Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA126367 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The goal of these studies was to delineate mechanisms of crosstalk between the atherosclerotic arterial wall of the aorta and the peripheral nervous system (PNS) in aged hyperlipidemic ApoE-deficient mice. We had observed by immunohistochemistry and morphometry that axon density of the PNS in adventitia segments that were located adjacent to advanced atherosclerotic plaques of aged hyperlipidemic ApoE-deficient mice were markedly higher than those adventitia segments that did not show adjacent atherosclerotic plaques in the intima layer. It is noteworthy in this connection that neither the media nor the intimal layer are innervated by axon endings. However, the adventitia layer of arteries is a conduit for axons and nerves of the PNS connecting the peripheral ganglia and peripheral organs including the spleen. In addition, we discovered (see references below) that atherosclerosis is sensed by the immune system of aged ApoE-deficient mice resulting in the formation of artery tertiary lymphoid organs in the adventitia layer of the arterial wall. To examine potential molecular mechanisms of the crosstalk between the disease aorta and the PNS, we isolated adventitia tissues and media tissues from aortas of ApoE-deficient mice and used wild-type mice as controls. Moreover, we observed that the sympathetic nervous system paraaortic and periaortic ganglia in aged ApoE-deficient but not of aged wild-type mice were infiltrated by leukocytes indicating that atherosclerosis is associated with major alterations of the PNS including axonogenesis and ganglionitis. To identify potential molecules involved in the crosstalk, we isolated respective tissues (media, adventitia, ganglia) by laser capture microdissection and generated large scale mRNA expression arrays to construct transcript maps that were assembled into transcript atlases. Publications related to this approach: Artery Tertiary Lymphoid Organs Control Aorta Immunity and Protect against Atherosclerosis via Vascular Smooth Muscle Cell Lymphotoxin β Receptors. Hu D, Mohanta SK, Yin C, Peng L, Ma Z, Srikakulapu P, Grassia G, MacRitchie N, Dever G, Gordon P, Burton FL, Ialenti A, Sabir SR, McInnes IB, Brewer JM, Garside P, Weber C, Lehmann T, Teupser D, Habenicht L, Beer M, Grabner R, Maffia P, Weih F, Habenicht AJ. Immunity. 2015 Jun 16;42(6):1100-15. doi: 10.1016/j.immuni.2015.05.015. Artery tertiary lymphoid organs contribute to innate and adaptive immune responses in advanced mouse atherosclerosis. Mohanta SK, Yin C, Peng L, Srikakulapu P, Bontha V, Hu D, Weih F, Weber C, Gerdes N, Habenicht AJ. Circ Res. 2014 May 23;114(11):1772-87. doi: 10.1161/CIRCRESAHA.114.301137. Review. Control of dichotomic innate and adaptive immune responses by artery tertiary lymphoid organs in atherosclerosis. Weih F, Gräbner R, Hu D, Beer M, Habenicht AJ. Front Physiol. 2012 Jul 6;3:226. doi: 10.3389/fphys.2012.00226. Laser-capture microdissection of hyperlipidemic/ApoE⁻/⁻ mouse aorta atherosclerosis. Beer M, Doepping S, Hildner M, Weber G, Grabner R, Hu D, Mohanta SK, Srikakulapu P, Weih F, Habenicht AJ. Methods Mol Biol. 2011;755:417-28. doi: 10.1007/978-1-61779-163-5_35.
