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Seth Blackshaw

@sethblackshaw.bsky.social
3.4K followers 833 following 322 posts

Professor of Neuroscience. Studying neural development, regeneration, and control of innate behaviors at Johns Hopkins.

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Seth Blackshaw @sethblackshaw.bsky.social · 11/06/2026
This perspective piece reviews new omics, developmental genetic, and cell lineage studies to critically review current models of developing forebrain organization. Spoiler: there are _serious_ problems with the prosomere model.
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Seth Blackshaw @sethblackshaw.bsky.social · 26/02/2026
Proud to have been part of this work.
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Michel Cayouette @michelcayouette.bsky.social · 04/02/2026
Happy to announce that our latest paper is now out! Have you ever wondered how neural tissues control their size? In this paper, we show that cell division orientation is critical in both the cortex and retina. www.science.org/doi/10.1126/...
science.org
Oriented cell divisions induce basal progenitors and regulate neural expansion across tissues and species
A fundamental role for division orientation in progenitor output driving cortical and retinal growth is revealed.
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Seth Blackshaw @sethblackshaw.bsky.social · 30/01/2026
Indeed.
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Elizabeth Manning @emmanning.bsky.social · 26/01/2026
Excited to finally share the final/final.doc version of our paper. It's been a journey, but very proud of the result. Well done to all involved, especially @elsieplace.bsky.social @kchinnaiya.bsky.social , @thomasdwkim.bsky.social, @sethblackshaw.bsky.social 👏👏 www.nature.com/articles/s41...
nature.com
Resolving forebrain developmental organisation by analysis of differential growth patterns - Nature Communications
Experiments on the embryonic chick brain reveal distinct directional growth patterns and a tripartite hypothalamus, challenging the classic segmented prosomere model and offering an updated view of ho...
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
Second paper is a collaboration with Jim Handa's lab at Hopkins. Cigarette smoke exposure induces aging-related molecular changes in both mouse and human retinal pigment epithelium. www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
I'd like to close by thanking lead author Nicole Pannullo, who recently defended her thesis, who with Debarpita Datta, @claytonsantiago.bsky.social, Jared Hangman, Lizhi Jiang, and Leighton Duncan -- and support from NIH -- made this possible./end
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
One reason why the Sox8/9 mutant phenotype is so much less dramatic than that of Nfia/b/x mutants may be persistent compensatory expression of other Sox family members, most notably Sox2, which might compensate for the loss of Sox8/9./11
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
So what's going on here? While Sox8/9 suppress early-born cell type generation when misexpressed, and directly regulate transcription of NFI family genes, they are not required for maintaining late-stage temporal identity, being required for glial differentiation rather than specification./10
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
What about Sox8/9 function in mature Muller glia, where we previously showed that Nfia/b/x actively suppress neurogenic competence? As with Nfia/b/x mutants, we observe a modest induction of injury-induced proliferation, but no glial-derived neurogenesis or induction of Ascl1./9
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
scATAC-Seq and CUT&TAG data show that Sox8/9 predominantly function as transcriptional activators, in combination with other late-stage progenitor-specific factors such as NFIs. However, Sox8/9 mutants show no change in retinal cell fate specification or clear disruptions of temporal identity./8
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
Single-cell multiomic analysis of Sox8/9 double mutant glia show reduced Notch signaling and altered expression of many genes known to regulate cell adhesion and migration, as well as mature glial markers./7
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
Both Sox8 and Sox9 mutants resulted in progressive radial displacement of Muller glial cell nuclei towards the photoreceptor layer. This was enhanced in Sox8/9 double mutants./6
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
Early retinal progenitor-specific loss of function of Sox9 did not affect neurogenesis or cell fate specification, and despite much effort, we were unable to generate early progenitor-specific Sox8 or Sox8/9 double mutants. We shifted instead to selectively deleting these genes in neonates./5
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
When over expressed in early-stage E14 progenitors, both Sox8 and Sox9 repress generation of early-born retinal ganglion and amacrine cells and promote formation of later-born photoreceptors. This matches what we previously observed with NFI factors./4
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
Overexpression, conditional loss of function, and biochemical analysis all confirmed that this was the case for Nfia/b/x in retina. We asked if this was also the case for Sox8/9./3 www.sciencedirect.com/science/arti...
