Abstract P2-02-18: Higher mutation burden and mutant allele fraction of circulating tumor DNA corresponds to worse progression free survival in metastatic breast cancer patients

Introduction: Genomic profiling of circulating tumor DNA (ctDNA) allows non-invasive monitoring of tumor genetic changes and molecular heterogeneity. In addition to actionable mutations, mutational landscape derived from ctDNA could provide a better representation of overall tumor burden and tumor heterogeneity, as well as potentially impact clinical outcomes. To evaluate this hypothesis, this study assessed the association of mutation burden and average mutant allele fraction (MAF) with tumor subtype, therapeutic response, and survival in patients with metastatic breast cancer.

Methods: Whole blood samples from patients with metastatic breast cancer were collected during clinic visits before start of a new therapy. Plasma-derived cell-free DNA underwent complete next-generation sequencing of 73 cancer-related genes with the Guardant360 test. Mutation burden was defined as the number of genes with mutations, and average MAF was calculated as the sum of the highest MAF for each mutated gene divided by the number of genes with mutations. Time to progression was measured from the date of new treatment initiation after circulating tumor DNA collection to the date of progression. Multivariate cox proportional hazard models assessed the association of mutation burden and average MAF with progression free survival (PFS), adjusted for age, receptor subtype (hormone receptor positive, HR+; human epidermal growth factor 2 positive, HER2+; triple negative breast cancer, TNBC), treatment subtype (chemotherapy vs. targeted therapy), and number of prior metastatic breast cancer therapies. A p value of 0.05 was considered statistically significant.

Results: The study population consisted of 158 women with metastatic breast cancer (108 HR+, 14 HER2+, 19 TNBC) with a median age of 59 years and a median of 2 prior metastatic breast cancer therapies. Median follow up time was 4.0 months, and median PFS was 15.7 months. Mutation burden was greater in triple negative compared to hormone receptor positive breast cancer (7.5 vs. 4.8, p = 0.02) but no different in patients with > 2 prior metastatic therapies vs. not (5.1 vs. 4.7, p = 0.60) and age >45 vs. not (5.0 vs. 3.9; p = 0.26). In univariate models, high mutation burden (> median of 2) and high MAF (> median of 1.4) were significantly associated with worse PFS (Table). These results were similar in effect size and significance when adjusted for age, receptor subtype, treatment subtype, and number of prior metastatic breast cancer therapies. Impact of mutation burden on response to specific therapies will be presented at the meeting.

VariableHazard Ratio95% Confidence Intervalp valueHigh mutation burden1.991.12-3.540.02High mutant allele fraction1.881.06-3.330.03

Conclusions: Higher ctDNA mutation burden and average MAF is associated with worse progression free survival and possibly reflects a more treatment refractory phenotype. Whether immunotherapy, alone or in combination, could influence the clinical outcomes in metastatic breast cancer patients with high ctDNA mutation burden is unclear and warrants additional research.

Citation Format: Keenan T, Juric D, Niemierko A, Spring L, Park H, Malvarosa G, Beeler M, Moy B, Ellisen L, Isakoff S, Bardia A. Higher mutation burden and mutant allele fraction of circulating tumor DNA corresponds to worse progression free survival in metastatic breast cancer patients [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-02-18.

Nonpolar m-plane GaN/AlGaN heterostructures with intersubband transitions in the 5-10 THz band

This paper assesses intersubband (ISB) transitions in the 1-10 THz frequency range in nonpolar m-plane GaN/AlGaN multi-quantum-wells deposited on free-standing semi-insulating GaN substrates. The quantum wells (QWs) were designed to contain two confined electronic levels, decoupled from the neighboring wells. Structural analysis reveals flat and regular QWs in the two perpendicular in-plane directions, with high-angle annular dark-field scanning transmission electron microscopy images showing inhomogeneities of the Al composition in the barriers along the growth axis. We do not observe extended structural defects (stacking faults or dislocations) introduced by the epitaxial process. Low-temperature ISB absorption from 1.5 to 9 THz (6.3-37.4 meV) is demonstrated, covering most of the 7-10 THz band forbidden to GaAs-based technologies.

