Aging alters murine peritoneal macrophages in a sex-dimorphic fashion

Aging is accompanied by general immune dysfunction, which is hypothesized to underlie the pathogenesis of many age-related diseases. In addition, there is accumulating evidence that aging is highly sex-dimorphic. However, the interactions of age and sex on the genomic and functional landscape of immune cells remain largely unexplored. To address this question, we have interrogated cells of the peritoneal cavity, an easily accessible immune niche, during aging in both sexes of C57BL/6 mice using single cell RNA-seq and flow cytometry. Interestingly, we found that macrophages were the most affected by age and sex among peritoneal immune cells, and that their frequency significantly dropped with aging. Macrophages are important for the initiating and resolving of inflammation, and dysfunction can contribute to inflammaging. Thus, we decided to further investigate the potentially sex-dimorphic impact of aging on the genomic landscape and function of peritoneal macrophages. We generated bulk RNA-seq data from purified peritoneal macrophages and identified genes modulated with aging as a function of sex. Complementing this ‘omic’ dataset, we performed an array of functional assays using purified peritoneal macrophages. We observed sex-dependent functional alterations, such as female-specific decrease in phagocytic ability. From our RNA-seq analysis, we identified potential regulators of phagocytosis that are significantly downregulated with age only in females. We are currently validating whether the potential regulators may indeed drive the observed female-specific decrease in phagocytic capabilities. Ultimately, this project will help delineate sex dimorphic mechanisms modulating immune aging.

This work was supported by a Diana Jacobs Kalman/AFAR Scholarships for Research in the Biology of Aging and NIA T32 AG052374 (to R.J.L.), GCRLE-2020 post-doctoral fellowship from the Global Consortium for Reproductive Longevity and Equality at the Buck Institute, made possible by the Bia-Echo Foundation, (to M.K.), and NIA R00 AG049934, Pew Biomedical Scholar award #00034120, an innovator grant from the Rose Hills foundation, and the Kathleen Gilmore Biology of Aging research award (to B.A.B). This work was also partially supported by NCI Cancer Center Support Grant P30 CA014089 through the use of shared resources.

Time isn't kind to female T-cells

While investigating sex-differences in T-cell aging, Mkhikian et al., identified a role for excessive IL-7 signaling and N-glycan branching in age-related mouse and human female T-cell dysfunction. These findings point to the increasingly-recognized importance of the impact of biological sex on immune aging and delineate new targetable pathways in age-related immune dysfunction.

Protocol for analysis of mouse neutrophil NETosis by flow cytometry

Studies involving neutrophils are steadily increasing, thus creating a need for more optimized and thorough protocols for studying neutrophil function. Here, we present our protocol for extracting mouse bone marrow neutrophils, estimating the purity of isolated neutrophils, and assessing their ability to induce NETosis upon an external cue. We test two isolation protocols that can be used to attain neutrophils to assess NETosis induction. This approach allows for the parallel assessment of NETosis induction in cohorts larger than 10 samples. For complete details on the use and execution of this protocol, please refer to Lu et al., 2021.

NHR-8 and P-glycoproteins uncouple xenobiotic resistance from longevity in chemosensory C. elegans mutants

Longevity is often associated with stress resistance, but whether they are causally linked is incompletely understood. Here we investigate chemosensory-defective Caenorhabditis elegans mutants that are long-lived and stress resistant. We find that mutants in the intraflagellar transport protein gene osm-3 were significantly protected from tunicamycin-induced ER stress. While osm-3 lifespan extension is dependent on the key longevity factor DAF-16/FOXO, tunicamycin resistance was not. osm-3 mutants are protected from bacterial pathogens, which is pmk-1 p38 MAP kinase dependent, while TM resistance was pmk-1 independent. Expression of P-glycoprotein (PGP) xenobiotic detoxification genes was elevated in osm-3 mutants and their knockdown or inhibition with verapamil suppressed tunicamycin resistance. The nuclear hormone receptor nhr-8 was necessary to regulate a subset of PGPs. We thus identify a cell-nonautonomous regulation of xenobiotic detoxification and show that separate pathways are engaged to mediate longevity, pathogen resistance, and xenobiotic detoxification in osm-3 mutants.

