Tumor microenvironment and lymphocyte infiltration

There is ample evidence that the presence of tumor-infiltrating T lymphocytes is associated with a favorable prognostic in patients. These observations suggest that a limiting step to immune resistance and immunotherapy could be the capacity of tumor-specific T cells to reach tumor bed. In this article, we review some factors that may influence this infiltration, and in particular the nature of the vasculature, the expression of chemokines or tumor antigens and the presence of dendritic cells and CD4⁺ T lymphocytes.     

Tumor microenvironment: Interactions and therapy

Tumor microenvironment (TME) is a host for a complex network of heterogeneous stromal cells with overlapping or opposing functions depending on the dominant signals within this milieu. Reciprocal paracrine interactions between cancer cells with cells within the tumor stroma often reshape the TME in favor of the promotion of tumor. These complex interactions require more sophisticated approaches for cancer therapy, and, therefore, advancing knowledge about dominant drivers of cancer within the TME is critical for designing therapeutic schemes. This review will provide knowledge about TME architecture, multiple signaling, and cross communications between cells within this milieu, and its targeting for immunotherapy of cancer.     

Glioma progression is shaped by genetic evolution and microenvironment interactions

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Biological relevance of colony morphology and phenotypic switching by Burkholderia pseudomallei

Melioidosis is a notoriously protracted illness and is difficult to cure. We hypothesize that the causative organism, Burkholderia pseudomallei, undergoes a process of adaptation involving altered expression of surface determinants which facilitates persistence in vivo and that this is reflected by changes in colony morphology. A colony morphotyping scheme and typing algorithm were developed using clinical B. pseudomallei isolates. Morphotypes were divided into seven types (denoted I to VII). Type I gave rise to other morphotypes (most commonly type II or III) by a process of switching in response to environmental stress, including starvation, iron limitation, and growth at 42 degrees C. Switching was associated with complex shifts in phenotype, one of which (type I to type II) was associated with a marked increase in production of factors putatively associated with in vivo concealment. Isogenic types II and III, derived from type I, were examined using several experimental models. Switching between isogenic morphotypes occurred in a mouse model, where type II appeared to become adapted for persistence in a low-virulence state. Isogenic type II demonstrated a significant increase in intracellular replication fitness compared with parental type I after uptake by epithelial cells in vitro. Isogenic type III demonstrated a higher replication fitness following uptake by macrophages in vitro, which was associated with a switch to type II. Mixed B. pseudomallei morphologies were common in individual clinical specimens and were significantly more frequent in samples of blood, pus, and respiratory secretions than in urine and surface swabs. These findings have major implications for therapeutics and vaccine development.     

Parental effects and the evolution of phenotypic memory

Despite growing evidence for nongenetic inheritance, the ecological conditions that favour the evolution of heritable parental or grandparental effects remain poorly understood. Here, we systematically explore the evolution of parental effects in a patch‐structured population with locally changing environments. When selection favours the production of a mix of offspring types, this mix differs according to the parental phenotype, implying that parental effects are favoured over selection for bet‐hedging in which the mixture of offspring phenotypes produced does not depend on the parental phenotype. Positive parental effects (generating a positive correlation between parental and offspring phenotype) are favoured in relatively stable habitats and when different types of local environment are roughly equally abundant, and can give rise to long‐term parental inheritance of phenotypes. By contrast, unstable habitats can favour negative parental effects (generating a negative correlation between parental and offspring phenotype), and under these circumstances, even slight asymmetries in the abundance of local environmental states select for marked asymmetries in transmission fidelity.     

CTL-mediated selective pressure influences dynamic evolution and pathogenic functions of HIV-1 Nef

HIV-1 Nef plays multiple roles in modulating immune responses, even though it is a dominant CTL target itself. How Nef accomplishes the balance between such conflicting selective pressures remains elusive. By genetic and functional studies, we found that Arg75Thr and Tyr85Phe mutations, located in a well-conserved proline-rich region in Nef, were differently associated with escape from CTL responses specific for two overlapping HLA-B35-restricted epitopes. CTLs specific for an epitope, that selected Tyr85Phe, were elicited earlier and had more potent functional avidities than did those that selected Arg75Thr. Although the double mutant could escape from both CTLs, the mutations are rarely observed in combination naturally. Introduction of both mutations reduced Nef's HLA class I down-regulation activity and increased the susceptibility of virus-infected cells to recognition by CTLs targeting other epitopes. Moreover, the mutant Nef was impaired in the association with activated cellular kinases and in the enhancement of viral replication. These results highlight CTL immunosurveillance as important modulators of Nef's biological activity in the infected host.     

