Development of an Immune-Pathology Informed Radiomics Model for Non-Small Cell Lung Cancer.
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ABSTRACT:
SUBMITTER: Tang C
PROVIDER: S-EPMC5792427 | biostudies-literature | 2018 Jan
REPOSITORIES: biostudies-literature
Publications
Development of an Immune-Pathology Informed Radiomics Model for Non-Small Cell Lung Cancer.
Tang Chad C Hobbs Brian B Amer Ahmed A Li Xiao X Behrens Carmen C Canales Jaime Rodriguez JR Cuentas Edwin Parra EP Villalobos Pamela P Fried David D Chang Joe Y JY Hong David S DS Welsh James W JW Sepesi Boris B Court Laurence L Wistuba Ignacio I II Koay Eugene J EJ
Scientific reports 20180131 1
With increasing use of immunotherapy agents, pretreatment strategies for identifying responders and non-responders is useful for appropriate treatment assignment. We hypothesize that the local immune micro-environment of NSCLC is associated with patient outcomes and that these local immune features exhibit distinct radiologic characteristics discernible by quantitative imaging metrics. We assembled two cohorts of NSCLC patients treated with definitive surgical resection and extracted quantitativ ...[more]
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Project description:Growing evidence suggests that the efficacy of immunotherapy in non-small cell lung cancers (NSCLCs) is associated with the immune microenvironment within the tumor. We aimed to explore radiologic phenotyping using a radiomics approach to assess the immune microenvironment in NSCLC. Two independent NSCLC cohorts (training and test sets) were included. Single-sample gene set enrichment analysis was used to determine the tumor microenvironment, where type 1 helper T (Th1) cells, type 2 helper T (Th2) cells, and cytotoxic T cells were the targets for prediction with computed tomographic (CT) radiomic features. Multiple algorithms were in the modeling followed by final model selection. The training dataset comprised 89 NSCLCs and the test set included 60 cases of lung squamous cell carcinoma and adenocarcinoma. A total of 239 CT radiomic features were used. A linear discriminant analysis model was selected for the final model of Th2 cell group prediction. The area under the curve value of the final model on the test set was 0.684. Predictors of the linear discriminant analysis model were skewness (total and outer pixels), kurtosis, variance (subsampled from delta [subtraction inner pixels from outer pixels]), and informational measure of correlation. The performances of radiomics on test set of Th1 and cytotoxic T cell were not accurate enough to be predictable. A radiomics approach can be used to interrogate an entire tumor in a noninvasive manner and provide added diagnostic value to identify the immune microenvironment of NSCLC, in particular, Th2 cell signatures.
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Project description:BackgroundTumor mutational burden (TMB) is one of the most significant predictive biomarkers of immunotherapy efficacy in non-small cell lung cancer (NSCLC). Radiomics allows high-throughput extraction and analysis of advanced and quantitative medical imaging features. This study develops and validates a radiomic model for predicting TMB level and the response to immunotherapy based on CT features in NSCLC.MethodPre-operative chest CT images of 127 patients with NSCLC were retrospectively studied. The 3D-Slicer software was used to outline the region of interest and extract features from the CT images. Radiomics prediction model was constructed by LASSO and multiple logistic regression in a training dataset. The model was validated by receiver operating characteristic (ROC) curves and calibration curves using external datasets. Decision curve analysis was used to assess the value of the model for clinical application.ResultsA total of 1037 radiomic features were extracted from the CT images of NSCLC patients from TCGA. LASSO regression selected three radiomics features (Flatness, Autocorrelation and Minimum), which were associated with TMB level in NSCLC. A TMB prediction model consisting of 3 radiomic features was constructed by multiple logistic regression. The area under the curve (AUC) value in the TCGA training dataset was 0.816 (95% CI: 0.7109-0.9203) for predicting TMB level in NSCLC. The AUC value in external validation dataset I was 0.775 (95% CI: 0.5528-0.9972) for predicting TMB level in NSCLC, and the AUC value in external validation dataset II was 0.762 (95% CI: 0.5669-0.9569) for predicting the efficacy of immunotherapy in NSCLC.ConclusionThe model based on CT radiomic features helps to achieve cost effective improvement in TMB classification and precise immunotherapy treatment of NSCLC patients.