2022-02-27 | GSE93954 | GEO
Project description:The goal of these studies was to delineate mechanisms of crosstalk between the atherosclerotic arterial wall of the aorta and the peripheral nervous system (PNS) in aged hyperlipidemic ApoE-deficient mice. We had observed by immunohistochemistry and morphometry that axon density of the PNS in adventitia segments that were located adjacent to advanced atherosclerotic plaques of aged hyperlipidemic ApoE-deficient mice were markedly higher than those adventitia segments that did not show adjacent atherosclerotic plaques in the intima layer. It is noteworthy in this connection that neither the media nor the intimal layer are innervated by axon endings. However, the adventitia layer of arteries is a conduit for axons and nerves of the PNS connecting the peripheral ganglia and peripheral organs including the spleen. In addition, we discovered (see references below) that atherosclerosis is sensed by the immune system of aged ApoE-deficient mice resulting in the formation of artery tertiary lymphoid organs in the adventitia layer of the arterial wall. To examine potential molecular mechanisms of the crosstalk between the disease aorta and the PNS, we isolated adventitia tissues and media tissues from aortas of ApoE-deficient mice and used wild-type mice as controls. Moreover, we observed that the sympathetic nervous system paraaortic and periaortic ganglia in aged ApoE-deficient but not of aged wild-type mice were infiltrated by leukocytes indicating that atherosclerosis is associated with major alterations of the PNS including axonogenesis and ganglionitis. To identify potential molecules involved in the crosstalk, we isolated respective tissues (media, adventitia, ganglia) by laser capture microdissection and generated large scale mRNA expression arrays to construct transcript maps that were assembled into transcript atlases. Publications related to this approach: Artery Tertiary Lymphoid Organs Control Aorta Immunity and Protect against Atherosclerosis via Vascular Smooth Muscle Cell Lymphotoxin β Receptors. Hu D, Mohanta SK, Yin C, Peng L, Ma Z, Srikakulapu P, Grassia G, MacRitchie N, Dever G, Gordon P, Burton FL, Ialenti A, Sabir SR, McInnes IB, Brewer JM, Garside P, Weber C, Lehmann T, Teupser D, Habenicht L, Beer M, Grabner R, Maffia P, Weih F, Habenicht AJ. Immunity. 2015 Jun 16;42(6):1100-15. doi: 10.1016/j.immuni.2015.05.015. Artery tertiary lymphoid organs contribute to innate and adaptive immune responses in advanced mouse atherosclerosis. Mohanta SK, Yin C, Peng L, Srikakulapu P, Bontha V, Hu D, Weih F, Weber C, Gerdes N, Habenicht AJ. Circ Res. 2014 May 23;114(11):1772-87. doi: 10.1161/CIRCRESAHA.114.301137. Review. Control of dichotomic innate and adaptive immune responses by artery tertiary lymphoid organs in atherosclerosis. Weih F, Gräbner R, Hu D, Beer M, Habenicht AJ. Front Physiol. 2012 Jul 6;3:226. doi: 10.3389/fphys.2012.00226. Laser-capture microdissection of hyperlipidemic/ApoE⁻/⁻ mouse aorta atherosclerosis. Beer M, Doepping S, Hildner M, Weber G, Grabner R, Hu D, Mohanta SK, Srikakulapu P, Weih F, Habenicht AJ. Methods Mol Biol. 2011;755:417-28. doi: 10.1007/978-1-61779-163-5_35. apoE-Adventitia arrays were submitted previously (GSM252007, GSM252008, GSM252009, GSM252010, GSM252011, GSM252014, GSM252015, GSM252016; GSE10000, GSE40156) and are now submitted together with new wild-type adventitia arrays not previously published in order to make all adventitia of ApoE-deficient mice and wild-type mice available in one new submission/location.
2022-02-27 | GSE94044 | GEO
Project description:Atherosclerosis is a transmural chronic inflammatory condition of small and large arteries that is associated with adaptive immune responses at all disease stages. However, impacts of adaptive immune reactions on clinically apparent atherosclerosis such as intima lesion (plaque) rupture, thrombosis, myocardial infarction, and aneurysm largely remain to be identified. It is increasingly recognized that leukocyte infiltrates in plaque, media, and adventitia are distinct but their specific roles have not been defined. To map these infiltrates, we employed laser capture microdissection (LCM) to isolate the three arterial wall laminae using apoE-/- mouse aorta as a model. RNA from LCM-separated tissues was extracted and large scale whole genome expression microarrays were prepared. We observed that the quality of the resulting gene expression maps was compromised by tissue RNA carried over from adjacent laminae during LCM. To account for these flaws, we established quality controls and algorithms to improve the predictive power of LCM-derived microarray data. Our approach creates robust transcriptome atlases of normal and atherosclerotic aorta. Assessing LCM transcriptomes for immunity-related mRNAs indicated markedly distinctive gene expression patterns in the three laminae of the atherosclerotic aorta. These mouse mRNA expression data banks can now be mined to address a wide range of questions in cardiovascular biology. Wild-type and apoE-deficient mice on the C57BL/6J genetic background were maintained on a standard mouse chow. Total aortae were removed at the age of 78 weeks, abdominal aorta was separated from the remainder of the tissue and arterial wall laminae were separated by laser capture microdissection as described (Beer et al. 2011). Following RNA quality controls, microarrays were prepared following MIAME guidelines as described previously (Uzonyi et al. 2006; Graebner et al. 2009; Lotzer et al. 2010).
