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Testosterone supplementation during energy deficit promotes whole body lean mass accretion, but the mechanisms underlying that effect remain unclear. To elucidate those mechanisms, skeletal muscle molecular adaptations were assessed from muscle biopsies collected before, 1 h, and 6 h after exercise and a mixed meal (40 g protein, 1 h postexercise) following 14 days of weight maintenance (WM) and 28 days of an exercise- and diet-induced 55% energy deficit (ED) in 50 physically active nonobese men treated with 200 mg testosterone enanthate/wk (TEST) or placebo (PLA) during the ED. Participants ( n = 10/group) exhibiting substantial increases in leg lean mass and total testosterone (TEST) were compared with those exhibiting decreases in both of these measures (PLA). Resting androgen receptor (AR) protein content was higher and fibroblast growth factor-inducible 14 (Fn14), IL-6 receptor (IL-6R), and muscle ring-finger protein-1 gene expression was lower in TEST vs. PLA during ED relative to WM ( P < 0.05). Changes in inflammatory, myogenic, and proteolytic gene expression did not differ between groups after exercise and recovery feeding. Mechanistic target of rapamycin signaling (i.e., translational efficiency) was also similar between groups at rest and after exercise and the mixed meal. Muscle total RNA content (i.e., translational capacity) increased more during ED in TEST than PLA ( P < 0.05). These findings indicate that attenuated proteolysis at rest, possibly downstream of AR, Fn14, and IL-6R signaling, and increased translational capacity, not efficiency, may drive lean mass accretion with testosterone administration during energy deficit.

HIV-infected individuals are at an increased risk of osteoporosis despite effective viral suppression. Observations that myostatin null mice have increased bone mass led us to hypothesize that simian immunodeficiency virus (SIV)-associated bone loss may be attenuated by blocking myostatin/TGFβ signaling. In this proof-of-concept study, pair-housed juvenile male rhesus macaques were inoculated with SIVmac239. Four weeks later, animals were treated with vehicle or Fc-conjugated soluble activin receptor IIB (ActR2B·Fc, iv. 10 mg ∗ kg−1 ∗ week−1) – an antagonist of myostatin and related members of TGFβ superfamily. Limb and trunk bone mineral content (BMC) and density (BMD) using dual-energy X-Ray absorptiometry, circulating markers of bone growth and turnover, and serum testosterone levels were measured at baseline and during the 12-week intervention period. The increase in BMC was significantly greater in the ActRIIB.Fc-treated group (+8 g) than in the placebo group (−4 g) (p < 0.05). BMD also increased significantly more in the ActRIIB.Fc-treated macaques (+0.03 g/cm2) than in the placebo-treated animals (+0 g/cm2) (p < 0.005). Serum osteocalcin was about two-fold higher in the ActRIIB.Fc-treated group than in the placebo group (p < 0.05), but serum C-terminal telopeptide and testosterone levels did not differ significantly between groups. The expression levels of TNFalpha (p < 0.05), GADD45 (p

Sustained periods of severe energy deficit during military operations, produced by significant increases in aerobic-type physical work and limited dietary intake, result in conditions that degrade lean body mass (LBM) and lower-body muscle function, which may be mediated by concomitant reductions in circulating testosterone. Therefore, we studied the effects of restoring testosterone by supplementation (200 mg testosterone enanthate/wk, TEST), compared to placebo (1 mL sesame seed oil/wk, PLA), on body composition and lower-body muscular strength and endurance during 28 d of severe exercise- and diet-induced energy deficit in non-obese, young men. Following energy deficit, concentrations of free testosterone decreased, total testosterone remained unchanged, and sex-hormone binding globulin (SHBG) increased in PLA; whereas, total and free testosterone increased and SHBG was unchanged in TEST, such that, total and free testosterone were greater and SHBG concentrations were lower in TEST than PLA. During energy deficit, TEST attenuated weight loss and increased DXA-derived LBM compared to PLA, but both groups had a similar increase in type I slow twitch myosin heavy chain cross-sectional area (CSA) and decrease in type II fast twitch myosin heavy chain CSA. Lower-body muscle function declines and adverse event rates did not differ by group during energy deficit. Supplemental testosterone may be an effective pharmacological LBM enhancement strategy during short-term periods of exercise- and diet-induced energy deficit in non-obese, young men, but does not appear to mitigate lower-body functional decline. Funding:The research reported in this publication is supported by the Collaborative Research to Optimize Warfighter Nutrition II and III projects and the Joint Program Committee-5, funded by the US Department of Defense. Declaration of Interest: J.C.W., O.T.C., and K.M.G. reported that their institution received funding from the US Department of Defense for work associated with this publication. H.R.L. reported receiving personal fees from Pfizer, Inc., for work outside this publication. All remaining authors declare no competing interests. The opinions or assertions contained herein are the private views of the authors and are not to be construed as official or as reflecting the views of the Army or the Department of Defense. Any citations of commercial organizations and trade names in this report do not constitute an official Department of the Army endorsement of approval of the products or services of these organizations. Ethical Approval: This study was approved by the Pennington Biomedical Research Center (PBRC) Institutional Review Board and the Human Research Protection Office of the US Army Medical Research and Materiel Command.

Objectives To determine reference values for laboratory tests in individuals aged 85 and older. Design Cross-sectional cohort study. Setting International. Participants Long Life Family Study (LLFS) participants (N~5,000, age: range 25–110, median 67, 45% male). Measurements Serum biomarkers were selected based on association with aging-related diseases and included complete blood count, lipids (triglycerides, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, total cholesterol), 25-hydroxyvitamin D2 and D3, vitamin D epi-isomer, diabetes mellitus–related biomarkers (adiponectin, insulin, insulin-like growth factor 1, glucose, glycosylated hemoglobin, soluble receptor for advanced glycation endproduct), kidney disease–related biomarkers (albumin, creatinine, cystatin), endocrine biomarkers (dehydroepiandrosterone, sex-hormone binding globulin, testosterone), markers of inflammation (interleukin 6, high-sensitivity C-reactive protein, N-terminal pro b-type natriuretic peptide), ferritin, and transferrin. Results Of 38 measured biomarkers, 34 were significantly correlated with age. Summary statistics were generated for all biomarkers according to sex and 5-year age increments from 50 and up after excluding participants with diseases and treatments that were associated with biomarkers. A biomarker data set was also generated that will be useful for other investigators seeking to compare biomarker levels between studies. Conclusion Levels of several biomarkers change with older age in healthy individuals. The descriptive statistics identified herein will be useful in future studies and, if replicated in additional studies, might also become useful in clinical practice. The availability of the reference data set will facilitate appropriate calibration of biomarkers measured in different laboratories.

