Lobule enrichment LE scores for each cluster i and each lobule j were calculated by:. For this analysis, we used coarse cell type definitions shown coloured in the Fig. For lobule composition testing and replicate consistency analysis below, we downsampled granule cells to 60, nuclei the next most numerous cell type were the MLI and PLI clusters with 45, nuclei. This assignment was used because not all regions had representation from all individuals profiled, and some had representation from only two individuals.
We calculated lobule enrichment scores for each cluster using each of the replicate sets separately; we then calculated the Pearson correlation between the two sets of lobule enrichment scores for each cluster. We would expect correlation to be high for clusters when lobule enrichment is biologically consistent.
However, we confirmed that lobule enrichment for this cluster was strongly consistent with Allen Brain Atlas expression staining Extended Data Fig. To characterize molecular variation across cell types, we attempted to quantify the continuity of scaled gene expression across a given cell type pair, ordered by pseudotime rank calculated using Monocle2. For each gene, we fit a logistic curve to the scaled gene expression values and calculated the maximum slope m of the resulting curve, after normalizing for both the number of cells and dynamic range of the logistic fit.
To limit computational complexity, we downsampled cell type pairs to 5, total nuclei. We fit curves and computed m values for the most significantly differentially expressed genes across five cell type pairs Fig.
We then plotted the cumulative distribution of m values for the top genes for each cell type pair; genes were selected based on ordering by absolute Spearman correlation between scaled gene expression and pseudotime rank. After generation of digital gene expression matrices for the peri- and postnatal mouse profiles, we filtered out nuclei with fewer than UMIs.
We applied the LIGER workflow similarly to the adult mouse data analysis , to identify clusters corresponding to major developmental pathways. We then isolated the cluster corresponding to GABAergic progenitors marked by expression of Tfap2b and other canonical markers.
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Ding, J. A metabolome atlas of the aging mouse brain. Nat Commun 12, Download citation. Received : 16 December Accepted : 24 September Published : 15 October Anyone you share the following link with will be able to read this content:. Sorry, a shareable link is not currently available for this article.
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Advanced search. Skip to main content Thank you for visiting nature. Download PDF. Subjects Ageing Metabolomics Neural ageing Sphingolipids. Abstract The mammalian brain relies on neurochemistry to fulfill its functions. Introduction The brain is one of the most structurally and functionally complex organs in mammals 1 , 2 , 3 , 4. Full size image. Reporting summary Further information on research design is available in the Nature Research Reporting Summary linked to this article.
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Search Search articles by subject, keyword or author. The pupil is to the right and the region encompassing the sphincter muscle is indicated. H Flat mounts of untreated iris immunostained as indicated. For each immunostaining analysis in this and subsequent figures, iris cross sections were stained from at least five mice and iris whole mounts were stained from at least two mice. All images are at the same magnification. This analysis localized transcripts for Nos1 to dilator muscle, Ttn to sphincter muscle, and myosin heavy chain Myh11 to both dilator and sphincter muscles Figure 3B and C.
Transcripts coding for synaptotagmin-1 Syt1 , a calcium sensor that regulates neurotransmitter release, localized to sphincter 1 and sphincter 2 cells Figure 3B and C. As predicted from the UMAP analysis, Adra1a transcripts are enriched in dilator muscle and Chrm3 transcripts are enriched in sphincter muscle Figure 3D. A Dot plot as described in Figure 2A showing transcript abundances across a subset of iris cell types for transcripts coding for markers shown in B—D.
B—D Cross sections of untreated iris hybridized with the indicated probes. For each in situ hybridization analysis in this and subsequent figures, iris cross sections were hybridized from at least three mice. Except for the adrenergic and cholinergic receptors, the physiologic significance of differential gene expression in the different iris smooth muscle subtypes is unclear.
A similar elastic role in the sphincter 1 cells appears plausible in light of the 4-fold change in pupil diameter — and, hence, sphincter muscle length — with dilation and constriction. Why Titin would not similarly be required in dilator muscle is unclear.