2011-11-03 | E-GEOD-21419 | biostudies-arrayexpress
Project description:Tertiary lymphoid organs (TLOs) emerge in response to nonresolving inflammation but their roles in adaptive immunity remain unknown. Here, we explored artery TLOs (ATLOs) to delineate atherosclerosis T cell responses in apoe-/- mice during aging. Though the T cell repertoire showed systemic age-associated contractions in size and modifications in subtype composition and activation, wt and apoe-/- mice were equally affected. In contrast, ATLOs - but not wt aortae, apoe-/- aorta segments without ATLOs or atherosclerotic plaques - promoted T cell recruitment, altered characteristics of T cell motility, primed and imprinted T cells in situ, generated CD4+/FoxP3-, CD4+/FoxP3+, CD8+/FoxP3- effector and central memory cells, and converted naïve CD4+/FoxP3- T cells into induced Treg cells. ATLOs also showed substantially increased antigen presentation capability by conventional dendritic cells (DCs) and monocyte-derived DCs but not by plasmacytoid DCs. Thus, the senescent immune system specifically employs ATLOs to control dichotomic atherosclerosis T cell immune responses. We assembled transcriptome maps of wt and apoe-/- aortae and aorta-draining RLNs and identified ATLOs as major sites of atherosclerosis-specific T cell responses during aging: Transcriptome atlases of wt and apoe-/- abdominal aortae and associated draining RLNs were constructed from laser capture microdissection (LCM)-based whole genome mRNA expression microarrays yielding 6 maps: wt adventitia (tissue-1); wt RLN (tissue-2); apoe-/- ATLOs (tissue-3); apoe-/- RLN (tissue-4); apoe-/- adventitia without adjacent plaques (tissue-5), and plaques (tissue-6). Several two-tissue comparisons within the transcriptome atlases are noteworthy: Unexpectedly, transcriptomes of wt and apoe-/- RLNs were virtually identical; additonal data revealed that transcriptomes of RLNs were strikingly similar to those of inguinal LNs which do not drain the aorta adventitia (as shown of India ink injection experiments of surgically exposed aortae); in sharp contrast, wt adventitia versus ATLOs revealed 1405 differentially expressed transcripts many of which encoded members of GO terms immune response and inflammatory response; the ATLO-plaque comparison also showed > 1000 differentially expressed transcripts; however, wt adventitia versus apoe-/- adventitia without plaque showed few genes (< 5 % of differentially expressed transcripts of the wt adventitia-ATLO comparison). Thus, the aorta transcriptome atlases support the conclusion that neither aorta-draining apoe-/- RLNs nor ILNs participate in atherosclerosis-specific T cell responses. In addition, they demonstrate that T cell responses in the diseased aorta are highly territorialized. Finally, these data show that the immune responses carried out in ATLOs differ significantly from those carried out in plaques. We next identified three major clusters within the transcriptome atlases through ANOVA analyses and application of strict filters: An adventitia cluster, a plaque/ATLO cluster, and a LN/plaque cluster. The total number of differentially expressed genes in each cluster were examined for GO terms immune response, inflammatory response, T cell activation, positive regulation of T cell response, and T cell proliferation. Within the adventitia cluster, similarities of transcriptomes of wt adventitia and apoe-/- adventitia without associated plaque versus ATLOs indicate that a robust number of immune response-regulating genes are selectively expressed in ATLOs which are located within a distance of few µm of the adventitia without associated plaques indicating a very high degree of territoriality of the atherosclerosis T cell response. Furthermore, unlike the total number of differentially regulated transcripts, the majority of transcripts among GO terms immune response and inflammatory response, was up-regulated. Inspection of the plaque/ATLO cluster provided further information: The majority of immune response regulating genes where expressed at a higher level in ATLOs when compared to plaques though plaques also contained a significant number of immune response regulating genes; the reverse is true for genes regulating inflammation. Finally, the lymph node cluster revealed that though the majority of immune response regulating genes resides in both wt and apoe-/- RLNs (with little differences between them) ATLOs express a selected set of immune response regulating genes at a higher level when compared to LNs. In addition, the inflammatory component of ATLOs when compared to LNs is documented by the finding that many more genes