Autism (NRCAM)
This web page was produced as an assignment for Gen677 at UW-Madison Spring 2009.
Conclusions
My project began by analyzing DNA and protein sequence alignments between the human NrCAM isoforms and its homologues in various organisms. It became apparent through these analyses that the NrCAM protein is highly conserved in mammals, while avian species and worms were less conserved. This high degree of homology will be important in thinking about appropriate model organisms in which tho study NrCAM. This similarity among mammals is also evident in the phylogenetic trees created based upon various multiple alignments as mammals cluster together. Chimps and humans are most closely related and both are closely related to mice and rats as expected. I think that the presence of a homologue in C. elegans is extremely important, as it becomes possible to do functional assays rapidly and repeatedly in order to better understand the role of NrCAM during central nervous system development, and the role it plays after neural networks are established. The mouse homologue is important to study for similar reasons and may be able to provide better information due to the greater complexity of its nervous system and brain.
Through gene ontology, I was able to understand that NrCAM has putative functions that are highly related to the development and maintenance of the central nervous system. It made sense then that NrCAM was implicated in autism due to the variety of cognitive delays both socially and academically. Predicted functions such as axon guidance, neuron migration, synaptogenesis, and cell-cell adhesion provided support the idea that NrCAM is involved in central nervous system development. There were also some phenotypes described in C. elegans RNAi studies which knocked down LAD-1, the homologue to NrCAM in C. elegans. These phenotypes included abnormal axon trajectory and lethality which indicate that the LAD-1 protein is very important in development.
The structure of the human NrCAM gene isoform implicated in autism contains various motifs, however none jump out as being critical for the function of the gene or as specific targets for research. These motifs included things such as heat shock factor and homeo domain factor motifs which did not really provide me with any direction to research. It is worth noting that there was not much overlap between the two DNA motif programs used: MOTIF and MEME. Analysis of NrCAM protein domains provided more information than the DNA motif analysis, as the human protein and all of the homologous proteins looked at shared domains in similar regions of the protein. This is important as it could allow researchers to investigate which protein domains are most important in the function of NrCAM in several model organisms.
There are a number of proteins that have been identified to interact with NrCAM by experimental evidence or through text mining. These interactions have not been well characterized for the most part, however they do warrant further research to learn more about their role in autism. These proteins include some ankyrin binding proteins which are consistent with NrCAM's role in ankyrin binding, as well as an activated leukocyte cell adhesion molecule which could have implications for NrCAM in other areas of research as well.
Altogether, this semester's analysis has allowed me to conclude several things about the research of NrCAM in autism. First, NrCAM seems to be a good target gene for autism studies based upon its predicted functions in central nervous system development, its increased expression in neuronal tissues, and RNAi studies in C. elegans showing axon growth defects and lethality as a result of LAD-1 knockdown. Also, there are a number of model organisms which have NrCAM homologues with high homology including mouse, rat, chimp, and worm. In addition, these homologous proteins share similar if not identical protein domains with the human protein so studies targeting specific domains would be possible. Lastly, the NrCAM gene and protein has a number of interacting partners that might be investigated to further develop the role of NrCAM in autism.
Through gene ontology, I was able to understand that NrCAM has putative functions that are highly related to the development and maintenance of the central nervous system. It made sense then that NrCAM was implicated in autism due to the variety of cognitive delays both socially and academically. Predicted functions such as axon guidance, neuron migration, synaptogenesis, and cell-cell adhesion provided support the idea that NrCAM is involved in central nervous system development. There were also some phenotypes described in C. elegans RNAi studies which knocked down LAD-1, the homologue to NrCAM in C. elegans. These phenotypes included abnormal axon trajectory and lethality which indicate that the LAD-1 protein is very important in development.
The structure of the human NrCAM gene isoform implicated in autism contains various motifs, however none jump out as being critical for the function of the gene or as specific targets for research. These motifs included things such as heat shock factor and homeo domain factor motifs which did not really provide me with any direction to research. It is worth noting that there was not much overlap between the two DNA motif programs used: MOTIF and MEME. Analysis of NrCAM protein domains provided more information than the DNA motif analysis, as the human protein and all of the homologous proteins looked at shared domains in similar regions of the protein. This is important as it could allow researchers to investigate which protein domains are most important in the function of NrCAM in several model organisms.
