Transcriptome analysis of age-, gender- and diet-associated changes in murine thymus

The poorly conducted orchestra of steroid hormones, oxidative stress and inflammation in frailty needs a maestro: Regular physical exercise

This review outlines the various factors associated with unhealthy aging which includes becoming frail and dependent. With many people not engaging in recommended exercise, facilitators and barriers to engage with exercise must be investigated to promote exercise uptake and adherence over the lifespan for different demographics, including the old, less affluent, women, and those with different cultural-ethnic backgrounds. Governmental and locally funded public health messages and environmental facilitation (gyms, parks etc.) can play an important role. Studies have shown that exercise can act as a conductor to balance oxidative stress, immune and endocrine functions together to promote healthy aging and reduce the risk for age-related morbidities, such as cardiovascular disease and atherosclerosis, and promote cognition and mood over the lifespan. Like a classic symphony orchestra, consisting of four groups of related musical instruments - the woodwinds, brass, percussion, and strings - the aging process should also perform in harmony, with compassion, avoiding the aggrandizement of any of its individual parts during the presentation. This review discusses the wide variety of molecular, cellular and endocrine mechanisms (focusing on the steroid balance) underlying this process and their interrelationships.

Ageing transcriptome meta-analysis reveals similarities and differences between key mammalian tissues

By combining transcriptomic data with other data sources, inferences can be made about functional changes during ageing. Thus, we conducted a meta-analysis on 127 publicly available microarray and RNA-Seq datasets from mice, rats and humans, identifying a transcriptomic signature of ageing across species and tissues. Analyses on subsets of these datasets produced transcriptomic signatures of ageing for brain, heart and muscle. We then applied enrichment analysis and machine learning to functionally describe these signatures, revealing overexpression of immune and stress response genes and underexpression of metabolic and developmental genes. Further analyses revealed little overlap between genes differentially expressed with age in different tissues, despite ageing differentially expressed genes typically being widely expressed across tissues. Additionally we show that the ageing gene expression signatures (particularly the overexpressed signatures) of the whole meta-analysis, brain and muscle tend to include genes that are central in protein-protein interaction networks. We also show that genes underexpressed with age in the brain are highly central in a co-expression network, suggesting that underexpression of these genes may have broad phenotypic consequences. In sum, we show numerous functional similarities between the ageing transcriptomes of these important tissues, along with unique network properties of genes differentially expressed with age in both a protein-protein interaction and co-expression networks.

Irf3 from mandarin fish thymus initiates interferon transcription

Interferon regulatory factors (IRFs) are transcription factors of the interferon (IFN)-inducible signaling pathway essential for host immunity against antimicrobial infection by virus and bacteria. Interferon regulatory factor 3 (IRF3) regulates the expression of IFNs and IFN-stimulated genes by binding to the IFN stimulatory response element (ISRE). In this study, we analyze the thymus transcriptome of the mandarin fish Siniperca chuatsi and report the functional analysis of Irf3 from the thymus as an emerging model of antiviral approaches. The predicted S. chuatsi IRF3 (Sc-Irf3) protein has 465 amino acid residues and evolutionarily conserved domains and is clustered in the IRF3 subfamily on a phylogenetic tree. Sc-Irf3 upon transgenic expression was mainly found in the cytoplasm through Western blot analysis and microscopy, but it translocated to the nucleus after polyinosinic:polycytidylic acid (ploly I:C) treatment. Endogenous Sc-irf3 RNA expression was detected in all eight adult organs examined. Importantly, Sc-irf3 RNA expression was significantly upregulated by ploly(I:C) treatment in the adult organs. Concurrently, reporter assays revealed that Sc-Irf3 increased the transcriptional activity of the ifnβ promoter, a minimal ISRE-containing promoter, and ifn promoter of mandarin fish. Therefore, Sc-Irf3 plays a major role in the IFN immune defense system against virus infection.

A novel mechanism of tumor-induced thymic atrophy in mice bearing H22 hepatocellular carcinoma

Background

Thymic atrophy was discovered in tumor-bearing mice in recent years.

Methods

Flow cytometry was carried out including Annexin V-FITC/PI double staining, PI staining, Terminal dUTP nick-end labeling, CD3-FITC/CD19-PE and CD8-FITC/CD4-PE double staining. Enzyme-linked immunosorbent assay and polymerase chain reaction were also investigated.

