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Cited by 158Acute Myeloid Leukemia ResearchCancer Genomics and DiagnosticsSingle-cell and spatial transcriptomics

Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution

Open access
Rodriguez-Meira, Alba, Norfo, Ruggiero, Wen, Sean, Chédeville, Agathe L., Rahman, Haseeb, O’Sullivan, Jennifer, Wang, Guanlin, Louka, Eleni +26 more·2023·Nature Genetics
DOI 10.1038/s41588-023-01480-1PMC PMC10484789
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Abstract

Understanding the genetic and nongenetic determinants of tumor protein 53 ( TP53 ) - mutation-driven clonal evolution and subsequent transformation is a crucial step toward the design of rational therapeutic strategies. Here we carry out allelic resolution single-cell multi-omic analysis of hematopoietic stem/progenitor cells (HSPCs) from patients with a myeloproliferative neoplasm who transform to TP53- mutant secondary acute myeloid leukemia (sAML). All patients showed dominant TP53 ‘multihit’ HSPC clones at transformation, with a leukemia stem cell transcriptional signature strongly predictive of adverse outcomes in independent cohorts, across both TP53- mutant and wild-type (WT) AML. Through analysis of serial samples, antecedent TP53 -heterozygous clones and in vivo perturbations, we demonstrate a hitherto unrecognized effect of chronic inflammation, which suppressed TP53 WT HSPCs while enhancing the fitness advantage of TP53- mutant cells and promoted genetic evolution. Our findings will facilitate the development of risk-stratification, early detection and treatment strategies for TP53 -mutant leukemia, and are of broad relevance to other cancer types.

AI snapshot

Written from the paper’s full text.

TL;DR

In TP53-mutant secondary AML arising from myeloproliferative neoplasms, allelic-resolution single-cell multi-omics identifies dominant TP53 multihit HSPC clones with complex copy-number alterations and a leukemia stem cell transcriptional signature that predicts adverse AML outcomes. Chronic inflammation suppresses TP53-WT pre-LSCs while enhancing the fitness and genetic evolution of TP53-mutant cells.

Key findings

  • Across 33 TP53-sAML patients, TP53-sAML showed complex genetic heterogeneity: multiple TP53 mutations in 11/33 patients, high VAF >50% in 82% (18/22) of single-TP53-mutation cases, CNAs in all analyzed patients, complex karyotype in 87% (20/23), and TP53 locus deletion/copy-neutral LOH in 43% (10/23).
  • TARGET-seq of 17,517 Lin−CD34+ HSPCs from 14 TP53-sAML patients, 9 healthy donors, and 8 MF patients showed dominant TP53 multihit clones in all cases, with four clonal-evolution patterns; TP53 multihit clones were enriched in progenitors and nearly all carried at least one clonally dominant CNA (only 3.4 ± 1.2% TP53-mutant cells lacked CNA evidence).
  • A 44-gene p53LSC signature derived from single-cell transcriptomes predicted poor survival in independent BeatAML and TCGA cohorts irrespective of TP53 mutational status; TP53-mutant AML also showed erythroid-biased transcription with increased GATA1 and reduced CEBPA/GATA1 ratio.
  • In serial CP-MPN/pre-TP53-sAML samples, TP53-heterozygous HSPCs from pre-TP53-sAML (n = 296) versus CP TP53-MPN (n = 273) showed inflammatory pathway changes; in mouse chimeras, poly(I:C) or LPS promoted Trp53-mutant myeloid/HSC/LSK expansion, reduced WT competitors, and increased karyotypic abnormalities in Trp53-mutant LSKs.

Methods

  • Allelic-resolution TARGET-seq was used for simultaneous single-cell genotyping, whole-transcriptome profiling, and immunophenotypic index sorting of Lin−CD34+ HSPCs, alongside bulk targeted NGS and SNP arrays; samples included 33 TP53-sAML patients, 14 TP53-sAML patients for single-cell analysis, 9 age-matched HDs, 8 MF patients, and CP-MPN/pre-TP53-sAML cohorts.
  • Functional validation used patient-derived xenografts, LTC-IC and short-term cultures, TP53 knockdown in JAK2V617F MPN CD34+ cells, and mouse bone marrow chimeras with Vav-iCre Trp53R172H/+ or SCL-CreERT Trp53R172H/+ cells treated with poly(I:C) or LPS.
  • Computational analysis included SCITE clonal hierarchy reconstruction, inferCNV CNA inference, Monocle3/scVelo trajectory analysis, GSEA, differential expression, and lasso Cox survival modeling in BeatAML and TCGA bulk expression cohorts.

Limitations

  • Stated by the authors: because CNAs were universally present and inextricably linked with TP53 multihit status, the study cannot disentangle the impact of TP53 multihit mutation versus patient-specific CNAs.
  • Stated by the authors: the data do not distinguish whether the erythroid lineage switch is primarily an instructive versus permissive effect of TP53 mutation, and further studies are required to characterize the key inflammatory mediators and molecular mechanisms, which are unlikely to be restricted to a single axis.
  • Evident from the text: some functional and validation experiments rely on small numbers, including PDX models (n = 1 for IF0131; n = 3 for GR001), pre-LSC functional assays from 3 TP53-sAML patients, and CP/pre-TP53-sAML TARGET-seq cohorts of 4–5 patients per group.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1038/s41588-023-01480-1

Cites

91 of 91 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

30 of 47 cited sources checked · 15 supported · 0 flagged · accuracy not yet measured

  • Findingown data

    HSPCs WT for all mutations analyzed were present in 10 of 14 TP53-sAML patients.

    “HSPCs WT for all mutations analyzed were present in 10 of 14 patients (Extended Data Fig. 2b–o), providing a valuable population of cells for intrapatient comparison with mutation-positive cells17.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [17] Giustacchini, A. et al. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia. Nat. Med. 23, 692–702 (2017). source

      The supplied passages are an IRIS repository page, with no results section or page number from the paper. Searches for the 10-of-14 wild-type HSPC finding and TP53-sAML returned only repository text, so our indexed copy does not establish the claim. (LLM, conf=0.75)

      Experimental — accuracy not yet measured
  • Findingcitation

    Similar findings were observed in TP53 knock-out or mutant isogenic MOLM13 cell lines.

