Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Nam, Anna S.; Dusaj, Neville; Izzo, Franco; Murali, Rekha; Myers, Robert M.; Mouhieddine, Tarek H.; Sotélo, Jesús Alfonso López; Benbarche, Salima; Waarts, Michael R.; Gaiti, Federico; Tahri, Sabrin; Levine, Ross L.; Abdel-Wahab, Omar; Godley, Lucy A.; Chaligné, Ronan; Ghobrial, Irène M.; Landau, Dan A.

doi:10.1038/s41588-022-01179-9

Cited by 80 publications

(83 citation statements)

References 180 publications

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“…We emphasize that the limited size of our cohort reduced the power to detect the many small associations between genetics and expression that may occur within tumours, and also means that we were unlikely to observe recurrent events across cancers. Future single cell analyses, rather than the tumour glands used here, are likely to be better powered to reveal DNA–RNA associations 58 . However, we argue that the large effects, which we were generally powered to see, are those most likely to be relevant for tumour biology.…”

Section: Discussionmentioning

confidence: 99%

Phenotypic plasticity and genetic control in colorectal cancer evolution

Househam

Heide

Cresswell

et al. 2022

Nature

103

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Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather ‘plastic’. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour.

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Section: Discussionmentioning

confidence: 99%

Phenotypic plasticity and genetic control in colorectal cancer evolution

Househam

Heide

Cresswell

et al. 2022

Nature

103

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“…These findings contrasted with the more subtle transcriptional impact of CALR - mutations, since mutated and wildtype cells are co-mingled throughout differentiation 20, 39 . We previously demonstrated that the whole transcriptomic data alone could not distinguish mutated versus wildtype cells in early clonal processes such as CALR -mutated MPN 20 (also confirmed in JAK2 -mutated MPN 40, 41 and DNMT3A -mutated clonal hematopoiesis 42 ), necessitating the development of GoT. Given the strong transcriptional impact of IFNa, we focused on deciphering the effects of IFNa on the overall HSC population first, before dissecting the differential impact on mutated versus wildtype cells.…”

Section: Resultsmentioning

confidence: 99%

“…Analysis of the GoT library was carried out as described previously 20 using Ironthrone pipeline V2.1 42 . Amplicon reads (Read 2) were screened for the presence of the primer sequence and the shared sequence (i.e.…”

Section: Methodsmentioning

confidence: 99%

“…A mismatch of 20% was allowed for all sequence matching steps. Only UMIs with at least 2 or more supporting reads were retained for final genotyping assignments, after the UMI collapse algorithm 42, 86 . Filtered cells were then genotyped as follows: cells with at least one mutant UMI were categorized as mutant cells whereas cells with no mutant UMI and at least one wildtype UMI were identified as wildtype.…”

Section: Methodsmentioning

confidence: 99%

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Type 1 interferon remodels normal and neoplastic hematopoiesis in human

Lama

Rosenberg

Kubas-Meyer

et al. 2022

Preprint

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Inflammatory cytokines perturb hematopoietic stem cell (HSC) homeostasis and modulate the fitness of neoplastic HSC clones in mouse models. However, the study of cytokines in human hematopoiesis is challenging due to the concerted activities of multiple cytokines across physiologic and pathologic processes. To overcome this limitation, we leveraged serial bone marrow samples from patients with CALR-mutated myeloproliferative neoplasms who were treated with recombinant interferon-alpha (IFNa). We interrogated baseline and IFNa-treated CD34+ stem and progenitor cells using single-cell multi-omics platforms that directly link, within the same cell, the mutation status, whole transcriptomes and immunophenotyping or chromatin accessibility. We identified a novel IFNa-induced inflammatory granulocytic progenitor defined by expression and activities of RFX2/3 and AP-1 transcription factors, with evidence supporting a direct differentiation from HSCs. On the other hand, IFNa also induced a significant B-lymphoid progenitor expansion and proliferation, associated with enhanced activities of PU.1 and its co-regulator TCF3, as well as decreased accessibility of megakaryocytic-erythroid transcription factor GATA1 binding sites in HSCs. In the neoplastic hematopoiesis, the lymphoid expansion was constrained by a preferential myeloid skewing of the mutated cells, linked with increased myeloid proliferation and enhanced CEBPA and GATA1 activities compared to wildtype cells. Further, IFNa caused a downregulation of the TNFa signaling pathway, with downregulation of NFKB and AP-1 transcription factors. Thus, IFNa simultaneously initiated both - pro-inflammatory and anti-inflammatory - cell states within the same hematopoiesis, and its phenotypic impact varied as a function of the underlying HSC state and mutation status.

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“…It has been demonstrated that the expression of DNMT3A is higher in pancreatic cancer compared with normal pancreatic tissues [4]. DNMT3A plays a cancer-promoting role in colorectal cancer [5], breast cancer [6], gastric cancer [7] and prostate cancer [8], whereas it makes an absolutely opposite difference to hematological malignant tumours [9]. DNMT3A promotes the proliferation of glioma [10] and hepatocellular carcinoma [11].…”

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confidence: 99%

DNMT3A promotes the proliferation and metastasis of esophageal squamous cell carcinoma via upregulating HDAC9

Pan

Feng

Ding

et al. 2022

Preprint

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Background Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide and is characterized by high morbidity and mortality. However, the detailed molecular mechanisms underlying malignant progression of ESCC remain unclear. Methods 140 patients with esophageal squamous cell carcinoma who underwent surgery were enrolled in this study. Clinicopathologic characteristics and Kaplan–Meier survival analysis were performed to investigate DNMT3A expression and HDAC9 expression. Cell functional experiments were implemented both in vivo and in vitro to investigate the effects on ESCC cell proliferation and metastasis. Recombinant lentivirus–meditated gene overexpression or knockdown showed that HDAC9 participated in DNMT3A-mediated ESCC progression in vivo and in vitro, and this was further confirmed by HDAC inhibitor (SAHA) and immunohistochemical. Results We first demonstrated that DNMT3A expression was significantly higher in ESCC tissues than in corresponding adjacent non-cancerous tissues, and high DNMT3A expression was associated with poor prognosis. Then we confirmed that DNMT3A promoted proliferation and metastasis of ESCC cells in vivo and in vitro, suggesting that DNMT3A may be a promising therapeutic target for preventing esophageal cancer. Additionally, we found that DNMT3A up-regulated HDAC9, and HDAC9 overexpression significantly reversed the inhibitory effect caused by DNMT3A gene knockdown. In addition, we further confirmed the involvement of HDAC9 in DNMT3A-mediated carcinogenesis using HDAC inhibitor (SAHA). At last, we also validated HDAC9 expression was significantly higher in ESCC tissues than in corresponding adjacent non-tumour tissues, and high HDAC9 expression was positively associated with poor prognosis. Interestingly, Spearman correlation analysis confirmed a significant positive correlation between DNMT3A and HDAC9 expression. and ESCC patients with simultaneous DNMT3A and HDAC9 expression have the worst prognosis. Conclusions These results suggest that HDAC9 is involved in DNMT3A-mediated progression of ESCC, and targeting DNMT3A and HDAC9 may be a potential ESCC therapeutic strategy.

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Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Cited by 80 publications

References 180 publications

Phenotypic plasticity and genetic control in colorectal cancer evolution

Phenotypic plasticity and genetic control in colorectal cancer evolution

Type 1 interferon remodels normal and neoplastic hematopoiesis in human

DNMT3A promotes the proliferation and metastasis of esophageal squamous cell carcinoma via upregulating HDAC9

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