Landscape of genetic lesions in 944 patients with myelodysplastic syndromes
Open accessAbstract
High-throughput DNA sequencing significantly contributed to diagnosis and prognostication in patients with myelodysplastic syndromes (MDS). We determined the biological and prognostic significance of genetic aberrations in MDS. In total, 944 patients with various MDS subtypes were screened for known/putative mutations/deletions in 104 genes using targeted deep sequencing and array-based genomic hybridization. In total, 845/944 patients (89.5%) harbored at least one mutation (median, 3 per patient; range, 0-12). Forty-seven genes were significantly mutated with TET2, SF3B1, ASXL1, SRSF2, DNMT3A, and RUNX1 mutated in >10% of cases. Many mutations were associated with higher risk groups and/or blast elevation. Survival was investigated in 875 patients. By univariate analysis, 25/48 genes (resulting from 47 genes tested significantly plus PRPF8) affected survival (P<0.05). The status of 14 genes combined with conventional factors revealed a novel prognostic model ('Model-1') separating patients into four risk groups ('low', 'intermediate', 'high', 'very high risk') with 3-year survival of 95.2, 69.3, 32.8, and 5.3% (P<0.001). Subsequently, a 'gene-only model' ('Model-2') was constructed based on 14 genes also yielding four significant risk groups (P<0.001). Both models were reproducible in the validation cohort (n=175 patients; P<0.001 each). Thus, large-scale genetic and molecular profiling of multiple target genes is invaluable for subclassification and prognostication in MDS patients.
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Dysregulated iron metabolism is a hallmark of a large subset of MDS with ringed sideroblasts (MDS-RS), characterized by aberrant iron accumulation in erythroblast mitochondria and accounting for ~30% of all MDS cases.
“dysregulated iron metabolism is a hallmark of a large subset of MDS with ringed sideroblasts (MDS-RS), characterized by aberrant iron accumulation in erythroblast mitochondria and accounting for ~30% of all MDS cases (42).”
From Eprenetapopt triggers ferroptosis, inhibits NFS1 cysteine desulfurase, and synergizes with serine and glycine dietary restriction (2022) · cites this paper as [42]
The Results section reports 292 patients with MDS subtypes featuring increased ring sideroblasts among a cohort of 944—approximately 31% of this cohort. It does not establish that MDS-RS accounts for 30% of all MDS cases, or discuss dysregulated iron metabolism or iron accumulation in erythroblast mitochondria. (LLM, conf=0.88)
Experimental — accuracy not yet measuredTP53 gene mutations are detected in approximately 10%-20% of patients with de novo MDS or AML and 30%-40% of patients with therapy-related disease.
“TP53 gene mutations are detected in approximately 10%-20% of patients with de novo myelodysplastic syndromes (MDS)1-4 or acute myeloid leukemia (AML)5,6 and 30%-40% of patients with therapy-related disease.7”
From Eprenetapopt (APR-246) and Azacitidine in <i>TP53</i> -Mutant Myelodysplastic Syndromes (2021) · cites this paper as [2]
The Results (Frequency and spectrum of gene mutations; page unavailable) identify TP53 mutations in patients with MDS, but place their frequency at 2–10%, not approximately 10–20%. The paper does not give a separate frequency for de novo MDS. In the citing sentence, this source is among citations 1–4 attached to the MDS portion, not the AML or therapy-related figures. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIn the context of MDS, eprenetapopt is currently only indicated in ~7% of all MDS cases.
“In the context of MDS, eprenetapopt is currently only indicated in ~7% of all MDS cases (42).”
