in non-epidemic areas.

Pulmonary MRI Radiomics and Machine Learning: Effect of Intralesional Heterogeneity on Classification of Lesion

RATIONALE AND OBJECTIVES

To investigate the effect of intralesional heterogeneity on differentiating benign and malignant pulmonary lesions, quantitative magnetic resonance imaging (MRI) radiomics, and machine learning methods were adopted.

MATERIALS AND METHODS

A total of 176 patients with multiparametric MRI were involved in this exploratory study. To investigate the effect of intralesional heterogeneity on lesion classification, a radiomics model called tumor heterogeneity model was developed and compared to the conventional radiomics model based on the entire tumor. In tumor heterogeneity model, each lesion was divided into five sublesions depending on the spatial location through clustering algorithm. From the five sublesions in multi-parametric MRI sequences, 1100 radiomics features were extracted. The recursive feature elimination method was employed to select features and support vector machine classifier was used to distinguish benign and malignant lesion. The performance of classification was evaluated with the receiver operating characteristic curve and the area under the curve (AUC) was the figure of merit. The 3-fold cross-validation (CV) with and without nesting was used to validate the model, respectively.

RESULTS

The tumor heterogeneity model (AUC = 0.74 ± 0.04 and 0.90 ± 0.03, CV with and without nesting, respectively) outperforms conventional model (AUC = 0.68 ± 0.04 and 0.87 ± 0.03). The difference between the two models is statistically significant (p = 0.03) for lesions greater than 18.80 cm³.

CONCLUSION

Intralesional heterogeneity influences the classification of pulmonary lesions. The tumor heterogeneity model tends to perform better than conventional radiomics model.

Dynamic Cancer Cell Heterogeneity: Diagnostic and Therapeutic Implications

Though heterogeneity of cancers is recognized and has been much discussed in recent years, the concept often remains overlooked in different routine examinations. Indeed, in clinical or biological articles, reviews, and textbooks, cancers and cancer cells are generally presented as evolving distinct entities rather than as an independent heterogeneous cooperative cell population with its self-oriented biology. There are, therefore, conceptual gaps which can mislead the interpretations/diagnostic and therapeutic approaches. In this short review, we wish to summarize and discuss various aspects of this dynamic evolving heterogeneity and its biological, pathological, clinical, diagnostic, and therapeutic implications, using thyroid carcinoma as an illustrative example.

New method for quantification of intratumoral heterogeneity: a feasibility study on Ktrans maps from preclinical DCE-MRI

OBJECT

To develop new imaging biomarkers of therapeutic efficacy through the quantification of intratumoral microvascular heterogeneity.

MATERIALS AND METHODS

The described method was a combination of non-supervised clustering and extraction of intratumoral complexity features (ICF): number of non-connected objects, volume fraction. It was applied to a set of 3D DCE-MRI K^trans maps acquired previously on tumor bearing mice prior to and on day 4 of anti-angiogenic treatment. Evolutions of ICF were compared to conventional summary statistics (CSS) and to heterogeneity related whole tumor texture features (TF) on treated (n = 9) and control (n = 6) mice.

RESULTS

Computed optimal number of clusters per tumor was 4. Several intratumoral features extracted from the clusters were able to monitor a therapy effect. Whereas no feature significantly changed for the control group, 6 features significantly changed for the treated group (4 ICF, 2 CSS). Among these, 5 also significantly differentiated the two groups (3 ICF, 2 CSS). TF failed in demonstrating differences within and between the two groups.

DISCUSSION

ICF are potential imaging biomarkers for anti-angiogenic therapy assessment. The presented method may be expected to have advantages with respect to texture analysis-based methods regarding interpretability of results and setup of standardized image analysis protocols.

Prediction of lymphovascular space invasion using a combination of tenascin-C, cox-2, and PET/CT radiomics in patients with early-stage cervical squamous cell carcinoma

BACKGROUND

Lymphovascular space invasion is an independent prognostic factor in early-stage cervical cancer. However, there is a lack of non-invasive methods to detect lymphovascular space invasion. Some researchers found that Tenascin-C and Cyclooxygenase-2 was correlated with lymphovascular space invasion. Radiomics has been studied as an emerging tool for distinguishing tumor pathology stage, evaluating treatment response, and predicting prognosis. This study aimed to establish a machine learning model that combines radiomics based on PET imaging with tenascin-C (TNC) and cyclooxygenase-2 (COX-2) for predicting lymphovascular space invasion (LVSI) in patients with early-stage cervical cancer.