    “Similar findings were observed in TP53 knock-out or mutant isogenic MOLM13 cell lines (Extended Data Fig. 5m)28.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [28] Boettcher, S. et al. A dominant-negative effect drives selection of TP53 missense mutations in myeloid malignancies. Science 365, 599–604 (2019). source
  • Premisecitation

    Bromodomain inhibitors combined with JAK2 inhibition markedly reduce serum levels of inflammatory cytokines.

    “as reported for bromodomain inhibitors, which, when combined with JAK2 inhibition, markedly reduce the serum levels of inflammatory cytokines51.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [51] Kleppe, M. et al. Dual targeting of oncogenic activation and inflammatory signaling increases therapeutic efficacy in myeloproliferative neoplasms. Cancer Cell 33, 29–43 (2018). source
  • Premisecitation

    Loss of the Trp53-WT allele confers an additional fitness advantage to Trp53-mutant HSPC following DNA damage.

    “loss of the Trp53-WT allele confers an additional fitness advantage to Trp53-mutant HSPC following DNA damage as previously described28”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [28] Boettcher, S. et al. A dominant-negative effect drives selection of TP53 missense mutations in myeloid malignancies. Science 365, 599–604 (2019). source
  • Findingown data

    Treatment of chimeric mice with LPS led to a similar increase in the number of Trp53-mutant PB myeloid cells and LSKs.

    “Treatment of chimeric mice with LPS (Fig. 5a), which induces an inflammatory response mediated through the release of IL1β and IL6 (ref. 37), among others, led to a similar increase in the number of Trp53-mutant PB myeloid cells and LSKs (Fig. 5f,g).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [37] Ngkelo, A., Meja, K., Yeadon, M., Adcock, I. & Kirkham, P. A. LPS induced inflammatory responses in human peripheral blood mononuclear cells is mediated through NOX4 and Giα dependent PI-3kinase signalling. J. Inflamm. 9, 1 (2012). source

      The citation is attached to the explanation that LPS induces inflammation through IL-1β and IL-6 release, not to the citing authors’ finding about Trp53-mutant cells. The Results and Discussion report LPS-induced IL-6 release from human PBMCs, but not IL-1β release; the Introduction says only that LPS mimics some effects of IL-1β. No page numbers are available in our copy. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim. 33
  • May combine two claims. 49

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    The shRNA sequence for p53 knockdown has been previously cloned into the lentiviral vector pRRLsin-PGK-eGFP-WPRE and validated.

    “shRNA sequence for p53 knockdown has been previously cloned into the lentiviral vector pRRLsin-PGK-eGFP-WPRE and validated87.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [87] Mahfoudhi, E. et al. P53 activation inhibits all types of hematopoietic progenitors and all stages of megakaryopoiesis. Oncotarget 7, 31980–31992 (2016). source

      The Materials and Methods section (Lentivirus production; page unavailable) lists p53-targeting shRNA sequences in GFP-encoding lentiviruses. The Results section (Effects of p53 stabilization on late stages of megakaryocyte differentiation; page unavailable) shows that two shRNAs reduced p53 RNA and protein, supporting their knockdown activity. Neither passage identifies the vector as pRRLsin-PGK-eGFP-WPRE or states that the sequences were cloned into it. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Deletion of Trp53 combined with JAK2 V617F mutation leads to highly penetrant myeloid leukemia in mice.

    “Furthermore, deletion of Trp53 combined with JAK2 V617F mutation leads to highly penetrant myeloid leukemia in mice11,14.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [11] Rampal, R. et al. Genomic and functional analysis of leukemic transformation of myeloproliferative neoplasms. Proc. Natl Acad. Sci. USA 111, E5401–E5410 (2014). source
    • cites [14] Tsuruta-Kishino, T. et al. Loss of p53 induces leukemic transformation in a murine model of Jak2 V617F-driven polycythemia vera. Oncogene 36, 3300–3311 (2017). source

  • May combine two claims.

    Findingown data

    Three distinct clusters of HSPCs were identified in TP53-sAML, including one characterized by overexpression of erythroid genes.

    “Three distinct clusters of HSPCs were identified in TP53-sAML, including one characterized by overexpression of erythroid genes, of particular note as erythroleukemia is a rare entity, associated with adverse outcomes and TP53 mutation43,44.”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [43] Boddu, P. et al. Erythroleukemia-historical perspectives and recent advances in diagnosis and management. Blood Rev. 32, 96–105 (2018). source
    • cites [44] Iacobucci, I. et al. Genomic subtyping and therapeutic targeting of acute erythroleukemia. Nat. Genet. 51, 694–704 (2019). source

      The Results sections on TP53 alterations and genomic determinants of outcome link acute erythroleukemia to TP53 mutations and poor prognosis. Our copy does not report three HSPC clusters in TP53-sAML or establish that erythroleukemia is rare. In the citing sentence, the cluster finding appears to be the citing authors’ own result; the citations follow the background statement about erythroleukemia. (LLM, conf=0.85)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Interpretationown data

    The data are compatible with a fitness advantage of monosomy 7 cells, a recurrent event in TP53-sAML, driven by activation of signaling pathways that may relate to deletion of chromosome 7 genes such as EZH2.

    “Together, these data are compatible with a fitness advantage of monosomy 7 cells, a recurrent event in TP53-sAML (Extended Data Fig. 1b,c), driven by activation of signaling pathways that may relate to deletion of chromosome 7 genes such as EZH2 (ref. 20).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [20] Booth, C. A. G. et al. Ezh2 and Runx1 mutations collaborate to initiate lympho-myeloid leukemia in early thymic progenitors. Cancer Cell 33, 274–291 (2018). source

      The Discussion (page unavailable) reports that Ezh2 loss increased expression of oncogenic Flt3-ITD signaling in a mouse model of early thymic progenitor leukemia, supporting the proposed link between EZH2 loss and signaling. It does not establish that chromosome 7 deletion activates signaling or gives monosomy 7 cells a fitness advantage in TP53-sAML; the paper cautions that its findings cannot be extrapolated to other contexts without validation. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    p53 target genes positively regulated are as defined in ref. 77.

