HER2-enriched subtype and novel molecular subgroups drive aromatase inhibitor resistance and an increased risk of relapse in early ER+/HER2+ breast cancer

BACKGROUND: Oestrogen receptor positive/ human epidermal growth factor receptor positive (ER+/HER2+) breast cancers (BCs) are less responsive to endocrine therapy than ER+/HER2- tumours. Mechanisms underpinning the differential behaviour of ER+HER2+ tumours are poorly characterised. Our aim was to identify biomarkers of response to 2 weeks’ presurgical AI treatment in ER+/HER2+ BCs. METHODS: All available ER+/HER2+ BC baseline tumours (n=342) in the POETIC trial were gene expression profiled using BC360™ (NanoString) covering intrinsic subtypes and 46 key biological signatures. Early response to AI was assessed by changes in Ki67 expression and residual Ki67 at 2 weeks (Ki672wk). Time-To-Recurrence (TTR) was estimated using Kaplan-Meier methods and Cox models adjusted for standard clinicopathological variables. New molecular subgroups (MS) were identified using consensus clustering. FINDINGS: HER2-enriched (HER2-E) subtype BCs (44.7% of the total) showed poorer Ki67 response and higher Ki672wk (p<0.0001) than non-HER2-E BCs. High expression of ERBB2 expression, homologous recombination deficiency (HRD) and TP53 mutational score were associated with poor response and immune-related signatures with High Ki672wk. Five new MS that were associated with differential response to AI were identified. HER2-E had significantly poorer TTR compared to Luminal BCs (HR 2.55, 95% CI 1.14–5.69; p=0.0222). The new MS were independent predictors of TTR, adding significant value beyond intrinsic subtypes. INTERPRETATION: Our results show HER2-E as a standardised biomarker associated with poor response to AI and worse outcome in ER+/HER2+. HRD, TP53 mutational score and immune-tumour tolerance are predictive biomarkers for poor response to AI. Lastly, novel MS identify additional non-HER2-E tumours not responding to AI with an increased risk of relapse

Started From the Egg, Now We’re Here: Examining the Development of Consistent Individual Variation in Growth and Behavior of Captive-Reared, Precocial Wood Ducks (Aix sponsa)

Individuals within a population often vary in the range and kind of behaviors that they exhibit. This variation, when consistent across time and/or context, has been termed animal personality. How and why consistent individual differences are maintained within populations when they have far-reaching fitness consequences remains a fundamental inquiry. Links between individual state and behavior have been hypothesized as an important component in the maintenance of this variation. Furthermore, understanding the development of consistent differences in state, behavior, and their relationship is of pivotal importance in addressing this question. With this dissertation we aimed to longitudinally examine the relationship between growth and personality across ontogeny in captive-reared Wood Ducks (Aix sponsa). In 2016 and 2017, we collected Wood Duck eggs from wild populations in the Central Valley of California and artificially incubated them at the University of California, Davis. We then reared hatched individuals in a controlled environment, collecting morphometric and behavioral data on a weekly basis using standardized assays. We found that individual differences in behaviors associated with sensitivity to predation risk (tonic immobility as well as activity, space-use, and response to a startling stimulus in a modified Open Field Test) remained relatively consistent across development. Repeatability of these behaviors qualitatively increased as ducklings aged while within-individual variance in behavioral expression decreased significantly, suggesting canalization. Duckling size also consistently varied and was significantly related to behavioral expression among-individuals, though the relationship was complex and age dependent. In a common garden setting, we found no evidence of feedback between size and behavior within-individuals as a driver of behavioral differentiation, suggesting that the observed variation in behaviors is not proximately driven by covariance with size during development. Experimentally increasing the perception of predation risk within the developmental environment significantly decreased size and growth rates as ducklings aged but had a limited effect on expression of select behaviors and their relationship with duckling size throughout ontogeny. Experimental treatments also appeared to generate negative feedback between a metric for Activity &amp; Space-use and body mass within-individuals, potentially leading to lowered repeatability and convergence of this behavioral type. Herein we discuss the methodology of measuring consistent individual differences in behavior, the possible causes of the relationships we discovered, the implications of our findings for Wood Ducks (a precocial waterfowl species), and the broader implications of our study for the understanding of personality, its development, and its ecological impacts.

3_WBC and IR

White blood cell counts with I

2_fledge with IR

Fledging success with IR

1_IR_observed vs. expected

#### 1. Observed vs. expected IR ### Data sheet includes obsetved and simulated (expected) values from both populations (NY and CA), given in 4 ways. #### (1) Adults in sample = known breeders (according to CERVUS) at Scale = Broad local scale #### (2-4) Adults in sample = All local adults at three different scales: Scale = Broad local scale, Intermediate local scale, and neighborhood scale. ### Analyses in the manuscript are run (1) with known breeders (according to CERVUS) at Scale = Broad local scale, and (2-4) at each of the three scales, using all local adults. #### All analyses are subsetted by population (CA or NY) and use the following model: model1<-lm(IR~Treatment) summary(model1

Code_MolEcol_Townsend et al 2018

Description of data files and associated cod

Data from: Apparent inbreeding preference despite inbreeding depression in the American crow

Although matings between relatives can have negative effects on offspring fitness, apparent inbreeding preference has been reported in a growing number of systems, including those with documented inbreeding depression. Here, we examined evidence for inbreeding depression and inbreeding preference in two populations (Clinton, New York and Davis, California, USA) of the cooperatively breeding American crow (Corvus brachyrhynchos). We then compared observed inbreeding strategies with theoretical expectations for optimal, adaptive levels of inbreeding, given the inclusive fitness benefits and population-specific magnitude of inbreeding depression. We found that low heterozygosity at a panel of 33 microsatellite markers was associated with low survival probability (fledging success) and low white blood cell counts among offspring in both populations. Despite these costs, our data were more consistent with inbreeding preference than avoidance: the observed heterozygosity among 396 sampled crow offspring was significantly lower than expected if local adults were mating by random chance. This pattern was consistent across a range of spatial scales in both populations. Theoretically adaptive levels of inbreeding, given the magnitude of inbreeding depression, were predicted to be very low in the California population, whereas complete disassociative mating was predicted in the New York population. Sexual conflict might have contributed to the apparent absence of inbreeding avoidance in crows. These data add to an increasing number of examples of an “inbreeding paradox,” where inbreeding appears to be preferred despite inbreeding depression