The review articles in this issue provide an improved appreciation for microRNA (miRNA) as an essential feature of lineage commitment and regulatory guidance during tissue development that, when absent or hampered, often lead to disease states. In the coming years, there is much to be learned about adaptive (and maladaptive) states by examining how the expression of miRNAs is influenced by the genetic architecture of miR genes, clusters, and mirtrons, as well as miRNA polymorphism and polymorphism in their mRNA targets. We are also introduced to several modes of miRNA regulation (negative feedback, positive feedback, and cross regulatory) that monitor, modulate, or resolve signaling pathways in a variety of biologic processes that include sepsis response, fibrosis, acute exercise, and steroid biology. Perhaps the homeostasis or micromanagement of these miRNA regulatory systems, when perturbed, arrive at new stable networked interactions that have an undesired effect of promoting or antagonizing disease severity and cancer progression. Clearly, a better understanding of these miRNA regulatory networks, as well as improved therapeutic tools for guiding miRNA expression and their targets toward desired outcomes, will be the subject of many advances in miRNA biology over the coming years.

Efficient muscle regeneration requires the clearance of dead and dying tissue via phagocytosis before remodeling. We have previously shown that mice lacking stem cell antigen-1 (Sca-1) display a defect in skeletal muscle regeneration characterized by increased fibrosis and decreased turnover of the extracellular matrix. In the present study we demonstrate that Sca-1−/− mice have a defect in their capacity to recruit soluble IgM, and subsequently C3 complement, to damaged muscle. We hypothesize that this defect in recruitment delays or decreases phagocytosis by macrophages, contributing to the previously observed fibrotic phenotype of these mice. As the primary source of soluble IgM is peritoneal B-1a cells, which are a subset of self-renewing B cells, we analyzed this cell population and observed a significant reduction in B-1a cells in Sca-1−/− animals. Interestingly, these mice are protected from ischemia-reperfusion injury, an acute inflammatory reaction also mediated by IgM and C3 complement that has been linked to a deficit in B-1a cells in previous studies. Collectively, these data reveal a novel role for Sca-1 in innate immunity during muscle regeneration and indicate that further elucidation of immuno-myogenic processes will help to better understand and promote muscle regeneration.

Sca-1 (stem cell antigen-1) is a member of the Ly-6 family of proteins and regulates cell proliferation, differentiation, and self-renewal in multiple tissues. In skeletal muscle, Sca-1 inhibits both proliferation and differentiation of myogenic cells. Sca-1 expression is dynamically regulated during muscle regeneration, and mice lacking Sca-1 display increased fibrosis following muscle injury. Here, we show that Sca-1 expression is negatively regulated by TGF-β1 and that this inhibition is dependent on Smad3. We demonstrate that levels of TGF-β1 in skeletal muscle rapidly increase on injury and that the majority of this TGFβ1 is produced by infiltrating macrophages. Sca-1 is expressed in multiple cell types, and we demonstrate that TGF-β1 represses Sca-1 expression in T cells and other immune cell populations derived from the spleen, indicating that regulation by TGF-β1 is a general feature of Sca-1 expression in multiple cell types. Elucidation of the mechanisms by which Sca-1 expression is regulated may aid in the understanding of muscle homeostasis, potentially identifying novel therapeutic targets for muscle diseases.—Long, K., Montano, M., Pavlath, G. K. Sca-1 is negatively regulated by TGF-β1 in myogenic cells.

Muscle atrophy remains a significant concern in multiple inflammatory conditions, including injury, sepsis, cachexia, and HIV‐associated wasting. Herein, we show that inflammatory stressors, including TNF‐α, IFN‐γ, or lipopolysaccharide, potently induced the novel expression of the RNA editor ADAR1, an observation not previously described in muscle cells. We also observed that cytokine stimulation suppressed muscle‐associated microRNAs, an observation also not previously demonstrated. To map potential effects of ADAR1 induction in the muscle program, we conducted knockdown and overexpression studies in the mouse C2C12 muscle precursor cell (MPC) line and in primary human MPCs. We show that knockdown of stress‐induced ADAR1 increased inflammation‐mediated declines in the muscle differentiation markers Myogenin and myosin heavy chain, and knockdown reduced levels of active phosphorylated Akt (phospho‐Akt), but had no effect on microRNA transcript levels, suggesting a role for ADAR1 in buffering inflammatory stress effects on myogenic transcription and protein synthesis pathways. In addition, overexpression of recombinant ADAR1 suppressed active phosphorylated double‐stranded RNA (dsRNA)‐dependent protein kinase (phospho‐PKR), consistent with a role for ADAR1 in limiting inflammation‐driven catabolic atrophy pathways. Collectively, these data identify a novel regulatory role for ADAR1 activation under inflammatory stress to both promote muscle protein synthesis pathways and limit atrophy pathways. Clin Trans Sci 2010; Volume 3: 73–80

Testosterone treatment induces erythrocytosis that could potentially affect blood viscosity and cardiovascular risk. We thus investigated the effects of testosterone administration on blood viscosity and erythrocyte deformability using mouse models. Blood viscosity, erythrocyte deformability, and hematocrits were measured in normal male and female mice, as well as in females and castrated males after short-term (2 wk) and long-term (5–7 mo) testosterone intervention (50 mg/kg, weekly). Castrated males for long-term intervention were studied in parallel with the normal males to assess the effect of long-term testosterone deprivation. An additional short-term intervention study was conducted in females with a lower testosterone dose (5 mg/kg). Our results indicate no rheological difference among normal males, females, and castrated males at steady-state. Short-term high-dose testosterone increased hematocrit and whole-blood viscosity in both females and castrated males. This effect diminished after long-term treatment, in association with increased erythrocyte deformability in the testosterone-treated mice, suggesting the presence of adaptive mechanism. Considering that cardiovascular events in human trials are seen early after intervention, rheological changes as potential mediator of vascular events warrant further investigation.

