Author: Alex

I am currently in the process of figuring out which genes are common to each of the data sets. This will involve building a program to find the common genes. I have a good idea of how to do it; it’s a relatively simple problem. The only hangups will probably be translating all the datasets into one universal comparable format, but given enough time to iron out the kinks in all 5 data sets, I think I can manage easily. Eventually, I’ll make a neat Venn diagram illustrating what genes are common to what datasets.

I’m also learning more and more about bayesian probability. This is the basis of the functional interaction network we will eventually use. Anna’s postdoc Ibrahim explained the basics to me. This is a new concept to me, so this week, I’ll also learn more about that as well.

This week, we searched for genes related to both schizophrenia and cell motility in order to build out gold standard of genes upon which to base our program off of.

My job was to find collections of genes related to Schizophrenia (SZ), while Miriam searched for cell motility genes. Our program is planned to have the capability to weight evidence for the strength of the data, so even uncertain genes will be really helpful.

The first set of associated genetic information is from the Schizophrenia Working Group of the Psychiatric Genomics Consortium. In a Genome Wide Association Study (GWAS) from 36,989 cases, they identified 108 loci that contained SNPs significantly more likely to be present in people with SZ. The threshold for significance is a p value of less than 5×10^-8, making this study one of the strongest sets of SZ gene data. However, while most of these SNPs are located near protein coding genes, all but 10 are located within non-coding regions. A regulatory region being near a protein coding gene does not necessarily mean that the gene is actually regulated by that region. Instead, the region might regulate some other gene in some other area. However, regionality with a regulator does imply a higher probability of being regulated by the regulator, so this locational information might be useful in the weaker evidence standards.

http://www.nature.com/nature/journal/v511/n7510/abs/nature13595.html?lang=en

The next set of data is from the Schizophrenia Research Forum on SZGene.org. It contains every genetic association study paper for SZ genes that’s available. It’s a nice collection, but none of the genes reached the GWAS p value threshold of 10^-8. This evidence will have to be weighted proportional to the strength of the studies themselves.

Another set of data comes from an expression study on human induced pluripotent stem cells. The cells were differentiated to neurons and underwent qPCR. This data, however, is in vitro, whereas the developmental aspect of SZ requires a degree of specificity and communication. https://www.nature.com/nature/journal/v473/n7346/full/nature09915.html

There is another gene expression dataset, but this time, it’s from dead people. While the region of the brain is much more specific (prefrontal cortex), this expression data comes long after development. However, they did find 1 gene, inhibited it in a pluripotent stem cell, and found abnormal cell motility. Therefore, this data may be useful to our study. http://www.nature.com/neuro/journal/v19/n11/full/nn.4399.html

The last genetic data set covers the conformational structure of the chromatin in the nucleus. Brain specific intrachromatin contacts can upregulate protein coding genes promoted by the contact. Thus, they established a strong correlation between gene expression and chromatin contact using 3 neonatal brain slices from separate subjects. They were able to locate the points of contact for the remaining 98 loci in the initial gene, giving a more broad picture of genetic interaction. http://www.nature.com/nature/journal/v538/n7626/full/nature19847.html

We’ll probably use all of these data sets. The next question is how.

This week we looked at a paper describing the relationship between cellular focal adhesions, cell motility, and schizophrenia. http://www.sciencedirect.com/science/article/pii/S0006322313000917

Previous gene expression assays from olfactory mucosa neurons, which are excellent for disease modeling because of their multipotentcy, from patients with schizophrenia found differential expression in focal adhesion related genes, such as integrin genes (http://dmm.biologists.org/content/3/11-12/785.long). Differential expression was also found in the Focal Adhesion Kinase (FAK) pathway, which is central to the construction and maintenance of Focal Adhesions. Focal Adhesions are necessary for binding the cell to the extracellular matrix, which keeps it lodged in one place. Focal Adhesions are also important for cell motility insofar as cells need some sort of friction to move around. The fatty acid lipid membrane is very flexible and slippery due to its hydrophobicity; it needs the focal adhesions to provide an equal and opposite force for cellular motion. Imagine you’re on an ice rink, but your shoes can penetrate the ice and grip it so that you can walk.

However, these researchers found an increased level of cell motility in neurons of schizophrenic patients. Schizophrenic cells are faster and travel farther than control cells. Schizophrenic cells were also found to be less adherent, with less cells binding to plates when creating cell cultures. They found a reduced level of phosphylated FAK (pFAK) in patient cells but found that inhibiting FAK returned cell motility to control levels. They also found that inhibiting α3β1 integrins and α8β1 integrins also returned motility to normal. This implies that instead of the reduced level of FAK being the cause of the increased motility, the cause is instead a malfunction in the FAK pathway itself, of which α3β1 integrin and α8β1 integrin are a part of. They also found that patient focal adhesions were smaller, less common, and disassembled faster.

Unfortunately, there are an enormous amount of genes involved in cell motility and the FAK pathway. Any one of them could be affecting FAK, integrins, and cell motility at large. Hopefully our functional network programs will help elucidate some suspects.

This coming week, my primary goal will be identifying genes and pathways prominent in Schizophrenia pathology, while Miriam will be finding ones associated with cell motility

9/8/17

We are starting off the year neck deep in our literature review! First, we’re looking at how some researchers built the GIANT network, a functional interaction network built around tissue specificity ¹. This type of network would be very useful to us given that we’re looking at neuronal motility genes, which needs to be specific to neurons since a ton of other cells move around.

How to Build a Tissue Specific Functional Gene Interaction Network

1. Don’t build a tissue specific functional gene interaction network

   First, they built a “gold standard” of gene pairs that most definitely not tissue specific by selecting specific biological process gene collections from the Gene Ontology Consortium (GO). Gene pairs that were co-annotated to be functionally related were placed as the positive examples. Gene pairs that were not co-annotated to be functionally related were placed in the not-functionally-related-bin, unless they were: (A) in two different GO groups that had a significant number of shared genes, or (B) if the two genes were in GO groups that had nothing to do with each other. These gene pairs were ignored. They found 604,038 functionally related genes and 12,425,713 unrelated pairs.

2. Ignore the 13 million pair list you just made

   Next, they matched Human Protein Reference Database gene to tissue annotations to the BRENDA Tissue Ontology. Tissues with less than ten genes were deemed worthless. They then grabbed a separate list of genes that are expressed ubiquitously and removed them from their respective sets of newly categorized genes and placed them into a “ubiquitous” bucket. Thus, they made a set of gene sets of genes expressed exclusively in specific tissues (T) and a set of genes expressed ubiquitously (U).

3. Integrate the Two lists

   

   Greene et al, 2015

Going back to the tissue naive list of gene pairs, every gene was labeled depending on its tissue specificity. The gene pairs were then categorized according to each gene’s tissue specificity. The pairs with genes “specifically co-expressed in the tissue [T-T and T-U]” were marked as tissue specific, whereas the remaining gene pairs were marked as negative. The integrations were limited to 144 tissues with at least 10 positive tissue specific gene pairs.

4. Train a Bayesian Classifier for Each Tissue

They also trained a tissue naive classifier using the the original naive pair list. Since there was little independence, which is needed for Bayes classifiers, the dependency was calculated and accounted for. The classifiers then were able to make genome wide predictions about that specific tissue.

Hopefully I can learn more about the nuts and bolts of GIANT. These tools seem incredibly powerful, and might be used to find targets we might have never thought of. I will continue researching throughout the week.

1. Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG. (2015). Understanding multicellular function and disease with human tissue-specific networks. Nature Genetics. 10.1038/ng.3259w. ↩︎