Dynamic and scalable assessment of the senescence-associated secretory phenotype (SASP).

Dual-faced cellular senescence is responsible for beneficial biological processes and for age-related pathologies. Senescent cells under stable proliferation arrest develop numerous senescence-associated phenotypes such as the potent pro-inflammatory secretome called the senescence-associated secretory phenotype (SASP). The SASP shapes the senescent microenvironment and influences the biology of adjacent cells, including the modulation of proliferation and migration/invasion, reinforcement/induction of peripheral senescence, and immune cell activity or recruitment. The SASP is a dynamic process with multiple waves of secreted factors described to interlace over a period of many days. Whether the senescence phenotype reaches a mature stable state remains controversial. Overall, the complexity of the context-dependent and timely SASP compositions and its varied microenvironmental impact demonstrate the importance of properly assessing SASP over time. In this chapter, we focus on scalable and dynamic experimental procedures to prepare SASP conditioned medium over time from cells receiving senescence-inducing stimuli. This SASP-containing conditioned medium can be used to assess the composition of the SASP, study SASP-related signaling pathways or evaluate the paracrine microenvironmental impact of senescent cells.

Aging and aging-related diseases: from molecular mechanisms to interventions and treatments.

Aging is a gradual and irreversible pathophysiological process. It presents with declines in tissue and cell functions and significant increases in the risks of various aging-related diseases, including neurodegenerative diseases, cardiovascular diseases, metabolic diseases, musculoskeletal diseases, and immune system diseases. Although the development of modern medicine has promoted human health and greatly extended life expectancy, with the aging of society, a variety of chronic diseases have gradually become the most important causes of disability and death in elderly individuals. Current research on aging focuses on elucidating how various endogenous and exogenous stresses (such as genomic instability, telomere dysfunction, epigenetic alterations, loss of proteostasis, compromise of autophagy, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, deregulated nutrient sensing) participate in the regulation of aging. Furthermore, thorough research on the pathogenesis of aging to identify interventions that promote health and longevity (such as caloric restriction, microbiota transplantation, and nutritional intervention) and clinical treatment methods for aging-related diseases (depletion of senescent cells, stem cell therapy, antioxidative and anti-inflammatory treatments, and hormone replacement therapy) could decrease the incidence and development of aging-related diseases and in turn promote healthy aging and longevity.

Comprehensive assessment of cellular senescence in the tumor microenvironment.

Cellular senescence (CS), a state of permanent growth arrest, is intertwined with tumorigenesis. Due to the absence of specific markers, characterizing senescence levels and senescence-related phenotypes across cancer types remain unexplored. Here, we defined computational metrics of senescence levels as CS scores to delineate CS landscape across 33 cancer types and 29 normal tissues and explored CS-associated phenotypes by integrating multiplatform data from ~20 000 patients and ~212 000 single-cell profiles. CS scores showed cancer type-specific associations with genomic and immune characteristics and significantly predicted immunotherapy responses and patient prognosis in multiple cancers. Single-cell CS quantification revealed intra-tumor heterogeneity and activated immune microenvironment in senescent prostate cancer. Using machine learning algorithms, we identified three CS genes as potential prognostic predictors in prostate cancer and verified them by immunohistochemical assays in 72 patients. Our study provides a comprehensive framework for evaluating senescence levels and clinical relevance, gaining insights into CS roles in cancer- and senescence-related biomarker discovery.

Psychosocial stress and epigenetic aging.

Aging is the single most important risk factor for diseases that are currently the leading causes of morbidity and mortality. However, there is considerable inter-individual variability in risk for aging-related disease, and studies suggest that biological age can be influenced by multiple factors, including exposure to psychosocial stress. Among markers of biological age that can be affected by stress, the present article focuses on the so-called measures of epigenetic aging: DNA methylation-based age predictors that are measured in a range of tissues, including the brain, and can predict lifespan and healthspan. We review evidence linking exposure to diverse types of psychosocial stress, including early-life stress, cumulative stressful experiences, and low socioeconomic status, with accelerated epigenetic aging as a putative mediator of the effects of psychosocial environment on health and disease. The chapter also discusses methodological differences that may contribute to discordant findings across studies to date and plausible mechanisms that may underlie the effects of stress on the aging epigenome. Future studies examining the effects of adversity on epigenetic and other indicators of biological weathering may provide important insights into the pathogenesis of aging-related disease states.

