By Josh Sanes

Vision begins in the retina, a part of the brain that lines the back of the eyeball. It contains complex neural circuits composed of numerous cell types that sense light, process visual signals, and transmit them to the rest of the brain through the optic nerve.  When any of those steps fail, vision is disrupted and all too often lost altogether.  For example, age-related macular degeneration results from loss of the light-sensing cells (photoreceptors) and glaucoma results from loss of the cells that send signals through the optic nerve (retinal ganglion cells).   Together, over 200 million people world-wide suffer from one of these two diseases.

Over the past several years, our lab and others have used new molecular methods to comprehensively catalog retinal cell types and inventory the genes that each expresses. We now have what is called a “cell atlas” of the human retina – as well as the retinas of several model species, including mice and monkeys. However, the retina does not act alone: it is surrounded by a complex set of ocular tissues that are also critically important for vision.   For example, the lens helps focus light on the retina, but if cataracts form, it becomes cloudy and images no longer reach the retina. The iris controls the amount of light that reaches the retina but if it becomes inflamed, a condition called uveitis, vision can be lost suddenly. Moreover, some retinal diseases involve multiple structures.  Death of photoreceptors in macular degeneration results in large part from damage to an overlying layer of supporting cells called retinal pigment epithelium.  Death of retinal ganglion cells in glaucoma is often triggered by increases in intraocular pressure resulting from defects in a tissue called trabecular meshwork responsible for draining the fluid that nourishes the front part of the eye. The pressure, in turn, leads to changes in specialized region of the optic nerve, the optic nerve head, that in turn strangle the axons of the ganglion cells.  In short, understanding blindness requires knowing a lot about the whole eye.

To address this challenge, we applied the method we had used to analyze retina. Called single cell (or single nucleus) RNA sequencing, it allows us to determine the genes expressed by thousands of single cells at high enough speed and low enough cost to enable complete, relatively unbiased sampling.  Altogether, we obtained so-called “transcriptomes” from nearly 700,000 cells derived from 16 different ocular tissues and then used computational methods to divide them into cell types. The results in our new paper, the final one of a series of four publications, complete a cell atlas of the human eye.

What have we found?  Altogether, we identified nearly 160 cell types in the human eye. Some are specific to individual structures such as the lens or retina, while others are shared by multiple structures.  Some cell types are unique, such as the retinal pigment epithelium, while others can be grouped into classes, some of which are quite heterogeneous.  For example, we identified five distinct types of astrocytes, non-neuronal cells that support neurons in a variety of ways. Some of the types are extremely distinct from other types, whereas some form similar groups, often representing stages in the development of cells that are generated even in adults. Together, the results provide a resource for scientists studying the development, structure and function of the eye.

In addition to its value for basic science, the atlas provides new information about ocular diseases. Literally hundreds of ocular diseases have been identified; some are very common (such as macular degeneration, cataract and glaucoma, mentioned above) while others are quite rare. Over the past few decades, hundreds of genes have been implicated in the pathogenesis of these diseases.  In some cases, mutations of single genes lead to disease, while in others, rather common variations in fully functional genes lead to increased susceptibility to the disease. Currently, most efforts to find treatments for ocular diseases involve targeting these genes in one way or another. However, to design an effective therapy, it is critically important to know where the gene is expressed. Our atlas provides this information. Taking the example of glaucoma, we found various of its susceptibility genes to be differentially expressed in numerous cell types, including specific types within the retina, trabecular meshwork and optic nerve head – and even in surprising types, such as retinal pigment epithelium. This analysis provides a blueprint that can now be used to assess which cell type or types express any disease-associated gene, thereby suggesting ways to design effective therapeutic strategies.

Josh Sanes is the Jeff C. Tarr Professor of Molecular and Cellular Biology at Harvard and the Founding Director of the Center for Brain Science

Also featured on the MCB Department website.

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Learn more in the original research article:
Transcriptomic analysis of the ocular posterior segment completes a cell atlas of the human eye.
Monavarfeshani A, Yan W, Pappas C, Odenigbo KA, He Z, Segrè AV, van Zyl T, Hageman GS, Sanes JR. Proc Natl Acad Sci U S A. 2023 Aug 22;120(34):e2306153120. doi: 10.1073/pnas.2306153120. Epub 2023 Aug 11.