Multi-omic profiling of primary mouse neutrophils predicts a pattern of sex and age-related functional regulation

Neutrophils are the most abundant human white blood cell and constitute a first line of defense in the innate immune response. Neutrophils are short-lived cells, and thus the impact of organismal aging on neutrophil biology, especially as a function of biological sex, remains poorly understood. Here, we describe a multi-omic resource of mouse primary bone marrow neutrophils from young and old female and male mice, at the transcriptomic, metabolomic and lipidomic levels. We identify widespread regulation of neutrophil 'omics' landscapes with organismal aging and biological sex. In addition, we leverage our resource to predict functional differences, including changes in neutrophil responses to activation signals. To date, this dataset represents the largest multi-omics resource for neutrophils across sex and ages. This resource identifies neutrophil characteristics which could be targeted to improve immune responses as a function of sex and/or age.

Protocol for isolation of adult mouse ear pinnae-derived primary fibroblasts

Researchers need in vitro models that mirror the biology of organisms. Primary fibroblasts play essential roles in wound healing and are present in many tissues. They are widely used in studies of cell cycle control, reprogramming, and aging. Though extraction protocols exist, alternatives that maximize use of available resources are useful. Here, we present our protocol for extracting primary fibroblasts from adult mouse ear pinnae, an often-discarded source of primary cells, which consistently yield large, pure numbers of primary fibroblasts.

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Primary fibroblasts are isolated from adult mouse ear pinnae, an often-unused tissue

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Fibroblasts can be isolated from mice of varying sex, age, and genotype

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Fibroblast cultures are highly pure, with >90% THY1.2 or PDGFRα staining

Functional genomics of inflamm-aging and immunosenescence

The aging population is at a higher risk for age-related diseases and infections. This observation could be due to immunosenescence: the decline in immune efficacy of both the innate and the adaptive immune systems. Age-related immune decline also links to the concept of 'inflamm-aging,' whereby aging is accompanied by sterile chronic inflammation. Along with a decline in immune function, aging is accompanied by a widespread of 'omics' remodeling. Transcriptional landscape changes linked to key pathways of immune function have been identified across studies, such as macrophages having decreased expression of genes associated to phagocytosis, a major function of macrophages. Therefore, a key mechanism underlying innate immune cell dysfunction during aging may stem from dysregulation of youthful genomic networks. In this review, we discuss both molecular and cellular phenotypes of innate immune cells that contribute to age-related inflammation.

Genome-wide surveillance of transcription errors in response to genotoxic stress

Mutagenic compounds are a potent source of human disease. By inducing genetic instability, they can accelerate the evolution of human cancers or lead to the development of genetically inherited diseases. Here, we show that in addition to genetic mutations, mutagens are also a powerful source of transcription errors. These errors arise in dividing and nondividing cells alike, affect every class of transcripts inside cells, and, in certain cases, greatly exceed the number of mutations that arise in the genome. In addition, we reveal the kinetics of transcription errors in response to mutagen exposure and find that DNA repair is required to mitigate transcriptional mutagenesis after exposure. Together, these observations have far-reaching consequences for our understanding of mutagenesis in human aging and disease, and suggest that the impact of DNA damage on human physiology has been greatly underestimated.

The microbiome: an emerging key player in aging and longevity

Revolutionary advancements of high-throughput sequencing and metagenomic tools have provided new insights to microbiome function, including a bidirectional relationship between the microbiome and host aging. The intestinal tract is the largest surface in the human body that directly interacts with foreign antigens - it is covered with extremely complex and diverse community of microorganisms, known as the gut microbiome. In a healthy gut, microbial communities maintain a homeostatic metabolism and reside within the host in a state of immune tolerance. Abnormal shifts in the gut microbiome, however, have been implicated in the pathogenesis of age-related chronic diseases, including obesity, cardiovascular diseases and neurodegenerative diseases. The gut microbiome is emerging as a key factor in the aging process. In this review, we describe studies of humans and model organisms that suggest a direct causal role of the gut microbiome on host aging. Additionally, we also discuss sex-dimorphism in the gut microbiome and its possible roles in age-related sex-dimorphic phenotypes. We also provide an overview of widely used microbiome analysis methods and tools which could be used to explore the impact of microbiome remodeling on aging.

Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation

Our understanding of the molecular regulation of aging and age-related diseases is still in its infancy, requiring in-depth characterization of the molecular landscape shaping these complex phenotypes. Emerging classes of molecules with promise as aging modulators include transposable elements, circRNAs and the mitochondrial transcriptome. Analytical complexity means that these molecules are often overlooked, even though they exhibit strong associations with aging and, in some cases, may directly contribute to its progress. Here, we review the links between these novel factors and age-related phenotypes, and we suggest tools that can be easily incorporated into existing pipelines to better understand the aging process.

Extensive sex-dimorphism in age-related transcriptional remodeling in mouse peritoneal macrophages

Chronic low-level inflammation is one of the hallmarks of aging. In addition, age-related diseases share common inflammatory mechanisms, a phenomenon named “inflamm-aging”. To date, the effect of age and sex on the genomic landscape of macrophages is largely unexplored, especially regarding sex-dimorphic trajectories in aging macrophages. Based on accumulating evidence indicating aging is highly sex-dimorphic, we hypothesize that aging will affect the phenotype of immune cells, such as macrophages, in a sex-dimorphic manner. To test our hypothesis, we used female and male C57BL/6N mice aged 4 and 20 months to investigate resident peritoneal macrophages. We generated RNA-seq data from purified peritoneal macrophages and identified genes modulated with aging as a function of sex. Complementing this ‘omic’ dataset, we performed an array of functional assays for these cells in several cohorts of aging mice, including immunophenotyping, metabolic profiling, lysosomal acidification tracking, phagocytic efficiency, etc. We observed sex-dependent functional decline, such as a male-specific decrease in macrophage ability to acidify lysosomes upon exposure to Zymosan. Interestingly, aspects of age-related functional changes may be mediated by age-related changes in circulating sex hormones. We are currently analyzing our single cell RNA-seq datasets from peritoneal lavages of naïve aging female and male mice, and generating complementary datasets that are profiling chromatin-level changes to identify putative drivers of age-related transcriptional and functional remodeling in macrophages. Ultimately, this project will help delineate sex dimorphic mechanisms modulating “inflamm-aging”.

Sex-dimorphic trajectories in aging macrophage populations

The existence of human supercentenarians reveals a surprising predictor for exceptional longevity: being female. Not only are 33 out of 34 living supercentenarians women, women are also more resistant to most diseases responsible for age-related morbidity in the US. However, because most molecular aging studies generally opt to use only one sex, sex-driven differences in aging remain poorly understood. A key compartment that can actively respond to sex-specific inputs throughout life is the immune system. Indeed, the majority of age-related diseases share common inflammatory mechanisms, a phenomenon described as “inflamm-aging”. Macrophages play an important role in the inflammatory response throughout life, and are considered major mediators of this phenomenon. Thus, to unbiasedly dissect sex differences in immune aging, we generated ‘omics’ data from 4 and 20 months old female and male mice. Intriguingly, we found that transcriptional aging in primary macrophage populations varies strongly between sexes, with up to 20-fold more aging changes in female vs. male cells. Pathways specifically downregulated in females with aging included lysosome, inflammation and phagolysosome. We confirmed experimentally that metabolic preferences of macrophages are indeed directly modulated in this context (e.g. glycolytic preference for male-derived cells). Our results support the notion that there are functional differences in aging trajectories in the immune system of female vs. male mice. Our research could provide new insights into the molecular underpinnings of sex-dimorphism in aging and disease.