Results

According to our experiments, we demonstrated that no signs of apoptosis in thymocytes were found in H22-bearing mice, while the proportions of CD4⁺ T cells and CD8⁺ T cells in thymuses were remarkably increased, the opposite tendency was found in peripheral bloods, and only CD3⁺CD8⁺ T cells were discovered in H22 solid tumors. We further discovered that the level of thymosin alpha 1 (Tα1) and the expression of Wnt4 in thymus of H22-bearing mice were significantly improved than control, which indicated the active proliferation and differentiation of thymocytes. Our study revealed that CD8⁺ T cells could not effectively eliminate H22 cells independently when CD4⁺ T cells were suppressed by tumors, while the body would only enhance the differentiation and maturation of T cells in thymuses and release them to solid tumor to reinforce antitumor immunocompetence, leading to a vicious cycle which finally led to thymic atrophy.

Conclusion

Our data propose a novel mechanism of tumor-induced thymic atrophy regulated by abnormal immunoreaction and may provide new ideas for the immunotherapy of tumors.

Age and sex differences in microRNAs expression during the process of thymus aging

The gender-biased thymus involution and the importance of microRNAs (miRNAs, miRs) expression in modulating the thymus development have been reported in many studies. However, how males and females differ in so many ways in thymus involution remains unclear. To address this question, we investigated the miRNA expression profiles in both untreated 3- and 12-month-old female and male mice thymuses. The results showed that 7 and 18 miRNAs were defined as the sex- and age-specific miRNAs, respectively. The expression of miR-181c-5p, miR-20b-5p, miR-98b-5p, miR-329-3p, miR-341-5p, and miR-2137 showed significant age-difference in mice thymus by quantitative polymerase chain reaction. High expression levels of miR-2137 were detected in mice thymic epithelial cells and gradually increased during the process of thymus aging. MiR-27b-3p and miR-378a-3p of the female-biased miRNAs were confirmed as the sex- and estrogen-responsive miRNAs in mice thymus in vivo. Their potential target genes and the pathway were identified by the online software. Possible regulation roles of sex- and age-specific miRNA expression during the process of thymus aging were discussed. Our results suggested that these miRNAs may be potential biomarkers for the study of sex- and age-specific thymus aging and involution.

Ghrelin augments murine T-cell proliferation by activation of the phosphatidylinositol-3-kinase, extracellular signal-regulated kinase and protein kinase C signaling pathways

Thymic atrophy occurs during normal aging, and is accelerated by exposure to chronic stressors that elevate glucocorticoid levels and impair the naïve T cell output. The orexigenic hormone ghrelin was recently shown to attenuate age-associated thymic atrophy. Here, we report that ghrelin enhances the proliferation of murine CD4+ primary T cells and a CD4+ T-cell line. Ghrelin induced activation of the ERK1/2 and Akt signaling pathways, via upstream activation of phosphatidylinositol-3-kinase and protein kinase C, to enhance T-cell proliferation. Moreover, ghrelin induced expression of the cell cycle proteins cyclin D1, cyclin E, cyclin-dependent kinase 2 (CDK2) and retinoblastoma phosphorylation. Finally, ghrelin activated the above-mentioned signaling pathways and stimulated thymocyte proliferation in young and older mice in vivo.

T cell aging: a review of the transcriptional changes determined from genome-wide analysis

Age carries a detrimental impact on T cell function. In the past decade, analyses of the genome-scale transcriptional changes of T cells during aging have yielded a large amount of data and provided a global view of gene expression changes in T cells from aged hosts as well as subsets of T cells accumulated with age. Here, we aim to review the changes of gene expression in thymocytes and peripheral mature T cells, as well as the subsets of T cells accumulated with age, and discuss the gene networks and signaling pathways that are altered with aging in T cells. We also discuss future direction for furthering the understanding of the molecular basis of gene expression alterations in aged T cells, which could potentially provide opportunities for gene-based clinical interventions.

Meta-profiles of gene expression during aging: limited similarities between mouse and human and an unexpectedly decreased inflammatory signature

BACKGROUND

Skin aging is associated with intrinsic processes that compromise the structure of the extracellular matrix while promoting loss of functional and regenerative capacity. These processes are accompanied by a large-scale shift in gene expression, but underlying mechanisms are not understood and conservation of these mechanisms between humans and mice is uncertain.