Neisseria gonorrhoeae is an obligate human pathogen that represents a significant health concern, particularly in the developing world. Although generally associated with an acute inflammatory infection of urogenital epithelia cells, infections have been noted in multiple tissues and many infected individuals can become asymptomatic carriers. Few studies of immune response to N. gonorrhoeae infection in peripheral blood have evaluated the production of T helper cytokines (TH1/TH2) induced early after infection. We developed a quantitative realtime PCR assay based on the gonococcal rmpIII gene to monitor dose-response effects of infection on cytokine release from peripheral blood mononuclear cells (PBMCs). We observed upregulation of CD69 transcription and surface CD25 expression on lymphocytes, consistent with early T-cell activation. We observed dosage-dependent transcription of the chemotactic factor IL-8 and previously unreported activation of the chemoattractant MCP-2. Multiplex analysis of broad cytokine protein production revealed a differential increase in the TH1 and TH2 associated cytokines: IL-2, IL-4, IL-8, IL-10, IL-12, IFN-gamma, TNF-alpha and MCP-1. Markov models of protein accumulation implicated a cross-regulated response to infection, notably for IL-8, IL-10 and IL-12. Taken together, the cytokine profile we observed early in response to whole gonococcal bacteria was broader than has been previously described and may have relevance for the contribution of antagonistic signaling events early in infection and in understanding peripheral immune mechanisms engaged to control infection.

Perinatal transmission of human immunodeficiency virus (HIV)-1 represents a major problem in many regions of the world, especially Southern Africa. With the exception of viral and proviral load, the role for maternal cofactors in perinatal transmission outcome is largely unknown. In this study, an assessment was made of peripheral blood mononuclear cells (PBMC) gene-expression profiles to better understand transcriptional changes associated with HIV-1 infection and perinatal transmission among young adult mothers with infants in Botswana. Peripheral blood mononuclear cells specimens were used from 25 HIV+ drug naive and 20 HIV− healthy mothers, similar in age and location, collected in 1999–2000 and 2003, and processed with the exact same methods, as previously described. Expression profiling of 22 277 microarray gene probes implicated a broad initiation of innate response gene-sets, including toll-like receptor, interferon-stimulated and antiviral RNA response pathways in association with maternal HIV-1 infection. Maternal transmission status was further associated with host genes that influence RNA processing and splicing patterns. In addition to real-time polymerase chain reaction validation of specific genes, enriched category validation of PBMC profiles was conducted using two independent data sets for either HIV-1 infection or an unrelated RNA virus, severe acute respiratory virus infection. HIV-1 pathogen-specific host profiles should prove a useful tool in infection and transmission intervention efforts worldwide. Supplementary information The online version of this article (doi:10.1038/sj.gene.6364297) contains supplementary material, which is available to authorized users.

The association between sexual activity and human herpes virus-8 (HHV-8) infection has been established, but the mode of acquisition is still unclear. Blood samples from 238 individuals from Northern Cameroon were tested to evaluate the incidence of herpes simplex virus-2 (HSV-2), human immunodeficiency virus (HIV), Treponema pallidum, and HHV-8 infections and to identify their possible association. The presence of HSV-2 antibodies was associated significantly with gender, age, and HIV, HHV-8 antilatent, and T. pallidum antibodies, but not with HHV-8 antilytic antibodies. In a multivariate model older age, female gender, seropositivity for HIV, for HHV-8 latent antigens and for T. pallidum were associated independently with seropositivity for HSV-2. HSV-2-seropositive individuals had significantly higher titers of antibodies to both lytic (P = 0.019) and latent (P = 0.021) HHV-8 antigens. These results suggest that HSV-2 infection can contribute to sexual transmission of HHV-8 infection. J. Med. Virol. 74:467–472, 2004. © 2004 Wiley-Liss, Inc.

The major group of human immunodeficiency viruses (HIV-1) that comprise the current global pandemic have diversified during their worldwide spread and may be divided into at least 10 distinct subtypes or clades, A through J. Subtype B predominates in North America and Europe, subtype E predominates in Southeast Asia, and subtype C predominates in sub-Saharan Africa. Functional distinctions in long terminal repeat (LTR) architecture among HIV subtypes have been identified, thus raising the possibility that regulatory divergence among the subtypes of HIV-1 has occurred. In addition to the transcriptional specificity of the HIV-1 LTR, productive HIV-1 replication is also dependent upon the viral Tat protein. Therefore, we sought to investigate whether interactions between host signaling pathways and the NF-kappaB regions of different HIV-1 subtypes, together with subtype-specific interactions between Tat, TAR, and cellular proteins, modulate the efficiency of HIV-1 clade-specific gene transcription. We demonstrate that the NF-kappaB sites of subtypes B and E both bind NF-kappaB-related complexes. However, the duplicated kappaB sites of the C subtype do not compete for NF-kappaB binding. Also, clade E Tat protein possesses the highest transactivation capacity, regardless of the LTR context. Furthermore, preliminary evidence suggests that the acetylation of subtype-specific Tat proteins may correlate with their transactivation efficiency.

