Normally, it takes 22 weeks for the disease to run its course in mice. During the 22-week period, we analyzed the complete transcriptome of the brain at 10 different time points. At each time point, we subtracted the transcriptomes of the normal mice from the transcriptomes of the diseased mice, thus ending with only the genes that were differentially expressed (DEGs). However, even after subtracting the normal genes from the diseased mice, we were left with about a third of the mouse brain genes that were differentially expressed. Normally, about 17,000 genes are active in a mouse’s brain, and in this case about 7,400 were differentially expressed—thus
Inhibitors,research,lifescience,medical representing an enormous signal-to-noise challenge. Noise can be divided into two types: technical noise that comes from generating and manipulation of data, and biological noise that arises as a SB203580 cost consequence of the different biologies operating in an organ such as the brain. If you assay
a phenotype such as the brain transcriptome, the result is almost always the sum of a number of different biologies. If only one specific Inhibitors,research,lifescience,medical phenomenon is of interest, such as neural degeneration, Inhibitors,research,lifescience,medical all the other biological phenomena must be subtracted away. Figure 6. A schematic view of the mouse prion experiment. Different strains of mice were created to subtract away the non-neurodegenerative phenomena from the roughly 7,400 genes that were differentially expressed in the prion-diseased mouse brain. For instance, a mouse which was a double knock-out for the prion gene was created, so, when injected with infectious prion particles, it did not contract the disease. However, its brain transcriptome changed, reflecting DEGs arising from other biologies that could be subtracted away. This subtraction process was repeated with the other carefully selected Inhibitors,research,lifescience,medical mouse strains that reflected other
irrelevant biologies that could be subtracted away as well. After eliminating all the non-neurodegenerative phenomena, the slightly more than 300 genes that were left encoded the core of the neurodegenerative response. Four basic Inhibitors,research,lifescience,medical processes delineate the dynamic histopathology of this disease: Prion accumulation and replication, glial activation, and two different forms of neurodegeneration: synaptic degeneration and neuronal cell death. The identified genes were mapped across multiple time points and across the identified interaction networks that encode for these four processes. The picture that emerged was that from in the beginning of the disease both normal and diseased mouse networks were the same (Figure 7). However, as the disease progressed, more and more networks were recruited into the disease state. One other very striking observation was the temporal sequential perturbation of the four major identified networks to the diseased state.9–10 The disease started in the most unique network of prion accumulation and replication and then progressed to the other networks (Figure 8).