Distinct profiles of cytotoxic granules in memory CD8 T cells correlate with functions, differentiation stage, and antigen exposure

RAPPORT DE SYNTHÈSE : Les profils des granules cytotoxiques des cellules T CD8 mémoires sont corrélés à la fonction, à leur état de différentiation et à l'exposition à l'antigène. Les lymphocytes T-CD8 cytotoxiques exercent leur fonction antivirale et antitumorale surtout par la sécrétion des granules cytotoxiques. En général, ce sont l'activité de dégranulation et les granules cytotoxiques (contenant perforine et différentes granzymes) qui définissent les lymphocytes T-CD8 cytotoxiques. Dans cette étude, nous avons investigué l'expression de granzyme K par cytométrie en flux, en comparaison avec l'expression de granzyme A, granzyme B et de perforine. L'expression des granules cytotoxiques a été déterminée dans lymphocytes T-CD8 qui étaient spécifiques pour des différents virus, en particulier spécifique pour le virus d'influenza (flu), le virus Ebstein Barr (EBV), le virus de cytomégalie (CMV) et le virus de l'immunodéficience humaine (HIV). Nous avons observé une dichotomie entre l'expression du granzyme K et de la perforine dans les lymphocytes T-CD8 qui étaient spécifiques aux virus mentionnés. Les profils des lymphocytes T-CD8 spécifiques à flu étaient positifs soit pour granzyme A et granzyme K soit pour le granzyme K seul, mais dans l'ensemble négatifs pour perforine et granzyme B. Les cellules spécifiques à CMV étaient dans la plupart positives pour perforine, granzyme B et A, mais négatives pour le granzyme K. Les cellules spécifiques à EBV et HIV étaient dans la majorité positives pour granzyme A, B et K, et dans la moitié des cas négatives pour la perforine. Nous avons également analysé, selon les marqueurs de mémoire de CD45 et CD127, les profils de différentiation cellulaire: Les cellules avec les granules cytotoxiques contenant exclusivement le granzyme K, étaient associées à un état de différentiation précoce. Au contraire, les protéines cytolytiques perforine, granzyme A et B, correspondent à une différentiation avancée. En outre, les protéines perforine et granzyme B, mais pas les granzymes A et K, sont corrélées à une activité cytotoxique. Finalement, des changements dans l'exposition d'antigène in vitro et in vivo suivant une infection primaire d' HIV ou une vaccination modulent le profil de granules cytotoxiques. Ces résultats nous permettent d'étendre la compréhension de la relation entre les différents profils de granules cytotoxiques des lymphocytes T-CD8 et leur fonction, leur état de différentiation et l'exposition à l'antigène.

Fourier transform convolution integrals applied to generalized Born molecular volume.

Generalized Born methods are currently among the solvation models most commonly used for biological applications. We reformulate the generalized Born molecular volume method initially described by (Lee et al, 2003, J Phys Chem, 116, 10606; Lee et al, 2003, J Comp Chem, 24, 1348) using fast Fourier transform convolution integrals. Changes in the initial method are discussed and analyzed. Finally, the method is extensively checked with snapshots from common molecular modeling applications: binding free energy computations and docking. Biologically relevant test systems are chosen, including 855-36091 atoms. It is clearly demonstrated that, precision-wise, the proposed method performs as good as the original, and could better benefit from hardware accelerated boards.

Peroxisome proliferator-activated receptors: three isotypes for a multitude of functions.

The peroxisome proliferator-activated receptors (PPARs) are fatty acid and eicosanoid inducible nuclear receptors, which occur in three different isotypes. Upon activator binding, they modulate the expression of various target genes implicated in several important physiological pathways. During the past few years, the identification of both PPAR ligands, natural and synthetic, and PPAR targets and their associated functions has been one of the most important achievements in the field. It underscores the potential therapeutic application of PPAR-specific compounds on the one side, and the crucial biological roles of endogenous PPAR ligands on the other.

Ex vivo characterization of human CD8+ T subsets with distinct replicative history and partial effector functions.

