Universal DNA methylation age across mammalian tissues.

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.

Sustained IFN-I stimulation impairs MAIT cell responses to bacteria by inducing IL-10 during chronic HIV-1 infection.

Mucosal-associated invariant T (MAIT) cells in HIV-1-infected individuals are functionally impaired by poorly understood mechanisms. Single-cell transcriptional and surface protein analyses revealed that peripheral MAIT cells from HIV-1-infected subjects were highly activated with the up-regulation of interferon (IFN)-stimulated genes as compared to healthy individuals. Sustained IFN-α treatment suppressed MAIT cell responses to Escherichia coli by triggering high-level interleukin-10 (IL-10) production by monocytes, which subsequently inhibited the secretion of IL-12, a crucial costimulatory cytokine for MAIT cell activation. Blocking IFN-α or IL-10 receptors prevented MAIT cell dysfunction induced by HIV-1 exposure in vitro. Moreover, blocking the IL-10 receptor significantly improved anti-Mycobacterium tuberculosis responses of MAIT cells from HIV-1-infected patients. Our findings demonstrate the central role of the IFN-I/IL-10 axis in MAIT cell dysfunction during HIV-1 infection, which has implications for the development of anti-IFN-I/IL-10 strategies against bacterial coinfections in HIV-1-infected patients.

Schwann cell-derived Desert hedgehog controls the development of peripheral nerve sheaths.

We show that Schwann cell-derived Desert hedgehog (Dhh) signals the formation of the connective tissue sheath around peripheral nerves. mRNAs for dhh and its receptor patched (ptc) are expressed in Schwann cells and perineural mesenchyme, respectively. In dhh-/- mice, epineurial collagen is reduced, while the perineurium is thin and disorganized, has patchy basal lamina, and fails to express connexin 43. Perineurial tight junctions are abnormal and allow the passage of proteins and neutrophils. In nerve fibroblasts, Dhh upregulates ptc and hedgehog-interacting protein (hip). These experiments reveal a novel developmental signaling pathway between glia and mesenchymal connective tissue and demonstrate its molecular identity in peripheral nerve. They also show that Schwann cell-derived signals can act as important regulators of nerve development.

A High Frequency of HIV-Specific Circulating Follicular Helper T Cells Is Associated with Preserved Memory B Cell Responses in HIV Controllers.

Follicular helper T cells (Tfh) play an essential role in the affinity maturation of the antibody response by providing help to B cells. To determine whether this CD4+ T cell subset may contribute to the spontaneous control of HIV infection, we analyzed the phenotype and function of circulating Tfh (cTfh) in patients from the ANRS CO21 CODEX cohort who naturally controlled HIV-1 replication to undetectable levels and compared them to treated patients with similarly low viral loads. HIV-specific cTfh (Tet+), detected by Gag-major histocompatibility complex class II (MHC-II) tetramer labeling in the CD45RA- CXCR5+ CD4+ T cell population, proved more frequent in the controller group (P = 0.002). The frequency of PD-1 expression in Tet+ cTfh was increased in both groups (median, >75%) compared to total cTfh (<30%), but the intensity of PD-1 expression per cell remained higher in the treated patient group (P = 0.02), pointing to the persistence of abnormal immune activation in treated patients. The function of cTfh, analyzed by the capacity to promote IgG secretion in cocultures with autologous memory B cells, did not show major differences between groups in terms of total IgG production but proved significantly more efficient in the controller group when measuring HIV-specific IgG production. The frequency of Tet+ cTfh correlated with HIV-specific IgG production (R = 0.71 for Gag-specific and R = 0.79 for Env-specific IgG, respectively). Taken together, our findings indicate that key cTfh-B cell interactions are preserved in controlled HIV infection, resulting in potent memory B cell responses that may play an underappreciated role in HIV control.IMPORTANCE The rare patients who spontaneously control HIV replication in the absence of therapy provide a unique model to identify determinants of an effective anti-HIV immune response. HIV controllers show signs of particularly efficient antiviral T cell responses, while their humoral response was until recently considered to play only a minor role in viral control. However, emerging evidence suggests that HIV controllers maintain a significant but "silent" antiviral memory B cell population that can be reactivated upon antigenic stimulation. We report that cTfh help likely contributes to the persistence of controller memory B cell responses, as the frequency of HIV-specific cTfh correlated with the induction of HIV-specific antibodies in functional assays. These findings suggest that T follicular help may contribute to HIV control and highlight the need for inducing such help in HIV vaccine strategies that aim at eliciting persistent B cell responses.

