Dataset Information

High-dimensional regression analysis links magnetic resonance imaging features and protein expression and signaling pathway alterations in breast invasive carcinoma.

ABSTRACT: Background:Imaging features derived from MRI scans can be used for not only breast cancer detection and measuring disease extent, but can also determine gene expression and patient outcomes. The relationships between imaging features, gene/protein expression, and response to therapy hold potential to guide personalized medicine. We aim to characterize the relationship between radiologist-annotated tumor phenotypic features (based on MRI) and the underlying biological processes (based on proteomic profiling) in the tumor. Methods:Multiple-response regression of the image-derived, radiologist-scored features with reverse-phase protein array expression levels generated association coefficients for each combination of image-feature and protein in the RPPA dataset. Significantly-associated proteins for features were analyzed with Ingenuity Pathway Analysis software. Hierarchical clustering of the results of the pathway analysis determined which features were most strongly correlated with pathway activity and cellular functions. Results:Each of the twenty-nine imaging features was found to have a set of significantly correlated molecules, associated biological functions, and pathways. Conclusions:We interrogated the pathway alterations represented by the protein expression associated with each imaging feature. Our study demonstrates the relationships between biological processes (via proteomic measurements) and MRI features within breast tumors.

SUBMITTER: Lehrer M

PROVIDER: S-EPMC5854291 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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High-dimensional regression analysis links magnetic resonance imaging features and protein expression and signaling pathway alterations in breast invasive carcinoma.

Lehrer Michael M Bhadra Anindya A Aithala Sathvik S Ravikumar Visweswaran V Zheng Youyun Y Dogan Basak B Bonaccio Emerlinda E Burnside Elizabeth S ES Morris Elizabeth E Sutton Elizabeth E Whitman Gary J GJ Net Jose J Brandt Kathy K Ganott Marie M Zuley Margarita M Rao Arvind A

Oncoscience 20180101 1-2

<h4>Background</h4>Imaging features derived from MRI scans can be used for not only breast cancer detection and measuring disease extent, but can also determine gene expression and patient outcomes. The relationships between imaging features, gene/protein expression, and response to therapy hold potential to guide personalized medicine. We aim to characterize the relationship between radiologist-annotated tumor phenotypic features (based on MRI) and the underlying biological processes (based on ...[more]

PMID: 29556516

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Project description:BackgroundFibromyalgia is a centralized multidimensional chronic pain syndrome, but its pathophysiology is not fully understood.MethodsWe applied 3D magnetic resonance spectroscopic imaging (MRSI), covering multiple cortical and subcortical brain regions, to investigate the association between neuro-metabolite (e.g. combined glutamate and glutamine, Glx; myo-inositol, mIno; and combined (total) N-acetylaspartate and N-acetylaspartylglutamate, tNAA) levels and multidimensional clinical/behavioural variables (e.g. pain catastrophizing, clinical pain severity and evoked pain sensitivity) in women with fibromyalgia (N = 87).ResultsPain catastrophizing scores were positively correlated with Glx and tNAA levels in insular cortex, and negatively correlated with mIno levels in posterior cingulate cortex (PCC). Clinical pain severity was positively correlated with Glx levels in insula and PCC, and with tNAA levels in anterior midcingulate cortex (aMCC), but negatively correlated with mIno levels in aMCC and thalamus. Evoked pain sensitivity was negatively correlated with levels of tNAA in insular cortex, MCC, PCC and thalamus.ConclusionsThese findings support single voxel placement targeting nociceptive processing areas in prior 1 H-MRS studies, but also highlight other areas not as commonly targeted, such as PCC, as important for chronic pain pathophysiology. Identifying target brain regions linked to multidimensional symptoms of fibromyalgia (e.g. negative cognitive/affective response to pain, clinical pain, evoked pain sensitivity) may aid the development of neuromodulatory and individualized therapies. Furthermore, efficient multi-region sampling with 3D MRSI could reduce the burden of lengthy scan time for clinical research applications of molecular brain-based mechanisms supporting multidimensional aspects of fibromyalgia.SignificanceThis large N study linked brain metabolites and pain features in fibromyalgia patients, with a better spatial resolution and brain coverage, to understand a molecular mechanism underlying pain catastrophizing and other aspects of pain transmission. Metabolite levels in self-referential cognitive processing area as well as pain-processing regions were associated with pain outcomes. These results could help the understanding of its pathophysiology and treatment strategies for clinicians.

Project description:Background: Multiparametric magnetic resonance imaging (mpMRI) has emerged as a non-invasive modality to diagnose and monitor prostate cancer. Quantitative metrics on the regions of abnormality have shown to be useful descriptors to discriminate clinically significant cancers. In this study, we evaluate the reproducibility of quantitative imaging features using repeated mpMRI on the same patients. Methods: We retrospectively obtained the deidentified records of patients, who underwent two mpMRI scans within 2 weeks of the first baseline scan. The patient records were obtained as deidentified data (including imaging), obtained through the TCIA (The Cancer Imaging Archive) repository and analyzed in our institution with an institutional review board-approved Health Insurance Portability and Accountability Act-compliant retrospective study protocol. Indicated biopsied regions were used as a marker for our study radiologists to delineate the regions of interest. We extracted 307 quantitative features in each mpMRI modality [T2-weighted MR sequence image (T2w) and apparent diffusion coefficient (ADC) with b values of 0 and 1,400 mm/s2] across the two sequential scans. Concordance correlation coefficients (CCCs) were computed on the features extracted from sequential scans. Redundant features were removed by computing the coefficient of determination (R 2) among them and replaced with a feature that had the highest dynamic range within intercorrelated groups. Results: We have assessed the reproducibility of quantitative imaging features among sequential scans and found that habitat region characterization improves repeatability in ADC maps. There were 19 T2w features and two ADC features in radiologist drawn regions (native raw image), compared to 18 T2w and 15 ADC features in habitat regions (sphere), which were reproducible (CCC ?0.65) and non-redundant (R 2 ? 0.99). We also found that z-transformation of the images prior to feature extraction reduced the number of reproducible features with no detrimental effect. Conclusion: We have shown that there are quantitative imaging features that are reproducible across sequential prostate mpMRI acquisition at a preset level of filters. We also found that a habitat approach improves feature repeatability in ADC. A validated set of reproducible image features in mpMRI will allow us to develop clinically useful disease risk stratification, enabling the possibility of using imaging as a surrogate to invasive biopsies.

Dataset Information

High-dimensional regression analysis links magnetic resonance imaging features and protein expression and signaling pathway alterations in breast invasive carcinoma.

Publications

High-dimensional regression analysis links magnetic resonance imaging features and protein expression and signaling pathway alterations in breast invasive carcinoma.

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