Seth Blackshaw



733 N. Broadway
329 MRB (Miller Research Building)
Baltimore MD 21205

Neuroscience; Neurology; Ophthalmology

The vertebrate central nervous system (CNS) is an amazingly complex structure composed of distinct subtypes of neurons and glia.  Our lab aims to identify the molecular mechanisms that control the generation of the major cell types of the vertebrate retina and hypothalamus, which both arise from the ventral embryonic forebrain.  The retina is perhaps the best-characterized CNS region at the cellular level, and is an ideal system for uncovering the gene regulatory networks that control neural and glial cell fate specification. We aim to identity genes that pattern progenitors in time, and regulate their ability to proliferate and give rise to specific types of retinal cells at different stages during the course of neurogenesis.  To do this, we have generated single-cell RNA and ATAC-Seq profiles of developing mouse retina, and have used this to identify NFI family transcription factors as key regulators of cell cycle exit and generation of late-born retinal bipolar and Müller glia.

We are using similar approaches to identify the gene regulatory networks that control spatial patterning and cell fate specification in the developing mammalian hypothalamus.  By identifying genes that control how major cell types of the hypothalamus are formed, we gain the ability to selectively manipulate their function and determine their contribution to a broad range of innate behaviors.  We have used our findings to identify key cell types that control circadian rhythmicity and sleep.  In particular, we have recently shown that a population of Lhx6-positive neurons sense sleep pressure, and directly inhibit the activity of wake-active hypothalamic neurons.  Working with other groups at Hopkins, we are now seeking to better understand the formation and organization of hypothalamic circuitry controlling sleep.

Mature glial cells of both the retina and hypothalamus retain the ability to give rise to neurons in certain species.  In zebrafish, retinal Müller glia do this readily following injury, while hypothalamic tanycytes of mammals retain limited neurogenic competence.  We are now integrating single cell RNA and ATAC-Seq data from zebrafish and mammals to gain insight into how this process is controlled, with the ultimate goals of replacing rod and cone photoreceptors lost to disease and rewiring hypothalamic circuitry that controls core homeostatic processes.

Finally, our group has a long-standing interest in developing new techniques and reagents for facilitating these studies.  Working together with other groups at Hopkins, we have developed the HuProt human proteome array, which currently contains over 23,000 unique full-length proteins, and a collection of over 1400 HuProt-validated immunoprecipitation-grade monoclonal antibodies against human transcription factors.  Recently, we have also co-developed a range of new computational tools for identifying evolutionarily conserved gene regulatory networks from single-cell RNA and ATAC-Seq data sets.


Stein-O’Brien GL, Clark BS, Sherman T, Hu Q, Sealfon R, Wolf A, Zibetti C, Liu S, Qian J, Colantuoni C, Beer M, Blackshaw S, Goff LA, and Fertig EJ.  Decomposing cell identity for transfer learning across platforms, tissues and species.  Cell Systems, in press.

Clark BS, Stein-O’Brien GL, Shiau F, Cannon GH, Davis E, Sherman T, Rajaii F, James-Esposito RE, Gronostajski RM, Fertig EJ, Goff LA, and Blackshaw S.   Comprehensive analysis of retinal development at single cell resolution identifies NFI factors as essential for mitotic exit and specification of late-born cells.  Neuron, in press.

Zibetti C, Liu S, Wan J, Qian J, and Blackshaw S.  Lhx2 regulates temporal changes in chromatin accessibility and transcription factor binding in retinal progenitor cells.  Comm Biology 2019, 2:142.

Yoo S, Cha D, Kim DW, Hoang T, and Blackshaw S.  Tanycyte-independent regulation of leptin signaling. Frontiers in Neuroscience 2019, https ://

Ling JP, Wilks C, Charles R, Ghosh D, Jiang L, Santiago CP, Pang B, Venkataraman A, Clark BS, Nellore A, Langmead B, and Blackshaw S. ASCOT identifies key regulators of neuronal subtype-specific RNA splicing.  bioRxiv 2018, 501882.

Newman EA, Wan J, Wang J, Jiang, Qian J, and Blackshaw S. Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes. Dev Biol 2018 439:102-111.

Newman EA, Wu D, Makoto MM, Zhang J, and Blackshaw S.  Canonical Wnt signaling regulates patterning, differentiation and nucleogenesis in mouse hypothalamus and prethalamus. Dev Biol 2018, 442:236-248.