METHODS

One hundred and twelve patients with early-stage cervical squamous cell carcinoma who underwent PET/CT examination were retrospectively analyzed. Four hundred one radiomics features based on PET/CT images were extracted and integrated into radiomics score (Rad-score). Immunohistochemical analysis was performed to evaluate TNC and COX-2 expression. Mann-Whitney U test was used to distinguish differences in the Rad-score, TNC, and COX-2 between LVSI and non-LVSI groups. The correlations of characteristics were tested by Spearman analysis. Machine learning models including radiomics model, protein model and combined model were established by logistic regression algorithm and evaluated by ROC curve. Pairwise comparisons of ROC curves were tested by DeLong test.

RESULTS

The Rad-score of patients with LVSI was significantly higher than those without. A significant correlation was shown between LVSI and Rad-score (r = 0.631, p < 0.001). TNC was correlated to both the Rad-score (r = 0.244, p = 0.024) and COX-2 (r = 0.227, p = 0.036). The radiomics model had the best predictive performance among all models in training and external dataset (AUCs: 0.914, 0.806, respectively, p < 0.001). However, in testing dataset, the combined model had better efficiency for predicting LVSI than other models (AUCs: 0.801 vs. 0.756 and 0.801 vs. 0.631, respectively).

CONCLUSION

The machine learning model of the combination of PET radiomics with COX-2 and TNC provides a new tool for detecting LVSI in patients with early-stage cervical cancer. In the future, multicentric studies on larger sample of patients will be used to test the model.

TRIAL REGISTRATION

This is a retrospective study and there is no experimental intervention on human participants. The Ethics Committee has confirmed that retrospectively registered is not required.

Predictive Radiomic Models for the Chemotherapy Response in Non-Small-Cell Lung Cancer based on Computerized-Tomography Images

The heterogeneity and complexity of non-small cell lung cancer (NSCLC) tumors mean that NSCLC patients at the same stage can have different chemotherapy prognoses. Accurate predictive models could recognize NSCLC patients likely to respond to chemotherapy so that they can be given personalized and effective treatment. We propose to identify predictive imaging biomarkers from pre-treatment CT images and construct a radiomic model that can predict the chemotherapy response in NSCLC. This single-center cohort study included 280 NSCLC patients who received first-line chemotherapy treatment. Non-contrast CT images were taken before and after the chemotherapy, and clinical information were collected. Based on the Response Evaluation Criteria in Solid Tumors and clinical criteria, the responses were classified into two categories: response (n = 145) and progression (n = 135), then all data were divided into two cohorts: training cohort (224 patients) and independent test cohort (56 patients). In total, 1629 features characterizing the tumor phenotype were extracted from a cube containing the tumor lesion cropped from the pre-chemotherapy CT images. After dimensionality reduction, predictive models of the chemotherapy response of NSCLC with different feature selection methods and different machine-learning classifiers (support vector machine, random forest, and logistic regression) were constructed. For the independent test cohort, the predictive model based on a random-forest classifier with 20 radiomic features achieved the best performance, with an accuracy of 85.7% and an area under the receiver operating characteristic curve of 0.941 (95% confidence interval, 0.898–0.982). Of the 20 selected features, four were first-order statistics of image intensity and the others were texture features. For nine features, there were significant differences between the response and progression groups (p < 0.001). In the response group, three features, indicating heterogeneity, were overrepresented and one feature indicating homogeneity was underrepresented. The proposed radiomic model with pre-chemotherapy CT features can predict the chemotherapy response of patients with non-small cell lung cancer. This radiomic model can help to stratify patients with NSCLC, thereby offering the prospect of better treatment.

Radiomics Nomograms Based on Non-enhanced MRI and Clinical Risk Factors for the Differentiation of Chondrosarcoma from Enchondroma

BACKGROUND

Differentiating chondrosarcoma from enchondroma using conventional MRI remains challenging. An effective method for accurate preoperative diagnosis could affect the management and prognosis of patients.

PURPOSE

To validate and evaluate radiomics nomograms based on non-enhanced MRI and clinical risk factors for the differentiation of chondrosarcoma from enchondroma.

STUDY TYPE

Retrospective.

