Candidate Luminal B Breast Cancer Genes Identified by Genome,Gene Expression and DNA Methylation Profiling

Breast cancers (BCs) of the luminal B subtype are estrogen receptor-positive (ER+), highly proliferative, resistant to standard therapies and have a poor prognosis. To better understand this subtype we compared DNA copy number aberrations (CNAs), DNA promoter methylation, gene expression profiles, and somatic mutations in nine selected genes, in 32 luminal B tumors with those observed in 156 BCs of the other molecular subtypes. Frequent CNAs included 8p11-p12 and 11q13.1-q13.2 amplifications, 7q11.22-q34, 8q21.12-q24.23, 12p12.3-p13.1, 12q13.11-q24.11, 14q21.1-q23.1, 17q11.1-q25.1, 20q11.23-q13.33 gains and 6q14.1-q24.2, 9p21.3-p24,3, 9q21.2, 18p11.31-p11.32 losses. A total of 237 and 101 luminal B-specific candidate oncogenes and tumor suppressor genes (TSGs) presented a deregulated expression in relation with their CNAs, including 11 genes previously reported associated with endocrine resistance. Interestingly, 88% of the potential TSGs are located within chromosome arm 6q, and seven candidate oncogenes are potential therapeutic targets. A total of 100 candidate oncogenes were validated in a public series of 5,765 BCs and the overexpression of 67 of these was associated with poor survival in luminal tumors. Twenty-four genes presented a deregulated expression in relation with a high DNA methylation level. FOXO3, PIK3CA and TP53 were the most frequent mutated genes among the nine tested. In a meta-analysis of next-generation sequencing data in 875 BCs, KCNB2 mutations were associated with luminal B cases while candidate TSGs MDN1 (6q15) and UTRN (6q24), were mutated in this subtype. In conclusion, we have reported luminal B candidate genes that may play a role in the development and/or hormone resistance of this aggressive subtype.     

The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes

Bacterial pathogens typically infect only a limited range of hosts; however, the genetic mechanisms governing host-specificity are poorly understood. The α-proteobacterial genus Bartonella comprises 21 species that cause host-specific intraerythrocytic bacteremia as hallmark of infection in their respective mammalian reservoirs, including the human-specific pathogens Bartonella quintana and Bartonella bacilliformis that cause trench fever and Oroya fever, respectively. Here, we have identified bacterial factors that mediate host-specific erythrocyte colonization in the mammalian reservoirs. Using mouse-specific Bartonella birtlesii, human-specific Bartonella quintana, cat-specific Bartonella henselae and rat-specific Bartonella tribocorum, we established in vitro adhesion and invasion assays with isolated erythrocytes that fully reproduce the host-specificity of erythrocyte infection as observed in vivo. By signature-tagged mutagenesis of B. birtlesii and mutant selection in a mouse infection model we identified mutants impaired in establishing intraerythrocytic bacteremia. Among 45 abacteremic mutants, five failed to adhere to and invade mouse erythrocytes in vitro. The corresponding genes encode components of the type IV secretion system (T4SS) Trw, demonstrating that this virulence factor laterally acquired by the Bartonella lineage is directly involved in adherence to erythrocytes. Strikingly, ectopic expression of Trw of rat-specific B. tribocorum in cat-specific B. henselae or human-specific B. quintana expanded their host range for erythrocyte infection to rat, demonstrating that Trw mediates host-specific erythrocyte infection. A molecular evolutionary analysis of the trw locus further indicated that the variable, surface-located TrwL and TrwJ might represent the T4SS components that determine host-specificity of erythrocyte parasitism. In conclusion, we show that the laterally acquired Trw T4SS diversified in the Bartonella lineage to facilitate host-restricted adhesion to erythrocytes in a wide range of mammals.     

Naturally recruited herbaceous vegetation in abandoned Belgian limestone quarries: towards habitats of conservation interest analogues?

We examined if naturally recruited herbaceous vegetation in abandoned Belgian limestone quarries tend towards plant communities analogous to semi-natural habitats of conservation interest. We studied taxon-based assemblages (using two-dimensional non-metric multidimensional scaling ordination) and functional patterns (relative to Grime’s competitor, stress tolerator and ruderal plant strategies (CSR) classification) of plant communities (n = 360 plots) among three different time periods after quarry abandonment (< 3 y, 3–20 y, >?20 y). We compared those successional assemblages with those of habitat of conservation interest plant communities (n = 53 plots): lowland hay meadows and rupicolous, xerophilous and mesophilous calcareous grasslands. Our results indicate that naturally recruited herbaceous vegetation compositionally resembled mesophilous grassland, even though initial substrate conditions were more similar to rupicolous or xerophilous grasslands. The specific successional pathway we found in CSR state-space differs from Grime's predictions because there was a functional shift in plant assemblages from dominance by ruderals to dominance by stress-tolerant species. The differences in successional trajectories we found on different types of rock substrate suggest that conservation management should adopt a site-specific approach, recognizing that the highest probabilities of success on hard limestone will be restoration to calcareous grassland analogues.     

Interactions between land use,habitat use,and population increase in greater snow geese: what are the consequences for natural wetlands?

The North American greater snow goose population has increased dramatically during the last 40 years. We evaluated whether refuge creation, changes in land use on the wintering and staging grounds, and climate warming have contributed to this expansion by affecting the distribution, habitat use, body condition, and migration phenology of birds. We also reviewed the effects of the increasing population on marshes on the wintering grounds, along the migratory routes and on the tundra in summer. Refuges established before 1970 may have contributed to the initial demographic increase. The most important change, however, was the switch from a diet entirely based on marsh plants in spring and winter (rhizomes of Scirpus/Spartina) to one dominated by crops (corn/young grass shoots) during the 1970s and 1980s. Geese now winter further north along the US Atlantic coast, leading to reduced hunting mortality. Their migratory routes now include portions of southwestern Québec where corn production has increased exponentially. Since the mid‐1960s, average temperatures have increased by 1–2.4°C throughout the geographic range of geese, which may have contributed to the northward shift in wintering range and an earlier migration in spring. Access to spilled corn in spring improved fat reserves upon departure for the Arctic and may have contributed to a high fecundity. The population increase has led to intense grazing of natural wetlands used by geese although these habitats are still largely undamaged. The foraging in fields allowed the population to exceed limits imposed by natural marshes in winter and spring, but also prevented permanent damage because of their overgrazing.     

Effects of 5'deoxy-5'-methylthioadenosine on the metabolism of S-adenosyl methionine

The treatment of transformed rat cells with micromolar amounts of 5'deoxy 5'methyl thioadenosine induces rapid effects on the rate of methylation of DNA concomitantly with alterations of intracellular pools of S-adenosyl methionine and S-adenosyl homocysteine. Pulse chase labelling experiments indicate that 5'deoxy 5'methylthioadenosine does not inhibit the degradation of S-adenosyl homocysteine but inhibits the consumption of S-adenosyl methionine. In vitro transmethylation assays performed with heterologous DNA show that low doses of the thioethernucleoside do not significantly affect the DNA methyltransferase activity of cellular extracts. The biological role of 5'deoxy 5'methylthioadenosine, a natural molecule formed during the synthesis of polyamines is discussed.