In this chapter we discuss translational models for studying infectious diseases, with a focus on HIV. We introduce acute infection and chronic infection, discuss how infections influence immune response, and discuss cells and target tissues of infection. We discuss aspects of innate immune response, such as cytokine production and TLR signaling. Adaptive immune response with production of antigen-specific effectors, including neutralizing antibody response and cytolytic T cell response (e.g. cytotoxic T lymphocyte (CTL)), is discussed. Host conditions arising from infection are discussed, including accelerated aging phenotypes, microbiome alterations and co-infection. Model systems used to study HIV, including cell lines and animal models, are described, along with their limitations. Recent efforts on eradication of the hidden reservoir of latent virus are discussed.

We have discussed model systems and analytical tools available to the translational researcher, including various cellular and organismal models ( Chapters 1– 2), as well as methods for monitoring outcomes in research using biomarkers, gene expression and genome association studies ( Chapters 3– 4). In this chapter, we provide examples of recent translational research occurring in the aging and longevity field. The examples chosen are intended to illustrate the breadth of ongoing research in aging biology. We also discuss efforts to understand what biological mechanisms contribute to the aging process, as well as what biomedical challenges posed by aging can potentially be influenced by translational research-driven intervention to optimize lifespan and healthspan.

In this chapter, we discuss translational approaches to skeletal muscle injury, repair and regeneration. We introduce muscle stem cells, known as satellite cells, and discuss the muscle stem cell niche. We discuss muscle differentiation, myogenesis and how this process is affected in aging. We briefly describe various muscle regulatory pathways that influence muscle growth, including the androgen pathway and testosterone, the IGF pathway, amino acid pathways, Wnt and calcium signaling, and follistatin. We also discuss negative muscle regulators and atrophy-promoting pathways including myostatin, transforming growth factor (TGF) signaling, inflammation and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) signaling. We discuss muscle loss phenotypes such as cachexia and age-associated decline in mass and function, that is, sarcopenia. We discuss approaches to improve muscle mass and function, such as exercise, SARMs and anabolic supplementation.

We address the problem of comparing interindividual genomic sequence diversity between two populations. Although the methods are general, for concreteness we focus on comparing two human immunodeficiency virus (HIV) infected populations. From a viral isolate(s) taken from each individual in a sample of persons from each population, suppose one or multiple measurements are made on the genetic sequence of a coding region of HIV. Given a definition of genetic distance between sequences, the goal is to test if the distribution of interindividual distances differs between populations. If distances between all pairs of sequences within each group are used, then data-dependencies arising from the use of multiple sequences from individuals invalidates the use of a standard two-sample test such as the t-test. Where this problem has been recognized, a typical solution has been to apply a standard test to a reduced dataset comprised of one sequence or a consensus sequence from each patient. Disadvantages of this procedure are that the conclusion of the test depends on the choice of utilized sequences, often an arbitrary decision, and exclusion of replicate sequences from the analysis may needlessly sacrifice statistical power. We present a new test free of these drawbacks, which is based on a statistic that linearly combines all possible standard test statistics calculated from independent sequence subsamples. We describe statistical power advantages of the test and illustrate its use by application to nucleotide sequence distances measured from HIV-1 infected populations in southern Africa (GenBank accession numbers AF110959--AF110981) and North America/Europe. The test makes minimal assumptions, is maximally efficient and objective, and is broadly applicable.

Zinc finger-containing GLI proteins are involved in the development of Caenorhabditis elegans, Xenopus, Drosophila , zebrafish, mice, and humans. In this study, we show that an isoform of human GLI-2 strongly synergizes with the Tat transactivating proteins of human immunodeficiency virus types 1 and 2 (HIV-1 and -2) and markedly stimulates viral replication. GLI-2 also synergizes with the previously described Tat cofactor cyclin T1 to stimulate Tat function. Surprisingly, GLI-2/Tat synergy is not dependent on either a typical GLI DNA binding site or an intact Tat activation response element but does require an intact TATA box. Thus, GLI-2/Tat synergy results from a mechanism of action which is novel both for a GLI protein and for a Tat cofactor. These findings link the GLI family of transcriptional and developmental regulatory proteins to Tat function and HIV replication.

The human immunodeficiency virus type 1 (HIV-1) epidemic within southern Africa is predominantly associated with the HIV-1C subtype. Functional analysis of the enhancer region within the long terminal repeat (LTR) indicates that HIV-1C isolates have >/=3 NF-kappaB binding sites, unlike other subtypes, which have only 1 or 2 sites. A correlation was shown between NF-kappaB enhancer configuration and responsiveness to the proinflammatory cytokine tumor necrosis factor (TNF)-alpha within the context of naturally occurring subtype LTRs, subtype-specific NF-kappaB enhancer regions cloned upstream of an isogenic HXB2 core promoter or a heterologous SV40 minimal promoter, and full-genome subtype clones. In all cases, TNF-alpha activation was correlated with the subtype configuration of the NF-kappaB enhancer. Whether the naturally occurring gain-of-function in the NF-kappaB enhancer of HIV-1C observed in this study can provide a selective advantage for the virus in vivo remains to be determined and warrants further study.

At least 10 different genetic human immunodeficiency virus type 1 (HIV-1) subtypes (A-J) are responsible for the AIDS pandemic. Much of the understanding of HIV-1 disease progression derives from studies in the developed world where HIV infection is almost exclusively subtype B. This has led many to question whether the properties and consequences of HIV-1 infection can be generalized across subtypes that afflict the majority of infected persons in the developing world. From 1985 to 1997, a prospective study of registered female sex workers in Senegal tracked the introduction and spread of HIV-1 subtypes A, C, D, and G. In clinical follow-up, the AIDS-free survival curves differed by HIV-1 subtype. Women infected with a non-A subtype were 8 times more likely to develop AIDS than were those infected with subtype A (hazard ratio=8.23; P=. 009), the predominant subtype in the study. These data suggest that HIV-1 subtypes may differ in rates of progression to AIDS.