Methods and Strategies for Procurement, Isolation, Characterization, and Assessment of Senescence of Human Mesenchymal Stem Cells from Adipose Tissue.

Human adipose-derived mesenchymal stem (stromal) cells (hADSC) represent an attractive source of the cells for numerous therapeutic applications in regenerative medicine. These cells are also an efficient model to study biological pathways of stem cell action, tissue injury and disease. Like any other primary somatic cells in culture, industrial-scale expansion of mesenchymal stromal cells (MSC) leads to the replicative exhaustion/senescence as defined by the "Hayflick limit." The senescence is not only greatly effecting in vivo potency of the stem cell cultures but also might be the cause and the source of clinical inconsistency arising from infused cell preparations. In this light, the characterization of hADSC replicative and stressor-induced senescence phenotypes is of great interest.This chapter summarizes some of the essential protocols and assays used at our laboratories and clinic for the human fat procurement, isolation, culture, differentiation, and characterization of mesenchymal stem cells from adipose tissue and the stromal vascular fraction. Additionally, we provide manuals for characterization of hADSC senescence in a culture based on stem cells immunophenotype, proliferation rate, migration potential, and numerous other well-accepted markers of cellular senescence. Such methodological framework will be immensely helpful to design standards and surrogate measures for hADSC-based therapeutic applications.

Interpersonal-level discrimination indices, sociodemographic factors, and telomere length in African-Americans and Whites.

OBJECTIVE: Studies have linked self-reported discrimination to telomere attrition, a biological marker of accelerated cellular aging. However, it is unknown whether intersections between social categories-race, socioeconomic status (SES), sex, and age-influence the association of varying forms of discrimination with telomere length. We examined these associations in a socioeconomically and racially/ethnically diverse urban sample. METHODS: Cross-sectional data were from 341 middle-aged (30-64 years) African American and White, community participants in the Healthy Aging in Neighborhoods of Diversity across the Life Span Study (HANDLS). Multiple regression models examined up to 3-way interactions between a discrimination measure (i.e., everyday, racial, gender, lifetime burden, and frequency of discrimination across sources) and two social categories. RESULTS: After adjusting for depressive symptoms, waist circumference, and lifetime substance use, two themes emerged: 1) among women with higher SES, a) greater lifetime discrimination burden (b = -0.23, p = .011), gender discrimination (b = -0.29, p = .040), and racial discrimination (b = -0.24, p = 0.023) and 2) among younger adults, irrespective of race and sex, greater frequency of discrimination across sources (b = 0.002, p = .008) was associated with shorter telomeres. CONCLUSIONS: Irrespective of race, women with higher SES and younger adults reporting greater discrimination may be at particular risk for accelerated aging. Telomere attrition promotes and accelerates chronic health conditions for which there are health disparities. Future research explicating intersections among specific discrimination indices and social categories is warranted.

STING SNP R293Q Is Associated with a Decreased Risk of Aging-Related Diseases.

BACKGROUND: Aging is a multifactorial process driven by several conditions. Among them, inflamm-aging is characterized by chronic low-grade inflammation driving aging-related diseases. The aged immune system is characterized by the senescence-associated secretory phenotype, resulting in the release of proinflammatory cytokines contributing to inflamm-aging. Another possible mechanism resulting in inflamm-aging could be the increased release of danger- associated molecular patterns (DAMPs) by increased cell death in the elderly, leading to a chronic low-grade inflammatory response. Several pattern recognition receptors of the innate immune system are involved in recognition of DAMPs. The DNA-sensing cGAS-STING pathway plays a pivotal role in combating viral and bacterial infections and recognizes DNA released by cell death during the process of aging, which in turn may result in increased inflamm-aging. OBJECTIVE: The aim of this study was to investigate whether a variation within the STING gene with known impaired function may be associated with protection from aging-related diseases by decreasing the process of inflamm-aging. METHODS: STING (Tmem173) R293Q was genotyped in a cohort of 3,397 aged subjects (65-103 years). The distribution of the variant allele in healthy subjects and subjects suffering from aging-associated diseases was compared by logistic regression analysis. RESULTS: We show here that STING 293Q allele carriers were protected from aging-associated diseases (OR = 0.823, p = 0.038). This effect was much stronger in the subgroup of subjects suffering from chronic lung diseases (OR = 0.730, p = 0.009). CONCLUSION: Our results indicate that decreased sensitivity of the innate immune receptors is associated with healthy aging, most likely due to a decreased process of inflamm-aging.