RESULTS

We used genome-wide expression profiling to investigate the aging skin transcriptome. In humans, age-related shifts in gene expression were sex-specific. In females, aging increased expression of transcripts associated with T-cells, B-cells and dendritic cells, and decreased expression of genes in regions with elevated Zeb1, AP-2 and YY1 motif density. In males, however, these effects were contrasting or absent. When age-associated gene expression patterns in human skin were compared to those in tail skin from CB6F1 mice, overall human-mouse correspondence was weak. Moreover, inflammatory gene expression patterns were not induced with aging of mouse tail skin, and well-known aging biomarkers were in fact decreased (e.g., Clec7a, Lyz1 and Lyz2). These unexpected patterns and weak human-mouse correspondence may be due to decreased abundance of antigen presenting cells in mouse tail skin with age.

CONCLUSIONS

Aging is generally associated with a pro-inflammatory state, but we have identified an exception to this pattern with aging of CB6F1 mouse tail skin. Aging therefore does not uniformly heighten inflammatory status across all mouse tissues. Furthermore, we identified both intercellular and intracellular mechanisms of transcriptome aging, including those that are sex- and species-specific.

MCL1 increases primitive thymocyte viability in female mice and promotes thymic expansion into adulthood

Increasing the pool of cells at early T-cell developmental stages enhances thymopoiesis and is especially beneficial when T-cell production is compromised by radiation or aging. Within the immature double-negative (DN; CD4(-)CD8(-)) thymocyte subpopulation, the DN1 subset contains the most primitive cells including the rare early T-cell progenitors (ETPs). In the present study, a human MCL1 transgene, under the control of its endogenous promoter, resulted in enlargement of an undistorted thymus in C57/BL6 mice. Enlargement occurred in females but not males, being seen at 1 month of age and maintained during progression into adulthood as the thymus underwent involution. The small DN1 subset was expanded disproportionally (ETPs increasing from ∼0.016 to 0.03% of thymocytes), while more mature thymocytes were increased proportionally (1.5-fold) along with the stroma. DN1 cells from transgenic females exhibited increased viability with maintained proliferation, and their survival in primary culture was extended. Exposure of transgenic females to γ-irradiation also revealed an expanded pool of radioresistant DN1 cells exhibiting increased viability. While the viability of DN1 cells from transgenic males was equivalent to that of their non-transgenic counterparts directly after harvest, it was enhanced in culture-suggesting that the effect of the transgene was suppressed in the in vivo environment of the male. Viability was increased in ETPs from transgenic females, but unchanged in more mature thymocytes, indicating that primitive cells were affected selectively. The MCL1 transgene thus increases the viability and pool size of primitive ETP/DN1 cells, promoting thymopoiesis and radioresistance in peripubescent females and into adulthood.

Thymic fatness and approaches to enhance thymopoietic fitness in aging

With advancing age, the thymus undergoes striking fibrotic and fatty changes that culminate in its transformation into adipose tissue. As the thymus involutes, reduction in thymocytes and thymic epithelial cells precede the emergence of mature lipid-laden adipocytes. Dogma dictates that adipocytes are 'passive' cells that occupy non-epithelial thymic space or 'infiltrate' the non-cellular thymic niches. The provenance and purpose of ectopic thymic adipocytes during aging in an organ that is required for establishment and maintenance of T cell repertoire remains an unsolved puzzle. Nonetheless, tantalizing clues about elaborate reciprocal relationship between thymic fatness and thymopoietic fitness are emerging. Blocking or bypassing the route toward thymic adiposity may complement the approaches to rejuvenate thymopoiesis and immunity in elderly.

Maternal protein restriction affects gene expression profiles in the kidney at weaning with implications for the regulation of renal function and lifespan

Nutritionally induced alterations in early growth can influence health and disease in later adult life. We have demonstrated previously that low birthweight resulting from maternal protein restriction during pregnancy followed by accelerated growth in rodents was associated with shortened lifespan, whereas protein restriction and slow growth during lactation increased lifespan. Thus early life events can also have a long lasting impact on longevity. In the present study, we show that long-lived PLP (postnatal low protein) mice were protected from developing albuminuria, whereas short-lived recuperated mice demonstrated an age-dependent increase in albuminuria in old age. Microarray analysis of kidneys from 21-day-old mice revealed that gene expression profiles were differentially affected depending on whether protein restriction was imposed during pregnancy or lactation. The differentially expressed genes were involved in diverse biological functions such as cytoprotective functions, vitamin D synthesis, protein homoeostasis, regulation of antioxidant enzymes and cellular senescence. Significantly, up-regulation of Hmox1 (haem oxygenase 1) in kidneys from PLP mice suggests that tissues of long-lived mice are equipped with a better cytoprotective function. In contrast, up-regulation of Nuak2 (NUAK family, SNF1-like kinase 2) and down-regulation of Lonp2 (Lon peptidase 2), Foxo3a (forkhead box O3a), Sod1 (copper/zinc superoxide dismutase) and Sesn1 (sestrin 1) in the kidneys of recuperated offspring suggest that protein homoeostasis and resistance to oxidative stress are compromised, leading to accelerated cellular senescence in these shorter-lived mice.

