Show Notes
Lilljebjörn H et al., Nat Commun - Single-cell and bulk sequencing of 120 AML cases reveal two NPM1-mutated subtypes with distinct immune evasion mechanisms and divergent responses to hematopoietic stem cell transplantation. Key terms: acute myeloid leukemia, single-cell RNA-seq, NPM1, immune evasion, hematopoietic stem cell transplantation.
Study Highlights:
Bulk RNA-seq profiles are strongly confounded by variable mature cell-type signatures that can conceal subtype-specific blast programs. Single-cell multimodal sequencing of AML identified four main clusters of immature leukemic cells and separated NPM1-mutated cases into NPM1class I and NPM1class II. NPM1class I is marked by MHC class II downregulation and shows a significant survival benefit from HSCT, while NPM1class II resists allogeneic T cell killing ex vivo and does not benefit from HSCT. A 180-gene signature, and a shorter 30-gene panel, distinguished the classes across external bulk cohorts and associated each subtype with different co-mutation patterns.
Conclusion:
Single-cell transcriptional profiling defines two clinically relevant NPM1 subtypes with distinct immune evasion strategies that may inform HSCT decisions and immunotherapy approaches.
Music:
Enjoy the music based on this article at the end of the episode.
First author:
Lilljebjörn H
Journal:
Nature Communications
DOI:
10.1038/s41467-025-66546-6
Reference:
Lilljebjörn H, Henningsson R, Rissler M, Landberg N, Puente-Moncada N, von Palffy S, Rissler V, Stanek P, Desponds J, Lazarevic V, Lehmann S, Fontes M, Ågerstam H, Sandén C, Orsmark-Pietras C, Zhong X, Juliusson G, Thorsson H, Fioretos T. The AML cellular state space unveils NPM1 immune evasion subtypes with distinct clinical outcomes. Nat Commun. 2025;16:10592. https://doi.org/10.1038/s41467-025-66546-6
License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/
Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00
Official website https://basebybase.com
On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.
Episode link: https://basebybase.com/episodes/npm1-immune-evasion-subtypes
️ Episode:
220: The AML cellular state space reveals NPM1 immune evasion subtypes
️ Season:
1
Article title:
The AML cellular state space unveils NPM1 immune evasion subtypes with distinct clinical outcomes
QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-12-06.
QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript sections describing AML heterogeneity, single-cell sequencing approaches, isolation of AML immature cells, the NPM1 class I/II dichotomy, MHC-II downregulation and CIITA, intrinsic T cell resistance, ex vivo T cell assays, HSCT outcomes, and the minimal 30-gene panel for clinical implementation.
- transcript topics: AML heterogeneity and leukemia stem cells; Single-cell multimodal sequencing (scRNA-seq + scADT-seq); Isolation and characterization of AML immature cells; NPM1-mutated AML: NPM1 class I and NPM1 class II; MHC class II downregulation and CIITA regulation; Intrinsic T cell resistance and alternative checkpoint pathways
QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0
Metadata Audited:
- article_doi
- article_title
- article_journal
- license
Factual Items Audited:
- AML heterogeneity and leukemia stem cells drive relapse
- Single-cell multimodal sequencing identifies AML immature cells and two NPM1 subtypes
- NPM1 class I downregulates MHC II and HSCT improves survival
- NPM1 class II shows intrinsic resistance to donor T cells and lacks HSCT benefit
- Ex vivo T cell co-culture shows differential sensitivity between NPM1 classes I and II
- A minimal 30-gene expression panel can distinguish the two NPM1 subtypes for clinical use
QC result: Pass.