Chromosomal speciation and phenotypic evolution in the house mouse

Chromosomal races of the house mouse (Mus musculus domesticus) in Valtellina and Orobian Alps (Northern Italy) are known for their very fast raciation. Here we present a study using geometric morphometries on size and shape changes in the skull and the mandible of three races (Orobian, Upper Valtellina, Poschiavo) occurring in this area and forming a presumably monophyletic group. One of the races (Upper Valtellina) went extinct recently in an area of sympatry with the Poschiavo race, so that data on genetics (chromosomes and allozymes), behaviour and morphology were available to investigate causes of phenotypic divergence during speciation with a recent extinction event. The evaluation of partial warp scores and the uniform component shows that morphological changes have been fast and that these races can be recognized on the basis of skull shape. Patterns of evolution in shape changes were visualized by combining the chromosomal phylogeny and shape space, summarizing therefore both the phenetic and cladistic relationships. Shape changes follow the cladogenetic sequence depicted by chromosomal fusions. The examination of Procrustes distances shows that the different parts of the skull evolved at different rates after speciation, with shifts in the integration of the various structures (olfactory, auditory, feeding, visualization, etc.). Among the possible causes, aggressive behaviour was advocated for sudden changes in the shape of the skull.     

Induction of phenotypic plasticity in rattlesnake trophic morphology by diet manipulation

Gape‐limited predators are restricted in the shape and size of prey items they can ingest by their trophic morphology. Evolutionary theory predicts that gape‐limited predators, such as rattlesnakes, should possess plasticity in their trophic morphology to allow them to respond to environmental cues about their prey base. This study examined the effects of two possible influences over trophic morphology in the pit‐viper Crotalus viridis viridis. Snakes from six litters were exposed to diet manipulations performed over 480 days. By day 480, snakes from two prey‐size treatments exhibited significantly different head shapes. Snakes reared on whole rodents had broader heads, whereas snakes force‐fed homogenized prey had narrower heads. Shape differences varied among litters, suggesting that not all litters responded the same to diet manipulations. Results suggest that trophic morphology of rattlesnakes is plastic, at least in some litters, and can be induced by prey items. J. Morphol. 275:1339–1348, 2014. © 2014 Wiley Periodicals, Inc.     

Adaptation to marginal habitats by evolution of increased phenotypic plasticity

In an island population receiving immigrants from a larger continental population, gene flow causes maladaptation, decreasing mean fitness and producing continued directional selection to restore the local mean phenotype to its optimum. We show that this causes higher plasticity to evolve on the island than on the continent at migration-selection equilibrium, assuming genetic variation of reaction norms is such that phenotypic variance is higher on the island, where phenotypes are not canalized. For a species distributed continuously in space along an environmental gradient, higher plasticity evolves at the edges of the geographic range, and in environments where phenotypes are not canalized. Constant or evolving partially adaptive plasticity also alleviates maladaptation owing to gene flow in a heterogeneous environment and produces higher mean fitness and larger population size in marginal populations, preventing them from becoming sinks and facilitating invasion of new habitats. Our results shed light on the widely observed involvement of partially adaptive plasticity in phenotypic clines, and on the mechanisms causing geographic variation in plasticity.     

Adaptive evolution of reproductive and vegetative traits driven by breeding systems

The evolution of inflorescence size, a key trait in reproductive success, was studied in the genus Acer under a perspective of adaptive evolution. Breeding systems, hypothesized to indicate different levels of mating competition, were considered as the selective scenarios defining different optima of inflorescence size. Larger inflorescences, which increase male fitness by generating larger floral displays, were hypothesized to be selected under scenarios with higher competition with unisexuals. An identical approach was used to test if the same selective regimes could be driving the evolution of leaf size, a vegetative trait that was found to be correlated with inflorescence size. A Brownian motion model of inflorescence/leaf-size evolution (which cannot distinguish between changes caused by pure drift processes and changes caused by natural selection in rapidly and randomly changing environments) was compared with several adaptive Ornstein-Uhlenbeck (OU) models, which can quantify the effects of both stochasticity and natural selection. The best-fitting model for inflorescence/leaf-size evolution was an OU model with three optima that increased with the level of mating competition. Both traits evolved under the same selective regimes and in the same direction, confirming a pattern of correlated evolution. These results show that a selective regime hypothetically related to the evolution of a reproductive trait can also explain the evolution of a vegetative trait.     