Genes and gene expression modules associated with caloric restriction and aging in the laboratory mouse

BACKGROUND

Caloric restriction (CR) counters deleterious effects of aging and, for most mouse genotypes, increases mean and maximum lifespan. Previous analyses of microarray data have identified gene expression responses to CR that are shared among multiple mouse tissues, including the activation of anti-oxidant, tumor suppressor and anti-inflammatory pathways. These analyses have provided useful research directions, but have been restricted to a limited number of tissues, and have focused on individual genes, rather than whole-genome transcriptional networks. Furthermore, CR is thought to oppose age-associated gene expression patterns, but detailed statistical investigations of this hypothesis have not been carried out.

RESULTS

Systemic effects of CR and aging were identified by examining transcriptional responses to CR in 17 mouse tissue types, as well as responses to aging in 22 tissues. CR broadly induced the expression of genes known to inhibit oxidative stress (e.g., Mt1, Mt2), inflammation (e.g., Nfkbia, Timp3) and tumorigenesis (e.g., Txnip, Zbtb16). Additionally, a network-based investigation revealed that CR regulates a large co-expression module containing genes associated with the metabolism and splicing of mRNA (e.g., Cpsf6, Sfpq, Sfrs18). The effects of aging were, to a considerable degree, similar among groups of co-expressed genes. Age-related gene expression patterns characteristic of most mouse tissues were identified, including up regulation of granulin (Grn) and secreted phosphoprotein 1 (Spp1). The transcriptional association between CR and aging varied at different levels of analysis. With respect to gene subsets associated with certain biological processes (e.g., immunity and inflammation), CR opposed age-associated expression patterns. However, among all genes, global transcriptional effects of CR were only weakly related to those of aging.

CONCLUSION

The study of aging, and of interventions thought to combat aging, has much to gain from data-driven and unbiased genomic investigations. Expression patterns identified in this analysis characterize a generalized response of mammalian cells to CR and/or aging. These patterns may be of importance in determining effects of CR on overall lifespan, or as factors that underlie age-related disease. The association between CR and aging warrants further study, but most evidence indicates that CR does not induce a genome-wide "reversal" of age-associated gene expression patterns.

Composition and function of haemolymphatic tissues in the European common shrew

BACKGROUND

Studies of wild animals responding to their native parasites are essential if we are to understand how the immune system functions in the natural environment. While immune defence may bring increased survival, this may come at a resource cost to other physiological traits, including reproduction. Here, we tested the hypothesis that wild common shrews (Sorex araneus), which produce large numbers of offspring during the one breeding season of their short life span, forgo investment in immunity and immune system maintenance, as increased longevity is unlikely to bring further opportunities for mating. In particular, we predicted that adult shrews, with shorter expected lifespans, would not respond as effectively as young animals to infection.

METHODOLOGY/PRINCIPAL FINDINGS

We examined haemolymphatic tissues from wild-caught common shrews using light and transmission electron microscopy, applied in conjunction with immunohistology. We compared composition and function of these tissues in shrews of different ages, and the extent and type of inflammatory reactions observed in response to natural parasitic infections. All ages seemed able to mount systemic, specific immune responses, but adult shrews showed some signs of lymphatic tissue exhaustion: lymphatic follicles in adults (n = 21) were both smaller than those in sub-adults (n = 18; Wald = 11.1, p<0.05) and exhibited greater levels of depletion (Wald = 13.3, p<0.05).

CONCLUSIONS/SIGNIFICANCE

Contrary to our expectations, shrews respond effectively to their natural parasites, and show little indication of immunosenescence as adults. The pancreas of Aselli, a unique lymphoid organ, may aid in providing efficient immune responses through the storage of large numbers of plasma cells. This may allow older animals to react effectively to previously encountered parasites, but infection by novel agents, and eventual depletion of plasma cell reserves, could both still be factors in the near-synchronous mortality of adult shrews observed shortly after breeding.