Wang J, Zibetti C, Shang P, Sripathi SR, Zhang P, Cano M, Ji H, Merbs SL, Zack DJ, Handa J, Sinha D, Blackshaw S* and Qian J*.  A widespread decrease in chromatin accessibility in age-related macular degeneration.  Nat Comm 2018 9:1364 (* indicates co-corresponding author).

de Melo J, Venkataraman A, Clark BS, Shiau F, Zibetti C, and Blackshaw S.  Ldb1 and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in retina.  Development 2018 145. pii: dev159970. doi: 10.1242/dev.159970

Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang K Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Seva G. Khambadkone5, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Anderson S, Myers RM, Boeke JD, Fenyo D,  Whiteley G, Bader JS, Pino  I, Eichinger  DJ, Zhu H, and Blackshaw S.  A toolbox of immunoprecipitation-grade monoclonal antibodies against human transcription factors.  Nat Methods 2018  doi: 10.1038/nmeth.4632.

Liu K, Kim J, Kim DW, Zhang S, Denaxa M, Bao H, Lim SA, Kim E, Liu C, Wickersham IR, Pachinis V, Hattar S, Song J, Brown SR, and Blackshaw S. Lhx6-positive GABAergic neurons of the zona incerta promote sleep.  Nature 2017 548:582-587.

Bedont JL, LeGates TA, Buhr E, Bathini A, Ling J, Wong P, van Gelder R, Mongrain V, Hattar  S, and Blackshaw S, An Lhx1-Regulated Transcriptional Network Controls Sleep-Wake Coupling and Thermal Resistance of the Central Circadian Clockworks.  Curr Biol 2017 27:128-136.

De Melo J, Zibetti C, Clark BS, Hwang W, Miranda-Angulo AL, Qian J, Blackshaw S. Lhx2 Is an Essential Factor for Retinal Gliogenesis and Notch Signaling.  J Neurosci 2016 36:2391-405.

De Melo J, Clark BS, and Blackshaw S. Multiple intrinsic factors act in concert with Lhx2 to direct retinal gliogenesis.  Sci Reports 2016 6:32757.

Thein T, de Melo J, Zibetti C, Clark BS, Juarez F, and Blackshaw S.  Control of lens development by Lhx2-regulated neuroretinal FGFs.   Development 2016 143: 3994-4002

Salvatierra J, Lee DA, Zibetti C, Duran-Moreno M, Yoo S, Newman EA, Wang H, Bedont JL, de Melo J, Miranda-Angulo AL, Gil-Perotin S, Garcia-Verdugo JM, and Blackshaw S. The LIM homeodomain factor Lhx2 is required for hypothalamic tanycyte specification and differentiation.  J Neurosci 2014 34:16809-20.

Bedont JL, LeGates TA, Slat EA , Byerly MS, Wang H, Hu J, Rupp AC, Qian J, Wong GW, Herzog ED, Hattar S, and Blackshaw S.  Lhx1 controls terminal differentiation and circadian function of the suprachiasmatic nucleus. Cell Reports 2014 7:609-22.

Jeong JS, Jiang L, Albino E, Marrero J, Rho HS, Hu S, Woodard C, Vera C,  Bayron-Poueymirou D, Rivera-Pacheco ZA, Ramos L, Torres-Castro C, Bonaventura J, Boeke JD, Pino I, Eichinger DJ, Zhu H and Blackshaw S.  A human proteome microarray-based pipeline for efficient production of monospecific monoclonal antibodies.  Mol Cell Proteomics 2012 11:O111.016253.

De Melo J, Miki K, Rattner A, Smallwood P, Hirokawa K, Monuki ES, Campochario P, and Blackshaw S.  Injury-independent induction of reactive gliosis in retinal Muller glia by loss of function of the LIM homeodomain transcription factor Lhx2.  Proc Natl Acad Sci USA 2012 109:4657-62.

Lee DA, Pak T, Bedont JL, Wang H, Miranda-Angulo A, Takiar V, Charubhumi V, Balordi F, Takebayashi H, Fishell G, Ford E and Blackshaw S.  Tanycytes of the median eminence form a dietary-responsive neurogenic niche.  Nat Neurosci 2012 15:700-2.

Shimogori T, Lee D A, Miranda-Angulo A, Yang Y, Yoshida A, Jiang L, Kataoka A, Wang H, Mashiko H,  Avetisyan M A, Qi L, Qian J, and Blackshaw S.  A genomic atlas of mouse hypothalamic development. Nat Neurosci 2010 13:767-75.

Onishi A, Peng GH, Chen S, Blackshaw S. Pias3-dependent SUMOylation controls mammalian cone photoreceptor differentiation. Nat Neurosci 2010 13:1059-65