    “p53 targets positively regulated from ref. 77 were used to compute a TP53-target gene score”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [77] Fischer, M. Census and evaluation of p53 target genes. Oncogene 36, 3943–3956 (2017). source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The Tg(Tal1-cre/ERT)42-056Jrg mouse line has been previously described.

    “Trp53tm2Tyj (ref. 88), Commd10Tg(Vav1-icre)A2Kio (ref. 89; Jackson Laboratory, 008610) and Tg(Tal1-cre/ERT)42-056Jrg (ref. 90) have been previously described.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [90] Göthert, J. R. et al. In vivo fate-tracing studies using the Scl stem cell enhancer: embryonic hematopoietic stem cells significantly contribute to adult hematopoiesis. Blood 105, 2724–2732 (2005). source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    In total, 100 erythroid genes and 135 myeloid genes were identified from the single-cell dataset.

    “In total, 100 erythroid genes and 135 myeloid genes were identified from this single-cell dataset (Supplementary Table 3) and were used to compute the scores presented in Extended Data Fig. 5g–j.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [24] Granja, J. M. et al. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat. Biotechnol. 37, 1458–1465 (2019). source

      The paper’s hematopoiesis discussion (page unavailable) identifies erythroid and myeloid lineages and examples of lineage-associated genes. Searches for “100 erythroid,” “135 myeloid,” and the claimed gene counts did not find a passage reporting those totals or the gene sets used for the cited scores. (LLM, conf=0.72)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Ninety-six multiple rate kinetics (MURK) genes possess coordinated step-change in transcription and hence violate the assumptions behind scVelo.

    “Ninety-six multiple rate kinetics (MURK) genes previously shown to possess coordinated step-change in transcription and hence violate the assumptions behind scVelo were removed82.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [82] Barile, M. et al. Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. Genome Biol. 22, 197 (2021). source

      The Results section, “Analysis of unspliced reads reveals complex expression kinetics,” links MURK genes’ increased transcription rates to incorrect scVelo velocity predictions, and the Discussion says removing them can improve predictions. But the Methods section, “MURK gene identification,” reports 89 mouse genes and 97 human genes, not 96; the Discussion also notes that MURK genes can occur where scVelo predictions are correct. (LLM, conf=0.90)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    TP53-heterozygous HSPC from pre-TP53-sAML patients showed downregulation of TNFα- and TGFβ-associated gene signatures, with upregulated expression of oxidative phosphorylation, DNA repair and interferon (IFN) response genes, without changes in IFN receptor expression levels or concurrent IFN treatment.

    “TP53-heterozygous HSPC from pre-TP53-sAML patients showed downregulation of TNFα- and TGFβ-associated gene signatures, both of which are known to be associated with HSC attrition32,33, with upregulated expression of oxidative phosphorylation, DNA repair and interferon (IFN) response genes (Supplementary Table 5 and Fig. 4c–e), without changes in IFN receptor expression levels or concurrent IFN”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [32] Bryder, D. et al. Self-renewal of multipotent long-term repopulating hematopoietic stem cells is negatively regulated by Fas and tumor necrosis factor receptor activation. J. Exp. Med. 194, 941–952 (2001). source
    • cites [33] Jacobsen, F. W., Stokke, T. & Jacobsen, S. E. Transforming growth factor-beta potently inhibits the viability-promoting activity of stem cell factor and other cytokines and induces apoptosis of primitive murine hematopoietic progenitor cells. Blood 86, 2957–2966 (1995). source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    TP53 is the most commonly mutated gene in human cancer.

    “Because TP53 is the most commonly mutated gene in human cancer3,52”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [3] Kastenhuber, E. R. & Lowe, S. W. Putting p53 in context. Cell 170, 1062–1078 (2017). source
    • cites [52] The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020). source

      The ‘Panorama of driver mutations in cancer’ section reports TP53 driver mutations in 954 tumours, supporting that TP53 is commonly mutated in the studied cohort. Our copy does not establish that it is the single most commonly mutated gene across human cancers. (LLM, conf=0.83)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingcitation

    TP53-sAML differed from de novo AML with an enrichment into HSC and early erythroid populations, whereas de novo AML was enriched in myeloid progenitors.

    “TP53-sAML differed from de novo AML with an enrichment into HSC and early erythroid populations, whereas de novo AML was enriched in myeloid progenitors (Fig. 2c,d)25.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [25] Van Galen, P. et al. Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity. Cell 176, 1265–1281 (2019). source

      The Results section on AML cellular hierarchies links clusters enriched for TP53 mutations to differing cell compositions, but does not compare TP53-associated secondary AML with de novo AML. Searches for secondary AML, early erythroid populations, and de novo AML with myeloid progenitors found no passage establishing the claimed contrast. The indexed passages provide no page numbers. (LLM, conf=0.73)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    There is emerging evidence that clonal HSCs can become inflammation-adapted and by altering the response to inflammatory challenges, mutations can thus confer a fitness advantage to HSCs.

    “There is emerging evidence that clonal HSCs can become inflammation-adapted47–49 and by altering the response to inflammatory challenges, mutations can thus confer a fitness advantage to HSCs.”
    Quote in the paperSubstantial claim2 of 3 sources checked
    • cites [47] Caiado, F., Pietras, E. M. & Manz, M. G. Inflammation as a regulator of hematopoietic stem cell function in disease, aging, and clonal selection. J. Exp. Med. 218, e20201541 (2021). source
    • cites [48] Hormaechea-Agulla, D. et al. Chronic infection drives Dnmt3a-loss-of-function clonal hematopoiesis via IFNγ signaling. Cell Stem Cell 28, 1428–1442 (2021). source
    • cites [49] Avagyan, S. et al. Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis. Science 374, 768–772 (2021). source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    TP53-mutant subclones are present in 16% of chronic phase MPN (CP-MPN), and in most cases this does not herald the development of TP53-sAML.

