Gene Expression Predicts Physiology of Aging

<div><p>(A) Cross-section of histologically unremarkable deltoid muscle from a 48-y-old woman demonstrating relatively equivalent sizes of types I and II muscle fibers. Arrows denote fibers types as distinguished by enzyme histochemistry (cryosection, 200×, myosin ATPase at pH 9.4).</p><p>(B) Cross-section of deltoid muscle from an 88-y-old woman demonstrating selective atrophy of type II muscle fibers that stain darkly by ATPase enzyme histochemistry (cryosection, 200×, myosin ATPase at pH 9.4).</p><p>(C) Histograms showing a correlation between muscle physiology and gene expression for age-regulated genes. Top panel: for each of the 250 age-regulated genes, we calculated the partial correlation coefficients between the type II/type I muscle fiber diameter ratio and gene expression excluding age variation (<i>x</i>-axis). Bottom panel: same as top panel, except that correlation coefficients were calculated for all 31,948 genes. The squared partial correlation coefficient denotes the amount that changes in gene expression account for variance in type II/type I muscle fiber diameter ratios while excluding the effects of age.</p><p>(D) Histogram showing the likelihood of finding 92 genes with |<i>r</i>| > 0.2 from a set of random genes. We performed a Monte Carlo experiment by randomly selecting sets of 250 genes from the genome, and calculating how many genes in the set had |<i>r</i>| > 0.2 as in (C). The procedure was repeated 1,000 times and the histogram shows the number of genes from each random selection that have |<i>r</i>| > 0.2. The arrow shows the number of genes exceeding this threshold (92) from the set of 250 age-regulated genes (<i>p</i> < 0.001). We also determined the total number of genes in the genome with |<i>r</i>| > 0.2, and then showed that 92 genes from a set of 250 is significant (hypergeometric distribution; <i>p</i> < 1 × 10⁻⁴).</p></div

A Common Signature for Aging in Muscle, the Kidney, and the Brain

<p>Shown are expression data from sets of extracellular matrix genes, cell growth genes, complement activation genes, cytosolic ribosomal genes, chloride transport genes, and electron transport chain genes. Rows are human tissues (M, muscle; K, kidney; B, brain). Columns correspond to individual genes in each gene set. Scale represents the slope of the change in log₂ expression level with age <i>(β_1j).</i> Gray indicates genes were not present in the dataset. A navigable version showing identities of specific genes can be found at <a href="http://cmgm.stanford.edu/~kimlab/aging_muscle" target="_blank">http://cmgm.stanford.edu/~kimlab/aging_muscle</a>.</p

The Electron Transport Chain Decreases Expression with Age in Humans, Mice, and Flies

<p>Rows represent either human tissues or model organisms. Columns correspond to individual human genes and homologs to human genes defined by reciprocal best BLAST hits in other species. Scale represents the normalized slope of the change in log₂ expression level with age (<i>β_1j</i>). Data from different species were normalized by dividing the slope of expression with age by the standard deviation of all similar slopes in the dataset. Gray indicates genes were not present in that species. A navigable version of this figure showing identities of specific genes can be found at <a href="http://cmgm.stanford.edu/~kimlab/aging_muscle" target="_blank">http://cmgm.stanford.edu/~kimlab/aging_muscle</a>.</p

Sensitivity of VHL-1–Regulated Genes to Defects in Extracellular Matrix-Associated Proteins

<div><p>RNase protection assays showing altered expression of VHL-1–regulated genes that are HIF-1 independent (upper six panels) and HIF-1 dependent (F22B5.4) in worms bearing mutations affecting (A) procollagen prolyl and lysyl hydroxylases and (B) other extracellular matrix-associated proteins. A common pattern of upregulation is observed in <i>hif-1; vhl-1, vhl-1, dpy-18, let-268, gon-1, mig-17,</i> and <i>unc-6</i> worms but not other mutants. This contrasts with the HIF-1–dependent gene F22B5.4, which is upregulated in <i>vhl-1</i> worms but none of the other mutants.</p> <p>(C) RNase protection assay for C01B4.9 illustrating DPY-18–mediated changes in expression that are independent of HIF-1.</p></div

Responses of VHL-1–Dependent, HIF-1–Independent Genes to <i>egl-9</i> Inactivation, Hypoxia, and 2-Oxoglutarate Dioxygenase Inhibitors

<p>RNase protection assays showing regulation of VHL-1–dependent, HIF-1–independent genes by (A) EGL-9 and hypoxia and (B) pharmacological inhibitors of 2-oxoglutarate dioxygenases: DIP and DMOG. None of the genes is regulated by EGL-9, but two genes (C01B4.7 and C01B4.8) show modest induction by hypoxia, DIP, and DMOG.</p

Age-Regulated Genes

<div><p>(A) Shown are expression levels for gene <i>CDO1</i>. White and black circles represent expression from cortex and medulla, respectively. The y-axis indicates log₂ (expression level), and the x-axis indicates age of patient (years). Dotted and solid lines indicate best fit slopes for the cortex and medulla values, respectively.</p> <p>(B) For every gene, we calculated a one-sided p̃ -value that its expression changes with age. Shown is a histogram representing all of the genes represented by the Affymetrix DNA chip. Genes that decrease with age have p̃ -values near zero, and genes that increase with age have p̃ -values near one. If there were no age-regulated genes (i.e., the true <i>β_kj</i> = 0 for every gene <i>j</i>), then the histogram of p̃ -values would be flat (i.e., have a uniform distribution on the interval from zero to one). The x-axis shows the p̃ -value, and the y-axis shows the number of genes with that p̃ -value. There are 985 genes with a <i>p-</i>value less than 0.001. </p></div

Chronicity Index of Kidney Samples

<p>Histology from patient 40 is shown on the left, demonstrating a normal glomerulus (G), tubules and interstitial space (T), and arteriole (A), respectively (chronicity score of zero). Histology from patient 62 is shown on the right, demonstrating glomerulosclerosis (g), tubular atrophy and interstitial fibrosis (t), and arterial intimal hyalinosis (a), respectively (chronicity score of ten). Hematoxylin and eosin staining of paraffin-embedded sections.</p

Differential Expression in the Cortex and the Medulla

<p>For each gene, we calculated a p̃ -value for expression differences in the cortex versus the medulla. Shown is a histogram of these p̃ -values. Genes enriched in the cortex are in a peak on the left, and genes enriched in the medulla are in a peak on the right. The x-axis indicates p̃ -value, and the y-axis indicates number of genes. </p

Chronicity Index Increases with Age

<p>Shown is the chronicity index versus age for most of the kidney samples used in this study. The line shows the least squared fit through the data points.</p

Expression of the 447 Genes as a Function of Age

<p>Rows correspond to age-regulated genes, ordered from most highly induced to most highly repressed. Columns correspond to individual patients, ordered from youngest to oldest. The age of certain patients is shown for reference. Left panel refers to data from cortex samples, and right panel depicts data from medulla samples. The first row shows the chronicity index (ChI; morphological appearance and physiological state of the kidney),from blue (healthiest) to yellow (least healthy) as indicated in the scale bar. Key genes discussed in the text are marked. Scale shows log₂ of the expression level (Exp). A navigable version of this figure can be found at <a href="http://cmgm.stanford.edu/~kimlab/aging_kidney/explorer.html" target="_blank">http://cmgm.stanford.edu/~kimlab/aging_kidney/explorer.html</a>.</p