POPULATION

A total of 103 patients with pathologically confirmed chondrosarcoma (n = 53) and enchondroma (n = 50) were randomly divided into training (n = 68) and validation (n = 35) groups.

FIELD STRENGTH/SEQUENCE

Axial non-contrast-enhanced T1-weighted images (T1WI) and fat-suppressed T2-weighted images (T2WI-FS) were acquired at 3.0 T.

ASSESSMENT

Clinical risk factors (sex, age, and tumor location) and diagnosis assessment based on morphologic MRI by three radiologists were recorded. Three radiomics signatures were established based on the T1WI, T2WI-FS, and T1WI + T2WI-FS sequences. Three clinical radiomics nomograms were developed based on the clinical risk factors and three radiomics signatures.

STATISTICAL TESTS

The area under the receiver operating characteristic curve (AUC) was used to evaluate the performance of radiomics signatures and clinical radiomics nomograms.

RESULTS

Tumor location was an important clinical risk factor (P < 0.05). The radiomics signature based on T1WI and T1WI + T2WI-FS features performed better than that based on T2WI-FS in the validation group (AUC in the validation group: 0.961, 0.938, and 0.833, respectively; P < 0.05). In the validation group, the three clinical radiomics nomograms (T1WI, T2WI-FS, and T1WI + T2WI-FS) achieved AUCs of 0.938, 0.935, and 0.954, respectively. In all patients, the clinical radiomics nomogram based on T2WI-FS (AUC = 0.967) performed better than that based on T2WI-FS (AUC = 0.901, P < 0.05).

DATA CONCLUSION

The proposed clinical radiomics nomogram showed promising performance in differentiating chondrosarcoma from enchondroma.

LEVEL OF EVIDENCE

4 TECHNICAL EFFICACY: Stage 2.

Delta Radiomics Can Predict Distant Metastasis in Locally Advanced Rectal Cancer: The Challenge to Personalize the Cure

PURPOSE

Distant metastases are currently the main cause of treatment failure in locally advanced rectal cancer (LARC) patients. The aim of this research is to investigate a correlation between the variation of radiomics features using pre- and post-neoadjuvant chemoradiation (nCRT) magnetic resonance imaging (MRI) with 2 years distant metastasis (2yDM) rate in LARC patients.

METHODS AND MATERIALS

Diagnostic pre- and post- nCRT MRI of LARC patients, treated in a single institution from May 2008 to June 2015 with an adequate follow-up time, were retrospectively collected. Gross tumor volumes (GTV) were contoured by an abdominal radiologist and blindly reviewed by a radiation oncologist expert in rectal cancer. The dataset was firstly randomly split into 90% training data, for features selection, and 10% testing data, for the validation. The final set of features after the selection was used to train 15 different classifiers using accuracy as target metric. The models' performance was then assessed on the testing data and the best performing classifier was then selected, maximising the confusion matrix balanced accuracy (BA).

RESULTS

Data regarding 213 LARC patients (36% female, 64% male) were collected. Overall 2yDM was 17%. A total of 2,606 features extracted from the pre- and post- nCRT GTV were tested and 4 features were selected after features selection process. Among the 15 tested classifiers, logistic regression proved to be the best performing one with a testing set BA, sensitivity and specificity of 78.5%, 71.4% and 85.7%, respectively.

CONCLUSIONS

This study supports a possible role of delta radiomics in predicting following occurrence of distant metastasis. Further studies including a consistent external validation are needed to confirm these results and allows to translate radiomics model in clinical practice. Future integration with clinical and molecular data will be mandatory to fully personalized treatment and follow-up approaches.

Prediction of the World Health Organization Grade of rectal neuroendocrine tumors based on CT histogram analysis

OBJECTIVES

To investigate the diagnostic value of contrast-enhanced computed tomography (CECT) histogram analysis in predicting the World Health Organization (WHO) grade of rectal neuroendocrine tumors (R-NETs).

MATERIALS AND METHODS

A total of 61 (35 G1, 12 G2, 10 G3, and 4 NECs) patients who underwent preoperative CECT and treated with surgery to be confirmed as R-NETs were included in this study from January 2014 to May 2019. We depicted ROIs and measured the CECT texture parameters (mean, median, 10th, 25th, 75th, 90th percentiles, skewness, kurtosis, and entropy) from arterial phase (AP) and venous phase (VP) images by two radiologists. We calculated intraclass correlation coefficient (ICC) and compared the histogram parameters between low-grade (G1) and higher grade (HG) (G2/G3/NECs) by applying appropriate statistical method. We obtained the optimal parameters to identify G1 from HG using receiver operating characteristic (ROC) curves.

