Seth Blackshaw

Very proud to have Leah working with us.

Leah Elias, Ph.D., is our Featured Fellow! Elias' postdoctoral research in @sethblackshaw.bsky.social's lab is dissecting how the need for restorative sleep is encoded into our brains at the level of cellular circuits and molecular signals. Her findings may reveal novel therapeutic targets ...
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Exciting new study shows that organoid-derived human retinal ganglion cells survive when apoptosis is genetically inhibited.

Kudos to everyone who contributed to this, particularly Pin Lyu, Isabella Palazzo, Yang Jin, Leah Campbell, and co-corresponding authors David Hyde and Jiang Qian./end

Muller glia-specific expression of Yamanaka factors induces modest but significantrejuvenative effects on rod and bipolar cells. Similar approaches may prove equally informative in humans./36

Finally, spatial transcriptomics proved particularly informative in identifying prorejuvenative effects of mouse Muller glia and heterogeneity in aging rods./35

Age-dependent changes in gene expression and regulation often unexpectedly (to us at least) represented homeostatic changes that potentially counteract the effects of inflammation and other deleterious aging-regulated processes. Reversing the age-dependent changes may prove counterproductive./34

Mostly, though, if you want to study the translation relevance of aging, work in humans. These datasets will likely prove useful in evaluating organoid-based models of retinal aging, and help identify age-dependent mechanisms increasing risk for AMD and glaucoma progression./33

Aging mouse and human retinas don’t have all that much in common with one another at the level of gene expression or regulation, or cell-cell signaling. although a few common and potentially useful homologies were identified./32

So after all that, what are the take home messages. First, There’s a lot to take from this data, but I think that the main points are that age-dependent expression changes are _highly_ species, sex, and cell type-specific./31

After one month of doxycycline treatment, Xenium and clock analysis showed rods and bipolars, though not Muller glia, were modestly but significantly rejuvenated. NicheNet confirmed rods shifted toward a young-like, photoreceptor-enriched state resembling Niche 8./30

Inspired by this, we tested rejuvenation strategies. We selectively expressed Yamanaka factors Oct4, Sox2, and Klf4 in Muller glia using a tamoxifen-inducible GlastCreER system with tetON control, driving low-level, sustained expression in adult mouse retina./29

Using NicheNet, we identified rod-specific age-dependent niches: Niche 8, enriched in young rods with photoreceptor genes, and Niche 11, enriched in aged rods with Col4a3 and proinflammatory Ly75. These niches highlight distinct pro-youth vs. pro-aging states./28

Xenium spatial data also revealed some surprising aging-related cell-cell interactions. Muller glia exerted broad pro-rejuvenative effects on neighboring cells, especially rod photoreceptors, bipolar cells, and amacrine interneurons, suggesting they help buffer against aging-related decline./27

Gene expression changes observed using snRNA-Seq generally replicated in Xenium analysis. This shows plots of several aging-regulated genes in Muller glia./27

To further examine aging-dependent changes in situ, we performed Xenium5k analysis in mouse retina, simultaneously measuring ~5,000 genes at 1 μm resolution. This mapped all major retinal cell types and enabled construction of cell-type-specific aging clocks across the tissue./26

But as with gene expression and regulation, we detected few evolutionarily conserved patterns of cell-cell signaling./25

In all three species, aged cells showed more complex patterns of cell-cell signaling, with Muller glia acting as signaling hubs, particularly in zebrafish and mouse./24

In mouse Muller glia, we saw upregulation of gliogenesis-related TFs such as Nfix, Hes5, and Sox9 in aged cells. This may reflect compensatory gliogenic activity. Interestingly, this pattern was absent in humans, which showed weaker age-linked inflammatory shifts./23

Photoreceptor-specific TFs such as Crx, Neurod1, and Nrl also changed with age, in both young and old cells. This likely reflects homeostatic compensation, as inflammation and stress suppress photoreceptor gene programs, forcing ongoing regulatory adjustments./22

In rod photoreceptors, stress- and metabolism-related transcription factors, including FoxO3, Esrrg, Stat1, and the glucocorticoid receptor Nr3c1, became more active with age. These factors align with known stress response and inflammatory signaling pathways./21

By integrating scRNA-Seq with scATAC-Seq, we mapped transcription factor activity in young vs. aged cells. This revealed robust age-dependent regulatory shifts, though again with strong dependence on species and cell type, and limited evolutionary conservation./20

Still, a few broad regulators emerged: fat4, an atypical cadherin, was age-regulated in zebrafish; Stat1, an inflammatory signal transducer, in mice; and metallothionein 1F, a stress response gene, in humans. These may represent conserved functional stress axes./19

Gene regulation with aging is also highly cell-type specific. Very few genes showed consistent aging patterns across more than two or three retinal cell types. Each population ages in a distinct transcriptional trajectory, with limited overlap across lineages./18

Pairwise conservation was not higher between human and mouse than between either species and zebrafish. This is notable because mouse is often assumed to better model human aging, but our data suggest zebrafish may be equally informative for some comparisons./17

Indeed, only a tiny handful of genes displayed consistent aging-related changes across zebrafish, mice, and humans. Most genes altered in one species showed little or no regulation in the others, underscoring evolutionary divergence in retinal aging mechanisms./16

This divergence extends to specific genes themselves. For any given retinal cell type, only a few individual genes showed conserved patterns of aging regulation across species, highlighting how little evolutionary conservation exists at the gene-specific level./15

Muller glia showed the largest number of aging-related changes in mice, but far fewer in humans and zebrafish. This demonstrates that even for the same cell class, patterns of aging-dependent gene regulation diverge sharply across species and biological contexts./14

Species, sex, and cell-type differences stand out most. For example, retinal ganglion cells (RGCs) in human females showed the largest number of age-regulated genes. Yet in mice and zebrafish, RGCs showed mid-range numbers, and in human males, changes were minimal./13

Humans, in particular, displayed striking sex-dependent differences. Many genes regulated with aging—including inflammation and autophagy genes—shifted far more strongly in one sex than the other, highlighting sex as a critical variable in human retinal aging./12