The transcriptional landscape of mTEChi and mTEClo.

Cell Subset ◽

Cell Types ◽

Thymic Epithelial Cells ◽

Surface Receptors ◽

Mhc Ii ◽

Histocompatibility Complex ◽

Self Tolerance ◽

Medullary thymic epithelial cells, or mTEC, are cells of the thymus that can be sorted and classified based on expression of the class II major histocompatibility complex, MHC-II (1-3). mTEChi and mTEClo can be further segregated by expression of the CD80 marker, but there are few systematic analyses of the unique transcriptional behavior of each mTEC cell subset (4-6). We performed global differential gene expression profiling by comparing the transcriptomes of mTEChi and mTEClo (7) to determine the most significant transcriptional differences between these two cell subsets of the thymus. We found nearly a dozen groups of gene that distinctly identify these two cell types from each other. These included phospholipase-type enzymes, transcription factors, transcriptional coactivators and epigenetic proteins, cell signaling intermediates, cell surface receptors, molecules involved in ubiquitination, taste receptors, cathepsins, and interleukin-13. mTEChi and mTEClo can be discerned with facility as discrete cell types independent of MHC-II and CD80 expression through systematic comparative transcriptional profiling and the molecular descriptions provided here can be used as a resource for future investigations into the organ primarily responsible for providing lymphocyte self-tolerance instruction.

The expression of ERV3 is elevated in Aire -/- mTEChi.

10.31219/osf.io/2uh7j ◽

2019 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Gene Expression ◽

Major Histocompatibility Complex ◽

Gene Expression Analysis ◽

Thymic Epithelial Cells ◽

Differential Gene Expression Analysis ◽

Mhc Ii ◽

Aire Gene ◽

Histocompatibility Complex ◽

Endogenous retroviral (ERV) element 3 is a gene for the retroviral envelope (env) that has been inserted into the human genome over the course of human evolution (1,2). To understand how Aire functions in shaping the transcriptional profile of cells that train lymphocytes what it means to be self through antigen presentation of tissue-restricted antigens, I performed differential gene expression analysis of murine medullary thymic epithelial cells expressing high levels of the class II major histocompatibility complex MHC-II (mTEChi) that possess a deletion of the Aire gene (3). I found that ERV3 was among the most differentially regulated genes in mTEChi transcriptome when comparing Aire -/- and Aire +/+ mTEChi and that ERV3 expression was significantly elevated in Aire -/- mTEChi. This data indicates that a molecule that functions at the level of transcription to enhance the expression of tissue-restricted antigens for the induction of immunological privilege restricts (at least in part) the expression of an endogenous retroviral sequence.

Stage-selective differential expression of eukaryotic initiation factor (Eif) genes in the medullary epithelial cells of the murine thymus.

10.31219/osf.io/hmnfq ◽

2020 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Epithelial Cells ◽

Adult Development ◽

Microarray Dataset ◽

Cell Types ◽

Initiation Factor ◽

Thymic Epithelial Cells ◽

Initiation Factors ◽

Eukaryotic Initiation Factors ◽

The thymus is the site of positive and negative selection in mammals (1), the process by which developing lymphocytes are selected for or deleted based on their ability to encounter foreign or self antigen, respectively, with optimal binding affinity (2, 3). The thymus consists of a medulla and a cortex , with mTEC, or medullary thymic epithelial cells expressing high or low amounts of the class II major histocompatibility complex (mTEChi and mTEClo) (4, 5). To understand how the mTEC transcriptome changes over mammalian adult development, we performed global differential gene expression profiling using a public microarray dataset to compare the transcriptomes of mTEC at months 1, 3, and 6 (6). We found that multiple eukaryotic initiation factors, or Eif genes, were differentially expressed by mTEClo and mTEChi. These data suggest a unique requirement for specific eukaryotic initiation factors during translation of proteins in the mTEClo and mTEChi cell types of the thymus.

Comparative transcriptional profiling of medullary and cortical thymic cell types identifies epigenetic and transcription factors that uniquely define the mTEChi and cTEC lineages.

10.31219/osf.io/nx23j ◽

2020 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Global Gene Expression ◽

Cell Types ◽

Self Tolerance ◽

In Trans ◽

The thymus has the unique ability to impart lymphocytes in trans the concept of self-tolerance by negative selection and to enforce positive selection of lymphocytes that express optimal T-cell receptors (1,2). The thymus possesses a cortex and a medulla (4), and epithelial cells known as mTEC and cTEC are intimately involved in these processes (5). Here I compared the transcriptomes of mTEChi and cTEC (6) using global differential gene expression analysis. I present a series of epigenetic molecules and transcription factors that represent the most significant differences in the global gene expression profiles between these two cell types.