RESULTS

The capability of AP and VP histogram parameters for differentiating G1 from HG was similar in several histogram parameters (mean, median, 10th, 25th, 75th, and 90th percentiles) (all p < 0.001). Skewness, kurtosis, and entropy on AP images showed no significant differences between G1 and HG (p = 0.853, 0.512, 0.557, respectively). Entropy on VP images was significantly different (p = 0.017) between G1 and HG, however, skewness and kurtosis showed no significant differences (p = 0.654, 0.172, respectively). ROC analysis showed a good predictive performance between G1 and HG, and the 75th (AP) generated the highest area under the curve (AUC = 0.871), followed by the 25th (AP), mean (VP), and median (VP) (AUC = 0.864). Combined the size of tumor and the 75th (AP) generated the highest AUC.

CONCLUSIONS

CECT histogram parameters, including arterial and venous phases, can be used as excellent indicators for predicting G1 and HG of rectal neuroendocrine tumors, and the size of the tumor is also an important independent predictor.

Multiparametric Analysis of Longitudinal Quantitative MRI data to Identify Distinct Tumor Habitats in Preclinical Models of Breast Cancer

This study identifies physiological tumor habitats from quantitative magnetic resonance imaging (MRI) data and evaluates their alterations in response to therapy. Two models of breast cancer (BT-474 and MDA-MB-231) were imaged longitudinally with diffusion-weighted MRI and dynamic contrast-enhanced MRI to quantify tumor cellularity and vascularity, respectively, during treatment with trastuzumab or albumin-bound paclitaxel. Tumors were stained for anti-CD31, anti-Ki-67, and H&E. Imaging and histology data were clustered to identify tumor habitats and percent tumor volume (MRI) or area (histology) of each habitat was quantified. Histological habitats were correlated with MRI habitats. Clustering of both the MRI and histology data yielded three clusters: high-vascularity high-cellularity (HV-HC), low-vascularity high-cellularity (LV-HC), and low-vascularity low-cellularity (LV-LC). At day 4, BT-474 tumors treated with trastuzumab showed a decrease in LV-HC (p = 0.03) and increase in HV-HC (p = 0.03) percent tumor volume compared to control. MDA-MB-231 tumors treated with low-dose albumin-bound paclitaxel showed a longitudinal decrease in LV-HC percent tumor volume at day 3 (p = 0.01). Positive correlations were found between histological and imaging-derived habitats: HV-HC (BT-474: p = 0.03), LV-HC (MDA-MB-231: p = 0.04), LV-LC (BT-474: p = 0.04; MDA-MB-231: p < 0.01). Physiologically distinct tumor habitats associated with therapeutic response were identified with MRI and histology data in preclinical models of breast cancer.

[Radiomics models based on non-enhanced MRI can differentiate chondrosarcoma from enchondroma]

OBJECTIVE

To develop and validate radiomics models based on non-enhanced magnetic resonance (MR) imaging for differentiating chondrosarcoma from enchondroma.

METHODS

We retrospectively evaluated a total of 68 patients (including 27 with chondrosarcoma and 41 with enchondroma), who were randomly divided into training group (n=46) and validation group (n=22). Radiomics features were extracted from T₁WI and T₂WI-FS sequences of the whole tumor by two radiologists independently and selected by Low Variance, Univariate feature selection, and least absolute shrinkage and selection operator (LASSO). Radiomics models were constructed by multivariate logistic regression analysis based on the features from T₁WI and T₂WI-FS sequences. The receiver-operating characteristics (ROC) curve and intraclass correlation coefficient (ICC) analyses of the radiomics models and conventional MR imaging were performed to determine their diagnostic accuracy.