There are a number of proteins that have been identified to interact with NrCAM by experimental evidence or through text mining. These interactions have not been well characterized for the most part, however they do warrant further research to learn more about their role in autism. These proteins include some ankyrin binding proteins which are consistent with NrCAM's role in ankyrin binding, as well as an activated leukocyte cell adhesion molecule which could have implications for NrCAM in other areas of research as well.
Altogether, this semester's analysis has allowed me to conclude several things about the research of NrCAM in autism. First, NrCAM seems to be a good target gene for autism studies based upon its predicted functions in central nervous system development, its increased expression in neuronal tissues, and RNAi studies in C. elegans showing axon growth defects and lethality as a result of LAD-1 knockdown. Also, there are a number of model organisms which have NrCAM homologues with high homology including mouse, rat, chimp, and worm. In addition, these homologous proteins share similar if not identical protein domains with the human protein so studies targeting specific domains would be possible. Lastly, the NrCAM gene and protein has a number of interacting partners that might be investigated to further develop the role of NrCAM in autism.
Stephen Wiltshire, who was diagnosed with autism at age 3, was able to sketch the London skyline in exact scale completely from memory. Wiltshire took five days to complete the magnificent drawing after only one trip by helicopter over the city.
Image retrieved from
http://aavey.wordpress.com/2008/04/02/
see-the-amazing-picture-by-an-autistic-artist
-who-drew-london-from-memory-after-a-single-helicopter-trip/.
Image retrieved from
http://aavey.wordpress.com/2008/04/02/
see-the-amazing-picture-by-an-autistic-artist
-who-drew-london-from-memory-after-a-single-helicopter-trip/.
Future directions
Based on what I have learned this semester about the human NrCAM gene and protein and homologous in several organism, there a few directions that I would like future NrCAM research to go. I would like to describe some of the analysis that I believe should be done to better understand the role of NrCAM in autism with the hope of using this knowledge to benefit individuals with autism.
First, I think it is absolutely necessary for researchers to conduct larger disease-gene association studies to better characterize the relationship between mutations in the NrCAM gene and autism. The current evidence that NrCAM mutations are from a single association study in which 7 SNPs were identified to have a significant correlation with autism. This study was done in a population made up entirely of Japanese children, thus the results may not be applicable to individuals of different ethnicities. The haplotype mapping studies done in this population may not be useful in studying individuals of other ethnic backgrounds as well. This is a major concern to address before NrCAM research moves forward as scientists should confirm that NrCAM mutations are shown to be associated with autism in a population with varied ethnic backgrounds. In order to properly study NrCAM's role in autism, researchers will need to invest a lot of money in their studies, thus it should be made clear that NrCAM is a good target gene to study in the first place.
Once NrCAM has been confirmed as an appropriate target gene for autism researchers, I would propose that science use some of the model organisms included in my analysis to study the functionality of NrCAM in the development of the nervous system. It is important for scientists to validate many of the predicted functions of NrCAM and investigate how mutations in the three domains present in the NrCAM protein affect its functionality. These studies would be easiest to do in the worm, mouse, or rat model as these organisms are easy to study in the laboratory. I think scientists should focus on each of the domains separately and mutate these regions to determine the functional relevance of the domain, and also understand which mutations might be responsible for autistic-like symptoms in the model organisms used. I would also propose that researchers look more into the potential modifications of the NrCAM protein such as phosphorylation because there is currently not much information in this area. These post-translational modifications could have significant effects on the interactions of the protein in the body. The high levels of homology between the human protein and its homologues is encouraging for these studies as we might be able to gain some valuable information about the NrCAM protein from model organisms that are relatively easy to work with.
