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

In the paper

“shRNA sequence for p53 knockdown has been previously cloned into the lentiviral vector pRRLsin-PGK-eGFP-WPRE and validated87.”

What the sources say

• Partly supported

  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)

  cites [87] Mahfoudhi, E. et al. P53 activation inhibits all types of hematopoietic progenitors and all stages of megakaryopoiesis. Oncotarget 7, 31980–31992 (2016). sourceExperimental — accuracy not yet measured

In the paper

“Furthermore, deletion of Trp53 combined with JAK2 V617F mutation leads to highly penetrant myeloid leukemia in mice11,14.”

What the sources say

• Supported

  In “Loss of Tp53 Cooperates with JAK2V617F to Promote AML” (page not supplied), the authors report transplanting JAK2V617F-expressing, Tp53-null mouse bone marrow into recipients; all recipients developed lethal disease within 110 days. The same section identifies the disease as AML, supporting the claim of highly penetrant myeloid leukemia in this mouse model. (LLM, conf=0.93)

  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
• ?Not checked — no full text of the sourcecites [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

In the paper

“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.”

What the sources say

• Supported

  The citation follows the clause describing erythroleukemia as rare, associated with adverse outcomes and TP53 mutation—not the preceding finding about HSPC clusters. Section 2, “Morphologic and clinical features” (page unavailable), describes acute erythroleukemia as 1% of de novo AML and reports a dismal prognosis for the rarer pure erythroid form. Section 4.2.2, “TP53” (page unavailable), reports frequent TP53 mutations or abnormalities in erythroleukemia. (LLM, conf=0.92)

  cites [43] Boddu, P. et al. Erythroleukemia-historical perspectives and recent advances in diagnosis and management. Blood Rev. 32, 96–105 (2018). source
• Partly supported

  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)

  cites [44] Iacobucci, I. et al. Genomic subtyping and therapeutic targeting of acute erythroleukemia. Nat. Genet. 51, 694–704 (2019). sourceExperimental — accuracy not yet measured

In the paper

“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).”

What the sources say

• Partly supported

  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)

  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). sourceExperimental — accuracy not yet measured

In the paper

“p53 targets positively regulated from ref. 77 were used to compute a TP53-target gene score”

What the sources say

• Supported

  The Introduction (page not provided) says the survey compiles a list of p53 target genes. The section surveying 16 high-throughput data sets distinguishes genes activated by p53 from those repressed by p53 and identifies a set of p53-activated targets. This supports citing the paper as the source of a positively regulated target-gene set; the score calculation is the citing authors’ own method. (LLM, conf=0.92)

  cites [77] Fischer, M. Census and evaluation of p53 target genes. Oncogene 36, 3943–3956 (2017). source

In the paper

“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.”

What the sources say

• Supported

  The “Generation of transgenic mice” section identifies founder line #42-056 and says it is referred to as HSC-SCL-Cre-ERT. The “Mice” section describes how the Cre-ERT transgenic mice were made, supporting the citation as a prior description of the line. (LLM, conf=0.91)

  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

In the paper

“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.”

What the sources say

• ?Could not verify

  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)

  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). sourceExperimental — accuracy not yet measured

In the paper

“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.”

What the sources say

• Partly supported

  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)

  cites [82] Barile, M. et al. Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. Genome Biol. 22, 197 (2021). sourceExperimental — accuracy not yet measured

In the paper

“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”

What the sources say

• Supported

  Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  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
• ?Not checked — no full text of the sourcecites [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

In the paper

“Because TP53 is the most commonly mutated gene in human cancer3,52”

What the sources say

• Supported

  In “The diversity of TP53 mutational events produces distinct functional consequences” (page not available), the paper says approximately half of all cancers harbor a TP53 mutation and describes TP53 alteration as “the most frequent event in human cancer.” Together, these support the citing sentence’s characterization of TP53 as the most commonly mutated gene. (LLM, conf=0.88)

  cites [3] Kastenhuber, E. R. & Lowe, S. W. Putting p53 in context. Cell 170, 1062–1078 (2017). source
• Partly supported

  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)

  cites [52] The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020). sourceExperimental — accuracy not yet measured

In the paper

“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.”

What the sources say

• ?Could not verify

  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)

  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). sourceExperimental — accuracy not yet measured

In the paper

“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.”

