Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.

Purpose: Mitogen-activated protein kinase (MAPK) phosphatase-1 (MKP-1) dephosphorylates mitogen-activated protein kinase [extracellular signal-regulated kinase (ERK), c-Jun NH 2 -terminal kinase (JNK), and p38], mediates breast cancer chemoresistance, and is repressible by doxorubicin in breast cancer cells. We aimed to characterize doxorubicin effects on MKP-1 and phospho-MAPKs in human breast cancers and to further study the clinical relevance of MKP-1 expression in this disease. Experimental Design: Doxorubicin effects on MKP-1, phospho-ERK1/2 (p-ERK1/2), phospho-JNK (p-JNK), and phospho-p38 were assayed in a panel of human breast cancer cells by Western blot and in human breast cancer were assayed ex vivo by immunohistochemistry (n = 50). MKP-1 expression was also assayed in a range of normal to malignant breast lesions (n = 30) and in a series of patients (n = 96) with breast cancer and clinical follow-up. Results: MKP-1 was expressed at low levels in normal breast and in usual ductal hyperplasia and at high levels in in situ carcinoma. MKP-1 was overexpressed in ∼50% of infiltrating breast carcinomas. Similar to what was observed in breast cancer cell lines, ex vivo exposure of breast tumors to doxorubicin down-regulated MKP-1, and upregulated p-ERK1/2 and p-JNK, in the majority of cases. However, in a proportion of tumors overexpressing MKP-1, doxorubicin did not significantly affect MKP-1 or phospho-MAPKs. With regard to patient outcome, MKP-1 overexpression was an adverse prognostic factor for relapse both by univariate (P < 0.001) and multivariate analysis (P = 0.002). Conclusions: MKP-1 is overexpressed during the malignant transformation of the breast and independently predicts poor prognosis. Furthermore, MKP-1 is repressed by doxorubicin in many human breast cancers.

The NFκB family is composed by five subunits (p65/RelA, c-Rel, RelB, p105-p50/ NFκB 1 , p100-p52/NFκB 2 ) and controls the expression of many genes that participate in cell cycle, apoptosis, and other key cellular processes. In a canonical pathway, NFκB activation depends on the IKK complex activity, which is formed by three subunits (IKKa and IKKb and IKKg/NEMO). There is an alternative NFκB activation pathway that does not require IKKb or IKKg/NEMO, in which RelB is a major player. We report in a panel of human breast cancer cells that the IKK/NFκB system is generally overexpressed in breast cancer cells and there is heterogeneity in expression levels of individual members between different cell lines. Doxorubicin, an anticancer agent used in patients with breast cancer, activated NFκB and appeared to be less effective in cells expressing predominantly members of the canonical IKK/NFκB. Two NFκB inhibitors, bortezomib and NEMO-Binding Domain Inhibitory Peptide, prevented doxorubicin-induced NFκB activation and increased doxorubicin antitumor effects in BT-474 cells. Transient down-regulation of members of the canonical pathway (p65, p52, c-Rel and IKKg/ NEMO) by siRNA in HeLa cells increased doxorubicin cytotoxicity. In contrast, silencing of RelB, a key subunit of the alternative pathway, had no evident effects on doxorubicin cytotoxicity. To conclude, NFκB inhibition sensitized cells to doxorubicin, implying directly p65, p52, c-Rel and IKKg/NEMO subunits in chemoresistance, but not RelB. These findings suggest that selective inhibition of the canonical NFκB pathway is sufficient to improve doxorubicin antitumor effects.

35Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores 36 worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we 37 present the genome and metabolic network of the closely related species, Ectocarpus subulatus 38Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains 39show new traces of viral sequences and the activity of large retrotransposons, which may also be 40 related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to 41 contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of 42 genes involved in the production of halogenated defence compounds, and the presence of fewer cell 43 wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene 44 families down-regulated in low salinities, and conserved those that were up-regulated in the same 45 condition. However, 96% of genes that differed between the two examined Ectocarpus species, as 46 well as all genes under positive selection, were found to encode proteins of unknown function. This 47 Organellar genomes 131 Plastid and mitochondrial genomes from E. subulatus have 95.5% and 91.5% sequence identity with 132 their Ectocarpus sp. Ec32 counterparts in the conserved regions respectively. Only minor structural 133 differences were observed between organellar genomes of both Ectocarpus genomes, as detailed in 134Supporting Information Text S1. 135

Background:NF-κB signalling appears deregulated in breast tumours. The purpose of this study was to determine whether the non-canonical NF-κB pathway, is activated in oestrogen receptor positive (ER+) breast cancer, to identify any correlation between its activity and the clinico-pathological phenotype and to explore whether NF-κB2 and RelB subunits and/or any of their target genes might be used as a predictive marker.Methods:Two independent cohorts of ER+ early breast cancer patients treated with adjuvant endocrine therapy were included in the study. Activation of RelB and NF-κB2 subunits was determined in a training set of 121 patients by measuring DNA-binding activities in nuclear extracts from fresh frozen specimens by an ELISA-based assay. Samples of 15 ER− breast cancer patients were also included in the study. In a large validation cohort of 207 patients, nuclear immunostaining of RelB and NF-κB2 on formalin-fixed paraffin-embedded specimens was performed. Statistical correlation within clinico-pathological factors, disease-free survival (DFS) and overall survival (OS) was evaluated. Publicly available gene expression and survival data have been interrogated aimed to identify target genes.Results:Activation of NF-κB2 and RelB was found in 53.7 and 49.2% of the 121 ER+ tumours analysed, with similar levels to ER− breast tumours analysed in parallel for comparisons. In the validation cohort, we obtained a similar proportion of cases with activation of NF-κB2 and RelB (59.9 and 32.4%), with a 39.6% of co-activation. Multiplexing immunofluorescence in breast cancer tissue confirmed an inverse spatial distribution of ER with NF-κB2 and RelB nuclear expression in tumour cells. Interestingly, NF-κB2 and RelB mRNA expression was inversely correlated with ER gene (ESR1) levels (P<0.001, both) and its activation was significantly associated with worse DFS (P=0.005 and P=0.035, respectively) in ER+ breast cancer. Moreover, the co-activation of both subunits showed a stronger association with early relapse (P=0.002) and OS (P=0.001). Finally, higher expression of the non-canonical NF-κB target gene myoglobin was associated with a poor outcome in ER+ breast cancer (DFS, P<0.05).Conclusions:The non-canonical NF-κB pathway activation is inversely associated with oestrogen receptor expression in ER+ breast cancer and predicts poor survival in this subgroup. The myoglobin gene expression has been identified as a possible surrogate marker of the non-canonical NF-κB pathway activation in these tumours.

35Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores 36 worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we 37 present the genome and metabolic network of the closely related species, Ectocarpus subulatus 38Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains 39show new traces of viral sequences and the activity of large retrotransposons, which may also be 40 related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to 41 contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of 42 genes involved in the production of halogenated defence compounds, and the presence of fewer cell 43wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene 44 families down-regulated in low salinities, and conserved those that were up-regulated in the same 45 condition. However, 96% of genes that differed between the two examined Ectocarpus species, as 46 well as all genes under positive selection, were found to encode proteins of unknown function. This 47 underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of 48 establishing E. subulatus as a comparative model for future functional studies. 49 50 Organellar genomes 131 Plastid and mitochondrial genomes from E. subulatus have 95.5% and 91.5% sequence identity with 132 their Ectocarpus sp. Ec32 counterparts in the conserved regions respectively. Only minor structural 133 differences were observed between organellar genomes of both Ectocarpus genomes, as detailed in 134Supporting Information Text S1. 135