Nanoproteomics analysis reveals single C. elegans heterogeneity during aging
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ABSTRACT: Aging was long assumed to be a passive and stochastic process caused by random damage accumulation, however,such theories fail to explain the program-like features of the aging process. Measuring the aging process in C. elegans at individual level provides an opportunity to analyze both the programmed (age-related changes at population level) and stochastic (inter-individual differences in isogenic population) components during the aging process. Here, we performed quantitative proteomic analyses on more than 150 worm individuals of different ages and aged individuals with different mobility. The analysis of inter-individual variations helps dissect the programmed and stochastic components during the aging process, and key proteins underlying the lifespan plasticity among the genetically identical worm individuals. Using a high temporal resolution single worm proteomic landscape, we found that the aging process was non-linearly progressed, with each stage marked by distinct age-related changes. The fast-aging individuals are depleted with such secreted proteins and over-activation of lysosome degradation processes, providing a first molecular link for the programmed enhanced offspring growth and death of the parent individual. This mechanistic link indicates that programmed events at least in part explain the heterogeneity of adult aging.
Project description:Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro-proteomics for the analysis of C. elegans, a eukaryote composed of 959 somatic cells and ~1,500 germ cells, measuring the worm proteome at a single organism level to a depth of ~ 3,000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (> 6 orders of magnitude), including many chromatin-associated factors involved in chromosome structure and gene regulation. We apply the micro-proteomics workflow to measure the global proteome response to heat-shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat-shock, including variable induction of heat-shock proteins. The micro-proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource.
Project description:Immune responses generally decline with age. We used multiple ‘omics’ technologies to capture population- and individual- level changes in the human immune system of 135 healthy adult individuals of different ages sampled longitudinally over a nine-year period. We observe a high inter-individual variability in the rates of change of cellular frequencies that correlate with baseline values, allowing identification of steady state levels towards which a cell subset converges and the ordered convergence of multiple cell subsets towards an older adult homeostasis. These form a high dimensional trajectory of immune-aging (IMM-AGE) that describes a person’s immune status better than chronological age. We show the IMM-AGE score predicts all-cause mortality beyond well-established risk factors in the Framingham Heart Study.
Project description:Immune responses generally decline with age. We used multiple ‘omics’ technologies to capture population- and individual- level changes in the human immune system of 135 healthy adult individuals of different ages sampled longitudinally over a nine-year period. We observe a high inter-individual variability in the rates of change of cellular frequencies that correlate with baseline values, allowing identification of steady state levels towards which a cell subset converges and the ordered convergence of multiple cell subsets towards an older adult homeostasis. These form a high dimensional trajectory of immune-aging (IMM-AGE) that describes a person’s immune status better than chronological age. We show the IMM-AGE score predicts all-cause mortality beyond well-established risk factors in the Framingham Heart Study.
Project description:Immune responses generally decline with age. We used multiple ‘omics’ technologies to capture population- and individual- level changes in the human immune system of 135 healthy adult individuals of different ages sampled longitudinally over a nine-year period. We observe a high inter-individual variability in the rates of change of cellular frequencies that correlate with baseline values, allowing identification of steady state levels towards which a cell subset converges and the ordered convergence of multiple cell subsets towards an older adult homeostasis. These form a high dimensional trajectory of immune-aging (IMM-AGE) that describes a person’s immune status better than chronological age. We show the IMM-AGE score predicts all-cause mortality beyond well-established risk factors in the Framingham Heart Study.
Project description:The endosymbiont population of the hydrothermal vent tube worm Riftia pachyptila consists of a single 16S phylotype of sulfur-oxidizing gammaproteobacteria. The intracellular symbiont exhibits remarkable morphological heterogeneity, from small rod-shaped or coccoid cells to large cocci, which were suggested to be part of a common cell cycle. To assess whether these morphological differences are accompanied by distinct metabolic profiles, we physically enriched individual symbiont cells sizes by density gradient centrifugation and subjected these enrichments to metaproteomic analysis and statistical evaluation using clustering and random forests. Unlike previous molecular studies, which examined the metabolism of the symbiont population as whole, we were thus able to unravel comprehensive protein abundance patterns of individual symbiont subpopulations. Supported by microscopic analyses, our metaproteomic results show that Riftia symbiont cells of different sizes are stages of a physiological differentiation process: Small symbionts actively divide and may establish cellular symbiont-host interaction, as indicated by highest abundance of the cell division key protein FtsZ and highly abundant chaperones and porins in this initial phase. We furthermore present evidence that large symbionts, on the other hand, do not divide, but still replicate DNA, leading to DNA endoreduplication. Highest abundance of enzymes for CO2 fixation, carbon storage and biosynthesis indicates that in its late differentiation stage, the symbiont’s metabolism is efficiently geared on the production of organic material. We propose that this symbiont aging process enhances the productivity of the symbiosis as a whole.
Project description:Analysis of the extent to which inter-individual variation in mRNA decay contributes to inter-individual variation in gene expression levels in humans. The study examines properties of genome-wide decay rates and the relationship between mRNA decay and gene expression across genes, across individuals, and finally across genotype classes.
Project description:We have investigated whether gene expression signatures can be used to predict inter-individual responses to DNA damaging agents We used microarrays to detail inter-individual variation in gene expression across a healthy population under basal and damage induced conditions Keywords: dose (MNNG)
Project description:Using neutrophils from a cohort of normal individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation.
Project description:DNA methylation has been comprehensively profiled in normal and cancer cells, but the dynamics that form, maintain and reprogram differentially methylated regions remain enigmatic. We show that methylation patterns within populations of cells from individual somatic tissues are heterogeneous and polymorphic. Using in vitro evolution of immortalized fibroblasts for over 300 generations, we track the dynamics of polymorphic methylation at regions developing significant differential methylation on average. The data indicate that changes in population-averaged methylation occur through a stochastic process that generates a stream of local and uncorrelated methylation aberrations. Despite the stochastic nature of the process, nearly deterministic epigenetic remodeling emerges on average at loci that lose or gain resistance to methylation accumulation. Changes in the susceptibility to methylation accumulation are correlated with changes in histone modifications and CTCF occupancy. Characterizing epigenomic polymorphism within cell populations is therefore critical for understanding methylation dynamics in normal and cancer cells. Gene expression profiled in duplicate throughout the microevolutionary timecourse using Affymetrix Gene 1.0 ST arrays.
Project description:The interleukin-23 (IL-23) pathway plays a critical role in the pathogenesis of multiple chronic inflammatory disorders, however, inter-individual variability in IL-23-induced signal transduction in circulating human lymphocytes has not been well-defined. In this study, we observed marked, reproducible inter-individual differences in IL-23 responsiveness (measured by STAT3 phosphorylation) in peripheral blood CD8+CD45RO+ memory T and CD3+CD56+ NKT cells. To define mechanisms that might be contributing to the differential IL-23-induced STAT3 activation between individuals, we examined mRNA expression differences in CD8+CD45RO+ memory T cells between IL-23 responsive and non-responsive individuals.