A multi-organ proteomic atlas of a murine model of extreme age
Ontology highlight
ABSTRACT:
INSTRUMENT(S): timsTOF fleX
ORGANISM(S): Mus Musculus (ncbitaxon:10090)
SUBMITTER: 
Benjamin C Orsburn
PROVIDER: MSV000094381 | MassIVE | Fri Mar 22 13:30:00 GMT 2024
SECONDARY ACCESSION(S): PXD050910
REPOSITORIES: MassIVE
Similar Datasets
Project description:17 organs were harvested from 4 12 week old and 4 84 week old male mice. Proteomics for this set was performed by diaPASEF analysis using an EvoSep 60 speed method.
2023-05-16 | MSV000091961 | MassIVE
Project description:The early-life organ development and maturation process shapes the fundamental blueprint for later-life phenotype. However, the proteome atlas of self-multi-organs from infancy to adulthood is currently not available. Herein, we present a comprehensive proteomic analysis of ten mice organs (brain, heart, lung, liver, kidney, spleen, stomach, intestine, muscle and skin) acquired from the same individuals at three essential developmental stages (1-week, 4-week and 8-week after birth) by data-independent acquisition mass spectrometry.
2024-05-02 | PXD041400 | Pride
Project description:Complex organisms are composed of organs and tissues which evolved to their present state as they function together to improve an organism's overall reproductive fitness. Studies of individual organs help us understand their basic functions but this reductionist approach misses the larger context of the whole organism. This problem can be circumvented if all the organs in an organism were comprehensively studied by the same methodology and analyzed together. Using honey bees (Apis mellifera L.) as a model system,we report here the first whole proteome of a complex organism,measuring 29 different tissue types among the three honey bee castes: queen,drone,and worker. The data reveal that,e.g.,workers have a heightened capacity to deal with environmental toxins and queens have a far more robust immune system than their nestmates. Most intriguingly,our analysis reveals the path by which organs of complex organisms probably evolved.Raw data were processed by MaxQuant (v1.2.0.13) using default parameters, plus lysine and N-terminal dimethylation for three isotopologues for relative quantitation. Data were searched against the Apis Official Gene Set version 2 with common contaminants, containing a total of 22037 sequences. Normalized intensity ratios were used for relative quantitation.
2013-09-10 | PXD000084 | Pride
Project description:Quantitative proteomic analysis from organs of mice either mock-infected or infected with group a streptococcus. Proteomic analysis was performed on an Orbitrap fusion with TMT based quantification using an SPS MS3 method to reduce interference effects.
2017-08-07 | MSV000081425 | MassIVE
Project description:Awareness of estrogen's effects on health is broadening rapidly. The effects of long-term high levels of estrogen on the body involve multiple organs. Here we use both single cell chromatin accessibility and RNA sequencing data to analyze the potential effect of estrogen on major organ at single cell levels.
2024-07-25 | GSE243770 | GEO
Project description:Awareness of estrogen's effects on health is broadening rapidly. The effects of long-term high levels of estrogen on the body involve multiple organs. Here we use both single cell chromatin accessibility and RNA sequencing data to analyze the potential effect of estrogen on major organ at single cell levels.
2024-07-25 | GSE243769 | GEO
Project description:Group A Streptococcus (GAS) remains one of the top 10 deadliest human pathogens worldwide despite its sensitivity to penicillin. Although the most common GAS infection is pharyngitis (strep throat), it also causes life-threatening systemic infections. A series of complex networks between host and pathogen drive invasive infections, which have not been comprehensively mapped. Attempting to map these interactions, we examined organ-level protein dynamics using a mouse model of systemic GAS infection. We quantified over 11,000 proteins, defining organ-specific markers for all analyzed tissues. From this analysis, an atlas of dynamically regulated proteins and pathways was constructed. Through statistical methods, we narrowed organ-specific markers of infection to 34 from the defined atlas. We show these markers are trackable in blood of infected mice, and a subset has been observed in plasma samples from GAS-infected clinical patients. This proteomics-based strategy provides insight into host defense responses, establishes potentially useful targets for therapeutic intervention, and presents biomarkers for determining affected organs during bacterial infection.