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Project description:Lung cancer is a leading cause of cancer-related death, and >80% of lung cancer diagnoses are non-small-cell lung cancer (NSCLC). However, when using current staging and prognostic indices, the prognosis can vary significantly. In the present study, we calculated a prognostic index for predicting overall survival (OS) in NSCLC patients. The data of 545 NSCLC patients were retrospectively reviewed. Univariate and multivariate Cox proportional hazards regression analyses were performed to evaluate the prognostic value of clinicopathological factors. Age (hazard ratio [HR] = 1.25, 95% confidence interval [CI] = 1.02-1.54), TNM stage (III, HR = 1.64, 95% CI = 1.08-2.48; IV, HR = 2.33, 95% CI = 1.48-3.69), lung lobectomy (HR = 1.96, 95% CI = 1.45-2.66), chemotherapy (HR = 1.42, 95% CI = 1.15-1.74), and pretreatment hemoglobin level (HR = 1.61, 95% CI = 1.28-2.02) were independent prognosticators. A prognostic index for NSCLC (PInscl, 0-6 points) was calculated based on age (≥65 years, 1 point), tumor-node-metastasis (TNM) stage (III, 1 point; IV, 2 points), lung lobectomy (no, 1 point), chemotherapy (no, 1 point), and pretreatment hemoglobin level (low, 1 point). In comparison with the "PInscl = 0" subgroup (survival time = 2.71 ± 1.86 years), the "PInscl = 2" subgroup (survival time = 1.86 ± 1.24 years), "PInscl = 3" subgroup (survival time = 1.45 ± 1.07 years), "PInscl = 4" subgroup (survival time = 1.17 ± 1.06 years), "PInscl = 5" subgroup (survival time = 0.81 ± 0.78 years), and "PInscl = 6" subgroup (survival time = 0.65 ± 0.56 years) exhibited significantly shorter survival times. Kaplan-Meier survival analysis showed that patients with higher PInscl scores had poorer OS than those with lower scores (log-rank test: χ2 = 155.82, P < 0.0001). The area under the curve of PInscl for predicting the 1-year OS was 0.73 (95 % CI = 0.69-0.77, P < 0.001), and the PInscl had a better diagnostic performance than the Karnofsky performance status or TNM stage (P < 0.01). In conclusion, the PInscl, which is calculated from age, TNM stage, lung lobectomy, chemotherapy, and pretreatment hemoglobin level, significantly predicted OS in NSCLC patients.
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Project description:BackgroundThe aim of this study was to build and validate a radiomics nomogram by integrating the radiomics features extracted from the CT images and known clinical variables (TNM staging, etc.) to individually predict the overall survival (OS) of patients with non-small cell lung cancer (NSCLC).MethodsA total of 1,480 patients with clinical data and pretreatment CT images during January 2013 and May 2018 were enrolled in this study. We randomly assigned the patients into training (N = 1036) and validation cohorts (N = 444). We extracted 1,288 quantitative features from the CT images of each patient. The Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression model was applied in feature selection and radiomics signature building. The radiomics nomogram used for the prognosis prediction was built by combining the radiomics signature and clinical variables that were derived from clinical data. Calibration ability and discrimination ability were analyzed in both training and validation cohorts.ResultsEleven radiomics features were selected by LASSO Cox regression derived from CT images, and the radiomics signature was built in the training cohort. The radiomics signature was significantly associated with NSCLC patients' OS (HR = 3.913, p < 0.01). The radiomics nomogram combining the radiomics signature with six clinical variables (age, sex, chronic obstructive pulmonary disease, T stage, N stage, and M stage) had a better prognostic performance than the clinical nomogram both in the training cohort (C-index, 0.861, 95% CI: 0.843-0.879 vs. C-index, 0.851, 95% CI: 0.832-0.870; p < 0.001) and in the validation cohort (C-index, 0.868, 95% CI: 0.841-0.896 vs. C-index, 0.854, 95% CI: 0.824-0.884; p = 0.002). The calibration curves demonstrated optimal alignment between the prediction and actual observation.ConclusionThe established radiomics nomogram could act as a noninvasive prediction tool for individualized survival prognosis estimation in patients with NSCLC. The radiomics signature derived from CT images may help clinicians in decision-making and hold promise to be adopted in the patient care setting as well as the clinical trial setting.