From Eprenetapopt triggers ferroptosis, inhibits NFS1 cysteine desulfurase, and synergizes with serine and glycine dietary restriction (2022) · cites this paper as [42]
The Results section (Frequency and spectrum of gene mutations; page unavailable) places TP53 mutations in the 2–10% range among the MDS cases studied, which is consistent with approximately 7% but does not establish that exact estimate. The paper does not address eprenetapopt or say that its use is indicated in those cases. (LLM, conf=0.82)
Experimental — accuracy not yet measuredSplicing factor mutations are common in AML and other blood malignancies and are often mutually exclusive, indicating that cancers harboring such mutations may rely on an intact splicing machinery for survival.
“Splicing factor mutations are common in AMl and other blood malignancies and are often mutually exclusive (Haferlach et al. 2014;Papaemmanuil et al. 2016), indicating that cancers harboring such mutations may rely on an intact splicing machinery for survival (lee et al. 2018).”
From From serendipity to strategy: molecular glue degraders in cancer therapeutics (2025) · cites this paper as Haferlach et al. 2014
The Results (Frequency and spectrum of gene mutations) report frequent RNA-splicing mutations in myelodysplastic syndromes, a blood malignancy. The Results (Correlation of gene mutations) describe negative correlations involving splicing-factor mutations, but do not establish that splicing-factor mutations are often mutually exclusive with one another or that they are common in AML. The survival inference is attached to Lee et al. (2018), not Haferlach et al. (LLM, conf=0.88)
Experimental — accuracy not yet measured
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Self-citation
- Authors
- Haferlach, T., Nagata, Y., Grossmann, V, Okuno, Y., Bacher, U., Nagae, G., Schnittger, S., Sanada, M., Kon, A., Alpermann, T., Yoshida, K., Roller, A., Nadarajah, N., Shiraishi, Y., Shiozawa, Y., Chiba, K., Tanaka, H., Koeffler, H. P., Klein, H.-U., Dugas, M., Aburatani, H., Kohlmann, A., Miyano, S., Haferlach, C., Kern, W., & Ogawa, S.
- Affiliations
- Munich Leukemia Laboratory (Germany) (DE)
- Kyoto University (JP)
- The University of Tokyo (JP)
- Research Center for Advanced Science and Technology, The University of Tokyo (JP)
- Institute of Medical Science, The University of Tokyo (JP)
- Cedars-Sinai Medical Center (US)
- University of Münster (DE)
- Corresponding author
- Haferlach, T
- Ogawa, S
- ORCID
- Venue
- Leukemia
- Published
- 2013-11-13
- Volume
- 28
- Issue
- 2
- Pages
- 241-247
- ISSN
- 0887-6924 (ISSN-L)
- 1476-5551
- PMC
- PMC3918868
- OpenAlex
- W2026134786
- Cited by
- 1,532
- References
- 32
- Citations by year
- 2026: 56 · 2025: 85 · 2024: 102 · 2023: 132 · 2022: 133 · 2021: 177 · 2020: 167 · 2019: 134 · 2018: 117 · 2017: 136 · 2016: 126 · 2015: 105 · 2014: 56 · 2013: 3 · 2012: 2
- FWCI
- 69.37
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc-sa
- www.springer.com/tdm (unspecified)
- Locations
- Leukemia (publishedVersion, cc-by-nc-sa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- National University of Singapore (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-sa)
- Funders
- U.S. Public Health Service (08C46598A)
- Japan Society for the Promotion of Science (24390242, 24659458, 21790907, 25670446, 24221011, 23249052)
- Topics
- Health Sciences › Medicine › Hematology › Acute Myeloid Leukemia Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- myelodysplastic syndrome, somatic mutations, prognostic model, risk stratification, TET2, SF3B1, ASXL1, SRSF2, DNMT3A, RUNX1, PRPF8, survival
- MeSH terms
- Adult, Aged, Aged, 80 and over, Female, Gene Frequency, Genetic Markers, Humans, Male, Middle Aged, Mutation, Myelodysplastic Syndromes, Prognosis, Proportional Hazards Models, Polymorphism, Single Nucleotide, Young Adult, Genetic Association Studies, High-Throughput Nucleotide Sequencing, Mutation Rate
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