Comparison of early and late feline immunodeficiency virus encephalopathies.

DESIGN: The study of the early and late stages of encephalopathy following infection by the feline immunodeficiency virus (FIV) was carried out with laboratory and naturally infected cats. INTERVENTIONS: Animals infected experimentally were injected with three different isolates of the virus, administered either intracerebrally or intravenously, and sacrificed at 7 days, 1 and 6 months (intracerebral injection), and 2, 6 and 12 months (intravenous injection) post-inoculation, respectively. CONCLUSIONS: General features of encephalopathy were found to be identical, regardless of the method of inoculation or the viral strain used. Moderate gliosis and glial nodules, sometimes associated with perivascular infiltrates and white matter pallor, were observed at 1 month (intracerebral injection) and 2 months (intravenous injection), and remained unchanged until 12 months post-inoculation. The fact that these initial stages are identical for intravenously and intracerebrally inoculated cats suggests that the virus enters the brain very quickly in intravenously infected animals. Encephalopathy in cats naturally infected with FIV only consisted of gliosis, glial nodules, white matter pallor, meningeal perivascular calcification and meningitis. These lesions were more frequent and more severe in the group coinfected with feline leukaemia virus and feline infectious peritonitis virus. Although multinucleated cells were rare, the strong similarities between HIV and simian immunodeficiency virus encephalopathies at comparable stages support the view that FIV infection may represent an interesting model for a physiopathological approach of HIV infection of the central nervous system.

Chromosome 3 linked frontotemporal dementia (FTD-3).

BACKGROUND: The authors have identified and studied a large kindred in which frontotemporal dementia (FTD) is inherited as an autosomal dominant trait. The trait has been mapped to the pericentromeric region of chromosome 3. METHODS: The authors report on the clinical, neuroimaging, neuropsychological, and pathologic features in this unique pedigree collected during 17 years of study. RESULTS: Twenty-two individuals in three generations have been affected; the age at onset varies between 46 and 65 years. The disease presents with a predominantly frontal lobe syndrome but there is also evidence for temporal and dominant parietal lobe dysfunction. Late in the illness individuals develop a florid motor syndrome with pyramidal and extrapyramidal features. Structural imaging reveals generalized cerebral atrophy; H2 15 O-PET scanning in two individuals relatively early and late in the disease shows a striking global reduction in cerebral blood flow affecting all lobes. On macroscopic pathologic examination, there is generalized cerebral atrophy affecting the frontal lobes preferentially. Microscopically, there is neuronal loss and gliosis without specific histopathologic features. CONCLUSIONS: FTD-3 shares clinical and pathologic features with other forms of FTD and fulfills international consensus criteria for FTD. There is involvement of the parietal lobes clinically, radiologically, and pathologically in FTD-3 in contrast to some forms of FTD. This more diffuse involvement of the cerebral cortex leads to a distinctive, global pattern of reduced blood flow on PET scanning.

Dietary protein alters age-induced change in hypothalamic GABA and immune response.

The effect of dietary protein on hypothalamic GABAergic activity and immune response of rats in relation to age was studied. The age-induced (due to increase of age from three to 18 months) decrease in hypothalamic GABAergic activity and immune response were potentiated with the supplementation of protein rich diet under both short- and long-term conditions. Long-term consumption of protein-poor diet, in contrast, produced activation of hypothalamic GABAergic activity with an immunopotentiation with the increase of age from three to 18 months; whereas, short-term supplementation of low protein diet did not show any effect. The results of the present study may indicate that the activation or inhibition of hypothalamic GABAergic activity by immunopotentiation or immunosuppression during aging depends on the variation of the amount of dietary protein as well as the duration of its supplementation.

A divergent simian immunodeficiency virus from sooty mangabey with an atypical Tat-TAR structure.