RESULTS

The ICC value for interreader agreement of the radiomics features ranged from 0.779 to 0.923, which indicated good agreement. Ten and 11 features were selected from the T₁WI and T₂WI-FS sequences to construct radiomics models, respectively. The areas under the curve (AUCs) of T₁WI and T₂WI-FS models were 0.990 and 0.925 in training group and 0.915 and 0.855 in the validation group, respectively, showing no significant differences between the two sequence-based models (P&gt;0.05). In all the cases, the AUCs of the two radiomics models based on T₁WI and T₂WI-FS sequences and conventional MR imaging were 0.955, 0.901 and 0.569, respectively, demonstrating a significantly higher diagnostic accuracy of the two sequence-based radiomics models than conventional MR imaging (P&lt;0.01).

CONCLUSIONS

The radiomics models based on T₁WI and T₂WI-FS non-enhanced MR imaging can be used for the differentiation of chondrosarcoma from enchondroma.

PET/MRI and genetic intrapatient heterogeneity in head and neck cancers

PURPOSE

The relation between functional imaging and intrapatient genetic heterogeneity remains poorly understood. The aim of our study was to investigate spatial sampling and functional imaging by FDG-PET/MRI to describe intrapatient tumour heterogeneity.

METHODS

Six patients with oropharyngeal cancer were included in this pilot study. Two tumour samples per patient were taken and sequenced by next-generation sequencing covering 327 genes relevant in head and neck cancer. Corresponding regions were delineated on pretherapeutic FDG-PET/MRI images to extract apparent diffusion coefficients and standardized uptake values.

RESULTS

Samples were collected within the primary tumour (n = 3), within the primary tumour and the involved lymph node (n = 2) as well as within two independent primary tumours (n = 1). Genetic heterogeneity of the primary tumours was limited and most driver gene mutations were found ubiquitously. Slightly increasing heterogeneity was found between primary tumours and lymph node metastases. One private predicted driver mutation within a primary tumour and one in a lymph node were found. However, the two independent primary tumours did not show any shared mutations in spite of a clinically suspected field cancerosis. No conclusive correlation between genetic heterogeneity and heterogeneity of PET/MRI-derived parameters was observed.

CONCLUSION

Our limited data suggest that single sampling might be sufficient in some patients with oropharyngeal cancer. However, few driver mutations might be missed and, if feasible, spatial sampling should be considered. In two independent primary tumours, both lesions should be sequenced. Our data with a limited number of patients do not support the concept that multiparametric PET/MRI features are useful to guide biopsies for genetic tumour characterization.

Bridging the translational gap: Implementation of multimodal small animal imaging strategies for tumor burden assessment in a co-clinical trial

In designing co-clinical cancer studies, preclinical imaging brings unique challenges that emphasize the gap between man and mouse. Our group is developing quantitative imaging methods for the preclinical arm of a co-clinical trial studying immunotherapy and radiotherapy in a soft tissue sarcoma model. In line with treatment for patients enrolled in the clinical trial SU2C-SARC032, primary mouse sarcomas are imaged with multi-contrast micro-MRI (T1 weighted, T2 weighted, and T1 with contrast) before and after immune checkpoint inhibition and pre-operative radiation therapy. Similar to the patients, after surgery the mice will be screened for lung metastases with micro-CT using respiratory gating. A systems evaluation was undertaken to establish a quantitative baseline for both the MR and micro-CT systems against which others systems might be compared. We have constructed imaging protocols which provide clinically-relevant resolution and contrast in a genetically engineered mouse model of sarcoma. We have employed tools in 3D Slicer for semi-automated segmentation of both MR and micro-CT images to measure tumor volumes efficiently and reliably in a large number of animals. Assessment of tumor burden in the resulting images was precise, repeatable, and reproducible. Furthermore, we have implemented a publicly accessible platform for sharing imaging data collected during the study, as well as protocols, supporting information, and data analyses. In doing so, we aim to improve the clinical relevance of small animal imaging and begin establishing standards for preclinical imaging of tumors from the perspective of a co-clinical trial.