Tumor microenvironment: the role of the tumor stroma in cancer

The tumor microenvironment, composed of non-cancer cells and their stroma, has become recognized as a major factor influencing the growth of cancer. The microenvironment has been implicated in the regulation of cell growth, determining metastatic potential and possibly determining location of metastatic disease, and impacting the outcome of therapy. While the stromal cells are not malignant per se, their role in supporting cancer growth is so vital to the survival of the tumor that they have become an attractive target for chemotherapeutic agents. In this review, we will discuss the various cellular and molecular components of the stromal environment, their effects on cancer cell dynamics, and the rationale and implications of targeting this environment for control of cancer. Additionally, we will emphasize the role of the bone marrow-derived cell in providing cells for the stroma.     

Assessing the impacts of phenotypic plasticity on evolution

In the past decade, there has been a resurgent interest in whether and how phenotypic plasticity might impact evolutionary processes. Of fundamental importance is how the environment influences individual phenotypic development while simultaneously selecting among phenotypic variants in a population. Conceptual and theoretical treatments of the evolutionary implications of plasticity are numerous, as are criticisms of the conclusions. As such, the time is ripe for empirical evidence to catch up with theoretical predictions. To this end, I provide a summary of eight hypotheses at the core of this issue, highlighting various approaches by which they can be tested. My goal is to provide practical guidance to those seeking to understand the complex ways by which phenotypic plasticity can influence evolutionary innovation and diversification.     

Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern

ABSTRACT: BACKGROUND: The photosynthetic oxygen-evolving photo system II (PS II) produces almost the entire oxygen in the atmosphere. This unique biochemical system comprises a functional core complex that is encoded by psbA and other genes. Unraveling the evolutionary dynamics of this gene is of particular interest owing to its direct role in oxygen production. psbA underwent gene duplication in leptosporangiates, in which both copies have been preserved since. Because gene duplication is often followed by the non-fictionalization of one of the copies and its subsequent erosion, preservation of both psbA copies pinpoint functional or regulatory specialization events. The aim of this study was to investigate the molecular evolution of psbA among fern lineages. RESULTS: We sequenced psbA, which encodes D1 protein in the core complex of PSII, in 20 species representing 8 orders of extant ferns; then we searched for selection and convolution signatures in psbA across the 11 fern orders. Collectively, our results indicate that: (1) selective constraints among D1 protein relaxed after the duplication in 4 leptosporangiate orders; (2) a handful positively selected codons were detected within species of single copy psbA, but none in duplicated ones; (3) a few sites among D1 protein were involved in co-evolution process which may intimate significant functional/structural communications between them. CONCLUSIONS: The strong competition between ferns and angiosperms for light may have been the main cause for a continuous fixation of adaptive amino acid changes in psbA, in particular after its duplication. Alternatively, a single psbA copy may have undergone bursts of adaptive changes at the molecular level to overcome angiosperms competition. The strong signature of positive Darwinian selection in a major part of D1 protein is testament to this. At the same time, species own two psbA copies hardly have positive selection signals among the D1 protein coding sequences. In this study, eleven co-evolving sites have been detected via different molecules, which may be more important than others.     

Adaptative evolution of the Vkorc1 gene in Mus musculus domesticus is influenced by the selective pressure of anticoagulant rodenticides

Anticoagulant rodenticides are commonly used to control rodent pests worldwide. They specifically inhibit the vitamin K epoxide reductase (VKORC1), which is an enzyme encoded by the Vkorc1 gene, involved in the recycling of vitamin K. Therefore, they prevent blood clotting. Numerous mutations of Vkorc1 gene were reported in rodents, and some are involved in the resistant to rodenticides phenotype. Two hundred and sixty‐six mice tails were received from 65 different locations in France. Coding sequences of Vkorc1 gene were sequenced in order to detect mutations. Consequences of the observed mutations were evaluated by the use of recombinant VKORC1. More than 70% of mice presented Vkorc1 mutations. Among these mice, 80% were homozygous. Contrary to brown rats for which only one predominant Vkorc1 genotype was found in France, nine missense single mutations and four double mutations were observed in house mice. The single mutations lead to resistance to first‐generation antivitamin K (AVKs) only and are certainly associated with the use of these first‐generation molecules by nonprofessionals for the control of mice populations. The double mutations, probably obtained by genetic recombination, lead to in vitro resistance to all AVKs. They must be regarded as an adaptive evolution to the current use of second‐generation AVKs. The intensive use of first‐generation anticoagulants probably allowed the selection of a high diversity of mutations, which makes possible the genetic recombination and consequently provokes the emergence of the more resistant mutated Vkorc1 described to date.