Ubiquitin ligase MARCH 8 cooperates with CD83 to control surface MHC II expression in thymic epithelium and CD4 T cell selection

Journal of Experimental Medicine ◽

10.1084/jem.20160312 ◽

2016 ◽

Vol 213 (9) ◽

pp. 1695-1703 ◽

Cited By ~ 26

Author(s):

Haiyin Liu ◽

Reema Jain ◽

Jing Guan ◽

Vivian Vuong ◽

Satoshi Ishido ◽

...

Keyword(s):

T Cell ◽

Ubiquitin Ligase ◽

Cell Types ◽

Surface Expression ◽

Cd4 T Cell ◽

Control Surface ◽

Thymic Epithelial Cells ◽

Cell Selection ◽

Mhc Ii ◽

T Cell Selection

Major histocompatibility complex class II (MHC II) expression is tightly regulated, being subjected to cell type–specific mechanisms that closely control its levels at the cell surface. Ubiquitination by the E3 ubiquitin ligase MARCH 1 regulates MHC II expression in dendritic cells and B cells. In this study, we demonstrate that the related ligase MARCH 8 is responsible for regulating surface MHC II in thymic epithelial cells (TECs). March8−/− mice have elevated MHC II at the surface of cortical TECs and autoimmune regulator (AIRE)− medullary TECs (mTECs), but not AIRE+ mTECs. Despite this, thymic and splenic CD4+ T cell numbers and repertoires remained unaltered in March8−/− mice. Notably, the ubiquitination of MHC II by MARCH 8 is controlled by CD83. Mice expressing a mutated form of CD83 (Cd83anu/anu mice) have impaired CD4+ T cell selection, but deleting March8 in Cd83anu/anu mice restored CD4+ T cell selection to normal levels. Therefore, orchestrated regulation of MHC II surface expression in TECs by MARCH 8 and CD83 plays a major role in CD4+ T cell selection. Our results also highlight the specialized use of ubiquitinating machinery in distinct antigen-presenting cell types, with important functional consequences and implications for therapeutic manipulation.

Transcriptional profiling predicts running promotes cerebrovascular remodeling in young but not midlife mice

BMC Genomics ◽

10.1186/s12864-019-6230-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Kate E. Foley ◽

Hongtian Stanley Yang ◽

Leah C. Graham ◽

Gareth R. Howell

Keyword(s):

Cognitive Decline ◽

Potential Therapeutic Intervention

Cell Types ◽

Brain Health ◽

New Approach ◽

Age Related ◽

Voluntary Running ◽

Differential Gene ◽

Age Related Cognitive Decline ◽

Abstract Background The incidence of dementia and cognitive decline is increasing with no therapy or cure. One of the reasons treatment remains elusive is because there are various pathologies that contribute to age-related cognitive decline. Specifically, with Alzheimer’s disease, targeting to reduce amyloid beta plaques and phosphorylated tau aggregates in clinical trials has not yielded results to slow symptomology, suggesting a new approach is needed. Interestingly, exercise has been proposed as a potential therapeutic intervention to improve brain health and reduce the risk for dementia, however the benefits throughout aging are not well understood. Results To better understand the effects of exercise, we preformed transcriptional profiling on young (1–2 months) and midlife (12 months) C57BL/6 J (B6) male mice after 12 weeks of voluntary running. Data was compared to age-matched sedentary controls. Interestingly, the midlife running group naturally broke into two cohorts based on distance ran - either running a lot and more intensely (high runners) or running less and less intensely (low runners). Midlife high runners had lower LDL cholesterol as well as lower adiposity (%fat) compared to sedentary, than midlife low runners compared to sedentary suggesting more intense running lowered systemic markers of risk for age-related diseases including dementias. Differential gene analysis of transcriptional profiles generated from the cortex and hippocampus showed thousands of differentially expressed (DE) genes when comparing young runners to sedentary controls. However, only a few hundred genes were DE comparing either midlife high runners or midlife low runners to midlife sedentary controls. This indicates that, in our study, the effects of running are reduced through aging. Gene set enrichment analyses identified enrichment of genes involved in extracellular matrix (ECM), vascular remodeling and angiogenesis in young runners but not midlife runners. These genes are known to be expressed in multiple vascular-related cell types including astrocytes, endothelial cells, pericytes and smooth muscle cells. Conclusions Taken together these results suggest running may best serve as a preventative measure to reduce risk for cerebrovascular decline. Ultimately, this work shows that exercise may be more effective to prevent dementia if introduced at younger ages.

