- Email: [email protected]
Allen Brain Atlas maps 21 000 genes of the mouse brain
Newsdesk
Allen Brain Atlas maps 21 000 genes of the mouse brain Neuroscientists studying the recently completed Allen Brain Atlas are calling the online geneexpression map of the mouse brain “revolutionary”, “majestic”, and “very cool”. They also say the atlas reveals a brain that is considerably more complicated than many of them thought. From Seattle, Michael McCarthy reports. pinpointing the expression patterns of each gene of the entire mouse genome—some 21 000 genes—to a resolution of 10 microns, showing not only in which regions the genes are being expressed, but in which cells. Paul Allen, who with Bill Gates III started Microsoft and is, according to Forbes magazine, the sixth richest man in the world, founded the non-profit Allen Institute for Brain Science in 2001 with a US$100 million 5-year grant. A year later Allen convened a panel of scientists and charged them to come up with a project that would have “significant” impact on the field of brain science. Allan Jones, the institute’s chief scientific officer, said Allen wanted to find a “unique investment” that would “change the field”. The panel’s recommendation: create a gene expression map of the mouse brain. The institute took the project on and with a staff of 80, which includes neurologists, anatomists, information architects, and other specialists, set up a fully automated in situ hybridisation system. The “walk-away” automated systems allowed the project to run nearly “24/7”, says Jones. 3 years— and $41 million—later the atlas was completed. For standardisation, all sections were made from 56-day-old, male C57BL/6J mice, a strain that has been used for other major brain anatomy reference works. To complete the project the team processed 170 genes, generating 16 000 microscopic sections, a day. All told, the project generated 250 000 microscopic slides, 85 million images, and 600 terabytes of data—enough data to fill 20 000 30-gigabyte iPods. Anyone can use the atlas. Access is free, and no registration or logon is
http://neurology.thelancet.com Vol 5 November 2006
required. The institute asks only that it be credited if atlas data are used. The institute does not make any claim on patents or other intellectual property rights on inventions developed by use of atlas data. Allen considers the atlas to be his “gift to science”. Even before the institute announced the completion of the atlas, the website was receiving 4 million “hits” a week. Analysis of the visitors’ internet addresses indicates that some 250 scientists visit the site each day, says Jones. Most are from US academic institutions but use by international scientists and researchers from pharmaceutical and biotechnology companies is heavy as well. Ben Barres, a professor of neurobiology who studies the development and function of glial cells at Stanford University in Palo Alto, California, is already using atlas data in his publications. “So far, I’ve found the data to be incredibly accurate”, says Barres. “It’s proven to be a huge resource that has just dropped from the sky.”
For the Allen Brain Atlas see http://www.brainatlas.org
The printed journal includes an image merely for illustration Allen Brain Atlas
Robert Williams, a professor of anatomy and neurobiology at the University of Tennessee Health Science Center in Memphis, was sitting in a workshop recently when a haematologist giving a talk mentioned that the gene Ezh2 was a marker for blood stem cells. “I wonder”, Williams thought to himself, “if Ezh2 is expressed in the brain.” So from his laptop Williams directed his web browser to the Allen Brain Atlas, a web-based threedimensional map of gene expression in the mouse brain created by the Allen Institute for Brain Science in Seattle, Washington, USA. In minutes, Williams was looking at detailed images showing not only that Ezh2 was expressed in the brain but also the precise anatomical location of the brain cells expressing the gene. “It was the tiniest amount of label”, Williams says, “but it was exactly in the two places where you’d expect to see label: in the nerve proliferative cells of the dentate gyrus, called the subgranular layer, and in the lateral ventricular regions that give rise to the rostral migratory stream.” Williams, who is also co-director of the university’s Center for Genomics and Bioinfomatics, says conducting such “in silico” experiments with the Allen Brain Atlas has become routine for him. “You have a question, you go to the resource, and in 5 minutes you have your answer—without ever picking up a pipette” he says. “It doesn’t even surprise me any more.” The Allen Institute has been posting its brain-map data online as they became available since 2004. However, last month the Seattle team announced it had completed the map,
Coronal section of mouse brain: Nissl stained (L) and graphical representation (R)
907
Newsdesk
Allen Brain Atlas
The printed journal includes an image merely for illustration
Computationally reconstructed three dimensional rendering of mouse brain
908
The printed journal includes an image merely for illustration Allen Brain Atlas
Barres adds that the atlas is also proving to be a great time saver. In the past, about the only way for a laboratory to see whether and whereabouts a gene of interest was expressed in the brain was for the laboratory to do its own in situ hybridisation, he says. “But this is a technique that takes a lot of technical expertise. You have to invest a lot of time to learn how to do it and how to do it well.” “Now, you can go to the Allen Brain Atlas and get your answers in seconds”, Barres says. “The amount of man-years of work, not to mention dollars, this is going to save people is incredible.” The data are also surprising, says Barres. In particular, he has been “bowled over” by the heterogeneity of the oligodendrocytes. “Up until this point I thought that all the oligodendrocytes were pretty much the same, but when you go through the atlas you realise right away that some of the genes we’ve identified are expressed in oligodendrocytes in one part of the brain and other genes are expressed in oligodendrocytes in a different part.” This variation may explain why in multiple sclerosis certain parts of the white matter are preferentially involved, he says. Also surprising to researchers is the large number of genes that are expressed in the brain. Before the Allen Brain Atlas data came out, experts predicted that only about 60–70% of the genome
