Abstract P4-01-11: Genomic alterations of cell-free DNA in early breast cancer patients with recurrence

Cell-free DNA (cfDNA), as a non-invasive strategy, provides substantial benefit to overcome tumor heterogeneity. Surveillance of recurrence after standard treatment in early breast cancer (BC) using cfDNA, enables to detect minimal residual disease (MRD), also to identify genomic alterations driving recurrences. We aimed to assess the role of cfDNA in detecting MRD by investigating genomic alterations of 1)primary, recurred tumor and 2)cfDNA at time of recurrence using deep targeted sequencing. Fifty-four early BC patients were enrolled prospectively between 2014 and 2017 at time of recurrence. Median disease free interval was 28.5 months (rage 6.2-49.8). 62.7% (32/51) were hormone receptor (HR) positive (28 HRpos/HER2neg, 4 HRpos/HER2pos), 11.8% (6/51) were HRneg/HER2pos and 25.5% (13/51) were triple negative BCs. 59.3% (32/54) patients developed loco-regional recurrence (15 local recurrence only, 13 regional only, 4 with both) and distant metastasis was observed among 40.7% (22/54) patients. Cell-free DNA was extracted from 5cc blood at time of recurrence. Deep targeted sequencing was performed using customized NGS panel –encompassing 426 cancer-related target coding region, 242 fusion and amplification-related region- of cfDNA and FFPE(formalin fixed paraffin embedded) tumor samples archived from surgical resection or biopsy. Deep targeted sequencing data was successfully performed in 72.1% (31/43) plasma samples and sequencing yield was significantly lower when stored for more than 2yrs (46.2% vs 83.3%).

Mutations of cfDNA and tumor (primary, recurred) were analyzed. Mean sequencing depth of cfDNA and FFPE were x425.7 and x777.6 respectively. Median number of pathogenic mutations found in primary tumor, cfDNA and recurred tumor were 27(range 12-99), 25(range 8-85) and 9(range 0-23). Among mutations found in primary tumor, 27.4% were shared mutations (range 8.1%-72.7%) with recurred tumor and 26.1% were shared mutations (range 4.7%-69.2%) observed in cfDNA sample. Among mutations found in recurred tumor, 40.9% were observed in cfDNA (range 17.7-87.5%). In primary tumor, median number of mutations with allelic fraction (MAF)>10% were 12 (range 4-21) and at least one mutation was found in cfDNA at time of recurrence. Among mutations with MAF>10%, 59.4% and 69.1% were found in cfDNA and recurred tumor. Known oncogenic mutations of PIK3CA, TP53, GATA3, AKT1, ESR1, RELN, ERBB2, ERBB3, BRCA1 mutation were found. PIK3CA gene (p.H1047R) was found in two cases both in primary tumor and cfDNA at recurrence (MAF 11.4% vs 5.3% and 12.3% vs 15.4%) suggesting de novo driver mutation. One patient developed regional recurrence during adjuvant aromatase inhibitor with ESR1 V392I mutation in both cfDNA and recurred tumor (MAF 48.1 and 54.5%), while another patient's recurred tumor during aromatase inhibitor harbored ESR1 D538G mutation exclusively in recurred tumor with MAF <1%. Both patients had no ESR1 hotpot mutation in primary tumor.

Our data showed sequencing yield of 83.3% in plasma samples within 2yr. Pathogenic mutations in primary tumor, especially when MAF>10%, half of them was observed in cfDNA at time of recurrence. ESR1 mutation should be included in cfDNA surveillance for patients undergoing endocrine therapy even absent in primary tumor.

Citation Format: Kim J, Jo WK, Kim KY, Kim BJ, Lee SB, Lee HJ, Yu JH, Kim HJ, Chung IY, Ko BS, Kim S-B, Jung KH, Ahn JH, Chang S, Lee JW, Son BH, Ahn SH. Genomic alterations of cell-free DNA in early breast cancer patients with recurrence [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-01-11.

Evaluation of changes in the locomotion and histology of sciatic nerve following experimental autoimmune encephalomyelitis

Introduction: Involvement of peripheral nerves in the experimental model of multiple sclerosis (MS) is rarely observed. The objective of this study was to investigate the changes in the locomotion in a mouse model of experimental autoimmune encephalomyelitis (EAE) and correlate with histological changes, if any, in the sections of sciatic nerve and lumbar part of spinal cord. Material and Methods: C57BL/6 mice (10 weeks, n = 8) were immunized with single subcutaneous injection of 300 μg of MOG35-55 and 200 μL of complete Freund's adjuvant (CFA) to produce EAE models. Limp tail with weakness of hindlimb was observed on day 10 and improvement in the weakness was observed on day 20 onwards. Footprint analysis was done to evaluate the impairment in the locomotion on day 0, 5, 10, 15 and 20 of the experiment. Results: One way repeated measure ANOVA found significant reduction in the mean hindlimb stride length on day 10 and 15 (left) and on day 15 and day 20 (right) when compared to mean stride length in day 0 (p<0.05). Histological analysis showed evidence of macrophage infiltration around the dilated blood vessels in the epineurium of sciatic nerve and evidence of damage in the myelinated white matter of lateral funiculus of the lumbar sections of the spinal cord in EAE mice. Conclusion: It is concluded that in mouse model of EAE, the impairment oflocomotion due to damage in the lumbar part of spinal cord can be associated with inflammatory changes in the sciatic nerve.

