Abstract 212: True2 duplex sequencing reveals a diverse landscape of unique somatic mutations beyond the surgical margins of high- and low-grade diffuse gliomas

Introduction: High- and low-grade diffuse gliomas commonly recur regardless of therapy. Here, we sought to detect and profile molecular evidence of disease in nearby brain tissue absent of tumor by standard-of-care clinical imaging.

Methods: Twenty-two patients presenting to the University of Utah with radiographic evidence of a new high- to low-grade intrinsic brain tumor were enrolled after providing written informed consent. Using intraoperative stereotactic guidance, tissue was acquired from bulky tumor (36 samples) and beyond the surgical margins in peritumoral edema (29 samples). All samples underwent somatic mutation discovery using a custom-designed 114 kb panel (115 genes) and True2 duplex sequencing. True2 is a duplex adapter-based technology developed and empirically validated to achieve >95% sensitivity for an allele frequency ≥0.1% at a false positive rate of <1 per 100 kb panel positions.

Results: Somatic mutations were detected in all samples regardless of radiographic location. The mean number of mutations was similar between bulky tumor and peritumoral edema (5.6±2.4 vs. 5.1±2.9 mutations/sample, respectively; P=0.48). Although the mean allele frequency of variants was higher in tumor compared to edema (16.0±21.2% vs. 11.2±17.4%, respectively; P=0.017), there was a strong overlap in the allele frequency ranges (tumor: 0.07% to 90.3% vs. edema: 0.10% to 75.6%). Notably, one-third of all the somatic mutations detected had an allele frequency <0.5%. Common diagnostic mutations specific to each tumor type were present in both tumor and edema - TERT promoter mutations in glioblastoma and oligodendroglioma; IDH1/2 mutations in astrocytoma and oligodendroglioma. In edema, mutations associated with glioblastoma but unique to a single sample occurred in TP53, EGFR, PTEN, NF1, ATRX, SCN9A, and MTOR at an allele frequency ranging from 0.10% to 20.22%. The edema of astrocytomas similarly harbored unique mutations in TP53, PTEN, and NF1, but mutations in EGFR, ATRX, SCN9A, and MTOR were absent. In contrast to both glioblastoma and astrocytoma, oligodendrogliomas exhibited a diverse collection of unique CIC and PAFAH1B3 mutations in edema at an allele frequency between 0.13% and 3.63%.

Conclusions: The application of True2 technology to conduct a discovery search for very-low frequency somatic mutations found the molecular burden between tumor and adjacent edema to be remarkably similar. Our findings indicate an extensive tumor presence beyond the surgical margins in diffuse gliomas with unique and abundant somatic mutations that may form the foundation of recurrent lesions. Molecular analysis of adjacent tissue identified as radiographically unaffected by bulky tumor to better characterize the mutational landscape of migratory subclones may directly impact personalized medicine for high- and low-grade diffuse glioma patients.

Citation Format: Hunter Underhill, Michael Karsy, Christian Davidson, Sabine Hellwig, Samuel Stevenson, Sydney Vincenti, Charlie Dean, Brion Harrison, Eric Goold, Mary Bronner, Howard Colman, Randy Jensen. True2 duplex sequencing reveals a diverse landscape of unique somatic mutations beyond the surgical margins of high- and low-grade diffuse gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 212.

COMP-10. THE MUTATIONAL PROFILE OF GLIOBLASTOMA-DERIVED CELL-FREE DNA IN PLASMA REPRESENTS A DISTINCT SUBSET OF THE SOMATIC MUTATIONS PRESENT IN GLIOBLASTOMA SOLID TUMOR DNA

