Predicting TP53 mutational status of breast cancers on clinical DCE MRI using directional-gradient based radiogenomic descriptors
Nathaniel Braman1, Prateek Prasanna1, Donna Plecha2, Hannah Gilmore2, Lyndsay Harris2, Kristy Miskimen1, Tao Wan3, Vinay Varadan1, and Anant Madabhushi1

1Case Western Reserve University, Cleveland, OH, United States, 2University Hospitals, Cleveland, OH, United States, 3Beihang University, Beijing, China, People's Republic of

Synopsis

In this work, we report preliminary success in the prediction of TP53 mutational status in breast cancer from DCE-MRI using a computer-extracted radiogenomic descriptor of multi-scale disorder, Co-occurrence of Local Anisotropic Gradient Orientations (CoLlAGe). A set of 8 distinguishing CoLlAGe features yielded accuracy of 78% in predicting TP53 mutational status and outperformed standard DCE-MRI pharmacokinetic parameters in an unsupervised hierarchical clustering. A non-invasive means of discerning TP53 mutational status may allow clinicians to more easily determine prognosis, assess treatment response, and inform treatment strategy.

Purpose

Mutation of TP53, a critical tumor suppressor protein, is a marker of breast cancer prognosis and can potentially predict preoperative treatment response.1 Currently, TP53 mutational status is determined through DNA sequencing of biopsied tissue. Radiogenomics is defined as the attempt to identify associations between radiomic (computer extracted image features from radiographic imaging) and genomic features for the prediction of pathological biology and outcomes. In this work, we explore a radiogenomic approach to non-invasively predict TP53 mutational status from DCE-MRI. TP53 inactivation creates disorder across multiple spatial scales, e.g. uncontrolled cytoskeleton formation2 distorts micro-architecture, while unregulated division creates disordered cell clusters. Standard DCE-MRI pharmacokinetic (PK) features – computed by modeling contrast agent uptake from intensity of post-contrast DCE-MRI phases – quantify tumor-associated changes in permeability, but offer no means of capturing multi-scale disorder patterns. In this work we explored the ability of a computer-extracted radiogenomic descriptor, Co-occurrence of Local Anisotropic Gradient Orientations (CoLlAGe), to predict the TP53 mutational status from routine clinical breast DCE-MRI alone. Additionally we also compared the approach with the predictive power of PK parameters obtained from DCE-MRI. CoLlAGe involves computing pixel-wise gradient orientations, determining dominant orientations via Principal Component Analysis, and extracting second order statistical features from the co-occurrence matrix of dominant orientations. The hypothesis behind our approach is that CoLlAGe will identify subtle microarchitecture differences on MRI associated with breast cancers with and without the TP53 mutation through a multi-scale quantification of disorder across local image gradients.

Methods

The ability of CoLlAGe to predict TP53 mutational status was compared against PK features on 23 DCE-MRI breast cancer cases with known TP53 mutational status. Breast tumors were obtained from patients on a preoperative clinical trial and whole-exome DNA sequencing was performed with an average coverage of 100X, followed by alignment, variant calling,3 and variant filtering to eliminate potential germline variants. 13 breast cancers harboring non-synonymous TP53 mutations were annotated as TP53MUT, while the remaining 10 samples were classified as TP53WT. 1.5 or 3.0 T STIR and T1w fat saturation axial scans were obtained with an 8 or 16 channel dedicated breast coil. Patients were imaged after administration of gadolinium contrast agent through intravenous injection, and tumor extent was manually annotated onto images by a radiologist. DCE-MRI PK parameters reflecting vascular permeability to contrast agent (Ktrans: volume transfer coefficient, Kep: flux rate constant, Ve: extracellular volume ratio) were computed from DCE-MRI post-contrast phases using Toft’s model4 for comparison. A supervised hierarchical clustering of CoLlAGe parameters was used to identify features capable of distinguishing TP53MUT and TP53WT. The ability of CoLlAGe and PK features to predict mutational status was assessed through separation of tumors corresponding to DNA sequencing-confirmed mutational status in a furthest distance unsupervised hierarchical clustering.

