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PDF file, 36K, Number of risk allele carriers.

Background: Heritable risk for breast cancer includes an increasing number of common, low effect risk variants. We conducted a multistage genetic association study in a series of independent epidemiologic breast cancer study populations to identify novel breast cancer risk variants.Methods: We tested 1,162 SNPs of greatest nominal significance from stage I of the Cancer Genetic Markers of Susceptibility breast cancer study (CGEMS; 1,145 cases, 1,142 controls) for evidence of replicated association with breast cancer in the Nashville Breast Cohort (NBC; 599 cases, 1,161 controls), the Collaborative Breast Cancer Study (CBCS; 1,552 cases, 1,185 controls), and BioVU Breast Cancer Study (BioVU; 1,172 cases, 1,172 controls).Results: Among these SNPs, a series of validated breast cancer risk variants yielded expected associations in the study populations. In addition, we observed two previously unreported loci that were significantly associated with breast cancer risk in the CGEMS, NBC, and CBCS study populations and had a consistent, although not statistically significant, risk effect in the BioVU study population. These were rs1626678 at 10q25.3 near ENO4 and KIAA1598 (meta-analysis age-adjusted OR = 1.13 [1.07–1.20], P = 5.6 × 10−5), and rs8046508 at 16q23.1 in the eighth intron of WWOX (meta-analysis age-adjusted OR = 1.20 [1.10–1.31], P = 3.5 × 10−5).Conclusions: Our data supports the association of two novel loci, at 10q25.3 and 16q23.1, with risk of breast cancer.Impact: The expanding compendium of known breast cancer genetic risk variants holds increasing power for clinical risk prediction models of breast cancer, improving upon the Gail model. Cancer Epidemiol Biomarkers Prev; 21(9); 1565–73. ©2012 AACR.

Supplementary Table 1 from A Multistage Association Study Identifies a Breast Cancer Genetic Locus at NCOA7

Supplementary Table 2 from A Multistage Association Study Identifies a Breast Cancer Genetic Locus at NCOA7

Supplementary Figure 1 from A Multistage Association Study Identifies a Breast Cancer Genetic Locus at NCOA7

Estrogen metabolism and growth factor signaling pathway genes play key roles in breast cancer development. We evaluated associations between breast cancer and tagging single-nucleotide polymorphisms (SNP) of 107 candidate genes of these pathways using single allele- and haplotype-based tests. We first sought concordance of associations between two study populations: the Nashville Breast Cohort (NBC; 510 cases, 988 controls), and the Cancer Genetic Markers of Susceptibility (CGEMS) breast cancer study (1,145 cases, 1,142 controls). Findings across the two study populations were concordant at tagging SNPs of six genes, and at previously published SNPs of FGFR2. We sought further replication of results for EGFR, NCOA7, and FGFR2 in the independent Collaborative Breast Cancer Study (CBCS; 1,552 cases, 1,185 controls). Associations at NCOA7 and FGFR2 replicated across all three studies. The association at NCOA7 on 6q22.32, detected by a haplotype spanning the initial protein-coding exon (5′-rs9375411, rs11967627, rs549438, rs529858, rs490361, rs17708107-3′), has not been previously reported. The haplotype had a significant inverse association with breast cancer in each study [ORHet: 0.69 (NBC), 0.76 (CGEMS), 0.79 (CBCS)], and a meta-analysis ORHet of 0.75 (95% CI, 0.65–0.87, P = 1.4 × 10−4) in the combined study populations. The haplotype frequency was 0.07 among cases, and 0.09 among controls; homozygotes were infrequent and each ORHom was not significant. NCOA7 encodes a nuclear receptor coactivator that interacts with estrogen receptor α to modulate its activity. These observations provide consistent evidence that genetic variants at the NCOA7 locus may confer a reduced risk of breast cancer. Cancer Res; 71(11); 3881–8. ©2011 AACR.

The aim of this professional Doctor of Creative Industries (DCI) Research Project was to investigate music-making practice and self as a practitioner in the process of creating and producing a DIY music artefact, specifically to investigate why I as the practitioner felt an authentic connection with one form of music-making (acoustic instrument-based) and not a connection with another form of music-making (digital virtual-based). As a phenomenologist, I situated self into this auto-ethnographic study in the dual roles of researcher and practitioner, developing first-person narratives of my personal journey, critical reflection, and reflexive practice. The holistic and multidimensional nature of this research has provided rich and nuanced data, illuminating the co-constituted nature of self, interpreting meaning, and practice. In particular, the research study contextualizes contemporary DIY creative practice relative to three interdependent tenets: Music & Sound-making practice, meaning-making, and self-making, where these tenets are understood in terms of hybridity, agency, and subjectivity. The emergent cultural production artefact exemplifies a broader interpretation of Music & Sound-making practice: an authentic, subjective, auto-ethnographic Music & Soundscape.

