Abstract 4354: An exosome-based ESR1 monitoring RT-qPCR technology that rapidly and accurately detects circulating tumor acquired resistance variants at ≤0.1% frequency in liquid biopsy samples

Introduction: Hormone receptor-positive/human epidermal growth factor receptor 2-negative (HR+/HER2-) breast cancer is the most common type of breast cancer. Patients with HR+/HER2- metastatic breast cancer (mBC) often become resistant to aromatase inhibitors commonly used in endocrine therapy (ET). Estrogen receptor (ESR1) ligand binding domain mutations are frequently detected in HR+ mBC and have been reported to be associated with ET resistance, noting up to 60% patients with mBC will develop resistance to treatment via acquired resistance in ESR1. Recent studies have shown that monitoring of ESR1 mutations in plasma may serve as a predictive biomarker of acquired resistance to ET, showcasing a strong need for sensitive nucleic acid-based assays. We describe a comprehensive methodology for targeted clinical RT-qPCR monitoring of ESR1 mutations in plasma that utilizes both exosomal nucleic acids and cfDNA to report multiple mutations, provide a streamlined workflow, and accommodate a range of inputs from clinically relevant samples.

Methods: Exosomal nucleic acids (exosomal DNA and RNA) and circulating cell-free DNA (cfDNA) were co-isolated using the ExoLution Plus Isolation Kit (Exosome Diagnostics). RT-qPCR-based target enrichment was performed using modified QuantideX reagents (Asuragen) and mutations were confirmed on the QuantStudio qPCR Platform (ThermoFisher). Bioinformatic analyses were conducted using custom software.

Results: We developed novel technologies and tested greater than samples across key ET resistance mutations, utilizing contrived samples as needed due to availability. Preliminary studies demonstrated that ESR1 exosomal RNA + cfDNA ranged from approximately 9,500 copies to 64,000 copies in a set of 2mL female presumed normal plasma samples; these results suggest that even 2mL plasma could provide sufficient exosomal RNA/DNA + cfDNA for mutation detection at variant frequencies less than or equal to 0.01%. The ESR1 RT-qPCR showed greater than 90% analytical sensitivity (at less than or equal to 1% mutant allele frequency) and greater than90% analytical specificity. Further, the technology detected less than 10 mutant copies for most tested mutants, showing an LOD of at least 0.1% (5 mutant copies in a background of 5,000 WT copies).

Conclusion: A fast, efficient, and sensitive ESR1 RT-qPCR panel approach was developed and evaluated, demonstrating the reliable and specific detection of rare variants in liquid biopsy specimens. Importantly, this prototype technology has potential to address several challenges associated with mutation monitoring in liquid biopsies by expanding detection of mutant analytes (exosomal RNA and DNA), improving analytical sensitivity (novel reagents and software), and increasing accessibility (qPCR instrument install base).

Citation Format: Sarah Statt, Julie Thibert, Kurt Franzen, Aquiles Sanchez, Liangjing Chen, Megan Yociss, Elliot Hallmark, Melissa Church, Stela Filipovic-Sadic, Gary Latham, Johan Skog. An exosome-based ESR1 monitoring RT-qPCR technology that rapidly and accurately detects circulating tumor acquired resistance variants at ≤0.1% frequency in liquid biopsy samples. [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 4354.

Use of human-derived stem cells to create a novel, in vitro model designed to explore FMR1 CGG repeat instability amongst female premutation carriers

OBJECTIVE

Create a model, using reprogrammed cells, to provide a platform to identify the mechanisms of CGG repeat instability amongst female fragile X mental retardation 1 gene (FMR1) premutation (PM) carriers.

METHODS

Female PM carriers (with and without POI) and healthy controls were enrolled from June 2013 to April 2014. Patient-derived fibroblasts (FB) were reprogrammed to induced pluripotent stem cells (iPSC) using viral vectors, encoding KLF4, OCT4, SOX2, and MYC. FMR1 CGG repeat-primed PCR was used to assess the triplet repeat structure of the FMR1 gene. FMR1 promoter methylation (%) was determined using FMR1 methylation PCR (mPCR). Quantification of FMR1 transcripts by RT-qPCR was used to evaluate the effect of reprogramming on gene transcription, as well as to correlate patient phenotype with FMR1 expression. Production of FMR1 protein (FMRP) was determined using a liquid bead array-based immunoassay.

RESULTS

Upon induction to pluripotency, all control clones exhibited maintenance of progenitor cell CGG repeat number, whereas 10 of 12 clones derived from PM carriers maintained their input CGG repeat number, one of which expanded and one contracted. As compared to parent FB, iPSC clones exhibited a skewed methylation pattern; however, downstream transcription and translation appeared unaffected. Further, the PM carriers, regardless of phenotype, exhibited similar FMR1 transcription and translation to the controls.