BET bromodomain antagonist JQ1 reactivates HIV-1, while suppressing T cell activation genes, and upregulating histone modification genes that favor increased Tat activity. The persistence of latent HIV-1 remains a major challenge in therapeutic efforts to eradicate infection. We report the capacity for HIV reactivation by a selective small molecule inhibitor of BET family bromodomains, JQ1, a promising therapeutic agent with antioncogenic properties. JQ1 reactivated HIV transcription in models of latent T cell infection and latent monocyte infection. We also tested the effect of exposure to JQ1 to allow recovery of replication-competent HIV from pools of resting CD4+ T cells isolated from HIV-infected, ART-treated patients. In one of three patients, JQ1 allowed recovery of virus at a frequency above unstimulated conditions. JQ1 potently suppressed T cell proliferation with minimal cytotoxic effect. Transcriptional profiling of T cells with JQ1 showed potent down-regulation of T cell activation genes, including CD3, CD28, and CXCR4, similar to HDAC inhibitors, but JQ1 also showed potent up-regulation of chromatin modification genes, including SIRT1, HDAC6, and multiple lysine demethylases (KDMs). Thus, JQ1 reactivates HIV-1 while suppressing T cell activation genes and up-regulating histone modification genes predicted to favor increased Tat activity. Thus, JQ1 may be useful in studies of potentially novel mechanisms for transcriptional control as well as in translational efforts to identify therapeutic molecules to achieve viral eradication.

Background Despite the success of highly active antiretroviral therapy (HAART), HIV infected individuals remain at increased risk for frailty and declines in physical function that are more often observed in older uninfected individuals. This may reflect premature or accelerated muscle aging. Methods Skeletal muscle gene expression profiles were evaluated in three uninfected independent microarray datasets including young (19 to 29 years old), middle aged (40 to 45 years old) and older (65 to 85 years old) subjects, and a muscle dataset from HIV infected subjects (36 to 51 years old). Using Bayesian analysis, a ten gene muscle aging signature was identified that distinguished young from old uninfected muscle and included the senescence and cell cycle arrest gene p21/Cip1 (CDKN1A). This ten gene signature was then evaluated in muscle specimens from a cohort of middle aged (30 to 55 years old) HIV infected individuals. Expression of p21/Cip1 and related pathways were validated and further analyzed in a rodent model for HIV infection. Results We identify and replicate the expression of a set of muscle aging genes that were prematurely expressed in HIV infected, but not uninfected, middle aged subjects. We validated select genes in a rodent model of chronic HIV infection. Because the signature included p21/Cip1, a cell cycle arrest gene previously associated with muscle aging and fibrosis, we explored pathways related to senescence and fibrosis. In addition to p21/Cip1, we observed HIV associated upregulation of the senescence factor p16INK4a (CDKN2A) and fibrosis associated TGFβ1, CTGF, COL1A1 and COL1A2. Fibrosis in muscle tissue was quantified based on collagen deposition and confirmed to be elevated in association with infection status. Fiber type composition was also measured and displayed a significant increase in slow twitch fibers associated with infection. Conclusions The expression of genes associated with a muscle aging signature is prematurely upregulated in HIV infection, with a prominent role for fibrotic pathways. Based on these data, therapeutic interventions that promote muscle function and attenuate pro-fibrotic gene expression should be considered in future studies.

Bone homeostasis can be compromised by an increase in osteoclast-mediated resorption and/or a decrease in osteoblast-mediated bone deposition. While many efforts have focused on treating osteoclast resorption, there has been less emphasis on identifying strategies for promoting osteoblast function. Herein, we describe a high-throughput screening assay to select for small molecules that augment bone morphogenetic protein-2 (BMP-2)-mediated osteoblast lineage commitment. After an initial screen of 5405 compounds; consisting of FDA-approved drugs, known bioactives, and compounds with novel chemical makeup, we identified 45 small molecules that promoted osteoblast commitment. Of the 45 candidates, there was a broad array of classes that included nine retinoid analogs/derivatives and four immunosuppressants, notably rapamycin and FK-506, which were chosen for further study. Treatment of osteoblast precursor cells with rapamycin or FK-506, either alone, or synergistically with BMP-2, increased levels of phospho-Smad 1/5/8 protein and transcription of Runx-2, Osx and Smad-7, consistent with a role in promoting osteoblast differentiation. Only FK-506 was able to enhance osteocalcin transcripts and Alizarin Red staining, both late markers for differentiation. When osteoblast differentiation was suppressed with exogenous TGF-β1 treatment, rapamycin (but not FK-506) was able to rescue expression of differentiation markers, indicating distinct but overlapping activity of these compounds. Collectively, these data add to an understanding of pathways engaged in osteoblastogenesis, support a role for non-redundant immunosuppressant signaling, and provide a novel approach for the discovery of potentially therapeutic compounds that affect bone remodeling.

Healthy aging is thought to reflect the combined influence of environmental factors (lifestyle choices) and genetic factors. To explore the genetic contribution, we undertook a genome-wide association study of exceptional longevity (EL) in 1055 centenarians and 1267 controls. Using these data, we built a genetic model that includes 150 single-nucleotide polymorphisms (SNPs) and found that it could predict EL with 77% accuracy in an independent set of centenarians and controls. Further in silico analysis revealed that 90% of centenarians can be grouped into 19 clusters characterized by different combinations of SNP genotypes—or genetic signatures—of varying predictive value. The different signatures, which attest to the genetic complexity of EL, correlated with differences in the prevalence and age of onset of age-associated diseases (e.g., dementia, hypertension, and cardiovascular disease) and may help dissect this complex phenotype into subphenotypes of healthy aging.

After interruption of highly active antiretroviral therapy, 15 out of 53 patients with the X4 HIV strain had a significantly larger decrease in CD4 + T cell count ( P = 0.001) and shorter length of treatment interruption ( P = 0.02) than patients with the R5 strain. At treatment resumption, HIV inferred tropism switched from the X4 strain to the R5 variant in 9 patients (60%). These patients had a prolonged length of treatment interruption compared to that of those who still carried the X4 strain.

