Indiana University Bloomington

Justin Kumar

Justin Kumar

Ph.D., Purdue University, 1996
Postdoctoral Fellow, University of Southern California, 1996-1997; Emory University, School of Medicine, 1998-2002

Email address: jkumar(at)

Research Interests

The compound eye of the fruit fly, Drosophila melanogaster, is an excellent model system for studying such diverse topics as tissue determination, compartment boundary establishment, cell fate specification, cell proliferation and apoptosis, planar cell polarity, signal transduction and cell-cell communication. The retina is a particularly good experimental model in part because it contains a limited number of cell types that follow a precise and stereotyped mode of development. Additionally, more than thirty years of study by dozens of laboratories has produced a detailed survey of the eye's cellular, molecular and morphological development.

Eye formation begins during embryogenesis when two groups of cells within the developing head delaminate from the surface ectoderm, proliferate rapidly and organize themselves into monolayer epithelial sheets called eye-antennal imaginal discs. During the earliest stages of retinal development, cells within the eye imaginal disc, to our inspection, are completely unpatterned and undifferentiated. However, as each disc serves as the template from which the adult eye is created, over the course of several days, the imaginal discs are transformed into the adult compound eyes each of which contains approximately 800 unit eyes or ommatidia.

My research group is focused on a number of questions (described below) that are central to understanding how tissues in general, and the eye in particular, are initially specified and then patterned. We use a wide range of molecular, biochemical and cellular methods to analyze the genes and proteins that control each step in retinal development. We also make extensive use of scanning, light and confocal microscopy to analyze the cellular and developmental consequences to eye development in instances in which genes critical to retinal formation have been disrupted.

Regulation of Tissue Specification

In addition to the retina, nearly all structures of the adult fly are derived from imaginal discs. Each type of disc must initiate a unique developmental program that will set it aside and down a path that is molecularly distinct from the other discs. Approximately fourteen known selector genes govern the process of specifying the retina. These factors are collectively referred to as the eye specification or retinal determination network and each gene encodes a nuclear protein; some of which are DNA binding proteins while others serve as transcriptional co-activators, kinases or phosphatases. Removal of any member of the core eye specification network leads to severe if not total loss of retinal tissue. On the other hand, forced expression of these factors results in the redirection of non-retinal tissues towards an eye fate. We are working towards understanding how this network promotes eye development and what are the cellular and molecular consequences of disrupting this regulatory system.

Connecting Specification to Proliferation

The eye primordium initially consists of approximately twenty cells. As the embryo hatches and the emerging larva undergoes consecutive rounds of molting and growth, the eye imaginal disc undergoes dramatic increases in cell proliferation and will eventually reach a size of nearly 20,000 cells. The loss of specific selector genes result not only in the loss of tissue identity but also lead to dramatically lowered rates of cell proliferation and increased numbers of apoptotic cells. We are pursuing potential links between tissue specification and cell proliferation. One potential outcome of these studies is likely to be a better understanding of how tumors initiate their growth.

Establishment of Compartment Boundaries

One of the earliest events to take place in the developing retina is the subdivision of the eye field into dorsal and ventral compartments. Initially, gene expression is relatively uniform throughout the entire tissue. However, during the first larval instar individual selector genes are expressed specifically within either the dorsal or ventral halves of the developing eye field. This has the effect of influencing the direction that photoreceptors will rotate immediately upon their birth. The most visible outcome of this process is the mirror-image orientation of the ommatidia across the equator in the adult retina, which is critical for proper vision. We are interested in identifying the entire gene regulatory network that subdivides the retina into discrete compartments.

Regulation of Pattern Formation

Overt patterning of the retina begins during the final larval instar when a wave of differentiation initiates at the posterior margin of the eye field and subsequently sweeps across the epithelium much like a wave travels across an ocean. The leading edge of this mobile compartment boundary is called the morphogenetic furrow. As the furrow passes cells are organized into clusters that are the rudiments of the future unit eyes. Over the years a number of signaling pathways have been shown to regulate the initiation of pattern formation and the progression of the furrow. It has also been shown that, if unchecked, the furrow actually moves too rapidly across the epithelium. To prevent this from occurring, the eye makes use of a protein sequestration mechanism to functionally inactivate factors that are required for the movement of the furrow. This results in a slowing of pattern formation to a speed that is compatible with the rate of cell proliferation. We are focused on furthering our understanding of how pattern formation is initiated, maintained and regulated within the developing retina.

The developing eye is an excellent system for studying eye development in vertebrate systems including humans because there are functional orthologs in humans for nearly all of the genes that govern each of the processes described above. More importantly, several human retinal disorders are attributed to mutations within the human versions of the fly genes. We believe that these observations will now make it considerably easier to look through the faceted lens of flies and into the eyes of humans.

Representative Publications

Spratford, C.M. & Kumar, J.P. (2013). Extramacrochaetae imposes order on the Drosophila eye by refining the activity of the Hedgehog signaling gradient. Development, 140(9), 1994-2004.

Weasner, B.M. & Kumar, J.P. (2013). Competition amongst gene regulatory networks imposes order within the eye-antennal disc of Drosophila. Development, 140(1), 205-215.

Kumar, J.P. (2012) Building an ommatidium one cell at a time. Developmental Dynamics, 241(1), 136-149.

Anderson, A.M., Weasner, B.M., Weasner, B.P. & Kumar, J.P. (2012). Dual transcriptional activities of Sine Oculis define its roles in normal and ectopic eye development. Development, 139(5), 991-1000.

