Retinal Circuit Development and Genetics

About our work

We are using molecular genetic approaches to study the development of neuronal cell types, with a particular focus on neuronal arbor formation in retinal neurons. Using sparse Cre-loxP recombination, we specifically label individual neurons or neuronal cell classes, and visualize their morphology and connectivity. By combining conditional gene ablation with reporter gene replacement, we are able to visualize neurons in which specific genes have been ablated, and study the consequences of loss of gene function on the development of the neurons. Targeting specific neuronal populations through mouse genetic manipulations enables us also to study the roles of these neurons in visual circuitry. Current research directions in the lab:

Developing methodologies for sparse genetic labeling of neuronal arbors.
Defining the transcriptional requirements for the formation of Retinal Ganglion Cell (RGC) types.
Designing tools for physiological and behavioral analysis of normal and pathological vision.

Below are some visual representations of our work:

Microscope image of embyonic retinal ganglion cells

Embryonic day 12 RGCs leaving the eye (right) and crossing the midline at the optic chiasm (left).

Dorsal, lateral, and ventral view of retinal ganglion cells leaving the brain

RGC axons innervating retinorecipient areas of the brain.

Diagram of Brn3a, Brn3c, and Brn3b dendrite morphologies

Dendrite Morphologies of RGCs expressing Brn3 transcription factors.

Comparison of 3 RGC types: Ret CreERt2/WT, Brn3a CKOAP/WT; Ret CreERt2/WT, Brn3b CKOAP/WT; Ret CreERt2/WT, Brn3c CKOAP/WT

RGC types expressing cRet in combination with Brn3 transcription factors.

Gene diagram for Dre recombinase, Cre recombinase, and Cre activity

Intersecting three different genetic loci using site specific recombination. The first locus drives Dre recombinase, a second locus drives Cre recombinase in a Dre dependent manner, and a third locus reports Cre activity, in the cell expressing all three loci.

Gene expression level diagram, normalized to maximum level for each gene

Selected transcription factors expressed in RGCs and retinas and differentially regulated by Brn3 transcription factors.

Stained microscope images of CEK293 cells overexpressing Brn3 transcriptional target genes

HEK293 cells overexpressing Brn3 transcriptional target genes expressed in RGCs and believed to influence neuronal morphology.

Example of a multielectrode channel detecting spike trains from two neighboring RGCs. Top to bottom: (i) Raw trace, (ii) Filtered trace with detected and sorted Spikes from the two RGCs, (iii) Sorted, and clustered overlayed spike cutouts color coded by RGC cluster.

Diagram comparing attributes of "ON" and "OFF" retinal ganglion cells

Examples of receptive field properties of “ON” (top) and “OFF” (bottom) RGCs, as revealed by multielectrode array recordings of retinas exposed to full field (b), checkerboard (c) or tiled spots (d) stimuli. The action potential template for each cell is shown in (a).

Selected publications

Kiyama T, Long Y, Chen CK, Whitaker CM, Shay A, Wu H, Badea TC, Mohsenin A, Parker-Thornburg J, Klein WH, Mills SL, Massey SC, Mao CA. Essential Roles of Tbr1 in the Formation and Maintenance of the Orientation-Selective J-RGCs and a Group of OFF-Sustained RGCs in Mouse. Cell Rep. 2019 Apr 16;27(3):900-915.e5. PubMed PMID: 30995485.

Goel M, Li T, Badea TC. Differential expression and subcellular localization of Copines in mouse retina. J Comp Neurol. 2019 Mar 13. PubMed PMID: 30866042.

Ghinia MG, Novelli E, Sajgo S, Badea TC, Strettoi E. Brn3a and Brn3b knockout mice display unvaried retinal fine structure despite major morphological and numerical alterations of ganglion cells. J Comp Neurol. 2019 Jan 1;527(1):187-211. PubMed PMID: 27391320.

Ghahari A, Kumar SR, Badea TC. Identification of Retinal Ganglion Cell Firing Patterns Using Clustering Analysis Supplied with Failure Diagnosis. Int J Neural Syst. 2018 Oct;28(8):1850008. PubMed PMID: 29631502.

Muzyka VV, Brooks M, Badea TC. Postnatal developmental dynamics of cell type specification genes in Brn3a/Pou4f1 Retinal Ganglion Cells. Neural Dev. 2018 Jun 29;13(1):15. PubMed PMID: 29958540.

