An immune response characterizes early Alzheimer’s disease pathology and subjective cognitive impairment in hydrocephalus biopsies

Early Alzheimer’s disease (AD) pathology can be found in cortical biopsies taken during shunt placement for Normal Pressure Hydrocephalus. This represents an opportunity to study early AD pathology in living patients. Here we report RNA-seq data on 106 cortical biopsies from this patient population. A restricted set of genes correlate with AD pathology in these biopsies, and co-expression network analysis demonstrates an evolution from microglial homeostasis to a disease-associated microglial phenotype in conjunction with increasing AD pathologic burden, along with a subset of additional astrocytic and neuronal genes that accompany these changes. Further analysis demonstrates that these correlations are driven by patients that report mild cognitive symptoms, despite similar levels of biopsy β-amyloid and tau pathology in comparison to patients who report no cognitive symptoms. Taken together, these findings highlight a restricted set of microglial and non-microglial genes that correlate with early AD pathology in the setting of subjective cognitive decline.


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Life sciences study design
All studies must disclose on these points even when the disclosure is negative. In this study, we perform RNA-seq on 106 NPH samples that were banked at our institution under IRB-AAAA4666, which allows for the distribution of de-identified tissue samples and clinical data to researchers as "Not Human Subject Research." We sequenced all available NPH samples that were banked under this protocol at the time the study was done that had a RIN of 6 or higher.
As stated in our manuscript, we sequenced all samples with a RIN score of 6 and higher; no other exclusion criteria was used; this led to sequencing of 106 samples.
In our manuscript, we show that our findings translate to established autopsy-based AD RNA-seq datasets. As we show in our manuscript, three of our WGCNA modules that correlate with AD pathology in our NPH data (saddlebrown, orange, and darkgrey) also correlate with AD pathology in bulk RNA-seq date from AD autopsy tissue, while our mediumpurple3 module does not. This prompts an extensive comparison with other autopsy datasets that support the notion that a decline in homeostatic genes in AD that is seen in our NPH data is generally not seen in other autopsy datasets, with the exception of entorhinal cortex data.
This is a retrospective study, and so there is no randomization of subjects because we did not experiment on our subjects. As stated in our Methods, we regressed out variability in gene expression not attributable to our primary variables of interest (beta-amyloid and tau) using surrogate variable analysis, which is a commonly used method to identify known and unknown confounders and covariates in data.
All biopsy samples were processed and sequenced with researchers blinded to any associated metadata. Analysis of immunofluorescent images (Figure 8) was performed blinded to patient's cognitive status.
The antibodies that the hospital uses in pathologic diagnosis (the first four mentioned above) have their quality continuously monitored on positive and negative control tissue by the clinical service, as these antibodies are used by the Pathology Department in the diagnosis of clinical samples. The antibodies that we used ourselves (the last two mentioned above) have been previously validated for IF and IHC by the manufacturers, as shown on their websites. More importantly, the beta-amyloid antibody stains plaques in NPH biopsy tissue that reportedly had beta-amyloid plaques on clinical examination. The IBA-1 antibody also stains