| S-EPMC7868092 | biostudies-literature
Project description:The craniofacial bones provide structural support for the skull and accommodate the vulnerable brain tissue with a protective cavity. The bone tissue undergoes constant turnover, which relies on skeletal stem cells (SSCs) and/or mesenchymal stem cells (MSCs) and their niches. SSCs/MSCs and their perivascular niche within the bone marrow are well characterized in long bones. As for cranial bones, besides bone marrow, the suture mesenchyme has been identified as a unique niche for SSCs/MSCs of craniofacial bones. However, a comprehensive study of the two different cranial stem cell niches at single-cell resolution is still lacking. In addition, during the progression of aging, age-associated changes in cranial stem cell niches and resident cells remain uncovered. In this study, we investigated age-related changes in cranial stem cell niches via single-cell RNA sequencing (scRNA-seq). The transcriptomic profiles and cellular compositions have been delineated, indicating alterations of the cranial bone marrow microenvironment influenced by inflammaging. Moreover, we identified a senescent mesenchymal cell subcluster and several age-related immune cell subclusters by reclustering and pseudotime trajectory analysis, which might be closely linked to inflammaging. Finally, differentially expressed genes (DEGs) and cell-cell communications were analyzed during aging, revealing potential regulatory factors. Overall, this work highlights the age-related changes in cranial stem cell niches, which deepens the current understanding of cranial bone and suture biology and may provide therapeutic targets for antiaging and regenerative medicine.
| S-EPMC10652347 | biostudies-literature
Project description:Vascular dysfunction and organ failure are two distinct, albeit highly interconnected clinical outcomes linked to morbidity and mortality in human sepsis. The mechanisms driving vascular and parenchymal damage are dynamic and display significant molecular crosstalk between organs and tissues. Therefore, assessing their individual contribution to disease progression is technically challenging. Here, we hypothesize that dysregulated vascular responses predispose the organism to organ failure. To address this hypothesis, we have evaluated four major organs in a murine model of S. aureus sepsis by combining in vivo labeling of the endothelial proteome, data-independent acquisition (DIA) mass spectrometry, and an integrative computational pipeline. The data reveal, with unprecedented depth and throughput, that a septic insult evokes organ-specific proteome responses that are highly compartmentalized, synchronously coordinated, and significantly correlated with the progression of the disease. This includes abundant vascular shedding, dysregulation of the intrinsic pathway of coagulation, compartmentalization of the acute phase-response, and abundant upregulation of glycocalyx components. Vascular proteome changes were also found to precede bacterial invasion and leukocyte infiltration into the organs, as well as to precede changes in various well-established cellular and biochemical correlates of systemic coagulopathy and tissue dysfunction. Importantly, our data suggests a potential role for the vascular proteome as a determinant of the susceptibility of the organs to undergo failure during sepsis.
2022-03-10 | MSV000089030 | MassIVE
Project description:Expression of full-length LINE-1 mRNA, the first step in the L1 copy-and-paste amplification cycle, is a prerequisite for L1-associated genomic instability resulting from DNA damage and insertional mutagenesis. We used our stringent bioinformatics method to parse L1 mRNA transcripts and measure the level of full-length L1 mRNA expressed in mouse and rat organs at a locus-specific resolution. We find that expression of L1 loci in rodents exhibits striking organ specificity with less than 0.8% of loci shared between different organs of the same organism. This organ specificity in L1 mRNA expression is preserved in male and female mice and across different age groups. Unexpectedly, we discovered notable differences in L1 mRNA expression between sexes with only 5% of expressed L1 loci shared between male and female mice. Moreover, we report that the levels of total L1 mRNA expression and the number and spectrum of expressed L1 loci fluctuate with age as independent variables, demonstrating different patterns in different organs and sexes. Overall, our comparisons between organs and sexes and across ages ranging from 2 to 22 months establish previously unforeseen dynamic changes in L1 mRNA expression in vivo. These milestone findings establish a previously lacking atlas of endogenous L1 mRNA expression across a broad range of biological variables that will guide future studies addressing the understanding of mechanisms that govern expression of a limited number of L1 loci in any given organ and the impact of environmental and genetic perturbations on L1 mRNA expression and its involvement in disease initiation and progression.
2021-06-01 | GSE158831 | GEO