Shouts out: @davidweinshenker.bsky.social for aid interpreting NM results but accidentally omitted from text's acknowledgments; @madhavitippani.bsky.social for NM quantification in the tissue; and @martinowk.bsky.social for her mentorship, patience w/ me (sometimes), + newfound LC enthusiasm! (8/8)

Finally, we made 2 web tools to share to this unprecedently large human LC xscriptomic data. A 3rd (that visualizes high-res H&E and NM with and spatial gene xpr.) on the way (last URL). We hope these help the #bluespot #LC #catecholamines community! Tools at: research.libd.org/LFF_spatial_... (7/8)

Controlled for age, sex, E4/E2, and genomic ancestry, higher APOE gene expression was associated with paler NM! ~180 other genes also assoc with NM (Bonf. p <0.05, 23k genes tested), inc. several autophagocytosis and axon-to-soma transport (processes that also clear intracell tau path)! (6/8)

I got creative here and ran analyses I'm extra stoked about: modeling gene xpr relationships with quantitative measures of how dark the LC neuronal pigment, neuromelanin (NM) was in individual transcriptomic spots. (5/x)

AD risk varies with APOE alleles (E4-risk, E2-protective), with the E4 risk effect in European ancestry (EA) >> in African ancestry (AA). (E2 has similar effects in both groups). E4-E2 DE was much stronger in LC of EA donors and most E4-E2 DE w/in LC was specific to 1 ancestry group. (4/8)

Differential expression analyses of course focused on the LC. Between sexes, there was subtle but highly signif. DE of cholesterol synthesis pathway genes. These genes do not show astrocytic expression patterns, suggesting LC neurons themselves synthesize cholesterol in a sex-biased manner(!) (3/8)

AFA(We)K, no group has yet succeeded in high-throughput, high-yield single-cell/nucleus seq of LC. Thankfully, spatial transcriptomics helped us get RNAseq of the LC consistently across donors. (The rest of the 55µm-diameter spots, though, are mismashes of cell types): (2/8)