CONCLUSIONS

This is the first study to establish a stem cell model aimed to understand FMR1 CGG repeat instability amongst female PM carriers. Our preliminary data indicate that CGG repeat number, transcription, and translation are conserved upon induction to pluripotency.

Novel insight into mutational landscape of head and neck squamous cell carcinoma

Development of head and neck squamous cell carcinoma (HNSCC) is characterized by accumulation of mutations in several oncogenes and tumor suppressor genes. We have formerly described the mutation pattern of HNSCC and described NOTCH signaling pathway alterations. Given the complexity of the HNSCC, here we extend the previous study to understand the overall HNSCC mutation context and to discover additional genetic alterations. We performed high depth targeted exon sequencing of 51 highly actionable cancer-related genes with a high frequency of mutation across many cancer types, including head and neck. DNA from primary tumor tissues and matched normal tissues was analyzed for 37 HNSCC patients. We identified 26 non-synonymous or stop-gained mutations targeting 11 of 51 selected genes. These genes were mutated in 17 out of 37 (46%) studied HNSCC patients. Smokers harbored 3.2-fold more mutations than non-smokers. Importantly, TP53 was mutated in 30%, NOTCH1 in 8% and FGFR3 in 5% of HNSCC. HPV negative patients harbored 4-fold more TP53 mutations than HPV positive patients. These data confirm prior reports of the HNSCC mutational profile. Additionally, we detected mutations in two new genes, CEBPA and FES, which have not been previously reported in HNSCC. These data extend the spectrum of HNSCC mutations and define novel mutation targets in HNSCC carcinogenesis, especially for smokers and HNSCC without HPV infection.

Activation of the NOTCH pathway in head and neck cancer

NOTCH1 mutations have been reported to occur in 10% to 15% of head and neck squamous cell carcinomas (HNSCC). To determine the significance of these mutations, we embarked upon a comprehensive study of NOTCH signaling in a cohort of 44 HNSCC tumors and 25 normal mucosal samples through a set of expression, copy number, methylation, and mutation analyses. Copy number increases were identified in NOTCH pathway genes, including the NOTCH ligand JAG1. Gene set analysis defined a differential expression of the NOTCH signaling pathway in HNSCC relative to normal tissues. Analysis of individual pathway-related genes revealed overexpression of ligands JAG1 and JAG2 and receptor NOTCH3. In 32% of the HNSCC examined, activation of the downstream NOTCH effectors HES1/HEY1 was documented. Notably, exomic sequencing identified 5 novel inactivating NOTCH1 mutations in 4 of the 37 tumors analyzed, with none of these tumors exhibiting HES1/HEY1 overexpression. Our results revealed a bimodal pattern of NOTCH pathway alterations in HNSCC, with a smaller subset exhibiting inactivating NOTCH1 receptor mutations but a larger subset exhibiting other NOTCH1 pathway alterations, including increases in expression or gene copy number of the receptor or ligands as well as downstream pathway activation. Our results imply that therapies that target the NOTCH pathway may be more widely suitable for HNSCC treatment than appreciated currently.

A multiplex technology platform for the rapid detection of relevant mutations in the EGFR signaling pathway

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Background: Determination of the mutational status of key gene effectors along the EGFR signaling pathway plays a critical role in the management of metastatic colorectal cancer (mCRC) and other cancer types. We previously reported the rapid, multiplex, and sensitive detection of 7 common KRAS mutations in mCRC FFPE specimens using the Signature KRAS Mutations (RUO) kit. We show here that the same technology platform can be applied to the detection of additional clinically relevant mutations in the EGFR, BRAF, KRAS, NRAS and HRAS genes.

Methods: Mutation panels were designed for multiplex PCR amplification of an internal control gene and discrete mutation regions in independent target genes. PCR products were hybridized on a liquid bead array carrying target-specific probes and sorted by flow cytometry using a Luminex 200 system. Genomic DNA was extracted from cell lines and representative flash frozen, FFPE or FNA clinical specimens using laboratory-validated extraction methods.

Results: Using model plasmids and cell lines we developed specific assays for distinct mutations in KRAS codon 12/13, KRAS 3' UTR (rs61764370), BRAF codon 600/601, HRAS codon 12/61, NRAS codon 61, and EGFR exon 19/20/21. The various assays reached 0.1 to 5% analytical sensitivity and could be further combined in multiplex panels relevant to specific applications. The Signature KRAS/BRAF Mutations (RUO) kit, an assay for 12 KRAS mutations in codon 12/13 and BRAF V600E, was validated in over 250 mCRC FFPE specimens with >99% agreement with clinically validated methods. Specific detection of these 13 mutations and 6 HRAS/NRAS mutations was also demonstrated in thyroid nodule FNA specimens. Single-well detection of EGFR deletions in exon 19 together with the point mutations L858R and T790M was also successfully evaluated in lung specimens.