Glioblastoma’s mutational landscape varies widely in the same tumor. Using conventional criteria to identify mutations from a focal tissue specimen (e.g., variant allele frequency > 5%) undersamples glioblastoma’s broad clonal diversity, which may limit detection of glioblastoma-derived circulating cell-free DNA in plasma (i.e., circulating tumor DNA; ctDNA). Here, we sought to enhance somatic variant identification in solid tumor DNA to improve detection and characterize glioblastoma-derived ctDNA. Tumor DNA and plasma cell-free DNA (collected < 24 hours prior to the surgical procedure) were isolated from eight glioblastoma patients. DNA was capture-enriched using a custom-designed, glioblastoma-targeted, next-generation sequencing panel (124 genes, 118 kb) followed by paired-end sequencing. Samples were prepared in duplicate with molecular barcodes to enable detection of very-low frequency variants. Somatic mutations in tumor DNA were identified using variable allele frequency thresholds and were considered positive in ctDNA if present in both duplicate samples. Using a lower allele frequency threshold to identify mutations in tumor DNA significantly increased detection of ctDNA (F(1.04,7.29)=14.81, P=0.006). At a solid tumor allele frequency threshold of ≥ 5%, only a single patient (12.5%) had tumor mutations detected in ctDNA. However, at a threshold ≥ 1%, all patients (100%) had at least one tumor mutation detected in ctDNA. Moreover, at a threshold ≥ 0.5%, 7 out of 8 patients (87.5%) had > 12 tumor mutations present in ctDNA. The increased detection of ctDNA enabled the subsequent discovery that somatic mutations in APC, KIT, MSH6, and NF1 were more likely to be present in ctDNA compared to somatic mutations in ATRX, LZTR1, SLC26A3, and TERT which were absent in ctDNA (χ 2=8.0, P=0.005). Thus, stronger sampling of glioblastoma’s genetic heterogeneity in tumor DNA improves detection of ctDNA allowing comparisons between mutational profiles that may lead to the identification of similarities and differences with key biologic and/or clinical implications.

MR imaging of carotid plaque composition during lipid-lowering therapy a prospective assessment of effect and time course

OBJECTIVES

The purpose of this study was to test the lipid depletion hypothesis and to establish the time course of change in carotid plaque morphology and composition during lipid therapy using high-resolution magnetic resonance imaging (MRI).

BACKGROUND

Lipid therapy is thought to improve plaque stability and reduce cardiovascular events by targeting the plaque rupture risk features such as large lipid core, thin fibrous cap, and high level of inflammatory infiltrates. However, the plaque stabilizing process during lipid therapy has not been clearly demonstrated in humans and in vivo.

METHODS

Subjects with coronary or carotid artery disease, apolipoprotein B ≥120 mg/dl, and lipid treatment history <1 year, were randomly assigned to atorvastatin monotherapy or to atorvastatin-based combination therapies with appropriate placebos for 3 years. All subjects underwent high-resolution, multicontrast bilateral carotid MRI scans at baseline and annually for 3 years. All images were analyzed for quantification of wall area and plaque composition blinded to therapy, laboratory results, and clinical course.

RESULTS

After 3 years of lipid therapy, the 33 subjects with measurable lipid-rich necrotic core (LRNC) at baseline had a significant reduction in plaque lipid content: LRNC volume decreased from 60.4 ± 59.5 mm(3) to 37.4 ± 69.5 mm(3) (p < 0.001) and %LRNC (LRNC area/wall area in the lipid-rich regions) from 14.2 ± 7.0% to 7.4 ± 8.2% (p < 0.001). The time course showed that %LRNC decreased by 3.2 (p < 0.001) in the first year, by 3.0 (p = 0.005) in the second year, and by 0.91 (p = 0.2) in the third year. Changes in LRNC volume followed the same pattern. Percent wall volume (100 × wall/outer wall, a ratio of volumes) in the lipid-rich regions significantly decreased from 52.3 ± 8.5% to 48.6 ± 9.7% (p = 0.002). Slices containing LRNC had significantly more percent wall volume reduction than those without (-4.7% vs. -1.4%, p = 0.02).

CONCLUSIONS

Intensive lipid therapy significantly depletes carotid plaque lipid. Statistically significant plaque lipid depletion is observed after 1 year of treatment and continues in the second year, and precedes plaque regression. (Using Magnetic Resonance Imaging to Evaluate Carotid Artery Plaque Composition in People Receiving Cholesterol-Lowering Medications [The CPC Study]; NCT00715273).

Localized measurement of atherosclerotic plaque inflammatory burden with dynamic contrast-enhanced MRI

Inflammation plays an important role in progression and rupture of atherosclerotic plaque. Dynamic contrast-enhanced MRI has been proposed as a tool to evaluate inflammation in vivo by measuring the transfer constant and partial plasma volume, which are influenced by inflammation. This study sought to demonstrate the ability of dynamic contrast-enhanced MRI to provide localized measurements of transfer constant and partial plasma volume within plaque regions of different compositions. In order to do that, a highly automatic procedure for localized measurement of dynamic contrast-enhanced MRI parameters was developed. In 47 subjects, the average transfer constant and partial plasma volume were highest in loose matrix and fibrous tissue and substantially lower in intraplaque hemorrhage, lipid rich/necrotic core, and calcification. In addition, except for hemorrhage and calcification, statistically significant differences of transfer constant and partial plasma volume were observed for any pair of these components. This suggests that transfer constant and partial plasma volume could be helpful to differentiate different plaque components and that dynamic contrast-enhanced MRI has the potential to assess inflammatory burden in specific regions.