Integrative analysis of scRNAs-seq and scATAC-seq revealed transit-amplifying thymic epithelial cells expressing autoimmune regulator

10.1101/2021.10.04.463004 ◽

2021 ◽

Author(s):

Takahisa Miyao ◽

Maki Miyauchi ◽

S. Thomas Kelly ◽

Tommy W. Terooatea ◽

Tatsuya Ishikawa ◽

...

Keyword(s):

Epithelial Cells ◽

Single Cell ◽

Tolerance Induction ◽

Integrative Analysis ◽

Thymic Epithelial Cells ◽

Self Tolerance ◽

Cell Assays ◽

Specific Antigens ◽

Accessible Chromatin

SummaryMedullary thymic epithelial cells (mTECs) are critical for self-tolerance induction in T cells via promiscuous expression of tissue-specific antigens (TSAs), which are controlled by transcriptional regulator AIRE. Whereas AIRE-expressing (Aire+) mTECs undergo constant turnover in the adult thymus, mechanisms underlying differentiation of postnatal mTECs remain to be discovered. Integrative analysis of single-cell assays for transposase accessible chromatin (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) suggested the presence of proliferating mTECs with a specific chromatin structure, which express high levels of Aire and co-stimulatory molecules CD80 (Aire+CD80hi). Proliferating Aire+CD80hi mTECs detected by using Fucci technology express a minimal level of Aire-dependent TSAs and are converted into quiescent Aire+CD80hi mTECs expressing high levels of TSAs after a transit amplification. These data provide evidence for the existence of transit amplifying Aire+mTEC precursors during Aire+mTEC differentiation process of the postnatal thymus.

Transcriptional profiling reveals running promotes cerebrovascular remodeling in young but not aged mice

10.1101/574673 ◽

2019 ◽

Author(s):

Kate E. Foley ◽

Stanley Yang ◽

Leah C. Graham ◽

Gareth R. Howell

Keyword(s):

Cognitive Decline ◽

Potential Therapeutic Intervention

Cell Types ◽

Brain Health ◽

New Approach ◽

Age Related ◽

Voluntary Running ◽

Differential Gene ◽

Age Related Cognitive Decline ◽

AbstractBackgroundThe incidence of dementia and cognitive decline is increasing with no therapy or cure. One of the reasons treatment remains elusive is because there are various pathologies that contribute to age-related cognitive decline. Specifically, with Alzheimer’s disease, targeting to reduce amyloid beta plaques and phosphorylated tau aggregates in clinical trials has not yielded results to slow symptomology, suggesting a new approach is needed. Interestingly, exercise has been proposed as a potential therapeutic intervention to improve brain health and reduce the risk for dementia, however the benefits throughout aging are not well understood.ResultsTo better understand the effects of exercise, we preformed transcriptional profiling on young (1-2 months) and midlife (12 months) C57BL/6J (B6) male mice after 12 weeks of voluntary running. Data was compared to age-matched sedentary controls. Interestingly, the midlife running group naturally broke into two cohorts based on distance ran - either running a lot and more intensely (high runners) or running less and less intensely (low runners). Midlife high runners had lower LDL cholesterol as well as lower adiposity (%fat) compared to sedentary, than midlife low runners compared to sedentary suggesting more intense running lowered systemic markers of risk for age-related diseases including dementias. Differential gene analysis of transcriptional profiles generated from the cortex and hippocampus showed thousands of differentially expressed (DE) genes when comparing young runners to sedentary controls. However, only a few hundred genes were DE comparing either midlife high runners or midlife low runners to midlife sedentary controls. This indicates that, in our study, the effects of running are reduced through aging. Gene set enrichment analyses identified enrichment of genes involved in extracellular matrix (ECM), vascular remodeling and angiogenesis in young runners but not midlife runners. These genes are known to be expressed in multiple vascular-related cell types including astrocytes, endothelial cells, pericytes and smooth muscle cells.ConclusionsTaken together these results suggest running may best serve as a preventative measure to reduce risk for cerebrovascular decline. Ultimately, this work shows that exercise may be more effective to prevent dementia if introduced at younger ages.

Extrathymic Aire-expressing cells support maternal-fetal tolerance

Science Immunology ◽

10.1126/sciimmunol.abf1968 ◽

2021 ◽

Vol 6 (61) ◽

pp. eabf1968

Author(s):

Eva Gillis-Buck ◽

Haleigh Miller ◽

Marina Sirota ◽

Stephan J. Sanders ◽

Vasilis Ntranos ◽

...