Conclusions: The Signature technology platform is a specific, sensitive and flexible tool for the assessment of various mutations in different tissue types. The development and validation of broader mutation panels would likely facilitate the rapid molecular characterization of individual tumor specimens and the optimization of personalized treatments for mCRC and other cancer types.

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Seismic data from man-made impacts on the moon

Unusually long reverberations were recorded from two lunar impacts by a seismic station installed on the lunar surface by the Apollo 12 astronauts. Seismic data from these impacts suggest that the lunar mare in the region of the Apollo 12 landing site consists of material with very low seismic velocities near the surface, with velocity increasing with depth to 5 to 6 kilometers per second (for compressional waves) at a depth of 20 kilometers. Absorption of seismic waves in this structure is extremely low relative to typical continental crustal materials on earth. It is unlikely that a major boundary similar to the crustmantle interface on earth exists in the outer 20 kilometers of the moon. A combination of dispersion and scattering of surface waves probably explains the lunar seismic reverberation. Scattering of these waves implies the presence of heterogeneity within the outer zone of the mare on a scale of from several hundred meters (or less) to several kilometers. Seismic signals from 160 events of natural origin have been recorded during the first 7 months of operation of the Apollo 12 seismic station. At least 26 of the natural events are small moonquakes. Many of the natural events are thought to be meteoroid impacts.

Probing structure/function relationships of HIV-1 reverse transcriptase with styrene oxide N2-guanine adducts

Details of the interactions between the human immunodeficiency virus (HIV-1) reverse transcriptase and substrate DNA were probed both by introducing site-specific and stereospecific modifications into DNA and by altering the structure of potential critical residues in the polymerase. Unadducted 11-mer DNAs and 11-mer DNAs containing R and S enantiomers of styrene oxide at N2-guanine were ligated with two additional oligonucleotides to create 63-mers that served as templates for HIV-1 reverse transcriptase replication. Oligonucleotides that primed synthesis 5 bases 3' to the adducts could be extended up to 1 base 3' and opposite the lesion. However, when the positions of the 3'-OH of the priming oligonucleotides were placed 1, 2, 3, 4, 5, and 6 bases downstream of the styrene oxide guanine adducts, replication was initiated, only to be blocked after incorporating 4, 5, 6, and 7 bases beyond the lesion. The sites of this adduct-induced termination corresponded to the position of the DNA where alpha-helix H makes contact with the DNA minor groove, 3-5 bases upstream of the growing 3' end. In addition, mutants of the polymerase in alpha-helix H (W266A and G262A) alter the termination probabilities caused by these DNA adducts, suggesting that alpha-helix H is a sensitive monitor of modifications in the minor groove of newly synthesized template-primer DNA several bases distal to the 3'-OH.

Minimal effects of dextroamphetamine on scopolamine-induced cognitive impairments in humans

The central anticholinergic drug scopolamine has been used to model aspects of the memory impairment that occurs in Alzheimer's disease and in aging. To determine whether nonspecific stimulant effects can attenuate the cognitive impairment induced by scopolamine, we studied the effects of scopolamine and the stimulant dextroamphetamine in 17 young normal volunteers. After a baseline day of cognitive testing, subjects participated in two study days, in which they received dextroamphetamine (d-AMP) (0.25 mg/kg p.o.) + scopolamine (0.5 mg i.v.) and placebo + scopolamine, in randomized order under double-blind conditions. There were no statistically significant differences in cognitive test performance between the two drug conditions with the exception of one of the category retrieval tasks. Stimulant effects were documented to occur by other measures. We conclude that d-AMP at the dose used does not attenuate the memory impairment induced by scopolamine.

Oral administration of heptylphysostigmine in healthy volunteers: a preliminary study

Heptylphysostigmine (HP) is a reversible cholinesterase (ChE) inhibitor with greater lipophilicity and longer inhibitory action than the parent compound, physostigmine (Phy). Single (0.1-0.6 mg/kg) and multiple 5-day (0.1-0.3 mg/kg) doses of HP were administered to 21 young normal volunteers. The relationship between logarithmic dose (mg/kg) and peak inhibition of red blood cell (RBC) ChE was linear with dose. In one subject given 0.6 mg/kg of HP, concentration in plasma was 0.68 ng/ml at 2 h and gradually declined to below the detection limit by 4 h. Peak plasma and RBC ChE inhibitions of 31.2% and 55.8% were achieved at 2 h for both with a 0.6 mg/kg dose. Chronic studies did not result in any accumulation of ChE inhibition up to 0.2 mg/kg b.i.d., whereas at 0.3 mg/kg b.i.d. 10-15% RBC ChE inhibition was maintained. Higher levels of ChE inhibition can be achieved with HP than with its parent compound, Phy. Red blood cell ChE inhibition recovered more slowly than plasma even though the maximum inhibition was similar for both enzymes.

