Using a next-generation sequencing approach to DNA metabarcoding for identification of adulteration and potential sources of mercury in commercial cat and dog foods

Studies have demonstrated that some commercial pet (i.e., cat and dog) food products contain high concentrations of mercury (Hg), and some products have Hg concentrations that are higher than expected based on the ingredients included in the package ingredient list. Additionally, concentrations of methylmercury, a particularly toxic form of Hg commonly associated with fish-based ingredients, are largely unstudied despite the widespread use of such ingredients in pet food products. This study aimed to quantify total Hg and methylmercury in a variety of commercial pet food products (n = 127), and use genetic tools to determine if specific ingredients contributed to high Hg concentrations in the final product. Results indicate that total Hg concentrations were above suggested maximum tolerable limits in three of the tested pet food products, and that methylmercury concentrations were at safe levels in all tested products. Next-generation amplicon sequencing using ten barcode primers was conducted to target distinct taxa and to determine if one primer set outperformed the others in amplifying the often heavily degraded DNA found in pet food products. The 16sUniF_16sUniR primer set generated a relatively higher number of reads across the broadest set of taxa, although several of the primer sets were useful in identifying common animal- and plant-based ingredients in commercial pet food products. Combined with the Hg results, it was demonstrated that pet food product ingredients are consistent among and between product lots. However, these results also revealed that adulteration is prevalent in pet food products.

Comparison of co-located ice-core and tree-ring mercury records indicates potential radial translocation of mercury in whitebark pine

Tree-ring records are a potential archive for reconstructing long-term historical trends in atmospheric mercury (Hg) concentrations. Although Hg preserved in tree rings has been shown to be derived largely from the atmosphere, quantitative relationships linking atmospheric concentrations to those in tree rings are limited. In addition, few tree-ring-based Hg records have been evaluated against co-located proxies of atmospheric Hg deposition or direct atmospheric measurements. Here we develop long-term Hg records extending from 1800 to 2018 CE using cores collected from two stands of whitebark pine located near the Upper Fremont Glacier in the Wind River Range, Wyoming, where a long-term record of atmospheric Hg deposition previously was developed from an ice core. The tree ring record showed that Hg concentrations increased beginning in 1800 CE to a broad peak centered at ~1960 CE, before decreasing to present, generally paralleling the ice-core record of Hg deposition. The exact timing and magnitude of the Hg increases in the trees, however, is offset earlier relative to the ice-core record. These discrepancies potentially arise from biotic processes that impact Hg uptake and preservation in whitebark pine, and results from an advection-diffusion model indicate that the temporal differences are consistent with radial movement of Hg within the trees. The forms of atmospheric Hg and seasonality may also impact the Hg record preserved by each archive, but are less likely to affect long-term trends. Further work is needed to assess radial Hg translocation in more controlled studies with larger sample sizes.

Abstract P2-04-03: Differential effect of chemotherapy on immune gene expression signatures based on molecular subtype of breast cancer

Background: Neoadjuvant chemotherapy (NAC) is frequently used in triple negative breast cancers (TNBC), and patients who achieve pathological complete response (pCR) following NAC have improved outcomes over those with residual disease (non-pCR). Unfortunately only 30% of TNBC patients achieve pCR, with no good treatment options for other 70% with non-pCR. Tumor infiltrating lymphocytes (TILs) in TNBC are predictive of pCR to NAC, and TILs found in the residual disease further prognosticate patients with residual disease into an improved prognosis subset. These data suggest there is an immune component to TNBC that might be affected by chemotherapy. Given the advent of immunotherapy trials in breast cancer, specifically in combination with NAC, there is an unmet need to gain a better understanding of the immune microenvironment in TNBC.

Objective: We investigated the role of NAC on the immune microenvironment by examining breast cancer samples before (diagnostic biopsy) and after (residual disease) NAC, as these data are pertinent to the design and analysis of ongoing clinical trials in breast cancer combining immunotherapy with concurrent chemotherapy.