Tumor Ensemble-Based Modeling and Visualization of Emergent Angiogenic Heterogeneity in Breast Cancer

There is a critical need for new tools to investigate the spatio-temporal heterogeneity and phenotypic alterations that arise in the tumor microenvironment. However, computational investigations of emergent inter- and intra-tumor angiogenic heterogeneity necessitate 3D microvascular data from 'whole-tumors' as well as "ensembles" of tumors. Until recently, technical limitations such as 3D imaging capabilities, computational power and cost precluded the incorporation of whole-tumor microvascular data in computational models. Here, we describe a novel computational approach based on multimodality, 3D whole-tumor imaging data acquired from eight orthotopic breast tumor xenografts (i.e. a tumor 'ensemble'). We assessed the heterogeneous angiogenic landscape from the microvascular to tumor ensemble scale in terms of vascular morphology, emergent hemodynamics and intravascular oxygenation. We demonstrate how the abnormal organization and hemodynamics of the tumor microvasculature give rise to unique microvascular niches within the tumor and contribute to inter- and intra-tumor heterogeneity. These tumor ensemble-based simulations together with unique data visualization approaches establish the foundation of a novel 'cancer atlas' for investigators to develop their own in silico systems biology applications. We expect this hybrid image-based modeling framework to be adaptable for the study of other tissues (e.g. brain, heart) and other vasculature-dependent diseases (e.g. stroke, myocardial infarction).

Noninvasive evaluation of 18F-FDG/18F-FMISO-based Micro PET in monitoring hepatic metastasis of colorectal cancer

This study aimed to explore the application of two radiotracers (¹⁸F-fluorodeoxyglucose (FDG) and ¹⁸F-fluoromisonidazole (FMISO)) in monitoring hepatic metastases of human colorectal cancer (CRC). Mouse models of CRC hepatic metastases were established by implantation of the human CRC cell lines LoVo and HT29 by intrasplenic injection. Wound healing and Transwell assays were performed to examine cell migration and invasion abilities. Radiotracer-based cellular uptake in vitro and micro-positron emission tomography imaging of liver metastases in vivo were performed. The incidence of liver metastases in LoVo-xenografted mice was significantly higher than that in HT29-xenografted ones. The SUVmax/mean values of ¹⁸F-FMISO, but not ¹⁸F-FDG, in LoVo xenografts were significantly greater than in HT29 xenografts. In vitro, LoVo cells exhibited stronger metastatic potential and higher radiotracer uptake than HT29 cells. Mechanistically, the expression of HIF-1α and GLUT-1 in LoVo cells and LoVo tumor tissues was remarkably higher than in HT29 cells and tissues. Linear regression analysis demonstrated correlations between cellular ¹⁸F-FDG/¹⁸F-FMISO uptake and HIF-1α/GLUT-1 expression in vitro, as well as between ¹⁸F-FMISO SUVmax and GLUT-1 expression in vivo. ¹⁸F-FMISO uptake may serve as a potential biomarker for the detection of liver metastases in CRC, whereas its clinical use warrants validation.

A new method for the high-precision assessment of tumor changes in response to treatment

Motivation

Imaging demonstrates that preclinical and human tumors are heterogeneous, i.e. a single tumor can exhibit multiple regions that behave differently during both development and also in response to treatment. The large variations observed in control group, tumors can obscure detection of significant therapeutic effects due to the ambiguity in attributing causes of change. This can hinder development of effective therapies due to limitations in experimental design rather than due to therapeutic failure. An improved method to model biological variation and heterogeneity in imaging signals is described. Specifically, linear Poisson modeling (LPM) evaluates changes in apparent diffusion co-efficient between baseline and 72 h after radiotherapy, in two xenograft models of colorectal cancer. The statistical significance of measured changes is compared to those attainable using a conventional t-test analysis on basic apparent diffusion co-efficient distribution parameters.

Results

When LPMs were applied to treated tumors, the LPMs detected highly significant changes. The analyses were significant for all tumors, equating to a gain in power of 4-fold (i.e. equivalent to having a sample size 16 times larger), compared with the conventional approach. In contrast, highly significant changes are only detected at a cohort level using t-tests, restricting their potential use within personalized medicine and increasing the number of animals required during testing. Furthermore, LPM enabled the relative volumes of responding and non-responding tissue to be estimated for each xenograft model. Leave-one-out analysis of the treated xenografts provided quality control and identified potential outliers, raising confidence in LPM data at clinically relevant sample sizes.

Availability and implementation

TINA Vision open source software is available from www.tina-vision.net.

Supplementary information

Supplementary data are available at Bioinformatics online.