What the sources say

• Supported

  The “Inflammation-adapted mutant HSCs” section reports evidence that CHIP-mutant HSPCs may adapt to sustained inflammatory cues. It also states that mutations making HSCs insensitive to inflammatory effects can confer a relative fitness advantage in an inflammatory environment. (LLM, conf=0.94)

  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
• Supported

  The Discussion reports that Dnmt3a-loss-of-function HSCs resist stress-induced apoptosis and differentiation more than wild-type HSCs, conferring a selection advantage under inflammatory conditions. Its summary also states that chronic IFNγ signaling drives expansion of these clones in a mouse model, supporting the claim that mutations can alter inflammatory responses and confer HSC fitness advantages. (LLM, conf=0.94)

  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
• ?Not checked — no full text of the sourcecites [49] Avagyan, S. et al. Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis. Science 374, 768–772 (2021). source

In the paper

“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).”

What the sources say

• Supported

  The Results section on ultra-deep NGS reports TP53 mutations in 41 of 254 treated chronic-phase MPN patients (16.1%). The Results section on leukemic transformation reports AML in 3 of 50 patients with TP53 mutations, with TP53-mutated AML confirmed in one; this supports the claim that transformation to TP53-mutated AML did not occur in most observed cases. The finding is bounded by the study cohort and follow-up. (LLM, conf=0.92)

  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

In the paper

“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.”

What the sources say

• Supported

  Section 2.1 describes the generation of Vav-iCre transgenic mice and says one Vav-iCre line was selected for further analysis. This supports the citation’s use to identify a previously described Vav-iCre mouse line. (LLM, conf=0.88)

  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

In the paper

“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.”

What the sources say

• Supported

  The citation attached to this source supports the broad claim that inflammation regulates HSC function and affects HSC fate. The Introduction describes HSCs integrating inflammatory cues and says inflammation impacts their function; the Concluding remarks describe the varied functional effects of inflammatory challenges. The more specific DNA-damage and depletion clause carries a different citation. (LLM, conf=0.92)

  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
• ?Not checked — no full text of the sourcecites [41] Walter, D. et al. Exit from dormancy provokes DNA-damage-induced attrition in haematopoietic stem cells. Nature 520, 549–552 (2015). source

In the paper

“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),”

What the sources say

• ?Could not verify

  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)

  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). sourceExperimental — accuracy not yet measured
• ?Could not verify

  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)

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

In the paper

“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).”

In the paper

“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).”

In the paper

“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.”

What the sources say

• ?Not checked — no full text of the sourcecites [21] Ledergor, G. et al. Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma. Nat. Med. 24, 1867–1876 (2018). source

In the paper

“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.”

In the paper

“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).”

In the paper

“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).”

In the paper

“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%.”

In the paper

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

In the paper

“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).”

In the paper

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

In the paper

“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).”

In the paper

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

In the paper

“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).”

In the paper

“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).”

In the paper

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

In the paper

“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).”

In the paper

“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).”

In the paper

“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).”

In the paper

“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).”

In the paper

“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.”

In the paper

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

In the paper

“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.”

What the sources say

• ?Not checked — no full text of the sourcecites [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

In the paper

“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).”

In the paper

“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).”

In the paper

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

In the paper

“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).”

In the paper

“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.”

In the paper

“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.”

In the paper

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

In the paper

“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).”

In the paper

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

In the paper

“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).”

In the paper

“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).”

In the paper

“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%).”

In the paper

“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).”

What the sources say

• ?Not checked — no full text of the sourcecites [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
• ?Not checked — no full text of the sourcecites [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
• ?Not checked — no full text of the sourcecites [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

In the paper

“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.”

In the paper

“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).”

In the paper

“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.”

What the sources say

• ?Not checked — no full text of the sourcecites [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

In the paper

“A minimum of ten reads was required for variant calling.”

In the paper

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

In the paper

“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%).”

In the paper

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

In the paper

“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).”

In the paper

“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.”

In the paper

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

In the paper

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

In the paper

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

In the paper

“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.”

In the paper

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

What the sources say

• ?Not checked — no full text of the sourcecites [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

In the paper

“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).”

In the paper

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

In the paper

“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.”

In the paper

“Notably, our data do not distinguish whether this lineage-switch is primarily an instructive versus permissive effect of TP53-mutation46.”

What the sources say

• ?Not checked — no full text of the sourcecites [46] Enver, T. & Jacobsen, S. E. Developmental biology: instructions writ in blood. Nature 461, 183–184 (2009). source

In the paper

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