Intraband absorption in self-assembled Ge-doped GaN/AlN nanowire heterostructures

We report the observation of transverse-magnetic-polarized infrared absorption assigned to the s-p(z) intraband transition in Ge-doped GaN/AlN nanodisks (NDs) in self-assembled GaN nanowires (NWs). The s-p(z) absorption line experiences a blue shift with increasing ND Ge concentration and a red shift with increasing ND thickness. The experimental results in terms of interband and intraband spectroscopy are compared to theoretical calculations of the band diagram and electronic structure of GaN/AlN heterostructured NWs, accounting for their three-dimensional strain distribution and the presence of surface states. From the theoretical analysis, we conclude that the formation of an AlN shell during the heterostructure growth applies a uniaxial compressive strain which blue shifts the interband optical transitions but has little influence on the intraband transitions. The presence of surface states with density levels expected for m-GaN plane charge-deplete the base of the NWs but is insufficient to screen the polarization-induced internal electric field in the heterostructures. Simulations show that the free-carrier screening of the polarization-induced internal electric field in the NDs is critical to predicting the photoluminescence behavior. The intraband transitions, on the other hand, are blue-shifted due to many-body effects, namely, the exchange interaction and depolarization shift, which exceed the red shift induced by carrier screening.

Adiabaticity and localization in one-dimensional incommensurate lattices

We experimentally investigate the role of localization on the adiabaticity of loading a Bose-Einstein condensate into a one-dimensional optical potential comprised of a shallow primary lattice plus one or two perturbing lattice(s) of incommensurate period. We find that even a very weak perturbation causes dramatic changes in the momentum distribution and makes adiabatic loading of the combined lattice much more difficult than for a single period lattice. We interpret our results using a band-structure model and the one-dimensional Gross-Pitaevskii equation.

Comparison of methods for retroviral mediated transfer of glucocerebrosidase gene to CD34+ hematopoietic progenitor cells

Gaucher disease is an excellent candidate for gene therapy by transduction of hematopoitic stem cells. In this study, we compared methods which allow an increase in transfer of the glucocerebrosidase gene to human hematopoietic progenitor cells. Several techniques were employed, including the use of cytokines, bone marrow stroma, fibronectin, centrifugal enhancement and in vitro long-term culture. The effect of prestimulation with cytokines interleukin-3 (IL-3), interleukin-6 (IL-6) and stem cell factor (SCF) on transduction of cord blood CD34+ cells was examined. The results suggest that 16-h prestimulation was sufficient for efficient transduction. We examined the effect of bone marrow stroma and fibronectin, both of which increased transduction efficiency up to 36% and 44%, respectively, as measured by PCR for the integrated GC-cDNA in clonogenic cells (9% without any support). Transduction efficiency of 83% was obtained using 2-h centrifugation. Combining centrifugation and in vitro culture in long-term bone marrow culture media containing cytokines (IL-3/IL-6/SCF), CD34+ cells from cord blood and peripheral blood of 3 Gaucher patients were transduced weekly for 21 d. The results of 6 separate experiments consistently demonstrated transduction efficiency of 100% after 7-d in vitro culture. This transduction protocol combining centrifugation and in vitro long-term culture is an attractive method and can be applied to clinical trials.

Gaucher's disease: studies of gene transfer to haematopoietic cells

Transfer of the gene coding for glucocerebrosidase (GC) via a retroviral vector (MFG-GC) to haematopoietic progenitors results in engraftment and life-long expression of the human protein at high levels in transplanted mice. Studies of human CD34 cells were carried out to evaluate their potential use in a gene therapy approach to Gaucher's disease. High transduction efficiency and correction of the enzyme deficiency was possible in CD34 cells obtained from patients with Gaucher's disease. Based on these results, a clinical trial of gene therapy was designed and initiated. Preliminary results of this study indicate the persistence or engraftment of genetically corrected cells in the transplanted patients.