After antigenic challenge, naive T lymphocytes enter a program of proliferation and differentiation during the course of which they acquire effector functions and may ultimately become memory cells. In humans, the pathways of effector and memory T-cell differentiation remain poorly defined. Here we describe the properties of 2 CD8+ T-lymphocyte subsets, RA+CCR7-27+28+ and RA+CCR7-27+28-, in human peripheral blood. These cells display phenotypic and functional features that are intermediate between naive and effector T cells. Like naive T lymphocytes, both subsets show relatively long telomeres. However, unlike the naive population, these T cells exhibit reduced levels of T-cell receptor excision circles (TRECs), indicating they have undergone additional rounds of in vivo cell division. Furthermore, we show that they also share effector-type properties. At equivalent in vivo replicative history, the 2 subsets express high levels of Fas/CD95 and CD11a, as well as increasing levels of effector mediators such as granzyme B, perforin, interferon gamma, and tumor necrosis factor alpha. Both display partial ex vivo cytolytic activity and can be found among cytomegalovirus-specific cytolytic T cells. Taken together, our data point to the presence of T cells with intermediate effector-like functions and suggest that these subsets consist of T lymphocytes that are evolving toward a more differentiated effector or effector-memory stage.

Functions of the peroxisome proliferator-activated receptor (PPAR) alpha and beta in skin homeostasis, epithelial repair, and morphogenesis.

The three peroxisome proliferator-activated receptors (PPAR alpha, PPAR beta, and PPAR gamma) are ligand-activated transcription factors belonging to the nuclear hormone receptor superfamily. They are regarded as being sensors of physiological levels of fatty acids and fatty acid derivatives. In the adult mouse skin, they are found in hair follicle keratinocytes but not in interfollicular epidermis keratinocytes. Skin injury stimulates the expression of PPAR alpha and PPAR beta at the site of the wound. Here, we review the spatiotemporal program that triggers PPAR beta expression immediately after an injury, and then gradually represses it during epithelial repair. The opposing effects of the tumor necrosis factor-alpha and transforming growth factor-beta-1 signalling pathways on the activity of the PPAR beta promoter are the key elements of this regulation. We then compare the involvement of PPAR beta in the skin in response to an injury and during hair morphogenesis, and underscore the similarity of its action on cell survival in both situations.

Estimating parameters for generalized mass action models using constraint propagation.

As modern molecular biology moves towards the analysis of biological systems as opposed to their individual components, the need for appropriate mathematical and computational techniques for understanding the dynamics and structure of such systems is becoming more pressing. For example, the modeling of biochemical systems using ordinary differential equations (ODEs) based on high-throughput, time-dense profiles is becoming more common-place, which is necessitating the development of improved techniques to estimate model parameters from such data. Due to the high dimensionality of this estimation problem, straight-forward optimization strategies rarely produce correct parameter values, and hence current methods tend to utilize genetic/evolutionary algorithms to perform non-linear parameter fitting. Here, we describe a completely deterministic approach, which is based on interval analysis. This allows us to examine entire sets of parameters, and thus to exhaust the global search within a finite number of steps. In particular, we show how our method may be applied to a generic class of ODEs used for modeling biochemical systems called Generalized Mass Action Models (GMAs). In addition, we show that for GMAs our method is amenable to the technique in interval arithmetic called constraint propagation, which allows great improvement of its efficiency. To illustrate the applicability of our method we apply it to some networks of biochemical reactions appearing in the literature, showing in particular that, in addition to estimating system parameters in the absence of noise, our method may also be used to recover the topology of these networks.

Calcineurin as a Multifunctional Regulator: Unraveling Novel Functions in Fungal Stress Responses, Hyphal Growth, Drug Resistance, and Pathogenesis.

Calcineurin signaling plays diverse roles in fungi in regulating stress responses, morphogenesis and pathogenesis. Although calcineurin signaling is conserved among fungi, recent studies indicate important divergences in calcineurin-dependent cellular functions among different human fungal pathogens. Fungal pathogens utilize the calcineurin pathway to effectively survive the host environment and cause life-threatening infections. The immunosuppressive calcineurin inhibitors (FK506 and cyclosporine A) are active against fungi, making targeting calcineurin a promising antifungal drug development strategy. Here we summarize current knowledge on calcineurin in yeasts and filamentous fungi, and review the importance of understanding fungal-specific attributes of calcineurin to decipher fungal pathogenesis and develop novel antifungal therapeutic approaches.

Tissue-specific opposing functions of the inflammasome adaptor ASC in the regulation of epithelial skin carcinogenesis.