Understanding and exploiting topographical data via standard machine learning techniques is challenging, mainly due to the large dynamic range of values present in elevation data and the lack of direct relationships between anthropogenic phenomena and topography, when considering topographic–geology couplings, for instance. Here we consider the first hurdle, dynamic range, in an effort to apply Convolutional Neural Network (CNN) approaches for prediction of human activity. CNN for learning 3-D elevation data relies on data normalization approaches, which only consider locally available points, thereby discarding contextual information and eliminating global contrast cues. We present a fully invertible and data-driven global partitioning elevation normalization (GPEN) preprocessing technique, which is intended to ameliorate the impact of limited data dynamic range. Global elevation populations are derived and used to formulate a distribution, which is used to adopt a partitioning scheme to remap all values according to global occurrence frequency, while preserving partition contrast. Using USGS 3-D Elevation Project and Microsoft building footprint data, we conduct a binary classification experiment predicting building footprint presence from elevation data, with and without a global remapping using the SegNet convolutional encoder-decoder model. The results of the experiment show more rapid model convergence, reduced regionalization errors, and enhanced classification metrics when compared to standard normalization preprocessing techniques. GPEN demonstrates performance over 10% higher than the next best conventional preprocessing method, with a mean overall accuracy of 94.76%. GPEN may show promise as an alternative normalization for deep learning with topological data.

Purpose of Review Immunotherapy is emerging as an effective treatment option for metastatic triple-negative breast cancer. In this review, we summarize clinical data of immunotherapy in triple-negative breast cancer and comment on future directions in the field. Recent Findings IMpassion130 was a phase III trial that demonstrated progression-free survival benefit, and potentially overall survival benefit, of first-line chemotherapy (nab-paclitaxel) plus anti-programmed death ligand 1 (PD-L1) atezolizumab, among PD-L1-positive metastatic triple-negative breast cancers. Studies are ongoing to evaluate other combination therapies with immune checkpoint blockade in TNBC, and to evaluate efficacy in PD-L1-negative tumors and in later lines of therapy. Summary Immunotherapy is now a standard option in the treatment of triple-negative breast cancer. Ongoing trials may expand the degree of clinical benefit. Further work is ongoing to identify novel predictive biomarkers, which in the future may enable a personalized approach of combination immunotherapy.

BackgroundPembrolizumab plus curative-intent dose-dense anthracycline-based chemotherapy (ddAC) is associated with improved outcome in PD-L1-negative TNBC,1 whereas in the metastatic setting, clinical benefit of chemoimmunotherapy (taxane or gemcitabine/carboplatin) is restricted to PD-L1-positive patients.2 We hypothesize that this discordance could be related to immunomodulatory differences of the various chemotherapies. On-treatment serial monitoring of peripheral blood and tumoral T cells can be used to compare the effects of various regimens. We also hypothesize that T cell clonal expansion may differ across the regimens, and that tumor-enriched T cell clones are more likely to be tumor-reactive and expand following chemoimmunotherapy.MethodsBlood and tumor samples were collected from patients enrolled in a phase Ib clinical trial of palliative pembrolizumab and paclitaxel or capecitabine for metastatic TNBC, and from a contemporaneous cohort of patients treated with ddAC. T-cells were characterized using fresh whole blood flow cytometry and T-cell receptor (TCR) immunosequencing (immunoSEQ, Adaptive Biotechnologies) of DNA digests. Longitudinal regression was used to test the hypothesis that tumor-enriched T-cell clonotypes are more likely to expand in peripheral blood following therapy.ResultsWhen combined with pembrolizumab, paclitaxel versus capecitabine had similar effects on T-cells, resulting in a time-dependent lymphodepletion across all major T cell subsets (average CD3+ T cell fold-change capecitabine: -0.42, paclitaxel: -0.56, p = 0.80 t-test), whereas ddAC was associated with more profound lymphodepletion (CD3+ average fold-change: -1.21). Notably, ddAC was associated with higher odds of novel clonotype detection compared to capecitabine (odds ratio (OR): 3.42, 95% CI: 3.34–3.5) as well as compared to paclitaxel (OR: 1.53, 95% CI: 1.47–1.60). Significant expansion of tumoral clonotypes occurred in five patients receiving chemoimmunotherapy (average 4.2 unique clonotypes per patient, range 2–11). These clonotypes did not significantly expand over time in the blood. Similarly, T-cell clonotypes that were enriched within tumor did not exhibit measurable differences in serial trend within the peripheral blood.ConclusionsEffects to T cell subsets and clonotypes are similar between capecitabine and paclitaxel when combined with pembrolizumab. ddAC was more profoundly lymphotoxic, but resulted in greater clonotype expansion. These findings offer mechanistic insight onto the differences in clinical activity observed with chemoimmunotherapy in early stage versus metastatic TNBC. We observed no strong association between tumor clonotype enrichment and peripheral clonotype expansion, highlighting the unmet need to develop methods of monitoring tumor-reactive T cell clones in the context of immunotherapy.AcknowledgementsThe authors would like to acknowledge collaborators at the Earle A. Chiles Research Institute and Adaptive Biotechnologies for mentorship and guidance. Support for the clinical trial (NCT02734290), which comprised the metastatic cohort was provided by Merck and the Providence Opportunity Fund. Laboratory services were provided at no cost by Adaptive BiotechnologiesTrial RegistrationNCT02734290ReferencesSchmid P, Cortes J, Pusztai L, et al. Pembrolizumab for early triple-negative breast cancer. N Engl J Med 2020 Feb 27;382(9):810–821. doi: 10.1056/NEJMoa1910549.Cortes J, Cescon DW, Rugo HS, et al. Pembrolizumab plus chemotherapy versus placebo plus chemotherapy for previously untreated locally recurrent inoperable or metastatic triple-negative breast cancer (KEYNOTE-355): a randomised, placebo-controlled, double-blind, phase 3 clinical trial. Lancet 2020;396(10265):1817–1828. doi:10.1016/S0140-6736(20)32531-9Ethics ApprovalAll patients provided written, informed consent. The study protocols for the collection of specimens from the early-stage breast cancer cohort and from the metastatic TNBC clinical trial were separately approved by independent review boards at Providence Portland Medical Center and Cedars Sinai Medical Center (mTNBC clinical trial only).