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Project description:Delta-radiomics is a branch of radiomics in which features are confronted after time or after introducing an external factor (such as treatment with chemotherapy or radiotherapy) to extrapolate prognostic data or to monitor a certain condition. Immune checkpoint inhibitors (ICIs) are currently revolutionizing the treatment of non-small cell lung cancer (NSCLC); however, there are still many issues in defining the response to therapy. Contrast-enhanced CT scans of 33 NSCLC patients treated with ICIs were analyzed; altogether, 43 lung lesions were considered. The radiomic features of the lung lesions were extracted from CT scans at baseline and at first reassessment, and their variation (delta, Δ) was calculated by means of the absolute difference and relative reduction. This variation was related to the final response of each lesion to evaluate the predictive ability of the variation itself. Twenty-seven delta features have been identified that are able to discriminate radiologic response to ICIs with statistically significant accuracy. Furthermore, the variation of nine features significantly correlates with pseudo-progression.
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Project description:Purpose: Radiotherapy is a promising treatment option for lung cancer, but patients' responses vary. The purpose of the study was to investigate the potential of radiomics and clinical signature for predicting the radiotherapy sensitivity and overall survival of inoperable stage III and IV non-small-cell lung cancer (NSCLC) patients. Materials: This retrospective study collected 104 inoperable stage III and IV NSCLC patients at the Yunnan Cancer Hospital from October 2016 to September 2020. They were divided into radiation-sensitive and non-sensitive groups. We used analysis of variance (ANOVA) to select features and support vector machine (SVM) to build the radiomic model. Furthermore, the logistic regression method was used to screen out clinically relevant predictive factors and construct the combined model of radiomics-clinical features. Finally, survival was estimated using the Kaplan-Meier method. Results: There were 40 patients in the radiation-sensitive group and 64 in the non-sensitive group. These patients were divided into training set (73 cases) and testing set (31 cases) according to the ratio of 7:3. Nine radiomics features and one clinical feature were significantly associated with radiotherapy sensitivity. Both the radiomics model and combined model have good predictive performance (the areas under the curve (AUC) values of the testing set were 0.864 (95% confidence interval [CI]: 0.683-0.996) and 0.868 (95% CI: 0.689-1.000), respectively). Only platelet level status was associated with overall survival. Conclusion: The combined model constructed based on radiomics and clinical features can effectively identify the radiation-sensitive population and provide valuable clinical information. Patients with higher platelet levels may have a poor prognosis.
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Project description:Increasing evidence suggests radiomics features extracted from computed tomography (CT) images may be useful in prognostic models for patients with nonsmall cell lung cancer (NSCLC). This study was designed to determine whether such features can be reproducibly obtained from cone-beam CT (CBCT) images taken using medical Linac onboard-imaging systems in order to track them through treatment.Test-retest CBCT images of ten patients previously enrolled in a clinical trial were retrospectively obtained and used to determine the concordance correlation coefficient (CCC) for 68 different texture features. The volume dependence of each feature was also measured using the Spearman rank correlation coefficient. Features with a high reproducibility (CCC > 0.9) that were not due to volume dependence in the patient test-retest set were further examined for their sensitivity to differences in imaging protocol, level of scatter, and amount of motion by using two phantoms. The first phantom was a texture phantom composed of rectangular cartridges to represent different textures. Features were measured from two cartridges, shredded rubber and dense cork, in this study. The texture phantom was scanned with 19 different CBCT imagers to establish the features' interscanner variability. The effect of scatter on these features was studied by surrounding the same texture phantom with scattering material (rice and solid water). The effect of respiratory motion on these features was studied using a dynamic-motion thoracic phantom and a specially designed tumor texture insert of the shredded rubber material. The differences between scans acquired with different Linacs and protocols, varying amounts of scatter, and with different levels of motion were compared to the mean intrapatient difference from the test-retest image set.Of the original 68 features, 37 had a CCC >0.9 that was not due to volume dependence. When the Linac manufacturer and imaging protocol were kept consistent, 4-13 of these 37 features passed our criteria for reproducibility more than 50% of the time, depending on the manufacturer-protocol combination. Almost all of the features changed substantially when scatter material was added around the phantom. For the dense cork, 23 features passed in the thoracic scans and 11 features passed in the head scans when the differences between one and two layers of scatter were compared. Using the same test for the shredded rubber, five features passed the thoracic scans and eight features passed the head scans. Motion substantially impacted the reproducibility of the features. With 4 mm of motion, 12 features from the entire volume and 14 features from the center slice measurements were reproducible. With 6-8 mm of motion, three features (Laplacian of Gaussian filtered kurtosis, gray-level nonuniformity, and entropy), from the entire volume and seven features (coarseness, high gray-level run emphasis, gray-level nonuniformity, sum-average, information measure correlation, scaled mean, and entropy) from the center-slice measurements were considered reproducible.Some radiomics features are robust to the noise and poor image quality of CBCT images when the imaging protocol is consistent, relative changes in the features are used, and patients are limited to those with less than 1 cm of motion.
