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.


Ling J, Bygrave A, Santiago CP, Trinh V, Carmen R, Yu M, Li Y, Han J, Taneja K, Liu Y, Dongmo R, Babola T, Parker P, Jiang L, Leavey P, Smith J, Vistein R, Gimmen M, Dubner B, Teodorescu P, Kanold P, Bergles D, Langmead B, Sun S, Nielsen K, Peachey N, Singh M, Dalton W, Rajaii F, Huganir R, and Blackshaw S. Cell-specific regulation of gene expression using splicing-dependent frameshifting. Nature Communications (2022) 13:5773.

Kim DW, Place E, Chinnaiya K, Manning E, Sun C, Dai W, Burbridge S, Placzek M, and Blackshaw S. Single cell analysis of early hypothalamic regionalization and neurogenesis in chick.  Cell Reports (2022) 38:110251.

Kim DW, Liu K, Wang ZQ, Zhang YS, Bathini A, Brown MP, Lin SH, Washington PW, Sun C, Lindtner S, Lee B, Wang H, Shimogori T, Rubenstein JLR, and Blackshaw S. Gene regulatory networks controlling differentiation, survival, and diversification of hypothalamic Lhx6 neurons. Comm Bio (2021) 4:95.

Brodie-Kommit J, Brian S. Clark BS, Shi Q, Shiau F, Kim DW, Langel J, Sheely C, Schmidt T, Badea T, Glaser T, Zhao H, Singer J, Blackshaw S*, and Hattar S* (*indicates corresponding author). Atoh7-independent specification of retinal ganglion cell identity. Sci Advances (2021) 7:eabe4983.

Lyu P, Hoang T, Santiago CP, Thomas ED, Timms AE, Appel H, Gimmen M, Le N, Jiang L, Kim DW, Chen S, Espinoza D, Telger AE, Weir K, Clark BS, Cherry TJ, Qian J, and Blackshaw S.  Integrated multiomic analysis identifies gene regulatory networks controlling temporal patterning, neurogenesis and cell fate specification in the mammalian retina. Cell Reports (2021) 37:109994.

Yoo S,  Kim J, Lyu P, Hoang TV, Ma A, Trinh V, Dai W, Jiang L, Leavy P, Won JK, Park SH, Qian J, Brown SP, and Blackshaw S. Control of neurogenic competence in mammalian hypothalamic tanycytes. Science Advances (2021) 7:eabg3777.

Hoang T, Wang J, Boyd P, Wang F, Santiago C, Jiang L, Lahne M, Todd LJ, Saez C, Yoo S, Keuthan C, Palazzo I, Squires N, Campbell WA , Jia M, Rajaii F, Payail T, Wang G , Ash J, Fischer AJ, Hyde DR, Qian J, and Blackshaw S. Cross-species transcriptomic and epigenomic analysis reveals key regulators of injury response and neuronal regeneration in vertebrate retinas.  Science (2020) 370(6519):eabb8598.

Kim DW, Washington PW, Wang ZQ, Lin S, Sun C, Jiang L, and Blackshaw S.  The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development.  Nat Comm (2020) 11:4360.

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.  Nat Comm (2020) 11:37.

Lu Y, Shiau F, Yi W, Lu S, Wu Q, Pearson J, Kallman A, Hoang T, Zhong S, Zuo Z, Zhao F, Zhang M, Tsai N, Zhuo Y, He S, Zhang J, Stein-O’Brien GL, Duan X, Fertig EJ, Goff LA, Zack DJ, Handa JT, Xue T*, Bremner R*, Blackshaw S*, Wang X* and Clark BS* (* indicates corresponding author).  Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development.  Dev Cell (2020) 53:473-491.

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 (2019) 102:1111-1126.

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 ://

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.

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

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.

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.