Close-up of area around the third ventricle
would be expressed in the brain. The atlas data, however, indicate that 80% of genes are expressed in the brain. Gene expression also appears to be surprisingly uniform throughout the brain, says the institute’s Jones. Although some genes are expressed more often in certain areas, almost none appears to be expressed in just one specific area. “Relatively few areas have unique gene expression patterns”, Jones notes. The findings suggest that with 80% of genes expressed there are many potential drug targets, Jones says, but, at the same time, because they are expressed so diffusely throughout brain, it will likely be hard to find “magic bullets” that will not have sideeffects. The atlas is also revealing that many known areas of the brain have small substructures within them that have not been seen before. “It’s been a bit like peeling an onion”, says Jones, “with every structure we look at in detail we continue to divide into smaller functional areas.” The data suggest “we don’t even know how many different types of cells there are in the brain”, says Prof Susumu Tonegawa, a 1987 Nobel Laureate who studies learning and memory at Massachusetts Institute of Technology in Cambridge, Massachusetts. “The fine anatomy of the brain will have to be revised based on their results.”
Now that the atlas is complete, the institute plans build on its work through collaborative projects with academic, government, and industry researchers, including projects to extend the map to the retina and spinal cord and to compare normal mouse brain with brains from mouse models of human neurological and psychological disease, and with areas of human brain known to play a role in diseases such as Parkinson’s, Alzheimer’s, and schizophrenia. There is some concern that the institute is shifting its focus to the human brain too soon. “It’s not that human research is not important”, says Barres, “but we still don’t understand the mouse brain—and once we figure out how the mouse brain works, the rest is trivial.” Nevertheless, there is more than enough in the atlas today to occupy researchers for years, says Barres. “I suspect a huge percentage of the in situ hybridisations that are posted on the site have never been looked at by anyone”, Barres says—genes that neurologists have never even thought were expressed in the brain. Williams agrees: “I’m surprised at the number of marvellous stories lurking in that dataset; if I were a graduate student looking for a thesis project, I’d pick analysis of the Allen Brain Atlas.”
Michael McCarthy
http://neurology.thelancet.com Vol 5 November 2006
Allen Brain Atlas maps 21 000 genes of the mouse brain Neuroscientists studying the recently completed Allen Brain Atlas are calling the online geneexpression map of the mouse brain “revolutionary”, “majestic”, and “very cool”. They also say the atlas reveals a brain that is considerably more complicated than many of them thought. From Seattle, Michael McCarthy reports. pinpointing the expression patterns of each gene of the entire mouse genome—some 21 000 genes—to a resolution of 10 microns, showing not only in which regions the genes are being expressed, but in which cells. Paul Allen, who with Bill Gates III started Microsoft and is, according to Forbes magazine, the sixth richest man in the world, founded the non-profit Allen Institute for Brain Science in 2001 with a US$100 million 5-year grant. A year later Allen convened a panel of scientists and charged them to come up with a project that would have “significant” impact on the field of brain science. Allan Jones, the institute’s chief scientific officer, said Allen wanted to find a “unique investment” that would “change the field”. The panel’s recommendation: create a gene expression map of the mouse brain. The institute took the project on and with a staff of 80, which includes neurologists, anatomists, information architects, and other specialists, set up a fully automated in situ hybridisation system. The “walk-away” automated systems allowed the project to run nearly “24/7”, says Jones. 3 years— and $41 million—later the atlas was completed. For standardisation, all sections were made from 56-day-old, male C57BL/6J mice, a strain that has been used for other major brain anatomy reference works. To complete the project the team processed 170 genes, generating 16 000 microscopic sections, a day. All told, the project generated 250 000 microscopic slides, 85 million images, and 600 terabytes of data—enough data to fill 20 000 30-gigabyte iPods. Anyone can use the atlas. Access is free, and no registration or logon is
http://neurology.thelancet.com Vol 5 November 2006
required. The institute asks only that it be credited if atlas data are used. The institute does not make any claim on patents or other intellectual property rights on inventions developed by use of atlas data. Allen considers the atlas to be his “gift to science”. Even before the institute announced the completion of the atlas, the website was receiving 4 million “hits” a week. Analysis of the visitors’ internet addresses indicates that some 250 scientists visit the site each day, says Jones. Most are from US academic institutions but use by international scientists and researchers from pharmaceutical and biotechnology companies is heavy as well. Ben Barres, a professor of neurobiology who studies the development and function of glial cells at Stanford University in Palo Alto, California, is already using atlas data in his publications. “So far, I’ve found the data to be incredibly accurate”, says Barres. “It’s proven to be a huge resource that has just dropped from the sky.”
