# Hotspot gene mutations and treatment response in myelodysplastic syndromes (MDS): predictive biomarkers and targeted strategies

**Authors:** Rui Zhang, Wei Kou, Tao Wu, Rui Zhou

PMC · DOI: 10.3389/fmed.2025.1712877 · Frontiers in Medicine · 2026-01-05

## TL;DR

This paper explores how specific gene mutations in myelodysplastic syndromes affect treatment responses and highlights the potential for personalized therapies.

## Contribution

The study systematically connects key gene mutations with treatment outcomes, offering insights for individualized therapy in MDS.

## Key findings

- ASXL1 mutations predict resistance to demethylating agents but respond well to HMAs and Venetoclax.
- TP53 multi-hit lesions correlate with poor survival but show high response rates to eprenetapopt-azacitidine.
- IDH1/2 inhibitors achieve durable remissions in MDS patients with specific mutations.

## Abstract

The myelodysplastic syndromes (MDS) are clonal hematopoietic stem cell disorders characterized by cytopenia and a high risk of transformation to acute myeloid leukemia. In recent years, next-generation sequencing (NGS) has revealed common hotspot gene mutations in MDS, which are not only involved in disease progression, but also affect the responsiveness of different therapeutic strategies. Current research has revealed that ASXL1 mutations in MDS predict demethylating agents (HMAs) resistance, the combination of HMAs and Venetoclax (VEN) achieved an ORR of 87%. DNMT3A R882 mutations induce decitabine sensitivity via hemi-methylated enhancer trapping, and TET2 mutations enhance HMAs efficacy only in ASXL1 wild-type contexts (ORR 62.1% vs. co-mutated 19%). RUNX1 aberrations reduce chemotherapy responses (18.9% ORR in high-risk MDS) through DNA repair impairment, while BCOR/EZH2 loss drives cytarabine resistance. TP53 multi-hit lesions correlate with poor survival (OS <12 months) but respond to eprenetapopt-azacitidine (ORR 73%), and IDH1/2 inhibitors achieve durable remissions (ivosidenib ORR 83.3%, mOS 35.7 months). In this paper, we systematically illustrate the correlation between key gene mutations and the response to HMAs, chemotherapy and targeted therapies in MDS patients. This article summarizes the current evidence on gene mutations as predictive biomarkers and discusses the direction of individualized therapy.

## Linked entities

- **Genes:** ASXL1 (ASXL transcriptional regulator 1) [NCBI Gene 171023], DNMT3A (DNA methyltransferase 3 alpha) [NCBI Gene 1788], TET2 (tet methylcytosine dioxygenase 2) [NCBI Gene 54790], RUNX1 (RUNX family transcription factor 1) [NCBI Gene 861], BCOR (BCL6 corepressor) [NCBI Gene 54880], EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) [NCBI Gene 2146], TP53 (tumor protein p53) [NCBI Gene 7157], IDH1 (isocitrate dehydrogenase (NADP(+)) 1) [NCBI Gene 3417], IDH2 (isocitrate dehydrogenase (NADP(+)) 2) [NCBI Gene 3418]
- **Chemicals:** Venetoclax (PubChem CID 49846579), decitabine (PubChem CID 451668), azacitidine (PubChem CID 9444), eprenetapopt (PubChem CID 52918385), ivosidenib (PubChem CID 71657455)
- **Diseases:** myelodysplastic syndromes (MONDO:0018881), acute myeloid leukemia (MONDO:0015667)

## Full-text entities

- **Genes:** TET2 (tet methylcytosine dioxygenase 2) [NCBI Gene 54790] {aka IMD75, KIAA1546, MDS}, BCOR (BCL6 corepressor) [NCBI Gene 54880] {aka ANOP2, MAA2, MCOPS2}, EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) [NCBI Gene 2146] {aka ENX-1, ENX1, EZH2b, KMT6, KMT6A, WVS}, ASXL1 (ASXL transcriptional regulator 1) [NCBI Gene 171023] {aka BOPS, MDS}, RUNX1 (RUNX family transcription factor 1) [NCBI Gene 861] {aka AML1, AML1-EVI-1, AMLCR1, CBF2alpha, CBFA2, EVI-1}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, DNMT3A (DNA methyltransferase 3 alpha) [NCBI Gene 1788] {aka DNMT3A2, HESJAS, M.HsaIIIA, TBRS}
- **Diseases:** cytopenia (MESH:D006402), MDS (MESH:D009190), acute myeloid leukemia (MESH:D015470), stem cell disorders (MESH:D000092423)
- **Chemicals:** cytarabine (MESH:D003561), HMAs (-), VEN (MESH:C579720), decitabine (MESH:D000077209), ivosidenib (MESH:C000627630)
- **Species:** Homo sapiens (human, species) [taxon 9606]

## Full text

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## Figures

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## References

89 references — full list in the complete paper: https://tomesphere.com/paper/PMC12812748/full.md

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Source: https://tomesphere.com/paper/PMC12812748