    “Notwithstanding the established role of TP53 mutation in MPN transformation, TP53-mutant subclones are also present in 16% of chronic phase MPN (CP-MPN), and in most cases, this does not herald the development of TP53-sAML (ref. 15).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [15] Kubesova, B. et al. Low-burden TP53 mutations in chronic phase of myeloproliferative neoplasms: association with age, hydroxyurea administration, disease type and JAK2 mutational status. Leukemia 32, 450–461 (2018). source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The Commd10Tg(Vav1-icre)A2Kio mouse line has been previously described.

    “Trp53tm2Tyj (ref. 88), Commd10Tg(Vav1-icre)A2Kio (ref. 89; Jackson Laboratory, 008610) and Tg(Tal1-cre/ERT)42-056Jrg (ref. 90) have been previously described.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [89] De Boer, J. et al. Transgenic mice with hematopoietic and lymphoid specific expression of Cre. Eur. J. Immunol. 33, 314–325 (2003). source

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    Inflammation is a cardinal regulator of HSC function with many effects on HSC fate and function, including proliferation-induced DNA-damage and depletion of HSCs.

    “Inflammation is a cardinal regulator of HSC function with many effects on HSC fate and function47, including proliferation-induced DNA-damage and depletion of HSCs41.”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [47] Caiado, F., Pietras, E. M. & Manz, M. G. Inflammation as a regulator of hematopoietic stem cell function in disease, aging, and clonal selection. J. Exp. Med. 218, e20201541 (2021). source
    • cites [41] Walter, D. et al. Exit from dormancy provokes DNA-damage-induced attrition in haematopoietic stem cells. Nature 520, 549–552 (2015). source

  • May combine two claims.

    Findingown data

    TP53 multihit HSPCs clustered separately from TP53-WT pre-LSCs in two distinct populations with enrichment of LSC and erythroid-associated transcription, respectively, and a differentiation trajectory toward the erythroid-biased population.

    “Integration of single-cell transcriptomes and diffusion map analysis of HSPCs from TP53-sAML patients showed that TP53 multihit HSPCs clustered separately from TP53-WT pre-LSCs in two distinct populations with enrichment of LSC and erythroid-associated transcription, respectively (Fig. 2a and Supplementary Table 3), and a differentiation trajectory toward the erythroid-biased population (Fig. 2b),”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [22] Mesa, R. A. et al. Leukemic transformation in myelofibrosis with myeloid metaplasia: a single-institution experience with 91 cases. Blood 105, 973–977 (2005). source

      The Methods and karyotypic-changes sections describe bone marrow histology and cytogenetic analysis in patients with myelofibrosis; no page numbers are available in our copy. Searches for TP53 multihit HSPCs, single-cell transcriptomes, diffusion maps, and an erythroid-biased differentiation trajectory found no passage addressing the claim. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
    • cites [23] Passamonti, F. et al. Leukemic transformation of polycythemia vera: a single center study of 23 patients. Cancer 104, 1032–1036 (2005). source

      The Cytogenetic Findings and Discussion passages (page numbers unavailable) report karyotypes and clinical outcomes in patients with leukemia following polycythemia vera. Searches for TP53 multihit HSPCs, single-cell transcriptomes, diffusion maps, and an erythroid-biased differentiation trajectory found no passage addressing the claimed populations or trajectory. (LLM, conf=0.76)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    A similar enrichment was observed for TP53 multihit cells when mapped on a Lin-CD34+ MF cellular hierarchy, with erythroid-biased populations being highly enriched in immunophenotypically defined MEPs.

    “A similar enrichment was observed for TP53 multihit cells when mapped on a Lin-CD34+ MF cellular hierarchy (Extended Data Fig. 5d,e), with erythroid-biased populations being highly enriched in immunophenotypically defined MEPs (Extended Data Fig. 5f).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    TP53 multihit LSCs showed enrichment of cell cycle, inflammatory, signaling pathways and LSC-associated transcription, whereas TP53 multihit erythroid cells were depleted of the latter.

    “TP53 multihit LSCs showed enrichment of cell cycle, inflammatory, signaling pathways and LSC-associated transcription, whereas TP53 multihit erythroid cells were depleted of the latter (Extended Data Fig. 4d).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Force-directed graph analysis revealed separate clustering of TP53-mutant HSPC in comparison with healthy and MF donor cells, with a high degree of interpatient heterogeneity.

    “Force-directed graph analysis revealed separate clustering of TP53-mutant HSPC in comparison with healthy and MF donor cells, with a high degree of interpatient heterogeneity (Extended Data Fig. 4a) as observed in other hematopoietic malignancies21.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [21] Ledergor, G. et al. Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma. Nat. Med. 24, 1867–1876 (2018). source

  • May combine two claims.

    Findingown data

    TP53 knock-down led to increased erythroid (CD71+CD235a+) and decreased myeloid (CD14+/CD15+/CD11b+) differentiation in vitro.

    “TP53 knock-down led to increased erythroid (CD71+CD235a+) and decreased myeloid (CD14+/CD15+/CD11b+) differentiation in vitro (Fig. 2i), and consequently decreased CEBPA/GATA1 expression ratio (Fig. 2j), suggesting that p53 may directly contribute to the aberrant myelo-erythroid differentiation observed.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    HSPC immunophenotype was similar for pre-TP53-sAML and CP TP53-MPN patients, and clearly distinct from the TP53-sAML stage.

    “HSPC immunophenotype was similar for pre-TP53-sAML and CP TP53-MPN patients (Extended Data Fig. 9a–c), and clearly distinct from the TP53-sAML stage (Extended Data Fig. 9d).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Poly(I:C) treatment promoted the selection of myeloid Trp53-mutant cells in the PB, with a myeloid bias induced by the inflammatory stimulus in PB leukocytes specifically associated with Trp53-mutation.

