Although the number of cell types in the vertebrate retina varies greatly, most appear to share a common origin. Karthik Shekhar and his colleagues raised some eyebrows when they collected cow and pig eyes from Boston butchers, but the eyes—which ended up coming from 17 different species, including humans—provided insights into the evolution of the vertebrate retina and may lead to better animal models for human eye diseases.
The retina is like a tiny computer, containing various types of cells that work together to process visual information and then transmit the information to other parts of the brain. Shekhar's previous research showed that there are 130 types of cells in the mouse retina alone. The researchers conducted a comparative analysis of multiple cell types in the retina and concluded that most have an ancient evolutionary history. Differences in these cell types at the molecular level provide clues to their functions and how they participate in building our visual world.
The remarkable preservation of retinal cells across species suggests that when the last common ancestor of all mammals roamed the Earth about 200 million years ago, its retinas were comparable in complexity to those of modern mammals. In fact, there are clear signs that some of these cell types can be traced back to the common ancestor of all vertebrates (i.e., mammals, reptiles, birds, and jawed fish) more than 400 million years ago.
The research results were published in the journal Nature on December 13, as part of 10 papers reporting the latest results of the BRAIN Project Cell Census Network to create an atlas of adult mouse brain cell types. The first author is Joshua Hahn, a graduate student in chemical and biomolecular engineering in Sheika's group at the University of California, Berkeley. This work was a collaboration with Joshua Sanis' group at Harvard University.
Surprising discovery in vertebrate vision
These findings are surprising because vertebrate vision varies greatly between species. Fish need to see underwater, mice and cats need good night vision, and monkeys and humans have evolved very sharp daytime vision for hunting and foraging. Some animals see bright colors, while others are content to see the world in black and white.
However, many cell types are shared across a range of vertebrate species, suggesting that the gene expression programs that define these types likely date back to a common ancestor of jawed vertebrates, the researchers concluded.
For example, the team found that one cell type, the "dwarf" retinal ganglion cells responsible for our ability to see fine detail, is not unique to primates as had been thought. By analyzing large-scale gene expression data using statistical inference methods, the researchers discovered evolutionary counterparts of dwarf cells in all other mammals, albeit at much smaller proportions.
"What we're seeing is that what was thought to be unique to primates is clearly not unique. It's a reshaped version of a cell type that's probably very ancient," said Shekhar, an assistant professor of chemical and biomolecular engineering at UC Berkeley. "The retina of early vertebrates may have been extremely complex, but its inventory of parts has been used, expanded, repurposed, or refurbished in all species since. Ed."
Coincidentally, one of Shekhar's colleagues at UC Berkeley, Teresa Puthussery of the School of Optometry, reported last month in the journal Nature that another cell type thought to have disappeared in the human eye - a type of retinal ganglion cell responsible for gaze stabilization - still exists. Puthussery and her colleagues used information from a previous paper Shekhar co-authored to select molecular markers that would help identify this cell type in primate retinal tissue samples.
Similarities of Vertebrate Eyes
In a sense, these findings are not entirely surprising, since vertebrate eyes have a similar structure: light is detected by photoreceptors, which relay signals to bipolar, horizontal, and amniotic cells, which in turn connect to retinal ganglion cells, which then relay the results to the brain's visual cortex. Shekhar uses new technologies, specifically single-cell genomics, to simultaneously examine the molecular makeup of thousands to tens of thousands of neurons in the visual system, from the retina to the visual cortex.
Because the number of identified retinal cell types varies widely among vertebrates—about 70 in humans and 130 in mice, according to previous research by Shekhar and colleagues—the origins of these different cell types have been a mystery.
Shekhar said one possibility uncovered by the new study is that as primate brains became more complex, primates began to rely less on signal processing within the eyes and more on analysis in the visual cortex. As a result, there are significantly fewer molecularly unique cell types in the human eye.
The evolution of the human retina
"Our study suggests that the human retina may have evolved during evolution to swap cell types that perform complex visual calculations with cell types that basically just transmit relatively unprocessed images of the visual world to the brain, so that we could do more complex things with those cell types. We gave up speed in exchange for sophistication," Shekhar said.
The team's new detailed map of various vertebrate retinal cell types could aid research into human eye diseases. Shekhar's research group is also studying the molecular signature of glaucoma, the leading cause of irreversible blindness in the world and the second most common cause of blindness in the United States after macular degeneration.
However, although mice are the most popular model animal for studying glaucoma, they have few dwarf retinal ganglion cell counterparts. These cell types make up only 2 to 4 percent of the total ganglion cells in mice, whereas 90 percent of retinal ganglion cells in humans are dwarf cells.
"This work has important clinical implications because ultimately, midget cells may be the human glaucoma cells we should be most concerned about," Shekhar said. "Understanding their counterparts in mice will hopefully help us better design and interpret these mouse models of glaucoma."
Single-cell transcriptomics in retinal research
For the past eight years, Shekhar and Sanes have been applying single-cell genomics methods to analyze mRNA molecules in cells, classifying them based on their gene expression fingerprints. The technique gradually helped identify an increasing number of unique cell types in the retina, many of which Shekor began while doing postdoctoral research at the Broad Institute with Aviv Regev, one of the pioneers of single-cell genomics. It was in her laboratory that Shekol began working with renowned retinal neurobiologist Sanes, who became Shekol's co-mentor and collaborator.
In the current study, they hope to extend the single-cell transcriptome approach to other species to understand how retinal cell types have changed through evolution. In total, they collected eyes from 17 species: humans, two species of monkeys (macaques and marmosets), four rodents (three mice and a soil squirrel), three ungulates (cows, sheep and pigs), tree shrews, opossums, ferrets, chickens, lizards, zebrafish and lampreys.
Transcriptome experiments by Sanes' team at Harvard University and computational analyzes by Shekhar's team at the University of California, Berkeley, resulted in the discovery of many new cell types in each species. They then mapped these cell types onto a smaller set of "prototypes" -- cell types that are likely descendants of the same ancestral cell types in early vertebrates.
For bipolar cells, a type of neuron located between photoreceptors and retinal ganglion cells, they found 14 different prototypes. Most extant species contain 13 to 16 bipolar cell types, suggesting that these types have evolved little. In contrast, they found 21 orthogonal types of retinal ganglion cells, with greater variation between species. So far, research has identified more than 40 different types in mice and about 20 in humans.
Evolutionary divergence and conservation
Interestingly, there is clear evolutionary differentiation between retinal ganglion cell types compared with other retinal categories, suggesting that natural selection acts more strongly on the differentiation of neuron types that carry information from the retina to the rest of the brain.
They also found that many transcription factors involved in the differentiation of mouse retinal cell types are highly conserved, suggesting that the molecular steps leading to retinal development may also be evolutionarily conserved.
Based on the new findings, Shekhar refocused his glaucoma research on mouse pygmy cell analogs, alpha cells.
Compiled source: ScitechDaily