Radiomics and radiogenomics for precision radiotherapy

Imaging plays an important role in the diagnosis and staging of cancer, as well as in radiation treatment planning and evaluation of therapeutic response. Recently, there has been significant interest in extracting quantitative information from clinical standard-of-care images, i.e. radiomics, in order to provide a more comprehensive characterization of image phenotypes of the tumor. A number of studies have demonstrated that a deeper radiomic analysis can reveal novel image features that could provide useful diagnostic, prognostic or predictive information, improving upon currently used imaging metrics such as tumor size and volume. Furthermore, these imaging-derived phenotypes can be linked with genomic data, i.e. radiogenomics, in order to understand their biological underpinnings or further improve the prediction accuracy of clinical outcomes. In this article, we will provide an overview of radiomics and radiogenomics, including their rationale, technical and clinical aspects. We will also present some examples of the current results and some emerging paradigms in radiomics and radiogenomics for clinical oncology, with a focus on potential applications in radiotherapy. Finally, we will highlight the challenges in the field and suggest possible future directions in radiomics to maximize its potential impact on precision radiotherapy.

Textural features of dynamic contrast-enhanced MRI derived model-free and model-based parameter maps in glioma grading

BACKGROUND

Presurgical glioma grading by dynamic contrast-enhanced MRI (DCE-MRI) has unresolved issues.

PURPOSE

The aim of this study was to investigate the ability of textural features derived from pharmacokinetic model-based or model-free parameter maps of DCE-MRI in discriminating between different grades of gliomas, and their correlation with pathological index.

STUDY TYPE

Retrospective.

SUBJECTS

Forty-two adults with brain gliomas.

FIELD STRENGTH/SEQUENCE

3.0T, including conventional anatomic sequences and DCE-MRI sequences (variable flip angle T1-weighted imaging and three-dimensional gradient echo volumetric imaging).

ASSESSMENT

Regions of interest on the cross-sectional images with maximal tumor lesion. Five commonly used textural features, including Energy, Entropy, Inertia, Correlation, and Inverse Difference Moment (IDM), were generated.

RESULTS

All textural features of model-free parameters (initial area under curve [IAUC], maximal signal intensity [Max SI], maximal up-slope [Max Slope]) could effectively differentiate between grade II (n = 15), grade III (n = 13), and grade IV (n = 14) gliomas (P < 0.05). Two textural features, Entropy and IDM, of four DCE-MRI parameters, including Max SI, Max Slope (model-free parameters), vp (Extended Tofts), and vp (Patlak) could differentiate grade III and IV gliomas (P < 0.01) in four measurements. Both Entropy and IDM of Patlak-based K^trans and vp could differentiate grade II (n = 15) from III (n = 13) gliomas (P < 0.01) in four measurements. No textural features of any DCE-MRI parameter maps could discriminate between subtypes of grade II and III gliomas (P < 0.05). Both Entropy and IDM of Extended Tofts- and Patlak-based vp showed highest area under curve in discriminating between grade III and IV gliomas. However, intraclass correlation coefficient (ICC) of these features revealed relatively lower inter-observer agreement. No significant correlation was found between microvascular density and textural features, compared with a moderate correlation found between cellular proliferation index and those features.

DATA CONCLUSION

Textural features of DCE-MRI parameter maps displayed a good ability in glioma grading.

LEVEL OF EVIDENCE

3 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018;47:1099-1111.

Systems heterogeneity: An integrative way to understand cancer heterogeneity

The concept of systems heterogeneity was firstly coined and explained in the Special Issue, as a new alternative to understand the importance and complexity of heterogeneity in cancer. Systems heterogeneity can offer a full image of heterogeneity at multi-dimensional functions and multi-omics by integrating gene or protein expression, epigenetics, sequencing, phosphorylation, transcription, pathway, or interaction. The Special Issue starts with the roles of epigenetics in the initiation and development of cancer heterogeneity through the interaction between permanent genetic mutations and dynamic epigenetic alterations. Cell heterogeneity was defined as the difference in biological function and phenotypes between cells in the same organ/tissue or in different organs, as well as various challenges, as exampled in telocytes. The single cell heterogeneity has the value of identifying diagnostic biomarkers and therapeutic targets and clinical potential of single cell systems heterogeneity in clinical oncology. A number of signaling pathways and factors contribute to the development of systems heterogeneity. Proteomic heterogeneity can change the strategy and thinking of drug discovery and development by understanding the interactions between proteins or proteins with drugs in order to optimize drug efficacy and safety. The association of cancer heterogeneity with cancer cell evolution and metastasis was also overviewed as a new alternative for diagnostic biomarkers and therapeutic targets in clinical application.