    “Similar to the Vav-iCre model, poly(I:C) treatment promoted the selection of myeloid Trp53-mutant cells in the PB (Extended Data Fig. 10k), with a myeloid bias induced by the inflammatory stimulus in PB leukocytes specifically associated with Trp53-mutation (Fig. 5i,j and Extended Data Fig. 10l).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Multiple TP53 mutations were present in one-third (n = 11) of TP53-sAML patients, including 2 patients with 3 TP53 mutations.

    “Multiple TP53 mutations were present in one-third (n = 11) of patients, including 2 patients with 3 TP53 mutations; 82% (18 of 22) of patients with a single TP53 mutation showed a high variant allelic frequency (VAF) of >50%.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    A second 'TP53-sAML LSC' cluster allowed identification of a p53LSC-signature, which can predict outcomes in AML independently of TP53 status.

    “A second ‘TP53-sAML LSC’ cluster allowed us to identify a p53LSC-signature, which can predict outcomes in AML independently of TP53 status.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Analysis of the BeatAML cohort revealed increased GATA1 and reduced CEBPA expression in association with TP53 mutation, with consequent reduction in the CEBPA/GATA1 expression ratio.

    “Analysis of the BeatAML cohort revealed increased GATA1 and reduced CEBPA expression in association with TP53 mutation (Extended Data Fig. 5l), with consequent reduction in the CEBPA/GATA1 expression ratio (Fig. 2h).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Compared to TP53-sAML samples, CP TP53-MPN had a lower VAF and number of TP53 mutations.

    “Compared to TP53-sAML samples, CP TP53-MPN had a lower VAF and number of TP53 mutations (Extended Data Fig. 8a–d).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Pre-LSC LTC-IC activity was similar to HDs and increased compared to MF patients, with preserved terminal differentiation capacity and confirmed TP53 WT genotype.

    “Pre-LSC LTC-IC activity was similar to HDs and increased compared to MF patients, with preserved terminal differentiation capacity and confirmed TP53 WT genotype (Fig. 3i and Extended Data Fig. 7d–g).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    In total, 9 and 44 genes were retained from the p53-all-cells and p53-LSC gene sets, respectively.

    “In total, 9 and 44 genes were retained from the p53-all-cells and p53-LSC gene sets, respectively.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In short-term liquid culture, pre-LSCs showed reduced clonogenicity, with retained CD34 expression and decreased proliferation.

    “In short-term liquid culture, pre-LSCs showed reduced clonogenicity, with retained CD34 expression and decreased proliferation (Fig. 3j and Extended Data Fig. 7h–i).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Erythroid scores were increased in TP53 mutant compared to TP53-WT AML, whereas there was no significant difference in myeloid scores.

    “Erythroid scores were increased in TP53 mutant compared to TP53-WT AML, whereas there was no significant difference in myeloid scores (Fig. 2e–f, Extended Data Fig. 5g–j and scores described in Supplementary Table 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    CNAs were present in all TP53-sAML patients analyzed, and 87% (20 of 23) had a complex karyotype (≥3 CNAs).

    “CNAs were present in all patients analyzed, and 87% (20 of 23) had a complex karyotype (≥3 CNAs; Extended Data Fig. 1a–g).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Mice transplanted with CD34+ cells from two TP53-sAML patients developed leukemia in 27-31 weeks with high numbers of human CD34+ myeloid blast cells in the bone marrow, with a progenitor phenotype, TP53 mutations and CNAs similar to the dominant clone from patients' primary cells.

    “Mice developed leukemia in 27–31 weeks with high numbers of human CD34+ myeloid blast cells in the bone marrow (BM; Extended Data Fig. 3b–d), with a progenitor phenotype, TP53 mutations and CNAs similar to the dominant clone from patients’ primary cells (Fig. 1i and Extended Data Fig. 3e–l).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The fitness advantage of Trp53-mutant HSCs and LSKs was exerted both through an increase in the numbers of Trp53R172H/+ HSPCs and a reduction in the numbers of WT competitors.

    “Crucially, the fitness advantage of Trp53-mutant HSCs and LSKs was exerted both through an increase in the numbers of Trp53R172H/+ HSPCs and a reduction in the numbers of WT competitors (Fig. 5d,e and Extended Data Fig. 10f,g).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Sorted CD34+ TP53-multi-hit cells exhibited potential for erythroid differentiation in vivo and in vitro, supporting that this occurs downstream of the LSC population.

    “Sorted CD34+ TP53-multi-hit cells exhibited potential for erythroid differentiation in vivo and in vitro, supporting that this occurs downstream of the LSC population (Extended Data Fig. 5a–c).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Increased GATA1 expression was found in Lin-CD34+ TP53 multihit HSPCs, whereas CEBPA was only expressed at low levels.

    “We next investigated the expression of key transcription factors for erythroid/granulomonocytic commitment and found increased GATA1 expression in Lin-CD34+ TP53 multihit HSPCs, whereas CEBPA was only expressed at low levels (Fig. 2g).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    High p53LSC-signature score was strongly associated with TP53 mutation status, although some TP53-WT patients also showed a high p53LSC score.

    “High p53LSC-signature score (Extended Data Fig. 6a,b) was strongly associated with TP53 mutation status, although some TP53-WT patients also showed a high p53LSC score.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Pre-LSCs were enriched in HSC-associated genes and mapped onto HSC clusters in healthy and MF donor hematopoietic hierarchies.

    “Pre-LSCs were enriched in HSC-associated genes and mapped onto HSC clusters in healthy and MF donor hematopoietic hierarchies (Fig. 3a,b).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Numbers of WT competitor erythroid progenitors were reduced upon poly(I:C) treatment, whereas Trp53-mutation was associated with an increase in erythroid progenitors that was not impacted by inflammation.