Alpha-catenins heterodimerize with beta-catenins at adherins junctions and they regulate actin filament assembly, coordinating junctional and cytoskeletal architectures Takeichi, The localization to sphincter cells of NeuN, neuronal activity-regulated pentraxin-2 NPTX2 , and synaptotagmin-1 SYT1 — all of which are enriched in the nervous system — suggests that gene expression in sphincter cells has a partially neuronal character. The cell-type-specific transcriptomes derived from snRNAseq provide an opportunity to systematically assess signal transduction components that regulate iris smooth muscle function.
Our transcriptome analysis shows that of all the genes coding for rhodopsin-like proteins in the mouse genome, Opn4 is the most highly expressed in the iris. Interestingly, it is expressed in both dilator and constrictor muscles, and it is also expressed in iris PE cells Figure 2—figure supplement 1A.
Transcripts for cryptochromes-1 and -2 Cry1 and Cry2 , flavin-based light sensors implicated in circadian rhythms, are also widely expressed in the iris Figure 2—figure supplement 1A. The distribution of adrenergic and muscarinic receptors implies that 1 dilator muscles receive adrenergic input principally via ADRA1A, 2 sphincter muscles receive cholinergic input principally via CHRM3 — consistent with the defect in pupil constriction observed in Chrm3 knockout mice Matsui et al.
The distribution of alpha-adrenergic receptor transcripts also implies that stroma 2 cells are sensitive to adrenergic ligands via ADRA1B receptors Figure 2—figure supplement 1D. Transcription factor ZIC1 localizes exclusively to the nuclei of these two epithelia Figure 4.
A Dot plot as described in Figure 2A showing transcript abundances across a subset of iris cell types for the markers shown in B—D. B Flat mounts of untreated iris immunostained as indicated. C,D Cross sections of untreated iris immunostained as indicated.
Stroma 1 cells express multiple melanogenesis-related genes, including endothelin receptor beta Ednrb , microphthalmia-associated transcription factor Mitf , dopachrome tautomerase dopachroma delta-isomerase, Dct , tyrosinase-related protein-1 Tyrp1 , and tyrosinase Tyr , indicating that they serve as a secondary site of melanin synthesis in addition to the principal site of melanin synthesis and accumulation in the iris PE.
A Dot plot as described in Figure 2A showing transcript abundances across a subset of iris cell types for the markers shown in B and C.
C Cross sections of untreated iris immunostained as indicated. The distribution of immune cells in the rodent iris — principally macrophages and dendritic cells — has been defined previously by immunocytochemistry of iris flat mounts McMenamin, ; McMenamin, The murine iris is uniformly tiled by irregularly shaped stellate cells, of which the majority are macrophages and the minority are dendritic cells Figure 5—figure supplement 1B.
One of the most striking properties of the iris is its mechanical flexibility. These large-scale changes in tissue structure suggested the possibility that iris dilation might also produce changes in gene expression. A Images of isolated eyes from mice with dilated pupils, constricted pupils, or no treatment. Red arrowheads mark the edge of the pupil. B Flat mounts of dilated and untreated irises showing the pattern of nerve fibers left and blood vessels right.
All images are at the same magnification and are oriented with the pupil to the right. C Scatter plots of single nucleus sn RNAseq read counts log 10 average normalized expression and R 2 values for pairwise comparisons of all transcripts for dilated vs. D Summary plot showing the difference in R 2 values between the dilated vs. As noted in connection with Figure 1E and Figure 1—figure supplements 1 and 2 , the transcriptomes of constricted and untreated irises are virtually indistinguishable across all cell types, presumably because the untreated pupil diameter is relatively small, so that pharmacologic constriction produces only a modest additional reduction in its diameter.
Therefore, comparisons between the transcriptomes of constricted and untreated irises can be used to estimate technical variability. Scatter plots of snRNAseq read counts for the constricted vs. For seven of the ten iris cell types, there was more scatter in the dilated vs. The dilator muscle showed the largest transcriptome changes, with a reduction in R 2 from 0.
The three cell types that showed little change in R 2 or a small trend in the opposite direction were endothelial cells, CB epithelial cells, and CB cells. Examples of transcripts that increased or decreased with dilation defined as a log 2 -fold change greater than 0. The dot plots in Figure 6—figure supplement 1 also illustrate the near identity of constricted and untreated snRNAseq read counts.