Results & Discussion

Through visual inspection of supervised cluster expression maps, skewness, and kurtosis of the information measure of correlation were identified as discriminating radiogenomic features. The skewness and kurtosis of the information measure of correlation alone were found to be 74% accurate (77% sensitivity, 70% specificity) in distinguishing TP53MUT and TP53WT (Figure 1). In figure 2, the difference in expression of this feature is shown with TP53MUT and TP53WT examples. Three additional distinguishing features for skewness (inertia, sum average, difference variance) and kurtosis (energy, entropy, correlation) were identified and included in an 8 feature unsupervised clustering. We identified two distinct clusters, representing TP53MUT and TP53WT, with accuracy of 78% (85% sensitivity, 70% specificity) (Figure 3, a.). TP53WT over-expressed skewness and kurtosis of information measure of correlation, while these features were under-expressed in TP53MUT. Interestingly, the TP53MUT cluster contained two sub-clusters, which differed in expression of skewness of the sum variance, inertia, and difference variance. All three misclassified WT tumors were sorted to the TP53MUT sub-cluster with high expression of these features. A potential explanation for these two mutant phenotypes is differing inter-tumor TP53 inactivation.5 Meanwhile, PK parameters produced two main clusters: the first bearing 38% of mutants and 44% of WT, the second 54% of mutants and 56% of WT. A third, separate cluster comprised a single mutant study (Figure 3, b.).

Conclusion

We reported preliminary success in the prediction of TP53 mutational status in breast cancer from DCE-MRI through analysis using CoLlAGe features. CoLlAGe demonstrated higher accuracy in sorting TP53 mutant and WT studies than standard DCE-MRI PK parameters. A non-invasive means of discerning TP53 mutational status may allow clinicians to easily determine prognosis, assess treatment response, and inform treatment strategy.

Acknowledgements

Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under award numbers R21CA167811-01, R21CA179327-01, R21CA195152-01, U24CA199374-01the National Institute of Diabetes and Digestive and Kidney Diseases under award number R01DK098503-02, the DOD Prostate Cancer Synergistic Idea Development Award (PC120857); the DOD Lung Cancer Idea Development New Investigator Award (LC130463),the DOD Prostate Cancer Idea Development Award; the Ohio Third Frontier Technology development Grant, the CTSC Coulter Annual Pilot Grant, the Case Comprehensive Cancer Center Pilot Grantthe VelaSano Grant from the Cleveland Clinicthe Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering at Case Western Reserve University. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

References

1. Kandioler-Eckersberger, D. et al. TP53 mutation and p53 overexpression for prediction of response to neoadjuvant treatment in breast cancer patients. Clin. Cancer Res. Off. J. Am. Assoc. Cancer Res. 6, 50–56 (2000).

2. Araki, K. et al. p53 regulates cytoskeleton remodeling to suppress tumor progression. Cell. Mol. Life Sci. 72, 4077–4094 (2015).

3. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).

4. Tofts, P. S. Modeling tracer kinetics in dynamic Gd-DTPA MR imaging. J. Magn. Reson. Imaging 7, 91–101 (1997).

5. Soussi, T. & Lozano, G. p53 mutation heterogeneity in cancer. Biochem. Biophys. Res. Commun. 331, 834–842 (2005).

Figures

Skewness vs. kurtosis of the information measure of correlation. These two features alone separate TP53 mutant (red) and WT (blue) studies with 74% accuracy, indicated by the gray dashed line.

CoLlAGe feature images showing expression of information measure of correlation within (a). TP53 WT and (b). TP53 mutant breast cancer studies. CoLlAGe maps are overlaid onto original DCE-MRI images, showing qualitative heatmap of CoLlAGe values.

Unsupervised clustering of (top) skewness/kurtosis of CoLlAGe features and (bottom) PK/intensity parameters. Rows display patients and columns display features. In (top), CoLlAGe features distribute patients into distinct groups: TP53MUT (red) and TP53WT group (blue). Sorting by PK parameters is seemingly random in (bottom).



Proc. Intl. Soc. Mag. Reson. Med. 24 (2016)
0188