Study design

MATERIALS AND METHODS

Study design

The goal of this study was to identify a molecular driver of CgR. First, we identified neurotranscriptomic correlates of both enrichment (in mice) and CgR (in humans burdened with neuropathology) in an unbiased manner. Second, we manipulated these TFs in a neurodegenerative disease model and measured properties of neuronal excitability. For all studies, mice were age- and gender-matched to keep treatment and control groups as similar as possible. Enrichment studies lasted 1 month to ensure robustness of the environmental manipulation. For mouse sequencing and immunohistochemistry experiments, all groups were processed and stained at the same time. Imaging quantification was carried out in a blinded fashion by a researcher who did not perform the immunohistochemistry. For human sequencing experiments, samples were processed in batches that spanned both resilient and nonresilient individuals in case of batch effects. Inclusion criteria for cognitively resilient and nonresilient individuals were based on the neuropathological and cognitive spread of the ROS/MAP cohort, with care to match groups on other clinical metrics and demographic data. We excluded outliers in the human snRNA sequencing experiment based on overall sequencing quality and cell clustering.

Statistics

Molecular results are presented as means ± SEM, assuming a normal distribution. All nonsequencing statistical analyses used Prism GraphPad software to compute significance. Data limited to two experimental groups were analyzed by two-tailed unpaired t tests. Data consisting of three or more groups were analyzed by one- or two-way ANOVAs followed by pairwise multiple comparisons tests. The statistical test, P values, and sample size (n) for each experiment are specified in the figure legends. No statistical method was used to estimate sample size, but they are consistent with previous publications while attempting to eliminate waste and animal mortality. Molecular analyses used a minimum of three biological replicates per condition, and validation experiments used a distinct set of animals. Behavioral tests were run on at least two independent cohorts of animals, with one reported in the main figures.

All other methods can be found in the supplemental methods.