In this review, we describe recent advances in the field of RNA regulatory biology and relate these advances to aging science. We introduce a new term, RNA surveillance, an RNA regulatory process that is conserved in metazoans, and describe how RNA surveillance represents molecular cross-talk between two emerging RNA regulatory systems—RNA interference and RNA editing. We discuss how RNA surveillance mechanisms influence mRNA and microRNA expression and activity during lifespan. Additionally, we summarize recent data from our own laboratory linking the RNA editor, ADAR, with exceptional longevity in humans and lifespan in Caenorhabditis elegans. We present data showing that transcriptional knockdown of RNA interference restores lifespan losses in the context of RNA editing defects, further suggesting that interaction between these two systems influences lifespan. Finally, we discuss the implications of RNA surveillance for sarcopenia and muscle maintenance, as frailty is a universal feature of aging. We end with a discussion of RNA surveillance as a robust regulatory system that can change in response to environmental stressors and represents a novel axis in aging science.

Background The strong familiality of living to extreme ages suggests that human longevity is genetically regulated. The majority of genes found thus far to be associated with longevity primarily function in lipoprotein metabolism and insulin/IGF-1 signaling. There are likely many more genetic modifiers of human longevity that remain to be discovered. Methodology/Principal Findings Here, we first show that 18 single nucleotide polymorphisms (SNPs) in the RNA editing genes ADARB1 and ADARB2 are associated with extreme old age in a U.S. based study of centenarians, the New England Centenarian Study. We describe replications of these findings in three independently conducted centenarian studies with different genetic backgrounds (Italian, Ashkenazi Jewish and Japanese) that collectively support an association of ADARB1 and ADARB2 with longevity. Some SNPs in ADARB2 replicate consistently in the four populations and suggest a strong effect that is independent of the different genetic backgrounds and environments. To evaluate the functional association of these genes with lifespan, we demonstrate that inactivation of their orthologues adr-1 and adr-2 in C. elegans reduces median survival by 50%. We further demonstrate that inactivation of the argonaute gene, rde-1, a critical regulator of RNA interference, completely restores lifespan to normal levels in the context of adr-1 and adr-2 loss of function. Conclusions/Significance Our results suggest that RNA editors may be an important regulator of aging in humans and that, when evaluated in C. elegans, this pathway may interact with the RNA interference machinery to regulate lifespan.

Background Many microarray experiments produce temporal profiles in different biological conditions but common cluster techniques are not able to analyze the data conditional on the biological conditions. Results This article presents a novel technique to cluster data from time course microarray experiments performed across several experimental conditions. Our algorithm uses polynomial models to describe the gene expression patterns over time, a full Bayesian approach with proper conjugate priors to make the algorithm invariant to linear transformations, and an iterative procedure to identify genes that have a common temporal expression profile across two or more experimental conditions, and genes that have a unique temporal profile in a specific condition. Conclusion We use simulated data to evaluate the effectiveness of this new algorithm in finding the correct number of clusters and in identifying genes with common and unique profiles. We also use the algorithm to characterize the response of human T cells to stimulations of antigen-receptor signaling gene expression temporal profiles measured in six different biological conditions and we identify common and unique genes. These studies suggest that the methodology proposed here is useful in identifying and distinguishing uniquely stimulated genes from commonly stimulated genes in response to variable stimuli. Software for using this clustering method is available from the project home page.

[Background] One of the challenges of the analysis of pooling-based genome wide association studies is to identify authentic associations among potentially thousands of false positive associations. [Results] We present a hierarchical and modular approach to the analysis of genome wide genotype data that incorporates quality control, linkage disequilibrium, physical distance and gene ontology to identify authentic associations among those found by statistical association tests. The method is developed for the allelic association analysis of pooled DNA samples, but it can be easily generalized to the analysis of individually genotyped samples. We evaluate the approach using data sets from diverse genome wide association studies including fetal hemoglobin levels in sickle cell anemia and a sample of centenarians and show that the approach is highly reproducible and allows for discovery at different levels of synthesis. [Conclusion] Results from the integration of Bayesian tests and other machine learning techniques with linkage disequilibrium data suggest that we do not need to use too stringent thresholds to reduce the number of false positive associations. This method yields increased power even with relatively small samples. In fact, our evaluation shows that the method can reach almost 70% sensitivity with samples of only 100 subjects., Supported by NHLBI grants R21 HL080463 (PS); R01 HL68970 (MHS); K-24, AG025727 (TP); K23 AG026754 (D.T.).

HIV-associated wasting and weight loss remain clinically significant concerns even in the era of potent antiretroviral therapy. Although androgen treatment increases muscle mass, the cell-intrinsic mechanisms engaged remain poorly understood.This study was an unbiased approach to identify expression profiles associated with testosterone treatment using genome-wide microarray analysis of skeletal muscle biopsies.Forty-four HIV-positive men with weight loss were randomized to receive either 300 mg testosterone enanthate or placebo injections im weekly for 16 wk. Muscle biopsies were obtained at baseline and on treatment d 14. A subset of specimens was chosen for microarray analysis, with changes in selected genes confirmed by real-time PCR, Western blot analysis, and in vitro culture of muscle precursor cells.Significantly greater gains in body mass (+2.05 and -1.07 kg, respectively; P = 0.003) and lean body mass by dual-energy x-ray absorptiometry (2.93 vs. 0.35 kg, respectively; P = 0.003) were observed in subjects treated with testosterone compared with placebo. Microarray analysis revealed up-regulation in genes involved in myogenesis and muscle protein synthesis, immune regulation, metabolic pathways, and chromatin remodeling. Representative genes were confirmed by real-time PCR and protein expression studies. In an independent analysis, gene networks that differentiate healthy young men from older men with sarcopenia had substantial overlap with those activated by testosterone treatment.These data provide new insights into the mechanisms of androgen action and have implications for both development of muscle biomarkers and anabolic therapies for wasting and sarcopenia.

