Impact of Confounding Factors in Human Postmortem Brain Tissues on Gene Expression Profiles: A Comparison of Patients With Schizophrenia, Bipolar Disorder, and Nonpsychiatric Controls

Controlling for confounding factors in postmortem brain studies of psychiatric disorders is crucial, particularly in gene expression analyses. Potential confounding factors include sex, age at death, medication history, agonal state, postmortem interval (PMI), tissue storage duration, tissue pH, and RNA integrity number (RIN). pH and RIN are considered particularly important in gene expression analysis because they accurately reflect mRNA quality. We previously found that pH and RIN affected the levels of genes related to the cell cycle and RNA processing, respectively, and both affected genes involved in energy production and the immune system. In this study, we investigated the influence of confounding factors on gene expression profiles in psychiatric disorders. We measured gene expression levels in the prefrontal cortex of 25 deceased patients with schizophrenia, 10 with bipolar disorder, and 21 nonpsychiatric controls via RNA sequencing, and identified genes associated with pH, RIN, PMI, sex, age at death, tissue storage duration, and antipsychotic drug dose. We identified key molecular pathways through Ingenuity Pathway Analysis. The total number of mRNA variants significantly correlated with gene expression, and each confounding factor was as follows: 139 for sex, 87 for age, 99 for PMI, 35 386 for pH, 11 373 for RIN, and 13 414 for storage duration. We identified strong associations with metabolic, immune, energy production, and DNA repair pathways. The expression of certain genes was strongly associated with different confounding factors; therefore, it is necessary to consider these factors when interpreting the gene expression profile in brain tissue.