    “Numbers of WT competitor erythroid progenitors were reduced upon poly(I:C) treatment as expected38, whereas Trp53-mutation was associated with an increase in erythroid progenitors that was not impacted by inflammation (Fig. 5k and Extended Data Fig. 10n) in line with the erythroid bias detected in patient samples.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [38] Libregts, S. F. et al. Chronic IFN-γ production in mice induces anemia by reducing erythrocyte life span and inhibiting erythropoiesis through an IRF-1/PU.1 axis. Blood 118, 2578–2588 (2011). source

  • May combine two claims.

    Findingown data

    scVelo analysis showed the absence of a transcriptional differentiation trajectory in pre-LSCs, unlike HD HSCs.

    “To explore this hypothesis, we carried out scVelo analysis, which showed the absence of a transcriptional differentiation trajectory in pre-LSCs, unlike HD HSCs (Fig. 3d).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Pre-LSCs showed increased expression of HSC and Wnt β-catenin genes and decreased cell cycle genes as compared to HD and MF cells.

    “Pre-LSCs showed increased expression of HSC and Wnt β-catenin genes and decreased cell cycle genes as compared to HD and MF cells (Fig. 3e–g and Supplementary Table 3).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    A minor homozygous TP53-mutated clone initially present in one CP TP53-MPN patient was undetectable after 4 years.

    “A minor homozygous TP53-mutated clone initially present in one CP TP53-MPN patient was undetectable after 4 years (Extended Data Fig. 9h).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    All TP53 multihit clones harbored at least one highly clonally-dominant CNA, with very few TP53-mutant cells without evidence of a CNA (3.4 ± 1.2%).

    “CNA analysis using single-cell transcriptomes showed that all TP53 multihit clones harbored at least one highly clonally-dominant CNA, with very few TP53-mutant cells without evidence of a CNA (3.4 ± 1.2%) and an additional 5 of 14 (36%) patients also showing cytogenetically-distinct subclones (Fig. 1f,g and Extended Data Fig. 2p,q).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Analysis of a large AML cohort revealed overexpression of erythroid genes as a more widespread phenomenon in TP53-mutant AML, with disrupted balance of GATA1 and CEBPA expression.

    “Analysis of a large AML cohort also revealed overexpression of erythroid genes as a more widespread phenomenon in TP53-mutant AML, with disrupted balance of GATA1 and CEBPA expression.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    CNAs identified by inferCNV were manually curated by removing those with size <10 kb, merging adjacent CNA calls with identical CNA status into larger CNA intervals and comparing them to SNP-Array bulk CNA calls.

    “CNAs identified by inferCNV were manually curated by removing those with size <10 kb, merging adjacent CNA calls with identical CNA status into larger CNA intervals and comparing them to SNP-Array bulk CNA calls.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Experiments involving the isolation of human HSPCs included single color stained controls and Fluorescence Minus One controls.

    “Experiments involving the isolation of human HSPCs included single color stained controls (CompBeads, BD Biosciences) and Fluorescence Minus One controls (FMOs).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductown data

    TARGET-seq analysis enabled comparison of TP53 multihit HSPC to TP53-WT preleukemic stem cells from the same TP53-sAML patients as well as healthy and MF donors, to derive a specific TP53 multihit signature including known p53-pathway genes.

    “TARGET-seq analysis uniquely enabled the comparison of TP53 multihit HSPC to TP53-WT preleukemic stem cells (‘pre-LSCs’) from the same TP53-sAML patients as well as healthy and MF donors, to derive a specific TP53 multihit signature including known p53-pathway genes (Extended Data Fig. 4b,c).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    A series of stringent filtering steps were applied to reduce the rate of false positive calls in mosaic copy number event calling.

    “A series of stringent filtering steps were applied to reduce the rate of false positive calls.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The dominant leukemic clones in TP53-sAML were invariably characterized by multiple hits affecting TP53 (multihit state), indicating strong selective pressure for complete loss of WT TP53, together with the gain of CNAs and complex cytogenetic evolution, with very few TP53 multihit cells with a normal karyotype.

    “In summary, the dominant leukemic clones in TP53-sAML were invariably characterized by multiple hits affecting TP53 (multihit state), indicating strong selective pressure for complete loss of WT TP53, together with the gain of CNAs and complex cytogenetic evolution, with very few TP53 multihit cells with a normal karyotype (Fig. 1j).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    After QC, 7,123 cells passed QC for batch 1, 5,779 for batch 2 and 6,319 for batch 3 (79.3%, 68.9% and 80.3% of cells processed, respectively).

    “After these QC steps, 7,123 cells passed QC for batch 1, 5,779 for batch 2 and 6,319 for batch 3 (79.3%, 68.9% and 80.3% of cells processed, respectively).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Run quality control for targeted bulk sequencing included %DP_100X >95%, %DP_200X >90%, number of reads per sample, % reads q30 forward and reverse >85%, read quality mean >30, and percentage of mapped reads >75%.

    “Run quality control included %DP_100X (>95%), %DP_200X (>90%), number of reads per sample and % reads q30 forward and reverse (>85%), read quality mean (>30) and percentage of mapped reads (>75%).”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    CEBPA knockout or mutation is reported to cause a myeloid to erythroid lineage switch with increased expression of GATA1, and GATA1 interacts with and inhibits p53.

    “CEBPA knockout or mutation is reported to cause a myeloid to erythroid lineage switch with increased expression of GATA1 (refs. 29,30) and, in addition, GATA1 interacts with and inhibits p53 (ref. 45).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [29] Wagner, K. et al. Absence of the transcription factor CCAAT enhancer binding protein α results in loss of myeloid identity in bcr/abl-induced malignancy. Proc. Natl Acad. Sci. USA 103, 6338–6343 (2006). source
    • cites [30] Bereshchenko, O. et al. Hematopoietic stem cell expansion precedes the generation of committed myeloid leukemia-initiating cells in C/EBPα mutant AML. Cancer Cell 16, 390–400 (2009). source
    • cites [45] Trainor, C. D., Mas, C., Archambault, P., di Lello, P. & Omichinski, J. G. GATA-1 associates with and inhibits p53. Blood 114, 165–173 (2009). source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Quality control for single-cell 3′-biased RNA-sequencing used parameters: number of genes detected >500, percentage of ERCC-derived reads <35%, percentage of mitochondrial reads <0.25%, percentage of unmapped reads <75%, and minimum reads per cell per batch (2,000 batch1, 5,000 batch2, 20,000 batch3).

