Single-molecule imaging of transcription dynamics in somatic stem cells

Wheat, Justin C.; Sella, Yehonatan; Willcockson, Michael A.; Skoultchi, Arthur I.; Bergman, Aviv; Singer, Robert H.; Steidl, Ulrich

doi:10.1038/s41586-020-2432-4

Cited by 73 publications

(77 citation statements)

References 45 publications

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“…Further studies are warranted to explore to what extent the increase of cell-to-cell variability in the stem cell compartment is contributing to MDS pathophysiology. Altogether our study is in full agreement with the wealth of recent studies that have highlighted the intensity and importance of gene expression stochasticity in all systems examined to date ( 46–50 ). More generally, this study highlights the need to consider the role of stochastic gene expression in complex physiological processes and pathologies such as cancer ( 51, 52 ) paving the way for possible noise-based therapies through epigenetic regulation ( 53 ).…”

Section: Discussionsupporting

confidence: 91%

Hematopoietic differentiation is characterized by a transient peak of entropy at a single cell level

Dussiau

Boussaroque

Gaillard³

et al. 2021

Preprint

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Hematopoietic differentiation has been considered as a multistep process which is metaphorically represented as linear trajectories with discrete steps from hematopoietic stem cells to mature cells. While the transcriptional state of cells at the beginning or at the end of these trajectories are relatively well described from bulk analysis, what happens in the intermediate states has remained elusive until the use of single cell approaches allowed to capture the dynamic changes of transcriptomic states.Applying Shannon entropy to measure cell-to-cell variability among cells at the same stage of differentiation, we observed a transient peak of gene expression variability in all the hematopoietic differentiation pathways. Strikingly, genes with the highest entropy variation in a given differentiation pathway matched genes known as pathway-specific, whereas genes with the highest expression variation were common to all pathways. Finally, we showed that the level of cell-to-cell variation is increased in the most immature compartment of hematopoiesis in myelodysplastic syndromes.These data suggest that differentiation may not be as deterministic and linear as previously thought, but could be better conceptualized as a dynamical stochastic process with a transient stage of cellular indetermination.

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Section: Discussionsupporting

confidence: 91%

Hematopoietic differentiation is characterized by a transient peak of entropy at a single cell level

Dussiau

Boussaroque

Gaillard³

et al. 2021

Preprint

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“…We pushed the usability of our framework a step further by combining it with standard fixation techniques after live imaging via the development of sample holder patterned with a cold stamp technique, allowing the tracking of immunolabelled cells back in time and space and compare their features to all of the other cells over the entire organoid growth. Unlike lineage tracing in single cell RNA sequencing, which clusters cells only by their RNA phenotypic fingerprint or a barcode 25 , with our approach we can focus on the missing spatiotemporal organization in a causal way, as we follow the same cells over time. Consequently, we can now address, in unprecedented detail, the evolution of cells that can give rise to the first symmetry breaking event, keeping track of local interaction within the whole organoid.…”

Section: Discussionmentioning

confidence: 99%

Multiscale light-sheet organoid imaging framework

G¹,

Ortiz²,

Strnad³

et al. 2021

Preprint

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We present an imaging framework capable of turning long term light-sheet imaging of organoids into digital organoids. The framework takes advantage of deep learning techniques to faithfully segment single organoids, their lumen, cells and nuclei in 3D and over long periods of time. In parallel, large lineage trees for each organoid are predicted and corrected to iteratively improve the tracking and segmentation performances over time. To visualize the extracted information, we developed a web-based 'Digital Organoid Viewer' that allows a unique understanding of the multivariate and multiscale data by linking 2D lineage trees with the corresponding 3D segmentation meshes. We also backtracked single cells of interest after fixation obtaining detailed information about their history within the entire organoid context. Furthermore, we show nuclei merging events that arise from cytokinesis failure and that these polyploid never reside in the intestinal crypt, hinting at a tissue scale control and feedback on cellular fidelity. Molecularly, these cytokinesis failures depend on a regenerative state of the organoids and are regulated by Lats1 and RXR and we propose a model of tissue integrity by multi-scale check points. This discovery sheds light on the robustness of a regenerative YAP cellular state, questioning the role of polyploidy in intestinal regeneration.

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“…60). More recent work by Wheat and colleagues directly illustrated that transcriptional dynamics of several identity-defining transcription factors in HSPCs exhibit infrequent and stochastic burst-like behavior by means of imaging single mRNA molecules (4). This suggests a model by which HSPCs reside in a "transcriptional space" rather than a fate-determined "transcriptionally primed" state with restricted directionality and limited fate potential.…”

Section: Aacrjournalsorg the Role Of The Gene Regulatory Network And Nongenetic Diversity In Normal Hematopoiesis And Leukemogenesismentioning

confidence: 99%

“…Importantly, the hematopoietic system comprises all cellular components of the blood and is, therefore, uniquely dynamic, diverse, and tightly responsive to the host's environment. Classically thought to differentiate unidirectionally and governed by strict hierarchical rules, it is now appreciated that hematopoietic stem and progenitor cells (HSPC) comprise a highly plastic continuum of cell states and populations, exhibiting more plasticity than previously thought and providing an elegant model for evolutionary adaptability (2)(3)(4). Hematopoiesis is maintained throughout life despite an onslaught of genetic and environmental insults; however, certain molecular footprints exist that may mark the early stages of its derailment.…”

Section: Introductionmentioning

confidence: 99%

An Evolutionary Approach to Clonally Complex Hematologic Disorders

Schwenger

Steidl

2021

Blood Cancer Discovery

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Emerging clonal complexity has brought into question the way in which we perceive and, in turn, treat disorders of the hematopoietic system. Former models of cellintrinsic clonal dominance driven by acquisition of driver genes in a stereotypic sequence are often insufficient in explaining observations such as clonal hematopoiesis, and new paradigms are in order.Here, we review the evidence within the hematologic malignancy field and also borrow from perspectives rooted in evolutionary biology to reframe pathogenesis of hematologic disorders as dynamic processes involving complex interplays of genetic and nongenetic subclones and the tissue microenvironment in which they reside.Significance: Hematopoietic malignant and premalignant syndromes exhibit vast clonal diversity that is subject to selection imposed by the tissue microenvironment, as well as artificial selection by therapy. Tackling these disorders requires an appreciation of heterogeneity at both genetic and nongenetic levels, which can be borrowed from evolutionary biology principles. Models and drug development strategies that veer away from targeting solely dominant clones and, instead, embrace this complexity to outsmart it are required for long-term remission.

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Single-molecule imaging of transcription dynamics in somatic stem cells

Cited by 73 publications

References 45 publications

Hematopoietic differentiation is characterized by a transient peak of entropy at a single cell level

Hematopoietic differentiation is characterized by a transient peak of entropy at a single cell level

Multiscale light-sheet organoid imaging framework

An Evolutionary Approach to Clonally Complex Hematologic Disorders

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