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Project description:BackgroundThe tumor immune microenvironment (TIME) phenotypes have been reported to mainly impact the efficacy of immunotherapy. Given the increasing use of immunotherapy in cancers, knowing an individual's TIME phenotypes could be helpful in screening patients who are more likely to respond to immunotherapy. Our study intended to establish, validate, and apply a machine learning model to predict TIME profiles in non-small cell lung cancer (NSCLC) by using 18F-FDG PET/CT radiomics and clinical characteristics.MethodsThe RNA-seq data of 1145 NSCLC patients from The Cancer Genome Atlas (TCGA) cohort were analyzed. Then, 221 NSCLC patients from Daping Hospital (DPH) cohort received18F-FDG PET/CT scans before treatment and CD8 expression of the tumor samples were tested. The Artificial Intelligence Kit software was used to extract radiomic features of PET/CT images and develop a radiomics signature. The models were established by radiomics, clinical features, and radiomics-clinical combination, respectively, the performance of which was calculated by receiver operating curves (ROCs) and compared by DeLong test. Moreover, based on radiomics score (Rad-score) and clinical features, a nomogram was established. Finally, we applied the combined model to evaluate TIME phenotypes of NSCLC patients in The Cancer Imaging Archive (TCIA) cohort (n = 39).ResultsTCGA data showed CD8 expression could represent the TIME profiles in NSCLC. In DPH cohort, PET/CT radiomics model outperformed CT model (AUC: 0.907 vs. 0.861, P = 0.0314) to predict CD8 expression. Further, PET/CT radiomics-clinical combined model (AUC = 0.932) outperformed PET/CT radiomics model (AUC = 0.907, P = 0.0326) or clinical model (AUC = 0.868, P = 0.0036) to predict CD8 expression. In the TCIA cohort, the predicted CD8-high group had significantly higher immune scores and more activated immune pathways than the predicted CD8-low group (P = 0.0421).ConclusionOur study indicates that 18F-FDG PET/CT radiomics-clinical combined model could be a clinically practical method to non-invasively detect the tumor immune status in NSCLCs.
| S-EPMC9105942 | biostudies-literature
Project description:Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death in the world. Immunological analysis of the tumor microenvironment (immunoscore) shows great promise for improved prognosis and prediction of response to immunotherapy. However, the exact immune cell composition in NSCLC remains unclear. Here, we used flow cytometry to characterize the immune infiltrate in NSCLC tumors, non-cancerous lung tissue, regional lymph node, and blood. The cellular identity of >95% of all CD45+ immune cells was determined. Thirteen distinct immune cell types were identified in NSCLC tumors. T cells dominated the lung cancer landscape (on average 47% of all CD45+ immune cells). CD4+ T cells were the most abundant T cell population (26%), closely followed by CD8+ T cells (22%). Double negative CD4-CD8- T cells represented a small fraction (1.4%). CD19+ B cells were the second most common immune cell type in NSCLC tumors (16%), and four different B cell sub-populations were identified. Macrophages and natural killer (NK) cells composed 4.7 and 4.5% of the immune cell infiltrate, respectively. Three types of dendritic cells (DCs) were identified (plasmacytoid DCs, CD1c+ DCs, and CD141+ DCs) which together represented 2.1% of all immune cells. Among granulocytes, neutrophils were frequent (8.6%) with a high patient-to-patient variability, while mast cells (1.4%), basophils (0.4%), and eosinophils (0.3%) were less common. Across the cohort of patients, only B cells showed a significantly higher representation in NSCLC tumors compared to the distal lung. In contrast, the percentages of macrophages and NK cells were lower in tumors than in non-cancerous lung tissue. Furthermore, the fraction of macrophages with high HLA-DR expression levels was higher in NSCLC tumors relative to distal lung tissue. To make the method readily accessible, antibody panels and flow cytometry gating strategy used to identify the various immune cells are described in detail. This work should represent a useful resource for the immunomonitoring of patients with NSCLC.
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