Ultimately I believe it will be important for scientists to do similar functional studies using a model organism in which behavioral and social phenotypes can be more easily studied such as the chimpanzee, which also shares high homology with the human protein. I propose this due to the fact that autism can include variety of social and behavioral deficits which would be hard to study in a worm or rodent model. Deficits in emotional responses to certain stimuli, interaction with peers, or learning and memory deficits would be easier to characterize in the chimpanzee, and provide more accurate portrayals of behavioral phenotypes due to mutations in NrCAM. These studies would require a great deal of evidence in worm or mouse models because the cost of doing such experiments in a chimpanzee model would be very high. Nonetheless, I believe that it is extremely important to study the behavioral implications of NrCAM mutations.
Finally, I would like to propose that additional studies be done to better characterize the interactions between NrCAM and some of its interaction partners as identified in the STRING protein networks. I plan to look more into the DNA motifs and protein domains of the proteins identified by STRING to interact with NrCAM, especially the ankyrin binding proteins and the activated leukocyte cell adhesion molecule. It is highly unlikely that autism is a result of mutations in a single protein, thus the role of the proteins it interacts with is important. Proteomic analysis looking at the expression profiles of NrCAM and its interacting partners could provide insight into the other proteins that are important during the development of the nervous system and would therefore by worth investigating in autism.
First, I think it is absolutely necessary for researchers to conduct larger disease-gene association studies to better characterize the relationship between mutations in the NrCAM gene and autism. The current evidence that NrCAM mutations are from a single association study in which 7 SNPs were identified to have a significant correlation with autism. This study was done in a population made up entirely of Japanese children, thus the results may not be applicable to individuals of different ethnicities. The haplotype mapping studies done in this population may not be useful in studying individuals of other ethnic backgrounds as well. This is a major concern to address before NrCAM research moves forward as scientists should confirm that NrCAM mutations are shown to be associated with autism in a population with varied ethnic backgrounds. In order to properly study NrCAM's role in autism, researchers will need to invest a lot of money in their studies, thus it should be made clear that NrCAM is a good target gene to study in the first place.
Once NrCAM has been confirmed as an appropriate target gene for autism researchers, I would propose that science use some of the model organisms included in my analysis to study the functionality of NrCAM in the development of the nervous system. It is important for scientists to validate many of the predicted functions of NrCAM and investigate how mutations in the three domains present in the NrCAM protein affect its functionality. These studies would be easiest to do in the worm, mouse, or rat model as these organisms are easy to study in the laboratory. I think scientists should focus on each of the domains separately and mutate these regions to determine the functional relevance of the domain, and also understand which mutations might be responsible for autistic-like symptoms in the model organisms used. I would also propose that researchers look more into the potential modifications of the NrCAM protein such as phosphorylation because there is currently not much information in this area. These post-translational modifications could have significant effects on the interactions of the protein in the body. The high levels of homology between the human protein and its homologues is encouraging for these studies as we might be able to gain some valuable information about the NrCAM protein from model organisms that are relatively easy to work with.
Ultimately I believe it will be important for scientists to do similar functional studies using a model organism in which behavioral and social phenotypes can be more easily studied such as the chimpanzee, which also shares high homology with the human protein. I propose this due to the fact that autism can include variety of social and behavioral deficits which would be hard to study in a worm or rodent model. Deficits in emotional responses to certain stimuli, interaction with peers, or learning and memory deficits would be easier to characterize in the chimpanzee, and provide more accurate portrayals of behavioral phenotypes due to mutations in NrCAM. These studies would require a great deal of evidence in worm or mouse models because the cost of doing such experiments in a chimpanzee model would be very high. Nonetheless, I believe that it is extremely important to study the behavioral implications of NrCAM mutations.
Finally, I would like to propose that additional studies be done to better characterize the interactions between NrCAM and some of its interaction partners as identified in the STRING protein networks. I plan to look more into the DNA motifs and protein domains of the proteins identified by STRING to interact with NrCAM, especially the ankyrin binding proteins and the activated leukocyte cell adhesion molecule. It is highly unlikely that autism is a result of mutations in a single protein, thus the role of the proteins it interacts with is important. Proteomic analysis looking at the expression profiles of NrCAM and its interacting partners could provide insight into the other proteins that are important during the development of the nervous system and would therefore by worth investigating in autism.
