Pantazatos, S. | Search bioRxiv

bioRxiv2019

Towards establishing internal validity for correlated gene expression measures in imaging genomics of functional networks: why distance corrections and external face validity alone fall short. Reply to "Distance is not everything in imaging genomics of functional networks: reply to a commentary on Correlated gene expression supports synchronous activity in brain networks"

The primary claim of the Richiardi et. al. 2015 Science article1 is that a measure of correlated gene expression, significant strength fraction (SSF), is related to resting state fMRI (rsfMRI) networks. However, there is still debate about this claim and whether spatial proximity, in the form of contiguous clusters, accounts entirely, or only partially, for SSF2,3. Here, thirteen distributed networks were simulated by combining 34 contiguous clusters randomly placed throughout cortex, with resulting edge distance distributions similar to rsfMRI networks. Cluster size was modulated (6-15mm radius) to test its influence on SSF false positive rate (SSF-FPR) among the simulated noise networks. The contribution of rsfMRI networks on SSF-FPR was examined by comparing simulations using: 1) all cortical samples 2) all samples with non-rsfMRI cluster centers and 3) only non-rsfMRI samples. Results show that SSF-FPR is influenced only by cluster size (r>0.9, p<0.001), not by rsfMRI samples. Simulations using 14mm radius clusters most resembled rsfMRI networks. When thresholding at p<10-4, the SSF-FPR was 0.47. Genes that maximize SF have high global spatial autocorrelation. In conclusion, SSF is unrelated to rsfMRI networks. The main conclusion of Richiardi et. al. 2015 is based on a finding that is [~]50% likely to be a false positive, not less than 0.01% as originally reported in the article1. We discuss why distance corrections alone and external face validity are insufficient to establish a trustworthy relationship between correlated gene expression measures and rsfMRI networks, and propose more rigorous approaches to preclude common pitfalls in related studies.

neuroscience↗

bioRxiv2017

Transcriptomic characterization of MRI contrast, focused on the T1-w/T2-w ratio in the cerebral cortex

Magnetic resonance (MR) images of the brain are of immense clinical and research utility. At the atomic and subatomic levels, the sources of MR signals are well understood. However, at the macromolecular scale, we lack a comprehensive understanding of what determines MR signal contrast. To address this gap, we used genome-wide measurements to correlate gene expression with MR signal intensity across the cortex in the Allen Human Brain Atlas. We focused on the ratio of T1-weighted and T2-weighted intensities (T1-w/T2-w) which is considered to be a useful proxy for myelin content. Positive correlations between myelin-associated genes and the ratio supported its use as a myelin marker. However, stronger correlations were observed for neurofilaments, and genes linked to the production of formaldehyde (which cross-links protein to create larger molecules). There was also an association with protein mass, with genes coding for heavier proteins expressed in regions with high T1-w/T2-w values. Oligodendrocyte gene markers were strongly correlated but this was not driven by myelin-associated genes, suggesting this signal is from non-myelinating satellite oligodendrocytes. We find the strongest support for the previous finding of high aerobic glycolysis in regions with low T1-w/T2-w ratio. Specifically, many mitochondrial genes were negatively correlated with T1-w/T2-w ratio. Genes up-regulated by pH in the brain were also highly correlated with the ratio, suggesting the pH gradient in mitochondria may explain the aerobic glycolysis association. Expression of protease subunit genes was also inversely associated with the ratio, in agreement with the protein mass correlation. While we corroborate associations with myelin and synaptic plasticity, differences in the T1-w/T2-w ratio appear to be more attributable to molecule size, satellite oligodendrocyte proportion, mitochondrial number, alkalinity, and axon caliber. Using disease-associated gene lists, we observed an enrichment of negative T1-w/T2-w ratio correlations with human immunodeficiency virus (HIV) associated genes. Expanding our analysis to the whole brain results in strong positive T1-w/T2-w associations for immune system, inflammatory disease, and microglial genes. In contrast, neuron markers and synaptic plasticity genes are negatively enriched. Lastly, our results vary little when our analysis is performed on T1-w or inverted T2-w intensities alone, possibly because the noise reduction properties of the ratio are not needed for postmortem brain scans. These results provide a molecular characterization of MR contrast that will aid interpretation of future MR studies of the brain.

neuroscience↗