MiR-34a and stroke: Assessment of non-modifiable biological risk factors in cerebral ischemia.

Aging of the nervous system, and the occurrence of age-related brain diseases such as stroke, are associated with changes to a variety of cellular processes controlled by many distinct genes. MicroRNAs (miRNAs), short non-coding functional RNAs that can induce translational repression or site-specific cleavage of numerous target mRNAs, have recently emerged as important regulators of cellular senescence, aging, and the response to neurological insult. Here, we focused on the assessment of the role of miR-34a in stroke. We noted increases in miR-34a expression in the blood of stroke patients as well as in blood and brain of mice subjected to experimental stroke. Our methodical genetic manipulation of miR-34a expression substantially impacted stroke-associated preclinical outcomes and we have in vitro evidence that these changes may be driven at least in part by disruptions to blood brain barrier integrity and mitochondrial oxidative phosphorylation in endothelial cells. Finally, aging, independent of brain injury, appears to be associated with shifts in circulating miRNA profiles. Taken together, these data support a role for miRNAs, and specifically miR-34a, in brain aging and the physiological response to age-related neurological insult, and lay the groundwork for future investigation of this novel therapeutic target.

Construction of the Leaf Senescence Database and Functional Assessment of Senescence-Associated Genes.

Leaf senescence is the last phase of plant development and a highly coordinated process regulated by a large number of senescence-associated genes (SAGs). By broad literature survey, we constructed a leaf senescence database (LSD) in 2011 and updated it to Version 2.0 in 2014 ( http://www.eplantsenescence.org/ and http://psd.cbi.pku.edu.cn/ ) which contains a total of 5357 genes and 324 mutants from 44 species. These SAGs were retrieved based on genetic, genomic, proteomic, physiological, or other experimental evidence and were classified into different categories according to their functions in leaf senescence or morphological phenotype of mutants. To provide comprehensive information for SAGs, we made extensive annotation by both manual and computational approaches. In addition, we predicted putative orthologues of the SAGs in other species. LSD has a user-friendly interface to allow users to make text queries or BLAST searches and to download SAGs sequences for local analysis. Functional analyses of putative SAGs reveal that WRKY75, AZF2, NAC16, and WRKY26 are positive regulators of leaf senescence, while MKP2 and CTR1 perform negative regulation to leaf senescence. This database has been served as a valuable resource for basic research on the function of SAGs and evolution of plant leaf senescence, as well as for the exploration of genetic traits in agronomically important plants.

Quantitative assessment of higher-order chromatin structure of the INK4/ARF locus in human senescent cells.

Somatic cells can be reset to oncogene-induced senescent (OIS) cells or induced pluripotent stem (iPS) cells by expressing specified factors. The INK4/ARF locus encodes p15(INK4b) , ARF, and p16(INK4a) genes in human chromosome 9p21, the products of which are known as common key reprogramming regulators. Compared with growing fibroblasts, the CCCTC-binding factor CTCF is remarkably up-regulated in iPS cells with silencing of the three genes in the locus and is reversely down-regulated in OIS cells with high expression of p15(INK4b) and p16(INK4a) genes. There are at least three CTCF-enriched sites in the INK4/ARF locus, which possess chromatin loop-forming activities. These CTCF-enriched sites and the p16(INK4a) promoter associate to form compact chromatin loops in growing fibroblasts, while CTCF depletion disrupts the loop structure. Interestingly, the loose chromatin structure is found in OIS cells. In addition, the INK4/ARF locus has an intermediate type of chromatin compaction in iPS cells. These results suggest that senescent cells have distinct higher-order chromatin signature in the INK4/ARF locus.