For the Allen Brain Atlas see http://www.brainatlas.org
The printed journal includes an image merely for illustration Allen Brain Atlas
Robert Williams, a professor of anatomy and neurobiology at the University of Tennessee Health Science Center in Memphis, was sitting in a workshop recently when a haematologist giving a talk mentioned that the gene Ezh2 was a marker for blood stem cells. “I wonder”, Williams thought to himself, “if Ezh2 is expressed in the brain.” So from his laptop Williams directed his web browser to the Allen Brain Atlas, a web-based threedimensional map of gene expression in the mouse brain created by the Allen Institute for Brain Science in Seattle, Washington, USA. In minutes, Williams was looking at detailed images showing not only that Ezh2 was expressed in the brain but also the precise anatomical location of the brain cells expressing the gene. “It was the tiniest amount of label”, Williams says, “but it was exactly in the two places where you’d expect to see label: in the nerve proliferative cells of the dentate gyrus, called the subgranular layer, and in the lateral ventricular regions that give rise to the rostral migratory stream.” Williams, who is also co-director of the university’s Center for Genomics and Bioinfomatics, says conducting such “in silico” experiments with the Allen Brain Atlas has become routine for him. “You have a question, you go to the resource, and in 5 minutes you have your answer—without ever picking up a pipette” he says. “It doesn’t even surprise me any more.” The Allen Institute has been posting its brain-map data online as they became available since 2004. However, last month the Seattle team announced it had completed the map,
Coronal section of mouse brain: Nissl stained (L) and graphical representation (R)
907
Newsdesk
Allen Brain Atlas
The printed journal includes an image merely for illustration
Computationally reconstructed three dimensional rendering of mouse brain
908
The printed journal includes an image merely for illustration Allen Brain Atlas
Barres adds that the atlas is also proving to be a great time saver. In the past, about the only way for a laboratory to see whether and whereabouts a gene of interest was expressed in the brain was for the laboratory to do its own in situ hybridisation, he says. “But this is a technique that takes a lot of technical expertise. You have to invest a lot of time to learn how to do it and how to do it well.” “Now, you can go to the Allen Brain Atlas and get your answers in seconds”, Barres says. “The amount of man-years of work, not to mention dollars, this is going to save people is incredible.” The data are also surprising, says Barres. In particular, he has been “bowled over” by the heterogeneity of the oligodendrocytes. “Up until this point I thought that all the oligodendrocytes were pretty much the same, but when you go through the atlas you realise right away that some of the genes we’ve identified are expressed in oligodendrocytes in one part of the brain and other genes are expressed in oligodendrocytes in a different part.” This variation may explain why in multiple sclerosis certain parts of the white matter are preferentially involved, he says. Also surprising to researchers is the large number of genes that are expressed in the brain. Before the Allen Brain Atlas data came out, experts predicted that only about 60–70% of the genome
Close-up of area around the third ventricle
would be expressed in the brain. The atlas data, however, indicate that 80% of genes are expressed in the brain. Gene expression also appears to be surprisingly uniform throughout the brain, says the institute’s Jones. Although some genes are expressed more often in certain areas, almost none appears to be expressed in just one specific area. “Relatively few areas have unique gene expression patterns”, Jones notes. The findings suggest that with 80% of genes expressed there are many potential drug targets, Jones says, but, at the same time, because they are expressed so diffusely throughout brain, it will likely be hard to find “magic bullets” that will not have sideeffects. The atlas is also revealing that many known areas of the brain have small substructures within them that have not been seen before. “It’s been a bit like peeling an onion”, says Jones, “with every structure we look at in detail we continue to divide into smaller functional areas.” The data suggest “we don’t even know how many different types of cells there are in the brain”, says Prof Susumu Tonegawa, a 1987 Nobel Laureate who studies learning and memory at Massachusetts Institute of Technology in Cambridge, Massachusetts. “The fine anatomy of the brain will have to be revised based on their results.”
Now that the atlas is complete, the institute plans build on its work through collaborative projects with academic, government, and industry researchers, including projects to extend the map to the retina and spinal cord and to compare normal mouse brain with brains from mouse models of human neurological and psychological disease, and with areas of human brain known to play a role in diseases such as Parkinson’s, Alzheimer’s, and schizophrenia. There is some concern that the institute is shifting its focus to the human brain too soon. “It’s not that human research is not important”, says Barres, “but we still don’t understand the mouse brain—and once we figure out how the mouse brain works, the rest is trivial.” Nevertheless, there is more than enough in the atlas today to occupy researchers for years, says Barres. “I suspect a huge percentage of the in situ hybridisations that are posted on the site have never been looked at by anyone”, Barres says—genes that neurologists have never even thought were expressed in the brain. Williams agrees: “I’m surprised at the number of marvellous stories lurking in that dataset; if I were a graduate student looking for a thesis project, I’d pick analysis of the Allen Brain Atlas.”
Michael McCarthy
http://neurology.thelancet.com Vol 5 November 2006