Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia

Beneyto-Calabuig, Sergi; Merbach, Anne Kathrin; Kniffka, Jonas-Alexander; Antes, Magdalena; Szu-Tu, Chelsea; Rohde, Christian; Waclawiczek, Alexander; Stelmach, Patrick; Gräßle, Sarah; Pervan, Philip; Janssen, Maike; Landry, Jonathan J. M.; Beneš, Vladimı́r; Jauch, Anna; Brough, Michaela; Bauer, Marcus; Besenbeck, Birgit; Felden, Julia; Bäumer, Sebastian; Hundemer, Michael; Sauer, Tim; Pabst, Caroline; Wickenhauser, Claudia; Angenendt, Linus; Schliemann, Christoph; Trumpp, Andreas; Haas, Simon; Scherer, Michael; Raffel, Simon; Müller‐Tidow, Carsten; Velten, Lars

doi:10.1016/j.stem.2023.04.001

Cited by 40 publications

(28 citation statements)

References 53 publications

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“…( Figure 4D ). To extend our analysis to the context of therapies, we took advantage of another published scRNA-seq dataset of human bone marrow, with sequential samples at diagnosis and relapse from patients treated with the BCL-2 inhibitor venetoclax 31,55 . As for the previous dataset, we first annotated healthy cell types ( Figure 4E ).…”

Section: Resultsmentioning

confidence: 99%

Interpreting single-cell messages in normal and aberrant hematopoiesis with the Cell Marker Accordion

Busarello,

Biancon,

Lauria

et al. 2024

Preprint

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Single-cell technologies offer a unique opportunity to explore cellular heterogeneity in hematopoiesis, reveal malignant hematopoietic cells with clinically significant features and measure gene signatures linked to pathological pathways. However, reliable identification of cell types is a crucial bottleneck in single-cell analysis. Available databases contain dissimilar nomenclature and non-concurrent marker sets, leading to inconsistent annotations and poor interpretability. Furthermore, current tools focus mostly on physiological cell types, lacking extensive applicability in disease. We developed the Cell Marker Accordion, a user-friendly platform for the automatic annotation and biological interpretation of single-cell populations based on consistency weighted markers. We validated our approach on peripheral blood and bone marrow single-cell datasets, using surface markers and expert-based annotation as the ground truth. In all cases, we significantly improved the accuracy in identifying cell types with respect to any single source database. Moreover, the Cell Marker Accordion can identify disease-critical cells and pathological processes, extracting potential biomarkers in a wide variety of contexts in human and murine single-cell datasets. It characterizes leukemia stem cell subtypes, including therapy-resistant cells in acute myeloid leukemia patients; it identifies malignant plasma cells in multiple myeloma samples; it dissects cell type alterations in splicing factor-mutant cells from myelodysplastic syndrome patients; it discovers activation of innate immunity pathways in bone marrow from mice treated with METTL3 inhibitors. The breadth of these applications elevates the Cell Marker Accordion as a flexible, faithful and standardized tool to annotate and interpret hematopoietic populations in single-cell datasets focused on the study of hematopoietic development and disease.

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Section: Resultsmentioning

confidence: 99%

Interpreting single-cell messages in normal and aberrant hematopoiesis with the Cell Marker Accordion

Busarello,

Biancon,

Lauria

et al. 2024

Preprint

View full text Add to dashboard Cite

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“…Mitochondrial variants stand out with their high mutation rate, copy number, and heteroplasmy and low sequencing cost among various types of endogenous markers. This allows simultaneously interrogating clonality and gene expression or chromatin state profiles in single-cell level (Beneyto-Calabuig et al, 2023; Lareau et al, 2021; Ludwig et al, 2019; Penter et al, 2021; Walker et al, 2022; Wang et al, 2022; Xu et al, 2019). The development of MAESTER (mitochondrial alteration enrichment from single-cell transcriptomes to establish relatedness) expands the application of mtDNA as a natural genetic cell barcode for clonal tracking to high throughput single-cell RNA sequencing (Miller et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Single-cell mitochondrial variant enrichment resolved clonal tracking and spatial architecture in human embryonic hematopoiesis

Xue,

Chao,

Lin

et al. 2023

Preprint

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The ability to perform lineage tracing at the single-cell level is critical to reconstructing dynamic transitions during cell differentiation. However, prospective tracing approaches inevitably encounter outstanding challenges including barcoding precision, barcode diversity, and detection efficiency, which can skew inferred lineage relationships. Human pluripotent stem cells (hPSC) even face risks of DNA-damage-induced toxicity-related cell death. We explored the use of naturally occurring somatic mutations in mitochondrial transcripts detected in single-cell RNA-seq as genetic lineage barcodes in HPSC. In this study, we used an enrichment of scRNA-seq mitochondrial reads and a robust computational method to identify clonally relevant mitochondrial variants as endogenous genetic barcodes for clonal tracking of early embryonic hematopoiesis from hPSC. We modeled the development of embryonic tissues from hPSCs and delineated the ontogeny of hematopoietic cells by mitochondrial variant lineage tracing. We identified multiple waves of erythropoiesis in time-series scRNA-seq data. We further applied mitochondrial variant lineage tracing to spatial transcriptomics and identified the clonal development of both erythro-myeloid progenitors and their niche cells. Our study highlights the power of mitochondrial variants as an endogenous marker for clonal tracking in modeling human development from stem cells.

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“…Whole genome sequencing provides such a dense lineage picture thanks to the mapping of soma�c DNA muta�ons 13,14 , but it suffers from very limited throughput and lacks informa�on about the cell state. On the other hand, spontaneous mitochondrial DNA (mtDNA) muta�ons can be captured by single-cell RNA-seq or ATAC-seq [15][16][17][18] . However, a recent preprint analyzed both mtDNA and nuclear soma�c muta�ons from clonally expanded hematopoie�c stem cells, and found that most apparent mitochondrial gene�c varia�on does not reflect the phylogene�c signal obtained from wholegenome sequencing of the nuclear genome 19 , raising doubts whether cellular phylogenies can be faithfully reconstructed with that approach.…”

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confidence: 99%

Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan

Scherer,

Singh,

Braun

et al. 2024

Preprint

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SummaryCurrent approaches to lineage tracing of stem cell clones require genetic engineering or rely on sparse somatic DNA variants, which are difficult to capture at single-cell resolution. Here, we show that targeted single-cell measurements of DNA methylation at single-CpG resolution deliver joint information about cellular differentiation state and clonal identities. We develop EPI-clone, a droplet-based method for transgene-free lineage tracing, and apply it to study hematopoiesis, capturing hundreds of clonal trajectories across almost 100,000 single-cells. Using ground-truth genetic barcodes, we demonstrate that EPI-clone accurately identifies clonal lineages throughout hematopoietic differentiation. Applied to unperturbed hematopoiesis, we describe an overall decline of clonal complexity during murine ageing and the expansion of rare low-output stem cell clones. In aged human donors, we identified expanded hematopoietic clones with and without genetic lesions, and various degrees of clonal complexity. Taken together, EPI-clone enables accurate and transgene-free single-cell lineage tracing at scale.

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Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia

Cited by 40 publications

References 53 publications

Interpreting single-cell messages in normal and aberrant hematopoiesis with the Cell Marker Accordion

Interpreting single-cell messages in normal and aberrant hematopoiesis with the Cell Marker Accordion

Single-cell mitochondrial variant enrichment resolved clonal tracking and spatial architecture in human embryonic hematopoiesis

Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan

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