Assessment of chronological lifespan dependent molecular damages in yeast lacking mitochondrial antioxidant genes.

The free radical theory of aging states that oxidative damage to biomolecules causes aging and that antioxidants neutralize free radicals and thus decelerate aging. Mitochondria produce most of the reactive oxygen species, but at the same time have many antioxidant enzymes providing protection from these oxidants. Expecting that cells without mitochondrial antioxidant genes would accumulate higher levels of oxidative damage and, therefore, will have a shorter lifespan, we analyzed oxidative damages to biomolecules in young and chronologically aged mutants lacking the mitochondrial antioxidant genes: GRX2, CCP1, SOD1, GLO4, TRR2, TRX3, CCS1, SOD2, GRX5, and PRX1. Among these mutants, ccp1Δ, trx3Δ, grx5Δ, prx1Δ, mutants were sensitive to diamide, and ccs1Δ and sod2Δ were sensitive to both diamide and menadione. Most of the mutants were less viable in stationary phase. Chronologically aged cells produced higher amount of superoxide radical and accumulated higher levels of oxidative damages. Even though our results support the findings that old cells harbor higher amount of molecular damages, no significant difference was observed between wild type and mutant cells in terms of their damage content.

CCancer: a bird's eye view on gene lists reported in cancer-related studies.

CCancer is an automatically collected database of gene lists, which were reported mostly by experimental studies in various biological and clinical contexts. At the moment, the database covers 3369 gene lists extracted from 2644 papers published in approximately 80 peer-reviewed journals. As input, CCancer accepts a gene list. An enrichment analyses is implemented to generate, as output, a highly informative survey over recently published studies that report gene lists, which significantly intersect with the query gene list. A report on gene pairs from the input list which were frequently reported together by other biological studies is also provided. CCancer is freely available at http://mips.helmholtz-muenchen.de/proj/ccancer.

Nuclear size measurement is a simple method for the assessment of hepatocellular aging in non-alcoholic fatty liver disease: Comparison with telomere-specific quantitative FISH and p21 immunohistochemistry.

Telomere-specific quantitative fluorescent in situ hybridization (Q-FISH) accurately evaluates hepatocellular aging on histological sections, but it requires appropriate tissue processing. To establish a more simple method for the assessment of hepatocellular aging, the usefulness of nuclear size measurement was clarified using biopsy liver samples from 64 patients with non-alcoholic fatty liver disease (NAFLD), a model for oxidative stress-associated hepatocellular aging, and 11 control individuals. Relative telomere intensity (RTI) was measured on Q-FISH, and the relative nuclear size (RNS) was calculated as the average nuclear size of the hepatocytes divided by that of lymphocytes. In normal individuals and NAFLD patients, the RTI and RNS were negatively correlated. The degree of nuclear enlargement in NAFLD patients was larger than that in normal individuals with the same telomere length, possibly reflecting telomere-independent senescence. In NAFLD patients with RNS >2.0, the regenerative responses, indicated by the ratio of Ki-67-positive index to serum alanine aminotransferase level, were significantly reduced. The RNS positively correlated with the p21 expression, another marker of senescence. This all indicates that nuclear enlargement progresses in parallel with reduced regenerative responses, telomere shortening, and p21 upregulation. Nuclear size measurement is an effective method for estimation of hepatocellular aging.

No association between socio-economic status and white blood cell telomere length.

It has been hypothesized that more socio-economically deprived individuals age faster and, thus, have shorter telomeres than their more affluent counterparts. A weak association between white blood cell telomere length and socio-economic status in a large heterogeneous sample of females has recently been reported. In 318 individuals from a homogeneous birth cohort, we found no evidence of an association between any measure of socio-economic status and peripheral blood mononucleocyte telomere length at age 50 after control for lifestyle variables, gender and paternal age at birth. The results of this, and the previous study, suggest that there is little evidence of a strong or consistent correlation between white blood cell telomere length and markers of socio-economic status.

A life course perspective on telomere length and social inequalities in aging.

Longitudinal studies will be needed to test the idea that social class in adult life, or in childhood, influences the rate of change in telomere length in peripheral blood samples.

How old are you now?

Cherkas et al. provide a new, biological approach to a classic problem in anthropology--the estimation of age.