Methods: RNA was extracted from 51 paired (pre- and post-NAC) breast cancer specimens with extensive residual disease, and analyzed by nCounter analysis for expression of >750 immune-related genes. Functional immune signature scores were generated, compared between matched pre- and post-NAC, and stratified by breast cancer molecular subtype (luminal (n=4), Her2-enriched (n=5), basal-like (n=17)). DNA extracted from a subset of these samples was utilized for T cell receptor sequencing to explore changes in T cell clonality following NAC in each subtype.

Results: Across all subtypes of breast cancer, immune scores decreased after NAC consistent with a broad decrease in TILs observed histologically. When samples were stratified by molecular subtype using the PAM50 analysis, luminal A/B and basal-like patients demonstrated a decrease in immune signatures after NAC, while Her2-enriched patients exhibited a global increase in immune scores. Importantly, basal-like patients had the greatest immune signature changes, including decreases in T cell functions and CD8+ T cell, T helper and T regulatory signatures (p>0.05). Conversely, these signatures were increased after NAC in the Her2-enriched molecular subtype. Analyses of T-cell clonality are ongoing, but should yield insight into the effect of NAC on the landscape of effector T-cells in the micro-environment.

Conclusions: Our work suggests that NAC decreases immune infiltrate signatures,</del> specifically related to effector T cells in patients who do not achieve pCR. However, we observed an increase after NAC in the same signatures in Her2-enriched patients, suggesting that these patients' tumors may respond differently to chemotherapy on the immune-molecular level. As clinical trials progress in TNBC with the combination of chemotherapy and immune therapy, more work is needed to understand who might benefit from these therapy regimens.

Citation Format: Hicks MJ, Estrada MV, Sanders ME, Salgado R, Cook RS, Arteaga CL, Balko JM. Differential effect of chemotherapy on immune gene expression signatures based on molecular subtype of breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-04-03.

Abstract P6-12-09: Pan-HER, an antibody mixture with antitumor activity against drug-resistant HER2-overexpressing breast cancers with high ERBB ligand expression

Background: Amplification/overexpression of ERBB receptors and/or ligands has been associated with resistance to anti-HER2 therapies. Pan-HER is a mixture of six antibodies targeting each of the ERBB receptors, EGFR, HER2 and HER3, with synergistic pairs of antibodies. Each pair of antibodies simultaneously blocks ligand binding and/or induces target degradation, thus preventing compensatory mechanisms to anti-ERBB therapies. We examined the antitumor activity of Pan-HER against drug-sensitive and -resistant HER2+ breast cancer cells and xenografts.

Results: Pan-HER exhibited potent growth inhibitory activity against a panel of HER2+ breast cancer cells (BT474, MDA-453, MDA-361, SUM190, HCC1954, UACC893 and SKBR3). Growth inhibition was associated with internalization and degradation of EGFR, HER2 and HER3. Pan-HER was superior to the combination of trastuzumab/pertuzumab (TP) against HER2+/PIK3CA mutant MDA-361, HCC1954, UACC893 and MDA-453 cells. We next compared the effect of Pan-HER against BT474, HCC1954 and MDA-361 xenografts established in nude mice to that of trastuzumab/lapatinib (TL), TP and T-DM1. All treatments were effective across the panel of xenografts. In mice with MDA-361 tumors, Pan-HER and TP were superior to TL. Immunoblot analysis showed significant downregulation of EGFR, HER2 and HER3 only in tumors treated with Pan-HER. After a complete response, treatment was discontinued. Among mice with BT474 xenografts treated with TP, TL and T-DM1, 25-50% of mice exhibited a tumor recurrence within 50 weeks of follow-up, while no recurrences were registered in mice treated with Pan-HER. Tumors recurring after TP and T-DM1 expressed significantly higher HER3 and P-HER3 protein levels and NRG1 mRNA levels. HCC1954 xenografts recurring after T-DM1 also overexpressed NRG1 mRNA compared to tumors before therapy.