A chronic inflammatory microenvironment favors tumor progression through molecular mechanisms that are still incompletely defined. In inflammation-induced skin cancers, IL-1 receptor- or caspase-1-deficient mice, or mice specifically deficient for the inflammasome adaptor protein ASC (apoptosis-associated speck-like protein containing a CARD) in myeloid cells, had reduced tumor incidence, pointing to a role for IL-1 signaling and inflammasome activation in tumor development. However, mice fully deficient for ASC were not protected, and mice specifically deficient for ASC in keratinocytes developed more tumors than controls, suggesting that, in contrast to its proinflammatory role in myeloid cells, ASC acts as a tumor-suppressor in keratinocytes. Accordingly, ASC protein expression was lost in human cutaneous squamous cell carcinoma, but not in psoriatic skin lesions. Stimulation of primary mouse keratinocytes or the human keratinocyte cell line HaCaT with UVB induced an ASC-dependent phosphorylation of p53 and expression of p53 target genes. In HaCaT cells, ASC interacted with p53 at the endogenous level upon UVB irradiation. Thus, ASC in different tissues may influence tumor growth in opposite directions: it has a proinflammatory role in infiltrating cells that favors tumor development, but it also limits keratinocyte proliferation in response to noxious stimuli, possibly through p53 activation, which helps suppressing tumors.

Antagonistic functions of LMNA isoforms in energy expenditure and lifespan.

Alternative RNA processing of LMNA pre-mRNA produces three main protein isoforms, that is, lamin A, progerin, and lamin C. De novo mutations that favor the expression of progerin over lamin A lead to Hutchinson-Gilford progeria syndrome (HGPS), providing support for the involvement of LMNA processing in pathological aging. Lamin C expression is mutually exclusive with the splicing of lamin A and progerin isoforms and occurs by alternative polyadenylation. Here, we investigate the function of lamin C in aging and metabolism using mice that express only this isoform. Intriguingly, these mice live longer, have decreased energy metabolism, increased weight gain, and reduced respiration. In contrast, progerin-expressing mice show increased energy metabolism and are lipodystrophic. Increased mitochondrial biogenesis is found in adipose tissue from HGPS-like mice, whereas lamin C-only mice have fewer mitochondria. Consistently, transcriptome analyses of adipose tissues from HGPS and lamin C-only mice reveal inversely correlated expression of key regulators of energy expenditure, including Pgc1a and Sfrp5. Our results demonstrate that LMNA encodes functionally distinct isoforms that have opposing effects on energy metabolism and lifespan in mammals.

Redundant functions of TCF-1 and LEF-1 during T and NK cell development, but unique role of TCF-1 for Ly49 NK cell receptor acquisition.

Members of the TCF/LEF (T cell factor / lymphoid enhancer factor) family of DNA-binding factors play important roles during embryogenesis, the establishment and/or maintenance of self-renewing tissues such as the immune system and for malignant transformation. Specifically, it has been shown that TCF-1 is required for T cell development. A role for LEF-1 became apparent when mice harbored two hypomorphic TCF-1 alleles and consequently expressed low levels of TCF-1. Here we show that NK cell development is similarly regulated by redundant functions of TCF-1 and LEF-1, whereby TCF-1 contributes significantly more to NK cell development than LEF-1. Despite this role for NK cell development, LEF-1 is not required for the establishment of a repertoire of MHC class I-specific Ly49 receptors on NK cells. The proper formation of this repertoire depends to a large extent on TCF-1. These findings suggest common and distinct functions of TCF-1 and LEF-1 during lymphocyte development.

Robust Estimators of the Generalized Log-Gamma Distribution

We propose robust estimators of the generalized log-gamma distribution and, more generally, of location-shape-scale families of distributions. A (weighted) Q tau estimator minimizes a tau scale of the differences between empirical and theoretical quantiles. It is n(1/2) consistent; unfortunately, it is not asymptotically normal and, therefore, inconvenient for inference. However, it is a convenient starting point for a one-step weighted likelihood estimator, where the weights are based on a disparity measure between the model density and a kernel density estimate. The one-step weighted likelihood estimator is asymptotically normal and fully efficient under the model. It is also highly robust under outlier contamination. Supplementary materials are available online.