To independently assess the changes seen with snRNAseq, we focused on three dilator muscle transcripts that were among the most strongly induced by dilation: Egr1 , a zinc-finger transcription factor that is an immediate-early response gene in diverse cell types; Slc26a4 , a broad-specificity anion exchanger that is expressed in multiple epithelia; and Tmem , a membrane protein of unknown function Figure 7A.
Similarly, ISH shows the accumulation of Slc26a4 and Tmem transcripts in dilator muscle with pupil dilation, whereas the abundance of Adrala transcripts remains unchanged Figure 7C , quantified in Figure 7—figure supplement 1. Confirming the snRNAseq data, quantification of the ISH signals showed accumulation of Anks1b , Btg2 , Junb , and Pde10a transcripts in dilator muscle and Tmem transcripts in sphincter muscle with pupil dilation Figure 7—figure supplement 1.
For each cell type, the symbols for the dilated iris blue are above the symbols for the untreated iris red. B Cross sections of dilated left and untreated right irises immunostained as indicated. C Cross sections of dilated left and untreated right irises hybridized with the indicated probes.
D Immunostaining of irises harvested 30 min left and 90 min right after the onset of dilation. Other cyclic nucleotide phosphodiesterase transcripts — including Pde1c , Pde3b , Pde4d , Pde7b — are also upregulated, suggesting that negative regulation of cyclic nucleotide signaling is a general feature of iris dilation Supplementary file 3. In dilator muscle, the second most highly induced transcript is Btg2 , and, unlike Pde10a , Btg2 induction is specific to dilator muscle Supplementary file 3.
BTG2 could play a regulatory role in the iris dilator muscle analogous to its role in cardiac muscle. Changes in iris structure at the macroscopic level must have counterparts at the cellular level. Early electron micrographic studies visualized ultrastructural responses to dilation or constriction on the plasma membrane morphology of iris PE cells and the surface morphology of sphincter and dilator muscles Lim and Webber, a ; Lim and Webber, b ; Murata et al.
Still largely unexplored are the effects of changes in iris structure on nuclear morphology. Current evidence suggests that changes in nuclear morphology alter chromatin organization, gene expression, and intracellular signals Kirby and Lammerding, ; Lele et al.
The identification of 1 transcription factors that mark defined iris cell type and 2 antibodies that can be used to immunolocalize those proteins in iris whole mounts presented an opportunity to visualize nuclear morphology in defined cell types in response to changes in iris structure Figure 8A. For untreated, dilated, and constricted irises, the length:width ratio was quantified for fluorescently stained nuclei in Z-stacked confocal images of iris flat mounts Figure 8B and.
As the 2D projection of a 3D ellipsoid exhibits a length:width ratio less than or equal to the actual 3D ratio, our analysis may underrepresent the elongation of some nuclei. A Flat mounts of untreated, dilated, or constricted irises, immunostained for the indicated nuclear markers.
Cell types are defined by the indicated marker. Each data point is an individual nucleus. The data for each condition in each plot are derived from three mice. The biological effects of these changes in nuclear morphology remain to be determined. Lineage tracing experiments in avian embryos provided the first evidence that some anterior ocular structures were derived, at least partially, from the neural crest via its contribution to the peri-ocular mesenchyme Johnston et al.
Neural crest lineage tracing in mice using Cre-LoxP to mark cells has produced conflicting results, with one laboratory describing no contribution of neural crest cell to the iris with a Wnt1-Cre driver Gage et al. We have revisited this issue using SoxCre Matsuoka et al. SoxCre labels migratory neural crest cells and Wnt1-Cre2 labels multiple cells within the embryonic CNS, including premigratory neural crest Debbache et al. For each Cre driver line, the fraction of cells of a given type that expressed the H2B-GFP reporter was determined from iris flat mounts and is summarized in Figure 9A.