sciencedirect.com
Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina
Gene regulatory networks (GRNs), consisting of transcription factors and their target sites, control neurogenesis and cell-fate specification in the d…
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
Sox8/9 play an important role in regulating brain and spinal cord astrocyte and oligodendrocyte differentiation, often acting cooperatively with Nfia. Our multiomic analysis of retinal progenitors identified NFI and SoxE factor as more broadly promoting late-stage temporal identity, however./2
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Seth Blackshaw @sethblackshaw.bsky.social · 16/01/2026
The lab's first paper of the new year is out. In it, we investigate the role of the late stage retinal progenitor-enriched SoxE family factors Sox8 and Sox9 in controlling retinal development./1 www.biorxiv.org/content/10.6...
biorxiv.org
Sox8 and Sox9 regulate differentiation and nuclear positioning of retinal Müller glia
Temporal patterning of retinal progenitor cells governs the sequential generation of retinal cell types, with gliogenesis occurring late in development. Sox8 and Sox9, members of the SoxE transcription factor family, are highly expressed in late-stage retinal progenitor cells and mature Müller glia, yet their functional roles remain incompletely defined. Here we employed gain- and loss-of-function approaches, single-cell multiomic profiling, and injury models to investigate Sox8/9 function. Overexpression of SOX8 and/or SOX9 in early-stage retinal progenitor cells suppressed early-born cell fates and promoted photoreceptor generation, consistent with a role in late-stage temporal identity. Conversely, conditional deletion of Sox8 and/or Sox9 in late-stage progenitors did not impair Müller glia specification, but caused radial displacement of Müller glia nuclei into the outer retina and modest changes in glial gene expression. Loss of Sox8/9 in mature Müller glia modestly increased proliferation post-injury without inducing neurogenic competence. These findings suggest that Sox8/9 are dispensable for gliogenesis and repression of neurogenic competence, but are essential for proper laminar positioning and maturation of retinal Müller glia. ### Competing Interest Statement S.B. is a cofounder, shareholder, and scientific advisory board member of CDI Labs LLC, and receives research support from Genentech. National Eye Institute, https://ror.org/03wkg3b53, R01EY036173
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Cold Spring Harbor Laboratory @cshlnews.bsky.social · 13/01/2026
We’re thrilled to share that CSHL Associate Professor Jeremy Borniger (@jborniger.bsky.social) has received the 2026 Bakewell Emerging Leader Award from The Mark Foundation. His lab is exploring synthetic torpor—a hibernation-like state—as a novel way to slow cancer growth. #ScienceMakesLifeBetter
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Nature Communications @natcomms.nature.com · 14/01/2026
New featured article! Resolving forebrain developmental organisation by analysis of differential growth patterns @emmanning.bsky.social @elsieplace.bsky.social @kchinnaiya.bsky.social @sethblackshaw.bsky.social @thomasdwkim.bsky.social dlvr.it/TQLWh5
Several stages of brain development in a chick embryo
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Seth Blackshaw @sethblackshaw.bsky.social · 08/01/2026
Congratulation!