CHUM: collaborative healthcare utilization model--an example of a self-directed team in a hospital setting

Self-directed work teams are innovative tools used in industry to improve productivity and quality. Work teams are complementary to the process of Total Quality Management (TQM) and build on the same foundations of customer satisfaction, goal setting, and staff education and training (Arikian, 1991; Sheehy & Musselwhite, 1990). The Collaborative Healthcare Utilization Model (CHUM) encompasses a self-directed team which enables nurse managers and physicians to lead a busy, tertiary care surgical service. The opportunity to develop CHUM arose when a middle management (director) position was removed from the nursing division. Development of the self-directed team included "selling" the idea and piloting the venture in an environment where work teams are not part of the organizational structure. The authors describe their experience in introducing a self-directed team into a hospital setting.

Intervention study in high school students with elevated blood pressures. Dietary experiment with polyunsaturated fatty acids

A blood pressure-lowering effect of increased prostaglandin synthesis via polyunsaturated fatty acids has been demonstrated in animal experiments. To our knowledge, for the first time an attempt was made to lower elevated blood pressures in adolescents (age 15-18 years) through a diet enriched in polyunsaturated fatty acids. This community-based dietary trial involved 30 students in the diet group and 20 students in the control group without any dietary intervention. Within 6 weeks the systolic blood pressure decreased by almost 11 mm Hg in the diet group and by 6 mm Hg in the control group. Diastolic blood pressure fell by 2 and 1 mm Hg, respectively. The effect on blood pressure was markedly different in normal weight adolescents. Systolic blood pressure in the diet group decreased by 14 mm Hg but only by 5 mm Hg in the control group. Diastolic blood pressure levels fell by 4 mm Hg in the diet group and increased by 4 mm Hg in the control group. Unfortunately, the numbers in these two comparison groups were rather small. The majority (70%) of adolescents with high blood pressure was overweight (greater than or equal to 20% above normal weight). However, for the small group of normal weight adolescents, the diet enriched with polyunsaturated fatty acids may be suitable to reduce elevated blood pressure levels.

Aftershocks and Intensity of the Managua Earthquake of 23 December 1972

Two portable seismic stations and a fixed array of five seismometers were used to record aftershocks in the vicinity of Managua, Nicaragua, after the earthquake of 23 December 1972. Approximately 3000 aftershocks were recorded during a 20-day period in January 1973. Left lateral motion along at least two faults, both trending N40 degrees E, is inferred from the seismic data. This is in good agreement with dislocations mapped at the surface in Managua. The data suggest that the shallow earthquakes of the Managua region are a consequence of north-south compressional stresses and east-west tensional stresses. This is consistent with regional plate movements deduced in other investigations.

New Seismic Data on the State of the Deep Lunar Interior

Direct shear-wave arrivals from seismtic events originating on the far side of the moon are not observed at some of the stations of the Apollo seismic network. These data suggest that the material in the lunar interior at a depth of 1000 to 1100 kilometers is more dissipative for seismic shear waves than the lithosphere above, and possibly exists in a partially molten state akin to the earth's asthenosphere.

Lunar Crust: Structure and Composition

Lunar seismic data from artificial impacts recorded at three Apollo seismometers are interpreted to determine the structure of the moon's interior to a depth of about 100 kilomneters. In the Fra Mauro region of Oceanus Procellarum, the moon has a layered crust 65 kilometers thick. The seismic velocities in the upper 25 kilometers are consistent with those in lunar basalts. Between 25 and 65 kilometers, the nearly constant velocity (6.8 kilometers per second) corresponds to velocities in gabbroic and anorthositic rocks. The apparent velocity is high (about 9 kilometers per second) in the lunar mantle immediately below the crust.

Moonquakes

Although the average rate of seismic energy release within the moon appears to be far below that of the earth, over 100 events believed to be moonquakes have been recorded by the two seismic stations installed on the lunar surface during Apollo missions 12 and 14. With few exceptions, the moonquakes occur at monthly intervals near times of perigee and apogee and show correlations with the longer-term (7-month) lunar gravity variations. The repeating moonquakes are believed to occur at not less than 10 different locations. However, a single focal zone accounts for 80 percent of the total seismic energy detected. This active zone appears to be 600 kilometers south-southwest of the Apollo 12 and 14 sites and deep within the moon. Each focal zone must be small (less than 10 kilometers in linear dimension) and fixed in location over a 14-month period. Cumulative strain at each location is inferred. Thus, the moonquakes appear to be releasing internal strain of unknown origin, the release being triggered by tidal stresses.