As seen in the iris flat mount and cross-sectional images in Figure 9 and Figure 9—figure supplement 1 , co-labeling with H2B-GFP was widespread with the Wnt1-Cre2 driver but limited to stroma 1 and stroma 2 cells with the SoxCre driver. The data are consistent with a model in which 1 a subset of migratory neural crest cells, defined by SoxCre expression, contribute exclusively to the stromal cell populations and provide all or nearly all of the stromal cell progenitors, and 2 migratory neural crest cells that express Wnt1-Cre2 but not SoxCre contribute the majority of the progenitors for iris PE, dilator, and sphincter 2 cells, but contribution minimally to the sphincter 1 population.
The vast majority of sphincter 1 cells presumably arise either from an unlabeled neural crest population or from local ocular progenitors. Iris cell types were identified by immunostaining for the nuclear-localized markers listed. The intensities of GFP and the cell type markers vary among nuclei.
A nucleus was considered to exhibit co-localization if both signals were present, regardless of intensity. For sphincter muscle, the number of cells scored for each Cre driver ranged from to For each of the other cell types, the number of cells scored for each Cre driver ranged from to The work described here is presented as a resource for future investigations of the mammalian iris. We have 1 used snRNAseq to define all of the major cell types in the mouse iris, which has led to the discovery of two types of stromal cells and two types of sphincter cells; 2 validated a series of molecular markers that can be used to visualize each of the major iris cell types; 3 identified transcriptome changes and distortions in nuclear morphology associated with iris dilation; and 4 clarified the neural crest contribution to the iris by showing that Wnt1-Cre -expressing progenitors contribute to nearly all iris cell types, whereas SoxCre -expressing progenitors contribute only to stromal cells.
As described more fully below, this work should be useful as a point of reference for investigations of iris development, disease, and pharmacology, for the isolation and propagation of defined iris cell types, and for iris cell engineering and transplantation.
Going forward, it will be of interest to obtain and compare similar snRNAseq data from the irises of other species, most especially from humans. The present work defines the molecular heterogeneity among different classes of iris smooth muscle cells. Smooth muscle cells are present in multiple organs and they control a wide range of physiological functions, including vascular tone, airway resistance, gastrointestinal GI motility, and pupil diameter.
The comprehensive determination of the abundances of transcripts for all known receptors, channels, and signaling components for sphincter 1, sphincter 2, and dilator muscles constrains the possible ligand-receptor systems that control contraction and relaxation in each of these muscle types.
The iris PE cell transcriptome provides a foundation for strategies to genetically engineer these cells and monitor their state of trans-differentiation in cell culture.
Over the past 30 years, the iris PE has been studied as a potential source of cells for autologous transplantation to replace dying or dysfunctional retinal pigment epithelial RPE cells in individuals with age-related macular degeneration. These studies were motivated by the surgical accessibility of human iris PE cells, which can be harvested from a small iridectomy sample and expanded in culture, and by earlier work showing that the iris PE in non-mammalian vertebrates can transdifferentiate into other ocular cell types Hu et al.
In three clinical trials of sub-retinal transplantation of iris PE in age-related macular degeneration patients, there have been minimal complications but also minimal effect on the clinical course of the disease Lappas et al.
Some sections in slide View Image and slide View Image will show a portion of this distal tubule with unusually closely packed nuclei. This region is the macula densa which is located at the end of the ascending straight tubule where the distal convoluted tubule begins slide View Image. The macula densa together with the juxtaglomerular cells and the extraglomerular mesangial cells lacis cells form the "juxtaglomerular apparatus". Juxtaglomerular cells are specialized smooth muscle cells found in the wall of the afferent and to some extend the efferent arteriole which secrete renin.
You cannot distinguish juxtaglomerular cells in these preparations but you could detect them by immunological techniques, e. Move to the medulla slide View Image , where straight proximal and distal tubules as well as collecting ducts are found.
Blood vessels note outlines of red blood cells in slide are also seen. In the medulla is the loop of Henle, usually composed of:. The thick portions have an histology characteristic of either proximal or distal tubule. The thin portion is lined by a simple squamous epithelium and cannot reliably be distinguished from capillaries unless blood cells are present in the capillaries as in slide View Image.
