Alzheimer's disease affects over 55 million people worldwide, yet the precise molecular changes happening inside individual brain cells remain poorly understood. I wanted to dig into that question - not at the tissue level, but at single-cell resolution.
So I built a full scRNA-seq analysis pipeline in Python using Scanpy, working with a publicly available dataset of 63,608 nuclei from human prefrontal cortex tissue (sourced from CZ CELLxGENE). The donors spanned three Braak stages: 0 (cognitively normal), 2 (early Alzheimer's), and 6 (severe Alzheimer's).
Here's what I found and how I found it.
The Dataset
The data came from a study on the molecular characterisation of selectively vulnerable neurons in AD. It covers the superior frontal gyrus, a prefrontal region known to be hit hard by neurodegeneration - and includes seven major brain cell types:
