| 1. |
- Kvastad, Linda, et al.
(författare)
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The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
- 2021
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Ingår i: Communications Biology. - : Springer Nature. - 2399-3642. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- The RNA integrity number (RIN) is a frequently used quality metric to assess the completeness of rRNA, as a proxy for the corresponding mRNA in a tissue. Current methods operate at bulk resolution and provide a single average estimate for the whole sample. Spatial transcriptomics technologies have emerged and shown their value by placing gene expression into a tissue context, resulting in transcriptional information from all tissue regions. Thus, the ability to estimate RNA quality in situ has become of utmost importance to overcome the limitation with a bulk rRNA measurement. Here we show a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at cellular resolution. We demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows. Kvastad et al. develop the spatial RNA Integrity Number (sRIN) assay that evaluates the RNA integrity at cellular resolution. This method improves the resolution of a similar method called the RNA Integrity Number (RIN), demonstrating spatial variation in the quality of RNA samples.
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| 2. |
- Llorens-Bobadilla, Enric, et al.
(författare)
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Solid-phase capture and profiling of open chromatin by spatial ATAC
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Current methods for epigenomic profiling are limited in the ability to obtain genome wideinformation with spatial resolution. Here we introduce spatial ATAC, a method that integratestransposase-accessible chromatin profiling in tissue sections with barcoded solid-phase captureto perform spatially resolved epigenomics. We show that spatial ATAC enables the discoveryof the regulatory programs underlying spatial gene expression during mouse organogenesis,lineage differentiation and in human pathology.
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| 3. |
- Llorens-Bobadilla, Enric, et al.
(författare)
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Solid-phase capture and profiling of open chromatin by spatial ATAC
- 2023
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Ingår i: Nature Biotechnology. - : Nature Research. - 1087-0156 .- 1546-1696. ; 41:8, s. 1085-1088
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Tidskriftsartikel (refereegranskat)abstract
- Current methods for epigenomic profiling are limited in their ability to obtain genome-wide information with spatial resolution. We introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.
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| 4. |
- Mold, Jeff E., et al.
(författare)
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Divergent clonal differentiation trajectories establish CD8(+) memory T cell heterogeneity during acute viral infections in humans
- 2021
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 35:8
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Tidskriftsartikel (refereegranskat)abstract
- The CD8(+) T cell response to an antigen is composed of many T cell clones with unique T cell receptors, together forming a heterogeneous repertoire of effector and memory cells. How individual T cell clones contribute to this heterogeneity throughout immune responses remains largely unknown. In this study, we longitudinally track human CD8(+) T cell clones expanding in response to yellow fever virus (YFV) vaccination at the single-cell level. We observed a drop in clonal diversity in blood from the acute to memory phase, suggesting that clonal selection shapes the circulating memory repertoire. Clones in the memory phase display biased differentiation trajectories along a gradient from stem cell to terminally differentiated effector memory fates. In secondary responses, YFV- and influenza-specific CD8(+) T cell clones are poised to recapitulate skewed differentiation trajectories. Collectively, we show that the sum of distinct clonal phenotypes results in the multifaceted human T cell response to acute viral infections.
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| 5. |
- Stenudd, Moa, et al.
(författare)
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Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties
- 2022
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Ingår i: Cell Reports. - : CELL PRESS. - 2211-1247. ; 38:9
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Tidskriftsartikel (refereegranskat)abstract
- Spinal cord ependymal cells display neural stem cell properties in vitro and generate scar-forming astrocytes and remyelinating oligodendrocytes after injury. We report that ependymal cells are functionally heterogeneous and identify a small subpopulation (8% of ependymal cells and 0.1% of all cells in a spinal cord segment), which we denote ependymal A (EpA) cells, that accounts for the in vitro stem cell potential in the adult spinal cord. After spinal cord injury, EpA cells undergo self-renewing cell division as they give rise to differentiated progeny. Single-cell transcriptome analysis revealed a loss of ependymal cell gene expression programs as EpA cells gained signaling entropy and dedifferentiated to a stem-cell-like transcriptional state after an injury. We conclude that EpA cells are highly differentiated cells that can revert to a stem cell state and constitute a therapeutic target for spinal cord repair.
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| 6. |
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| 7. |
- Zamboni, Margherita
(författare)
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On astrocytes and neural stem cells : a study of reactive and canonical neurogenesis
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The mammalian central nervous system has limited regenerative capacity and the long-lasting functional impairment resulting from trauma and neurodegenerative disease derives from a failure to repopulate neuronal cell populations that are lost to injury. The studies included in the present thesis aim at proposing astrocytes as a novel source for achieving widespread replacement of neurons. Central to this work are notions within the field of astrocyte biology, adult neurogenesis, and regenerative medicine, which are discussed in the literature review. Astrocytes are an abundant cell population that supports neuronal development, survival and activity in health and participate in inflammation and injury resolution in disease. Learning about astrocyte biology allows us to develop tools for selectively targeting these cells or their specific functions. It will also help us learn about heterogeneous subtypes with distinctive functional properties or differential potential for regenerative repair. Adult neurogenesis is the process through which new neurons are added throughout life to a pre-existing neural circuitry. This process has been extensively explored in model organisms, but it has been challenging to achieve the same level of resolution and detail for the study of human neurogenesis. It is nevertheless important to identify and characterize neurogenic cells in the human brain and investigate their functional impact on cognition, as well as how their dysregulation may be linked to neurodegenerative and psychiatric diseases. In the context of this thesis, learning about the molecular dynamics driving neurogenesis allowed us to demonstrate that astrocytes, once recruited, unfold a process of differentiation like that seen in neural stem cells (Paper I and Paper II). We, furthermore, profiled the transcriptome of young and adult human hippocampal cells and depicted, for the first time, a comprehensive molecular framework that describes the neurogenic program in the human dentate gyrus (Paper III). Cell replacement therapies are obtaining promising results in pre-clinical settings and are starting to be successfully used in patients to replace specific cell populations depleted due to neurodegeneration or injury. The present thesis discusses the two main strategies to approach cell replacement, namely transplantation and recruitment of endogenous cells with stem cell properties. The latter has gained momentum in recent years to overcome limitations characteristic of cell transplantation. Work within this thesis is aimed in this direction and provides evidence that parenchymal astrocytes can be considered latent neural stem cells and can be recruited to replace neurons after injury (Paper I and Paper II). From the methodological point of view, genomics technologies and computational approaches are important concepts to this thesis and have been applied, here, to study canonical and reactive neurogenesis. Published single-cell omics data across organs, developmental times, and species have enabled comprehensive investigations of cell processes and interactions that had remained until now elusive. Here, we leveraged transcriptome-wide analysis to investigate the molecular dynamics underlying astrocyte-mediated neurogenesis in the striatum (Paper I) and the cortex (Paper II), and to study human hippocampal neurogenesis with an unparalleled level of detail, which we used to identify markers of neural progenitors and to compare molecular processes across species (Paper III).
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