Signal features of the atherosclerotic plaque at 3.0 Tesla versus 1.5 Tesla: impact on automatic classification

PURPOSE

To investigate the impact of different field strengths on determining plaque composition with an automatic classifier.

MATERIALS AND METHODS

We applied a previously developed automatic classifier-the morphology enhanced probabilistic plaque segmentation (MEPPS) algorithm-to images from 20 subjects scanned at both 1.5 Tesla (T) and 3T. Average areas per slice of lipid-rich core, intraplaque hemorrhage, calcification, and fibrous tissue were recorded for each subject and field strength.

RESULTS

All measurements showed close agreement at the two field strengths, with correlation coefficients of 0.91, 0.93, 0.95, and 0.93, respectively. None of these measurements showed a statistically significant difference between field strengths in the average area per slice by a paired t-test, although calcification tended to be measured larger at 3T (P = 0.09).

CONCLUSION

Automated classification results using an identical algorithm at 1.5T and 3T produced highly similar results, suggesting that with this acquisition protocol, 3T signal characteristics of the atherosclerotic plaque are sufficiently similar to 1.5T characteristics for MEPPS to provide equivalent performance.

Reader and platform reproducibility for quantitative assessment of carotid atherosclerotic plaque using 1.5T Siemens, Philips, and General Electric scanners

PURPOSE

To evaluate the platform and reader reproducibility of quantitative carotid plaque measurements.

MATERIALS AND METHODS

A total of 32 individuals with >or=15% carotid stenosis by duplex ultrasound were each imaged once by a 1.5T General Electric (GE) whole body scanner and twice by either a 1.5T Philips scanner or a 1.5T Siemens scanner. A standardized multisequence protocol and identical phased-array carotid coils were used. Expert readers, blinded to subject information, scanner type, and time point, measured the lumen, wall, and total vessel areas and determined the modified American Heart Association lesion type (AHA-LT) on the cross-sectional images.

RESULTS

AHA-LT was consistently identified across the same (kappa = 0.75) and different scan platforms (kappa = 0.75). Furthermore, scan-rescan coefficients of variation (CV) of wall area measurements on Siemens and Philips scanners ranged from 6.3% to 7.5%. However, wall area measurements differed between Philips and GE (P = 0.003) and between Siemens and GE (P = 0.05). In general, intrareader reproducibility was higher than interreader reproducibility for AHA-LT identification as well as for quantitative measurements.

CONCLUSION

All three scanners produced images that allowed AHA-LT to be consistently identified. Reproducibility of quantitative measurements by Siemens and Philips scanners were comparable to previous studies using 1.5T GE scanners. However, bias was introduced with each scanner and the use of different readers substantially increased variability. We therefore recommend using the same platform and the same reader for scans of individual subjects undergoing serial assessment of carotid atherosclerosis.

The vulnerable, or high-risk, atherosclerotic plaque: noninvasive MR imaging for characterization and assessment

"Vulnerable" plaques are atherosclerotic plaques that have a high likelihood to cause thrombotic complications, such as myocardial infarction or stroke. Plaques that tend to progress rapidly are also considered to be vulnerable. Besides luminal stenosis, plaque composition and morphology are key determinants of the likelihood that a plaque will cause cardiovascular events. Noninvasive magnetic resonance (MR) imaging has great potential to enable characterization of atherosclerotic plaque composition and morphology and thus to help assess plaque vulnerability. A classification for clinical, as well as pathologic, evaluation of vulnerable plaques was recently put forward in which five major and five minor criteria to define vulnerable plaques were proposed. The purpose of this review is to summarize the status of MR imaging with regard to depiction of the criteria that define vulnerable plaques by using existing MR techniques. The use of MR imaging in animal models and in human disease in various vascular beds, particularly the carotid arteries, is presented.