BackgroundIt has previously been shown that immune checkpoint blockade (ICB) with anti-programmed death 1/ligand 1 (anti-PD-1/L1) improves survival when combined with chemotherapy in PD-L1-positive first-line triple-negative metastatic breast cancer (MBC). Given the lower efficacy of ICB in hormone receptor positive (HR+) or PD-L1-negative disease, and in later lines of therapy, novel combinations are necessary. Dual ICB with nivolumab (anti-PD-1) and ipilimumab (anti-CTLA-4) has shown success in other solid tumors but has not been extensively studied in MBC. Furthermore, MBCs often express the androgen receptor (AR), which can be targeted to modulate immune response. AR blockade may stimulate thymic production of naïve T-cell clones by modulating the Notch pathway,1 whereas ICB can amplify the immune activity of recent thymic emigrants by blocking PD-1-mediated peripheral tolerance.2MethodsThis is an open-label, Simon 2-stage phase II trial investigating the dual ICB (nivolumab 240mg IV q2w; ipilimumab 1mg/kg IV q6w) and AR blockade (bicalutamide, 150mg PO daily) in MBC. Two cohorts will be studied: AR-positive TNBC [ > 1% by IHC, constituting ~50% of TNBCs]; and HR+ MBC (of which the great majority are AR-positive). Eligible patients must have RECIST1.1 measurable disease, Eastern Cooperative Oncology Group performance score 0 or 1, adequate hematological/hepatic function, and received no more than 1 prior course of non-curative chemotherapy. Target accrual is n=15 per arm (stage I), with a maximum of 46 patients per cohort. Current cohort accrual n=15 HR+ and n=5 TNBC. The primary endpoint is week 24 clinical benefit by iRECIST criteria, with success defined as >20% improvement over historical control (30% per EMBRACE clinical trial).3 Safety will be evaluated by CTCAE v4.0. Biomarkers of recent thymic activation will be evaluated via quantitative deep sequencing of T-cell receptors (TcR, ImmunoSEQ assay), TcR excision circles (TRECs), and flow cytometry using markers for recent thymic emigration (CD3+CD45RA+CD45RO-CD31+)Trial RegistrationNCT03650894. The trial is open at Providence Cancer Institute (Portland, OR) and Memorial Sloan Kettering Cancer Center (New York, NY).ReferencesVelardi E, Tsai JJ, Holland AM, et al. Sex steroid blockade enhances thympoesis modulating notch signaling. J Exp Med 2014;211(12):2341–49.Thangavelu G, Parkman JC, Ewen CL, et al. Programmed death-1 is required for systemic self-tolerance in newlygenerated T cells during the establishment of immune homeostasis. Journal of autoimmunity 2011;36(3–4):301–12.Kaufman PA, Awada A, Twevles C, et al. Phase III open-label randomized study of eribulin mesylate versus capecitabine in patients with locally advanced or metastatic breast cancer previously treated with an anthracycline and a taxane. J Clin Oncol 2015;33(6):594–601.Ethics ApprovalThis study was approved by the IRB department and Providence Portland Medical Center, Clinical Trials Department for study NCT03650894.ConsentWritten, informed consent is obtained from each participant.