Widespread sex dimorphism in aging and age-related diseases

Although aging is a conserved phenomenon across evolutionary distant species, aspects of the aging process have been found to differ between males and females of the same species. Indeed, observations across mammalian studies have revealed the existence of longevity and health disparities between sexes, including in humans (i.e. with a female or male advantage). However, the underlying mechanisms for these sex differences in health and lifespan remain poorly understood, and it is unclear which aspects of this dimorphism stem from hormonal differences (i.e. predominance of estrogens vs. androgens) or from karyotypic differences (i.e. XX vs. XY sex chromosome complement). In this review, we discuss the state of the knowledge in terms of sex dimorphism in various aspects of aging and in human age-related diseases. Where the interplay between sex differences and age-related differences has not been explored fully, we present the state of the field to highlight important future research directions. We also discuss various dietary, drug or genetic interventions that were shown to improve longevity in a sex-dimorphic fashion. Finally, emerging tools and models that can be leveraged to decipher the mechanisms underlying sex differences in aging are also briefly discussed.

Remodeling of the H3 nucleosomal landscape during mouse aging

In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and deregulation of gene expression correlates with aging. A key layer in the study of gene regulation mechanisms lies at the level of chromatin: cellular chromatin states (i.e. the 'epigenome') can tune transcriptional profiles, and, in line with the prevalence of transcriptional alterations with aging, accumulating evidence suggests that the chromatin landscape is altered with aging across cell types and species. However, although alterations in the chromatin make-up of cells are considered to be a hallmark of aging, little is known of the genomic loci that are specifically affected by age-related chromatin state remodeling and of their biological significance. Here, we report the analysis of genome-wide profiles of core histone H3 occupancy in aging male mouse tissues (i.e. heart, liver, cerebellum and olfactory bulb) and primary cultures of neural stem cells. We find that, although no drastic changes in H3 levels are observed, local changes in H3 occupancy occur with aging across tissues and cells with both regions of increased or decreased occupancy. These changes are compatible with a general increase in chromatin accessibility at pro-inflammatory genes and may thus mechanistically underlie known shift in gene expression programs during aging.

Measuring Phagocytosis in Bone Marrow-Derived Macrophages and Peritoneal Macrophages with Aging

The majority of age-related diseases share common inflammatory mechanisms, a phenomenon which has been described as "inflamm-aging," and genetic variants in immune and inflammatory genes are significantly associated with exceptional human longevity and/or age-related diseases. Consistently, aging is associated with increased macrophage infiltration into tissues. Macrophages are a key component of the innate immune system and the inflammatory response, which accomplish key tasks such as phagocytosis, antigen presentation, and cytokine production. Phagocytosis is the process by which specialized cells that can clear harmful foreign particles, pathogens, and dead or dying cells. Upon phagocytosis, foreign particles are internalized in vesicles, forming phagosomes. Phagosomes go on to fuse with lysosomes, and the ingested particles are neutralized by lysosomal enzymes. Macrophages have two main origins: tissue-resident macrophages differentiate from specific embryonic progenitors, whereas monocyte-derived macrophages differentiate from bone-marrow progenitors. Because of their key role in inflammation and damage repair, macrophages are a key cell type in age-related inflammatory diseases. Here, we describe an efficient method to quantify the phagocytotic ability of two types of primary macrophages in aging mice: bone marrow-derived macrophages (BMDMs) and tissue-resident peritoneal macrophages.

SEX-DIMORPHISM IN THE GENOMIC REGULATION OF AGING

The current cohort of human supercentenarians reveals a surprising predictor for achieving such an exceptional longevity: being female. Indeed, out of 34 living supercentenarians, 33 are women. We obtained samples from 4 and 20 months old female and male mice. Our data indicates that cytokine levels are differentially regulated with age in males vs. females, with pro-inflammatory cytokines specifically upregulated in the serum of old males, but not females. Because of the central role of macrophages in inflammation and their infiltration in tissues with age, we have generated RNA-seq from purified macrophages of aging animals. Female macrophages displayed ~7-20-fold more transcriptional remodeling with aging than males. Pathways specifically downregulated in females with aging included lysosome, inflammation and phagolysosome. Consistently, our data shows that aged female, but not male macrophages, display decreased phagocytic efficiency. Our results support the notion that there are differences in aging trajectories in female vs. male mice.