SIVsm, the simian immunodeficiency virus that naturally infects sooty mangabeys in West Africa, is the closest lentiviral relative of human immunodeficiency virus type 2 (HIV-2). To determine the genetic characteristics of SIVsm in its natural host, we sequenced the full-length genome of SIVsmSL92b, a primary isolate obtained from a pet sooty mangabey in Sierra Leone. SIVsmSL92b proved to be the most divergent member of the HIV-2/SIVsm lineage found thus far, having as much as 35% nucleotide divergence from other HIV-2 genomes. A phylogenetic association between SIVsmSL92b and HIV-2 PA subtype E, which had been previously revealed by the analysis of partial gag sequences, was extended to the pol gene. SIVsmSL92b showed several divergent features, including a short Tat protein of 104 residues and an atypical TAR structure. Specifically, only one of the duplicate TAR elements contained the conserved hexanucleotide loop sequence CUGGGX important for Tat-cyclin T1 binding. These features suggested that the mechanism of SIVsmSL92b Tat and TAR interaction differed from that described for HIV-2. Taken together, these findings indicated that the structural diversity within the HIV-2/SIVsm lineage was greater than previously appreciated.

Early stages of feline immunodeficiency virus infection in lymph nodes and spleen.

Analysis of the early stages of infection within the lymphoid organs is crucial for the understanding of the physiopathology of HIV infection. Such analysis can only be performed using animal models. Cats were infected with two strains of FIV and killed at regular intervals for a classic pathologic study along with a quantification of the viral load by in situ hybridization in the spleen and the lymph nodes. The pathological study showed a persistent follicular reaction, which peaked 15 days postinoculation (p.i.). The in situ hybridization study showed two types of labeling. The first was spot labeling corresponding to cells actively replicating the virus. The second consisted of a more diffuse labeling linked to the follicular dendritic cells (FDCs) demonstrating by colocalization of virus detected by in situ hybridization associated with the FDCs, specifically labeled by immunohistochemistry. The number of productive cells is few and identical for the two viruses tested. Despite a slight peak at 15 days p.i., the number of infected cells persists while slightly decreasing over time. The FDC virus load appears jointly with the appearance of antibody and remains permanent until the end of the study at 3 years p.i. These results show that in the FIV model, there is a chronic permanent infection in the lymphoid organs. Furthermore, as compared with the SIV-macaque model, there is a correlation between the low number of infected cells detected in these organs in the early phase and the extended length of the asymptomatic period, which contrasts with the high level of the FDC virus load lasting during the same period.

The relationship between the interferon alpha response and viral burden in primary SIV infection.

The interferon alpha (IFN-alpha) response of rhesus macaques was investigated during primary infection with pathogenic and attenuated simian immunodeficiency virus (SIV). IFN-alpha was detected in the serum of animals as early as day 4 after inoculation of SIVmac251, but remained barely detected in animals infected with the attenuated virus SIVmac251 delta nef. The peak of IFN-alpha secretion preceded that of antigenemia in animals infected with pathogenic virus, indicating that the IFN-alpha response did not prevent viral spread. In addition, elevated levels of IFN-alpha in the serum after the acute stage of infection was associated with persisting antigenemia. The analysis of lymph nodes (LNs) by in situ hybridization showed that, similar to the results obtained with peripheral blood, the induction of IFN-alpha in lymphoid organs was rapidly detected in animals infected with the pathogenic virus, but remained very limited in animals infected with the attenuated virus. Quantitation of the hybridization signal indicated that IFN-alpha-producing cells were numerous in the LNs of animals that had a high viral burden. Taken together, these findings indicate that the IFN-alpha response is unable to contain the initial burst of SIV replication.

Highly attenuated SIVmac142 is immunogenic but does not protect against SIVmac251 challenge.