Characterization of Age- and Gender-related Changes in the Spleen and Thymus from Control Cynomolgus Macaques Used in Toxicity Studies

Age- and gender-related lymphoid tissue variability in control male and female monkeys of various ages (under three years; three to six years; seven to fifteen years) was characterized. Spleen and thymus organ weights, organ-to-body and organ-to-brain ratios, morphology by light microscopy, and B- and T-cell immunohistochemistry (IHC) were evaluated. Splenic weights and ratios were not significantly different between various age groups or genders, except males and females in the three-to-six-years age group, who exhibited statistically significant changes from the under-three-years age group. No differences in the number of primary follicles, secondary follicles with germinal centers, B-cell follicles, and periarterial lymphoid sheath were seen between age groups or genders, and no trends were noted in the spleen. By IHC, no differences were observed in B- and T-cell splenic densities. Several age- and gender-related changes in weights and ratios were noted in the thymus. The thymus had a trend toward increased interlobular fat infiltration with increasing age in both males and females. Thymic delineation of the cortex and medulla was significantly decreased in the seven-to-fifteen-years age group for males only. The cortex-to-medulla ratio was significantly lower only in males in the seven-to-fifteen-years age group. B- and T-cell cellular density did not change across various ages.

Aging of the immune system as a prognostic factor for human longevity

Accumulating data are documenting an inverse relationship between immune status, response to vaccination, health, and longevity, suggesting that the immune system becomes less effective with advancing age and that this is clinically relevant. The mechanisms and consequences of age-associated immune alterations, designated immunosenescence, are briefly reviewed here.

Effects of aging and calorie restriction on the global gene expression profiles of mouse testis and ovary

Background

The aging of reproductive organs is not only a major social issue, but of special interest in aging research. A long-standing view of 'immortal germ line versus mortal soma' poses an important question of whether the reproductive tissues age in similar ways to the somatic tissues. As a first step to understand this phenomenon, we examine global changes in gene expression patterns by DNA microarrays in ovaries and testes of C57BL/6 mice at 1, 6, 16, and 24 months of age. In addition, we compared a group of mice on ad libitum (AL) feeding with a group on lifespan-extending 40% calorie restriction (CR).

Results

We found that gene expression changes occurred in aging gonads, but were generally different from those in somatic organs during aging. For example, only two functional categories of genes previously associated with aging in muscle, kidney, and brain were confirmed in ovary: genes associated with complement activation were upregulated, and genes associated with mitochondrial electron transport were downregulated. The bulk of the changes in gonads were mostly related to gonad-specific functions. Ovaries showed extensive gene expression changes with age, especially in the period when ovulation ceases (from 6 to 16 months), whereas testes showed only limited age-related changes. The same trend was seen for the effects of CR: CR-mediated reversal of age-associated gene expression changes, reported in somatic organs previously, was limited to a small number of genes in gonads. Instead, in both ovary and testis, CR caused small and mostly gonad-specific effects: suppression of ovulation in ovary and activation of testis-specific genes in testis.

Conclusion

Overall, the results are consistent with unique modes of aging and its modification by CR in testis and ovary.

AGEMAP: a gene expression database for aging in mice

We present the AGEMAP (Atlas of Gene Expression in Mouse Aging Project) gene expression database, which is a resource that catalogs changes in gene expression as a function of age in mice. The AGEMAP database includes expression changes for 8,932 genes in 16 tissues as a function of age. We found great heterogeneity in the amount of transcriptional changes with age in different tissues. Some tissues displayed large transcriptional differences in old mice, suggesting that these tissues may contribute strongly to organismal decline. Other tissues showed few or no changes in expression with age, indicating strong levels of homeostasis throughout life. Based on the pattern of age-related transcriptional changes, we found that tissues could be classified into one of three aging processes: (1) a pattern common to neural tissues, (2) a pattern for vascular tissues, and (3) a pattern for steroid-responsive tissues. We observed that different tissues age in a coordinated fashion in individual mice, such that certain mice exhibit rapid aging, whereas others exhibit slow aging for multiple tissues. Finally, we compared the transcriptional profiles for aging in mice to those from humans, flies, and worms. We found that genes involved in the electron transport chain show common age regulation in all four species, indicating that these genes may be exceptionally good markers of aging. However, we saw no overall correlation of age regulation between mice and humans, suggesting that aging processes in mice and humans may be fundamentally different.