We next examined the effect of Pan-HER against trastuzumab-resistant HR6 (BT474) cells (Ritter et al. CCR 2007) and HCC1954 and UACC893 cells with acquired resistance to T-DM1 (TDR; IC50 >5-, >6- and 600-fold in HR6, UACC893-TDR and HCC1954-TDR cells, respectively, vs. parental cells). All T-DM1-resistant cells expressed significantly higher HER3 and P-HER3 protein levels and NRG1 mRNA and protein levels. Treatment with the HER3 neutralizing antibody LJM716 resensitized HR6 and HCC1954-TDR cells to T-DM1, suggesting a causal association between the NRG1-HER3 axis and drug resistance. Mice with HR6 tumors were treated with Pan-HER, TL, TP and T-DM1. Only Pan-HER arrested HR6 tumor growth and downregulated EGFR, HER2, HER3, P-HER3 and P-AKT. Finally, HCC1954-TDR tumors rapidly grew in vivo despite treatment with T-DM1. Administration of Pan-HER to mice bearing HCC1954-TDR xenografts growing in the presence of T-DM1, induced rapid tumor regressions.

Conclusions: These data suggest that multitarget therapeutic interventions, such as Pan-HER, which simultaneously remove and/or block all ERBB receptors and ligands, are a feasible and effective approach against HER2-overexpressing cancers both sensitive and resistant to anti-HER2 therapies.

Citation Format: Schwarz LJ, Hutchinson KE, Estrada MV, Sanders ME, Dugger TC, Formisano L, Guerrero AL, Red-Brewer M, Young CD, Lantto J, Pedersen MW, Kragh M, Horak ID, Arteaga CL. Pan-HER, an antibody mixture with antitumor activity against drug-resistant HER2-overexpressing breast cancers with high ERBB ligand expression [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-12-09.

Abstract P6-10-02: MHC-II positive breast tumors are more immunogenic and may preferentially select for LAG-3-positive tumor immune infiltrates

Background: Lymphocyte-activation gene 3 (LAG-3) is a T-cell checkpoint regulator and a current target in immunotherapy trials. LAG-3's main ligand is MHC class II (MHC-II), to which it binds with higher affinity than CD4. Binding of LAG3 to MHC-II antigen-presenting cells negatively regulates cellular proliferation, activation, and homeostasis of T cells, similarly to CTLA-4 and PD-1, suggesting that antibodies targeting LAG-3 may demonstrate similar anti-tumor immune effects.

Hypothesis: We recently reported an association of MHC-II on tumor cells and its involvement in mediating sensitivity to PD-1/PD-L1 monoclonal antibodies. MHC-II demonstrates a strong bimodal expression pattern on tumor cells from a variety of tissues, including those of the breast. In breast cancer patients, tumor-specific MHC-II expression on TNBCs is correlated with a 'hot' immune environment. We hypothesized that 1) MHC-II expression may drive potent anti-tumor immune responses and 2) MHC-II-positive tumors that generate immunotolerance may develop a specific immune checkpoint dependency on LAG-3, since LAG-3 is the inhibitory receptor for MHC-II-mediated antigen presentation.

Methods: To determine the functionality of MHC-II in driving anti-tumor immune responses, we constitutively expressed the MHC-II master regulator CIITA in MMTV-neu mouse tumor cells and determined their ability to form tumors in immunocompetent syngeneic hosts. To evaluate the association of MHC-II+ tumors with LAG-3 expression, we evaluated LAG-3-positivity by immunohistochemistry (IHC) in lymphocytic infiltrates in a series of 111 post-NAC TNBC specimens from patients with residual disease remaining after presurgical chemotherapy. Tumor-infiltrating lymphocytes (TILs) were scored by H&E, PD-L1 and MHC-II (HLA-DR) were scored in the stroma and tumor compartments using automated quantitative immunofluorescence (AQUA).

Results: Enforced expression of MHC-II via constitutive expression of CIITA caused rejection in 60% of mice, while only 11% of mice rejected MMTV-neu tumors expressing the vector control (Fisher's exact p=0.04). All rejecting mice were immune to rechallenge with parental (non-CIITA-expressing) MMTV-neu cells, suggesting a memory effector response.

Clinically, 11/102 patients (10.8%) had LAG-3+ immune cells in their tumor. LAG-3+ tumors were strongly correlated with MHC-II positivity in tumor cells (p<0.0001). Presence of LAG-3+ cells also correlated strongly with overall TILs (p<0.0001), and PD-L1 expression on TILs (p<0.02). Since the likelihood of identifying LAG3+ lymphocytes is confounded by the inclusion of poorly-infiltrated tumors, we performed a subset analysis on only those tumors with substantial TILs (>20%). When this subset was analyzed, LAG-3 positivity retained its association with tumor MHC-II expression (p=0.0001), while the association of LAG-3 with stromal PD-L1 was reduced below the level of significance (p=0.052).