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Seth Blackshaw @sethblackshaw.bsky.social · 08/01/2026
Nice summary on our paper on mechanisms controlling development and evolution of the cone-dominant ground squirrel retina, which is now in final form at eLife. www.lifescienceeditors.com/2026/01/06/h...
lifescienceeditors.com
How ground squirrels enhanced their retinas - Scientific editing and writing experts - Life Science Editors
Scientific editing and writing experts for manuscripts and grants
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Development, Regeneration and Neurophysiology @drn-sheffield.bsky.social · 08/01/2026
rdcu.be/eX8JD DRN new publication alert: Manning et al., 2025, @emmanning.bsky.social, co-led by Marysia Placzek and Elsie Place @elsieplace.bsky.social, in collaboration with Seth Blackshaw @sethblackshaw.bsky.social
rdcu.be
Resolving forebrain developmental organisation by analysis of differential growth patterns
Nature Communications - Experiments on the embryonic chick brain reveal distinct directional growth patterns and a tripartite hypothalamus, challenging the classic segmented prosomere model and...
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Reposted by Seth Blackshaw
Samer Hattar @samerhattar.bsky.social · 07/01/2026
A new paper from my lab. I will have a full description soon. rdcu.be/eX1Ld
rdcu.be
ipRGC properties prevent light from shifting the SCN clock during daytime
Nature - The inability of intrinsically photosensitive retinal ganglion cells to shift the circadian clock in the suprachiasmatic nucleus during daytime is caused by light-dependent depolarization...
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Seth Blackshaw @sethblackshaw.bsky.social · 22/12/2025
I want to give my deepest thanks to Tomomi Shimogori -- with whom this all started nearly 20 years ago -- and more recently Marysia and Elsie. It has been an honor and privilege to work with you all.
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Seth Blackshaw @sethblackshaw.bsky.social · 22/12/2025
I have no illusions that this will stop the ongoing trickle of prosomere-promoting single-color in situ hybridization studies in one Frontiers journal or another. I hope this will lead the Allen Brain Atlas to finally revise their developmental mouse reference atlas, however.
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Seth Blackshaw @sethblackshaw.bsky.social · 22/12/2025
And finally combining multiomic-based gene regulatory network and genetic analysis in mouse earlier this year: www.cell.com/cell-reports...
cell.com
Decoding gene networks controlling hypothalamic and prethalamic neuron development
Kim et al. map gene regulatory networks of the developing mouse hypothalamus and prethalamus using single-cell multiomics, identifying regulators of regionalization and neurogenesis. They further show...
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Seth Blackshaw @sethblackshaw.bsky.social · 22/12/2025
Moving to chick here: www.cell.com/cell-reports...
cell.com
Single-cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamic-like progenitors
Using scRNA-seq in the developing chick hypothalamus, Kim et al. identify progenitors during hypothalamic specification, regionalization, and early neurogenesis and demonstrate evolutionary conservati...
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Seth Blackshaw @sethblackshaw.bsky.social · 22/12/2025
Moving to single-cell analysis in mouse: www.nature.com/articles/s41...
nature.com
The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development - Nature Communications
The cellular and molecular mechanisms regulating hypothalamic patterning and differentiation are unclear. Here, the authors profiled the transcriptome of the developing hypothalamus at single cell lev...
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Seth Blackshaw @sethblackshaw.bsky.social · 22/12/2025
Starting here: www.nature.com/articles/nn....
nature.com
A genomic atlas of mouse hypothalamic development - Nature Neuroscience
This Resource chronicles dynamic gene expression patterns in the developing hypothalamus from embryonic day 10.5 through maturity. The authors find that Shh must be expressed in the hypothalamic basal...
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Seth Blackshaw @sethblackshaw.bsky.social · 22/12/2025
Contrast with the prosomere model, which puts that telencephalon and hypothalamus as dorsal and ventral halves of the "secondary prosencephalon". The data here match the conclusions drawn from what's now a long series of molecular studies of both mouse and chick hypothalamic development.
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Seth Blackshaw @sethblackshaw.bsky.social · 22/12/2025
Huge kudos to Marysia Płaczek, Elsie Place and Liz Manning on this. Tl:dr -- most of the hypothalamus and prethalamus form the dorsal and ventral portions of a common forebrain compartment, as do the ZLI and retro(supra)mammilary complex.