regulating inflammation reside in ATLOs even when compared to those of plaques. Key words: T cell response in atherosclerosis; Laser capture microdissection; transcriptome atlas of atherosclerosis. Citations: Gräbner R. et al. Lymphotoxin beta receptor signaling promotes tertiary lymphoid organogenesis in the aorta adventitia of aged ApoE-/- mice. J Exp Med 2009 Jan 16;206(1):233-48. PMID: 19139167; Moos M. et al. The lamina adventitia is the major site of immune cell accumulation in standard chow-fed apolipoprotein E-deficient mice. Arterioscler Thromb Vasc Biol. 2005 Nov;25(11):2386-91. Epub 2005 Sep 22. PMID: 16179593; Beer M. et al. Laser-capture microdissection of hyperlipidemic/ApoE-/- mouse aorta atherosclerosis. Methods Mol Biol. 2011;755:417-28. PMID: 21761324; Weih F. et al. Control of Dichotomic Innate and Adaptive Immune Responses by Artery Tertiary Lymphoid Organs in Atherosclerosis. Front Physiol. 2012;3:226. Epub 2012 Jul 6. PMID: 22783198. Wild-type and apoE-deficient mice on the C57BL/6J genetic background were maintained on a standard mouse chow. Total aortae were removed at the age of 6 (n=3), 32 (n=3), or 78 (n=3) w and microarrays were prepared from total RNA extracts or extracts of atherosclerotic lesions and adventitiae obtained by the use of a laser dissection microscope. In addition, aorta associated LNs or distant LNs were prepared from both mouse genotypes.
2013-10-30 | E-GEOD-40156 | biostudies-arrayexpress
Project description:This dataset contains RNA-Seq data for cells within spatially defined subdomains of the human embryo dorsal aorta, subdissected from tissue sections using laser capture microdissection. This dataset explores dorsal-ventral polarisation across the dorsal aorta, the site of hematopoietic stem cell emergence.
2020-09-17 | GSE151875 | GEO
Project description:Atherosclerosis is a transmural chronic inflammatory condition of small and large arteries that is associated with adaptive immune responses at all disease stages. However, impacts of adaptive immune reactions on clinically apparent atherosclerosis such as intima lesion (plaque) rupture, thrombosis, myocardial infarction, and aneurysm largely remain to be identified. It is increasingly recognized that leukocyte infiltrates in plaque, media, and adventitia are distinct but their specific roles have not been defined. To map these infiltrates, we employed laser capture microdissection (LCM) to isolate the three arterial wall laminae using apoE-/- mouse aorta as a model. RNA from LCM-separated tissues was extracted and large scale whole genome expression microarrays were prepared. We observed that the quality of the resulting gene expression maps was compromised by tissue RNA carried over from adjacent laminae during LCM. To account for these flaws, we established quality controls and algorithms to improve the predictive power of LCM-derived microarray data. Our approach creates robust transcriptome atlases of normal and atherosclerotic aorta. Assessing LCM transcriptomes for immunity-related mRNAs indicated markedly distinctive gene expression patterns in the three laminae of the atherosclerotic aorta. These mouse mRNA expression data banks can now be mined to address a wide range of questions in cardiovascular biology.
2011-11-03 | GSE21419 | GEO
Project description:Laser Capture Microdissection isolation of preovulatory granulosa cells from WT and bERKO ovaries
| PRJNA190701 | ENA
Project description:Tertiary lymphoid organs (TLOs) emerge in response to nonresolving inflammation but their roles in adaptive immunity remain unknown. Here, we explored artery TLOs (ATLOs) to delineate atherosclerosis T cell responses in apoe-/- mice during aging. Though the T cell repertoire showed systemic age-associated contractions in size and modifications in subtype composition and activation, wt and apoe-/- mice were equally affected. In contrast, ATLOs - but not wt aortae, apoe-/- aorta segments without ATLOs or atherosclerotic plaques - promoted T cell recruitment, altered characteristics of T cell motility, primed and imprinted T cells in situ, generated CD4+/FoxP3-, CD4+/FoxP3+, CD8+/FoxP3- effector and central memory cells, and converted naïve CD4+/FoxP3- T cells into induced Treg cells. ATLOs also showed substantially increased antigen presentation capability by conventional dendritic cells (DCs) and monocyte-derived DCs but not by plasmacytoid DCs. Thus, the senescent immune system specifically employs ATLOs to control dichotomic atherosclerosis T cell immune responses. We assembled transcriptome maps of wt and apoe-/- aortae and aorta-draining RLNs and identified ATLOs as major sites of