Cytokine mobilization of peripheral blood stem cells in patients with Gaucher disease with a view to gene therapy

As clinical trials for gene therapy in Gaucher disease (GD) begin, questions regarding the biology of the hematopoietic stem cell in this disease remain unanswered. This study demonstrates the ability to mobilize and collect CD34+ cells in three patients with the disorder. Our RAC/FDA-approved clinical trial utilizes mobilized peripheral blood stem cells (PBSC) as the target cells for gene transfer. In this approach, a white blood cell fraction is collected by apheresis, enriched for CD34+ cells, and transduced with a retroviral vector carrying the glucocerebrosidase (GC) gene. Transduced cells from the patient with activity corrected to at least normal levels will be returned to the patient without myelosuppressive therapy. We report here the effect of cytokines in mobilizing PBSC in three patients with GD. Two (patients 1 and 2) were given granulocyte colony-stimulating factor (G-CSF) at a dose of 5 micrograms/kg/d and one (patient 3) was given 10 micrograms/kg/d for 10 days. Leukaphereses were done daily for 5 days and the products enriched for CD34+ cells using the clinical Ceprate (CellPro) column. The CD34+ cells in all fractions were monitored daily during mobilization and leukaphereses. Subset analysis for the expression of Thy-1, CD38, HLA-DR, and CD33 on the CD34+ cells was performed. An increase in CD34+ cells in the peripheral blood was noted from day 5 onward (up to a six-fold increase). Up to a 625-fold enrichment in CD34+ cells in the apheresis product was noted using the clinical Ceprate column. Totals of 1.2, 3.5, and 2.1 x 10(6) CD34+ cells/kg were collected in the three patients. A diminution in the percent of CD34+/Thy-1+ cells was noted with enrichment. In vitro retroviral transduction of the CD34-enriched cells using centrifugation promoted transduction protocol previously described (Bahnson AB et al., Centrifugal enhancement of retroviral-mediated gene transfer. Journal of Virology Methods 54:131, 1995) and modified for clinical use, demonstrated a mean transduction efficiency of 37% (range 8.3-87.1%) in clonogenic cells and up to 50% in long-term culture-initiating cells (LTC-IC) at week 6. Significantly, we have been able to achieve up to a 50-fold increase in the level of GC above deficient levels in the patients' CD34+ enriched cells when maintained in vitro in culture. The study demonstrates that up to a six-fold increase in CD34+ cells in the PB can be achieved with cytokines in patients with GD. CD34+ cells can be collected in numbers sufficient for conventional transplantation and transduced efficiently in vitro. In gene therapy trials for genetic disorders to date, myelosuppressive therapy is not advocated. The clinical trial will demonstrate whether this number of transduced CD34+ cells will be adequate for competitive engraftment of genetically corrected PBSC.

Effect of anger on colon motor and myoelectric activity in irritable bowel syndrome

The present investigation was designed to study the effect of anger on colon motor and myoelectric activity in irritable bowel syndrome. Patients with irritable bowel syndrome were compared with normal controls during resting and two anger stressors: criticism of performance on an intelligence test and during a delay of assistance for a diagnostic procedure. At rest patients with irritable bowel syndrome had higher motor and spike potential activity than normal subjects; however, the difference was only significant for spike activity. Anger significantly increased colon motor and spike potential activity in the groups compared with the resting state. Patients with irritable bowel syndrome produced significantly higher motor and spike potential activity when angered. They also reported themselves to be more hostile and appeared angrier than normal controls after the study. However, they did not report themselves to be more anxious or depressed, suggesting that the observed changes in colonic function of both groups were due to anger. Patients with irritable bowel syndrome scored significantly higher than controls on the Minnesota Multiphasic Personality Inventory scales of hypochondriasis, hysteria, and depression, but these personality factors did not significantly influence their anger level before the study. The results are discussed in terms of the role of learning in the colon and the abnormal reinforcement of bowel behavior in patients with irritable bowel syndrome.