Molecular Diagnostic Assays and Clinicopathologic Implications of MET Exon 14 Skipping Mutation in Non-small-cell Lung Cancer

BACKGROUND

Recent studies revealed MET exon 14 skipping (METex14) as a biomarker that predicts the response to MET inhibitors in non-small-cell lung cancer (NSCLC). However, METex14 genomic alterations exhibit a highly diverse sequence composition, posing a challenge for clinical diagnostic testing. This study aimed to find a reasonable diagnostic assay for METex14 and identify its clinicopathologic implications.

MATERIALS AND METHODS

We performed a comprehensive analysis of METex14 in 414 EGFR/KRAS/ALK/ROS1-negative (quadruple negative) surgically resected NSCLCs. We used real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Sanger sequencing for the first assay, followed by next-generation sequencing (NGS; hybrid-capture targeted DNA/RNA sequencing). Clinicopathologic implications of the METex14 group were analyzed in a total of 880 NSCLCs.

RESULTS

METex14 was confirmed in 13 (3.1%) patients by DNA- and RNA-NGS. After comparison of assay results, qRT-PCR and NGS demonstrated the highest concordance rate. The mean variant allele frequency was 10.5% and 49% in DNA- and RNA-NGS, respectively. DNA-NGS revealed various lengths of indel and substitutions around and in exon 14. Moreover, METex14 was associated with adenocarcinoma (4.8%; 11/230) or sarcomatoid carcinoma (9.5%; 2/21), old age, never-smokers, and early stage of disease.

CONCLUSIONS

METex14 occurs in about 3% of NSCLCs and has characteristic clinicopathologic features. NGS should be the first assay of choice as a multiplex testing. Sanger sequencing can detect METex14, but sensitivity can be hampered by large deletions or low allele frequency. qRT-PCR, an mRNA-based method, is sensitive and specific and can be appropriate for screening METex14 as a single gene testing.

Biological and Mechanical Evaluation of Novel Prototype Dental Composites

The breakdown of the polymeric component of contemporary composite dental restorative materials compromises their longevity, while leachable compounds from these materials have cellular consequences. Thus, a new generation of composite materials needed to be designed to have a longer service life and ensure that any leachable compounds are not harmful to appropriate cell lines. To accomplish this, we have developed concurrent thiol-ene-based polymerization and allyl sulfide-based addition-fragmentation chain transfer chemistries to afford cross-linked polymeric resins that demonstrate low shrinkage and low shrinkage stress. In the past, the filler used in dental composites mainly consisted of glass, which is biologically inert. In several of our prototype composites, we introduced fluorapatite (FA) crystals, which resemble enamel crystals and are bioactive. These novel prototype composites were benchmarked against similarly filled methacrylate-based bisphenol A diglycidyl ether dimethacrylate / triethylene glycol dimethacrylate (bisGMA/TEGDMA) composite for their cytotoxicity, mechanical properties, biofilm formation, and fluoride release. The leachables at pH 7 from all the composites were nontoxic to dental pulp stem cells. There was a trend toward an increase in total toughness of the glass-only-filled prototype composites as compared with the similarly filled bisGMA/TEGDMA composite. Other mechanical properties of the glass-only-filled prototype composites were comparable to the similarly filled bisGMA/TEGDMA composite. Incorporation of the FA reduced the mechanical properties of the prototype and bisGMA/TEGDMA composite. Biofilm mass and colony-forming units per milliliter were reduced on the glass-only-filled prototype composites as compared with the glass-only-filled bisGMA/TEGDMA composite and were significantly reduced by the addition of FA to all composites. Fluoride release at pH 7 was greatest after 24 h for the bisGMA/TEGDMA glass + FA composite as compared with the similarly filled prototypes, but overall the F^- release was marginal and not at a concentration to affect bacterial metabolism.

Administration of slow release exogenous melatonin modulates oxidative stress profiles and in vitro fertilizing ability of the cryopreserved mithun (Bos frontalis) spermatozoa

Mithun (Bos frontalis) is a unique domestic free range bovine species of North Eastern hilly regions of India. The present study was designed to assess the seasonal effect of slow release exogenous melatonin (MT) implant on semen quality parameters (SQP) and in vitro zona binding ability (IVZ) of spermatozoa. The experimental animals were divided into Gr I: Control (n = 5) and Gr II: Treatment (n = 5; melatonin implant @ 18mg/50 kg bwt). A total of 20 semen samples/group in winter, spring, autumn and summer seasons (n = 160), twice per week were collected. Following cryopreservation, samples were evaluated for motility parameters (forward progressive, mobility & velocity by computer assisted sperm analyser (CASA), viability, acrosome integrity, plasma membrane and nuclear abnormality, functional status of mitochondria, enzymatic, antioxidant and oxidative profiles, and IVZ. The study revealed significant (p < 0.05) improvement in total motility, viability, acrosome-, plasma membrane-, and nuclear-integrity, and antioxidant profiles; with highest values in spring and lowest in summer season in the fresh semen in Gr II than the Control. A significant (p < 0.05) improvement in motility parameters, membrane potential of mitochondria, antioxidant profiles and reduction in sperm and nuclear abnormalities, leakage of intracellular enzymes and oxidative stress and IVZ index & binding percentage in post-thaw semen samples in melatonin supplemented than in un-supplemented control group was observed. It can be concluded from the study that slow-release melatonin supplementation can be effectively utilized to improve the antioxidant profiles and reduction of oxidative stress, with cascading beneficial effects on semen quality parameters and fertility status of the mithun bull.