The deepest portions of the medulla have only thin segments and collecting ducts. The epithelium of the collecting ducts becomes higher as these ducts pass toward the papilla where they are called "papillary ducts" or ducts of Bellini slide View Image. As an artifact in some slides, the collecting duct epithelium may be pulled away from its basement membrane in some areas of the papilla, leaving a white space between the epithelium and its underlying connective tissue.
Urine is released at the papilla through openings area cribrosa into one of the minor calices which you will note are lined with transitional epithelium slide View Image somewhat damaged in slide View Image as is the rest of the urinary tract. It is worth noting that, from this point onward, the osmolarity of the urine can no longer be modified since transitional epithelium is essentially impermeable to salts and water.
Now that you have seen the arrangement of various nephron components in the kidney, go back and follow the blood supply. Slide is helpful to study the blood supply even though the tubular epithelium in this slide is in bad shape! You will remember from gross anatomy that the renal artery enters the hilus of the kidney, and divides successively into lobar, interlobar these are difficult to identify with certainty in histological sections, but they are the large arteries among the pyramids that are upstream of the arcuate arteries and finally into arcuate arteries, which are accompanied by the corresponding veins.
Observe interlobar arteries and veins in slide View Image , sizable vessels passing along the lateral sides of the medullary pyramid. Arcuate arteries and veins follow the base of the medullary pyramid along the boundary between the renal medulla and the renal cortex. From the arcuate arteries, relatively straight branches, the interlobular arteries and vein slide View Image extend up between the lobules of the cortex where they branch off into the intralobular arteries and, in turn, the afferent arterioles in slide View Image that supply the glomeruli within each lobule.
Human kidneys do not have interlobular arteries, just afferent arterioles. Even though most of the RBCs have been washed out of the tissue in slide , the arcuate and interlobular vessels should still be identifiable by the smooth muscle in their walls also, note that arcuate vessels are generally lining the base of the medullary pyramid along the cortico-medullary boundary.
Efferent arterioles do not worry about distinguishing between afferent vs. The majority of these capillaries then coalesce to enter the interlobular veins, allowing the blood to pass back to the general circulation. However, efferent arterioles from some glomeruli near the medulla i. The multiple small vessels arterioles that are more like dilated capillaries arising from the efferent arterioles and descending into the medulla and the somewhat larger venules ascending from it are clustered to form the vasa recta, which you observed earlier in slide as radiating reddish or brownish stripes in the medulla.
The close association of arterioles and venules in the vasa recta provide counter-current exchange to help prevent loss of the high electrolyte concentration present in the inner medulla, necessary for the concentration of urine.
Capillaries receiving blood from arterioles of the vasa recta are seen throughout the lower medulla. The venules of the vasa recta empty into arcuate or interlobular veins. Blood enters the kidney through the large renal arteries.
At the hilum, the renal arteries branch and become interlobar arteries. Interlobar arteries travel through the medulla to the corticomedullary junction where the arteries branch into arcuate arteries that run along the corticomedullary junction. The arcuate arteries further branch and become interlobular arteries that run through the renal cortex. From the interlobular arteries come afferent arterioles that become the glomerulus.
Exiting from the glomerulus is the efferent arteriole. After leaving glomeruli in the cortical region, the efferent arteriole leads to the peritubular capillary network.
Efferent arterioles of the juxtamedullary glomeruli become the vasa rectae, which can be seen in the medulla. The vasa rectae and peritubular capillary network drain directly into interlobular veins. Peritubular capillaries drain into stellate veins and then into interlobular veins. From there blood travels to the arcuate veins, interlobar veins and finally leaves through the renal vein. This section of kidney cortex was cut parallel to the surface of the kidney, and thus shows medullary rays in cross section in View Image.
Observe such rays to see cross sections of straight proximal and distal tubules as well as collecting ducts. Also, you may have a more favorable view of maculae densae in this slide. In this cross section of a monkey kidney, you will recognize cortex at the periphery and a medullary pyramid in the center. Many of the tubules in the cortex are swollen, making it somewhat more difficult to distinguish proximal tubules from distal and collecting tubules. An opaque red gelatin was injected through the renal artery of this kidney, filling many of the arteries and capillaries.
Observe the distribution of blood vessels.
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