Datta, R.R., Weasner, B.P. & Kumar, J.P. (2011). A dissection of the Teashirt and Tiptop genes reveals a novel mechanism for regulating transcription factor activity. Developmental Biology, 360, 391-402

Kumar, J.P. (2011). My what big eyes you have: how the Drosophila retina grows. Developmental Neurobiology, 71, 1133-1152

Datta, R., Cruckshank, T. & Kumar J.P. (2011). Differential selection within the Drosophila retinal determination network and evidence for functional divergence between paralog pairs. Evolution and Development, 13, 58-71

Kumar, J.P. (2010). Retinal determination: the beginning of eye development. Current Topics in Developmental Biology, 93, 1-28

Salzer, C.L. & Kumar, J.P. (2010). Identification of retinal transformation hot spots in developing Drosophila epithelia. PLoS One, 5, 1-8

Salzer, C.L., Elias, Y. & Kumar, J.P. (2010). The retinal determination gene eyes absent is regulated by the EGF Receptor pathway throughout development in Drosophila. Genetics, 184, 185-197.

Datta R.R., Lurye, J.L. & Kumar, J.P. (2009). Restriction of ectopic eye formation by Drosophila Teashirt and Tiptop to the developing antenna. Developmental Dynamics, 238, 2202-2210.

Kumar, J.P. (2009). The Sine Oculis Homeobox (SIX) family of transcription factors as regulators of development and disease. Cellular and Molecular Life Sciences, 66, 565-583.

Weasner, B,M., Weasner, B., DeYoung, S.M., Michaels, S.D. & Kumar, J.P. (2009). Dual transcriptional activities of the Pax6 gene eyeless regulate tissue specificity of ectopic eye formation in Drosophila. Developmental Biology, 334, 492-502.

Weasner, B.P. & Kumar, J.P. (2009). The non-conserved C-terminal segments of Sine oculis homeobox (SIX) proteins confer functional specificity. Genesis, 47, 514-523.

Salzer, C.L. & Kumar, J.P. (2009). Position dependent responses to discontinuities in the retinal determination network. Developmental Biology, 326, 121-130.

Kumar, J.P. (2009) The molecular circuitry governing eye development in Drosophila. Biochimica et Biophysica Acta, 1789, 306-314.

Luhur, A.L & Kumar, J.P. (2008). Advances in microRNA Biology. Fly, 2, 123-124.

Yao, J.G., Weasner, B.M., Wang, L.H., Jang, C.C., Weasner, B.P., Tang, C.Y. Salzer, C.S., Chen, C.H., Sun, Y.H. & Kumar, J.P. (2008). Differential Requirements for the Pax6(5a) genes eyegone and twin of eyegone during eye development in Drosophila. Developmental Biology, 315, 535-551.

Weasner, B.P., Salzer, C.L. & Kumar, J.P. (2007). Sine oculis, a member of the SIX family of transcription factors directs eye development. Developmental Biology, 303, 756-771.

Anderson, J.L., Salzer, C.L. & Kumar J.P. (2006). Regulation of the retinal determination gene, dachshund, in the embryonic head and developing eye of Drosophila. Developmental Biology, 297, 536-549.

Anderson, J.L., Bhandari, R. & Kumar, J.P. (2005). A genetic screen identifies putative targets and binding partners of CREB Binding Protein (CBP) in the developing Drosophila eye. Genetics, 171, 1566-1672.

Roederer, K., Cozy, L., Anderson, J.L. & Kumar, J.P. (2005). A novel dominant negative mutation within the Six domain of the conserved eye specification gene, sine oculis, inhibits eye development in Drosophila. Developmental Dynamics, 232, 753-766.

Weasner, B.P., Anderson, J.L. & Kumar, J.P. (2004). Eye specification in Drosophila. Proceedings of the Indian National Sience Academy Part A, 70, 517-530.

Kumar, J.P., Jamal, T., Doetsch, A., Turner, F.R. & Duffy, J.B. (2004). CREB Binding Protein (CBP) functions at successive stages of eye development in Drosophila. Genetics, 168, 877-893.

Kumar, J.P., Hsiung, F., Powers, M.A. & Moses, K. (2003). Nuclear translocation of activated MAP kinase is developmentally regulated in the developing Drosophila eye. Development, 130, 3703-3714,

Kumar, J.P. (2002). The Epidermal Growth Factor Receptor in Drosophila eye development. In Results and Problems in Cell Differentiation, Granderath, S. (ed), 37, 282-292.

Kumar, J.P., Wilkie, G.S., Tekotte, H., Moses, K. & Davis, I. (2001). Perturbing nuclear transport in the Drosophila eye imaginal disc causes specific axon guidance defects. Developmental Biology, 240, 315-325.

Kumar, J.P. & Moses, K. (2001). The EGF Receptor and Notch signaling pathways act upstream of Eyeless/Pax6 to control eye specification. Cell, 104, 687-697.

Kumar, J.P. (2001). Signaling pathways in Drosophila and vertebrate retinal development. Nature Reviews Genetics, 2,846-857.

Kumar, J.P. & Moses, K. (2001). The EGF Receptor and Notch signaling pathways control the initiation of the morphogenetic furrow during Drosophila eye development. Development 128, 2689-2697.

Kumar, J.P. & Moses, K. (2001). Eye specification in Drosophila: perspectives and implications. Seminars in Cell and Developmental Biology, 12, 469-474.

Kumar, J.P. & Moses, K. (2001). Analysis of eye specification gene expression during Drosophila embryogenesis. Development, Genes and Evolution, 211, 406-414.

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