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
formation
2 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 TP53
MUT, while the remaining 10 samples were classified
as TP53
WT. 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 model
4 for comparison.
A supervised hierarchical clustering of CoLlAGe parameters was used to identify
features capable of distinguishing TP53
MUT and TP53
WT. 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 TP53
MUT and TP53
WT
(Figure 1). In figure 2, the difference in expression of this feature is
shown with TP53
MUT and TP53
WT
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 TP53
MUT and TP53
WT, with accuracy of 78% (85% sensitivity, 70%
specificity) (Figure 3, a.). TP53
WT over-expressed skewness and
kurtosis of information measure of correlation,
while these features were under-expressed in TP53
MUT. Interestingly,
the TP53
MUT 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
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