Human samples
Post-mortem human brain tissue samples for immunohistochemistry were obtained from patients who had enrolled in and provided consent for a brain donation programme through the Neuropathology Brain Bank and Research CoRE at the Icahn School of Medicine at Mount Sinai. These samples were collected in accordance with ethical guidelines and institutional review board approval at the Icahn School of Medicine at Mount Sinai, ensuring the privacy and dignity of the donors while supporting ongoing neurological research. Tissue was obtained from donors who had provided written informed consent for research use either directly or through their next of kin. Three post-mortem brain samples (frontal cortex) were obtained from patients affected by Alzheimer’s disease neuropathological changes. Neuropathological assessments were performed at the respective centres using standardized criteria, including the Consortium to Establish a Registry for Alzheimer’s Disease neuritic plaque assessment and Braak neurofibrillary tangle staging51,52. In this study, we did not recruit participants; we only de-identified post-mortem brain samples from individuals. Research with de-identified autopsy material does not meet the federal regulatory definition of human subject research, as defined in 45 Code of Federal Regulations Part 46. However, Health Insurance Portability and Accountability Act requirements still apply.
Human samples of induced pluripotent stem cell lines were generated by the Icahn School of Medicine at Mount Sinai, University of California, Irvine Alzheimer’s Disease Research Center (UCI ADRC)and Washington University Alzheimer’s Disease Research Center (WashU ADRC) Induced Pluripotent Stem Cell Core from subject fibroblasts or peripheral blood mononuclear cells (PBMCs) with approved Institutional Review Boards and Human Stem Cell Research Oversight committee protocols at the Icahn School of Medicine at Mount Sinai, UCI ADRC and WashU ADRC Induced Pluripotent Stem Cell Core. The consent for reprogramming human somatic cells to human samples of induced pluripotent stem cell was obtained through the Human Stem Cell Research Oversight protocols 19-04, 2013-9561 and 2017-1061. Informed consent was received from each participant who donated fibroblasts or PBMCs.
Human demographic information, including sex, age, AD diagnosis, Braak state, post-mortem interval and/or clinical cognitive status, can be found in Supplementary Table 2. This study does not report on race, ethnicity or other socially relevant groupings to minimize the likelihood of unintentional identification of de-identified samples.
Mice
Mice were housed in cages with two to five animals per cage, with a 12-h light/dark cycle (lights on from 0700 to 1900 hours), a constant temperature (23 °C) and ad libitum access to food and water. Humidity averaged 38%, with a high of 58% and a low of 31% over a 24-h period. All animal protocols were approved by the Institutional Animal Care and Use Committee at Icahn School of Medicine at Mount Sinai and performed according to the National Institutes of Health (NIH) guidelines.
The Spi1fl/+ (ref. 41), Cx3cr1CreErt2/+(Litt) (ref. 53), Sykfl/fl (ref. 54), Cd28fl/fl (ref. 55) and 5xFAD25 (also known as Tg6799) mice were purchased from The Jackson Laboratory (006922, 021160, 017309, 024282 and 034840, respectively). The Plcg2fl/+ mouse56 was generously provided by T. Inoue and T. Kurosaki (RIKEN Institute). The Eef1a1LSL.eGFPL10a/+ mouse was generously provided by A. Domingos (Instituto Gulbenkian de Ciência) and J. Friedman (Rockefeller University). The Mx1::GFP mouse57 was generously provided by A. García-Sastre (Icahn School of Medicine at Mount Sinai).
To achieve ectopic expression of the Spi1 gene, a floxed transcriptional STOP cassette followed by FLAG-tagged mouse Spi1 complementary DNA (cDNA) was targeted into the Rosa R26 locus of embryonic stem cells using the TV-targeting vector for homologous recombination at the ROSA26 locus, generously provided by K. Rajewsky58 and available at Addgene (plasmid no. 11739), as previously described. A schematic is shown in Extended Data Fig. 4a. In brief, a transcriptional STOP cassette consisting of six SV40 polyadenylation sites was flanked by loxP recognition sequences to facilitate Cre-mediated deletion and subsequent activation of exogenous FLAG-tagged Spi1. The original plasmid with mouse Spi1 sequence was provided by C. Vakoc24,59 (Cold Spring Harbor Laboratory). Routine genotyping of Rosa26LSL.FLAG-Spi1/+ mice (Extended Data Fig. 4a) was performed using the following primers:
5′-GTG TTG CAA TAC CTT TCT GGG AGT T
5′-GGA AGT CTT GTC CCT CCA ATT TTA CAC
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