    “Quality control was performed using the following parameters: number of genes detected >500, percentage of ERCC-derived reads <35%, percentage of mitochondrial reads <0.25% and percentage of unmapped reads <75%. Cells with less than 2,000 reads in batch1, 5,000 reads in batch2 and 20,000 reads in batch3 were further excluded.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    Chronic inflammation promotes the survival and genetic evolution of TP53-mutated cells while suppressing WT hematopoiesis, ultimately promoting the clonal expansion of TP53-mutant HSPCs.

    “Collectively, these results support a model whereby chronic inflammation promotes the survival and genetic evolution of TP53-mutated cells while suppressing WT hematopoiesis, ultimately promoting the clonal expansion of TP53-mutant HSPCs (Fig. 6e).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The Trp53tm2Tyj mouse line has been previously described.

    “Trp53tm2Tyj (ref. 88), Commd10Tg(Vav1-icre)A2Kio (ref. 89; Jackson Laboratory, 008610) and Tg(Tal1-cre/ERT)42-056Jrg (ref. 90) have been previously described.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [88] Olive, K. P. et al. Mutant p53 gain of function in two mouse models of Li-Fraumeni syndrome. Cell 119, 847–860 (2004). source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    A minimum of ten reads was required for variant calling.

    “A minimum of ten reads was required for variant calling.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    All cells were karyotyped, excluding metaphases severely damaged for technical reasons.

    “All cells were karyotyped, excluding metaphases severely damaged for technical reasons.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    If TP53 mutations are bi-allelic, the expected number of WT/HOM and HOM/WT would be higher than HOM/HOM cells considering TARGET-seq expected ADO rates (1-5%).

    “If TP53 mutations are bi-allelic, the expected number of WT/HOM and HOM/WT would be higher than HOM/HOM cells considering TARGET-seq expected ADO rates (1–5%).”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: ADO is unbiased toward HOM or WT.
    • The authors state this as an assumption: ADO events at each TP53 site are independent.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    All pathogenic variants were manually checked using Integrative Genomics Viewer software.

    “All pathogenic variants were manually checked using Integrative Genomics Viewer software.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Primary human samples were analyzed with approvals from the Inserm Institutional Review Board Ethical Committee (project C19-73, agreement 21-794, CODECOH DC-2020-4324) and from the INForMeD Study (REC: 199833, 26 July 2016, University of Oxford).

    “Primary human samples (PB or BM; described in Supplementary Table 1) were analyzed with approvals from the Inserm Institutional Review Board Ethical Committee (project C19-73, agreement 21-794, CODECOH DC-2020-4324) and from the INForMeD Study (REC: 199833, 26 July 2016, University of Oxford).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    Allelic resolution genotyping of leukemic HSPCs revealed a strong selective pressure for gain of TP53 missense mutation, loss of the TP53-WT allele and acquisition of complex CNAs, including cases with parallel genetic evolution during TP53-sAML LSC expansion.

    “Allelic resolution genotyping of leukemic HSPCs revealed a strong selective pressure for gain of TP53 missense mutation, loss of the TP53-WT allele and acquisition of complex CNAs, including cases with parallel genetic evolution during TP53-sAML LSC expansion.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Inflammation leads to the accumulation of HSCs that have acquired DNA damage, promoting genetic evolution that underlies disease progression.

    “leading to the accumulation of HSCs that have acquired DNA damage, thus promoting genetic evolution that underlies disease progression.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Variants with ambiguous or low coverage assignments for a particular cell were excluded from the analysis.

    “Variants with ambiguous or low coverage assignments for a particular cell were excluded from the analysis.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The analysis of the M-FISH hybridized cells was blinded.

    “The analysis of the M-FISH hybridized cells was blinded.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    HSCs that would otherwise undergo inflammation-associated and DNA-damage-induced attrition are rescued by TP53 mutation, ultimately leading to the accumulation of HSCs that have acquired DNA damage, thus promoting genetic evolution that underlies disease progression.

    “We propose that HSCs that would otherwise undergo inflammation-associated and DNA-damage-induced attrition are rescued by TP53 mutation, ultimately leading to the accumulation of HSCs that have acquired DNA damage, thus promoting genetic evolution that underlies disease progression.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The 17-gene LSC17 gene set was retrieved from ref. 31.

    “The 17-gene LSC17 gene set was retrieved from ref. 31.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [31] Ng, S. W. et al. A 17-gene stemness score for rapid determination of risk in acute leukaemia. Nature 540, 433–437 (2016). source

  • May combine two claims.

    Interpretationown data

    Through integration of single-cell multi-omic analysis with in vitro and in vivo functional assays, TP53-WT pre-LSCs are cell-extrinsically suppressed while chronic inflammation promotes the fitness advantage of TP53-mutant cells, ultimately leading to clonal selection.

    “Through the integration of single-cell multi-omic analysis with in vitro and in vivo functional assays, we show that TP53-WT pre-LSCs are cell-extrinsically suppressed while chronic inflammation promotes the fitness advantage of TP53-mutant cells, ultimately leading to clonal selection (Fig. 6e).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The quality of cDNA traces was checked using a high-sensitivity DNA kit in a Bioanalyzer instrument.

    “The quality of cDNA traces was checked using a high-sensitivity DNA kit in a Bioanalyzer instrument (Agilent Technologies).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    Only homozygous alternate genotype calls below the 0.05 cut-off were reported.