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Seth Blackshaw @sethblackshaw.bsky.social · 22/12/2025
It's been quite a year for hypothalamic development. With this heroic analysis of developmental cell lineage, coupled with earlier multimode-based gene regulatory network analysis, the prosomere model looks like it has passed into history. www.nature.com/articles/s41...
nature.com
Resolving forebrain developmental organisation by analysis of differential growth patterns - Nature Communications
Experiments on the embryonic chick brain reveal distinct directional growth patterns and a tripartite hypothalamus, challenging the classic segmented prosomere model and offering an updated view of ho...
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Elise Cutts @elisecutts.bsky.social · 11/12/2025
On our evolutionary branch, a few genes got an update unique to humans. Some used to think those variants might have been difference that made all the difference: the key to becoming human. This month's Q&A with Barbara Molz @mpi-nl.bsky.social gets into new results that tell a different story. 🧪
reviewertoo.com
There's no gene for being human
A Q&A on genetics and human evolution with Barbara Molz
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Seth Blackshaw @sethblackshaw.bsky.social · 12/12/2025
Second, not only does Ptpb1 not repress neurogenesis in adult glia, it doesn't do much in the developing CNS either. Scratch another master regulator off the list. doi.org/10.7554/eLif...
doi.org
Ptbp1 is not required for retinal neurogenesis and cell fate specification
Loss of function of Ptbp1 in retinal progenitors leads to changes in RNA splicing but does not affect neurogenesis and cell fate specification.
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Seth Blackshaw @sethblackshaw.bsky.social · 12/12/2025
A couple of papers are finally out too. First, Meis factors are (unfortunately) not sufficient to respecify temporal identity in retinal progenitor cells. www.nature.com/articles/s41...
nature.com
Overexpression of Meis factors in late-stage retinal progenitors yields complex effects on temporal patterning and neurogenesis - Scientific Reports
The vertebrate retina serves as a model for studying neurogenesis and cell fate specification, with retinal progenitor cells following a tightly regulated temporal sequence to generate distinct cell t...
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Seth Blackshaw @sethblackshaw.bsky.social · 12/12/2025
Recent Hopkins Hub article highlighting our work on optic nerve regeneration in axolotl. Congratulations to Ted! hub.jhu.edu/2025/12/11/s...
hub.jhu.edu
Could axolotls hold the key to restoring human vision?
Axolotls can regenerate optic nerves, retinas, and parts of their brain. Provost's Undergraduate Research Award-winner Ted Chor wants to understand how.
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Seth Blackshaw @sethblackshaw.bsky.social · 07/10/2025
Very proud to have Leah working with us.
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Jane Coffin Childs Fund for Medical Research @jcchildsfund.bsky.social · 07/10/2025
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 ... 1/
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Seth Blackshaw @sethblackshaw.bsky.social · 30/09/2025
Exciting new study shows that organoid-derived human retinal ganglion cells survive when apoptosis is genetically inhibited.
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Seth Blackshaw @sethblackshaw.bsky.social · 12/09/2025
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
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Seth Blackshaw @sethblackshaw.bsky.social · 12/09/2025
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
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Seth Blackshaw @sethblackshaw.bsky.social · 12/09/2025
Finally, spatial transcriptomics proved particularly informative in identifying prorejuvenative effects of mouse Muller glia and heterogeneity in aging rods./35
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Seth Blackshaw @sethblackshaw.bsky.social · 12/09/2025
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
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Seth Blackshaw @sethblackshaw.bsky.social · 12/09/2025
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
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Seth Blackshaw @sethblackshaw.bsky.social · 12/09/2025
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
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Seth Blackshaw @sethblackshaw.bsky.social · 12/09/2025
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
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Seth Blackshaw @sethblackshaw.bsky.social · 12/09/2025
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
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Seth Blackshaw @sethblackshaw.bsky.social · 12/09/2025
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
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Seth Blackshaw @sethblackshaw.bsky.social · 12/09/2025
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
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