We report here the use of the highly attenuated SIVmac142 clone, unable to establish permanent infection of rhesus macaques, in a vaccine trial. Four rhesus macaques were immunized over a long time period with HUT-78 cells infected with wild-type SIVmac142 or, in order to reinforce the safety use of the vaccine, a deleted mutant with similar in vitro infectivity. The first two injections were done with living cells and the remaining boosts with cells emulsified in muramyl dipeptide adjuvant. Three control macaques were injected with uninfected HUT-78 cells. Over 3 years, we have been unable except once to detect viral infections by three methods. However, antibodies directed against the viral Gag proteins and envelope glycoproteins were detected by immunoblots and/or in vitro neutralization assays. All macaques were challenged intravenously with a low dose (10 animal infectious doses) of a highly pathogenic biological clone of SIVmac251 grown on macaque PBMCs. All seven animals became persistently viremic following challenge. The cell-associated viral loads of the vaccinated monkeys were not reduced relative to those of unvaccinated controls during the first weeks postchallenge even if vaccinated monkeys did not present a transient CD4 decrease. Thus, our data reinforced the notion that the efficacy of live attenuated SIV requires the establishment of persistent infection.

Population genetics of the FRAXE and FRAXF GCC repeats, and a novel CGG repeat, in Xq28.

Most of the rare folate sensitive fragile sites cloned to date arise from expansion of a CGG:CCG trinucleotide repeat array. Analysis of the CAG repeat at the Huntington Disease (HD) locus showed a positively skewed repeat distribution leading to the proposal that microsatellites are subject to a mutational bias toward expansion. Such a mutational bias predicts an increase in mean repeat size at all microsatellite loci. We present an analysis of repeats at two fragile site loci, FRAXE and FRAXF, and a novel CGG repeat in Xq28, in five different human populations, which suggests that these loci may also be subject to the same mutation process. The novel repeat array may represent the first evidence for the existence of a fourth fragile site in Xq27.3-28.

Fragile X syndrome.

The fragile X syndrome is characterized by mental handicap, facial dysmorphism and expression of a fragile site at Xq27.3. An expansion of a CGG repeat in the 5' end of the fragile X mental retardation 1 (FMR1) gene results in the absence of the encoded fragile X mental retardation protein, known to play an important role in RNA processing and probably the developmental maturation of brain neurons.

Cytokine patterns and viral load in lymph nodes during the early stages of SIV infection.

To elucidate the initial pathogenic events in lymphoid organs, the major reservoir of virus in HIV infection, follow-up of viral load and cytokine mRNA production was performed in the rhesus macaque SIV mac251 model. In the first experiment, lymph nodes (LN) obtained from animals sacrificed at early time points following intravenous (i.v.) inoculation with a high viral dose, showed that the production of cytokine mRNA in LN (IFN gamma, IL1 beta, IL2, IL4, IL12p40, IL6, IL10, TNF alpha and TNF beta) was correlated with viral replication and persisted during the two months post-inoculation (p.i.). In the second experiment, LN were sequentially analysed in two groups of animals receiving i.v. a high or a low viral dose. The initial higher local production of IFN gamma mRNA in LN was associated with weak viraemia, the capacity of the host to decrease productive infection in LN measured at one and two months p.i., and slow disease progression.

The cytoplasmic domain of simian immunodeficiency virus transmembrane protein modulates infectivity.

A striking characteristic of the simian immunodeficiency virus (SIV) and of the human immunodeficiency virus type 2 (HIV-2) is the presence of a nonsense mutation in the env gene resulting in the synthesis of a truncated transmembrane protein lacking the cytoplasmic domain. By mutagenesis of an infectious molecular clone of SIVmac142, we investigated the function of the cytoplasmic domain and the significance of the env nonsense mutation. When the nonsense codon (TAG) was replaced by a glutamine codon (CAG), the virus infected HUT78 cells with markedly delayed kinetics. This negative effect was counterselected in vitro as reversion of the slow phenotype frequently occurred. The sequencing of one revertant revealed the presence of a new stop codon three nucleotides 5' to the original mutation. Deletions or an additional nonsense mutation introduced 3' to the original stop codon did not modify SIV infectivity. In contrast, the same deletions or nonsense mutation introduced in the clone in which the stop codon was replaced by CAG abolished infectivity. These results indicated that the envelope domain located 3' to the stop codon is not necessary for in vitro replication. However, the presence of this domain in SIV transmembrane protein leads to a reduced infectivity. This negative effect might correspond to a function controlling the rate of spread of the virus during in vivo infection.

Is age-induced decline in immune response associated with hypothalamic glutamate receptor density and dietary protein?

