GEO series

Clonal expansion of cytotoxic CD8+ T cells in lecanemab-associated ARIA

GSE316096 Homo sapiens (human) Single-cell RNA-seq 18 samples Submitted 2026/01/20 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 18 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Clonal expansion of cytotoxic CD8⁺ T cells in lecanemab-associated ARIANature communications · 2026

Summary (written by the submitters)

Amyloid-related imaging abnormalities (ARIA) remain the principal safety concern limiting adoption of anti-amyloid therapies such as lecanemab, yet their underlying biology is poorly defined. To address this, we performed deep multi-omic profiling of peripheral blood mononuclear cells from three Alzheimer's disease (AD) patients who developed ARIA and three matched controls.

Read the full summary ↓

Single-cell RNA sequencing, CITE-seq, V(D)J clonotyping, and metabolomic/lipidomic profiling revealed a coordinated reprogramming of the CD8+ compartment in ARIA+ patients. CD8+ TEM and TEMRA subsets were numerically expanded, transcriptionally enriched for cytotoxic and migratory programs, and exhibited increased clonal expansion. Transcription factor inference and metabolomics converged on a glycolytic bias, supporting short-lived effector activity. Ligand-receptor modeling identified ARIA-associated signaling from CD14+ and CD16+ monocytes that augmented antigen presentation, adhesion, and chemokine axes directed toward effector CD8s. Finally, integration with an external cerebrovascular atlas confirmed that ARIA-associated TEM/TEMRAs are transcriptionally "addressed" for vascular engagement.

Published in

Clonal expansion of cytotoxic CD8⁺ T cells in lecanemab-associated ARIA

Johnson LA, Saito K, Pallerla AV et al. · Nature communications 2026 · PMID 41617706 · doi:10.1038/s41467-026-68921-3

This dataset

Open GSE316096 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE316096_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1400587. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41617706) ↗

Study design

18 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM9444420 PBMCs, AD patient, lecanemab, control, 75-79F, E3/E4, Gene Expression
GSM9444421 PBMCs, AD patient, lecanemab, control, 75-79F, E3/E4, CITE-seq ADT
GSM9444422 PBMCs, AD patient, lecanemab, control, 75-79F, E3/E4, TCR VDJ
GSM9444423 PBMCs, AD patient, lecanemab, ARIA-E, 70-74F, E3/E4, Gene Expression
GSM9444424 PBMCs, AD patient, lecanemab, ARIA-E, 70-74F, E3/E4, CITE-seq ADT
GSM9444425 PBMCs, AD patient, lecanemab, ARIA-E, 70-74F, E3/E4, TCR VDJ
GSM9444426 PBMCs, AD patient, lecanemab, control, 70-74M, E4/E4, Gene Expression
GSM9444427 PBMCs, AD patient, lecanemab, control, 70-74M, E4/E4, CITE-seq ADT
GSM9444428 PBMCs, AD patient, lecanemab, control, 70-74M, E4/E4, TCR VDJ
GSM9444429 PBMCs, AD patient, lecanemab, ARIA-H, 65-69M, E4/E4, Gene Expression
GSM9444430 PBMCs, AD patient, lecanemab, ARIA-H, 65-69M, E4/E4, CITE-seq ADT
GSM9444431 PBMCs, AD patient, lecanemab, ARIA-H, 65-69M, E4/E4, TCR VDJ
GSM9444432 PBMCs, AD patient, lecanemab, control, 75-79F, E4/E4, Gene Expression
GSM9444433 PBMCs, AD patient, lecanemab, control, 75-79F, E4/E4, CITE-seq ADT
GSM9444434 PBMCs, AD patient, lecanemab, control, 75-79F, E4/E4, TCR VDJ
GSM9444435 PBMCs, AD patient, lecanemab, ARIA-E+H, 70-74F, E4/E4, Gene Expression
GSM9444436 PBMCs, AD patient, lecanemab, ARIA-E+H, 70-74F, E4/E4, CITE-seq ADT
GSM9444437 PBMCs, AD patient, lecanemab, ARIA-E+H, 70-74F, E4/E4, TCR VDJ

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