MRI of atherosclerosis in clinical trials

Magnetic resonance imaging (MRI) of the arterial wall has emerged as a viable technology for characterizing atherosclerotic lesions in vivo, especially within carotid arteries and other large vessels. This capability has facilitated the use of carotid MRI in clinical trials to evaluate therapeutic effects on atherosclerotic lesions themselves. MRI is specifically able to characterize three important aspects of the lesion: size, composition and biological activity. Lesion size, expressed as a total wall volume, may be more sensitive than maximal vessel narrowing (stenosis) as a measure of therapeutic effects, as it reflects changes along the entire length of the lesion and accounts for vessel remodeling. Lesion composition (e.g. lipid, fibrous and calcified content) may reflect therapeutic effects that do not alter lesion size or stenosis, but cause a transition from a vulnerable plaque composition to a more stable one. Biological activity, most notably inflammation, is an emerging target for imaging that is thought to destabilize plaque and which may be a systemic marker of vulnerability. The ability of MRI to characterize each of these features in carotid atherosclerotic lesions gives it the potential, under certain circumstances, to replace traditional trials involving large numbers of subjects and hard end-points--heart attacks and strokes--with smaller, shorter trials involving imaging end-points. In this review, the state of the art in MRI of atherosclerosis is presented in terms of hardware, image acquisition protocols and post-processing. Also, the results of validation studies for measuring lesion size, composition and inflammation will be summarized. Finally, the status of several clinical trials involving MRI of atherosclerosis will be reviewed.

Predictors of carotid atherosclerotic plaque progression as measured by noninvasive magnetic resonance imaging

The purpose of this in vivo MRI study was to quantify changes in atherosclerotic plaque morphology prospectively and to identify factors that may alter the rate of progression in plaque burden. Sixty-eight asymptomatic subjects with >or=50% stenosis, underwent serial carotid MRI examinations over an 18-month period. Clinical risk factors for atherosclerosis, and medications were documented prospectively. The wall and total vessel areas, matched across time-points, were measured from cross-sectional images. The normalized wall index (NWI=wall area/total vessel area), as a marker of disease severity, was documented at baseline and at 18 months. Multiple regression analysis was used to correlate risk factors and morphological features of the plaque with the rate of progression/regression. On average, the wall area increased by 2.2% per year (P=0.001). Multiple regression analysis demonstrated that statin therapy (P=0.01) and a normalized wall index >0.64 (P=0.001) were associated with a significantly reduced rate of progression in mean wall area. All other documented risk factors were not significantly associated with changes in wall area. Findings from this study suggest that increased normalized wall index and the use of statin therapy are associated with reduced rates of plaque progression amongst individuals with advanced, asymptomatic carotid atherosclerosis.

Association Between Carotid Plaque Characteristics and Subsequent Ischemic Cerebrovascular Events

Background and Purpose— MRI is able to quantify carotid plaque size and composition with good accuracy and reproducibility and provides an opportunity to prospectively examine the relationship between plaque features and subsequent cerebrovascular events. We tested the hypothesis that the characteristics of carotid plaque, as assessed by MRI, are possible predictors of future ipsilateral cerebrovascular events.

Methods— A total of 154 consecutive subjects who initially had an asymptomatic 50% to 79% carotid stenosis by ultrasound with ≥12 months of follow-up were included in this study. Multicontrast-weighted carotid MRIs were performed at baseline, and participants were followed clinically every 3 months to identify symptoms of cerebrovascular events.

Results— Over a mean follow-up period of 38.2 months, 12 carotid cerebrovascular events occurred ipsilateral to the index carotid artery. Cox regression analysis demonstrated a significant association between baseline MRI identification of the following plaque characteristics and subsequent symptoms during follow-up: presence of a thin or ruptured fibrous cap (hazard ratio, 17.0; P ≤0.001), intraplaque hemorrhage (hazard ratio, 5.2; P =0.005), larger mean intraplaque hemorrhage area (hazard ratio for 10 mm 2 increase, 2.6; P =0.006), larger maximum %lipid-rich/necrotic core (hazard ratio for 10% increase, 1.6; P =0.004), and larger maximum wall thickness (hazard ratio for a 1-mm increase, 1.6; P =0.008).

Conclusions— Among patients who initially had an asymptomatic 50% to 79% carotid stenosis, arteries with thinned or ruptured fibrous caps, intraplaque hemorrhage, larger maximum %lipid-rich/necrotic cores, and larger maximum wall thickness by MRI were associated with the occurrence of subsequent cerebrovascular events. Findings from this prospective study provide a basis for larger multicenter studies to assess the risk of plaque features for subsequent ischemic events.

Calcification in invasive tracheal aspergillosis demonstrated on ultrasound: a new finding

Invasion of the major airways is a rare manifestation of respiratory tract involvement by Aspergillus sp. and is seen almost exclusively in immunocompromised patients. We present calcification as a new feature of this condition and its demonstration by ultrasound in a 15-year-old boy with severe neutropenia secondary to aplastic anaemia.