Conclusions: MHC-II expression causes increased immune activation in breast cancers, consistent with our previous findings. MHC-II positivity in breast tumors may identify a population with preferential dependence on the LAG-3 checkpoint, which may be important for future immunotherapy trials.

Citation Format: Balko JM, Loi S, Giltnane JM, Combs S, Estrada MV, Sanchez V, Rimm D, Sanders ME, Salgado R, Gomez H, Johnson DB. MHC-II positive breast tumors are more immunogenic and may preferentially select for LAG-3-positive tumor immune infiltrates [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-10-02.

Abstract P6-07-02: Targeted next generation sequencing of advanced breast cancers identifies potentially actionable alterations and variants of standard biomarkers in the majority of patients

Background: Molecular tumor profiling is increasingly important in the management of oncologic patients. Targeted next-generation sequencing (T-NGS), using formalin fixed paraffin embedded (FFPE) clinical samples, allows for molecular characterization of genes with known or potential therapeutic and prognostic importance in cancer. Actionable alterations include those with on- or off-label therapeutic implications, those that might be biomarkers of response to clinical trial agents, or those which are non-indicators for response.

Design: We correlated information on patients with metastatic or refractory locoregional recurrence of breast cancer (BC) with potentially actionable genetic alterations detected by a commercially available T-NGS assay, which sequences the coding regions of 315 genes and introns of 28 genes involved in rearrangements selected for their demonstrated role in solid malignancy. We developed an informatics pipeline to capture test results in real-time and store them for subsequent research analysis. Results were analyzed by clinical subtype (estrogen receptor positive [ER+]; HER-2 amplified [HER2+]; triple-negative [TN]) for actionable alterations, most frequently altered genes/pathways and variants of standard biomarkers not detected by routine studies.

Results: Between 11/2013 and 4/2015, 141 FFPE samples from 139 patients were tested by T-NGS. At least one potentially actionable genetic alteration was identified in 98% of patients (median 5.5 alterations/tumor [range 0-18]). 64% had alterations predicting sensitivity to approved BC therapies and 10% to approved therapies in other tumor types. An additional 1231 variants of uncertain significance (VUS) (median 9 per tumor [range 0-28]) were identified. The most frequently altered genes were TP53 (64%), PIK3CA (37%) and MYC (24%). Genes involved in cell cycle, DNA damage and PIK3CA/mTOR pathways were highly altered among all receptor subtypes. The RAS/MAPK pathway was more commonly altered in ER+ (28%) vs. HER2+ (13%) and TN (17%). CCND1 amplifications were found in 16% (57% ER+, 30% HER2+, 13% TN) and FGFR1 amplifications in 13% (61% ER+, 22% HER2, 17% TN). Co-amplification of 8p and 11q (including FGFR1/ZNF703 and CCND1/FGF3/FGF4/FGF19) was found in 28% of patients (ER+ 21%, HER2+ 25%, TN 7.5%). The combination of PIK3CA mutation and MAP3K1/MAP2K4 alteration occurred in 12% of patients (82% ER+, 18% TN). 4 ESR1 mutations and 2 amplifications (all in ER+) as well as 4 HER2 mutations (1 ER+ and 3 TN) were also identified. The number of patients receiving genotype-directed treatments informed by T-NGS results and patient outcome after genotype-directed treatment will be subsequently presented.

Conclusion: Mutation profiling using T-NGS identified potentially actionable alterations in a majority of advanced BC patients, providing novel yet rational therapeutic options and facilitating clinical trial enrollment. T-NGS results will be used to guide therapy in increasing numbers of BC patients.

Citation Format: Estrada MV, Warner J, Rioth M, Balko JM, Rexer B, Sanders ME. Targeted next generation sequencing of advanced breast cancers identifies potentially actionable alterations and variants of standard biomarkers in the majority of patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-07-02.