atherosclerosis-specific T cell responses during aging: Transcriptome atlases of wt and apoe-/- abdominal aortae and associated draining RLNs were constructed from laser capture microdissection (LCM)-based whole genome mRNA expression microarrays yielding 6 maps: wt adventitia (tissue-1); wt RLN (tissue-2); apoe-/- ATLOs (tissue-3); apoe-/- RLN (tissue-4); apoe-/- adventitia without adjacent plaques (tissue-5), and plaques (tissue-6). Several two-tissue comparisons within the transcriptome atlases are noteworthy: Unexpectedly, transcriptomes of wt and apoe-/- RLNs were virtually identical; additonal data revealed that transcriptomes of RLNs were strikingly similar to those of inguinal LNs which do not drain the aorta adventitia (as shown of India ink injection experiments of surgically exposed aortae); in sharp contrast, wt adventitia versus ATLOs revealed 1405 differentially expressed transcripts many of which encoded members of GO terms immune response and inflammatory response; the ATLO-plaque comparison also showed > 1000 differentially expressed transcripts; however, wt adventitia versus apoe-/- adventitia without plaque showed few genes (< 5 % of differentially expressed transcripts of the wt adventitia-ATLO comparison). Thus, the aorta transcriptome atlases support the conclusion that neither aorta-draining apoe-/- RLNs nor ILNs participate in atherosclerosis-specific T cell responses. In addition, they demonstrate that T cell responses in the diseased aorta are highly territorialized. Finally, these data show that the immune responses carried out in ATLOs differ significantly from those carried out in plaques. We next identified three major clusters within the transcriptome atlases through ANOVA analyses and application of strict filters: An adventitia cluster, a plaque/ATLO cluster, and a LN/plaque cluster. The total number of differentially expressed genes in each cluster were examined for GO terms immune response, inflammatory response, T cell activation, positive regulation of T cell response, and T cell proliferation. Within the adventitia cluster, similarities of transcriptomes of wt adventitia and apoe-/- adventitia without associated plaque versus ATLOs indicate that a robust number of immune response-regulating genes are selectively expressed in ATLOs which are located within a distance of few µm of the adventitia without associated plaques indicating a very high degree of territoriality of the atherosclerosis T cell response. Furthermore, unlike the total number of differentially regulated transcripts, the majority of transcripts among GO terms immune response and inflammatory response, was up-regulated. Inspection of the plaque/ATLO cluster provided further information: The majority of immune response regulating genes where expressed at a higher level in ATLOs when compared to plaques though plaques also contained a significant number of immune response regulating genes; the reverse is true for genes regulating inflammation. Finally, the lymph node cluster revealed that though the majority of immune response regulating genes resides in both wt and apoe-/- RLNs (with little differences between them) ATLOs express a selected set of immune response regulating genes at a higher level when compared to LNs. In addition, the inflammatory component of ATLOs when compared to LNs is documented by the finding that many more genes regulating inflammation reside in ATLOs even when compared to those of plaques. Key words: T cell response in atherosclerosis; Laser capture microdissection; transcriptome atlas of atherosclerosis. Citations: Gräbner R. et al. Lymphotoxin beta receptor signaling promotes tertiary lymphoid organogenesis in the aorta adventitia of aged ApoE-/- mice. J Exp Med 2009 Jan 16;206(1):233-48. PMID: 19139167; Moos M. et al. The lamina adventitia is the major site of immune cell accumulation in standard chow-fed apolipoprotein E-deficient mice. Arterioscler Thromb Vasc Biol. 2005 Nov;25(11):2386-91. Epub 2005 Sep 22. PMID: 16179593; Beer M. et al. Laser-capture microdissection of hyperlipidemic/ApoE-/- mouse aorta atherosclerosis. Methods Mol Biol. 2011;755:417-28. PMID: 21761324; Weih F. et al. Control of Dichotomic Innate and Adaptive Immune Responses by Artery Tertiary Lymphoid Organs in Atherosclerosis. Front Physiol. 2012;3:226. Epub 2012 Jul 6. PMID: 22783198.
2013-10-30 | GSE40156 | GEO
Project description:Gene Expression in Perivenous Hepatocytes: A Laser Capture Microdissection and Transcriptomic Analysis.
| PRJNA209474 | ENA
Project description:Laser capture microdissection/RNA-Seq analyses of Hoxa9,10,11/Hoxd9,10,11 mutant limb development
| PRJNA277715 | ENA