    “Only homozygous alternate genotype calls below this 0.05 cut-off were reported in Extended Data Figs. 2b–o and 9e–m; the results of the binomial test are reported for each patient and mutation in Supplementary Table 8.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: ADO is unbiased toward HOM or WT.
    • The authors state this as an assumption: ADO events at each TP53 site are independent.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Our data do not distinguish whether the lineage-switch is primarily an instructive versus permissive effect of TP53-mutation.

    “Notably, our data do not distinguish whether this lineage-switch is primarily an instructive versus permissive effect of TP53-mutation46.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [46] Enver, T. & Jacobsen, S. E. Developmental biology: instructions writ in blood. Nature 461, 183–184 (2009). source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Patients and normal donors provided written informed consent in accordance with the Declaration of Helsinki for sample collection and use in research.

    “Patients and normal donors provided written informed consent in accordance with the Declaration of Helsinki for sample collection and use in research.”
    Quote in the paperNot a substantial claim
70 of 70

  • The authors state this as an assumption.

    Little is known about the additional genetic and nongenetic determinants of clonal evolution following the acquisition of a TP53 mutation.

    “However, little is known about the additional genetic and nongenetic determinants of clonal evolution following the acquisition of a TP53 mutation.”

  • The authors state this as an assumption.

    ADO is unbiased toward HOM or WT.

    “(1) ADO is unbiased toward HOM or WT”

  • The authors state this as an assumption.

    ADO events at each TP53 site are independent.

    “(2) ADO events at each TP53 site are independent.”

  • The authors state this as an assumption.

    All possible mutation trees are equally likely a priori.

    “where all possible mutation trees are equally likely a priori.”

  • The paper relies on this without support.

    The proportional hazards assumption holds for the Cox regression models used to estimate hazard ratios.

    “The Cox proportional hazards regression model implemented by the survival R package (version 3.5–5) was fitted to estimate the hazard ratio associated with each feature.”
5 of 5

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Previously, induction of IFNa in mice have yielded mixed results demonstrating either an upregulation or downregulation of TNFa.

    “Previously, induction of IFNa in mice have yielded mixed results demonstrating either an upregulation 2 or downregulation 53 of TNFa.”

    From Type 1 interferon perturbates clonal competition by reshaping human blood development (2026) · cites this paper as [53]

    The Results section (‘Inflammation promotes TP53-associated clonal dominance’; page unavailable) reports downregulated TNFα-associated gene signatures in human TP53-heterozygous cells, alongside increased interferon-response genes. It specifies that these patients had no concurrent interferon treatment. This does not establish that inducing IFNα in mice downregulated TNFα—the part of the sentence to which this citation is attached. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • TWIST1 has been implicated in mediating the downregulation of TNFa upon type 1 IFN treatment.

    “TWIST1 has been implicated in mediating the downregulation of TNFa upon type 1 IFN treatment 53”

    From Type 1 interferon perturbates clonal competition by reshaping human blood development (2026) · cites this paper as [53]

    The Results section, “Inflammation promotes TP53-associated clonal dominance” (page unavailable), reports reduced TNFα-associated gene signatures alongside increased IFN-response genes in TP53-mutant cells, explicitly without concurrent IFN treatment. Searches for TWIST1 and type I IFN-mediated TNFα downregulation found no passage in our copy linking TWIST1 to that effect. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

Cites

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Related

Authors
Rodriguez-Meira, A., Norfo, R., Wen, S., Chédeville, A. L., Rahman, H., O’Sullivan, J., Wang, G., Louka, E., Kretzschmar, W. W., Paterson, A., Brierley, C., Martin, J.-E., Demeule, C., Bashton, M., Sousos, N., Moralli, D., Subha Meem, L., Carrelha, J., Wu, B., Hamblin, A., Guermouche, H., Pasquier, F., Marzac, C., Girodon, F., Vainchenker, W., Drummond, M., Harrison, C., Chapman, J. R., Plo, I., Jacobsen, S. E. W., Psaila, B., Thongjuea, S., Antony-Debré, I., & Mead, A. J.
Affiliations
  • University of Modena and Reggio Emilia (IT)
  • University of Oxford (GB)
  • Inserm (FR)
  • Karolinska University Hospital (SE)
  • Memorial Sloan Kettering Cancer Center (US)
  • CHU Dijon Bourgogne (FR)
  • Northumbria University (GB)
  • Centre for Human Genetics (GB)
  • Beatson West of Scotland Cancer Centre (GB)
  • Guy's and St Thomas' NHS Foundation Trust (GB)
Corresponding author
Mead, Adam J.
ORCID
Venue
Nature Genetics
Publisher
Springer Science and Business Media LLC
Published
2023-09
Volume
55
Issue
9
Pages
1531-1541
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
DOI
10.1038/s41588-023-01480-1
PMC
PMC10484789
OpenAlex
W4386415929
Cited by
158
References
91
Citations by year
2026: 43 · 2025: 62 · 2024: 44 · 2023: 8 · 2022: 1
FWCI
32.40
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Genetics (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, other-oa)
  • PubMed Central (submittedVersion, cc-by)
  • IRIS UNIMORE (University of Modena and Reggio Emilia) (submittedVersion, cc-by)
Funders
  • Cancer Research UK (C42639/A26988, C5255/A20936)
  • RCUK | Medical Research Council (MC_PC_19049)
  • Wellcome Trust (222800/Z/21/Z)
  • Emergence Canceropole Ile de France, Association pour la Recherche contre le cancer, Siric-Socrate, INCA-PLBIO
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 › Single-cell and spatial transcriptomics
Keywords
TP53 mutation, secondary acute myeloid leukemia, myeloproliferative neoplasms, clonal evolution, chronic inflammation, hematopoietic stem and progenitor cells, leukemia stem cells, tumor suppressor inactivation, risk stratification, single-cell multi-omics
MeSH terms
Multiomics, Alleles, Humans, Inflammation, Leukemia, Neoplasm Proteins, Tumor Suppressor Protein p53

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-28.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-28.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

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