Manipulation of dietary protein has been found to be the most useful dictator in the age-associated decline of neuroimmune activity in mammals. In the present study, we sought to clarify the effect of dietary protein on age-induced alterations of hypothalamic glutamatergic activity and immune response. The hypothalamic glutamatergic activity and immune response were found to increase and decrease, respectively, with the increase in age of rats from young (3 months) to old (18 months) maintained with normal (20%) protein diet. Intake of low (5%) protein diet (LPD) and high (40%) protein diet (HPD) under short-term period (7 days) failed to alter the age-associated loss of immune response and increase in hypothalamic glutamatergic activity. However, long-term (30 days) supplementation of LPD retarded the age-induced decline in immune response and increase in hypothalamic glutamatergic activity, whereas, HPD consumption under similar condition potentiated the age-related immunosuppression and increase in hypothalamic glutamatergic activity. These results suggest that (a) the age-associated immunosuppression may be inversely related to the hypothalamic glutamatergic activity and (b) consumption of diets having variable quantity of protein without variation of calorie content modulates immune response and hypothalamic glutamatergic activity depending upon age and duration of dietary supplementation.

Kinetics of primary SIV infection in lymph nodes.

The very early stages of SIV infection in lymph nodes of rhesus monkeys were characterized by in situ hybridization. Massive viral replication was detected in macrophages and lymphocytes during the first week of infection. In a second phase, SIV RNA concentrated in the developing germinal centers, and colocalized with the follicular dendritic cells. The down-regulation of the viral load in lymph nodes varied depending on the animal, indicating early differences in the susceptibility to SIV infection.

Target cells during early SIV encephalopathy.

Early encephalopathy was studied in rhesus macaques in the first month following intravenous (i.v.) infection with SIV-mac-251. Histopathological analysis of brain tissues showed slight gliosis, associated with perivascular infiltrates and occasional glial nodules. Immunophenotyping of brain tissue showed microgliosis with expression of MHC class II molecule and macrophage infiltration associated with a few lymphocytes. At the early stage of infection, most infected cells were perivascular, suggesting that infiltrating cells are the main route of entry of the virus into the brain. Using combined immunochemistry and in situ hybridization, it was shown that these infected perivascular cells were mostly macrophages. Later, SIV infected a limited number of cells expressing the same CD68 monocyte/macrophage/microglia marker. Using different genome probes, hypotheses concerning SIV RNA expression during early brain infection were tested. It was shown that the latent brain infection was not due to a complete transcription block, but rather to productive replication of SIV at a low level in a small number of target cells in the brain. Injection of SIV by the intracerebral (i.c.) route induced the same slight encephalitis as observed in i.v. inoculated animals. The very small number of infected cells found around the site of i.c. inoculation suggests that resident microglia are poorly susceptible to infection by SIV.

Variable course of primary simian immunodeficiency virus infection in lymph nodes: relation to disease progression.

To investigate the dynamics of spread of simian immunodeficiency virus (SIV) in the lymphoid organs, we sequentially analyzed the viral burden in lymph nodes (LN) of eight rhesus macaques inoculated intravenously with a high or low dose of the pathogenic SIVmac 251 isolate. For each animal, four axillary or inguinal LN were collected during the first weeks of infection and a fifth LN was taken 6 or 8 months later to estimate disease progression. Measurement of SIV RNA by in situ hybridization showed that all of the macaques studied had a phase of acute viral replication in LN between 7 and 14 days postinoculation which paralleled that observed in the blood. In a second phase, productive infection was controlled and viral particles were trapped in the germinal centers that developed in LN. While the peaks of productive infection were similar for the eight animals, marked differences in the numbers of productively infected cells that persisted in LN after primary infection were seen. Differences were less pronounced in the blood, where productive infection was efficiently controlled in all cases. The persistence of productively infected cells in LN after primary infection was found to be associated with more rapid disease progression, as measured by the decrease of the T4/T8 ratio and the occurrence of clinical signs. However, the persistence of a significant level of viral particles in germinal centers was observed even in animals that remained healthy over a 1- to 2-year observation period. This study indicates that the course of primary SIV infection in LN is variable, and it suggests that the initial capacity of the host to control productive infection in LN may determine the rate of disease progression.