Parmhans N, Sajgo S, Niu J, Luo W, Badea TC. Characterization of retinal ganglion cell, horizontal cell, and amacrine cell types expressing the neurotrophic receptor tyrosine kinase Ret. J Comp Neurol. 2018 Mar 1;526(4):742-766. PubMed PMID: 29218725.

Kretschmer F, Tariq M, Chatila W, Wu B, Badea TC. Comparison of optomotor and optokinetic reflexes in mice. J Neurophysiol. 2017 Jul 1;118(1):300-316. PubMed PMID: 28424291.

Sajgo S, Ghinia MG, Brooks M, Kretschmer F, Chuang K, Hiriyanna S, Wu Z, Popescu O, Badea TC. Molecular codes for cell type specification in Brn3 retinal ganglion cells. Proc Natl Acad Sci U S A. 2017 May 16;114(20):E3974-E3983. PubMed PMID: 28465430.

Somasundaram P, Wyrick GR, Fernandez DC, Ghahari A, Pinhal CM, Simmonds Richardson M, Rupp AC, Cui L, Wu Z, Brown RL, Badea TC, Hattar S, Robinson PR. C-terminal phosphorylation regulates the kinetics of a subset of melanopsin-mediated behaviors in mice. Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):2741-2746. Feb 21. PubMed PMID: 28223508.

Sajgo S, Ali S, Popescu O, Badea TC. Dynamic expression of transcription factor Brn3b during mouse cranial nerve development. J Comp Neurol. 2016 Apr 1;524(5):1033-61. PubMed PMID: 26356988.

Kretschmer F, Sajgo S, Kretschmer V, Badea TC. A system to measure the Optokinetic and Optomotor response in mice. J Neurosci Methods. 2015 Dec 30;256:91-105. PubMed PMID: 26279344.

Chuang K, Nguyen E, Sergeev Y, Badea TC. Novel Heterotypic Rox Sites for Combinatorial Dre Recombination Strategies. G3 (Bethesda). 2015 Dec 29;6(3):559-71. PubMed PMID: 26715092.

Sajgo S, Ghinia MG, Shi M, Liu P, Dong L, Parmhans N, Popescu O, Badea TC. Dre - Cre sequential recombination provides new tools for retinal ganglion cell labeling and manipulation in mice. PLoS One. 2014 Mar 7;9(3):e91435. PubMed PMID: 24608965.

Shi M, Kumar SR, Motajo O, Kretschmer F, Mu X, Badea TC. Genetic interactions between Brn3 transcription factors in retinal ganglion cell type specification. PLoS One. 2013 Oct 8;8(10):e76347. PubMed PMID: 24116103.

Badea TC, Williams J, Smallwood P, Shi M, Motajo O, Nathans J. Combinatorial expression of Brn3 transcription factors in somatosensory neurons: genetic and morphologic analysis. J Neurosci. 2012 Jan 18;32(3):995-1007. PubMed PMID: 22262898.

Matsuoka RL, Chivatakarn O, Badea TC, Samuels IS, Cahill H, Katayama K, Kumar SR, Suto F, Chédotal A, Peachey NS, Nathans J, Yoshida Y, Giger RJ, Kolodkin AL. Class 5 transmembrane semaphorins control selective Mammalian retinal lamination and function. Neuron. 2011 Aug 11;71(3):460-73. PubMed PMID: 21835343.

Chen SK, Badea TC, Hattar S. Photoentrainment and pupillary light reflex are mediated by distinct populations of ipRGCs. Nature. 2011 Jul 17;476(7358):92-5. PubMed PMID: 21765429.

Matsuoka RL, Nguyen-Ba-Charvet KT, Parray A, Badea TC, Chédotal A, Kolodkin AL. Transmembrane semaphorin signalling controls laminar stratification in the mammalian retina. Nature. 2011 Feb 10;470(7333):259-63. PubMed PMID: 21270798.

Badea TC, Nathans J. Morphologies of mouse retinal ganglion cells expressing transcription factors Brn3a, Brn3b, and Brn3c: analysis of wild type and mutant cells using genetically-directed sparse labeling. Vision Res. 2011 Jan 28;51(2):269-79. PubMed PMID: 20826176.