There is considerable evidence that co-infection with the sexually transmitted pathogen Neisseria gonorrhoeae (Gc) can increase the likelihood of both transmitting and acquiring HIV-1 worldwide. However, less information is available on how host immune response to co-infection differs with immune response to HIV-1 infection alone. To evaluate HIV-1 burden effects on host response to co-infection with Gc, we performed gene-expression profiling of human PBMCs infected over a broad range of viral titers (HIV-1 series) and upon exposure to a single infectious dose of Gc (HIV-1/Gc series). The transcriptional profiles differed substantially between each series (P < 0.0001). Major shifts in the transcriptional landscape were identified in contour plots based on fold stimulation and hierarchical clustering. Prominent regions of transcriptional activity were evaluated for statistical enrichment to identify up-regulated pathways associated with immune response, infection and T-cell stimulation. Notably, gene enrichment was dependent on HIV-1 burden and shifted during co-infection to reveal a disproportionate effect on lymphocyte signaling, apoptosis and proteasome activity. Further evaluation of these findings may help to better understand the role of viral burden in defining cellular contribution to host immune response upon co-infection with secondary sexually transmitted pathogens.

A longitudinal study of the replication capacity of HIV strains isolated from 18 patients failing highly active antiretroviral therapy (HAART) was undertaken at the time of genotypic guided change of therapy and after 12 months. Patients were divided in two groups according to the response to therapy: immune responders (12 patients with immune recovery defined as having more than 100 CD4 cells compared to baseline value), and failing patients (six patients without immune recovery). At enrollment no significant difference in terms of CD4 cell count and HIV plasma viremia was detected between the two groups. One year after change of therapy, all patients experienced a decrease in the replication capacity of HIV strains. The HIV replication capacity of the failing and of immune-responder patients decreased from 60% (range 14-96%) to 26.4% (range 0.4-74.5) and from 46.8% (range 15-98%) to 3.6% (range 0.1-26.8%), respectively. At month 12, the difference of HIV replication capacity between the two groups reached a statistical significance (P

Maternal plasma human immunodeficiency virus (HIV) type 1 RNA load has a role in perinatal transmission, but significant overlap in the range of plasma virus loads among transmitters and nontransmitters is often observed, which makes it difficult to predict transmission outcome. We measured several virus markers in a drug-naive population of HIV-1-infected mothers in Botswana. Maternal plasma HIV-1 RNA load, peripheral blood mononuclear cell-associated blood HIV-1 DNA load, and cervicovaginal fluid (CVF) HIV-1 DNA load were determined using quantitative real-time polymerase chain reaction. The overall rate of transmission among these mother-infant pairs was 35.7%. Median infant age was 2.5 months. An association between increased plasma HIV-1 RNA load and perinatal transmission was observed (odds ratio [OR], 2.20/1-log virus load; 95% confidence interval [CI], 1.15-4.18). However, the association between increased blood HIV-1 DNA load and perinatal transmission was stronger (OR, 10.30; 95% CI, 2.11-50.38). When blood HIV-1 DNA load was combined with CVF HIV-1 DNA load, the association with transmission increased (OR, 25.0; 95% CI 2.73-228.60).

To better understand the virological aspect of the expanding AIDS epidemic in southern Africa, a set of 23 near-full-length clones of human immunodeficiency virus type 1 (HIV-1) representing eight AIDS patients from Botswana were sequenced and analyzed phylogenetically. All study viruses from Botswana belonged to HIV-1 subtype C. The interpatient diversity of the clones from Botswana was higher than among full-length isolates of subtype B or among a set of full-length HIV-1 genomes of subtype C from India (mean value of 9.1% versus 6.5 and 4.3%, respectively; P

The global diversity of human immunodeficiency virus type 1 (HIV-1) genotypes, termed subtypes A to J, is considerable and growing. However, relatively few studies have provided evidence for an associated phenotypic divergence. Recently, we demonstrated subtype-specific functional differences within the long terminal repeat (LTR) region of expanding subtypes (M. A. Montano, V. A. Novitsky, J. T. Blackard, N. L. Cho, D. A. Katzenstein, and M. Essex, J. Virol. 71:8657–8665, 1997). Notably, all HIV-1E isolates were observed to contain a defective upstream NF-κB site and a unique TATA-TAR region. In this study, we demonstrate that tumor necrosis factor alpha (TNF-α) stimulation of the HIV-1E LTR was also impaired, consistent with a defective upstream NF-κB site. Furthermore, repair of the upstream NF-κB site within HIV-1E partially restored TNF-α responsiveness. We also show, in gel shift assays, that oligonucleotides spanning the HIV-1E TATA box displayed a reduced efficiency in the assembly of the TBP-TFIIB-TATA complex, relative to an HIV-1B TATA oligonucleotide. In transfection assays, the HIV-1E TATA, when changed to the canonical HIV-1B TATA sequence (ATA A AA→ATA T AA) unexpectedly reduces both heterologous HIV-1B Tat and cognate HIV-1E Tat activation of an HIV-1E LTR-driven reporter gene. However, Tat activation, irrespective of subtype, could be rescued by introducing a cognate HIV-1B TAR. Collectively, these observations suggest that the expanding HIV-1E genotype has likely evolved an alternative promoter configuration with altered NF-κB and TATA regulatory signals in contradistinction with HIV-1B.

Phylogenetic characterization of primary isolates from 17 HIV-1-infected individuals within a recent epidemic in the city of Odessa, Ukraine was conducted. The isolates were drawn from two time periods, 1993 and 1996. The 1996 isolates coincided with the first apparent expansion of HIV-1 among injection drug users (IDU). Multi-locus phylogenetic analysis indicated that HIV-1 gag, env, tat, and long terminal repeat (LTR) sequences all conformed to the HIV-1 classification of a subcluster within subtype A. There was no evidence for intersubtype recombinants among these isolates. A number of potential signature sequences, particularly within env, were identified in these two time periods, possibly suggesting a selective pressure on viral evolution among IDU. Results of this study are consistent with a recent introduction and subsequent independent evolution of an HIV-1 subtype A subcluster among IDU in the Southern Ukraine. This study demonstrates a congruence of multi-locus phylogenetic analysis, and suggests that non-B genetic subtypes, such as HIV-1 subtype A, may become relevant to the study of IDU transmission in the future.

