Shanshan Jiang1, Xianlong Wang1, Hao Yu1, Jiandong Xi1, Jingwen Wu1, Lisong Liang1, Shilong Lu1, Tianyu Zou1, Jinyuan Zhou2, and Zhibo Wen1
1Department of Radiology, Southern Medical University Zhujiang Hospital, Guangzhou, China, People's Republic of, 2Department of Radiology, Johns Hopkins University, Baltimore, MD, United States
Synopsis
The correlation between endogenous protein-based
APT-weighted (APTw) imaging and gene expression in glioblastoma (GBM) was
investigated. 16 patients with newly
diagnosed GBM were studied.
APTw/FLAIR hyperintensity area ratio (AFR), and APTw hyperintensity/gadolinium
contrast-enhanced T1w enhancement area ratio (ATR) were calculated.
Interoperative paired tumor and adjacent normal tissues were sampled for
genomic analysis. BRCA1 and CDK4 were
significantly downregulated
in the high AFR group
(adjusted P= 0.000953 and 0.025187), and SLAMF9 and MIA
were significantly downregulated in
the high ATR
group (adjusted P= 1.08E-11 and 0.00997). APT imaging has great potential for unveiling
some special genomic changes in GBM.Target audience
Researchers and clinicians who are interested
in novel diagnostic image methods and radiogenomics in gliomas.
Purpose
Glioblastoma (GBM) is the most dismal primary brain tumor that relentlessly defies
therapy. New biological understanding helped to perfect treatment strategies,
especially for targeted, molecular based therapies that are individualized on
particular biological or genomic modifications in each unique patient. Amide proton transfer (APT) imaging is a novel
MRI technique in which amide protons of endogenous mobile proteins
in tissue (such as those in the cytoplasm) are detected [1]. The APT-weighted (APTw)
signal is well correlated with the Ki-67 index and cell density, and may be a valuable
imaging biomarker to identify the spatial extent and pathological grade of
malignant gliomas [2,3]. The
correlation between proteome and genome is fundamental duo to the central dogma
of molecular biology. The research was designed to explore the differentially
expressed genes (DEGs) related to the protein-based APT imaging phenotype of
GBM.
Materials and Methods
MRI scanning:
16 patients with GBM were recruited and scanned
on a Philips 3T MRI scanner. The sequences performed for each patient included
T1w, T2w, FLAIR, APT imaging, and gadolinium
contrast-enhanced T1w. A multi-offset, multi-acquisition imaging
acquisition scheme was used for APT imaging (saturation power = 2 μT;
saturation time = 800 msec; matrix = 128×128; field of view = 240×240 mm2;
and slice thickness = 6 mm; scan time = 3 min) [2]. APTw images were calculated using a
magnetization transfer ratio (MTR) asymmetry at ±3.5ppm.
APTw phenotype:
Two experienced neuro-oncologic radiologists
assessed APTw imaging or conversional MR imaging morphologic features. APTw
signal intensities and hyperintense area, FLAIR hyperintense area, and gadolinium
contrast-enhanced T1w enhancement area were recorded. APTw/FLAIR
hyperintense area ratio (AFR), as well as APTw hyperintense/gadolinium
contrast-enhanced T1w enhancement area ratio (ATR) were calculated. The
AFR cutoff value was 0.8, and all patients were divided into two groups: high AFR
and low AFR. The ATR cutoff value was 0.9, and all patients were divided into
two groups: high ATR and low ATR.
RNA
extraction, library construction and sequencing:
Paired tumor and adjacent normal tissues were obtained
intraoperatively. Global gene expression and genomic DNA
measurements (RNA-seq) from the matched specimens with use of research
identifiers were performed in these patients, as previously described [4]. [A1] A
threshold of the FDR ≤ 0.05 and an absolute value of log2
Ratio ≥ 1 were used to identify
differentially expressed genes (DEGs). GO and KEGG enrichment analyses were
performed for DEGs as described by Zhang [5]. Workflow is showed in Fig. 1.
Results and Discussion
Radiogenomics analysis:
By analyzing the radiogenomic correlation
between APTw image features and message RNA expression, BRCA1 and CDK4 genes were
found to be significantly downregulated in
the high AFR tumor tissue compared to the low AFR group. SLAMF9 and
MIA genes
were found to be significantly downregulated in
the high ATR tumor
tissues compared to the low ATR group (see Figs. 2 and 3).
Gene function interpretation:
BRCA1: BRCA1
(Breast Cancer 1, Early Onset) encodes a nuclear phosphoprotein that
plays a role in maintaining genomic stability, and it also acts as a tumor
suppressor. The BRCA1 protein is involved in repairing damaged DNA. BRCA1 protein
expression may be an important predictive biomarker of overall survival in GBM [6].
CDK4: CDK4 (Cyclin-Dependent Kinase 4) is a
Protein Coding gene. Among its related pathways are PI3K-Akt
signaling pathway and Glioma. GO annotations related to this gene include
protein complex binding and cyclin binding.
SLAMF9: SLAMF9
(SLAM Family Member 9) is a Protein Coding gene. GO annotations related to this
gene include receptor activity. This gene may play a role in the
immune response.
MIA: MIA (Melanoma Inhibitory Activity) is a
Protein Coding gene. Among its related pathways is Neural
Crest Differentiation. GO
annotations related to this gene include growth factor activity [7].
Conclusion
Our
initial findings demonstrated a novel correlation in molecular imaging and gene
characteristics of gliomas, and revealed the potential genetic and biologic
significance of the non-invasive protein-based APTw imaging features, which may
facilitate the
GBM precision medicine that depends on genomics.
Acknowledgements
No acknowledgement found.References
[1] Zhou et al. Nature Med. 9, 1085 (2003).
[2]
Wen et al. NeuroImage 51, 616 (2010).
[3] Togao et al. Neuro-Oncology 16, 441
(2014).
[4] Bredel et al. Cancer Res. 65, 8679 (2005).
[5] Zhang et al. BMC
genomics. 14, 279 (2013).
[6] www.nrgoncology.org.
[7] www.genecards.org.