Keyword(s):

Thymic Epithelial Cells ◽

Activated T Cells ◽

Healthy Pregnancy ◽

Follicular Helper ◽

Immune Mediated ◽

Self Tolerance ◽

Selective Ablation ◽

Early Mouse

Healthy pregnancy requires tolerance to fetal alloantigens as well as syngeneic embryonic and placental antigens. Given the importance of the autoimmune regulator (Aire) gene in self-tolerance, we investigated the role of Aire-expressing cells in maternal-fetal tolerance. We report that maternal ablation of Aire-expressing (Aire+) cells during early mouse pregnancy caused intrauterine growth restriction (IUGR) in both allogeneic and syngeneic pregnancies. This phenotype is immune mediated, as IUGR was rescued in Rag1-deficient mice, and involved a memory response, demonstrated by recurrence of severe IUGR in second pregnancies. Single-cell RNA sequencing demonstrated that Aire+ cell depletion in pregnancy results in expansion of activated T cells, particularly T follicular helper cells. Unexpectedly, selective ablation of either Aire-expressing medullary thymic epithelial cells or extrathymic Aire-expressing cells (eTACs) mapped the IUGR phenotype exclusively to eTACs. Thus, we report a previously undescribed mechanism for the maintenance of maternal-fetal immune homeostasis and demonstrate that eTACs protect the conceptus from immune-mediated IUGR.

Aire-dependent production of XCL1 mediates medullary accumulation of thymic dendritic cells and contributes to regulatory T cell development

Journal of Experimental Medicine ◽

10.1084/jem.20102327 ◽

2011 ◽

Vol 208 (2) ◽

pp. 383-394 ◽

Cited By ~ 180

Author(s):

Yu Lei ◽

Adiratna Mat Ripen ◽

Naozumi Ishimaru ◽

Izumi Ohigashi ◽

Takashi Nagasawa ◽

...

Keyword(s):

T Cells ◽

Dendritic Cells ◽

Chemokine Receptor ◽

T Cell Development ◽

Cell Development ◽

Thymic Epithelial Cells ◽

Naturally Occurring ◽

Self Tolerance ◽

Deficient Mice

Dendritic cells (DCs) in the thymus (tDCs) are predominantly accumulated in the medulla and contribute to the establishment of self-tolerance. However, how the medullary accumulation of tDCs is regulated and involved in self-tolerance is unclear. We show that the chemokine receptor XCR1 is expressed by tDCs, whereas medullary thymic epithelial cells (mTECs) express the ligand XCL1. XCL1-deficient mice are defective in the medullary accumulation of tDCs and the thymic generation of naturally occurring regulatory T cells (nT reg cells). Thymocytes from XCL1-deficient mice elicit dacryoadenitis in nude mice. mTEC expression of XCL1, tDC medullary accumulation, and nT reg cell generation are diminished in Aire-deficient mice. These results indicate that the XCL1-mediated medullary accumulation of tDCs contributes to nT reg cell development and is regulated by Aire.

Development and function of murine B220+CD11c+NK1.1+ cells identify them as a subset of NK cells

Journal of Experimental Medicine ◽

10.1084/jem.20070991 ◽

2007 ◽

Vol 204 (11) ◽

pp. 2561-2568 ◽

Cited By ~ 118

Author(s):

Amanda L. Blasius ◽

Winfried Barchet ◽

Marina Cella ◽

Marco Colonna

Keyword(s):

Nk Cells ◽

Nk Cell ◽

Ex Vivo ◽

Cell Subset ◽

Lymphoid Organs ◽

Surface Receptors ◽

Histocompatibility Complex ◽

Function Expression ◽

Interleukin 15 ◽

And Function

Lymphoid organs contain a B220+CD11c+NK1.1+ cell population that was recently characterized as a novel dendritic cell (DC) subset that functionally overlaps with natural killer (NK) cells and plasmacytoid DCs (PDCs). Using Siglec-H and NK1.1 markers, we unambiguously dissected B220+CD11c+ cells and found that PDCs are the only professional interferon (IFN)-α–producing cells within this heterogeneous population. In contrast, B220+CD11c+NK1.1+ cells are a discrete NK cell subset capable of producing higher levels of IFN-γ than conventional NK cells. Unlike DCs, only a minute fraction of B220+CD11c+NK1.1+ cells in the spleen expressed major histocompatibility complex class II ex vivo or after stimulation with CpG. Consistent with being a NK cell subset, B220+CD11c+NK1.1+ cells depended primarily on interleukin 15 and common cytokine receptor γ chain signaling for their development. In terms of function, expression of distinctive cell surface receptors, and location in lymphoid organs, NK1.1+B220+CD11c+ appear to be the murine equivalent of human CD56bright NK cells.