The current AIDS pandemic represents the uneven spread of multiple genetically related subtypes (A to J) of human immunodeficiency virus type 1 (HIV-1). Notably, HIV-1 E in southeast Asia and HIV-1 C in sub-Saharan Africa are expanding faster and are likely of greater global significance than the HIV-1 B subtype prevalent in the United States and Europe. While many studies have focused on genetic variation among structural genes, we chose to conduct a comparative analysis of the long terminal repeats of HIV-1 E and HIV-1 C isolates and report subtype-specific differences in enhancer copy numbers and sequences, as well as divergent activation in response to the cellular transcriptional activators Rel-p65 and NFATc and viral Tat. This study is the first to identify functional distinctions in promoter architecture between HIV-1 subtypes and raises the possibility that regulatory divergence among the subtypes of HIV-1 has occurred. Divergent transcriptional regulation may explain some of the epidemiologically observed differences in transmission and pathogenesis and underscores the need for further comparative analysis of HIV-1 regulation.

Like most complex phenotypes, exceptional longevity is thought to reflect a combined influence of environmental (e.g., lifestyle choices, where we live) and genetic factors. To explore the genetic contribution, we undertook a genome-wide association study of exceptional longevity in 801 centenarians (median age at death 104 years) and 914 genetically matched healthy controls. Using these data, we built a genetic model that includes 281 single nucleotide polymorphisms (SNPs) and discriminated between cases and controls of the discovery set with 89% sensitivity and specificity, and with 58% specificity and 60% sensitivity in an independent cohort of 341 controls and 253 genetically matched nonagenarians and centenarians (median age 100 years). Consistent with the hypothesis that the genetic contribution is largest with the oldest ages, the sensitivity of the model increased in the independent cohort with older and older ages (71% to classify subjects with an age at death>102 and 85% to classify subjects with an age at death>105). For further validation, we applied the model to an additional, unmatched 60 centenarians (median age 107 years) resulting in 78% sensitivity, and 2863 unmatched controls with 61% specificity. The 281 SNPs include the SNP rs2075650 in TOMM40/APOE that reached irrefutable genome wide significance (posterior probability of association = 1) and replicated in the independent cohort. Removal of this SNP from the model reduced the accuracy by only 1%. Further in-silico analysis suggests that 90% of centenarians can be grouped into clusters characterized by different "genetic signatures" of varying predictive values for exceptional longevity. The correlation between 3 signatures and 3 different life spans was replicated in the combined replication sets. The different signatures may help dissect this complex phenotype into sub-phenotypes of exceptional longevity.

Phenotypic heterogeneity is a well known characteristic of sickle cell anemia. Patients have different rates of hemolysis-related complications, like pulmonary hypertension, priapism and leg ulceration, and viscosity/vasoocclusion-related complications, like painful episodes, acute chest syndrome and osteonecrosis; they also have variation in levels of HbF and hematocrit. To integrate individual disease variables into a global measure of severity, we developed a Bayesian network model that described the complex associations of 25 clinical and laboratory variables, deriving a score that we used to define disease severity (0, least severe to 1, most severe) as the risk of death within 5 years (Sebastiani et al, Blood 2007). This initial network, validated in 2 unrelated patient populations, did not incorporate the genetic heterogeneity that is likely to modulate its components. Accordingly, we studied the association of single nucleotide polymorphisms (964 SNPs) in candidate genes (315 genes) using a Bayesian beta regression model of the severity score in 741 HBB glu6val homozygotes, aged more than 18 years. Forty-three SNPs in about 25 genes were associated with disease severity. Some associated SNPs tag genes that affect nitric oxide and oxidative biology and the endothelium, such as NOS1, ASS, KL, HMOX1, ECE1, KDR, FLT1. Homozygosity for an intronic SNP in ECE1 is associated with a increase of severity (OR=3.5). As expected, some associations were consistent with our previous findings. For example, the same SNP in ECE1 and TGFBR3, that was highly predictive of severity, was also strongly associated with sickle cell stroke (Sebastiani et al, Nature Genet 2005). Also, the association with severity of genes in the TGF-beta signaling pathway, including BMP6 and TGFBR3, were also associated with individual disease complications. Other associated genes play a less obvious role in the pathobiology of disease, e.g., HAO2, but are very strongly associated with the phenotype of severity (probability of a chance association, for HAO2, 10−6). Several of the genes associated with severity, including KL, PRKCA, FLT1 and MET have been related to aging, as suggested by gene expression profiling and studies in model organisms for aging. In genome-wide studies of the genetic basis of exceptional longevity, we found associations with some of the same genes that were associated with severity in sickle cell anemia. Perhaps increased oxidative stress, and the relentless progression of vasculopathy in sickle cell anemia, cause accelerated tissue damage that is modulated by a set of genes similar to those involved in the normal aging process. We suggest that the disease severity score can be used as a phenotype integrating many features of the disease, for genetic association studies. As we add the results of unbiased genome-wide association studies to capture polymorphisms not included in candidate gene studies, we can develop a predictive network with even greater reliability than one using only clinical and laboratory variables. Such networks might also identify pathways that could be targeted to alter the course of disease.

Retroviruses such as human immunodeficiency virus type 1 (HIV-1) contain two RNA strands per virion, and recombination can occur frequently during reverse transcription. Recombination may occur between HIV-1 genomes of the same subtype or among genomes of two or more distinct subtypes present in an individual. In the current study, we found that recombinatorial events were not limited to viral structural genes such as gag and env, but rather, recombination could likewise occur within the 5′ long terminal repeat (LTR). Intersubtype recombinant LTRs among HIV-1 subtypes A, C, and D were found in Tanzanian infants. By introducing novel LTR sequences, these recombinant LTR viruses may further increase the adaptive potential and fitness of HIV-1.