INVESTIGATING THE ROLE OF AHR IN MEDIATING SEX DIFFERENCES OF AGING MACROPHAGES

“Inflamm-aging” describes a state of chronic low-grade inflammation which occurs with age in the absence of infection. This process is related to many chronic age-related diseases. Aryl hydrocarbon receptor (Ahr), is a transcription factor that is thought to decrease inflammation, and decrease of Ahr with aging only in females was previously observed in a macrophage RNA-seq with aging. Based on this, I hypothesized that 1) Ahr expression will decrease with age in female cells; and 2) phagocytic activity and Ahr expression in macrophages will increase when exposed to estrogens (E2). To test these hypotheses, Ahr signaling was quantified by RT-qPCR in aging male and female mice BMDMs, and in macrophages that were treated with E2. I also performed a phagocytosis assay on macrophages treated with E2. I found a significant downregulation of Ahr in old female BMDMs. Ahrr (Ahr Repressor) was significantly downregulated in both old female and males with aging. Arnt (Ahr Nuclear Translocator) did not significantly change with aging. The qPCR performed on the E2 treated cells showed no significant trend for Ahr regulation. Finally, the phagocytosis assay revealed an overall increase in phagocytosis activity in cells treated with estrogen. Our hypotheses were supported by data showing a decrease in Ahr expression with age and increase in phagocytosis activity in estrogen treated cells. The RT-qPCR results for the E2 treated cells did not support our hypothesis, but could stem from a relatively short exposure time for estrogen.

MOTS-c: A Mitochondrial-Encoded Regulator of the Nucleus

Mitochondria are increasingly being recognized as information hubs that sense cellular changes and transmit messages to other cellular components, such as the nucleus, the endoplasmic reticulum (ER), the Golgi apparatus, and lysosomes. Nonetheless, the interaction between mitochondria and the nucleus is of special interest because they both host part of the cellular genome. Thus, the communication between genome-bearing organelles would likely include gene expression regulation. Multiple nuclear-encoded proteins have been known to regulate mitochondrial gene expression. On the contrary, no mitochondrial-encoded factors are known to actively regulate nuclear gene expression. MOTS-c (mitochondrial open reading frame of the 12S ribosomal RNA type-c) is a recently identified peptide encoded within the mitochondrial 12S ribosomal RNA gene that has metabolic functions. Notably, MOTS-c can translocate to the nucleus upon metabolic stress (e.g., glucose restriction and oxidative stress) and directly regulate adaptive nuclear gene expression to promote cellular homeostasis. It is hypothesized that cellular fitness requires the coevolved mitonuclear genomes to coordinate adaptive responses using gene-encoded factors that cross-regulate the opposite genome. This suggests that cellular gene expression requires the bipartite split genomes to operate as a unified system, rather than the nucleus being the sole master regulator.

Multi-level remodeling of transcriptional landscapes in aging and longevity

In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and gene expression has been observed to be deregulated with aging. In this review, we discuss the current knowledge on the transcriptional alterations that have been described to occur with age in metazoans. First, we discuss age-related transcriptional changes in protein-coding genes, the expected functional impact of such changes, and how known pro-longevity interventions impact these changes. Second, we discuss the changes and impact of emerging aspects of transcription in aging, including age-related changes in splicing, lncRNAs and circRNAs. Third, we discuss the changes and potential impact of transcription of transposable elements with aging. Fourth, we highlight small ncRNAs and their potential impact on the regulation of aging phenotypes. Understanding the aging transcriptome will be key to identify important regulatory targets, and ultimately slow-down or reverse aging and extend healthy lifespan in humans.